bluuebunny/crossref_metadata_2025 huggingface dataset:
Laminin-111 protein therapy prevents muscle disease in the
mdx
mouse model for Duchenne muscular dystrophy
Authors: Rooney Jachinta E. , Gurpur Praveen B. , Burkin Dean J.
Published: April 2009

Duchenne muscular dystrophy (DMD) is a devastating neuromuscular disease caused by mutations in the gene encoding dystrophin. Loss of dystrophin results in reduced sarcolemmal integrity and increased susceptibility to muscle damage. The α
7
β
1
-integrin is a laminin-binding protein up-regulated in the skeletal muscle of DMD patients and in the
mdx
mouse model. Transgenic overexpression of the α
7
-integrin alleviates muscle disease in dystrophic mice, making this gene a target for pharmacological intervention. Studies suggest laminin may regulate α
7
-integrin expression. To test this hypothesis, mouse and human myoblasts were treated with laminin and assayed for α
7
-integrin expression. We show that laminin-111 (α
1
, β
1
, γ
1
), which is expressed during embryonic development but absent in normal or dystrophic skeletal muscle, increased α
7
-integrin expression in mouse and DMD patient myoblasts. Injection of laminin-111 protein into the
mdx
mouse model of DMD increased expression of α
7
-integrin, stabilized the sarcolemma, restored serum creatine kinase to wild-type levels, and protected muscle from exercised-induced damage. These findings demonstrate that laminin-111 is a highly potent therapeutic agent for the
mdx
mouse model of DMD and represents a paradigm for the systemic delivery of extracellular matrix proteins as therapies for genetic diseases.
Von Willebrand factor-binding protein is a hysteretic conformational activator of prothrombin
Authors: Kroh Heather K. , Panizzi Peter , Bock Paul E.
Published: April 2009

Von Willebrand factor-binding protein (VWbp), secreted by
Staphylococcus aureus
, displays secondary structural homology to the 3-helix bundle, D1 and D2 domains of staphylocoagulase (SC), a potent conformational activator of the blood coagulation zymogen, prothrombin (ProT). In contrast to the classical proteolytic activation mechanism of trypsinogen-like serine proteinase zymogens, insertion of the first 2 residues of SC into the NH
2
-terminal binding cleft on ProT (molecular sexuality) induces rapid conformational activation of the catalytic site. Based on plasma-clotting assays, the target zymogen for VWbp may be ProT, but this has not been verified, and the mechanism of ProT activation is unknown. We demonstrate that VWbp activates ProT conformationally in a mechanism requiring its Val
1
-Val
2
residues. By contrast to SC, full time-course kinetic studies of ProT activation by VWbp demonstrate that it activates ProT by a substrate-dependent, hysteretic kinetic mechanism. VWbp binds weakly to ProT (
K
D
2.5 μM) to form an inactive complex, which is activated through a slow conformational change by tripeptide chromogenic substrates and its specific physiological substrate, identified here as fibrinogen (Fbg). This mechanism increases the specificity of ProT activation by delaying it in a slow reversible process, with full activation requiring binding of Fbg through an exosite expressed on the activated ProT*·VWbp complex. The results suggest that this unique mechanism regulates pathological fibrin (Fbn) deposition to VWF-rich areas during
S. aureus
endocarditis.
Experimental characterization of disordered and ordered aggregates populated during the process of amyloid fibril formation
Authors: Carulla Natàlia , Zhou Min , Arimon Muriel , Gairí Margarida , Giralt Ernest , Robinson Carol V. , Dobson Christopher M.
Published: April 2009

Recent experimental evidence points to intermediates populated during the process of amyloid fibril formation as the toxic moieties primarily responsible for the development of increasingly common disorders such as Alzheimer's disease and type II diabetes. We describe here the application of a pulse-labeling hydrogen-deuterium (HD) exchange strategy monitored by mass spectrometry (MS) and NMR spectroscopy (NMR) to characterize the aggregation process of an SH3 domain under 2 different conditions, both of which ultimately lead to well-defined amyloid fibrils. Under one condition, the intermediates appear to be largely amorphous in nature, whereas under the other condition protofibrillar species are clearly evident. Under the conditions favoring amorphous-like intermediates, only species having no protection against HD exchange can be detected in addition to the mature fibrils that show a high degree of protection. By contrast, under the conditions favoring protofibrillar-like intermediates, MS reveals that multiple species are present with different degrees of HD exchange protection, indicating that aggregation occurs initially through relatively disordered species that subsequently evolve to form ordered aggregates that eventually lead to amyloid fibrils. Further analysis using NMR provides residue-specific information on the structural reorganizations that take place during aggregation, as well as on the time scales by which they occur.
Genetic reductionist approach for dissecting individual roles of GGDEF proteins within the c-di-GMP signaling network in
Salmonella
Authors: Solano Cristina , García Begoña , Latasa Cristina , Toledo-Arana Alejandro , Zorraquino Violeta , Valle Jaione , Casals Joan , Pedroso Enrique , Lasa Iñigo
Published: April 2009

