bluuebunny/crossref_metadata_2025 huggingface dataset:
Raver1, a dual compartment protein, is a ligand for PTB/hnRNPI and microfilament attachment proteins
Authors: Hüttelmaier Stefan , Illenberger Susanne , Grosheva Irina , Rüdiger Manfred , Singer Robert H. , Jockusch Brigitte M.
Published: July 2002

By screening a yeast two-hybrid library with COOH-terminal fragments of vinculin/metavinculin as the bait, we identified a new protein termed raver1. Raver1 is an 80-kD multidomain protein and widely expressed but to varying amounts in different cell lines. In situ and in vitro, raver1 forms complexes with the microfilament-associated proteins vinculin, metavinculin, and α-actinin and colocalizes with vinculin/metavinculin and α-actinin at microfilament attachment sites, such as cell–cell and cell matrix contacts of epithelial cells and fibroblasts, respectively, and in costameres of skeletal muscle. The NH2-terminal part of raver1 contains three RNA recognition motifs with homology to members of the heterogeneous nuclear RNP (hnRNP) family. Raver1 colocalizes with polypyrimidine tract binding protein (PTB)/hnRNPI, a protein involved in RNA splicing of microfilament proteins, in the perinucleolar compartment and forms complexes with PTB/hnRNPI. Hence, raver1 is a dual compartment protein, which is consistent with the presence of nuclear location signal and nuclear export sequence motifs in its sequence. During muscle differentiation, raver1 migrates from the nucleus to the costamere. We propose that raver1 may coordinate RNA processing and targeting as required for microfilament anchoring in specific adhesion sites.
Proteolytic release of CD44 intracellular domain and its role in the CD44 signaling pathway
Authors: Okamoto Isamu , Kawano Yoshiaki , Murakami Daizo , Sasayama Takashi , Araki Norie , Miki Toru , Wong Albert J. , Saya Hideyuki
Published: July 2002

CD44 is a widely distributed cell surface adhesion molecule and is implicated in diverse biological processes. However, the nature of intracellular signaling triggered by CD44 remains to be elucidated. Here, we show that CD44 undergoes sequential proteolytic cleavage in the ectodomain and intracellular domain, resulting in the release of a CD44 intracellular domain (ICD) fragment. Consequently, CD44ICD acts as a signal transduction molecule, where it translocates to the nucleus and activates transcription mediated through the 12-O-tetradecanoylphorbol 13-acetate–responsive element, which is found in numerous genes involved in diverse cellular processes. Expression of an uncleavable CD44 mutant as well as metalloprotease inhibitor treatment blocks CD44-mediated transcriptional activation. In search of the underlying mechanism, we have found that CD44ICD potentiates transactivation mediated by the transcriptional coactivator CBP/p300. Furthermore, we show that cells expressing CD44ICD produce high levels of CD44 messenger RNA, suggesting that the CD44 gene is one of the potential targets for transcriptional activation by CD44ICD. These observations establish a novel CD44 signaling pathway and shed new light on the functional link between proteolytic processing of an adhesion molecule at the cell surface and transcriptional activation in the nucleus.
The Central Executioner of Apoptosis: Multiple Connections between Protease Activation and Mitochondria in Fas/APO-1/CD95- and Ceramide-induced Apoptosis
Authors: Susin Santos A. , Zamzami Naoufal , Castedo Maria , Daugas Eric , Wang Hong-Gang , Geley Stephan , Fassy Florence , Reed John C. , Kroemer Guido
Published: July 2002

According to current understanding, cytoplasmic events including activation of protease cascades and mitochondrial permeability transition (PT) participate in the control of nuclear apoptosis. However, the relationship between protease activation and PT has remained elusive. When apoptosis is induced by cross-linking of the Fas/APO-1/CD95 receptor, activation of interleukin-1β converting enzyme (ICE; caspase 1) or ICE-like enzymes precedes the disruption of the mitochondrial inner transmembrane potential (ΔΨm). In contrast, cytosolic CPP32/ Yama/Apopain/caspase 3 activation, plasma membrane phosphatidyl serine exposure, and nuclear apoptosis only occur in cells in which the ΔΨm is fully disrupted. Transfection with the cowpox protease inhibitor crmA or culture in the presence of the synthetic ICE-specific inhibitor Ac-YVAD.cmk both prevent the ΔΨm collapse and subsequent apoptosis. Cytosols from anti-Fas–treated human lymphoma cells accumulate an activity that induces PT in isolated mitochondria in vitro and that is neutralized by crmA or Ac-YVAD.cmk. Recombinant purified ICE suffices to cause isolated mitochondria to undergo PT-like large amplitude swelling and to disrupt their ΔΨm. In addition, ICE-treated mitochondria release an apoptosis-inducing factor (AIF) that induces apoptotic changes (chromatin condensation and oligonucleosomal DNA fragmentation) in isolated nuclei in vitro. AIF is a protease (or protease activator) that can be inhibited by the broad spectrum apoptosis inhibitor Z-VAD.fmk and that causes the proteolytical activation of CPP32. Although Bcl-2 is a highly efficient inhibitor of mitochondrial alterations (large amplitude swelling + ΔΨm collapse + release of AIF) induced by prooxidants or cytosols from ceramide-treated cells, it has no effect on the ICE-induced mitochondrial PT and AIF release. These data connect a protease activation pathway with the mitochondrial phase of apoptosis regulation. In addition, they provide a plausible explanation of why Bcl-2 fails to interfere with Fas-triggered apoptosis in most cell types, yet prevents ceramide- and prooxidant-induced apoptosis.
Compensatory Prostaglandin E2 Biosynthesis in Cyclooxygenase 1 or 2 Null Cells
Authors: Kirtikara Kanyawim , Morham Scott G. , Raghow Rajendra , Laulederkind Stanley J. F. , Kanekura Takuro , Goorha Sarita , Ballou Leslie R.
Published: July 2002

