bluuebunny/crossref_metadata_2025 huggingface dataset:
Validation of the Aura Microwave Limb Sounder HNO3 measurements
Authors: Santee M. L. , Lambert A. , Read W. G. , Livesey N. J. , Cofield R. E. , Cuddy D. T. , Daffer W. H. , Drouin B. J. , Froidevaux L. , Fuller R. A. , Jarnot R. F. , Knosp B. W. , Manney G. L. , Perun V. S. , Snyder W. V. , Stek P. C. , Thurstans R. P. , Wagner P. A. , Waters J. W. , Muscari G. , de Zafra R. L. , Dibb J. E. , Fahey D. W. , Popp P. J. , Marcy T. P. , Jucks K. W. , Toon G. C. , Stachnik R. A. , Bernath P. F. , Boone C. D. , Walker K. A. , Urban J. , Murtagh D.
Published: December 2007

We assess the quality of the version 2.2 (v2.2) HNO3 measurements from the Microwave Limb Sounder (MLS) on the Earth Observing System Aura satellite. The MLS HNO3 product has been greatly improved over that in the previous version (v1.5), with smoother profiles, much more realistic behavior at the lowest retrieval levels, and correction of a high bias caused by an error in one of the spectroscopy files used in v1.5 processing. The v2.2 HNO3 data are scientifically useful over the range 215 to 3.2 hPa, with single‐profile precision of ∼0.7 ppbv throughout. Vertical resolution is 3–4 km in the upper troposphere and lower stratosphere, degrading to ∼5 km in the middle and upper stratosphere. The impact of various sources of systematic uncertainty has been quantified through a comprehensive set of retrieval simulations. In aggregate, systematic uncertainties are estimated to induce in the v2.2 HNO3 measurements biases that vary with altitude between ±0.5 and ±2 ppbv and multiplicative errors of ±5–15% throughout the stratosphere, rising to ∼±30% at 215 hPa. Consistent with this uncertainty analysis, comparisons with correlative data sets show that relative to HNO3 measurements from ground‐based, balloon‐borne, and satellite instruments operating in both the infrared and microwave regions of the spectrum, MLS v2.2 HNO3 mixing ratios are uniformly low by 10–30% throughout most of the stratosphere. Comparisons with in situ measurements made from the DC‐8 and WB‐57 aircraft in the upper troposphere and lowermost stratosphere indicate that the MLS HNO3 values are low in this region as well, but are useful for scientific studies (with appropriate averaging).
Phonological Awareness Intervention: Beyond the Basics
Authors: Schuele C. Melanie , Boudreau Donna
Published: December 2007

Purpose

The purpose of this article is to advance practitioners' knowledge base of best practices in phonological awareness intervention to facilitate the implementation of evidence- or research-based practices in everyday clinical practice. Although most speech-language pathologists (SLPs) have a basic knowledge of phonological awareness, this article provides additional information on the variables to consider in the design and implementation of phonological awareness intervention; access to this information has a clear impact on practitioners' efforts to move research to practice.

Method

We reviewed the relevant literature on the nature and development of phonological awareness and phonological awareness intervention to identify evidence-based intervention practices. We draw on clinical experience to supplement the research literature, particularly where the research literature provides limited direction.

Implications

SLPs have a unique contribution to make in school-based teams' efforts to facilitate literacy development in children, particularly children who are at risk for reading disability. Research provides much information to guide clinicians in the design and implementation of phonological awareness intervention.
Promoting Literacy in Students With ASD: The Basics for the SLP
Authors: Lanter Elizabeth , Watson Linda R.
Published: December 2007

Purpose

This article provides a tutorial for speech-language pathologists (SLPs) concerning approaches for improving the reading skills of students with autism spectrum disorder (ASD). SLPs are encouraged to modify their role to include a literacy focus, not only because of inclusion and standardized reading tests, but also because SLPs offer skills to enrich the literacy skills of students with ASD.

Method

This article is organized to provide guidance on approaches associated with reading achievements in 3 stages of development: (a) emergent, (b) conventional, and (c) skilled reading. For each, we provide a brief overview of major achievements observed in students with typical development as well as a synopsis of what is currently known concerning the achievements of students with ASD. We then provide suggestions concerning specific approaches that can be used to further the reading and oral language skills of students with ASD within the particular stage.

Implications

This article suggests literacy interventions that target critical oral language and literacy skills that have been well documented as areas of need among many students with ASD. SLPs can draw on this information when designing and implementing transdiciplinary literacy interventions for this growing population of students whose literacy needs are currently underserved.
Absenteeism Rates in Students Receiving Services for CDs, LDs, and EDs: A Macroscopic View of the Consequences of Disability
Authors: Redmond Sean M. , Hosp John L.
Published: December 2007

Purpose

Elevated levels of absenteeism have been reported for students receiving special education services, especially students with learning disabilities (LDs) and emotional disturbances (EDs). In contrast, little is known about absenteeism rates associated with students with communication disorders (CDs).

Method

Archival records of student attendance for the 1997–2001 academic years from a mid-sized urban school district in the Intermountain West were used to examine absenteeism rates in students receiving services for CDs, LDs, and EDs. Two cohort samples were generated (K–4th grade and 5th–9th grade).

Results

Students with CDs displayed absenteeism rates that were comparable to those of students receiving general education. Significant group and group × grade effects were found. Students in the LD and ED groups displayed elevated levels of absenteeism, especially at Grade 9.

