bluuebunny/crossref_metadata_2025 huggingface dataset:
Visualizing odorant receptor trafficking in living cells down to the single-molecule level
Authors: Jacquier V. , Prummer M. , Segura J.-M. , Pick H. , Vogel H.
Published: September 2006

Despite the importance of trafficking for regulating G protein-coupled receptor signaling, for many members of the seven transmembrane helix protein family, such as odorant receptors, little is known about this process in live cells. Here, the complete life cycle of the human odorant receptor OR17-40 was directly monitored in living cells by ensemble and single-molecule imaging, using a double-labeling strategy. While the overall, intracellular trafficking of the receptor was visualized continuously by using a GFP tag, selective imaging of cell surface receptors was achieved by pulse-labeling an acyl carrier protein tag. We found that OR17-40 efficiently translocated to the plasma membrane only at low expression, whereas at higher biosynthesis the receptor accumulated in intracellular compartments. Receptors in the plasma membrane showed high turnover resulting from constitutive internalization along the clathrin pathway, even in the absence of ligand. Single-molecule microscopy allowed monitoring of the early, dynamic processes in odorant receptor signaling. Although mobile receptors initially diffused either freely or within domains of various sizes, binding of an agonist or an antagonist increased partitioning of receptors into small domains of ≈190 nm, which likely are precursors of clathrin-coated pits. The binding of a ligand, therefore, resulted in modulation of the continuous, constitutive internalization. After endocytosis, receptors were directed to early endosomes for recycling. This unique mechanism of continuous internalization and recycling of OR17-40 might be instrumental in allowing rapid recovery of odor perception.
Granulocyte colony-stimulating factor preferentially stimulates proliferation of monosomy 7 cells bearing the isoform IV receptor
Authors: Sloand Elaine M. , Yong Agnes S. M. , Ramkissoon Shakti , Solomou Elena , Bruno Tullia C. , Kim Sonnie , Fuhrer Monika , Kajigaya Sachiko , Barrett A. John , Young Neal S.
Published: September 2006

Granulocyte colony-stimulating factor (GCSF) administration has been linked to the development of monosomy 7 in severe congenital neutropenia and aplastic anemia. We assessed the effect of pharmacologic doses of GCSF on monosomy 7 cells to determine whether this chromosomal abnormality developedde novoor arose as a result of favored expansion of a preexisting clone. Fluorescencein situhybridization (FISH) of chromosome 7 was used to identify small populations of aneuploid cells. When bone marrow mononuclear cells from patients with monosomy 7 were cultured with 400 ng/ml GCSF, all samples showed significant increases in the proportion of monosomy 7 cells. In contrast, bone marrow from karyotypically normal aplastic anemia, myelodysplastic syndrome, or healthy individuals did not show an increase in monosomy 7 cells in culture. In bone marrow CD34 cells of patients with myelodysplastic syndrome and monosomy 7, GCSF receptor (GCSFR) protein was increased. Although no mutation was found in genomic GCSFR DNA, CD34 cells showed increased expression of the GCSFR class IV mRNA isoform, which is defective in signaling cellular differentiation. GCSFR signal transduction via the Jak/Stat system was abnormal in monosomy 7 CD34 cells, with increased phosphorylated signal transducer and activation of transcription protein, STAT1-P, and increased STAT5-P relative to STAT3-P. Our results suggest that pharmacologic doses of GCSF increase the proportion of preexisting monosomy 7 cells. The abnormal response of monosomy 7 cells to GCSF would be explained by the expansion of undifferentiated monosomy 7 clones expressing the class IV GCSFR, which is defective in signaling cell maturation.
Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize
Authors: Yennawar Neela H. , Li Lian-Chao , Dudzinski David M. , Tabuchi Akira , Cosgrove Daniel J.
Published: September 2006

Expansins are small extracellular proteins that promote turgor-driven extension of plant cell walls. EXPB1 (also called Zea m 1) is a member of the β-expansin subfamily known in the allergen literature as group-1 grass pollen allergens. EXPB1 induces extension and stress relaxation of grass cell walls. To help elucidate expansin's mechanism of wall loosening, we determined the structure of EXPB1 by x-ray crystallography to 2.75-Å resolution. EXPB1 consists of two domains closely packed and aligned so as to form a long, shallow groove with potential to bind a glycan backbone of ≈10 sugar residues. The structure of EXPB1 domain 1 resembles that of family-45 glycoside hydrolase (GH45), with conservation of most of the residues in the catalytic site. However, EXPB1 lacks a second aspartate that serves as the catalytic base required for hydrolytic activity in GH45 enzymes. Domain 2 of EXPB1 is an Ig-like β-sandwich, with aromatic and polar residues that form a potential surface for polysaccharide binding in line with the glycan binding cleft of domain 1. EXPB1 binds to maize cell walls, most strongly to xylans, causing swelling of the cell wall. Tests for hydrolytic activity by EXPB1 with various wall polysaccharides proved negative. Moreover, GH45 enzymes and a GH45-related protein called “swollenin” lacked wall extension activity comparable to that of expansins. We propose a model of expansin action in which EXPB1 facilitates the local movement and stress relaxation of arabinoxylan–cellulose networks within the wall by noncovalent rearrangement of its target.
Partitioning of atmospherically relevant ions between bulk water and the water/vapor interface
Authors: Pegram Laurel M. , Record M. Thomas
Published: September 2006

