bluuebunny/crossref_metadata_2025 huggingface dataset:
Chromatin structure can strongly facilitate enhancer action over a distance
Authors: Rubtsov Mikhail A. , Polikanov Yury S. , Bondarenko Vladimir A. , Wang Yuh-Hwa , Studitsky Vasily M.
Published: November 2006

Numerous DNA transactions in eukaryotic nuclei are regulated by elements (enhancers) that can directly interact with their targets over large regions of DNA organized into chromatin. The mechanisms allowing communication over a distance in chromatin are unknown. We have established an experimental system allowing quantitative analysis of the impact of chromatin structure on distant transcriptional regulation. Assembly of relaxed or linear DNA templates into subsaturated chromatin results in a strong increase of the efficiency of distant enhancer–promoter E–P communication and activation of transcription. The effect is directly proportional to the efficiency of chromatin assembly and cannot be explained only by DNA compaction. Transcription activation on chromatin templates is enhancer- and activator-dependent, and must be accompanied by direct E–P interaction and formation of a chromatin loop. Previously we have shown that DNA supercoiling can strongly facilitate E–P communication on histone-free DNA. The effects of chromatin assembly and DNA supercoiling on the communication are quantitatively similar, but the efficiency of enhancer action in subsaturated chromatin does not depend on the level of unconstrained DNA supercoiling. Thus chromatin structure
per se
can support highly efficient communication over a distance and functionally mimic the supercoiled state characteristic for prokaryotic DNA.
Pathogen escape from host immunity by a genome program for antigenic variation
Authors: Barbour Alan G. , Dai Qiyuan , Restrepo Blanca I. , Stoenner Herbert G. , Frank Steven A.
Published: November 2006

The vector-borne bacterium
Borrelia hermsii
, a relapsing fever agent, switches gene expression of a surface protein between different antigenic variants, thereby causing sequential waves of immune escape within hosts and increasing the likelihood of transmission. Analogous programmed systems of antigenic variation occur in African trypanosomes and
Plasmodium falciparum
. In these examples, switch rates to individual variants differ over a wide range. We studied how
B. hermsii
determines switch rates in two experimental infections: one where variants were identified by specific antisera and one based on identification by DNA sequence. Unexpressed loci of variant antigens copy into a single expression site at rates determined by extragenic features of silent loci rather than similarity between coding sequences of variants at silent sites and the single expression site. Two elements, in particular, determine switch rates. One set of elements overlaps the 5′ ends of the expressed gene and the silent loci; greater sequence identity between elements was associated with a higher switch rate. The second set of elements flanks the expression site on the 3′ side and occurs at variable distances downstream from silent loci; the nearer an element to a silent locus, the greater the switch rate of that locus into the expression site. In combination, these two features of the genome provide a simple mechanism to modulate switch rate whereby silent loci form a hierarchy of switch rates into the expression site. Although the switching hierarchy causes changes in individual cells that are stochastic, ordering of variants within hosts is semipredictable.
Analysis of retrotransposon structural diversity uncovers properties and propensities in angiosperm genome evolution
Authors: Vitte Clémentine , Bennetzen Jeffrey L.
Published: November 2006

Analysis of LTR retrotransposon structures in five diploid angiosperm genomes uncovered very different relative levels of different types of genomic diversity. All species exhibited recent LTR retrotransposon mobility and also high rates of DNA removal by unequal homologous recombination and illegitimate recombination. The larger plant genomes contained many LTR retrotransposon families with >10,000 copies per haploid genome, whereas the smaller genomes contained few or no LTR retrotransposon families with >1,000 copies, suggesting that this differential potential for retroelement amplification is a primary factor in angiosperm genome size variation. The average ratios of transition to transversion mutations (Ts/Tv) in diverging LTRs were >1.5 for each species studied, suggesting that these elements are mostly 5-methylated at cytosines in an epigenetically silenced state. However, the diploid wheat
Triticum monococcum
and barley have unusually low Ts/Tv values (respectively, 1.9 and 1.6) compared with maize (3.9), medicago (3.6), and lotus (2.5), suggesting that this silencing is less complete in the two Triticeae. Such characteristics as the ratios of point mutations to indels (insertions and deletions) and the relative efficiencies of DNA removal by unequal homologous recombination compared with illegitimate recombination were highly variable between species. These latter variations did not correlate with genome size or phylogenetic relatedness, indicating that they frequently change during the evolutionary descent of plant lineages. In sum, the results indicate that the different sizes, contents, and structures of angiosperm genomes are outcomes of the same suite of mechanistic processes, but acting with different relative efficiencies in different plant lineages.
Designer short peptide surfactants stabilize G protein-coupled receptor bovine rhodopsin
Authors: Zhao Xiaojun , Nagai Yusuke , Reeves Philip J. , Kiley Patrick , Khorana H. Gobind , Zhang Shuguang
Published: November 2006

