bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome characteristics of a generalist marine bacterial lineage
Authors: Newton Ryan J , Griffin Laura E , Bowles Kathy M , Meile Christof , Gifford Scott , Givens Carrie E , Howard Erinn C , King Eric , Oakley Clinton A , Reisch Chris R , Rinta-Kanto Johanna M , Sharma Shalabh , Sun Shulei , Varaljay Vanessa , Vila-Costa Maria , Westrich Jason R , Moran Mary Ann
Published: January 2010

Members of the marine Roseobacter lineage have been characterized as ecological generalists, suggesting that there will be challenges in assigning well-delineated ecological roles and biogeochemical functions to the taxon. To address this issue, genome sequences of 32 Roseobacter isolates were analyzed for patterns in genome characteristics, gene inventory, and individual gene/pathway distribution using three predictive frameworks: phylogenetic relatedness, lifestyle strategy and environmental origin of the isolate. For the first framework, a phylogeny containing five deeply branching clades was obtained from a concatenation of 70 conserved single-copy genes. Somewhat surprisingly, phylogenetic tree topology was not the best model for organizing genome characteristics or distribution patterns of individual genes/pathways, although it provided some predictive power. The lifestyle framework, established by grouping isolates according to evidence for heterotrophy, photoheterotrophy or autotrophy, explained more of the gene repertoire in this lineage. The environment framework had a weak predictive power for the overall genome content of each strain, but explained the distribution of several individual genes/pathways, including those related to phosphorus acquisition, chemotaxis and aromatic compound degradation. Unassembled sequences in the Global Ocean Sampling metagenomic data independently verified this global-scale geographical signal in some Roseobacter genes. The primary findings emerging from this comparative genome analysis are that members of the lineage cannot be easily collapsed into just a few ecologically differentiated clusters (that is, there are almost as many clusters as isolates); the strongest framework for predicting genome content is trophic strategy, but no single framework gives robust predictions; and previously unknown homologs to genes for H2 oxidation, proteorhodopsin-based phototrophy, xanthorhodpsin-based phototrophy, and CO2 fixation by Form IC ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) expand the possible mechanisms for energy and carbon acquisition in this remarkably versatile bacterial lineage.
Offsetting virulence and antibiotic resistance costs by MRSA
Authors: Collins James , Rudkin Justine , Recker Mario , Pozzi Clarissa , O'Gara James P , Massey Ruth C
Published: January 2010

The prevalence of diverse MRSA (methicillin-resistant Staphylococcus aureus) types in both hospital and community settings is a major health problem worldwide. Here we compare hospital-acquired MRSAs with large type II SCCmec elements with those prevalent in both hospital and community settings with smaller type IV SCCmec elements. We find that the type II but not the type IV SCCmec element causes the bacteria to reduce their levels of costly toxin expression. We compare the relative growth rates of these MRSA types and show that the type II SCCmec carrying MRSAs are more affected than those carrying type IV elements and from this we hypothesize that offsetting the costs associated with antibiotic resistance and toxin expression is why the type II are confined to hospital environments where antibiotic use, the prevalence of immunocompromised individuals and vector-mediated transmission is high. In contrast, those MRSAs that are also successful in the community can maintain their high levels of toxin expression due to a lower fitness burden associated with the smaller SCCmec element.
TATA binding protein binds to single stranded DNA: A new model for eukaryotic transcription
Authors: Irani Rostem
Published: January 2010

Although the players mediating the initiation of eukaryotic transcription appear to be known, the mechanism is not. In this paper we report findings on the interaction between the TATA box binding protein (TBP) and DNA, using a novel optical technology, that point to a potential plausible physical mechanism, and at the same time tie together a number of otherwise disparate observations. TBP plays a central and ubiquitous role in initiating eukaryotic transcription, binding to promoters with and without the canonical 5’ TATA(A/T)A(A/T)(G/A) 3’ motif1. It also tends to bind to double-stranded DNA promiscuously, and though affinity is lower, the number of binding opportunities is greater. TBP-DNA complexes have been characterized structurally2,3 and thermodynamically4,5, the standard model representing the TBP double-helix complex as the biologically significant entity. Here we show, using a label-free detection method termed Spectral Reflectance Imaging Biosensor6 (SRIB) that TBP binds to single stranded (ss), as well as double stranded (ds), oligonucleotides with the TATA motif, and binds the single-stranded form preferentially. Moreover, TBP binds preferentially to single stranded pyrimidine-rich sequences over purine-rich sequences, which is similar to the Single-Stranded DNA-binding protein (SSB) binding pattern. These observations suggest a new model for eukaryotic transcription in which TBP destabilizes the double helix, thereby initiating the open complex bubble necessary for transcription. Furthermore, the role of TBP as a multifunctional protein is discussed.
Analysis of the SIM1 Contribution to Polygenic Obesity in the French Population
Authors: Ghoussaini Maya , Stutzmann Fanny , Couturier Cyril , Vatin Vincent , Durand Emmanuelle , Lecoeur Cécile , Degraeve Franck , Heude Barbara , Tauber Maithé , Hercberg Serge , Levy‐Marchal Claire , Tounian Patrick , Weill Jacques , Traurig Michael , Bogardus Clifton , Baier Leslie J. , Michaud Jacques L. , Froguel Philippe , Meyre David
Published: January 2010

