bluuebunny/crossref_metadata_2025 huggingface dataset:
Magneto-seismology: effect of inhomogeneous magnetic field on transversal coronal loop oscillations
Authors: Verth G.
Published: May 2008

The extreme-ultraviolet (EUV) imagers onboard the planned Solar Dynamics Observatory (SDO) and Solar Orbiter (SO) will offer us the best chance yet of using observations of post-flare loop oscillations to probe the fine structure of the corona. Recently developed magnetohydrodynamic (MHD) wave theory has shown that the properties of loop oscillations depend on their plasma fine structure. Up to this point, many studies have concentrated solely on the effect of plasma density stratification on coronal loop oscillations. In this paper we develop MHD wave theory which models the effect of an inhomogeneous magnetic field on coronal loop oscillations. The results have the potential to be used in testing the efficacy of photospheric magnetic field extrapolations and have important implications regarding magneto-seismology of the corona.
Influence of longitudinal structure in the fast modes of prominence threads
Authors: Díaz A. J. , Oliver R. , Ballester J. L.
Published: May 2008

Recent high-resolution observations have pointed out that prominences are made of small threads (also named fibrils) piled up to form the body of the prominence. These fine structures also seem to support their own oscillatory modes, while their effect on the global modes of the prominences are less certain. We study the effect of adding a smooth transition layer between the prominence material and the corona along the magnetic field line, since previous studies have considered a jump in density in this interface. Then we compare the results with previous models and check that these transition layers do not affect significantly the periods of the modes.
Exploring short period oscillations in filaments
Authors: Kolobov D. Y. , Kobanov N. I. , Chupin S. A.
Published: May 2008

The authors analyse sources of false Doppler velocity signals of high frequencies (10 mHz and higher) in observations of filaments. In ground-based observations, spectrograph noise and image shifting at the spectrograph entrance slit are the main causes of the false signal. It is shown that using differential methods and telluric lines as reference lines significantly reduces the influence of the first factor. Periodical image shifting along the spectrograph slit can be compensated for during data reduction. In some cases detected high-frequency oscillations appear to be real.
Integrated approach to the coronal heating problem
Authors: Taroyan Y.
Published: May 2008

Solving the coronal heating problem involves dealing with a number of theoretical and observational steps. These include designing instruments, deriving required observables from observations, developing theories and finding the unique footprints of theoretical models. Each of these steps poses its unique challenges to theoreticians and observers. It is important to treat the heating problem in an integrated manner, whereby each component of the problem is treated in its relationship to the other parts rather than in isolation. The paper presents a brief review of recent developments in the field with an emphasis on forward modeling and inversion which play a central role in solving the heating problem by providing the necessary interaction between theories and observations.
Evolution of Alfvén wave-driven solar winds to red giants
Authors: Suzuki Takeru K.
Published: May 2008

In this talk we introduce our recent results of global 1D MHD simulations for the acceleration of solar and stellar winds. We impose transverse photospheric motions corresponding to the granulations, which generate outgoing Alfvén waves. The Alfvén waves effectively dissipate by 3-wave coupling and direct mode conversion to compressive waves in density-stratified atmosphere. We show that the coronal heating and the solar wind acceleration in the open magnetic field regions are natural consequence of the footpoint fluctuations of the magnetic fields at the surface (photosphere). We also discuss winds from red giant stars driven by Alfvén waves, focusing on different aspects from the solar wind. We show that red giants wind are highly structured with intermittent magnetized hot bubbles embedded in cool chromospheric material.
Gaussian pulse propagation in coronal loops
Authors: Mendoza-Briceño César A. , Sigalotti Leonardo Di G. , Guerra Jordan A.
Published: May 2008

We study the linear evolution of a Gaussian pulse injected at different locations along a one-dimensional (1D), hot (T ≥ 6.3 MK) coronal loop, including the dissipative effects of thermal conduction, viscosity, heating, and radiative cooling. We consider both homogeneous and stratified loops of different lengths (50 ≤ L ≤ 400 Mm) and values of the pulse width (or standard deviation, βg/L) between 0.005 and 0.02. We find that a Gaussian velocity pulse can generate propagating waves whose amplitudes increase with increasing width of the pulse. The shape of the waves is quite irregular owing to the superposition of the several harmonics composing the Gaussian pulse. Wave damping due to the combined effects of thermal conduction and viscosity is faster in the shortest and hottest loops. The decay times and periods of the waves are within the observed values of decaying modes of hot SUMER loop oscillations.
A minimal model of parallel electric field generation in a transversely inhomogeneous plasma
Authors: Tsiklauri David
Published: May 2008