Recently, surface-sensitive spectroscopy data and molecular dynamics simulations have generated intense interest in the distribution of electrolyte ions between bulk water and the air/water interface. A partitioning model for cations and anions developed for biopolymer surface is extended here to interpret the effects of selected acids, bases, and salts on the surface tension of water. Data for electrolytes were analyzed by using a lower-bound value for the number of water molecules in the surface region [0.2 H
2
O Å
−2
(approximately two layers of water)], obtained by assuming that both Na
+
and SO
4
2−
(i.e., Na
2
SO
4
) are fully excluded from this region. Surface–bulk partition coefficients of atmospherically relevant anions and the proton are determined. Notably, we find that H
+
is most strongly surface-accumulated, I
−
is modestly accumulated, NO
3
−
is evenly distributed, and OH
−
is weakly excluded.
Aberrant MHC class II expression in mouse joints leads to arthritis with extraarticular manifestations similar to rheumatoid arthritis
Authors: Kanazawa Satoshi , Ota Shusuke , Sekine Chiyoko , Tada Toyohiro , Otsuka Takanobu , Okamoto Takashi , Sønderstrup Grete , Peterlin B. Matija
Published: September 2006

Genetic susceptibility to rheumatoid arthritis (RA) is associated with certain MHC class II molecules. To clarify the role of these determinants in RA, we generated the D1CC transgenic mouse that expressed genes involved in antigen processing and presentation by the MHC class II pathway in joints. The class II transactivator, which was transcribed from the rat collagen type II promoter and enhancer, directed the expression of these genes. In D1CC mice congenic for the H-2q(DBA/1) background, small amounts of bovine collagen type II in adjuvant induced reproducibly an inflammatory arthritis resembling RA. Importantly, these stimuli had no effect in DBA/1 mice. Eighty-nine percent of D1CC mice developed chronic disease with joint swelling, redness, and heat in association with synovial proliferation as well as pannus formation and mononuclear infiltration of synovial membranes. Granulomatous lesions resembling rheumatoid nodules and interstitial pneumonitis also were observed. As in patients with RA, anticyclic citrullinated peptide antibodies were detected during the inflammatory stage. Finally, joints in D1CC mice displayed juxtaarticular demineralization, severe joint space narrowing, and erosions, which led to ankylosis, but without the appearance of osteophytes. Thus, aberrant expression of MHC class II in joints facilitates the development of severe erosive inflammatory polyarthritis, which is very similar to RA.
Tree-ring isotope records of tropical cyclone activity
Authors: Miller Dana L. , Mora Claudia I. , Grissino-Mayer Henri D. , Mock Cary J. , Uhle Maria E. , Sharp Zachary
Published: September 2006

The destruction wrought by North Atlantic hurricanes in 2004 and 2005 dramatically emphasizes the need for better understanding of tropical cyclone activity apart from the records provided by meteorological data and historical documentation. We present a 220-year record of oxygen isotope values of α-cellulose in longleaf pine tree rings that preserves anomalously low isotope values in the latewood portion of the ring in years corresponding with known 19th and 20th century landfalling/near-coastal tropical storms and hurricanes. Our results suggest the potential for a tree-ring oxygen isotope proxy record of tropical cyclone occurrence extending back many centuries based on remnant pine wood from protected areas in the southeastern U.S.
Transducer of regulated CREB-binding proteins (TORCs) induce PGC-1α transcription and mitochondrial biogenesis in muscle cells
Authors: Wu Zhidan , Huang Xueming , Feng Yajun , Handschin Christoph , Feng Yan , Gullicksen P. Scott , Bare Olivia , Labow Mark , Spiegelman Bruce , Stevenson Susan C.
Published: September 2006

PGC-1α (peroxisome proliferator-activated receptor γ coactivator 1α) is a master regulator of mitochondrial biogenesis and plays an important role in several other aspects of energy metabolism. To identify upstream regulators of PGC-1α gene transcription, 10,000 human full-length cDNAs were screened for induction of the PGC-1α promoter. A number of activators of PGC-1α transcription were found; the most potent activator was the transducer of regulated CREB (cAMP response element-binding protein) binding protein (TORC) 1, a coactivator of CREB. The other two members of the TORC family, TORC2 and TORC3, also strongly activated PGC-1α transcription. TORCs dramatically induced PGC-1α gene transcription through CREB. Forced expression of TORCs in primary muscle cells induced the endogenous mRNA of PGC-1α and its downstream target genes in the mitochondrial respiratory chain and TCA cycle. Importantly, these changes in gene expression resulted in increased mitochondrial oxidative capacity measured by cellular respiration and fatty acid oxidation. Finally, we demonstrated that the action of TORCs in promoting mitochondrial gene expression and function requires PGC-1α. Previous studies had indicated that TORCs function as a calcium- and cAMP-sensitive coincidence detector and mediate individual and synergistic effects of these two pathways. Our results, together with previous findings, strongly suggest that TORCs play a key role in linking these external signals to the transcriptional program of adaptive mitochondrial biogenesis by activating PGC-1α gene transcription.
The training needs of doctors working in English and Welsh prisons: A survey of doctors
Authors: Gray Andrew , Pearce Sarah , Marks Linda
Published: September 2006

