bluuebunny/crossref_metadata_2025 huggingface dataset:
High quality x-ray absorption spectroscopy measurements with long energy range at high pressure using diamond anvil cell
Authors: Hong Xinguo , Newville Matthew , Prakapenka Vitali B. , Rivers Mark L. , Sutton Stephen R.
Published: July 2009

We describe an approach for acquiring high quality x-ray absorption fine structure (XAFS) spectroscopy spectra with wide energy range at high pressure using diamond anvil cell (DAC). Overcoming the serious interference of diamond Bragg peaks is essential for combining XAFS and DAC techniques in high pressure research, yet an effective method to obtain accurate XAFS spectrum free from DAC induced glitches has been lacking. It was found that these glitches, whose energy positions are very sensitive to the relative orientation between DAC and incident x-ray beam, can be effectively eliminated using an iterative algorithm based on repeated measurements over a small angular range of DAC orientation, e.g., within ±3° relative to the x-ray beam direction. Demonstration XAFS spectra are reported for rutile-type GeO2 recorded by traditional ambient pressure and high pressure DAC methods, showing similar quality at 440 eV above the absorption edge. Accurate XAFS spectra of GeO2 glass were obtained at high pressure up to 53 GPa, providing important insight into the structural polymorphism of GeO2 glass at high pressure. This method is expected be applicable for in situ XAFS measurements using a diamond anvil cell up to ultrahigh pressures.
Intramolecular interactions of L-phenylalanine revealed by inner shell chemical shift
Authors: Ganesan Aravindhan , Wang Feng
Published: July 2009

Intramolecular interactions of the functional groups, carboxylic acid, amino, and phenyl in L-phenylalanine have been revealed through inner shell chemical shift. The chemical shift and electronic structures are studied using its derivatives, 2-phenethylamine (PEA) and 3-phenylpropionic acid (PPA), through substitutions of the functional groups on the chiral carbon Cα, i.e., carboxylic acid (–COOH) and amino (–NH2) groups. Inner shell ionization spectra of L-phenylalanine are simulated using density functional theory based B3LYP/TZVP and LB94/et-pVQZ models, which achieve excellent agreement with the most recently available synchrotron sourced x-ray photoemission spectroscopy of L-phenylalanine (Elettra, Italy). The present study reveals insight into behavior of the peptide bond (CO–NH) through chemical shift of the C1–Cα–Cβ(–Cγ) chain and intramolecular interactions with phenyl. It is found that the chemical shift of the carbonyl C1(=O) site exhibits an apparently redshift (smaller energy) when interacting with the phenyl aromatic group. Removal of the amino group (–NH2) from L-phenylalanine (which forms PPA) brings this energy on C1 close to that in L-alanine (δ<0.01 eV). Chemical environment of Cα and Cβ exhibits more significant differences in L-alanine than in the aromatic species, indicating that the phenyl group indeed affects the peptide bond in the amino acid fragment. No direct evidences are found that the carbonyl acid and amino group interact with the phenyl ring through conventional hydrogen bonds.
Tapered photoconductive terahertz field probe tip with subwavelength spatial resolution
Authors: Wächter Markus , Nagel Michael , Kurz Heinrich
Published: July 2009

In this work a photoconductive probe tip applicable for near- and far-field measurements in the terahertz frequency regime is demonstrated as a powerful alternative to existing terahertz scanning near-field optical microscopy approaches. The probe tip is based on a triangular-shaped patch of freestanding low-temperature-grown GaAs of only 1.3 μm thickness with a pair of tapered metallic wires on top. Using nonresonant electric field enhancement at the tip of the probing device, 10 μm wide metallic structures are spatially resolved and a bandwidth of 2 THz is demonstrated.
Disilane chemisorption on SixGe1−x(100)-(2×1): Molecular mechanisms and implications for film growth rates
Authors: Ng Rachel Qiao-Ming , Tok E. S. , Kang H. Chuan
Published: July 2009

At low temperatures, hydrogen desorption is known to be the rate-limiting process in silicon germanium film growth via chemical vapor deposition. Since surface germanium lowers the hydrogen desorption barrier, SixGe(1−x) film growth rate increases with the surface germanium fraction. At high temperatures, however, the molecular mechanisms determining the epitaxial growth rate are not well established despite much experimental work. We investigate these mechanisms in the context of disilane adsorption because disilane is an important precursor used in film growth. In particular, we want to understand the molecular steps that lead, in the high temperature regime, to a decrease in growth rate as the surface germanium increases. In addition, there is a need to consider the issue of whether disilane adsorbs via silicon-silicon bond dissociation or via silicon-hydrogen bond dissociation. It is usually assumed that disilane adsorption occurs via silicon-silicon bond dissociation, but in recent work we provided theoretical evidence that silicon-hydrogen bond dissociation is more important. In order to address these issues, we calculate the chemisorption barriers for disilane on silicon germanium using first-principles density functional theory methods. We use the calculated barriers to estimate film growth rates that are then critically compared to the experimental data. This enables us to establish a connection between the dependence of the film growth rate on the surface germanium content and the kinetics of the initial adsorption step. We show that the generally accepted mechanism where disilane chemisorbs via silicon-silicon bond dissociation is not consistent with the data for film growth kinetics. Silicon-hydrogen bond dissociation paths have to be included in order to give good agreement with the experimental data for high temperature film growth rate.
Laser wavelength effects in ultrafast near-field laser nanostructuring of Si
Authors: Zorba Vassilia , Mao Xianglei , Russo Richard E.
Published: July 2009

