bluuebunny/crossref_metadata_2025 huggingface dataset:
Charge losses in expanding plasma created by an XeCl laser
Authors: Lorusso Antonella , Krása Josef , Rohlena Karel , Nassisi Vincenzo , Belloni Fabio , Doria Domenico
Published: February 2005

The emission of multiply charged Cuq+ ions from a plasma produced by 308 nm excimer laser is analyzed with respect to the distance from the irradiated target. The critical zone, outside which the charge states of ions of the expanding plasma are frozen, was determined to be approximately 20 cm from the target. This value was estimated using a charge-freezing criterion expressed by a distance dependence of the total charge carried by the ions Q∝L−2, which describes the dilution of plasma by its expansion into a vacuum without collisional recombination processes.
Low-frequency noise characteristics of HfSiON gate-dielectric metal-oxide-semiconductor-field-effect transistors
Authors: Min Bigang , Devireddy Siva Prasad , Çelik-Butler Zeynep , Shanware Ajit , Green Keith , Chambers J. J. , Visokay M. V. , Colombo Luigi
Published: February 2005

High dielectric constant materials are being developed as possible replacements for SiO2 as the gate dielectric. Although these materials do overcome the issue of gate leakage current because of increased thickness for a given equivalent capacitance, several other problems arise, such as degraded carrier mobility and higher low-frequency noise due to increased fixed charges and traps in the high-k film. HfSiON gate-dielectric metal-oxide-semiconductor field-effect transistors (MOSFETs), presented here, offer lower 1∕f noise compared to other high-k materials, but the noise levels are relatively higher than in SiO2 devices. Oxide-trap-induced correlated carrier number-mobility fluctuations dominate in all of these devices. Measured noise characteristics as well as extracted oxide trap density values are discussed for various geometries and sizes. The latter, measured to be 1.5×1019–1.6×1020cm−3eV−1, is higher than that for SiO2 MOSFETs with similar dimensions (4.1×1016–7.8×1016cm−3eV−1). This work represents an investigation of interface generated flicker noise on HfSiON gate stacks.
Scanning acoustic force microscopy characterization of thermal expansion effects on the electromechanical properties of film bulk acoustic resonators
Authors: San Paulo A. , Liu X. , Bokor J.
Published: February 2005

This letter demonstrates the application of scanning acoustic force microscopy for the characterization of film bulk acoustic resonators beyond detection of the gigahertz vibration amplitude and acoustic wave field imaging. We present a method to measure thermal expansion effects on these resonators by modulating the driving signal amplitude and then varying the modulation frequency from a few hertz to several tens of kilohertz. For the particular device considered here, we show the influence of thermal expansion effects on its electromechanical response and the acoustic wave field images. The thermal relaxation time constant of the resonator is measured and compared with a theoretical estimation based on the heat transfer analysis of the system.
Detection of α particles with superconducting series-junction detectors
Authors: Kurakado M. , Sato H. , Takizawa Y. , Shiki S. , Shimizu H. M.
Published: February 2005

Superconducting series-junction detectors present the possibility of highly practical radiation detectors with high detection efficiencies, high count rates, and high energy-resolution even for radiation that is difficult to detect efficiently with traditional radiation detectors. A series-junction detector with an effective volume of 8×8×0.4mm3 has shown that the efficiency of signal charge production is high despite its large volume. The position dependence of signal heights of a series-junction detector with an effective area of 1.5×1.5mm2 was corrected, and the energy resolution was improved from 2.9% to 0.42%.
Near-field spectroscopy of phase segregation in white-light-emitting blends based on low-mass molecules
Authors: Salerno Marco , Mazzeo Marco , Frassanito Maria C. , Patanè Salvatore , Cingolani Roberto , Gigli Giuseppe
Published: February 2005

We report on the direct observation of phase segregation occurring in thin-film blends of a thiophene monomer and an ammino compound, used in the fabrication of organic white-light-emitting diodes. In the homogeneous and uniform regions of the films, the interaction between the two molecular components gives rise to exciplex states responsible for a broad redshifted photoluminescence emission band, which disappears in the film zones where segregation occurs. This effect has been observed with submicrometer spatial resolution by means of local spectroscopic measurements performed in a scanning near-field optical microscope.
5
nm
ruthenium thin film as a directly plateable copper diffusion barrier
Authors: Arunagiri T. N. , Zhang Y. , Chyan O. , El-Bouanani M. , Kim M. J. , Chen K. H. , Wu C. T. , Chen L. C.
Published: February 2005

Interfacial stability of electroplated copper on a 5nm ruthenium film supported by silicon, Cu∕(5nmRu)∕Si, was investigated using Rutherford backscattering and high-resolution analytical electron microscopy. Transmission electron microscopy (TEM) imaging shows that a 5nm Ru film is amorphous in contrast to the columnar microstructures of thicker films (20nm). Direct Cu plating on a 5nm Ru film yielded a homogeneous Cu film with over 90% plating efficiency. It is demonstrated that 5nm Ru can function as a directly plateable Cu diffusion barrier up to at least 300°C vacuum anneal. TEM reveals an interlayer between Ru∕Si, which expands at the expense of Ru upon annealing. Electron energy loss spectroscopy analyses show no oxygen (O) across the Cu∕(5nmRu)∕Si interfaces, thereby indicating that the interlayer is ruthenium silicide (RuxSiy). This silicidation is mainly attributed to the failure of the ultrathin Ru barrier at the higher annealing temperature.
Al
x
Ga
1
−
x
N
bulk single crystals
Authors: Geiser P. , Jun J. , Kazakov S. M. , Wägli P. , Karpinski J. , Batlogg B. , Klemm L.
Published: February 2005

