bluuebunny/crossref_metadata_2025 huggingface dataset:
N-cadherin is regulated by gonadal steroids in the adult hippocampus
Authors: Monks Douglas A. , Getsios Spiro , MacCalman Colin D. , Watson Neil V.
Published: July 2012

In the adult hippocampus, gonadal steroids induce neural remodeling
through cellular and molecular mechanisms that are largely unknown. The
calcium-dependent cell adhesion molecule N-cadherin, which
participates in the developmental organization of the nervous system,
has recently been localized to hippocampal synapses and is suspected to
participate in adult synaptic physiology. Little is currently known
about the regulation of cadherins in the adult central nervous system,
although posttranslational modifications are thought to account for
variability in N-cadherin expression levels. To evaluate the
possibility that gonadal steroids regulate N-cadherin in the adult
hippocampus, we examined hippocampal N-cadherin mRNA levels and protein
expression in castrated adult male rats treated with testosterone, or
its metabolites 17β-estradiol or dihydrotestosterone. Northern blot
analysis indicated increased hippocampal N-cadherin mRNA levels in the
adult rat hippocampus after treatment with 17β-estradiol but not
testosterone or dihydrotestosterone. Increased N-cadherin
immunoreactivity was observed in CA1 and CA3 pyramidal cells after
17β-estradiol treatment. Additionally, both 17β-estradiol and
testosterone treatment increased N-cadherin immunoreactivity in the
neuropil of the stratum lacunosum-moleculare, which includes apical
dendrites from pyramidal cells. In contrast, dihydrotestosterone
treatment had no effect on levels of N-cadherin protein expression in
CA1 or CA3 pyramidal cells or in the stratum lacunosum-moleculare.
These results demonstrate that, in the hippocampus, expression levels
of N-cadherin are dynamic in adulthood. To our knowledge, there have
been no other demonstrations of steroid regulation of cadherin
expression in neural populations. These results suggest a possible
adhesive mechanism for steroid-induced plasticity of the adult nervous
system.
A highly variable segment of human subterminal 16p reveals a history of population growth for modern humans outside Africa
Authors: Alonso Santos , Armour John A. L.
Published: July 2012

We have sequenced a highly polymorphic subterminal noncoding region
from human chromosome 16p13.3, flanking the 5′ end of the hypervariable
minisatellite MS205, in 100 chromosomes sampled from different African
and Euroasiatic populations. Coalescence analysis indicates that the
time to the most recent common ancestor (approximately 1 million years)
predates the appearance of anatomically modern human forms. The root of
the network describing this variability lies in Africa. African
populations show a greater level of diversity and deeper branches. Most
Euroasiatic variability seems to have been generated after a recent
out-of-Africa range expansion. A history of population growth is the
most likely scenario for the Euroasiatic populations. This pattern of
nuclear variability can be reconciled with inferences based on
mitochondrial DNA.
Overexpression of the inositol phosphatase SopB in human 293 cells stimulates cellular chloride influx and inhibits nuclear mRNA export
Authors: Feng Yucheng , Wente Susan R. , Majerus Philip W.
Published: July 2012

SopB is an inositol phosphate phosphatase that is a virulence
factor in
Salmonella
species. We have overexpressed SopB
cDNA in a tetracycline-dependent system in human embryonic 293 cells,
and used this model system to directly analyze the role of SopB in
altering inositol metabolite levels
in vivo
. Addition of
tetracycline to these cells resulted in the rapid induction of SopB
expression, which was coincident with perturbations in the cellular
levels of multiple soluble inositol phosphates. All of the changes
induced by SopB expression were reversed within 24 h on removal of
tetracycline from media. Specifically, cellular inositol
1,3,4,5,6-pentakisphosphate (InsP
5
) and inositol
hexakisphosphate (InsP
6
) levels were depleted within 4 to
6 h after inducing SopB expression. A transient rise in cellular
inositol 1,4,5,6-tetrakisphosphate was also observed and was
accompanied by increased chloride channel activity. This indicates that
SopB alone is sufficient for changes in chloride channel function in
cells infected with
Salmonella
organisms. Depletion of
inositol phosphates, including InsP
5
and InsP
6
metabolites, was coincident with the accumulation of polyadenylated RNA
in the nucleus. This suggested that a defect in nuclear export had
occurred. Moreover, the penetrance of the export defect required
localization of SopB to the nucleus. These results provide evidence
that inositol phosphate productions may be required for efficient mRNA
export in mammalian cells.
Rotation of the c subunit oligomer in fully functional F
1
F
o
ATP synthase
Authors: Tsunoda Satoshi P. , Aggeler Robert , Yoshida Masasuke , Capaldi Roderick A.
Published: July 2012

The F
1
F
o
-type ATP synthase is the smallest
motor enzyme known. Previous studies had established that the central
γ and ɛ subunits of the F
1
part rotate relative to a
stator of α
3
β
3
and δ subunits during
catalysis. We now show that the ring of c subunits in the
F
o
part moves along with the γ and ɛ subunits. This was
demonstrated by linking the three rotor subunits with disulfide bridges
between cysteine residues introduced genetically at the interfaces
between the γ, ɛ, and c subunits. Essentially complete
cross-linking of the γ, ɛ, and c subunits was achieved by using
CuCl
2
to induce oxidation. This fixing of the three
subunits together had no significant effect on ATP hydrolysis, proton
translocation, or ATP synthesis, and each of these functions retained
inhibitor sensitivity. These results unequivocally place the c subunit
oligomer in the rotor part of this molecular machine.
Directed evolution of ampicillin-resistant activity from a functionally unrelated DNA fragment: A laboratory model of molecular evolution
Authors: Yano Takato , Kagamiyama Hiroyuki
Published: July 2012