The generation of parallel electric fields by the propagation of ion cyclotron waves (with frequency 0.3 ωci) in the plasma with a transverse density inhomogeneity was studied. Using two-fluid, cold plasma linearised equations, it was shown for the first time that, in this particular context, E∥ generation can be understood by an analytic equation that couples E∥ to the transverse electric field of the driving ion cyclotron wave. It was proven that the minimal model required to reproduce the previous kinetic simulation results of E∥ generation [Tsiklauri et al 2005, Génot et al 2004] is the two-fluid, cold plasma approximation in the linear regime. By considering the numerical solutions it was also shown that the cause of E∥ generation is the electron and ion flow separation induced by the transverse density inhomogeneity. We also investigate how E∥ generation is affected by the mass ratio and found that amplitude attained by E∥ decreases linearly as inverse of the mass ratio mi/me. For realistic mass ratio of mi/me=1836, such empirical scaling law, within a time corresponding to 3 periods of the driving ion cyclotron wave, is producing E∥=14 Vm−1 for solar coronal parameters. Increase in mass ratio does not have any effect on final parallel (magnetic field aligned) speed attained by electrons. However, parallel ion velocity decreases linearly with inverse of the mass ratio mi/me. These results can be interpreted as following: (i) ion dynamics plays no role in the E∥ generation; (ii) E∥ ∝ 1/mi scaling is caused by the fact that ωd = 0.3 ωci ∝ 1/mi is decreasing with the increase of ion mass, and hence the electron fluid can effectively “short-circuit” (recombine with) the slowly oscillating ions, hence producing smaller E∥.
Overview of XRT performance and first results
Authors: Savcheva Antonia ,   the XRT Team
Published: May 2008

In this review we present a short introduction to the X-ray Telescope on Hinode. We discuss its capabilities and new features and compare it with Yohkoh SXT. We also discuss some of the first results that include observations of X-ray jets in coronal holes, shear change in flares, sigmoid eruptions and evolution, application of filter ratios and differential emission measure analysis, structure of active regions, fine structure of X-ray bright points, and modeling non-potential fields around filaments. Finally, we describe how XRT works with other ground and space-based instrumentation, in particular with TRACE, EIS, SOT, and SOLIS.
Damping of hydromagnetic waves by bulk viscosity
Authors: Ibáñez S. M. H.
Published: May 2008

It was shown in a previous paper (Ibáñez 2004) that for certain kind of plasmas the coefficient of second (bulk) viscosity can be orders of magnitude larger than the coefficients corresponding to the dynamical viscosity and to the thermometric conductivity. In the present paper, the damping effects of the second viscosity on the hydromagnetic waves propagation are analyzed. In particular, we study the effect of the second viscosity on the magnetoacustic waves propagating in a photoionized gas of arbitrary metallicity Z and mean energy E of the ionizing photons when an initial steady magnetic field H is present.
Qualitative analysis of wave propagation in a 3-D magnetic flux tube
Authors: Jaimes C. , Fedun V.
Published: May 2008

In this work wave propagation in a 3-D magnetic flux tube is solved numerically. The aim is to find interaction between kink waves and higher order modes (flute modes).

A 60x60x60 cube is set up, containing a vertically oriented uniform magnetic flux tube, to solve numerically. Waves are observed propagating after triggering them with solution to the linearized system.

The waves propagate acquiring a distinctive shape (seen in the crosscut of the tube at an arbitrary height showing the radial velocity maps). It is discarded that this is caused by the existence of higher order modes and is found that the radial dependence of the phase speed creates the motion.

It was also found that the study of the profile of the radial velocity map of a slice of the system is a very intuitive way of analysing the modes of waves propagating through the flux tube.
Twisting flux tubes as a cause of micro-flaring activity
Authors: Jess D. B. , McAteer R. T. J. , Mathioudakis M. , Keenan F. P. , Andic A. , Bloomfield D. S.
Published: May 2008

High-cadence optical observations of an H-α blue-wing bright point near solar AR NOAA 10794 are presented. The data were obtained with the Dunn Solar Telescope at the National Solar Observatory/Sacramento Peak using a newly developed camera system, the rapid dual imager. Wavelet analysis is undertaken to search for intensity-related oscillatory signatures, and periodicities ranging from 15 to 370 s are found with significance levels exceeding 95%. During two separate microflaring events, oscillation sites surrounding the bright point are observed to twist. We relate the twisting of the oscillation sites to the twisting of physical flux tubes, thus giving rise to reconnection phenomena. We derive an average twist velocity of 8.1 km/s and detect a peak in the emitted flux between twist angles of 180° and 230°.
Therapeutic Mechanisms of Suicidal Ideation
Authors: Coleman Daniel , Casey John T.
Published: May 2008

The treatment processes associated with reduced suicidal ideation have received little research attention. This study evaluates the influence on suicidal ideation of theory-based intrapsychic processes: maladaptive cognition and defensive style. Thirty-three community mental health patients completed questionnaires at two time points. Decreases in automatic thoughts were a strong correlate of decreased suicidal ideation, and decreases in immature defenses were a moderate strength correlate. These relationships remained significant even when controlling for initial level of depression. The theorized mechanisms of cognitive-behavioral and psychodynamic therapy had the expected effects on suicidal ideation. The strong association of decreased maladaptive cognitions with decreased suicidal ideation supports further development of cognitive-behavioral suicide interventions and clinical use of cognitive interventions. Psychodynamic processes in suicidal ideation and behavior warrant further exploration.
A Pediatric Weight Management Program for High‐risk Populations: A Preliminary Analysis
Authors: Skelton Joseph A. , DeMattia Laure G. , Flores Glenn
Published: May 2008

Objective: To determine whether a multidisciplinary pediatric weight management program effectively improves BMI, BMI z‐score, and cardiovascular risk factors (CVRFs) in high‐risk populations.

Methods and Procedures: A retrospective chart review was performed on children seen in the NEW Kids Program at the Children's Hospital of Wisconsin, a family‐based clinic that treats pediatric obesity using medical management, nutrition education, behavioral intervention, and physical activity. Inclusion criteria were program participation for ≥9 months and >4 visits. Analyses were performed to identify factors associated with pre‐ to postintervention changes in BMI, BMI z‐score, and CVRF laboratory values.