Conclusion

The outcomes of this study support the characterization of the socioemotional concomitants associated with CDs as being typologically different and exerting a weaker influence on student’s health levels than those associated with either LDs or EDs.
Language Intervention Practices for School-Age Children With Spoken Language Disorders: A Systematic Review
Authors: Cirrin Frank M. , Gillam Ronald B.
Published: December 2007

Purpose

This systematic review focuses on peer-reviewed articles published since 1985 that assess the outcomes of language intervention practices for school-age students with spoken language disorders.

Method

We conducted computer searches of electronic databases and hand searches of other sources for studies that used experimental designs that were considered to be reliable and valid: randomized clinical trials, nonrandomized comparison studies, and multiple-baseline single-subject design studies.

Results

The review yielded 21 studies concerning the efficacy or effectiveness of language intervention practices with school-age children since 1985. Eleven of the studies limited participants to children in kindergarten and first grade, and no studies were located that focused on students in middle grades or high school. The relatively high quality of the studies that met our criteria, and the moderate-to-high effect sizes we calculated for the majority of studies, suggests that clinicians can have some confidence in the specific language intervention practices examined.

Conclusion

The fact that only 21 studies met our criteria means that there is relatively little evidence supporting the language intervention practices that are currently being used with school-age children with language disorders. We outline significant gaps in the evidence and discuss the implications for clinical practice in schools.
Mice with targeted
Slc4a10
gene disruption have small brain ventricles and show reduced neuronal excitability
Authors: Jacobs Stefan , Ruusuvuori Eva , Sipilä Sampsa T. , Haapanen Aleksi , Damkier Helle H. , Kurth Ingo , Hentschke Moritz , Schweizer Michaela , Rudhard York , Laatikainen Linda M. , Tyynelä Jaana , Praetorius Jeppe , Voipio Juha , Hübner Christian A.
Published: December 2007

Members of the SLC4 bicarbonate transporter family are involved in solute transport and pH homeostasis. Here we report that disrupting the
Slc4a10
gene, which encodes the Na
+
-coupled Cl
−
–HCO
3
−
exchanger Slc4a10 (NCBE), drastically reduces brain ventricle volume and protects against fatal epileptic seizures in mice. In choroid plexus epithelial cells, Slc4a10 localizes to the basolateral membrane. These cells displayed a diminished recovery from an acid load in KO mice. Slc4a10 also was expressed in neurons. Within the hippocampus, the Slc4a10 protein was abundant in CA3 pyramidal cells. In the CA3 area, propionate-induced intracellular acidification and attenuation of 4-aminopyridine-induced network activity were prolonged in KO mice. Our data indicate that Slc4a10 is involved in the control of neuronal pH and excitability and may contribute to the secretion of cerebrospinal fluid. Hence, Slc4a10 is a promising pharmacological target for the therapy of epilepsy or elevated intracranial pressure.
Heterogeneity in EGF-binding affinities arises from negative cooperativity in an aggregating system
Authors: Macdonald Jennifer L. , Pike Linda J.
Published: December 2007

Scatchard analysis of the binding of EGF to its receptor yields concave up plots that indicate the presence of two classes of binding sites. However, how two independent classes of sites arise from the expression of a single EGF receptor protein has never been adequately explained. Using a new analytical approach involving the simultaneous fitting of binding isotherms from cells expressing increasing levels of EGF receptors, we show that
125
I-EGF-binding data can be completely explained by a model involving negative cooperativity in an aggregating system. This approach provides an experimentally determined value for the monomer–dimer equilibrium constant, which, for wild-type EGF receptors, corresponds to ≈50,000 receptors per cell. Therefore, changes in receptor expression within the physiological range can modulate the outcome of a signaling stimulus. Analysis of the L680N-EGF receptor mutant, in which the formation of asymmetric kinase domain dimers is blocked, indicates that the kinase dimers make a substantial energetic contribution to the ligand-independent association of EGF receptor monomers, but are not necessary for negative cooperativity. The model accurately predicts the behavior of receptor mutants, such as the dimerization-defective Y246D-EGF receptor, which exhibit a single class of binding sites and provides a framework for understanding secondary dimer formation and lateral signaling in the EGF receptor family.
Clathrin light chains function in mannose phosphate receptor trafficking via regulation of actin assembly
Authors: Poupon Viviane , Girard Martine , Legendre-Guillemin Valerie , Thomas Sebastien , Bourbonniere Lyne , Philie Jacynthe , Bright Nicholas A. , McPherson Peter S.
Published: December 2007

Clathrin-coated vesicles (CCVs) are major carriers for endocytic cargo and mediate important intracellular trafficking events at the trans-Golgi network (TGN) and endosomes. Whereas clathrin heavy chain provides the structural backbone of the clathrin coat, the role of clathrin light chains (CLCs) is poorly understood. We now demonstrate that CLCs are not required for clathrin-mediated endocytosis but are critical for clathrin-mediated trafficking between the TGN and the endosomal system. Specifically, CLC knockdown (KD) causes the cation-independent mannose-6 phosphate receptor (CI-MPR) to cluster near the TGN leading to a delay in processing of the lysosomal hydrolase cathepsin D. A recently identified binding partner for CLCs is huntingtin-interacting protein 1-related (HIP1R), which is required for productive interactions of CCVs with the actin cytoskeleton. CLC KD causes mislocalization of HIP1R and overassembly of actin, which accumulates in patches around the clustered CI-MPR. A dominant-negative CLC construct that disrupts HIP1R/CLC interactions causes similar alterations in CI-MPR trafficking and actin assembly. Thus, in mammalian cells CLCs function in intracellular membrane trafficking by acting as recruitment proteins for HIP1R, enabling HIP1R to regulate actin assembly on clathrin-coated structures.
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation
Authors: Brylinski Michal , Skolnick Jeffrey
Published: December 2007