Membrane proteins play vital roles in every aspect of cellular activities. To study diverse membrane proteins, it is crucial to select the right surfactants to stabilize them for analysis. Despite much effort, little progress has been made in elucidating their structure and function, largely because of a lack of suitable surfactants. Here we report the stabilization of a G protein-coupled receptor bovine rhodopsin in solution, using a new class of designer short and simple peptide surfactants. These surfactants consist of seven amino acids with a hydrophilic head, aspartic acid or lysine, and a hydrophobic tail with six consecutive alanines. These peptide surfactants not only enhance the stability of bovine rhodopsin in the presence of lipids and the common surfactantsn-dodecyl-β-d-maltoside and octyl-d-glucoside, but they also significantly stabilize rhodopsin under thermal denaturation conditions, even after lipids are removed. These peptide surfactants are simple, versatile, effective, and affordable. They represent a designer molecular nanomaterial for use in studies of diverse elusive membrane proteins.
Imaging alveolar–capillary gas transfer using hyperpolarized
129
Xe MRI
Authors: Driehuys Bastiaan , Cofer Gary P. , Pollaro Jim , Mackel Julie Boslego , Hedlund Laurence W. , Johnson G. Allan
Published: November 2006

Effective pulmonary gas exchange relies on the free diffusion of gases across the thin tissue barrier separating airspace from the capillary red blood cells (RBCs). Pulmonary pathologies, such as inflammation, fibrosis, and edema, which cause an increased blood–gas barrier thickness, impair the efficiency of this exchange. However, definitive assessment of such gas-exchange abnormalities is challenging, because no methods currently exist to directly image the gas transfer process. Here we exploit the solubility and chemical shift of
129
Xe, the magnetic resonance signal of which has been enhanced by 10
5
with hyperpolarization, to differentially image its transfer from the airspaces into the tissue barrier spaces and RBCs in the gas exchange regions of the lung. Based on a simple diffusion model, we estimate that this MR imaging method for measuring
129
Xe alveolar-capillary transfer is sensitive to changes in blood–gas barrier thickness of ≈5 μm. We validate the successful separation of tissue barrier and RBC images and show the utility of this method in a rat model of pulmonary fibrosis where
129
Xe replenishment of the RBCs is severely impaired in regions of lung injury.
Golgi twins in late mitosis revealed by genetically encoded tags for live cell imaging and correlated electron microscopy
Authors: Gaietta Guido M. , Giepmans Ben N. G. , Deerinck Thomas J. , Smith W. Bryan , Ngan Lucy , Llopis Juan , Adams Stephen R. , Tsien Roger Y. , Ellisman Mark H.
Published: November 2006

Combinations of molecular tags visible in light and electron microscopes become particularly advantageous in the analysis of dynamic cellular components like the Golgi apparatus. This organelle disassembles at the onset of mitosis and, after a sequence of poorly understood events, reassembles after cytokinesis. The precise location of Golgi membranes and resident proteins during mitosis remains unclear, partly due to limitations of molecular markers and the resolution of light microscopy. We generated a fusion consisting of the first 117 residues of α-mannosidase II tagged with a fluorescent protein and a tetracysteine motif. The mannosidase component guarantees docking into the Golgi membrane, with the tags exposed in the lumen. The fluorescent protein is optically visible without further treatment, whereas the tetracysteine tag can be reduced acutely with a membrane-permeant phosphine, labeled with ReAsH, monitored in the light microscope, and used to trigger the photoconversion of diaminobenzidine, allowing 4D optical recording on live cells and correlated ultrastructural analysis by electron microscopy. These methods reveal that Golgi reassembly is preceded by the formation of four colinear clusters at telophase, two per daughter cell. Within each daughter, the smaller cluster near the midbody gradually migrates to rejoin the major cluster on the far side of the nucleus and asymmetrically reconstitutes a single Golgi apparatus, first in one daughter cell and then in the other. Our studies provide previously undescribed insights into Golgi disassociation and reassembly during mitosis and offer a powerful approach to follow recombinant protein distribution in 4D imaging and correlated high-resolution analysis.
Transcription factor profiling in individual hematopoietic progenitors by digital RT-PCR
Authors: Warren Luigi , Bryder David , Weissman Irving L. , Quake Stephen R.
Published: November 2006

We report here a systematic, quantitative population analysis of transcription factor expression within developmental progenitors, made possible by a microfluidic chip-based “digital RT-PCR” assay that can count template molecules in cDNA samples prepared from single cells. In a survey encompassing five classes of early hematopoietic precursor, we found markedly heterogeneous expression of the transcription factor PU.1 in hematopoietic stem cells and divergent patterns of PU.1 expression within flk2
−
and flk2
+
common myeloid progenitors. The survey also revealed significant differences in the level of the housekeeping transcript GAPDH across the surveyed populations, which demonstrates caveats of normalizing expression data to endogenous controls and underscores the need to put gene measurement on an absolute, copy-per-cell basis.
On the definition of a criterion of immunogenicity
Authors: Pradeu Thomas , Carosella Edgardo D.
Published: November 2006

The main objective of immunology is to establish why and when an immune response occurs, that is, to determine a criterion of immunogenicity. According to the consensus view, the proper criterion of immunogenicity lies in the discrimination between self and nonself. Here we challenge this consensus by suggesting a simpler and more comprehensive criterion, the criterion of continuity. Moreover, we show that this criterion may be considered as an interpretation of the immune “self.” We conclude that immunologists can continue to speak of the self, provided that they admit that the self/nonself discrimination is not an adequate criterion of immunogenicity.
Low micronutrient intake may accelerate the degenerative diseases of aging through allocation of scarce micronutrients by triage
Authors: Ames Bruce N.
Published: November 2006