Results: A total of 66 patients met inclusion criteria; the mean age was 11 years (s.d. ± 3.4), 56% were racial/ethnic minorities, 45% were Medicaid recipients, 48% resided in impoverished communities, and 38% had a BMI ≥40 kg/m2. Of the 66 patients, 91% had more than one weight‐related comorbidity, 88% had CVRFs, and the preintervention mean BMI was 37 kg/m2. After the intervention, there was an overall increase in absolute BMI, but a small, yet significant decrease in BMI z‐score (mean −0.03 ± 0.16; P < 0.05). There were significant pregroup to postgroup improvements in total cholesterol, low‐density lipoprotein, and triglycerides levels (P < 0.05). Insurance coverage, race/ethnicity, gender, age, and initial BMI were not significantly associated with changes in BMI or BMI z‐score.

Discussion: A multidisciplinary pediatric weight management program can improve the weight status of high‐risk populations, including minorities, Medicaid recipients, patients with multiple comorbidities and CVRFs, and the severely obese.
Epidemiological Survey for the Prevalence of Overweight and Abdominal Obesity in Greek Adolescents
Authors: Tzotzas Themistoklis , Kapantais Efthymios , Tziomalos Konstantinos , Ioannidis Ioannis , Mortoglou Anastasios , Bakatselos Spiridon , Kaklamanou Myrto , Lanaras Leonidas , Kaklamanos Ioannis
Published: May 2008

This study was designed to provide estimates of overweight (OW), obesity (OB), and abdominal OB (AO) in a representative sample of adolescents throughout the whole of Greece. A total of 14,456 adolescents aged 13–19 years (6,677 boys and 7,779 girls) had direct measurements (height, weight, waist circumference (WC)) taken at school during 2003. The overall prevalence of OW including OB in the population studied was 29.4% in boys and 16.7% in girls. OB prevalence was also higher in boys than in girls (6.1% vs. 2.7%), whereas prevalence of AO was higher in girls than in boys (21.7% vs. 13.5%). Rates of OW, OB, and AO were significantly more prevalent in the Greek than in the foreign male population (immigrants). OW% in adolescent girls was independently associated with smoking and alcohol consumption. The prevalence of OW and OB in Greek adolescents is high, particularly in boys, comparable with that reported for most Mediterranean European countries. AO, mainly in adolescent girls, also appears high. Preventive and treatment strategies are urgently needed to combat this OB epidemic in Greece.
A Decreased Mitochondrial DNA Content Is Related to Insulin Resistance in Adolescents
Authors: Gianotti Tomas F. , Sookoian Silvia , Dieuzeide Guillermo , García Silvia I. , Gemma Carolina , González Claudio D. , Pirola Carlos J.
Published: May 2008

The aim of this study was to investigate whether mitochondrial DNA (mtDNA) content is associated with insulin resistance (IR) in a sample of adolescents with features of metabolic syndrome. We further studied the link between polymorphisms in three genes involved in mitochondrial biogenesis and the presence of deleted mtDNA and mtDNA content. Data and blood samples were collected from 175 adolescents out of a cross‐sectional, population‐based study of 934 high school students. On the basis of the median value of homeostasis model assessment of IR (HOMA‐IR) of the whole sample (2.2), the population was divided into two groups: noninsulin resistance (NIR) and IR. mtDNA quantification using nuclear DNA (nDNA) as a reference was carried out using a real‐time quantitative PCR method. Genotyping for peroxisome proliferator‐activated receptor‐γ (PPAR‐γ) (pro12Ala), PPAR‐ γ coactivator‐1α (PGC‐1α) (Gly482Ser), and Tfam (rs1937 and rs12247015) polymorphisms was performed by PCR‐based restriction fragment length polymorphism. Long‐extension PCR was performed to amplify the whole mitochondrial genome. The mtDNA/nDNA ratio was significantly lower in the IR group (median: 9.08, range: 68.94) in comparison with the NIR group (12.24, 71.92) (P < 0.03). Besides, the mtDNA/nDNA ratio was inversely correlated with HOMA (R: −0.18, P < 0.02), glucose (R: −0.21, P < 0.008), and uric acid (R: −0.18, P < 0.03). Genotypes for the PPAR‐ γ, PGC‐1α, and Tfam variants were not associated with the mtDNA/nDNA ratio. Long‐extension PCR did not show significant levels of mtDNA deletions. In conclusion, our findings indicate that reduced mtDNA content in peripheral leukocytes is associated with IR. This result seems not to be related with the previously mentioned variants in genes involved in the regulation of mitochondrial biogenesis.
Predictors of Excessive and Inadequate Gestational Weight Gain in Hispanic Women
Authors: Chasan‐Taber Lisa , Schmidt Michael D. , Pekow Penelope , Sternfeld Barbara , Solomon Caren G. , Markenson Glenn
Published: May 2008