We study the effect of laser wavelength (400 and 800 nm) on the near-field processing of crystalline silicon (Si) in the femtosecond pulse duration regime through subwavelength apertures. Distinct differences in the obtained nanostructures are found in each case both in terms of their physical sizes as well as their structure, which can be tuned between craters and protrusions. A single or a few femtosecond pulses can deliver enough energy on the substrate to induce subdiffraction limited surface modification, which is among the smallest ever reported in subwavelength apertured near-field scanning optical microscope schemes.
Jahn–Teller distortions in the photodetachment spectrum of PtCl62−: A four-component relativistic study
Authors: Pernpointner Markus , Rapps Thomas , Cederbaum Lorenz S.
Published: July 2009

In this work the mutual influence of Jahn–Teller (JT) and spin-orbit effects on the photoelectron spectrum of PtCl62− is analyzed. For this purpose potential energy surfaces of PtCl6− along the JT active modes are calculated in the four-component Dirac–Coulomb (DC) framework and the possible JT stabilizations are determined. For the relativistic calculation we set out from the one-particle propagator implemented on the basis of the DC Hamiltonian. A correlated four-component approach is favorable for complexes with a strongly relativistic central atom due to the complicated interplay of electron correlation and relativity. PtCl62− possesses a long enough lifetime which makes it amenable to precise experimental measurements. In the photoelectron spectrum of PtCl62− some peaks could not be unambiguously assigned either originating from a JT splitting or representing individual spin-orbit components. In previously calculated dianionic tetrahalide platinum complexes PtX42− (X=F,Cl,Br) it was observed that spin-orbit effects dominate over the d-orbital-induced JT effects. The same trend also persists in the currently studied hexachlorocomplex where sizable platinum-induced spin-orbit splittings give rise to features that supersede any JT structures.
Investigating DNA barcoding options for the identification of Caladenia (Orchidaceae) species
Authors: Farrington Lachlan , MacGillivray Phyllis , Faast Renate , Austin Andrew
Published: July 2009

The application of molecular techniques for defining evolutionary units in Caladenia has largely focussed on addressing relationships at the subgeneric and deeper levels. However, in light of the morphological complexity present in this diverse genus, molecular markers offer additional characters for the refinement of taxonomy at the species level. In the present study, we explored the utility of marker systems with demonstrated application for defining fine-scale units, both in terms of phylogenetic information and in the context of DNA barcoding. We also provide a working example of the use of molecular techniques for identifying the source plants of pollinia collected from passively sampled pollinators and for identifying sterile plants.
Implications of pollination by food and sexual deception for pollinator specificity, fruit set, population genetics and conservation of Caladenia (Orchidaceae)
Authors: Phillips Ryan D. , Faast Renate , Bower Colin C. , Brown Graham R. , Peakall Rod
Published: July 2009

Caladenia is very unusual in that it contains species that attract pollinators by two different strategies, food and sexual deception. Among the sexually deceptive species, baiting for pollinators has shown that within populations orchid species are typically pollinated by a single species of thynnine wasp. However, some wasp species can be pollinators of more than one species of orchid usually when their ranges do not overlap. There is a trend for closely related orchids to exploit wasps from the same genus, with different lineages of orchids often pollinated by different genera. Very little is known about pollination of food-deceptive Caladenia species, although it is evident they attract a suite of generalist food-seeking insects. Food-deceptive species have a higher pollination rate than do sexually deceptive species. Studies of population genetics and pollen movements are few, although they suggest a pattern of fine-scale genetic structuring within populations, owing to predominantly restricted seed dispersal and low genetic differentiation among populations as a consequence of rare long-distance seed-dispersal events. Both evolutionary and ecological research of Caladenia will greatly benefit from a better understanding of the insect species involved in pollination, their ecological requirements and the ecological and genetic consequences of food and sexual deception.
Dormancy in Caladenia: a Bayesian approach to evaluating latency
Authors: Tremblay Raymond L. , Perez Maria-Eglée , Larcombe Matthew , Brown Andrew , Quarmby Joe , Bickerton Doug , French Garry , Bould Andrew
Published: July 2009

Dormancy is common in many terrestrial orchids in southern Australia and other temperate environments. The difficulty for conservation and management when considering dormancy is ascertaining whether non-emergent plants are dormant or dead. Here we use a multi-state capture–recapture method, undertaken over several seasons, to determine the likelihood of a plant becoming dormant or dying following its annual emergent period and evaluate the frequency of the length of dormancy. We assess the transition probabilities from time series of varying lengths for the following nine terrestrial orchids in the genus Caladenia: C. amoena, C. argocalla, C. clavigera, C. elegans, C. graniticola, C. macroclavia, C. oenochila, C. rosella and C. valida from Victoria, South Australia and Western Australia. We used a Bayesian approach for estimating survivorship, dormancy and the likelihood of death from capture–recapture data. Considering all species together, the probability of surviving from one year to the next was ~86%, whereas the likelihood of observing an individual above ground in two consecutive years was ~74%. All species showed dormancy of predominantly 1 year, whereas dormancy of three or more years was extremely rare (<2%). The results have practical implications for conservation, in that (1) population sizes of Caladenia species are more easily estimated by being able to distinguish the likelihood of an unseen individual being dormant or dead, (2) population dynamics of individuals can be evaluated by using a 1–3-year dormancy period and (3) survey effort is not wasted on monitoring individuals that have not emerged for many years.
Population dynamics of Caladenia: Bayesian estimates of transition and extinction probabilities
Authors: Tremblay Raymond L. , Perez Maria-Eglée , Larcombe Matthew , Brown Andrew , Quarmby Joe , Bickerton Doug , French Garry , Bould Andrew
Published: July 2009

