bluuebunny/crossref_metadata_2025 huggingface dataset:
Melanin-concentrating hormone is a critical mediator of the leptin-deficient phenotype
Authors: Segal-Lieberman Gabriella , Bradley Richard L. , Kokkotou Efi , Carlson Michael , Trombly Daniel J. , Wang Xiaomei , Bates Sarah , Myers Martin G. , Flier Jeffrey S. , Maratos-Flier Eleftheria
Published: August 2003

Energy homeostasis is regulated by a complex network involving peripheral
and central signals that determine food intake and energy expenditure.
Melanin-concentrating hormone (MCH) plays an essential role in this process.
Animals treated with MCH develop hyperphagia and obesity. Ablation of the
prepro-MCH gene leads to a lean phenotype, as does ablation of the rodent MCH
receptor, MCHR-1. MCH is overexpressed in the leptin-deficient
ob
/
ob
mouse, and we hypothesized that ablation of MCH in
this animal would lead to attenuation of its obese phenotype. Compared with
ob
/
ob
animals, mice lacking both leptin and MCH (double
null) had a dramatic reduction in body fat. Surprisingly, the hyperphagia of
the
ob
/
ob
mouse was unaffected. Instead, leanness was
secondary to a marked increase in energy expenditure resulting from both
increased resting energy expenditure and locomotor activity. Furthermore,
double-null mice showed improvements in other parameters impaired in
ob
/
ob
mice. Compared with
ob
/
ob
mice,
double-null animals had increased basal body temperature, improved response to
cold exposure, lower plasma glucocorticoid levels, improved glucose tolerance,
and reduced expression of stearoyl-CoA desaturase 1 (SCD-1). These results
highlight the importance of MCH in integration of energy homeostasis
downstream of leptin and, in particular, the role of MCH in regulation of
energy expenditure.
Polar auxin transport in the wood-forming tissues of hybrid aspen is under simultaneous control of developmental and environmental signals
Authors: Schrader J. , Baba K. , May S. T. , Palme K. , Bennett M. , Bhalerao R. P. , Sandberg G.
Published: August 2003

Recent research has highlighted the importance of auxin concentration
gradients during plant development. Establishment of these gradients is
believed to involve polar auxin transport through specialized carrier
proteins. We have used an experimental system, the wood-forming tissue of
hybrid aspen, which allows tissue-specific expression analysis of auxin
carrier genes and quantification of endogenous concentrations of the hormone.
As part of this study, we isolated the putative polar auxin transport genes,
PttLAX1
–
PttLAX3
and
PttPIN1
–
PttPIN3
, belonging to the AUX1-like family of
influx and PIN1-like efflux carriers, respectively. Analysis of
PttLAX
and
PttPIN
expression suggests that specific
positions in a concentration gradient of the hormone are associated with
different stages of vascular cambium development and expression of specific
members of the auxin transport gene families. We were also able demonstrate
positive feedback of auxin on polar auxin transport genes. Entry into dormancy
at the end of a growing season leads to a loss of auxin transport capacity,
paralleled by reduced expression of
PttLAX
and
PttPIN
genes.
Furthermore, data from field experiments show that production of the molecular
components of the auxin transport machinery is governed by environmental
controls. Our findings collectively demonstrate that trees have developed
mechanisms to modulate auxin transport in the vascular meristem in response to
developmental and environmental cues.
Selective thyroid hormone receptor-β activation: A strategy for reduction of weight, cholesterol, and lipoprotein (a) with reduced cardiovascular liability
Authors: Grover Gary J. , Mellström Karin , Ye Liu , Malm Johan , Li Yi-Lin , Bladh Lars-Göran , Sleph Paul G. , Smith Mark A. , George Rocco , Vennström Björn , Mookhtiar Kasim , Horvath Ryan , Speelman Jessica , Egan Donald , Baxter John D.
Published: August 2003

Few treatments for obesity exist and, whereas efficacious therapeutics for
hyperlipidemia are available, further improvements are desirable. Thyroid
hormone receptors (TRs) regulate both body weight and cholesterol levels.
However, thyroid hormones also have deleterious effects, particularly on the
heart. The TRβ subtype is involved in cholesterol lowering and possibly
elevating metabolic rate, whereas TRα appears to be more important for
control of heart rate (HR). In the current studies, we examined the effect of
TRβ activation on metabolic rate and HR with either
TR
α
1
–
/
–
mice or the selective TRβ agonist KB-141 in mice, rats, and monkeys.
3,5,3′-triiodi-
l
-thyronine (T
3
) had a greater
effect on increasing HR in WT than in
TR
α
–
/
–
mice
(ED
15
values of 34 and 469 nmol/kg/day, respectively).
T
3
increased metabolic rate [whole body oxygen consumption
(MV
O
2
)] in both WT and
TR
α
–
/
–
mice, but
the effect in the
TR
α
1
–
/
–
mice at the highest dose was half that of the WT mice. Thus, stimulation of
MV
O
2
is likely due to both TRα and -β.
T
3
had equivalent potency for cholesterol reduction in WT and
TR
α
–
/
–
mice.
KB-141 increased MV
O
2
with selectivities of 16.5- and
11.2-fold vs. HR in WT and
TR
α
1
–
/
–
mice, respectively. KB-141 also increased MV
O
2
with a
10-fold selectivity and lowered cholesterol with a 27-fold selectivity vs. HR
in rats. In primates, KB-141 caused significant cholesterol, lipoprotein (a),
and body-weight reduction (up to 7% after 1 wk) with no effect on HR.
TRβ-selective agonists may constitute a previously uncharacterized class
of drugs to treat obesity, hypercholesterolemia, and elevated lipoprotein
(a).
ELG1
, a yeast gene required for genome stability, forms a complex related to replication factor C
Authors: Ben-Aroya Shay , Koren Amnon , Liefshitz Batia , Steinlauf Rivka , Kupiec Martin
Published: August 2003