SIM1 (single‐minded 1) haploinsufficiency is responsible for obesity in both humans and mice, but the contribution of frequent DNA variation to polygenic obesity is unknown. Sequencing of all exons, exon/intron boundaries, 870 base pairs (bp) of the putative promoter, and 1,095 bp of the 3′UTR of SIM1 gene in 143 obese children and 24 control adults identified 13 common variants. After analysis of the linkage disequilibrium (LD) structure, association study of eight variants was performed in 1,275 obese children and severely obese adults, in 1,395 control subjects, and in 578 obesity‐selected pedigrees. A nominal evidence of association was found for the nonsynonymous variant P352T C/A (rs3734354) (P = 0.01, OR = 0.81 (0.70–0.95)), the +2,004 TGA −/insT SNP (rs35180395) (P = 0.02, OR = 1.21 (1.02–1.43)), the +2,215A/G TGA SNP (rs9386126) (P = 0.002, OR = 0.81 (0.71–0.93)), and pooled childhood/adult obesity. Even though transmission disequilibrium test (TDT) further supported the association of P352T and +2,004 −/inst T with obesity, none of these nominal associations remained significant after a multiple testing Bonferroni correction. Therefore, our study excludes a major contribution of SIM1 common variants in exons, 5′ and 3′ UTR regions in polygenic obesity susceptibility in French Europeans.
Variations in BMI and Prevalence of Health Risks in Diverse Racial and Ethnic Populations
Authors: Stommel Manfred , Schoenborn Charlotte A.
Published: January 2010

When examining health risks associated with the BMI, investigators often rely on the customary BMI thresholds of the 1995 World Health Organization report. However, within‐interval variations in morbidity and mortality can be substantial, and the thresholds do not necessarily correspond to identifiable risk increases. Comparing the prevalence of hypertension, diabetes, coronary heart disease (CHD), asthma, and arthritis among non‐Hispanic whites, blacks, East Asians and Hispanics, we examine differences in the BMI‐health‐risk relationships for small BMI increments. The analysis is based on 11 years of data of the National Health Interview Survey (NHIS), with a sample size of 337,375 for the combined 1997–2007 Sample Adult. The analysis uses multivariate logistic regression models, employing a nonparametric approach to modeling the BMI‐health‐risk relationship, while relying on narrowly defined BMI categories. Rising BMI levels are associated with higher levels of chronic disease burdens in four major racial and ethnic groups, even after adjusting for many socio‐demographic characteristics and three important health‐related behaviors (smoking, physical activity, alcohol consumption). For all population groups, except East Asians, a modestly higher disease risk was noted for persons with a BMI <20 compared with persons with BMI in the range of 20–21. Using five chronic conditions as risk criteria, a categorization of the BMI into normal weight, overweight, or obesity appears arbitrary. Although the prevalence of disease risks differs among racial and ethnic groups regardless of BMI levels, the evidence presented here does not support the notion that the BMI‐health‐risk profile of East Asians and others warrants race‐specific BMI cutoff points.
Obese Women Have Lower Monosodium Glutamate Taste Sensitivity and Prefer Higher Concentrations Than Do Normal‐weight Women
Authors: Pepino M. Yanina , Finkbeiner Susana , Beauchamp Gary K. , Mennella Julie A.
Published: January 2010

The goal of this study was to determine whether obese women exhibit altered umami and sweet taste perception compared to normal‐weight women. A total of 57 subjects (23 obese and 34 normal weight) participated in a 2‐day study separated by 1 week. Half of the women in each group were evaluated using monosodium glutamate (MSG; prototypical umami stimulus) on the first test day and sucrose on the second test day; the order was reversed for the remaining women. We used two‐alternative forced‐choice staircase procedures to measure taste detection thresholds, forced‐choice tracking technique to measure preferences, the general Labeled Magnitude Scale (gLMS) to measure perceived intensity of suprathreshold concentrations, and a triangle test to measure discrimination between 29 mmol/l MSG and 29 mmol/l NaCl. Obese women required higher MSG concentrations to detect a taste and preferred significantly higher MSG concentrations in a soup‐like vehicle. However, their perception of MSG at suprathreshold concentrations, their ability to discriminate MSG from salt, and their preference for sucrose were similar to that observed in normal‐weight women. Regardless of their body weight category, 28% of the women did not discriminate 29 mmol/l MSG from 29 mmol/l NaCl (nondiscriminators). Surprisingly, we found that, relative to discriminators, nondiscriminators perceived less savoriness when tasting suprathreshold MSG concentrations and less sweetness from suprathreshold sucrose concentrations but had similar MSG and sucrose detection thresholds. Taken together, these data suggest that body weight is related to some components of umami taste and that different mechanisms are involved in the perception of threshold and suprathreshold MSG concentrations.
BMI and Waist Circumference as Predictors of Well‐being in Older Adults: Findings From the English Longitudinal Study of Ageing
Authors: Zaninotto Paola , Pierce Mary , Breeze Elizabeth , de Oliveira Cesar , Kumari Meena
Published: January 2010

