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1.  Pathogenic Fungus Microsporum canis Activates the NLRP3 Inflammasome 
Infection and Immunity  2014;82(2):882-892.
Microsporum canis is a pathogenic fungus with worldwide distribution that causes tinea capitis in animals and humans. M. canis also causes invasive infection in immunocompromised patients. To defy pathogenic fungal infection, the host innate immune system is the first line of defense. As an important arm of innate immunity, the inflammasomes are intracellular multiprotein complexes that control the activation of caspase-1, which cleaves proinflammatory cytokine pro-interleukin-1β (IL-1β) into its mature form. To determine whether the inflammasome is involved in the host defense against M. canis infection, we challenged human monocytic THP-1 cells and mouse dendritic cells with a clinical strain of M. canis isolated from patients with tinea capitis. We found that M. canis infection triggered rapid secretion of IL-1β from both THP-1 cells and mouse dendritic cells. Moreover, by using gene-specific shRNA and competitive inhibitors, we determined that M. canis-induced IL-1β secretion was dependent on NLRP3. The pathways proposed for NLRP3 inflammasome activation, namely, cathepsin B activity, K+ efflux, and reactive oxygen species production, were all required for the inflammasome activation triggered by M. canis. Meanwhile, Syk, Dectin-1, and Card9 were found to be involved in M. canis-induced IL-1β secretion via regulation of pro-IL-1β transcription. More importantly, our data revealed that M. canis-induced production of IL-1β was dependent on the NLRP3 inflammasome in vivo. Together, this study unveils that the NLRP3 inflammasome exerts a critical role in host innate immune responses against M. canis infection, and our data suggest that diseases that result from M. canis infection might be controlled by regulating the activation of inflammasomes.
doi:10.1128/IAI.01097-13
PMCID: PMC3911390  PMID: 24478101
2.  Trehalase Regulates Neuroepithelial Stem Cell Maintenance and Differentiation in the Drosophila Optic Lobe 
PLoS ONE  2014;9(7):e101433.
As one of the major hydrolases in Drosophila, trehalase (Treh) catalyzes the hydrolysis of trehalose into glucose providing energy for flight muscle activity. Treh is highly conserved from bacteria to humans, but little is known about its function during animal development. Here, we analyze the function of Treh in Drosophila optic lobe development. In the optic lobe, neuroepithelial cells (NEs) first divide symmetrically to expand the stem cell pool and then differentiate into neuroblasts, which divide asymmetrically to generate medulla neurons. We find that the knockdown of Treh leads to a loss of the lamina and a smaller medulla. Analyses of Treh RNAi-expressing clones and loss-of-function mutants indicate that the lamina and medulla phenotypes result from neuroepithelial disintegration and premature differentiation into medulla neuroblasts. Although the principal role of Treh is to generate glucose, the Treh loss-of-function phenotype cannot be rescued by exogenous glucose. Thus, our results indicate that in addition to being a hydrolase, Treh plays a role in neuroepithelial stem cell maintenance and differentiation during Drosophila optic lobe development.
doi:10.1371/journal.pone.0101433
PMCID: PMC4086926  PMID: 25003205
4.  Molecular Characterization, Expression Pattern, and Ligand-Binding Property of Three Odorant Binding Protein Genes from Dendrolimus tabulaeformis 
Journal of Chemical Ecology  2014;40(4):396-406.
