bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature-dependent carrier tunneling for self-assembled InAs/GaAs quantum dots with a GaAsN quantum well injector
Authors: Jin C. Y. , Ohta S. , Hopkinson M. , Kojima O. , Kita T. , Wada O.
Published: April 2010

We have investigated the carrier tunneling process in a quantum-dot (QD) tunnel injection structure, which employs a GaAs1−xNx quantum well (QW) as a carrier injector. The influence of the barrier thickness between the GaAs1−xNx well and InAs dot layer has been studied by temperature-dependent photoluminescence. Although the 2.5 nm barrier sample exhibits the best tunneling efficiency, a 3.0 nm thickness for the barrier is optimum to retain good optical properties. The carrier capture time from the GaAs1−xNx QW to QD ground states has been evaluated by time-resolved photoluminescence. The result indicates that efficient carrier tunneling occurs at temperatures above 150 K due to the temperature dependent nature of phonon-assisted processes.
Gilbert damping in perpendicularly magnetized Pt/Co/Pt films investigated by all-optical pump-probe technique
Authors: Mizukami S. , Sajitha E. P. , Watanabe D. , Wu F. , Miyazaki T. , Naganuma H. , Oogane M. , Ando Y.
Published: April 2010

To investigate the correlation between perpendicular magnetic anisotropy and intrinsic Gilbert damping, time-resolved magneto-optical Kerr effect was measured in Pt/Co(dCo)/Pt films. These films showed perpendicular magnetization at dCo=1.0 nm and a perpendicular magnetic anisotropy energy Kueff that was inversely proportional to dCo. With an analysis based on the Landau–Lifshitz–Gilbert equation, the intrinsic Gilbert damping constant α was evaluated by parameter-fitting of frequency and lifetime expressions to experimental data of angular variations in spin precession frequency and life-times. The α values increased significantly with decreasing dCo but not inversely proportional to dCo.
Distinct consequences of posttranslational modification by linear versus K63-linked polyubiquitin chains
Authors: Zhao Shengkai , Ulrich Helle D.
Published: April 2010

Polyubiquitin chains mediate a variety of biological processes, ranging from proteasomal targeting to inflammatory signaling and DNA repair. Their functional diversity is in part due to their ability to adopt distinct conformations, depending on how the ubiquitin moieties within the chain are linked. We have used the eukaryotic replication clamp PCNA, a natural target of lysine (K)63-linked polyubiquitylation, as a model substrate to directly compare the consequences of modification by different types of polyubiquitin chains. We show here that K63-polyubiquitylated PCNA is not subject to proteasomal degradation. In contrast, linear, noncleavable ubiquitin chains do not promote DNA damage tolerance, but function as general degradation signals. We find that a linear tetraubiquitin chain is sufficient to afford proteasomal targeting through the Cdc48-Npl4-Ufd1 complex without further modification. Although a minimum chain length of four is required for degradation, a longer chain does not further reduce the half-life of the respective substrate protein. Our results suggest that the cellular machinery responsible for recognition of ubiquitylated substrates can make subtle distinctions between highly similar forms of the polyubiquitin signal.
Disentangling collective trends from local dynamics
Authors: Barthélemy Marc , Nadal Jean-Pierre , Berestycki Henri
Published: April 2010

A single social phenomenon (such as crime, unemployment, or birthrate) can be observed through temporal series corresponding to units at different levels (i.e., cities, regions, and countries). Units at a given local level may follow a collective trend imposed by external conditions, but also may display fluctuations of purely local origin. The local behavior is usually computed as the difference between the local data and a global average (e.g, a national average), a viewpoint that can be very misleading. We propose here a method for separating the local dynamics from the global trend in a collection of correlated time series. We take an independent component analysis approach in which we do not assume a small average local contribution in contrast with previously proposed methods. We first test our method on synthetic series generated by correlated random walkers. We then consider crime rate series (in the United States and France) and the evolution of obesity rate in the United States, which are two important examples of societal measures. For the crime rates in the United States, we observe large fluctuations in the transition period of mid-70s during which crime rates increased significantly, whereas since the 80s, the state crime rates are governed by external factors and the importance of local specificities being decreasing. In the case of obesity, our method shows that external factors dominate the evolution of obesity since 2000, and that different states can have different dynamical behavior even if their obesity prevalence is similar.
Anonymization of electronic medical records for validating genome-wide association studies
Authors: Loukides Grigorios , Gkoulalas-Divanis Aris , Malin Bradley
Published: April 2010

Genome-wide association studies (GWAS) facilitate the discovery of genotype–phenotype relations from population-based sequence databases, which is an integral facet of personalized medicine. The increasing adoption of electronic medical records allows large amounts of patients’ standardized clinical features to be combined with the genomic sequences of these patients and shared to support validation of GWAS findings and to enable novel discoveries. However, disseminating these data “as is” may lead to patient reidentification when genomic sequences are linked to resources that contain the corresponding patients’ identity information based on standardized clinical features. This work proposes an approach that provably prevents this type of data linkage and furnishes a result that helps support GWAS. Our approach automatically extracts potentially linkable clinical features and modifies them in a way that they can no longer be used to link a genomic sequence to a small number of patients, while preserving the associations between genomic sequences and specific sets of clinical features corresponding to GWAS-related diseases. Extensive experiments with real patient data derived from the Vanderbilt's University Medical Center verify that our approach generates data that eliminate the threat of individual reidentification, while supporting GWAS validation and clinical case analysis tasks.
Induction of fatty acid synthesis is a key requirement for phagocytic differentiation of human monocytes
Authors: Ecker Josef , Liebisch Gerhard , Englmaier Marion , Grandl Margot , Robenek Horst , Schmitz Gerd
Published: April 2010