In the context of the transfer of the responsibility for prison health from the Prison Service to the National Health Service, a survey of doctors working in prisons reveals doctors’ own high priorities for training in the distinct patient contexts found in prison as well as in certain clinical conditions. The analysis identifies exclusive competences required only for doctors working in prisons and special interest competences that although applicable to practice in the community are particular strengths of doctors working in prisons because of the prevalence of conditions they are required to address.
The Virgo status
Authors: Acernese F , Amico P , Alshourbagy M , Antonucci F , Aoudia S , Avino S , Babusci D , Ballardin G , Barone F , Barsotti L , Barsuglia M , Beauville F , Bigotta S , Birindelli S , Bizouard M A , Boccara C , Bondu F , Bosi L , Bradaschia C , Braccini S , Brillet A , Brisson V , Brocco L , Buskulic D , Calloni E , Campagna E , Cavalier F , Cavalieri R , Cella G , Cesarini E , Chassande-Mottin E , Corda C , Cottone F , Clapson A-C , Cleva F , Coulon J-P , Cuoco E , Dari A , Dattilo V , Davier M , De Rosa R , Di Fiore L , Di Virgilio A , Dujardin B , Eleuteri A , Enard D , Ferrante I , Fidecaro F , Fiori I , Flaminio R , Fournier J-D , Francois O , Frasca S , Frasconi F , Freise A , Gammaitoni L , Garufi F , Gennai A , Giazotto A , Giordano G , Giordano L , Gouaty R , Grosjean D , Guidi G , Hebri S , Heitmann H , Hello P , Holloway L , Karkar S , Kreckelbergh S , La Penna P , Laval M , Leroy N , Letendre N , Lorenzini M , Loriette V , Loupias M , Losurdo G , Mackowski J-M , Majorana E , Man C N , Mantovani M , Marchesoni F , Marion F , Marque J , Martelli F , Masserot A , Mazzoni M , Milano L , Moins C , Moreau J , Morgado N , Mours B , Pai A , Palomba C , Paoletti F , Pardi S , Pasqualetti A , Passaquieti R , Passuello D , Perniola B , Piergiovanni F , Pinard L , Poggiani R , Punturo M , Puppo P , Qipiani K , Rapagnani P , Reita V , Remillieux A , Ricci F , Ricciardi I , Ruggi P , Russo G , Solimeno S , Spallicci A , Stanga R , Taddei R , Tonelli M , Toncelli A , Tournefier E , Travasso F , Vajente G , Verkindt D , Vetrano F , Viceré A , Vinet J-Y , Vocca H , Yvert M , Zhang Z
Published: September 2006

We report on the status of the Virgo detector, under commissioning. We will focus on the last year's activity. The two commissioning runs performed during 2005 allowed us to reach a sensitivity ofh∼ 6 × 10−22. The data obtained during the runs were used to test a few data analysis algorithms, namely coalescing binaries and burst searches. The main improvements made on the detector during this year will be described, as well as the plans and activities foreseen in the coming years.
Status of LIGO at the start of the fifth science run
Authors: Waldman Samuel J
Published: September 2006

In November 2005, the LIGO interferometer network began data taking for its latest data run (S5). All three interferometers are working at design sensitivities with duty cycles expected to reach 80%. The Hanford 4 km detector regularly achieves aneutron star inspiral range of 12 Mpc. The S5 data run will record one year of coincident science data at unprecedented sensitivity ending in mid 2007.
Hierarchical and multi-resolution representation of protein flexibility
Authors: Zhao Yong , Stoffler Daniel , Sanner Michel
Published: September 2006

Motivation: Conformational rearrangements during molecular interactions are observed in a wide range of biological systems. However, computational methods that aim at simulating and predicting molecular interactions are still largely ignoring the flexible nature of biological macromolecules as the number of degrees of freedom is computationally intractable when using brute force representations.

Results: In this article, we present a computational data structure called the Flexibility Tree (FT) that enables a multi-resolution and hierarchical encoding of molecular flexibility. This tree-like data structure allows the encoding of relatively small, yet complex sub-spaces of a protein's conformational space. These conformational sub-spaces are parameterized by a small number of variables and can be searched efficiently using standard global search techniques. The FT structure makes it straightforward to combine and nest a wide variety of motion types such as hinge, shear, twist, screw, rotameric side chains, normal modes and essential dynamics. Moreover, the ability to assign shapes to the nodes in a FT allows the interactive manipulation of flexible protein shapes and the interactive visualization of the impact of conformational changes on the protein's overall shape. We describe the design of the FT and illustrate the construction of such trees to hierarchically combine motion information obtained from a variety of sources ranging from experiment to user intuition, and describing conformational changes at different biological scales. We show that the combination of various types of motion helps refine the encoded conformational sub-spaces to include experimentally determined structures, and we demonstrate searching these sub-spaces for specific conformations.

Contact:  sanner@scripps.edu

Supplementary information: Supplementary Data are available at Bioinformatics online.
Benefits of Zataria multiflora Boiss in Experimental Model of Mouse Inflammatory Bowel Disease
Authors: Nakhai Leila Ashtaral , Mohammadirad Azadeh , Yasa Narges , Minaie Bagher , Nikfar Shekoufeh , Ghazanfari Ghazal , Zamani Mohammad Jafar , Dehghan Gholamreza , Jamshidi Hamidreza , Boushehri Vahid Shetab , Khorasani Reza , Abdollahi Mohammad
Published: September 2006

