bluuebunny/crossref_metadata_2025 huggingface dataset:
Short-chain fatty acids stimulate the migration of neutrophils to inflammatory sites
Authors: Vinolo Marco A. R. , Rodrigues Hosana G. , Hatanaka Elaine , Hebeda Cristina B. , Farsky Sandra H. P. , Curi Rui
Published: April 2009

SCFAs (short-chain fatty acids) are produced by anaerobic bacterial fermentation. Increased concentrations of these fatty acids are observed in inflammatory conditions, such as periodontal disease, and at sites of anaerobic infection. In the present study, the effect of the SCFAs acetate, propionate and butyrate on neutrophil chemotaxis and migration was investigated. Experiments were carried out in rats and in vitro. The following parameters were measured: rolling, adherence, expression of adhesion molecules in neutrophils (L-selectin and β2 integrin), transmigration, air pouch influx of neutrophils and production of cytokines [CINC-2αβ (cytokine-induced neutrophil chemoattractant-2αβ), IL-1β (interleukin-1β), MIP-1α (macrophage inflammatory protein-1α) and TNF-α (tumour necrosis factor-α)]. SCFAs induced in vivo neutrophil migration and increased the release of CINC-2αβ into the air pouch. These fatty acids increased the number of rolling and adhered cells as evaluated by intravital microscopy. SCFA treatment increased L-selectin expression on the neutrophil surface and L-selectin mRNA levels, but had no effect on the expression of β2 integrin. Propionate and butyrate also increased in vitro transmigration of neutrophils. These results indicate that SCFAs produced by anaerobic bacteria raise neutrophil migration through increased L-selectin expression on neutrophils and CINC-2αβ release.
Hypothesis test for synchronization: Twin surrogates revisited
Authors: Romano M. Carmen , Thiel Marco , Kurths Jürgen , Mergenthaler Konstantin , Engbert Ralf
Published: April 2009

The method of twin surrogates has been introduced to test for phase synchronization of complex systems in the case of passive experiments. In this paper we derive new analytical expressions for the number of twins depending on the size of the neighborhood, as well as on the length of the trajectory. This allows us to determine the optimal parameters for the generation of twin surrogates. Furthermore, we determine the quality of the twin surrogates with respect to several linear and nonlinear statistics depending on the parameters of the method. In the second part of the paper we perform a hypothesis test for phase synchronization in the case of experimental data from fixational eye movements. These miniature eye movements have been shown to play a central role in neural information processing underlying the perception of static visual scenes. The high number of data sets (21 subjects and 30 trials per person) allows us to compare the generated twin surrogates with the “natural” surrogates that correspond to the different trials. We show that the generated twin surrogates reproduce very well all linear and nonlinear characteristics of the underlying experimental system. The synchronization analysis of fixational eye movements by means of twin surrogates reveals that the synchronization between the left and right eye is significant, indicating that either the centers in the brain stem generating fixational eye movements are closely linked, or, alternatively that there is only one center controlling both eyes.
Cantori of the dissipative sawtooth map
Authors: Celletti Alessandra , Guzzo Massimiliano
Published: April 2009

We investigate the existence of cantori for a dissipative version of the sawtooth map. Making use of an explicit parametric representation of the solution, we prove that cantori exist for any irrational value of the frequency. We also perform a numerical study aimed to determine some dynamical properties of the dissipative sawtooth map.
Two-sided estimates of minimum-error distinguishability of mixed quantum states via generalized Holevo–Curlander bounds
Authors: Tyson Jon
Published: April 2009

We prove a concise factor-of-2 estimate for the failure rate of optimally distinguishing an arbitrary ensemble of mixed quantum states, generalizing work of Holevo [Theor. Probab. Appl. 23, 411 (1978)] and Curlander [Ph.D. Thesis, MIT, 1979]. A modification to the minimal principle of Cocha and Poor [Proceedings of the 6th International Conference on Quantum Communication, Measurement, and Computing (Rinton, Princeton, NJ, 2003)] is used to derive a suboptimal measurement which has an error rate within a factor of 2 of the optimal by construction. This measurement is quadratically weighted and has appeared as the first iterate of a sequence of measurements proposed by Ježek et al. [Phys. Rev. A 65, 060301 (2002)]. Unlike the so-called pretty good measurement, it coincides with Holevo’s asymptotically optimal measurement in the case of nonequiprobable pure states. A quadratically weighted version of the measurement bound by Barnum and Knill [J. Math. Phys. 43, 2097 (2002)] is proven. Bounds on the distinguishability of syndromes in the sense of Schumacher and Westmoreland [Phys. Rev. A 56, 131 (1997)] appear as a corollary. An appendix relates our bounds to the trace-Jensen inequality.
Interior- and surface-bound excess electron states in large water cluster anions
Authors: Madarász Ádám , Rossky Peter J. , Turi László
Published: April 2009

