bluuebunny/crossref_metadata_2025 huggingface dataset:
Untangling the folding mechanism of the 52‐knotted protein UCH‐L3
Authors: Andersson Fredrik I. , Pina David G. , Mallam Anna L. , Blaser Georg , Jackson Sophie E.
Published: March 2009

Proteins possessing deeply embedded topological knots in their structure add a stimulating new challenge to the already complex protein‐folding problem. The most complicated knotted topology observed to date belongs to the human enzyme ubiquitin C‐terminal hydrolase UCH‐L3, which is an integral part of the ubiquitin–proteasome system. The structure of UCH‐L3 contains five distinct crossings of its polypeptide chain, and it adopts a 52‐knotted topology, making it a fascinating target for folding studies. Here, we provide the first in depth characterization of the stability and folding of UCH‐L3. We show that the protein can unfold and refold reversibly in vitro without the assistance of molecular chaperones, demonstrating that all the information necessary for the protein to find its knotted native structure is encoded in the amino acid sequence, just as with any other globular protein, and that the protein does not enter into any deep kinetic traps. Under equilibrium conditions, the unfolding of UCH‐L3 appears to be two‐state, however, multiphasic folding and unfolding kinetics are observed and the data are consistent with a folding pathway in which two hyperfluorescent intermediates are formed. In addition, a very slow phase in the folding kinetics is shown to be limited by proline‐isomerization events. Overall, the data suggest that a knotted topology, even in its most complex form, does not necessarily limit folding in vitro, however, it does seem to require a complex folding mechanism which includes the formation of several distinct intermediate species.
Construction of a novel detection system for protein–protein interactions using yeast G‐protein signaling
Authors: Fukuda Nobuo , Ishii Jun , Tanaka Tsutomu , Fukuda Hideki , Kondo Akihiko
Published: March 2009

In the current study, we report the construction of a novel system for the detection of protein–protein interactions using yeast G‐protein signaling. It is well established that the G‐protein γ subunit (Gγ) is anchored to the inner leaflet of the plasma membrane via lipid modification in the C‐terminus, and that this localization of Gγ is required for signal transduction. In our system, mutated Gγ (Gγcyto) lacking membrane localization ability was genetically prepared by deletion of the lipid modification site. Complete disappearance of G‐protein signal was observed when Gγcyto was expressed in the cytoplasm of yeast cells from which the endogenous Gγ gene had been deleted. In order to demonstrate the potential use of our system, we utilized the Staphylococcus aureus ZZ domain and the Fc portion of human immunoglobulin G (IgG) as a model interaction pair. To design our detection system for protein–protein interaction, the ZZ domain was altered so that it associates with the inner leaflet of the plasma membrane, and the Fc part was then fused to Gγcyto. The Fc–Gγcyto fusion protein migrated towards the membrane via the ZZ–Fc interaction, and signal transduction was therefore restored. This signal was successfully detected by assessing growth inhibition and transcription in response to G‐protein signaling. Finally, several Z variants displaying affinity constants ranging from 8.0 × 103 to 6.8 × 108 m−1 were prepared, and it was demonstrated that our system was able to discriminate subtle differences in affinity. In conclusion, our system appears to be a reliable and versatile technique for detection of protein–protein interactions, and may prove useful in future protein interaction studies.
Inner retinal ischaemia: current understanding and needs for further investigations
Authors: Bek Toke
Published: March 2009

Inner retinal ischaemia is involved in the pathogenesis of major vision‐threatening diseases such as retinal vein thrombosis, diabetic retinopathy and retinopathy of prematurity. However, the pathogenesis of inner retinal ischaemia has not been fully elucidated, which represents an impediment to the development and improvement of techniques to prevent and treat these diseases on a rational basis. This paper provides a comprehensive review of current knowledge of the pathophysiology of inner retinal ischaemia, including clinical, anatomical and physiological aspects of disease development. It is suggested that chronic inner retinal ischaemia caused by capillary occlusion may develop secondary to an increase in hydrostatic pressure in the vessels. Further knowledge of the pathophysiology of inner retinal ischaemia can be obtained by identifying the mechanisms that lead to increased hydrostatic pressure in the capillary bed and establishing the structural and functional basis for the different response patterns in the central and peripheral areas of the retina that develop secondary to this increased hydrostatic pressure. Further elucidation of these unknown response patterns requires both in vitro and in vivo studies of retinal vascular pathophysiology. It is conceivable that a more detailed knowledge of these response patterns may help in the design of new treatments for retinal ischaemia and its vision‐threatening consequences.
Imperfect durability and the Coase conjecture
Authors: Deneckere Raymond , Liang Meng‐Yu
Published: March 2009

This article considers a market served by a monopolist who sells a durable good that depreciates stochastically over time. We show that there exist three types of stationary equilibria: a Coase Conjecture equilibrium, a monopoly equilibrium, and a reputational equilibrium. When the depreciation rate is low, the Coase Conjecture equilibrium is the unique equilibrium. For intermediate values of the depreciation rate, all three equilibrium types coexist. When the depreciation rate is high, the monopoly equilibrium is the unique equilibrium. Consequently, when selling a good of sufficiently low durability, the monopolist does not lose any of her monopoly power. Furthermore, the steady‐state output in the reputational equilibrium falls below the monopoly quantity. Hence, in durable goods markets, welfare losses due to monopoly power may be larger than in markets for perishables.
Rules of proof, courts, and incentives
Authors: Demougin Dominique , Fluet Claude
Published: March 2009

