bluuebunny/crossref_metadata_2025 huggingface dataset:
Fluctuation theory and (very) early statistical energy analysis (SEA) (L)
Authors: Lyon Richard H.
Published: May 2003

The equivalence between a noise source in combination with a resistance, and a thermal bath, is a part of fluctuation theory. This observation was the motivation for the author’s 1960 calculation of the power flow between modes of vibration excited by random noise sources. The resulting relation between power flow and uncoupled energy of vibration is therefore more than a thermal analogy; it is an actual representation of two thermal baths in contact. In a sense, the answer was known before the calculation was performed; the power flow had to be proportional to the differences in modal energy. The calculation merely determined the thermal conductivity of the connection. The relations for groups of modes in contact and the proportionality between power flow and actual modal energy came later.
Measuring the porosity and the tortuosity of porous materials via reflected waves at oblique incidence
Authors: Fellah Z. E. A. , Berger S. , Lauriks W. , Depollier C. , Aristégui C. , Chapelon J.-Y.
Published: May 2003

An ultrasonic reflectivity method is proposed for measuring porosity and tortuosity of porous materials having a rigid frame. Porosity is the relative fraction by volume of the air contained within a material. Tortuosity is a geometrical parameter which intervenes in the description of the inertial effects between the fluid filled the porous material and its structure at high frequency range. It is generally easy to evaluate the tortuosity from transmitted waves, this is not the case for porosity because of its weak sensitivity in transmitted mode. The proposed method is based on measurement of reflected wave by the first interface of a slab of rigid porous material. This method is obtained from a temporal model of the direct and inverse scattering problems for the propagation of transient ultrasonic waves in a homogeneous isotropic slab of porous material having a rigid frame [Z. E. A. Fellah, M. Fellah, W. Lauriks, and C. Depollier, J. Acoust. Soc. Am. 113, 61 (2003)]. Reflection and transmission scattering operators for a slab of porous material are derived from the responses of the medium to an incident acoustic pulse at oblique incidence. The porosity and tortuosity are determined simultaneously from the measurements of reflected waves at two oblique incidence angles. Experimental and numerical validation results of this method are presented.
Microseism and infrasound generation by cyclones
Authors: Bowen Samuel P. , Richard Jacques C. , Mancini Jay D. , Fessatidis Vassilios , Crooker Benjamin
Published: May 2003

A two-dimensional cylindrical shear-flow wave theory for the generation of microseisms and infrasound by hurricanes and cyclones is developed as a linearized theory paralleling the seminal work by Longuet-Higgins which was limited to one-dimensional plane waves. Both theories are based on Bernoulli’s principle. A little appreciated consequence of the Bernoulli principle is that surface gravity waves induce a time dependent pressure on the sea floor through a vertical column of water. A significant difference exists between microseisms detected at the bottom of each column and seismic signals radiated into the crust through coherence over a region of the sea floor. The dominant measured frequency of radiated microseisms is matched by this new theory for seismic data gathered at the Fordham Seismic Station both for a hurricane and a mid-latitude cyclone in 1998. Implications for Bernoulli’s principle and this cylindrical stress flow theory on observations in the literature are also discussed.
Pulse register phonation in Diana monkey alarm calls
Authors: Riede Tobias , Zuberbühler Klaus
Published: May 2003

The adult male Diana monkeys (Cercopithecus diana) produce predator-specific alarm calls in response to two of their predators, the crowned eagles and the leopards. The acoustic structure of these alarm calls is remarkable for a number of theoretical and empirical reasons. First, although pulsed phonation has been described in a variety of mammalian vocalizations, very little is known about the underlying production mechanism. Second, Diana monkey alarm calls are based almost exclusively on this vocal production mechanism to an extent that has never been documented in mammalian vocal behavior. Finally, the Diana monkeys’ pulsed phonation strongly resembles the pulse register in human speech, where fundamental frequency is mainly controlled by subglottal pressure. Here, we report the results of a detailed acoustic analysis to investigate the production mechanism of Diana monkey alarm calls. Within calls, we found a positive correlation between the fundamental frequency and the pulse amplitude, suggesting that both humans and monkeys control fundamental frequency by subglottal pressure. While in humans pulsed phonation is usually considered pathological or artificial, male Diana monkeys rely exclusively on pulsed phonation, suggesting a functional adaptation. Moreover, we were unable to document any nonlinear phenomena, despite the fact that they occur frequently in the vocal repertoire of humans and nonhumans, further suggesting that the very robust Diana monkey pulse production mechanism has evolved for a particular functional purpose. We discuss the implications of these findings for the structural evolution of Diana monkey alarm calls and suggest that the restricted variability in fundamental frequency and robustness of the source signal gave rise to the formant patterns observed in Diana monkey alarm calls, used to convey predator information.
The relation of lung volume initiation to selected acoustic properties of speech
Authors: Watson Peter J. , Ciccia Angela H. , Weismer Gary
Published: May 2003

