bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of Structural Genomics: Expectations and Outcomes
Authors: Chandonia John-Marc , Brenner Steven E.
Published: January 2006

Structural genomics (SG) projects aim to expand our structural knowledge of biological macromolecules while lowering the average costs of structure determination. We quantitatively analyzed the novelty, cost, and impact of structures solved by SG centers, and we contrast these results with traditional structural biology. The first structure identified in a protein family enables inference of the fold and of ancient relationships to other proteins; in the year ending 31 January 2005, about half of such structures were solved at a SG center rather than in a traditional laboratory. Furthermore, the cost of solving a structure at the most efficient SG center in the United States has dropped to one-quarter of the estimated cost of solving a structure by traditional methods. However, the efficiency of the top structural biology laboratories—even though they work on very challenging structures—is comparable to that of SG centers; moreover, traditional structural biology papers are cited significantly more often, suggesting greater current impact.
Light Scattered by Air
Authors: Van Hecke Gerald R.
Published: January 2006

Sky in a Bottle
.
By Peter Pesic
. MIT Press, Cambridge, MA, 2005. 270 pp. $24.95, £16.95. ISBN 0-262-16234-2.

The author weaves together observations and considerations of light, color, atmosphere, and vision to chart the development of our understanding of why Earth's sky is blue.
A Molecular Framework for Plant Regeneration
Authors: Xu Jian , Hofhuis Hugo , Heidstra Renze , Sauer Michael , Friml Jiří , Scheres Ben
Published: January 2006

Plants and some animals have a profound capacity to regenerate organs from adult tissues. Molecular mechanisms for regeneration have, however, been largely unexplored. Here we investigate a local regeneration response in Arabidopsis roots. Laser-induced wounding disrupts the flow of auxin—a cell-fate–instructive plant hormone—in root tips, and we demonstrate that resulting cell-fate changes require the PLETHORA, SHORTROOT, and SCARECROW transcription factors. These transcription factors regulate the expression and polar position of PIN auxin efflux–facilitating membrane proteins to reconstitute auxin transport in renewed root tips.

Thus, a regeneration mechanism using embryonic root stem-cell patterning factors first responds to and subsequently stabilizes a new hormone distribution.
Chromosomes Can Congress to the Metaphase Plate Before Biorientation
Authors: Kapoor Tarun M. , Lampson Michael A. , Hergert Polla , Cameron Lisa , Cimini Daniela , Salmon E. D. , McEwen Bruce F. , Khodjakov Alexey
Published: January 2006

The stable propagation of genetic material during cell division depends on the congression of chromosomes to the spindle equator before the cell initiates anaphase. It is generally assumed that congression requires that chromosomes are connected to the opposite poles of the bipolar spindle (“bioriented”). In mammalian cells, we found that chromosomes can congress before becoming bioriented. By combining the use of reversible chemical inhibitors, live-cell light microscopy, and correlative electron microscopy, we found that monooriented chromosomes could glide toward the spindle equator alongside kinetochore fibers attached to other already bioriented chromosomes. This congression mechanism depended on the kinetochore-associated, plus end–directed microtubule motor CENP-E (kinesin-7).
South-Seeking Magnetotactic Bacteria in the Northern Hemisphere
Authors: Simmons Sheri L. , Bazylinski Dennis A. , Edwards Katrina J.
Published: January 2006

Magnetotactic bacteria contain membrane-bound intracellular iron crystals (magnetosomes) and respond to magnetic fields. Polar magnetotactic bacteria in vertical chemical gradients are thought to respond to high oxygen levels by swimming downward into areas with low or no oxygen (toward geomagnetic north in the Northern Hemisphere and geomagnetic south in the Southern Hemisphere). We identified populations of polar magnetotactic bacteria in the Northern Hemisphere that respond to high oxygen levels by swimming toward geomagnetic south, the opposite of all previously reported magnetotactic behavior. The percentage of magnetotactic bacteria with south polarity in the environment is positively correlated with higher redox potential. The coexistence of magnetotactic bacteria with opposing polarities in the same redox environment conflicts with current models of the adaptive value of magnetotaxis.
The Cellular Localization Pattern of Varicella-Zoster Virus ORF29p Is Influenced by Proteasome-Mediated Degradation
Authors: Stallings Christina L. , Duigou Gregory J. , Gershon Anne A. , Gershon Michael D. , Silverstein Saul J.
Published: January 2006

Varicella-zoster virus (VZV) open reading frame 29 (ORF29) encodes a single-stranded DNA binding protein. During lytic infection, ORF29p is localized primarily to infected-cell nuclei, whereas during latency it appears in the cytoplasm of infected neurons. Following reactivation, ORF29p accumulates in the nucleus. In this report, we analyze the cellular localization patterns of ORF29p during VZV infection and during autonomous expression. Our results demonstrate that ORF29p is excluded from the nucleus in a cell-type-specific manner and that its cellular localization pattern may be altered by subsequent expression of VZV ORF61p or herpes simplex virus type 1 ICP0. In these cases, ORF61p and ICP0 induce nuclear accumulation of ORF29p in cell lines where it normally remains cytoplasmic. One cellular system utilized by ICP0 to influence protein abundance is the proteasome degradation pathway. Inhibition of the 26S proteasome, but not heat shock treatment, resulted in accumulation of ORF29p in the nucleus, similar to the effect of ICP0 expression. Immunofluorescence microscopy and pulse-chase experiments reveal that stabilization of ORF29p correlates with its nuclear accumulation and is dependent on a functional nuclear localization signal. ORF29p nuclear translocation in cultured enteric neurons and cells derived from an astrocytoma is reversible, as the protein's distribution and stability revert to the previous states when the proteasomal activity is restored. Thus, stabilization of ORF29p leads to its nuclear accumulation. Although proteasome inhibition induces ORF29p nuclear accumulation, this is not sufficient to reactivate latent VZV or target the immediate-early protein ORF62p to the nucleus in cultured guinea pig enteric neurons.
A Comparative Study of Adsorption of Aliphatic Amines at a Gold Electrode
Authors: Łuczak Teresa
Published: January 2006