We present the results of mixed quantum/classical simulations on relaxed thermal nanoscale water cluster anions, (H2O)n−, with n=200, 500, 1000, and 8000. By using initial equilibration with constraints, we investigate stable/metastable negatively charged water clusters with both surface-bound and interior-bound excess electron states. Characterization of these states is performed in terms of geometrical parameters, energetics, and optical absorption spectroscopy of the clusters. The calculations provide data characterizing these states in the gap between previously published calculations and experiments on smaller clusters and the limiting cases of either an excess electron in bulk water or an excess electron at an infinite water/air interface. The present results are in general agreement with previous simulations and provide a consistent picture of the evolution of the physical properties of water cluster anions with size over the entire size range, including results for vertical detachment energies and absorption spectra that would signify their presence. In particular, the difference in size dependence between surface-bound and interior-bound state absorption spectra is dramatic, while for detachment energies the dependence is qualitatively the same.
Bulk viscosity and compressibility measurement using acoustic spectroscopy
Authors: Dukhin Andrei S. , Goetz Philip J.
Published: April 2009

Bulk viscosity is a somewhat obscure parameter that appears in the hydrodynamic equations for Newtonian liquids when compressibility is important and, together with the dynamic viscosity, controls sound attenuation. Whereas dynamic viscosity reflects only “translational” molecular motion, in contrast the bulk viscosity reflects the relaxation of both “rotational” and “vibrational” degrees of molecular freedom. Several molecular theories yield predictive expressions for both bulk and dynamic viscosities, but experimentally the situation is quite out of balance, in that there is extensive data for the dynamic viscosity of all sorts of liquids, but a paucity of data for bulk viscosity, just a few values for water and a handful of exotic liquids. We compare three possible experimental techniques for measuring bulk viscosity, namely, Brillouin spectroscopy, Laser transient grating spectroscopy, and acoustic spectroscopy. We then formulate some arguments suggesting that acoustic spectroscopy is not only the most suitable for measuring bulk viscosity, but that it also offers a verification procedure that can confirm that the measured parameter agrees with theoretical definition of bulk viscosity for a Newtonian liquid. In addition, acoustic spectroscopy provides a measurement of sound speed, which cannot only improve the attenuation measurement but as a side benefit can also be used to calculate liquid compressibility. We apply this technique for measuring the bulk viscosity and compressibility of twelve commonly assumed Newtonian liquids, two of which surprisingly fails to pass a verification test described here to test the Newtonian hypothesis. Then, we test correlation between measured bulk viscosity and several other intensive properties of these liquids, such as density, dynamic viscosity, dielectric permittivity, and compressibility. We have not discovered any meaningful correlation. This suggests that bulk viscosity is an independent parameter that reflects peculiar properties of liquids and can be used in the set of independent equations describing molecular interaction in liquids.
Numerical studies of slow rhythms emergence in neural microcircuits: Bifurcations and stability
Authors: Komarov M. A. , Osipov G. V. , Suykens J. A. K. , Rabinovich M. I.
Published: April 2009

There is a growing body of evidence that slow brain rhythms are generated by simple inhibitory neural networks. Sequential switching of tonic spiking activity is a widespread phenomenon underlying such rhythms. A realistic generative model explaining such reproducible switching is a dynamical system that employs a closed stable heteroclinic channel (SHC) in its phase space. Despite strong evidence on the existence of SHC, the conditions on its emergence in a spiking network are unclear. In this paper, we analyze a minimal, reciprocally connected circuit of three spiking units and explore all possible dynamical regimes and transitions between them. We show that the SHC arises due to a Neimark–Sacker bifurcation of an unstable cycle.
A new eye-safe lidar design for studying atmospheric aerosol distributions
Authors: Cao Nianwen , Zhou Xiaobing , Li Shusun , Chen Zhongrong
Published: April 2009

This paper presents the design, eye-safe characteristics, and performance of a new eye-safe infrared lidar system for studying city fog. It includes a compact infrared (1574 nm) transmitter, a telescope receiver, and a computer to acquire, store, and process and analyze the measurement data. The development of such a system makes it possible for routine aerosol monitoring in a populated area using lidar technology. A simulation study and a field test show that the system was capable of aerosol monitoring in cities. This lidar system will be used to study the distribution of aerosol over an urban area of 100–200 km2 and will be useful for routine multidimensional aerosol measurements with high resolution in an urban environment.

At the request of the authors and editor, this article is being retracted effective 16 February 2010.
Heat acclimation of grapevine leaf photosynthesis: mezo- and macroclimatic aspects
Authors: Zsófi Zsolt , Váradi Gyula , Bálo Borbála , Marschall Marianna , Nagy Zoltán , Dulai Sándor
Published: April 2009