A disproportionate number of threatened plant species in Australia are found in the genus Caladenia, although little has been published on their life history. Here we examine data from nine species to evaluate some of the basic life-history strategies in Caladenia, specifically the transitions between life-history stages. We constructed life-history transition models of the orchids by using a Bayesian approach, we evaluated the growth rate of populations, compared transition values among species and determined which stage influenced the population growth most. We assessed extinction likelihood and considered the effect of variation in transitions among states on the probability of extinction. Bayesian model selection showed differences between species regarding their life cycle. The probability of individuals flowering in two consecutive years is extremely rare and was found to be common in only one species, C. amoena. All other species had a high likelihood of returning to a vegetative state, and some were likely to enter dormancy after flowering. High elasticities in the transition from the dormant to dormant stage suggest that dormancy has a large impact on population persistence. The quasi-extinction rate suggests that C. rosella, C. clavigera, C. graniticola and C. macroclavia are most at risk when all species have an equal initial population size. Conservation management should focus on studies to identify cues that influence flowering in consecutive years, emergence from dormancy and increasing recruitment.
An introduction to Caladenia R.Br. - Australasia's jewel among terrestrial orchids
Authors: Dixon Kingsley W. , Hopper Stephen D.
Published: July 2009

Caladenia is a genus of more than 250 species of geophytic orchids in the Tribe Diurideae endemic to the Australasian Region. The genus in this broad sense has an exceptional diversity of insect pollination adaptations among its colourfully adorned species, from food-rewarding generalists to specialists achieving pollination by sexual deception of male thynnid wasps. The exploration of diversity in Caladenia involves many of the great names in the foundation of Australasian plant systematics, as well as reflecting a remarkable second phase of discovery and description over the past three decades. Molecular phylogenetics has greatly clarified relationships of Caladenia and established six major clades within the genus. Some researchers regard these clades as genera themselves, whereas they are treated as subgenera herein to maximise nomenclatural stability and information retrieval. More work is needed to adequately document relationships within each of these clades, and disputed matters of typification greatly influence nomenclature applied to many species if the six clades are recognised as genera. Given the relatively recent and ongoing discovery of so many new species in Caladenia, the biology of these orchids is only now being documented comprehensively. Significant advances in pollination ecology, mycorrhizal studies, horticulture and conservation biology are emerging that highlight the extraordinary ecological sensitivity and conservation vulnerability of the genus. Indeed, the high species number and complex biotic connections have resulted in no other genus of terrestrial orchids possessing such a large number of rare and threatened taxa. Some of this rich body of new data is presented by a diverse range of laboratories and researchers in this special issue.
Receptor guanylyl cyclases in Inka cells targeted by eclosion hormone
Authors: Chang Jer-Cherng , Yang Ruey-Bing , Adams Michael E. , Lu Kuang-Hui
Published: July 2009

A signature of eclosion hormone (EH) action in insect ecdysis is elevation of cGMP in Inka cells, leading to massive release of ecdysis triggering hormone (ETH) and ecdysis initiation. Although this aspect of EH-induced signal transduction is well known, the receptor mediating this process has not been identified. Here, we describe a receptor guanylyl cyclase BdmGC-1 and its isoform BdmGC-1B in the Oriental fruit flyBactrocera dorsalisthat are activated by EH. The B form exhibits the conserved domains and putative N-glycosylation sites found in BdmGC-1, but possesses an additional 46-amino acid insertion in the extracellular domain and lacks the C-terminal tail of BdmGC-1. Combined immunolabeling and in situ hybridization reveal that BdmGC-1 is expressed in Inka cells. Heterologous expression of BdmGC-1 in HEK cells leads to robust increases in cGMP following exposure to low picomolar concentrations of EH. The B-isoform responds only to higher EH concentrations, suggesting different physiological roles of these cyclases. We propose that BdmGC-1 and BdmGC-1Β are high- and low-affinity EH receptors, respectively.
Multiplexed imaging of surface enhanced Raman scattering nanotags in living mice using noninvasive Raman spectroscopy
Authors: Zavaleta Cristina L. , Smith Bryan R. , Walton Ian , Doering William , Davis Glenn , Shojaei Borzoyeh , Natan Michael J. , Gambhir Sanjiv S.
Published: July 2009

Raman spectroscopy is a newly developed, noninvasive preclinical imaging technique that offers picomolar sensitivity and multiplexing capabilities to the field of molecular imaging. In this study, we demonstrate the ability of Raman spectroscopy to separate the spectral fingerprints of up to 10 different types of surface enhanced Raman scattering (SERS) nanoparticles in a living mouse after s.c. injection. Based on these spectral results, we simultaneously injected the five most intense and spectrally unique SERS nanoparticles i.v. to image their natural accumulation in the liver. All five types of SERS nanoparticles were successfully identified and spectrally separated using our optimized noninvasive Raman imaging system. In addition, we were able to linearly correlate Raman signal with SERS concentration after injecting four spectrally unique SERS nanoparticles either s.c. (
R
2
= 0.998) or i.v. (
R
2
= 0.992). These results show great potential for multiplexed imaging in living subjects in cases in which several targeted SERS probes could offer better detection of multiple biomarkers associated with a specific disease.
Muscle stem cell behavior is modified by microRNA-27 regulation of Pax3 expression
Authors: Crist Colin G. , Montarras Didier , Pallafacchina Giorgia , Rocancourt Didier , Cumano Ana , Conway Simon J. , Buckingham Margaret
Published: July 2009