Adsorption of aliphatic amines (C1-C4) at the gold electrode was studied by tensammetry. It has been established that the experimental dependence between the gold surface coverage (Θ) and the bulk amine concentration (cA) fits satisfactorily both by the Frumkin and Flory-Huggins isotherms. The standard Gibbs energy of adsorption, ∆G°ad at Emax for Θ < 0.8 has been found to increase in the order methylamine < ethylamine < propylamine < butylamine. This is rationalised in terms of surface-adsorbate, adsorbate-adsorbate and adsorbate-solvent interactions.
Cleavage of the Epimines of 1,6-Anhydrohexoses with Fluoride Anion
Authors: Kroutil Jiří , Jeništová Klára
Published: January 2006

Aziridine ring cleavage reactions of fiveN-nosylepimines (2-6) having D-talo, D-galacto, D-manno, and D-alloconfigurations with potassium hydrogendifluoride under various reaction conditions have been performed. The cleavage regioselectively afforded diaxial isomers of vicinal amino-fluoro derivatives of 1,6-anhydro-β-D-gluco- and mannopyranose7-11in 51-94% yields. Removal of 2-nitrobenzenesulfonyl protecting group with benzenethiol has been attempted in the case of compound10.
Conformational Preferences of Ethyl 2,3-Dideoxy-3-[(α-D-glucopyranosyl)methyl]-β-L- and -D-arabino-hexopyranosides
Authors: Vích Ondřej , Kniežo Ladislav , Dvořáková Hana , Raich Ivan , Valenta Štěpán
Published: January 2006

Conformational behavior of twoC-disaccharides, containing D-glucopyranose moiety at the non-reducing end and L- or D-2-deoxy-arabino-hexopyranose moiety at the reducing end, has been studied using MM3 calculations and NMR experiments. The obtained results show that the conformational preference around theC-glycosidic bond is the same in both compounds and corresponds with theexo-anomeric effect. On the other hand, both compounds differ markedly in the conformational arrangement around theC-aglycone bond where the population of conformers is controlled by 1,3-diaxial-like interactions.
COSMOLOGICAL SOLUTION FROM D-BRANE MOTION IN NS5-BRANES BACKGROUND
Authors: YAVARTANOO HOSSEIN
Published: January 2006

We study dynamics of a D3-brane propagating in the vicinity of k coincident NS5 branes. We show that when gs is small, there exists a regime in which dynamics of the D-brane is governed by Dirac–Born–Infeld action while higher order derivative in the expansion cannot be neglected. This leads to a restriction on how fast scalar field may roll. We analyze the motion of a rolling scalar field in this regime, and extend the analysis to cosmological systems obtained by coupling this type of field theory to four-dimensional gravity. It also leads to some FRW cosmologies, some of which are related to those obtained with tachyon matter.
BOUNDARY STATES IN THE NAPPI–WITTEN MODEL
Authors: HIKIDA YASUAKI
Published: January 2006

We investigate D-branes in the Nappi–Witten model. Classically symmetric D-branes are classified by the (twisted) conjugacy classes of the Nappi–Witten group, which specify the geometry of the corresponding D -branes. Quantum description of the D-branes is given by boundary states, and we need one-point functions of closed strings to construct the boundary states. We compute the one-point functions solving conformal bootstrap constraints, and check that the classical limit of the boundary states reproduces the geometry of D-branes.
Pin–Hole Luminosity Monitor with Feedback
Authors: NOREM JAMES H. , SPENCER JAMES E.
Published: January 2006

Previously, the generalized luminosity [Formula: see text] was defined and calculated for all incident channels based on an NLC e+e- design. Alternatives were then considered to improve the differing beam-beam effects in the e-e-, eγ and γγ channels. Regardless of the channel, there was a large flux of outgoing, high energy photons that were produced from the beam-beam interaction e.g. beamstrahlung that needs to be disposed of and whose flux depended on [Formula: see text]. One approach to this problem is to consider it a resource and attempt to take advantage of it by disposing of these straight–ahead photons in more useful ways than simply dumping them. While there are many options for monitoring the luminosity, any method that allows feedback and optimization in real time and in a non-intercepting and non-interfering way during normal data taking is extremely important – especially if it provides other capabilities such as high resolution tuning of spot sizes and can be used for all incident channels without essential modifications to their setup. Our "pin-hole" camera appears to be such a device if it can be made to work with high energy photons in ways that are compatible with the many other constraints and demands on space around the interaction region. The basis for using this method is that it has, in principle, the inherent resolution and bandwidth to monitor the very small spot sizes and their stabilities that are required for very high, integrated luminosity. While there are many possible, simultaneous uses of these outgoing photon beams, we limit our discussion to a single, blind, proof-of-principle experiment that was done on the FFTB line at SLAC to certify the concept of a camera obscura for high energy photons.
Luminosity, Energy and Polarization Studies for the Linear Collider: Comparing e+e- and e-e- for NLC and TESLA
Authors: Woods M. , Moffeit K. C. , Raubenheimer T. O. , Seryi A. , Sramek C. , Florimonte A.
Published: January 2006