To establish an experimental system to directly observe molecular
evolution, a DNA fragment that confers ampicillin resistance on
Escherichia coli
was cloned from an archaeal genomic
DNA. The activity of this clone was enhanced by 50 rounds of directed
evolution by using DNA shuffling. Analysis of the evolved DNA fragments
shows that two genetic regions have coevolved: One region, which has no
obvious ORF, is essential for the activity, whereas the other, which
appears to encode a protein, is not essential but enhances the activity
of the former region. Analysis of the evolutionary intermediates shows
that negative mutations are effectively removed while beneficial
mutations accumulate and illustrates how a protein has evolved over the
course of the evolution experiments. Although the mechanism of the
activity remains unclear, the evolved DNA fragments also confer
resistance to other drugs that inhibit bacterial cell-wall synthesis.
The present system would serve as an experimental model to study
evolutionary dynamics in the laboratory and provide the concept of
screening natural libraries to obtain starting materials for directed
evolution.
The critical role of DNA in the equilibrium between OmpR and phosphorylated OmpR mediated by EnvZ in
Escherichia coli
Authors: Qin Ling , Yoshida Takeshi , Inouye Masayori
Published: July 2012

Escherichia coli
modulates its porin expression
through a histidine kinase, EnvZ, and its cognate response regulator,
OmpR. EnvZ is a bifunctional enzyme that possesses both OmpR kinase and
phosphorylated OmpR (OmpR-P) phosphatase activities and thus controls
the cellular level of OmpR-P. In an
in vitro
-assay
system, the addition of OmpR to the reaction mixture consisting of the
cytoplasmic domain of EnvZ (EnvZc) and ATP produces a barely detectable
amount of OmpR-P because of the dual activities of EnvZ. Here we report
that DNA fragments containing the upstream promoter regions of the
porin genes (
ompF
and
ompC
) can shift the
equilibrium between OmpR and OmpR-P dramatically toward OmpR-P. Among
the four reactions occurring in the mixture, only the EnvZ phosphatase
activity was inhibited severely by the specific DNA, in contrast to the
previous report by Kenney and her associates that DNA stimulates OmpR
phosphorylation by EnvZ [Ames, S. K., Frankema, N. & Kenney,
L. J. (1999)
Proc. Natl. Acad. Sci. USA
96,
11792–11797]. The autophosphorylation of EnvZc and the
phosphotransfer from phosphorylated EnvZc to OmpR were not affected by
DNA, whereas the autodephosphorylation of OmpR-P was inhibited
slightly. We propose that the apparent inhibitory effect of DNA on the
EnvZ phosphatase function is caused by sequestrating OmpR-P from the
reaction as a result of OmpR-P binding to DNA.
Protein–protein interactions with subunits of human nuclear RNase P
Authors: Jiang Taijiao , Altman Sidney
Published: July 2012

A yeast two-hybrid system was used to analyze interactions among the protein subunits of human nuclear RNase P themselves and with other interacting partners encoded in a HeLa cell cDNA library. Subunits hpop1, Rpp21, Rpp29, Rpp30, Rpp38, and Rpp40 are involved in extensive, but weak, protein–protein interactions in the holoenzyme complex. Rpp14, Rpp20, and Rpp30 were found to have strong interactions with proteins encoded in the cDNA library. The small heat shock protein 27, which interacts with Rpp20 in the two-hybrid assay, binds to Rpp20 during affinity chromatography and can be found to be associated with, and enhances the activity of, highly purified RNase P. RNase P activity in HeLa cell nuclei also increases under the stress of heat shock.
Characterization of a quinone reductase activity for the mitomycin C binding protein (MRD): Functional switching from a drug-activating enzyme to a drug-binding protein
Authors: He Min , Sheldon Paul J. , Sherman David H.
Published: July 2012

Self-protection in the mitomycin C (MC)-producing microorganism
Streptomyces lavendulae
includes MRD, a protein that
binds MC in the presence of NADH and functions as a component of a
unique drug binding-export system. Characterization of MRD revealed
that it reductively transforms MC into
1,2-
cis
-1-hydroxy-2,7-diaminomitosene, a compound that
is produced in the reductive MC activation cascade. However, the
reductive reaction catalyzed by native MRD is slow, and both MC and the
reduced product are bound to MRD for a relatively prolonged period.
Gene shuffling experiments generated a mutant protein
(MRD
E55G
) that conferred a 2-fold increase in MC resistance
when expressed in
Escherichia coli
. Purified
MRD
E55G
reduces MC twice as fast as native MRD, generating
three compounds that are identical to those produced in the reductive
activation of MC. Detailed amino acid sequence analysis revealed that
the region around E55 in MRD strongly resembles the second active site
of prokaryotic catalase-peroxidases. However, native MRD has an
aspartic acid (D52) and a glutamic acid (E55) residue at the positions
corresponding to the catalytic histidine and a nearby glycine residue
in the catalase-peroxidases. Mutational analysis demonstrated that
MRD
D52H
and MRD
D52H/E55G
conferred only
marginal resistance to MC in
E. coli
. These findings
suggest that MRD has descended from a previously unidentified quinone
reductase, and mutations at the active site of MRD have greatly
attenuated its catalytic activity while preserving substrate-binding
capability. This presumed evolutionary process might have switched MRD
from a potential drug-activating enzyme into the drug-binding component
of the MC export system.
Predicting the reactivity of proteins from their sequence alone: Kazal family of protein inhibitors of serine proteinases
Authors: Lu Stephen M. , Lu Wuyuan , Qasim M. A. , Anderson Stephen , Apostol Izydor , Ardelt Wojciech , Bigler Theresa , Chiang Yi Wen , Cook James , James Michael N. G. , Kato Ikunoshin , Kelly Clyde , Kohr William , Komiyama Tomoko , Lin Tiao-Yin , Ogawa Michio , Otlewski Jacek , Park Soon-Jae , Qasim Sabiha , Ranjbar Michael , Tashiro Misao , Warne Nicholas , Whatley Harry , Wieczorek Anna , Wieczorek Maciej , Wilusz Tadeusz , Wynn Richard , Zhang Wenlei , Laskowski Michael
Published: July 2012