Prostaglandin E2 (PGE2) production in immortalized, nontransformed cells derived from wild-type, cyclooxygenase 1–deficient (COX-1−/−) or cyclooxygenase 2–deficient (COX-2−/−) mice was examined after treatment with interleukin (IL)-1β, tumor necrosis factor α, acidic fibroblast growth factor, and phorbol ester (phorbol myristate acetate). Compared with their wild-type counterparts, COX-1−/− or COX-2−/− cells exhibited substantially enhanced expression of the remaining functional COX gene. Furthermore, both basal and IL-1–induced expression of cytosolic phospholipase A2 (cPLA2), a key enzyme-regulating substrate mobilization for PGE2 biosynthesis, was also more pronounced in both COX-1−/− and COX-2−/− cells. Thus, COX-1−/− and COX-2−/− cells have the ability to coordinate the upregulation of the alternate COX isozyme as well as cPLA2 genes to overcome defects in prostaglandin biosynthetic machinery. The potential for cells to alter and thereby compensate for defects in the expression of specific genes such as COX has significant clinical implications given the central role of COX in a variety of disease processes and the widespread use of COX inhibitors as therapeutic agents.
Requirement of CD3 Complex–associated Signaling Functions for Expression of Rearranged T Cell Receptor β VDJ Genes in Early Thymic Development
Authors: Würch Andreas , Biro Judit , Potocnik Alexandre J. , Falk Ingrid , Mossmann Horst , Eichmann Klaus
Published: July 2002

During αβ thymocyte development, the clonotypic αβ–T cell receptor (TCR) is preceded by sequentially expressed immature versions of the TCR–CD3 complex: the pre-TCR, containing a clonotypic TCR-β chain and invariant pre-Tα, is expressed on pre-T cells before rearrangement of the TCR-α locus. Moreover, clonotype-independent CD3 complexes (CIC) appear on pro-T cells before VDJ rearrangements of TCR-β genes. The pre-TCR is known to mediate TCR-β selection, the prerequisite for maturation of CD4−8− double negative (DN) thymocytes to the CD4+8+ double positive stage. A developmental function of CIC has so far not been delineated. In mice single deficient and double deficient for CD3ζ/η and/or p56lck, we observe a pronounced reduction in the proportions of CD25+ DN thymocytes that express intracellular TCR-β chains. TCR-β transcripts are reduced in parallel with TCR-β polypeptide chains whereas no reduction in TCR-β locus rearrangements could be detected. Wild-type levels of TCR-β transcripts and of cells expressing TCR-β polypeptide chains are induced by treatment with anti-CD3ε mAb. The data suggest that the initial expression of rearranged TCR-β VDJ genes in pro-T cell to pre-T cell progression is dependent on CD3 complex signaling, and thus define a putative developmental function for CIC.
Simultaneous Disruption of Interleukin (IL)-4 and IL-13 Defines Individual Roles in T Helper Cell Type 2–mediated Responses
Authors: McKenzie Grahame J. , Fallon Padraic G. , Emson Claire L. , Grencis Richard K. , McKenzie Andrew N.J.
Published: July 2002

Using a single vector targeting strategy, we have generated mice with a combined deficiency of interleukin (IL)-4 and IL-13 to clarify their roles in T helper type 2 (Th2) cell responses. Using immunological challenges normally characterized by a Th2-like response, we have compared the responses of the double-deficient mice with those generated by wild-type, IL-4–deficient, and IL-13–deficient mice. Using a pulmonary granuloma model, induced with Schistosoma mansoni eggs, we demonstrate that although eosinophil infiltration, immunoglobulin E, and IL-5 production are reduced in the IL-4–deficient mice and IL-13–deficient mice, they are abolished only in the combined absence of both cytokines. Furthermore, IL-4/13–deficient animals are severely impaired in their ability to expel the gastrointestinal nematode Nippostrongylus brasiliensis. Unexpectedly, N. brasiliensis–infected IL-4/13–deficient mice developed elevated IL-5 and eosinophilia, indicating that compensatory mechanisms exist for the expression of IL-5, although serum IgE remained undetectable. IL-4/13–deficient mice default to a Th1-like phenotype characterized by the expression of interferon γ and the production of IgG2a and IgG2b. We conclude that IL-4 and IL-13 cooperate to initiate rapid Th2 cell–driven responses, and that although their functions overlap, they perform additive roles.
Clonal Deleterious Mutations in the Iκbα Gene in the Malignant Cells in Hodgkin's Lymphoma
Authors: Jungnickel Berit , Staratschek-Jox Andrea , Bräuninger Andreas , Spieker Tilmann , Wolf Jürgen , Diehl Volker , Hansmann Martin-Leo , Rajewsky Klaus , Küppers Ralf
Published: July 2002