Inflammatory bowel disease (IBD) is a chronic condition of the intestine with unknown etiology involving multiple immune, genetic and environmental factors. We were interested to examine the effect of total extract from Zataria multiflora Boiss, a folk medicinal plant on prevention and treatment of experimental IBD. Z. multiflora was administered (400, 600, 900 p.p.m.) through drinking water to IBD mice induced by intrarectal administration of acetic acid. Prednisolone was used as the standard drug for comparison. Biochemical, macroscopic and microscopic examinations of colon were performed. Biochemical evaluation of inflamed colon was done using assay of myeloperoxidase (MPO) activity and thiobarbituric acid reactive substances (TBARS) concentration as indicators of free radical activity and cell lipid peroxidation. The activity of MPO and lipid peroxidation products (TBARS) increased in acetic acid‐treated groups while recovered by pretreatment of animals with Z. multiflora (400–900 p.p.m.) and prednisolone. Z. multiflora (600 and 900 p.p.m.) and prednisolone‐treated groups showed significantly lower score values of macroscopic and microscopic characters when compared with the acetic acid‐treated group. The beneficial effect of Z. multiflora (900 p.p.m.) was comparable with that of prednisolone. The antioxidant, antimicrobial and anti‐inflammatory potentials of Z. multiflora might be the mechanisms by which this herbal extract protects animals against experimentally induced IBD. Proper clinical investigation should be carried out to confirm the activity in human.
A transcription factor-binding domain of the coactivator CBP is essential for long-term memory and the expression of specific target genes
Authors: Wood Marcelo A. , Attner Michelle A. , Oliveira Ana M.M. , Brindle Paul K. , Abel Ted
Published: September 2006

Transcriptional activation is a key process required for long-term memory formation. Recently, the transcriptional coactivator CREB-binding protein (CBP) was shown to be critical for hippocampus-dependent long-term memory and hippocampal synaptic plasticity. As a coactivator with intrinsic histone acetyltransferase activity, CBP interacts with numerous transcription factors and contains multiple functional domains. Currently, it is not known which transcription factor-binding domain of CBP is essential for memory storage. Using mice that carry inactivating mutations in the CREB-binding (KIX) domain of the coactivator CBP (CBPKIX/KIXmice), we show that the KIX domain is required for long-term memory storage. These results are the first to identify an in vivo function for the KIX domain of CBP in the brain, and they suggest that KIX-interacting transcription factors recruit CBP histone acetyltransferase activity during long-term memory storage. One such KIX-interacting factor is the transcription factor CREB. Using quantitative real-time RT-PCR, we find that the expression of specific CREB target genes is reduced in the hippocampi ofCBPKIX/KIXmice during memory consolidation. The recruitment of the transcriptional coactivator CBP via the KIX domain thus imparts target gene-dependent selectivity to CREB-driven transcriptional regulation, thereby activating genes required for the long-term storage of hippocampus-dependent memory.
Roles for Drosophila mushroom body neurons in olfactory learning and memory
Authors: Akalal David-Benjamin G. , Wilson Curtis F. , Zong Lin , Tanaka Nobuaki K. , Ito Kei , Davis Ronald L.
Published: September 2006

Olfactory learning assays in Drosophila have revealed that distinct brain structures known as mushroom bodies (MBs) are critical for the associative learning and memory of olfactory stimuli. However, the precise roles of the different neurons comprising the MBs are still under debate. The confusion surrounding the roles of the different neurons may be due, in part, to the use of different odors as conditioned stimuli in previous studies. We investigated the requirements for the different MB neurons, specifically the α/β versus the γ neurons, and whether olfactory learning is supported by different subsets of MB neurons irrespective of the odors used as conditioned stimuli. We expressed the rutabaga (rut)-encoded adenylyl cyclase in either the γ or α/β neurons and examined the effects on restoring olfactory associative learning and memory of rut mutant flies. We also expressed a temperature-sensitive shibire (shi) transgene in these neuron sets and examined the effects of disrupting synaptic vesicle recycling on Drosophila olfactory learning. Our results indicate that although we did not detect odor-pair-specific learning using GAL4 drivers that primarily express in γ neurons, expression of the transgenes in a subset of α/β neurons resulted in both odor-pair-specific rescue of the rut defect as well as odor-pair-specific disruption of learning using shits1.
Early boost and slow consolidation in motor skill learning
Authors: Hotermans Christophe , Peigneux Philippe , Maertens de Noordhout Alain , Moonen Gustave , Maquet Pierre
Published: September 2006

Motorskill learning is a dynamic process that continues covertly after training has ended and eventually leads to delayed increments in performance. Current theories suggest that this off-line improvement takes time and appears only after several hours. Here we show an early transient and short-lived boost in performance, emerging as early as 5–30 min after training but no longer observed 4 h later. This early boost is predictive of the performance achieved 48 h later, suggesting its functional relevance for memory processes.
Distinct roles for medial temporal lobe structures in memory for objects and their locations
Authors: Buffalo Elizabeth A. , Bellgowan Patrick S.F. , Martin Alex
Published: September 2006

The ability to learn and retain novel information depends on a system of structures in the medial temporal lobe (MTL) including the hippocampus and the surrounding entorhinal, perirhinal, and parahippocampal cortices. Damage to these structures produces profound memory deficits; however, the unique contribution to memory of each of these structures remains unclear. Here we have used functional magnetic resonance imaging (fMRI) to determine whether the perirhinal and parahippocampal cortices show differential memory-related activity. Based on the distinct patterns of cortical input to these two areas, we reasoned that these structures might show differential activity for spatial and object recognition memory. In each of 11 subjects, we found that the perirhinal cortex was active during both spatial and object memory encoding, while the anterior parahippocampal cortex was active only during spatial encoding. These data support the idea that MTL structures make distinct contributions to recognition memory performance.
Two mutations preventing PDZ–protein interactions of GluR1 have opposite effects on synaptic plasticity
Authors: Boehm Jannic , Ehrlich Ingrid , Hsieh Helen , Malinow Roberto
Published: September 2006

