bluuebunny/crossref_metadata_2025 huggingface dataset:
Variation in dopamine genes influences responsivity of the human reward system
Authors: Dreher Jean-Claude , Kohn Philip , Kolachana Bhaskar , Weinberger Daniel R. , Berman Karen Faith
Published: December 2008

In humans, dopamine neurotransmission is influenced by functional polymorphisms in the dopamine transporter (
DAT
1) and catechol-
O
-methyltransferase (
COMT
) genes. Here, we used event-related functional magnetic resonance imaging to directly investigate the neurofunctional effects of the Val
158
Met
COMT
and variable number of tandem repeat
DAT
1 polymorphisms on distinct components of the reward system in humans. The results revealed a main effect of
COMT
genotype in the ventral striatum and lateral prefrontal cortex during reward anticipation (
P
< 0.001, uncorrected) and in the orbitofrontal cortex at the time of reward delivery (
P
< 0.005), met/met individuals exhibiting the highest activation. The main effect of
DAT
1 genotype was seen in robust blood-oxygen-level-dependent response differences in the caudate nucleus and ventral striatum during reward anticipation (
P
< 0.001) and in the lateral prefrontal cortex and midbrain at the time of reward delivery, with carriers of the
DAT
1 9-repeat allele showing the highest activity. Moreover, an interaction between the
COMT
and
DAT
1 genes was found in the ventral striatum and lateral prefrontal cortex during reward anticipation and in the lateral prefrontal and orbitofrontal cortices as well as in the midbrain at the time of reward delivery, with carriers of the
DAT
1 9-repeat allele and
COMT
met/met allele exhibiting the highest activation, presumably reflecting functional change consequent to higher synaptic dopamine availability. Taken together, these results indicate that genetically influenced variations in dopamine transmission modulate the response of brain regions involved in anticipation and reception of rewards and suggest that these responses may contribute to individual differences in reward-seeking behavior and in predisposition to neuropsychiatric disorders.
Regulatory logic of neuronal diversity: Terminal selector genes and selector motifs
Authors: Hobert Oliver
Published: December 2008

Individual neuronal cell types are defined by the expression of unique batteries of terminal differentiation genes. The elucidation of the
cis
-regulatory architecture of several distinct, single neuron type-specific gene batteries in
Caenorhabditis elegans
has revealed a strikingly simple
cis
-regulatory logic, in which small
cis
-regulatory motifs are activated in postmitotic neurons by autoregulating transcription factors (TFs). Loss of the TFs results in the loss of the identity of the individual neuron type. I propose to term these TFs “terminal selector genes” and their cognate
cis
-regulatory target sites “terminal selector motifs.” Terminal selector genes assign individual neuronal identities by directly controlling the expression of downstream, terminal differentiation genes and act in specific regulatory network configurations. The simplicity of the
cis
-regulatory logic on which the terminal selector gene concept is based may contribute to the evolvability of neuronal diversity.
A regulatory module embedded in the coding region of
Hoxa2
controls expression in rhombomere 2
Authors: Tümpel Stefan , Cambronero Francisco , Sims Carrie , Krumlauf Robb , Wiedemann Leanne M.
Published: December 2008

Here, we define a gene regulatory network for
Hoxa2
, responsible for temporal and spatial expression in hindbrain development.
Hoxa2
plays an important role in regulating the regional identity of rhombomere 2 (r2) and is the only
Hox
gene expressed in this segment. In this study, we found that a
Hoxa2 cis
-regulatory module consists of five elements that direct expression in r2 of the developing hindbrain. Surprisingly, the module is imbedded in the second coding exon of
Hoxa2
and therefore may be constrained by both protein coding and gene regulatory requirements. This highly conserved enhancer consists of two consensus Sox binding sites and several additional elements that act in concert to direct strong r2 specific expression. Our findings provide important insight into the regulation of segmental identity in the anterior hindbrain. Furthermore, they have broader implications in designing arrays and interpreting data from global analyses of gene regulation because regulatory input from coding regions needs to be considered.
Gene regulatory network subcircuit controlling a dynamic spatial pattern of signaling in the sea urchin embryo
Authors: Smith Joel , Davidson Eric H.
Published: December 2008

We dissect the transcriptional regulatory relationships coordinating the dynamic expression patterns of two signaling genes,
wnt8
and
delta
, which are central to specification of the sea urchin embryo endomesoderm.
cis
-Regulatory analysis shows that transcription of the gene encoding the Notch ligand Delta is activated by the widely expressed Runx transcription factor, but spatially restricted by HesC-mediated repression through a site in the
delta
5′UTR. Spatial transcription of the
hesC
gene, however, is controlled by Blimp1 repression. Blimp1 thus represses the repressor of
delta
, thereby permitting its transcription. The
blimp1
gene is itself linked into a feedback circuit that includes the
wnt8
signaling ligand gene, and we showed earlier that this circuit generates an expanding torus of
blimp1
and
wnt8
expression. The finding that
delta
expression is also controlled at the
cis
-regulatory level by the
blimp1-wnt8
torus-generating subcircuit now explains the progression of Notch signaling from the mesoderm to the endoderm of the developing embryo. Thus the specific
cis
-regulatory linkages of the gene regulatory network encode the coordinated spatial expression of Wnt and Notch signaling as they sweep outward across the vegetal plate of the embryo.
A gene regulatory network armature for T lymphocyte specification
Authors: Georgescu Constantin , Longabaugh William J. R. , Scripture-Adams Deirdre D. , David-Fung Elizabeth-Sharon , Yui Mary A. , Zarnegar Mark A. , Bolouri Hamid , Rothenberg Ellen V.
Published: December 2008