Members of the nuclear factor (NF)-κB family of transcription factors play a crucial role in cellular activation, immune responses, and oncogenesis. In most cells, they are kept inactive in the cytosol by complex formation with members of the inhibitor of NF-κB (IκB) family, whose degradation activates NF-κB in response to diverse stimuli. In Hodgkin's lymphoma (HL), high constitutive nuclear activity of NF-κB is characteristic of the malignant Hodgkin and Reed-Sternberg (H/RS) cells, which occur at low number in a background of nonneoplastic inflammatory cells. In single H/RS cells micromanipulated from histological sections of HL, we detect clonal deleterious somatic mutations in the IκBα gene in two of three Epstein-Barr virus (EBV)-negative cases but not in two EBV-positive cases (in which a viral oncogene may account for NF-κB activation). There was no evidence for IκBα mutations in two non-HL entities or in normal germinal center B cells. This study establishes deleterious IκBα mutations as the first recurrent genetic defect found in H/RS cells, indicating a role of IκBα defects in the pathogenesis of HL and implying that IκBα is a tumor suppressor gene.
A Discrete Subpopulation of Dendritic Cells Transports Apoptotic Intestinal Epithelial Cells to T Cell Areas of Mesenteric Lymph Nodes
Authors: Huang Fang-Ping , Platt Nicholas , Wykes Michelle , Major James R. , Powell Timothy J. , Jenkins Christopher D. , MacPherson G. Gordon
Published: July 2002

This study identifies a dendritic cell (DC) subset that constitutively transports apoptotic intestinal epithelial cell remnants to T cell areas of mesenteric lymph nodes in vivo. Rat intestinal lymph contains two DC populations. Both populations have typical DC morphology, are major histocompatibility complex class IIhi, and express OX62, CD11c, and B7. CD4+/OX41+ DCs are strong antigen-presenting cells (APCs). CD4−/OX41− DCs are weak APCs and contain cytoplasmic apoptotic DNA, epithelial cell–restricted cytokeratins, and nonspecific esterase (NSE)+ inclusions, not seen in OX41+ DCs. Identical patterns of NSE electrophoretic variants exist in CD4−/OX41− DCs, intestinal epithelial cells, and mesenteric node DCs but not in other DC populations, macrophages, or tissues. Terminal deoxynucleotidyl transferase–mediated dUTP-biotin nick-end labeling (TUNEL)-positive DCs and strongly NSE+ DCs are present in intestinal lamina propria. Peyer's patches and mesenteric but not other lymph nodes contain many strongly NSE+ DCs in interfollicular and T cell areas. Similar DCs are seen in the ileum and in T cell areas of mesenteric nodes in gnotobiotic rats. These results show that a distinct DC subset constitutively endocytoses and transports apoptotic cells to T cell areas and suggest a role for these DCs in inducing and maintaining peripheral self-tolerance.
Regulation by Chemokines of Circulating Dendritic Cell Precursors, and the Formation of Portal Tract–Associated Lymphoid Tissue, in a Granulomatous Liver Disease
Authors: Yoneyama Hiroyuki , Matsuno Kenjiro , Zhang Yanyun , Murai Masako , Itakura Meiji , Ishikawa Sho , Hasegawa Go , Naito Makoto , Asakura Hitoshi , Matsushima Kouji
Published: July 2002

We have studied the recruitment and roles of distinct dendritic cell (DC) precursors from the circulation into Propionibacterium acnes–induced granulomas in mouse liver. During infection, F4/80−B220−CD11c+ DC precursors appeared in the circulation, migrated into the perisinusoidal space, and matured within newly formed granulomas. Recruited DCs later migrated to the portal area to interact with T cells in what we term “portal tract–associated lymphoid tissue” (PALT). Macrophage inflammatory protein 1α attracted blood DC precursors to the sinusoidal granuloma, whereas secondary lymphoid organ chemokine (SLC) attracted mature DCs to the newly identified PALT. Anti-SLC antibody diminished PALT expansion while exacerbating granuloma formation. Therefore, circulating DC precursors can migrate into a solid organ like liver, and participate in the granulomatous reaction in response to specific chemokines.
Very Low Affinity B Cells Form Germinal Centers, Become Memory B Cells, and Participate in Secondary Immune Responses When Higher Affinity Competition Is Reduced
Authors: Dal Porto Joseph M. , Haberman Ann M. , Kelsoe Garnett , Shlomchik Mark J.
Published: July 2002

To understand the relationship between the affinity of the B cell antigen receptor (BCR) and the immune response to antigen, two lines of immunoglobulin H chain transgenic (Tg) mice were created. H50Gμa and T1(V23)μa mice express μ H chain transgenes that associate with the λ1 L chains to bind the (4-hydroxy-3-nitrophenyl)acetyl hapten with association constants (Kas) of only 1.2 × 105 M−1 and 3 × 104 M−1, respectively. Both lines mounted substantial antibody-forming cell (AFC) and germinal center (GC) responses. H50Gμa Tg mice also generated memory B cells. T1(V23)μa B cells formed AFC and GCs, but were largely replaced in late GCs by antigen-specific cells that express endogenous BCRs. Thus, B lymphocytes carrying BCRs with affinities previously thought to be irrelevant in specific immune responses are in fact capable of complete T cell–dependent immune responses when relieved of substantial competition from other B cells. The failure to observe such B cells normally in late primary responses and in memory B cell populations is the result of competition, rather than an intrinsic inability of low affinity B cells.
Adenosine Triphosphate and the Late Steps in Calcium-dependent Exocytosis at a Ribbon Synapse
Authors: Heidelberger Ruth
Published: July 2002