The detection of ligand-binding sites is often the starting point for protein function identification and drug discovery. Because of inaccuracies in predicted protein structures, extant binding pocket-detection methods are limited to experimentally solved structures. Here, FINDSITE, a method for ligand-binding site prediction and functional annotation based on binding-site similarity across groups of weakly homologous template structures identified from threading, is described. For crystal structures, considering a cutoff distance of 4 Å as the hit criterion, the success rate is 70.9% for identifying the best of top five predicted ligand-binding sites with a ranking accuracy of 76.0%. Both high prediction accuracy and ability to correctly rank identified binding sites are sustained when approximate protein models (<35% sequence identity to the closest template structure) are used, showing a 67.3% success rate with 75.5% ranking accuracy. In practice, FINDSITE tolerates structural inaccuracies in protein models up to a rmsd from the crystal structure of 8–10 Å. This is because analysis of weakly homologous protein models reveals that about half have a rmsd from the native binding site <2 Å. Furthermore, the chemical properties of template-bound ligands can be used to select ligand templates associated with the binding site. In most cases, FINDSITE can accurately assign a molecular function to the protein model.
An alcohol binding site on the neural cell adhesion molecule L1
Authors: Arevalo Enrique , Shanmugasundararaj Sivananthaperumal , Wilkemeyer Michael F. , Dou Xiaowei , Chen Suzhen , Charness Michael E. , Miller Keith W.
Published: December 2007

Prenatal ethanol exposure causes fetal alcohol spectrum disorders (FASD) in part by disrupting the neural cell adhesion molecule L1. L1 gene mutations cause neuropathological abnormalities similar to those of FASD. Ethanol and 1-butanol inhibit L1-mediated cell–cell adhesion (L1 adhesion), whereas 1-octanol antagonizes this action. To test the hypothesis that there are alcohol binding sites on L1, we used 3-azibutanol and 3-azioctanol, the photoactivatable analogs of 1-butanol and 1-octanol, to photolabel the purified Ig1–4 domain of human L1 (hL1 Ig1–4). 3-Azibutanol (11 mM), like ethanol, inhibited L1 adhesion in NIH/3T3 cells stably transfected with hL1, whereas subanesthetic concentrations of 3-azioctanol (14 μM) antagonized ethanol inhibition of L1 adhesion. 3-Azibutanol (100–1,000 μM) and 3-azioctanol (10–100 μM) photoincorporated into Tyr-418 on Ig4 and into two adjacent regions in the N terminus, Glu-33 and Glu-24 to Glu-27. A homology model of hL1 Ig1–4 (residues 33–422), based on the structure of the Ig1–4 domains of axonin-1, suggests that Glu-33 and Tyr-418 hydrogen-bond at the interface of Ig1 and Ig4 to stabilize a horseshoe conformation of L1 that favors homophilic binding. Furthermore, this alcohol binding pocket lies within 7 Å of Leu-120 and Gly-121, residues in which missense mutations cause neurological disorders similar to FASD. These data suggest that ethanol or selected mutations produce neuropathological abnormalities by disrupting the domain interface between Ig1 and Ig4. Characterization of alcohol agonist and antagonist binding sites on L1 will aid in understanding the molecular basis for FASD and might accelerate the development of ethanol antagonists.
Substrate specificity and redox potential of AhpC, a bacterial peroxiredoxin
Authors: Parsonage Derek , Karplus P. Andrew , Poole Leslie B.
Published: December 2007

Typical 2-Cys peroxiredoxins (Prxs) are ubiquitous peroxidases that are involved in peroxide scavenging and/or the regulation of peroxide signaling in eukaryotes. Despite their prevalence, very few Prxs have been reliably characterized in terms of their substrate specificity profile and redox potential even though these values are important for gaining insight into physiological function. Here, we present such studies focusing on
Salmonella typhimurium
alkyl hydroperoxide reductase C component (
St
AhpC), an enzyme that has proven to be an excellent prototype of this largest and most widespread class of Prxs that includes mammalian Prx I–Prx IV. The catalytic efficiencies of
St
AhpC (
k
cat
/
K
m
) are >10
7
M
−1
·s
−1
for inorganic and primary hydroperoxide substrates and ≈100-fold less for tertiary hydroperoxides, with the difference being exclusively caused by changes in
K
m
. The oxidative inactivation of AhpC through reaction with a second molecule of peroxide shows parallel substrate specificity. The midpoint reduction potential of
St
AhpC is determined to be −178 ± 0.4 mV, a value much higher than most other thiol-based redox proteins. The relevance of these results for our understanding of Prx and the physiological role of
St
AhpC is discussed.
Interaction with host SGS3 is required for suppression of RNA silencing by tomato yellow leaf curl virus V2 protein
Authors: Glick Efrat , Zrachya Avi , Levy Yael , Mett Anahit , Gidoni David , Belausov Eduard , Citovsky Vitaly , Gafni Yedidya
Published: December 2007

The V2 protein of tomato yellow leaf curl geminivirus (TYLCV) functions as an RNA-silencing suppressor that counteracts the innate immune response of the host plant. The host-cell target of V2, however, remains unknown. Here we show that V2 interacts directly with SlSGS3, the tomato homolog of the
Arabidopsis
SGS3 protein (AtSGS3), which is known to be involved in the RNA-silencing pathway.
SlSGS3
genetically complemented an
AtSGS3
mutation and restored RNA silencing, indicating that SlSGS3 is indeed a functional homolog of AtSGS3. A point mutant of V2 that is unable to bind SlSGS3 also lost its ability to suppress RNA silencing, suggesting a correlation between the V2–SlSGS3 interaction
in planta
and the suppressor activity of V2.
Differential patterning of cGMP in vascular smooth muscle cells revealed by single GFP-linked biosensors
Authors: Nausch Lydia W. M. , Ledoux Jonathan , Bonev Adrian D. , Nelson Mark T. , Dostmann Wolfgang R.
Published: December 2007

