bluuebunny/crossref_metadata_2025 huggingface dataset:
Whites as a Minority and the New Biracial Coalition in New Orleans and Memphis
Authors: Liu Baodong
Published: February 2006

In 2005, Hurricane Katrina flooded more than 80% of the city of New Orleans. As the stories of hurricane victims, mostly African Americans, dominated the national news coverage, New Orleans' racial politics in particular, and the racial divisions in general, once again invited public debate. Why did a city that had been firmly controlled by African-American politicians from the mayor's office to the city council exhibit such a clear racial image? What role did Whites play in the city's political establishment? This project was supported by research grants from the American Political Science Association and the University of Wisconsin, which allowed the author to travel to Memphis and New Orleans to collect original data and interview the mayor of Memphis and other politicians. The author would also like to thank Susan Reed, Martin Gruberg, Wayne Parent, and David Siemers for their helpful comments on an earlier version of the article. Special thanks go to the three reviewers and the editors ofPS: Political Science and Politics, and to Laura Fisher-Guex, James Vanderleeuw, and Susan Howell for their invaluable assistance with the data-collection/recording process.
Drawing the Line on District Competition: A
Rejoinder
Authors: Abramowitz Alan , Alexander Brad , Gunning Matthew
Published: February 2006

In “Drawing the Line on District Competition,” Michael McDonald
(2006) challenges our conclusion that redistricting is not
responsible for declining competition in House elections. McDonald
claims that this conclusion is incorrect largely because our measure
of district partisanship in 1992 is flawed. According to McDonald,
using the normalized 1992 major party presidential vote as a measure
of House district partisanship in 1992 seriously overstates the
competitiveness of House districts in that year because of the
impact of the vote for Ross Perot. McDonald recommends instead using
the 1988 presidential vote to measure district partisanship in 1992,
or using a procedure developed by Gelman and King (1994a) to
estimate the partisan bias of House districts. With either of these
methods, McDonald claims that a significant proportion of the
decline in competitive districts between 1990 and 2002 was caused by
redistricting. In addition, contrary to our finding that nonpartisan
redistricting commissions have failed to produce increased
competition in House elections, McDonald claims that nonpartisan
redistricting in Arizona provides a positive example of what can be
accomplished by nonpartisan redistricting commissions elsewhere.
Asian American Political Participation: Research
Challenges for an Emerging Minority
Authors: Jacob Anil G.
Published: February 2006

Asian Americans are among the fastest-growing minority groups in the
United States. In recent years, their impact on politics has been
the focus of a growing number of scholars in the social sciences,
which raises the definitional question: Who are Asian Americans? The
working definition deployed here is that an Asian American is a
person who “resides in the United States on a permanent or long-term
basis, regardless of citizenship or other legal status” (Lien,
Conway, and Wong 2004). However, the definition of who an Asian is
has undergone significant expansion over the last 150 years because
of “shifts in the racial and ethnic makeup of the U.S. population
and changes in social attitudes and political concerns regarding
racial and ethnic minorities” (Lien, Conway, and Wong 2004). These
concerns expressed themselves in various modes of political
participation; referred to in the literature as the “Asian American
movement” (Wei 1993), these have ranged from litigation to the
boycott activities of Asian Americans on a variety of issues. I would like to extend my gratitude to
Jane Junn of Rutgers University as well as to members of the
APSA Committee on the Status of Asian Pacific Americans in the
Profession for encouragement and valuable feedback on this
article.
Doing a Literature Review
Authors: Knopf Jeffrey W.
Published: February 2006

Students entering a graduate program often encounter a new type of
assignment that differs from the papers they had to write in high
school or as college undergraduates: the literature review (also
known as a critical review essay). Put briefly, a literature review
summarizes and evaluates a body of writings about a specific topic.
The need to conduct such reviews is by no means limited to graduate
students; scholarly researchers generally carry out literature
reviews throughout their research careers. In a world where the
Internet has broadened the range of potentially relevant sources,
however, doing a literature review can pose challenges even to an
experienced researcher. In drafting
this overview, I have incorporated some points made by Paul
Pitman in a lecture delivered to students at the Naval
Postgraduate School. I have also incorporated some suggestions
contained in a handout prepared by John Odell for students in
the School of International Relations at the University of
Southern California.
Learning Political Engagement from the Experts: Advocacy
Groups, Neighborhood Councils, and Constituency
Service
Authors: Freyss Siegrun Fox
Published: February 2006

This article describes an uncommon approach to service learning. To
demonstrate points of access to the political system, I place
students in my class with experts of the political advocacy process,
not with charitable nonprofits. And to reach a wide spectrum of
students, I integrate the service-learning component in one section
of the basic American and state government course, which is a
general education requirement for all college graduates in the state
of California. This report explains the approach, evaluates the
course based on student responses, identifies reasons for its
success, and points out some of the limits encountered. The article
follows the tradition of Battistoni (2000), Battistoni and Hudson
(1997, 1), Zlotkowski (1998), and others by sharing insights into
the theory and practice of service learning in political science, in
the hopes of making transparent the advantages and limits of this
form of experiential learning. I am
grateful to the department of political science, the college of
natural and social sciences, and the dean of undergraduate
studies at the California State University, Los Angeles, for
supporting my modification of one section of the POLS 150 course
to include a service-learning component. I also wish to thank
Ted Anagnoson and Jan Mackay for their constructive comments as
I developed my service-learning course. The researchers at the
Carnegie Foundation for the Advancement of Teaching deserve a
word of appreciation for including my course in the Political
Engagement Project, and finally a thank you should go to the
anonymous reviewer of the original manuscript.
From Fukuoka to Santiago: Institutionalization of
Political Science in Latin America
Authors: Altman David
Published: February 2006