This study examined the relationship of speech breathing to other elements of speech production. It was hypothesized that initiating speech from different lung volumes would have an effect on different elements of the acoustic output. It was postulated that effects may be brought about by mechanical interaction as well as a dispersion of effort to mechanically unlinked elements of speech production, such as articulatory behavior. To this end, selected acoustic variables were studied in eight young healthy women who initiated speech from low, typical, and high lung volume levels. The acoustic variables studied were selected because they have been shown to be sensitive indicators of speech production performance. It was found that with increasing lung volume initiation levels, average sound pressure level, average fundamental frequency, and declination rate of fundamental frequency increased. It was also observed that vowel space was significantly smaller during low lung volume initiation levels relative to typical lung volume initiation levels. Vowel space reduction is discussed relative to “gaining down.”
Using links between speech perception and speech production to evaluate different acoustic metrics: A preliminary report
Authors: Newman Rochelle S.
Published: May 2003

This paper examines whether correlations between speech perception and speech production exist, and, if so, whether they might provide a way of evaluating different acoustic metrics. The cues listeners use for many phonemic distinctions are not known, often because many different acoustic cues are highly correlated with one another, making it difficult to distinguish among them. Perception-production correlations may provide a new means of doing so. In the present paper, correlations were examined between acoustic measures taken on listeners’ perceptual prototypes for a given speech category and on their average production of members of that category. Significant correlations were found for VOT among stop consonants, and for spectral peaks (but not centroids or skewness) for voiceless fricatives. These results suggest that correlations between speech perception and production may provide a methodology for evaluating different proposed acoustic metrics.
Correlations between acoustic properties and bone density in bovine cancellous bone from 0.5 to 2 MHz
Authors: Lee Kang Il , Roh Heui-Seol , Yoon Suk Wang
Published: May 2003

Correlations between acoustic properties and bone density were investigated in the 12 defatted bovine cancellous bone specimens in vitro. Speed of sound (SOS) and broadband ultrasonic attenuation (BUA) were measured in three different frequency bandwidths from 0.5 to 2 MHz using three matched pairs of transducers with the center frequencies of 1, 2.25, and 3.5 MHz. The relative orientation between ultrasonic beam and bone specimen was the mediolateral (ML) direction of the bovine tibia. SOS shows significant linear positive correlation with apparent density for all three pairs of transducers. However, BUA shows relatively weak correlation with apparent density. SOS and BUA are only weakly correlated with each other. The linear combination of SOS and BUA in a multiple regression model leads to a significant improvement in predicting apparent density. The correlations among SOS, BUA, and bone density can be effectively and clearly represented in the three-dimensional space by the multiple regression model. These results suggest that the frequency range up to 1.5 MHz and the multiple regression model in the three-dimensional space can be useful in the osteoporosis diagnosis.
Gestural overlap of stop-consonant sequences: Evidence from analysis and synthesis
Authors: Zhao Sherry , Stevens Kenneth N.
Published: May 2003

This study uses an analysis-by-synthesis approach to discover possible principles governing the coordination of oral and laryngeal articulators in the production of English stop-consonant sequences. Individual recordings were made of two male and two female native American-English speakers reading phrases which include voiced and voiceless stop consonants in word-initial (V♯CV) and word-final (VC♯V) positions, as well as in VC♯CV stop–stop consonant sequences. Articulatory timing estimates were made based on analyzing acoustic data including formant movements, closure durations, release bursts, and spectrum shape at low frequencies. Based on the gestural estimates, the same consonant sequences were generated using HLsyn, a quasiarticulatory synthesizer. The synthetic utterances were acoustically and perceptually compared to the actual utterances in order to verify and refine the articulatory timing estimates from which possible principles could be derived. Preliminary results agree with earlier findings of more overlapping of oral gestures in sequences with front-to-back order of place of articulation than those with back-to-front order [Chitoran, Goldstein, and Byrd, Lab. Phonology 7, 419–448 (2002)]. Furthermore, overlapping of laryngeal gestures is suggested by the smaller acoustical loss at the glottis in vowels after voiced–voiceless sequences than voiceless–voiceless sequences.
Relation between peak pressure and spectrum for small caliber muzzle report and ballistic shock
Authors: White Michael J. , Pater Larry L.
Published: May 2003

It might seem impossible to reconstruct the peak signal level of an impulsive sound from its spectrum if the phase information is not kept. Without such an estimate, sound propagation assessments made in the frequency domain are at a disadvantage when it is the peak level that is desired. From a set of experimental measurements of small caliber firearm noise at Camp Guernsey, muzzle report and ballistic shock signals were time-gated to obtain 1/3-octave sound exposure spectra and peak levels from each signal. The rms bandwidth of each signal was determined by summing the squared frequency, weighted by the relative 1/3-octave band exposures. Finally, a relation was presumed only such that the sound exposure was equal to a product of squared peak pressure, the reciprocal of the rms bandwidth, and an undetermined constant. Constants equal to 3 dB for muzzle blast and 3.5 dB for ballistic shock fit the data sets, with approximately 3 dB standard error. Greater error tended to coincide with smaller measured bandwidths, by overestimating the peak level.
High-frequency seafloor studies using buried directional receivers
Authors: Lyons Anthony P. , Osler John C.
Published: May 2003