The aim of this study is to examine the association of BMI and waist circumference (WC), with a quality of life (QoL) indicator designed for older ages (CASP19), and with depressive symptoms (Centre for Epidemiologic Studies Depression Scale). We included 8,688 individuals aged ≥52 years who participants of Wave 2 (2004–2005) and Wave 3 (2006–2007) of the English Longitudinal Study of Ageing (ELSA). To explore cross‐sectional relationships (2004–2005), we fitted regression models for BMI and WC (included simultaneously) as our predictors of QoL and depressive symptoms adjusted for covariates. To explore longitudinal relationships, BMI and waist at baseline (2004–2005) were related to the each outcome variable measured at follow‐up (2006–2007), and adjusted for baseline characteristics (2004–2005). For a given BMI, larger WC was associated with lower QoL and higher risk of depressive symptoms for women in cross‐sectional and longitudinal analyses. By contrast for a given WC increased BMI for women was positively associated with QoL and lower odds of depressive symptoms. In men, for a given BMI, increased WC was related to QoL only cross‐sectionally; neither WC nor BMI at baseline were associated with depressive symptoms (cross‐sectionally or longitudinally). In conclusion among older people, for a given BMI, increased WC was related with higher risk of poor QoL and, for women, of depressive symptoms; whereas for a given WC, increased BMI had a protective effect on QoL for women.
Industrial Analysis with Vibrational Spectroscopy
Authors: Barnett Neil W , Dent G , Chalmers John M , Chalmers John M , Dent G
Published: January 2010

Industrial Analysis with Vibrational Spectroscopy is an integrated work which emphasises the synergy and complementary nature of the techniques of infrared and Raman spectroscopy in industrial laboratories. The book is written in a pragmatic and straight-forward manner and is illustrated throughout with examples of real-world, everyday problems and applications. It provides a developed, realistic insight into industrial analysis with vibrational spectroscopy for both undergraduate and academic researcher, while additionally providing a straight-forward working tool of value to the industrial laboratory worker.
Template synthesis of ordered arrays of mesoporous titania spheres
Authors: Chen Jianfeng , Hua Zhongjiong , Yan Yushan , Zakhidov Anvar A. , Baughman Ray H. , Xu Lianbin
Published: January 2010

Three-dimensionally ordered arrays of submicron-sized mesoporous titania spheres with high surface area and high crystallinity have been prepared through triblock copolymer templating within the confinement of polymer inverse opals.
Excitation-wavelength-dependent photoluminescence of a pyromellitic diimidenanowire network
Authors: Zhang Hairong , Xu Xiaohe , Ji Hai-Feng
Published: January 2010

Nanowires from deposition of PMDI from the gas phase and their unique excitation-wavelength-dependent photoluminescence are demonstrated. The luminescence peaks of the PMDI nanowires red-shifted as the excitation wavelength increased. The relationship between the luminescence peak and the excitation wavelength is nearly linear in a broad range of excitation.
Protein nanoarrays on a highly-oriented lamellar surface
Authors: Matsusaki Michiya , Omichi Masaaki , Kadowaki Koji , Kim Bong Hoon , Kim Sang Ouk , Maruyama Ikuro , Akashi Mitsuru
Published: January 2010

Unidirectional protein nanoarrays were fabricated on a highly-aligned block copolymer lamellar surface, and these bioactive protein nanoarrays will be useful in biological assays.
Spin capturing with nitrones: radical coupling reactions with concurrent introduction of mid-chain functionality
Authors: Wong Edgar H. H. , Boyer Cyrille , Stenzel Martina H. , Barner-Kowollik Christopher , Junkers Tanja
Published: January 2010

Nitrones are demonstrated to efficiently mediate radical coupling reactions on the example of the conjugation of ATRP-made polymers, yielding macromolecules with distinct functional alkoxyamine centres in mid-chain locations of the chains.
Facile synthesis of linear-dendritic cholesteryl-poly(ε-caprolactone)-b-(l-lysine)G2 by thiol-ene and azide-alkyne “click” reactions
Authors: Javakhishvili Irakli , Binder Wolfgang H. , Tanner Susanne , Hvilsted Søren
Published: January 2010

A rodcoil dendron comprising cholesterol, poly(ε-caprolactone), and dendritic l-lysine has been synthesized via combination of ring-opening polymerization and sequential orthogonal “click” reactions.
Quick extended x-ray absorption fine structure instrument with millisecond time scale, optimized for in situ applications
Authors: Khalid S. , Caliebe W. , Siddons P. , So I. , Clay B. , Lenhard T. , Hanson J. , Wang Q. , Frenkel A. I. , Marinkovic N. , Hould N. , Ginder-Vogel M. , Landrot G. L. , Sparks D. L. , Ganjoo A.
Published: January 2010

In order to learn about in situ structural changes in materials at subseconds time scale, we have further refined the techniques of quick extended x-ray absorption fine structure (QEXAFS) and quick x-ray absorption near edge structure (XANES) spectroscopies at beamline X18B at the National Synchrotron Light Source. The channel cut Si (111) monochromator oscillation is driven through a tangential arm at 5 Hz, using a cam, dc motor, pulley, and belt system. The rubber belt between the motor and the cam damps the mechanical noise. EXAFS scan taken in 100 ms is comparable to standard data. The angle and the angular range of the monochromator can be changed to collect a full EXAFS or XANES spectrum in the energy range 4.7–40.0 KeV. The data are recorded in ascending and descending order of energy, on the fly, without any loss of beam time. The QEXAFS mechanical system is outside the vacuum system, and therefore changing the mode of operation from conventional to QEXAFS takes only a few minutes. This instrument allows the acquisition of time resolved data in a variety of systems relevant to electrochemical, photochemical, catalytic, materials, and environmental sciences.
Polarization-charge tunnel junctions for ultraviolet light-emitters without p-type contact
Authors: Schubert Martin F.
Published: January 2010