Here, we report the design of unprecedented, non-FRET based cGMP-biosensors, named FlincGs, to assess the dynamics of nitric oxide (NO) and atrial natriuretic peptide (ANP) induced synthesis of intracellular cGMP, [cGMP]
i
. Regulatory fragments of PKG I α, PKG I β, and an N-terminal deletion mutant of PKG I α were fused to circular permutated EGFP to generate α-, β-, and δ-FlincG, with high dynamic ranges and apparent
K
D,cGMP
values of 35 nM, 1.1 μM, and 170 nM, respectively. All indicators displayed significant selectivity for cGMP over cAMP, and 1.5- to 2.1-fold increases in fluorescence intensity at 510 nm when excited at 480 nm. Surprisingly, FlincGs displayed an additional excitation peak at 410 nm. δ-FlincG permitted ratiometric (480/410 nm) measurements, with a cGMP-specific 3.5-fold ratio change. In addition, δ-FlincG presented cGMP association and dissociation kinetics sufficiently fast to monitor rapid changes of [cGMP]
i
in intact cells. In unpassaged, adenoviral transfected vascular smooth muscle (VSM) cells, δ-FlincG had an EC
50,cGMP
of 150 nM, and revealed transient global cGMP elevations to sustained physiological NO (EC
50,DEA/NO
= 4 nM), and the decay phase depended on the activity of PDE-5. In contrast, ANP elicited sustained submembrane elevations in [cGMP]
i
, which were converted to global cGMP elevations by inhibition of PDE-5 by sildenafil. These results indicate that FlincG is an innovative tool to elucidate the dynamics of a central biological signal, cGMP, and that NO and natriuretic peptides induce distinct cGMP patterning under the regulation of PDE-5, and therefore likely differentially engage cGMP targets.
The genetic design of signaling cascades to record receptor activation
Authors: Barnea Gilad , Strapps Walter , Herrada Gilles , Berman Yemiliya , Ong Jane , Kloss Brian , Axel Richard , Lee Kevin J.
Published: December 2007

We have developed an experimental strategy to monitor protein interactions in a cell with a high degree of selectivity and sensitivity. A transcription factor is tethered to a membrane-bound receptor with a linker that contains a cleavage site for a specific protease. Activation of the receptor recruits a signaling protein fused to the protease that then cleaves and releases the transcription factor to activate reporter genes in the nucleus. This strategy converts a transient interaction into a stable and amplifiable reporter gene signal to record the activation of a receptor without interference from endogenous signaling pathways. We have developed this assay for three classes of receptors: G protein-coupled receptors, receptor tyrosine kinases, and steroid hormone receptors. Finally, we use the assay to identify a ligand for the orphan receptor GPR1, suggesting a role for this receptor in the regulation of inflammation.
Effect of aging on regional cerebral blood flow responses associated with osmotic thirst and its satiation by water drinking: A PET study
Authors: Farrell M. J. , Zamarripa F. , Shade R. , Phillips P. A. , McKinley M. , Fox P. T. , Blair-West J. , Denton D. A. , Egan G. F.
Published: December 2007

Levels of thirst and ad libitum drinking decrease with advancing age, making older people vulnerable to dehydration. This study investigated age-related changes in brain responses to thirst and drinking in healthy men. Thirst was induced with hypertonic infusions (3.1 ml/kg 0.51M NaCl) in young (Y) and older (O) subjects. Regional cerebral blood flow (rCBF) was measured with positron emission tomography (PET). Thirst activations were identified by correlating rCBF with thirst ratings. Average rCBF was measured from regions of interest (ROI) corresponding to activation clusters in each group. The effects of drinking were examined by correlating volume of water drunk with changes in ROI rCBF from maximum thirst to postdrinking. There were increases in blood osmolality (Y, 2.8 ± 1.8%; O, 2.2 ± 1.4%) and thirst ratings (Y, 3.1 ± 2.1; O, 3.7 ± 2.8) from baseline to the end of the hypertonic infusion. Older subjects drank less water (1.9 ± 1.6 ml/kg) than younger subjects (3.9 ± 1.9 ml/kg). Thirst-related activation was evident in S1/M1, prefrontal cortex, anterior midcingulate cortex (aMCC), premotor cortex, and superior temporal gyrus in both groups. Postdrinking changes of rCBF in the aMCC correlated with drinking volumes in both groups. There was a greater reduction in aMCC rCBF relative to water drunk in the older group. Aging is associated with changes in satiation that militate against adequate hydration in response to hyperosmolarity, although it is unclear whether these alterations are due to changes in primary afferent inflow or higher cortical functioning.
Zimbabwean Farm Workers in Northern South Africa
Authors: Rutherford Blair , Addison Lincoln
Published: December 2007

This article analyses the precarious livelihoods of Zimbabweans working on commercial farms in northern South Africa. Based on research carried out in 2004 and 2005, we examine how these Zimbabweans seek pathways of survival and, for a few, potential accumulation across space, sectors, and international boundaries. The article analyses how these Zimbabwean farm workers are situated in an ambivalent legal terrain, the neo-liberal restructuring of agriculture and the articulation of paternalistic rule into a far more authoritarian logic of rule on the farms, all of which have made the border-zone a ‘state of exception’ for them which conditions their livelihoods. The article highlights that although these processes intensify labour exploitation, they also recalibrate the survival strategies of Zimbabweans and generate varied forms of resistance.
Genome-wide analysis demonstrates conserved localization of messenger RNAs to mitotic microtubules
Authors: Blower Michael D. , Feric Elma , Weis Karsten , Heald Rebecca
Published: December 2007