The ATP dependence of the kinetics of Ca2+-dependent exocytosis after flash photolysis of caged Ca2+ was studied by capacitance measurements with submillisecond resolution in single synaptic terminals of retinal bipolar neurons. After control experiments verified that this combination of techniques is valid for the study of exocytosis in synaptic terminals, a comparison was made between the Ca2+ dependence of the rate of exocytosis in synaptic terminals internally dialyzed with MgATP, MgATP-γ-S, or no added Mg2+ or nucleotide. The Ca2+ threshold for release, the maximum rate of release, and the overall relationship between the rate of synaptic vesicle fusion and [Ca2+]i were found to be independent of MgATP. A decrease in the average rate at near-threshold [Ca2+]i was observed in terminals with MgATP-γ-S, but due to the small sample size is of unclear significance. The Ca2+ dependence of the delay between the elevation of [Ca2+]i and the beginning of the capacitance rise was also found to be independent of MgATP. In contrast, MgATP had a marked effect on the ability of terminals to respond to multiple stimuli. Terminals with MgATP typically exhibited a capacitance increase to a second stimulus that was >70% of the amplitude of the first response and to a third stimulus with a response amplitude that was >50% of the first, whereas terminals without MgATP responded to a second stimulus with a response <35% of the first and rarely responded to a third flash. These results suggest a major role for MgATP in preparing synaptic vesicles for fusion, but indicate that cytosolic MgATP may have little role in events downstream of calcium entry, provided that [Ca2+]i near release sites is elevated above ≈30 μM.
P2 Receptor Modulation of Voltage-gated Potassium Currents in Brown Adipocytes
Authors: Wilson S.M. , Pappone P.A.
Published: July 2002

Using patch voltage-clamp techniques, we find there are two components to the voltage-gated potassium current (IKv) in rat brown adipocytes. The components differ in their gating and responses to purinergic stimulation, but not their pharmacology. IKv-A recovers from inactivation at physiological membrane potentials, while IKv-B inactivation recovers at more negative potentials. Both currents are >90% blocked by similar concentrations of quinine and tetraethylammonium, but not by β-dendrotoxin, charybdotoxin, or apamin. The two current components are differentially modulated by extracellular ATP. ATP shifts the voltage dependence of IKv-A inactivation negative by 38 ± 5 mV (n = 35, ±SEM) and shifts activation by −14 ± 2 mV in whole-cell experiments. ATP did not affect the steady state inactivation voltage dependence of IKv-B, but did apparently convert IKv-A into IKv-B. The pharmacology of the inactivation shift is consistent with mediation by a P2 purinergic receptor. Purinergic stimulation of perforated-patch clamped cells causes hyperpolarizing shifts in the window current of IKv-A by shifting inactivation −18 ± 4 mV and activation −7 ± 2 mV (n = 16). Since perforated-patch recordings will most closely resemble in vivo cell responses, this ATP-induced shift in the window current may facilitate IKv activation when the cell depolarizes. IKv activity is necessary for the proliferation and differentiation of brown adipocytes in culture (Pappone, P.A., and S.I. Ortiz-Miranda. 1993. Am. J. Physiol. 264:C1014–C1019) so purinergic modulation of IKv may be important in altering adipocyte growth and development.
Opening and Closing of KcnkØ Potassium Leak Channels Is Tightly Regulated
Authors: Zilberberg Noam , Ilan Nitza , Gonzalez-Colaso Rosana , Goldstein Steve A.N.
Published: July 2002

Potassium-selective leak channels control neuromuscular function through effects on membrane excitability. Nonetheless, their existence as independent molecular entities was established only recently with the cloning of KCNKØ from Drosophila melanogaster. Here, the operating mechanism of these 2 P domain leak channels is delineated. Single KCNKØ channels switch between two long-lived states (one open and one closed) in a tenaciously regulated fashion. Activation can increase the open probability to ∼1, and inhibition can reduce it to ∼0.05. Gating is dictated by a 700-residue carboxy-terminal tail that controls the closed state dwell time but does not form a channel gate; its deletion (to produce a 300-residue subunit with two P domains and four transmembrane segments) yields unregulated leak channels that enter, but do not maintain, the closed state. The tail integrates simultaneous input from multiple regulatory pathways acting via protein kinases C, A, and G.
On normal solvability of the Riemann problem with singular coefficient
Authors: Rakowski M. , Spitkovsky I.
Published: July 2002

Suppose

G
G

is a singular matrix function on a simple, closed, rectifiable contour

Γ
\Gamma

. We present a necessary and sufficient condition for normal solvability of the Riemann problem with coefficient

G
G

in the case where

G
G

admits a spectral (or generalized Wiener-Hopf) factorization

G

+

Λ

G

−

G_{+} \Lambda G_{-}

with

G

−

±
1

G_{-}^{\pm 1}

essentially bounded. The boundedness of

G

−

±
1

G_{-}^{\pm 1}

is not required when

G
G

takes injective values a.e. on

Γ
\Gamma

.
Sur le rang du 2-groupe de classes de 𝑄({√{𝑚}},{√{𝑑}}) où 𝑚=2 ou un premier 𝑝≡1(𝑚𝑜𝑑4)
Authors: Azizi Abdelmalek , Mouhib Ali
Published: July 2002

On the rank of the

2
2

-class group of

Q
(

m

,

d

)

Q({\sqrt {m}},{\sqrt {d}})

. Let

d
d

be a square-free positive integer and

p
p

be a prime such that

p
≡
1

(
m
o
d

4
)

p\equiv 1\,(mod\, 4)

. We set

K
=
Q
(

m

,

d

)

K = Q({\sqrt {m}},{\sqrt {d}})

, where

m
=
2

m=2

or

m
=
p

m=p

. In this paper, we determine the rank of the

2
2

-class group of

K
K

.