The regulated trafficking of GluR1 contributes significantly to synaptic plasticity, but studies addressing the function of the GluR1 C-terminal PDZ-ligand domain in this process have produced conflicting results. Here, we resolve this conflict by showing that apparently similar C-terminal mutations of the GluR1 PDZ-ligand domain result in opposite physiological phenotypes during activity- and CamKII-induced synaptic plasticity.
Single-item memory, associative memory, and the human hippocampus
Authors: Gold Jeffrey J. , Hopkins Ramona O. , Squire Larry R.
Published: September 2006

We tested recognition memory for items and associations in memory-impaired patients with bilateral lesions thought to be limited to the hippocampal region. In Experiment 1 (Combined memory test), participants studied words and then took a memory test in which studied words, new words, studied word pairs, and recombined word pairs were presented in a mixed order. In Experiment 2 (Separated memory test), participants studied single words and then took a memory test involving studied word and new words. In a separate test, they studied word pairs and then took a memory test involving studied word pairs and recombined word pairs. In both experiments, patients were impaired at memory for single items as well as memory for associations, suggesting that the hippocampus is important for both of these memory functions. In Experiment 1, patients appeared to be more impaired at associative memory than item memory. In Experiment 2, patients were similarly impaired at associative memory and item memory. These different findings are considered, including the fact that in Experiment 1 the results depended on the fact that controls produced unexpectedly low false-alarm rates to recombined pairs. We discuss single-item and associative memory from the perspective that the hippocampus and adjacent cortex work cooperatively to signal recognition and that simple dichotomies do not adequately describe the division of labor within the medial temporal lobe.
Learning in the absence of experience-dependent regulation of NMDAR composition
Authors: Lebel David , Sidhu Nishchal , Barkai Edi , Quinlan Elizabeth M.
Published: September 2006

Olfactory discrimination (OD) learning consists of two phases: an initial N-methyl-d-aspartate (NMDA) receptor–sensitive rule-learning phase, followed by an NMDA receptor (NMDAR)–insensitive pair-learning phase. The rule-learning phase is accompanied by changes in the composition and function of NMDARs at synapses in the piriform cortex, resulting in a high level of the NR2a subunit relative to NR2b. Here we show that the learning-induced changes in NMDAR composition in the adult piriform cortex are due to a decrease in the level of the NR2b subunit protein, rather than an increase in the level of NR2a. Chronic administration of an NMDAR open channel blocker during training delays OD learning and blocks learning-induced changes in NMDAR subunit composition. However, the animals still learn the OD task. Our data demonstrate that learning can occur in the absence of activity-dependent regulation of NMDAR composition, suggesting differences in the mechanism for long-term maintenance of NMDAR-dependent and NMDAR-independent learning.
Behavioral interference and C/EBPβ expression in the insular-cortex reveal a prolonged time period for taste memory consolidation
Authors: Merhav Maayan , Kuulmann-Vander Shelly , Elkobi Alina , Jacobson-Pick Shlomit , Karni Avi , Rosenblum Kobi
Published: September 2006

Memory consolidation is defined as the time window during which the memory trace is susceptible to behavioral, electrical, or pharmacological interventions. Here, we presented rats with two novel tastes at consecutive time intervals. Clear interference was evident when a novel taste formed the second taste input whereby, surprisingly, the time window for interference was found to last more than 10 h. In addition, we detected an increase of C/EBPβ protein expression in the gustatory cortex 18 h after novel taste learning. This modulation was attenuated by a subsequent novel taste. Our findings reveal temporal constraints and a lingering nature of taste memory consolidation.
Role of centrifugal projections to the olfactory bulb in olfactory processing
Authors: Kiselycznyk Carly L. , Zhang Steven , Linster Christiane
Published: September 2006

While there is evidence that feedback projections from cortical and neuromodulatory structures to the olfactory bulb are crucial for maintaining the oscillatory dynamics of olfactory bulb processing, it is not clear how changes in dynamics are related to odor perception. Using electrical lesions of the olfactory peduncle, sparing output from the olfactory bulb while decreasing feedback inputs to the olfactory bulb, we demonstrate here a role for feedback inputs to the olfactory bulb in the formation of odor–reward associations, but not for maintaining primary bulbar odor representations, as reflected by spontaneous odor discrimination.
Localization of Green Fluorescent Protein Fusions with the Seven Arabidopsis Vacuolar Sorting Receptors to Prevacuolar Compartments in Tobacco BY-2 Cells
Authors: Miao Yansong , Yan Pak Kan , Kim Hyeran , Hwang Inhwan , Jiang Liwen
Published: September 2006

We have previously demonstrated that vacuolar sorting receptor (VSR) proteins are concentrated on prevacuolar compartments (PVCs) in plant cells. PVCs in tobacco (Nicotiana tabacum) BY-2 cells are multivesicular bodies (MVBs) as defined by VSR proteins and the BP-80 reporter, where the transmembrane domain (TMD) and cytoplasmic tail (CT) sequences of BP-80 are sufficient and specific for correct targeting of the reporter to PVCs. The genome of Arabidopsis (Arabidopsis thaliana) contains seven VSR proteins, but little is known about their individual subcellular localization and function. Here, we study the subcellular localization of the seven Arabidopsis VSR proteins (AtVSR1–7) based on the previously proven hypothesis that the TMD and CT sequences correctly target individual VSR to its final destination in transgenic tobacco BY-2 cells. Toward this goal, we have generated seven chimeric constructs containing signal peptide (sp) linked to green fluorescent protein (GFP) and TMD/CT sequences (sp-GFP-TMD/CT) of the seven individual AtVSR. Transgenic tobacco BY-2 cell lines expressing these seven sp-GFP-TMD-CT fusions all exhibited typical punctate signals colocalizing with VSR proteins by confocal immunofluorescence. In addition, wortmannin caused the GFP-marked prevacuolar organelles to form small vacuoles, and VSR antibodies labeled these enlarged MVBs in transgenic BY-2 cells. Wortmannin also caused VSR-marked PVCs to vacuolate in other cell types, including Arabidopsis, rice (Oryza sativa), pea (Pisum sativum), and mung bean (Vigna radiata). Therefore, the seven AtVSRs are localized to MVBs in tobacco BY-2 cells, and wortmannin-induced vacuolation of PVCs is a general response in plants.
Divergence of the Dof Gene Families in Poplar, Arabidopsis, and Rice Suggests Multiple Modes of Gene Evolution after Duplication
Authors: Yang Xiaohan , Tuskan Gerald A. , Cheng (Max) Zong-Ming
Published: September 2006