We present results from luminosity, energy and polarization studies at a future Linear Collider. We compare e+e- and e-e- modes of operation and consider both NLC and TESLA beam parameter specifications at a center-of-mass energy of 500 GeV. Realistic colliding beam distributions are used, which include dynamic effects of the beam transport from the Damping Rings to the Interaction Point. Beam-beam deflections scans and their impact for beam-based feedbacks are considered. A transverse kink instability is studied, including its impact on determining the luminosity-weighted center-of-mass energy. Polarimetry in the extraction line from the IP is presented, including results on beam distributions at the Compton IP and at the Compton detector.
Store-operated Ca2+ entry modulates sarcoplasmic reticulum Ca2+ loading in neonatal rabbit cardiac ventricular myocytes
Authors: Huang Jingbo , van Breemen Casey , Kuo Kuo-Hsing , Hove-Madsen Leif , Tibbits Glen F.
Published: January 2006

Store-operated Ca2+ entry (SOCE), which is Ca2+ entry triggered by the depletion of intracellular Ca2+ stores, has been observed in many cell types, but only recently has it been suggested to occur in cardiomyocytes. In the present study, we have demonstrated SOCE-dependent sarcoplasmic reticulum (SR) Ca2+ loading (loadSR) that was not altered by inhibition of L-type Ca2+ channels, reverse mode Na+/Ca2+ exchange (NCX), or nonselective cation channels. In contrast, lowering the extracellular [Ca2+] to 0 mM or adding either 0.5 mM Zn2+ or the putative store-operated channel (SOC) inhibitor SKF-96365 (100 μM) inhibited loadSR at rest. Interestingly, inhibition of forward mode NCX with 30 μM KB-R7943 stimulated SOCE significantly and resulted in enhanced loadSR. In addition, manipulation of the extracellular and intracellular Na+ concentrations further demonstrated the modulatory role of NCX in SOCE-mediated SR Ca2+ loading. Although there is little knowledge of SOCE in cardiomyocytes, the present results suggest that this mechanism, together with NCX, may play an important role in SR Ca2+ homeostasis. The data reported herein also imply the presence of microdomains unique to the neonatal cardiomyocyte. These findings may be of particular importance during open heart surgery in neonates, in which uncontrolled SOCE could lead to SR Ca2+ overload and arrhythmogenesis.
Disulfonic stilbene permeation and block of the anion channel from the sarcoplasmic reticulum of rabbit skeletal muscle
Authors: Laver Derek R. , Bradley Katherine M.
Published: January 2006

Block of a sarcoplasmic reticulum anion channel (SCl channel) by disulfonic stilbene derivatives [DIDS, dibenzamidostilbene-2,2′-disulfonic acid (DBDS), and 4,4′-dinitrostilbene-2,2′-disulfonic acid (DNDS)] was investigated in planar bilayers using SO[Formula: see text] as the conducting ion. All molecules caused reversible voltage-dependent channel block when applied to either side of the membrane. DIDS also produced nonreversible channel block from both sides within 1–3 min. Reversible inhibition was associated with a decrease in channel open probability and mean open duration but not with any change in channel conductance. The half inhibitory concentration for cis- and trans-inhibition had voltage dependencies with minima of 190 nM and 33 μM for DBDS and 3.4 and 55 μM for DNDS. Our data supports a permeant blocker mechanism, in which stilbenes block SCl channels by lodging in the permeation pathway, where they may dissociate to either side of the membrane and thus permeate the channel. The stilbenes acted as open channel blockers where the binding of a single molecule occludes the channel. DBDS and DNDS, from opposite sides of the membrane, competed for common sites on the channel. Dissociation rates exhibited biphasic voltage dependence, indicative of two dissociation processes associated with ion movement in opposite directions within the trans-membrane electric field. The kinetics of DNDS and DBDS inhibition predict that there are two stilbene sites in the channel that are separated by 14–24 Å and that the pore constriction is ∼10 Å in diameter.
α7β1-Integrin regulates mechanotransduction and prevents skeletal muscle injury
Authors: Boppart Marni D. , Burkin Dean J. , Kaufman Stephen J.
Published: January 2006

α7β1-Integrin links laminin in the extracellular matrix with the cell cytoskeleton and therein mediates transduction of mechanical forces into chemical signals. Muscle contraction and stretching ex vivo result in activation of intracellular signaling molecules that are integral to postexercise injury responses. Because α7β1-integrin stabilizes muscle and provides communication between the matrix and cytoskeleton, the role of this integrin in exercise-induced cell signaling and skeletal muscle damage was assessed in wild-type and transgenic mice overexpressing the α7BX2 chain. We report here that increasing α7β1-integrin inhibits phosphorylation of molecules associated with muscle damage, including the mitogen-activated protein kinases (JNK, p38, and ERK), following downhill running. Likewise, activation of molecules associated with hypertrophy (AKT, mTOR, and p70S6k) was diminished in mice overexpressing integrin. While exercise resulted in Evans blue dye-positive fibers, an index of muscle damage, increased integrin protected mice from injury. Moreover, exercise leads to an increase in α7β1 protein. These experiments provide the first evidence that α7β1-integrin is a negative regulator of mechanotransduction in vivo and provides resistance to exercise-induced muscle damage.
Implication of CO inactivation on myoglobin function
Authors: Chung Youngran , Huang Shih-Jwo , Glabe Alan , Jue Thomas
Published: January 2006

