bluuebunny/crossref_metadata_2025_split huggingface dataset:
Parietal and hippocampal contribution to topokinetic and topographic memory
Authors: Berthoz Alain 
Published: October 2002

This paper reviews the involvement of the parietal cortex and the hippocampus in three kinds of spatial memory tasks which all require a memory of a previously experienced movement in space. The first task compared, by means of positron emission tomography (PET) scan techniques, the production, in darkness, of self–paced saccades (SAC) with the reproduction, in darkness, of a previously learned sequence of saccades to visual targets (SEQ). The results show that a bilateral increase of activity was seen in the depth of the intraparietal sulcus and the medial superior parietal cortex (superior parietal gyrus and precuneus) together with the frontal sulcus but only in the SEQ task, which involved memory of the previously seen targets and possibly also motor memory.The second task is the vestibular memory contingent task, which requires that the subject makes, in darkness, a saccade to the remembered position of a visual target after a passively imposed whole–body rotation. Deficits in this task, which involves ‘vestibular memory’, were found predominantly in patients with focal vascular lesions in the parieto–insular (vestibular) cortex, the supplementary motor area–supplementary eye field area, and the prefrontal cortex.The third task requires mental navigation from the memory of a previously learned route in a real environment (the city of Orsay in France). A PET scan study has revealed that when subjects were asked to remember visual landmarks there was a bilateral activation of the middle hippocampal regions, left inferior temporal gyrus, left hippocampal regions, precentral gyrus and posterior cingulate gyrus. If the subjects were asked to remember the route, and their movements along this route, bilateral activation of the dorsolateral cortex, posterior hippocampal areas, posterior cingulate gyrus, supplementary motor areas, right middle hippocampal areas, left precuneus, middle occipital gyrus, fusiform gyrus and lateral premotor area was found. Subtraction between the two conditions reduced the activated areas to the left hippocampus, precuneus and insula.These data suggest that the hippocampus and parietal cortex are both involved in the dynamic aspects of spatial memory, for which the name ’topokinetic memory’ is proposed. These dynamic aspects could both overlap and be different from those involved in the cartographic and static aspects of ‘topographic’ memory.
Population growth rate and its determinants: an overview
Authors: Sibly Richard M. , Hone Jim 
Published: October 2002

We argue that population growth rate is the key unifying variable linking the various facets of population ecology. The importance of population growth rate lies partly in its central role in forecasting future population trends; indeed if the form of density dependence were constant and known, then the future population dynamics could to some degree be predicted. We argue that population growth rate is also central to our understanding of environmental stress: environmental stressors should be defined as factors which when first applied to a population reduce population growth rate. The joint action of such stressors determines an organism's ecological niche, which should be defined as the set of environmental conditions where population growth rate is greater than zero (where population growth rate =r= loge(Nt+1/Nt)). While environmental stressors have negative effects on population growth rate, the same is true of population density, the case of negative linear effects corresponding to the well–known logistic equation. Following Sinclair, we recognize population regulation as occurring when population growth rate is negatively density dependent. Surprisingly, given its fundamental importance in population ecology, only 25 studies were discovered in the literature in which population growth rate has been plotted against population density. In 12 of these the effects of density were linear; in all but two of the remainder the relationship was concave viewed from above.Alternative approaches to establishing the determinants of population growth rate are reviewed, paying special attention to the demographic and mechanistic approaches. The effects of population density on population growth rate may act through their effects on food availability and associated effects on somatic growth, fecundity and survival, according to a 'numerical response', the evidence for which is briefly reviewed. Alternatively, there may be effects on population growth rate of population density in addition to those that arise through the partitioning of food between competitors; this is 'interference competition'. The distinction is illustrated using a replicated laboratory experiment on a marine copepod,Tisbe battagliae. Application of these approaches in conservation biology, ecotoxicology and human demography is briefly considered. We conclude that population regulation, density dependence, resource and interference competition, the effects of environmental stress and the form of the ecological niche, are all best defined and analysed in terms of population growth rate.
Induction of Mitochondrial Alternative Oxidase in Response to a Cell Signal Pathway Down-Regulating the Cytochrome Pathway Prevents Programmed Cell Death
Authors: Vanlerberghe Greg C. , Robson Christine A. , Yip Justine Y.H. 
Published: October 2002