Polarization-charge tunnel junctions for ultraviolet light-emitters (λ<360 nm) are modeled using the k⋅p multiband quantum transmitting boundary method. It is shown that polarization-charge tunnel junctions can carry sufficient current to be viable for ultraviolet emitters. Sources of inefficiency in existing ultraviolet emitters are discussed, including poor hole-injection efficiency and optical absorption in the p-type GaN contact layers. It is demonstrated that polarization-charge tunnel junctions can deliver improvements in both areas, by eliminating the need for p-type contacts, and by enabling the use of a p-side-down structure, which is shown to have favorable characteristics for carrier transport compared to conventional p-side-up structures.
Mitigation implications of midcentury targets that preserve long-term climate policy options
Authors: O’Neill Brian C. , Riahi Keywan , Keppo Ilkka
Published: January 2010

Midcentury targets have been proposed as a guide to climate change policy that can link long-term goals to shorter-term actions. However no explicit mitigation analyses have been carried out of the relationship between midcentury conditions and longer-term outcomes. Here we use an integrated assessment modeling framework with a detailed representation of the energy sector to examine the dependence of climate change outcomes in 2100 on emissions levels, atmospheric concentrations, and technology characteristics in 2050. We find that midcentury conditions are crucial determinants of longer-term climate outcomes, and we identify feasibility thresholds describing conditions that must be met by midcentury to keep particular long-term options open. For example, to preserve the technical feasibility of a 50% likelihood of keeping global average temperature at < 2 °C above preindustrial in 2100, global emissions must be reduced by about 20% below 2000 levels by 2050. Results are sensitive to several assumptions, including the nature of future socio-economic development. In a scenario with high demand for energy and land, being below 2 °C with 50% likelihood requires a 50% reduction in emissions below 2000 levels by 2050, which is only barely feasible with known technologies in that scenario. Results suggest that a greater focus on midcentury targets could facilitate the development of policies that preserve potentially desirable long-term options.
Generation of regulatory dendritic cells and CD4
+
Foxp3
+
T cells by probiotics administration suppresses immune disorders
Authors: Kwon Ho-Keun , Lee Choong-Gu , So Jae-Seon , Chae Chang-Suk , Hwang Ji-Sun , Sahoo Anupama , Nam Jong Hee , Rhee Joon Haeng , Hwang Ki-Chul , Im Sin-Hyeog
Published: January 2010

The beneficial effects of probiotics have been described in many diseases, but the mechanism by which they modulate the immune system is poorly understood. In this study, we identified a mixture of probiotics that up-regulates CD4
+
Foxp3
+
regulatory T cells (Tregs). Administration of the probiotics mixture induced both T-cell and B-cell hyporesponsiveness and down-regulated T helper (Th) 1, Th2, and Th17 cytokines without apoptosis induction. It also induced generation of CD4
+
Foxp3
+
Tregs from the CD4
+
CD25
−
population and increased the suppressor activity of naturally occurring CD4
+
CD25
+
Tregs. Conversion of T cells into Foxp3
+
Tregs is directly mediated by regulatory dendritic cells (rDCs) that express high levels of IL-10, TGF-β, COX-2, and indoleamine 2,3-dioxygenase. Administration of probiotics had therapeutical effects in experimental inflammatory bowel disease, atopic dermatitis, and rheumatoid arthritis. The therapeutical effect of the probiotics is associated with enrichment of CD4
+
Foxp3
+
Tregs in the inflamed regions. Collectively, the administration of probiotics that enhance the generation of rDCs and Tregs represents an applicable treatment of inflammatory immune disorders.
Remosomes: RSC generated non-mobilized particles with approximately 180 bp DNA loosely associated with the histone octamer
Authors: Shukla Manu Shubhdarshan , Syed Sajad Hussain , Montel Fabien , Faivre-Moskalenko Cendrine , Bednar Jan , Travers Andrew , Angelov Dimitar , Dimitrov Stefan
Published: January 2010

Chromatin remodelers are sophisticated nano-machines that are able to alter histone-DNA interactions and to mobilize nucleosomes. Neither the mechanism of their action nor the conformation of the remodeled nucleosomes are, however, yet well understood. We have studied the mechanism of Remodels Structure of Chromatin (RSC)-nucleosome mobilization by using high-resolution microscopy and biochemical techniques. Atomic force microscopy and electron cryomicroscopy (EC-M) analyses show that two types of products are generated during the RSC remodeling: (
i
) stable non-mobilized particles, termed remosomes that contain about 180 bp of DNA associated with the histone octamer and, (
ii
) mobilized particles located at the end of DNA. EC-M reveals that individual remosomes exhibit a distinct, variable, highly-irregular DNA trajectory. The use of the unique “one pot assays” for studying the accessibility of nucleosomal DNA towards restriction enzymes, DNase I footprinting and
ExoIII
mapping demonstrate that the histone-DNA interactions within the remosomes are strongly perturbed, particularly in the vicinity of the nucleosome dyad. The data suggest a two-step mechanism of RSC-nucleosome remodeling consisting of an initial formation of a remosome followed by mobilization. In agreement with this model, we show experimentally that the remosomes are intermediate products generated during the first step of the remodeling reaction that are further efficiently mobilized by RSC.
Genomic disorders: A window into human gene and genome evolution
Authors: Carvalho Claudia M. B. , Zhang Feng , Lupski James R.
Published: January 2010