Heat sensitivity of grapevine (Vitis vinifera L. cv. Kékfrankos) photosynthesis was studied in two vineyards (Eger-Kőlyuktető, flat; and Eger-Nagyeged hill, steep slope) with different mesoclimates and water supply conditions in two climatically different years. 2007 was drier and warmer, with higher vapour pressure deficit (VPD) than 2005. Pre-dawn water potential measurements indicated mild water deficit at the steep-sloped vineyard. In July 2005 mild water deficit enhanced the thermostability of grapevine photosynthesis, as reflected in the temperature dependence of optimal quantum yield (Fv/Fm) and in the critical temperature of initial fluorescence (F0Tc). Decreased Fv/Fm and actual quantum yield (ΔF/Fm′) was recorded at most temperatures in September at the water-stressed (steep slope) site. This time, F0Tcs were also lower due to early leaf senescence. In September 2007, heat sensitivity of Fv/Fm was similar to 2005, and ΔF/Fm′ indicated higher thermostability at both sites, but keeping the consistent difference between the two vineyards. The critical points of steady-state fluorescence (FsTc) were higher by 3−6°C at both vineyards in 2007 than in 2005. Although, in September thermolabile F0 signals were measured at the water-stressed vineyard, the heat sensitivity was not decreased in light adapted state, assumingly as a result of enhanced xanthophyll cycle pigment pool size. The higher xanthophyll pigments pool size (V + A + Z) in 2007 (compared to 2005) at the unstressed (flat) vineyard suggests that high temperature and VPD play a role in changing (V + A + Z)/(chl a + b), and, thus, results in higher thermostability under high light conditions.
Willow species (genus: Salix) with contrasting habitat affinities differ in their photoprotective responses to water stress
Authors: Savage Jessica A. , Cavender-Bares Jeannine , Verhoeven Amy
Published: April 2009

Although many Mediterranean and xeric plant species enhance their xanthophyll-mediated thermal dissipation under drought conditions, there has been limited research on photoprotective mechanism in droughted plants from other habitats. To investigate whether wetland plants utilise this mechanism under drought conditions, and whether species differ in their responses depending on their habitat affinities, we investigated the response of six willow (Salix) species to a short-term drought. In a greenhouse, 40 individuals per species were dried down over 4 weeks. Periodically during the drought, predawn and midday chlorophyll fluorescence measurements were taken and leaf discs were collected for pigment analysis with HPLC. Predawn water potential was also monitored throughout the experiment. All six species increased xanthophyll cycle activity and their capacity to dissipate excess energy during the drought by increasing their total de-epoxidised xanthophyll concentration and the concentration of zeaxanthin in proportion to chlorophyll. In general, habitat generalists had greater photoprotective responses than wetland specialists, while the wetland specialists had higher pre-drought nonphotochemical quenching. These differences are consistent with their contrasting photosynthetic rates. The observed variation in species drought responses suggests that their photoprotective strategies vary with habitat affinity.
The phonology of mixed languages
Authors: van Gijn Rik
Published: April 2009

Mixed languages are said to be the result of a process of intertwining (e.g. Bakker & Muysken 1995, Bakker 1997), a regular process in which the grammar of one language is combined with the lexicon of another. However, the outcome of this process differs from language pair to language pair. As far as morphosyntax is concerned, people have discussed these different outcomes and the reasons for them extensively, e.g. Bakker 1997 for Michif, Mous 2003 for Ma’a, Muysken 1997a for Media Lengua and 1997b for Callahuaya. The issue of phonology, however, has not generated a large debate. This paper compares the phonological systems of the mixed languages Media Lengua, Callahuaya, Mednyj Aleut, and Michif. It will be argued that the outcome of the process of intertwining, as far as phonology is concerned, is at least partly determined by the extent to which unmixed phonological domains exist.
Auditory P300 Event‐Related Potentials and Neurocognitive Functions in Opioid Dependent Men and Their Brothers
Authors: Singh Shubh Mohan , Basu Debasish , Kohli Adarsh , Prabhakar Sudesh
Published: April 2009

Event‐related‐potentials (especially P300) and cognitive functioning as potential endophenotypes have not been studied in opioid dependence. We compared auditory P300 and cognitive functions in opioid‐dependent men, their brothers and normal controls in an exploratory study with a view to find shared genetic factors in the development of opioid dependence. Twenty abstinent opioid‐dependent males, their brothers and twenty matched controls were administered Wisconsin card sorting test (WCST), digit span test, trail making test‐B, and auditory event‐related potentials (P300) from an oddball task were recorded. The opioid dependent group performed the worst, the brothers group was intermediate, and the control group performed the best on tests of WCST, digit span and trail making test‐B. The opioid dependent group had the smallest amplitudes and longest latencies of P300, and was followed by the brothers group who had an intermediate position and the control group who had the largest amplitudes and the shortest latencies. P300 and executive neurocognitive functions can be considered endophenotypes for the genetic study of vulnerability to opioid dependence. These are reflective of executive dysfunction and disrupted behavioral inhibition and the intermediate position of brothers suggests a common genetic substrate as a component of the etiology.
Are Women at Greater Risk? An Examination of Alcohol‐Related Consequences and Gender
Authors: Sugarman Dawn E. , DeMartini Kelly S. , Carey Kate B.
Published: April 2009

Men typically drink more than women; however, women achieve higher BACs (blood alcohol concentration) than men at equivalent consumption levels. This study investigated the unique effect of gender on individual alcohol problems by controlling both consumption and intoxication in a sample of 1,331 undergraduate drinkers. Gender independently influenced the risk of experiencing seven of nine negative consequences: (a) being female increased risk for tolerance, blacking out, passing out, drinking after promising not to, and getting injured; (b) being male increased risk for damaging property and going to school drunk. Gender patterns should be explored in a wider set of alcohol‐related problems.
A Randomized, Double‐Blind, Placebo‐Controlled Trial of Naltrexone in the Treatment of Concurrent Alcohol Use Disorder and Pathological Gambling
Authors: Toneatto Tony , Brands Bruna , Selby Peter
Published: April 2009