Odorant binding proteins (OBPs) play important roles in insect olfactory processes. The Chinese pine caterpillar moth, Dendrolimus tabulaeformis (Lepidoptera, Lasiocampidae) is a serious economic pest in China, and the pheromones of this species have been identified to monitor their presence. However, the molecular mechanisms by which D. tabulaeformis perceive pheromones and host volatiles remain unknown. In this study, we identified and characterized three new OBPs, including one pheromone binding protein (PBP1) and two general odor binding proteins (GOBPs), from antennal cDNA of D. tabulaeformis. The deduced amino acid sequences of DtabPBP1, DtabGOBP1, and DtabGOBP2 revealed mature proteins of 140, 147, and 140 amino acids, respectively. Each has six cysteine residues in conserved positions relative to other known OBPs. Amino-acid alignments indicated that the two GOBPs are more conserved (DtabGOBP1 is 52.9–67.4 % identical to orthologs from other Lepidoptera, and DtabGOBP2 is 55.2–81.8 % identical) than the PBP (32.5–46.0 %). Real-time PCR indicated tissue- and sex-specific expression patterns of the three genes. DtabPBP1 was mainly expressed in the antennae of males, whereas female antennae had only 1.09 % the expression in male antennae. Both DtabGOBP1 and DtabGOBP2 were more highly expressed in antennae than in other tissues, while DtabGOBP1 was more abundant in male antennae and DtabGOBP2 in female antennae. In addition, the binding specificities of the three proteins were investigated, and all three OBPs exhibited high binding affinities for the pheromone component (5Z,7E)-5,7-dodecadien-1-yl propionate (Z5,E7-12:OPr). This suggests a role in binding pheromone for GOBPs, as well as PBP1, in D. tabulaeformis.
Electronic supplementary material
The online version of this article (doi:10.1007/s10886-014-0412-6) contains supplementary material, which is available to authorized users.
doi:10.1007/s10886-014-0412-6
PMCID: PMC4008786  PMID: 24728949
Pheromone binding proteins; General odorant binding proteins; Real-time PCR; Fluorescence competitive binding assay; Forest insect; Economic pest; Lepidoptera
5.  Insight into others’ minds: spatio-temporal representations by intrinsic frame of reference 
Recent research has seen a growing interest in connections between domains of spatial and social cognition. Much evidence indicates that processes of representing space in distinct frames of reference (FOR) contribute to basic spatial abilities as well as sophisticated social abilities such as tracking other’s intention and belief. Argument remains, however, that belief reasoning in social domain requires an innately dedicated system and cannot be reduced to low-level encoding of spatial relationships. Here we offer an integrated account advocating the critical roles of spatial representations in intrinsic frame of reference. By re-examining the results from a spatial task (Tamborello etal., 2012) and a false-belief task (Onishi and Baillargeon, 2005), we argue that spatial and social abilities share a common origin at the level of spatio-temporal association and predictive learning, where multiple FOR-based representations provide the basic building blocks for efficient and flexible partitioning of the environmental statistics. We also discuss neuroscience evidence supporting these mechanisms. We conclude that FOR-based representations may bridge the conceptual as well as the implementation gaps between the burgeoning fields of social and spatial cognition.
doi:10.3389/fnhum.2014.00058
PMCID: PMC3924045  PMID: 24592226
theory of mind; false belief; spatial cognition; frame of reference; predictive learning
6.  The Chloroplast Min System Functions Differentially in Two Specific Nongreen Plastids in Arabidopsis thaliana 
PLoS ONE  2013;8(7):e71190.
The nongreen plastids, such as etioplasts, chromoplasts, etc., as well as chloroplasts, are all derived from proplastids in the meristem. To date, the Min system members in plants have been identified as regulators of FtsZ-ring placement, which are essential for the symmetrical division of chloroplasts. However, the regulation of FtsZ-ring placement in nongreen plastids is poorly understood. In this study, we investigated the division site placement of nongreen plastids by examining the etioplasts as representative in Arabidopsis Min system mutants. Surprisingly, the shape and number of etioplasts in cotyledons of arc3, arc11 and mcd1 mutants were similar to that observed in wild-type plants, whereas arc12 and parc6 mutants exhibited enlarged etioplasts that were reduced in number. In order to examine nongreen plastids in true leaves, we silenced the ALB3 gene in these Min system mutant backgrounds to produce immature chloroplasts without the thylakoidal network using virus induced gene silencing (VIGS). Interestingly, consistent with our observations in etioplasts, enlarged and fewer nongreen plastids were only detected in leaves of parc6 (VIGS-ALB3) and arc12 (VIGS-ALB3) plants. Further, the FtsZ-ring assembled properly at the midpoint in nongreen plastids of arc3, arc11 and mcd1 (VIGS-ALB3) plants, but organized into multiple rings in parc6 (VIGS-ALB3) and presented fragmented filaments in arc12 (VIGS-ALB3) plants, suggesting that division site placement in nongreen plastids requires fewer components of the plant Min system. Taken together, these results suggest that division site placement in nongreen plastids is different from that in chloroplasts.