Abstract
Treatment of tobacco (Nicotiana tabacum L. cv Petit Havana SR1) cells with cysteine (Cys) triggers a signal pathway culminating in a large loss of mitochondrial cytochrome (cyt) pathway capacity. This down-regulation of the cyt path likely requires events outside the mitochondrion and is effectively blocked by cantharidin or endothall, indicating that protein dephosphorylation is one critical process involved. Generation of reactive oxygen species, cytosolic protein synthesis, and Ca2+ flux from organelles also appear to be involved. Accompanying the loss of cyt path is a large induction of alternative oxidase (AOX) protein and capacity. Induction of AOX allows the cells to maintain high rates of respiration, indicating that the lesion triggered by Cys is in the cyt path downstream of ubiquinone. Consistent with this, transgenic (AS8) cells unable to induce AOX (due to the presence of an antisense transgene) lose all respiratory capacity upon Cys treatment. This initiates in AS8 a programmed cell death pathway, as evidenced by the accumulation of oligonucleosomal fragments of DNA as the culture dies. Alternatively, wild-type cells remain viable and eventually recover their cyt path. Induction of AOX in response to a chemical inhibition of the cyt path (by antimycin A) is also dependent upon protein dephosphorylation and the generation of reactive oxygen species. Common events required for both down-regulation of the cyt path and induction of AOX may represent a mechanism to coordinate the biogenesis of these two electron transport paths. Such coordinate regulation may be necessary, not only to satisfy metabolic demands, but also to modulate the initiation of a programmed cell death pathway responsive to mitochondrial respiratory status.
Barley Cbf3 Gene Identification, Expression Pattern, and Map Location
Authors: Choi Dong-Woog , Rodriguez Edmundo M. , Close Timothy J. 
Published: October 2002

Abstract
Although cold and drought adaptation in cereals and other plants involve the induction of a large number of genes, inheritance studies in Triticeae (wheat [Triticum aestivum], barley [Hordeum vulgare], and rye [Secale cereale]) have revealed only a few major loci for frost or drought tolerance that are consistent across multiple genetic backgrounds and environments. One might imagine that these loci could encode highly conserved regulatory factors that have global effects on gene expression; therefore, genes encoding central regulators identified in other plants might be orthologs of these Triticeae stress tolerance genes. The CBF/DREB1 regulators, identified originally in Arabidopsis as key components of cold and drought regulation, merit this consideration. We constructed barley cDNA libraries, screened these libraries and a barley bacterial artificial chromosome library using rice (Oryza sativa) and barley Cbf probes, found orthologs of ArabidopsisCBF/DREB1 genes, and examined the expression and genetic map location of the barley Cbf3 gene,HvCbf3. HvCbf3 was induced by a chilling treatment. HvCbf3 is located on barley chromosome 5H between markers WG364b and saflp58 on the barley cv Dicktoo × barley cv Morex genetic linkage map. This position is some 40 to 50 cM proximal to the winter hardiness quantitative trait locus that includes the Vrn-1H gene, but may coincide with the wheat 5A Rcg1 locus, which governs the threshold temperature at which cor genes are induced. From this, it remains possible that HvCbf3 is the basis of a minor quantitative trait locus in some genetic backgrounds, though that possibility remains to be thoroughly explored.
Using Genomic Resources to Guide Research Directions. The Arabinogalactan Protein Gene Family as a Test Case
Authors: Schultz Carolyn J. , Rumsewicz Michael P. , Johnson Kim L. , Jones Brian J. , Gaspar Yolanda M. , Bacic Antony 
Published: October 2002