Bacteria have developed an exclusive signal transduction system involving multiple diguanylate cyclase and phosphodiesterase domain-containing proteins (GGDEF and EAL/HD-GYP, respectively) that modulate the levels of the same diffusible molecule, 3′-5′-cyclic diguanylic acid (c-di-GMP), to transmit signals and obtain specific cellular responses. Current knowledge about c-di-GMP signaling has been inferred mainly from the analysis of recombinant bacteria that either lack or overproduce individual members of the pathway, without addressing potential compensatory effects or interferences between them. Here, we dissected c-di-GMP signaling by constructing a
Salmonella
strain lacking all GGDEF-domain proteins and then producing derivatives, each restoring 1 protein. Our analysis showed that most GGDEF proteins are constitutively expressed and that their expression levels are not interdependent. Complete deletion of genes encoding GGDEF-domain proteins abrogated virulence, motility, long-term survival, and cellulose and fimbriae synthesis. Separate restoration revealed that 4 proteins from
Salmonella
and 1 from
Yersinia pestis
exclusively restored cellulose synthesis in a c-di-GMP–dependent manner, indicating that c-di-GMP produced by different GGDEF proteins can activate the same target. However, the restored strain containing the STM4551-encoding gene recovered all other phenotypes by means of gene expression modulation independently of c-di-GMP. Specifically, fimbriae synthesis and virulence were recovered through regulation of
csgD
and the plasmid-encoded
spvAB
mRNA levels, respectively. This study provides evidence that the regulation of the GGDEF-domain proteins network occurs at 2 levels: a level that strictly requires c-di-GMP to control enzymatic activities directly, restricted to cellulose synthesis in our experimental conditions, and another that involves gene regulation for which c-di-GMP synthesis can be dispensable.
Spatial dynamics of ecological public goods
Authors: Wakano Joe Yuichiro , Nowak Martin A. , Hauert Christoph
Published: April 2009

The production, consumption, and exploitation of common resources ranging from extracellular products in microorganisms to global issues of climate change refer to public goods interactions. Individuals can cooperate and sustain common resources at some cost or defect and exploit the resources without contributing. This generates a conflict of interest, which characterizes social dilemmas: Individual selection favors defectors, but for the community, it is best if everybody cooperates. Traditional models of public goods do not take into account that benefits of the common resource enable cooperators to maintain higher population densities. This leads to a natural feedback between population dynamics and interaction group sizes as captured by “ecological public goods.” Here, we show that the spatial evolutionary dynamics of ecological public goods in “selection-diffusion” systems promotes cooperation based on different types of pattern formation processes. In spatial settings, individuals can migrate (diffuse) to populate new territories. Slow diffusion of cooperators fosters aggregation in highly productive patches (activation), whereas fast diffusion enables defectors to readily locate and exploit these patches (inhibition). These antagonistic forces promote coexistence of cooperators and defectors in static or dynamic patterns, including spatial chaos of ever-changing configurations. The local environment of cooperators and defectors is shaped by the production or consumption of common resources. Hence, diffusion-induced self-organization into spatial patterns not only enhances cooperation but also provides simple mechanisms for the spontaneous generation of habitat diversity, which denotes a crucial determinant of the viability of ecological systems.
Immunization by vaccine-coated microneedle arrays protects against lethal influenza virus challenge
Authors: Zhu Qiyun , Zarnitsyn Vladimir G. , Ye Ling , Wen Zhiyuan , Gao Yulong , Pan Lei , Skountzou Ioanna , Gill Harvinder S. , Prausnitz Mark R. , Yang Chinglai , Compans Richard W.
Published: April 2009

Influenza prophylaxis would benefit from a simple method to administer influenza vaccine into skin without the need for hypodermic needles. In this study, solid metal microneedle arrays (MNs) were investigated as a system for cutaneous vaccine delivery using influenza virus antigen. The MNs with 5 monument-shaped microneedles per array were produced and coated with inactivated influenza virus A/PR/8/34 (IIV). As much as 10 μg of viral proteins could be coated onto an array of 5 microneedles, and the coated IIV was delivered into skin at high efficiency within minutes. The coated MNs were used to immunize mice in comparison with conventional intramuscular injection at the same dose. Analysis of immune responses showed that a single immunization with IIV-coated MNs induced strong antibody responses against influenza virus, with significant levels of hemagglutination inhibition activities (>1:40), which were comparable to those induced by conventional intramuscular immunization. Moreover, mice immunized by a single dose of IIV coated on MNs were effectively protected against lethal challenge by a high dose of mouse-adapted influenza virus A/PR/8/34. These results show that MNs are highly effective as a simple method of vaccine delivery to elicit protective immune responses against virus infection.
A model for the regulatory network controlling the dynamics of kinetochore microtubule plus-ends and poleward flux in metaphase
Authors: Fernandez Nicolas , Chang Qiang , Buster Daniel W. , Sharp David J. , Ma Ao
Published: April 2009