doi:10.1371/journal.pone.0071190
PMCID: PMC3728212  PMID: 23936263
7.  COORDINATED ACTIVATION OF THE RAC-GAP β2-CHIMAERIN BY AN ATYPICAL PROLINE-RICH DOMAIN AND DIACYLGLYCEROL 
Nature communications  2013;4:1849.
Chimaerins, a family of GTPase activating proteins (GAPs) for the small G-protein Rac, have been implicated in development, neuritogenesis, and cancer. These Rac-GAPs are regulated by the lipid second messenger diacylglycerol (DAG) generated by tyrosine-kinases such as the epidermal growth factor receptor (EGFR). Here we identify an atypical Pro-rich motif in chimaerins that binds to the adaptor protein Nck1. Unlike most Nck1 partners, chimaerins bind to the third SH3 domain of Nck1. This association is mediated by electrostatic interactions of basic residues within the Pro-rich motif with acidic clusters in the SH3 domain. EGF promotes the binding of β2-chimaerin to Nck1 in the cell periphery in a DAG-dependent manner. Moreover, β2-chimaerin translocation to the plasma membrane and its peripheral association with Rac1 requires Nck1. Our studies underscore a coordinated mechanism for β2-chimaerin activation that involves lipid interactions via the C1 domain and protein-protein interactions via the N-terminal Pro-rich region.
doi:10.1038/ncomms2834
PMCID: PMC3700536  PMID: 23673634
8.  The Parietal Cortex in Sensemaking: The Dissociation of Multiple Types of Spatial Information 
According to the data-frame theory, sensemaking is a macrocognitive process in which people try to make sense of or explain their observations by processing a number of explanatory structures called frames until the observations and frames become congruent. During the sensemaking process, the parietal cortex has been implicated in various cognitive tasks for the functions related to spatial and temporal information processing, mathematical thinking, and spatial attention. In particular, the parietal cortex plays important roles by extracting multiple representations of magnitudes at the early stages of perceptual analysis. By a series of neural network simulations, we demonstrate that the dissociation of different types of spatial information can start early with a rather similar structure (i.e., sensitivity on a common metric), but accurate representations require specific goal-directed top-down controls due to the interference in selective attention. Our results suggest that the roles of the parietal cortex rely on the hierarchical organization of multiple spatial representations and their interactions. The dissociation and interference between different types of spatial information are essentially the result of the competition at different levels of abstraction.
doi:10.1155/2013/152073
PMCID: PMC3654633  PMID: 23710165
9.  Shotgun Proteomic Analysis of Plasma from Dairy Cattle Suffering from Footrot: Characterization of Potential Disease-Associated Factors 
PLoS ONE  2013;8(2):e55973.
The plasma proteome of healthy dairy cattle and those with footrot was investigated using a shotgun LC-MS/MS approach. In total, 648 proteins were identified in healthy plasma samples, of which 234 were non-redundant proteins and 123 were high-confidence proteins; 712 proteins were identified from footrot plasma samples, of which 272 were non-redundant proteins and 138 were high-confidence proteins. The high-confidence proteins showed significant differences between healthy and footrot plasma samples in molecular weight, isoelectric points and the Gene Ontology categories. 22 proteins were found that may differentiate between the two sets of plasma proteins, of which 16 potential differential expression (PDE) proteins from footrot plasma involved in immunoglobulins, innate immune recognition molecules, acute phase proteins, regulatory proteins, and cell adhesion and cytoskeletal proteins; 6 PDE proteins from healthy plasma involved in regulatory proteins, cytoskeletal proteins and coagulation factors. Of these PDE proteins, haptoglobin, SERPINA10 protein, afamin precursor, haptoglobin precursor, apolipoprotein D, predicted peptidoglycan recognition protein L (PGRP-L) and keratan sulfate proteoglycan (KS-PG) were suggested to be potential footrot-associated factors. The PDE proteins PGRP-L and KS-PG were highlighted as potential biomarkers of footrot in cattle. The resulting protein lists and potential differentially expressed proteins may provide valuable information to increase understanding of plasma protein profiles in cattle and to assist studies of footrot-associated factors.