This article helps fill the void in U.S. political science's approach
to Latin American political science and its institutionalization.
One example of that void is that PS: Political Science &
Politics has recently published several pieces on the
state of the discipline in diverse regions of the world but, despite
its relative importance, none on the state of the discipline in
Latin America (see, for example, Bogaç and Turan 2004; Rizayev 2004;
and Sharapova 2005). This omission is remarkable because this
continent has both nourished U.S. political science by providing
several outstanding colleagues, many of whom have generated
controversial and important arguments against the dominant paradigms
in the discipline, and because, for better or worse, Latin America
has been considered the “backyard” of the United States. Arguably,
because of its economic, social, and political ties with the U.S.,
any major change in Latin America would have greater and more
immediate implications for the U.S. than similar events elsewhere in
the world. These topics are particularly pertinent with the upcoming
conference of the International Political Science Association (IPSA)
being held in Santiago, Chile, in 2009, and the APSA's new efforts
to recruit members from overseas, especially from not-so privileged
countries.
George A. Graham
Authors: Rowse Mary E.
Published: February 2006

George Adams Graham, political scientist and emeritus educator,
passed away on February 25, 2005, at his home in Chapel Hill, North
Carolina. He was 100. Among Dr. Graham's most lasting achievements
will be his work professionalizing and improving governance of the
public sector.
Marjorie Mowlam
Authors: Loewenberg Gerhard
Published: February 2006

Marjorie Mowlam, who received her Ph.D. in political science from the
University of Iowa in 1977, died at Pilgrim's Hospice in the United
Kingdom on August 19th at age 55 from the recurrence of a
brain tumor that had been first diagnosed nine years earlier. In the
interval between that diagnosis and her death, she rose to become
Britain's most popular politician on the strength of her
accomplishment as secretary of state for Northern Ireland in
negotiating the Good Friday Accords in 1998. When she subsequently
fell from Tony Blair's good graces and was sidelined to the Cabinet
Office, her personal popularity only rose further. To Blair's
embarrassment, she received a standing ovation at the Labour Party
Conference in 1998 in the middle of the prime minister's report to
the delegates.
Reliabilität von Kurzformen gängiger psychometrischer Instrumente zur Evaluation des therapeutischen Fortschritts in Psychotherapie und Psychiatrie
Authors: Lutz Wolfgang , Tholen Sven , Schürch Eva , Berking Matthias
Published: February 2006

Zusammenfassung. Im Rahmen der sich in den letzten Jahren immer stärker etablierenden Wissenschaftler-Praktiker-Netzwerke und Qualitätssicherungsstudien in der Psychotherapie und Psychiatrie wird der Einsatz von ökonomischen, aber multidimensionalen und veränderungssensitiven klinischen Messinstrumenten zur Verlaufs- und Ergebnismessung therapeutischer Behandlungen immer wichtiger. In der vorliegenden Arbeit wird die Entwicklung von Kurzfragebögen vier gängiger Messinstrumente (der Symptom-Checkliste, SCL-90-R; dem Emotionalitätsinventar, EMI; dem Inventar Interpersonaler Probleme, IIP und dem Inkongruenzfragebogen, INK) sowie die Validität, Reliabilität und Veränderungssensitivität dieser Kurzfragebögen anhand einer Stichprobe der Allgemeinbevölkerung (N = 436), einer Stichprobe ambulanter Psychotherapiepatienten (N = 169) sowie einer Stichprobe von Patienten in stationärer Psychotherapie (N = 134) dargestellt. Die psychometrischen Eigenschaften dieser Kurzformen sowie ein daraus generierter auf 43 Items beruhender Gesamtwert für die allgemeine psychische Beeinträchtigung erlauben den kombinierten Einsatz dieser Instrumente für eine kontinuierliche und ökonomische Erhebung des therapeutischen Fortschritts.
Bevölkerungsrepräsentative Normierung der Skala zur Allgemeinen Selbstwirksamkeitserwartung
Authors: Hinz Andreas , Schumacher Jörg , Albani Cornelia , Schmid Gabriele , Brähler Elmar
Published: February 2006

Zusammenfassung. Für die Skala zur Allgemeinen Selbstwirksamkeitserwartung von Jerusalem und Schwarzer steht eine Normierung anhand einer repräsentativen deutschen Bevölkerungsstichprobe bisher aus. Im Jahr 2001 wurde eine bevölkerungsrepräsentative Erhebung (N = 2019; Alter: 16-95 Jahre) durchgeführt, bei welcher neben der Skala zur Allgemeinen Selbstwirksamkeitserwartung auch andere Fragebögen eingesetzt wurden: Gießener Beschwerdebogen, Systems of Belief Inventory, Portraits Values Questionnaire und Resilience Scale. Die eindimensionale Struktur der Skala zur Allgemeinen Selbstwirksamkeitserwartung wurde bestätigt. Männer und jüngere Personen haben höhere Mittelwerte als Frauen und ältere Personen. Unter Validierungsgesichtspunkten ist die Nähe zur Resilienzskala (r = .68) hervorzuheben. Es werden Normwerte in Form von T-Werten und Prozenträngen mitgeteilt.
Influence of electric field on the hydrogen bond network of water
Authors: Suresh S. J. , Satish A. V. , Choudhary A
Published: February 2006