An additivity-based sequence to reactivity algorithm for the
interaction of members of the Kazal family of protein inhibitors with
six selected serine proteinases is described. Ten consensus variable
contact positions in the inhibitor were identified, and the 19 possible
variants at each of these positions were expressed. The free energies
of interaction of these variants and the wild type were measured. For
an additive system, this data set allows for the calculation of all
possible sequences, subject to some restrictions. The algorithm was
extensively tested. It is exceptionally fast so that all possible
sequences can be predicted. The strongest, the most specific possible,
and the least specific inhibitors were designed, and an evolutionary
problem was solved.
The surface coat of procyclic
Trypanosoma brucei:
Programmed expression and proteolytic cleavage of procyclin in the tsetse fly
Authors: Acosta-Serrano Alvaro , Vassella Erik , Liniger Matthias , Renggli Christina Kunz , Brun Reto , Roditi Isabel , Englund Paul T.
Published: July 2012

Trypanosoma brucei,
the protozoan parasite causing
sleeping sickness, is transmitted by a tsetse fly vector. When the
tsetse takes a blood meal from an infected human, it ingests
bloodstream form trypanosomes that quickly differentiate into procyclic
forms within the fly's midgut. During this process, the parasite loses
the 10
7
molecules of variant surface glycoprotein that
formed its surface coat, and it develops a new coat composed of several
million procyclin molecules. Procyclins, the products of a small
multigene family, are glycosyl phosphatidylinositol-anchored proteins
containing characteristic amino acid repeats at the C terminus [either
EP (EP procyclin, a form of procyclin rich in Glu-Pro repeats) or GPEET
(GPEET procyclin, a form of procyclin rich in Glu-Pro-Glu-Glu-Thr
repeats)]. We have used a sensitive and accurate mass spectrometry
method to analyze the appearance of different procyclins during the
establishment of midgut infections in tsetse flies. We found that
different procyclin gene products are expressed in an orderly manner.
Early in the infection (day 3), GPEET2 is the only procyclin detected.
By day 7, however, GPEET2 disappears and is replaced by several
isoforms of glycosylated EP, but not the unglycosylated isoform EP2.
Unexpectedly, we discovered that the N-terminal domains of all
procyclins are quantitatively removed by proteolysis in the fly, but
not in culture. These findings suggest that one function of the
protease-resistant C-terminal domain, containing the amino acid
repeats, is to protect the parasite surface from digestive enzymes in
the tsetse fly gut.
Forced unfolding modulated by disulfide bonds in the Ig domains of a cell adhesion molecule
Authors: Carl Philippe , Kwok Carol H. , Manderson Gavin , Speicher David W. , Discher Dennis E.
Published: July 2012

Cell adhesion molecules (CAMs) mediate cell attachment and stress
transfer through extracellular domains. Here we forcibly unfold the Ig
domains of a prototypical Ig superfamily CAM that contains intradomain
disulfide bonds. The Ig domains of all such CAMs have conformations
homologous to cadherin extracellular domains, titin Ig-type domains,
and fibronectin type-III (FNIII) domains. Atomic force microscopy has
been used to extend the five Ig domains of Mel-CAM (melanoma CAM)—a
protein that is overexpressed in metastatic melanomas—under conditions
where the disulfide bonds were either left intact or disrupted through
reduction. Under physiological conditions where intradomain disulfide
bonds are intact, partial unfolding was observed at forces far smaller
than those reported previously for either titin's Ig-type domains or
tenascin's FNIII domains. This partial unfolding under low force may
be an important mechanism for imparting elasticity to cell–cell
contacts, as well as a regulatory mechanism for adhesive interactions.
Under reducing conditions, Mel-CAM's Ig domains were found to fully
unfold through a partially folded state and at slightly higher forces.
The results suggest that, in divergent evolution of all such domains,
stabilization imparted by disulfide bonds relaxes requirements for
strong, noncovalent, folded-state interactions.
Myozenin: An α-actinin- and γ-filamin-binding protein of skeletal muscle Z lines
Authors: Takada Fumio , Woude Douglas L. Vander , Tong Hui-Qi , Thompson Terri G. , Watkins Simon C. , Kunkel Louis M. , Beggs Alan H.
Published: July 2012

To better understand the structure and function of Z lines, we used
sarcomeric isoforms of α-actinin and γ-filamin to screen a human
skeletal muscle cDNA library for interacting proteins by using the
yeast two-hybrid system. Here we describe myozenin
(
MYOZ
), an α-actinin- and γ-filamin-binding Z line
protein expressed predominantly in skeletal muscle. Myozenin is
predicted to be a 32-kDa, globular protein with a central glycine-rich
domain flanked by α-helical regions with no strong homologies to any
known genes. The
MYOZ
gene has six exons and maps to
human chromosome 10q22.1-q22.2. Northern blot analysis demonstrated
that this transcript is expressed primarily in skeletal muscle with
significantly lower levels of expression in several other tissues.
Antimyozenin antisera stain skeletal muscle in a sarcomeric pattern
indistinguishable from that seen by using antibodies for α-actinin,
and immunogold electron microscopy confirms localization specifically
to Z lines. Thus, myozenin is a skeletal muscle Z line protein that may
be a good candidate gene for limb-girdle muscular dystrophy or other
neuromuscular disorders.
β-Arrestin 1 and 2 differentially regulate heptahelical receptor signaling and trafficking
Authors: Kohout Trudy A. , Lin Fang-Tsyr , Perry Stephen J. , Conner David A. , Lefkowitz Robert J.
Published: July 2012