Skeletal muscle stem cells are regulated by Pax3/7. During development, Pax3 is required for the maintenance of these cells in the somite and their migration to sites of myogenesis; high levels of Pax3 interfere with muscle cell differentiation, both in the embryo and in the adult. Quantitative fine-tuning of Pax3 is critical, and microRNAs provide a potential mechanism. We identify microRNA-27b (miR-27b), which directly targets the 3′-UTR of Pax3 mRNA, as such a regulator. miR-27b is expressed in the differentiating skeletal muscle of the embryonic myotome and in activated satellite cells of adult muscle. In vivo overexpression of a miR-27b transgene in Pax3-positive cells in the embryo leads to down-regulation of Pax3, resulting in interference with progenitor cell migration and in premature differentiation. In a complementary experiment, miR-27b inhibitors were transfected into cultures of adult muscle satellite cells that normally express miR-27b at the onset of differentiation, when Pax3 protein levels undergo rapid down-regulation. Interference with miR-27b function results in continuing Pax3 expression leading to more proliferation and a delay in the onset of differentiation. Pax7 levels are not affected. Introduction of miR-27b antagomirs at a site of muscle injury in vivo also affects Pax3 expression and regeneration in vivo. We therefore conclude that miR-27b regulates Pax3 protein levels and this down-regulation ensures rapid and robust entry into the myogenic differentiation program.
Cooperative hunting and meat sharing 400–200 kya at Qesem Cave, Israel
Authors: Stiner Mary C. , Barkai Ran , Gopher Avi
Published: July 2009

Zooarchaeological research at Qesem Cave, Israel demonstrates that large-game hunting was a regular practice by the late Lower Paleolithic period. The 400- to 200,000-year-old fallow deer assemblages from this cave provide early examples of prime-age-focused ungulate hunting, a human predator–prey relationship that has persisted into recent times. The meat diet at Qesem centered on large game and was supplemented with tortoises. These hominins hunted cooperatively, and consumption of the highest quality parts of large prey was delayed until the food could be moved to the cave and processed with the aid of blade cutting tools and fire. Delayed consumption of high-quality body parts implies that the meat was shared with other members of the group. The types of cut marks on upper limb bones indicate simple flesh removal activities only. The Qesem cut marks are both more abundant and more randomly oriented than those observed in Middle and Upper Paleolithic cases in the Levant, suggesting that more (skilled and unskilled) individuals were directly involved in cutting meat from the bones at Qesem Cave. Among recent humans, butchering of large animals normally involves a chain of focused tasks performed by one or just a few persons, and butchering guides many of the formalities of meat distribution and sharing that follow. The results from Qesem Cave raise new hypotheses about possible differences in the mechanics of meat sharing between the late Lower Paleolithic and Middle Paleolithic.
The evolutionary origins of beneficial alleles during the repeated adaptation of garter snakes to deadly prey
Authors: Feldman Chris R. , Brodie Edmund D. , Brodie Edmund D. , Pfrender Michael E.
Published: July 2009

Where do the genetic variants underlying adaptive change come from? Are currently adaptive alleles recruited by selection from standing genetic variation within populations, moved through introgression from other populations, or do they arise as novel mutations? Here, we examine the molecular basis of repeated adaptation to the toxin of deadly prey in 3 species of garter snakes (Thamnophis) to determine whether adaptation has evolved through novel mutations, sieving of existing variation, or transmission of beneficial alleles across species. Functional amino acid substitutions in the skeletal muscle sodium channel (Nav1.4) are largely responsible for the physiological resistance of garter snakes to tetrodotoxin found in their newt (Taricha) prey. Phylogenetic analyses reject the hypotheses that the unique resistance alleles observed in multipleThamnophisspecies were present before the split of these lineages, or that alleles were shared among species through occasional hybridization events. Our results demonstrate that adaptive evolution has occurred independently multiple times in garter snakes via the de novo acquisition of beneficial mutations.
Cation specific binding with protein surface charges
Authors: Hess Berk , van der Vegt Nico F. A.
Published: July 2009

Biological organization depends on a sensitive balance of noncovalent interactions, in particular also those involving interactions between ions. Ion-pairing is qualitatively described by the law of “matching water affinities.” This law predicts that cations and anions (with equal valence) form stable contact ion pairs if their sizes match. We show that this simple physical model fails to describe the interaction of cations with (molecular) anions of weak carboxylic acids, which are present on the surfaces of many intra- and extracellular proteins. We performed molecular simulations with quantitatively accurate models and observed that the order K+< Na+< Li+of increasing binding affinity with carboxylate ions is caused by a stronger preference for forming weak solvent-shared ion pairs. The relative insignificance of contact pair interactions with protein surfaces indicates that thermodynamic stability and interactions between proteins in alkali salt solutions is governed by interactions mediated through hydration water molecules.
The structure of DNA overstretched from the 5′5′ ends differs from the structure of DNA overstretched from the 3′3′ ends
Authors: Danilowicz Claudia , Limouse Charles , Hatch Kristi , Conover Alyson , Coljee Vincent W. , Kleckner Nancy , Prentiss Mara
Published: July 2009

