bluuebunny/crossref_metadata_2025 huggingface dataset:
Energy limits on runaway electrons in tokamak plasmas
Authors: Martín-Solís J. R. , Esposito B. , Sánchez R. , Alvarez J. D.
Published: July 2002

A test particle description of the runaway dynamics is used to analyze some of the main mechanisms limiting the runaway energy in a tokamak plasma. It is found that the synchrotron radiation losses associated with the electron gyromotion around the magnetic field lines can explain the energy limit of runaway electrons found experimentally by observing their bremsstrahlung spectra during the current ramp-up of low density Ohmic discharges in the Joint European Torus (JET) [Nucl. Fusion 25, 1011 (1985)]. The model is applied to the problem of determining the influence of a resonance between the electron gyromotion and the magnetic field ripple of the tokamak on the radiation loss and energy limits of runaway electrons. The equilibrium energy at the resonance and the conditions under which the ripple mechanism can create an upper bound on the runaway energy are investigated. Predictions are discussed on the effect of the ripple resonance on the maximum energy attainable by disruption generated runaway electrons in JET and the projected International Thermonuclear Experimental Reactor (ITER) [ITER EDA Agreement and Protocol 2, International Atomic Energy Agency, Vienna, 1994].
Resistive wall mode stabilization in toroidal geometry
Authors: Bondeson A. , Gimblett C. G. , Hastie R. J.
Published: July 2002

The possibility of stabilizing ideal magnetohydrodynamical (MHD) instabilities by resistive walls and slow plasma rotation (rotation frequencies comparable to resistive tearing growth rates) was proposed recently by Finn [Phys. Plasmas 2, 3782 (1995)] on the basis of cylindrical theory. In the present paper we analyze toroidal effects (pressure gradients and favorable averaged curvature) [Glasser et al., Phys. Fluids 18, 875 (1975)] on this “resistive window.” It is found that in toroidal geometry the resistive window for the distance of the wall from the plasma scales as S−1/3 (S is the ratio of resistive to Alfvénic time scales) and thus becomes very small in large tokamaks. Other differences between toroidal and cylindrical theories of resistive wall mode stability are discussed.
Local transit-time damping of electrostatic wave packets
Authors: Skjæraasen O. , Melatos A. , Robinson P. A. , Pécseli H. , Trulsen J.
Published: July 2002

The theory of local transit-time damping is generalized to coherent electrostatic wave packets with nonzero mean wave number in an unmagnetized plasma. A general analytic formula for the phase-averaged power dissipated locally within an arbitrary three-dimensional wave packet is derived to second order in the fields. This expression is evaluated explicitly for a representative one-dimensional field structure. The result agrees with independent numerical test-particle calculations to within numerical rounding errors for small to moderate field amplitudes, which justify the perturbation expansions. The resulting damping involves both Landau (resonant) and non-Landau (nonresonant) terms, the latter having been omitted in previous works. It is found that the dissipated power depends sensitively on the ratio of the particle velocity to the phase velocity of the packet, the ratio of the wavelength to the size of the packet, and the form of the particle distribution. In general, particles remove energy from some parts of the packet and deposit it in others, thus reshaping it.
On finite β stabilization of the toroidal ion temperature gradient mode
Authors: Hirose A.
Published: July 2002

It is shown that finite beta stabilization of the toroidal ion temperature gradient (ITG) mode is attributable to the electron ballooning parameter (normalized electron pressure gradient) αe. A modest αe, much smaller than that required from the drift reversal α (normalized total pressure gradient) ≳2q2 where q is the safety factor, can effectively stabilize the ITG mode.
Superballistic transport in tearing driven magnetic turbulence
Authors: Zimbardo G. , Greco A. , Veltri P.
Published: July 2002

Ion transport is studied in a magnetic field reversal with a constant electric field and with a model tearing driven magnetic turbulence. Superdiffusive and superballistic transport regimes are found for the mean square displacements in the plane of the current sheet, 〈Δx2〉∝tγ, with anomalous diffusion exponents γ up to 4. It is shown that the jump length l scales as l∝τν, with τ the jump duration and ν>1, and that γ can be interpreted in terms of the Klafter, Blumen, and Shlesinger model [Phys. Rev. A 35, 3081 (1987)] for continuous time random walk. Since velocity increases with the length of the free path, we have accelerated Lévy flights.
Nonlocal simulation of the transition from ballooning to ion temperature gradient mode turbulence in the tokamak edge
Authors: Hallatschek K. , Zeiler A.
Published: July 2002

The transition from resistive ballooning to ion temperature gradient (ITG) mode turbulence in the tokamak edge is studied in three dimensions using the electrostatic reduced Braginskii equations with ion temperature dynamics. In contrast to most previous simulations of plasma edge turbulence, which assume the parameters (density, temperature, collisionality, etc.) to be constant in space and time (local approximation), a realistic spatial variation and the nonlinear dependence of the parameters on the fluctuating quantities is taken into account. The influence of nonlocal effects is studied by a scan in the ratio of profile to turbulence scale length. For a large ratio, good agreement between local and nonlocal results on the ITG mode and ballooning turbulence is found. With increasing nonlocality, however, the anomalous transport is more and more suppressed. For the ITG mode, the turbulence quench is due to a decrease of the linear growth rate, while for the ballooning mode a novel, inherently nonlocal saturation mechanism is identified.
Novel configuration of self-electro-optic effect device based on asymmetric quantum wells
Authors: Khurgin J.
Published: July 2002