Tight regulation of kinetochore microtubule dynamics is required to generate the appropriate position and movement of chromosomes on the mitotic spindle. A widely studied but mysterious aspect of this regulation occurs during metaphase when polymerization of kinetochore microtubule plus-ends is balanced by depolymerization at their minus-ends. Thus, kinetochore microtubules maintain a constant net length, allowing chromosomes to persist at the spindle equator, but consist of tubulin subunits that continually flux toward spindle poles. Here, we construct a feasible network of regulatory proteins for controlling kinetochore microtubule plus-end dynamics, which was combined with a Monte Carlo algorithm to simulate metaphase tubulin flux. We also test the network model by combining it with a force-balancing model explicitly taking force generators into account. Our data reveal how relatively simple interrelationships among proteins that stimulate microtubule plus-end polymerization, depolymerization, and dynamicity can induce robust flux while accurately predicting apparently contradictory results of knockdown experiments. The model also provides a simple and robust physical mechanism through which the regulatory networks at kinetochore microtubule plus- and minus-ends could communicate.
Genome-wide association and meta-analysis of bipolar disorder in individuals of European ancestry
Authors: Scott Laura J. , Muglia Pierandrea , Kong Xiangyang Q. , Guan Weihua , Flickinger Matthew , Upmanyu Ruchi , Tozzi Federica , Li Jun Z. , Burmeister Margit , Absher Devin , Thompson Robert C. , Francks Clyde , Meng Fan , Antoniades Athos , Southwick Audrey M. , Schatzberg Alan F. , Bunney William E. , Barchas Jack D. , Jones Edward G. , Day Richard , Matthews Keith , McGuffin Peter , Strauss John S. , Kennedy James L. , Middleton Lefkos , Roses Allen D. , Watson Stanley J. , Vincent John B. , Myers Richard M. , Farmer Ann E. , Akil Huda , Burns Daniel K. , Boehnke Michael
Published: April 2009

Bipolar disorder (BP) is a disabling and often life-threatening disorder that affects ≈1% of the population worldwide. To identify genetic variants that increase the risk of BP, we genotyped on the Illumina HumanHap550 Beadchip 2,076 bipolar cases and 1,676 controls of European ancestry from the National Institute of Mental Health Human Genetics Initiative Repository, and the Prechter Repository and samples collected in London, Toronto, and Dundee. We imputed SNP genotypes and tested for SNP-BP association in each sample and then performed meta-analysis across samples. The strongest association
P
value for this 2-study meta-analysis was 2.4 × 10
−6
. We next imputed SNP genotypes and tested for SNP-BP association based on the publicly available Affymetrix 500K genotype data from the Wellcome Trust Case Control Consortium for 1,868 BP cases and a reference set of 12,831 individuals. A 3-study meta-analysis of 3,683 nonoverlapping cases and 14,507 extended controls on >2.3 M genotyped and imputed SNPs resulted in 3 chromosomal regions with association
P
≈ 10
−7
: 1p31.1 (no known genes), 3p21 (>25 known genes), and 5q15 (
MCTP1
). The most strongly associated nonsynonymous SNP rs1042779 (OR = 1.19,
P
= 1.8 × 10
−7
) is in the
ITIH1
gene on chromosome 3, with other strongly associated nonsynonymous SNPs in
GNL3
,
NEK4
, and
ITIH3
. Thus, these chromosomal regions harbor genes implicated in cell cycle, neurogenesis, neuroplasticity, and neurosignaling. In addition, we replicated the reported
ANK3
association results for SNP rs10994336 in the nonoverlapping GSK sample (OR = 1.37,
P
= 0.042). Although these results are promising, analysis of additional samples will be required to confirm that variant(s) in these regions influence BP risk.
Larger groups are more successful in innovative problem solving in house sparrows
Authors: Liker András , Bókony Veronika
Published: April 2009

Group living offers well-known benefits to animals, such as better predator avoidance and increased foraging success. An important additional, but so far neglected, advantage is that groups may cope more effectively with unfamiliar situations through faster innovations of new solutions by some group members. We tested this hypothesis experimentally by presenting a new foraging task of opening a familiar feeder in an unfamiliar way to house sparrows in small and large groups (2 versus 6 birds). Group size had strong effects on problem solving: sparrows performed 4 times more and 11 times faster openings in large than in small groups, and all members of large groups profited by getting food sooner (7 times on average). Independently from group size, urban groups were more successful than rural groups. The disproportionately higher success in large groups was not a mere consequence of higher number of attempts, but was also related to a higher effectiveness of problem solving (3 times higher proportion of successful birds). The analyses of the birds' behavior suggest that the latter was not explained by either reduced investment in antipredator vigilance or reduced neophobia in large groups. Instead, larger groups may contain more diverse individuals with different skills and experiences, which may increase the chance of solving the task by some group members. Increased success in problem solving may promote group living in animals and may help them to adapt quickly to new situations in rapidly-changing environments.
Contactin-2/TAG-1-directed autoimmunity is identified in multiple sclerosis patients and mediates gray matter pathology in animals
Authors: Derfuss Tobias , Parikh Khyati , Velhin Sviataslau , Braun Magdalena , Mathey Emily , Krumbholz Markus , Kümpfel Tania , Moldenhauer Anja , Rader Christoph , Sonderegger Peter , Pöllmann Walter , Tiefenthaller Christian , Bauer Jan , Lassmann Hans , Wekerle Hartmut , Karagogeos Domna , Hohlfeld Reinhard , Linington Christopher , Meinl Edgar
Published: April 2009