Many overlapping surveillance and repair mechanisms operate in eukaryotic
cells to ensure the stability of the genome. We have screened to isolate yeast
mutants exhibiting increased levels of recombination between repeated
sequences. Here we characterize one of these mutants,
elg1
. Strains
lacking Elg1p exhibit elevated levels of recombination between homologous and
nonhomologous chromosomes, as well as between sister chromatids and direct
repeats. These strains also exhibit increased levels of chromosome loss. The
Elg1 protein shares sequence homology with the large subunit of the clamp
loader replication factor C (RFC) and with the product of two additional genes
involved in checkpoint functions and genome maintenance:
RAD24
and
CTF18
. Elg1p forms a complex with the Rfc2–5 subunits of RFC
that is distinct from the previously described RFC-like complexes containing
Rad24 and Ctf18. Genetic data indicate that the Elg1, Ctf18, and Rad24
RFC-like complexes work in three separate pathways important for maintaining
the integrity of the genome and for coping with various genomic stresses.
Shrinkage-based similarity metric for cluster analysis of microarray data
Authors: Cherepinsky Vera , Feng Jiawu , Rejali Marc , Mishra Bud
Published: August 2003

The current standard correlation coefficient used in the analysis of
microarray data was introduced by M. B. Eisen, P. T. Spellman, P. O. Brown,
and D. Botstein [(1998)
Proc. Natl. Acad. Sci. USA
95,
14863–14868]. Its formulation is rather arbitrary. We give a
mathematically rigorous correlation coefficient of two data vectors based on
James–Stein shrinkage estimators. We use the assumptions described by
Eisen
et al.
, also using the fact that the data can be treated as
transformed into normal distributions. While Eisen
et al.
use zero as
an estimator for the expression vector mean μ, we start with the assumption
that for each gene, μ is itself a zero-mean normal random variable [with
a priori
distribution

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], and
use Bayesian analysis to obtain
a posteriori
distribution of μ in
terms of the data. The shrunk estimator for μ differs from the mean of the
data vectors and ultimately leads to a statistically robust estimator for
correlation coefficients. To evaluate the effectiveness of shrinkage, we
conducted
in silico
experiments and also compared similarity metrics
on a biological example by using the data set from Eisen
et al.
For
the latter, we classified genes involved in the regulation of yeast cell-cycle
functions by computing clusters based on various definitions of correlation
coefficients and contrasting them against clusters based on the activators
known in the literature. The estimated false positives and false negatives
from this study indicate that using the shrinkage metric improves the accuracy
of the analysis.
Advantages of external periodic events to the evolution of biochemical oscillatory reactions
Authors: Tsuchiya Masa , Ross John
Published: August 2003

We compare, by calculations on a simple model of glycolysis, the
evolutionary development of oscillatory reaction mechanisms in the presence
and absence of external periodic events, such as an oscillatory or constant
influx of glucose in an open reaction system. The chosen model has autonomous
oscillations for given choices of the parameters of the feedback loops
responsible for the oscillations, and for a given range of the total adenylate
pool concentration. We change first one, then two of the parameters, so that
there are no autonomous oscillations, and then vary these parameters with a
genetic algorithm method in which the parameters are represented by binary
strings that evolve by selection, crossover, and mutations; the optimization
goal is the attainment of a high ATP/ADP concentration ratio in the system.
This goal is taken to provide evolutionary advantages and is shown to be
achieved more quickly in the presence of external periodic events, rather than
constant influx of glucose. The results suggest the possibility of the
enhanced evolutionary development of oscillatory biological reactions at
shores where waves impinge on rocks and bring nutrients periodically.
Measurements have shown that animals and plants grow more rapidly in the
presence of such wave action than in its absence.
Regulation of the murine renal vitamin D receptor by 1,25-dihydroxyvitamin D3and calcium
Authors: Healy Kevin D. , Zella Julia B. , Prahl Jean M. , DeLuca Hector F.
Published: August 2003

Renal vitamin D receptor (VDR) is required for 1,25-dihydroxyvitamin D3-[1,25(OH)2D3]-induced renal reabsorption of calcium and for 1,25(OH)2D3-induced 1,25(OH)2D324-hydroxylase. The long-term effect of vitamin D and dietary calcium on the expression of renal VDR was examined in the nonobese diabetic mouse. Vitamin D-deficient and vitamin D-replete mice were maintained on diets containing 0.02%, 0.25%, 0.47%, and 1.20% calcium with or without 50 ng of 1,25(OH)2D3per day. Vitamin D-replete mice on a 1.20% calcium diet had renal VDR levels of 165 fmol/mg protein. Calcium restriction caused renal VDR levels to decrease to <30 fmol/mg protein in vitamin D-deficient mice and to ≈80 fmol/mg protein in vitamin D-replete mice. When dietary calcium was present, 50 ng of 1,25(OH)2D3elevated the VDR levels 2- to 10-fold, depending on vitamin D status and the level of calcium. In the absence of either vitamin D or calcium, the VDR mRNA was expressed at a basal level. 1,25(OH)2D3supplementation caused relative VDR mRNA to increase 8- to 10-fold in the vitamin D-deficient mouse when dietary calcium was available. This increase was completely absent in the calcium-restricted mice. Thisin vivostudy demonstrates that 1,25(OH)2D3and calcium are both required for renal VDR mRNA expression above a basal level, furthering our understanding of the complex regulation of renal VDR by 1,25(OH)2D3and calcium.
Functional mutants of the sequence-specific transcription factor p53 and implications for master genes of diversity
Authors: Resnick Michael A. , Inga Alberto
Published: August 2003