Knowledge of the acoustic arrival angle can be useful for studying penetration mechanisms and for estimating sediment sound speed dispersion. The arrival angle of acoustic energy penetrating the sediment water interface, however, is difficult to measure using sparsely distributed pressure sensors. The arrival angle, as well as amplitude information, can be unambiguously obtained by measuring particle motion with directional receivers. An experiment was conducted off of Elba Island in 1999 to assess the feasibility of using of high-frequency accelerometers to measure directionality. Measurements of acoustic penetration onto a sandy seafloor were obtained over wide frequency range (2.5 to 29 kHz) using the accelerometers. Results from the experiment demonstrating this novel measurement technique will be presented, as will issues concerning accelerometer design and calibration.
Statistical evidence that musical universals derive from the acoustic characteristics of human speech
Authors: Schwartz David , Howe Catharine , Purves Dale
Published: May 2003

Listeners of all ages and societies produce a similar consonance ordering of chromatic scale tone combinations. Despite intense interest in this perceptual phenomenon over several millennia, it has no generally accepted explanation in physical, psychological, or physiological terms. Here we show that the musical universal of consonance ordering can be understood in terms of the statistical relationship between a pattern of sound pressure at the ear and the possible generative sources of the acoustic energy pattern. Since human speech is the principal naturally occurring source of tone-evoking (i.e., periodic) sound energy for human listeners, we obtained normalized spectra from more than 100000 recorded speech segments. The probability distribution of amplitude/frequency combinations derived from these spectra predicts both the fundamental frequency ratios that define the chromatic scale intervals and the consonance ordering of chromatic scale tone combinations. We suggest that these observations reveal the statistical character of the perceptual process by which the auditory system guides biologically successful behavior in response to inherently ambiguous sound stimuli.
Audible-frequency methods in assessment of soft tissues
Authors: Sarvazyan Armen P.
Published: May 2003

One of the reasons why MHz-range ultrasonic compressional waves have become a powerful tool for medical diagnostics is that their wavelength is of the order of a millimeter, adequate for imaging an anatomical structural. Other types of acoustic waves that can be generated in soft tissue, such as shear and surface waves, are two–three orders of magnitude slower and, respectively, have a millimeter range wavelength in the audible-frequency range. These waves can be effectively used for imaging and soft tissue characterization in terms of the shear elasticity modulus. This paper is a summary of the studies on applications of the surface and shear waves for diagnostic assessment of soft tissue elasticity and dynamic viscosity performed by the author and his coworkers over three decades. A number of techniques for measuring shear elastic moduli of soft tissue using both wave propagation and the acoustic impedance methods are described. Audible-frequency methods and devices for assessment of skin in dermatological applications, for the detection of breast cancer, for imaging of brain and muscle tissues are analyzed. Various embodiments of the Shear Wave Imaging modality are considered. The reasons for a limited success of the audible-frequency methods despite their great potential in ultrasonic medical imaging and diagnostics are discussed.
Signal Transduction by MAP Kinases: Regulation by Phosphorylation-Dependent Switches
Authors: Whitmarsh Alan J. , Davis Roger J.
Published: May 2003

The kinases of mitogen-activated protein (MAP) kinase cascades transmit signals through sequential phosphorylation and activation of the enzymes. However, recent evidence indicates that protein-protein interactions between the kinases themselves or with substrates or other components are also a critical means of regulation. Whitmarsh and Davis summarize these findings with emphasis on new evidence from yeast that, when phosphorylated, a MAP kinase kinase actually switches from a negative regulator that binds to and inhibits its target MAP kinase to a positive regulator of that same enzyme.
MEETING REPORT: Signaling Themes Shared Between Peptide and Steroid Hormones at the Plasma MembraneA review of the meeting "Steroid Receptor Family Members in the Plasma Membrane: The Proteins and their Functions," FASEB Summer Research Conference, Copper Mountain, Colorado, 8 through 13 August 1999
Authors: Watson Cheryl S.
Published: May 2003

Steroid hormone receptors are primarily thought of as transcriptional regulators that are activated by ligand binding. However, there is also evidence for "nongenomic" actions of steroid hormones. Cheryl Watson summarizes a recent meeting that brought together researchers exploring these rapid effects of steroid hormones that occur in the absence of new protein synthesis. Current evidence for the existence of membrane steroid receptors, which may or may not be related to the well-known nuclear receptors, is discussed.
Tangled Webs: Evidence of Cross-Talk Between c-Raf-1 and Akt
Authors: Jun Toni , Gjoerup Ole , Roberts Thomas M.
Published: May 2003

The apparent cross-communication that can occur between different cell signaling pathways indicates that some signaling mechanisms may be more complex than originally envisaged. Jun
et al.
discuss recent studies suggesting that two signaling pathways that can be activated by the same growth factor receptor, the Ras-Raf pathway and the phosphatidylinositol 3-kinase (PI3K)–Akt (protein kinase B) pathway, can integrate with each other to generate a particular response, depending on the cell type and the stage of cell differentiation.
Growth Factors and Gene Expression: Fresh Insights from Arrays
Authors: Hill Caroline S. , Treisman Richard
Published: May 2003