Understanding the inherent response of water to an external electric (E)-field is useful towards decoupling the role of E-field and surface in several practically encountered situations, such as that near an ion, near a charged surface, or within a biological nanopore. While this problem has been studied in some detail through simulations in the past, it has not been very amenable for theoretical analysis owing to the complexities presented by the hydrogen (H) bond interactions in water. It is also difficult to perform experiments with water in externally imposed, high E-fields owing to dielectric breakdown problems; it is hence all the more important that theoretical progress in this area complements the progress achieved through simulations. In an attempt to fill this lacuna, we develop a theory based on relatively simple concepts of reaction equilibria and Boltzmann distribution. The results are discussed in three parts: one pertaining to a comparison of the key features of the theory vis a vis published simulation/experimental results; second pertaining to insights into the H-bond stoichiometry and molecular orientations at different field strengths and temperatures; and the third relating to a surprising but explainable finding that H-bonds can stabilize molecules whose dipoles are oriented perpendicular to the direction of field (in addition to the E-field and H-bonds both stabilizing molecules with dipoles aligned in the direction of the field).
Substitution and chemical environment effects on the absorption spectrum of indigo
Authors: Jacquemin Denis , Preat Julien , Wathelet Valérie , Perpète Eric A.
Published: February 2006

The UV/visible spectra of a series of indigo derivatives have been evaluated by using ab initio methods. The combination of the Polarizable continuum model for estimating bulk solvent effects with the TD-B3LYP∕6-311+G(2d,p)∕∕B3LYP∕6-311G(d,p) level of approximation, leads to an accurate description of the wavelength of maximum absorption of indigoïds compounds. Using this procedure, we have assessed the effects of both the surroundings (solvent and solid state) and the substitution pattern. For the latter, we obtained a mean absolute deviation of only 7 nm (0.02 eV) compared to experiment, for a set of 86 molecules/solvents.
Theoretical study of the hydrated Gd3+ ion: Structure, dynamics, and charge transfer
Authors: Clavaguéra Carine , Calvo Florent , Dognon Jean-Pierre
Published: February 2006

The dynamical processes taking place in the first coordination shells of the gadolinium (III) ion are important for improving the contrast agent efficiency in magnetic-resonance imaging. An extensive study of the gadolinium (III) ion solvated by a water cluster is reported, based on molecular dynamics simulations. The AMOEBA force field [P. Y. Ren and J. W. Ponder, J. Phys. Chem. B 107, 5933 (2003)] that includes many-body polarization effects is used to describe the interactions among water molecules, and is extended here to treat the interactions between them and the gadolinium ion. In this purpose accurate ab initio calculations have been performed on Gd3+–H2O for extracting the relevant parameters. Structural data of the first two coordination shells and some dynamical properties such as the water exchange rate between the first and second coordination shells are compared to available experimental results. We also investigate the charge transfer processes between the ion and its solvent, using a fluctuating charges model fitted to reproduce electronic structure calculations on [Gd(H2O)n]3+ complexes, with n ranging from 1 to 8. Charge transfer is seen to be significant (about one electron) and correlated with the instantaneous coordination of the ion.
Remarkable identities related to the (quantum) elliptic Calogero-Sutherland model
Authors: Langmann Edwin
Published: February 2006

We present remarkable functional identities related to the elliptic Calogero-Sutherland (eCS) system. We derive them from a second quantization of the eCS model within a quantum field theory model of anyons on a circle and at finite temperature. The identities involve two eCS Hamiltonians with arbitrary and, in general, different particle numbers N and M, and a particular function of N+M variables arising as anyon correlation function of N particles and M antiparticles. In addition to identities obtained from anyons with the same statistics parameter λ, we also obtain “dual” relations involving “mixed” correlation functions of anyons with two different statistics parameters λ and 1∕λ. We also give alternative, elementary proofs of these identities by direct computations.
First-principles studies of chiral step reconstructions of Cu(100) by adsorbed glycine and alanine
Authors: Rankin Rees B. , Sholl David S.
Published: February 2006

Adsorption of amino acids on Cu(100) is known experimentally to induce surface reconstructions featuring intrinsically chiral Cu(3,1,17) facets, but no information about the geometry of the molecules on these chiral facets is available. We present density-functional theory calculations for the structure of glycine and alanine at moderate coverages on Cu(3,1,17). As might be expected, molecules prefer to bind at the step edges on this surface rather than on the surface’s (100)-oriented terraces. The adsorption of enantiopure alanine on Cu(3,1,17) is predicted to be weakly enantiospecific, with S-alanine being more stable on Cu(3,1,17)S than R-alanine. By comparing the surface energies of Cu(100) and Cu(3,1,17) in the presence of adsorbed glycine or alanine, our calculations provide insight into the driving force for chiral reconstructions of Cu(100) by amino acids.
Hydrolysis of Al3+ from constrained molecular dynamics
Authors: Ikeda Takashi , Hirata Masaru , Kimura Takaumi
Published: February 2006

