bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of starch accumulation by granule-associated plant 14-3-3 proteins
Authors: Sehnke Paul C. , Chung Hwa-Jee , Wu Ke , Ferl Robert J.
Published: July 2012

In higher plants the production of starch is orchestrated by
chloroplast-localized biosynthetic enzymes, namely starch synthases,
ADP-glucose pyrophosphorylase, and starch branching and debranching
enzymes. Diurnal regulation of these enzymes, as well as
starch-degrading enzymes, influences both the levels and composition of
starch, and is dependent in some instances upon phosphorylation-linked
regulation. The phosphoserine/threonine-binding 14-3-3 proteins
participate in environmentally responsive phosphorylation-related
regulatory functions in plants, and as such are potentially involved in
starch regulation. We report here that reduction of the ɛ subgroup of
Arabidopsis
14-3-3 proteins by antisense technology
resulted in a 2- to 4-fold increase in leaf starch accumulation.
Dark-governed starch breakdown was unaffected in these “antisense
plants,” indicating an unaltered starch-degradation pathway and
suggesting a role for 14-3-3 proteins in regulation of starch
synthesis. Absorption spectra and gelatinization properties indicate
that the starch from the antisense plants has an altered branched
glucan composition. Biochemical characterization of protease-treated
starch granules from both
Arabidopsis
leaves and maize
endosperm showed that 14-3-3 proteins are internal intrinsic granule
proteins. These data suggest a direct role for 14-3-3 proteins in
starch accumulation. The starch synthase III family is a possible
target for 14-3-3 protein regulation because, uniquely among
plastid-localized starch metabolic enzymes, all members of the family
contain the conserved 14-3-3 protein
phosphoserine/threonine-binding consensus motif. This
possibility is strengthened by immunocapture using antibodies to DU1, a
maize starch synthase III family member, and direct interaction with
biotinylated 14-3-3 protein, both of which demonstrated an
association between 14-3-3 proteins and DU1 or DU1-like proteins.
REF proteins mediate the export of spliced and unspliced mRNAs from the nucleus
Authors: Rodrigues João P. , Rode Michaela , Gatfield David , Blencowe Benjamin J. , Carmo-Fonseca Maria , Izaurralde Elisa
Published: July 2012

The REF family of evolutionarily conserved heterogeneous
ribonucleoprotein (hnRNP)-like proteins consists of one central
RNP-type RNA binding domain flanked by Arg–Gly-rich regions of
variable length. Members of this protein family bind directly to RNA
and the mRNA export factor TAP/Mex67p, and it has been suggested that
they facilitate the recruitment of TAP/Mex67p to cellular mRNPs. We
show that the variable regions are necessary for binding of REFs to RNA
and to TAP. Antibodies specific to REFs prevent their interaction with
RNA
in vitro
. After microinjection into
Xenopus
oocytes, these antibodies inhibit mRNA nuclear
export. This inhibition of export is observed whether or not the mRNAs
are generated by splicing. The antibodies do not interfere with
pre-mRNA splicing or with the nuclear export of constitutive transport
element (CTE)-containing RNAs (directly mediated by TAP), so REF
proteins must play a critical role in mRNA nuclear export, acting
downstream of splicing and upstream of TAP/Mex67p. We also show that
recombinant REFs stimulate directly the export of mRNAs that are
otherwise exported inefficiently. Together, our data indicate that REFs
are directly implicated in the export of mRNAs from the nucleus. More
generally, we show that spliced and unspliced mRNAs use common export
factors to reach the cytoplasm.
Lack of type XV collagen causes a skeletal myopathy and cardiovascular defects in mice
Authors: Eklund Lauri , Piuhola Jarkko , Komulainen Jyrki , Sormunen Raija , Ongvarrasopone Chalermporn , Fässler Reinhard , Muona Anu , Ilves Mika , Ruskoaho Heikki , Takala Timo E. S. , Pihlajaniemi Taina
Published: July 2012

Type XV collagen occurs widely in the basement membrane zones of
tissues, but its function is unknown. To understand the biological role
of this protein, a null mutation in the
Col15a1
gene was
introduced into the germ line of mice. Despite the complete lack of
type XV collagen, the mutant mice developed and reproduced normally,
and they were indistinguishable from their wild-type littermates.
However,
Col15a1
-deficient mice showed progressive
histological changes characteristic for muscular diseases after 3
months of age, and they were more vulnerable than controls to
exercise-induced muscle injury. Despite the antiangiogenic role of type
XV collagen-derived endostatin, the development of the vasculature
appeared normal in the null mice. Nevertheless, ultrastructural
analyses revealed collapsed capillaries and endothelial cell
degeneration in the heart and skeletal muscle. Furthermore, perfused
hearts showed a diminished inotropic response, and exercise resulted in
cardiac injury, changes that mimic early or mild heart disease. Thus,
type XV collagen appears to function as a structural component needed
to stabilize skeletal muscle cells and microvessels.
What is a moment? Transient synchrony as a collective mechanism for spatiotemporal integration
Authors: Hopfield J. J. , Brody Carlos D.
Published: July 2012