We analyze the design of legal principles and procedures for court decision making in civil litigation. The objective is the provision of incentives for potential tort‐feasors to exert care when evidence is imperfect and may be distorted by the parties. Efficiency is consistent with courts adjudicating on the basis of the preponderance of evidence standard together with common law exclusionary rules. Inefficient equilibria may nevertheless also arise under these rules. Burden of proof guidelines are then useful as a coordination device. Alternatively, guidelines are unnecessary if courts are allowed a more active or inquisitorial role in contrast to that of passive adjudicator.
Industry dynamics with stochastic demand
Authors: Bergin James , Bernhardt Dan
Published: March 2009

We study the dynamics of an industry subject to aggregate demand shocks where the productivity of a firm's technology evolves stochastically over time. To characterize the intertemporal evolution of the distribution of firms, we discuss in particular how exit decisions, aggregate output, profits, and distributions of firm productivities vary (a) across different demand realization paths; (b) along a demand history path, detailing the effects of continued good or bad market conditions; and (c) for different anticipated future market conditions. We show how poor demand conditions can lead to increased exit of low‐productivity firms at all future dates and states and raise welfare due to the impact on exit decisions.
Can cost increases increase competition? Asymmetric information and equilibrium prices
Authors: Dell'Ariccia Giovanni , Marquez Robert
Published: March 2009

We present an analysis of competition under asymmetric information where prices react asymmetrically to changes in firms' marginal costs. When one firm has private information about some customers, an increase in an uninformed firm's marginal cost leads to a price increase, as usual. However, an increase in the informed firm's marginal cost causes the equilibrium price to fall by improving the distribution of customers served by the uninformed firm. The model applies to settings where information asymmetries are important determinants of competition, such as credit, insurance, labor markets, or for the sale of goods where repeat business is important.
Human ClCa1 modulates anionic conduction of calcium‐dependent chloride currents
Authors: Hamann Martine , Gibson Adele , Davies Noel , Jowett Amanda , Walhin Jean Philippe , Partington Leanne , Affleck Karen , Trezise Derek , Main Martin
Published: March 2009

Proteins of the CLCA gene family including the human ClCa1 (hClCa1) have been suggested to constitute a new family of chloride channels mediating Ca2+‐dependent Cl− currents. The present study examines the relationship between the hClCa1 protein and Ca2+‐dependent Cl− currents using heterologous expression of hClCa1 in HEK293 and NCIH522 cell lines and whole cell recordings. By contrast to previous reports claiming the absence of Cl− currents in HEK293 cells, we find that HEK293 and NCIH522 cell lines express constitutive Ca2+‐dependent Cl− currents and show that hClCa1 increases the amplitude of Ca2+‐dependent Cl− currents in those cells. We further show that hClCa1 does not modify the permeability sequence but increases the Cl− conductance while decreasing the GSCN−/GCl− conductance ratio from ∼2–3 to ∼1. We use an Eyring rate theory (two barriers, one site channel) model and show that the effect of hClCa1 on the anionic channel can be simulated by its action on lowering the first and the second energy barriers. We conclude that hClCa1 does not form Ca2+‐dependent Cl− channels per se or enhance the trafficking/insertion of constitutive channels in the HEK293 and NCIH522 expression systems. Rather, hClCa1 elevates the single channel conductance of endogenous Ca2+‐dependent Cl− channels by lowering the energy barriers for ion translocation through the pore.
A Continuous Protein Design Model Using Artificial Power Law in Topology Optimization
Authors: Koh Sung K. , Liu Guangjun , Zhu Wen-Hong
Published: March 2009

A continuous protein synthesis formulation based on the design principles applied to topology optimization problems is proposed in this paper. In contrast to conventional continuous protein design methods, the power law (PL) protein design formulation proposed in this paper can handle any number of residue types to accomplish the goal of protein synthesis, and hence provides a general continuous formulation for protein synthesis. Moreover, a discrete sequence with minimum energy can be determined by the PL design method as it inherits the feature of material penalization used in designing a structural topology. Since a continuous optimization method is implemented to solve the PL design formulation, the entire design process is more efficient and robust than conventional design methods employing stochastic or enumerative search methods. The performance of the proposed PL design formulation is explored by designing simple lattice protein models, for which an exhaustive search can be carried out to identify a sequence with minimum energy. We used residue probabilities as an initial guess for the design optimization to enhance the capability and efficiency of the PL design formulation. The comparison with the exchange replica method indicates that the PL design method is millions of times more efficient than the conventional stochastic protein design method.
Improving the B-Spline Method of Dynamically-Compensated Cam Design by Minimizing or Restricting Vibrations in High-Speed Cam-Follower Systems
Authors: Jiang J. K. , Iwai Y. R.
Published: March 2009

This paper presents an improved method for dynamically-compensated (tuned) cam design by minimizing or restricting vibrations in high-speed cam-follower systems. Using this approach, cams can be synthesized with a variety of design requirements and reduced residual vibrations. An example of the dynamically-compensated B-spline method illustrates the application process and demonstrates the improvement effect. While preserving the features of the B-spline method, the improved design method allows the cams to satisfy requirements, such as pressure angle, radius of curvature, and contact stress, and also reduces the residual vibrations caused by deviations in actual cam speed or system damping ratio from their design values.
Complementary Intersection Method for System Reliability Analysis
Authors: Youn Byeng D. , Wang Pingfeng
Published: March 2009