Monocytes are precursors of macrophages. Here we demonstrate that macrophage colony-stimulating factor (M-CSF)-dependent differentiation of primary human monocytes from healthy volunteers induces transcription of SREBP-1c target genes required for fatty acid (FA) biosynthesis and impairs transcription of SREBP-2 target genes required for cholesterol synthesis. Detailed lipid metabolic profiling showed that this transcriptional regulation leads to a dramatically increased fatty acid synthesis as driving force for enhanced phospholipid synthesis. During cell differentiation the major lipid class switches from cholesterol in monocytes to phosphatidylcholine in macrophages. Ultrastructural analysis revealed that this transcriptional and metabolic regulation is essential for development of macrophage filopodia and cellular organelles including primary lysosomes, endoplasmic reticulum, and Golgi network. Additional functional studies showed that suppression of fatty acid synthesis prevents phagocytosis representing a central macrophage function. Therefore induction of fatty acid synthesis is a key requirement for phagocyte development and function.
An ATPase promotes autophosphorylation of the pattern recognition receptor XA21 and inhibits XA21-mediated immunity
Authors: Chen Xuewei , Chern Mawsheng , Canlas Patrick E. , Ruan Deling , Jiang Caiying , Ronald Pamela C.
Published: April 2010

Cell-surface pattern recognition receptors (PRRs) are key components of the innate immune response in animals and plants. These receptors typically carry or associate with non-RD kinases to control early events of innate immunity signaling. Despite their importance, the mode of regulation of PRRs is largely unknown. Here we show that the rice PRR, XA21, interacts with XA21 binding protein 24 (XB24), a previously undescribed ATPase. XB24 promotes autophosphorylation of XA21 through its ATPase activity. Rice lines silenced for
Xb24
display enhanced XA21-mediated immunity, whereas rice lines overexpressing XB24 are compromised for immunity. XB24 ATPase enzyme activity is required for XB24 function. XA21 is degraded in the presence of the pathogen-associated molecular pattern Ax21 when XB24 is overexpressed. These results demonstrate a function for this large class of broadly conserved ATPases in PRR-mediated immunity.
Hydrodynamic synchronization of colloidal oscillators
Authors: Kotar Jurij , Leoni Marco , Bassetti Bruno , Lagomarsino Marco Cosentino , Cicuta Pietro
Published: April 2010

Two colloidal spheres are maintained in oscillation by switching the position of an optical trap when a sphere reaches a limit position, leading to oscillations that are bounded in amplitude but free in phase and period. The interaction between the oscillators is only through the hydrodynamic flow induced by their motion. We prove that in the absence of stochastic noise the antiphase dynamical state is stable, and we show how the period depends on coupling strength. Both features are observed experimentally. As the natural frequencies of the oscillators are made progressively different, the coordination is quickly lost. These results help one to understand the origin of hydrodynamic synchronization and how the dynamics can be tuned. Cilia and flagella are biological systems coupled hydrodynamically, exhibiting dramatic collective motions. We propose that weakly correlated phase fluctuations, with one of the oscillators typically precessing the other, are characteristic of hydrodynamically coupled systems in the presence of thermal noise.
Constraining the chlorine monoxide (ClO)/chlorine peroxide (ClOOCl) equilibrium constant from Aura Microwave Limb Sounder measurements of nighttime ClO
Authors: Santee Michelle L. , Sander Stanley P. , Livesey Nathaniel J. , Froidevaux Lucien
Published: April 2010

The primary ozone loss process in the cold polar lower stratosphere hinges on chlorine monoxide (ClO) and one of its dimers, chlorine peroxide (ClOOCl). Recently, analyses of atmospheric observations have suggested that the equilibrium constant, K
eq
, governing the balance between ClOOCl formation and thermal decomposition in darkness is lower than that in the current evaluation of kinetics data. Measurements of ClO at night, when ClOOCl is unaffected by photolysis, provide a useful means of testing quantitative understanding of the ClO/ClOOCl relationship. Here we analyze nighttime ClO measurements from the National Aeronautics and Space Administration Aura Microwave Limb Sounder (MLS) to infer an expression for K
eq
. Although the observed temperature dependence of the nighttime ClO is in line with the theoretical ClO/ClOOCl equilibrium relationship, none of the previously published expressions for K
eq
consistently produces ClO abundances that match the MLS observations well under all conditions. Employing a standard expression for K
eq
,
A
 × exp(
B
/
T
), we constrain the parameter
A
to currently recommended values and estimate
B
using a nonlinear weighted least squares analysis of nighttime MLS ClO data. ClO measurements at multiple pressure levels throughout the periods of peak chlorine activation in three Arctic and four Antarctic winters are used to estimate
B
. Our derived
B
leads to values of K
eq
that are ∼1.4 times smaller at stratospherically relevant temperatures than currently recommended, consistent with earlier studies. Our results are in better agreement with the newly updated (2009) kinetics evaluation than with the previous (2006) recommendation.
A mechanical model of actin stress fiber formation and substrate elasticity sensing in adherent cells
Authors: Walcott Sam , Sun Sean X.
Published: April 2010