We investigated the hydrolysis reactions of Al3+ in AlCl3 aqueous solution using the constrained molecular dynamics based on the Car-Parrinello molecular-dynamics method. By employing the proton-aluminum coordination number as a reaction coordinate in the constrained molecular dynamics the deprotonation as well as dehydration processes are successfully realized. From our free-energy difference of ΔG0≃8.0kcalmol−1 the hydrolysis constant pKa1 is roughly estimated as 5.8, comparable to the literature value of 5.07. We show that the free-energy difference for the hydrolysis of Al3+ in acidic conditions is at least 4kcalmol−1 higher than that in neutral condition, indicating that the hydrolysis reaction is inhibited by the presence of excess protons located around the hydrated ion, in agreement with the change of the predominant species by pH.
Real-time in situ growth study of TiN- and TiCxNy-based superhard nanocomposite coatings using spectroscopic ellipsometry
Authors: Jedrzejowski P. , Amassian A. , Bousser E. , Klemberg-Sapieha J. E. , Martinu L.
Published: February 2006

We investigate in situ and in real-time the growth of superhard ternary nanocomposite (nc)-TiN∕amorphous (a)-Si3N4 and quaternary nc-TiCxNy∕a-SiCN films. Using nondestructive, noncontact spectroscopic ellipsometry and appropriate ellipsometric models, we determine the variation of optical constants, film resistivity, and electron scattering time and mean free path as a function of thickness and particle size. Based on the optical and electrical behavior, we propose a microstructural model of superhard nanocomposite films, postulating the interconnectivity between individual nanoparticles, presence of defects in the individual grains, and particle size varying in the initial stage of the film growth.
Photoluminescent silicon nanocrystals synthesized by reactive laser ablation
Authors: Riabinina Daria , Durand Christophe , Chaker Mohamed , Rosei Federico
Published: February 2006

We report the synthesis of Si nanocrystals embedded in a SiO2 matrix using reactive laser ablation in oxygen atmosphere followed by annealing. We observe a strong photoluminescence signal, which is related to the oxygen background pressure used for synthesis. The average nanoparticle size, obtained independently by fitting photoluminescence spectra and from x-ray diffraction patterns, decreases from 16to2nm with increasing oxygen pressure from 0.01to1.1mTorr. The maximum photoluminescence intensity is observed at 0.8mTorr, which corresponds to a crystal size of 2.2±0.4nm. We find that the concentration of nonoxidized Si, which is controlled by the oxygen pressure, determines the final nanocrystal size.
Ferroelectric properties of SrRuO3∕BaTiO3∕SrRuO3 ultrathin film capacitors free from passive layers
Authors: Kim Y. S. , Jo J. Y. , Kim D. J. , Chang Y. J. , Lee J. H. , Noh T. W. , Song T. K. , Yoon J.-G. , Chung J.-S. , Baik S. I. , Kim Y.-W. , Jung C. U.
Published: February 2006

Structural studies on ultrathin SrRuO3∕BaTiO3∕SrRuO3 capacitors, with BaTiO3 thicknesses of between 5nm and 30nm, show well-defined interfaces between ferroelectric BaTiO3 and electrode SrRuO3 layers. In these capacitors, we cannot observe any extrinsic electrical effects due to either the formation of an insulating interfacial passive layer or passive-layer-induced charge injection. Such high-quality interfaces result in very good fatigue endurance, even for the 5nm thick BaTiO3 capacitor.
Terahertz-wave generation from quasi-phase-matched GaP for 1.55μm pumping
Authors: Tomita Isao , Suzuki Hiroyuki , Ito Hiroshi , Takenouchi Hirokazu , Ajito Katsuhiro , Rungsawang Rakchanok , Ueno Yuko
Published: February 2006

We have realized a terahertz (THz)-wave source employing difference frequency generation (DFG) from a quasi-phase-matched GaP stack pumped at 1.55μm. We observed THz waves with enhanced power by quasi-phase matching (QPM) in the ⟨110⟩ direction of GaP with a ⟨111⟩ polarization direction for the incidence of two pump lights with the same propagation and polarization directions. We obtained THz-wave power proportional to the product of two pump-light powers due to DFG. We also confirmed that power peaks appeared at around 1 and 2.6THz reflecting the first- and the third-order QPM, respectively.
Disaster in Agriculture: Or Foot and Mouth Mobilities
Authors: Law John
Published: February 2006

This paper is an exploration of the dynamics of the outbreak of foot and mouth disease in the United Kingdom in 2001. Following Perrow's analysis of the catastrophic breakdown of technological systems, the author treats the UK agricultural system as a set of flows that are both tightly coupled and complex. This suggests that the stability of the agricultural system is precarious, and that when it is disrupted (as it was with the arrival of the foot and mouth virus) the consequences may be large scale and catastrophic. The foot and mouth outbreak, and more generally, aspects of global agriculture, are thus understood as ‘normal accidents’.
Mobility/Stability: British Asian Cultures of ‘Landscape and Englishness’
Authors: Tolia-Kelly Divya P
Published: February 2006