There are many sources of genetic diversity, ranging from programmed
mutagenesis in antibody genes to random mutagenesis during species evolution
or development of cancer. We propose that mutations in DNA sequence-specific
transcription factors that target response elements (REs) in many genes can
also provide for rapid and broad phenotypic diversity, if the mutations lead
to altered binding affinities at individual REs. To test this concept, we
examined the
in vivo
transactivation capacity of wild-type human and
murine p53 and 25 partial function mutants. The p53s were expressed in yeast
from a rheostatable promoter, and the transactivation capacities toward >15
promoter REs upstream of a reporter gene were measured. Surprisingly, there
was wide variation in transactivation by the mutant p53s toward the various
REs. This is the first study to address directly the impact of mutations in a
sequence-specific transcription factor on transactivation from a wide array of
REs. We propose a master gene hypothesis for phenotypic diversity where the
master gene is a single transcriptional activator (or repressor) that
regulates many genes through different REs. Mutations of the master gene can
lead to a variety of simultaneous changes in both the selection of targets and
the extent of transcriptional modulation at the individual targets, resulting
in a vast number of potential phenotypes that can be created with minimal
mutational changes without altering existing protein–protein
interactions.
Insights into the mode of inhibition of human mitochondrial monoamine oxidase B from high-resolution crystal structures
Authors: Binda Claudia , Li Min , Hubálek Frantisek , Restelli Nadia , Edmondson Dale E. , Mattevi Andrea
Published: August 2003

Monoamine oxidase B (MAO-B) is an outer mitochondrial membrane-bound enzyme
that catalyzes the oxidative deamination of arylalkylamine neurotransmitters
and has been a target for a number of clinically used drug inhibitors. The
1.7-Å structure of the reversible isatin–MAO-B complex has been
determined; it forms a basis for the interpretation of the enzyme's structure
when bound to either reversible or irreversible inhibitors.
1,4-Diphenyl-2-butene is found to be a reversible MAO-B inhibitor, which
occupies both the entrance and substrate cavity space in the enzyme.
Comparison of these two structures identifies Ile-199 as a “gate”
between the two cavities. Rotation of the side chain allows for either
separation or fusion of the two cavities. Inhibition of the enzyme with
N
-(2-aminoethyl)-
p
-chlorobenzamide results in the formation
of a covalent N(5) flavin adduct with the phenyl ring of the inhibitor
occupying a position in the catalytic site overlapping that of isatin.
Inhibition of MAO-B with the clinically used
trans
-2-phenylcyclopropylamine results in the formation of a covalent
C(4a) flavin adduct with an opened cyclopropyl ring and the phenyl ring in a
parallel orientation to the flavin. The peptide bond between the
flavin-substituted Cys-397 and Tyr-398 is in a
cis
conformation,
which allows the proper orientation of the phenolic ring of Tyr-398 in the
active site. The flavin ring exists in a twisted nonplanar conformation, which
is observed in the oxidized form as well as in both the N(5) and the C(4a)
adducts. An immobile water molecule is H-bonded to Lys-296 and to the N(5) of
the flavin as observed in other flavin-dependent amine oxidases. The active
site cavities are highly apolar; however, hydrophilic areas exist near the
flavin and direct the amine moiety of the substrate for binding and catalysis.
Small conformational changes are observed on comparison of the different
inhibitor–enzyme complexes. Future MAO-B drug design will need to
consider “induced fit” contributions as an element in
ligand–enzyme interactions.
Expression ofBCR/ABLandBCL-2in myeloid progenitors leads to myeloid leukemias
Authors: Jaiswal Siddhartha , Traver David , Miyamoto Toshihiro , Akashi Koichi , Lagasse Eric , Weissman Irving L.
Published: August 2003

Chronic myelogenous leukemia is a myeloproliferative disorder (MPD) that, over time, progresses to acute leukemia. Both processes are closely associated with the t(9;22) chromosomal translocation that creates theBCR/ABLfusion gene in hematopoietic stem cells (HSCs) and their progeny. Chronic myelogenous leukemia is therefore classified as an HSC disorder in which a clone of multipotent HSCs is likely to be malignantly transformed, although direct evidence for malignant t(9;22)+HSCs is lacking. To test whether HSC malignancy is required, we generated hMRP8p210BCR/ABLtransgenic mice in which expression ofBCR/ABLis absent in HSCs and targeted exclusively to myeloid progenitors and their myelomonocytic progeny. Four of 13BCR/ABLtransgenic founders developed a chronic MPD, but only one progressed to blast crisis. To address whether additional oncogenic events are required for progression to acute disease, we crossed hMRP8p210BCR/ABLmice to apoptosis-resistant hMRP8BCL-2mice. Of 18 double-transgenic animals, 9 developed acute myeloid leukemias that were transplantable to wild-type recipients. Taken together, these data indicate that a MPD can arise in mice without expression ofBCR/ABLin HSCs and that additional mutations inhibiting programmed cell death may be critical in the transition of this disease to blast-crisis leukemia.
A morphometric analysis of auditory brain regions in congenitally deaf adults
Authors: Emmorey Karen , Allen John S. , Bruss Joel , Schenker Natalie , Damasio Hanna
Published: August 2003