A new configuration of self-electro-optic effect device (SEED), based on combination of two asymmetric quantum wells, is proposed. The new device, the so-called scissors SEED, does not require the existence of sharp exciton transitions and therefore can in principle operate in a wider range of wavelengths and temperatures than conventional SEED.
Brain signatures of artificial language processing: Evidence challenging the critical period hypothesis
Authors: Friederici Angela D. , Steinhauer Karsten , Pfeifer Erdmut
Published: July 2002

Adult second language learning seems to be more difficult
and less efficient than first language acquisition during childhood. By
using event-related brain potentials, we show that adults who
learned a miniature artificial language display a similar real-time
pattern of brain activation when processing this language as native
speakers do when processing natural languages. Participants trained in
the artificial language showed two event-related brain potential
components taken to reflect early automatic and late controlled
syntactic processes, whereas untrained participants did not. This
result challenges the common view that late second language learners
process language in a principally different way from native speakers.
Our findings demonstrate that a small system of grammatical rules can
be syntactically instantiated by the adult speaker in a way that
strongly resembles native-speaker sentence processing.
A regulator of G protein signaling interaction surface linked to effector specificity
Authors: Sowa Mathew E. , He Wei , Wensel Theodore G. , Lichtarge Olivier
Published: July 2002

Proteins of the regulator of G protein signaling (RGS) family accelerate GTP hydrolysis by the α subunits (G
α
) of G proteins, leading to rapid recovery of signaling cascades. Many different RGS proteins can accelerate GTP hydrolysis by an individual G
α
, and GTP hydrolysis rates of different G
α
s can be enhanced by the same RGS protein. Consequently, the mechanisms for specificity in RGS regulation and the residues involved remain unclear. Using the evolutionary trace (ET) method, we have identified a cluster of residues in the RGS domain that includes the RGS-G
α
binding interface and extends to include additional functionally important residues on the surface. One of these is within helix α3, two are in α5, and three are in the loop connecting α5 and α6. A cluster of surface residues on G
α
previously identified by ET, and composed predominantly of residues from the switch III region and helix α3, is spatially contiguous with the ET-identified residues in the RGS domain. This cluster includes residues proposed to interact with the γ subunit of G
tα
's effector, cGMP phosphodiesterase (PDEγ). The proximity of these clusters suggests that they form part of an interface between the effector and the RGS-G
α
complex. Sequence variations in these residues correlate with PDEγ effects on GTPase acceleration. Because ET identifies residues important for all members of a protein family, these residues likely form a general site for regulation of G protein-coupled signaling cascades, possibly by means of effector interactions.
Localized neuronal activation in the zebra finch brain is related to the strength of song learning
Authors: Bolhuis Johan J. , Zijlstra Guus G. O. , den Boer-Visser Ardie M. , Van der Zee Eddy A.
Published: July 2002

Songbirds (Oscines) learn their songs from a tutor. It is not known where in the brain the memories of these learned sounds are stored. Recent evidence suggests that song perception in songbirds involves neuronal activation in brain regions that have not traditionally been implicated in the control of song production or song learning, notably the caudal part of the neostriatum (NCM) and of the hyperstriatum ventrale. Zebra finch males (
Taeniopygia guttata castanotis
) were reared without their father and exposed to a tape-recorded song during the sensitive period for song learning. When, as adults, they were reexposed to the tutor song, the males showed increased expression of the protein products of the immediate early genes
egr-1
(ZENK) and c-
fos
in the NCM and caudal hyperstriatum ventrale, but not in the conventional “song-control nuclei.” The strength of the immediate early gene response (which is a reflection of neuronal activation) in the NCM correlated significantly and positively with the number of song elements that the birds had copied from the tutor song. These results show localized neural activation in response to tutor song exposure that correlates with the strength of song learning.
Curvature of co-links uncovers hidden thematic layers in the World Wide Web
Authors: Eckmann Jean-Pierre , Moses Elisha
Published: July 2002

Beyond the information stored in pages of the World Wide Web, novel types of “meta-information” are created when pages connect to each other. Such meta-information is a collective effect of independent agents writing and linking pages, hidden from the casual user. Accessing it and understanding the interrelation between connectivity and content in the World Wide Web is a challenging problem [Botafogo, R. A. & Shneiderman, B. (1991) in
Proceedings of Hypertext
(Assoc. Comput. Mach., New York), pp. 63–77 and Albert, R. & Barabási, A.-L. (2002)
Rev. Mod. Phys.
74, 47–97]. We demonstrate here how thematic relationships can be located precisely by looking only at the graph of hyperlinks, gleaning content and context from the Web without having to read what is in the pages. We begin by noting that reciprocal links (co-links) between pages signal a mutual recognition of authors and then focus on triangles containing such links, because triangles indicate a transitive relation. The importance of triangles is quantified by the clustering coefficient [Watts, D. J. & Strogatz, S. H. (1999)
Nature (London)
393, 440–442], which we interpret as a curvature [Bridson, M. R. & Haefliger, A. (1999)
Metric Spaces of Non-Positive Curvature
(Springer, Berlin)]. This curvature defines a World Wide Web landscape whose connected regions of high curvature characterize a common topic. We show experimentally that reciprocity and curvature, when combined, accurately capture this meta-information for a wide variety of topics. As an example of future directions we analyze the neural network of
Caenorhabditis elegans
, using the same methods.
Polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational release factors
Authors: Uno Makiko , Ito Koichi , Nakamura Yoshikazu
Published: July 2002