This paper examines the way in which the (British) Asian diaspora creates a territory of belonging and a cultural nationalism within the British landscape. New, British Asian cultures of Englishness are figured through the experience of mobility from ‘other’ landscapes to England. The expression of new hybrids of cultural nationalism based on cultures of Englishness and landscape are presented in the tangible forms of Asian women's drawings of ‘landscapes of belonging’ and their material cultures at home. The Englishness that is expressed through these cultures is examined as a mobile culture that has shifted in meaning and form through the various migrations of the diaspora from sites of colonial governance. The acknowledgement of mobility reveals how new cultural nationalisms rely on souvenirs and sacred objects, contributing to a new moral aesthetics of home and thus creating an inclusive culture of Englishness. The home incorporates a new space where the Englishness of Victoriana and textures of Indianess or Africaness are sites of memorial to mobility itself. The British Asian diaspora creates spatially transferable, mobile cultures of nationalism, expressed through material registers of English landscape aesthetics. The English landscape itself is examined as refractive of lived landscapes abroad and explored through the diasporic lens. Englishness in this paper is based on a ‘territory of culture’, unfixed from any singular national identity, land, or discrete national culture, but located in the cultures of desire of belonging to England.
In vitro
generated extracellular matrix and fluid shear stress synergistically enhance 3D osteoblastic differentiation
Authors: Datta Néha , P. Pham Quynh , Sharma Upma , Sikavitsas Vassilios I. , Jansen John A. , Mikos Antonios G.
Published: February 2006

This study instituted a unique approach to bone tissue engineering by combining effects of mechanical stimulation in the form of fluid shear stresses and the presence of bone-like extracellular matrix (ECM) on osteodifferentiation. Rat marrow stromal cells (MSCs) harvested from bone marrow were cultured on titanium (Ti) fiber mesh discs for 12 days in a flow perfusion system to generate constructs containing bone-like ECM. To observe osteodifferentiation and bone-like matrix deposition, these decellularized constructs and plain Ti fiber meshes were seeded with MSCs (Ti/ECM and Ti, respectively) and cultured in the presence of fluid shear stresses either with or without the osteogenic culture supplement dexamethasone. The calcium content, alkaline phosphatase activity, and osteopontin secretion were monitored as indicators of MSC differentiation. Ti/ECM constructs demonstrated a 75-fold increase in calcium content compared with their Ti counterparts after 16 days of culture. After 16 days, the presence of dexamethasone enhanced the effects of fluid shear stress and the bone-like ECM by increasing mineralization 50-fold for Ti/ECM constructs; even in the absence of dexamethasone, the Ti/ECM constructs exhibited approximately a 40-fold increase in mineralization compared with their Ti counterparts. Additionally, denatured Ti/ECM* constructs demonstrated a 60-fold decrease in calcium content compared with Ti/ECM constructs after 4 days of culture. These results indicate that the inherent osteoinductive potential of bone-like ECM along with fluid shear stresses synergistically enhance the osteodifferentiation of MSCs with profound implications on bone-tissue-engineering applications.
Peptide-matrix-mediated gene transfer of an oxygen-insensitive hypoxia-inducible factor-1α variant for local induction of angiogenesis
Authors: Trentin Diana , Hall Heike , Wechsler Sandra , Hubbell Jeffrey A.
Published: February 2006

Hypoxia-inducible factor (HIF) constitutes a target in therapeutic angiogenesis. HIF-1α functions as a sensor of hypoxia and induces expression of vascular endothelial growth factor (VEGF), which then induces angiogenesis. To explore the potential of HIF-1α gene therapy in stimulating wound healing, we delivered a gene encoding a stabilized form of HIF-1α, lacking the oxygen-sensitive degradation domain, namely HIF-1αΔODD, by using a previously characterized peptide-based gene delivery vector in fibrin as a surgical matrix. The peptide vector consisted of multiple domains: (
i
) A cysteine-flanked lysine hexamer provided DNA interactions that were stable extracellularly but destabilized intracellularly after reduction of the formed disulfide bonds. This DNA-binding domain was fused to either (
ii
) a fibrin-binding peptide for entrapment within the matrix or (
iii
) a nuclear localization sequence for efficient nuclear targeting. The HIF-1αΔODD gene was expressed and translocated to the nucleus under normoxic conditions, leading to up-regulation of vascular endothelial growth factor (VEGF)-A
165
mRNA and protein levels
in vitro
. When the peptide-DNA nanoparticles entrapped in fibrin matrices were applied to full-thickness dermal wounds in the mouse (10 μg per wound in 30 μl of fibrin), angiogenesis was increased comparably strongly to that induced by VEGF-A
165
protein (1.25 μg per wound in 30 μl of fibrin). However, the maturity of the vessels induced by HIF-1αΔODD was significantly higher than that induced by VEGF-A
165
protein, as shown by stabilization of the neovessels with smooth muscle. Nonviral, local administration of this potent angiogenesis-inducing gene by using this peptide vector represents a powerful approach in tissue engineering and therapeutic angiogenesis.
SmyD1, a histone methyltransferase, is required for myofibril organization and muscle contraction in zebrafish embryos
Authors: Tan Xungang , Rotllant Josep , Li Huiqing , DeDeyne Patrick , Du Shao Jun
Published: February 2006

Histone modification has emerged as a fundamental mechanism for control of gene expression and cell differentiation. Recent studies suggest that SmyD1, a novo SET domain-containing protein, may play a critical role in cardiac muscle differentiation. However, its role in skeletal muscle development and its mechanism of actions remains elusive. Here we report that SmyD1a and SmyD1b, generated by alternative splicing ofSmyD1gene, are histone methyltransferases that play a key role in skeletal and cardiac muscle contraction. SmyD1a and SmyD1b are specifically expressed in skeletal and cardiac muscles of zebrafish embryos. Knockdown of SmyD1a and SmyD1b expression by morpholino antisense oligos resulted in malfunction of skeletal and cardiac muscles. The SmyD1 morphant embryos (embryos injected with morpholino oligos) could not swim and had no heartbeat. Myofibril organization in the morphant embryos was severely disrupted. The affected myofibers appeared as immature fibers with centrally located nuclei. Together, these data indicate that SmyD1a and SmyD1b are histone methyltransferases and play a critical role in myofibril organization during myofiber maturation.
CSPα-deficiency causes massive and rapid photoreceptor degeneration
Authors: Schmitz Frank , Tabares Lucia , Khimich Darina , Strenzke Nicola , de la Villa-Polo Pedro , Castellano-Muñoz Manuel , Bulankina Anna , Moser Tobias , Fernández-Chacón Rafael , Südhof Thomas C.
Published: February 2006