Myoglobin (Mb) has a purported role in facilitating O2 diffusion in tissue, especially as cellular Po2 drops or the respiration demand increases. Inhibiting Mb with CO under conditions that accentuate the facilitated diffusion role should then elicit a significant physiological response. In one set of experiments, the perfused myocardium received buffer with decreasing Po2 (225, 129, and 64 mmHg). Intracellular Po2 declined, as reflected in the 1H NMR Val E11 signal of MbO2 (67%, 32%, and 18%). The addition of 6% CO further reduced the available MbO2 (11%, 9%, and 7%), as evidenced by the decline of the MbO2 Val E11 signal intensity at −2.76 ppm. In a second set of experiments, electrical stimulation increased the heart rate (300, 450, and 540 beats/min) and correspondingly the O2 consumption rate (MV̇o2). Intracellular Po2 also declined, as reflected in the slight drop in the MbO2 signal (100%, 96%, and 82%). MV̇o2 increased (100%, 114%, 165%). The addition of 3% CO in the stimulated hearts further decreased the available MbO2 (46%, 44%, and 29%). In all cases, CO inactivation of Mb does not induce any change in the respiration rate, contractile function, and high-energy phosphate levels. Moreover, the MbCO/MbO2 partition coefficient shifts dramatically from its in vitro value during hypoxia and increased work. The observation suggests a modulation of an intracellular O2 gradient. Overall, the experimental observations provide no evidence of a facilitated diffusion role for Mb in perfused myocardium and implicate a physiologically responsive intracellular O2 gradient.
PVD9902, a porcine vas deferens epithelial cell line that exhibits neurotransmitter-stimulated anion secretion and expresses numerous HCO3− transporters
Authors: Carlin Ryan W. , Sedlacek Roger L. , Quesnell Rebecca R. , Pierucci-Alves Fernando , Grieger David M. , Schultz Bruce D.
Published: January 2006

Epithelial ion transport disorders, including cystic fibrosis, adversely affect male reproductive function by nonobstructive mechanisms and by obstruction of the distal duct. Continuous cell lines that could be used to define ion transport mechanisms in this tissue are not readily available. In the present study, porcine vas deferens epithelial cells were isolated by standard techniques, and the cells spontaneously immortalized to form a porcine vas deferens epithelial cell line that we have titled PVD9902. Cells were maintained in continuous culture for >4 yr and 200 passages in a typical growth medium. Frozen stocks were generated, and thawed cells exhibited growth characteristics indistinguishable from their nonfrozen counterparts. Molecular and immunocytochemical studies confirmed the origin and epithelial nature of these cells. When seeded on permeable supports, PVD9902 cells grew as electrically tight (>6,000 Ω·cm2), confluent monolayers that responded to forskolin with an increase in short-circuit current ( Isc; 8 ± 1 μA/cm2) that required Cl−, HCO3−, and Na+, and was partially sensitive to bumetanide. mRNA was expressed for a number of anion transporters, including CFTR, electrogenic Na+-HCO3− cotransporter 1b (NBCe1b), downregulated in adenoma, pendrin, and Cl−/formate exchanger. Both forskolin and isoproterenol caused an increase in cellular cAMP levels. In addition, PVD9902 cell monolayers responded to physiological (i.e., adenosine, norepinephrine) and pharmacological [i.e., 5′-( N-ethylcarboxamido)adenosine, isoproterenol] agonists with increases in Isc. Unlike their freshly isolated counterparts, however, PVD9902 cells did not respond to glucocorticoid exposure with an increase in amiloride-sensitive Isc. RT-PCR analysis revealed the presence of both glucocorticoid and mineralocorticoid receptor mRNA as well as mRNA for the α- and γ-subunits of the epithelia Na+ channels (α- and γ-ENaC), but not β-ENaC. Nonetheless, PVD9902 cells recapitulated most observations in freshly isolated cells and thus represent a powerful new tool to characterize mechanisms that contribute to male reproductive function.
Protein kinase D protects against oxidative stress-induced intestinal epithelial cell injury via Rho/ROK/PKC-δ pathway activation
Authors: Song Jun , Li Jing , Lulla Andrew , Evers B. Mark , Chung Dai H.
Published: January 2006

Protein kinase D (PKD) is a novel protein serine kinase that has recently been implicated in diverse cellular functions, including apoptosis and cell proliferation. The purpose of our present study was 1) to define the activation of PKD in intestinal epithelial cells treated with H2O2, an agent that induces oxidative stress, and 2) to delineate the upstream signaling mechanisms mediating the activation of PKD. We found that the activation of PKD is induced by H2O2 in both a dose- and time-dependent fashion. PKD phosphorylation was attenuated by rottlerin, a selective PKC-δ inhibitor, and by small interfering RNA (siRNA) directed against PKC-δ, suggesting the regulation of PKD activity by upstream PKC-δ. Activation of PKD was also blocked by a Rho kinase (ROK)-specific inhibitor, Y-27632, as well as by C3, a Rho protein inhibitor, demonstrating that the Rho/ROK pathway also mediates PKD activity in intestinal cells. In addition, H2O2-induced PKC-δ phosphorylation was inhibited by C3 treatment, further suggesting that PKC-δ is downstream of Rho/ROK. Interestingly, H2O2-induced intestinal cell apoptosis was enhanced by PKD siRNA. Together, these results clearly demonstrate that oxidative stress induces PKD activation in intestinal epithelial cells and that this activation is regulated by upstream PKC-δ and Rho/ROK pathways. Importantly, our findings suggest that PKD activation protects intestinal epithelial cells from oxidative stress-induced apoptosis. These findings have potential clinical implications for intestinal injury associated with oxidative stress (e.g., necrotizing enterocolitis in infants).
Functional link between TNF biosynthesis and CaM-dependent activation of inducible nitric oxide synthase in RAW 264.7 macrophages
Authors: Weber Thomas J. , Smallwood Heather S. , Kathmann Loel E. , Markillie Lye Meng , Squier Thomas C. , Thrall Brian D.
Published: January 2006