Choice of a T lymphoid fate by hematopoietic progenitor cells depends on sustained Notch–Delta signaling combined with tightly regulated activities of multiple transcription factors. To dissect the regulatory network connections that mediate this process, we have used high-resolution analysis of regulatory gene expression trajectories from the beginning to the end of specification, tests of the short-term Notch dependence of these gene expression changes, and analyses of the effects of overexpression of two essential transcription factors, namely PU.1 and GATA-3. Quantitative expression measurements of >50 transcription factor and marker genes have been used to derive the principal components of regulatory change through which T cell precursors progress from primitive multipotency to T lineage commitment. Our analyses reveal separate contributions of Notch signaling, GATA-3 activity, and down-regulation of PU.1. Using BioTapestry (
www.BioTapestry.org
), the results have been assembled into a draft gene regulatory network for the specification of T cell precursors and the choice of T as opposed to myeloid/dendritic or mast-cell fates. This network also accommodates effects of E proteins and mutual repression circuits of Gfi1 against Egr-2 and of TCF-1 against PU.1 as proposed elsewhere, but requires additional functions that remain unidentified. Distinctive features of this network structure include the intense dose dependence of GATA-3 effects, the gene-specific modulation of PU.1 activity based on Notch activity, the lack of direct opposition between PU.1 and GATA-3, and the need for a distinct, late-acting repressive function or functions to extinguish stem and progenitor-derived regulatory gene expression.
Transformation and isolation of allelic exchange mutants of
Chlamydia psittaci
using recombinant DNA introduced by electroporation
Authors: Binet Rachel , Maurelli Anthony T.
Published: December 2008

To facilitate genetic investigations in the obligate intracellular pathogens
Chlamydia
, the ability to construct variants by homologous recombination was investigated in
C. psittaci
6BC. The single rRNA operon was targeted with a synthetic 16S rRNA allele, harboring three nucleotide substitutions over 398 bp, which imparts resistance to kasugamycin (Ksm) and spectinomycin (Spc) and causes loss of one HpaI restriction site. A fourth, silent mutation was introduced 654 bp downstream in the beginning of the 23S rRNA gene.
C. psittaci
6BC infectious particles were electroporated with various concentrations of circular or linearized plasmids containing different lengths of the rRNA region homologous to the chromosomal copy except for the four nucleotide substitutions. Ksm and Spc were added 18 h after inoculation onto confluent cell monolayers in the plaque assay. Resistant plaques were picked and expanded with selection 10 days later before collecting DNA for analysis by PCR, restriction mapping, sequencing, or Southern. Spontaneous resistance to Ksm and Spc was never observed in mock electroporated bacteria (frequency <6.2 × 10
−9
). Conversely, double resistance and replacement of the 16S rRNA gene were observed when
C. psittaci
was electroporated with the recombination substrates. Highest efficiency was obtained with 10 μg of circular vector prepared in a DNA methylase-deficient
Escherichia coli
(1.9 ± 1.1 × 10
−6
,
n
= 7). Coinheritance of the silent 23S rRNA mutation was seen in 46 of 67 recombinants analyzed, illustrating DNA exchange of up to 1,052 bp in length. These findings provide the first step toward genetic manipulation of
Chlamydia
.
The
Drosophila
cell adhesion molecule Klingon is required for long-term memory formation and is regulated by Notch
Authors: Matsuno Motomi , Horiuchi Junjiro , Tully Tim , Saitoe Minoru
Published: December 2008

The
ruslan
(
rus
) mutant was previously identified in a behavioral screen for mutants defective in long-lasting memory, which consists of two consolidated memory types, anesthesia-resistant memory, and protein synthesis-dependent long-term memory (LTM). We demonstrate here that
rus
is a new allele of
klingon
(
klg
), which encodes a homophilic cell adhesion molecule. Klg is acutely required for LTM but not anesthesia-resistant memory formation, and Klg expression increases upon LTM induction. LTM formation also requires activity of the Notch cell-surface receptor. Although defects in Notch have been implicated in memory loss because of Alzheimer's disease, downstream signaling linking Notch to memory have not been determined. Strikingly, we found that Notch activity increases upon LTM induction and regulates Klg expression. Furthermore, Notch-induced enhancement of LTM is disrupted by a
klg
mutation. We propose that Klg is a downstream effector of Notch signaling that links Notch activity to memory.
Structural basis for antagonism of human interleukin 18 by poxvirus interleukin 18-binding protein
Authors: Krumm Brian , Meng Xiangzhi , Li Yongchao , Xiang Yan , Deng Junpeng
Published: December 2008