The mechanism of stop codon recognition during translation has long been a puzzle. Only recently has it been established that a tripeptide in the bacterial release factors (RFs) 1 and 2 serves as the “anticodon” in deciphering stop codons in mRNA. However, the molecular basis of the accuracy of stop codon recognition is unknown. Although specific tripeptides in the RFs are primarily responsible for selective reading of cognate stop codons, charge-flip variant RF proteins, altered at conserved Glu residues adjacent to the tripeptide-anticodon, are shown here to be crucial to codon recognition. Changes of these Glu residues are capable of triggering polypeptide release at noncognate stop codons and also at sense codons. These changes also reverse the growth inhibition by RFs containing “harmful” tripeptide-anticodon changes. These findings suggest that electrostatic interactions involving negative charges in domain C of the RFs mediate their accurate docking in the ribosome. Our results also establish that the charge flipping creates a phenotype/translation termination by “codon bypassing” via relaxed positioning of the RF tripeptide-anticodon in the decoding pocket of the ribosome.
HemK, a class of protein methyl transferase with similarity to DNA methyl transferases, methylates polypeptide chain release factors, and
hemK
knockout induces defects in translational termination
Authors: Nakahigashi Kenji , Kubo Naoko , Narita Shin-ichiro , Shimaoka Takeshi , Goto Simon , Oshima Taku , Mori Hirotada , Maeda Maki , Wada Chieko , Inokuchi Hachiro
Published: July 2002

HemK, a universally conserved protein of unknown function, has high amino acid similarity with DNA-(adenine-N6) methyl transferases (MTases). A certain mutation in
hemK
gene rescues the photosensitive phenotype of a ferrochelatase-deficient (
hemH)
mutant in
Escherichia coli
. A
hemK
knockout strain of
E. coli
not only suffered severe growth defects, but also showed a global shift in gene expression to anaerobic respiration, as determined by microarray analysis, and this shift may lead to the abrogation of photosensitivity by reducing the oxidative stress. Suppressor mutations that abrogated the growth defects of the
hemK
knockout strain were isolated and shown to be caused by a threonine to alanine change at codon 246 of polypeptide chain release factor (RF) 2, indicating that
hemK
plays a role in translational termination. Consistent with such a role, the
hemK
knockout strain showed an enhanced rate of read-through of nonsense codons and induction of transfer-mRNA-mediated tagging of proteins within the cell. By analysis of the methylation of RF1 and RF2
in vivo
and
in vitro
, we showed that HemK methylates RF1 and RF2
in vitro
within the tryptic fragment containing the conserved GGQ motif, and that
hemK
is required for the methylation within the same fragment of, at least, RF1
in vivo
. This is an example of a protein MTase containing the DNA MTase motif and also a protein-(glutamine-N5) MTase.
Sterol regulation of human fatty acid synthase promoter I requires nuclear factor-Y- and Sp-1-binding sites
Authors: Xiong Shunbin , Chirala Subrahmanyam S. , Wakil Salih J.
Published: July 2002

To understand cholesterol-mediated regulation of human fatty acid synthase promoter I, we tested various 5′-deletion constructs of promoter I-luciferase reporter gene constructs in HepG2 cells. The reporter gene constructs that contained only the Sp-1-binding site (nucleotides −82 to −74) and the two tandem sterol regulatory elements (SREs; nucleotides −63 to −46) did not respond to cholesterol. Only the reporter gene constructs containing a nuclear factor-Y (NF-Y) sequence, the CCAAT sequence (nucleotides −90 to −86), an Sp-1 sequence, and the two tandem SREs responded to cholesterol. The NF-Y-binding site, therefore, is essential for cholesterol response. Mutating the SREs or the NF-Y site and inserting 4 bp between the Sp-1- and NF-Y-binding sites both resulted in a minimal cholesterol response of the reporter genes. Electrophoretic mobility-shift assays using anti-SRE-binding protein (SREBP) and anti-NF-Ya antibodies confirmed that these SREs and the NF-Y site bind the respective factors. We also identified a second Sp-1 site located between nucleotides −40 and −30 that can substitute for the mutated Sp-1 site located between nucleotides −82 and −74. The reporter gene expression of the wild-type promoter and the Sp-1 site (nucleotides −82 to −74) mutant promoter was similar when SREBP1a [the N-terminal domain of SREBP (amino acids 1–520)] was constitutively overexpressed, suggesting that Sp-1 recruits SREBP to the SREs. Under the same conditions, an NF-Y site mutation resulted in significant loss of reporter gene expression, suggesting that NF-Y is required to activate the cholesterol response.
Contributions of distinct quaternary contacts to cooperative operator binding by Mnt repressor
Authors: Berggrun Arie , Sauer Robert T.
Published: July 2002