Abstract
Arabinogalactan proteins (AGPs) are extracellular hydroxyproline-rich proteoglycans implicated in plant growth and development. The protein backbones of AGPs are rich in proline/hydroxyproline, serine, alanine, and threonine. Most family members have less than 40% similarity; therefore, finding family members using Basic Local Alignment Search Tool searches is difficult. As part of our systematic analysis of AGP function in Arabidopsis, we wanted to make sure that we had identified most of the members of the gene family. We used the biased amino acid composition of AGPs to identify AGPs and arabinogalactan (AG) peptides in the Arabidopsis genome. Different criteria were used to identify the fasciclin-like AGPs. In total, we have identified 13 classical AGPs, 10 AG-peptides, three basic AGPs that include a short lysine-rich region, and 21 fasciclin-like AGPs. To streamline the analysis of genomic resources to assist in the planning of targeted experimental approaches, we have adopted a flow chart to maximize the information that can be obtained about each gene. One of the key steps is the reformatting of the Arabidopsis Functional Genomics Consortium microarray data. This customized software program makes it possible to view the ratio data for all Arabidopsis Functional Genomics Consortium experiments and as many genes as desired in a single spreadsheet. The results for reciprocal experiments are grouped to simplify analysis and candidate AGPs involved in development or biotic and abiotic stress responses are readily identified. The microarray data support the suggestion that different AGPs have different functions.
ADP-Ribosylation Factor 1 of Arabidopsis Plays a Critical Role in Intracellular Trafficking and Maintenance of Endoplasmic Reticulum Morphology in Arabidopsis
Authors: Lee Mi Hee , Min Myung Ki , Lee Yong Jik , Jin Jing Bo , Shin Dong Han , Kim Dae Heon , Lee Kwang-Hee , Hwang Inhwan 
Published: October 2002

Abstract
ADP-ribosylation factors (Arf), a family of small GTP-binding proteins, play important roles in intracellular trafficking in animal and yeast cells. Here, we investigated the roles of two Arf homologs, Arf1 and Arf3 of Arabidopsis, in intracellular trafficking in plant cells. We generated dominant negative mutant forms of Arf 1 and Arf3 and examined their effect on trafficking of reporter proteins in protoplasts. Arf1[T31N] inhibited trafficking of H+-ATPase:green fluorescent protein (GFP) and sialyltransferase (ST):GFP to the plasma membrane and the Golgi apparatus. In addition, Arf1[T31N] caused relocalization of the Golgi reporter protein ST:GFP to the endoplasmic reticulum (ER). In protoplasts expressing Arf1[T31N], ST:red fluorescent protein remained in the ER, whereas H+-ATPase:GFP was mistargeted to another organelle. Also, expression of Arf1[T31N] in protoplasts resulted in profound changes in the morphology of the ER. The treatment of protoplasts with brefeldin A had exactly the same effect as Arf1[T31N] on various intracellular trafficking pathways. In contrast, Arf3[T31N] did not affect trafficking of any of these reporter proteins. Inhibition experiments using mutants with various domains swapped between Arf1 and Arf3 revealed that the N-terminal domain is interchangeable for trafficking inhibition. However, in addition to the T31N mutation, motifs in domains II, III, and IV of Arf1 were necessary for inhibition of trafficking of H+-ATPase:GFP. Together, these results strongly suggest that Arf1 plays a role in the intracellular trafficking of cargo proteins in Arabidopsis, and that Arf1 functions through a brefeldin A-sensitive factor.
Loss-of-Function Mutations in the Ethylene ReceptorETR1 Cause Enhanced Sensitivity and Exaggerated Response to Ethylene in Arabidopsis
Authors: Cancel Jesse D. , Larsen Paul B. 
Published: October 2002

Abstract
Ethylene signaling in Arabidopsis begins at a family of five ethylene receptors that regulate activity of a downstream mitogen-activated protein kinase kinase kinase, CTR1. Triple and quadruple loss-of-function ethylene receptor mutants display a constitutive ethylene response phenotype, indicating they function as negative regulators in this pathway. No ethylene-related phenotype has been described for single loss-of-function receptor mutants, although it was reported that etr1 loss-of-function mutants display a growth defect limiting plant size. In actuality, this apparent growth defect results from enhanced responsiveness to ethylene; a phenotype manifested in all tissues tested. The phenotype displayed by etr1 loss-of-function mutants was rescued by treatment with an inhibitor of ethylene perception, indicating that it is ethylene dependent. Identification of an ethylene-dependent phenotype for a loss-of-function receptor mutant gave a unique opportunity for genetic and biochemical analysis of upstream events in ethylene signaling, including demonstration that the dominant ethylene-insensitive phenotype of etr2-1 is partially dependent on ETR1. This work demonstrates that mutational loss of the ethylene receptor ETR1 alters responsiveness to ethylene in Arabidopsis and that enhanced ethylene response in Arabidopsis not only results in increased sensitivity but exaggeration of response.
Independent Activation of Cold Acclimation by Low Temperature and Short Photoperiod in Hybrid Aspen
Authors: Welling Annikki , Moritz Thomas , Palva E. Tapio , Junttila Olavi 
Published: October 2002