Al x Ga 1 − x N bulk single crystals have been grown by a solution growth technique in a cubic anvil cell with a solid pressure medium. GaN powder pellets as starting materials serve as a nitrogen source for crystallization in a Ga∕Al alloy. The growth process (up to 3days at T=1750°C, p=30kbar) yields crystals up to 0.6×0.4×0.2mm3 in size. X-ray diffraction investigations confirm the growth of the AlxGa1−xN phase. The crystal composition is studied by mass spectrometry, showing aluminum contents as high as x=27%. The near-band-gap photoluminescence spectra in AlxGa1−xN are blueshifted with respect to GaN and indicate Al concentrations in agreement with results from mass spectrometry and from the measured lattice parameter contraction.
Femtosecond spectroscopy of defect modes in silica glasses
Authors: Guillon C. , Burgin J. , Langot P. , Vallée F. , Hehlen B.
Published: February 2005

The D1 and D2 defect modes are investigated in the time domain in normal and densified silica using a high sensitivity femtosecond pump-probe technique with 15fs pulses. Their frequency and width are precisely determined even when they are partly masked by a broad background in spontaneous Raman spectroscopy. These results open up many possibility for investigation of local structures in glasses.
Comparison of the properties of GaN grown on complex Si-based structures
Authors: Zhou S. Q. , Vantomme A. , Zhang B. S. , Yang H. , Wu M. F.
Published: February 2005

With the aim of investigating the possible integration of optoelectronic devices, epitaxial GaN layers have been grown on Si(111) semiconductor-on-insulator (SOI) and on Si∕CoSi2∕Si(111) using metalorganic chemical vapor deposition. The samples are found to possess a highly oriented wurtzite structure, a uniform thickness, and abrupt interfaces. The epitaxial orientation is determined as GaN(0001)∕∕Si(111),GaN[112¯0]∕∕Si[11¯0], and GaN[101¯0]∕∕Si[1¯1¯2], and the GaN layer is tensilely strained in the direction parallel to the interface. According to Rutherford backscattering/channeling spectrometry and (0002) rocking curves, the crystalline quality of GaN on Si(111) SOI is better than that of GaN on silicide. Room-temperature photoluminescence of GaN∕SOI reveals a strong near-band-edge emission at 368 nm (3.37 eV) with a full width at half-maximum of 59 meV.
In situ growth of c-axis-oriented Ca3Co4O9 thin films on Si (100)
Authors: Hu Y. F. , Si W. D. , Sutter E. , Li Qiang
Published: February 2005

High-quality c-axis-oriented Ca3Co4O9 thin films have been grown directly on Si (100) wafers by pulsed-laser deposition without prechemical treatment of the substrate surface. Cross-sectional transmission electron microscopy shows good crystallinity of the Ca3Co4O9 films. The Seebeck coefficient and resistivity of the Ca3Co4O9 thin films on Si (100) substrate are 126μV∕K and 4.3mΩcm, respectively, at room temperature, comparable to the single-crystal samples. This advance demonstrates the possibility of integrating the cobaltate-based high thermoelectric materials with the current state-of-the-art silicon technology for thermoelectricity-on-a-chip applications.
Monte Carlo simulation of Joule heating in bulk and strained silicon
Authors: Pop Eric , Dutton Robert W. , Goodson Kenneth E.
Published: February 2005

This work examines the details of Joule heating in silicon with a Monte Carlo method including efficient, analytic models for the electron bands, acoustic and optical phonon dispersion. We find that a significant portion of the initially generated phonons have low group velocity, and therefore low contribution to heat transport, e.g., optical phonons or acoustic modes near the Brillouin zone edge. The generated phonon spectrum in strained silicon is different from bulk silicon at low electric fields due to band splitting and scattering selection rules which favor g-type and reduce f-type phonon emission. However, heat generation is essentially the same in strained and bulk silicon at high fields, when electrons have enough energy to emit across the entire phonon spectrum despite the strain-induced band splitting. The results of this study are important for electro-thermal analysis of future silicon nanoscale devices.
Predicting rogue waves in random oceanic sea states
Authors: Islas A. L. , Schober C. M.
Published: February 2005

Using the inverse spectral theory of the nonlinear Schrödinger (NLS) equation we correlate the development of rogue waves in oceanic sea states characterized by the Joint North Sea Wave Project (JONSWAP) spectrum with the proximity to homoclinic solutions of the NLS equation. We find in numerical simulations of the NLS equation that rogue waves develop for JONSWAP initial data that are “near” NLS homoclinic data, while rogue waves do not occur for JONSWAP data that are “far” from NLS homoclinic data. We show the nonlinear spectral decomposition provides a simple criterium for predicting the occurrence and strength of rogue waves.
Early origins of polycystic ovary syndrome
Authors: Dumesic Daniel A. , Schramm R. Dee , Abbott David H.
Published: February 2005