A previous paper described a network of simple integrate-and-fire
neurons that contained output neurons selective for specific
spatiotemporal patterns of inputs; only experimental results were
described. We now present the principles behind the operation of this
network and discuss how these principles point to a general class of
computational operations that can be carried out easily and naturally
by networks of spiking neurons. Transient synchrony of the action
potentials of a group of neurons is used to signal “recognition”
of a space–time pattern across the inputs of those neurons.
Appropriate synaptic coupling produces synchrony when the inputs to
these neurons are nearly equal, leaving the neurons unsynchronized or
only weakly synchronized for other input circumstances. When the input
to this system comes from timed past events represented by decaying
delay activity, the pattern of synaptic connections can be set such
that synchronization occurs only for selected spatiotemporal patterns.
We show how the recognition is invariant to uniform time warp and
uniform intensity change of the input events. The fundamental
recognition event is a transient collective synchronization,
representing “many neurons now agree,” an event that is then
detected easily by a cell with a small time constant. If such
synchronization is used in neurobiological computation, its hallmark
will be a brief burst of gamma-band electroencephalogram noise when and
where such a recognition event or decision occurs.
The MinE ring required for proper placement of the division site is a mobile structure that changes its cellular location during the
Escherichia coli
division cycle
Authors: Fu Xiaoli , Shih Yu-Ling , Zhang Yan , Rothfield Lawrence I.
Published: July 2012

Placement of the division site at midcell in
Escherichia
coli
requires the MinE protein. MinE acts by imparting
topological specificity to the MinCD division inhibitor, preventing the
inhibitor from acting at the midcell site while permitting it to block
division at other unwanted sites along the length of the cell. It was
previously shown that MinE assembled into a ring structure that
appeared to be localized near midcell, apparently explaining the
ability of MinE to specifically counteract MinCD at midcell. We report
here that the MinE ring is not fixed in position near midcell but is a
dynamic structure that undergoes a repetitive cycle of movement first
to one cell pole and then to the opposite pole. Taken together with
studies of the dynamic behavior of the MinD protein, the results
suggest that the topological specificity of division site placement may
not involve a localized action of MinE to counteract the MinCD division
inhibitor at midcell but rather the ability of MinE to move the
division inhibitor away from midcell and to the cell poles.
A numerical strategy for efficient modeling of the equatorial wave guide
Authors: Majda Andrew J. , Khouider Boualem
Published: July 2012

Convection in the tropics is observed to involve a
wide-ranging hierarchy of scales from a few kilometers to the planetary
scales and also has a profound impact on short-term climate. The
mechanisms responsible for this behavior present a major unsolved
problem. A promising emerging approach to address these issues is
cloud-resolving modeling. Here a family of numerical models is
introduced specifically to model the feedback of small-scale deep
convection on tropical planetary waves and tropical circulation in a
highly efficient manner compatible with the approach through
cloud-resolving modeling. Such a procedure is also useful for
theoretical purposes. The basic idea in the approach is to use
low-order truncation in the meriodonal direction through Gauss–Hermite
quadrature projected onto a simple discrete radiation condition. In
this fashion, the cloud-resolving modeling of equatorially trapped
planetary waves reduces to the solution of a small number of purely
zonal two-dimensional wave systems along a few judiciously chosen
meriodonal layers that are coupled only by some additional source
terms. The approach is analyzed in detail with full mathematical rigor
for linearized equatorial primitive equations with source terms.
Evidence of termite foraging by Swartkrans early hominids
Authors: Backwell Lucinda R. , d'Errico Francesco
Published: July 2012

Previous studies have suggested that modified bones from the Lower
Paleolithic sites of Swartkrans and Sterkfontein in South Africa
represent the oldest known bone tools and that they were used by
Australopithecus robustus
to dig up tubers. Macroscopic
and microscopic analysis of the wear patterns on the purported bone
tools, pseudo bone tools produced naturally by known taphonomic
processes, and experimentally used bone tools confirm the anthropic
origin of the modifications. However, our analysis suggests that these
tools were used to dig into termite mounds, rather than to dig for
tubers. This result indicates that early hominids from southern Africa
maintained a behavioral pattern involving a bone tool material culture
that may have persisted for a long period and strongly supports the
role of insectivory in the early hominid diet.
The E2F6 transcription factor is a component of the mammalian Bmi1-containing polycomb complex
Authors: Trimarchi Jeffrey M. , Fairchild Brian , Wen Jessica , Lees Jacqueline A.
Published: July 2012

The E2F transcription factors play a key role in the regulation of
cellular proliferation and terminal differentiation. E2F6 is the most
recently identified and the least well understood member of the E2F
family. It is only distantly related to the other E2Fs and lacks the
sequences responsible for both transactivation and binding to the
retinoblastoma protein. Consistent with this finding, E2F6 can behave
as a dominant negative inhibitor of the other E2F family members. In
this study, we continue to investigate the possible role(s) of E2F6
in vivo
. We report the isolation of RYBP, a recently
identified member of the mammalian polycomb complex, as an
E2F6-interacting protein. Mapping studies indicate that RYBP binds
within the known “repression domain” of E2F6. Moreover, we
demonstrate that endogenous E2F6 and polycomb group
proteins, including RYBP, Ring1, MEL-18, mph1, and the oncoprotein
Bmi1, associate with one another. These findings suggest that the
biological properties of E2F6 are mediated through its ability to
recruit the polycomb transcriptional repressor complex.
Trapping the transition state of an ATP-binding cassette transporter: Evidence for a concerted mechanism of maltose transport
Authors: Chen Jue , Sharma Susan , Quiocho Florante A. , Davidson Amy L.
Published: July 2012

High-affinity uptake into bacterial cells is mediated by a large
class of periplasmic binding protein-dependent transport systems,
members of the ATP-binding cassette superfamily. In the maltose
transport system of
Escherichia coli
, the periplasmic
maltose-binding protein binds its substrate maltose with high affinity
and, in addition, stimulates the ATPase activity of the
membrane-associated transporter when maltose is present. Vanadate
inhibits maltose transport by trapping ADP in one of the two
nucleotide-binding sites of the membrane transporter immediately after
ATP hydrolysis, consistent with its ability to mimic the transition
state of the γ-phosphate of ATP during hydrolysis. Here we report
that the maltose-binding protein becomes tightly associated with the
membrane transporter in the presence of vanadate and simultaneously
loses its high affinity for maltose. These results suggest a general
model explaining how ATP hydrolysis is coupled to substrate transport
in which a binding protein stimulates the ATPase activity of its
cognate transporter by stabilizing the transition state.
The structure of the ultraspiracle ligand-binding domain reveals a nuclear receptor locked in an inactive conformation
Authors: Clayton Gina M. , Peak-Chew Sew Y. , Evans Ronald M. , Schwabe John W. R.
Published: July 2012