The two widely coexpressed isoforms of β-arrestin (termed
βarrestin 1 and 2) are highly similar in amino acid sequence.
The β-arrestins bind phosphorylated heptahelical receptors to
desensitize and target them to clathrin-coated pits for endocytosis. To
better define differences in the roles of β-arrestin 1 and 2, we
prepared mouse embryonic fibroblasts from knockout mice that lack one
of the β-arrestins (βarr1-KO and βarr2-KO) or both
(βarr1/2-KO), as well as their wild-type (WT) littermate controls.
These cells were analyzed for their ability to support desensitization
and sequestration of the β
2
-adrenergic receptor
(β
2
-AR) and the angiotensin II type 1A receptor
(AT
1A
-R). Both βarr1-KO and βarr2-KO cells showed
similar impairment in agonist-stimulated β
2
-AR and
AT
1A
-R desensitization, when compared with their WT control
cells, and the βarr1/2-KO cells were even further impaired.
Sequestration of the β
2
-AR in the βarr2-KO cells was
compromised significantly (87% reduction), whereas in the βarr1-KO
cells it was not. Agonist-stimulated internalization of the
AT
1A
-R was only slightly reduced in the βarr1-KO but was
unaffected in the βarr2-KO cells. In the βarr1/2-KO cells, the
sequestration of both receptors was dramatically reduced. Comparison of
the ability of the two β-arrestins to sequester the
β
2
-AR revealed β-arrestin 2 to be 100-fold more potent
than β-arrestin 1. Down-regulation of the β
2
-AR was
also prevented in the βarr1/2-KO cells, whereas no change was
observed in the single knockout cells. These findings suggest that
sequestration of various heptahelical receptors is regulated
differently by the two β-arrestins, whereas both isoforms are capable
of supporting receptor desensitization and down-regulation.
The role of zinc in the binding of killer cell Ig-like receptors to class I MHC proteins
Authors: Valés-Gómez Mar , Erskine Robert A. , Deacon Matthew P. , Strominger Jack L. , Reyburn Hugh T.
Published: July 2012

The binding of killer cell Ig-like Receptors (KIR) to their Class I
MHC ligands was shown previously to be characterized by extremely rapid
association and dissociation rate constants. During experiments to
investigate the biochemistry of receptor–ligand binding in more
detail, the kinetic parameters of the interaction were observed to
alter dramatically in the presence of Zn
2+
but not other
divalent cations. The basis of this phenomenon is
Zn
2+
-induced multimerization of the KIR molecules as
demonstrated by BIAcore, analytical ultracentrifugation, and chemical
cross-linking experiments. Zn
2+
-dependent multimerization
of KIR may be critical for formation of the clusters of KIR and HLA-C
molecules, the “natural killer (NK) cell immune synapse,”
observed at the site of contact between the NK cell and target cell.
Luteinizing hormone-releasing hormone (LH-RH) antagonist Cetrorelix down-regulates the mRNA expression of pituitary receptors for LH-RH by counteracting the stimulatory effect of endogenous LH-RH
Authors: Kovacs Magdolna , Schally Andrew V. , Csernus Balazs , Rekasi Zoltan
Published: July 2012

The mechanisms through which LH-RH antagonists suppress
gonadotroph functions and LH-RH receptor (LH-RH-R) production are
incompletely understood. To elucidate these mechanisms, we investigated
the effects of Cetrorelix on the mRNA expression of pituitary LH-RH-R
and luteinizing hormone (LH) secretion in three experimental systems
with different pituitary LH-RH environments. Ovariectomy induced
3.61-fold and 6.34-fold increases in the mRNA expression of pituitary
LH-RH-R in rats after 11 and 21 days, respectively. After (5 h) a
single injection of 100 μg Cetrorelix, no significant decrease
occurred in the mRNA levels of pituitary LH-RH-R in ovariectomized
(OVX) rats with high pituitary exposure to LH-RH, but there was a
significant 23.2% reduction in cycling rats with normal hypophysial
LH-RH environment. Prolonged treatment for 10 days with a Cetrorelix
depot formulation releasing 100 μg/day decreased the concentration
of mRNA for pituitary LH-RH-R by 72.6% in OVX rats, but only by 32.9%
in normal rats. The decline in serum LH was 98.7% in OVX rats and
63.2% in normal rats, resulting in a minimal 0.1–0.2 ng/ml LH
concentration in both groups. A continuous exposure of pituitary cells
to 100 nM Cetrorelix in the superfusion system, which is devoid of
LH-RH, did not cause any significant changes in LH-RH-R mRNA level.
These studies demonstrate that prolonged exposure to Cetrorelix
in vivo
, but not
in vitro
, down-regulates
the mRNA expression of the pituitary receptors for LH-RH. Our findings
indicate that LH-RH antagonists exert their inhibitory effects on the
gene expression of pituitary LH-RH-R by counteracting the stimulatory
effect of endogenous LH-RH.
Genetic transformation of HeLa cells by
Agrobacterium
Authors: Kunik Talya , Tzfira Tzvi , Kapulnik Yoram , Gafni Yedidya , Dingwall Colin , Citovsky Vitaly
Published: July 2012

Agrobacterium tumefaciens
is a soil phytopathogen
that elicits neoplastic growths on the host plant species. In nature,
however,
Agrobacterium
also may encounter organisms
belonging to other kingdoms such as insects and animals that feed on
the infected plants. Can
Agrobacterium
, then, also
infect animal cells? Here, we report that
Agrobacterium
attaches to and genetically transforms several types of human cells. In
stably transformed HeLa cells, the integration event occurred at the
right border of the tumor-inducing plasmid's transferred-DNA (T-DNA),
suggesting bona fide T-DNA transfer and lending support to the notion
that
Agrobacterium
transforms human cells by a mechanism
similar to that which it uses for transformation of plants cells.
Collectively, our results suggest that
Agrobacterium
can
transport its T-DNA to human cells and integrate it into their genome.
The insect endosymbiont
Sodalis glossinidius
utilizes a type III secretion system for cell invasion
Authors: Dale Colin , Young Simon A. , Haydon Daniel T. , Welburn Susan C.
Published: July 2012