The prenatally androgenised female rhesus monkey has become a model for polycystic ovary syndrome (PCOS) in women, with early prenatal androgenisation entraining a permanent PCOS-like phenotype characterised by luteinising hormone (LH) hypersecretion due to reduced hypothalamic sensitivity to steroid negative feedback and relative insulin excess associated with increased abdominal adiposity. These combined reproductive and metabolic abnormalities occur in combination with ovarian hyperandrogenism and follicular arrest in adulthood, and with premature follicle differentiation and impaired embryo development during gonadotrophin therapy for in vitro fertilization (IVF). The ability of prenatal androgen excess in fetal rhesus monkeys to entrain multiple organ systems in utero provides evidence that the hormonal environment of intrauterine life programmes target tissue differentiation, raising the possibility that hyperandrogenism in human fetal development promotes PCOS in adulthood. This hypothesis developed in prenatally androgenised female rhesus monkeys, however, also must include data from clinical studies of PCOS to clarify the homology between human and non-human primates in intrafollicular steroidogenesis and its impact on oocyte developmental competency. By doing so, future studies promise to develop new clinical strategies that will lead to improved pregnancy outcome and reduced pregnancy loss in women with disorders of insulin action, including PCOS, obesity and diabetes mellitus.
Rewards and risks of human embryo creation: a personal view
Authors: Leese Henry J.
Published: February 2005

Understanding how a single cell, the fertilised egg, can develop into all the tissues in the body has been referred to as one of the two great problems facing biology; the other is how the brain works. To be working on the early human embryo is a reward in itself. To see such knowledge applied to improve the lives of infertile couples provides special rewards. There are considerable technical challenges in these activities due to the paucity of experimental material, particularly in the human. A major intellectual challenge is to understand the mechanisms that regulate early embryo development, especially the role of signal molecules intrinsic to the embryo and those that are maternally derived. Central to this issue are notions of embryo autonomy and plasticity; the extent to which the same genotype can give rise to different phenotypes in response to environmental perturbations and the need to discover how severe such changes have to be to induce irreversible changes that can compromise the health of the offspring. Research areas that could be fruitful include stress-induced causal effects, cell signalling and the concept of ‘quiet metabolism’. Managing assisted conception practices and their associated risks requires a regulatory framework to ensure the safety and efficacy of the new technologies. However, there is a danger of over-regulation, a cultural phenomenon characterised by a rise in audit and decline in trust. The challenge is to devise regulation in assisted reproduction technologies proportionate to the risks. The ultimate rewards will come from understanding how the human genome operates in functional terms. The ideal system in which to study this is the human blastocyst, an autonomous, functional group of mammalian cells.
Diet during pregnancy, neonatal outcomes and later health
Authors: Moore Vivienne M. , Davies Michael J.
Published: February 2005

Renewed interest in nutrition during pregnancy has been generated by the hypothesis that adult disease has origins in early life. Animal experiments clearly show that altering maternal diet before and during pregnancy can induce permanent changes in the offspring’s birth size, adult health and lifespan. Among women living in Western societies, cigarette smoking is the most important factor known to reduce fetal growth, followed by low pre-pregnancy weight and low gestational weight gain. Obesity is also associated with pregnancy complications and adverse neonatal outcomes, so inadequate or excessive energy intake is not optimal for the developing fetus. Against a history of inconsistent results, several recent studies suggest that in Western settings the balance of macronutrients in a woman’s diet can influence newborn size. Effects appear to be modest, but this relationship may not encapsulate the full significance for health of the child, as there is emerging evidence of associations with long-term metabolic functioning that are independent of birth size. Consequences of inadequate maternal nutrition, for the offspring, may depend on timing during gestation, reflecting critical windows for fetal development. Where women are not malnourished, changing a woman’s nutritional plane during pregnancy may be detrimental to the unborn baby, and systematic reviews of the literature on dietary supplementation during pregnancy indicate few benefits and possible risks. In view of this, improved diet before pregnancy deserves greater attention.
Assisted reproductive technologies and birth outcomes: overview of recent systematic reviews
Authors: Bower Carol , Hansen Michèle
Published: February 2005

Several systematic reviews have been published recently on birth outcomes of infants conceived through assisted reproductive technologies (ART), compared with infants conceived spontaneously. These outcomes include perinatal mortality, preterm birth, low birthweight and birth defects. Methodological limitations of many of the individual studies (including small sample size, potential for bias in ascertainment of outcomes and considering singletons and multiples together) were obviated in these reviews by excluding studies where methods were considered inadequate, by conducting meta-analyses using data from all methodologically sound studies (small and large) and by examining singletons separately. Overall, the reviews indicate few differences between outcomes in ART twins compared with twins conceived spontaneously. However, in singleton ART infants, there are around two-fold increases in risk of perinatal mortality, low birthweight and preterm birth, about a 50% increase in small for gestational age and a 30–35% increase in birth defects, compared with singletons conceived spontaneously. Couples considering ART should be counselled about the increased risk of adverse outcomes. Epidemiologists, in conjunction with clinical and laboratory colleagues, should now focus on large, methodologically sound studies with long-term follow up that seek to identify the reasons for these increased risks and their long-term consequences, whether they are associated with particular technologies and causes of infertility, and how they might be reduced.
Fetal programming: the perspective of single and twin pregnancies
Authors: Davies Michael J.
Published: February 2005