Gene duplications alter the genetic constitution of organisms and can be a driving force of molecular evolution in humans and the great apes. In this context, the study of genomic disorders has uncovered the essential role played by the genomic architecture, especially low copy repeats (LCRs) or segmental duplications (SDs). In fact, regardless of the mechanism, LCRs can mediate or stimulate rearrangements, inciting genomic instability and generating dynamic and unstable regions prone to rapid molecular evolution. In humans, copy-number variation (CNV) has been implicated in common traits such as neuropathy, hypertension, color blindness, infertility, and behavioral traits including autism and schizophrenia, as well as disease susceptibility to HIV, lupus nephritis, and psoriasis among many other clinical phenotypes. The same mechanisms implicated in the origin of genomic disorders may also play a role in the emergence of segmental duplications and the evolution of new genes by means of genomic and gene duplication and triplication, exon shuffling, exon accretion, and fusion/fission events.
Competition-colonization dynamics in an RNA virus
Authors: Ojosnegros Samuel , Beerenwinkel Niko , Antal Tibor , Nowak Martin A. , Escarmís Cristina , Domingo Esteban
Published: January 2010

During replication, RNA viruses rapidly generate diverse mutant progeny which differ in their ability to kill host cells. We report that the progeny of a single RNA viral genome diversified during hundreds of passages in cell culture and self-organized into two genetically distinct subpopulations that exhibited the competition-colonization dynamics previously recognized in many classical ecological systems. Viral colonizers alone were more efficient in killing cells than competitors in culture. In cells coinfected with both competitors and colonizers, viral interference resulted in reduced cell killing, and competitors replaced colonizers. Mathematical modeling of this coinfection dynamics predicted selection to be density dependent, which was confirmed experimentally. Thus, as is known for other ecological systems, biodiversity and even cell killing of virus populations can be shaped by a tradeoff between competition and colonization. Our results suggest a model for the evolution of virulence in viruses based on internal interactions within mutant spectra of viral quasispecies.
Amyloid fibers provide structural integrity to
Bacillus subtilis
biofilms
Authors: Romero Diego , Aguilar Claudio , Losick Richard , Kolter Roberto
Published: January 2010

Bacillus subtilis
forms biofilms whose constituent cells are held together by an extracellular matrix. Previous studies have shown that the protein TasA and an exopolysaccharide are the main components of the matrix. Given the importance of TasA in biofilm formation, we characterized the physicochemical properties of this protein. We report that purified TasA forms fibers of variable length and 10–15 nm in width. Biochemical analyses, in combination with the use of specific dyes and microscopic analyses, indicate that TasA forms amyloid fibers. Consistent with this hypothesis, TasA fibers required harsh treatments (e.g., formic acid) to be depolymerized. When added to a culture of a
tasA
mutant, purified TasA restored wild-type biofilm morphology, indicating that the purified protein retained biological activity. We propose that TasA forms amyloid fibers that bind cells together in the biofilm.
Ubiquitin not only serves as a tag but also assists degradation by inducing protein unfolding
Authors: Hagai Tzachi , Levy Yaakov
Published: January 2010

Protein ubiquitination controls the cellular fate of numerous eukaryotic proteins. Despite its importance, many fundamental questions remain regarding its mechanism. One such question is how ubiquitination alters the biophysical properties of the modified protein and whether these alterations are significant in the cellular context. In this study, we investigate the effects of ubiquitination on the folding thermodynamics and mechanism of various substrates using computational tools and find that ubiquitination changes the thermal stability of modified proteins in a manner relevant to cellular processes. These changes depend on the substrate modification site and on the type of ubiquitination. Ubiquitination of the substrate Ubc7 at the residues that are modified in vivo prior to proteasomal degradation uniquely results in significant thermal destabilization and a local unwinding near the modification site, which indicates that ubiquitination possibly facilitates the unfolding process and improves substrate degradation efficiency. With respect to the substrate p19
4inkd
, our results support a synergetic effect of ubiquitination and phosphorylation on the degradation process via enhanced thermal destabilization. Our study implies that, in addition to its known role as a recognition signal, the ubiquitin attachment may be directly involved in the cellular process it regulates by changing the biophysical properties of the substrate.
Wee1B, Myt1, and Cdc25 function in distinct compartments of the mouse oocyte to control meiotic resumption
Authors: Oh Jeong Su , Han Seung Jin , Conti Marco
Published: January 2010

After a long period of quiescence at dictyate prophase I, termed the germinal vesicle (GV) stage, mammalian oocytes reenter meiosis by activating the Cdc2–cyclin B complex (maturation-promoting factor [MPF]). The activity of MPF is regulated by Wee1/Myt1 kinases and Cdc25 phosphatases. In this study, we demonstrate that the sequestration of components that regulate MPF activity in distinct subcellular compartments is essential for their function during meiosis. Down-regulation of either Wee1B or Myt1 causes partial meiotic resumption, and oocytes reenter the cell cycle only when both proteins are down-regulated. Shortly before GV breakdown (GVBD), Cdc25B is translocated from the cytoplasm to the nucleus, whereas Wee1B is exported from the nucleus to the cytoplasm. These movements are regulated by PKA inactivation and MPF activation, respectively. Mislocalized Wee1B or Myt1 is not able to maintain meiotic arrest. Thus, cooperation of Wee1B, Myt1, and Cdc25 is required to maintain meiotic arrest and relocation of these components before GVBD is necessary for meiotic reentry.
A sex-specific role for androgens in angiogenesis
Authors: Sieveking Daniel P. , Lim Patrick , Chow Renée W.Y. , Dunn Louise L. , Bao Shisan , McGrath Kristine C.Y. , Heather Alison K. , Handelsman David J. , Celermajer David S. , Ng Martin K.C.
Published: January 2010