Inadequate dietary intakes of vitamins and minerals are widespread, most likely due to excessive consumption of energy-rich, micronutrient-poor, refined food. Inadequate intakes may result in chronic metabolic disruption, including mitochondrial decay. Deficiencies in many micronutrients cause DNA damage, such as chromosome breaks, in cultured human cells or
in vivo
. Some of these deficiencies also cause mitochondrial decay with oxidant leakage and cellular aging and are associated with late onset diseases such as cancer. I propose DNA damage and late onset disease are consequences of a triage allocation response to micronutrient scarcity. Episodic shortages of micronutrients were common during evolution. Natural selection favors short-term survival at the expense of long-term health. I hypothesize that short-term survival was achieved by allocating scarce micronutrients by triage, in part through an adjustment of the binding affinity of proteins for required micronutrients. If this hypothesis is correct, micronutrient deficiencies that trigger the triage response would accelerate cancer, aging, and neural decay but would leave critical metabolic functions, such as ATP production, intact. Evidence that micronutrient malnutrition increases late onset diseases, such as cancer, is discussed. A multivitamin-mineral supplement is one low-cost way to ensure intake of the Recommended Dietary Allowance of micronutrients throughout life.
Calpain is required for macroautophagy in mammalian cells
Authors: Demarchi Francesca , Bertoli Cosetta , Copetti Tamara , Tanida Isei , Brancolini Claudio , Eskelinen Eeva-Liisa , Schneider Claudio
Published: November 2006

Ubiquitously expressed micro- and millicalpain, which both require the calpain small 1 (CAPNS1) regulatory subunit for function, play important roles in numerous biological and pathological phenomena. We have previously shown that the product of GAS2, a gene specifically induced at growth arrest, is an inhibitor of millicalpain and that its overexpression sensitizes cells to apoptosis in a p53-dependent manner (Benetti, R., G. Del Sal, M. Monte, G. Paroni, C. Brancolini, and C. Schneider. 2001. EMBO J. 20:2702–2714). More recently, we have shown that calpain is also involved in nuclear factor κB activation and its relative prosurvival function in response to ceramide, in which calpain deficiency strengthens the proapoptotic effect of ceramide (Demarchi, F., C. Bertoli, P.A. Greer, and C. Schneider. 2005. Cell Death Differ. 12:512–522). Here, we further explore the involvement of calpain in the apoptotic switch and find that in calpain-deficient cells, autophagy is impaired with a resulting dramatic increase in apoptotic cell death. Immunostaining of the endogenous autophagosome marker LC3 and electron microscopy experiments demonstrate that autophagy is impaired in CAPNS1-deficient cells. Accordingly, the enhancement of lysosomal activity and long-lived protein degradation, which normally occur upon starvation, is also reduced. In CAPNS1-depleted cells, ectopic LC3 accumulates in early endosome-like vesicles that may represent a salvage pathway for protein degradation when autophagy is defective.
Specific inhibition of GPI-anchored protein function by homing and self-association of specific GPI anchors
Authors: Nicholson Thomas B. , Stanners Clifford P.
Published: November 2006

The functional specificity conferred by glycophosphatidylinositol (GPI) anchors on certain membrane proteins may arise from their occupancy of specific membrane microdomains. We show that membrane proteins with noninteractive external domains attached to the same carcinoembryonic antigen (CEA) GPI anchor, but not to unrelated neural cell adhesion molecule GPI anchors, colocalize on the cell surface, confirming that the GPI anchor mediates association with specific membrane domains and providing a mechanism for specific signaling. This directed targeting was exploited by coexpressing an external domain-defective protein with a functional protein, both with the CEA GPI anchor. The result was a complete loss of signaling capabilities (through integrin–ECM interaction) and cellular effect (differentiation blockage) of the active protein, which involved an alteration of the size of the microdomains occupied by the active protein. This work clarifies how the GPI anchor can determine protein function, while offering a novel method for its modulation.
Tau-dependent microtubule disassembly initiated by prefibrillar β-amyloid
Authors: King Michelle E. , Kan Ho-Man , Baas Peter W. , Erisir Alev , Glabe Charles G. , Bloom George S.
Published: November 2006

Alzheimer's Disease (AD) is defined histopathologically by extracellular β-amyloid (Aβ) fibrils plus intraneuronal tau filaments. Studies of transgenic mice and cultured cells indicate that AD is caused by a pathological cascade in which Aβ lies upstream of tau, but the steps that connect Aβ to tau have remained undefined. We demonstrate that tau confers acute hypersensitivity of microtubules to prefibrillar, extracellular Aβ in nonneuronal cells that express transfected tau and in cultured neurons that express endogenous tau. Prefibrillar Aβ42 was active at submicromolar concentrations, several-fold below those required for equivalent effects of prefibrillar Aβ40, and microtubules were insensitive to fibrillar Aβ. The active region of tau was localized to an N-terminal domain that does not bind microtubules and is not part of the region of tau that assembles into filaments. These results suggest that a seminal cell biological event in AD pathogenesis is acute, tau-dependent loss of microtubule integrity caused by exposure of neurons to readily diffusible Aβ.
ZBP1 regulates mRNA stability during cellular stress
Authors: Stöhr Nadine , Lederer Marcell , Reinke Claudia , Meyer Sylke , Hatzfeld Mechthild , Singer Robert H. , Hüttelmaier Stefan
Published: November 2006