Gray matter pathology is increasingly recognized as an important feature of multiple sclerosis (MS), but the nature of the immune response that targets the gray matter is poorly understood. Starting with a proteomics approach, we identified contactin-2/transiently expressed axonal glycoprotein 1 (TAG-1) as a candidate autoantigen recognized by both autoantibodies and T helper (Th) 1/Th17 T cells in MS patients. Contactin-2 and its rat homologue, TAG-1, are expressed by various neuronal populations and sequestered in the juxtaparanodal domain of myelinated axons both at the axonal and myelin sides. The pathogenic significance of these autoimmune responses was then explored in experimental autoimmune encephalitis models in the rat. Adoptive transfer of TAG-1–specific T cells induced encephalitis characterized by a preferential inflammation of gray matter of the spinal cord and cortex. Cotransfer of TAG-1–specific T cells with a myelin oligodendrocyte glycoprotein-specific mAb generated focal perivascular demyelinating lesions in the cortex and extensive demyelination in spinal cord gray and white matter. This study identifies contactin-2 as an autoantigen targeted by T cells and autoantibodies in MS. Our findings suggest that a contactin-2–specific T-cell response contributes to the development of gray matter pathology.
Timing of HAART defines the integrity of memory B cells and the longevity of humoral responses in HIV-1 vertically-infected children
Authors: Pensieroso Simone , Cagigi Alberto , Palma Paolo , Nilsson Anna , Capponi Claudia , Freda Elio , Bernardi Stefania , Thorstensson Rigmor , Chiodi Francesca , Rossi Paolo
Published: April 2009

HIV-1 infection induces a progressive disruption of the B cell compartment impairing long-term immune responses to routine immunizations. Depletion of specific memory B cell pools occurs during the 1st stages of the infection and cannot be reestablished by antiretroviral treatment. We reasoned that an early control of viral replication through treatment could preserve the normal development of the memory B cell compartment and responses to routine childhood vaccines. Accordingly, we evaluated the effects of different highly-active antiretroviral therapy (HAART) schedules in 70 HIV-1 vertically-infected pediatric subjects by B cell phenotypic analyses, antigen-specific B cell enzyme-linked immunosorbent spot (ELISpot) and ELISA for common vaccination and HIV-1 antigens. Initiation of HAART within the 1st year of life permits the normal development and maintenance of the memory B cell compartment. On the contrary, memory B cells from patients treated later in time are remarkably reduced and their function is compromised regardless of viral control. A cause for concern is that both late-treated HIV-1 controllers and noncontrollers loose protective antibody titers against common vaccination antigens. Timing of HAART initiation is the major factor predicting the longevity of B cell responses in vaccinated HIV-1-infected children.
Quantum control experiment reveals solvation-induced decoherence
Authors: van der Walle P. , Milder M. T. W. , Kuipers L. , Herek J. L.
Published: April 2009

Coherent control holds the promise of becoming a powerful spectroscopic tool for the study of complex molecular systems. Achieving control requires coherence in the quantum system under study. In the condensed phase, coherence is typically lost rapidly because of fluctuating interactions between the solvated molecule and its surrounding environment. We investigate the degree of attainable control on a dye molecule when the fluctuations of its environment are systematically varied. A single successful learning curve for optimizing stimulated emission from the dye in solution is reapplied for a range of solvents with varying viscosity, revealing a striking trend that is correlated directly with the dephasing time. Our results provide clear evidence that the environment limits the leverage of control on the molecular system. This insight can be used to enhance the yield of control experiments greatly.
Fat-induced satiety factor oleoylethanolamide enhances memory consolidation
Authors: Campolongo Patrizia , Roozendaal Benno , Trezza Viviana , Cuomo Vincenzo , Astarita Giuseppe , Fu Jin , McGaugh James L. , Piomelli Daniele
Published: April 2009

The ability to remember contexts associated with aversive and rewarding experiences provides a clear adaptive advantage to animals foraging in the wild. The present experiments investigated whether hormonal signals released during feeding might enhance memory of recently experienced contextual information. Oleoylethanolamide (OEA) is an endogenous lipid mediator that is released when dietary fat enters the small intestine. OEA mediates fat-induced satiety by engaging type-α peroxisome proliferator-activated receptors (PPAR-α) in the gut and recruiting local afferents of the vagus nerve. Here we show that post-training administration of OEA in rats improves retention in the inhibitory avoidance and Morris water maze tasks. These effects are blocked by infusions of lidocaine into the nucleus tractus solitarii (NTS) and by propranolol infused into the basolateral complex of the amygdala (BLA). These findings suggest that the memory-enhancing signal generated by OEA activates the brain via afferent autonomic fibers and stimulates noradrenergic transmission in the BLA. The actions of OEA are mimicked by PPAR-α agonists and abolished in mutant mice lacking PPAR-α. The results indicate that OEA, acting as a PPAR-α agonist, facilitates memory consolidation through noradrenergic activation of the BLA, a mechanism that is also critically involved in memory enhancement induced by emotional arousal.
7SK snRNP/P-TEFb couples transcription elongation with alternative splicing and is essential for vertebrate development
Authors: Barboric Matjaz , Lenasi Tina , Chen Hui , Johansen Eric B. , Guo Su , Peterlin B. Matija
Published: April 2009

Eukaryotic gene expression is commonly controlled at the level of RNA polymerase II (RNAPII) pausing subsequent to transcription initiation. Transcription elongation is stimulated by the positive transcription elongation factor b (P-TEFb) kinase, which is suppressed within the 7SK small nuclear ribonucleoprotein (7SK snRNP). However, the biogenesis and functional significance of 7SK snRNP remain poorly understood. Here, we report that LARP7, BCDIN3, and the noncoding 7SK small nuclear RNA (7SK) are vital for the formation and stability of a cell stress-resistant core 7SK snRNP. Our functional studies demonstrate that 7SK snRNP is not only critical for controlling transcription elongation, but also for regulating alternative splicing of pre-mRNAs. Using a transient expression splicing assay, we find that 7SK snRNP disintegration promotes inclusion of an alternative exon via the increased occupancy of P-TEFb, Ser2-phosphorylated (Ser2-P) RNAPII, and the splicing factor SF2/ASF at the minigene. Importantly, knockdown of
larp7
or
bcdin3
orthologues in zebrafish embryos destabilizes 7SK and causes severe developmental defects and aberrant splicing of analyzed transcripts. These findings reveal a key role for P-TEFb in coupling transcription elongation with alternative splicing, and suggest that maintaining core 7SK snRNP is essential for vertebrate development.
The coreceptor CD2 uses plasma membrane microdomains to transduce signals in T cells
Authors: Kaizuka Yoshihisa , Douglass Adam D. , Vardhana Santosh , Dustin Michael L. , Vale Ronald D.
Published: April 2009