Résumé. Soit

K
=
Q
(

m

,

d

)

K = Q({\sqrt {m}},{\sqrt {d}})

, un corps biquadratique où

m
=
2

m=2

ou bien un premier

p
≡
1

(
m
o
d

4
)

p\equiv 1\,(mod\,4)

et

d
d

étant un entier positif sans facteurs carrés. Dans ce papier, on détermine le rang du

2
2

-groupe de classes de

K
K

.
Competitive exclusion and coexistence for competitive systems on ordered Banach spaces
Authors: Hsu S. , Smith H. , Waltman Paul
Published: July 2002

The dynamics of competitive maps and semiflows defined on the product of two cones in respective Banach spaces is studied. It is shown that exactly one of three outcomes is possible for two viable competitors. Either one or the other population becomes extinct while the surviving population approaches a steady state, or there exists a positive steady state representing the coexistence of both populations.
Curve-straightening and the Palais-Smale condition
Authors: Linnér Anders
Published: July 2002

This paper considers the negative gradient trajectories associated with the modified total squared curvature functional

∫

k

2

+
ν
d
s

\int k^{2} +\nu ds

. The focus is on the limiting behavior as

ν
\nu

tends to zero from the positive side. It is shown that when

ν
=
0

\nu =0

spaces of curves exist in which some trajectories converge and others diverge. In one instance the collection of critical points splits into two subsets. As

ν
\nu

tends to zero the critical curves in the first subset tend to the critical points present when

ν
=
0

\nu =0

. Meanwhile, all the critical points in the second subset have lengths that tend to infinity. It is shown that this is the only way the Palais-Smale condition fails in the present context. The behavior of the second class of critical points supports the view that some of the trajectories are ‘dragged’ all the way to ‘infinity’. When the curves are rescaled to have constant length the Euler figure eight emerges as a ‘critical point at infinity’. It is discovered that a reflectional symmetry need not be preserved along the trajectories. There are examples where the length of the curves along the same trajectory is not a monotone function of the flow-time. It is shown how to determine the elliptic modulus of the critical curves in all the standard cases. The modulus

p
p

must satisfy

2
E
(
p
)

/

K
(
p
)
=
1
±

|

g

|

/

L
~

2E(p)/K(p)=1\pm |g|/\widetilde L

when the space is limited to curves of fixed length

L
~

\widetilde L

and the endpoints are separated by the vector

g
g

.
Wavelets based on orthogonal polynomials
Authors: Fischer Bernd , Prestin Jürgen
Published: July 2002

We present a unified approach for the construction of polynomial wavelets. Our main tool is orthogonal polynomials. With the help of their properties we devise schemes for the construction of time localized polynomial bases on bounded and unbounded subsets of the real line. Several examples illustrate the new approach.
Detecting cryptically simple protein sequences using the SIMPLE algorithm
Authors: Albà M. Mar , Laskowski Roman A. , Hancock John M.
Published: July 2002

Motivation: Low-complexity or cryptically simple sequences are widespread in protein sequences but their evolution and function are poorly understood. To date methods for the detection of low complexity in proteins have been directed towards the filtering of such regions prior to sequence homology searches but not to the analysis of the regions per se. However, many of these regions are encoded by non-repetitive DNA sequences and may therefore result from selection acting on protein structure and/or function.

Results: We have developed a new tool, based on the SIMPLE algorithm, that facilitates the quantification of the amount of simple sequence in proteins and determines the type of short motifs that show clustering above a certain threshold. By modifying the sensitivity of the program simple sequence content can be studied at various levels, from highly organised tandem structures to complex combinations of repeats. We compare the relative amount of simplicity in different functional groups of yeast proteins and determine the level of clustering of the different amino acids in these proteins.

Availability: The program is available on request or online at http://www.biochem.ucl.ac.uk/bsm/SIMPLE

Contact: j.hancock@cs.rhul.ac.uk

* To whom correspondence should be addressed.
Racial Discrimination in Professional Basketball: Evidence from Nielsen Ratings
Authors: Kanazawa Mark T. , Funk Jonas P.
Published: July 2002

Using data on Nielsen ratings for locally televised NBA basketball games, we find strong evidence that viewership increases when there is greater participation by white players. This finding controls for a wide variety of other factors that could systematically affect Nielsen ratings, and signifies the presence of customer discrimination in the market for NBA players. We also find that higher Nielsen ratings allow NBA teams to realize greater advertising revenues, meaning that the marginal revenue product of white players exceeds that of comparable black players. This factor explains much of the race‐based salary gap that exists in professional basketball.
The Effect of Cocaine Prices on Crime
Authors: Desimone Jeff
Published: July 2002

The relationship between cocaine prices and crime has critical implications for U.S. drug policy, but is theoretically indeterminate because cocaine price changes affect crime through changes in both cocaine consumption and expenditures. This paper investigates this relationship in annual data from 1981–95 on 29 large U.S. cities, accounting for simultaneity by using two‐stage least squares with measures of wholesale supply factors and retail enforcement intensity as instruments for cocaine prices. Controlling for prices of other drugs, deterrence, socioeconomic factors, and city and year‐specific effects, a strong negative relationship exists between cocaine prices and six of seven FBI index crimes.
An intron in the YRA1 gene is required to control Yra1 protein expression and mRNA export in yeast
Authors: Rodríguez‐Navarro Susana , Sträßer Katja , Hurt Ed
Published: July 2002