It has been suggested that the structure that results when double-stranded DNA (dsDNA) is pulled from the 3′3′ ends differs from that which results when it is pulled from the 5′5′ ends. In this work, we demonstrate, using λ phage dsDNA, that the overstretched states do indeed show different properties, suggesting that they correspond to different structures. For 3′3′ pulling versus 5′5′ pulling, the following differences are observed: (
i
) the forces at which half of the molecules in the ensemble have made a complete force-induced transition to single stranded DNA are 141 ± 3 pN and 122 ± 4 pN, respectively; (
ii
) the extension vs. force curve for overstretched DNA has a marked change in slope at 127 ± 3 pN for 3′3′ and 110 ± 3 pN for 5′5′; (
iii
) the hysteresis (H) in the extension vs. force curves at 150 mM NaCl is 0.3 ± 0.8 pN μm for 3′3′ versus 13 ± 8 pN for 5′5′; and (
iv
) 3′3′ and 5′5′ molecules show different changes in hysteresis due to interactions with β-cyclodextrin, a molecule that is known to form stable host-guest complexes with rotated base pairs, and glyoxal that is known to bind stably to unpaired bases. These differences and additional findings are well-accommodated by the corresponding structures predicted on theoretical grounds.
Darwinian selection for sites of Asn-linked glycosylation in phylogenetically disparate eukaryotes and viruses
Authors: Cui Jike , Smith Temple , Robbins Phillips W. , Samuelson John
Published: July 2009

Numerous protists and rare fungi have truncated Asn-linked glycan precursors and lack N-glycan-dependent quality control (QC) systems for glycoprotein folding in the endoplasmic reticulum. Here, we show that the abundance of sequons (NXT or NXS), which are sites for N-glycosylation of secreted and membrane proteins, varies by more than a factor of 4 among phylogenetically diverse eukaryotes, based on a few variables. There is positive correlation between the density of sequons and the AT content of coding regions, although no causality can be inferred. In contrast, there appears to be Darwinian selection for sequons containing Thr, but not Ser, in eukaryotes that have N-glycan-dependent QC systems. Selection for sequons with Thr, which nearly doubles the sequon density in human secreted and membrane proteins, occurs by an increased conditional probability that Asn and Thr are present in sequons rather than elsewhere. Increasing sequon densities of the hemagglutinin (HA) of influenza viruses A/H3N2 and A/H1N1 during the past few decades of human infection also result from an increased conditional probability that Asn, Thr, and Ser are present in sequons rather than elsewhere. In contrast, there is no selection on sequons by this mechanism in HA of A/H5N1 or 2009 A/H1N1 (Swine flu). Very strong selection for sequons with both Thr and Ser in glycoprotein of
M
r
120,000 (gp120) of HIV and related retroviruses results from this same mechanism, as well as amino acid composition bias and increases in AT content. We conclude that there is Darwinian selection for sequons in phylogenetically disparate eukaryotes and viruses.
TRPA channels distinguish gravity sensing from hearing in Johnston's organ
Authors: Sun Yishan , Liu Lei , Ben-Shahar Yehuda , Jacobs Julie S. , Eberl Daniel F. , Welsh Michael J.
Published: July 2009

Although many animal species sense gravity for spatial orientation, the molecular bases remain uncertain. Therefore, we studied
Drosophila melanogaster
, which possess an inherent upward movement against gravity-negative geotaxis. Negative geotaxis requires Johnston's organ, a mechanosensory structure located in the antenna that also detects near-field sound. Because channels of the transient receptor potential (TRP) superfamily can contribute to mechanosensory signaling, we asked whether they are important for negative geotaxis. We identified distinct expression patterns for 5
TRP
genes; the
TRPV
genes
nanchung
and
inactive
were present in most Johnston's organ neurons, the
TRPN
gene
nompC
and the
TRPA
gene
painless
were localized to 2 subpopulations of neurons, and the
TRPA
gene
pyrexia
was expressed in cap cells that may interact with the neurons. Likewise, mutating specific
TRP
genes produced distinct phenotypes, disrupting negative geotaxis (
painless
and
pyrexia
), hearing (
nompC
), or both (
nanchung
and
inactive
). Our genetic, physiological and behavioral data indicate that the sensory component of negative geotaxis involves multiple
TRP
genes. The results also distinguish between different mechanosensory modalities and set the stage for understanding how TRP channels contribute to mechanosensation.
Brassinosteroid signaling and auxin transport are required to establish the periodic pattern of
Arabidopsis
shoot vascular bundles
Authors: Ibañes Marta , Fàbregas Norma , Chory Joanne , Caño-Delgado Ana I.
Published: July 2009

The plant vascular system provides transport and support capabilities that are essential for plant growth and development, yet the mechanisms directing the arrangement of vascular bundles within the shoot inflorescence stem remain unknown. We used computational and experimental biology to evaluate the role of auxin and brassinosteroid hormones in vascular patterning in
Arabidopsis
. We show that periodic auxin maxima controlled by polar transport and not overall auxin levels underlie vascular bundle spacing, whereas brassinosteroids modulate bundle number by promoting early procambial divisions. Overall, this study demonstrates that auxin polar transport coupled to brassinosteroid signaling is required to determine the radial pattern of vascular bundles in shoots.
Epigenetic changes during disease progression in a murine model of human chronic lymphocytic leukemia
Authors: Chen Shih-Shih , Raval Aparna , Johnson Amy J. , Hertlein Erin , Liu Te-Hui , Jin Victor X. , Sherman Mara H. , Liu Shu-Jun , Dawson David W. , Williams Katie E. , Lanasa Mark , Liyanarachchi Sandya , Lin Thomas S. , Marcucci Guido , Pekarsky Yuri , Davuluri Ramana , Croce Carlo M. , Guttridge Denis C. , Teitell Michael A. , Byrd John C. , Plass Christoph
Published: July 2009