The interaction between a T cell and an antigen-presenting cell (APC) can trigger a signaling response that leads to T cell activation. Prior studies have shown that ligation of the T cell receptor (TCR) triggers a signaling cascade that proceeds through the coalescence of TCR and various signaling molecules (e.g., the kinase Lck and adaptor protein LAT [linker for T cell activation]) into microdomains on the plasma membrane. In this study, we investigated another ligand–receptor interaction (CD58–CD2) that facilities T cell activation using a model system consisting of Jurkat T cells interacting with a planar lipid bilayer that mimics an APC. We show that the binding of CD58 to CD2, in the absence of TCR activation, also induces signaling through the actin-dependent coalescence of signaling molecules (including TCR-ζ chain, Lck, and LAT) into microdomains. When simultaneously activated, TCR and CD2 initially colocalize in small microdomains but then partition into separate zones; this spatial segregation may enable the two receptors to enhance signaling synergistically. Our results show that two structurally distinct receptors both induce a rapid spatial reorganization of molecules in the plasma membrane, suggesting a model for how local increases in the concentration of signaling molecules can trigger T cell signaling.
Cdc28/Cdk1 positively and negatively affects genome stability in S. cerevisiae
Authors: Enserink Jorrit M. , Hombauer Hans , Huang Meng-Er , Kolodner Richard D.
Published: April 2009

We studied the function of the cyclin-dependent kinase Cdc28 (Cdk1) in the DNA damage response and maintenance of genome stability using Saccharomyces cerevisiae. Reduced Cdc28 activity sensitizes cells to chronic DNA damage, but Cdc28 is not required for cell viability upon acute exposure to DNA-damaging agents. Cdc28 is also not required for activation of the DNA damage and replication checkpoints. Chemical–genetic analysis reveals that CDC28 functions in an extensive network of pathways involved in maintenance of genome stability, including homologous recombination, sister chromatid cohesion, the spindle checkpoint, postreplication repair, and telomere maintenance. In addition, Cdc28 and Mre11 appear to cooperate to prevent mitotic catastrophe after DNA replication arrest. We show that reduced Cdc28 activity results in suppression of gross chromosomal rearrangements (GCRs), indicating that Cdc28 is required for formation or recovery of GCRs. Thus, we conclude that Cdc28 functions in a genetic network that supports cell viability during DNA damage while promoting the formation of GCRs.
Active establishment of centromeric CENP-A chromatin by RSF complex
Authors: Perpelescu Marinela , Nozaki Naohito , Obuse Chikashi , Yang Hua , Yoda Kinya
Published: April 2009

Centromeres are chromosomal structures required for equal DNA segregation to daughter cells, comprising specialized nucleosomes containing centromere protein A (CENP-A) histone, which provide the basis for centromeric chromatin assembly. Discovery of centromere protein components is progressing, but knowledge related to their establishment and maintenance remains limited. Previously, using anti-CENP-A native chromatin immunoprecipitation, we isolated the interphase–centromere complex (ICEN). Among ICEN components, subunits of the remodeling and spacing factor (RSF) complex, Rsf-1 and SNF2h proteins, were found. This paper describes the relationship of the RSF complex to centromere structure and function, demonstrating its requirement for maintenance of CENP-A at the centromeric core chromatin in HeLa cells. The RSF complex interacted with CENP-A chromatin in mid-G1. Rsf-1 depletion induced loss of centromeric CENP-A, and purified RSF complex reconstituted and spaced CENP-A nucleosomes in vitro. From these data, we propose the RSF complex as a new factor actively supporting the assembly of CENP-A chromatin.
A single charged voltage sensor is capable of gating the Shaker K+ channel
Authors: Gagnon Dominique G. , Bezanilla Francisco
Published: April 2009

We sought to determine the contribution of an individual voltage sensor to Shaker's function. Concatenated heterotetramers of Shaker zH4 Δ(6–46) wild type (wt) in combination with a neutral S4 segment Shaker mutant (mut) with stoichiometries 2wt/2mut and 1wt/3mut were studied and compared with the 4wt concatenated homotetramer. A single charged voltage sensor is sufficient to open Shaker conductance with reduced delay (<1 ms) and at more hyperpolarized voltages compared with 4wt. In addition, the wt-like slow inactivation of 1wt/3mut was almost completely eliminated by mutations T449V-I470C in its single wt subunit, indicating that the subunits bearing a neutral S4 were unable to trigger slow inactivation. Our results strongly suggest that a neutral S4 segment of Shaker's subunit is voltage insensitive and its voltage sensor is in the activated position (i.e., ready for pore opening), and provide experimental support to the proposed model of independent voltage sensors with a final, almost voltage-independent concerted step.
Intracellular calcium strongly potentiates agonist-activated TRPC5 channels
Authors: Blair Nathaniel T. , Kaczmarek J. Stefan , Clapham David E.
Published: April 2009