Sodalis glossinidius
is a maternally transmitted
secondary endosymbiont residing intracellularly in tissues of the
tsetse flies,
Glossina
spp. In this study, we have used
Tn5 mutagenesis and a negative selection procedure to derive a
S. glossinidius
mutant that is incapable of invading
insect cells
in vitro
and is aposymbiotic when
microinjected into tsetse. This mutant strain harbors Tn5 integrated
into a chromosomal gene sharing high sequence identity with a type III
secretion system invasion gene (
invC
) previously
identified in
Salmonella enterica
. With the use of
degenerate PCR, we have amplified a further six
Sodalis
inv
/
spa
genes sharing high sequence identity
with type III secretion system genes encoded by
Salmonella
pathogenicity island 1. Phylogenetic
reconstructions based on the
inv
/
spa
genes of
Sodalis
and other members of the family
Enterobacteriaceae
have consistently identified a
well-supported clade containing
Sodalis
and the enteric
pathogens
Shigella
and
Salmonella
. These
results suggest that
Sodalis
may have evolved from an
ancestor with a parasitic intracellular lifestyle, possibly a
latter-day entomopathogen. These observations lend credence to a
hypothesis suggesting that vertically transmitted mutualistic
endosymbionts evolve from horizontally transmitted parasites through a
parasitism–mutualism continuum.
Female preproenkephalin-knockout mice display altered emotional responses
Authors: Ragnauth A. , Schuller A. , Morgan M. , Chan J. , Ogawa S. , Pintar J. , Bodnar R. J. , Pfaff D. W.
Published: July 2012

The endogenous opioid system has been implicated in
sexual behavior, palatable intake, fear, and anxiety. The present study
examined whether ovariectomized female transgenic
preproenkephalin-knockout (PPEKO) mice and their wild-type and
heterozygous controls displayed alterations in fear and anxiety
paradigms, sucrose intake, and lordotic behavior. To examine stability
of responding, three squads of the genotypes were tested across seasons
over a 20-month period. In a fear-conditioning paradigm, PPEKO mice
significantly increased freezing to both fear and fear + shock stimuli
relative to controls. In the open field, PPEKO mice spent significantly
less time and traversed significantly less distance in the center of an
open field than wild-type controls. Further, PPEKO mice spent
significantly less time and tended to be less active on the light side
of a dark–light chamber than controls, indicating that deletion of the
enkephalin gene resulted in exaggerated responses to fear or
anxiety-provoking environments. These selective deficits were observed
consistently across testing squads spanning 20 months and different
seasons. In contrast, PPEKO mice failed to differ from corresponding
controls in sucrose, chow, or water intake across a range
(0.0001–20%) of sucrose concentrations and failed to differ in either
lordotic or female approach to male behaviors when primed with
estradiol and progesterone, thereby arguing strongly for the
selectivity of a fear and anxiety deficit which was not caused by
generalized and nonspecific debilitation. These transgenic data
strongly suggest that opioids, and particularly enkephalin gene
products, are acting naturally to inhibit fear and anxiety.
Targeted inactivation of sister of P-glycoprotein gene (
spgp
) in mice results in nonprogressive but persistent intrahepatic cholestasis
Authors: Wang Renxue , Salem Myriam , Yousef Ibrahim M. , Tuchweber Beatriz , Lam Ping , Childs Sarah J. , Helgason Cheryl D. , Ackerley Cameron , Phillips M. James , Ling Victor
Published: July 2012

Mutations in the sister of P-glycoprotein (Spgp) or bile salt
export pump (BSEP) are associated with Progressive Familial
Intrahepatic Cholestasis (PFIC2). Spgp is predominantly expressed in
the canalicular membranes of liver. Consistent with
in
vitro
evidence demonstrating the involvement of Spgp in bile
salt transport, PFIC2 patients secrete less than 1% of biliary bile
salts compared with normal infants. The disease rapidly progresses to
hepatic failure requiring liver transplantation before adolescence. In
this study, we show that the knockout of
spgp
gene in
mice results in intrahepatic cholestasis, but with significantly less
severity than PFIC2 in humans. Some unexpected characteristics are
observed. Notably, although the secretion of cholic acid in mutant mice
is greatly reduced (6% of wild-type), total bile salt output in mutant
mice is about 30% of wild-type. Also, secretion of an unexpectedly
large amount of tetra-hydroxylated bile acids (not detected in
wild-type) is observed. These results suggest that hydroxylation and an
alternative canalicular transport mechanism for bile acids compensate
for the absence of Spgp function and protect the mutant mice from
severe cholestatic damage. In addition, the
spgp
−/−
mice display a significant
increase in the secretion of cholesterol and phospholipids into the
bile. This latter observation in
spgp
−/−
mice suggests that intrahepatic, rather than intracanalicular, bile
salts are the major driving force for the biliary lipid secretion. The
spgp
−/−
mice thus provide a unique model
for gaining new insights into therapeutic intervention for intrahepatic
cholestasis and understanding mechanisms associated with lipid
homeostasis.
Sequence and structural analyses of nuclear export signals in the NESdb database
Authors: Xu Darui , Farmer Alicia , Collett Garen , Grishin Nick V. , Chook Yuh Min
Published: July 2012