Human interleukin-18 (hIL-18) is a cytokine that plays an important role in inflammation and host defense against microbes. Its activity is regulated in vivo by a naturally occurring antagonist, the human IL-18-binding protein (IL-18BP). Functional homologs of human IL-18BP are encoded by all orthopoxviruses, including variola virus, the causative agent of smallpox. They contribute to virulence by suppressing IL-18-mediated immune responses. Here, we describe the 2.0-Å resolution crystal structure of an orthopoxvirus IL-18BP, ectromelia virus IL-18BP (ectvIL-18BP), in complex with hIL-18. The hIL-18 structure in the complex shows significant conformational change at the binding interface compared with the structure of ligand-free hIL-18, indicating that the binding is mediated by an induced-fit mechanism. EctvIL-18BP adopts a canonical Ig fold and interacts via one edge of its β-sandwich with 3 cavities on the hIL-18 surface through extensive hydrophobic and hydrogen bonding interactions. Most of the ectvIL-18BP residues that participate in these interactions are conserved in both human and viral homologs, explaining their functional equivalence despite limited sequence homology. EctvIL-18BP blocks a putative receptor-binding site on IL-18, thus preventing IL-18 from engaging its receptor. Our structure provides insights into how IL-18BPs modulate hIL-18 activity. The revealed binding interface provides the basis for rational design of inhibitors against orthopoxvirus IL-18BP (for treating orthopoxvirus infection) or hIL-18 (for treating certain inflammatory and autoimmune diseases).
Fossil evidence for the origin of spider spinnerets, and a proposed arachnid order
Authors: Selden Paul A. , Shear William A. , Sutton Mark D.
Published: December 2008

Silk production from opisthosomal glands is a defining characteristic of spiders (Araneae). Silk emerges from spigots (modified setae) borne on spinnerets (modified appendages). Spigots from
Attercopus fimbriunguis
, from Middle Devonian (386 Ma) strata of Gilboa, New York, were described in 1989 as evidence for the oldest spider and the first use of silk by animals. Slightly younger (374 Ma) material from South Mountain, New York, conspecific with
A. fimbriunguis
, includes spigots and other evidence that elucidate the evolution of early Araneae and the origin of spider silk. No known
Attercopus
spigots, including the original specimen, occur on true spinnerets but are arranged along the edges of plates. Spinnerets originated from biramous appendages of opisthosomal somites 4 and 5; although present in
Limulus
, no other arachnids have opisthosomal appendage homologues on these segments. The spigot arrangement in
Attercopus
shows a primitive state before the reexpression of the dormant genetic mechanism that gave rise to spinnerets in later spiders. Enigmatic flagellar structures originally described as Arachnida
incertae sedis
, are shown to be
Attercopus
anal flagella, as found in
Permarachne
, also originally described as a spider. An arachnid order, Uraraneida, is erected for a plesion, including these two genera, based on this combination of characters. The inability of Uraraneida precisely to control silk weaving suggests its original use as a wrapping, lining, or homing material.
Culture, population structure, and low genetic diversity in Pleistocene hominins
Authors: Premo L. S. , Hublin Jean-Jacques
Published: December 2008

Paleogenomic research has shown that modern humans, Neanderthals, and their most recent common ancestor have displayed less genetic diversity than living great apes. The traditional interpretation that low levels of genetic diversity in modern humans resulted from a relatively recent demographic bottleneck cannot account for similarly low levels of genetic diversity in Middle Pleistocene hominins. A more parsimonious hypothesis proposes that the effective population size of the human lineage has been low for more than 500,000 years, but the mechanism responsible for suppressing genetic diversity in Pleistocene hominin populations without similarly affecting that of their hominoid contemporaries remains unknown. Here we use agent-based simulation to study the effect of culturally mediated migration on neutral genetic diversity in structured populations. We show that, in populations structured by culturally mediated migration, selection can suppress neutral genetic diversity over thousands of generations, even in the absence of bottlenecks or expansions in census population size. In other words, selection could have suppressed the effective population size of Pleistocene hominins for as long as the degree of cultural similarity between regionally differentiated groups played an important role in mediating intraspecific gene flow.
Slow peptide bond formation by proline and other
N
-alkylamino acids in translation
Authors: Pavlov Michael Y. , Watts Richard E. , Tan Zhongping , Cornish Virginia W. , Ehrenberg Måns , Forster Anthony C.
Published: December 2008

Proteins are made from 19 aa and, curiously, one
N
-alkylamino acid (“imino acid”), proline (Pro). Pro is thought to be incorporated by the translation apparatus at the same rate as the 19 aa, even though the alkyl group in Pro resides directly on the nitrogen nucleophile involved in peptide bond formation. Here, by combining quench-flow kinetics and charging of tRNAs with cognate and noncognate amino acids, we find that Pro incorporates in translation significantly more slowly than Phe or Ala and that other
N
-alkylamino acids incorporate much more slowly. Our results show that the slowest step in incorporation of
N
-alkylamino acids is accommodation/peptidyl transfer after GTP hydrolysis on EF-Tu. The relative incorporation rates correlate with expectations from organic chemistry, suggesting that amino acid sterics and basicities affect translation rates at the peptidyl transfer step. Cognate isoacceptor tRNAs speed Pro incorporation to rates compatible with in vivo, although still 3–6 times slower than Phe incorporation from Phe-tRNA
Phe
depending on the Pro codon. Results suggest that Pro is the only
N
-alkylamino acid in the genetic code because it has a privileged cyclic structure that is more reactive than other
N
-alkylamino acids. Our data on the variation of the rate of incorporation of Pro from native Pro-tRNA
Pro
isoacceptors at 4 different Pro codons help explain codon bias not accounted for by the “tRNA abundance” hypothesis.
Circuitry-based gene expression profiles in GABA cells of the trisynaptic pathway in schizophrenics versus bipolars
Authors: Benes Francine M. , Lim Benjamin , Matzilevich David , Subburaju Sivan , Walsh John P.
Published: December 2008