Yra1p is an essential and conserved mRNA export factor in yeast. Strikingly, removal of the intron from YRA1 causes a dominant‐negative growth phenotype and a concomitant inhibition of mRNA export. However, both defects are neutralized by replacement of the intron of YRA1 by a different intron. Significantly, Yra1p is overproduced in yeast when expressed from its intronless gene, but Yra1p levels are the same as the wild type when expressed from an intron‐containing YRA1 gene. Thus, an intron in YRA1 controls Yra1p expression and mRNA export.
Constraints on models for the flagellar rotary motor
Authors: Berg Howard C.
Published: July 2002

Most bacteria that swim are propelled by flagellar filaments, each driven at its base by a rotary motor embedded in the cell wall and cytoplasmic membrane. A motor is about 45 nm in diameter and made up of about 20 different kinds of parts. It is assembled from the inside out. It is powered by a proton (or in some species, a sodium–ion) flux. It steps at least 400 times per revolution. At low speeds and high torques, about 1000 protons are required per revolution, speed is proportional to protonmotive force, and torque varies little with temperature or hydrogen isotope. At high speeds and low torques, torque increases with temperature and is sensitive to hydrogen isotope. At room temperature, torque varies remarkably little with speed from about –100 Hz (the present limit of measurement) to about 200 Hz, and then it declines rapidly, reaching zero at about 300 Hz. These are facts that motor models should explain. None of the existing models for the flagellar rotary motor completely do so.
Flexibility in photosynthetic electron transport: a newly identified chloroplast oxidase involved in chlororespiration
Authors: Cournac Laurent , Josse Eve-Marie , Joët Thierry , Rumeau Dominique , Redding Kevin , Kuntz Marcel , Peltier Gilles
Published: July 2002

Besides electron transfer reactions involved in the ‘Z’ scheme of photosynthesis, alternative electron transfer pathways have been characterized in chloroplasts. These include cyclic electron flow around photosystem I (PS I) or a respiratory chain called chlororespiration. Recent work has supplied new information concerning the molecular nature of the electron carriers involved in the non-photochemical reduction of the plastoquinone (PQ) pool. However, until now little is known concerning the nature of the electron carriers involved in PQ oxidation. By using mass spectrometric measurement of oxygen exchange performed in the presence of
18
O-enriched O
2
and
Chlamydomonas
mutants deficient in PS I, we show that electrons can be directed to a quinol oxidase sensitive to propyl gallate but insensitive to salicyl hydroxamic acid. This oxidase has immunological and pharmacological similarities with a plastid protein involved in carotenoid biosynthesis.
Altered spectra of hypermutation in DNA repair–deficient mice
Authors: Winter David B. , Gearhart Patricia J.
Published: July 2002

Affinity maturation of the humoral immune response is based on the ability of immunoglobulin variable genes to undergo a process of rapid and extensive somatic mutation followed by antigenic selection for antibodies with higher affinity. While the behaviour of this somatic hypermutation phenomenon has been well characterized over the last 20 years, the molecular mechanism responsible for inserting mutations has remained shrouded. To better understand this mechanism, we studied the interplay between hypermutation and other DNA associated activities such as DNA repair. There was no effect on the frequency and pattern of hypermutation in mice deficient for nucleotide excision repair, base excision repair and ataxia–telangiectasia mutated gene repair of double strand breaks. However, variable genes from mice lacking some components of mismatch repair had an increased frequency of tandem mutations and had more mutations of G and C nucleotides. These results suggest that the DNA polymerase(s) involved in the hypermutation pathway produces a unique spectra of mutations, which is then altered by mismatch repair and antigenic selection. We also describe the differential pattern of expression of some nuclear DNA polymerases in hypermutating versus non–hypermutating B lymphocytes. The rapidly dividing germinal centre B cells expressed DNA polymerases alpha, beta, delta, epsilon and zeta, whereas the resting non–germinal centre cells did not express polymerases alpha or epsilon at detectable levels, although they did express polymerases beta, delta and zeta. The lack of expression of polymerase epsilon in the non–germinal centre cells suggests that this enzyme has a critical role in chromosomal replication but does not participate in DNA repair in these cells.
Molecular virology of Kaposi's sarcoma–associated herpesvirus
Authors: Moore Patrick S. , Chang Yuan
Published: July 2002

Kaposi's sarcoma–associated herpesvirus (KSHV), the most recently discovered human tumour virus, is the causative agent of Kaposi's sarcoma, primary effusion lymphoma and some forms of Castleman's disease. KSHV is a rhadinovirus, and like other rhadinoviruses, it has an extensive array of regulatory genes obtained from the host cell genome. These pirated KSHV proteins include homologues to cellular CD21, three different β–chemokines, IL–6, BCL–2, several different interferon regulatory factor homologues, Fas–ligand ICE inhibitory protein (FLIP), cyclin D and a G–protein–coupled receptor, as well as DNA synthetic enzymes including thymidylate synthase, dihydrofolate reductase, DNA polymerase, thymidine kinase and ribonucleotide reductases. Despite marked differences between KSHV and Epstein–Barr virus, both viruses target many of the same cellular pathways, but use different strategies to achieve the same effects. KSHV proteins have been identified which inhibit cell–cycle regulation checkpoints, apoptosis control mechanisms and the immune response regulatory machinery. Inhibition of these cellular regulatory networks appears to be a defensive means of allowing the virus to escape from innate antiviral immune responses. However, due to the overlapping nature of innate immune and tumour–suppressor pathways, inhibition of these regulatory networks can lead to unregulated cell proliferation and may contribute to virus–induced tumorigenesis.
Rangelands, pastoralists and governments: interlinked systems of people and nature
Authors: Walker Brian H. , Janssen Marco A.
Published: July 2002

We analyse commercially operated rangelands as coupled systems of people and nature. The biophysical components include: (i) the reduction and recovery of potential primary production, reflected as changes in grass production per unit of rainfall; (ii) changes in woody plants dependent on the grazing and fire regimes; and (iii) livestock and wool dynamics influenced by season, condition of the rangeland and numbers of wild and feral animals. The social components include the managers, who vary with regard to a range of cognitive abilities and lifestyle choices, and the regulators who vary in regard to policy goals.