Mounting evidence suggests that in men, serum levels of testosterone are negatively correlated to cardiovascular and all-cause mortality. We studied the role of androgens in angiogenesis, a process critical in cardiovascular repair/regeneration, in males and females. Androgen exposure augmented key angiogenic events in vitro. Strikingly, this occurred in male but not female endothelial cells (ECs). Androgen receptor (AR) antagonism or gene knockdown abrogated these effects in male ECs. Overexpression of AR in female ECs conferred androgen sensitivity with respect to angiogenesis. In vivo, castration dramatically reduced neovascularization of Matrigel plugs. Androgen treatment fully reversed this effect in male mice but had no effect in female mice. Furthermore, orchidectomy impaired blood-flow recovery from hindlimb ischemia, a finding rescued by androgen treatment. Our findings suggest that endogenous androgens modulate angiogenesis in a sex-dependent manner, with implications for the role of androgen replacement in men.
The generalized Uhlenbeck–Goudsmit hypothesis: ‘magnetic’ Sa and ‘electric’ Za spins
Authors: Ivezić Tomislav
Published: January 2010

In this paper, the connection between the dipole moment tensor D

ab
and the spin four-tensor S

ab
is formulated in the form of the generalized Uhlenbeck–Goudsmit hypothesis, D

ab
=g

S

S

ab
. It is also found that the spin four-tensor S

ab
can be decomposed into two 4-vectors, the usual ‘space–space’ intrinsic angular momentum S

a
, which will be called ‘magnetic’ spin (mspin), and a new one, the ‘time–space’ intrinsic angular momentum Z

a
, which will be called ‘electric’ spin (espin). Both spins are equally good physical quantities. Taking into account the generalized Uhlenbeck–Goudsmit hypothesis, the decomposition of S

ab
and the decomposition of D

ab
into the dipole moments m

a
and d

a
, we find that an electric dipole moment (EDM) of a fundamental particle, as a four-dimensional (4D) geometric quantity, is determined by Z

a
and not, as generally accepted, by the spin S as a 3-vector. Also it is shown that neither the T inversion nor the P inversion are good symmetries in the 4D spacetime. In this geometric approach, only the world parity W, Wx

a
=- x

a
, is well defined in the 4D spacetime. Some consequences for elementary particle theories and experiments that search for EDM are briefly discussed.

Henceforth space by itself, and time by itself, are doomed to fade away into mere shadows and only a kind of union of the two will preserve an independent reality. H Minkowski
Effect of ion temperature on localized ion-acoustic waves with flat-topped electron distribution
Authors: Alinejad H , Sobhanian S
Published: January 2010

The effect of ion temperature on the propagation of arbitrary amplitude ion-acoustic solitary waves is studied in an unmagnetized plasma which consists of a positively charged, warm ion fluid and hot electrons obeying a flat-topped distribution. A flat distribution for trapped particles is considered corresponding to the nonlinear interaction between electrons and electrostatic wave potential during its evolution. The basic properties of large amplitude solitary waves are studied by deriving an energy integral equation involving the Sagdeev potential. It is shown that the effects of such electron behavior and ion temperature change the regions of existence of arbitrary amplitude compressive solitary waves. By expanding the Sagdeev potential to include higher order nonlinearities of the electric potential, an exact steady state solution is also obtained, which confirms the possibility of ion-acoustic solitary waves in the small amplitude limit. Furthermore, two asymptotic cases of the stationary solution are found which are related to the contribution of flat-trapped electrons.
Inelastic Coulomb scattering rate within the finite-temperature Hubbard approximation
Authors: Vazifehshenas T , Salavati-fard T
Published: January 2010

In this paper, we have calculated the inelastic Coulomb scattering rate within the temperature-dependent Hubbard approximation for the dielectric function of high-mobility two-dimensional electron gas systems at low temperatures. To provide a good comparison, the results calculated within the RPA and the Hubbard approximation are also given in this paper. We found that the inelastic Coulomb scattering rate increases if the finite-temperature Hubbard local field is used, especially at low electron density.
Ras and Calcium Signaling Pathways Converge at Raf1 via the Shoc2 Scaffold Protein
Authors: Yoshiki Sayaka , Matsunaga-Udagawa Rie , Aoki Kazuhiro , Kamioka Yuji , Kiyokawa Etsuko , Matsuda Michiyuki
Published: January 2010

Situated downstream of Ras is a key signaling molecule, Raf1. Increase in Ca2+concentration has been shown to modulate the Ras-dependent activation of Raf1; however, the mechanism underlying this effect remains elusive. Here, to characterize the role of Ca2+in Ras signaling to Raf1, we used a synthetic guanine nucleotide exchange factor (GEF) for Ras, eGRF. In HeLa cells expressing eGRF, Ras was activated by the cAMP analogue 007 as efficiently as by epidermal growth factor (EGF), whereas the activation of Raf1, MEK, and ERK by 007 was about half of that by EGF. Using a biosensor based on fluorescence resonance energy transfer, it was found that activation of Raf1 at the plasma membrane required not only Ras activation but also an increase in Ca2+concentration or inhibition of calmodulin. Furthermore, the Ca2+-dependent activation of Raf1 was found to be abrogated by knockdown of Shoc2, a scaffold protein that binds both Ras and Raf1. These observations indicated that the Shoc2 scaffold protein modulates Ras-dependent Raf1 activation in a Ca2+- and calmodulin-dependent manner.
Making Music Modern
Authors: Oja Carol J.
Published: January 2010