Significant reductions in GABAergic cell numbers and/or activity have been demonstrated in the hippocampus of subjects with schizophrenia and bipolar disorder. To understand how different subpopulations of interneurons are regulated, laser microdissection and gene expression profiling have been used to “deconstruct” the trisynaptic pathway, so that subtypes of GABA cells could be defined by their location in various layers of CA3/2 and CA1. The results suggest that the cellular endophenotypes for SZ and BD may be determined by multiple factors that include unique susceptibility genes for the respective disorders and altered integration among hippocampal GABA cells with extrinsic and intrinsic afferent fiber systems. The extensive and intricate data that has come from this study has provided insights into how a complex circuit, like the trisynaptic pathway, may be regulated in human hippocampus in both health and disease.
Molecular mechanism for the umami taste synergism
Authors: Zhang Feng , Klebansky Boris , Fine Richard M. , Xu Hong , Pronin Alexey , Liu Haitian , Tachdjian Catherine , Li Xiaodong
Published: December 2008

Umami is one of the 5 basic taste qualities. The umami taste of L-glutamate can be drastically enhanced by 5′ ribonucleotides and the synergy is a hallmark of this taste quality. The umami taste receptor is a heteromeric complex of 2 class C G-protein-coupled receptors, T1R1 and T1R3. Here we elucidate the molecular mechanism of the synergy using chimeric T1R receptors, site-directed mutagenesis, and molecular modeling. We propose a cooperative ligand-binding model involving the Venus flytrap domain of T1R1, where L-glutamate binds close to the hinge region, and 5′ ribonucleotides bind to an adjacent site close to the opening of the flytrap to further stabilize the closed conformation. This unique mechanism may apply to other class C G-protein-coupled receptors.
A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes
Authors: Lage Kasper , Hansen Niclas Tue , Karlberg E. Olof , Eklund Aron C. , Roque Francisco S. , Donahoe Patricia K. , Szallasi Zoltan , Jensen Thomas Skøt , Brunak Søren
Published: December 2008

Heritable diseases are caused by germ-line mutations that, despite tissuewide presence, often lead to tissue-specific pathology. Here, we make a systematic analysis of the link between tissue-specific gene expression and pathological manifestations in many human diseases and cancers. Diseases were systematically mapped to tissues they affect from disease-relevant literature in PubMed to create a disease–tissue covariation matrix of high-confidence associations of >1,000 diseases to 73 tissues. By retrieving >2,000 known disease genes, and generating 1,500 disease-associated protein complexes, we analyzed the differential expression of a gene or complex involved in a particular disease in the tissues affected by the disease, compared with nonaffected tissues. When this analysis is scaled to all diseases in our dataset, there is a significant tendency for disease genes and complexes to be overexpressed in the normal tissues where defects cause pathology. In contrast, cancer genes and complexes were not overexpressed in the tissues from which the tumors emanate. We specifically identified a complex involved in XY sex reversal that is testis-specific and down-regulated in ovaries. We also identified complexes in Parkinson disease, cardiomyopathies, and muscular dystrophy syndromes that are similarly tissue specific. Our method represents a conceptual scaffold for organism-spanning analyses and reveals an extensive list of tissue-specific draft molecular pathways, both known and unexpected, that might be disrupted in disease.
Prediction of incommensurate crystal structure in Ca at high pressure
Authors: Arapan Sergiu , Mao Ho-kwang , Ahuja Rajeev
Published: December 2008

Ca shows an interesting high-pressure phase transformation sequence, but, despite similar physical properties at high pressure and affinity in the electronic structure with its neighbors in the periodic table, no complex phase has been identified for Ca so far. We predict an incommensurate high-pressure phase of Ca from first principle calculations and describe a procedure of estimating incommensurate structure parameters by means of electronic structure calculations for periodic crystals. Thus, by using the ab initio technique for periodic structures, one can get not only reliable information about the electronic structure and structural parameters of an incommensurate phase, but also identify and predict such phases in new elements.
Differential trafficking of AMPA and NMDA receptors by SAP102 and PSD-95 underlies synapse development
Authors: Elias G. M. , Elias L. A. B. , Apostolides P. F. , Kriegstein A. R. , Nicoll R. A.
Published: December 2008

The development of glutamatergic synapses involves changes in the number and type of receptors present at the postsynaptic density. To elucidate molecular mechanisms underlying these changes, we combine
in utero
electroporation of constructs that alter the molecular composition of developing synapses with dual whole-cell electrophysiology to examine synaptic transmission during two distinct developmental stages. We find that SAP102 mediates synaptic trafficking of AMPA and NMDA receptors during synaptogenesis. Surprisingly, after synaptogenesis, PSD-95 assumes the functions of SAP102 and is necessary for two aspects of synapse maturation: the developmental increase in AMPA receptor transmission and replacement of NR2B-NMDARs with NR2A-NMDARs. In PSD-95/PSD-93 double-KO mice, the maturational replacement of NR2B- with NR2A-NMDARs fails to occur, and PSD-95 expression fully rescues this deficit. This study demonstrates that SAP102 and PSD-95 regulate the synaptic trafficking of distinct glutamate receptor subtypes at different developmental stages, thereby playing necessary roles in excitatory synapse development.
Replication protein A and proliferating cell nuclear antigen coordinate DNA polymerase selection in 8-oxo-guanine repair
Authors: Maga Giovanni , Crespan Emmanuele , Wimmer Ursula , van Loon Barbara , Amoroso Alessandra , Mondello Chiara , Belgiovine Cristina , Ferrari Elena , Locatelli Giada , Villani Giuseppe , Hübscher Ulrich
Published: December 2008