Tissue cells sense and respond to the stiffness of the surface on which they adhere. Precisely how cells sense surface stiffness remains an open question, though various biochemical pathways are critical for a proper stiffness response. Here, based on a simple mechanochemical model of biological friction, we propose a model for cell mechanosensation as opposed to previous more biochemically based models. Our model of adhesion complexes predicts that these cell-surface interactions provide a viscous drag that increases with the elastic modulus of the surface. The force-velocity relation of myosin II implies that myosin generates greater force when the adhesion complexes slide slowly. Then, using a simple cytoskeleton model, we show that an external force applied to the cytoskeleton causes actin filaments to aggregate and orient parallel to the direction of force application. The greater the external force, the faster this aggregation occurs. As the steady-state probability of forming these bundles reflects a balance between the time scale of bundle formation and destruction (because of actin turnover), more bundles are formed when the cytoskeleton time-scale is small (i.e., on stiff surfaces), in agreement with experiment. As these large bundles of actin, called stress fibers, appear preferentially on stiff surfaces, our mechanical model provides a mechanism for stress fiber formation and stiffness sensing in cells adhered to a compliant surface.
Larvae from afar colonize deep-sea hydrothermal vents after a catastrophic eruption
Authors: Mullineaux Lauren S. , Adams Diane K. , Mills Susan W. , Beaulieu Stace E.
Published: April 2010

The planktonic larval stage is a critical component of life history in marine benthic species because it confers the ability to disperse, potentially connecting remote populations and leading to colonization of new sites. Larval-mediated connectivity is particularly intriguing in deep-sea hydrothermal vent communities, where the habitat is patchy, transient, and often separated by tens or hundreds of kilometers. A recent catastrophic eruption at vents near 9°50′N on the East Pacific Rise created a natural clearance experiment and provided an opportunity to study larval supply in the absence of local source populations. Previous field observations have suggested that established vent populations may retain larvae and be largely self-sustaining. If this hypothesis is correct, the removal of local populations should result in a dramatic change in the flux, and possibly species composition, of settling larvae. Fortuitously, monitoring of larval supply and colonization at the site had been established before the eruption and resumed shortly afterward. We detected a striking change in species composition of larvae and colonists after the eruption, most notably the appearance of the gastropodCtenopelta porifera, an immigrant from possibly more than 300 km away, and the disappearance of a suite of species that formerly had been prominent. This switch demonstrates that larval supply can change markedly after removal of local source populations, enabling recolonization via immigrants from distant sites with different species composition. Population connectivity at this site appears to be temporally variable, depending not only on stochasticity in larval supply, but also on the presence of resident populations.
Why Hofmeister effects of many salts favor protein folding but not DNA helix formation
Authors: Pegram Laurel M. , Wendorff Timothy , Erdmann Robert , Shkel Irina , Bellissimo Dana , Felitsky Daniel J. , Record M. Thomas
Published: April 2010

The majority (∼70%) of surface buried in protein folding is hydrocarbon, whereas in DNA helix formation, the majority (∼65%) of surface buried is relatively polar nitrogen and oxygen. Our previous quantification of salt exclusion from hydrocarbon (C) accessible surface area (
ASA
) and accumulation at amide nitrogen (N) and oxygen (O)
ASA
leads to a prediction of very different Hofmeister effects on processes that bury mostly polar (N, O) surface compared to the range of effects commonly observed for processes that bury mainly nonpolar (C) surface, e.g., micelle formation and protein folding. Here we quantify the effects of salts on folding of the monomeric DNA binding domain (DBD) of
lac
repressor (
lac
DBD) and on formation of an oligomeric DNA duplex. In accord with this prediction, no salt investigated has a stabilizing Hofmeister effect on DNA helix formation. Our
ASA
-based analyses of model compound data and estimates of the surface area buried in protein folding and DNA helix formation allow us to predict Hofmeister effects on these processes. We observe semiquantitative to quantitative agreement between these predictions and the experimental values, obtained from a novel separation of coulombic and Hofmeister effects. Possible explanations of deviations, including salt-dependent unfolded ensembles and interactions with other types of surface, are discussed.
Sustained experience of emotion after loss of memory in patients with amnesia
Authors: Feinstein Justin S. , Duff Melissa C. , Tranel Daniel
Published: April 2010

Can the experience of an emotion persist once the memory for what induced the emotion has been forgotten? We capitalized on a rare opportunity to study this question directly using a select group of patients with severe amnesia following circumscribed bilateral damage to the hippocampus. The amnesic patients underwent a sadness induction procedure (using affectively-laden film clips) to ascertain whether their experience of sadness would persist beyond their memory for the sadness-inducing films. The experiment showed that the patients continued to experience elevated levels of sadness well beyond the point in time at which they had lost factual memory for the film clips. A second experiment using a happiness induction procedure yielded similar results, suggesting that both positive and negative emotional experiences can persist independent of explicit memory for the inducing event. These findings provide direct evidence that a feeling of emotion can endure beyond the conscious recollection for the events that initially triggered the emotion.
Correlated physiological and perceptual effects of noise in a tactile stimulus
Authors: Lak Armin , Arabzadeh Ehsan , Harris Justin A. , Diamond Mathew E.
Published: April 2010