We compiled >200 nuclear export signal (NES)–containing CRM1 cargoes in a database named NESdb. We analyzed the sequences and three-dimensional structures of natural, experimentally identified NESs and of false-positive NESs that were generated from the database in order to identify properties that might distinguish the two groups of sequences. Analyses of amino acid frequencies, sequence logos, and agreement with existing NES consensus sequences revealed strong preferences for the Φ1-X3-Φ2-X2-Φ3-X-Φ4 pattern and for negatively charged amino acids in the nonhydrophobic positions of experimentally identified NESs but not of false positives. Strong preferences against certain hydrophobic amino acids in the hydrophobic positions were also revealed. These findings led to a new and more precise NES consensus. More important, three-dimensional structures are now available for 68 NESs within 56 different cargo proteins. Analyses of these structures showed that experimentally identified NESs are more likely than the false positives to adopt α-helical conformations that transition to loops at their C-termini and more likely to be surface accessible within their protein domains or be present in disordered or unobserved parts of the structures. Such distinguishing features for real NESs might be useful in future NES prediction efforts. Finally, we also tested CRM1-binding of 40 NESs that were found in the 56 structures. We found that 16 of the NES peptides did not bind CRM1, hence illustrating how NESs are easily misidentified.
Interactions between the PDZ domains of Bazooka (Par-3) and phosphatidic acid: in vitro characterization and role in epithelial development
Authors: Yu Cao Guo , Harris Tony J. C.
Published: July 2012

Bazooka (Par-3) is a conserved polarity regulator that organizes molecular networks in a wide range of cell types. In epithelia, it functions as a plasma membrane landmark to organize the apical domain. Bazooka is a scaffold protein that interacts with proteins through its three PDZ (postsynaptic density 95, discs large, zonula occludens-1) domains and other regions. In addition, Bazooka has been shown to interact with phosphoinositides. Here we show that the Bazooka PDZ domains interact with the negatively charged phospholipid phosphatidic acid immobilized on solid substrates or in liposomes. The interaction requires multiple PDZ domains, and conserved patches of positively charged amino acid residues appear to mediate the interaction. Increasing or decreasing levels of diacylglycerol kinase or phospholipase D—enzymes that produce phosphatidic acid—reveal a role for phosphatidic acid in Bazooka embryonic epithelial activity but not its localization. Mutating residues implicated in phosphatidic acid binding revealed a possible role in Bazooka localization and function. These data implicate a closer connection between Bazooka and membrane lipids than previously recognized. Bazooka polarity landmarks may be conglomerates of proteins and plasma membrane lipids that modify each other's activities for an integrated effect on cell polarity.
Calculating Rural‐Urban Food Price Differentials from Unit Values in Household Expenditure Surveys: A Comparison with Existing Methods and A New Procedure
Authors: Majumder Amita , Ray Ranjan , Sinha Kompal
Published: July 2012

While purchasing power parity (PPP) between countries has received a great deal of attention, PPP calculations within countries have received less attention. The idea that one unit of currency has the same purchasing power in all regions in large countries is false. This paper addresses this limitation by proposing a methodology for calculating rural‐urban PPP in India. The paper introduces a concept of item‐specific PPP that exploits the analogy with an item‐specific equivalence scale. The methodology relies on demographically‐varying preferences to estimate PPP. The results underline the need to incorporate spatial differences in PPP calculations in countries with heterogeneous preferences.
Contact map prediction using a large-scale ensemble of rule sets and the fusion of multiple predicted structural features
Authors: Bacardit Jaume , Widera Paweł , Márquez-Chamorro Alfonso , Divina Federico , Aguilar-Ruiz Jesús S. , Krasnogor Natalio
Published: July 2012

Motivation: The prediction of a protein’s contact map has become in recent years, a crucial stepping stone for the prediction of the complete 3D structure of a protein. In this article, we describe a methodology for this problem that was shown to be successful in CASP8 and CASP9. The methodology is based on (i) the fusion of the prediction of a variety of structural aspects of protein residues, (ii) an ensemble strategy used to facilitate the training process and (iii) a rule-based machine learning system from which we can extract human-readable explanations of the predictor and derive useful information about the contact map representation.

Results: The main part of the evaluation is the comparison against the sequence-based contact prediction methods from CASP9, where our method presented the best rank in five out of the six evaluated metrics. We also assess the impact of the size of the ensemble used in our predictor to show the trade-off between performance and training time of our method. Finally, we also study the rule sets generated by our machine learning system. From this analysis, we are able to estimate the contribution of the attributes in our representation and how these interact to derive contact predictions.

Availability:  http://icos.cs.nott.ac.uk/servers/psp.html.

Contact:  natalio.krasnogor@nottingham.ac.uk

Supplementary information: Supplementary data are available at Bioinformatics online.
Acute heart failure patient profiles, management and in‐hospital outcome: results of the Italian Registry on Heart Failure Outcome
Authors: Oliva Fabrizio , Mortara Andrea , Cacciatore Giuseppe , Chinaglia Alessandra , Di Lenarda Andrea , Gorini Marco , Metra Marco , Senni Michele , Maggioni Aldo P. , Tavazzi Luigi ,   on the behalf of the IN‐HF Outcome Investigators
Published: July 2012

Aims

Registries and surveys improve knowledge of the ‘real world’. This paper aims to describe baseline clinical profiles, management strategies, and the in‐hospital outcome of patients admitted to hospital for an acute heart failure (AHF) episode.

Methods and results

IN‐HF Outcome is a nationwide, prospective, multicentre, observational study conducted in 61 Cardiology Centres in Italy. Up to December 2009, 5610 patients had been enrolled, 1855 (33%) with AHF and 3755 (67%) with chronic heart failure (CHF). Baseline and in‐hospital outcome data of AHF patients are presented. Mean age was 72 ± 12 years, and 39.8% were female. Hospital admission was due to new‐onset heart failure (HF) in 43% of cases. Co‐morbid conditions were observed more frequently in the worsening HF group, while those with de novo HF showed a higher heart rate, blood pressure, and more preserved left ventricular ejection fraction (LVEF). Electrical devices were previously implanted in 13.3% of the entire group. Inotropes were administered in 19.4% of the patients. The median duration of hospital stay was 10 days (interquartile range 7–15). All‐cause in‐hospital death was 6.4%, similar in worsening and de novo HF. Older age, hypotension, cardiogenic shock, pulmonary oedema, symptoms of hypoperfusion, hyponatraemia, and elevated creatinine were independent predictors of all‐cause death.