Ultraspiracle (USP) is the invertebrate homologue of the
mammalian retinoid X receptor (RXR). RXR plays a uniquely important
role in differentiation, development, and homeostasis through its
ability to serve as a heterodimeric partner to many other nuclear
receptors. RXR is able to influence the activity of its partner
receptors through the action of the ligand 9-
cis
retinoic acid. In contrast to RXR, USP has no known high-affinity
ligand and is thought to be a silent component in the heterodimeric
complex with partner receptors such as the ecdysone receptor. Here we
report the 2.4-Å crystal structure of the USP ligand-binding domain.
The structure shows that a conserved sequence motif found in dipteran
and lepidopteran USPs, but not in mammalian RXRs, serves to lock USP in
an inactive conformation. It also shows that USP has a large
hydrophobic cavity, implying that there is almost certainly a natural
ligand for USP. This cavity is larger than that seen previously for
most other nuclear receptors. Intriguingly, this cavity has partial
occupancy by a bound lipid, which is likely to resemble the natural
ligand for USP.
Electrophysiological characterization of specific interactions between bacterial sensory rhodopsins and their transducers
Authors: Schmies G. , Engelhard M. , Wood P. G. , Nagel G. , Bamberg E.
Published: July 2012

The halobacterial phototaxis receptors sensory rhodopsin I and II
(SRI, SRII) enable the bacteria to seek optimal light conditions for
ion pumping by bacteriorhodopsin and/or
halorhodopsin. The incoming signal is transferred across the plasma
membrane by means of receptor-specific transducer proteins that bind
tightly to their corresponding photoreceptors. To investigate the
receptor/transducer interaction, advantage is taken of the
observation that both SRI and SRII can function as proton pumps. SRI
from
Halobacterium salinarum
, which triggers the
positive phototaxis, the photophobic receptor SRII from
Natronobacterium pharaonis
(pSRII), as well as the
mutant pSRII-F86D were expressed in
Xenopus
oocytes.
Voltage-clamp studies confirm that SRI and pSRII function as
light-driven, outwardly directed proton pumps with a much stronger
voltage dependence than the ion pumps
bacteriorhodopsin and halorhodopsin. Coexpression
of SRI and pSRII-F86D with their corresponding transducers suppresses
the proton transport, revealing a tight binding and specific
interaction of the two proteins. These latter results may be exploited
to further analyze the binding interaction of the photoreceptors with
their downstream effectors.
Real-time visualization of intracellular hydrodynamics in single living cells
Authors: Potma Eric O. , de Boeij Wim P. , van Haastert Peter J. M. , Wiersma Douwe A.
Published: July 2012

Intracellular water concentrations in single living cells were
visualized by nonlinear coherent anti-Stokes Raman scattering (CARS)
microscopy. In combination with isotopic exchange measurements, CARS
microscopy allowed the real-time observation of transient intracellular
hydrodynamics at a high spatial resolution. Studies of the
hydrodynamics in the microorganism
Dictyostelium
discoideum
indicated the presence of a microscopic region near
the plasma membrane where the mobility of water molecules is severely
restricted. Modeling the transient hydrodynamics eventuated in the
determination of cell-specific cytosolic diffusion and plasma membrane
permeability constants. Our experiments demonstrate that CARS
microscopy offers an invaluable tool for probing single-cell water
dynamics.
Physical and functional association of glycolipid
N
-acetyl-galactosaminyl and galactosyl transferases in the Golgi apparatus
Authors: Giraudo Claudio G. , Daniotti Jose L. , Maccioni Hugo J. F.
Published: July 2012

Glycolipid glycosyltransferases catalyze the stepwise transfer of
monosaccharides from sugar nucleotides to proper glycolipid acceptors.
They are Golgi resident proteins that colocalize functionally in the
organelle, but their intimate relationships are not known. Here, we
show that the sequentially acting
UDP-GalNAc:lactosylceramide/GM3/GD3
β-1,4-
N
-acetyl-galactosaminyltransferase and the
UDP-Gal:GA2/GM2/GD2 β-1,3-galactosyltransferase associate
physically in the distal Golgi. Immunoprecipitation of the respective
epitope-tagged versions expressed in transfected CHO-K1 cells resulted
in their mutual coimmunoprecipitation. The immunocomplexes efficiently
catalyze the two transfer steps leading to the synthesis of GM1 from
exogenous GM3 in the presence of UDP-GalNAc and UDP-Gal. The N-terminal
domains (cytosolic tail, transmembrane domain, and few amino acids of
the stem region) of both enzymes are involved in the interaction
because (
i
) they reproduce the coimmunoprecipitation
behavior of the full-length enzymes, (
ii
) they compete with
the full-length counterpart in both coimmunoprecipitation and GM1
synthesis experiments, and (
iii
) fused to the cyan and
yellow fluorescent proteins, they localize these proteins to the Golgi
membranes in an association close enough as to allow fluorescence
resonance energy transfer between them. We suggest that these
associations may improve the efficiency of glycolipid synthesis by
channeling the intermediates from the position of product to the
position of acceptor along the transfer steps.
Induction of oxyradicals by arsenic: Implication for mechanism of genotoxicity
Authors: Liu Su X. , Athar Mohammad , Lippai Istvan , Waldren Charles , Hei Tom K.
Published: July 2012