Gene array technology allows researchers to evaluate patterns of gene expression at a genome-wide level. Two recent papers have applied this powerful technique to characterize how gene expression is changed in response to growth factors and mitogens. The studies focus on two important questions concerning specificity in signal transduction. First, are the multiple signaling pathways activated by a single growth factor receptor used to activate gene expression, and if so, do these pathways act combinatorially? Second, how does the initial genetic response of a cell to a signal stimulus relate to the patterns of gene expression that determine that cell's ultimate biological response to the stimulus? Hill and Treisman take a critical look at what these array technology studies tell us concerning these questions and discuss technical issues arising from them.
Getting Directions: Axon Guidance Receptors Find the Way
Authors: Merz David C. , Culotti Joseph G.
Published: May 2003

As neuronal growth cones explore the terrain, their migration is dictated by guidance cues in the environment. Some cues are considered bifunctional because they can elicit an attractive or repulsive response. However, the cytoplasmic tails of guidance cue receptors appear to also control how growth cones respond. Merz and Culotti discuss recent evidence that the cytoplasmic domains of the DCC and UNC-5 family of receptors control the response of neurons to netrins, and propose a model for mechanisms by which axon guidance receptors might function.
The NF-κB Activation Pathway:	A Paradigm in Information Transfer from Membrane to Nucleus
Authors: Rothwarf David M. , Karin Michael
Published: May 2003

Nuclear factor kappa B (NF-κB)/Rel proteins are dimeric, sequence-specific transcription factors involved in the activation of an exceptionally large number of genes in response to inflammation, viral and bacterial infections, and other stressful situations requiring rapid reprogramming of gene expression. In unstimulated cells, NF-κB is sequestered in an inactive form in the cytoplasm bound to inhibitory IκB proteins. Stimulation leads to the rapid phosphorylation, ubiquitinylation, and ultimately proteolytic degradation of IκB, which frees NF-κB to translocate to the nucleus and activate the transcription of its target genes. The multisubunit IκB kinase (IKK) responsible for the inducible phosphorylation of IκB appears to be the initial point of convergence for most stimuli that activate NF-κB. IKK contains two catalytic subunits, IKKα and IKKβ, both of which phosphorylate IκB at sites phosphorylated in vivo. Gene knockout studies indicate that IKKβ is primarily responsible for the activation of NF-κB in response to proinflammatory stimuli, whereas IKKα is essential for keratinocyte differentiation. The activity of IKK is regulated by phosphorylation. IKK contains a regulatory subunit, IKKγ, which is critical for activation of IKK and is postulated to serve as a recognition site for upstream activators. When phosphorylated, the IKK recognition site on IκBα serves as a specific recognition site for the κ-TrCP-like component of a Skp1-Cullin-F-box-type E3 ubiquitin-protein ligase. A variety of other signaling events, including phosphorylation of NF-κB, phosphorylation of IKK, new synthesis of IκBs, and the processing of NF-κB precursors provide mechanisms of modulating the amount and duration of NF-κB activity.
BOOK REVIEW: Intracellular Calcium--They Think It's All Over! It Isn't Quite Yet!A review of the book

Calcium as a Cellular Regulator

Edited by Ernesto Carafoli and Claude Klee  Oxford University Press, New York, 1999. 658 pp. $150.00 U.S. £105.00 U.K. ISBN 0-19-509421-2.
Authors: Campbell Anthony K.
Published: May 2003

Calcium is one of the key regulators of numerous intracellular processes, and literature related to this topic dates back to
the late 1800s. A recent book, filled with contributions from experts in the field of calcium analysis and function, summarizes
many of the roles of intracellular calcium and calcium regulation in various cell types. Anthony Campbell reviews this
compendium and explains why both experts and nonexperts in the calcium field may find this book useful, depending on what
they are looking for.
All Good Things Must Come to an End: How Is Notch Signaling Turned off?
Authors: Kopan Raphael
Published: May 2003

Turning off signaling pathways can be just as important for proper biological regulation as turning them on. The Notch signaling pathway controls development of the nervous system in
Drosophila
. Proteolysis of Notch appears to initiate signaling, but further proteolysis may also terminate signals from this pathway. Kopan discusses mechanisms that limit signaling by Notch, including recent evidence that degradation of specifically targeted proteins by the proteasome is required.
EGF Receptor Transactivation Mediated by the Proteolytic Production of EGF-like Agonists
Authors: Carpenter Graham
Published: May 2003

The epidermal growth factor (EGF) receptor is activated not only by EGF-like ligands, but also by stimuli that do not directly act on the receptor, including agonists of G protein–coupled receptors and certain environmental stresses such as ionizing radiation. Carpenter discusses two reports that indicate EGF receptor activation by such heterologous stimuli may occur through the action of proteases that release cell surface EGF-like growth factor precursors. This mechanism of EGF receptor transactivation appears to involve the generation of soluble agonists.
Environmental-Dependent Acceleration of a Developmental Switch: The Floral Transition
Authors: Simpson Gordon G. , Dean Caroline
Published: May 2003

The transition from vegetative growth to reproductive growth in plants in which flowers are produced requires the activation of specific genes. Simpson and Dean discuss two recent reports that characterize the
FLOWERING LOCUS T
(
FT
) gene in
Arabidopsis
, which is part of the floral transition pathway. Unlike many of the known genes that initiate flower production, the
FT
gene appears to encode a membrane-associated protein that could function in signaling from the cell surface.
Crossing Smads
Authors: Wrana Jeffrey L.
Published: May 2003