New York City witnessed a burst of creativity in the 1920s. This artistic renaissance is examined from the perspective of composers of classical and modern music who, along with writers, painters, and jazz musicians, were at the heart of early modernism in America. The book also illustrates how the aesthetic attitudes and institutional structures from the 1920s left a deep imprint on the arts over the 20th century. Aaron Copland, George Gershwin, Ruth Crawford Seeger, Virgil Thomson, William Grant Still, Edgard Varèse, Henry Cowell, Carl Ruggles, Marion Bauer, and Dane Rudhyar were the leaders of a talented new generation of American composers whose efforts made New York City the center of new music in the country. They founded composer societies—such as the International Composers' Guild, the League of Composers, the Pan American Association, and the Copland-Sessions Concerts—to promote the performance of their music, and nimbly negotiated cultural boundaries, aiming for recognition in Western Europe as much as at home. This book provides a new perspective on the period and a compelling collective portrait of the figures, puncturing many longstanding myths. American composers active in New York during the 1920s are explored in relation to the “Machine Age” and American Dada; the impact of spirituality on American dissonance; the crucial, behind-the-scenes role of women as patrons and promoters of modernist music; cross-currents between jazz and concert music; the critical reception of modernist music (especially in the writings of Carl Van Vechten and Paul Rosenfeld); and the international impulse behind neoclassicism. The book also examines the persistent biases of the time, particularly anti-Semitism, gender stereotyping, and longstanding racial attitudes.
1 Leo Ornstein: “Wild Man” of the 1910s
Authors: Oja Carol J.
Published: January 2010

The decade between 1910 and 1920 was the mysterious Paleolithic period of modernist music in America. In the middle of a hazy, emergent scene, a charismatic keyboard virtuoso and composer named Leo Ornstein dazzled New York City with a series of four recitals at the Bandbox Theatre in January and February 1915. Ornstein's concerts startled musical New York and even aroused orchestral conductors, in some measure, out of their lethargic method of program-making. Ornstein performed not only recent music by European composers such as Arnold Schoenberg, Alexander Scriabin, Maurice Ravel, Isaac Albeniz, Erich Korngold, and Cyril Scott, but also adventurous new works of his own. With a flair for flamboyance and self-promotion, Ornstein provided an early model of how a modernist composer might make a career in the United States. He showed that modernism could be successfully marketed through clever packaging.
6 Dane Rudhyar’s Vision of Dissonance
Authors: Oja Carol J.
Published: January 2010

Noise was but one tool for modernist composers in the early 20th century. For many, the principal challenge came in devising alternatives to the tonal system on which much Western music had been based. One particular group of Americans—the “ultra-moderns”—took this mission especially seriously. Including composers who spanned a range of styles, the ultra-moderns seized experimentation as their rallying cry, and dissonance as their ideal. One facet of the ultra-moderns' music—especially that of Carl Ruggles, Henry Cowell, and Ruth Crawford—has been largely forgotten over time: the degree to which they associated dissonance with spirituality. In this realm, the French-American composer and philosopher Dane Rudhyar (1895-1985) became their quiet leader. Although Rudhyar's perspective represented only one part of ultra-modernism in the United States, it was influential for a time, and affected the way some of the most difficult strains of new music were being composed and perceived. All in all, Rudhyar fused an abundant array of ideas and influences into a distinctive vision of American dissonance.
13 Neoclassicism: “Orthodox Europeanism” or Empowering Internationalism?
Authors: Oja Carol J.
Published: January 2010

The stylistic designation “neoclassicism” met with especially strong resistance from young composers in the United States during the 1920s. Although slippery to define, neoclassicism popped up all across the Western modernist spectrum, often encompassing stylistic principles of “clarity” and “simplicity” and a broad range of attempts in art, music, and literature to re-imagine materials from the past. Whatever its profile, as a loosely defined aesthetic it affected a significant body of American works written late in the decade. These included compositions by Aaron Copland, Virgil Thomson, Roy Harris, Roger Sessions, Carlos Chavez, Walter Piston, and other newcomers to the scene. Much of the ambivalence of American composers toward neoclassicism hung on the question of whether the aesthetic yielded orthodox Europeanism, or whether it represented an empowering form of internationalism. Selected works from the Copland-Sessions Concerts exhibit sprightly responses to varying aspects of the aesthetic, showing how American composers achieved individuality while responding to a transnational set of aesthetic values.
20 Crossing Over with George Gershwin, Paul Whiteman, and the Modernists
Authors: Oja Carol J.
Published: January 2010

On February 12, 1924, Rhapsody in Blue, composed by George Gershwin (1898-1937), premiered at Aeolian Hall in New York City. Soon a group of other composers joined him in a brief but intense movement to produce “highbrow jazz”, including John Alden Carpenter, Aaron Copland, Louis Gruenberg, and William Grant Still. The first three made their careers in concert music, and the last straddled both popular music and concert music. At the same time, parallel forays were being made by European modernists seeking a means of mediating between the rarefied aesthetic terrain of high modernism and the more accessible plains of jazz. Gershwin may have taken his biggest artistic leap of the mid-1920s with another work, the Concerto in F, which represented a more ambitious attempt to bridge independent musical categories. One of the trendsetters in the crossover movement was the jazz-band conductor Paul Whiteman (1890-1967).
Rejecting the Plan
Authors: Jarausch Konrad H.
Published: January 2010