It is widely accepted that gene duplication is a primary source of genetic novelty. However, the evolutionary fate of duplicated genes remains largely unresolved. The classical Ohno's Duplication-Retention-Non/Neofunctionalization theory, and the recently proposed alternatives such as subfunctionalization or duplication-degeneration-complementation, and subneofunctionalization, each can explain one or more aspects of gene fate after duplication. Duplicated genes are also affected by epigenetic changes. We constructed a phylogenetic tree using Dof (DNA binding with one finger) protein sequences from poplar (Populus trichocarpa) Torr. & Gray ex Brayshaw, Arabidopsis (Arabidopsis thaliana), and rice (Oryza sativa). From the phylogenetic tree, we identified 27 pairs of paralogous Dof genes in the terminal nodes. Analysis of protein motif structure of the Dof paralogs and their ancestors revealed six different gene fates after gene duplication. Differential protein methylation was revealed between a pair of duplicated poplar Dof genes, which have identical motif structure and similar expression pattern, indicating that epigenetics is involved in evolution. Analysis of reverse transcription-PCR, massively parallel signature sequencing, and microarray data revealed that the paralogs differ in expression pattern. Furthermore, analysis of nonsynonymous and synonymous substitution rates indicated that divergence of the duplicated genes was driven by positive selection. About one-half of the motifs in Dof proteins were shared by non-Dof proteins in the three plants species, indicating that motif co-option may be one of the forces driving gene diversification. We provided evidence that the Ohno's Duplication-Retention-Non/Neofunctionalization, subfunctionalization/duplication-degeneration-complementation, and subneofunctionalization hypotheses are complementary with, not alternative to, each other.
Separation of Arabidopsis Pollen Tetrads Is Regulated by QUARTET1, a Pectin Methylesterase Gene
Authors: Francis Kirk E. , Lam Sandy Y. , Copenhaver Gregory P.
Published: September 2006

Arabidopsis (Arabidopsis thaliana) QUARTET (QRT) genes are required for pollen separation during normal floral development. In qrt mutants, the four products of microsporogenesis remain fused and pollen grains are released as tetrads. In Arabidopsis, tetrad analysis in qrt mutants has been used to map all five centromeres, easily distinguish sporophytic from gametophytic mutations, and accurately assess crossover interference. Using a combination of forward and reverse genetics, we have identified the gene responsible for the qrt1 phenotype. Annotation predicts that QRT1 encodes a pectin methylesterase (PME), and enzymatic assays of QRT1 expressed in Escherichia coli indicate that QRT1 has PME activity. Promoter and transcription analysis demonstrate QRT1 is expressed in anther tissues shortly after meiosis is complete. Unexpectedly, the QRT1 promoter is also active in a variety of developmentally unrelated tissues, including developing guard cells, the hypocotyl-root transition zone, areas of lateral root emergence, and floral nectaries. PMEs constitute a large gene family in Arabidopsis, are involved in cell wall loosening, and have been implicated in various aspects of floral development and pollen tube elongation. The identification of QRT1 as a PME contributes to our understanding of pollen development and may help to provide valuable genetic tools in other plant species.
Up-Regulation of 1-Deoxy-d-Xylulose-5-Phosphate Synthase Enhances Production of Essential Oils in Transgenic Spike Lavender
Authors: Muñoz-Bertomeu Jesús , Arrillaga Isabel , Ros Roc , Segura Juan
Published: September 2006

Spike lavender (Lavandula latifolia) is an aromatic shrub cultivated worldwide for the production of essential oils. The major constituents of these oils are monoterpenes, which are obtained from isopentenyl diphosphate and dimethylallyl diphosphate precursors through the plastidial methylerythritol phosphate (MEP) pathway and/or the cytosolic mevalonate pathway. 1-Deoxy-d-xylulose-5-P synthase (DXS) catalyzes the first step of the MEP pathway. A cDNA coding for the Arabidopsis (Arabidopsis thaliana) DXS was constitutively expressed in spike lavender. Gas chromatography/mass spectrometry analyses revealed that transgenic plants accumulated significantly more essential oils compared to controls (from 101.5% to 359.0% and from 12.2% to 74.1% yield increase compared to controls in leaves and flowers, respectively). T0 transgenic plants were grown for 2 years, self-pollinated, and the T1 seeds obtained. The inheritance of the DXS transgene was studied in the T1 generation. The increased essential oil phenotype observed in the transgenic T0 plants was maintained in the progeny that inherited the DXS transgene. Total chlorophyll and carotenoid content in DXS progenies that inherited the transgene depended on the analyzed plant, showing either no variation or a significant decrease in respect to their counterparts without the transgene. Transgenic plants had a visual phenotype similar to untransformed plants (controls) in terms of morphology, growth habit, flowering, and seed germination. Our results demonstrate that the MEP pathway contributes to essential oil production in spike lavender. They also demonstrate that the DXS enzyme plays a crucial role in monoterpene precursor biosynthesis and, thus, in essential oil production in spike lavender. In addition, our results provide a strategy to increase the essential oil production in spike lavender by metabolic engineering of the MEP pathway without apparent detrimental effects on plant development and fitness.
CER4Encodes an Alcohol-Forming Fatty Acyl-Coenzyme A Reductase Involved in Cuticular Wax Production in Arabidopsis
Authors: Rowland Owen , Zheng Huanquan , Hepworth Shelley R. , Lam Patricia , Jetter Reinhard , Kunst Ljerka
Published: September 2006