Factors influencing gestational weight gain are incompletely understood, particularly among Hispanic women. We assessed medical, sociodemographic, behavioral, and psychosocial predictors of overall gestational weight gain, as well as gains below, within, or above the range recommended by the Institute of Medicine (IOM) within a prospective study of 770 Hispanic (predominantly Puerto Rican) prenatal care patients at a large tertiary care facility in Western Massachusetts. One third of women gained within the recommended range, 22% gained below, and 45% gained above the range. In multivariate analysis, women in the highest category of BMI (Ptrend < 0.001) and parity (Ptrend < 0.001) gained on average 9 lbs less than those in the lowest category. Increasing time in residence in the continental United States (Ptrend < 0.01) as well as a number of prenatal care visits (Ptrend = 0.03) were positively associated with weight gain. Overweight women (odds ratio (OR) = 2.2, 95% confidence interval (CI) 1.3, 3.8) and those over age 30 years (OR = 2.5, 95% CI 1.2, 5.0) were more likely to gain above the IOM range as compared to normal‐weight women and those aged 20–24, respectively. Women with <10 years of residence in the United States were 50% less likely to gain above the IOM range as compared to third‐generation women (95% CI 0.3, 0.9). Findings identify determinants of gestational weight gain which can form the basis of targeted interventions in this rapidly growing ethnic group.
Matching Auditory and Visual Signals: Is Sensory Modality Just Another Feature?
Authors: Benjamins Jeroen S , van der Smagt Maarten J , Verstraten Frans A J
Published: May 2008

In order to perceive the world coherently, we need to integrate features of objects and events that are presented to our senses. Here we investigated the temporal limit of integration in unimodal visual and auditory as well as crossmodal auditory–visual conditions. Participants were presented with alternating visual and auditory stimuli and were asked to match them either within or between modalities. At alternation rates of about 4 Hz and higher, participants were no longer able to match visual and auditory stimuli across modalities correctly, while matching within either modality showed higher temporal limits. Manipulating different temporal stimulus characteristics (stimulus offsets and/or auditory–visual SOAs) did not change performance. Interestingly, the difference in temporal limits between crossmodal and unimodal conditions appears strikingly similar to temporal limit differences between unimodal conditions when additional features have to be integrated. We suggest that adding a modality across which sensory input is integrated has the same effect as adding an extra feature to be integrated within a single modality.
Interactive Processes in Matching Identity and Expressions of Unfamiliar Faces: Evidence for Mutual Facilitation Effects
Authors: Levy Yonata , Bentin Shlomo
Published: May 2008

We investigated the interactions between matching identity and expressions of unfamiliar faces. In experiment 1, participants matched expressions in frontal and in oblique views, while we manipulated facial identity. In experiment 2, participants matched identity in frontal and in oblique views, while facial expressions were manipulated. Labeling of expressions was not required. Results showed mutual facilitation between matching facial identity and facial expressions, in accuracy as well as in reaction times. Thus, matching expressions was better and faster for same-identity images in oblique as well as in frontal views (experiment 1), and matching identity was better and faster for same-expression images in oblique as well as in frontal views (experiment 2). The discussion focuses on the implications of these results for the structural encoding of facial identity and facial expressions.
Pasture yield and soil physical property responses to soil compaction from treading and grazing—a review
Authors: Drewry J. J. , Cameron K. C. , Buchan G. D.
Published: May 2008

This paper reviews animal treading and the associated effects on soil physical properties and pasture productivity from treading-induced soil compaction and pugging. Response curve relationships between soil physical properties (e.g. macroporosity, air-filled porosity, bulk density) and pasture and crop yield are reviewed. Optimum soil macroporosity for maximum pasture and crop yield ranges from 6 to 17% v/v, but there is a paucity of yield response curves for pastoral systems, particularly critical or optimum values of soil physical properties. There is little information available on the effects of cattle treading on soil physical properties and consequently pasture yield in seasons when soil pugging and poaching is minimised. Such information is needed to provide practical and rigorously tested decision support tools for land managers during grazing seasons. Knowledge of yield response curves, and critical or optimum values of soil physical properties for field pasture-based grazing systems, is required for improved farm-system production and economic decision support.
Microbial CO2 production from surface and subsurface soil as affected by temperature, moisture, and nitrogen fertilisation
Authors: Jin Xiaobin , Wang Shenmin , Zhou Yinkang
Published: May 2008

The Sanjiang Plain of north-east China is presently the second largest freshwater marsh in China. The drainage and use of marshes for agricultural fields occurred in the past 50 years, resulting in the increase in cultivated land from about 2.9 × 108 m2 in 1893 to 4.57 × 1010 m2 in 1994. Under human disturbance in the past half century, the environment in Sanjiang Plain has had significant change. We hypothesised that environmental factors such as soil moisture, soil temperature, and soil N levels affect the rates of soil organic C mineralisation and the nature of the controls on microbial CO2 production to change with depth through the soil profile in the freshwater marsh in the Sanjiang Plain. In a series of experiments, we measured the influence of soil temperature, soil water content, and nitrogen additions on soil microbial CO2 production rates. The results showed that Q10 values (the factor by which the CO2 production rate increases when the temperature is increased by 10°C) significantly increased with soil depth through the soil profile (P < 0.05). The average Q10 values for the surface soils were 2.7 (0–0.2 m), significantly lower than that (average Q10 values 3.3) for the subsurface samples (0.2–0.6 m) (P < 0.05), indicating that C mineralisation rates were more sensitive to temperature in subsurface soil horizons than in surface horizons. The maximum respiration rate was measured at 60% water hold capacity for each sample. The quadratic equation function adequately describes the relationship between soil respiration and soil water content, and the R2 values were > 0.80. The sensitivity of microbial CO2 production rate response to soil water content for surface soils (0–0.2 m) was slightly lower than for subsurface soils (0.2–0.6 m). The responses of actual soil respiration rates to nitrogen fertilisation were different for surface and subsurface soils. In the surface soils (0–0.2 m), the addition of N caused a slight decreased in respiration rates compared with the control, whereas, in the subsurface soils (0.2–0.6 m), the addition of N tended to increase microbial CO2 production rates, and the addition of 10 µg N/g soil treatment caused twice the increase in C mineralisation rates of the control. Our results suggested that the responses of microbial CO2 production to changes in soil moisture, soil temperature, and soil N levels varied with soil depth through the profile, and subsurface soil organic C was more sensitive to temperature increase and nitrogen inputs in the freshwater marsh of the Sanjiang Plain.
Effect of continuous cropping on potassium forms and potassium adsorption characteristics in calcareous soils of Iran
Authors: Samadi A. , Dovlati B. , Barin M.
Published: May 2008