Inflammatory responses stimulated by bacterial endotoxin LPS involve Ca2+-mediated signaling, yet the cellular sensors that determine cell fate in response to LPS remain poorly understood. We report that exposure of RAW 264.7 macrophage-like cells to LPS induces a rapid increase in CaM abundance, which is associated with the modulation of the inflammatory response. Increases in CaM abundance precede nuclear localization of key transcription factors (i.e., NF-κB p65 subunit, phospho-c-Jun, Sp1) and subsequent increases in the proinflammatory cytokine TNF-α and inducible nitric oxide synthase (iNOS). Cellular apoptosis after LPS challenge is blocked upon inhibition of iNOS activity using the pharmacological inhibitor 1400W. LPS-mediated iNOS expression and apoptosis also were inhibited by siRNA-mediated silencing of TNF induction, indicating TNF induction both precedes and is necessary for subsequent regulation of iNOS expression. Increasing the level of cellular CaM by stable transfection results in reductions in LPS-induced expression of TNF and iNOS, along with reduced activation of their transcriptional regulators and concomitant protection against apoptosis. Thus the level of CaM available for Ca2+-dependent signaling regulation plays a key role in determining the expression of the proinflammatory and proapoptotic cascade during cellular activation by LPS. These results indicate a previously unrecognized central role for CaM in maintaining cellular homeostasis in response to LPS such that, under resting conditions, cellular concentrations of CaM are sufficient to inhibit the biosynthesis of proinflammatory mediators associated with macrophage activation. Although CaM and iNOS protein levels are coordinately increased as part of the oxidative burst, limiting cellular concentrations of CaM due to association with iNOS (and other high-affinity binders) commit the cell to an unchecked inflammatory cascade leading to apoptosis.
Reports of the length dependence of fatigue are greatly exaggerated
Authors: MacNaughton M. B. , MacIntosh B. R.
Published: January 2006

Relative force depression associated with muscle fatigue is reported to be greater when assessed at short vs. long muscle lengths. This appears to be due to a rightward shift in the force-length relationship. This rightward shift may be caused by stretch of in-series structures, making sarcomere lengths shorter at any given muscle length. Submaximal force-length relationships (twitch, double pulse, 50 Hz) were evaluated before and after repetitive contractions (50 Hz, 300 ms, 1/s) in an in situ preparation of the rat medial gastrocnemius muscle. In some experiments, fascicle lengths were measured with sonomicrometry. Before repetitive stimulation, fascicle lengths were 11.3 ± 0.8, 12.8 ± 0.9, and 14.4 ± 1.2 mm at lengths corresponding to −3.6, 0, and 3.6 mm where 0 is a reference length that corresponds with maximal active force for double-pulse stimulation. After repetitive stimulation, there was no change in fascicle lengths; these lengths were 11.4 ± 0.8, 12.6 ± 0.9, and 14.2 ± 1.2 mm. The length dependence of fatigue was, therefore, not due to a stretch of in-series structures. Interestingly, the rightward shift that was evident when active force was calculated in the traditional way (subtraction of the passive force measured before contraction) was not seen when active force was calculated by subtracting the passive force that was associated with the fascicle length reached at the peak of the contraction. This calculation is based on the assumption that passive force decreases as the fascicles shorten during a fixed-end contraction. This alternative calculation revealed similar postfatigue absolute active force depression at all lengths. In relative terms, a length dependence of fatigue was still evident, but this was greatly diminished compared with that observed when active force was calculated with the traditional method.
Basal Ganglia Orient Eyes to Reward
Authors: Hikosaka Okihide , Nakamura Kae , Nakahara Hiroyuki
Published: January 2006

Expectation of reward motivates our behaviors and influences our decisions. Indeed, neuronal activity in many brain areas is modulated by expected reward. However, it is still unclear where and how the reward-dependent modulation of neuronal activity occurs and how the reward-modulated signal is transformed into motor outputs. Recent studies suggest an important role of the basal ganglia. Sensorimotor/cognitive activities of neurons in the basal ganglia are strongly modulated by expected reward. Through their abundant outputs to the brain stem motor areas and the thalamocortical circuits, the basal ganglia appear capable of producing body movements based on expected reward. A good behavioral measure to test this hypothesis is saccadic eye movement because its brain stem mechanism has been extensively studied. Studies from our laboratory suggest that the basal ganglia play a key role in guiding the gaze to the location where reward is available. Neurons in the caudate nucleus and the substantia nigra pars reticulata are extremely sensitive to the positional difference in expected reward, which leads to a bias in excitability between the superior colliculi such that the saccade to the to-be-rewarded position occurs more quickly. It is suggested that the reward modulation occurs in the caudate where cortical inputs carrying spatial signals and dopaminergic inputs carrying reward-related signals are integrated. These data support a specific form of reinforcement learning theories, but also suggest further refinement of the theory.
Comparison of Midbrain and Thalamic Space-Specific Neurons in Barn Owls
Authors: Pérez María Lucía , Peña José Luis
Published: January 2006