RNA localization is of critical importance in many fundamental cell biological and developmental processes by regulating the spatial control of gene expression. To investigate how spindle-localized RNAs might influence mitosis, we comprehensively surveyed all messenger RNAs (mRNAs) that bound to microtubules during metaphase in both Xenopus laevis egg extracts and mitotic human cell extracts. We identify conserved classes of mRNAs that are enriched on microtubules in both human and X. laevis. Active mitotic translation occurs on X. laevis meiotic spindles, and a subset of microtubule-bound mRNAs (MT-mRNAs) associate with polyribosomes. Although many MT-mRNAs associate with polyribosomes, we find that active translation is not required for mRNA localization to mitotic microtubules. Our results represent the first genome-wide survey of mRNAs localized to a specific cytoskeletal component and suggest that microtubule localization of specific mRNAs is likely to function in mitotic regulation and mRNA segregation during cell division.
Mice deficient in involucrin, envoplakin, and periplakin have a defective epidermal barrier
Authors: Sevilla Lisa M. , Nachat Rachida , Groot Karen R. , Klement John F. , Uitto Jouni , Djian Philippe , Määttä Arto , Watt Fiona M.
Published: December 2007

The cornified envelope is assembled from transglutaminase cross-linked proteins and lipids in the outermost epidermal layers and is essential for skin barrier function. Involucrin, envoplakin, and periplakin form the protein scaffold on which the envelope assembles. To examine their combined function, we generated mice deficient in all three genes. The triple knockouts have delayed embryonic barrier formation and postnatal hyperkeratosis (abnormal accumulation of cornified cells) resulting from impaired desquamation. Cornified envelopes form but are ultrastructurally abnormal, with reduced lipid content and decreased mechanical integrity. Expression of proteases is reduced and the protease inhibitor, serpina1b, is highly upregulated, resulting in defective filaggrin processing and delayed degradation of desmoglein 1 and corneodesmosin. There is infiltration of CD4+ T cells and a reduction in resident γδ+ T cells, reminiscent of atopic dermatitis. Thus, combined loss of the cornified envelope proteins not only impairs the epidermal barrier, but also changes the composition of T cell subpopulations in the skin.
Zasp is required for the assembly of functional integrin adhesion sites
Authors: Jani Klodiana , Schöck Frieder
Published: December 2007

The integrin family of heterodimeric transmembrane receptors mediates cell–matrix adhesion. Integrins often localize in highly organized structures, such as focal adhesions in tissue culture and myotendinous junctions in muscles. Our RNA interference screen for genes that prevent integrin-dependent cell spreading identifies Z band alternatively spliced PDZ-motif protein (zasp), encoding the only known Drosophila melanogaster Alp/Enigma PDZ-LIM domain protein. Zasp localizes to integrin adhesion sites and its depletion disrupts integrin adhesion sites. In tissues, Zasp colocalizes with βPS integrin in myotendinous junctions and with α-actinin in muscle Z lines. Zasp also physically interacts with α-actinin. Fly larvae lacking Zasp do not form Z lines and fail to recruit α-actinin to the Z line. At the myotendinous junction, muscles detach in zasp mutants with the onset of contractility. Finally, Zasp interacts genetically with integrins, showing that it regulates integrin function. Our observations point to an important function for Zasp in the assembly of integrin adhesion sites both in cell culture and in tissues.
Two translocating hydrophilic segments of a nascent chain span the ER membrane during multispanning protein topogenesis
Authors: Kida Yuichiro , Morimoto Fumiko , Sakaguchi Masao
Published: December 2007

During protein integration into the endoplasmic reticulum, the N-terminal domain preceding the type I signal-anchor sequence is translocated through a translocon. By fusing a streptavidin-binding peptide tag to the N terminus, we created integration intermediates of multispanning membrane proteins. In a cell-free system, N-terminal domain (N-domain) translocation was arrested by streptavidin and resumed by biotin. Even when N-domain translocation was arrested, the second hydrophobic segment mediated translocation of the downstream hydrophilic segment. In one of the defined intermediates, two hydrophilic segments and two hydrophobic segments formed a transmembrane disposition in a productive state. Both of the translocating hydrophilic segments were crosslinked with a translocon subunit, Sec61α. We conclude that two translocating hydrophilic segment in a single membrane protein can span the membrane during multispanning topogenesis flanking the translocon. Furthermore, even after six successive hydrophobic segments entered the translocon, N-domain translocation could be induced to restart from an arrested state. These observations indicate the remarkably flexible nature of the translocon.
Of Mice and Metaphysics: Natural Selection and Realized Population-Level Properties
Authors: Haug Matthew C.
Published: December 2007

In this paper, I answer a fundamental question facing any view according to which natural selection is a population-level causal process—namely, how is the causal process of natural selection related to, yet not preempted by, causal processes that occur at the level of individual organisms? Without an answer to this grounding question, the population-level causal view appears unstable—collapsing into either an individual-level causal interpretation or the claim that selection is a purely formal, statistical phenomenon. I argue that a causal account of realization provides an answer to the grounding question. By applying this account of realization to the natural selection of melanism in rock pocket mice, I show how an alternative, formal account of realization, favored by proponents of the statistical interpretation, misses biologically important features. More generally, this paper shows how metaphysical issues about realization normally discussed in the philosophy of mind apply to debates in philosophy of biology. Thus, it is a first step toward fleshing out the oft-noted similarities between debates in these areas.
Dynamic Partitioning and the Conventionality of Kinds
Authors: Barrett Jeffrey A.
Published: December 2007