Mnt, a tetrameric repressor encoded by bacteriophage P22, uses
N-domain dimers to contact each half of its operator site. Experiments
with a double mutant and structural homology with the P22 Arc repressor
suggest that contacts made by Arg-28 and stabilized by Glu-33 are
largely responsible for dimer–dimer cooperativity in Mnt. These
dimer–dimer contacts are energetically more important for operator
binding than solution tetramerization, which is mediated by an
independent C-terminal coiled-coil domain. Indeed, once one dimer of
the Mnt tetramer contacts an operator half site, binding of the second
dimer occurs with an effective concentration much lower than that
expected if both dimers were flexibly tethered. These results suggest
that binding of the second dimer introduces some strain into the
protein–DNA complex, a mechanism that could serve to limit the
affinity of operator binding and to prevent strong binding of the Mnt
tetramer to nonoperator sites.
Identification of proacrosin binding protein sp32 precursor as a human cancer/testis antigen
Authors: Ono Toshiro , Kurashige Takushi , Harada Naoki , Noguchi Yuji , Saika Takashi , Niikawa Norio , Aoe Motoi , Nakamura Shinichiro , Higashi Toshihiro , Hiraki Akio , Wada Hisashi , Kumon Hiromi , Old Lloyd J. , Nakayama Eiichi
Published: July 2002

Serological expression cloning of antigens eliciting a humoral
immune response to a syngeneic mouse sarcoma identified
pem
(mouse placenta and embryonic expression gene) as a
new member of the cancer/testis family. To identify the human
homologue of
pem
, mouse
pem
sequences and
pem
-related expressed sequence tags from human testis
were used as PCR primers for amplification using human testis cDNA.
However, rather than
pem
, another gene, designated
OY-TES-1
, was isolated and found to be the human
homologue of proacrosin binding protein sp32 precursor originally
identified in mouse, guinea pig, and pig.
OY-TES-1
maps
to chromosome 12p12-p13 and contains 10 exons. Southern blot analysis
suggests the presence of two
OY-TES-1-
related genes in
the human genome. In normal tissues,
OY-TES-1
mRNA was
expressed only in testis, whereas in malignant tissues, a variable
proportion of a wide array of cancers, including bladder, breast, lung,
liver, and colon cancers, expressed
OY-TES-1
.
Serological survey of 362 cancer patients with a range of different
cancers showed antibody to OY-TES-1 in 25 patients. No OY-TES-1 sera
reactivity was found in 20 normal individuals. These findings indicate
that OY-TES-1 is an additional member of the cancer/testis family of
antigens and that OY-TES-1 is immunogenic in humans.
Truncated hexa-octahedral magnetite crystals in ALH84001: Presumptive biosignatures
Authors: Thomas-Keprta Kathie L. , Clemett Simon J. , Bazylinski Dennis A. , Kirschvink Joseph L. , McKay David S. , Wentworth Susan J. , Vali Hojatollah , Gibson Everett K. , McKay Mary Fae , Romanek Christopher S.
Published: July 2002

McKayet al.[(1996)Science273, 924–930] suggested that carbonate globules in the meteorite ALH84001 contained the fossil remains of Martian microbes. We have characterized a subpopulation of magnetite (Fe3O4) crystals present in abundance within the Fe-rich rims of these carbonate globules. We find these Martian magnetites to be both chemically and physically identical to terrestrial, biogenically precipitated, intracellular magnetites produced by magnetotactic bacteria strain MV-1. Specifically, both magnetite populations are single-domain and chemically pure, and exhibit a unique crystal habit we describe as truncated hexa-octahedral. There are no known reports of inorganic processes to explain the observation of truncated hexa-octahedral magnetites in a terrestrial sample. In bacteria strain MV-1 their presence is therefore likely a product of Natural Selection. Unless there is an unknown and unexplained inorganic process on Mars that is conspicuously absent on the Earth and forms truncated hexa-octahedral magnetites, we suggest that these magnetite crystals in the Martian meteorite ALH84001 were likely produced by a biogenic process. As such, these crystals are interpreted as Martian magnetofossils and constitute evidence of the oldest life yet found.
Analysis of endoplasmic reticulum trafficking signals by combinatorial screening in mammalian cells
Authors: Zerangue Noa , Malan Michael J. , Fried Sharon R. , Dazin Paul F. , Jan Yuh Nung , Jan Lily Yeh , Schwappach Blanche
Published: July 2002

To improve the accuracy of predicting membrane protein sorting
signals, we developed a general methodology for defining trafficking
signal consensus sequences in the environment of the living cell. Our
approach uses retroviral gene transfer to create combinatorial
expression libraries of trafficking signal variants in mammalian cells,
flow cytometry to sort cells based on trafficking phenotype, and
quantitative trafficking assays to measure the efficacy of individual
signals. Using this strategy to analyze arginine- and lysine-based
endoplasmic reticulum localization signals, we demonstrate that small
changes in the local sequence context dramatically alter signal
strength, generating a broad spectrum of trafficking phenotypes.
Finally, using sequences from our screen, we found that the potency of
di-lysine, but not di-arginine, mediated endoplasmic reticulum
localization was correlated with the strength of interaction with
α-COP.
Complete genomic sequence of
Pasteurella multocida
,Pm70
Authors: May Barbara J. , Zhang Qing , Li Ling Ling , Paustian Michael L. , Whittam Thomas S. , Kapur Vivek
Published: July 2002