Cysteine string protein (CSP) α is an abundant synaptic vesicle protein that contains a DNA-J domain characteristic of Hsp40-type cochaperones. Previous studies showed that deletion of CSPα in mice leads to massive lethal neurodegeneration but did not clarify how the neurodegeneration affects specific subpopulations of neurons. Here, we analyzed the effects of the CSPα deficiency on tonically active ribbon synapses of the retina and the inner ear. We show that CSPα-deficient photoreceptor terminals undergo dramatic and rapidly progressive neurodegeneration that starts before eye opening and initially does not affect other retinal synapses. These changes are associated with progressive blindness. In contrast, ribbon synapses of auditory hair cells did not exhibit presynaptic impairments in CSPα-deficient mice. Hair cells, but not photoreceptor cells or central neurons, express CSPβ, thereby accounting for the lack of a hair-cell phenotype in CSPα knockout mice. Our data demonstrate that tonically active ribbon synapses in retina are particularly sensitive to the deletion of CSPα and that expression of at least one CSP isoform is essential to protect such tonically active synapses from neurodegeneration.
Structure and mechanism of the
Propionibacterium acnes
polyunsaturated fatty acid isomerase
Authors: Liavonchanka Alena , Hornung Ellen , Feussner Ivo , Rudolph Markus Georg
Published: February 2006

Conjugated linoleic acids (CLAs) affect body fat gain, carcinogenesis, insulin resistance, and lipid peroxidation in mammals. Several isomers of CLA exist, of which the (9
Z
, 11
E
) and (10
E
, 12
Z
) isomers have beneficial effects on human metabolism but are scarce in foods. Bacterial polyunsaturated fatty acid isomerases are promising biotechnological catalysts for CLA production. We describe six crystal structures of the
Propionibacterium acnes
polyunsaturated fatty acid isomerase PAI in apo- and product-bound forms. The three-domain flavoprotein has previously undescribed folds outside the FAD-binding site. Conformational changes in a hydrophobic channel toward the active site reveal a unique gating mechanism for substrate specificity. The geometry of the substrate-binding site explains the length preferences for C18 fatty acids. A catalytic mechanism for double-bond isomerization is formulated that may be altered to change substrate specificity for syntheses of rare CLAs from easily accessible precursors.
Gene expression changes associated with progression and response in chronic myeloid leukemia
Authors: Radich Jerald P. , Dai Hongyue , Mao Mao , Oehler Vivian , Schelter Jan , Druker Brian , Sawyers Charles , Shah Neil , Stock Wendy , Willman Cheryl L. , Friend Stephen , Linsley Peter S.
Published: February 2006

Chronic myeloid leukemia (CML) is a hematopoietic stem cell disease with distinct biological and clinical features. The biologic basis of the stereotypical progression from chronic phase through accelerated phase to blast crisis is poorly understood. We used DNA microarrays to compare gene expression in 91 cases of CML in chronic (42 cases), accelerated (17 cases), and blast phases (32 cases). Three thousand genes were found to be significantly (
P
< 10
−10
) associated with phase of disease. A comparison of the gene signatures of chronic, accelerated, and blast phases suggest that the progression of chronic phase CML to advanced phase (accelerated and blast crisis) CML is a two-step rather than a three-step process, with new gene expression changes occurring early in accelerated phase before the accumulation of increased numbers of leukemia blast cells. Especially noteworthy and potentially significant in the progression program were the deregulation of the WNT/β-catenin pathway, the decreased expression of Jun B and Fos, alternative kinase deregulation, such as Arg (Abl2), and an increased expression of PRAME. Studies of CML patients who relapsed after initially successful treatment with imatinib demonstrated a gene expression pattern closely related to advanced phase disease. These studies point to specific gene pathways that might be exploited for both prognostic indicators as well as new targets for therapy.
MyD88-dependent and -independent signaling by IL-1 in neurons probed by bifunctional Toll/IL-1 receptor domain/BB-loop mimetics
Authors: Davis Christopher N. , Mann Enrique , Behrens M. Margarita , Gaidarova Svetlana , Rebek Mitra , Rebek Julius , Bartfai Tamas
Published: February 2006