The adenine misincorporated by replicative DNA polymerases (pols) opposite 7,8-dihydro-8-oxoguanine (8-oxo-G) is removed by a specific glycosylase, leaving the lesion on the DNA. Subsequent incorporation of C opposite 8-oxo-G on the resulting 1-nt gapped DNA is essential for the removal of the 8-oxo-G to prevent G–C to T–A transversion mutations. By using model DNA templates, purified DNA pols β and λ and knockout cell extracts, we show here that the auxiliary proteins replication protein A and proliferating cell nuclear antigen act as molecular switches to activate the DNA pol λ- dependent highly efficient and faithful repair of A:8-oxo-G mismatches in human cells and to repress DNA pol β activity. By using an immortalized human fibroblast cell line that has the potential to induce cancer in mice, we show that the development of a tumoral phenotype in these cells correlated with a differential expression of DNA pols λ and β.
Genetic analysis of interactions with eukaryotic rRNA identify the mitoribosome as target in aminoglycoside ototoxicity
Authors: Hobbie Sven N. , Akshay Subramanian , Kalapala Sarath K. , Bruell Christian M. , Shcherbakov Dmitry , Böttger Erik C.
Published: December 2008

Aminoglycoside ototoxicity has been related to a surprisingly large number of cellular structures and metabolic pathways. The finding that patients with mutations in mitochondrial rRNA are hypersusceptible to aminoglycoside-induced hearing loss has indicated a possible role for mitochondrial protein synthesis. To study the molecular interaction of aminoglycosides with eukaryotic ribosomes, we made use of the observation that the drug binding site is a distinct domain defined by the small subunit rRNA, and investigated drug susceptibility of bacterial hybrid ribosomes carrying various alleles of the eukaryotic decoding site. Compared to hybrid ribosomes with the A site of human cytosolic ribosomes, susceptibility of mitochondrial hybrid ribosomes to various aminoglycosides correlated with the relative cochleotoxicity of these drugs. Sequence alterations that correspond to the mitochondrial deafness mutations A1555G and C1494T increased drug-binding and rendered the ribosomal decoding site hypersusceptible to aminoglycoside-induced mistranslation and inhibition of protein synthesis. Our results provide experimental support for aminoglycoside-induced dysfunction of the mitochondrial ribosome. We propose a pathogenic mechanism in which interference of aminoglycosides with mitochondrial protein synthesis exacerbates the drugs' cochlear toxicity, playing a key role in sporadic dose-dependent and genetically inherited, aminoglycoside-induced deafness.
Dividing glial cells maintain differentiated properties including complex morphology and functional synapses
Authors: Ge Woo-Ping , Zhou Wei , Luo Qingming , Jan Lily Yeh , Jan Yuh Nung
Published: December 2008

It is generally believed that dividing cells gain complex features of differentiation only after exiting the cell cycle because cell division and differentiation are both under such tight regulation that their coexistence is deemed unlikely. As the major proliferating cell type in the mammalian CNS, NG2 glial cells (NG2 cells) account for 5–8% of the glial cell population and form synaptic contacts with neurons. Here we report that NG2 cells divide while maintaining their differentiation, including morphological features, such as the elaboration of multiple complex cellular processes and physiological features including active glutamatergic and GABAergic synaptic responses. Not only do NG2 cells continue to receive excitatory and inhibitory synaptic inputs as they undergo mitosis, a subpopulation of dividing NG2 cells can fire action potentials upon depolarization, thereby revealing that these dividing NG2 cells retain voltage-gated ion channels as well as transmitter receptors for signal processing. These findings provide a clear counterexample of the widely perceived incompatibility between cell division and differentiation.
A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3β
Authors: Hirota Tsuyoshi , Lewis Warren G. , Liu Andrew C. , Lee Jae Wook , Schultz Peter G. , Kay Steve A.
Published: December 2008

The circadian clock controls daily oscillations of gene expression at the cellular level. We report the development of a high-throughput circadian functional assay system that consists of luminescent reporter cells, screening automation, and a data analysis pipeline. We applied this system to further dissect the molecular mechanisms underlying the mammalian circadian clock using a chemical biology approach. We analyzed the effect of 1,280 pharmacologically active compounds with diverse structures on the circadian period length that is indicative of the core clock mechanism. Our screening paradigm identified many compounds previously known to change the circadian period or phase, demonstrating the validity of the assay system. Furthermore, we found that small molecule inhibitors of glycogen synthase kinase 3 (GSK-3) consistently caused a strong short period phenotype in contrast to the well-known period lengthening by lithium, another presumed GSK-3 inhibitor. siRNA-mediated knockdown of GSK-3β also caused a short period, confirming the phenotype obtained with the small molecule inhibitors. These results clarify the role of GSK-3β in the period regulation of the mammalian clockworks and highlight the effectiveness of chemical biology in exploring unidentified mechanisms of the circadian clock.
Imaging the glycome
Authors: Laughlin Scott T. , Bertozzi Carolyn R.
Published: December 2008