We present here the complete genome sequence of a common avian
clone of
Pasteurella multocida
, Pm70. The genome of Pm70
is a single circular chromosome 2,257,487 base pairs in length and
contains 2,014 predicted coding regions, 6 ribosomal RNA operons, and
57 tRNAs. Genome-scale evolutionary analyses based on pairwise
comparisons of 1,197 orthologous sequences between
P.
multocida
,
Haemophilus influenzae
, and
Escherichia coli
suggest that
P.
multocida
and
H. influenzae
diverged ≈270
million years ago and the γ subdivision of the proteobacteria
radiated about 680 million years ago. Two previously undescribed open
reading frames, accounting for ≈1% of the genome, encode large
proteins with homology to the virulence-associated filamentous
hemagglutinin of
Bordetella pertussis
. Consistent with
the critical role of iron in the survival of many microbial pathogens,
in silico
and whole-genome microarray analyses
identified more than 50 Pm70 genes with a potential role in iron
acquisition and metabolism. Overall, the complete genomic sequence and
preliminary functional analyses provide a foundation for future
research into the mechanisms of pathogenesis and host specificity of
this important multispecies pathogen.
Comprehensive analysis of CpG islands in human chromosomes 21 and 22
Authors: Takai Daiya , Jones Peter A.
Published: July 2002

CpG islands are useful markers for genes in organisms containing 5-methylcytosine in their genomes. In addition, CpG islands located in the promoter regions of genes can play important roles in gene silencing during processes such as X-chromosome inactivation, imprinting, and silencing of intragenomic parasites. The generally accepted definition of what constitutes a CpG island was proposed in 1987 by Gardiner-Garden and Frommer [Gardiner-Garden, M. & Frommer, M. (1987)
J. Mol. Biol.
196, 261–282] as being a 200-bp stretch of DNA with a C+G content of 50% and an observed CpG/expected CpG in excess of 0.6. Any definition of a CpG island is somewhat arbitrary, and this one, which was derived before the sequencing of mammalian genomes, will include many sequences that are not necessarily associated with controlling regions of genes but rather are associated with intragenomic parasites. We have therefore used the complete genomic sequences of human chromosomes 21 and 22 to examine the properties of CpG islands in different sequence classes by using a search algorithm that we have developed. Regions of DNA of greater than 500 bp with a G+C equal to or greater than 55% and observed CpG/expected CpG of 0.65 were more likely to be associated with the 5′ regions of genes and this definition excluded most
Alu
-repetitive elements. We also used genome sequences to show strong CpG suppression in the human genome and slight suppression in
Drosophila melanogaster
and
Saccharomyces cerevisiae
. This finding is compatible with the recent detection of 5-methylcytosine in
Drosophila
, and might suggest that
S. cerevisiae
has, or once had, CpG methylation.
Global analysis of proteasomal substrate specificity using positional-scanning libraries of covalent inhibitors
Authors: Nazif Tamim , Bogyo Matthew
Published: July 2002

The proteasome is a large protease complex consisting of
multiple catalytic subunits that function simultaneously to digest
protein substrates. This complexity has made deciphering the role each
subunit plays in the generation of specific protein fragments
difficult. Positional scanning libraries of peptide vinyl sulfones were
generated in which the amino acid located directly at the site of
hydrolysis (P1 residue) was held constant and sequences distal to that
residue (P2, P3, and P4 positions) were varied across all natural amino
acids (except cysteine and methionine). Binding information for each of
the individual catalytic subunits was obtained for each library under a
variety of different conditions. The resulting specificity profiles
indicated that substrate positions distal to P1 are critical for
directing substrates to active subunits in the complex. Furthermore,
specificity profiles of IFN-γ-regulated subunits closely matched
those of their noninducible counterparts, suggesting that subunit
swapping may modulate substrate processing by a mechanism that does
require a change in the primary sequence specificity of individual
catalytic subunits in the complex. Finally, specificity profiles were
used to design specific inhibitors of a single active site in the
complex. These reagents can be used to further establish the role of
each subunit in substrate processing by the proteasome.
Ciliary neurotrophic factor activates leptin-like pathways and reduces body fat, without cachexia or rebound weight gain, even in leptin-resistant obesity
Authors: Lambert P. D. , Anderson K. D. , Sleeman M. W. , Wong V. , Tan J. , Hijarunguru A. , Corcoran T. L. , Murray J. D. , Thabet K. E. , Yancopoulos G. D. , Wiegand S. J.
Published: July 2002

Ciliary Neurotrophic Factor (CNTF) was first characterized as
a trophic factor for motor neurons in the ciliary ganglion and spinal
cord, leading to its evaluation in humans suffering from motor neuron
disease. In these trials, CNTF caused unexpected and substantial weight
loss, raising concerns that it might produce cachectic-like effects.
Countering this possibility was the suggestion that CNTF was working
via a leptin-like mechanism to cause weight loss, based on the findings
that CNTF acts via receptors that are not only related to leptin
receptors, but also similarly distributed within hypothalamic nuclei
involved in feeding. However, although CNTF mimics the ability of
leptin to cause fat loss in mice that are obese because of genetic
deficiency of leptin (ob/ob mice), CNTF is also effective in
diet-induced obesity models that are more representative of human
obesity, and which are resistant to leptin. This discordance again
raised the possibility that CNTF might be acting via nonleptin
pathways, perhaps more analogous to those activated by cachectic
cytokines. Arguing strongly against this possibility, we now show that
CNTF can activate hypothalamic leptin-like pathways in diet-induced
obesity models unresponsive to leptin, that CNTF improves prediabetic
parameters in these models, and that CNTF acts very differently than
the prototypical cachectic cytokine, IL-1. Further analyses of
hypothalamic signaling reveals that CNTF can suppress food intake
without triggering hunger signals or associated stress responses that
are otherwise associated with food deprivation; thus, unlike forced
dieting, cessation of CNTF treatment does not result in binge
overeating and immediate rebound weight gain.
Leukotriene A
4
hydrolase: Selective abrogation of leukotriene B
4
formation by mutation of aspartic acid 375
Authors: Rudberg Peter C. , Tholander Fredrik , Thunnissen Marjolein M. G. M. , Samuelsson Bengt , Haeggström Jesper Z.
Published: July 2002