Spatial receptive fields of neurons in the auditory pathway of the barn owl result from the sensitivity to combinations of interaural time (ITD) and level differences across stimulus frequency. Both the forebrain and tectum of the owl contain such neurons. The neural pathways, which lead to the forebrain and tectal representations of auditory space, separate before the midbrain map of auditory space is synthesized. The first nuclei that belong exclusively to either the forebrain or the tectal pathways are the nucleus ovoidalis (Ov) and the external nucleus of the inferior colliculus (ICx), respectively. Both receive projections from the lateral shell subdivision of the inferior colliculus but are not interconnected. Previous studies indicate that the owl's tectal representation of auditory space is different from those found in the owl's forebrain and the mammalian brain. We addressed the question of whether the computation of spatial cues in both pathways is the same by comparing the ITD tuning of Ov and ICx neurons. Unlike in ICx, the relationship between frequency and ITD tuning had not been studied in single Ov units. In contrast to the conspicuous frequency independent ITD tuning of space-specific neurons of ICx, ITD selectivity varied with frequency in Ov. We also observed that the spatially tuned neurons of Ov respond to lower frequencies and are more broadly tuned to ITD than in ICx. Thus there are differences in the integration of frequency and ITD in the two sound-localization pathways. Thalamic neurons integrate spatial information not only within a broader frequency band but also across ITD channels.
Cortico-Cerebellar Coherence During a Precision Grip Task in the Monkey
Authors: Soteropoulos Demetris S. , Baker Stuart N.
Published: January 2006

We studied the synchronization of single units in macaque deep cerebellar nuclei (DCN) with local field potentials (LFPs) in primary motor cortex (M1) bilaterally during performance of a precision grip task. Analysis was restricted to periods of steady holding, during which M1 oscillations are known to be strongest. Significant coherence between DCN units and M1 LFP oscillations bilaterally was seen at ∼10–40 Hz (contralateral M1: 25/87 units; ipsilateral: 9/87 units). Averaged coherence between DCN units and contralateral M1 LFP showed a prominent ∼17-Hz coherence peak and an average phase of approximately −π/2 radians, implying that the DCN units fired around the time of maximal depolarization of M1 cells. The lack of a time delay between DCN and M1 activity suggests that the cerebellum and cortex may form a pair of phase coupled oscillators. Although coherence values were low (mean peak coherence, 0.018), we used a computational model to show that this probably resulted from the nonlinearity of spike generating mechanisms within the DCN. DCN unit discharge and DCN LFPs also showed significant coherence at ∼10–40 Hz, with similarly low magnitude (mean peak coherence, 0.012). The average coherence phase was −2.5 radians for the 6- to 14-Hz range and −1.1 radians for the 17- to 41-Hz range, suggesting different frequency-specific underlying mechanisms. Finally, 4/40 pairs of simultaneously recorded DCN units showed a significant cross-correlation peak, and 16/40 pairs showed significant unit-unit coherence. The extensive oscillatory synchronization observed between cerebellum and motor cortex may have functional importance in sensorimotor processing.
Chemical and Cold Sensitivity of Two Distinct Populations of TRPM8-Expressing Somatosensory Neurons
Authors: Xing Hong , Ling Jennifer , Chen Meng , Gu Jianguo G.
Published: January 2006

The cold- and menthol-sensing TRPM8 receptor has been proposed to have both nonnociceptive and nociceptive functions. However, one puzzle is how this single type of receptor may be used by somatosensory neurons to code for two distinct sensory modalities. Using acutely dissociated rat dorsal root ganglion (DRG) neurons without culture, we show that TRPM8 receptors are expressed on two distinct classes of somatosensory neurons. One class is sensitive to menthol and features nonnociceptive neuron properties, including capsaicin-insensitive, ATP-insensitive, transient acid response, and expression of TTX-sensitive sodium channels only. This class is termed the menthol-sensitive/capsaicin-insensitive neuron class (MS/CIS). The other class is also sensitive to menthol but has characteristics of nociceptive neurons including capsaicin-sensitive, ATP-sensitive, prolonged acid response, and expression of both TTX-sensitive and TTX-resistant sodium channels. This class is termed the menthol-sensitive/capsaicin-sensitive neuron class (MS/CS). The presence of these two neuron classes in acutely dissociated DRG neurons support the idea that TRPM8 receptors can have both nonnociceptive and nociceptive functions. While both neuron classes respond to menthol and cold, the overall responses induced by menthol and cold are significantly larger in MS/CIS than in MS/CS neurons. Furthermore, low concentrations of menthol produce strong selection of the MS/CIS neuron population over the MS/CS neuron population. On the other hand, the population selection becomes weaker with higher concentrations of menthol. TRPM8 current density shows significant higher in MS/CIS neurons than in MS/CS neurons, suggesting different expression levels of TRPM8 receptors between the two neuron populations, and this difference may provide a mean of selective activation of MS/CIS neurons at low stimulation intensity.
Chemoprevention of Human Prostate Cancer by Oral Administration of Green Tea Catechins in Volunteers with High-Grade Prostate Intraepithelial Neoplasia: A Preliminary Report from a One-Year Proof-of-Principle Study
Authors: Bettuzzi Saverio , Brausi Maurizio , Rizzi Federica , Castagnetti Giovanni , Peracchia Giancarlo , Corti Arnaldo
Published: January 2006