Molecular imaging enables visualization of specific molecules in vivo and without substantial perturbation to the target molecule's environment. Glycans are appealing targets for molecular imaging but are inaccessible with conventional approaches. Classic methods for monitoring glycans rely on molecular recognition with probe-bearing lectins or antibodies, but these techniques are not well suited to in vivo imaging. In an emerging strategy, glycans are imaged by metabolic labeling with chemical reporters and subsequent ligation to fluorescent probes. This technique has enabled visualization of glycans in living cells and in live organisms such as zebrafish. Molecular imaging with chemical reporters offers a new avenue for probing changes in the glycome that accompany development and disease.
Coreference between singular epicenes and the plural pronoun
Authors: Neubauer Marion
Published: December 2008

This corpus-based study examines the resolution of coreference between formally singular epicene antecedents and their anaphoric pronouns within the framework of Cognitive Grammar. These antecedents are expected to most directly evoke a singular conceptual entity, and, consequently, coreference is assumed to be most effectively established by using a singular pronoun, whereas the plural anaphor would have to be accounted for by metonymic antecedence. Yet, the high frequency of they found in the study suggests that epicene generics are predominantly conceptualized as referring to plural entities, despite their morphological singularity. This conceptual plurality proves to be salient enough to persist even if the gender of the referent(s) is known. Finally, a small portion of tokens evincing coreference between notionally singular antecedents and they can only be accounted for by acknowledging that the anaphor actively contributes information to its anchor, thus refuting the claim that pronouns merely resume their antecedents.
La vérité et le fabliau. Le cas d'Estormi
Authors: Abramowicz Maciej
Published: December 2008

L’article propose d’étudier le phénomène de la véridiction dans le genre du fabliau à partir de l’exemple d’Estormi. Les auteurs de fabliaux postulent souvent, en dépit de l’invraisemblance des intrigues, qu’ils relatent un fait qui s’est réellement produit. La question se pose de savoir comment un genre dont la fictivité ne suscite aucun doute peut-il être véhicule de la vérité? L’étude des instances d’énonciation et de l’organisation du récit montre que la vérité du fabliau ne s’épuise pas dans la fiction de la référentialité, l’illusion du réel réalisée grâce au vraisemblable ponctuel. Ineséparable de la vérité du dévoilement, la pseudo-référentialité fait partie de la vérité syncrétique qui naît du mélange de la représentation, de la moralisation et du mélange des discours dont l’unique lieu de manifestation est l’oeuvre littéraire. Sa présence s’avère indispensable pour réaliser l’objectif assigné à l’oeuvre qui est, dans le cas du fabliau, de faire rire.
Absence of SPARC results in increased cardiac rupture and dysfunction after acute myocardial infarction
Authors: Schellings Mark W.M. , Vanhoutte Davy , Swinnen Melissa , Cleutjens Jack P. , Debets Jacques , van Leeuwen Rick E.W. , d'Hooge Jan , Van de Werf Frans , Carmeliet Peter , Pinto Yigal M. , Sage E. Helene , Heymans Stephane
Published: December 2008

The matricellular protein SPARC (secreted protein, acidic and rich in cysteine, also known as osteonectin) mediates cell–matrix interactions during wound healing and regulates the production and/or assembly of the extracellular matrix (ECM). This study investigated whether SPARC functions in infarct healing and ECM maturation after myocardial infarction (MI). In comparison with wild-type (WT) mice, animals with a targeted inactivation of SPARC exhibited a fourfold increase in mortality that resulted from an increased incidence of cardiac rupture and failure after MI. SPARC-null infarcts had a disorganized granulation tissue and immature collagenous ECM. In contrast, adenoviral overexpression of SPARC in WT mice improved the collagen maturation and prevented cardiac dilatation and dysfunction after MI. In cardiac fibroblasts in vitro, reduction of SPARC by short hairpin RNA attenuated transforming growth factor β (TGF)–mediated increase of Smad2 phosphorylation, whereas addition of recombinant SPARC increased Smad2 phosphorylation concordant with increased Smad2 phosphorylation in SPARC-treated mice. Importantly, infusion of TGF-β rescued cardiac rupture in SPARC-null mice but did not significantly alter infarct healing in WT mice. These findings indicate that local production of SPARC is essential for maintenance of the integrity of cardiac ECM after MI. The protective effects of SPARC emphasize the potential therapeutic applications of this protein to prevent cardiac dilatation and dysfunction after MI.
Maresins: novel macrophage mediators with potent antiinflammatory and proresolving actions
Authors: Serhan Charles N. , Yang Rong , Martinod Kimberly , Kasuga Kie , Pillai Padmini S. , Porter Timothy F. , Oh Sungwhan F. , Spite Matthew
Published: December 2008