An essential constituent of the integrated stress response (ISR) is a reversible translational suppression. This mRNA silencing occurs in distinct cytoplasmic foci called stress granules (SGs), which transiently associate with processing bodies (PBs), typically serving as mRNA decay centers. How mRNAs are protected from degradation in these structures remains elusive. We identify that Zipcode-binding protein 1 (ZBP1) regulates the cytoplasmic fate of specific mRNAs in nonstressed cells and is a key regulator of mRNA turnover during the ISR. ZBP1 association with target mRNAs in SGs was not essential for mRNA targeting to SGs. However, ZBP1 knockdown induced a selective destabilization of target mRNAs during the ISR, whereas forced expression increased mRNA stability. Our results indicate that although targeting of mRNAs to SGs is nonspecific, the stabilization of mRNAs during cellular stress requires specific protein–mRNA interactions. These retain mRNAs in SGs and prevent premature decay in PBs. Hence, mRNA-binding proteins are essential for translational adaptation during cellular stress by modulating mRNA turnover.
Oxidized phosphatidylserine–CD36 interactions play an essential role in macrophage-dependent phagocytosis of apoptotic cells
Authors: Greenberg Michael E. , Sun Mingjiang , Zhang Renliang , Febbraio Maria , Silverstein Roy , Hazen Stanley L.
Published: November 2006

The phagocytosis of apoptotic cells within an organism is a critical terminal physiological process in programmed cell death. Evidence suggests that apoptotic cell engulfment and removal by macrophages is facilitated by phosphatidylserine (PS) displayed at the exofacial surface of the plasma membrane; however, neither the macrophage receptors responsible for PS recognition, nor characterization of the PS molecular species potentially involved, have been clearly defined. We show that the class B scavenger receptor CD36 plays an essential role in macrophage clearance of apoptotic cells in vivo. Further, macrophage recognition of apoptotic cells via CD36 is shown to occur via interactions with membrane-associated oxidized PS (oxPS) and, to a lesser extent, oxidized phosphatidylcholine, but not nonoxidized PS molecular species. Mass spectrometry analyses of oxPS species identify structures of candidate ligands for CD36 in apoptotic membranes that may facilitate macrophage recognition. Collectively, these results identify oxPS–CD36 interactions on macrophages as potential participants in a broad range of physiologic processes where macrophage-mediated engulfment of apoptotic cells is involved.
Soluble Amyloid Oligomers Increase Bilayer Conductance by Altering Dielectric Structure
Authors: Sokolov Yuri , Kozak J. Ashot , Kayed Rakez , Chanturiya Alexandr , Glabe Charles , Hall James E.
Published: November 2006

The amyloid hypothesis of Alzheimer's toxicity has undergone a resurgence with increasing evidence that it is not amyloid fibrils but a smaller oligomeric species that produces the deleterious results. In this paper we address the mechanism of this toxicity. Only oligomers increase the conductance of lipid bilayers and patch-clamped mammalian cells, producing almost identical current–voltage curves in both preparations. Oligomers increase the conductance of the bare bilayer, the cation conductance induced by nonactin, and the anion conductance induced by tetraphenyl borate. Negative charge reduces the sensitivity of the membrane to amyloid, but cholesterol has little effect. In contrast, the area compressibility of the lipid has a very large effect. Membranes with a large area compressibility modulus are almost insensitive to amyloid oligomers, but membranes formed from soft, highly compressible lipids are highly susceptible to amyloid oligomer-induced conductance changes. Furthermore, membranes formed using the solvent decane (instead of squalane) are completely insensitive to the presence of oligomers. One simple explanation for these effects on bilayer conductance is that amyloid oligomers increase the area per molecule of the membrane-forming lipids, thus thinning the membrane, lowering the dielectric barrier, and increasing the conductance of any mechanism sensitive to the dielectric barrier.
Turning Cones Off: the Role of the 9-Methyl Group of Retinal in Red Cones
Authors: Estevez Maureen E. , Ala-Laurila Petri , Crouch Rosalie K. , Cornwall M. Carter
Published: November 2006

Our ability to see in bright light depends critically on the rapid rate at which cone photoreceptors detect and adapt to changes in illumination. This is achieved, in part, by their rapid response termination. In this study, we investigate the hypothesis that this rapid termination of the response in red cones is dependent on interactions between the 9-methyl group of retinal and red cone opsin, which are required for timely metarhodopsin (Meta) II decay. We used single-cell electrical recordings of flash responses to assess the kinetics of response termination and to calculate guanylyl cyclase (GC) rates in salamander red cones containing native visual pigment as well as visual pigment regenerated with 11-cis 9-demethyl retinal, an analogue of retinal in which the 9-methyl group is missing. After exposure to bright light that photoactivated more than ∼0.2% of the pigment, red cones containing the analogue pigment had a slower recovery of both flash response amplitudes and GC rates (up to 10 times slower at high bleaches) than red cones containing 11-cis retinal. This finding is consistent with previously published biochemical data demonstrating that red cone opsin regenerated in vitro with 11-cis 9-demethyl retinal exhibited prolonged activation as a result of slowed Meta II decay. Our results suggest that two different mechanisms regulate the recovery of responsiveness in red cones after exposure to light. We propose a model in which the response recovery in red cones can be regulated (particularly at high light intensities) by the Meta II decay rate if that rate has been inhibited. In red cones, the interaction of the 9-methyl group of retinal with opsin promotes efficient Meta II decay and, thus, the rapid rate of recovery.
Predicting transcription factor affinities to DNA from a biophysical model
Authors: Roider Helge G. , Kanhere Aditi , Manke Thomas , Vingron Martin
Published: November 2006