Although arsenic is a well-established human carcinogen, the
mechanisms by which it induces cancer remain poorly understood. We
previously showed arsenite to be a potent mutagen in human–hamster
hybrid (A
L
) cells, and that it induces predominantly
multilocus deletions. We show here by confocal scanning microscopy with
the fluorescent probe
5′,6′-chloromethyl-2′,7′-dichlorodihydrofluorescein diacetate that
arsenite induces, within 5 min after treatment, a dose-dependent
increase of up to 3-fold in intracellular oxyradical production.
Concurrent treatment of cells with arsenite and the radical scavenger
DMSO reduced the fluorescent intensity to control levels. ESR
spectroscopy with 4-hydroxy-2,2,6,6-tetramethyl-1-hydroxypiperidine
(TEMPOL-H) as a probe in conjunction with superoxide dismutase and
catalase to quench superoxide anions and hydrogen peroxide,
respectively, indicates that arsenite increases the levels of
superoxide-driven hydroxyl radicals in these cells. Furthermore,
reducing the intracellular levels of nonprotein sulfhydryls (mainly
glutathione) in A
L
cells with buthionine S-R-sulfoximine
increases the mutagenic potential of arsenite by more than 5-fold. The
data are consistent with our previous results with the radical
scavenger DMSO, which reduced the mutagenicity of arsenic in these
cells, and provide convincing evidence that reactive oxygen species,
particularly hydroxyl radicals, play an important causal role in the
genotoxicity of arsenical compounds in mammalian cells.
Monophyly and extensive extinction of advanced eusocial bees: Insights from an unexpected Eocene diversity
Authors: Engel Michael S.
Published: July 2012

Advanced eusociality sometimes is given credit for the ecological
success of termites, ants, some wasps, and some bees. Comprehensive
study of bees fossilized in Baltic amber has revealed an unsuspected
middle Eocene (
ca.
45 million years ago) diversity of
eusocial bee lineages. Advanced eusociality arose once in the bees with
significant post-Eocene losses in diversity, leaving today only two
advanced eusocial tribes comprising less than 2% of the total bee
diversity, a trend analogous to that of hominid evolution. This pattern
of changing diversity contradicts notions concerning the role of
eusociality for evolutionary success in insects.
ATM-dependent expression of the insulin-like growth factor-I receptor in a pathway regulating radiation response
Authors: Peretz Shani , Jensen Ryan , Baserga Renato , Glazer Peter M.
Published: July 2012

The ATM gene is mutated in the syndrome of ataxia telangiectasia
(AT), associated with neurologic dysfunction, growth abnormalities, and
extreme radiosensitivity. Insulin-like growth factor-I receptor
(IGF-IR) is a cell surface receptor with tyrosine kinase activity that
can mediate mitogenesis, cell transformation, and inhibition of
apoptosis. We report here that AT cells express low levels of
IGF-IR and show decreased IGF-IR promoter activity compared with
wild-type cells. Complementation of AT cells with the ATM cDNA results
in increased IGF-IR promoter activity and elevated IGF-IR levels,
whereas expression in wild-type cells of a dominant negative fragment
of ATM specifically reduces IGF-IR expression, results consistent with
a role for ATM in regulating IGF-IR expression at the level of
transcription. When expression of IGF-IR cDNA is forced in AT cells via
a heterologous viral promoter, near normal radioresistance is conferred
on the cells. Conversely, in ATM cells complemented with the ATM cDNA,
specific inhibition of the IGF-IR pathway prevents correction of the
radiosensitivity. Taken together, these results establish a fundamental
link between ATM function and IGF-IR expression and suggest that
reduced expression of IGF-IR contributes to the radiosensitivity of AT
cells. In addition, because IGF-I plays a major role in human growth
and metabolism and serves as a survival and differentiation factor for
developing neuronal tissue, these results may provide a basis for
understanding other aspects of the AT syndrome, including the growth
abnormalities, insulin resistance, and neurodegeneration.
Induction of pre-B cell proliferation afterde novosynthesis of the pre-B cell receptor
Authors: Hess Jochen , Werner Annick , Wirth Thomas , Melchers Fritz , Jäck Hans-Martin , Winkler Thomas H.
Published: July 2012

The assembly of a pre-B cell receptor (pre-BCR) composed of an Ig μ heavy chain (μH-chain), the surrogate light (SL) chain, and the Igα/β dimer is critical for late pro-B cells to advance to the pre-B cell stage. By using a transgenic mouse model, in which μH-chain synthesis is solely driven by a tetracycline-controlled transactivator, we show thatde novosynthesis of μH-chain in transgenic pro-B cells not only induces differentiation but also proliferation. This positive effect of μH-chain synthesis on proliferation requires the presence of SL chain and costimulatory signals provided by stromal cells or IL-7. We conclude that pre-BCR signaling induces clonal expansion of early pre-B cells.
The major murine systemic lupus erythematosus susceptibility locus,Sle1, is a cluster of functionally related genes
Authors: Morel Laurence , Blenman Kim R. , Croker Byron P. , Wakeland Edward K.
Published: July 2012