The efficacy of naltrexone as a treatment for concurrent alcohol abuse or dependence and pathological gambling was evaluated in a randomized, double‐blind, placebo‐controlled trial. Fifty‐two, mostly male, subjects were recruited from the community and received 11 weeks of medication during which cognitive‐behavioral counseling was also provided. No significant group differences were found on any alcohol or gambling variable (ie, frequency, quantity, expenditures) at post‐treatment or at the one year follow‐up. However, a strong time effect was found suggesting that treatment, in general, was effective. The use of naltrexone to treat concurrent alcohol use and gambling problems was not supported.
Adult psychosocial outcomes of children with specific language impairment, pragmatic language impairment and autism
Authors: Whitehouse Andrew J. O. , Watt Helen J. , Line E. A. , Bishop Dorothy V. M.
Published: April 2009

Background: The few studies that have tracked children with developmental language disorder to adulthood have found that these individuals experience considerable difficulties with psychosocial adjustment (for example, academic, vocational and social aptitude). Evidence that some children also develop autistic symptomatology over time has raised suggestions that developmental language disorder may be a high‐functioning form of an autism spectrum disorder (ASD). It is not yet clear whether these outcomes vary between individuals with different subtypes of language impairment.

Aims: To compare the adult psychosocial outcomes of children with specific language impairment (SLI), pragmatic language impairment (PLI) and ASD.

Methods & Procedures: All participants took part in research as children. In total, there were 19 young adults with a childhood history of Specific Language Impairment (M age = 24;8), seven with PLI (M age = 22;3), 11 with high functioning ASD (M age = 21;9) and 12 adults with no history of developmental disorder (Typical; n = 12; M age = 21;6). At follow‐up, participants and their parents were interviewed to elicit information about psychosocial outcomes.

Outcomes & Results: Participants in the SLI group were most likely to pursue vocational training and work in jobs not requiring a high level of language/literacy ability. The PLI group tended to obtain higher levels of education and work in ‘skilled’ professions. The ASD participants had lower levels of independence and more difficulty obtaining employment than the PLI and SLI participants. All groups had problems establishing social relationships, but these difficulties were most prominent in the PLI and ASD groups. A small number of participants in each group were found to experience affective disturbances. The PLI and SLI groups showed lower levels of autistic symptomatology than the ASD group.

Conclusions & Implications: The between‐group differences in autistic symptomatology provide further evidence that SLI, PLI, and ASD are related disorders that vary along qualitative dimensions of language structure, language use and circumscribed interests. Childhood diagnosis showed some relation to adult psychosocial outcome. However, within‐group variation highlights the importance of evaluating children on a case‐by‐case basis.
Temporal evolution of H-mode pedestal in DIII-D
Authors: Groebner R.J. , Osborne T.H. , Leonard A.W. , Fenstermacher M.E.
Published: April 2009

The temporal evolution of pedestal parameters is examined in the initial edge localized mode (ELM)-free phase and inter-ELM phases of H-mode discharges in the DIII-D tokamak. These discharges are heated by deuterium neutral beam injection and achieve type-I ELMing conditions. Pedestal parameters exhibit qualitatively similar behaviour in both the ELM-free and inter-ELM phases. There is a trend for the widths and heights of pedestals for electron density, temperature and pressure to increase during these phases; the increase in width is most pronounced in the density and least pronounced in electron temperature. Near the separatrix, the ion temperature achieves higher values but a flatter profile as compared with the electron temperature. Higher heating powers lead to a faster evolution of the pedestal and to a shorter period until the onset of an ELM. For sufficiently long ELM-free or inter-ELM periods, some parameters, particularly gradients, approach a steady state. However, a simultaneous steady state in all parameters is not observed. The simultaneous increase in density width and pedestal density is opposite to the predictions of a simple model, which predicts that the density width is set by neutral penetration. Thus, additional physics must be added to the simple model to provide a more general description of pedestal behaviour. However, the barrier growth is qualitatively consistent with time-dependent theoretical models that predict a self-consistent temporal growth of the pedestal due to E × B shearing effects. In addition, an approximate linear correlation is observed between the density width and the square root of the pedestal ion temperature and also between the density width and the square root of the pedestal beta poloidal. These pedestal studies suggest that a complete model of the pedestal width in type-I ELMing discharges must be time dependent, include transport physics during inter-ELM periods and include the limits to pedestal evolution imposed by the ELM instability.
Plasma elongation effects on temperature gradient driven instabilities and geodesic acoustic modes
Authors: Gao Zhe , Peng Lili , Wang Ping , Dong Jiaqi , Sanuki H.
Published: April 2009