Epigenetic alterations, including gain or loss of DNA methylation, are a hallmark of nearly every malignancy. Changes in DNA methylation can impact expression of cancer-related genes including apoptosis regulators and tumor suppressors. Because such epigenetic changes are reversible, they are being aggressively investigated as potential therapeutic targets. Here we use the Eμ-TCL1 transgenic mouse model of chronic lymphocytic leukemia (CLL) to determine the timing and patterns of aberrant DNA methylation, and to investigate the mechanisms that lead to aberrant DNA methylation. We show that CLL cells from Eμ-TCL1 mice at various stages recapitulate epigenetic alterations seen in human CLL. Aberrant methylation of promoter sequences is observed as early as 3 months of age in these animals, well before disease onset. Abnormally methylated promoter regions include binding sites for the transcription factor FOXD3. We show that loss of
Foxd3
expression due to an NF-κB p50/p50:HDAC1 repressor complex occurs in TCL1-positive B cells before methylation. Therefore, specific transcriptional repression is an early event leading to epigenetic silencing of target genes in murine and human CLL. These results provide strong rationale for the development of strategies to target NF-κB components in CLL and potentially other B-cell malignancies.
Bell-like homeodomain selectively regulates the high-irradiance response of phytochrome A
Authors: Staneloni Roberto J. , Rodriguez-Batiller María José , Legisa Danilo , Scarpin María R. , Agalou Adamantia , Cerdán Pablo D. , Meijer Annemarie H. , Ouwerkerk Pieter B. F. , Casal Jorge J.
Published: July 2009

Plant responses mediated by phytochrome A display a first phase saturated by transient light signals and a second phase requiring sustained excitation with far-red light (FR). These discrete outcomes, respectively so-called very-low-fluence response (VLFR) and high-irradiance response (HIR), are appropriate in different environmental and developmental contexts but the mechanisms that regulate the switch remain unexplored. Promoter analysis of a light-responsive target gene revealed a motif necessary for HIR but not for VLFR. This motif is required for binding of the Bell-like homeodomain 1 (BLH1) to the promoter in in vitro and in yeast 1-hybrid experiments. Promoter substitutions that increased BLH1 binding also enhanced HIR.
blh1
mutants showed reduced responses to continuous FR and to deep canopy shadelight, but they retained normal responses to pulsed FR or red light and unfiltered sunlight. BLH1 enhanced
BLH1
expression and its promotion by FR. We conclude that BLH1 specifically regulates HIR and not VLFR of phytochrome A.
Observation of acoustic and subacoustic fast particles driven modes in Tore-Supra
Authors: Sabot R. , Macor A. , Nguyen C. , Decker J. , Elbeze D. , Eriksson L.-G. , Garbet X. , Goniche M. , Huysmans G. , Ladroit Y. , Maget P. , Segui J.L.
Published: July 2009

Energetic particles driven modes are one of the concerns for burning plasmas. On Tore-Supra, fast ions and electrons are generated by the RF heating systems and fast particles driven modes are detected with ECE and reflectometry diagnostics. In ICRH heated plasmas, modes are observed in the acoustic frequency range 30–70 kHz. The observed frequency agrees with the frequency predicted for both geodesic acoustic modes and beta Alfvén eigenmodes (BAE), but their structure and their excitation by fast ions advocate for an identification as BAE. Experimental analysis displays the existence of an excitation threshold depending on various parameters such as the ICRH power, the minority fraction and the density, in agreement with the theoretical prediction resulting from a balance between the fast ion drive and Landau damping by thermal ions. In lower hybrid current drive plasmas, electron fishbones have been detected below 20 kHz. Evolution of the fishbone modes with LH power was studied. Precession fishbones are observed at moderate power to be replaced by a mode at diamagnetic frequency at higher power. Precession fishbone frequency exhibits periodical jumps (0.1 s). These jumps are linked to spontaneous transitions between modes at different wavenumbers and a redistribution of the fast electrons in resonance with these modes. The number of excited modes and their wave number change with the LH power.
Pedestal stability comparison and ITER pedestal prediction
Authors: Snyder P.B. , Aiba N. , Beurskens M. , Groebner R.J. , Horton L.D. , Hubbard A.E. , Hughes J.W. , Huysmans G.T.A. , Kamada Y. , Kirk A. , Konz C. , Leonard A.W. , Lönnroth J. , Maggi C.F. , Maingi R. , Osborne T.H. , Oyama N. , Pankin A. , Saarelma S. , Saibene G. , Terry J.L. , Urano H. , Wilson H.R.
Published: July 2009