The transforming growth factor–β (TGF-β) superfamily of secreted polypeptide growth factors exerts extensive control over all aspects of development and homeostasis, and components of this pathway are often mutated in cancers and in several hereditary disorders. Apart from TGF-β, the superfamily also includes the activins and the bone morphogenetic proteins. These factors signal through heteromeric complexes of type II and type I serine-threonine kinase receptors, which activate the downstream Smad signal transduction pathway. Three classes of Smads have been defined: the receptor-regulated Smads (R-Smads), the common-mediator Smads (co-Smads), and the antagonistic or inhibitory Smads (I-Smads). Receptor complexes activate the Smad pathway by interacting and phosphorylating specific R-Smads. Phosphorylation of the R-Smads causes dissociation from the receptor and induces assembly into complexes with Smad4, a co-Smad. This heteromeric complex then translocates into the nucleus, where the Smads function as transcriptional comodulators by recruiting coactivators or corepressors to Smad DNA binding partners. Thus, Smads transmit signals directly from the receptor kinase into the nucleus. Crosstalk between Smads and other signaling pathways occurs both in the cytosol and in the nucleus. In the cytosol, Smad translocation might be inhibited by mitogen-activated protein kinase–dependent phosphorylation, whereas in the nucleus Smads interact with a number of transcription factors that themselves are primary targets of other signaling pathways. Furthermore, Smad-dependent regulation of these targets often requires input from the primary signaling pathway. In these examples, Smad signaling may represent a secondary signal that modifies the output of the primary pathway. Consequently, the transcriptional response to TGF-β family ligands may be dependent on what other signals are being received by the cell. Crosstalk may thus provide one explanation for the long-standing observation that the biological response to TGF-β is often dependent on the extracellular environment of the cell.
RIPping Notch Apart: A New Role for Endocytosis in Signal Transduction?
Authors: Krämer Helmut
Published: May 2003

Notch proteins are receptors that are important in mediating several developmental processes. Notch receptors are activated upon binding transmembrane ligands, the DSL proteins. Notch is cleaved at several sites and activation of Notch leads to the cleavage of the intracellular domain, which then is translocated to the nucleus and regulates the transcription of target genes. Krämer discusses how binding of Notch to the DSL ligand, Delta, leads to cleavage and trans-endocytosis of the Notch extracellular domain into the Delta-expressing cell. This trans-endocytosis event contributes to the cleavage and release of the active Notch intracellular domain. The Perspective is accompanied by a
movie
illustrating the trans-endocytosis of Notch.
Signal Transduction: Stuck with FYVE Domains
Authors: Corvera Silvia
Published: May 2003

The FYVE domain is a protein motif that allows the interaction of cytosolic proteins with membranes containing the lipid phosphatidylinositol 3-phosphate. Structural information about FYVE domains has come from two crystal structures and NMR analysis. Corvera discusses how these structures differ and what they tell us about how proteins with FYVE domains interact with biological membranes. The Perspective also addresses how proteins with FYVE domains and protein internalization are involved in signal transduction.
Use of Mass Spectrometry to Study Signaling Pathways
Authors: Pandey Akhilesh , Andersen Jens S. , Mann Matthias
Published: May 2003

Activation of cells by extracellular stimuli, such as growth factors, initiates a cascade of events involving posttranslational modifications, including phosphorylation, formation of protein complexes, and induction or repression of gene expression. Traditionally, genetic methods or specific biochemical assays have been used to identify molecules involved in signaling pathways. Lately, mass spectrometry, combined with elegant biochemical approaches, has become a powerful tool for identifying proteins and posttranslational modifications. With this protocol, we hope to bridge the gap between the biochemical and molecular aspects of signal transduction pathways and the mass spectrometric tools and techniques that are available to study them. We provide methods for large-scale cell culture and immunoprecipitation of tyrosine-phosphorylated proteins, silver staining of gels, trypsin digests, and protein identification by matrix-assisted laser desorption/ionization (MALDI) mass spectrometry and nanoelectrospray tandem mass spectrometry. We discuss the special requirements for the identification of phosphorylation sites in proteins by mass spectrometry. We describe enrichment of phosphopeptides from unseparated peptide mixtures by immobilized metal affinity column (IMAC) and the use of phosphatases to identify phosphorylated peptides. We also discuss specialized methods, such as precursor ion scanning in the negative mode and direct sequencing of phosphopeptides in the positive mode. Our goal is to provide detailed methods in use today for proteomic applications in general and for receptor-mediated signaling pathways in particular.
Measurement of Molecular Interactions in Living Cells by Fluorescence Resonance Energy Transfer Between Variants of the Green Fluorescent Protein
Authors: Siegel Richard M. , Chan Francis Ka-Ming , Zacharias David A. , Swofford Ruth , Holmes Kevin L. , Tsien Roger Y. , Lenardo Michael J.
Published: May 2003