TRPC5 is a calcium (Ca2+)-permeable nonselective cation channel expressed in several brain regions, including the hippocampus, cerebellum, and amygdala. Although TRPC5 is activated by receptors coupled to phospholipase C, the precise signaling pathway and modulatory signals remain poorly defined. We find that during continuous agonist activation, heterologously expressed TRPC5 currents are potentiated in a voltage-dependent manner (∼5-fold at positive potentials and ∼25-fold at negative potentials). The reversal potential, doubly rectifying current–voltage relation, and permeability to large cations such as N-methyl-d-glucamine remain unchanged during this potentiation. The TRPC5 current potentiation depends on extracellular Ca2+: replacement by Ba2+ or Mg2+ abolishes it, whereas the addition of 10 mM Ca2+ accelerates it. The site of action for Ca2+ is intracellular, as simultaneous fura-2 imaging and patch clamp recordings indicate that potentiation is triggered at ∼1 µM [Ca2+]. This potentiation is prevented when intracellular Ca2+ is tightly buffered, but it is promoted when recording with internal solutions containing elevated [Ca2+]. In cell-attached and excised inside-out single-channel recordings, increases in internal [Ca2+] led to an ∼10–20-fold increase in channel open probability, whereas single-channel conductance was unchanged. Ca2+-dependent potentiation should result in TRPC5 channel activation preferentially during periods of repetitive firing or coincident neurotransmitter receptor activation.
DHPR activation underlies SR Ca2+ release induced by osmotic stress in isolated rat skeletal muscle fibers
Authors: Pickering James D. , White Ed , Duke Adrian M. , Steele Derek S.
Published: April 2009

Changes in skeletal muscle volume induce localized sarcoplasmic reticulum (SR) Ca2+ release (LCR) events, which are sustained for many minutes, suggesting a possible signaling role in plasticity or pathology. However, the mechanism by which cell volume influences SR Ca2+ release is uncertain. In the present study, rat flexor digitorum brevis fibers were superfused with isoosmotic Tyrode's solution before exposure to either hyperosmotic (404 mOsm) or hypoosmotic (254 mOsm) solutions, and the effects on cell volume, membrane potential (Em), and intracellular Ca2+ ([Ca2+]i) were determined. To allow comparison with previous studies, solutions were made hyperosmotic by the addition of sugars or divalent cations, or they were made hypoosmotic by reducing [NaCl]o. All hyperosmotic solutions induced a sustained decrease in cell volume, which was accompanied by membrane depolarization (by 14–18 mV; n = 40) and SR Ca2+ release. However, sugar solutions caused a global increase in [Ca2+]i, whereas solutions made hyperosmotic by the addition of divalent cations only induced LCR. Decreasing osmolarity induced an increase in cell volume and a negative shift in Em (by 15.04 ± 1.85 mV; n = 8), whereas [Ca2+]i was unaffected. However, on return to the isoosmotic solution, restoration of cell volume and Em was associated with LCR. Both global and localized SR Ca2+ release were abolished by the dihydropyridine receptor inhibitor nifedipine by sustained depolarization of the sarcolemmal or by the addition of the ryanodine receptor 1 inhibitor tetracaine. Inhibitors of the Na-K-2Cl (NKCC) cotransporter markedly inhibited the depolarization associated with hyperosmotic shrinkage and the associated SR Ca2+ release. These findings suggest (1) that the depolarization that accompanies a decrease in cell volume is the primary event leading to SR Ca2+ release, and (2) that volume-dependent regulation of the NKCC cotransporter contributes to the observed changes in Em. The differing effects of the osmotic agents can be explained by the screening of fixed charges by divalent ions.
Ionic selectivity in L-type calcium channels by electrostatics and hard-core repulsion
Authors: Boda Dezső , Valiskó Mónika , Henderson Douglas , Eisenberg Bob , Gillespie Dirk , Nonner Wolfgang
Published: April 2009

A physical model of selective “ion binding” in the L-type calcium channel is constructed, and consequences of the model are compared with experimental data. This reduced model treats only ions and the carboxylate oxygens of the EEEE locus explicitly and restricts interactions to hard-core repulsion and ion–ion and ion–dielectric electrostatic forces. The structural atoms provide a flexible environment for passing cations, thus resulting in a self-organized induced-fit model of the selectivity filter. Experimental conditions involving binary mixtures of alkali and/or alkaline earth metal ions are computed using equilibrium Monte Carlo simulations in the grand canonical ensemble. The model pore rejects alkali metal ions in the presence of biological concentrations of Ca2+ and predicts the blockade of alkali metal ion currents by micromolar Ca2+. Conductance patterns observed in varied mixtures containing Na+ and Li+, or Ba2+ and Ca2+, are predicted. Ca2+ is substantially more potent in blocking Na+ current than Ba2+. In apparent contrast to experiments using buffered Ca2+ solutions, the predicted potency of Ca2+ in blocking alkali metal ion currents depends on the species and concentration of the alkali metal ion, as is expected if these ions compete with Ca2+ for the pore. These experiments depend on the problematic estimation of Ca2+ activity in solutions buffered for Ca2+ and pH in a varying background of bulk salt. Simulations of Ca2+ distribution with the model pore bathed in solutions containing a varied amount of Li+ reveal a “barrier and well” pattern. The entry/exit barrier for Ca2+ is strongly modulated by the Li+ concentration of the bath, suggesting a physical explanation for observed kinetic phenomena. Our simulations show that the selectivity of L-type calcium channels can arise from an interplay of electrostatic and hard-core repulsion forces among ions and a few crucial channel atoms. The reduced system selects for the cation that delivers the largest charge in the smallest ion volume.
Effect of the curvature and the β parameter on the nonlinear dynamics of a drift tearing magnetic island
Authors: Muraglia M. , Agullo O. , Yagi M. , Benkadda S. , Beyer P. , Garbet X. , Itoh S.-I. , Itoh K. , Sen A.
Published: April 2009