doi:10.1371/journal.pone.0055973
PMCID: PMC3572155  PMID: 23418487
10.  The RacGAP β-Chimaerin Selectively Mediates Stereotyped Hippocampal Axonal Pruning 
Cell  2012;149(7):1594-1606.
Summary
Axon pruning and synapse elimination are critical for establishing neural connectivity and synaptic plasticity. Stereotyped pruning of axons that originate in the hippocampal dentate gyrus (DG) and extend in the infrapyramidal tract (IPT) occurs during postnatal murine development by neurite retraction and resembles axon repulsion. The chemorepellent Sema3F is required for IPT axon pruning, dendritic spine remodeling and repulsion of DG axons. However, the signaling events that regulate IPT pruning are not known. We find that inhibition of the small G-protein Rac1 by the Rac GTPase activating protein (GAP) β2-Chimaerin (β2Chn) is essential for Sema3F-mediated IPT pruning. β2Chn selectively binds to the Sema3F receptor neuropilin-2. Sema3F activation of β2Chn is necessary for pruning both in vitro and in vivo, but is dispensable for axon repulsion and spine remodeling. Therefore, β2Chn contributes to a mechanistic distinction among DG axon pruning, repulsion, and dendritic spine remodeling, all mediated by the repellent Sema3F.
doi:10.1016/j.cell.2012.05.018
PMCID: PMC3395473  PMID: 22726444
11.  Characterization of the Unusual Bidirectional ves Promoters Driving VESA1 Expression and Associated with Antigenic Variation in Babesia bovis 
Eukaryotic Cell  2012;11(3):260-269.
Rapid clonal antigenic variation in Babesia bovis involves the variant erythrocyte surface antigen-1 (VESA1) protein expressed on the infected-erythrocyte surface. Because of the significance of this heterodimeric protein for demonstrated mechanisms of parasite survival and virulence, there is a need to understand how expression of the ves multigene family encoding this protein is controlled. As an initial step toward this goal, we present here initial characterization of the ves promoter driving transcription of VESA1a and -1b subunits. A series of transfection constructs containing various sequence elements from the in vivo locus of active ves transcription (LAT) were used to drive expression of the firefly luciferase gene in a dual luciferase-normalized assay. The results of this approach reveal the presence of two bidirectional promoter activities within the 434-bp intergenic region (IGr), influenced by putative regulatory sequences embedded within the flanking ves1α and ves1β genes. Repressor-like effects on the apposing gene were observed for intron 1 of both ves1α and ves1β. This effect is apparently not dependent upon intronic promoter activity and acts only in cis. The expression of genes within the ves family is likely modulated by local elements embedded within ves coding sequences outside the intergenic promoter region in concert with chromatin modifications. These results provide a framework to help us begin to understand gene regulation during antigenic variation in B. bovis.
doi:10.1128/EC.05318-11
PMCID: PMC3294438  PMID: 22286091
12.  Two Homologous Putative Protein Tyrosine Phosphatases, OsPFA-DSP2 and AtPFA-DSP4, Negatively Regulate the Pathogen Response in Transgenic Plants 
PLoS ONE  2012;7(4):e34995.