We investigated whether variation in auditory experience in humans during
development alters the macroscopic neuroanatomy of primary or auditory
association cortices. Volumetric analyses were based on MRI data from 25
congenitally deaf subjects and 25 hearing subjects, all right-handed. The
groups were matched for gender and age. Gray and white matter volumes were
determined for the temporal lobe, superior temporal gyrus, Heschl's gyrus
(HG), and the planum temporale. Deaf and hearing subjects did not differ in
the total volume or the gray matter volume of HG, which suggests that auditory
deafferentation does not lead to cell loss within primary auditory cortex in
humans. However, deaf subjects had significantly larger gray
matter–white matter ratios than hearing subjects in HG, with deaf
subjects exhibiting significantly less white matter in both left and right HG.
Deaf subjects also had higher gray matter–white matter ratios in the
rest of the superior temporal gyrus, but this pattern was not observed for the
temporal lobe as a whole. These findings suggest that auditory deprivation
from birth results in less myelination and/or fewer fibers projecting to and
from auditory cortices. Finally, the volumes of planum temporale and HG were
significantly larger in the left hemisphere for both groups, suggesting that
leftward asymmetries within “auditory” cortices do not arise from
experience with auditory processing.
Separating pitch chroma and pitch height in the human brain
Authors: Warren J. D. , Uppenkamp S. , Patterson R. D. , Griffiths T. D.
Published: August 2003

Musicians recognize pitch as having two dimensions. On the keyboard, these
are illustrated by the octave and the cycle of notes within the octave. In
perception, these dimensions are referred to as pitch height and pitch chroma,
respectively. Pitch chroma provides a basis for presenting acoustic patterns
(melodies) that do not depend on the particular sound source. In contrast,
pitch height provides a basis for segregation of notes into streams to
separate sound sources. This paper reports a functional magnetic resonance
experiment designed to search for distinct mappings of these two types of
pitch change in the human brain. The results show that chroma change is
specifically represented anterior to primary auditory cortex, whereas height
change is specifically represented posterior to primary auditory cortex. We
propose that tracking of acoustic information streams occurs in anterior
auditory areas, whereas the segregation of sound objects (a crucial aspect of
auditory scene analysis) depends on posterior areas.
Nuclear import of hepatitis B virus capsids and release of the viral genome
Authors: Rabe Birgit , Vlachou Angelika , Panté Nelly , Helenius Ari , Kann Michael
Published: August 2003

While studying the import of the hepatitis B virus genome into the nucleus
of permeabilized tissue culture cells, we found that viral capsids were
imported in intact form through the nuclear pore into the nuclear basket.
Import depended on phosphorylation of the capsid protein and was mediated by
the cellular transport receptors importin α and β. Virus-derived
capsids that contained the mature viral genome were able to release the viral
DNA and capsid protein into the nucleoplasm. The uncoating reaction was
independent of Ran, a GTP-binding enzyme responsible for dissociating other
imported cargoes from the inner face of the nuclear pore. Immature capsids
that did not contain the mature viral genome reached the basket but did not
release capsid proteins nor immature genomes into the nucleoplasm. The
different fate of mature and immature capsids after passing the nuclear pore
indicates that the outcome of a nuclear import event may be regulated within
the nuclear basket.
Traveling stripes on the skin of a mutant mouse
Authors: Suzuki Noboru , Hirata Masashi , Kondo Shigeru
Published: August 2003

In the course of animal development, complex structures form autonomously
from the apparently shapeless egg. How cells can produce spatial patterns that
are much larger than each cell is one of the key issues in developmental
biology. It has been suggested that spatial patterns in animals form through
the same principles by which dispatched structures are formed in the
nonbiological system. However, because of the complexity of biological
systems, molecular details of such phenomena have been rarely clarified. In
this article, we introduce an example of a pattern-forming phenomenon that
occurs in the skin of mutant mice. The mutant mouse has a defect in splicing
of the
Foxn1
(
Whn
or
nude
) gene, which terminates
hair follicle development just after pigment begins to accumulate in the
follicle. The immature follicles are rapidly discharged, and a new hair cycle
resumes. Eventually, the skin color of the mouse appears to oscillate. The
color oscillation is synchronous in juvenile mice, but the phase gradually
shifts among skin regions to eventually form traveling, evenly spaced stripes.
Although the time scale is quite different, the pattern change in the mutant
mouse shares characteristics with the nonlinear waves generated on excitable
media, such as the Belousov–Zhabotinskii reaction, suggesting that a
common principle underlies the wave pattern formation. Molecular details that
underlie the phenomenon can be conjectured from recent molecular studies.
Rapid loss of genetically based resistance to metals after the cleanup of a Superfund site
Authors: Levinton Jeffrey S. , Suatoni E. , Wallace William , Junkins Ruth , Kelaher Brendan , Allen Bengt J.
Published: August 2003

Over the period 1953–1979, a battery factory on the Hudson River in
New York released ≈53 tons of cadmium (Cd) and nickel hydride wastes into
Foundry Cove. The most common aquatic benthic species, the oligochaete
Limnodrilus hoffmeisteri
, rapidly evolved resistance to Cd. The
capacity for detoxification and internal storage of Cd resulted in a strong
potential for trophic transfer of Cd through the aquatic food web. As a result
of United States Superfund legislation, a major remediation effort in
1994–1995 removed the majority of the Cd, thereby removing the selective
force for resistance. The cleanup of this cove resulted in the maintenance of
resistant forms but then there ensued a rapid loss of resistance in
≈9–18 generations, showing the potential for ecological restoration
to rapidly reduce the potential for trophic transfer of Cd through the
ecosystem. This study demonstrates a genetic approach to the study of
ecological restoration and connects a genetic indicator of restoration to
transfer of toxic metals through ecosystems.
Chronic hepatitis associated with GB virus B persistence in a tamarin after intrahepatic inoculation of synthetic viral RNA
Authors: Martin Annette , Bodola Francis , Sangar David V. , Goettge Kathryn , Popov Vsevolod , Rijnbrand Rene , Lanford Robert E. , Lemon Stanley M.
Published: August 2003