Multiple pregnancy is associated with increased risk of adverse consequences for both mother and fetus(es), including increased rates of maternal hypertension and pre-eclampsia, spontaneous abortion, Caesarean delivery, low birthweight, birth prematurity, perinatal mortality, admission to neonatal intensive care and extended length of care, respiratory distress, cerebral palsy, developmental delay, contact with disability services and mortality to age 5 years. Premature birth, which affects 97% of triplets and 53.3% of twins in Australia, is not the sole factor involved. The rate of multiple pregnancy in Australia is 1.7%. This compares to 22.1% for pregnancies resulting from assisted reproduction technology (ART). As a result, 21.8% of babies born from ART are from a multiple pregnancy, in comparison to the USA where the majority of babies born from ART are from a multiple pregnancy. Additionally, the population rate of multiple births is rising due to the more frequent use of ART and continued multi-embryo transfers, which is operating against a background of rising implantation rates within ART clinics. Twins have been of interest from a programming perspective. However, analysis of associations between crude birthweight and subsequent metabolic risk factors or mortality in adulthood from chronic disease indicate that adaptations in pregnancy to support multi-fetal growth are not identical to fetal growth restriction in singleton pregnancies. Indeed, the process of ‘maternal constraint’ is incompletely understood and confounds such comparisons. From a programming perspective, it is a challenge to identify in twin pregnancies the transition from physiological adaptation to pathological growth restriction. Growth disparity between twins has been more illuminating of subtle adverse effects for the smaller of twin pairs in both blood pressure and insulin resistance in adulthood. Interestingly, these effects can be observed in both dizygotic and to a lesser degree in monozygotic twins, which indicates a role for both genetic and environmental factors in these measures. This suggests that, consistent with experimental studies in other species, the relationship between impaired growth in utero and chronic disease in later life is not simply mediated by a common genetic pathway.
Understanding cellular disruptions during early embryo development that perturb viability and fetal development
Authors: Lane Michelle , Gardner David K.
Published: February 2005

An inability to regulate ionic and metabolic homeostasis is related to a reduction in the developmental capacity of the embryo. The early embryo soon after fertilisation and up until compaction appears to have a reduced capacity to regulate its homeostasis. The reduced ability to regulate homeostasis, such as intracellular pH and calcium levels, by the precompaction-stage embryo appears to impact on the ability to regulate mitochondrial function and maintain adequate levels of energy production. This reduction in ATP production causes a cascade of events leading to disrupted cellular function and, perhaps ultimately, disrupted epigenetic regulation and aberrant placental and fetal development. In contrast, after compaction the embryo takes on a more somatic cell-like physiology and is better able to regulate its physiology and therefore appears less vulnerable to stress. Therefore, for human IVF it would seem important for the establishment of healthy pregnancies that the embryos are maintained in systems that are designed to minimise homeostatic stress, particularly for the cleavage-stage embryos, as exposure to stress is likely to culminate in impaired embryo function.
Ex vivo early embryo development and effects on gene expression and imprinting
Authors: Gardner David K. , Lane Michelle
Published: February 2005

The environment to which the mammalian embryo is exposed during the preimplantation period of development has a profound effect on the physiology and viability of the conceptus. It has been demonstrated that conditions that alter gene expression, and in some instances the imprinting status of specific genes, have all previously been shown to adversely affect cell physiology. Thus, questions are raised regarding the aetiology of abnormal gene expression and altered imprinting patterns, and whether problems can be averted by using more physiological culture conditions. It is also of note that the sensitivity of the embryo to its surroundings decreases as development proceeds. Post compaction, environmental conditions have a lesser effect on gene function. This, therefore, has implications regarding the conditions used for IVF and the culture of the cleavage stage embryo. The developmental competence of the oocyte also impacts gene expression in the embryo, and therefore superovulation has been implicated in abnormal methylation and imprinting in the resultant embryo. Furthermore, the genetics and dietary status of the mother have a profound impact on embryo development and gene expression. The significance of specific animal models for human assisted reproductive technologies (ART) is questioned, given that most cattle data have been obtained from in vitro-matured oocytes and that genes imprinted in domestic and laboratory animals are not necessarily imprinted in the human. Patients treated with ART have fertility problems, which in turn may predispose their gametes or embryos to greater sensitivities to the process of ART. Whether this is from the drugs involved in the ovulation induction or from the IVF, intracytoplasmic sperm injection or culture procedures themselves remains to be determined. Alternatively, it may be that epigenetic alterations are associated with infertility and symptoms are subsequently revealed through ART. Whatever the aetiology, continued long-term monitoring of the children conceived through ART is warranted.
The role of early embryonic environment on epigenotype and phenotype
Authors: Vickaryous Nicola , Whitelaw Emma
Published: February 2005