The potassium (K) status of 5 major soil types, under sugar beet cultivation for 35–40 years, and adjoining virgin lands were compared. Fifty-nine paired surface soil samples belonging to 24 soil series from the major sugar beet growing areas in Western Azarbaijan province located in the north-west of Iran were studied to ascertain whether relative K form sizes and K adsorption behaviour of the soils are being changed by long-term cropping. The samples were analysed for soil physical and chemical properties, mineralogy of clay fraction, different forms of K, and K adsorption characteristics. The soils are alkaline and calcareous. The K-bearing mineral illite is the dominant clay mineral in Typic calcixerepts, Typic haploxerepts, and Typic endoaquepts, whereas in Vertic calcixerepts and Vertic endoquepts, the clay mineralogy is dominated by smectite. A highly significant relationship (r2 = 77, P ≤ 0.001) was observed between CEC and smectite content. No changes in K-bearing minerals were detected due to cropping and K depletion. Soil solution K (So-K) constituted 1.7% of exchangeable K (Ex-K) and 1.4% of non-exchangeable K (NEx-K) for the cultivated soils and 1.8% of Ex-K and 2% of NEx-K for the adjacent virgin land. A pronounced significant decline (P ≤ 0.001) in the Ex-K content from 507 to 270 mg/kg (a drop of 45%) and a less significant degree (P ≤ 0.05) in the So-K content from 28 to 12 mg/L (a drop of 55%) were detected in the soil series of Typic calcixerepts as a result of long-term cropping. Continuous sugar beet cropping did not result in changes in the NEx-K contents in any soils except in Vertic endoaquepts containing low illite. A highly significant positive relationship (r2 = 0.79, P ≤ 0.001) was observed between values of NEx-K and illite contents, indicating that this form of K is mainly released from the frayed edges of illite. Paired t-test revealed that continuous sugar beet cultivation increased significantly (P ≤ 0.01) K adsorption in Typic calcixerepts, Typic haploxerepts, and Vertic endoaquepts, where exchangeable K was decreased as a result of intensive cultivation.
Biogenesis of extracellular microfibrils: Multimerization of the fibrillin-1 C terminus into bead-like structures enables self-assembly
Authors: Hubmacher Dirk , El-Hallous Ehab I. , Nelea Valentin , Kaartinen Mari T. , Lee Eunice R. , Reinhardt Dieter P.
Published: May 2008

Microfibrils are essential elements in elastic and nonelastic tissues contributing to homeostasis and growth factor regulation. Fibrillins form the core of these multicomponent assemblies. Various human genetic disorders, the fibrillinopathies, arise from mutations in fibrillins and are frequently associated with aberrant microfibril assembly. These disorders include Marfan syndrome, Weill–Marchesani syndrome, Beals syndrome, and others. Although homotypic and heterotypic fibrillin self-interactions are considered to provide critical initial steps, the detailed mechanisms for microfibril assembly are unknown. We show here that the C-terminal recombinant half of fibrillin-1 assembles into disulfide-bonded multimeric globular structures with peripheral arms and a dense core. These globules are similar to the beaded structures observed in microfibrils isolated from tissues. Only these C-terminal fibrillin-1 multimers interacted strongly with the fibrillin-1 N terminus, whereas the monomers showed very little self-interaction activity. The multimers strongly inhibited microfibril formation in cell culture, providing evidence that these recombinant assemblies can also interact with endogenous fibrillin-1. The C-terminal self-interaction site was fine-mapped to the last three calcium-binding EGF domains in fibrillin-1. These results suggest a new mechanism for microfibril formation where fibrillin-1 first oligomerizes via its C terminus before the partially or fully assembled bead-like structures can further interact with other beads via the fibrillin-1 N termini.
You wrote it; you own it!
Authors: Hill Emma , Rossner Mike
Published: May 2008

Authors of papers published in Rockefeller University Press journals (The Journal of Cell Biology, The Journal of Experimental Medicine, or The Journal of General Physiology) now retain copyright to their published work. This permits authors to reuse their own work in any way, as long as they attribute it to the original publication. Third parties may use our published materials under a Creative Commons license, six months after publication.
Interaction between Epsin/Yap180 Adaptors and the Scaffolds Ede1/Pan1 Is Required for Endocytosis
Authors: Maldonado-Báez Lymarie , Dores Michael R. , Perkins Edward M. , Drivas Theodore G. , Hicke Linda , Wendland Beverly
Published: May 2008