Progress in understanding the pathogenesis of hepatitis C virus (HCV) has
been slowed by the absence of tractable small animal models. Whereas GB virus
B (GBV-B, an unclassified flavivirus) shares a phylogenetic relationship and
several biologic attributes with HCV, including hepatotropism, it is not known
to cause persistent infection, a hallmark of HCV. Here, we document persistent
GBV-B infection in one of two healthy tamarins (
Saguinus oedipus
)
inoculated intrahepatically with infectious synthetic RNA. High-titer viremia
(10
8
to 10
9
genome equivalents per ml) and transiently
elevated serum alanine transaminase activities were present from weeks 4 to 12
postinoculation in both animals. However, whereas GBV-B was eliminated from
one animal by 20 weeks, the second animal remained viremic (10
3
to
10
7
genome equivalents per ml) for >2 years, with alanine
transaminase levels becoming elevated again before spontaneous resolution of
the infection. A liver biopsy taken late in the course of infection
demonstrated hepatitis with periportal mononuclear infiltrates, hepatocellular
microvesicular changes, cytoplasmic lipid droplets, and disordered
mitochondrial ultrastructure, findings remarkably similar to chronic hepatitis
C. GBV-B-infected hepatocytes contained numerous small vesicular membranous
structures resembling those associated with expression of HCV nonstructural
proteins, and sequencing of GBV-B RNA demonstrated a rate of molecular
evolution comparable to that of HCV. We conclude that GBV-B is capable of
establishing persistent infections in healthy tamarins, a feature that
substantially enhances its value as a model for HCV. Mitochondrial structural
changes and altered lipid metabolism leading to steatosis are conserved
features of the pathogenesis of chronic hepatitis caused by these genetically
distinct flaviviruses.
β1 subunits facilitate gating of BK channels by acting through the Ca
2
+
, but not the Mg
2
+
, activating mechanisms
Authors: Qian Xiang , Magleby Karl L.
Published: August 2003

The β1 subunit of BK (large conductance Ca
2
+
and
voltage-activated K
+
) channels is essential for many key
physiological processes, such as controlling the contraction of smooth muscle
and the tuning of hair cells in the cochlea. Although it is known that the
β1 subunit greatly increases the open probability of BK channels, little
is known about its mechanism of action. We now explore this mechanism by using
channels in which the Ca
2
+
- and
Mg
2
+
-dependent activating mechanisms have been disrupted
by mutating three sites to remove the Ca
2
+
and
Mg
2
+
sensitivity. We find that the presence of the
β1 subunit partially restores Ca
2
+
sensitivity to
the triply mutated channels, but not the Mg
2
+
sensitivity. We also find that the β1 subunit has no effect on the
Mg
2
+
sensitivity of WT BK channels, in contrast to its
pronounced effect of increasing the apparent Ca
2
+
sensitivity. These observations suggest that the β1 subunit increases
open probability by working through the Ca
2
+
-dependent,
rather than Mg
2
+
-dependent, activating mechanisms, and
that the action of the β1 subunit is not directly on the
Ca
2
+
binding sites, but on the allosteric machinery
coupling the sites to the gate. The differential effects of the β1
subunit on the Ca
2
+
and Mg
2
+
activation of the channel suggest that these processes act separately.
Finally, we show that

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inhibits,
rather than activates, BK channels in the presence of the β1 subunit for
intermediate levels of

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. This
Mg
2
+
inhibition in the presence of the β1 subunit
provides an additional regulatory mechanism of BK channel activity.
A gene expression-based method to diagnose clinically distinct subgroups of diffuse large B cell lymphoma
Authors: Wright George , Tan Bruce , Rosenwald Andreas , Hurt Elaine H. , Wiestner Adrian , Staudt Louis M.
Published: August 2003

To classify cancer specimens by their gene expression profiles, we created a statistical method based on Bayes' rule that estimates the probability of membership in one of two cancer subgroups. We used this method to classify diffuse large B cell lymphoma (DLBCL) biopsy samples into two gene expression subgroups based on data obtained from spotted cDNA microarrays. The germinal center B cell-like (GCB) DLBCL subgroup expressed genes characteristic of normal germinal center B cells whereas the activated B cell-like (ABC) DLBCL subgroup expressed a subset of the genes that are characteristic of plasma cells, particularly those encoding endoplasmic reticulum and golgi proteins involved in secretion. We next used this predictor to discover these subgroups within a second set of DLBCL biopsies that had been profiled by using oligonucleotide microarrays [Shipp, M. A.,et al.(2002)Nat. Med.8, 68–74]. The GCB and ABC DLBCL subgroups identified in this data set had significantly different 5-yr survival rates after multiagent chemotherapy (62% vs. 26%;P≤ 0.0051), in accord with analyses of other DLBCL cohorts. These results demonstrate the ability of this gene expression-based predictor to classify DLBCLs into biologically and clinically distinct subgroups irrespective of the method used to measure gene expression.
Plants reverse warming effect on ecosystem water balance
Authors: Zavaleta Erika S. , Thomas Brian D. , Chiariello Nona R. , Asner Gregory P. , Shaw M. Rebecca , Field Christopher B.
Published: August 2003