AbstractTemperate zone woody plants cold acclimate in response to both short daylength (SD) and low temperature (LT). We were able to show that these two environmental cues induce cold acclimation independently by comparing the wild type (WT) and the transgenic hybrid aspen (Populus tremula × Populus tremuloides Michx.) line 22 overexpressing the oat (Avena sativa) PHYTOCHROME A gene. Line 22 was not able to detect the SD and, consequently, did not stop growing in SD conditions. This resulted in an impaired freezing tolerance development under SD. In contrast, exposure to LT resulted in cold acclimation of line 22 to a degree comparable with the WT. In contrast to the WT, line 22 could not dehydrate the overwintering tissues or induce the production of dehydrins (DHN) under SD conditions. Furthermore, abscisic acid (ABA) content of the buds of line 22 were the same under SD and long daylength, whereas prolonged SD exposure decreased the ABA level in the WT. LT exposure resulted in a rapid accumulation of DHN in both the WT and line 22. Similarly, ABA content increased transiently in both the WT and line 22. Our results indicate that phytochrome A is involved in photoperiodic regulation of ABA and DHN levels, but at LT they are regulated by a different mechanism. Although SD and LT induce cold acclimation independently, ABA and DHN may play important roles in both modes of acclimation.
A Novel Plant Homeodomain Protein Interacts in a Functionally Relevant Manner with a Virus Movement Protein
Authors: Desvoyes Bénédicte , Faure-Rabasse Sandrine , Chen Min-Huei , Park Jong-Won , Scholthof Herman B. 
Published: October 2002

AbstractTomato bushy stunt virus and its cell-to-cell movement protein (MP; P22) provide valuable tools to study trafficking of macromolecules through plants. This study shows that wild-type P22 and selected movement-defective P22 amino acid substitution mutants were equivalent for biochemical features commonly associated with MPs (i.e. RNA binding, phosphorylation, and membrane partitioning). This generated the hypothesis that their movement defect was caused by improper interaction between the P22 mutants and one or more host factors. To test this, P22 was used as bait in a yeast (Saccharomyces cerevisiae) two-hybrid screen with a tobacco (Nicotiana tabacum) cDNA library, which identified a new plant homeodomain leucine-zipper protein that reproducibly interacted with P22 but not with various control proteins. These results were confirmed with an independent in vitro binding test. An mRNA for the host protein was detected in plants, and its accumulation was enhanced upon Tomato bushy stunt virusinfection of two plant species. The significance of this interaction was further demonstrated by the failure of the homeodomain protein to interact efficiently with two of the well-defined movement-deficient P22 mutants in yeast and in vitro. This is the first report, to our knowledge, that a new plant homeodomain leucine-zipper protein interacts specifically and in a functionally relevant manner with a plant virus MP.
Pheromone binding by polymorphic mouse major urinary proteins
Authors: Sharrow Scott D. , Vaughn Jeffrey L. , Žídek Lukáš , Novotny Milos V. , Stone Martin J. 
Published: October 2002