Lewis sender-receiver games illustrate how a meaningful term language might evolve from initially meaningless random signals (Lewis 1969; Skyrms 2006). Here we consider how a meaningful language with a primitive grammar might evolve in a somewhat more subtle sort of game. The evolution of such a language involves the co-evolution of partitions of the physical world into what may seem, at least from the perspective of someone using the language, to correspond to canonical natural kinds. While the evolved language may allow for the sort of precise representation that is required for successful coordinated action and prediction, the apparent natural kinds reflected in its structure may be purely conventional. This has both positive and negative implications for the limits of naturalized metaphysics.
A new construction of quantum error-correcting codes
Authors: Feng Keqin , Xing Chaoping
Published: December 2007

In this paper, we present a characterization of (binary and non-binary) quantum error-correcting codes. Based on this characterization, we introduce a method to construct

p
p

-ary quantum codes using Boolean functions satisfying a system of certain quadratic relations. As a consequence of the construction, we are able to construct quantum codes of minimum distance

2
2

. In particular, we produce a class of binary quantum
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis left-parenthesis n comma 2 Superscript n minus 2 Baseline minus one half StartBinomialOrMatrix n minus 1 Choose left-parenthesis n minus 1 right-parenthesis slash 2 EndBinomialOrMatrix comma 2 right-parenthesis right-parenthesis">

(
(
n
,

2

n
−
2

−

1
2

(

n
−
1

(
n
−
1
)

/

2

)

,
2
)
)

((n,2^{n-2}-\frac 12{n-1\choose (n-1)/2},2))

-codes for odd length

n
≥
5

n\ge 5

. For

n
≥
11

n\ge 11

, this improves the result by Rains in Quantum codes of minimal distance two, 1999, showing the existence of binary quantum

(
(
n
,
3
⋅

2

n
−
4

,
2
)
)

((n,3\cdot 2^{n-4},2))

-codes for odd

n
≥
5

n\ge 5

. Moreover, our binary quantum
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="left-parenthesis left-parenthesis n comma 2 Superscript n minus 2 Baseline minus one half StartBinomialOrMatrix n minus 1 Choose left-parenthesis n minus 1 right-parenthesis slash 2 EndBinomialOrMatrix comma 2 right-parenthesis right-parenthesis">

(
(
n
,

2

n
−
2

−

1
2

(

n
−
1

(
n
−
1
)

/

2

)

,
2
)
)

((n,2^{n-2}-\frac 12{n-1\choose (n-1)/2},2))

-codes of odd length achieve the Singleton bound asymptotically. Finally, based on our characterization some propagation rules of quantum codes are proposed and the rules are similar to those in classical coding theory. It turns out that some new quantum codes are found through these propagation rules.
The Cauchy problem and integrability of a modified Euler-Poisson equation
Authors: Tığlay Feride
Published: December 2007

We prove that the periodic initial value problem for a modified Euler-Poisson equation is well-posed for initial data in

H

s

(

T

m

)

H^{s}(\mathbb {T}^{m})

when

s
>
m

/

2
+
1

s>m/2+1

. We also study the analytic regularity of this problem and prove a Cauchy-Kowalevski type theorem. After presenting a formal derivation of the equation on the semidirect product space

D
i
f
f

⋉

C

∞

(

T

)

\mathrm {Diff} \ltimes C^{\infty }(\mathbb {T})

as a Hamiltonian equation, we concentrate on one space dimension (

m
=
1

m=1

) and show that the equation is bihamiltonian.
Free boundary regularity close to initial state for parabolic obstacle problem
Authors: Shahgholian Henrik
Published: December 2007

In this paper we study the behavior of the free boundary

∂
{
u
>
ψ
}

\partial \{u>\psi \}

, arising in the following complementary problem:
<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" alttext="StartLayout 1st Row left-parenthesis upper H u right-parenthesis left-parenthesis u minus psi right-parenthesis equals 0 comma u greater-than-or-equal-to psi left-parenthesis x comma t right-parenthesis normal i normal n upper Q Superscript plus Baseline comma upper H u less-than-or-equal-to 0 comma u left-parenthesis x comma t right-parenthesis greater-than-or-equal-to psi left-parenthesis x comma t right-parenthesis normal o normal n partial-differential Subscript p Baseline upper Q Superscript plus Baseline period EndLayout">

(
H
u
)
(
u
−
ψ
)
=
0
,

u
≥
ψ
(
x
,
t
)

i
n

 

Q
+

,
H
u
≤
0
,
u
(
x
,
t
)
≥
ψ
(
x
,
t
)

o
n

 

∂
p

Q
+

.

\begin{gather*} (Hu)(u-\psi )=0,\qquad u\geq \psi (x,t) \quad \mathrm {in}\ Q^+, Hu \leq 0, u(x,t) \geq \psi (x,t) \quad \mathrm {on}\ \partial _p Q^+. \end{gather*}

Here

∂
p

\partial _p

denotes the parabolic boundary,

H
H

is a parabolic operator with certain properties,

Q
+

Q^+

is the upper half of the unit cylinder in

R

n
+
1

\textbf {R}^{n+1}

, and the equation is satisfied in the viscosity sense. The obstacle

ψ
\psi

is assumed to be continuous (with a certain smoothness at

{

x
1

=
0

\{x_1=0

,

t
=
0
}

t=0\}

), and coincides with the boundary data

u
(
x
,
0
)
=
ψ
(
x
,
0
)

u(x,0)=\psi (x,0)

at time zero. We also discuss applications in financial markets.
The modal logic of forcing
Authors: Hamkins Joel , Löwe Benedikt
Published: December 2007