The major murine systemic lupus erythematosus (SLE) susceptibility locusSle1is syntenic to a chromosomal region linked with SLE susceptibility in multiple human studies. Congenic analyses have shown thatSle1breaks tolerance to chromatin, a necessary step for full disease induction that can be suppressed by specific modifier loci. In the present study, our fine mapping analysis of the location ofSle1has determined that three loci within this congenic interval, termedSle1a,Sle1b, andSle1c, can independently cause a loss of tolerance to chromatin. Each displays a distinctive profile of serological and cellular characteristics, with T and B cell functions being more affected bySle1aandSle1b, respectively. The epistatic interactions ofSle1with other susceptibility loci to cause severe nephritis cannot be accounted, however, by these three loci alone, suggesting the existence of an additional locus, termedSle1d. These findings indicate that the potent autoimmune phenotype caused by theSle1genomic interval reflects the combined impact of four, separate, susceptibility genes. This level of genetic complexity, combined with similar findings in other systems, supports the possibility that many complex trait loci reflect the impact of polymorphisms in linked clusters of genes with related functions.
Herpes simplex virus 1 α regulatory protein ICP0 functionally interacts with cellular transcription factor BMAL1
Authors: Kawaguchi Yasushi , Tanaka Michiko , Yokoymama Akihiko , Matsuda Go , Kato Kentaro , Kagawa Hiroyuki , Hirai Kanji , Roizman Bernard
Published: July 2012

The infected cell protein no. 0 (ICP0) of herpes simplex virus 1
(HSV-1) is a promiscuous transactivator shown to enhance the expression
of gene introduced into cells by infection or transfection. At the
molecular level, ICP0 is a 775-aa ring finger protein localized
initially in the nucleus and late in infection in the cytoplasm and
mediates the degradation of several proteins and stabilization of
others. None of the known functions at the molecular level account for
the apparent activity of ICP0 as a transactivator. Here we report that
ICP0 functionally interacts with cellular transcription factor BMAL1, a
member of the basic helix–loop–helix PER-ARNT-SIM (PAS) super family
of transcriptional regulators. Specifically, sequences mapped to the
exon II of ICP0 interacted with BMAL1 in the yeast two-hybrid system
and in reciprocal pull-down experiments
in vitro
.
Moreover, the enhancement of transcription of a luciferase reporter
construct whose promoter contained multiple BMAL1-binding sites by ICP0
and BMAL1 was significantly greater than that observed by ICP0 or BMAL1
alone. Although the level of BMAL1 present in nuclei of infected cells
remained unchanged between 3 and 8 h after infection, the level of
cytoplasmic BMAL1 was reduced at 8 h after infection. The
reduction of cytoplasmic BMAL1 was significantly greater in cells
infected with the ICP0-null mutant than in the wild-type virus-infected
cells, suggesting that ICP0 mediates partial stabilization of the
protein. These results indicate that ICP0 interacts physically and
functionally with at least one cellular transcription-regulatory
factor.
A zinc finger-containing papain-like protease couples subgenomic mRNA synthesis to genome translation in a positive-stranded RNA virus
Authors: Tijms Marieke A. , van Dinten Leonie C. , Gorbalenya Alexander E. , Snijder Eric J.
Published: July 2012

The genome expression of positive-stranded RNA viruses starts with
translation rather than transcription. For some viruses, the genome is
the only viral mRNA and expression is regulated primarily at the
translational level and by limited proteolysis of polyproteins. Other
virus groups also generate subgenomic mRNAs later in the reproductive
cycle. For nidoviruses, subgenomic mRNA synthesis (transcription) is
discontinuous and yields a 5′ and 3′ coterminal nested set of mRNAs.
Nidovirus transcription is not essential for genome replication, which
relies on the autoprocessing products of two replicase polyproteins
that are translated from the genome. We now show that the N-terminal
replicase subunit, nonstructural protein 1 (nsp1), of the nidovirus
equine arteritis virus is in fact dispensable for replication but
crucial for transcription, thereby coupling replicase expression and
subgenomic mRNA synthesis in an unprecedented manner. Nsp1 is composed
of two papain-like protease domains and a predicted N-terminal zinc
finger, which was implicated in transcription by site-directed
mutagenesis. The structural integrity of nsp1 is essential, suggesting
that the protease domains form a platform for the zinc finger to
operate in transcription.
On a common circle: Natural scenes and Gestalt rules
Authors: Sigman Mariano , Cecchi Guillermo A. , Gilbert Charles D. , Magnasco Marcelo O.
Published: July 2012

To understand how the human visual system analyzes images, it is
essential to know the structure of the visual environment. In
particular, natural images display consistent statistical properties
that distinguish them from random luminance distributions. We have
studied the geometric regularities of oriented elements (edges or line
segments) present in an ensemble of visual scenes, asking how much
information the presence of a segment in a particular location of the
visual scene carries about the presence of a second segment at
different relative positions and orientations. We observed strong
long-range correlations in the distribution of oriented segments that
extend over the whole visual field. We further show that a very simple
geometric rule, cocircularity, predicts the arrangement of segments in
natural scenes, and that different geometrical arrangements show
relevant differences in their scaling properties. Our results show
similarities to geometric features of previous physiological and
psychophysical studies. We discuss the implications of these findings
for theories of early vision.
Bimodal regulation of Na
+
–Ca
2+
exchanger by β-adrenergic signaling pathway in shark ventricular myocytes
Authors: Woo Sun-Hee , Morad Martin
Published: July 2012