Many signal transduction pathways operate through oligomerization of proteins into multi-subunit complexes. Although biochemical assays can identify potential protein-protein interactions, studying these interactions in living cells is more challenging. Fluorescence resonance energy transfer (FRET) has been used as a "spectroscopic ruler" to measure molecular proximity, but these methods have been limited by the need for chemical labeling of target proteins or labeled antibodies. We present methods for examining interactions between target proteins molecularly fused to cyan and yellow variants of the green fluorescent protein (GFP) by FRET in living cells. Flow cytometric and microscope-based methods are described that have been applied to a variety of interacting proteins.
Multiple Calcium Stores: Separate but Interacting
Authors: Lee Hon Cheung
Published: May 2003

Multiple mechanisms exist for increasing the concentration of intracellular calcium. This Perspective by Lee is one in a series on intracellular calcium release mechanisms and focuses on the calcium store operated by nicotinic acid adenine dinucleotide phosphate (NAADP). The characterization of the NAADP-operated calcium store as separate from the inositol trisphosphate (IP
3
)-operated and cyclic ADP-ribose (cADPR)-operated calcium stores is discussed. Lee also addresses the role of NAADP in regulating intracellular calcium fluctuations during fertilization and hormonal activation of pancreatic acinar cells.
Regulation of Mitogen-Activated Protein Kinase Signaling Networks by G Protein-Coupled Receptors
Authors: Gutkind J. Silvio
Published: May 2003

The family of receptors that transmit signals through the activation of heterotrimeric GTP-binding proteins (G proteins) constitutes the largest group of cell surface proteins involved in signal transduction. These receptors participate in a broad range of important biological functions and are implicated in a number of disease states. More than half of all drugs currently available influence G protein-coupled receptors (GPCRs). These receptors affect the generation of small molecules that act as intracellular mediators or second messengers, and can regulate a highly interconnected network of biochemical routes controlling the activity of several members of the mitogen-activated protein kinase (MAPK) superfamily. They include extracellular signal-regulated kinase 1 (ERK1) and ERK2 (or p44
MAPK
and p42
MAPK
), c-Jun NH
2
-terminal kinases (JNKs), ERK5 (or BMK), and p38 MAPKs, including p38α (or CSBP-1), p38β, p38γ (or SAPK3 or ERK6), and p38δ?(or SAPK4). This review will focus on the molecular mechanisms by which GPCRs signal to the nucleus through this intricate network of second messenger-generating systems and MAPK signaling pathways, thereby affecting the expression of genes whose products influence many biological processes, including normal and aberrant cell growth.
Cyclic ADP Ribose as a Calcium-Mobilizing Messenger
Authors: Galione Antony , Churchill Grant C.
Published: May 2003

This Perspective by Galione and Churchill is one in a series on intracellular calcium release mechanisms. The authors review the evidence for cyclic adenosine diphosphate ribose (cADPR) being a second messenger involved in regulating intracellular calcium. In addition, the physiological stimuli and responses mediated by cADPR are discussed. The Perspective is accompanied by a movie showing a calcium wave triggered by cADPR.
Steroid Receptor and Molecular Chaperone Encounters in the Nucleus
Authors: DeFranco Donald B. , Csermely Peter
Published: May 2003

Steroid hormone receptors interact with several different molecular chaperones. DeFranco and Csermely discuss how the molecular chaperones p23 and Hsp90 may serve to regulate the activity of the ligand-bound steroid receptors within the nucleus. The authors hypothesize that these chaperone proteins may have a proactive role in promoting recycling of receptors once they have interacted with chromatin and in allowing rebinding of ligand once the receptors have been recycled.
The Informational Content of Gradients of Wnt Proteins
Authors: Martinez Arias Alfonso
Published: May 2003

This perspective tackles the issues facing developmental biologists and cell biologists regarding how the molecular mechanisms for specifying cell fate are defined. This Perspective focuses on members of the Wnt family. The author proposes that Wnt proteins may act as stabilizing signals for earlier inductive events in certain systems, for example, in
Caenorhabditis elegans
during the migration of two neurons and in
Drosophila melanogaster
during the patterning of the wing.
The IAP Proteins: Caspase Inhibitors and Beyond
Authors: Richter Bettina W. M. , Duckett Colin S.
Published: May 2003

Apoptosis, or programmed cell death, occurs as an outcome of signals that direct cells to perish. Whether initiated by specifically activated receptors or induced through viral infection, apoptosis is an important means by which organisms maintain health and homeostasis. The apoptotic pathway uses several regulatory proteins that prevent uncontrolled cell death, which would be detrimental to the organism. Richter and Duckett review the recently discovered and characterized inhibitors of apoptosis proteins (IAPs). Not surprisingly, IAPs were first identified in viruses that were able to subvert apoptosis in infected cells. Evidence exists suggesting that, in addition to inhibiting apoptosis, IAPs are involved in signal transduction and cell cycle regulation. Richter and Duckett also review other recent observations indicating that some IAPs may have roles in protein ubiquitination. Although the various roles of the IAPs are beginning to be uncovered, new questions arise about the breadth of their functions and the proteins to which IAPs bind.
Neuronal Signal Transduction Pathways: Wasteland or the Promised Land?
Review and commentary on
Cerebral Signal Transduction: From First to Fourth Messengers
, edited by Maarten E. A. Reith.  The Humana Press, Totowa, NJ, 2000. 440 pp. $125.00
Authors: Roth Bryan L.
Published: May 2003