Protein phosphatases, together with protein kinases, regulate protein phosphorylation and dephosphorylation, and play critical roles in plant growth and biotic stress responses. However, little is known about the biological functions of plant protein tyrosine dual-specificity phosphatase (PFA-DSP) in biotic stresses. Here, we found that OsPFA-DSP2 was mainly expressed in calli, seedlings, roots, and young panicles, and localized in cytoplasm and nucleus. Ectopic overexpression of OsPFA-DSP2 in rice increased sensitivity to Magnaporthe grisea (M. grisea Z1 strain), inhibited the accumulation of hydrogen peroxide (H2O2) and suppressed the expression of pathogenesis-related (PR) genes after fungal infection. Interestingly, transgenic Arabidopsis plants overexpressing AtPFA-DSP4, which is homologous to OsPFA-DSP2, also exhibited sensitivity to Pseudomonas syringae pv. tomato DC3000 (Pst DC3000), reduced accumulation of H2O2 and decreased photosynthesic capacity after infection compared with Col-0. These results indicate that OsPFA-DSP2 and AtPFA-DSP4 act as negative regulators of the pathogen response in transgenic plants.
doi:10.1371/journal.pone.0034995
PMCID: PMC3325911  PMID: 22514699
13.  IDENTIFICATION OF THE Rac-GEF P-REX1 AS AN ESSENTIAL MEDIATOR OF ErbB SIGNALING IN BREAST CANCER 
Molecular cell  2010;40(6):877-892.
SUMMARY
While the small GTPase Rac1 and its effectors are well-established mediators of mitogenic and motile signaling by tyrosine-kinase receptors and have been implicated in breast tumorigenesis, little is known regarding the exchange factors (Rac-GEFs) that mediate ErbB receptor responses. Here we identify the PIP3-Gβγ-dependent Rac-GEF P-Rex1 as an essential mediator of Rac1 activation, motility, cell growth, and tumorigenesis driven by ErbB receptors in breast cancer cells. Notably, activation of P-Rex1 in breast cancer cells requires the convergence of inputs from ErbB receptors and a Gβγ- and PI3Kγ-dependent pathway. Moreover, we identified the GPCR CXCR4 as a crucial mediator of P-Rex1/Rac1 activation in response to ErbB ligands. P-Rex1 is highly overexpressed in human breast cancers and their derived cell lines, particularly those with high ErbB2 and ER expression. In addition to the prognostic and therapeutic implications, our findings reveal an ErbB effector pathway that is crucial for breast cancer progression.
doi:10.1016/j.molcel.2010.11.029
PMCID: PMC3038344  PMID: 21172654
P-Rex1; Rac-GEF; Rac1; ErbB receptors; PI3Kγ; Gβγ subunits; breast cancer
14.  A highly efficient rice green tissue protoplast system for transient gene expression and studying light/chloroplast-related processes 
Plant Methods  2011;7:30.
Background
Plant protoplasts, a proven physiological and versatile cell system, are widely used in high-throughput analysis and functional characterization of genes. Green protoplasts have been successfully used in investigations of plant signal transduction pathways related to hormones, metabolites and environmental challenges. In rice, protoplasts are commonly prepared from suspension cultured cells or etiolated seedlings, but only a few studies have explored the use of protoplasts from rice green tissue.
Results
Here, we report a simplified method for isolating protoplasts from normally cultivated young rice green tissue without the need for unnecessary chemicals and a vacuum device. Transfections of the generated protoplasts with plasmids of a wide range of sizes (4.5-13 kb) and co-transfections with multiple plasmids achieved impressively high efficiencies and allowed evaluations by 1) protein immunoblotting analysis, 2) subcellular localization assays, and 3) protein-protein interaction analysis by bimolecular fluorescence complementation (BiFC) and firefly luciferase complementation (FLC). Importantly, the rice green tissue protoplasts were photosynthetically active and sensitive to the retrograde plastid signaling inducer norflurazon (NF). Transient expression of the GFP-tagged light-related transcription factor OsGLK1 markedly upregulated transcript levels of the endogeneous photosynthetic genes OsLhcb1, OsLhcp, GADPH and RbcS, which were reduced to some extent by NF treatment in the rice green tissue protoplasts.