We present numerical simulation studies of 2D reduced MHD equations investigating the impact of the electronic β parameter and of curvature effects on the nonlinear evolution of drift tearing islands. We observe a bifurcation phenomenon that leads to an amplification of the pressure energy, the generation of E × B poloidal flow and a nonlinear diamagnetic drift that affects the rotation of the magnetic island. These dynamical modifications arise due to quasilinear effects that generate a zonal flow at the onset point of the bifurcation. Our simulations show that the transition point is influenced by the β parameter such that the pressure gradient through a curvature effect strongly stabilizes the transition. Regarding the modified rotation of the island, a model for the frequency is derived in order to study its origin and the effect of the β parameter. It appears that after the transition, an E × B poloidal flow as well as a nonlinear diamagnetic drift are generated due to an amplification of the stresses by pressure effects.
Design of a −1 MV dc UHV power supply for ITER NBI
Authors: Watanabe K. , Yamamoto M. , Takemoto J. , Yamashita Y. , Dairaku M. , Kashiwagi M. , Taniguchi M. , Tobari H. , Umeda N. , Sakamoto K. , Inoue T.
Published: April 2009

Procurement of a dc −1 MV power supply system for the ITER neutral beam injector (NBI) is shared by Japan and the EU. The Japan Atomic Energy Agency as the Japan Domestic Agency (JADA) for ITER contributes to the procurement of dc −1 MV ultra-high voltage (UHV) components such as a dc −1 MV generator, a transmission line and a −1 MV insulating transformer for the ITER NBI power supply. The inverter frequency of 150 Hz in the −1 MV power supply and major circuit parameters have been proposed and adopted in the ITER NBI. The dc UHV insulation has been carefully designed since dc long pulse insulation is quite different from conventional ac insulation or dc short pulse systems. A multi-layer insulation structure of the transformer for a long pulse up to 3600 s has been designed with electric field simulation. Based on the simulation the overall dimensions of the dc UHV components have been finalized. A surge energy suppression system is also essential to protect the accelerator from electric breakdowns. The JADA contributes to provide an effective surge suppression system composed of core snubbers and resistors. Input energy into the accelerator from the power supply can be reduced to about 20 J, which satisfies the design criteria of 50 J in total in the case of breakdown at −1 MV.
Existence of traveling domain solutions for a two-dimensional moving boundary problem
Authors: Choi Y. , Lui Roger
Published: April 2009

In this paper we prove the existence of a traveling domain solution for a two-dimensional moving boundary problem. Specifically, we prove the existence of a domain that travels to the right at a constant speed

k
k

and a function

b
b

which solves a porous medium type equation in the domain with constant Dirichlet boundary condition. The proof is by Schaefer’s fixed point theorem. The result may be viewed as an extension of the existence of traveling cell solutions of a one-dimensional cell motility model proved by the authors and Juliet Lee (2004).
Value functions and the Dirichlet problem for Isaacs equation in a smooth domain
Authors: Kovats Jay
Published: April 2009

In this paper, we investigate probabilistic solutions of the Dirichlet problem for the elliptic Isaacs equation in a smooth bounded domain in Euclidean space.
Fourier and Radon transform on harmonic 𝑁𝐴 groups
Authors: Ray Swagato , Sarkar Rudra
Published: April 2009

In this article we study the Fourier and the horocyclic Radon transform on harmonic

N
A

NA

groups (also known as Damek-Ricci spaces). We consider the geometric Fourier transform for functions on

L
p

L^p

-spaces and prove an analogue of the

L
2

L^2

-restriction theorem. We also prove some mixed norm estimates for the Fourier transform generalizing the Hausdorff-Young and Hardy-Littlewood-Paley inequalities. Unlike Euclidean spaces the domains of the Fourier transforms are various strips in the complex plane. All the theorems are considered on these entire domains of the Fourier transforms. Finally we deal with the existence of the Radon transform on

L
p

L^p

-spaces and obtain its continuity property.
Rahnuma: hypergraph-based tool for metabolic pathway prediction and network comparison
Authors: Mithani Aziz , Preston Gail M. , Hein Jotun
Published: April 2009

Summary:We present a tool called Rahnuma for prediction and analysis of metabolic pathways and comparison of metabolic networks. Rahnuma represents metabolic networks as hypergraphs and computes all possible pathways between two or more metabolites. It provides an intuitive way to answer biological ques- tions focusing on differences between organisms or the evolution of different species by allowing pathway-based metabolic network comparisons at an organism as well as at a phylogenetic level.

Availability: Rahnuma is available online at http://portal.stats.ox.ac.uk:8080/rahnuma/.