In shark heart, the Na
+
–Ca
2+
exchanger
serves as a major pathway for both Ca
2+
influx and efflux,
as there is only rudimentary sarcoplasmic reticulum in these hearts.
The modulation of the exchanger by a β-adrenergic agonist in
whole-cell clamped ventricular myocytes was compared with that of the
Na
+
–Ca
2+
exchanger blocker KB-R7943.
Application of 5 μM isoproterenol and 10 μM KB-R7943 suppressed
both the inward and the outward Na
+
–Ca
2+
exchanger current
(
I
Na
−
Ca
). The
isoproterenol effect was mimicked by 10 μM forskolin. Isoproterenol
and forskolin shifted the reversal potential
(
E
rev
) of
I
Na
−
Ca
by
approximately −23 mV and −30 mV, respectively. An equivalent
suppression of outward
I
Na
−
Ca
by KB-R7943
to that by isoproterenol produced a significantly smaller shift in
E
rev
of about −4 mV. The ratio of inward to
outward exchanger currents was also significantly larger in
isoproterenol- than in control- and KB-R7943-treated myocytes. Our data
suggest that the larger ratio of inward to outward exchanger currents
as well as the larger shift in
E
rev
with
isoproterenol results from the enhanced efficacy of Ca
2+
efflux via the exchanger. The protein kinase A-mediated bimodal
regulation of the exchanger in parallel with phosphorylation of the
Ca
2+
channel and enhancement of its current may have
evolved to satisfy the evolutionary needs for accelerated contraction
and relaxation in hearts of animals with vestigial sarcoplasmic
Ca
2+
release stores.
Plastid redox state and sugars: Interactive regulators of nuclear-encoded photosynthetic gene expression
Authors: Oswald Oliver , Martin Thomas , Dominy Peter J. , Graham Ian A.
Published: July 2012

Feedback regulation of photosynthesis by carbon metabolites has
long been recognized, but the underlying cellular mechanisms that
control this process remain unclear. By using an
Arabidopsis
cell culture, we show that a block in
photosynthetic electron flux prevents the increase in transcript levels
of chlorophyll a/b-binding protein and the small subunit of Rubisco
that typically occurs when intracellular sugar levels are depleted. In
contrast, the expression of the nitrate reductase gene, which is
induced by sugars, is not affected. These findings were confirmed
in planta
by using
Arabidopsis
carrying
the firefly luciferase reporter gene fused to the plastocyanin and
chlorophyll a/b-binding protein 2 gene promoters. Transcription from
both promoters increases on carbohydrate depletion. Blocking
photosynthetic electron transport with 3-(3′,
4′-dichlorophenyl)-1,1′-dimethylurea prevents this increase in
transcription. We conclude that plastid-derived redox signaling can
override the sugar-regulated expression of nuclear-encoded
photosynthetic genes. In the sugar-response mutant,
sucrose
uncoupled 6
(
sun6
),
plastocyanin
-
firefly luciferase transcription actually
increases in response to exogenous sucrose rather than decreasing as in
the wild type. Interestingly, plastid-derived redox signals do not
influence this defective pattern of sugar-regulated gene expression in
the
sun6
mutant. A model, which invokes a positive
inducer originating from the photosynthetic electron transport chain,
is proposed to explain the nature of the plastid-derived signal.
Placenta to cartilage: direct conversion of human placenta to chondrocytes with transformation by defined factors
Authors: Ishii Ryuga , Kami Daisuke , Toyoda Masashi , Makino Hatsune , Gojo Satoshi , Ishii Toshiharu , Umezawa Akihiro
Published: July 2012

Cellular differentiation and lineage commitment are considered to be robust and irreversible processes during development. Recent work has shown that mouse and human fibroblasts can be reprogrammed to a pluripotent state with a combination of four transcription factors. We hypothesized that combinatorial expression of chondrocyte-specific transcription factors could directly convert human placental cells into chondrocytes. Starting from a pool of candidate genes, we identified a combination of only five genes (5F pool)—BCL6, T (also called BRACHYURY), c-MYC, MITF, and BAF60C (also called SMARCD3)—that rapidly and efficiently convert postnatal human chorion and decidual cells into chondrocytes. The cells generated expressed multiple cartilage-specific genes, such as Collagen type II α1, LINK PROTEIN-1, and AGGRECAN, and exhibited characteristics of cartilage both in vivo and in vitro. Expression of the endogenous genes for T and MITF was initiated, implying that the cell conversion is due to not only the forced expression of the transgenes, but also to cellular reprogramming by the transgenes. This direct conversion system from noncartilage tissue to cartilaginous tissue is a substantial advance toward understanding cartilage development, cell-based therapy, and oncogenesis of chondrocytes.
Interplay between MEK-ERK signaling, cyclin D1, and cyclin-dependent kinase 5 regulates cell cycle reentry and apoptosis of neurons
Authors: Modi Prashant Kumar , Komaravelli Narayana , Singh Neha , Sharma Pushkar
Published: July 2012

In response to neurotoxic signals, postmitotic neurons make attempts to reenter the cell cycle, which results in their death. Although several cell cycle proteins have been implicated in cell cycle–related neuronal apoptosis (CRNA), the molecular mechanisms that underlie this important event are poorly understood. Here, we demonstrate that neurotoxic agents such as β-amyloid peptide cause aberrant activation of mitogen-activated kinase kinase (MEK)–extracellular signal-regulated kinase (ERK) signaling, which promotes the entry of neurons into the cell cycle, resulting in their apoptosis. The MEK-ERK pathway regulates CRNA by elevating the levels of cyclin D1. The increase in cyclin D1 attenuates the activation of cyclin-dependent kinase 5 (cdk5) by its neuronal activator p35. The inhibition of p35-cdk5 activity results in enhanced MEK-ERK signaling, leading to CRNA. These studies highlight how neurotoxic signals reprogram and alter the neuronal signaling machinery to promote their entry into the cell cycle, which eventually leads to neuronal cell death.
Regulation of SREBP during hypoxia requires Ofd1-mediated control of both DNA bindingand degradation
Authors: Porter Joshua R. , Lee Chih-Yung S. , Espenshade Peter J. , Iglesias Pablo A.
Published: July 2012