We compare agent–based and optimization models of a rangeland system. The agent–based model leads to recognition that policies select for certain management practices by creating a template that governs the trajectories of the behaviour of individuals, learning, and overall system dynamics. Conservative regulations reduce short–term loss in production but also restrict learning. A free–market environment leads to severe degradation but the surviving pastoralists perform well under subsequent variable conditions. The challenge for policy makers is to balance the needs for learning and for preventing excessive degradation. A genetic algorithm model optimizing for net discounted income and based on a population of management solutions (stocking rate, how much to suppress fire, etc.) indicates that robust solutions lead to a loss of about 40% compared with solutions where the sequence of rainfall was known in advance: this is a similar figure to that obtained from the agent–based model.

We conclude that, on the basis of Levin's three criteria, rangelands with their livestock and human managers do constitute complex adaptive systems. If this is so, then command–and–control approaches to rangeland policy and management are bound to fail.
A novel zinc finger protein is associated with U7 snRNP and interacts with the stem–loop binding protein in the histone pre-mRNP to stimulate 3′-end processing
Authors: Dominski Zbigniew , Erkmann Judith A. , Yang Xiaocui , Sànchez Ricardo , Marzluff William F.
Published: July 2002

The stem–loop binding protein (SLBP) is the posttranscriptional regulator of histone mRNA in metazoan cells. SLBP binds histone pre-mRNAs and facilitates 3′-end processing by promoting stable association of U7 snRNP with the pre-mRNA. To identify other factors involved in histone pre-mRNA processing, we used a modified yeast two-hybrid assay in which SLBP and its RNA target were coexpressed as bait. A novel zinc finger protein, hZFP100, which interacts with the SLBP/RNA complex but not with free SLBP, was cloned. The interaction requires regions of SLBP that are important for histone pre-mRNA processing. Antibodies to hZFP100 precipitate U7 snRNA, and expression of hZFP100 inXenopusoocytes stimulates processing of histone pre-mRNA, showing that hZFP100 is a component of the processing machinery.
KSR is a scaffold required for activation of the ERK/MAPK module
Authors: Roy François , Laberge Gino , Douziech Mélanie , Ferland-McCollough David , Therrien Marc
Published: July 2002

Mechanisms that regulate signal propagation through the ERK/MAPK pathway are still poorly understood. Several proteins are suspected to play critical roles in this process. One of these is Kinase Suppressor of Ras (KSR), a component previously identified in RAS-dependent genetic screens in Drosophila and Caenorhabditis elegans. Here, we show that KSR functions upstream of MEK within the ERK/MAPK module. In agreement with this, we found that KSR facilitates the phosphorylation of MEK by RAF. We further show that KSR associates independently with RAF and MEK, and that these interactions lead to the formation of a RAF/MEK complex, thereby positioning RAF in close proximity to its substrate MEK. These findings suggest that KSR functions as a scaffold that assembles the RAF/MEK functional pair.
Binding specificity and the ligand dissociation process in the E. coli biotin holoenzyme synthetase
Authors: Kwon Keehwan , Streaker Emily D. , Beckett Dorothy
Published: July 2002

The binding of the Escherichia coli biotin holoenzyme synthetase to the two ligands, biotin and bio‐5′‐AMP, is coupled to disorder‐to‐order transitions in the protein. In the structure of the biotin complex, a “glycine‐rich” loop that is disordered in the apo‐enzyme is folded over the ligand. Mutations in three residues in this loop result in significant changes in the affinity of the enzyme for both biotin and bio‐5′‐AMP. The kinetic basis of these losses in the affinity resides primarily in changes in the unimolecular rates of dissociation of the complexes. In this work, isothermal titration calorimetry has been employed to examine the detailed thermodynamics of binding of three loop mutants to biotin and bio‐5′‐AMP. The energetic features of dissociation of the protein•ligand complexes also have been probed by measuring the temperature dependencies of the unimolecular dissociation rates. Analysis of the data using the Eyring formalism yielded entropic and enthalpic contributions to the energetic barrier to dissociation. The thermodynamic results coupled with the known structures of the apo‐enzyme and biotin complex have been used to formulate a model for progression from the ground‐state complex to the transition state in biotin dissociation. In this model, the transition‐state is characterized by both partial disruption of noncovalent bonds and acquisition of some of the disorder that characterizes the glycine‐rich loop in the absence of ligand.
A test of proposed rules for helix capping: Implications for protein design
Authors: Sagermann Martin , Mårtensson Lars‐Göran , Baase Walter A. , Matthews Brian W.
Published: July 2002