Leukotriene A
4
(LTA
4
, 5S-
trans
-5,6-oxido-7,9-
trans
-11,14-
cis
-eicosatetraenoic acid) hydrolase (LTA4H)/aminopeptidase is a bifunctional zinc metalloenzyme that catalyzes the final and rate-limiting step in the biosynthesis of leukotriene B
4
(LTB
4
, 5S,12R-dihydroxy-6,14-
cis
-8,10-
trans
-eicosatetraenoic acid), a classical chemoattractant and immune modulating lipid mediator. Two chemical features are key to the bioactivity of LTB
4
, namely, the chirality of the 12
R
-hydroxyl group and the cis
-
trans
-
trans geometry of the conjugated triene structure. From the crystal structure of LTA4H, a hydrophilic patch composed of Gln-134, Tyr-267, and Asp-375 was identified in a narrow and otherwise hydrophobic pocket, believed to bind LTA
4
. In addition, Asp-375 belongs to peptide K21, a previously characterized 21-residue active site-peptide to which LTA
4
binds during suicide inactivation. In the present report we used site-directed mutagenesis and x-ray crystallography to show that Asp-375, but none of the other candidate residues, is specifically required for the epoxide hydrolase activity of LTA4H. Thus, mutation of Asp-375 leads to a selective loss of the enzyme's ability to generate LTB
4
whereas the aminopeptidase activity is preserved. We propose that Asp-375, possibly assisted by Gln-134, acts as a critical determinant for the stereoselective introduction of the 12
R
-hydroxyl group and thus the biological activity of LTB
4
.
Transforming growth factor β-inducible independent binding of SMAD to the Smad7 promoter
Authors: Denissova Natalia G. , Pouponnot Celio , Long Jianyin , He Dongming , Liu Fang
Published: July 2002

SMAD proteins can mediate transforming growth factor β (TGF-β)-inducible transcriptional responses. Whereas SMAD can recognize specific DNA sequences, it is usually recruited to a promoter through interaction with a DNA-binding partner. In an effort to search for TGF-β-inducible genes, we used a subtractive screening method and identified human Smad7, which can antagonize TGF-β signaling and is rapidly up-regulated by TGF-β. In this report, we show that TGF-β can stabilize Smad7 mRNA and activate Smad7 transcription. The Smad7 promoter is the first TGF-β responsive promoter identified in vertebrates that contains the 8-bp palindromic SMAD-binding element (SBE), an optimal binding site previously identified by a PCR-based selection from random oligonucleotides by using recombinant Smad3 and Smad4. We demonstrate that on TGF-β treatment, endogenous SMAD complex can bind to a Smad7 promoter DNA as short as 14 or 16 bp that contains the 8-bp SBE in gel mobility shift and supershift assays. Our studies provide strong evidence that SMAD proteins can bind to a natural TGF-β responsive promoter independent of other sequencespecific transcription factors. We further show that, whereas recombinant Smad3 binds to the SBE, endogenous or even transfected Smad3 cannot bind to the SBE in the absence of Smad4. These findings have important implications in the identification of target genes of the TGF-β/SMAD signaling pathways.
Amygdala-enriched genes identified by microarray technology are restricted to specific amygdaloid subnuclei
Authors: Zirlinger Mariela , Kreiman Gabriel , Anderson David J.
Published: July 2002

Microarray technology represents a potentially powerful method for
identifying cell type- and regionally restricted genes expressed in the
brain. Here we have combined a microarray analysis of differential gene
expression among five selected brain regions, including the amygdala,
cerebellum, hippocampus, olfactory bulb, and periaqueductal gray, with
in situ
hybridization. On average, 0.3% of the 34,000
genes interrogated were highly enriched in each of the five regions,
relative to the others.
In situ
hybridization performed
on a subset of amygdala-enriched genes confirmed in most cases the
overall region-specificity predicted by the microarray data and
identified additional sites of brain expression not examined on the
microarrays. Strikingly, the majority of these genes exhibited
boundaries of expression within the amygdala corresponding to
cytoarchitectonically defined subnuclei. These results define a unique
set of molecular markers for amygdaloid subnuclei and provide tools to
genetically dissect their functional roles in different emotional
behaviors.
Defective regulatory volume decrease in human cystic fibrosis tracheal cells because of altered regulation of intermediate conductance Ca
2+
-dependent potassium channels
Authors: Vázquez Esther , Nobles Muriel , Valverde Miguel A.
Published: July 2002