The pressure at the top of the edge transport barrier (or ‘pedestal height’) strongly impacts fusion performance, while large edge localized modes (ELMs), driven by the free energy in the pedestal region, can constrain material lifetimes. Accurately predicting the pedestal height and ELM behavior in ITER is an essential element of prediction and optimization of fusion performance. Investigation of intermediate wavelength MHD modes (or ‘peeling–ballooning’ modes) has led to an improved understanding of important constraints on the pedestal height and the mechanism for ELMs. The combination of high-resolution pedestal diagnostics, including substantial recent improvements, and a suite of highly efficient stability codes, has made edge stability analysis routine on several major tokamaks, contributing both to understanding, and to experimental planning and performance optimization. Here we present extensive comparisons of observations to predicted edge stability boundaries on several tokamaks, both for the standard (Type I) ELM regime, and for small ELM and ELM-free regimes. We further discuss a new predictive model for the pedestal height and width (EPED1), developed by self-consistently combining a simple width model with peeling–ballooning stability calculations. This model is tested against experimental measurements, and used in initial predictions of the pedestal height for ITER.
Laboratory Measurement of Yield and Composition of Dry‐Milled Corn Fractions Using a Shortened, Single‐Stage Tempering Procedure
Authors: Rausch Kent D. , Pruiett Larry E. , Wang Ping , Xu Li , Belyea Ronald L. , Tumbleson M. E.
Published: July 2009

The objective was to describe a laboratory‐scale dry‐milling procedure that used single‐stage tempering and determine the effect of hybrid on yields and fraction compositions in milled corn. Samples of 11 commercially available hybrids were processed through a laboratory dry‐milling procedure that used 1 kg samples of corn to produce milling fractions of large grits, small grits, fines, germ, and pericarp. Compositions of milling fractions (protein, neutral detergent fiber, ash, and crude fat) were determined. The procedure used a single‐stage tempering step that increased corn moisture from 15 to 23.5% wb during an 18‐min tempering period. Germ were separated from endosperm particles using a roller mill followed by screening over a sieve with 1.68‐mm openings. Coefficients of variability were small, indicating acceptable repeatability. Overall yield means were 39.2, 25.3, 13.8, 78.2, 14.3, and 6.8 g/100 g (db) for large grits, small grits, fines, total endosperm, germ, and pericarp, respectively. There were effects due to hybrid (P < 0.05) on fraction yields and compositions of milling fractions. Correlations (r) among endosperm fractions (large grits, small grits, and fines) ranged from 0.54 to |–0.92|. Correlations among endosperm fractions and germ and pericarp were <0.68. The developed dry‐milling method estimated milling yields among hybrids with low standard deviations relative to the means and should be a useful tool for research and industry in measuring dry‐milling characteristics.
Validity, prognostic value and optimal cutoff of respiratory muscle strength in patients with chronic heart failure changes with beta-blocker treatment
Authors: Frankenstein Lutz , Nelles Manfred , Meyer F. Joachim , Sigg Caroline , Schellberg Dieter , Remppis B. Andrew , Katus Hugo A. , Zugck Christian
Published: July 2009

Background

Training studies frequently use maximum inspiratory mouth occlusion pressure (PImax) as a therapeutic target and surrogate marker. For patients on β-blocker (BBL), prognostic data allowing this extrapolation do not exist. Furthermore, the effects of BBL, mainstay of modern chronic heart failure therapy, on respiratory muscle function remain controversial. Finally, no proper separate cutoff according to treatment exists.

Design

Prospective, observational inclusion of patients with stable systolic chronic heart failure and recording of 1 year and all-time mortality for endpoint analysis.

Methods

In 686 patients, 81% men, 494 patients on BBL, PImax was measured along with clinical evaluation. The median follow-up was 50 months (interquartile range: 26–75 months).

Results

Patients with or without BBL did not differ significantly for PImax, percentage of predicted PImax or other marker of disease severity. PImax was a significant (hazard ratio: 0.925; 95% confidence interval: 0.879–0.975; χ2: 8.62) marker of adverse outcome, independent of BBL-status or aetiology. Percentage of predicted PImax was not independent of PImax. The cutoff identified through receiver-operated characteristics for 1-year mortality was 4.14 kPa for patients on BBL and 7.29 kPa for patients not on BBL. When separated accordingly, 1-year mortality was 8.5 versus 21.4%, P = 0.02, for patients not on BBL and 4.3 versus 16.2%, P < 0.001, for patients on BBL.

Conclusion

This study fills the gap between trials targeting respiratory muscle on a functional basis and the resultant prognostic information with regard to BBL. BBL lowered the optimal PImax cutoff values for risk stratification without changing the measured values of PImax. This should be considered at inclusion and evaluation of trials and interpretation of exercise parameters.
Effects of a 14-month low-cost maintenance training program in patients with chronic systolic heart failure: a randomized study
Authors: Prescott Eva , Hjardem-Hansen Rasmus , Dela Flemming , Ørkild Bodil , Teisner Ane S. , Nielsen Henrik
Published: July 2009

Background

Exercise training is known to be beneficial in chronic heart failure (CH F) patients but there is a lack of studies following patient groups for longer duration with maintenance training programs to defer deconditioning.

Methods

Study base consisted of all patients diagnosed with CHF in a 3-year period. Sixty-six patients with systolic CHF (ejection fraction < 45, New York Heart Association II-III) were randomized to 12 months of either usual care or home-based maintenance exercise with group training sessions every 2 weeks after an initial 8-week training program. The primary endpoint was maximum workload; secondary endpoints were 6-min walk test, incremental shuttle walk test, sit-to-stand test, quality of life, and serological markers.