Motivation: Theoretical efforts to understand the regulation of gene expression are traditionally centered around the identification of transcription factor binding sites at specific DNA positions. More recently these efforts have been supplemented by experimental data for relative binding affinities of proteins to longer intergenic sequences. The question arises to what extent these two approaches converge. In this paper, we adopt a physical binding model to predict the relative binding affinity of a transcription factor for a given sequence.

Results: We find that a significant fraction of genome-wide binding data in yeast can be accounted for by simple count matrices and a physical model with only two parameters. We demonstrate that our approach is both conceptually and practically more powerful than traditional methods, which require selection of a cutoff. Our analysis yields biologically meaningful parameters, suitable for predicting relative binding affinities in the absence of experimental binding data.

Availability: The C source code for our TRAP program is freely available for non-commercial use at

Contact:  vingron@molgen.mpg.de
Evidence‐Based Research in Complementary and Alternative Medicine III: Treatment of Patients with Alzheimer′s Disease
Authors: Chiappelli Francesco , Navarro Audrey M. , Moradi David R. , Manfrini Ercolano , Prolo Paolo
Published: November 2006

This paper presents the novel domain of evidence‐based research (EBR) in the treatment of patients with Alzheimer′s disease (AD) from the perspective of traditional medicine and of complementary and alternative medicine. In earlier lectures we have described the process of evidence‐based medicine as a methodological approach to clinical practice that is directed to aid clinical decision‐making. Here, we present a practical example of this approach with respect to traditional pharmacological interventions and to complementary and alternative treatments for patients with AD.
Development switch in neural circuitry underlying odor-malaise learning
Authors: Shionoya Kiseko , Moriceau Stephanie , Lunday Lauren , Miner Cathrine , Roth Tania L. , Sullivan Regina M.
Published: November 2006

Fetal and infant rats can learn to avoid odors paired with illness before development of brain areas supporting this learning in adults, suggesting an alternate learning circuit. Here we begin to document the transition from the infant to adult neural circuit underlying odor-malaise avoidance learning using LiCl (0.3 M; 1% of body weight, ip) and a 30-min peppermint-odor exposure. Conditioning groups included: Paired odor-LiCl, Paired odor-LiCl-Nursing, LiCl, and odor-saline. Results showed that Paired LiCl-odor conditioning induced a learned odor aversion in postnatal day (PN) 7, 12, and 23 pups. Odor-LiCl Paired Nursing induced a learned odor preference in PN7 and PN12 pups but blocked learning in PN23 pups. 14C 2-deoxyglucose (2-DG) autoradiography indicated enhanced olfactory bulb activity in PN7 and PN12 pups with odor preference and avoidance learning. The odor aversion in weanling aged (PN23) pups resulted in enhanced amygdala activity in Paired odor-LiCl pups, but not if they were nursing. Thus, the neural circuit supporting malaise-induced aversions changes over development, indicating that similar infant and adult-learned behaviors may have distinct neural circuits.
Cholinergic neurons mediate CaMKII-dependent enhancement of courtship suppression
Authors: Mehren Jennifer E. , Griffith Leslie C.
Published: November 2006

In Drosophila, calcium/calmodulin-dependent protein kinase II (CaMKII) activity is crucial in associative courtship conditioning for both memory formation and suppression of courtship during training with a mated female. We have previously shown that increasing levels of constitutively active CaMKII, but not calcium-dependent CaMKII, in a subset of neurons can decrease the initial level of courtship and enhance the rate of suppression of courtship in response to a mated female. In this study, we demonstrate that a subpopulation of noncholinergic, nondopaminergic, non-GABAergic neurons can cause CaMKII-dependent reductions in initial courtship, but only cholinergic neurons enhance training-dependent suppression. These data suggest that processing of pheromonal signals in two subpopulations of neurons, likely antennal lobe projection neurons, is critical for behavioral plasticity.
Age-dependent glutamate induction of synaptic plasticity in cultured hippocampal neurons
Authors: Sapoznik Stav , Ivenshitz Miriam , Segal Menahem
Published: November 2006

A common denominator for the induction of morphological and functional plasticity in cultured hippocampal neurons involves the activation of excitatory synapses. We now demonstrate massive morphological plasticity in mature cultured hippocampal neurons caused by a brief exposure to glutamate. This plasticity involves a slow, 70%–80% increase in spine cross-section area associated with a significant reduction in the width of dendrites. These changes are age dependent and expressed only in cells >18 d in vitro (DIV). Activation of both NMDARs and AMPARs as well as a sustained rise of internal calcium levels are necessary for induction of this plasticity. On the other hand, blockade of network activity or mGluRs does not abolish the observed morphological plasticity. Electrophysiologically, a brief exposure to glutamate induces an increase in the magnitude of EPSCs evoked between pairs of neurons, as well as in mEPSC frequency and amplitude, in mature but not young cultures. These results demonstrate an age-dependent, rapid and robust morphological and functional change in cultured central neurons that may contribute to their ability to express long term synaptic plasticity.
A Membrane-Bound NAC Transcription Factor Regulates Cell Division inArabidopsis
Authors: Kim Youn-Sung , Kim Sang-Gyu , Park Jung-Eun , Park Hye-Young , Lim Mi-Hye , Chua Nam-Hai , Park Chung-Mo
Published: November 2006