The endogenous cellular and molecular mechanisms that control acute inflammation and its resolution are of wide interest. Using self-resolving inflammatory exudates and lipidomics, we have identified a new pathway involving biosynthesis of potent antiinflammatory and proresolving mediators from the essential fatty acid docosahexaenoic acid (DHA) by macrophages (MΦs). During the resolution of mouse peritonitis, exudates accumulated both 17-hydroxydocosahexaenoic acid, a known marker of 17S-D series resolvin (Rv) and protectin biosynthesis, and 14S-hydroxydocosa-4Z,7Z,10Z,12E,16Z,19Z-hexaenoic acid from endogenous DHA. Addition of either DHA or 14S-hydroperoxydocosa-4Z,7Z,10Z,12E,16Z,19Z-hexaenoic acid to activated MΦs converted these substrates to novel dihydroxy-containing products that possessed potent antiinflammatory and proresolving activity with a potency similar to resolvin E1, 5S,12R,18R-trihydroxyeicosa-6Z,8E,10E,14Z,16E-pentaenoic acid, and protectin D1, 10R,17S-dihydroxydocosa-4Z,7Z,11E,13E,15Z,19Z-hexaenoic acid. Stable isotope incorporation, intermediate trapping, and characterization of physical and biological properties of the products demonstrated a novel 14-lipoxygenase pathway, generating bioactive 7,14-dihydroxydocosa-4Z,8,10,12,16Z,19Z-hexaenoic acid, coined MΦ mediator in resolving inflammation (maresin), which enhances resolution. These findings suggest that maresins and this new metabolome may be involved in some of the beneficial actions of DHA and MΦs in tissue homeostasis, inflammation resolution, wound healing, and host defense.
Pure mapping class group acting on Teichmüller space
Authors: Fujikawa Ege
Published: December 2008

For a Riemann surface of analytically infinite type, the action of the quasiconformal mapping class group on the Teichmüller space is not discontinuous in general. In this paper, we consider pure mapping classes that fix all topological ends of a Riemann surface and prove that the pure mapping class group acts on the Teichmüller space discontinuously under a certain geometric condition of a Riemann surface. We also consider the action of the quasiconformal mapping class group on the asymptotic Teichmüller space. Non-trivial mapping classes can act on the asymptotic Teichmüller space trivially. We prove that all such mapping classes are contained in the pure mapping class group.
Silence in the Sewing Chamber:
Le Roman de Silence
Authors: Tolmie Jane
Published: December 2008

Following on from Howard Bloch's investigation of a ‘refusal of univocal meaning’ in the thirteenth-century
Roman de Silence
, this article examines the poem as inviting critics to investigate the collapse of binary systems such as male/female, in/out, language/silence, learned/natural, reward/punishment, innocent/guilty. Moving away from Bloch's focus on poetic language, this article examines the poem's systematic conflation of a woman's life with images of death and captivity. The action of the poem, and the characters within the poem, draw our attention to issues of gender performance in such a manner as to render it impossible for the poem's conservative ending to unsay or undo (to silence) the main body of the romance.
Sexualité douteuse et bestialité trompeuse dans
Bisclavret
de Marie de France
Authors: Bibring Tovi
Published: December 2008

L'image qu'un loup vorace suscite dans l'imaginaire médiéval renvoie à une sexualité doublement douteuse. La bête sauvage matérialise le désir aberré, discourtois, et déréglé, d'une part de l'animal et d'autre part de la personne qui la regarde. Dans le premier cas, la forme animalière d'un être humain (récit de métamorphose) ou la personnification d'un animal (fable), représenteraient une personnalité dévergondée. L'animalité aurait un terrain commun avec la lèpre, vue comme une maladie sexuelle. Dans le second cas, par une lecture moins symbolique et plus psychologique, la rencontre ou la connaissance d'un loup extérioriseraient les désirs cachés, non apprivoisés et non avoués surgissant lors d'une expérience narcissique spontanée. Le loup-garou n'existerait pas vraiment, il serait le reflet (le
signifiant
) de la personne en face de lui. Ces deux associations au loup expliquent la motivation des actions de l'épouse du baron Bisclavret dans la première partie du lai de Marie de France. Ayant peur de partager la couche d'un monstre mais en même temps de se voir elle-même monstrueuse, elle s'empare de ses vêtements laissés lors de la transformation, espérant ainsi l'éliminer à tout jamais. Cependant, et ceci constitue le second point de ma réflexion, la bestialité de Bisclavret est trompeuse. Contrairement à l'image populaire du loup, la forme animalière représente ici plutôt une lutte idéologique, pas uniquement celle du désir d'appartenance à la cour féodale comme il a été souvent dit, mais aussi celle qui existe, chez un être, entre l'âme et le corps.
Jacques Roubaud and the Ethics of Artifice
Authors: James Alison
Published: December 2008

Jacques Roubaud's multivolume prose cycle ‘
Le grand incendie de Londres
’ (1989–) has variously been termed a novel, a self-portrait, an autobiography, and a work of
autofiction
. Several factors contribute to this generic uncertainty: a long-standing suspicion, shared by critics and writers, of autobiography; Roubaud's status as a member of the Oulipo, a group associated with formal artifice rather than referential writing; and Roubaud's own equivocating or cryptic statements about ‘
Le grand incendie de Londres
’. Nevertheless, to label this complex work a fiction is to obscure its deep concern with the relationship between form and authenticity. This article argues that Roubaud's explicitly stated principle of truth-telling (
véridicité
) generates a complex and paradoxical strategy, based on a form of sincerity that foregrounds itself as artifice and constraint. Framed in mathematical, philosophical and rhetorical terms, Roubaud's theoretical pronouncements do not necessarily amount to a coherent conception of truth. However, they successfully provide the basis for a new type of autobiographical contract and for the creation of original narrative forms. Rhetorical artifice and Oulipian constraints provide the conditions for Roubaud's investigation of memory and his ethical engagement with the reader.
Salammbô
, la Bible et la matière du monde
Authors: Bouvier Agnès
Published: December 2008