Results

Six patients died and 43 completed the study. The initial 8-week training was associated with small but significant improvement in all of the functional tests. In both groups there was a significant decline in the maximum workload the next 12 months ( P = 0.03 and P < 0.001, respectively) but after an adjustment for difference between groups in baseline characteristics, maintenance intervention reduced the decline in the maximum workload by 8.0W (95% CI: 3.0–13.0, P = 0.002). No effect of maintenance intervention was observed for 6-min walk test, incremental shuttle walk test, sit-to-stand test, or quality of life. After 14 months changes in most markers of inflammation, endothelial damage, and glycemic control were more beneficial in the intervention group.

Conclusion

A low-cost maintenance intervention in CHF patients reduced the decline in the maximum workload compared with usual care but not in other measures of physical function. Results suggest beneficial effects of long-term maintenance training on glycemic control, inflammation, and endothelial function.
Guideline-oriented ambulatory lipid-lowering therapy of patients at high risk for cardiovascular events by cardiologists in clinical practice: the 2L cardio registry
Authors: Gitt Anselm K. , Juenger Claus , Jannowitz Christina , Karmann Barbara , Senges Juergen , Bestehorn Kurt
Published: July 2009

Background

Lipid-lowering treatment has been proven to decrease the rate of cardiovascular events in high-risk patients with manifest coronary artery disease (CAD) or CAD equivalent risk profile. Current treatment guidelines recommend low-density lipoprotein-cholesterol (LDL-C) less than 100 mg/dl (optional < 70 mg/dl) as the target level for this high-risk population. Little is known about the ambulatory treatment of high-risk patients in clinical practice and the achievement of guideline recommended target values.

Methods and results

In the ‘2L cardio’ registry in Germany, 295 cardiologists enrolled 6711 consecutive patients with known CAD, and/or diabetes mellitus, peripheral arterial disease (summarized as ‘coronary risk equivalent’, CE), on chronic statin treatment. They recorded actual LDL-C values at entry, probable changes in therapy, and the expected LDL-C values using a lipid calculator based on an earlier observational study in a similar setting. The three groups comprised 2618 patients with CAD plus CE (39.0%; median LDL-C 112 mg/dl), 3436 patients with CAD only (51.2%; median LDL-C 108 mg/dl), and 657 with CE only (9.8%; median LDL-C 124 mg/dl). They had LDL-C levels less than 100 mg/dl in 36.2% [95% confidence intervals (CI): 34.3–38.1], 39.7% (CI: 38.0–41.4), and 27.2% (CI: 23.7–30.7), respectively. Statin doses at entry were usually in the lower to intermediate range (e.g. simvastatin median 25 mg/day). Cardiologists switched to another statin in 10.1% (9.4–10.8), increased the dose of statins (if same drug) in 22.2% (CI: 21.1–23.2) and/or added a cholesterol absorption inhibitor in 23.7% (CI: 22.7–24.7) of the patients. The cardiologists’ intervention improved expected LDL-C levels in the total cohort by a mean of 9.0 mg/dl, but the 100 mg/dl LDL-C target was only reached in 51.3% (CI: 50.0–52.5) of the total cohort. CE patients appeared undertreated in terms of antiplatelet drugs.

Discussion

Through infrequent increases in statin doses and mainly through add-on of a cholesterol absorption inhibitor, cardiologists improved target level attainment. Compared with earlier studies in the outpatient setting, the treatment to target for LDL-C of high-risk CAD patients has improved, but is not satisfactory.
Impact of different diagnostic criteria on the prevalence and prognostic significance of exertional oscillatory ventilation in patients with chronic heart failure
Authors: Ingle Lee , Isted Aaron , Witte Klaus K. , Cleland John G.F. , Clark Andrew L.
Published: July 2009

Introduction

Exertional oscillatory ventilation (EOV) occurs in many patients with chronic heart failure. Two different definitions of EOV have been proposed by Corrá and Leite. We aimed to compare the prevalence of EOV and its prognostic significance in patients with chronic heart failure using the two diagnostic approaches.

Methods

Patients underwent a symptom-limited, treadmill-based exercise test with metabolic gas exchange measurements using the modified Bruce protocol. EOV was defined (i) as cyclic fluctuations in ventilation lasting for more than 60% of exercise duration, with an amplitude of greater than 15% of the average amplitude of cyclic fluctuations at rest (Corrá) and/or (ii) as three or more regular oscillations with regularity defined if the standard deviation of three consecutive cycle lengths was within 20% of the average coupled with a minimal average amplitude of ventilatory oscillation of 5I (Leite).

Results

Two hundred and forty patients (mean age 59 ± 13 years; 73% males; left ventricular ejection fraction 34 ± 6%; peak VO2 21.0 ± 4.6 ml/kg per min; VE/VCO2 slope 35 ± 9) were included in the study. The prevalence of EOV was 25% using the Corrá method and 31% using the Leite method. Fifty percent of patients diagnosed with EOV by the Corrá criteria and 58% diagnosed by the Leite criteria had died at 12-month follow-up. EOV (Corrá) was a predictor of mortality independent of peak VO2, VE/VCO2 slope, left ventricular ejection fraction, age, and 6-min walk test distance. A hazard ratio (HR) of 6.3 ( P < 0.0001; 95% confidence interval = 1.6–25.2) was evident for the Corrá method, which was higher than for the Leite method (HR = 4.9; P < 0.0001; 95% confidence interval = 2.6–18.2).

Conclusion

The prevalence of EOV was between 25 and 31% depending on the criteria used to define it. The presence of EOV was a powerful predictor of adverse outcome, and diagnosed with the Corrá criteria was associated with a higher HR than the Leite criteria.