The influence of epigenetic modifications to the genome on the phenotype of the adult organism is now a tractable problem in biology. This has come about through the development of methods that enable us to study the methylation state of the DNA and the packaging of the chromatin at specific gene loci. It is becoming clear that early embryogenesis is a critical period for the establishment of the epigenotype. Furthermore, it appears that this process is sensitive to environmental conditions. This is a concern in light of the increasing use of artificial reproductive technologies throughout the world.
Polar nuclear localization of H1T2, a histone H1 variant, required for spermatid elongation and DNA condensation during spermiogenesis
Authors: Martianov Igor , Brancorsini Stefano , Catena Raffaella , Gansmuller Anne , Kotaja Noora , Parvinen Martti , Sassone-Corsi Paolo , Davidson Irwin
Published: February 2005

Spermiogenesis entails a major biochemical and morphological restructuring of the germ cell involving replacement of the somatic histones by protamines packing the DNA into the condensed spermatid nucleus and elimination of the cytoplasm during the elongation phase. We describe H1T2, an histone H1 variant selectively and transiently expressed in male haploid germ cells during spermiogenesis. In round and elongating spermatids, H1T2 specifically localizes to a chromatin domain at the apical pole, revealing a polarity in the spermatid nucleus. Inactivation by homologous recombination shows that H1T2 is critical for spermiogenesis as male
H1t2
–/–
mice have greatly reduced fertility. Analysis of spermiogenesis in
H1t2
mutant mice shows delayed nuclear condensation and aberrant elongation. As a result, mutant spermatids are characterized by the presence of residual cytoplasm, acrosome detachment, and fragmented DNA. Hence, H1T2 is a protein required for proper cell restructuring and DNA condensation during the elongation phase of spermiogenesis.
Uncovering transcriptional regulation of metabolism by using metabolic network topology
Authors: Patil Kiran Raosaheb , Nielsen Jens
Published: February 2005

Cellular response to genetic and environmental perturbations is often reflected and/or mediated through changes in the metabolism, because the latter plays a key role in providing Gibbs free energy and precursors for biosynthesis. Such metabolic changes are often exerted through transcriptional changes induced by complex regulatory mechanisms coordinating the activity of different metabolic pathways. It is difficult to map such global transcriptional responses by using traditional methods, because many genes in the metabolic network have relatively small changes at their transcription level. We therefore developed an algorithm that is based on hypothesis-driven data analysis to uncover the transcriptional regulatory architecture of metabolic networks. By using information on the metabolic network topology from genome-scale metabolic reconstruction, we show that it is possible to reveal patterns in the metabolic network that follow a common transcriptional response. Thus, the algorithm enables identification of so-called reporter metabolites (metabolites around which the most significant transcriptional changes occur) and a set of connected genes with significant and coordinated response to genetic or environmental perturbations. We find that cells respond to perturbations by changing the expression pattern of several genes involved in the specific part(s) of the metabolism in which a perturbation is introduced. These changes then are propagated through the metabolic network because of the highly connected nature of metabolism.
Past trials influence perception of ambiguous motion quartets through pattern completion
Authors: Maloney L. T. , Martello M. F. Dal , Sahm C. , Spillmann L.
Published: February 2005

There are many celebrated examples of ambiguous perceptual configurations such as the Necker cube that abruptly and repeatedly “switch” among possible perceptual states. When such ambiguous configurations are presented intermittently, observers tend to see the same perceptual state on successive trials. The outcome of each trial apparently serves to “prime” the outcome of the following. We sought to determine how long the influence of a past trial persists by using ambiguous motion quartets as stimuli. We found large, significant effects of all four most recent trials, but the results were not consistent with any priming model. The results could be explained instead as perceptual completion of two kinds of temporal patterns, repeating and alternating. We conclude that the visual system does not passively remember perceptual state: it analyzes recent perceptual history and attempts to predict what will come next. These predictions can alter what is seen.
Antioxidants and photoprotection in a lichen as compared with its isolated symbiotic partners
Authors: Kranner Ilse , Cram W. John , Zorn Margret , Wornik Sabine , Yoshimura Isao , Stabentheiner Edith , Pfeifhofer Hartwig W.
Published: February 2005

Extreme desiccation and irradiation increase the formation of reactive oxygen species in organisms. Lichens are highly resistant to potential damage, but it is not known whether biochemical interaction between their fungal and algal partners is involved in conferring stress tolerance. Here, we show that antioxidant and photoprotective mechanisms in the lichen
Cladonia vulcani
are more effective by orders of magnitude than those of its isolated partners. When alone, both alga and fungus suffer oxidative damage during desiccation, but in the lichen, each appears to induce up-regulation of protective systems in the other. Without the fungal contact, the alga tolerates only very dim light and its photoprotective system is only partially effective; without the alga, the glutathione-based antioxidant system of the fungus is slow and ineffective. In the lichen, this mutually enhanced resistance to oxidative stress and, in particular, its desiccation tolerance are essential for life above ground. This lifestyle, in turn, increases the chance of dispersal of reproductive propagules and ensures their joint evolutionary success.
Interruption of ganglioside synthesis produces central nervous system degeneration and altered axon–glial interactions
Authors: Yamashita Tadashi , Wu Yun-Ping , Sandhoff Roger , Werth Norbert , Mizukami Hiroki , Ellis Jessica M. , Dupree Jeffrey L. , Geyer Rudolf , Sandhoff Konrad , Proia Richard L.
Published: February 2005