Models predict that global warming may increase aridity in water-limited
ecosystems by accelerating evapotranspiration. We show that interactions
between warming and the dominant biota in a grassland ecosystem produced the
reverse effect. In a 2-year field experiment, simulated warming increased
spring soil moisture by 5–10% under both ambient and elevated
CO
2
. Warming also accelerated the decline of canopy greenness
(normalized difference vegetation index) each spring by 11–17% by
inducing earlier plant senescence. Lower transpirational water losses
resulting from this earlier senescence provide a mechanism for the unexpected
rise in soil moisture. Our findings illustrate the potential for
organism–environment interactions to modify the direction as well as the
magnitude of global change effects on ecosystem functioning.
Ordering of water molecules between phospholipid bilayers visualized by coherent anti-Stokes Raman scattering microscopy
Authors: Cheng Ji-Xin , Pautot Sophie , Weitz David A. , Xie X. Sunney
Published: August 2003

We demonstrate ordered orientation of the hydration water at the surface of
phospholipid bilayers by use of coherent anti-Stokes Raman scattering (CARS)
microscopy, a highly sensitive vibrational imaging method recently developed.
We investigated negatively charged POPS
(1-palmitoyl-2-oleoyl-sn-glycero-3-phospho-
l
-serine) and neutral
POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) multilamellar onions
dispersed in deuterated dodecane. The imaging contrast based on the CARS
signal from the H
2
O stretching vibration shows a clear dependence
on the excitation field polarization. Our results provide direct experimental
evidence that water molecules close to the phospholipid bilayer surface are
ordered with the symmetry axis along the direction normal to the bilayer.
Moreover, the amount of ordered water molecules depends on the lipid polar
group. The spectral profile for the inter-lamellar water shows that the water
molecules bound to the bilayer surface are less hydrogen-bonded and exhibit a
higher vibrational frequency than bulk water.
Subcellular compartmentalization of human Nfu, an iron–sulfur cluster scaffold protein, and its ability to assemble a [4Fe–4S] cluster
Authors: Tong Wing-Hang , Jameson Guy N. L. , Huynh Boi Hanh , Rouault Tracey A.
Published: August 2003

Iron–sulfur (Fe–S) clusters serve as cofactors in many proteins
that have important redox, catalytic, and regulatory functions. In bacteria,
biogenesis of Fe–S clusters is mediated by multiple gene products
encoded by the
isc
and
nif
operons. In particular, genetic
and biochemical studies suggest that IscU, Nfu, and IscA function as scaffold
proteins for assembly and delivery of rudimentary Fe–S clusters to
target proteins. Here we report the characterization of human Nfu. A
combination of biochemical and spectroscopic techniques, including UV-visible
absorption and
57
Fe Mössbauer spectroscopies, have been used
to investigate the ability of purified human Nfu to assemble Fe–S
clusters. The results suggest that Nfu can assemble approximately one labile
[4Fe–4S] cluster per two Nfu monomers, and support the proposal that Nfu
is an alternative scaffold protein for assembly of clusters that are
subsequently used for maturation of targeted Fe–S proteins. Analyses of
genomic DNA, transcripts, and translation products indicate that alternative
splicing of a common pre-mRNA results in synthesis of two Nfu isoforms with
distinct subcellular localizations. Isoform I is localized in the
mitochondria, whereas isoform II is present in the cytosol and the nucleus.
These results, together with previous reports of subcellular distributions of
isoforms of human IscS and IscU in mitochondria, cytosol, and nucleus suggest
that the Fe–S cluster assembly machineries are compartmentalized in
higher eukaryotes.
Defective double-strand DNA break repair and chromosomal translocations by
MYC
overexpression
Authors: Karlsson Asa , Deb-Basu Debabrita , Cherry Athena , Turner Stephanie , Ford James , Felsher Dean W.
Published: August 2003

DNA repair mechanisms are essential for the maintenance of genomic
integrity. Disruption of gene products responsible for DNA repair can result
in chromosomal damage. Improperly repaired chromosomal damage can result in
the loss of chromosomes or the generation of chromosomal deletions or
translocations, which can lead to tumorigenesis. The
MYC
protooncogene is a transcription factor whose overexpression is frequently
associated with human neoplasia.
MYC
has not been previously
implicated in a role in DNA repair. Here we report that the overexpression of
MYC
disrupts the repair of double-strand DNA breaks, resulting in a
several-magnitude increase in chromosomal breaks and translocations. We found
that
MYC
inhibited the repair of γ irradiation DNA breaks in
normal human cells and blocked the repair of a single double-strand break
engineered to occur in an immortal cell line. By spectral karyotypic analysis,
we found that
MYC
even within one cell division cycle resulted in a
several-magnitude increase in the frequency of chromosomal breaks and
translocations in normal human cells. Hence,
MYC
overexpression may
be a previously undescribed example of a dominant mutator that may fuel
tumorigenesis by inducing chromosomal damage.
Defective mammary gland morphogenesis in mice lacking the progesterone receptor B isoform
Authors: Mulac-Jericevic Biserka , Lydon John P. , DeMayo Francesco J. , Conneely Orla M.
Published: August 2003