Conclusion

Our registry confirms that in‐hospital mortality in AHF is still high, with a long length of stay. Pharmacological treatment seems to be practically unchanged in the last decades, and the adherence to HF guidelines concerning implantable cardioverter defibrillators/cardiac resynchronization therapy is still very low. Some AHF phenotypes are characterized by worst prognosis and need specific research projects.
Nitric Oxide–Mediated Stress Imprint in Potato as an Effect of Exposure to a Priming Agent
Authors: Floryszak-Wieczorek Jolanta , Arasimowicz-Jelonek Magdalena , Milczarek Grzegorz , Janus Lukasz , Pawlak-Sprada Sylwia , Abramowski Dariusz , Deckert Joanna , Billert Hanna
Published: July 2012

We investigated how potato exposed to a chemical agent could activate nitric oxide (NO)-dependent events facilitating more potent defense responses to a subsequent pathogen attack. Obtained data revealed that all applied inducers, i.e., β-aminobutyric acid (BABA), γ-aminobutyric acid (GABA), laminarin, or 2,6-dichloroisonicotinic acid (INA), were active stimuli in potentiating NO synthesis in the primed potato. It is assumed, for the mechanism proposed in this paper, that priming involves reversible S-nitrosylated protein (S-nitrosothiols [SNO]) storage as one of the short-term stress imprint components, apart from epigenetic changes sensitized by NO. Based on BABA- and GABA-induced events, it should be stated that a rise in NO generation and coding the NO message in SNO storage at a relatively low threshold together with histone H2B upregulation might create short-term imprint activation, facilitating acquisition of a competence to react faster after challenge inoculation. Laminarin elicited strong NO upregulation with an enhanced SNO pool–altered biochemical imprint in the form of less effective local recall, nevertheless being fully protective in distal responses against P. infestans. In turn, INA showed the most intensified NO generation and abundant formation of SNO, both after the inducer treatment and challenge inoculation abolishing potato resistance against the pathogen. Our results indicate, for the first time, that a precise control of synthesized NO in cooperation with reversible SNO storage and epigenetic modifications might play an important role in integrating and coordinating defense potato responses in the priming phenomenon.
The Nicotiana benthamiana Mitogen-Activated Protein Kinase Cascade and WRKY Transcription Factor Participate in Nep1Mo-Triggered Plant Responses
Authors: Zhang Huajian , Li Deqing , Wang Meifang , Liu Jiewen , Teng Wenjun , Cheng Baoping , Huang Qian , Wang Min , Song Wenwen , Dong Suomeng , Zheng Xiaobo , Zhang Zhengguang
Published: July 2012

Many bacterial, fungal, and oomycete species secrete necrosis and ethylene-inducing peptide 1 (Nep1)-like proteins (NLP) that trigger programmed cell death (PCD) and innate immune responses in dicotyledonous plants. However, how NLP induce such immune responses is not understood. Here, we show that silencing of the MAPKKKα–MEK2–WIPK mitogen-activated protein kinase (MAPK) cascade through virus-induced gene silencing compromises hydrogen peroxide accumulation and PCD induced by Nep1Mo from Magnaporthe oryzae. WIPK interacts with NbWRKY2, a transcription factor in Nicotiana benthamiana, in vitro and in vivo, suggesting an effector pathway that mediates Nep1Mo-induced cell death. Unexpectedly, salicylic acid–induced protein kinase (SIPK)- and NbWRKY2-silenced plants showed impaired Nep1Mo-induced stomatal closure, decreased Nep1Mo-promoted nitric oxide (NO) production in guard cells, and a reduction in Nep1Mo-induced resistance against Phytophthora nicotianae. Expression studies by real-time polymerase chain reaction suggested that the MEK2–WIPK–NbWRKY2 pathway regulated Nep1Mo-triggered NO accumulation could be partly dependent on nitrate reductase, which was implicated in NO synthesis. Taken together, these studies demonstrate that the MAPK cascade is involved in Nep1Mo-triggered plant responses and MAPK signaling associated with PCD exhibits shared and distinct components with that for stomatal closure.
Evidence for a Minor Gene–for–Minor Gene Interaction Explaining Nonhypersensitive Polygenic Partial Disease Resistance
Authors: González Ana M. , Marcel Thierry C. , Niks Rients E.
Published: July 2012

Partial resistance is a quantitative type of resistance that, by definition of Parlevliet, is not based on hypersensitivity. It is largely pathotype nonspecific, although some minor isolate-specific responses have been reported. In order to elucidate the isolate specificity of individual genes for partial resistance, three barley recombinant inbred line mapping populations were analyzed for resistance to the leaf rust fungus Puccinia hordei. The mapping populations were inoculated with one isolate avirulent and two isolates virulent to resistance gene Rph7g. Six significant quantitative trait loci (QTLs) were detected. Of these, two (Rphq3 and Rphq11) were detected with only the avirulent isolate (1.2.1.) and one (Rphq18) only with both virulent isolates (CO-04 and 28.1). The effectiveness of these QTLs was tested with 14 isolates, using a tester set of genotypes containing alleles for resistance or susceptibility for these QTLs. QTL Rphq18 was effective to only two isolates, CO-04 and 28.1, whereas Rphq3 and Rphq11 were ineffective to CO-04 and 28.1 but effective to all other isolates, except one. This resulted in a significant Person's differential interaction, which is a hallmark of a gene–for–gene interaction. The minor gene–for–minor gene interaction is not based on hypersensitivity and there is no evidence that the resistance is based on genes belonging to the nucleotide-binding leucine-rich repeat class.
Rank Regression for Analyzing Ordinal Qualitative Data for Treatment Comparison
Authors: Fu L. Y. , Wang Y.-G. , Liu C. J.
Published: July 2012