Controlled release of membrane-tethered, dormant precursors is an intriguing activation mechanism that regulates diverse cellular functions in eukaryotes. An exquisite example is the proteolytic activation of membrane-bound transcription factors. The proteolytic cleavage liberates active transcription factors from the membranes that can enter the nucleus and evokes rapid transcriptional responses to incoming stimuli. Here, we show that a membrane-bound NAC (for NAM, ATAF1/2, CUC2) transcription factor, designated NTM1 (for NAC with transmembrane motif1), is activated by proteolytic cleavage through regulated intramembrane proteolysis and mediates cytokinin signaling during cell division in Arabidopsis thaliana. Cell proliferation was greatly reduced in an Arabidopsis mutant with retarded growth and serrated leaves in which a transcriptionally active NTM1 form was constitutively expressed. Accordingly, a subset of cyclin-dependent kinase (CDK) inhibitor genes (the KIP-related proteins) was induced in this mutant with a significant reduction in histone H4 gene expression and in CDK activity. Consistent with a role for NTM1 in cell cycling, a Ds element insertional mutant was morphologically normal but displayed enhanced hypocotyl growth with accelerated cell division. Interestingly, cytokinins were found to regulate NTM1 activity by controlling its stability. These results indicate that the membrane-mediated activation of NTM1 defines a molecular mechanism by which cytokinin signaling is tightly regulated during cell cycling.
SIAMESE, a Plant-Specific Cell Cycle Regulator, Controls Endoreplication Onset inArabidopsis thaliana
Authors: Churchman Michelle L. , Brown Matthew L. , Kato Naohiro , Kirik Viktor , Hülskamp Martin , Inzé Dirk , De Veylder Lieven , Walker Jason D. , Zheng Zhengui , Oppenheimer David G. , Gwin Taylor , Churchman Jason , Larkin John C.
Published: November 2006

Recessive mutations in the SIAMESE (SIM) gene of Arabidopsis thaliana result in multicellular trichomes harboring individual nuclei with a low ploidy level, a phenotype strikingly different from that of wild-type trichomes, which are single cells with a nuclear DNA content of ∼16C to 32C. These observations suggested that SIM is required to suppress mitosis as part of the switch to endoreplication in trichomes. Here, we demonstrate that SIM encodes a nuclear-localized 14-kD protein containing a cyclin binding motif and a motif found in ICK/KRP (for Interactors of Cdc2 kinase/Kip-related protein) cell cycle inhibitor proteins. Accordingly, SIM was found to associate with D-type cyclins and CDKA;1. Homologs of SIM were detected in other dicots and in monocots but not in mammals or fungi. SIM proteins are expressed throughout the shoot apical meristem, in leaf primordia, and in the elongation zone of the root and are localized to the nucleus. Plants overexpressing SIM are slow-growing and have narrow leaves and enlarged epidermal cells with an increased DNA content resulting from additional endocycles. We hypothesize that SIM encodes a plant-specific CDK inhibitor with a key function in the mitosis-to-endoreplication transition.
The Balance between theMIR164AandCUC2Genes Controls Leaf Margin Serration inArabidopsis
Authors: Nikovics Krisztina , Blein Thomas , Peaucelle Alexis , Ishida Tetsuya , Morin Halima , Aida Mitsuhiro , Laufs Patrick
Published: November 2006

CUP-SHAPED COTYLEDON1 (CUC1), CUC2, and CUC3 define the boundary domain around organs in the Arabidopsis thaliana meristem. CUC1 and CUC2 transcripts are targeted by a microRNA (miRNA), miR164, encoded by MIR164A, B, and C. We show that each MIR164 is transcribed to generate a large population of primary miRNAs of variable size with a locally conserved secondary structure around the pre-miRNA. We identified mutations in the MIR164A gene that deepen serration of the leaf margin. By contrast, leaves of plants overexpressing miR164 have smooth margins. Enhanced leaf serration was observed following the expression of an miR164-resistant CUC2 but not of an miR164-resistant CUC1. Furthermore, CUC2 inactivation abolished serration in mir164a mutants and the wild type, whereas CUC1 inactivation did not. Thus, CUC2 specifically controls leaf margin development. CUC2 and MIR164A are transcribed in overlapping domains at the margins of young leaf primordia, with transcription gradually restricted to the sinus, where the leaf margins become serrated. We suggest that leaf margin development is controlled by a two-step process in Arabidopsis. The pattern of serration is determined first, independently of CUC2 and miR164. The balance between coexpressed CUC2 and MIR164A then determines the extent of serration.
Music CD Purchase Decisions
Authors: North Adrian C. , Oishi Atsuko
Published: November 2006