Gangliosides, which are sialylated glycosphingolipids, are the major class of glycoconjugates on neurons and carry the majority of the sialic acid within the central nervous system (CNS). To determine the role of ganglioside synthesis within the CNS, mice carrying null mutations in two critical ganglioside-specific glycosyltransferase genes,
Siat9
(encoding GM3 synthase) and
Galgt1
(encoding GM2 synthase), were generated. These double-null mice were unable to synthesize gangliosides of the ganglio-series of glycosphingolipids, which are the major ganglioside class in the CNS. Soon after weaning, viable mice developed a severe neurodegenerative disease that resulted in death. Histopathological examination revealed striking vacuolar pathology in the white matter regions of the CNS with axonal degeneration and perturbed axon–glia interactions. These results indicate that ganglioside synthesis is essential for the development of a stable CNS, possibly by means of the promotion of interactions between axon and glia.
Reconstitution of papillomavirus E2-mediated plasmid maintenance in
Saccharomyces cerevisiae
by the Brd4 bromodomain protein
Authors: Brannon Angela R. , Maresca Julia A. , Boeke Jef D. , Basrai Munira A. , McBride Alison A.
Published: February 2005

The papillomavirus E2 protein functions in viral transcriptional regulation, DNA replication, and episomal genome maintenance. Viral genomes are maintained in dividing cells by attachment to mitotic chromosomes by means of the E2 protein. To investigate the chromosomal tethering function of E2, plasmid stability assays were developed in
Saccharomyces cerevisiae
to determine whether the E2 protein could maintain plasmids containing the yeast autonomous replication sequence replication element but with the centromeric element replaced by E2-binding sites. E2 expression was not sufficient to maintain such plasmids, but plasmid stability could be rescued by expression of the mammalian protein Brd4. In the presence of both Brd4 and E2 proteins, plasmids with multiple E2-binding sites were stable without selection.
S. cerevisiae
encodes a homolog of Brd4 named Bdf1 that does not contain the C-terminal domain that interacts with the E2 protein. A fusion protein of Bdf1 and the Brd4 C-terminal “tail” could support E2-mediated plasmid maintenance in yeast. Using a panel of mutated E2 proteins, we determined that plasmid stability required the ability of E2 to bind DNA and to interact with Brd4 and mammalian mitotic chromosomes but did not require its replication initiation and transactivation functions. The
S. cerevisiae
-based plasmid maintenance assays described here are invaluable tools for dissecting mechanisms of episomal viral genome replication and screening for additional host protein factors involved in plasmid maintenance.
Root-knot nematodes and bacterial Nod factors elicit common signal transduction events in
Lotus japonicus
Authors: Weerasinghe Ravisha R. , Bird David McK. , Allen Nina S.
Published: February 2005

The symbiosis responsible for nitrogen fixation in legume root nodules is initiated by rhizobial signaling molecules [Nod factors (NF)]. Using transgenically tagged microtubules and actin, we dynamically profiled the spatiotemporal changes in the cytoskeleton of living
Lotus japonicus
root hairs, which precede root-hair deformation and reflect one of the earliest host responses to NF. Remarkably, plant-parasitic root-knot nematodes (RKN) invoke a cytoskeletal response identical to that seen in response to NF and induce root-hair waviness and branching in legume root hairs via a signal able to function at a distance. Azide-killed nematodes do not produce this signal. A similar response to RKN was seen in tomato. Aspects of the host responses to RKN were altered or abolished by mutations in the NF receptor genes
nfr1
,
nfr5
, and
symRK
, suggesting that RKN produce a molecule with functional equivalence to NF, which we name NemF. Because the ability of RKN to establish feeding sites and reproduce was markedly reduced in the mutant lines, we propose that RKN have adapted at least part of the symbiont-response pathway to enhance their parasitic ability.
Specific collapse followed by slow hydrogen-bond formation of β-sheet in the folding of single-chain monellin
Authors: Kimura Tetsunari , Uzawa Takanori , Ishimori Koichiro , Morishima Isao , Takahashi Satoshi , Konno Takashi , Akiyama Shuji , Fujisawa Tetsuro
Published: February 2005

Characterization of the conformational landscapes for proteins with different secondary structures is important in elucidating the mechanism of protein folding. The folding trajectory of single-chain monellin composed of a five-stranded β-sheet and a helix was investigated by using a pH-jump from the alkaline unfolded to native state. The kinetic changes in the secondary structures and in the overall size and shape were measured by circular dichroism spectroscopy and small-angle x-ray scattering, respectively. The formation of the tertiary structure was monitored by intrinsic and extrinsic fluorescence. A significant collapse was observed within 300 μs after the pH-jump, leading to the intermediate with a small amount of secondary and tertiary structures but with an overall oblate shape. Subsequently, the stepwise formation of secondary and tertiary structures was detected. The current observation was consistent with the theoretical prediction that a more significant collapse precedes the formation of secondary structures in the folding of β-sheet proteins than that of helical proteins [Shea, J. E., Onuchic, J. N. & Brooks, C. L., III (2002)
Proc. Natl. Acad. Sci. USA
99, 16064–16068]. Furthermore, it was implied that the initial collapse was promoted by the formation of some specific structural elements, such as tight turns, to form the oblate shape.
Amyloid-β neurotoxicity is mediated by FISH adapter protein and ADAM12 metalloprotease activity
Authors: Malinin Nikolay L. , Wright Sarah , Seubert Peter , Schenk Dale , Griswold-Prenner Irene
Published: February 2005