Conclusions
We show here a simplified and highly efficient transient gene expression system using photosynthetically active rice green tissue protoplasts and its broad applications in protein immunoblot, localization and protein-protein interaction assays. These rice green tissue protoplasts will be particularly useful in studies of light/chloroplast-related processes.
doi:10.1186/1746-4811-7-30
PMCID: PMC3203094  PMID: 21961694
15.  Cognitive Control in Majority Search: A Computational Modeling Approach 
Despite the importance of cognitive control in many cognitive tasks involving uncertainty, the computational mechanisms of cognitive control in response to uncertainty remain unclear. In this study, we develop biologically realistic neural network models to investigate the instantiation of cognitive control in a majority function task, where one determines the category to which the majority of items in a group belong. Two models are constructed, both of which include the same set of modules representing task-relevant brain functions and share the same model structure. However, with a critical change of a model parameter setting, the two models implement two different underlying algorithms: one for grouping search (where a subgroup of items are sampled and re-sampled until a congruent sample is found) and the other for self-terminating search (where the items are scanned and counted one-by-one until the majority is decided). The two algorithms hold distinct implications for the involvement of cognitive control. The modeling results show that while both models are able to perform the task, the grouping search model fit the human data better than the self-terminating search model. An examination of the dynamics underlying model performance reveals how cognitive control might be instantiated in the brain for computing the majority function.
doi:10.3389/fnhum.2011.00016
PMCID: PMC3037790  PMID: 21369357
cognitive control; uncertainty; majority function; algorithms; computational modeling; neural networks
16.  Testing the behavioral interaction and integration of attentional networks 
Brain and cognition  2009;70(2):209-220.
One current conceptualization of attention subdivides it into functions of alerting, orienting, and executive control. Alerting describes the function of tonically maintaining the alert state and phasically responding to a warning signal. Automatic and voluntary orienting are involved in the selection of information among multiple sensory inputs. Executive control describes a set of more complex operations that includes monitoring and resolving conflicts in order to control thoughts or behaviors. Converging evidence supports this theory of attention by showing that each function appears to be subserved by anatomically distinct networks in the brain and differentially innervated by various neuromodulatory systems. Although much research has been dedicated to understanding the functional separation of these networks in both healthy and disease states, the interaction and integration among these networks still remain unclear. In this study, we aimed to characterize possible behavioral interaction and integration in healthy adult volunteers using a revised attentional network test (ANT-R) with cue-target interval and cue validity manipulations. We found that whereas alerting improves overall response speed, it exerts negative influence on executive control under certain conditions. A valid orienting cue enhances but an invalid cue diminishes the ability of executive control to overcome conflict. The results support the hypothesis of functional integration and interaction of these brain networks.
doi:10.1016/j.bandc.2009.02.002
PMCID: PMC2674119  PMID: 19269079
attention; attentional networks; alerting; orienting; executive control
17.  p23/Tmp21 Differentially Targets the Rac-GAP β2-Chimaerin and Protein Kinase C via Their C1 Domains 
Molecular Biology of the Cell  2010;21(8):1398-1408.
The ER/Golgi protein p23/Tmp21 acts as a C1 domain-docking protein that mediates perinuclear translocation of β-chimaerin. C1 domains from PKC isozymes can also interact with p23/Tmp21. Our study highlights the relevance of C1 domains in protein-protein interactions in addition to their well-established lipid-binding properties.
The C1 domains in protein kinase C (PKC) isozymes and other signaling molecules are responsible for binding the lipid second messenger diacylglycerol and phorbol esters, and for mediating translocation to membranes. Previous studies revealed that the C1 domain in α- and β-chimaerins, diacylglycerol-regulated Rac-GAPs, interacts with the endoplasmic reticulum/Golgi protein p23/Tmp21. Here, we found that p23/Tmp21 acts as a C1 domain-docking protein that mediates perinuclear translocation of β2-chimaerin. Glu227 and Leu248 in the β2-chimaerin C1 domain are crucial for binding p23/Tmp21 and perinuclear targeting. Interestingly, isolated C1 domains from individual PKC isozymes differentially interact with p23/Tmp21. For PKCε, it interacts with p23/Tmp21 specifically via its C1b domain; however, this association is lost in response to phorbol esters. These results demonstrate that p23/Tmp21 acts as an anchor that distinctively modulates compartmentalization of C1 domain-containing proteins, and it plays an essential role in β2-chimaerin relocalization. Our study also highlights the relevance of C1 domains in protein–protein interactions in addition to their well-established lipid-binding properties.