We investigated connections between the physiology of rat barrel cortex neurons and the sensation of vibration in humans. One set of experiments measured neuronal responses in anesthetized rats to trains of whisker deflections, each train characterized either by constant amplitude across all deflections or by variable amplitude (“amplitude noise”). Firing rate and firing synchrony were, on average, boosted by the presence of noise. However, neurons were not uniform in their responses to noise. Barrel cortex neurons have been categorized as regular-spiking units (putative excitatory neurons) and fast-spiking units (putative inhibitory neurons). Among regular-spiking units, amplitude noise caused a higher firing rate and increased cross-neuron synchrony. Among fast-spiking units, noise had the opposite effect: It led to a lower firing rate and decreased cross-neuron synchrony. This finding suggests that amplitude noise affects the interaction between inhibitory and excitatory neurons. From these physiological effects, we expected that noise would lead to an increase in the perceived intensity of a vibration. We tested this notion using psychophysical measurements in humans. As predicted, subjects overestimated the intensity of noisy vibrations. Thus the physiological mechanisms present in barrel cortex also appear to be at work in the human tactile system, where they affect vibration perception.
Probing myosin structural conformation in vivo by second-harmonic generation microscopy
Authors: Nucciotti V. , Stringari C. , Sacconi L. , Vanzi F. , Fusi L. , Linari M. , Piazzesi G. , Lombardi V. , Pavone F. S.
Published: April 2010

Understanding of complex biological processes requires knowledge of molecular structures and measurement of their dynamics in vivo. The collective chemomechanical action of myosin molecules (the molecular motors) in the muscle sarcomere represents a paradigmatic example in this respect. Here, we describe a label-free imaging method sensitive to protein conformation in vivo. We employed the order-based contrast enhancement by second-harmonic generation (SHG) for the functional imaging of muscle cells. We found that SHG polarization anisotropy (SPA) measurements report on the structural state of the actomyosin motors, with significant sensitivity to the conformation of myosin. In fact, each physiological/biochemical state we probed (relaxed, rigor, isometric contraction) produced a distinct value of polarization anisotropy. Employing a full reconstruction of the contributing elementary SHG emitters in the actomyosin motor array at atomic scale, we provide a molecular interpretation of the SPA measurements in terms of myosin conformations. We applied this method to the discrimination between attached and detached myosin heads in an isometrically contracting intact fiber. Our observations indicate that isometrically contracting muscle sustains its tetanic force by steady-state commitment of 30% of myosin heads. Applying SPA and molecular structure modeling to the imaging of unstained living tissues provides the basis for a generation of imaging and diagnostic tools capable of probing molecular structures and dynamics in vivo.
Hybrid PET-optical imaging using targeted probes
Authors: Nahrendorf Matthias , Keliher Edmund , Marinelli Brett , Waterman Peter , Feruglio Paolo Fumene , Fexon Lioubov , Pivovarov Misha , Swirski Filip K. , Pittet Mikael J. , Vinegoni Claudio , Weissleder Ralph
Published: April 2010

Fusion imaging of radionuclide-based molecular (PET) and structural data [x-ray computed tomography (CT)] has been firmly established. Here we show that optical measurements [fluorescence-mediated tomography (FMT)] show exquisite congruence to radionuclide measurements and that information can be seamlessly integrated and visualized. Using biocompatible nanoparticles as a generic platform (containing a
18
F isotope and a far red fluorochrome), we show good correlations between FMT and PET in probe concentration (
r
2
> 0.99) and spatial signal distribution (
r
2
> 0.85). Using a mouse model of cancer and different imaging probes to measure tumoral proteases, macrophage content and integrin expression simultaneously, we demonstrate the distinct tumoral locations of probes in multiple channels in vivo. The findings also suggest that FMT can serve as a surrogate modality for the screening and development of radionuclide-based imaging agents.
Contribution of the myosin VI tail domain to processive stepping and intramolecular tension sensing
Authors: Dunn Alexander R. , Chuan Peiying , Bryant Zev , Spudich James A.
Published: April 2010

Myosin VI is proposed to act as both a molecular transporter and as an anchor in vivo. A portion of the molecule
C
-terminal to the canonical lever arm, termed the medial tail (MT), has been proposed to act as either a lever arm extension or as a dimerization motif. We describe constructs in which the MT is interrupted by a glycine-rich molecular swivel. Disruption of the MT results in decreased processive run lengths measured using single-molecule fluorescence microscopy and a decreased step size under applied load as measured in an optical trap. We used single-molecule gold nanoparticle tracking and optical trapping to examine the mechanism of coordination between the heads of dimeric myosin VI. We detect two rate-limiting kinetic processes at low (< 200 micromolar) ATP concentrations. Our data can be explained by a model in which intramolecular tension greatly increases the affinity of the lead head for ADP, likely by slowing ADP release from the lead head. This mechanism likely increases both the motor’s processivity and its ability to act as an anchor under physiological conditions.
Global analysis of gene activity duringArabidopsisseed development and identification of seed-specific transcription factors
Authors: Le Brandon H. , Cheng Chen , Bui Anhthu Q. , Wagmaister Javier A. , Henry Kelli F. , Pelletier Julie , Kwong Linda , Belmonte Mark , Kirkbride Ryan , Horvath Steve , Drews Gary N. , Fischer Robert L. , Okamuro Jack K. , Harada John J. , Goldberg Robert B.
Published: April 2010