This chapter treats the return of the market economy in post-war Germany, which contrasted to Nazi exploitation and Communist planning and led to the economic miracle.
Embracing the West
Authors: Jarausch Konrad H.
Published: January 2010

This chapter deals with the process of Westernization during the 1960s, which transformed political preferences in the direction of the Western alliance and cultural practices towards American popular culture.
Searching for Normalcy
Authors: Jarausch Konrad H.
Published: January 2010

This chapter chronicles the German division, the drive for unification, and reflects upon the new challenges of a restored national state, in foreign policy as well as domestic affairs.
Introduction
Authors: Jarausch Konrad H.
Published: January 2010

This introductory chapter begins with a discussion of the aftermath of the German defeat and the atrocities committed under Nazi dictatorship. It then considers interpretations of Nazi barbarism. The chapter explains the purpose of the book, which is to explore German political culture during the second half of the 20th century. It looks at the practical rather than the intellectual ways in which Germans dealt with their problematic past.
“The Most Natural View of the Whole”
Authors: FOOTE THELMA WILLS
Published: January 2010

This chapter reveals that, by the 1740s, interracial socializing among colonial New York City's subaltern population of enslaved blacks, propertyless white servants, and transients troubled ruling elite and its binary racial division of society. It explains that with the additional threat of an impending Spanish invasion, the aggravation of an unsolved crime wave, and the outbreak of a mysterious rash of fire during the winter of 1741-42, fear of the city's dangerous classes crystallized in the discovery of the “plot of 1741-42,” an alleged conspiracy among enslaved blacks and several white outsiders accused of plotting together in secret to overthrow English rule, murder the city's white male settler population, enslave white females in harems, and establish a “Negro regime” under the protection of Catholic Spain.
“We Shall Never Be Quite Safe”
Authors: FOOTE THELMA WILLS
Published: January 2010

This chapter investigates examples of insubordination, ranging from the unruly behavior of the city's laboring class in the streets, marketplaces, dock areas, and taverns to the remarkable bids for freedom on the part of runaway servants and slaves. It points out that the largely unregulated population flows moving in and out of the port of New York compounded the problem of policing the city's servile population. It notes that the British war policy marked the abandonment of the long-standing disciplinary mechanism of governing the rulers and the majority settler population by cultivating a shaded interest between the rulers and the ruled in subjugation of the black population.
The Double Chorus in the St. Matthew Passion BWV 244
Authors: Melamed Daniel R.
Published: January 2010

Is Bach's St. Matthew Passion really for double-chorus and orchestra? The one thing everyone seems to know is that the St. Matthew Passion is a double-chorus composition. The idea that the work balances two matched ensembles against each other—a feature typically regarded as “symmetry”—has itself been a theme of almost every discussion of the St. Matthew Passion. But the view of the St. Matthew Passion as a symmetrical double-chorus work has arisen largely from the experience of modern performances that use two large choirs. Bach's original performing materials and analytical features of the work show that very little is actually scored for equal choruses, and that the two ensembles do not have the same status. Chorus 2 is subordinate to Chorus 1 and is better viewed as a ripieno ensemble that most often supports the work's concertists (Chorus 1), only occasionally gaining a measure of independence. This flexible and expanded role for a group of ripieno singers had its origins in a movement from Bach's St. John Passion and was particularly suited to the dialogue texts at the core of the St. Matthew Passion's libretto. It is also consistent with the particular performance forces Bach had at his disposal.
There Is No Such Thing as a Norm
Authors: Sherman Bernard D.
Published: January 2010

The mainstream repertory is so heavily Germanic that a novice of an earlier generation might easily have imagined that classical music had always been Teutonic territory. But in the art music of the Renaissance, the crucial region was what is now Belgium and northern France. Franco-Flemings like Dufay and Ockeghem dominated the 15th century, and their follower Josquin Desprez established the polyphonic style that dominated the 16th-century. This chapter presents an interview with Paul Hillier on Renaissance sacred music, the concept of definitive realization, size of an ensemble, how to perform a Renaissance piece, William Byrd’s Anglican works, instrumental accompaniment, voice production during the Renaissance, use of unwritten accidentals, barline as a musically significant element, transposition, intonation, improvisation, and authenticity and articulation in Renaissance music.
Beyond the Beautiful Pearl
Authors: Sherman Bernard D.
Published: January 2010

More than anything else in music, the art of singing can turn reasonable people into red-faced absolutists. That by itself guarantees that the most controversial area of Baroque performance today is singing. It probably explains why outsiders often have problems with early music singing. And after the opulent beauty of the singing of Renata Tebaldi, they often object to such elements as limited vibrato—although it is a mistake to assume that Baroque singers never use any vibrato. However, the early music community itself argues over Baroque singing. Reconstructing historical singing styles has proved more challenging than reconstructing instrumental styles. In the field of singing, far more than in the world of the harpsichord or the gamba, modern mainstream style weighs heavily upon us. This chapter presents an interview with Julianne Baird on Baroque singing, her admiration for Maria Callas and Mirella Freni, opera singing, the rising power of the composer and reverence for the score, vocal writing, articulation in Baroque singing, portamento, the use of non-vibrato by opera singers, and vibrato and rubato in Italian Baroque singing.