Based on a variety of genetic, biochemical, and neuropathological evidence, amyloid-β peptide (Aβ) has been suggested to be causal in Alzheimer's disease (AD). Aβ has been shown to mediate neurodegenerative and inflammatory changes associated with amyloid plaques, as well as exert direct neurotoxicity through oligomeric forms of Aβ. The mechanism of Aβ toxicity, however, remains largely unknown. In this work, we show that an early event after exposure of postmitotic neurons to Aβ is tyrosine phosphorylation of FISH adapter protein. FISH binds to and potentially regulates certain ADAM family members. We present evidence that FISH and ADAM12 mediate the neurotoxic effect of Aβ. Expression of an ADAM12 protease-deficient mutant (ADAM12ΔMP) blocks Aβ-induced neuronal death, and expression of an N-terminal fragment of FISH reduces Aβ toxicity. The C-terminal fragment of FISH containing the ADAMs binding region is found to be sufficient for induction of neuronal death, which is prevented by coexpression of the ADAM12ΔMP. Aβ treatment, as well as expression of the C-terminal toxic FISH fragment, induces accumulation of ADAM12 N-terminal cleavage product in conditioned medium, demonstrating activation of the ADAM metalloprotease/sheddase activity. ADAM12 protein is reduced in AD brains, pointing to a possible increase in ADAM12 proteolytic activity. These data suggest that Aβ toxicity is mediated by FISH and ADAM12 and may provide insights into therapeutic strategies for AD treatment.
The carboxyl-terminal region of cyclic nucleotide-modulated channels is a gating ring, not a permeation path
Authors: Johnson J. P. , Zagotta William N.
Published: February 2005

The recent elucidation of the structure of the carboxyl-terminal region of the hyperpolarization-activated cyclic nucleotide-modulated (HCN2) channel has prompted us to investigate a curious feature of this structure in HCN2 channels and in the related CNGA1 cyclic nucleotide-gated (CNG) channels. The crystallized fragment of the HCN2 channel contains both the cyclic nucleotide-binding domain (CNBD) and the C-linker region, which connects the CNBD to the pore. At the center of the fourfold-symmetric structure is a tunnel that runs perpendicular to the membrane. The narrowest part of the tunnel is ≈10 Å in diameter and is lined by a ring of negatively charged amino acids: D487, E488, and D489. Many ion channels have “charge rings” that focus permeant ions at the mouth of the pore and increase channel conductance. We used nonstationary fluctuation analysis and single-channel recording, coupled with site-directed mutagenesis and cysteine modification, to determine whether this part of HCN and CNG channels might be an extension of the permeation pathway. Our results indicate that modifying charge-ring amino acids affects gating but not ion permeation in HCN2 and CNG channels. Thus, this portion of the channel is not an obligatory part of the ion path but instead acts as a “gating ring.” The carboxyl-terminal region of these channels must hang below the pore much like the “hanging gondola” of voltage-gated potassium channels, but the permeation pathway must exit the protein before the level of the ring of charged amino acids.
Control of antiviral defenses through hepatitis C virus disruption of retinoic acid-inducible gene-I signaling
Authors: Foy Eileen , Li Kui , Sumpter Rhea , Loo Yueh-Ming , Johnson Cynthia L. , Wang Chunfu , Fish Penny Mar , Yoneyama Mitsutoshi , Fujita Takashi , Lemon Stanley M. , Gale Michael
Published: February 2005

Hepatitis C virus (HCV) is a major human pathogen that infects 170 million people. A hallmark of HCV is its ability to establish persistent infections reflecting the evasion of host immunity and interference with α/β-IFN innate immune defenses. We demonstrate that disruption of retinoic acid-inducible gene I (RIG-I) signaling by the viral NS3/4A protease contributes to the ability of HCV to control innate antiviral defenses. RIG-I was essential for virus or HCV RNA-induced signaling to the IFN-β promoter in human hepatoma cells. This signaling was disrupted by the protease activity of NS3/4A, which ablates RIG-I signaling of downstream IFN regulatory factor 3 and NF-κB activation, attenuating expression of host antiviral defense genes and interrupting an IFN amplification loop that otherwise suppresses HCV replication. Treatment of cells with an active site inhibitor of the NS3/4A protease relieved this suppression and restored intracellular antiviral defenses. Thus, NS3/4A control of RIG-I supports HCV persistence by preventing IFN regulatory factor 3 and NF-κB activation. Our results demonstrate that these processes are amenable to restoration through pharmacologic inhibition of viral protease function.
Immune evasion by hepatitis C virus NS3/4A protease-mediated cleavage of the Toll-like receptor 3 adaptor protein TRIF
Authors: Li Kui , Foy Eileen , Ferreon Josephine C. , Nakamura Mitsuyasu , Ferreon Allan C. M. , Ikeda Masanori , Ray Stuart C. , Gale Michael , Lemon Stanley M.
Published: February 2005