Most of the transcription factors (TFs) responsible for controlling seed development are not yet known. To identify TF genes expressed at specific stages of seed development, including those unique to seeds, we used Affymetrix GeneChips to profileArabidopsisgenes active in seeds from fertilization through maturation and at other times of the plant life cycle. Seed gene sets were compared with those expressed in prefertilization ovules, germinating seedlings, and leaves, roots, stems, and floral buds of the mature plant. Most genes active in seeds are shared by all stages of seed development, although significant quantitative changes in gene activity occur. Each stage of seed development has a small gene set that is either specific at the level of the GeneChip or up-regulated with respect to genes active at other stages, including those that encode TFs. We identified 289 seed-specific genes, including 48 that encode TFs. Seven of the seed-specific TF genes are known regulators of seed development and include theLEAFY COTYLEDON(LEC) genesLEC1, LEC1-LIKE, LEC2, andFUS3. The rest represent different classes of TFs with unknown roles in seed development. Promoter-β-glucuronidase(GUS) fusion experiments and seed mRNA localization GeneChip datasets showed that the seed-specific TF genes are active in different compartments and tissues of the seed at unique times of development. Collectively, these seed-specific TF genes should facilitate the identification of regulatory networks that are important for programming seed development.
A feed-forward loop amplifies nutritional regulation of PNPLA3
Authors: Huang Yongcheng , He Shaoqing , Li John Zhong , Seo Young-Kyo , Osborne Timothy F. , Cohen Jonathan C. , Hobbs Helen H.
Published: April 2010

The upsurge in prevalence of obesity has spawned an epidemic of nonalcoholic fatty liver disease (NAFLD). Previously, we identified a sequence variant (I148M) in patatin-like phospholipase domain-containing protein 3 (PNPLA3) that confers susceptibility to both hepatic triglyceride (TG) deposition and liver injury. To glean insights into the biological role of PNPLA3, we examined the molecular mechanisms by which nutrient status controls hepatic expression of PNPLA3. PNPLA3 mRNA levels, which were low in fasting animals, increased ∼90-fold with carbohydrate feeding. The increase was mimicked by treatment with a liver X receptor (LXR) agonist and required the transcription factor SREBP-1c. The site of SREBP-1c binding was mapped to intron 1 of
Pnpla3
using chromatin immunoprecipitation and electrophoretic mobility shift assays. SREBP-1c also promotes fatty acid synthesis by activating several genes encoding enzymes in the biosynthetic pathway. Addition of fatty acids (C16:0, C18:1, and C18:2) to the medium of cultured hepatocytes (HuH-7) increased PNPLA3 protein mass without altering mRNA levels. The posttranslational increase in PNPLA3 levels persisted after blocking TG synthesis with triascin C. Oleate (400 μM) treatment prolonged the half-life of PNPLA3 from 2.4 to 6.7 h. These findings are consistent with nutritional control of PNPLA3 being effected by a feed-forward loop; SREBP-1c promotes accumulation of PNPLA3 directly by activating
Pnpla3
transcription and indirectly by inhibiting PNPLA3 degradation through the stimulation of fatty acid synthesis.
Fetal liver hepatic progenitors are supportive stromal cells for hematopoietic stem cells
Authors: Chou Song , Lodish Harvey F.
Published: April 2010

Previously we showed that the ~2% of fetal liver cells reactive with an anti-CD3ε monoclonal antibody support ex vivo expansion of both fetal liver and bone marrow hematopoietic stem cells (HSCs); these cells express two proteins important for HSC ex vivo expansion, IGF2, and angiopoietin-like 3. Here we show that these cells do not express any CD3 protein and are not T cells; rather, we purified these HSC-supportive stromal cells based on the surface phenotype of SCF
+
DLK
+
. Competitive repopulating experiments show that SCF
+
DLK
+
cells support the maintenance of HSCs in ex vivo culture. These are the principal fetal liver cells that express not only angiopoietin-like 3 and IGF2, but also SCF and thrombopoietin, two other growth factors important for HSC expansion. They are also the principal fetal liver cells that express CXCL12, a factor required for HSC homing, and also α-fetoprotein (AFP), indicating that they are fetal hepatic stem or progenitor cells. Immunocytochemistry shows that >93% of the SCF
+
cells express DLK and Angptl3, and a portion of SCF
+
cells also expresses CXCL12. Thus SCF
+
DLK
+
cells are a highly homogenous population that express a complete set of factors for HSC expansion and are likely the primary stromal cells that support HSC expansion in the fetal liver.
Continued primer synthesis at stalled replication forks contributes to checkpoint activation
Authors: Van Christopher , Yan Shan , Michael W. Matthew , Waga Shou , Cimprich Karlene A.
Published: April 2010