The cystic fibrosis transmembrane conductance regulator (CFTR)
protein has the ability to function as both a chloride channel and a
channel regulator. The loss of these functions explains many of the
manifestations of the cystic fibrosis disease (CF), including lung and
pancreatic failure, meconium ileus, and male infertility. CFTR has
previously been implicated in the cell regulatory volume decrease (RVD)
response after hypotonic shocks in murine small intestine crypts, an
effect associated to the dysfunction of an unknown swelling-activated
potassium conductance. In the present study, we investigated the RVD
response in human tracheal CF epithelium and the nature of the
volume-sensitive potassium channel affected. Neither the human tracheal
cell line CFT1, expressing the mutant CFTR-ΔF508 gene, nor the
isogenic vector control line CFT1-LC3, engineered to express the βgal
gene, showed RVD. On the other hand, the cell line CFT1-LCFSN,
engineered to express the wild-type CFTR gene, presented a full RVD.
Patch-clamp studies of swelling-activated potassium currents in the
three cell lines revealed that all of them possess a potassium current
with the biophysical and pharmacological fingerprints of the
intermediate conductance Ca
2+
-dependent potassium channel
(IK, also known as KCNN4). However, only CFT1-LCFSN cells showed an
increase in IK currents in response to hypotonic challenges. Although
the identification of the molecular mechanism relating CFTR to the hIK
channel remains to be solved, these data offer new evidence on the
complex integration of CFTR in the cells where it is expressed.
Virulence of aMycobacterium tuberculosisclinical isolate in mice is determined by failure to induce Th1 type immunity and is associated with induction of IFN-α/β
Authors: Manca Claudia , Tsenova Liana , Bergtold Amy , Freeman Sherry , Tovey Michael , Musser James M. , Barry Clifton E. , Freedman Victoria H. , Kaplan Gilla
Published: July 2002

To understand how virulent mycobacteria subvert host immunity and establish disease, we examined the differential response of mice to infection with various human outbreakMycobacterium tuberculosisclinical isolates. One clinical isolate, HN878, was found to be hypervirulent, as demonstrated by unusually early death of infected immune-competent mice, compared with infection with other clinical isolates. The differential effect on survival required lymphocyte function because severe combined immunodeficiency (SCID) mice infected with HN878 or other clinical isolates all died at the same rate. The hypervirulence of HN878 was associated with failure to induceM. tuberculosis-specific proliferation and IFN-γ production by spleen and lymph node cells from infected mice. In addition, 2- to 4-fold lower levels of tumor necrosis factor-α (TNF-α), IL-6, IL-12, and IFN-γ mRNAs were observed in lungs of HN878-infected mice. IL-10, IL-4, and IL-5 mRNA levels were not significantly elevated in lungs of HN878 infected mice. In contrast, IFN-α mRNA levels were significantly higher in lungs of these mice. To further investigate the role of Type 1 IFNs, mice infected with HN878 were treated intranasally with purified IFN-α/β. The treatment resulted in increased lung bacillary loads and even further reduced survival. These results suggest that the hypervirulence of HN878 may be due to failure of this strain to stimulate Th1 type immunity. In addition, the lack of development of Th1 immunity in response to HN878 appears to be associated with increased induction of Type 1 IFNs.
Comprehensive copy number and gene expression profiling of the 17q23 amplicon in human breast cancer
Authors: Monni Outi , Bärlund Maarit , Mousses Spyro , Kononen Juha , Sauter Guido , Heiskanen Mervi , Paavola Paulina , Avela Kristiina , Chen Yidong , Bittner Michael L. , Kallioniemi Anne
Published: July 2002

The biological significance of DNA amplification in cancer is thought to be due to the selection of increased expression of a single or few important genes. However, systematic surveys of the copy number and expression of all genes within an amplified region of the genome have not been performed. Here we have used a combination of molecular, genomic, and microarray technologies to identify target genes for 17q23, a common region of amplification in breast cancers with poor prognosis. Construction of a 4-Mb genomic contig made it possible to define two common regions of amplification in breast cancer cell lines. Analysis of 184 primary breast tumors by fluorescencein situhybridization on tissue microarrays validated these results with the highest amplification frequency (12.5%) observed for the distal region. Based on GeneMap'99 information, 17 known genes and 26 expressed sequence tags were localized to the contig. Analysis of genomic sequence identified 77 additional transcripts. A comprehensive analysis of expression levels of these transcripts in six breast cancer cell lines was carried out by using complementary DNA microarrays. The expression patterns varied from one cell line to another, and several overexpressed genes were identified. Of these,RPS6KB1,MUL,APPBP2,andTRAP240as well as one uncharacterized expressed sequence tag were located in the two common amplified regions. In summary, comprehensive analysis of the 17q23 amplicon revealed a limited number of highly expressed genes that may contribute to the more aggressive clinical course observed in breast cancer patients with 17q23-amplified tumors.
Establishment and persistence of photoperiodic memory in hamsters
Authors: Prendergast Brian J. , Gorman Michael R. , Zucker Irving
Published: July 2002

Long summer days unequivocally stimulate, and short winter days inhibit reproduction in Siberian hamsters. By contrast, intermediate-duration day lengths (12.5–14 h long) either accelerate reproductive development or initiate regression of the reproductive apparatus. Which of these outcomes transpires depends on an animal's photoperiodic history, suggesting that hamsters must encode a representation of prior photoperiods. The duration of nocturnal melatonin secretion is the endocrine representation of day length, but nothing is known about how long it takes to establish photoperiodic histories or how long they endure. Hamsters exposed for 2 or more weeks to long summer day lengths acquired a long-day photoperiodic history that determined subsequent reproductive responses to intermediate-duration day lengths and melatonin signals. The memory for long-day lengths persisted in pinealectomized hamsters for 6.5 weeks, faded significantly after 13 weeks, and was functionally absent after 20 weeks. These findings indicate that hamsters are influenced only by relatively recent day lengths and melatonin signals and ignore earlier ones that might cause them to misinterpret the salience of current day lengths.
Drosophila Thor
participates in host immune defense and connects a translational regulator with innate immunity
Authors: Bernal Alejandro , Kimbrell Deborah A.
Published: July 2002