Cells adapt to changes in ambient oxygen by changing their gene expression patterns. In fission yeast, the sterol regulatory element–binding protein Sre1 is proteolytically cleaved under low oxygen, and its N-terminal segment (Sre1N) serves as a hypoxic transcription factor. When oxygen is present, the prolyl hydroxylase Ofd1 down-regulates Sre1N activity in two ways: first, by inhibiting its binding to DNA, and second, by accelerating its degradation. Here we use a mathematical model to assess what each of these two regulatory functions contributes to the hypoxic response of the cell. By disabling individual regulatory functions in the model, which would be difficult in vivo, we found that the Ofd1 function of inhibiting Sre1N binding to DNA is essential for oxygen-dependent Sre1N regulation. The other Ofd1 function of accelerating Sre1N degradation is necessary for the yeast to quickly turn off its hypoxic response when oxygen is restored. In addition, the model predicts that increased Ofd1 production at low oxygen plays an important role in the hypoxic response, and the model indicates that the Ofd1 binding partner Nro1 tunes the response to oxygen. This model quantifies our understanding of a novel oxygen-sensing mechanism that is widely conserved.
DELIMINATE—a fast and efficient method for loss-less compression of genomic sequences
Authors: Mohammed Monzoorul Haque , Dutta Anirban , Bose Tungadri , Chadaram Sudha , Mande Sharmila S.
Published: July 2012

Summary: An unprecedented quantity of genome sequence data is currently being generated using next-generation sequencing platforms. This has necessitated the development of novel bioinformatics approaches and algorithms that not only facilitate a meaningful analysis of these data but also aid in efficient compression, storage, retrieval and transmission of huge volumes of the generated data. We present a novel compression algorithm (DELIMINATE) that can rapidly compress genomic sequence data in a loss-less fashion. Validation results indicate relatively higher compression efficiency of DELIMINATE when compared with popular general purpose compression algorithms, namely, gzip, bzip2 and lzma.

Availability and implementation: Linux, Windows and Mac implementations (both 32 and 64-bit) of DELIMINATE are freely available for download at: http://metagenomics.atc.tcs.com/compression/DELIMINATE.

Contact:  sharmila@atc.tcs.com

Supplementary Information:  Supplementary data are available at Bioinformatics online.
Fusarium graminearum Tri12p Influences Virulence to Wheat and Trichothecene Accumulation
Authors: Menke Jon , Dong Yanhong , Kistler H. Corby
Published: July 2012

The gene Tri12 encodes a predicted major facilitator superfamily protein suggested to play a role in export of trichothecene mycotoxins produced by Fusarium spp. It is unclear, however, how the Tri12 protein (Tri12p) may influence trichothecene sensitivity and virulence of the wheat pathogen Fusarium graminearum. In this study, we establish a role for Tri12 in toxin accumulation and sensitivity as well as in pathogenicity toward wheat. Tri12 deletion mutants (tri12) are reduced in virulence and result in decreased trichothecene accumulation when inoculated on wheat compared with the wild-type strain or an ectopic mutant. Reduced radial growth of tri12 mutants on trichothecene biosynthesis induction medium was observed relative to the wild type and the ectopic strains. Diminished trichothecene accumulation was observed in liquid medium cultures inoculated with tri12 mutants. Wild-type fungal cells grown under conditions that induce trichothecene biosynthesis develop distinct subapical swelling and form large vacuoles. A strain expressing Tri12p linked to green fluorescent protein shows localization of the protein consistent with the plasma membrane. Our results indicate Tri12 plays a role in self-protection and influences toxin production and virulence of the fungus in planta.
Synergistic Interaction of CLAVATA1, CLAVATA2, and RECEPTOR-LIKE PROTEIN KINASE 2 in Cyst Nematode Parasitism of Arabidopsis
Authors: Replogle Amy , Wang Jianying , Paolillo Vitoria , Smeda John , Kinoshita Atsuko , Durbak Amanda , Tax Frans E. , Wang Xiaohong , Sawa Shinichiro , Mitchum Melissa G.
Published: July 2012

Plant-parasitic cyst nematodes secrete CLAVATA3 (CLV3)/ENDOSPERM SURROUNDING REGION (CLE)-like effector proteins. These proteins act as ligand mimics of plant CLE peptides and are required for successful nematode infection. Previously, we showed that the CLV2/CORYNE (CRN) heterodimer receptor complex is required for nematode CLE signaling. However, there was only a partial reduction in nematode infection when this signaling was disrupted, indicating that there might be additional nematode CLE receptors. In this study, we demonstrate that CLV1 and RECEPTOR-LIKE PROTEIN KINASE 2/TOADSTOOL2 (RPK2), two additional receptors that can transmit the CLV3 signal independent of CLV2/CRN for shoot apical meristem maintenance, also play a role in nematode CLE perception. Localization studies showed that both receptors are expressed in nematode-induced syncytia. Infection assays with clv1 and rpk2 single mutants revealed a decrease in both nematode infection and syncytium size. Significantly, further reduction in nematode infection was observed when rpk2 was combined with clv1 and clv2 mutants. Taken together, our results indicate that parallel signaling pathways involving CLV1, CLV2, and RPK2 are important for nematode parasitism.
AdpA, key regulator for morphological differentiation regulates bacterial chromosome replication
Authors: Wolański Marcin , Jakimowicz Dagmara , Zakrzewska-Czerwińska Jolanta
Published: July 2012