Stalled replication forks activate and are stabilized by the ATR (ataxia-telangiectasia mutated and Rad3 related)-mediated checkpoint, but ultimately, they must also recover from the arrest. Although primed single-stranded DNA (ssDNA) is sufficient for checkpoint activation, it is still unknown how this signal is generated at a stalled replication fork. Furthermore, it is not clear how recovery and fork restart occur in higher eukaryotes. Using Xenopus laevis egg extracts, we show that DNA replication continues at a stalled fork through the synthesis and elongation of new primers independent of the checkpoint. This synthesis is dependent on the activity of proliferating cell nuclear antigen, Pol-δ, and Pol-ε, and it contributes to the phosphorylation of Chk1. We also used defined DNA structures to show that for a fixed amount of ssDNA, increasing the number of primer–template junctions strongly enhances Chk1 phosphorylation. These results suggest that new primers are synthesized at stalled replication forks by the leading and lagging strand polymerases and that accumulation of these primers may contribute to checkpoint activation.
A yeast MAPK cascade regulates pexophagy but not other autophagy pathways
Authors: Manjithaya Ravi , Jain Shveta , Farré Jean-Claude , Subramani Suresh
Published: April 2010

Autophagy is important for many cellular processes such as innate immunity, neurodegeneration, aging, and cancer. Although the signaling events triggering autophagy have been studied, little is known regarding the signaling mechanisms by which autophagy is redirected to achieve selective removal of cellular components. We have used the degradation of a peroxisomal marker to investigate the role of protein kinases in selective autophagy of peroxisomes (pexophagy) in Saccharomyces cerevisiae. We show that the Slt2p mitogen-activated protein kinase (MAPK) and several upstream components of its signal transduction pathway are necessary for pexophagy but not for pexophagosome formation or other nonselective and selective forms of autophagy. Other extracellular signals that activate this pathway do not trigger pexophagy on their own, suggesting that this MAPK cascade is necessary but not sufficient to trigger pexophagy. We propose that pexophagy requires the simultaneous activation of this MAPK pathway and a hexose-sensing mechanism acting through protein kinase A and cyclic adenosine monophosphate.
Rnf8 deficiency impairs class switch recombination, spermatogenesis, and genomic integrity and predisposes for cancer
Authors: Li Li , Halaby Marie-Jo , Hakem Anne , Cardoso Renato , El Ghamrasni Samah , Harding Shane , Chan Norman , Bristow Robert , Sanchez Otto , Durocher Daniel , Hakem Razqallah
Published: April 2010

Signaling and repair of DNA double-strand breaks (DSBs) are critical for preventing immunodeficiency and cancer. These DNA breaks result from exogenous and endogenous DNA insults but are also programmed to occur during physiological processes such as meiosis and immunoglobulin heavy chain (IgH) class switch recombination (CSR). Recent studies reported that the E3 ligase RNF8 plays important roles in propagating DNA DSB signals and thereby facilitating the recruitment of various DNA damage response proteins, such as 53BP1 and BRCA1, to sites of damage. Using mouse models for Rnf8 mutation, we report that Rnf8 deficiency leads to impaired spermatogenesis and increased sensitivity to ionizing radiation both in vitro and in vivo. We also demonstrate the existence of alternative Rnf8-independent mechanisms that respond to irradiation and accounts for the partial recruitment of 53bp1 to sites of DNA damage in activated Rnf8−/− B cells. Remarkably, IgH CSR is impaired in a gene dose-dependent manner in Rnf8 mutant mice, revealing that these mice are immunodeficient. In addition, Rnf8−/− mice exhibit increased genomic instability and elevated risks for tumorigenesis indicating that Rnf8 is a novel tumor suppressor. These data unravel the in vivo pleiotropic effects of Rnf8.
Location of modulatory β subunits in BK potassium channels
Authors: Liu Guoxia , Niu Xiaowei , Wu Roland S. , Chudasama Neelesh , Yao Yongneng , Jin Xin , Weinberg Richard , Zakharov Sergey I. , Motoike Howard , Marx Steven O. , Karlin Arthur
Published: April 2010

Large-conductance voltage- and calcium-activated potassium (BK) channels contain four pore-forming α subunits and four modulatory β subunits. From the extents of disulfide cross-linking in channels on the cell surface between cysteine (Cys) substituted for residues in the first turns in the membrane of the S0 transmembrane (TM) helix, unique to BK α, and of the voltage-sensing domain TM helices S1–S4, we infer that S0 is next to S3 and S4, but not to S1 and S2. Furthermore, of the two β1 TM helices, TM2 is next to S0, and TM1 is next to TM2. Coexpression of α with two substituted Cys’s, one in S0 and one in S2, and β1 also with two substituted Cys’s, one in TM1 and one in TM2, resulted in two αs cross-linked by one β. Thus, each β lies between and can interact with the voltage-sensing domains of two adjacent α subunits.
Quality assessment of protein model-structures using evolutionary conservation
Authors: Kalman Matan , Ben-Tal Nir
Published: April 2010

Motivation: Programs that evaluate the quality of a protein structural model are important both for validating the structure determination procedure and for guiding the model-building process. Such programs are based on properties of native structures that are generally not expected for faulty models. One such property, which is rarely used for automatic structure quality assessment, is the tendency for conserved residues to be located at the structural core and for variable residues to be located at the surface.

Results: We present ConQuass, a novel quality assessment program based on the consistency between the model structure and the protein's conservation pattern. We show that it can identify problematic structural models, and that the scores it assigns to the server models in CASP8 correlate with the similarity of the models to the native structure. We also show that when the conservation information is reliable, the method's performance is comparable and complementary to that of the other single-structure quality assessment methods that participated in CASP8 and that do not use additional structural information from homologs.

Availability: A perl implementation of the method, as well as the various perl and R scripts used for the analysis are available at http://bental.tau.ac.il/ConQuass/.