Toll-like receptors (TLRs) bind pathogen-specific ligands early in infection, initiating signaling pathways that lead to expression of multiple protective cellular genes. Many viruses have evolved strategies that block the effector mechanisms induced through these signaling pathways, but viral interference with critical proximal receptor interactions has not been described. We show here that the NS3/4A serine protease of hepatitis C virus (HCV), a virus notorious for its ability to establish persistent intrahepatic infection, causes specific proteolysis of Toll-IL-1 receptor domain-containing adaptor inducing IFN-β (TRIF or TICAM-1), an adaptor protein linking TLR3 to kinases responsible for activating IFN regulatory factor 3 (IRF-3) and NF-κB, transcription factors controlling a multiplicity of antiviral defenses. NS3/4A-mediated cleavage of TRIF reduces its abundance and inhibits polyI:C-activated signaling through the TLR3 pathway before its bifurcation to IRF-3 and NF-κB. This uniquely broad mechanism of immune evasion potentially limits expression of multiple host defense genes, thereby promoting persistent infections with this medically important virus.
A critical role of helix 3–helix 5 interaction in steroid hormone receptor function
Authors: Zhang Junhui , Simisky Jessica , Tsai Francis T. F. , Geller David S.
Published: February 2005

The ligand-binding domains of steroid hormone receptors possess a conserved structure with 12 α-helices surrounding a central hydrophobic core. On agonist binding, a repositioned helix 12 forms a pocket with helix 3 (H3) and helix 5 (H5), where transcriptional coactivators bind. The precise molecular interactions responsible for activation of these receptors remain to be elucidated. We previously identified a H3–H5 interaction that permits progesterone-mediated activation of a mutant mineralocorticoid receptor. We were intrigued to note that the potential for such interaction is widely conserved in the nuclear receptor family, indicating a possible functional significance. Here, we demonstrate via transcriptional activation studies in cell culture that alteration of residues involved in H3–H5 interaction consistently produces a gain of function in steroid hormone receptors. These data suggest that H3–H5 interaction may function as a molecular switch regulating the activity of nuclear receptors and suggest this site as a general target for pharmacologic intervention. Furthermore, they reveal a general mechanism for the creation of nuclear receptors bearing increased activity, providing a potentially powerful tool for the study of physiologic pathways
in vivo
.
Ecosystem recovery after climatic extremes enhanced by genotypic diversity
Authors: Reusch Thorsten B. H. , Ehlers Anneli , Hämmerli August , Worm Boris
Published: February 2005

Contemporary climate change is characterized both by increasing mean temperature and increasing climate variability such as heat waves, storms, and floods. How populations and communities cope with such climatic extremes is a question central to contemporary ecology and biodiversity conservation. Previous work has shown that species diversity can affect ecosystem functioning and resilience. Here, we show that genotypic diversity can replace the role of species diversity in a species-poor coastal ecosystem, and it may buffer against extreme climatic events. In a manipulative field experiment, increasing the genotypic diversity of the cosmopolitan seagrassZostera marinaenhanced biomass production, plant density, and faunal abundance, despite near-lethal water temperatures due to extreme warming across Europe. Net biodiversity effects were explained by genotypic complementarity rather than by selection of particularly robust genotypes. Positive effects on invertebrate fauna suggest that genetic diversity has second-order effects reaching higher trophic levels. Our results highlight the importance of maintaining genetic as well as species diversity to enhance ecosystem resilience in a world of increasing uncertainty.
Disulfide trapping to localize small-molecule agonists and antagonists for a G protein-coupled receptor
Authors: Buck Elizabeth , Wells James A.
Published: February 2005

A key question regarding the signaling mechanism for G protein-coupled receptors (GPCRs) is what triggers agonism versus antagonism. Peptide analogs derived from the chemokine, complement fragment 5 anaphylatoxin (C5a), can act as agonists or antagonists to the C5a receptor, a member of the GPCR family [Gerber, B. O., Meng, E. C., Dotsch, V., Baranski, T. J. & Bourne, H. R. (2001)
J. Biol. Chem.
276, 3394–4000]. Recently, we showed that two Cys residues engineered near a proposed binding site in the C5a receptor on transmembrane helices III and VI can selectively and reversibly trap short Cys-containing 3-mer peptides derived from C5a by disulfide bond formation [Buck, E. A., Bourne, H. & Wells, J. A. (November 18, 2004)
J. Biol. Chem.
, 10.1074/jbc.C400500200]. Here, a library of 10,000 compounds, each containing an exchangeable thiol, was screened to identify specific small-molecule mimics that block binding of C5a. Some of the selected compounds acted as agonists and were as potent as the natural C5a ligand, and some acted as antagonists. A residue near these compounds, Ile-116 in helix III, functions as a “gatekeeper” to modulate these effects. A small substitution, Ile-116-Ala, enhanced affinity for some compounds and allowed antagonists to function as agonists; a larger substitution, Ile-116-Trp, decreased affinity and agonism. Thus, subtle changes in either the structure of the ligand or the receptor at the site between helix III, VI, and VII can switch the receptor on or off. This ligand binding and activation site may be similarly positioned in other members of the chemokine receptor family. Selective ligand trapping by reversible disulfide formation may serve to nucleate the development of small-molecule mimics.