Green tea catechins (GTCs) proved to be effective in inhibiting cancer growth in several experimental models. Recent studies showed that 30% of men with high-grade prostate intraepithelial neoplasia (HG-PIN) would develop prostate cancer (CaP) within 1 year after repeated biopsy. This prompted us to do a proof-of-principle clinical trial to assess the safety and efficacy of GTCs for the chemoprevention of CaP in HG-PIN volunteers. The purity and content of GTCs preparations were assessed by high-performance liquid chromatography [(−)-epigallocathechin, 5.5%; (−)-epicatechin, 12.24%; (−)-epigallocatechin-3-gallate, 51.88%; (−)-epicatechin-3-gallate, 6.12%; total GTCs, 75.7%; caffeine, <1%]. Sixty volunteers with HG-PIN, who were made aware of the study details, agreed to sign an informed consent form and were enrolled in this double-blind, placebo-controlled study. Daily treatment consisted of three GTCs capsules, 200 mg each (total 600 mg/d). After 1 year, only one tumor was diagnosed among the 30 GTCs-treated men (incidence, ∼3%), whereas nine cancers were found among the 30 placebo-treated men (incidence, 30%). Total prostate-specific antigen did not change significantly between the two arms, but GTCs-treated men showed values constantly lower with respect to placebo-treated ones. International Prostate Symptom Score and quality of life scores of GTCs-treated men with coexistent benign prostate hyperplasia improved, reaching statistical significance in the case of International Prostate Symptom Scores. No significant side effects or adverse effects were documented. To our knowledge, this is the first study showing that GTCs are safe and very effective for treating premalignant lesions before CaP develops. As a secondary observation, administration of GTCs also reduced lower urinary tract symptoms, suggesting that these compounds might also be of help for treating the symptoms of benign prostate hyperplasia. (Cancer Res 2006; 66(2): 1234-40)
Angiopoietin 2 Induces Glioma Cell Invasion by Stimulating Matrix Metalloprotease 2 Expression through the αvβ1 Integrin and Focal Adhesion Kinase Signaling Pathway
Authors: Hu Bo , Jarzynka Michael J. , Guo Ping , Imanishi Yorihisha , Schlaepfer David D. , Cheng Shi-Yuan
Published: January 2006

Accumulating evidence reveals a significant correlation between angiopoietin 2 (Ang2) expression and tumor invasion and metastasis in various human cancers, but the major focus of recent studies has been on the angiogenic effects of Ang2. We recently reported that Ang2-stimulated glioma cell invasion results from the up-regulation and activation of matrix metalloprotease 2 (MMP-2) in tumor cells. In this study, we identify a novel mechanism by which Ang2 stimulates MMP-2 expression leading to glioma cell invasion. We show that Ang2 interacts with αvβ1 integrin in Tie2-deficient human glioma cells, activating focal adhesion kinase (FAK), p130Cas, extracellular signal–regulated protein kinase (ERK) 1/2, and c-jun NH2-terminal kinase (JNK) and substantially enhancing MMP-2 expression and secretion. The Ang2/αvβ1 integrin signaling pathway was attenuated by functional inhibition of β1 and αv integrins, FAK, p130Cas, ERK1/2, and JNK. Furthermore, expression of a negative regulator of FAK, FAK-related nonkinase, by U87MG/Ang2–expressing glioma xenografts suppressed Ang2-induced MMP-2 expression and glioma cell infiltration in the murine brain. These data establish a functional link between Ang2 interaction with αvβ1 integrin and glioma cell invasion through the FAK/p130Cas/ERK1/2 and JNK-mediated signaling pathway. (Cancer Res 2006; 66(2): 775-83)
Differential Requirement for DNA Methyltransferase 1 in Maintaining Human Cancer Cell Gene Promoter Hypermethylation
Authors: Ting Angela H. , Jair Kam-wing , Schuebel Kornel E. , Baylin Stephen B.
Published: January 2006

Previous work has shown that DNA hypermethylation of tumor suppressor genes in colorectal cancer cells may be maintained in the absence of the major mammalian methyltransferase, DNA methyltransferase 1 (DNMT1). In an effort to dissect the dependency on DNMT1 to maintain such hypermethylation in different cancer types, we performed a systematic analysis of depletion of DNMT1 in colorectal (SW48), bladder (T24), and breast (T47D) cancer cells by DNMT1-specific small hairpin RNA (shRNA) targeting. We show that although DNMT1-deficient SW48 and T24 cells exhibited no observable growth defects and were able to maintain promoter hypermethylation, DNMT1-deficient T47D breast cells failed to form comparable numbers of colonies when stably selected for the incorporation of the DNMT1-specific shRNA expression vector, suggesting a growth defect with reduced levels of DNMT1. Further treatment of T47D cells with transient transfection of small interfering RNA targeting DNMT1 revealed that severely DNMT1-deficient T47D cells could not fully maintain promoter hypermethylation, and gene silencing was partially reversed at two of the three assayed loci. These observations suggest that human cancer cells may differ in their reliance on DNMT1 for maintaining DNA methylation. (Cancer Res 2006; 66(2): 729-35)
PTEN Autoregulates Its Expression by Stabilization of p53 in a Phosphatase-Independent Manner
Authors: Tang Yufang , Eng Charis
Published: January 2006

PTEN (phosphatase and tensin homologue, deleted on chromosome 10) is a tumor suppressor with dual phosphatase activity and mutations of its gene, PTEN, have been associated with many sporadic cancers and heritable neoplasia syndromes, including Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome. However, accumulating evidence now shows that PTEN may have novel functions other than as a phosphatase. In the present study, we show that PTEN is able to autoregulate its expression through the stabilization of another tumor suppressor p53. We further show that PTEN enhances p53 transactivation, a relationship that requires the interaction between PTEN and p53 and is PTEN phosphatase independent. We show that cell lines from Cowden syndrome and Bannayan-Riley-Ruvalcaba syndrome patients with germ line PTEN promoter mutations in the vicinity of the p53-binding motifs have altered p53 regulation. This seems to be due to reduced PTEN stability and decreased PTEN-p53 interactions. Our data provide clues to better understand the regulation of PTEN expression and the possible mechanisms of the pathogenesis of the subset of Cowden syndrome individuals with germ line promoter variation and who lack mutations in the PTEN coding region and splice sites. Importantly, this mechanism also holds for those sporadic tumors that lack intragenic mutations but have hemizygous deletion of PTEN, which includes the promoter region as manifested by loss-of-heterozygosity of 10q markers. The importance of our observations is underlined by the broad spectrum of neoplasias that harbor somatic PTEN or p53 alterations, or both. (Cancer Res 2006; 66(2): 736-42)
TheIn vivoExpansion Rate of Properly Stimulated Transferred CD8+ T Cells Exceeds That of an Aggressively Growing Mouse Tumor
Authors: Hwang Leroy N. , Yu Zhiya , Palmer Douglas C. , Restifo Nicholas P.
Published: January 2006