Contact:  nirb@tauex.tau.ac.il

Supplementary information:  Supplementary data are available at Bioinformatics online.
Modular rate laws for enzymatic reactions: thermodynamics, elasticities and implementation
Authors: Liebermeister Wolfram , Uhlendorf Jannis , Klipp Edda
Published: April 2010

Motivation: Standard rate laws are a key requisite for systematically turning metabolic networks into kinetic models. They should provide simple, general and biochemically plausible formulae for reaction velocities and reaction elasticities. At the same time, they need to respect thermodynamic relations between the kinetic constants and the metabolic fluxes and concentrations.

Results: We present a family of reversible rate laws for reactions with arbitrary stoichiometries and various types of regulation, including mass–action, Michaelis–Menten and uni–uni reversible Hill kinetics as special cases. With a thermodynamically safe parameterization of these rate laws, parameter sets obtained by model fitting, sampling or optimization are guaranteed to lead to consistent chemical equilibrium states. A reformulation using saturation values yields simple formulae for rates and elasticities, which can be easily adjusted to the given stationary flux distributions. Furthermore, this formulation highlights the role of chemical potential differences as thermodynamic driving forces. We compare the modular rate laws to the thermodynamic–kinetic modelling formalism and discuss a simplified rate law in which the reaction rate directly depends on the reaction affinity. For automatic handling of modular rate laws, we propose a standard syntax and semantic annotations for the Systems Biology Markup Language.

Availability: An online tool for inserting the rate laws into SBML models is freely available at www.semanticsbml.org

Contact:  wolfram.liebermeister@biologie.hu-berlin.de

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Analysis of the Potential Topical Anti‐Inflammatory Activity of Averrhoa carambola L. in Mice
Authors: Cabrini Daniela Almeida , Moresco Henrique Hunger , Imazu Priscila , Silva Cíntia Delai da , Pietrovski Evelise Fernandes , Mendes Daniel Augusto Gasparin Bueno , Prudente Arthur da Silveira , Pizzolatti Moacir Geraldo , Brighente Inês Maria Costa , Otuki Michel Fleith
Published: April 2010

Inflammatory skin disorders, such as psoriasis and atopic dermatitis, are very common in the population; however, the treatments currently available are not well tolerated and are often ineffective. Averrhoa carambola L. (Oxalidaceae) is an Asian tree that has been used in traditional folk medicine in the treatment of several skin disorders. The present study evaluates the topical anti‐inflammatory effects of the crude ethanolic extract of A. carambola leaves, its hexane, ethyl acetate, and butanol fractions and two isolated flavonoids on skin inflammation. Anti‐inflammatory activity was measured using a croton oil‐induced ear edema model of inflammation in mice. Topically applied ethanolic extract reduced edema in a dose‐dependent manner, resulting in a maximum inhibition of 73 ± 3% and an ID50 value of 0.05 (range: 0.02–0.13) mg/ear. Myeloperoxidase (MPO) activity was also inhibited by the extract, resulting in a maximum inhibition of 60 ± 6% (0.6 mg/ear). All of the fractions tested caused inhibition of edema formation and of MPO activity. Treatment with the ethyl acetate fraction was the most effective, resulting in inhibition levels of 75 ± 5 and 54 ± 8% for edema formation and MPO activity, respectively. However, treatment of mice with isolated compounds [apigenin‐6‐C‐β‐l‐fucopyranoside and apigenin‐6‐C‐(2″‐O‐α‐l‐rhamnopyranosyl)‐β‐l‐fucopyranoside] did not yield successful results. Apigenin‐6‐C‐(2″‐O‐α‐l‐rhamnopyranosyl)‐β‐l‐fucopyranoside caused only a mild reduction in edema formation (28 ± 11%). Taken together, these preliminary results support the popular use of A. carambola as an anti‐inflammatory agent and open up new possibilities for its use in skin disorders.
Antifungal Activity of Brazilian Propolis Microparticles against Yeasts Isolated from Vulvovaginal Candidiasis
Authors: Dota Kelen Fátima Dalben , Consolaro Marcia Edilaine Lopes , Svidzinski Terezinha Inez Estivalet , Bruschi Marcos Luciano
Published: April 2010

Propolis, a resinous compound produced by Apis mellifera L. bees, is known to possess a variety of biological activities and is applied in the therapy of various infectious diseases. The aim of this study was to evaluate the in vitro antifungal activity of propolis ethanol extract (PE) and propolis microparticles (PMs) obtained from a sample of Brazilian propolis against clinical yeast isolates of importance in the vulvovaginal candidiasis (VVC). PE was used to prepare the microparticles. Yeast isolates (n = 89), obtained from vaginal exudates of patients with VVC, were exposed to the PE and the PMs. Moreover, the main antifungal drugs used in the treatment of VVC (Fluconazole, Voriconazole, Itraconazole, Ketoconazole, Miconazole and Amphotericin B) were also tested. Minimum inhibitory concentration (MIC) was determined according to the standard broth microdilution method. Some Candida albicans isolates showed resistance or dose‐dependent susceptibility for the azolic drugs and Amphotericin B. Non‐C. albicans isolates showed more resistance and dose‐dependent susceptibility for the azolic drugs than C. albicans. However, all of them were sensitive or dose‐dependent susceptible for Amphotericin B. All yeasts were inhibited by PE and PMs, with small variation, independent of the species of yeast. The overall results provided important information for the potential application of PMs in the therapy of VVC and the possible prevention of the occurrence of new symptomatic episodes.
Transgenerational marking of cephalopods with an enriched barium isotope: a promising tool for empirically estimating post-hatching movement and population connectivity
Authors: Pecl Gretta T. , Doubleday Zoë A. , Danyushevsky Leonid , Gilbert Sarah , Moltschaniwskyj Natalie A.
Published: April 2010