AbstractMouse major urinary proteins (MUPs) have been proposed to play a role in regulating the release and capture of pheromones. Here, we report affinity measurements of five recombinant urinary MUP isoforms (MUPs‐I, II, VII, VIII, and IX) and one recombinant nasal isoform (MUP‐IV) for each of three pheromonal ligands, (±)‐2‐sec‐butyl‐4,5‐dihydrothiazole (SBT), 6‐hydroxy‐6‐methyl‐3‐heptanone (HMH), and (±)dehydro‐exo‐brevicomin (DHB). Dissociation constants for all MUP‐pheromone pairs were determined by isothermal titration calorimetry, and data for SBT were corroborated by measurements of intrinsic protein fluorescence. We also report the isolation of MUP‐IV protein from mouse nasal extracts, in which MUP‐IV mRNA has been observed previously. The affinity of each MUP isoform for SBT (Kd ∼ 0.04 to 0.9 μM) is higher than that for DHB (Kd ∼ 26 to 58 μM), which in turn is higher than that for HMH (Kd ∼ 50 to 200 μM). Isoforms I, II, VIII, and IX show very similar affinities for each of the ligands. MUP‐VII has approximately twofold higher affinity for SBT but approximately twofold lower affinity for the other pheromones, whereas MUP‐IV has ∼23‐fold higher affinity for SBT and approximately fourfold lower affinity for the other pheromones. The variations in ligand affinities of the MUP isoforms are consistent with structural differences in the binding cavities of the isoforms. The data indicate that the concentrations of available pheromones in urine may be influenced by changes in the expression levels of urinary MUPs or the excretion levels of other MUP ligands. The variation in pheromone affinities of the urinary MUP isoforms provides only limited support for the proposal that MUP heterogeneity plays a role in regulating profiles of available pheromones. However, the binding data support the proposed role of nasal MUPs in sequestering pheromones and possibly transporting them to their receptors.
Contact order and ab initio protein structure prediction
Authors: Bonneau Richard , Ruczinski Ingo , Tsai Jerry , Baker David 
Published: October 2002

AbstractAlthough much of the motivation for experimental studies of protein folding is to obtain insights for improving protein structure prediction, there has been relatively little connection between experimental protein folding studies and computational structural prediction work in recent years. In the present study, we show that the relationship between protein folding rates and the contact order (CO) of the native structure has implications for ab initio protein structure prediction. Rosetta ab initio folding simulations produce a dearth of high CO structures and an excess of low CO structures, as expected if the computer simulations mimic to some extent the actual folding process. Consistent with this, the majority of failures in ab initio prediction in the CASP4 (critical assessment of structure prediction) experiment involved high CO structures likely to fold much more slowly than the lower CO structures for which reasonable predictions were made. This bias against high CO structures can be partially alleviated by performing large numbers of additional simulations, selecting out the higher CO structures, and eliminating the very low CO structures; this leads to a modest improvement in prediction quality. More significant improvements in predictions for proteins with complex topologies may be possible following significant increases in high–performance computing power, which will be required for thoroughly sampling high CO conformations (high CO proteins can take six orders of magnitude longer to fold than low CO proteins). Importantly for such a strategy, simulations performed for high CO structures converge much less strongly than those for low CO structures, and hence, lack of simulation convergence can indicate the need for improved sampling of high CO conformations. The parallels between Rosetta simulations and folding in vivo may extend to misfolding: The very low CO structures that accumulate in Rosetta simulations consist primarily of local up–down β–sheets that may resemble precursors to amyloid formation.
Docking of protein models
Authors: Tovchigrechko Andrei , Wells Christopher A. , Vakser Ilya A. 
Published: October 2002

AbstractAn adequate description of entire genomes has to include information on the three‐dimensional (3D) structure of proteins. Most of these protein structures will be determined by high‐throughput modeling procedures. Thus, a structure‐based analysis of the network of protein–protein interactions in genomes requires docking methodologies that are capable of dealing with significant structural inaccuracies in the modeled structures of proteins. We present a systematic study of the applicability of our low‐resolution docking method to protein models of different accuracies. A representative nonredundant set of 475 cocrystallized protein–protein complexes was used to build an array of models of each protein in the set. A sophisticated procedure was created to generate the models with RMS deviations of 1, 2, 3, …, 10 Å from the crystal structure. The docking was performed for all the models, and the predictions were compared with the configurations of the original cocrystallized complexes. Statistical analysis showed that the low‐resolution docking can determine the gross structural features of protein–protein interactions for a significant percent of complexes of highly inaccurate protein models. Such predictions may serve as starting points for a more detailed structural analysis, as well as complement experimental and computational data on protein–protein interactions obtained by other techniques.