Plasma shaping effects on temperature gradient driven instabilities and geodesic acoustic oscillations are investigated with gyrokinetic theory and a local magnetohydrodynamic equilibrium model. In particular, we focus on the effect of the elongation κ, including its radial derivative s
κ = (r/κ)(∂κ/∂r), in the large aspect ratio limit. An analytical formula of the dependence of the geodesic acoustic mode (GAM) frequency on the elongation is given. It is found that the GAM frequency sharply decreases with increasing elongation by the dependence of [(2 − αs
κ)/(κ2 + 1)]1/2 with α = 0.5–1, which comes from the modification of ion classical polarization balanced by that of curvature drift polarization. The dependence of the critical threshold of the ETG/ITG instability on the elongation is numerically studied and a semi-analytical formula is given as (R
0/L

Tc)/(R
0/L

Tc)
s
κ=0,κ=1 = (1 + 0.36s
κ)[1 + 0.11(κ − 1)], where R
0 is the major radius and L

Tc is the critical scale length of the temperature gradient.
Network-based multiple locus linkage analysis of expression traits
Authors: Pan Wei
Published: April 2009

Motivation: We consider the problem of multiple locus linkage analysis for expression traits of genes in a pathway or a network. To capitalize on co-expression of functionally related genes, we propose a penalized regression method that maps multiple expression quantitative trait loci (eQTLs) for all related genes simultaneously while accounting for their shared functions as specified a priori by a gene pathway or network.

Results: An analysis of a mouse dataset and simulation studies clearly demonstrate the advantage of the proposed method over a standard approach that ignores biological knowledge of gene networks.

Contact:  weip@biostat.umn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Proust's Emotional Cavities: Vision and Affect in
A la recherche du temps perdu
Authors: Haustein Katja
Published: April 2009

Against the background of the ‘waning of affect’ in modern times

1

and the (post-)Freudian consignment of feelings to theories of drives, the ineluctable question emerges of where we can satisfactorily place emotionality at all nowadays. What role do feelings play in works of art? This article reflects on these questions by examining the relationship between vision (both bodily and photographic) and affect in Proust's
A la recherche du temps perdu
. Reading Proust's work as part of a growing tendency to hollow out the Romantic idea of emotion, the article explores the advancing displacement of ‘holistic emotionality’ by the rapid increase in ‘emotional cavities’. These are zones devoid of any emotional contact or correspondence between the narrator and the world he perceives. In close readings of the scenes connected with the death of the grandmother and of Albertine sleeping, this article argues that Proust introduces a new understanding of affect that neither theorizes it as essential and all-pervading nor simply disqualifies it in a modernist gesture of denial. Instead, Proust's work proposes a conception of affect that eventually appears as privatized, contingent and in peril.
The influence of context-dependent maternal effects on population dynamics: an experimental test
Authors: Plaistow S.J , Benton T.G
Published: April 2009

Parental effects arise when either the maternal or paternal phenotype influences the phenotypes of subsequent generations. Simple analytical models assume maternal effects are a mechanism creating delayed density dependence. Such models predict that maternal effects can very easily lead to population cycles. Despite this, unambiguous maternal-effect mediated cycles have not been demonstrated in any system. Additionally, much evidence has arisen to invalidate the underlying assumption that there is a simple positive correlation between maternal performance and offspring performance. A key issue in understanding how maternal effects may affect population dynamics is determining how the expression of parental effects changes in different environments. In this study, we tested the hypothesis that maternal effects influence population dynamics in a context-dependent way. Populations of the soil mite,Sancassania berlesei, were set up at high density (500 eggs) or low density (50 eggs), with eggs that were either laid by young mothers or old mothers (a previously documented maternal effect in this system). The influence of maternal age on both population and egg and body-size dynamics was only observed in the populations initiated under low density rather than high density. This difference was attributable to the context-dependence of maternal effects at the individual level. In low-density (high food) conditions, maternal effects have an impact on offspring reproductive performance, creating an impact on the population growth rate. In high density (low food), maternal effects impact more on juvenile survival (not adult size or reproduction), creating a smaller impact on the population growth rate. This context dependence of effects at the population level means that, in fluctuating populations, maternal effects cause intermittent delayed density dependence that does not lead to persistent cycles.
Completing the cycle: maternal effects as the missing link in plant life histories
Authors: Donohue Kathleen
Published: April 2009

Maternal effects on seed traits such as germination are important components of the life histories of plants because they represent the pathway from adult to offspring: the pathway that completes the life cycle. Maternal environmental effects on germination influence basic life-history expression, natural selection on germination, the expression of genetic variation for germination and even the genes involved in germination. Maternal effects on seed traits can even influence generation time and projected population growth rates. Whether these maternal environmental effects are imposed by the maternal genotype, the endosperm genotype or the embryonic genotype, however, is as yet unknown. Patterns of gene expression and protein synthesis in seeds indicate that the maternal genotype has the opportunity to influence its progeny's germination behaviour. Investigation of the phenotypic consequences of maternal environmental effects, regardless of its genetic determination, is relevant for understanding the variation in plant life cycles. Distinguishing the genotype(s) that control them is relevant for predicting the evolutionary trajectories and patterns of selection on progeny phenotypes and the genes underlying them.
GCN5 is a required cofactor for a ubiquitin ligase that targets NF-κB/RelA
Authors: Mao Xicheng , Gluck Nathan , Li Duo , Maine Gabriel N. , Li Haiying , Zaidi Iram W. , Repaka Aparna , Mayo Marty W. , Burstein Ezra
Published: April 2009