Progesterone (P) regulates female reproduction via two nuclear receptors,
PR-A and PR-B. Although both receptors display overlapping and distinct
transcription regulatory properties, their individual physiological roles are
unclear. To address the physiological role of PR-A, we generated a mouse model
in which expression of PR-B was specifically ablated
(PRBKO
–
/
–
). We show that
selective activation of PR-A in
PRBKO
–
/
–
mice is sufficient to
elicit normal ovarian and uterine responses to P but results in reduced
mammary gland morphogenesis. In the absence of PR-B, pregnancy-associated
ductal sidebranching and lobuloalveolar development are markedly reduced due
to decreased ductal and alveolar epithelial cell proliferation and decreased
survival of alveolar epithelium. In an effort to elucidate the molecular
genetic signaling pathways that are differentially regulated by PRs in the
mammary gland, we have identified receptor activator of nuclear factor
κB ligand (RANKL) as a paracrine mediator of P-dependent alveologenesis.
Further, we demonstrate that the defects in
PRBKO
–
/
–
mice are associated with
an inability of PR-A to activate the RANKL signaling pathway in response to P.
Our data indicate that functional interaction between PR-A and PR-B is not
required for reproductive activity and that selective modulation of PR-A
activity by progestin agonists may have a protective effect against both
uterine and mammary gland hyperplasias.
Atypical expansion in mice of the sensory neuron-specific
Mrg
G protein-coupled receptor family
Authors: Zylka Mark J. , Dong Xinzhong , Southwell Amber L. , Anderson David J.
Published: August 2003

The Mas-related genes (
Mrgs
) comprise a family of >50 G
protein-coupled receptors (GPCRs), many of which are expressed in specific
subsets of nociceptive sensory neurons in mice. In contrast, humans contain a
related but nonorthologous family of genes, called
MrgXs
or sensory
neuron-specific receptors, of which many fewer appear to be expressed in
sensory neurons. To determine whether the diversity of murine
Mrgs
is
generic to rodents or is an atypical feature of mice, we characterized
MrgA, MrgB, MrgC
, and
MrgD
subfamilies in rat and gerbil.
Surprisingly, although mice have ≈22
MrgA
and ≈14
MrgC
genes, rats and gerbils have just a single
MrgA
and
MrgC
gene. This murine-specific expansion likely reflects recent
retrotransposon-mediated unequal crossover events. The expression of
Mrgs
in rat sensory ganglia suggests that the extensive cellular
diversity in mice can be simplified to a core subset of approximately four
different genes (
MrgA, MrgB, MrgC
, and
MrgD
), defining a
similar number of neuronal subpopulations. Our results suggest more generally
that mouse–human genomic comparisons may sometimes reveal differences
atypical of rodents.
Nestin expression in hair follicle sheath progenitor cells
Authors: Li Lingna , Mignone John , Yang Meng , Matic Maja , Penman Sheldon , Enikolopov Grigori , Hoffman Robert M.
Published: August 2003

The intermediate filament protein, nestin, marks progenitor cells of the
CNS. Such CNS stem cells are selectively labeled by placing GFP under the
control of the nestin regulatory sequences. During early anagen or growth
phase of the hair follicle, nestin-expressing cells, marked by GFP
fluorescence in nestin-GFP transgenic mice, appear in the permanent upper hair
follicle immediately below the sebaceous glands in the follicle bulge. This is
where stem cells for the hair follicle outer-root sheath are thought to be
located. The relatively small, oval-shaped, nestin-expressing cells in the
bulge area surround the hair shaft and are interconnected by short dendrites.
The precise locations of the nestin-expressing cells in the hair follicle vary
with the hair cycle. During telogen or resting phase and in early anagen, the
GFP-positive cells are mainly in the bulge area. However, in mid- and late
anagen, the GFP-expressing cells are located in the upper outer-root sheath as
well as in the bulge area but not in the hair matrix bulb. These observations
show that the nestin-expressing cells form the outer-root sheath. Results of
the immunohistochemical staining showed that nestin, GFP, keratin 5/8, and
keratin 15 colocalize in the hair follicle bulge cells, outer-root sheath
cells, and basal cells of the sebaceous glands. These data indicate that
nestin-expressing cells, marked by GFP, in the hair follicle bulge are indeed
progenitors of the follicle outer-root sheath. The expression of the unique
protein, nestin, in both neural stem cells and hair follicle stem cells
suggests their possible relation.
The VirD2 pilot protein of
Agrobacterium
-transferred DNA interacts with the TATA box-binding protein and a nuclear protein kinase in plants
Authors: Bakó László , Umeda Masaaki , Tiburcio Antonio F. , Schell Jeff , Koncz Csaba
Published: August 2003

The bacterial virulence protein VirD2 plays an important role in nuclear
import and chromosomal integration of
Agrobacterium
-transferred DNA
in fungal, plant, animal, and human cells. Here we show that in nuclei of
alfalfa cells, VirD2 interacts with and is phosphorylated by CAK2Ms, a
conserved plant ortholog of cyclin-dependent kinase-activating kinases. CAK2Ms
binds to and phosphorylates the C-terminal regulatory domain of RNA polymerase
II largest subunit, which can recruit the TATA box-binding protein. VirD2 is
found in tight association with the TATA box-binding protein
in vivo
.
These results indicate that recognition of VirD2 is mediated by widely
conserved nuclear factors in eukaryotes.
Genome sequence of the cyanobacterium
Prochlorococcus marinus
SS120, a nearly minimal oxyphototrophic genome
Authors: Dufresne Alexis , Salanoubat Marcel , Partensky Frédéric , Artiguenave François , Axmann Ilka M. , Barbe Valérie , Duprat Simone , Galperin Michael Y. , Koonin Eugene V. , Le Gall Florence , Makarova Kira S. , Ostrowski Martin , Oztas Sophie , Robert Catherine , Rogozin Igor B. , Scanlan David J. , de Marsac Nicole Tandeau , Weissenbach Jean , Wincker Patrick , Wolf Yuri I. , Hess Wolfgang R.
Published: August 2003