Proteins used in signal transduction pathways are commonly found in different cell types and organs. However, specific proteins whose expression is highly restricted are also utilized for allowing discrete responsiveness to signals that are otherwise ignored by other cells. How the brain uses common and specific signal proteins for communication within and beyond the cerebrum has been an area of intense study. A new book concentrates on the signaling that occurs in the brain under normal and pathological conditions--memory, apoptosis, neurodegeneration, depression, and drug dependence--and is filled with chapters written by experts in neurobiology and neurophysiology. Bryan Roth reviews the book and discusses in detail several chapters that may lead to promising future research.
Tales from the Crypt: Evidence for Heptahelical Receptor Signaling in the Endocytic Pathway
Authors: Whistler Jennifer , Beattie Eric , von Zastrow Mark
Published: May 2003

In certain circumstances, internalized receptors are able to continue signaling after endocytosis. Whistler
et al
. discuss how the interaction of heterotrimeric GTP-binding protein (G protein)-coupled receptors with arrestins and their subsequent endocytosis may contribute to activation of the mitogen-activated protein kinase pathway. This Perspective delves into the role that scaffolds may play in organizing and specifying downstream signaling events that occur after internalization of G protein-coupled receptors.
Dissecting Intracellular Signaling Pathways with Membrane-Permeable Peptides
Authors: Chang Mike S. S. , Tam James P. , Sanders-Bush Elaine
Published: May 2003

Peptides can be designed that mimic protein interaction motifs and thus, can be used to specifically and selectively block particular steps in signal transduction cascades where protein interactions have been previously identified. This protocol describes methods to synthesize peptides coupled to a membrane-permeable sequence (MPS), designed from the signal sequence of Kaposi fibroblast growth factor, which has been previously shown to translocate covalently attached cargo peptides across the cell membrane. To increase efficiency, yield, and versatility in the preparation of these membrane-permeable peptides, a modular synthesis strategy based on two unprotected peptide segments was designed. The modular synthesis strategy allows the MPS and functional peptides to be synthesized separately. In this manner, the functional domain of a peptide or protein, synthesized by traditional fluoroenylmethyloxy-carbonyl (Fmoc) chemistry or derived from recombinant expression, may be purchased commercially to expedite synthesis. Subsequently, the MPS domain may be attached to any functional domain using a one-step conjugation reaction. This protocol provides detailed methods for peptide synthesis, activation of the MPS, and the subsequent conjugation protocol.
MAP Kinases and the Regulation of Nuclear Receptors
Authors: Kyriakis John M.
Published: May 2003

The activity of nuclear receptors or ligand-activated transcription factors can be regulated both positively and negatively by signals transduced through mitogen-activated protein kinase (MAPK) signaling cascades. Kyriakis discusses how cross talk between MAPK signaling and nuclear receptor signaling occurs and the effect this cross talk has on nuclear receptor function.
Nuclear Lipid Signaling
Authors: Irvine Robin
Published: May 2003

There is now abundant evidence for the existence of phospholipids in the nucleus that resist washing of nuclei with detergents. These lipids are apparently not in the nuclear envelope, but are actually within the nucleus, presumably not in a bilayer membrane but instead forming proteolipid complexes with unidentified proteins. This review discusses the experimental evidence that attempts to explain their existence. Among these nuclear lipids are the polyphosphoinositol lipids which, together with the enzymes that synthesize them, form an intranuclear phospholipase C (PI-PLC) signaling system that generates diacylglycerol and inositol-1,4,5-trisphosphate [Ins(1,4,5)
P
3
]. The isoforms of PI-PLC that are involved in this signaling system, and how they are regulated, are not yet clear. Generation of diacylglycerol within the nucleus is believed to recruit protein kinase C to the nucleus to phosphorylate intranuclear proteins. Generation of Ins(1,4,5)
P
3
may mobilize Ca
2+
from the space between the nuclear membranes and thus increase nucleoplasmic Ca
2+
. Less well understood are an increasing number of variations and complications on the "simple" idea of a PI-PLC system. These include, all apparently within the nucleus: (i) two separate routes of synthesis of phosphatidylinositol-4,5-bisphosphate; (ii) two different sources of diacylglycerol, one being from the PI-PLC pathway, and the other probably from phosphatidylcholine; (iii) several different isoforms of PKC translocating to the nuclei; (iv) increases in activity of the PI-PLC pathway at two different points in the cell cycle; (v) a pathway of phosphorylation of Ins(1,4,5)
P
3
, which may have several functions, including a role in the transfer of messenger RNA (mRNA) out of the nucleus; and (vi) the possible existence of other lipid signaling pathways that may include sphingolipids, phospholipase A2, and 3-phosphorylated inositol lipids.
Control of T Helper Cell Differentiation--in Search of Master Genes
Authors: Dong Chen , Flavell Richard A.
Published: May 2003