The transcription factor NF-κB is a critical regulator of inflammatory and cell survival signals. Proteasomal degradation of NF-κB subunits plays an important role in the termination of NF-κB activity, and at least one of the identified ubiquitin ligases is a multimeric complex containing Copper Metabolism Murr1 Domain 1 (COMMD1) and Cul2. We report here that GCN5, a histone acetyltransferase, associates with COMMD1 and other components of the ligase, promotes RelA ubiquitination, and represses κB-dependent transcription. In this role, the acetyltransferase activity of GCN5 is not required. Interestingly, GCN5 binds more avidly to RelA after phosphorylation on Ser 468, an event that is dependent on IKK activity. Consistent with this, we find that both GCN5 and the IκB Kinase (IKK) complex promote RelA degradation. Collectively, the data indicate that GCN5 participates in the ubiquitination process as an accessory factor for a ubiquitin ligase, where it provides a novel link between phosphorylation and ubiquitination.
Transcriptional control of brown adipocyte development and physiological function—of mice and men
Authors: Seale Patrick , Kajimura Shingo , Spiegelman Bruce M.
Published: April 2009

The last several years have seen an explosion of information relating to the transcriptional control of brown fat cell development. At the same time, new data have emerged that clearly demonstrate that adult humans do indeed have substantial amounts of functioning brown adipose tissue (BAT). Together, these advances are stimulating a reassessment of the role of brown adipose tissue in human physiology and pathophysiology. These data have also opened up exciting new opportunities for the development of entirely novel classes of therapeutics for metabolic diseases like obesity and type 2 diabetes.
Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses
Authors: Fullwood Melissa J. , Wei Chia-Lin , Liu Edison T. , Ruan Yijun
Published: April 2009

Comprehensive understanding of functional elements in the human genome will require thorough interrogation and comparison of individual human genomes and genomic structures. Such an endeavor will require improvements in the throughputs and costs of DNA sequencing. Next-generation sequencing platforms have impressively low costs and high throughputs but are limited by short read lengths. An immediate and widely recognized solution to this critical limitation is the paired-end tag (PET) sequencing for various applications, collectively called the PET sequencing strategy, in which short and paired tags are extracted from the ends of long DNA fragments for ultra-high-throughput sequencing. The PET sequences can be accurately mapped to the reference genome, thus demarcating the genomic boundaries of PET-represented DNA fragments and revealing the identities of the target DNA elements. PET protocols have been developed for the analyses of transcriptomes, transcription factor binding sites, epigenetic sites such as histone modification sites, and genome structures. The exclusive advantage of the PET technology is its ability to uncover linkages between the two ends of DNA fragments. Using this unique feature, unconventional fusion transcripts, genome structural variations, and even molecular interactions between distant genomic elements can be unraveled by PET analysis. Extensive use of PET data could lead to efficient assembly of individual human genomes, transcriptomes, and interactomes, enabling new biological and clinical insights. With its versatile and powerful nature for DNA analysis, the PET sequencing strategy has a bright future ahead.
New class of microRNA targets containing simultaneous 5′-UTR and 3′-UTR interaction sites
Authors: Lee Inhan , Ajay Subramanian S. , Yook Jong In , Kim Hyun Sil , Hong Su Hyung , Kim Nam Hee , Dhanasekaran Saravana M. , Chinnaiyan Arul M. , Athey Brian D.
Published: April 2009

MicroRNAs (miRNAs) are known to post-transcriptionally regulate target mRNAs through the 3′-UTR, which interacts mainly with the 5′-end of miRNA in animals. Here we identify many endogenous motifs within human 5′-UTRs specific to the 3′-ends of miRNAs. The 3′-end of conserved miRNAs in particular has significant interaction sites in the human-enriched, less conserved 5′-UTR miRNA motifs, while human-specific miRNAs have significant interaction sites only in the conserved 5′-UTR motifs, implying both miRNA and 5′-UTR are actively evolving in response to each other. Additionally, many miRNAs with their 3′-end interaction sites in the 5′-UTRs turn out to simultaneously contain 5′-end interaction sites in the 3′-UTRs. Based on these findings we demonstrate combinatory interactions between a single miRNA and both end regions of an mRNA using model systems. We further show that genes exhibiting large-scale protein changes due to miRNA overexpression or deletion contain both UTR interaction sites predicted. We provide the predicted targets of this new miRNA target class, miBridge, as an efficient way to screen potential targets, especially for nonconserved miRNAs, since the target search space is reduced by an order of magnitude compared with the 3′-UTR alone. Efficacy is confirmed by showing SEC24D regulation with hsa-miR-605, a miRNA identified only in primate, opening the door to the study of nonconserved miRNAs. Finally, miRNAs (and associated proteins) involved in this new targeting class may prevent 40S ribosome scanning through the 5′-UTR and keep it from reaching the start-codon, preventing 60S association.
Optimization and Troubleshooting in PCR
Authors: Roux Kenneth H.
Published: April 2009