La Bible est l'une des sources majeures de
Salammbô
. Pas n'importe quelle Bible: celle de Samuel Cahen (parue de 1831 à 1851). En quoi la Bible de Cahen peut-elle servir pour écrire Carthage? D'abord, parce que cette nouvelle traduction est une véritable encyclopédie du monde antique où tous les savoirs contemporains sont convoqués. Ensuite, parce qu'une traduction littérale de l'hébreu est une promesse d'accès à la langue de Carthage. Qu'est-ce que le punique en effet? Une branche de la famille des langues sémitiques, si proche de l'hébreu que tous les savants consultés par Flaubert affirment la quasi-identité des deux langues. Or, Cahen restitue l'hébreu dans sa matérialité, dans sa capacité à dire la matière, à faire adhérer les mots et les choses. Les notes de lecture de Flaubert sur la Bible de Cahen en vue de
Salammbô
montrent une attention passionnée pour les versets qui, rendant le texte à la matière, le rendent aussi à sa plus grande étrangeté: Carthage réinventée par Flaubert exprimera l'altérité absolue, en même temps que le vertige de l'appropriation de la substance du monde.
Extrusion and Characterization of Starch Films
Authors: Pushpadass Heartwin A. , Marx David B. , Wehling Randy L. , Hanna Milford A.
Published: December 2008

Starch plasticized with water, glycerol, and stearic acid was extruded and sheeted into films 0.4–0.6 mm thick. The ingredients were extruded in a conical twin‐screw extruder at a temperature profile of 50–120–120–120°C and a screw speed of 45 rpm. The effects of glycerol, water, and stearic acid on selected physical and functional properties of the films were studied. The tensile strength, tensile strain at break, and Young's modulus were 0.23–2.91 MPa, 45.79–90.83%, and 2.89–37.94 MPa, respectively. Differential scanning calorimetry thermograms exhibited two glass transitions and multiple melting endotherms, including that of amylose‐lipid complexes formed during extrusion. The enthalpy of gelatinization of starch in the extruded films was 0.7–4.1 J/g and was dependent largely on the plasticizer content. Fourier‐transform infrared spectra revealed significant interactions between the starch and plasticizer but the peaks shifted to higher wave numbers with increasing glycerol content. During extrusion in the presence of glycerol, the A‐type crystalline structure of starch was transformed to B‐type. It also was observed that the Vh crystallinity increased with increase in glycerol content due to tight packing of starch chains. The water vapor permeabilities of the starch films were 12.3–19.9 g·mm/hr·m2·kPa.
Polyinosinic‐polycytidylic acid liposome induces human hepatoma cells apoptosis which correlates to the up‐regulation of RIG‐I like receptors
Authors: Peng Shuo , Geng Jianlin , Sun Rui , Tian Zhigang , Wei Haiming
Published: December 2008

Toll‐like receptor 3 and RIG‐I like receptors (RLRs; MDA5, RIG‐I) are involved in cell growth inhibition and apoptosis. However, the toll‐like receptor 3‐related apoptotic pathway is insensitive to direct polyinosinic‐polycytidylic acid (dsRNA analog) stimulation in hepatoma cells. To determine whether the strategy of transferring polyinosinic‐polycytidylic acid into cells (polyinosinic‐polycytidylic acid‐liposome) could induce apoptosis in hepatoma cells through cytoplasm receptors, we examined the responses of innate immune receptors RLRs and toll‐like receptor 3 in response to different stimulation. We found that the apoptosis could exclusively be detected under polyinosinic‐polycytidylic acid‐liposome stimulation, which involved the activation of the caspase pathway. Besides, the expression of RIG‐I, MDA5, IFNβ and interferon‐stimulated gene 15 was increased significantly at an early stage. Moreover, the growth inhibition of polyinosinic‐polycytidylic acid‐liposome was confirmed in a mouse model. Taken together, these results suggest polyinosinic‐polycytidylic acid‐liposome could be used as a potential apoptotic agent in hepatocellular carcinoma cells and imply a potential therapeutic strategy. (Cancer Sci 2009; 100: 529–536)
Ablation of p120‐catenin enhances invasion and metastasis of human lung cancer cells
Authors: Liu Yang , Li Qing‐Chang , Miao Yuan , Xu Hong‐Tao , Dai Shun‐Dong , Wei Qiang , Dong Qian‐Ze , Dong Xin‐Jun , Zhao Yue , Zhao Chen , Wang En‐Hua
Published: December 2008

p120‐catenin, a member of the Armadillo gene family, has emerged as both a master regulator of cadherin stability and an important modulator of small GTPase activities. Therefore, it plays novel roles in tumor malignant phenotype, such as invasion and metastasis. We have reported previously that abnormal expression of p120‐catenin is associated with lymph node metastasis in lung squamous cell carcinomas (SCC) and adenocarcinomas. To investigate the role and possible mechanism of p120‐catenin in lung cancer, we knocked down p120‐catenin using small interfering RNA (siRNA). We found that ablation of p120‐catenin reduced the levels of E‐cadherin and β‐catenin proteins, as well as the mRNA of β‐catenin. Furthermore, p120‐catenin depletion inactivated RhoA, but increased the activity of Cdc42 and Rac1, and promoted proliferation and the invasive ability of lung cancer cells both in vitro and in vivo. Our data reveal that p120‐catenin gene knockdown enhances the metastasis of lung cancer cells, probably by either depressing cell–cell adhesion due to lower levels of E‐cadherin and β‐catenin, or altering the activity of small GTPase, such as inactivation of RhoA and activation of Cdc42/Rac1. (Cancer Sci 2009; 100: 441–448)