The spatial and temporal regulation of the interactions among the ∼60 proteins required for endocytosis is under active investigation in many laboratories. We have identified the interaction between monomeric clathrin adaptors and endocytic scaffold proteins as a critical prerequisite for the recruitment and/or spatiotemporal dynamics of endocytic proteins at early and late stages of internalization. Quadruple deletion yeast cells (ΔΔΔΔ) lacking four putative adaptors, Ent1/2 and Yap1801/2 (homologues of epsin and AP180/CALM proteins), with a plasmid encoding Ent1 or Yap1802 mutants, have defects in endocytosis and growth at 37°C. Live-cell imaging revealed that the dynamics of the early- and late-acting scaffold proteins Ede1 and Pan1, respectively, depend upon adaptor interactions mediated by adaptor asparagine-proline-phenylalanine motifs binding to scaffold Eps15 homology domains. These results suggest that adaptor/scaffold interactions regulate transitions from early to late events and that clathrin adaptor/scaffold protein interaction is essential for clathrin-mediated endocytosis.
Golgi-resident Small GTPase Rab33B Interacts with Atg16L and Modulates Autophagosome Formation
Authors: Itoh Takashi , Fujita Naonobu , Kanno Eiko , Yamamoto Akitsugu , Yoshimori Tamotsu , Fukuda Mitsunori
Published: May 2008

Macroautophagy is a mechanism of degradation of cytoplasmic components in all eukaryotic cells. In macroautophagy, cytoplasmic components are wrapped by double-membrane structures called autophagosomes, whose formation involves unique membrane dynamics, i.e., de novo formation of a double-membrane sac called the isolation membrane and its elongation. However, the precise regulatory mechanism of isolation membrane formation and elongation remains unknown. In this study, we showed that Golgi-resident small GTPase Rab33B (and Rab33A) specifically interacts with Atg16L, an essential factor in isolation membrane formation, in a guanosine triphosphate-dependent manner. Expression of a GTPase-deficient mutant Rab33B (Rab33B-Q92L) induced the lipidation of LC3, which is an essential process in autophagosome formation, even under nutrient-rich conditions, and attenuated macroautophagy, as judged by the degradation of p62/sequestosome 1. In addition, overexpression of the Rab33B binding domain of Atg16L suppressed autophagosome formation. Our findings suggest that Rab33 modulates autophagosome formation through interaction with Atg16L.
Nucleophosmin Is a Binding Partner of Nucleostemin in Human Osteosarcoma Cells
Authors: Ma Hanhui , Pederson Thoru
Published: May 2008

Nucleostemin (NS) is expressed in the nucleoli of adult and embryonic stem cells and in many tumors and tumor-derived cell lines. In coimmunoprecipitation experiments, nucleostemin is recovered with the tumor suppressor p53, and more recently we have demonstrated that nucleostemin exerts its role in cell cycle progression via a p53-dependent pathway. Here, we report that in human osteosarcoma cells, nucleostemin interacts with nucleophosmin, a nucleolar protein believed to possess oncogenic potential. Nucleostemin (NS) and nucleophosmin (NPM) displayed an extremely high degree of colocalization in the granular component of the nucleolus during interphase, and both proteins associated with prenucleolar bodies in late mitosis before the reformation of nucleoli. Coimmunoprecipitation experiments revealed that NS and NPM co-reside in complexes, and yeast two-hybrid experiments confirmed that they are interactive proteins, revealing the NPM-interactive region to be the 46-amino acid N-terminal domain of NS. In bimolecular fluorescence complementation studies, bright nucleolar signals were observed, indicating that these two proteins directly interact in the nucleolus in vivo. These results support the notion that cell cycle regulatory proteins congress and interact in the nucleolus, adding to the emerging concept that this nuclear domain has functions beyond ribosome production.
Dynamic Movement of the Calcium Sensor STIM1 and the Calcium Channel Orai1 in Activated T-Cells: Puncta and Distal Caps
Authors: Barr Valarie A. , Bernot Kelsie M. , Srikanth Sonal , Gwack Yousang , Balagopalan Lakshmi , Regan Carole K. , Helman Daniel J. , Sommers Connie L. , Oh-hora Masatsugu , Rao Anjana , Samelson Lawrence E.
Published: May 2008

The proteins STIM1 and Orai1 are the long sought components of the store-operated channels required in T-cell activation. However, little is known about the interaction of these proteins in T-cells after engagement of the T-cell receptor. We found that T-cell receptor engagement caused STIM1 and Orai1 to colocalize in puncta near the site of stimulation and accumulate in a dense structure on the opposite side of the T-cell. FRET measurements showed a close interaction between STIM1 and Orai1 both in the puncta and in the dense cap-like structure. The formation of cap-like structures did not entail rearrangement of the entire endoplasmic reticulum. Cap formation depended on TCR engagement and tyrosine phosphorylation, but not on channel activity or Ca2+influx. These caps were very dynamic in T-cells activated by contact with superantigen pulsed B-cells and could move from the distal pole to an existing or a newly forming immunological synapse. One function of this cap may be to provide preassembled Ca2+channel components to existing and newly forming immunological synapses.
Fuel price increase, subsidies, overcapacity, and resource sustainability
Authors: Sumaila Ussif Rashid , Teh Louise , Watson Reg , Tyedmers Peter , Pauly Daniel
Published: May 2008