It has been hypothesized that rapidly dividing tumor cells can outpace adoptively transferred antitumor lymphocytes when tumors are large. However, this hypothesis is at odds with clinical observations indicating that bulky tumors can be destroyed by small numbers of adoptively transferred antitumor T cells. We sought to measure the relative growth rates of T cells and tumor cells in a model using transgenic CD8+ T cells specific for the gp10025-33 H-2Db epitope (called pmel-1) to treat large, well-established s.c. B16 melanoma. We tested the effect of the immunization using an altered peptide ligand vaccine alone or in combination with interleukin-2 (IL-2) by analyzing the kinetics of T-cell expansion using direct enumeration. We found that pmel-1 T cells proliferated explosively during a 5-day period following transfer. Calculations from net changes in population suggest that, at the peak of cell division, pmel-1 T cells divide at a rate of 5.3 hours per cell division, which was much faster than B16 tumor cells during optimal growth (24.9 hours per cell division). These results clearly indicate that the notion of a kinetic “race” between the tumor and the lymphocyte is no contest when adoptively transferred cells are stimulated with immunization and IL-2. When appropriately stimulated, tumor-reactive T-cell expansion can far exceed the growth of even an aggressively growing mouse tumor. (Cancer Res 2006; 66(2): 1132-8)
The Gene Expression Program of Prostate Fibroblast Senescence Modulates Neoplastic Epithelial Cell Proliferation through Paracrine Mechanisms
Authors: Bavik Claes , Coleman Ilsa , Dean James P. , Knudsen Beatrice , Plymate Steven , Nelson Peter S.
Published: January 2006

The greatest risk factor for developing carcinoma of the prostate is advanced age. Potential molecular and physiologic contributors to the frequency of cancer occurrence in older individuals include the accumulation of somatic mutations through defects in genome maintenance, epigenetic gene silencing, oxidative stress, loss of immune surveillance, telomere dysfunction, chronic inflammation, and alterations in tissue microenvironment. In this context, the process of prostate carcinogenesis can be influenced through interactions between intrinsic cellular alterations and the extrinsic microenvironment and macroenvironment, both of which change substantially as a consequence of aging. In this study, we sought to characterize the molecular alterations that occur during the process of prostate fibroblast senescence to identify factors in the aged tissue microenvironment capable of promoting the proliferation and potentially the neoplastic progression of prostate epithelium. We evaluated three mechanisms leading to cell senescence: oxidative stress, DNA damage, and replicative exhaustion. We identified a consistent program of gene expression that includes a subset of paracrine factors capable of influencing adjacent prostate epithelial growth. Both direct coculture and conditioned medium from senescent prostate fibroblasts stimulated epithelial cell proliferation, 3-fold and 2-fold, respectively. The paracrine-acting proteins fibroblast growth factor 7, hepatocyte growth factor, and amphiregulin (AREG) were elevated in the extracellular environment of senescent prostate fibroblasts. Exogenous AREG alone stimulated prostate epithelial cell growth, and neutralizing antibodies and small interfering RNA targeting AREG attenuated, but did not completely abrogate the growth-promoting effects of senescent fibroblast conditioned medium. These results support the concept that aging-related changes in the prostate microenvironment may contribute to the progression of prostate neoplasia. (Cancer Res 2006; 66(2): 794-802)
Dietary Soy Isoflavones Inhibit Estrogen Effects in the Postmenopausal Breast
Authors: Wood Charles E. , Register Thomas C. , Franke Adrian A. , Anthony Mary S. , Cline J. Mark
Published: January 2006

Soy isoflavones are promising dietary agents for prevention of breast cancer. Isoflavones bind estrogen receptors (ER) and may variably act as either estrogen agonists or antagonists depending on the estrogen environment. In this study, we used a postmenopausal primate model to evaluate interactive effects of dietary soy isoflavones and estrogen on risk markers for breast cancer. The experiment followed a randomized factorial design in which 31 ovariectomized adult female cynomolgus monkeys were divided into social groups of three to four animals each and rotated through eight different diets containing the human equivalent of 0, 60, 120, or 240 mg/d soy isoflavones with a dose of oral micronized 17β-estradiol (E2) corresponding to either a low (0.09 mg/d) or a high (0.5 mg/d) postmenopausal estrogen environment. Treatment periods lasted 4 months with a 1-month washout period between diets. The highest isoflavone dose resulted in significantly lower breast proliferation and uterine size in the high-estrogen environment. These effects were accompanied by divergent changes in breast markers of ER activation in which pS2 expression was significantly lower and progesterone receptor expression was significantly higher following the 240 mg isoflavone dose. All isoflavone doses resulted in lower serum estrone and E2 concentrations in the high-estrogen environment. In contrast, isoflavone treatment had no significant estrogen agonist effects and minimal antagonistic effects in the lower-estrogen environment. These findings show that in the presence of estrogen higher doses of dietary soy isoflavones may alter ER signaling and induce selective antagonistic effects in the breast. (Cancer Res 2006; 66(2): 1241-9)