Pecl, G. T., Doubleday, Z. A., Danyushevsky, L., Gilbert, S., and Moltschaniwskyj, N. A. 2010. Transgenerational marking of cephalopods with an enriched barium isotope: a promising tool for empirically estimating post-hatching movement and population connectivity. – ICES Journal of Marine Science, 67: 1372–1380. Quantifying the movement of very small and young individuals, determining sources of recruitment, and identifying the contribution of populations from different regions and periods to fished stocks is a major ecological challenge. Transgenerational isotope labelling (TRAIL), a technique which enables offspring to be marked on a mass scale, is applied for the first time to cephalopods, facilitating field studies quantifying population connectivity. Four species were used: Sepioteuthis australis, Euprymna tasmanica, Octopus pallidus, and Octopus maorum. Gravid females were injected with the enriched stable isotope 137Ba in different body tissues at several different doses. Isotopic ratios 138Ba:137Ba were then quantified using laser ablation inductively coupled plasma-mass spectrometry on the hard structures (statoliths and stylets) of offspring produced by the injected females. Day-old hatchlings from both squid species had statoliths with isotopic ratios significantly different from natural ratios and control animals, but variability in the ratios in hatchlings produced by different females was independent of dose or injection location. No differences were observed in the statoliths and stylets removed from hatchlings and juveniles, respectively, from the two octopus species, although isotopic shifts were evident in the hard structures of the adults injected. The use of TRAIL is a technique that offers considerable potential to advance the understanding of post-hatching dispersal and population connectivity in cephalopod populations.
Nutrition as a facilitator of host‐race formation: the shift of a stem‐boring beetle to a gall host
Authors: BLAIR CATHERINE P. , SCHLANGER RITA V. , DIAMOND SARAH E. , ABRAHAMSON WARREN G.
Published: April 2010

1. The importance of host‐race formation to herbivorous insect diversity depends on the likelihood that successful populations can be established on a new plant host. A previously unexplored ecological aid to success on a novel host is better nutritional quality. The role of nutrition was examined in the shift of the stem‐boring beetle Mordellistena convicta to fly‐induced galls on goldenrod and the establishment there of a genetically distinct gall host race.

2. First, larvae of the host race inhabiting stems of Solidago gigantea were transplanted into stems and galls of greenhouse‐grown S. gigantea plants. At the end of larval development, the mean mass of larvae transplanted to galls was significantly greater than the mass of larvae transplanted to stems, indicating a likely nutritional benefit during the shift. This advantage was slightly but significantly diminished when the gall‐inducing fly feeding at the centre of the gall died early in the season. Additionally, there was a suggestion of a trade‐off in the increased mortality of smaller beetle larvae transplanted into galls.

3. In a companion experiment, S. gigantea gall‐race beetle larvae were likewise transplanted to S. gigantea stems and galls. Besides the expected greater mass in galls, the larvae also exhibited adaptations to the gall nutritional environment: larger inherent size, altered tunnelling behaviour, and no diminution of mass pursuant to gall‐inducer mortality.

4. In a third line of inquiry, chemical analyses of field‐collected S. gigantea plants revealed higher levels of mineral elements important to insect nutrition in galls as compared with stems.
Dormancy, germination and seed bank storage: a study in support of ex situ conservation of macrophytes of southwest Australian temporary pools
Authors: TUCKETT R. E. , MERRITT D. J. , HAY F. R. , HOPPER S. D. , DIXON K. W.
Published: April 2010

1. Vernal pools and rock pools (gnammas) in the Southwest Australian Floristic Region are forms of temporary wetlands that are under threat. Some of their aquatic macrophytes are rare and/or endemic, and there is a need to develop off‐site seed banks to assure their conservation. Here, we report results of the first comprehensive study of the seed germination, dormancy and seed storage behaviour of nine indigenous macrophyte species.

2. Seeds of Glossostigma drummondii, Myriophyllum balladoniense, M. lapidicola, M. petreaum and Triglochin linearis were non‐dormant, whereas those of Damasonium minus, Glossostigma sp. (currently undescribed), G. trichodes and Myriophyllum crispatum were dormant. Non‐dormant seeds germinated over a range of temperatures (5–20 °C) but temperatures at which highest germination occurred were species specific. All species demonstrated a germination preference for the light. Warm stratification substantially increased germination of dormant Glossostigma trichodes seeds and all dormancy‐breaking treatments partially overcame dormancy in Glossostigma spp.

3. Seeds possessed orthodox storage behaviour (tolerating drying to 5% moisture content and storage at −18 °C) and are thus amenable to seed banking as a means of ex situ conservation.

4. It appears that seeds of most species are able to germinate upon inundation as long as they are situated at the soil surface. Thus, species are opportunistic and respond to the first rains of the season providing prompt ecological cuing in an environment vulnerable to rapid drying events. Maintaining the integrity of the soil crust may be an important first step for on‐site conservation if seeds are in the superficial layers.