INTRODUCTION

The use of polymerase chain reaction (PCR) to generate large amounts of a desired product can be a double-edged sword. Failure to amplify under optimum conditions can lead to the generation of multiple undefined and unwanted products, even to the exclusion of the desired product. At the other extreme, no product may be produced. A typical response at this point is to vary one or more of the many parameters that are known to contribute to primer-template fidelity and primer extension. High on the list of optimization variables are Mg++ concentrations, buffer pH, and cycling conditions. With regard to the last, the annealing temperature is most important. The situation is further complicated by the fact that some of the variables are quite interdependent. For example, because dNTPs directly chelate a proportional number of Mg++ ions, an increase in the concentration of dNTPs decreases the concentration of free Mg++ available to influence polymerase function. This article discusses various optimization strategies, including touchdown PCR and hot-start PCR.
Fixation of Ilyanassa Snail Embryos and Larvae: Figure 1.
Authors: Gharbiah Maey , Cooley James , Leise Esther M. , Nakamoto Ayaki , Rabinowitz Jeremy S. , Lambert J. David , Nagy Lisa M.
Published: April 2009

INTRODUCTION

The marine gastropod Ilyanassa obsoleta is a long-standing and very useful model for studies of embryonic development. It is an especially important model for spiralian development, and for studies of asymmetric cell division. The embryos are amenable to classic embryological manipulation techniques, as well as a growing number of molecular approaches. Ilyanassa is also an important model for studies of metamorphosis, the ecology of parasitism, the effects of environmental contaminants on morphology and sexual function, and comparative neurobiology. Ilyanassa embryos are particularly well suited for RNA and protein localization studies because of the relatively large cells and favorable properties for imaging. This protocol describes how to fix and store Ilyanassa embryos and larvae for use in whole-mount in situ hybridization and immunohistochemical studies.
Isolating Protein from Ilyanassa Snail Embryos
Authors: Gharbiah Maey , Cooley James , Leise Esther M. , Nakamoto Ayaki , Rabinowitz Jeremy S. , Lambert J. David , Nagy Lisa M.
Published: April 2009

INTRODUCTION

The marine gastropod Ilyanassa obsoleta is a long-standing and very useful model for studies of embryonic development. It is an especially important model for spiralian development, and for studies of asymmetric cell division. The embryos are amenable to classic embryological manipulation techniques as well as a growing number of molecular approaches. Ilyanassa is also an important model for studies of metamorphosis, the ecology of parasitism, the effects of environmental contaminants on morphology and sexual function, and comparative neurobiology. This protocol describes the procedure for extracting protein from Ilyanassa embryos for use in techniques such as Western blotting or two-dimensional (2D) gel electrophoresis.
In Situ Hybridization of Helobdella (Leech) Embryos
Authors: Weisblat David A. , Kuo Dian-Han
Published: April 2009

INTRODUCTION

The purpose of this protocol is to reveal the localization of transcripts in the Helobdella (leech) embryo. In situ hybridization protocols for Helobdella embryos are derived from those used for zebrafish and Xenopus. The protocols are different for early- and late-stage embryos (stages 1-8 and stages 9-11, respectively) due to a difference in tissue permeability.
Quick Preparation of Genomic DNA from Drosophila
Authors: Huang Audrey M. , Rehm E. Jay , Rubin Gerald M.
Published: April 2009

INTRODUCTION

This protocol describes a standard miniprep for Drosophila melanogaster that requires very few flies and produces high-quality DNA. This method can also be used to isolate RNA when RNase-free conditions are utilized; an extra step must be taken to rid the sample of genomic DNA (e.g., RNase-free DNase digestion).
Emotional well‐being and mental health of looked after children in England
Authors: McAuley Colette , Davis Teresa
Published: April 2009

The national prevalence studies of the mental health of looked after children in Great Britain provide sobering reading. Forty‐five per cent of looked after children in England were found to have a diagnosable mental health disorder. In contrast, this is to one in 10 in the general population. Carers estimated that mental health problems were even more widespread. Children with mental health disorders were also more likely to have education, health and social issues. This paper discusses the findings and argues for early intervention along with inter‐departmental and interdisciplinary approaches. The recent Child and Adolescent Mental Health Services Review clearly indicates that issues of access to appropriate and timely Child and Adolescent Mental Health Services remain. However, the introduction of evidence‐based approaches is encouraging. Young people's views on the services they want and on what is important for emotional well‐being and mental health are important considerations.
Immunomodulatory drug FTY720 induces regulatory CD4+CD25+ T cellsin vitro
Authors: Zhou P J , Wang H , Shi G H , Wang X H , Shen Z J , Xu D
Published: April 2009