α‐helices within proteins are often terminated (capped) by distinctive configurations of the polypeptide chain. Two common arrangements are the Schellman motif and the alternative αL motif. Rose and coworkers developed stereochemical rules to identify the locations of such motifs in proteins of unknown structure based only on their amino acid sequences. To check the effectiveness of these rules, they made specific predictions regarding the structural and thermodynamic consequences of certain mutations in T4 lysozyme. We have constructed these mutants and show here that they have neither the structure nor the stability that was predicted. The results show the complexity of the protein‐folding problem. Comparison of known protein structures may show that a characteristic sequence of amino acids (a sequence motif) corresponds to a conserved structural motif. In any particular protein, however, changes in other parts of the sequence may result in a different conformation. The structure is determined by sequence as a whole, not by parts considered in isolation.
Low levels of asparagine deamidation can have a dramatic effect on aggregation of amyloidogenic peptides: Implications for the study of amyloid formation
Authors: Nilsson Melanie R. , Driscoll Miles , Raleigh Daniel P.
Published: July 2002

The polypeptide hormone amylin forms amyloid deposits in Type 2 diabetes mellitus and a 10‐residue fragment of amylin (amylin20–29) is commonly used as a model system to study this process. Studies of amylin20–29 and several variant peptides revealed that low levels of deamidation can have a significant effect on the secondary structure and aggregation behavior of these molecules. Results obtained with a variant of amylin20–29, which has the primary sequence SNNFPAILSS, are highlighted. This peptide is particularly interesting from a technical standpoint. In the absence of impurities the peptide does not spontaneously aggregate and is not amyloidogenic. This peptide can spontaneously deamidate, and the presence of less than 5% of deamidation impurities leads to the formation of aggregates that have the hallmarks of amyloid. In addition, small amounts of deamidated material can induce amyloid formation by the purified peptide. These results have fundamental implications for the definition of an amyloidogenic sequence and for the standards of purity of peptides and proteins used for studies of amyloid formation.
Evaluation of three‐dimensional finite element‐based deformable registration of pre‐ and intraoperative prostate imaging
Authors: Bharatha Aditya , Hirose Masanori , Hata Nobuhiko , Warfield Simon K. , Ferrant Matthieu , Zou Kelly H. , Suarez‐Santana Eduardo , Ruiz‐Alzola Juan , D'Amico Anthony , Cormack Robert A. , Kikinis Ron , Jolesz Ferenc A. , Tempany Clare M. C.
Published: July 2002

In this report we evaluate an image registration technique that can improve the information content of intraoperative image data by deformable matching of preoperative images. In this study, pretreatment 1.5 tesla (T) magnetic resonance (MR) images of the prostate are registered with 0.5 T intraoperative images. The method involves rigid and nonrigid registration using biomechanical finite element modeling. Preoperative 1.5 T MR imaging is conducted with the patient supine, using an endorectal coil, while intraoperatively, the patient is in the lithotomy position with a rectal obturator in place. We have previously observed that these changes in patient position and rectal filling produce a shape change in the prostate. The registration of 1.5 T preoperative images depicting the prostate substructure [namely central gland (CG) and peripheral zone (PZ)] to 0.5 T intraoperative MR images using this method can facilitate the segmentation of the substructure of the gland for radiation treatment planning. After creating and validating a dataset of manually segmented glands from images obtained in ten sequential MR‐guided brachytherapy cases, we conducted a set of experiments to assess our hypothesis that the proposed registration system can significantly improve the quality of matching of the total gland (TG), CG, and PZ. The results showed that the method statistically–significantly improves the quality of match (compared to rigid registration), raising the Dice similarity coefficient (DSC) from prematched coefficients of 0.81, 0.78, and 0.59 for TG, CG, and PZ, respectively, to 0.94, 0.86, and 0.76. A point‐based measure of registration agreement was also improved by the deformable registration. CG and PZ volumes are not changed by the registration, indicating that the method maintains the biomechanical topology of the prostate. Although this strategy was tested for MRI‐guided brachytherapy, the preliminary results from these experiments suggest that it may be applied to other settings such as transrectal ultrasound‐guided therapy, where the integration of preoperative MRI may have a significant impact upon treatment planning and guidance.
The use of quantitative temperature images to predict the optimal power for focused ultrasound surgery: In vivo verification in rabbit muscle and brain
Authors: McDannold Nathan , King Randy L. , Jolesz Ferenc A. , Hynynen Kullervo
Published: July 2002

In this study, we investigated the use of MRI‐derived thermal imaging for determining the exposure parameters for focused ultrasound (FUS) surgery. Since the temperature rise induced by a FUS beam scales linearly with power, the temperature maps acquired during subthreshold sonications can be used to determine the power necessary to produce thermal tissue damage with a desired size. Thermal images acquired during multiple sonications delivered at different locations in rabbit thigh muscle and brain tissue in vivo were analyzed to test this hypothesis. First, the linearity of the induced temperature rise with the acoustic power was tested. Next, the temperature maps acquired during preliminary low power sonications were scaled up until the estimated size of the tissue damage was equal to the tissue damage size of subsequent high power sonications. A threshold thermal dose was used to estimate the onset of thermal damage. The predicted power (based on amount of scaling required to reach the target size) was then compared to the true high power value. Overall, the temperature rise varied linearly with power (slope of vs 0.93 for pairs of sonications at each location in brain, muscle). The predicted power matched the true high power in the brain sonications The predicted power underestimated the true high power in the muscle sonications This under‐prediction was due to a deviation from linearity in those cases where tissue damage was detected in subsequent MR images (slope of vs 0.84 for no tissue damage, tissue damage). The source of this deviation was not clear from these experiments. Even with this underestimation of the power, this method will be useful because it will allow an estimate of the proper power to use during FUS surgery without exact knowledge of the tissue parameters.