Ordinal qualitative data are often collected for phenotypical measurements in plant pathology and other biological sciences. Statistical methods, such as t tests or analysis of variance, are usually used to analyze ordinal data when comparing two groups or multiple groups. However, the underlying assumptions such as normality and homogeneous variances are often violated for qualitative data. To this end, we investigated an alternative methodology, rank regression, for analyzing the ordinal data. The rank-based methods are essentially based on pairwise comparisons and, therefore, can deal with qualitative data naturally. They require neither normality assumption nor data transformation. Apart from robustness against outliers and high efficiency, the rank regression can also incorporate covariate effects in the same way as the ordinary regression. By reanalyzing a data set from a wheat Fusarium crown rot study, we illustrated the use of the rank regression methodology and demonstrated that the rank regression models appear to be more appropriate and sensible for analyzing nonnormal data and data with outliers.
Long‐acting somatostatin analogues decrease blood transfusion requirements in patients with refractory gastrointestinal bleeding associated with angiodysplasia
Authors: Bon C. , Aparicio T. , Vincent M. , Mavros M. , Bejou B. , Raynaud J.‐J. , Zampeli E. , Airinei G. , Sautereau D. , Benamouzig R. , Michopoulos S.
Published: July 2012

Background

Gastrointestinal angiodysplasias (GIADs) may be the cause of recurrent bleeding, despite endoscopic treatment.

Aim

To evaluate the effect of long‐acting somatostatin analogues on blood transfusion requirements, in patients with refractory bleeding due to GIADs.

Methods

Consecutive patients with recurrent bleeding from GIADs were enrolled. They received somatostatin analogue treatment for at least 6 months. The efficacy was evaluated in terms of blood transfusions, frequency of bleeding episodes and haemoglobin level during 6 months of treatment (Period During) compared to a 6‐months' period before treatment (Period Before).

Results

Fifteen patients were enrolled from 2007 to 2010. The median duration of somatostatin analogue treatment was 12 months (range: 6–36). The number of transfusions significantly decreased in Period During compared with Period Before [median number: 2 (0–14) vs. 10 (6–24); P < 0.001]. The percentage of patients who experienced a bleeding event was lower during somatostatin analogues treatment (20% vs. 73%; P = 0.01). The mean haemoglobin level was significantly higher when somatostatin analogues were offered [median: 10 g/dL (9–13) vs. 7 (5–8.5); P < 0.001]. None of the patients discontinued treatment due to side effects.

Conclusions

Long‐acting somatostatin analogues treatment decreased transfusion needs in patients with refractory bleeding from gastrointestinal angiodysplasias. Bleeding episodes were limited and haemoglobin improved during treatment. Long‐acting somatostatin analogues may represent an option for the management of patients with chronic bleeding due to gastrointestinal angiodysplasias.
SnTox5–Snn5: a novel Stagonospora nodorum effector–wheat gene interaction and its relationship with the SnToxA–Tsn1 and SnTox3–Snn3–B1 interactions
Authors: Friesen Timothy l. , Chu Chenggen , Xu Steven S. , Faris Justin D.
Published: July 2012

The Stagonospora nodorum–wheat interaction involves multiple pathogen‐produced necrotrophic effectors that interact directly or indirectly with specific host gene products to induce the disease Stagonospora nodorum blotch (SNB). Here, we used a tetraploid wheat mapping population to identify and characterize a sixth effector–host gene interaction in the wheat–S. nodorum system. Initial characterization of the effector SnTox5 indicated that it is a proteinaceous necrotrophic effector that induces necrosis on host lines harbouring the Snn5 sensitivity gene, which was mapped to the long arm of wheat chromosome 4B. On the basis of ultrafiltration, SnTox5 is probably in the size range 10–30 kDa. Analysis of SNB development in the mapping population indicated that the SnTox5–Snn5 interaction explains 37%–63% of the variation, demonstrating that this interaction plays a significant role in disease development. When the SnTox5–Snn5 and SnToxA–Tsn1 interactions occurred together, the level of SNB was increased significantly. Similar to several other interactions in this system, the SnTox5–Snn5 interaction is light dependent, suggesting that multiple interactions may exploit the same pathways to cause disease.
THE EFFECT OF INDORAMIN ON PERIPHERAL BLOOD FLOW
Authors: ROYDS R.B. , LOCKHART J.D.F.
Published: July 2012

The effect of indoramin, a new hypotensive agent, on peripheral blood flows of six normal subjects was determined and compared to placebo in a double‐blind, randomized study.

Indoramin (0.25 mg/kg), administered intravenously, resulted in an increased forearm muscle volume as measured by strain gauge plethysmography and an increase in the skin temperature of the hand but not to the skin of the chest.

It is concluded that these effects are the result of α‐adrenoceptor blockade.
THE EFFECT OF AGE ON THE HYDROXYLATION OF AMYLOBARBITONE SODIUM IN MAN
Authors: IRVINE R.E. , GROVE J. , TOSELAND P.A. , TROUNCE J.R.
Published: July 2012

Following a single oral dose of amylobarbitone sodium it has been shown that a group of young subjects convert a higher proportion of the dose to 3′‐hydroxyamylobarbitone than a group of elderly subjects.

Twenty‐four hours after the administration of the drug, the mean plasma level of amylobarbitone in the elderly group is significantly higher than in the group of young subjects.

It is concluded that the rate of hydroxylation of amylobarbitone sodium decreases with age.