Although researchers desire to evaluate system reliability accurately and efficiently over the years, little progress has been made on system reliability analysis. Up to now, bound methods for system reliability prediction have been dominant. However, two primary challenges are as follows: (1) Most numerical methods cannot effectively evaluate the probabilities of the second (or higher)–order joint failure events with high efficiency and accuracy, which are needed for system reliability evaluation and (2) there is no unique system reliability approximation formula, which can be evaluated efficiently with commonly used reliability methods. Thus, this paper proposes the complementary intersection (CI) event, which enables us to develop the complementary intersection method (CIM) for system reliability analysis. The CIM expresses the system reliability in terms of the probabilities of the CI events and allows the use of commonly used reliability methods for evaluating the probabilities of the second–order (or higher) joint failure events efficiently. To facilitate system reliability analysis for large-scale systems, the CI-matrix can be built to store the probabilities of the first- and second-order CI events. In this paper, three different numerical solvers for reliability analysis will be used to construct the CI-matrix numerically: first-order reliability method, second-order reliability method, and eigenvector dimension reduction (EDR) method. Three examples will be employed to demonstrate that the CIM with the EDR method outperforms other methods for system reliability analysis in terms of efficiency and accuracy.
High-Stiffness, Lock-and-Key Heat-Reversible Locator-Snap Systems for the Design for Disassembly
Authors: Shalaby Mohammed , Saitou Kazuhiro
Published: March 2009

Driven by the moral sense of obligation, legislative and social pressures, manufacturers now consider effective part reuse and material recycling at the end of product life at the design stage. It is a key consideration to use joints that can disengage with minimum labor, part damage, and material contamination. This paper extends our previous work on the design of high-stiffness reversible locator-snap system that can disengage nondestructively with localized heat (Shalaby and Saitou, 2006, “Optimal Heat-Reversible Snap Joints for Frame-Panel Assembly in Aluminum Space Frame Automotive Bodies,” Proceedings of the LCE2006: The 13th CIRP International Conference on Life Cycle Engineering, Leuven, Belgium, May 31–Jun. 2, pp. 411–416; Shalaby and Saitou, 2008, “Design for Disassembly With High-Stiffness, Heat-Reversible Locator-Snap Systems,” ASME J. Mech. Des., 130(12), p. 121701) to include (1) modeling for tolerance stack-up and (2) lock-and-key concept to ensure that snaps only disengage when the right procedure is followed. The design problem is posed as an optimization problem to find the locations, numbers, and orientations of locators and snaps, and the locations and sizes of heating areas, to release the snaps with minimum heat, compliance, and tolerance stack-up. The motion and structural requirements are considered constraints. Screw theory is employed to precalculate the set of feasible types and orientations of locators and snaps that are examined during optimization. Multi-objective genetic algorithm coupled with structural and thermal finite element analysis is used to solve the optimization problem. The method is applied on two case studies. The Pareto-optimal solutions present alternative designs with different trade-offs between the design objectives.
Odor Coding by a Mammalian Receptor Repertoire
Authors: Saito Harumi , Chi Qiuyi , Zhuang Hanyi , Matsunami Hiroaki , Mainland Joel D.
Published: March 2009

Identification of mammalian olfactory receptor agonists enables development of a predictive model of receptor activation.
The Precise Sequence of FGF Receptor Autophosphorylation Is Kinetically Driven and Is Disrupted by Oncogenic Mutations
Authors: Lew Erin D. , Furdui Cristina M. , Anderson Karen S. , Schlessinger Joseph
Published: March 2009

The order of FGFR1 tyrosine autophosphorylation is kinetically controlled and determined by primary and tertiary structures.
IL-17 Receptor Signaling Inhibits C/EBPβ by Sequential Phosphorylation of the Regulatory 2 Domain
Authors: Shen Fang , Li Nan , Gade Padmaja , Kalvakolanu Dhananjaya V. , Weibley Timothy , Doble Brad , Woodgett James R. , Wood Troy D. , Gaffen Sarah L.
Published: March 2009

The IL-17 receptor triggers dual, sequential phosphorylation of the transcription factor C/EBPβ, which represses the expression of target genes.
Direct Response to Notch Activation: Signaling Crosstalk and Incoherent Logic
Authors: Krejčí Alena , Bernard Fred , Housden Ben E. , Collins Stephanie , Bray Sarah J.
Published: March 2009

Identification of the direct target genes of Notch reveals complex input into multiple signaling pathways that goes beyond coordination of transcriptional networks.
Obesity Increases Vascular Senescence and Susceptibility to Ischemic Injury Through Chronic Activation of Akt and mTOR
Authors: Wang Chao-Yung , Kim Hyung-Hwan , Hiroi Yukio , Sawada Naoki , Salomone Salvatore , Benjamin Laura E. , Walsh Kenneth , Moskowitz Michael A. , Liao James K.
Published: March 2009

Chronic activation of Akt and mammalian target of rapamycin (mTOR) links diet-induced obesity with cardiovascular disease.
Rac1
Is a Critical Mediator of Endothelium-Derived Neurotrophic Activity
Authors: Sawada Naoki , Kim Hyung-Hwan , Moskowitz Michael A. , Liao James K.
Published: March 2009

Rac1 drives transcriptional programs in endothelial cells that alter endothelial barrier property and expression of neurotrophic factors.
Adaptive Inflammation
Authors: Adler Elizabeth M.
Published: March 2009

Inflammation is critical to inward vascular remodeling after hemodynamic changes.
Cone of Inactivation
Authors: Wong Wei
Published: March 2009

Rho GTPase activity in pollen tubes is restricted to the apical tip by a Rho GAP that is present throughout the apical region.
Keeping Fungal Invaders at Bay
Authors: Zahn Laura M.
Published: March 2009

Plant cells defend against fungal attack through an innate immunity pathway in which infection triggers glucosinolate synthesis, stimulating formation of a protective callose.
Chaperone to Neurodegeneration
Authors: Hurtley Stella M.
Published: March 2009

The degradation of a key neuronal survival factor by chaperone-mediated autophagy may contribute to Parkinson's disease.
2008: Signaling Breakthroughs of the Year
Authors: Adler Elizabeth M.
Published: March 2009