The increasing ease and frequency of digital music piracy and the global nature of the music industry make it important to understand why consumers in different national markets purchase music CDs. Study 1 identified 5 factors underlying CD purchasing, noting these differences between British and Japanese participants. Study 2 investigated relationships between these 5 factors and individual‐difference variables. Compliance was unrelated to scores on the Friendship factor. Experience seeking and scores on the Re‐Experience the Music factor were correlated negatively. Scores on the Friendship factor and innovativeness were unrelated, although innovativeness and scores on the Need to Control and Be Involved With Music factor were positively associated with product, purchase decision, and consumption involvements. Implications for marketing and future research are discussed.
Lifetime reproductive output of Calliphora vicina and Lucilia sericata in outdoor caged and field populations; flight vs. egg production?
Authors: DAVIES LEWIS
Published: November 2006

Abstract Females of the blowflies Calliphora vicina (Robineau‐Desvoidy) and Lucilia sericata (Meigen) (Diptera: Calliphoridae) maintained in sheltered outdoor cages and supplied with excess food, oviposited later than would have been expected from the temperature‐sum. The survival rates of the caged flies was high and the isolation of flies from predation, extreme temperatures and food shortages is likely to have contributed to this. Despite good survival rates, subsequent egg production over the greater part of the adult life span was reduced to ∼24% for C. vicina and ∼55% for L. sericata, of the potential expected from the published temperature‐sums required for the maturation of successive egg batches. The data suggest that under field‐cage conditions there is a considerable variation in egg development between individuals of the same age and that this variation should not be overlooked, since it may have significant implications in ecological and forensic investigations; however, the cause of this variability remains unclear. While lower than expected, the reproductive outputs recorded in the cages were nevertheless considerably greater than those that have been estimated for blowflies in the field and illustrate the potential for population increase in these species under favourable conditions. The possibility of a greater energy investment in flight activity relative to reproductive output in C. vicina compared to L. sericata is proposed.
Fine‐scale natal homing and localized movement as shaped by sex and spawning habitat in Chinook salmon: insights from spatial autocorrelation analysis of individual genotypes
Authors: NEVILLE H. M. , ISAAK D. J. , DUNHAM J. B. , THUROW R. F. , RIEMAN B. E.
Published: November 2006

Natal homing is a hallmark of the life history of salmonid fishes, but the spatial scale of homing within local, naturally reproducing salmon populations is still poorly understood. Accurate homing (paired with restricted movement) should lead to the existence of fine‐scale genetic structuring due to the spatial clustering of related individuals on spawning grounds. Thus, we explored the spatial resolution of natal homing using genetic associations among individual Chinook salmon (Oncorhynchus tshawytscha) in an interconnected stream network. We also investigated the relationship between genetic patterns and two factors hypothesized to influence natal homing and localized movements at finer scales in this species, localized patterns in the distribution of spawning gravels and sex. Spatial autocorrelation analyses showed that spawning locations in both sub‐basins of our study site were spatially clumped, but the upper sub‐basin generally had a larger spatial extent and continuity of redd locations than the lower sub‐basin, where the distribution of redds and associated habitat conditions were more patchy. Male genotypes were not autocorrelated at any spatial scale in either sub‐basin. Female genotypes showed significant spatial autocorrelation and genetic patterns for females varied in the direction predicted between the two sub‐basins, with much stronger autocorrelation in the sub‐basin with less continuity in spawning gravels. The patterns observed here support predictions about differential constraints and breeding tactics between the two sexes and the potential for fine‐scale habitat structure to influence the precision of natal homing and localized movements of individual Chinook salmon on their breeding grounds.
A spatial genetic structure and effects of relatedness on mate choice in a wild bird population
Authors: FOERSTER K. , VALCU M. , JOHNSEN A. , KEMPENAERS B.
Published: November 2006

Inbreeding depression, as commonly found in natural populations, should favour the evolution of inbreeding avoidance mechanisms. If natal dispersal, the first and probably most effective mechanism, does not lead to a complete separation of males and females from a common origin, a small‐scale genetic population structure may result and other mechanisms to avoid inbreeding may exist. We studied the genetic population structure and individual mating patterns in blue tits (Parus caeruleus). The population showed a local genetic structure in two out of four years: genetic relatedness between individuals (estimated from microsatellite markers) decreased with distance. This pattern was mainly caused by immigrants to the study area; these, if paired with fellow immigrants, were more related than expected by chance. Since blue tits did not avoid inbreeding with their social partner, we examined if individuals preferred less related partners at later stages of the mate choice process. We found no evidence that females or males avoided inbreeding through extra‐pair copulations or through mate desertion and postbreeding dispersal. Although the small‐scale genetic population structure suggests that blue tits could use a simple rule of thumb to select less related mates, females did not generally prefer more distantly breeding extra‐pair partners. However, the proportion of young fathered by an extra‐pair male in mixed paternity broods depended on the genetic relatedness with the female. This suggests that there is a fertilization bias towards less related copulation partners and that blue tits are able to reduce the costs of inbreeding through a postcopulatory process.
The utility of QTL‐Linked markers to detect selective sweeps in natural populations — a case study of theEDAgene and a linked marker in threespine stickleback
Authors: CANO J. M. , MATSUBA C. , MÄKINEN H. , MERILÄ J.
Published: November 2006