A set theoretical assertionψ\psiisforceableorpossible, written◊ψ\Diamond \psi, ifψ\psiholds in some forcing extension, andnecessary, written◻ψ\Box \psi, ifψ\psiholds in all forcing extensions. In this forcing interpretation of modal logic, we establish that if ZFC is consistent, then the ZFC-provable principles of forcing are exactly those in the modal theoryS4.2\mathsf {S4.2}.
Sequential Fourier-Feynman transform, convolution and first variation
Authors: Chang K. , Cho D. , Kim B. , Song T. , Yoo I.
Published: December 2007

Cameron and Storvick introduced the concept of a sequential Fourier-Feynman transform and established the existence of this transform for functionals in a Banach algebra

S

^

\hat {\mathcal S}

of bounded functionals on classical Wiener space. In this paper we investigate various relationships between the sequential Fourier-Feynman transform and the convolution product for functionals which need not be bounded or continuous. Also we study the relationships involving this transform and the first variation.
Uniform Sobolev inequalities and absolute continuity of periodic operators
Authors: Shen Zhongwei , Zhao Peihao
Published: December 2007

We establish certain uniform

L

p

−

L

q

L^{p}-L^{q}

inequalities for a family of second order elliptic operators of the form

(

D

+

k

)
A
(

D

+

k

)

T

( {\mathbf {D}} + {\mathbf {k}} ) A ( {\mathbf {D}}+ {\mathbf {k} })^{T}

on the

d
d

-torus, where

D

=
−
i
∇
,

k

∈

C

d

{\mathbf {D}} =-i\nabla , {\mathbf {k}}\in {\mathbb {C}} ^{d}

and

A
A

is a symmetric, positive definite

d
×
d

d\times d

matrix with real constant entries. Using these Sobolev type inequalities, we obtain the absolute continuity of the spectrum of the periodic Dirac operator on

R

d

{\mathbb R}^{d}

with singular potential. The absolute continuity of the elliptic operator div

(
ω
(

x

)
∇
)

(\omega ( {\mathbf {x}})\nabla )

on

R

d

{\mathbb R}^{d}

with a positive periodic scalar function

ω
(

x

)

\omega ( {\mathbf {x}} )

is also studied.
Effects of FeedingSpodoptera littoralison Lima Bean Leaves: IV. Diurnal and Nocturnal Damage Differentially Initiate Plant Volatile Emission
Authors: Arimura Gen-ichiro , Köpke Sabrina , Kunert Maritta , Volpe Veronica , David Anja , Brand Peter , Dabrowska Paulina , Maffei Massimo E. , Boland Wilhelm
Published: December 2007

Continuous mechanical damage initiates the rhythmic emission of volatiles in lima bean (Phaseolus lunatus) leaves; the emission resembles that induced by herbivore damage. The effect of diurnal versus nocturnal damage on the initiation of plant defense responses was investigated using MecWorm, a robotic device designed to reproduce tissue damage caused by herbivore attack. Lima bean leaves that were damaged by MecWorm during the photophase emitted maximal levels of β-ocimene and (Z)-3-hexenyl acetate in the late photophase. Leaves damaged during the dark phase responded with the nocturnal emission of (Z)-3-hexenyl acetate, but with only low amounts of β-ocimene; this emission was followed by an emission burst directly after the onset of light. In the presence of 13CO2, this light-dependent synthesis of β-ocimene resulted in incorporation of 75% to 85% of 13C, demonstrating that biosynthesis of β-ocimene is almost exclusively fueled by the photosynthetic fixation of CO2 along the plastidial 2-C-methyl-d-erythritol 4-P pathway. Jasmonic acid (JA) accumulated locally in direct response to the damage and led to immediate up-regulation of the P. lunatus β-ocimene synthase gene (PlOS) independent of the phase, that is, light or dark. Nocturnal damage caused significantly higher concentrations of JA (approximately 2–3 times) along with enhanced expression levels of PlOS. Transgenic Arabidopsis thaliana transformed with PlOS promoter∷β-glucuronidase fusion constructs confirmed expression of the enzyme at the wounded sites. In summary, damage-dependent JA levels directly control the expression level of PlOS, regardless of light or dark conditions, and photosynthesis is the major source for the early precursors of the 2-C-methyl-d-erythritol 4-P pathway.
Parasitism by Cuscuta pentagona Attenuates Host Plant Defenses against Insect Herbivores
Authors: Runyon Justin B. , Mescher Mark C. , De Moraes Consuelo M.
Published: December 2007

Considerable research has examined plant responses to concurrent attack by herbivores and pathogens, but the effects of attack by parasitic plants, another important class of plant-feeding organisms, on plant defenses against other enemies has not been explored. We investigated how attack by the parasitic plant Cuscuta pentagona impacted tomato (Solanum lycopersicum) defenses against the chewing insect beet armyworm (Spodoptera exigua; BAW). In response to insect feeding, C. pentagona-infested (parasitized) tomato plants produced only one-third of the antiherbivore phytohormone jasmonic acid (JA) produced by unparasitized plants. Similarly, parasitized tomato, in contrast to unparasitized plants, failed to emit herbivore-induced volatiles after 3 d of BAW feeding. Although parasitism impaired antiherbivore defenses, BAW growth was slower on parasitized tomato leaves. Vines of C. pentagona did not translocate JA from BAW-infested plants: amounts of JA in parasite vines grown on caterpillar-fed and control plants were similar. Parasitized plants generally contained more salicylic acid (SA), which can inhibit JA in some systems. Parasitized mutant (NahG) tomato plants deficient in SA produced more JA in response to insect feeding than parasitized wild-type plants, further suggesting cross talk between the SA and JA defense signaling pathways. However, JA induction by BAW was still reduced in parasitized compared to unparasitized NahG, implying that other factors must be involved. We found that parasitized plants were capable of producing induced volatiles when experimentally treated with JA, indicating that resource depletion by the parasite does not fully explain the observed attenuation of volatile response to herbivore feeding. Collectively, these findings show that parasitic plants can have important consequences for host plant defense against herbivores.
A Naturally Occurring Mutation in an Arabidopsis Accession Affects a β-d-Galactosidase That Increases the Hydrophilic Potential of Rhamnogalacturonan I in Seed Mucilage
Authors: Macquet Audrey , Ralet Marie-Christine , Loudet Olivier , Kronenberger Jocelyne , Mouille Gregory , Marion-Poll Annie , North Helen M.
Published: December 2007