The signaling breakthroughs of 2008 extended from protein crystals to cells and subcellular structures to whole genomes.
MicroRNAs: Opening a New Vein in Angiogenesis Research
Authors: Fish Jason E. , Srivastava Deepak
Published: March 2009

MicroRNAs regulate angiogenic signaling in endothelial cells.
Surviving Hard Times
Authors: Adler Elizabeth M.
Published: March 2009

LKB1-AMPK signaling enhances survival in dauer by limiting depletion of lipid stores.
Tassel Tussle
Authors: Zahn Laura M.
Published: March 2009

A gene that controls male floral development in maize is involved in synthesis of a hormone that suppresses female organ development.
CD30-ARNT Interaction
Authors: Ray L. Bryan
Published: March 2009

Signals from a cancer-associated receptor that activate a key pathway in the immune system are modulated by its binding to a stress-responsive transcription factor.
Neuro2A Differentiation by Gα
i/o
Pathway
Authors: Ma'ayan Avi , Jenkins Sherry L. , Barash Alexander , Iyengar Ravi
Published: March 2009

Neurite outgrowth can be stimulated by G protein-coupled receptors that signal through Gα
i
and Gα
o
proteins.
Staving Off Hunger
Authors: VanHook Annalisa M.
Published: March 2009

Signaling through metabotropic glutamate receptors affects the nematode starvation response.
Does a Fatty Diet Take a Toll on Leptin Signaling?
Authors: Adler Elizabeth M.
Published: March 2009

Activation of TLR4 signaling by saturated fatty acids plays an important role in the hypothalamic response to a high-fat diet.
Interleukin-1 Receptor, Sliced for Action
Authors: Ray L. Bryan
Published: March 2009

Intramembrane proteolysis enhances signaling by interleukin-1 receptor type 1.
Genome to Kinome: Species-Specific Peptide Arrays for Kinome Analysis
Authors: Jalal Shakiba , Arsenault Ryan , Potter Andrew A. , Babiuk Lorne A. , Griebel Philip J. , Napper Scott
Published: March 2009

Marrying bioinformatics and phosphorylation assays enables the empirical analysis of kinomes of multiple species.
Getting the Best from a Gradient
Authors: Ray L. Bryan
Published: March 2009

Effective patterning in a morphogen gradient requires inhibitory signals from stimulated cells that act on their neighbors.
Freedom of Materials
Authors: Yaffe Michael B.
Published: March 2009

Intellectual property concerns bring into conflict data sharing and accessibility of materials.
Transcription Factor for p75
NTR
Authors: Gough Nancy R.
Published: March 2009

Activation of the p75
NTR
and the TrkA neurotrophin receptors by nerve growth factor promotes the dissociation of the transcription factor Sall2 from the p75
NTR
, cell cycle arrest, and neurite outgrowth.
Broken Blood Vessels
Authors: Wong Wei
Published: March 2009

The signaling pathway mediated by the cerebral cavernous malformation protein 2 functions in endothelial cells to regulate angiogenesis.
Mitochondrial Stat3 Activity
Authors: Ray L. Bryan
Published: March 2009

A protein that has a nuclear function as a transcription factor also functions to support respiration in the mitochondria.
Yet Another Ubiquitin Arrangement for NF-κB
Authors: Gough Nancy R.
Published: March 2009

Linear polyubiquitylation of NEMO bypasses the need for Lys
63
-linked ubiquitylation in activating nuclear factor κB in response to tumor necrosis factor–α.
Axonal Regeneration in Nematodes
Authors: Hines Pamela J.
Published: March 2009

Axon regeneration in adult nematode worms has distinct signals that are independent of earlier developmental programs.
Emerging Roles of NAD
+
and Its Metabolites in Cell SignalingA report on the NAD2008 symposium, Hamburg, Germany, 14 to 17 September 2008.
Authors: Koch-Nolte Friedrich , Haag Friedrich , Guse Andreas H. , Lund Frances , Ziegler Mathias
Published: March 2009

Scientists discussed the molecular aspects of NAD
+
metabolism and signaling at a conference in Hamburg, Germany.
Smelly Kidneys
Authors: Ray L. Bryan
Published: March 2009

Olfactory receptors expressed in the kidney may allow regulation of filtration rates in response to chemicals in extracellular fluids.
The Sigma-1 Receptor—Orphan No More
Authors: Stern Peter
Published: March 2009

An endogenous compound is a ligand for a ubiquitously expressed receptor that binds many synthetic drugs and has been implicated in psychiatric disease.
TRPing Toward the Gradient
Authors: Adler Elizabeth M.
Published: March 2009

High-calcium microdomains that depend on Ca
2+
influx through TRPM7 play a role in regulating directional migration of lung fibroblasts.
The Lure of Lipids
Authors: VanHook Annalisa M.
Published: March 2009

Germ cell migration in the fruit fly relies on a lipid-modified attractant secreted by a system analogous to that of yeast mating pheromone.
Stress Flips the Switch
Authors: Foley John F.
Published: March 2009

Two proteins that compete for binding to human
VEGFA
mRNA regulate its translation.
More Roles for Cryptochromes
Authors: Gough Nancy R.
Published: March 2009

Characterization of blue light receptors in wheat reveals that they have roles in responding to osmotic stress and abscisic acid.
Slime Mold on Steroids
Authors: VanHook Annalisa M.
Published: March 2009

A steroid signal initiates the sporulation cascade in
Dictyostelium
.
Follow the Water
Authors: Gough Nancy R.
Published: March 2009

A new mutation in GNOM, a regulator of vesicle trafficking, defines separate roles for responding to gravity and moisture.
Supporting Sensory Signals
Authors: Adler Elizabeth M.
Published: March 2009

Loss of FGFR1 and FGFR2 signaling in nonmyelinating Schwann cells interferes with their ability to support sensory axons.
GPR3 and Alzheimer’s Disease
Authors: Hurtley Stella
Published: March 2009