Contact:  gail.preston@plants.ox.ac.uk

Supplementary information:  Supplementary data are available at the Bioinformatics online.
List-decoding methods for inferring polynomials in finite dynamical gene network models
Authors: Dingel Janis , Milenkovic Olgica
Published: April 2009

Motivation: The problem of reverse engineering the dynamics of gene expression profiles is of focal importance in systems biology. Due to noise and the inherent lack of sufficiently large datasets generated via high-throughput measurements, known reconstruction frameworks based on dynamical systems models fail to provide adequate settings for network analysis. This motivates the study of new approaches that produce stochastic lists of explanations for the observed network dynamics that can be efficiently inferred from small sample sets and in the presence of errors.

Results: We introduce a novel algebraic modeling framework, termed stochastic polynomial dynamical systems (SPDSs) that can capture the dynamics of regulatory networks based on microarray expression data. Here, we refer to dynamics of the network as the trajectories of gene expression profiles over time. The model assumes that the expression data is quantized in a manner that allows for imposing a finite field structure on the observations, and the existence of polynomial update functions for each gene in the network. The underlying reverse engineering algorithm is based on ideas borrowed from coding theory, and in particular, list-decoding methods for so called Reed-Muller codes. The list-decoding method was tested on synthetic data and on microarray expression measurements from the M3D database, corresponding to a subnetwork of the Escherichia coli SOS repair system, as well as on the complete transcription factor network, available at RegulonDB. The results show that SPDSs constructed via list-decoders significantly outperform other algebraic reverse engineering methods, and that they also provide good guidelines for estimating the influence of genes on the dynamics of the network.

Availability: Software codes for list-decoding algorithms suitable for direct application to quantized expression data will be publicly available at the authors' web-pages.

Contact:  janis.dingel@tum.de; milenkov@uiuc.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
Affinity Density: a novel genomic approach to the identification of transcription factor regulatory targets
Authors: Hazelett Dennis J. , Lakeland Daniel L. , Weiss Joseph B.
Published: April 2009

Methods: A new method was developed for identifying novel transcription factor regulatory targets based on calculating Local Affinity Density. Techniques from the signal-processing field were used, in particular the Hann digital filter, to calculate the relative binding affinity of different regions based on previously published in vitro binding data. To illustrate this approach, the complete genomes of Drosophila melanogaster and D.pseudoobscura were analyzed for binding sites of the homeodomain proteinc Tinman, an essential heart development gene in both Drosophila and Mouse. The significant binding regions were identified relative to genomic background and assigned to putative target genes. Valid candidates common to both species of Drosophila were selected as a test of conservation.

Results: The new method was more sensitive than cluster searches for conserved binding motifs with respect to positive identification of known Tinman targets. Our Local Affinity Density method also identified a significantly greater proportion of Tinman-coexpressed genes than equivalent, optimized cluster searching. In addition, this new method predicted a significantly greater than expected number of genes with previously published RNAi phenotypes in the heart.

Availability: Algorithms were implemented in Python, LISP, R and maxima, using MySQL to access locally mirrored sequence data from Ensembl (D.melanogaster release 4.3) and flybase (D.pseudoobscura). All code is licensed under GPL and freely available at http://www.ohsu.edu/cellbio/dev_biol_prog/affinitydensity/.

Contact:  hazelett@ohsu.edu
Optimizing static thermodynamic models of transcriptional regulation
Authors: Bauer Denis C. , Bailey Timothy L.
Published: April 2009

Motivation: Modeling transcriptional regulation using thermo-dynamic modeling approaches has become increasingly relevant as a way to gain a detailed understanding of transcriptional regulation. Thermodynamic models are able to model the interactions between transcription factors (TFs) and DNA that lead to a specific transcriptional output of the target gene. Such models can be ‘trained’ by fitting their free parameters to data on the transcription rate of a gene and the concentrations of its regulating factors. However, the parameter fitting process is computationally very expensive and this limits the number of alternative types of model that can be explored.

Results: In this study, we evaluate the ‘optimization landscape’ of a class of static, quantitative models of regulation and explore the efficiency of a range of optimization methods. We evaluate eight optimization methods: two variants of simulated annealing (SA), four variants of gradient descent (GD), a hybrid SA/GD algorithm and a genetic algorithm. We show that the optimization landscape has numerous local optima, resulting in poor performance for the GD methods. SA with a simple geometric cooling schedule performs best among all tested methods. In particular, we see no advantage to using the more sophisticated ‘LAM’ cooling schedule. Overall, a good approximate solution is achievable in minutes using SA with a simple cooling schedule.

Contact:  d.bauer@uq.edu.au; t.bailey@imb.uq.edu.au

Supplementary information:  Supplementary data are available at Bioinformatics online.
penalizedSVM: a R-package for feature selection SVM classification
Authors: Becker Natalia , Werft Wiebke , Toedt Grischa , Lichter Peter , Benner Axel
Published: April 2009

Summary: Support vector machine (SVMs) classification is a widely used and one of the most powerful classification techniques. However, a major limitation is that SVM cannot perform automatic gene selection. To overcome this restriction, a number of penalized feature selection methods have been proposed. In the R package ‘penalizedSVM’ implemented penalization functions L1 norm and Smoothly Clipped Absolute Deviation (SCAD) provide automatic feature selection for SVM classification tasks.

Availability: The R package ‘penalizedSVM’ is available from the Comprehensive R Archive Network (http://cran.r-project.org/) under GPL-2 or later.

Contact:  natalia.becker@dkfz.de

Supplementary information:  Supplementary data are available at Bioinformatics online.