Sumaila, U. R., Teh, L., Watson, R., Tyedmers, P., and Pauly, D. 2008. Fuel price increase, subsidies, overcapacity, and resource sustainability. – ICES Journal of Marine Science, 65: 832–840. Global fisheries are currently overcapitalized, resulting in overfishing in many of the world’s fisheries. Given that fuel constitutes a significant component of fishing costs, we expect recent increases in fuel prices to reduce overcapacity and overfishing. However, government fuel subsidies to the fishing sector reduce, if not completely negate, this positive aspect of increasing fuel costs. Here, we explore the theoretical basis for the expectation that the increasing fuel prices faced by fishing enterprises will reduce fishing pressure. Next, we estimate the amount of fuel subsidies to the fishing sector by governments globally to be in the range of US$4.2–8.5 billion per year. Hence, depending on how much of this subsidy existed before the recent fuel price increases, fishing enterprises, as a group, can absorb as much as this amount of increase in their fuel budget before any conservation benefits occur as a result of fuel price increases.
Poor condition and infection: a vicious circle in natural populations
Authors: Beldomenico Pablo M , Telfer Sandra , Gebert Stephanie , Lukomski Lukasz , Bennett Malcolm , Begon Michael
Published: May 2008

Pathogens may be important for host population dynamics, as they can be a proximate cause of morbidity and mortality. Infection dynamics, in turn, may be dependent on the underlying condition of hosts. There is a clear potential for synergy between infection and condition: poor condition predisposes to host infections, which further reduce condition and so on. To provide empirical data that support this notion, we measured haematological indicators of infection (neutrophils and monocytes) and condition (red blood cells (RBCs) and lymphocytes) in field voles from three populations sampled monthly for 2 years. Mixed-effect models were developed to evaluate two hypotheses, (i) that individuals with low lymphocyte and/or RBC levels are more prone to show elevated haematological indicators of infection when re-sampled four weeks later, and (ii) that a decline in indicators of condition is likely to follow the development of monocytosis or neutrophilia. We found that individuals with low RBC and lymphocyte counts had increased probabilities of developing monocytosis and higher increments in neutrophils, and that high indices of infection (neutrophilia and monocytosis) were generally followed by a declining tendency in the indicators of condition (RBCs and lymphocytes). The vicious circle that these results describe suggests that while pathogens overall may be more important in wildlife dynamics than has previously been appreciated, specific pathogens are likely to play their part as elements of an interactive web rather than independent entities.
The role of the chromatin remodeler Mi-2β in hematopoietic stem cell self-renewal and multilineage differentiation
Authors: Yoshida Toshimi , Hazan Idit , Zhang Jiangwen , Ng Samuel Y. , Naito Taku , Snippert Hugo J. , Heller Elizabeth J. , Qi Xiaoqing , Lawton Lee N. , Williams Christine J. , Georgopoulos Katia
Published: May 2008

The ability of somatic stem cells to self-renew and differentiate into downstream lineages is dependent on specialized chromatin environments that keep stem cell-specific genes active and key differentiation factors repressed but poised for activation. The epigenetic factors that provide this type of regulation remain ill-defined. Here we provide the first evidence that the SNF2-like ATPase Mi-2β of the Nucleosome Remodeling Deacetylase (NuRD) complex is required for maintenance of and multilineage differentiation in the early hematopoietic hierarchy. Shortly after conditional inactivation of Mi-2β, there is an increase in cycling and a decrease in quiescence in an HSC (hematopoietic stem cell)-enriched bone marrow population. These cycling mutant cells readily differentiate into the erythroid lineage but not into the myeloid and lymphoid lineages. Together, these effects result in an initial expansion of mutant HSC and erythroid progenitors that are later depleted as more differentiated proerythroblasts accumulate at hematopoietic sites exhibiting features of erythroid leukemia. Examination of gene expression in the mutant HSC reveals changes in the expression of genes associated with self-renewal and lineage priming and a pivotal role of Mi-2β in their regulation. Thus, Mi-2β provides the hematopoietic system with immune cell capabilities as well as with an extensive regenerative capacity.
Multiple pathways inhibit NHEJ at telomeres
Authors: Marcand Stéphane , Pardo Benjamin , Gratias Ariane , Cahun Sabrina , Callebaut Isabelle
Published: May 2008

The nonhomologous end-joining (NHEJ) repair pathway is inhibited at telomeres, preventing chromosome fusion. In budding yeast Saccharomyces cerevisiae, the Rap1 protein directly binds the telomere sequences and is required for NHEJ inhibition. Here we show that the Rap1 C-terminal domain establishes two parallel inhibitory pathways through the proteins Rif2 and Sir4. In addition, the central domain of Rap1 inhibits NHEJ independently of Rif2 and Sir4. Thus, Rap1 establishes several independent pathways to prevent telomere fusions. We discuss a possible mechanism that would explain Rif2 multifunctionality at telomeres and the recent evolutionary origin of Rif2 from an origin recognition complex (ORC) subunit.
Actively transcribed rRNA genes in S. cerevisiae are organized in a specialized chromatin associated with the high-mobility group protein Hmo1 and are largely devoid of histone molecules
Authors: Merz Katharina , Hondele Maria , Goetze Hannah , Gmelch Katharina , Stoeckl Ulrike , Griesenbeck Joachim
Published: May 2008