The Arabidopsis thaliana accession Shahdara was identified as a rare naturally occurring mutant that does not liberate seed mucilage on imbibition. The defective locus was found to be allelic to the mum2-1 and mum2-2 mutants. Map-based cloning showed that MUCILAGE-MODIFIED2 (MUM2) encodes the putative β-d-galactosidase BGAL6. Activity assays demonstrated that one of four major β-d-galactosidase activities present in developing siliques is absent in mum2 mutants. No difference was observed in seed coat epidermal cell structure between wild-type and mutant seed; however, weakening of the outer tangential cell wall by chemical treatment resulted in the release of mucilage from mum2 seed coat epidermal cells, and the mum2 mucilage only increased slightly in volume, relative to the wild type. Consistent with the absence of β-d-galactosidase activity in the mutant, the inner layer of mucilage contained more Gal. The allocation of polysaccharides between the inner and outer mucilage layers was also modified in mum2. Mass spectrometry showed that rhamnogalacturonan I in mutant mucilage had more branching between rhamnose and hexose residues relative to the wild type. We conclude that the MUM2/BGAL6 β-d-galactosidase is required for maturation of rhamnogalacturonan I in seed mucilage by the removal of galactose/galactan branches, resulting in increased swelling and extrusion of the mucilage on seed hydration.
The Arabidopsis MUM2 Gene Encodes a β-Galactosidase Required for the Production of Seed Coat Mucilage with Correct Hydration Properties
Authors: Dean Gillian H. , Zheng Huanquan , Tewari Jagdish , Huang Jun , Young Diana S. , Hwang Yeen Ting , Western Tamara L. , Carpita Nicholas C. , McCann Maureen C. , Mansfield Shawn D. , Haughn George W.
Published: December 2007

Seed coat development in Arabidopsis thaliana involves a complex pathway where cells of the outer integument differentiate into a highly specialized cell type after fertilization. One aspect of this developmental process involves the secretion of a large amount of pectinaceous mucilage into the apoplast. When the mature seed coat is exposed to water, this mucilage expands to break the primary cell wall and encapsulate the seed. The mucilage-modified2 (mum2) mutant is characterized by a failure to extrude mucilage on hydration, although mucilage is produced as normal during development. The defect in mum2 appears to reside in the mucilage itself, as mucilage fails to expand even when the barrier of the primary cell wall is removed. We have cloned the MUM2 gene and expressed recombinant MUM2 protein, which has β-galactosidase activity. Biochemical analysis of the mum2 mucilage reveals alterations in pectins that are consistent with a defect in β-galactosidase activity, and we have demonstrated that MUM2 is localized to the cell wall. We propose that MUM2 is involved in modifying mucilage to allow it to expand upon hydration, establishing a link between the galactosyl side-chain structure of pectin and its physical properties.
The Downy Mildew Effector Proteins ATR1 and ATR13 Promote Disease Susceptibility in Arabidopsis thaliana
Authors: Sohn Kee Hoon , Lei Rita , Nemri Adnane , Jones Jonathan D.G.
Published: December 2007

The downy mildew (Hyaloperonospora parasitica) effector proteins ATR1 and ATR13 trigger RPP1-Nd/WsB– and RPP13-Nd–dependent resistance, respectively, in Arabidopsis thaliana. To better understand the functions of these effectors during compatible and incompatible interactions of H. parasitica isolates on Arabidopsis accessions, we developed a novel delivery system using Pseudomonas syringae type III secretion via fusions of ATRs to the N terminus of the P. syringae effector protein, AvrRPS4. ATR1 and ATR13 both triggered the hypersensitive response (HR) and resistance to bacterial pathogens in Arabidopsis carrying RPP1-Nd/WsB or RPP13-Nd, respectively, when delivered from P. syringae pv tomato (Pst) DC3000. In addition, multiple alleles of ATR1 and ATR13 confer enhanced virulence to Pst DC3000 on susceptible Arabidopsis accessions. We conclude that ATR1 and ATR13 positively contribute to pathogen virulence inside host cells. Two ATR13 alleles suppressed bacterial PAMP (for Pathogen-Associated Molecular Patterns)-triggered callose deposition in susceptible Arabidopsis when delivered by DC3000 ΔCEL mutants. Furthermore, expression of another allele of ATR13 in plant cells suppressed PAMP-triggered reactive oxygen species production in addition to callose deposition. Intriguingly, although Wassilewskija (Ws-0) is highly susceptible to H. parasitica isolate Emco5, ATR13Emco5 when delivered by Pst DC3000 triggered localized immunity, including HR, on Ws-0. We suggest that an additional H. parasitica Emco5 effector might suppress ATR13-triggered immunity.