Interleukin (IL)-1β is a pluripotent proinflammatory cytokine that signals through the type-I IL-1 receptor (IL-1RI), a member of the Toll-like receptor family. In hypothalamic neurons, binding of IL-1β to IL-1RI mediates transcription-dependent changes that depend on the recruitment of the cytosolic adaptor protein myeloid differentiation primary-response protein 88 (MyD88) to the IL-1RI/IL-1 receptor accessory protein (IL-1RAcP) complex through homomeric Toll/IL-1 receptor (TIR)–TIR interactions. Through design and synthesis of bifunctional TIR mimetics that disrupt the interaction of MyD88 with the IL-1RI/IL-1RAcP complex, we analyzed the involvement of MyD88 in the signaling of IL-1β in anterior hypothalamic neurons. We show here that IL-1β-mediated activation of the protein tyrosine kinase Src depended on a MyD88 interaction with the IL-1RI/IL-1RAcP complex. The activation of the protein kinase Akt/PKB depended on the recruitment of the p85 subunit of PI3K to IL-1RI and independent of MyD88 association with the IL-1RI/IL-1RAcP complex. These bifunctional TIR–TIR mimetics represent a class of low-molecular-weight compounds with both an antiinflammatory and neuroprotective potential. These compounds have the potential to inhibit the MyD88-dependent proinflammatory actions of IL-1β, while permitting the potential neuronal survival supporting actions mediated by the MyD88-independent activation of the protein kinase Akt.
Activation of IFN pathways and plasmacytoid dendritic cell recruitment in target organs of primary Sjögren’s syndrome
Authors: Gottenberg Jacques-Eric , Cagnard Nicolas , Lucchesi Carlo , Letourneur Franck , Mistou Sylvie , Lazure Thierry , Jacques Sebastien , Ba Nathalie , Ittah Marc , Lepajolec Christine , Labetoulle Marc , Ardizzone Marc , Sibilia Jean , Fournier Catherine , Chiocchia Gilles , Mariette Xavier
Published: February 2006

Gene expression analysis of target organs might help provide new insights into the pathogenesis of autoimmune diseases. We used global gene expression profiling of minor salivary glands to identify patterns of gene expression in patients with primary Sjögren’s syndrome (pSS), a common and prototypic systemic autoimmune disease. Gene expression analysis allowed for differentiating most patients with pSS from controls. The expression of 23 genes in the IFN pathways, including two Toll-like receptors (TLR8 and TLR9), was significantly different between patients and controls. Furthermore, the increased expression of IFN-inducible genes, BAFF and IFN-induced transmembrane protein 1, was also demonstrated in ocular epithelial cells by quantitative RT-PCR.In vitroactivation showed that these genes were effectively modulated by IFNs in salivary gland epithelial cells, the target cells of autoimmunity in pSS. The activation of IFN pathways led us to investigate whether plasmacytoid dendritic cells were recruited in salivary glands. These IFN-producing cells were detected by immunohistochemistry in all patients with pSS, whereas none was observed in controls. In conclusion, our results support the pathogenic interaction between the innate and adaptive immune system in pSS. The persistence of the IFN signature might be related to a vicious circle, in which the environment interacts with genetic factors to drive the stimulation of salivary TLRs.
Synergistic roles of platelet-derived growth factor-BB and interleukin-1β in phenotypic modulation of human aortic smooth muscle cells
Authors: Chen Cheng-Nan , Li Yi-Shuan J. , Yeh Yi-Ting , Lee Pei-Ling , Usami Shunichi , Chien Shu , Chiu Jeng-Jiann
Published: February 2006

The phenotype of smooth muscle cells (SMCs) plays an important role in vascular function in health and disease. We investigated the mechanism of modulation of SMC phenotype (from contractile to synthetic) induced by the synergistic action of a growth factor (platelet-derived growth factor, PDGF-BB) and a cytokine (interleukin, IL-1β). Human aortic SMCs grown on polymerized collagen showed high expression levels of contractile markers (smooth muscle α-actin, myosin heavy chain, and calponin). These levels were not significantly affected by PDGF-BB and IL-1β individually, but decreased markedly after the combined usage of PDGF-BB and IL-1β. PDGF/IL-1β costimulation also induced a sustained phosphorylation of Akt and p70 ribosomal S6 kinase (p70S6K). The effects of PDGF/IL-1β costimulation on contractile marker expression and Akt and p70S6K phosphorylation were blocked by the phosphatidylinositol 3-kinase inhibitors wortmannin and LY294002 and by adenovirus expressing a dominant-negative Akt, and they were mimicked by constitutively active Akt. PDGF-BB/IL-1β induced a sustained phosphorylation of PDGF receptor (PDGFR)-β and its association with IL-1 receptor (IL-1R1). Such activation and association of receptors were blocked by a PDGFR-β neutralizing antibody (AF385), an IL-1R1 antagonist (IL-1ra), as well as a specific inhibitor of PDGFR-β phosphorylation (AG1295); these agents also eliminated the PDGF-BB/IL-1β-induced signaling and phenotypic modulation. PDGF-BB/IL-1β inhibited the polymerized collagen-induced serum response factor DNA binding activity in the nucleus, and this effect was mediated by the PDGFR-β/IL-1R1 association and phosphatidylinositol 3-kinase/Akt/p70S6K pathway. Our findings provide insights into the mechanism of SMC phenotypic modulation from contractile to synthetic, e.g., in atherosclerosis.
Cell-type-specific signatures of microRNAs on target mRNA expression
Authors: Sood Pranidhi , Krek Azra , Zavolan Mihaela , Macino Giuseppe , Rajewsky Nikolaus
Published: February 2006