A neuronal G protein–coupled receptor can stimulate the generation of the Aβ peptide implicated in Alzheimer’s disease.
Science Signaling
Podcast: 17 February 2009
Authors: Kino Tomoshige , VanHook Annalisa M.
Published: March 2009

The guanine nucleotide exchange factor Brx is required in lymphocytes for the expression of
nfat5
in response to osmotic stress.
Von Gierke’s Disease Adopts an Orphan (and Its Partner)
Authors: Cheng Alan , Saltiel Alan R.
Published: March 2009

The transcription of
glucose-6-phosphatase
is positively regulated by a nuclear receptor and coactivator.
DNA Kills
Authors: Ash Caroline
Published: March 2009

A family of proteins is identified that binds to foreign cytoplasmic DNA in mammalian cells and regulates the immune response.
Breaching the Barrier
Authors: VanHook Annalisa M.
Published: March 2009

Cytokine signaling induces blood-testis barrier permeability by promoting endocytosis of membrane proteins.
Pathways Talk at Endosomes
Authors: Gough Nancy R.
Published: March 2009

Epidermal growth factor receptor signaling controls the activity of Wnt and Notch pathways by regulating endosomal trafficking.
Digital Feedback
Authors: VanHook Annalisa M.
Published: March 2009

Three signaling pathways intersect to regulate vertebrate limb patterning.
Inverse Agonist to the Rescue
Authors: Ray L. Bryan
Published: March 2009

Inhibiting signaling by the β
2
-adrenergic receptor inhibits development of asthma in mice.
Drooling Over Purinergic Receptors
Authors: Wong Wei
Published: March 2009

ATP stimulates fluid secretion in mouse salivary glands through the P2X
7
receptor.
Signal Transduction Molecules as Targets for Cancer PreventionA report on the joint 3rd Hormel Institute Frontiers in Cancer Conference and 8th International Skin Carcinogenesis Conference held at The Hormel Institute, University of Minnesota, Austin, Minnesota, 4 to 7 October 2008.
Authors: Bode Ann M. , Dong Zigang
Published: March 2009

Two conferences at The Hormel Institute highlight early intervention and chemoprevention in targeting cancer.
Greasing the Path?
Authors: Adler Elizabeth M.
Published: March 2009

Lipids relieve open channel block of TRPL and NMDA channels by modulating membrane properties.
Destructive Duo
Authors: Foley John F.
Published: March 2009

The cellular prion protein acts as a receptor for β-amyloid.
Astrocytes in Alzheimer's
Authors: Hurtley Stella M.
Published: March 2009

In a mouse model of Alzheimer's disease, astrocytes respond globally to plaque formation.
Signaling al Dente
Authors: VanHook Annalisa M.
Published: March 2009

The transcription factors Msx1 and Osr2 control the distribution of BMP4 to restrict tooth development to a single row in mammals.
From Model to Marker
Authors: Jasny Barbara R.
Published: March 2009

A developmental marker in fruit flies also acts as a marker of renal cell cancer in humans.
MicroRNA Keeps Inflammation in Check
Authors: Ray L. Bryan
Published: March 2009

A negative feedback loop mediated by microRNA prevents excessive inflammation when dendritic cells encounter foreign stimuli.
Science Signaling
Podcast: 03 March 2009
Authors: Schlessinger Joseph , VanHook Annalisa M.
Published: March 2009

Autophosphorylation events that control the activity of the FGF receptor are kinetically controlled and disrupted by a mutation associated with glioblastoma.
A STIMulating CAD
Authors: Foley John F.
Published: March 2009

A discrete region within STIM1 directly binds to and activates Orai1 to trigger influx of Ca
2+
.
Reversible Phosphorylation of Histidine Residues in Proteins from Vertebrates
Authors: Klumpp Susanne , Krieglstein Josef
Published: March 2009

The importance of kinases and phosphatases to signaling mechanisms is extended by their regulation of histidine residues.
Fingertip Search
Authors: Chin Gilbert
Published: March 2009

Fingertip ridges improve the tactile perception of fine features.
From PINK(1) to Code Red
Authors: Ray L. Bryan
Published: March 2009

Impaired calcium regulation in the mitochondria can account for increased neuronal cell death in a model of Parkinson’s disease.
Back to the Dead
Authors: Foley John F.
Published: March 2009

Treating estrogen receptor α (ERα)–negative tumor cells with Wnt-5a restores ERα and renders them susceptible to tamoxifen-induced death.
Stalled at Endosomes
Authors: Gough Nancy R.
Published: March 2009

Hypoxic conditions or forced stabilization of HIF-2α inhibits epidermal growth factor receptor delivery to lysosomes.
Limiting Potential
Authors: Hurtley Stella
Published: March 2009

The protein RSY-1 inhibits synapse formation by antagonizing assembly molecules during presynaptic development.
Closing the Loop
Authors: Hines Pamela J.
Published: March 2009

The transcription factor CHE binds the promoter of the clock gene
CCA1
, adding to the molecular clock circuitry in plants.
Combination Therapy in Treatment of Experimental Pulmonary Aspergillosis: In Vitro and In Vivo Correlations of the Concentration- and Dose- Dependent Interactions between Anidulafungin and Voriconazole by Bliss Independence Drug Interaction Analysis
Authors: Petraitis Vidmantas , Petraitiene Ruta , Hope William W. , Meletiadis Joseph , Mickiene Diana , Hughes Johanna E. , Cotton Margaret P. , Stergiopoulou Theodouli , Kasai Miki , Francesconi Andrea , Schaufele Robert L. , Sein Tin , Avila Nilo A. , Bacher John , Walsh Thomas J.
Published: March 2009