Prochlorococcus marinus
, the dominant photosynthetic organism in
the ocean, is found in two main ecological forms: high-light-adapted genotypes
in the upper part of the water column and low-light-adapted genotypes at the
bottom of the illuminated layer.
P. marinus
SS120, the complete
genome sequence reported here, is an extremely low-light-adapted form. The
genome of
P. marinus
SS120 is composed of a single circular
chromosome of 1,751,080 bp with an average G+C content of 36.4%. It contains
1,884 predicted protein-coding genes with an average size of 825 bp, a single
rRNA operon, and 40 tRNA genes. Together with the 1.66-Mbp genome of
P.
marinus
MED4, the genome of
P. marinus
SS120 is one of the two
smallest genomes of a photosynthetic organism known to date. It lacks many
genes that are involved in photosynthesis, DNA repair, solute uptake,
intermediary metabolism, motility, phototaxis, and other functions that are
conserved among other cyanobacteria. Systems of signal transduction and
environmental stress response show a particularly drastic reduction in the
number of components, even taking into account the small size of the SS120
genome. In contrast, housekeeping genes, which encode enzymes of amino acid,
nucleotide, cofactor, and cell wall biosynthesis, are all present. Because of
its remarkable compactness, the genome of
P. marinus
SS120 might
approximate the minimal gene complement of a photosynthetic organism.
Glutathione synthetase homologs encode α-
l
-glutamate ligases for methanogenic coenzyme F
420
and tetrahydrosarcinapterin biosyntheses
Authors: Li Hong , Xu Huimin , Graham David E. , White Robert H.
Published: August 2003

Proteins in the ATP-grasp superfamily of amide bond-forming ligases have
evolved to function in a number of unrelated biosynthetic pathways. Previously
identified homologs encoding glutathione synthetase,
d
-alanine:
d
-alanine ligase and the bacterial ribosomal
protein S6:glutamate ligase have been vertically inherited within certain
organismal lineages. Although members of this specificity-diverse superfamily
share a common reaction mechanism, the nonoverlapping set of amino acid and
peptide substrates recognized by each family provided few clues as to their
evolutionary history. Two members of this family have been identified in the
hyperthermophilic marine archaeon
Methanococcus jannaschii
and shown
to catalyze the final reactions in two coenzyme biosynthetic pathways. The
MJ0620 (
mptN
) locus encodes a
tetrahydromethanopterin:α-
l
-glutamate ligase that forms
tetrahydrosarcinapterin, a single carbon-carrying coenzyme. The MJ1001
(
cofF
) locus encodes a
γ-F
420
-2:α-
l
-glutamate ligase, which caps
the γ-glutamyl tail of the hydride carrier coenzyme F
420
.
These two genes share a common ancestor with the ribosomal protein
S6:glutamate ligase and a putative α-aminoadipate ligase, defining the
first group of ATP-grasp enzymes with a shared amino acid substrate
specificity. As in glutathione biosynthesis, two unrelated amino acid ligases
catalyze sequential reactions in coenzyme F
420
polyglutamate
formation: a γ-glutamyl ligase adds 1–3
l
-glutamate
residues and the ATP-grasp-type ligase described here caps the chain with a
single α-linked
l
-glutamate residue. The analogous pathways
for glutathione, F
420
, folate, and murein peptide biosyntheses
illustrate convergent evolution of nonribosomal peptide biosynthesis through
the recruitment of single-step amino acid ligases.
Nonparametric regression to the mean
Authors: Müller Hans-Georg , Abramson Ian , Azari Rahman
Published: August 2003

Available data may reflect a true but unknown random variable of interest
plus an additive error, which is a nuisance. The problem in predicting the
unknown random variable arises in many applied situations where measurements
are contaminated with errors; it is known as the regression-to-the-mean
problem. There exists a well known solution when both the distributions of the
true underlying random variable and the contaminating errors are normal. This
solution is given by the classical regression-to-the-mean formula, which has a
data-shrinkage interpretation. We discuss the extension of this solution to
cases where one or both of these distributions are unknown and demonstrate
that the fully nonparametric case can be solved for the case of small
contaminating errors. The resulting nonparametric regression-to-the-mean
paradigm can be implemented by a straightforward data-sharpening algorithm
that is based on local sample means. Asymptotic justifications and practical
illustrations are provided.
The crystal structure of polygalacturonase-inhibiting protein (PGIP), a leucine-rich repeat protein involved in plant defense
Authors: Di Matteo A. , Federici L. , Mattei B. , Salvi G. , Johnson K. A. , Savino C. , De Lorenzo G. , Tsernoglou D. , Cervone F.
Published: August 2003

Polygalacturonase-inhibiting proteins (PGIPs) are plant cell wall proteins
that protect plants from fungal invasion. They interact with
endo
polygalacturonases secreted by phytopathogenic fungi, inhibit
their enzymatic activity, and favor the accumulation of oligogalacturonides,
which activate plant defense responses. PGIPs are members of the leucine-rich
repeat (LRR) protein family that in plants play crucial roles in development,
defense against pathogens, and recognition of beneficial microbes. Here we
report the crystal structure at 1.7-Å resolution of a PGIP from
Phaseolus vulgaris
. The structure is characterized by the presence of
two β-sheets instead of the single one originally predicted by modeling
studies. The structure also reveals a negatively charged surface on the LRR
concave face, likely involved in binding polygalacturonases. The structural
information on PGIP provides a basis for designing more efficient inhibitors
for plant protection.