As a novel immunosuppressant, FTY720 (2-amino-2-(2-[4-octylphenyl] ethyl)-1, 3-propanediol hydrochloride) has been used to prevent the allograft rejection in organ transplantation. FTY720 can prolong markedly survival of the allograft by inducing apoptosis of reactive lymphocytes and by redirecting the homing of lymphocytes. However, as the archetype of a new class of immune modulators, the potential effect of FTY720 on the immune response needs to be elucidated further. In this study, FTY720 was added into the mixed lymphocyte reaction (MLR) consisting of murine splenocytes from BALB/c and C57BL/6, to observe its direct effect on the induction of CD4+CD25+ regulatory T cells. It was demonstrated that the proportion of CD4+CD25+ and CD4+CD25+forkhead box P3 (FoxP3)+ T cells in MLR were increased significantly by FTY720 treatment, and the expression of FoxP3 mRNA in lymphocytes was also enhanced markedly by the drug. A synergetic effect was observed between FTY720 and co-stimulation blockades. Moreover, analysis of the function of FTY720-treated cells manifested an increased suppressive activity in an in vitro antigen-specific proliferation assay. In conclusion, FTY720 can increase the number and enhance the functional activity of CD4+CD25+ regulatory T cells in MLR, and these FTY720-treated cells possess the activity to down-regulate the alloreactivity of lymphocytes, indicating its potential use for therapeutic purposes.
Interleukin-17 and systemic lupus erythematosus: current concepts
Authors: Nalbandian A , Crispín J C , Tsokos G C
Published: April 2009

The emerging role of interleukin (IL)-17 as a hallmark proinflammatory cytokine of the adaptive immune system, produced primarily by a new T helper cell subset termed ‘Th17’, has received considerable attention. Differentiation of Th17 cells is driven by the simultaneous presence of transforming growth factor-β and certain inflammatory cytokines (e.g. IL-6, IL-21), and recent studies have shown that inflammation instigated by IL-17-producing cells is central to the development and pathogenesis of several human autoimmune diseases and animal models of autoimmunity. In this review, we focus on the information regarding IL-17 and systemic lupus erythematosus (SLE), a chronic autoimmune disease. The work that has explored the development and behaviour of IL-17-producing cells in SLE is discussed, and different mechanisms by which IL-17 could potentially augment inflammation and autoantibody production in the context of SLE are proposed.
Interpretation case study of the Sahl El Qaa area, southern Sinai Peninsula, Egypt
Authors: Rabeh Taha , Miranda Jorge Miguel , Carvalho Joao , Bocin Andrei
Published: April 2009

The study area is located in the Sinai Peninsula, which is considered one of the most promising regions for oil resources. Three different tectonic forces affect the area in the triple junction structures associated with the opening of the Gulf of Suez and the strike slip movement along the Gulf of Aqaba. The main goal of this work is to model the structure of the basement rocks in the study area using magnetic methods. To achieve this, a high‐resolution land magnetic survey was acquired and the results were combined with existing seismic reflection data. The magnetic interpretation was carried out using the analytical signal, horizontal gradient, Euler and Werner deconvolution and 3D magnetic modelling methods. We concluded that most of the deduced structures are trending in N–S, N35°–N45° west and E–W directions. The Aqaba trend (N15°–N25° east) is barely noticeable. The depth to the basement rocks ranges from 1 km to more than 2 km below sea level and these results are in agreement with the available well log data. In addition, interpretation of seismic reflection sections was carried out and compared with overlapping magnetic profiles interpreted using Euler deconvolution. They show that the sedimentary section was affected by the basement tectonics, with faults extending from the basement upwards through the sedimentary cover. These faults constitute good potential structural traps for oil accumulation.
Comparison between the Fourier finite‐difference method and the generalized‐screen method
Authors: Zhang Jin‐Hai , Wang Wei‐Min , Yao Zhen‐Xing
Published: April 2009

The Fourier finite‐difference propagator and the generalized‐screen propagator are two general high‐order forms of one‐way dual‐domain methods. We compare these two propagators mainly on phase accuracy, computational efficiency and 3D extension. A comparison of phase accuracy shows that the high‐order generalized‐screen propagator is preferable to the Fourier finite‐difference propagator for heterogeneous media with a weak velocity contrast and wide dip angle. With increasing velocity contrast, the accuracy improvement gained by the high‐order generalized‐screen propagator declines rapidly. The Fourier finite‐difference propagator is more robust and flexible to lateral velocity variations than the generalized‐screen propagator. The 2D Fourier finite‐difference propagator is superior to the 2D generalized‐screen propagator when the velocity contrast is stronger than 23%. Despite the two‐way splitting error, the 3D Fourier finite‐difference propagator is more accurate than the second‐order generalized‐screen propagator when the velocity contrast is stronger than 20% and is more accurate than the fourth‐order generalized‐screen propagator when the velocity contrast is stronger than 40%. Numerical experiments on the SEG/EAGE salt model demonstrate that the Fourier finite‐difference propagator behaves better than the generalized‐screen propagator when imaging steep salt boundary and faults beneath the salt body. Under the same hardware and software conditions, the computational cost of the Fourier finite‐difference propagator in our implementation is greater than that of the second‐order generalized‐screen propagator but smaller than that of the third‐order generalized‐screen propagator. Compared with the Fourier finite‐difference propagator, the generalized‐screen propagator requires fewer grid points per wavelength and has more potential to improve running speed in the presence of a much faster Fourier transform. These analyses are applicable for both forward modelling and depth migration.