We studied the antifungal activity of anidulafungin (AFG) in combination with voriconazole (VRC) against experimental invasive pulmonary aspergillosis (IPA) in persistently neutropenic rabbits and further explored the in vitro and in vivo correlations by using Bliss independence drug interaction analysis. Treatment groups consisted of those receiving AFG at 5 (AFG5 group) and 10 (AFG10 group) mg/kg of body weight/day, VRC at 10 mg/kg every 8 h (VRC group), AFG5 plus VRC (AFG5+VRC group), and AFG10 plus VRC (AFG10+VRC group) and untreated controls. Survival throughout the study was 60% for the AFG5+VRC group, 50% for the VRC group, 27% for the AFG10+VRC group, 22% for the AFG5 group, 18% for the AFG10 group, and 0% for control rabbits (P< 0.001). There was a significant reduction of organism-mediated pulmonary injury, measured by infarct scores, lung weights, residual fungal burdens, and galactomannan indexes, in AFG5+VRC-treated rabbits versus those treated with AFG5 and VRC alone (P< 0.05). In comparison, AFG10+VRC significantly lowered only infarct scores and lung weights in comparison to those of AFG10-treated animals (P< 0.05). AFG10+VRC showed no significant difference in other outcome variables. Significant Bliss synergy was found in vivo between AFG5 and VRC, with observed effects being 24 to 30% higher than expected levels if the drugs were acting independently. These synergistic interactions were also found between AFG and VRC in vitro. However, for AFG10+VRC, only independence and antagonism were observed among the outcome variables. We concluded that the combination of AFG with VRC in treatment of experimental IPA in persistently neutropenic rabbits was independent to synergistic at a dosage of 5 mg/kg/day but independent to antagonistic at 10 mg/kg/day, as assessed by Bliss independence analysis, suggesting that higher dosages of an echinocandin may be deleterious to the combination.
Population Pharmacokinetics of Ganciclovir in Solid-Organ Transplant Recipients Receiving Oral Valganciclovir
Authors: Perrottet N. , Csajka C. , Pascual M. , Manuel O. , Lamoth F. , Meylan P. , Aubert J. D. , Venetz J. P. , Soccal P. , Decosterd L. A. , Biollaz J. , Buclin T.
Published: March 2009

Valganciclovir (VGC) is an oral prodrug of ganciclovir (GCV) recently introduced for prophylaxis and treatment of cytomegalovirus infection. Optimal concentration exposure for effective and safe VGC therapy would require either reproducible VGC absorption and GCV disposition or dosage adjustment based on therapeutic drug monitoring (TDM). We examined GCV population pharmacokinetics in solid organ transplant recipients receiving oral VGC, including the influence of clinical factors, the magnitude of variability, and its impact on efficacy and tolerability. Nonlinear mixed effect model (NONMEM) analysis was performed on plasma samples from 65 transplant recipients under VGC prophylaxis or treatment. A two-compartment model with first-order absorption appropriately described the data. Systemic clearance was markedly influenced by the glomerular filtration rate (GFR), patient gender, and graft type (clearance/GFR = 1.7 in kidney, 0.9 in heart, and 1.2 in lung and liver recipients) with interpatient and interoccasion variabilities of 26 and 12%, respectively. Body weight and sex influenced central volume of distribution (V1= 0.34 liter/kg in males and 0.27 liter/kg in females [20% interpatient variability]). No significant drug interaction was detected. The good prophylactic efficacy and tolerability of VGC precluded the demonstration of any relationship with GCV concentrations. In conclusion, this analysis highlights the importance of thorough adjustment of VGC dosage to renal function and body weight. Considering the good predictability and reproducibility of the GCV profile after treatment with oral VGC, routine TDM does not appear to be clinically indicated in solid-organ transplant recipients. However, GCV plasma measurement may still be helpful in specific clinical situations.
Bone Penetration of Amoxicillin and Clavulanic Acid Evaluated by Population Pharmacokinetics and Monte Carlo Simulation
Authors: Landersdorfer Cornelia B. , Kinzig Martina , Bulitta Jürgen B. , Hennig Friedrich F. , Holzgrabe Ulrike , Sörgel Fritz , Gusinde Johannes
Published: March 2009

Amoxicillin (amoxicilline)-clavulanic acid has promising activity against pathogens that cause bone infections. We present the first evaluation of the bone penetration of a beta-lactam by population pharmacokinetics and pharmacodynamic profiling via Monte Carlo simulations. Twenty uninfected patients undergoing total hip replacement received a single intravenous infusion of 2,000 mg/200 mg amoxicillin-clavulanic acid before surgery. Blood and bone specimens were collected. Bone samples were pulverized under liquid nitrogen with a cryogenic mill, including an internal standard. The drug concentrations in serum and total bone were analyzed by liquid chromatography-tandem mass spectrometry. We used NONMEM and S-ADAPT for population pharmacokinetic analysis and a target time of the non-protein-bound drug concentration above the MIC for ≥50% of the dosing interval for near-maximal bactericidal activity in serum. The median of the ratio of the area under the curve (AUC) for bone/AUC for serum was 20% (10th to 90th percentile for between-subject variability [variability], 16 to 25%) in cortical bone and 18% (variability, 11 to 29%) in cancellous bone for amoxicillin and 15% (variability, 11 to 21%) in cortical bone and 10% (variability, 5.1 to 21%) in cancellous bone for clavulanic acid. Analysis in S-ADAPT yielded similar results. The equilibration half-lives between serum and bone were 12 min for amoxicillin and 14 min for clavulanic acid. For a 30-min infusion of 2,000 mg/200 mg amoxicillin-clavulanic acid every 4 h, amoxicillin achieved robust (≥90%) probabilities of target attainment (PTAs) for MICs of ≤12 mg/liter in serum and 2 to 3 mg/liter in bone and population PTAs above 95% against methicillin-susceptible
Staphylococcus aureus
in bone and serum. The AUC of amoxicillin-clavulanic acid was 5 to 10 times lower in bone than in serum, and amoxicillin-clavulanic acid achieved a rapid equilibrium and favorable population PTAs against pathogens commonly encountered in bone infections.
Predictive Value of Pharmacokinetics-Adjusted Phenotypic Susceptibility on Response to Ritonavir-Enhanced Protease Inhibitors (PIs) in Human Immunodeficiency Virus-Infected Subjects Failing Prior PI Therapy
Authors: Eron Joseph J. , Park Jeong-Gun , Haubrich Richard , Aweeka Francesca , Bastow Barbara , Pakes Gary E. , Yu Song , Wu Hulin , Richman Douglas D.
Published: March 2009