Synthesis of ribosomal RNAs (rRNAs) is the major transcriptional event in proliferating cells. In eukaryotes, ribosomal DNA (rDNA) is transcribed by RNA polymerase I from a multicopy locus coexisting in at least two different chromatin states. This heterogeneity of rDNA chromatin has been an obstacle to defining its molecular composition. We developed an approach to analyze differential protein association with each of the two rDNA chromatin states in vivo in the yeast Saccharomyces cerevisiae. We demonstrate that actively transcribed rRNA genes are largely devoid of histone molecules, but instead associate with the high-mobility group protein Hmo1.
Two strategies for gene regulation by promoter nucleosomes
Authors: Tirosh Itay , Barkai Naama
Published: May 2008

Chromatin structure is central for the regulation of gene expression, but its genome-wide organization is only beginning to be understood. Here, we examine the connection between patterns of nucleosome occupancy and the capacity to modulate gene expression upon changing conditions, i.e., transcriptional plasticity. By analyzing genome-wide data of nucleosome positioning in yeast, we find that the presence of nucleosomes close to the transcription start site is associated with high transcriptional plasticity, while nucleosomes at more distant upstream positions are negatively correlated with transcriptional plasticity. Based on this, we identify two typical promoter structures associated with low or high plasticity, respectively. The first class is characterized by a relatively large nucleosome-free region close to the start site coupled with well-positioned nucleosomes further upstream, whereas the second class displays a more evenly distributed and dynamic nucleosome positioning, with high occupancy close to the start site. The two classes are further distinguished by multiple promoter features, including histone turnover, binding site locations, H2A.Z occupancy, expression noise, and expression diversity. Analysis of nucleosome positioning in human promoters reproduces the main observations. Our results suggest two distinct strategies for gene regulation by chromatin, which are selectively employed by different genes.
Making Solutions from Dry Chemicals
Authors: Adams Dany Spencer
Published: May 2008

INTRODUCTION

Solution making most typically involves dissolving a dry chemical in water or other specified solvent. The amount of chemical to be added to a solvent depends on the final concentration or molarity (M) needed for the finished solution and the total amount in liters (L) of solution required. The easiest way to measure chemicals is by mass. Typically, to make a solution one must determine the mass of chemical needed, based on the desired final concentration (usually molarity), the molecular weight (MW) of the chemical, and the final volume of solution. This article describes the calculations involved in making solutions from dry chemicals.
Making Solutions from Hydrated Compounds
Authors: Adams Dany Spencer
Published: May 2008

INTRODUCTION

Solution making typically involves dissolving dry chemicals in water or other specified solvent. The amount of chemical to be added to a solvent depends on the final concentration or molarity (M) needed for the finished solution and the total amount in liters (L) of solution required. However, some chemicals come with water molecules attached. The molecular weight (MW) of such compounds, listed as formula weight (FW) on the bottle, includes the mass of the water. Whenever you would use the MW of an unhydrated compound in calculations, use instead the MW of the hydrated compound. If a recipe tells how many grams to use of the unhydrated compound, determine the target concentration and then calculate the grams to use of hydrated compound. When using a hydrated compound, the attached water molecules contribute water to the solution, potentially diluting the final concentration (if the solvent is water). Therefore, you must account for the contribution of water from the hydrated compound when determining the volume of solvent (water) to add. This article describes the calculations involved in making solutions from hydrated compounds.
Alkaline Phosphatase Treatment of Phosphopeptides: In-Solution Dephosphorylation prior to MALDI-MS Analysis
Authors: Steen Hanno , Stensballe Allan , Jensen Ole N.
Published: May 2008

INTRODUCTION

The use of the enzyme alkaline phosphatase allows identification of phosphopeptides in a mixture of predominantly nonphosphopeptides. Using a MALDI-MS instrument, the masses of peptides are acquired both before and after alkaline phosphatase treatment, which removes phospho-moieties from serine, threonine, and/or tyrosine. (Any peptide whose mass decreases by 80 Da, or a multiple thereof, is a phosphopeptide.) An advantage of using MALDI-MS for these experiments is that the peptide ions produced tend to be singly charged rather than multiply charged (as with ESI), thus making the interpretation easier. This protocol describes a method for in-solution dephosphorylation prior to MALDI-MS analysis.
Mapping Protein Distributions on Polytene Chromosomes by Immunostaining
Authors: Paro Renato
Published: May 2008

INTRODUCTION

The formidable size and structure of polytene chromosomes allow mapping of chromosomal protein distributions at very high resolution. This protocol describes the preparation of polytene chromosomes from Drosophila larvae, immunostaining of the chromosomes with a protein of interest, and counterstaining with Giemsa and Hoechst.
THE ROLE OF GLUCOCORTICOID HORMONES IN THE CONTROL OF EPIDERMAL MITOSIS
Authors: Bullough William S. , Laurence Edna B.
Published: May 2008

It has previously been established that the epidermal chalone inhibits epidermal mitotic activity more powerfully in the presence of adrenalin, although adrenalin itself is not a mitotic inhibitor. It is now shown that in low concentrations hydrocortisone has little if any antimitotic activity, that when it is present together with chalone and adrenalin it does not markedly increase their antimitotic activity, but that it does act to prolong the mitotic depression which they induce.

It is known that, without hydrocortisone, adrenalin rapidly escapes from epidermal cells so that the chalone action is weakened. It appears that the role of hydrocortisone may be to reduce the rate of adrenalin loss and thus to prolong the chalone‐adrenalin activity.

It is also shown that the rate of loss of adrenalin from epidermal cells is inhibited, though to a much lesser extent, in the presence of excess chalone.