Thor
has been identified as a new type of gene involved in
Drosophila
host immune defense.
Thor
is a member of the
4E-binding protein
(
4E-BP
) family, which in mammals has been defined as critical regulators in a pathway that controls initiation of translation through binding eukaryotic initiation factor 4E (eIF4E). Without an infection,
Thor
is expressed during all developmental stages and transcripts localize to a wide variety of tissues, including the reproductive system. In response to bacterial infection and, to a lesser extent, by wounding,
Thor
is up-regulated. The
Thor
promoter has the canonical NFκB and associated GATA recognition sequences that have been shown to be essential for immune induction, as well as other sequences commonly found for
Drosophila
immune response genes, including interferon-related regulatory sequences. In survival tests,
Thor
mutants show symptoms of being immune compromised, indicating that
Thor
may be critical in host defense. In contrast to
Thor
,
Drosophila eIF4E
is not induced by bacterial infection. These findings for
Thor
provide the first evidence that a
4E-BP
family member has a role in immune induction in any organism. Further, no gene in the translation initiation pathway that includes 4E-BP has been previously found to be immune induced. Our results suggest either a role for translational regulation in humoral immunity or a new, nontranslational function for
4E-BP
type genes.
Permissive proteolytic activity for visual cortical plasticity
Authors: Mataga Nobuko , Nagai Nobuo , Hensch Takao K.
Published: July 2002

The serine protease, tissue-type plasminogen activator (tPA) is a key regulator of extracellular proteolytic cascades. We demonstrate a requirement for tPA signaling in the experience-dependent plasticity of mouse visual cortex during the developmental critical period. Proteolytic activity by tPA in the binocular zone was typically increased within 2 days of monocular deprivation (MD). This regulation failed to occur in glutamic acid decarboxylase (GAD) 65 knockout mice, an animal model of impaired ocular dominance plasticity because of reduced γ-aminobutyric acid (GABA)-mediated transmission described previously. Loss of responsiveness to the deprived eye consequent to MD was conversely suppressed in mice lacking tPA despite normal levels of neuronal activity. Plasticity was restored in a gene dose-dependent manner, or by direct tPA infusion. Permissive amounts of tPA may, thus, couple functional to structural changes downstream of the excitatory-inhibitory balance that triggers visual cortical plasticity. Our results not only support a molecular cascade leading to neurite outgrowth after sensory deprivation, but also identify a valuable tool for further proteomic and genomic dissection of experience-dependent plasticity downstream of electrical activity.
Scavenger endothelial cells of vertebrates: A nonperipheral leukocyte system for high-capacity elimination of waste macromolecules
Authors: Seternes Tore , Sørensen Karen , Smedsrød Bård
Published: July 2002

Studies over the last two decades have shown that mammalian nonmacrophagic liver endothelial cells clear the blood from numerous physiological and foreign waste macromolecules, such as polysaccharides and proteins released during extracellular matrix turnover, intracellular macromolecules, modified serum proteins, and bacterial and fungal proteins [Smedsrød, B., Pertoft, H., Gustafson, S. & Laurent, T. C. (1990)
Biochem. J.
266, 313–327]. These macromolecules are released daily in gram-amounts in a normal human body and are effectively taken up and degraded by the liver endothelial cells. Recent studies show that bony fishes harbor a similar system of specialized nonmacrophagic scavenger endothelial cells in either kidney [Smedsrød, B., Gjøen, T., Sveinbjørnsson, B. & Berg, T. (1993)
J. Fish Biol.
42, 279–291] or heart [Sørensen, K. K., Melkko, J. & Smedsrød, B. (1998)
J. Exp. Biol.
201, 1707–1718], but not in liver. Using specific and extremely effective endocytosis, these fish scavenger endothelial cells function as their mammalian counterpart to eliminate soluble waste macromolecules from the circulation. We show here that species from all seven vertebrate classes carry a population of nonmacrophagic scavenger endothelial cells that efficiently eliminate an array of circulating waste macromolecules. Thus representing an important part of the vertebrate innate immune system, these scavenger endothelial cells display the following distribution in the different vertebrate classes: Gills in Agnatha and Chondrichtyes; heart or kidney in Osteichtyes; and liver in Amphibia, Reptilia, Aves, and Mammalia.
Synergistic transcriptional activation by one regulatory protein in response to two metabolites
Authors: Bundy Becky M. , Collier Lauren S. , Hoover Timothy R. , Neidle Ellen L.
Published: July 2002

BenM is a LysR-type bacterial transcriptional regulator that controls aromatic compound degradation in
Acinetobacter
sp. ADP1. Here,
in vitro
transcription assays demonstrated that two metabolites of aromatic compound catabolism, benzoate and
cis,cis
-muconate, act synergistically to activate gene expression. The level of BenM-regulated
benA
transcription was significantly higher in response to both compounds than the combined levels due to each alone. These compounds also were more effective together than they were individually in altering the DNase I footprint patterns of BenM-DNA complexes. This type of dual-inducer synergy provides great potential for rapid and large modulations of gene expression and may represent an important, and possibly widespread, feature of transcriptional control.