A waxy cuticle that serves as a protective barrier against uncontrolled water loss and environmental damage coats the aerial surfaces of land plants. It is composed of a cutin polymer matrix and waxes. Cuticular waxes are complex mixtures of very-long-chain fatty acids and their derivatives. We report here the molecular cloning and characterization of CER4, a wax biosynthetic gene from Arabidopsis (Arabidopsis thaliana). Arabidopsis cer4 mutants exhibit major decreases in stem primary alcohols and wax esters, and slightly elevated levels of aldehydes, alkanes, secondary alcohols, and ketones. This phenotype suggested that CER4 encoded an alcohol-forming fatty acyl-coenzyme A reductase (FAR). We identified eight FAR-like genes in Arabidopsis that are highly related to an alcohol-forming FAR expressed in seeds of jojoba (Simmondsia chinensis). Molecular characterization of CER4 alleles and genomic complementation revealed that one of these eight genes, At4g33790, encoded the FAR required for cuticular wax production. Expression of CER4 cDNA in yeast (Saccharomyces cerevisiae) resulted in the accumulation of C24:0 and C26:0 primary alcohols. Fully functional green fluorescent protein-tagged CER4 protein was localized to the endoplasmic reticulum in yeast cells by confocal microscopy. Analysis of gene expression by reverse transcription-PCR indicated that CER4 was expressed in leaves, stems, flowers, siliques, and roots. Expression of a β-glucuronidase reporter gene driven by the CER4 promoter in transgenic plants was detected in epidermal cells of leaves and stems, consistent with a dedicated role for CER4 in cuticular wax biosynthesis. CER4 was also expressed in all cell types in the elongation zone of young roots. These data indicate that CER4 is an alcohol-forming FAR that has specificity for very-long-chain fatty acids and is responsible for the synthesis of primary alcohols in the epidermal cells of aerial tissues and in roots.
The Role of Cytosolic α-Glucan Phosphorylase in Maltose Metabolism and the Comparison of Amylomaltase in Arabidopsis and Escherichia coli
Authors: Lu Yan , Steichen Jon M. , Yao Jian , Sharkey Thomas D.
Published: September 2006

Transitory starch of leaves is broken down hydrolytically, making maltose the predominant form of carbon exported from chloroplasts at night. Maltose metabolism in the cytoplasm of Escherichia coli requires amylomaltase (MalQ) and maltodextrin phosphorylase (MalP). Possible orthologs of MalQ and MalP in the cytosol of Arabidopsis (Arabidopsis thaliana) were proposed as disproportionating enzyme (DPE2, At2g40840) and α-glucan phosphorylase (AtPHS2, At3g46970). In this article, we measured the activities of recombinant DPE2 and AtPHS2 proteins with various substrates; we show that maltose and a highly branched, soluble heteroglycan (SHG) are excellent substrates for DPE2 and propose that a SHG is the in vivo substrate for DPE2 and AtPHS2. In E. coli, MalQ and MalP preferentially use smaller maltodextrins (G3–G7) and we suggest that MalQ and DPE2 have similar, but nonidentical, roles in maltose metabolism. To study this, we complemented a MalQ−  E. coli strain with DPE2 and found that the rescue was not complete. To investigate the role of AtPHS2 in maltose metabolism, we characterized a T-DNA insertion line of the AtPHS2 gene. The nighttime maltose level increased 4 times in the Atphs2-1 mutant. The comparison of maltose metabolism in Arabidopsis with that in E. coli and the comparison of the maltose level in plants lacking DPE2 or AtPHS2 indicate that an alternative route to metabolize the glucan residues in SHG exists. Other plant species also contain SHG, DPE2, and α-glucan phosphorylase, so this pathway for maltose metabolism may be widespread among plants.
Chloroplasts as a Nitric Oxide Cellular Source. Effect of Reactive Nitrogen Species on Chloroplastic Lipids and Proteins
Authors: Jasid Sebastián , Simontacchi Marcela , Bartoli Carlos G. , Puntarulo Susana
Published: September 2006