Naïve T helper (T
H
0) cells can differentiate into one of two distinct populations: T
H
1 and T
H
2. Each population is characterized by the expression of specific cytokines and their ability to participate in cell-mediated or humoral immune responses. Recent efforts at identifying the molecular mechanisms through which T
H
0 cells become T
H
1 or T
H
2 cells have been promising. A number of transcription factors, including GATA-3 and T-bet, have been identified that promote the differentiation of T
H
0 cells and the maintenance of the differentiated cell phenotype. Dong and Flavell review recent findings on proteins that control the fate of T
H
0 differentiation, whether by promotion or inhibition, and discuss the role of epigenesis in the differentiation process.
Conformational Display: A Role for Switch Polymorphism in the Superfamily of Regulatory GTPases
Authors: Sprang Stephen R.
Published: May 2003

Regulating signal transduction is serious business. If signals are improperly controlled, aberrant proliferation or inappropriate cell death may result. The Ras superfamily of small guanosine triphosphatases (GTPases) and the heterotrimeric G proteins require GTP binding into their active sites for subsequent activation. Hydrolysis of GTP to GDP precedes, and is a requirement for, inactivation. However, the changes in conformation that accompany GTP or GDP binding are now becoming fully appreciated. Sprang discusses the importance of conformation in the activation of GTPases and heterotrimeric G proteins, and the possibility that these proteins exist in several different conformations. Thus, rather than a simplistic on/off two-conformation model, these signaling proteins exist in several differing conformations that may be related to activation and effector protein binding.
IP
3
Receptor-Operated Calcium Entry
Authors: Mikoshiba Katsuhiko , Hattori Mitsuharu
Published: May 2003

This Perspective by Mikoshiba and Hattori is the third in a series on cellular calcium release mechanisms. The authors describe the regulated release of calcium from intracellular stores by the inositol 1,4,5 trisphosphate receptor (IP
3
R) and the relationship of this release mechanism to calcium influx from the extracellular milieu through store-operated calcium channels. They discuss a model proposing that intracellular and plasma membrane calcium channels are functionally and physically coupled.
Biolistic Transfection of Neurons
Authors: McAllister A. Kimberley
Published: May 2003

One method used to study gene function is through the manipulation of gene expression by transfecting cells with DNA constructs designed to overexpress or knock out particular proteins. Unfortunately, transfection of cells and tissues remains a rate-limiting step for molecular studies in many fields, especially neurobiology. Conventional transfection techniques are of limited effectiveness, particularly in intact tissue. This protocol describes an alternative method for transfecting cells, called biolistics. Biolistics is a physical method of transfection in which target tissue is bombarded with DNA-coated gold particles using a "gene gun," produced by Bio-Rad Laboratories. Cells penetrated by gold particles have a high likelihood of becoming transfected. Because biolistic transfection relies only on the physical penetration of a cell's membrane, it is possible to use biolistics to transfect cells that are resistant to transfection by other methods, such as neurons in primary culture and organotypic slice cultures. This protocol provides information on optimizing the biolistic parameters for transfecting neurons in both of these preparations. Once optimized, biolistic transfection is a reliable and efficient method for studying gene function in many cell types, especially postmitotic neurons.
Hydrogen Peroxide: A Key Messenger That Modulates Protein Phosphorylation Through Cysteine Oxidation
Authors: Rhee Sue Goo , Bae Yun Soo , Lee Seung-Rock , Kwon Jaeyul
Published: May 2003

Ligand-receptor interactions can generate the production of hydrogen peroxide (H
2
O
2
) in cells, the implications of which are becoming appreciated. Fluctuations in H
2
O
2
levels can affect the intracellular activity of key signaling components including protein kinases and protein phosphatases. Rhee
et al
. discuss recent findings on the role of H
2
O
2
in signal transduction. Specifically, H
2
O
2
appears to oxidize active site cysteines in phosphatases, thereby inactivating them. H
2
O
2
also can activate protein kinases; however, although the mechanism of activation for some kinases appears to be similar to that of phosphatase inactivation (cysteine oxidation), it is unclear how H
2
O
2
promotes increased activation of other kinases. Thus, the higher levels of intracellular phosphoproteins observed in cells most likely occur because of the concomitant inhibition of protein phosphatases and activation of protein kinases.
Regulation of Cx43 Gap Junctions: The Gatekeeper and the Password
Authors: Hossain Mohammad Z. , Boynton Alton L.
Published: May 2003

Gap junctions are regulatable pores that connect the cytoplasms of neighboring cells. Hossain and Boynton focus on connexin 43 gap junctions and their regulation by changing the phosphorylation status of the COOH-terminal domain of connexin 43 or by altering protein-protein interactions in this region. The COOH-terminal domain of connexin 43 appears to be a key player in regulating gap junctional communication (GJC) because many divergent signals in many different cell types modify this domain to inhibit GJC.
Receptor Cross Talk: Ligand-Gated Ion Channels Start to Communicate
Authors: Brandon Nicholas J. , Moss Stephen J.
Published: May 2003

Evidence is mounting for a direct mode of interaction between neurotransmitter receptors that modulates the activity of the interacting proteins. Brandon and Moss discuss two examples in which direct interactions between neurotransmitter receptors appear to regulate the receptors independently of the signal transduction cascades they activate. This type of interaction has important implications for rapid modulation of receptor function and the integration of multiple signals at a synapse.