doi:10.1091/mbc.E09-08-0735
PMCID: PMC2854097  PMID: 20164256
18.  Perception of Space by Multiple Intrinsic Frames of Reference 
PLoS ONE  2010;5(5):e10442.
It has been documented that when memorizing a physical space, the person's mental representation of that space is biased with distortion and segmentation. Two experiments reported here suggest that distortion and segmentation arise due to a hierarchical organization of the spatial representation. The spatial relations associated with salient landmarks are more strongly encoded and easier to recall than those associated with non-salient landmarks. In the presence of multiple salient landmarks, multiple intrinsic frames of reference are formed and spatial relations are anchored to each individual frame of reference. Multiple such representations may co-exist and interactively determine a person's spatial performance.
doi:10.1371/journal.pone.0010442
PMCID: PMC2862738  PMID: 20454617
19.  An Exploration of the Relations between External Representations and Working Memory 
PLoS ONE  2009;4(8):e6513.
It is commonly hypothesized that external representations serve as memory aids and improve task performance by means of expanding the limited capacity of working memory. However, very few studies have directly examined this memory aid hypothesis. By systematically manipulating how information is available externally versus internally in a sequential number comparison task, three experiments were designed to investigate the relation between external representations and working memory. The experimental results show that when the task requires information from both external representations and working memory, it is the interaction of information from the two sources that determines task performance. In particular, when information from the two sources does not match well, external representations hinder instead of enhance task performance. The study highlights the important role the coordination among different representations plays in distributed cognition. The general relations between external representations and working memory are discussed.
doi:10.1371/journal.pone.0006513
PMCID: PMC2714979  PMID: 19652712
20.  Phylogenetic analysis, structural evolution and functional divergence of the 12-oxo-phytodienoate acid reductase gene family in plants 
Background
The 12-oxo-phytodienoic acid reductases (OPRs) are enzymes that catalyze the reduction of double-bonds in α, β-unsaturated aldehydes or ketones and are part of the octadecanoid pathway that converts linolenic acid to jasmonic acid. In plants, OPRs belong to the old yellow enzyme family and form multigene families. Although discoveries about this family in Arabidopsis and other species have been reported in some studies, the evolution and function of multiple OPRs in plants are not clearly understood.
Results
A comparative genomic analysis was performed to investigate the phylogenetic relationship, structural evolution and functional divergence among OPR paralogues in plants. In total, 74 OPR genes were identified from 11 species representing the 6 major green plant lineages: green algae, mosses, lycophytes, gymnosperms, monocots and dicots. Phylogenetic analysis showed that seven well-conserved subfamilies exist in plants. All OPR genes from green algae were clustered into a single subfamily, while those from land plants fell into six other subfamilies, suggesting that the events leading to the expansion of the OPR family occurred in land plants. Further analysis revealed that lineage-specific expansion, especially by tandem duplication, contributed to the current OPR subfamilies in land plants after divergence from aquatic plants. Interestingly, exon/intron structure analysis showed that the gene structures of OPR paralogues exhibits diversity in intron number and length, while the intron positions and phase were highly conserved across different lineage species. These observations together with the phylogenetic tree revealed that successive single intron loss, as well as indels within introns, occurred during the process of structural evolution of OPR paralogues. Functional divergence analysis revealed that altered functional constraints have occurred at specific amino acid positions after diversification of the paralogues. Most notably, significant functional divergence was also found in all pairs, except for the II/IV, II/V and V/VI pairs. Strikingly, analysis of the site-specific profiles established by posterior probability revealed that the positive-selection sites and/or critical amino acid residues for functional divergence are mainly distributed in α-helices and substrate binding loop (SBL), indicating the functional importance of these regions for this protein family.