Although it is known that the human genome contains hundreds of microRNA (miRNA) genes and that each miRNA can regulate a large number of mRNA targets, the overall effect of miRNAs on mRNA tissue profiles has not been systematically elucidated. Here, we show that predicted human mRNA targets of several highly tissue-specific miRNAs are typically expressed in the same tissue as the miRNA but at significantly lower levels than in tissues where the miRNA is not present. Conversely, highly expressed genes are often enriched in mRNAs that do not have the recognition motifs for the miRNAs expressed in these tissues. Together, our data support the hypothesis that miRNA expression broadly contributes to tissue specificity of mRNA expression in many human tissues. Based on these insights, we apply a computational tool to directly correlate 3′ UTR motifs with changes in mRNA levels upon miRNA overexpression or knockdown. We show that this tool can identify functionally important 3′ UTR motifs without cross-species comparison.
Phanerozoic marine biodiversity dynamics in light of the incompleteness of the fossil record
Authors: Lu Peter J. , Yogo Motohiro , Marshall Charles R.
Published: February 2006

Long-term evolutionary dynamics have been approached through quantitative analysis of the fossil record, but without explicitly taking its incompleteness into account. Here we explore the temporal covariance structure of per-genus origination and extinction rates for global marine fossil genera throughout the Phanerozoic, both before and after corrections for the incompleteness of the fossil record. Using uncorrected data based on Sepkoski’s compendium, we find significant autocovariance within origination and extinction rates, as well as covariance between extinction and origination, not one, but two, intervals later, corroborating evidence for the unexplained temporal gap found by past studies. However, these effects vanish when the data are corrected for the incompleteness of the fossil record. Instead, we observe significant covariance only between extinction and origination in the immediately following intervals. The gap in the response of the biosphere to extinction in the uncorrected fossil record thus appears to be an artifact of the incompleteness of the fossil record, specifically due to episodic variation in the probability that taxa will be preserved, on time scales comparable to the temporal resolution of Sepkoski’s data. Our results also indicate that at that temporal resolution (the stage/substage of duration ≈5 million years), changes in origination and extinction do not persist for longer than one interval, except that elevated origination rates immediately after extinction may last for more than a single interval. Thus, although certain individual cases may deviate from the overall pattern, we find that in general the biosphere’s response to perturbation is immediate geologically and usually short-lived.
Analysis of
Pseudomonas aeruginosa
diguanylate cyclases and phosphodiesterases reveals a role for bis-(3′-5′)-cyclic-GMP in virulence
Authors: Kulesekara Hemantha , Lee Vincent , Brencic Anja , Liberati Nicole , Urbach Jonathan , Miyata Sachiko , Lee Daniel G. , Neely Alice N. , Hyodo Mamoru , Hayakawa Yoshihiro , Ausubel Frederick M. , Lory Stephen
Published: February 2006

The opportunistic pathogen
Pseudomonas aeruginosa
is responsible for systemic infections in immunocompromised individuals and chronic respiratory disease in patients with cystic fibrosis. Cyclic nucleotides are known to play a variety of roles in the regulation of virulence-related factors in pathogenic bacteria. A set of
P. aeruginosa
genes, encoding proteins that contain putative domains characteristic of diguanylate cyclases (DGCs) and phosphodiesterases (PDEs) that are responsible for the maintenance of cellular levels of the second messenger bis-(3′-5′)-cyclic dimeric GMP (c-di-GMP) was identified in the annotated genomes of
P. aeruginosa
strains PAO1 and PA14. Although the majority of these genes are components of the
P. aeruginosa
core genome, several are located on presumptive horizontally acquired genomic islands. A comprehensive analysis of
P. aeruginosa
genes encoding the enzymes of c-di-GMP metabolism (DGC- and PDE-encoding genes) was carried out to analyze the function of c-di-GMP in two disease-related phenomena, cytotoxicity and biofilm formation. Analysis of the phenotypes of DGC and PDE mutants and overexpressing clones revealed that certain virulence-associated traits are controlled by multiple DGCs and PDEs through alterations in c-di-GMP levels. A set of mutants in selected DGC- and PDE-encoding genes exhibited attenuated virulence in a mouse infection model. Given that insertions in different DGC and PDE genes result in distinct phenotypes, it seems likely that the formation or degradation of c-di-GMP by these enzymes is in highly localized and intimately linked to particular targets of c-di-GMP action.
Automated cell lineage tracing in
Caenorhabditis elegans
Authors: Bao Zhirong , Murray John I. , Boyle Thomas , Ooi Siew Loon , Sandel Matthew J. , Waterston Robert H.
Published: February 2006

The invariant cell lineage and cell fate of
Caenorhabditis elegans
provide a unique opportunity to decode the molecular mechanisms of animal development. To exploit this opportunity, we have developed a system for automated cell lineage tracing during
C. elegans
embryogenesis, based on 3D, time-lapse imaging and automated image analysis. Using ubiquitously expressed histone–GFP fusion protein to label cells/nuclei and a confocal microscope, the imaging protocol captures embryogenesis at high spatial (31 planes at 1 μm apart) and temporal (every minute) resolution without apparent effects on development. A set of image analysis algorithms then automatically recognizes cells at each time point, tracks cell movements, divisions and deaths over time and assigns cell identities based on the canonical naming scheme. Starting from the four-cell stage (or earlier), our software, named
starrynite
, can trace the lineage up to the 350-cell stage in 25 min on a desktop computer. The few errors of automated lineaging can then be corrected in a few hours with a graphic interface that allows easy navigation of the images and the reported lineage tree. The system can be used to characterize lineage phenotypes of genes and/or extended to determine gene expression patterns in a living embryo at the single-cell level. We envision that this automation will make it practical to systematically decipher the developmental genes and pathways encoded in the genome of
C. elegans
.