Sequence polymorphisms in coding genes and variability in quantitative trait loci (QTL)‐linked markers can be used to uncover the evolutionary mechanisms of traits involved in adaptive processes. We studied sequence variation in theEDAgene and allelic variation in 18 microsatellites — one of which (Gac4174) is linked with theEDAQTL — in low, partially and completely plated morphs from eight threespine stickleback European populations. The results agree with previous studies in thatEDApolymorphism is closely related to plate number variation:EDAsequences grouped populations into low and completely plated morphs, whereas microsatellites failed to do so. Furthermore, partially plated fish were heterozygous with respect to the distinctiveEDAalleles for completely and low plated morphs, indicating that completely plated morph alleles are not entirely dominant in controlling the expression of lateral plate number. An examination of population differentiation in plate number with quantitative genetic methods revealed that the degree of differentiation exceeded that expected from genetic drift alone (QST > FST). Our results support the adaptive genetic differentiation of plate morphs and the view that distinctiveEDAgene polymorphism occurs in similar sites across the distribution range of this species. Yet, allele frequency differentiation in the Gac4174 microsatellite locus, informative in experimental crosses for plate number variation, did not differ from that of neutral markers and, was therefore unable to detect the signature of natural selection responsible for population divergence.
Uncoupling of choline‐O‐sulphate utilization from osmoprotection in Pseudomonas putida
Authors: Galvão Teca Calcagno , De Lorenzo Víctor , Cánovas David
Published: November 2006

The genomic context of the recognized bet genes for choline‐O‐sulphate (COS) utilization in Pseudomonas putida KT2440 is such that betC (choline sulphatase) lies adjacent to an ATP‐binding cassette transporter and a LysR type regulator, but well away from betBA, encoding enzymes for transformation of choline into glycine betaine. The consequences of such genetic layout of the functions for COS metabolism have been examined with a suite of genetic and biochemical approaches. An early clue of the utilities of the bet‐encoded products was exposed by the phenotypes of a betC deletion. This mutant still accumulated intact COS but failed to use this compound as carbon or nitrogen source. Furthermore, betC expression was downregulated at high salt concentrations, showing that the principal role of this gene lied in COS metabolism, not in osmoprotection. In contrast, the betBA genes were required for choline transformation into the highly effective compatible solute glycine betaine (and the concomitant endurance to high salt) and also for its utilization as carbon or nitrogen source. Thus, unlike in the cases of Bacillus subtilis and Sinorhizobium meliloti, betC is unrelated to osmoprotection in Pseudomonas putida while the betBA genes are required for both betaine synthesis and tolerance to high osmotic pressure.
WFCAM, Spitzer/IRAC and SCUBA observations of the massive star-forming region DR21/W75 – II. Stellar content and star formation
Authors: Kumar M. S. N. , Davis C. J. , Grave J. M. C. , Ferreira B. , Froebrich D.
Published: November 2006

Wide-field near-infrared observations and Spitzer Space Telescope Infrared Array Camera (IRAC) observations of the DR21/W75 star formation regions are presented. The photometric data are used to analyse the extinction, stellar content and clustering in the entire region by using standard methods. A young stellar population is identified all over the observed field, which is found to be distributed in embedded clusters that are surrounded by a distributed halo population extending over a larger projected area. The Spitzer/IRAC data are used to compute a spectral index value, α, for each young stellar object in the field. We use these data to separate pure photospheres from disc excess sources. We find a small fraction of sources with α in excess of 2 to 3 (plus a handful with α∼ 4), which is much higher than the values found in the low-mass star-forming region IC 348 (α≤ 2). The sources with high values of α spatially coincide with the densest regions of the filaments and also with the sites of massive star formation. Star formation is found to be occurring in long filaments stretching to few parsecs that are fragmented over a scale of ∼1 pc. The spatial distribution of young stars are found to be correlated with the filamentary nebulae that are prominently revealed by 8- and 850-μm observations. Five filaments are identified that appear to converge on a centre that includes the DR21/DR21(OH) regions. The morphological pattern of filaments and clustering compare well with numerical simulations of star cluster formation by Bate et al.
Effect of long‐term and rapid cold hardening on the cold torpor temperature of an aphid
Authors: POWELL S. J. , BALE J. S.
Published: November 2006

Abstract The effect of long‐term (seasonal) acclimation and rapid cold hardening is investigated on the cold torpor temperature (CTmin) of adult grain aphids, Sitobion avenae, reared at 20 or 10 °C for more than 6 months before experimentation. Rapid cold hardening is induced by exposing aphids reared at 20 to 0 °C for 3 h and aphids reared at 10 to 0 °C for 30 min (acclimation regimes previously found to induce maximum rapid cold hardening). The effect of cooling aphids from the same rearing regimes from 10 to −10 °C at 1, 0.5 and 0.1 °C min−1 is also investigated. In the 20 °C acclimated population, rapid cold hardening and cooling at 0.1 °C min−1 both produce a significant decrease in CTmin from 1.5 ± 0.3 to –0.9 ± 0.3 and –1.3 ± 0.3 °C, respectively. Rapid cold hardening also results in a significant reduction in CTmin of the population reared at 10 °C from 0.8 ± 0.1 to –0.9 ± 0.2 °C. However, none of the cooling regimes tested reduces the CTmin of the winter‐acclimated (10 °C) population. The present study demonstrates that rapid cold‐hardening induced during the cooling phase of natural diurnal temperature cycles could lower the movement threshold of S. avenae, allowing insects to move and continue feeding at lower temperatures than would otherwise be possible.