The activities of protease inhibitors in vivo may depend on plasma concentrations and viral susceptibility. This nonrandomized, open-label study evaluated the relationship of the inhibitory quotient (IQ [the ratio of drug exposure to viral phenotypic susceptibility]) to the human immunodeficiency virus type 1 (HIV-1) viral load (VL) change for ritonavir-enhanced protease inhibitors (PIs). Subjects on PI-based regimens replaced their PIs with ritonavir-enhanced indinavir (IDV/r) 800/200 mg, fosamprenavir (FPV/r) 700/100 mg, or lopinavir (LPV/r) 400/200 mg twice daily. Pharmacokinetics were assessed at day 14; follow-up lasted 24 weeks. Associations between IQ and VL changes were examined. Fifty-three subjects enrolled, 12 on IDV/r, 33 on FPV/r, and 8 on LPV/r. Median changes (n-fold) (FC) of 50% inhibitory concentrations (IC50s) to the study PI were high. Median 2-week VL changes were −0.7, −0.1, and −1.0 log10for IDV/r, FPV/r, and LPV/r. With FPV/r, correlations between the IQ and the 2-week change in VL were significant (Spearman'srrange, −0.39 to −0.50;P≤ 0.029). The strongest correlation with response to FPV/r was the IC50FC (r= 0.57;P= 0.001), which improved when only adherent subjects were included (r= 0.68;P= 0.001). In multivariable analyses of the FPV/r arm that included FC, one measure of the drug concentration, corresponding IQ, baseline VL, and CD4, the FC to FPV was the only significant predictor of VL decline (P< 0.001). In exploratory analyses of all arms, the area under the concentration-time curve IQ was correlated with the week 2 VL change (r= −0.72;P< 0.001). In conclusion, in PI-experienced subjects with highly resistant HIV-1, short-term VL responses to RTV-enhanced FPV/r correlated best with baseline susceptibility. The IQ improved correlation in analyses of all arms where a greater range of virologic responses was observed.
Evaluation of Cefotaxime and Desacetylcefotaxime Concentrations in Cord Blood after Intrapartum Prophylaxis with Cefotaxime
Authors: Lepercq Jacques , Treluyer Jean Marc , Auger Christelle , Raymond Josette , Rey Elisabeth , Schmitz Thomas , Jullien Vincent
Published: March 2009

Preterm premature rupture of the membranes is associated with a high risk of neonatal sepsis. An increase in the incidence of early-onset neonatal sepsis due to ampicillin-resistant
Escherichia coli
in premature infants has been observed in the past few years. Intrapartum prophylaxis with ampicillin has proven to be efficient for the prevention of early neonatal sepsis due to group B streptococci. To date, there is no strategy for the prevention of early neonatal sepsis due to ampicillin-resistant
E. coli
. Our aim was to investigate whether a standardized dosage regimen of intrapartum cefotaxime could provide concentrations in the cord blood greater than the cefotaxime MIC
90
for
E. coli
. Seven pregnant women hospitalized with preterm premature rupture of the membranes and colonized with ampicillin-resistant isolates of the family
Enterobacteriaceae
were included. Cefotaxime was given intravenously during delivery, as follows: 2 g at the onset of labor and then 1 g every 4 h until delivery. Blood specimens were collected from the mother 30 min after the first injection and just before the second injection, and at birth, blood specimens were simultaneously collected from the mother and the umbilical cord. The concentrations of cefotaxime in the cord blood ranged from 0.5 to 8.5 mg/liter. The MIC
90
of cefotaxime for
E. coli
strains (0.125 mg/liter) was achieved in all cases. This preliminary study supports the use of cefotaxime for intrapartum prophylaxis in women colonized with ampicillin-resistant isolates of
Enterobacteriaceae
. The effectiveness of this regimen for the prevention of neonatal sepsis needs to be evaluated with a larger population.
Atorvastatin Is a Promising Partner for Antimalarial Drugs in Treatment of
Plasmodium falciparum
Malaria
Authors: Parquet Véronique , Briolant Sébastien , Torrentino-Madamet Marylin , Henry Maud , Almeras Lionel , Amalvict Rémy , Baret Eric , Fusaï Thierry , Rogier Christophe , Pradines Bruno
Published: March 2009