AdpA, one of the most pleiotropic transcription regulators in bacteria, controls expression of several dozen genes during
Streptomyces
differentiation. Here, we report a novel function for the AdpA protein: inhibitor of chromosome replication at the initiation stage. AdpA specifically recognizes the 5′ region of the
Streptomyces coelicolor
replication origin (
oriC
). Our
in vitro
results show that binding of AdpA protein decreased access of initiator protein (DnaA) to the
oriC
region
.
We also found that mutation of AdpA-binding sequences increased the accessibility of
oriC
to DnaA, which led to more frequent replication and acceleration of
Streptomyces
differentiation (at the stage of aerial hyphae formation). Moreover, we also provide evidence that AdpA and DnaA proteins compete for
oriC
binding in an ATP-dependent manner, with low ATP levels causing preferential binding of AdpA, and high ATP levels causing dissociation of AdpA and association of DnaA. This would be consistent with a role for ATP levels in determining when aerial hyphae emerge.
OBSERVATIONS ON THE EFFECT OF β‐ADRENOCEPTOR BLOCKING DRUGS ON GLYCERYL TRINITRATE TACHYCARDIA
Authors: EKUE J.M. KOFI , SHANKS R.G. , WALSH M.J.
Published: July 2012

The administration of 0.5 mg glyceryl trinitrate by chewing and keeping under the tongue increased heart rate in normal subjects in the supine and erect posture.

There was no significant difference between the responses in the same subject on repeated administration of glyceryl trinitrate on different days but there was a significant difference between the responses in different subjects.

The oral administration of practolol and propranolol reduced the responses to glyceryl trinitrate. The two drugs progressively reduced the increase in heart rate produced by glyceryl trinitrate; there was no significant difference between their effects. Propranolol produced a significantly greater reduction than practolol in the maximum heart rate that was produced by glyceryl trinitrate.

The administration of practolol (300 mg) twice daily by mouth to patients after an acute episode of ischaemic heart disease significantly reduced the increases in heart rate produced by standing and by glyceryl trinitrate in comparison to the responses in similar patients receiving a placebo.
PURINE AND PYRIMIDINE EXCRETION IN PSORIASIS: A COMPARISON WITH HEALTHY CONTROLS DURING ALLOPURINOL THERAPY
Authors: SIMMONDS H.A. , BOWYER A.
Published: July 2012

Urinary purine excretion has been investigated in two healthy controls and two patients with psoriasis, one a hyperuricaemic, one a normouricaemic. No difference was detected between the patients and controls. Therapy with allopurinol effectively lowered blood and urinary uric acid levels and produced a deficit in total urinary oxypurine excretion in both controls and patients with psoriasis. The concomitant increase in xanthine excretion was greater than the increase in hypoxanthine excretion and xanthine/hypoxanthine ratios (average 0.70 and 1.0 prior to therapy) were increased by allopurinol to an average of 3.0 and 3.8 respectively in the two groups. Allopurinol also reduced the excretion of 8‐hydroxy‐7‐methyl guanine but no effect on the excretion levels of other minor purine bases was noted.

Allopurinol was metabolized similarly by both patients and controls, 84% of the administered allopurinol being accounted for as urinary metabolites. 74% of the drug in the urine was excreted as oxipurinol, 26% as unchanged allopurinol plus allopurinol riboside, the remainder being oxipurinol riboside.

Pseudouridine excretion in 25 healthy controls was 86.5 ± 17.8 mg/24 hours. Pseudouridine excretion was not excessive in the patients with psoriasis and was not altered by allopurinol therapy.

No abnormality or difference in purine or pyrimidine excretion in either patient was detected prior to or during therapy which could be related to the epidermal lesion.
PLASMA CONCENTRATIONS OF METHIMAZOLE, A METABOLITE OF CARBIMAZOLE, IN HYPERTHYROID PATIENTS
Authors: SKELLERN G.G. , STENLAKE J.B. , WILLIAMS W.D. , McLARTY D.G.
Published: July 2012

Carbimazole was administered to nine hyperthyroid patients, and blood samples were taken at various time intervals for analysis of carbimazole, and its metabolite methimazole.

A technique was developed for the measurement of methimazole in serum, using a High‐Pressure Liquid Chromatograph, which could detect nanogram quantities of this metabolite.

After a single oral dose, the patients' blood levels appeared to fall into two groups, either those with a maximum concentration of methimazole between 30 and 60 min, or those whose maximum was 2 to 3 hours.

The results would suggest that there could be a correlation between the high level of methimazole in serum and the high thyroxine concentration found in some patients.
CHARCOAL HAEMOPERFUSION FOR PARACETAMOL OVERDOSE
Authors: GAZZARD B.G. , WILLSON R.A. , WESTON M.J. , THOMPSON R.P.H. , WILLIAMS R.
Published: July 2012

A controlled trial of charcoal haemoperfusion as an early treatment for paracetamol overdose showed no benefit.

The plasma clearances of paracetamol by the charcoal column were variable and disappointingly small (range 4–119 ml/minute). The cumulative amounts removed were also low, mean 1.4 g (range 0.2–5.2 g).

No clinical problems were encountered with the technique of haemoperfusion and in particular the drop in blood platelet counts was small (mean fall 16%).
EFFECT OF ANGIOTENSIN‐CONVERTING ENZYME INHIBITOR ON RESPONSE OF PLASMA RENIN ACTIVITY AND ALDOSTERONE TO TILTING IN MAN
Authors: COLLIER J.G. , JENKINS J.S. , KEDDIE J. , KHAN M.U.A. , ROBINSON B.F.
Published: July 2012

The effect of an angiotensin‐converting enzyme inhibitor (SQ 20,881; 0.5 mg/kg) on the response to tilting of plasma renin activity (PRA), plasma aldosterone and Cortisol was studied in five normal subjects.

PRA rose significantly in both the supine and upright positions following administration of SQ 20,881; no significant effect on aldosterone or Cortisol was observed.