Nitric oxide (NO) generation by soybean (Glycine max var. ADM 4800) chloroplasts was studied as an endogenous product assessed by the electron paramagnetic resonance spin-trapping technique. Nitrite and l-arginine (Arg) are substrates for enzymatic activities considered to be the possible sources of NO in plants. Soybean chloroplasts showed a NO production of 3.2 ± 0.2 nmol min−1 mg−1 protein in the presence of 1 mm NaNO2. Inhibition of photosynthetic electron flow by 3-(3,4-dichlorophenyl)-1,1-dimethyl urea resulted in a lower rate (1.21 ± 0.04 nmol min−1 mg−1 protein) of NO generation. Chloroplasts incubated with 1 mm Arg showed NO production of 0.76 ± 0.04 nmol min−1 mg−1 protein that was not affected either by omission of Ca2+ or by supplementation with Ca2+ and calmodulin to the incubation medium. This production was inhibited when chloroplasts were incubated in the presence of NO synthase inhibitors N  ω-nitro-l-Arg methyl ester hydrochloride and N  ω-nitro-l-Arg. In vitro exposure of chloroplasts to an NO donor (250 μ  m  S-nitrosoglutathione) decreased lipid radical content in membranes by 29%; however, incubation in the presence of 25 μ  m peroxynitrite (ONOO−) led to an increase in lipid-derived radicals (34%). The effect of ONOO− on protein oxidation was determined by western blotting, showing an increase in carbonyl content either in stroma or thylakoid proteins as compared to controls. Moreover, ONOO− treatment significantly affected both O2 evolution and chlorophyll fluorescence in thylakoids. Data reported here suggest that NO is an endogenous metabolite in soybean chloroplasts and that reactive nitrogen species could exert either antioxidant or prooxidant effects on chloroplast macromolecules.
Carotenoid Cleavage Dioxygenase (CmCCD4a) Contributes to White Color Formation in Chrysanthemum Petals
Authors: Ohmiya Akemi , Kishimoto Sanae , Aida Ryutaro , Yoshioka Satoshi , Sumitomo Katsuhiko
Published: September 2006

The white petals of chrysanthemum (Chrysanthemum morifolium Ramat.) are believed to contain a factor that inhibits the accumulation of carotenoids. To find this factor, we performed polymerase chain reaction-Select subtraction screening and obtained a clone expressed differentially in white and yellow petals. The deduced amino acid sequence of the protein (designated CmCCD4a) encoded by the clone was highly homologous to the sequence of carotenoid cleavage dioxygenase. All the white-flowered chrysanthemum cultivars tested showed high levels of CmCCD4a transcript in their petals, whereas most of the yellow-flowered cultivars showed extremely low levels. Expression of CmCCD4a was strictly limited to flower petals and was not detected in other organs, such as the root, stem, or leaf. White petals turned yellow after the RNAi construct of CmCCD4a was introduced. These results indicate that in white petals of chrysanthemums, carotenoids are synthesized but are subsequently degraded into colorless compounds, which results in the white color.
Branching Genes Are Conserved across Species. Genes Controlling a Novel Signal in Pea Are Coregulated by Other Long-Distance Signals
Authors: Johnson Xenie , Brcich Tanya , Dun Elizabeth A. , Goussot Magali , Haurogné Karine , Beveridge Christine A. , Rameau Catherine
Published: September 2006

Physiological and genetic studies with the ramosus (rms) mutants in garden pea (Pisum sativum) and more axillary shoots (max) mutants in Arabidopsis (Arabidopsis thaliana) have shown that shoot branching is regulated by a network of long-distance signals. Orthologous genes RMS1 and MAX4 control the synthesis of a novel graft-transmissible branching signal that may be a carotenoid derivative and acts as a branching inhibitor. In this study, we demonstrate further conservation of the branching control system by showing that MAX2 and MAX3 are orthologous to RMS4 and RMS5, respectively. This is consistent with the long-standing hypothesis that branching in pea is regulated by a novel long-distance signal produced by RMS1 and RMS5 and that RMS4 is implicated in the response to this signal. We examine RMS5 expression and show that it is more highly expressed relative to RMS1, but under similar transcriptional regulation as RMS1. Further expression studies support the hypothesis that RMS4 functions in shoot and rootstock and participates in the feedback regulation of RMS1 and RMS5 expression. This feedback involves a second novel long-distance signal that is lacking in rms2 mutants. RMS1 and RMS5 are also independently regulated by indole-3-acetic acid. RMS1, rather than RMS5, appears to be a key regulator of the branching inhibitor. This study presents new interactions between RMS genes and provides further evidence toward the ongoing elucidation of a model of axillary bud outgrowth in pea.
Green Light Adjusts the Plastid Transcriptome during Early Photomorphogenic Development
Authors: Dhingra Amit , Bies Dawn H. , Lehner Kevin R. , Folta Kevin M.
Published: September 2006

During the transition from darkness to light, a suite of light sensors guides gene expression, biochemistry, and morphology to optimize acclimation to the new environment. Ultraviolet, blue, red, and far-red light all have demonstrated roles in modulating light responses, such as changes in gene expression and suppression of stem growth rate. However, green wavebands induce stem growth elongation, a response not likely mediated by known photosensors. In this study, etiolated Arabidopsis (Arabidopsis thaliana) seedlings were treated with a short, dim, single pulse of green light comparable in fluence and duration to that previously shown to excite robust stem elongation. Genome microarrays were then used to monitor coincident changes in gene expression. As anticipated, phytochrome A-regulated, nuclear-encoded transcripts were induced, confirming proper function of the sensitive phytochrome system. In addition, a suite of plastid-encoded transcripts decreased in abundance, including several typically up-regulated after phytochrome and/or cryptochrome activation. Further analyses using RNA gel-blot experiments demonstrated that the response is specific to green light, fluence dependent, and detectable within 30 min. The response obeys reciprocity and persists in the absence of known photosensors. Plastid transcript down-regulation was also observed in tobacco (Nicotiana tabacum) with similar temporal and fluence-response kinetics. Together, the down-regulation of plastid transcripts and increase in stem growth rate represent a mechanism that tempers progression of early commitment to the light environment, helping tailor seedling development during the critical process of establishment.