Atorvastatin (AVA) is a 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitor. AVA exposure resulted in the reduced in vitro growth of 22
Plasmodium falciparum
strains, with the 50% inhibitory concentrations (IC
50
s) ranging from 2.5 μM to 10.8 μM. A significant positive correlation was found between the strains’ responses to AVA and mefloquine (
r
= 0.553;
P
= 0.008). We found no correlation between the responses to AVA and to chloroquine, quinine, monodesethylamodiaquine, lumefantrine, dihydroartemisinin, atovaquone, or doxycycline. These data could suggest that the mechanism of AVA uptake and/or the mode of action of AVA is different from those for other antimalarial drugs. The IC
50
s for AVA were unrelated to the occurrence of mutations in the transport protein genes involved in quinoline antimalarial drug resistance, such as the
P. falciparum crt
,
mdr1
,
mrp
, and
nhe-1
genes. Therefore, AVA can be ruled out as a substrate for the transport proteins (CRT, Pgh1, and MRP) and is not subject to the pH modification induced by the
P. falciparum
NHE-1 protein. The absence of in vitro cross-resistance between AVA and chloroquine, quinine, mefloquine, monodesethylamodiaquine, lumefantrine, dihydroartemisinin, atovaquone, and doxycycline argues that these antimalarial drugs could potentially be paired with AVA as a treatment for malaria. In conclusion, the present observations suggest that AVA is a good candidate for further studies on the use of statins in association with drugs known to have activities against the malaria parasite.
Intracellular Localization of the ABCC Proteins of
Leishmania
and Their Role in Resistance to Antimonials
Authors: Leprohon Philippe , Légaré Danielle , Ouellette Marc
Published: March 2009

The ABCC subfamily of proteins is composed of nine members in
Leishmania
. We report that all of these proteins have an intracellular localization and that the overexpression of at least four members, ABCC3, ABCC4, ABCC5, and ABCC7, can confer resistance to antimonials, the first-line drug against
Leishmania
.
Omeprazole Antagonizes Virulence and Inflammation in
Salmonella enterica
-Infected RAW264.7 Cells
Authors: Puiac Speranta , Negrea Aurel , Richter-Dahlfors Agneta , Plant Laura , Rhen Mikael
Published: March 2009

The proton pump inhibitor omeprazole reduced the intracellular replication of
Salmonella enterica
serovar Typhimurium in RAW264.7 cells without affecting bacterial growth in vitro or the viability of the host cells. The mechanism was bacteriostatic and interfered with replication mediated by the virulence-associated SPI2 type III secretion system. The proton pump inhibitor bafilomycin A
1
, in contrast, mediated killing of intracellular bacteria and imposed a marked cytotoxicity on RAW264.7 cells. The two compounds also differentially affected the proinflammatory responses of the infected cells. Bafilomycin A
1
enhanced nitric oxide production, whereas omeprazole delayed IκB degradation and blocked nitric oxide production and the secretion of proinflammatory cytokines. These results imply that omeprazole can be used to block the virulence factor-mediated intracellular replication of
S
. Typhimurium, and that its mechanism of growth inhibition is different from that mediated by bafilomycin A
1
.
Inhibition of Vaccinia Virus Replication by Two Small Interfering RNAs Targeting B1R and G7L Genes and Their Synergistic Combination with Cidofovir
Authors: Vigne Solenne , Duraffour Sophie , Andrei Graciela , Snoeck Robert , Garin Daniel , Crance Jean-Marc
Published: March 2009

In view of the threat of the potential use of variola virus in a terrorist attack, considerable efforts have been performed to develop new antiviral strategies against orthopoxviruses. Here we report on the use of RNA interference, either alone or in combination with cidofovir, as an approach to inhibit orthopoxvirus replication. Two selected small interfering RNAs (siRNAs), named siB1R-2 and siG7L-1, and a previously reported siRNA, i.e., siD5R-2 (which targets the viral D5R mRNA), were evaluated for antiviral activity against vaccinia virus (VACV) by plaque reduction and virus yield assays. siB1R-2 and siG7L-1, administered before or after viral infection, reduced VACV replication by more than 90%. Also, these two siRNAs decreased monkeypox virus replication by 95% at a concentration of 1 nM. siB1R-2 and siG7L-1 were demonstrated to specifically silence their corresponding transcripts, i.e., B1R and G7L mRNAs, without induction of a beta interferon response. Strong synergistic effects were observed when siB1R-2, siG7L-1, or siD5R-2 was combined with cidofovir. In addition, the antiviral activities of these three siRNAs were evaluated against VACV resistant to cidofovir and other acyclic nucleoside phosphonates. siG7L-1 and siD5R-2 remained active against four of five VACV mutants, while siB1R-2 showed activity against only one of the mutants. Our results showed that siRNAs are potent inhibitory agents in vitro, not only against wild-type VACV but also against several cidofovir-resistant VACV. Furthermore, we showed that a combined therapy using siRNA and cidofovir may be useful in the treatment of poxvirus infections.
Antibodies to Reticulocyte Binding Protein-Like Homologue 4 Inhibit Invasion of
Plasmodium falciparum
into Human Erythrocytes
Authors: Tham Wai-Hong , Wilson Danny W. , Reiling Linda , Chen Lin , Beeson James G. , Cowman Alan F.
Published: March 2009

Plasmodium falciparum
invasion into human erythrocytes relies on the interaction between multiple parasite ligands and their respective erythrocyte receptors. The sialic acid-independent invasion pathway is dependent on the expression of
P. falciparum
reticulocyte binding protein-like homologue 4 (PfRh4), as disruption of the gene abolishes the ability of parasites to switch to this pathway. We show that PfRh4 is present as an invasion ligand in culture supernatants as a 160-kDa proteolytic fragment. We confirm that PfRh4 binds to the surfaces of erythrocytes through recognition of an erythrocyte receptor that is neuraminidase resistant but trypsin and chymotrypsin sensitive. Serum antibodies from malaria-exposed individuals show reactivity against the binding domain of PfRh4. Purified immunoglobulin G raised in rabbits against the binding domain of PfRh4 blocked the binding of native PfRh4 to the surfaces of erythrocytes and inhibited erythrocyte invasion of parasites using sialic acid-independent invasion pathways and grown in neuraminidase-treated erythrocytes. Our results suggest PfRh4 is a potential vaccine candidate.