Conclusion
This study highlights the molecular evolution of the OPR gene family in all plant lineages and indicates critical amino acid residues likely relevant for the distinct functional properties of the paralogues. Further experimental verification of these findings may provide valuable information on the OPRs' biochemical and physiological functions.
doi:10.1186/1471-2148-9-90
PMCID: PMC2688005  PMID: 19416520
21.  Searching for the Majority: Algorithms of Voluntary Control 
PLoS ONE  2008;3(10):e3522.
Voluntary control of information processing is crucial to allocate resources and prioritize the processes that are most important under a given situation; the algorithms underlying such control, however, are often not clear. We investigated possible algorithms of control for the performance of the majority function, in which participants searched for and identified one of two alternative categories (left or right pointing arrows) as composing the majority in each stimulus set. We manipulated the amount (set size of 1, 3, and 5) and content (ratio of left and right pointing arrows within a set) of the inputs to test competing hypotheses regarding mental operations for information processing. Using a novel measure based on computational load, we found that reaction time was best predicted by a grouping search algorithm as compared to alternative algorithms (i.e., exhaustive or self-terminating search). The grouping search algorithm involves sampling and resampling of the inputs before a decision is reached. These findings highlight the importance of investigating the implications of voluntary control via algorithms of mental operations.
doi:10.1371/journal.pone.0003522
PMCID: PMC2567037  PMID: 18949039
22.  Downregulation of Rap1GAP Contributes to Ras Transformation▿  
Molecular and Cellular Biology  2007;27(19):6647-6658.
Although abundant in well-differentiated rat thyroid cells, Rap1GAP expression was extinguished in a subset of human thyroid tumor-derived cell lines. Intriguingly, Rap1GAP was downregulated selectively in tumor cell lines that had acquired a mesenchymal morphology. Restoring Rap1GAP expression to these cells inhibited cell migration and invasion, effects that were correlated with the inhibition of Rap1 and Rac1 activity. The reexpression of Rap1GAP also inhibited DNA synthesis and anchorage-independent proliferation. Conversely, eliminating Rap1GAP expression in rat thyroid cells induced a transient increase in cell number. Strikingly, Rap1GAP expression was abolished by Ras transformation. The downregulation of Rap1GAP by Ras required the activation of the Raf/MEK/extracellular signal-regulated kinase cascade and was correlated with the induction of mesenchymal morphology and migratory behavior. Remarkably, the acute expression of oncogenic Ras was sufficient to downregulate Rap1GAP expression in rat thyroid cells, identifying Rap1GAP as a novel target of oncogenic Ras. Collectively, these data implicate Rap1GAP as a putative tumor/invasion suppressor in the thyroid. In support of that notion, Rap1GAP was highly expressed in normal human thyroid cells and downregulated in primary thyroid tumors.
doi:10.1128/MCB.00155-07
PMCID: PMC2099240  PMID: 17646383
23.  A Subgroup of First-Degree Relatives of Crohn's Disease Patients Shows a Profile of Inflammatory Markers in the Blood Which Is More Typical of Crohn's Disease Patients Than of Normal Individuals 
Mediators of Inflammation  2006;2006(2):74785.
Introduction. Family member with IBD is the greatest risk factor for developing the disease. The hematological profile of first-degree relatives (FDRs) of Crohn's disease (CD) patients was studied in order to identify healthy FDRs at risk to develop disease. Materials and methods. Thirty CD patients, 90 FDRs, and 28 non-related individuals (controls) were enrolled. Hematological profile and C-reactive protein were determined. Results. All hematological parameters were significantly different in CD patients compared to controls, with significantly higher levels of CRP, WBC, PMN, MONO, and PLT and lower Hb and lymphocyte count. The hematological profile of FDRs showed values between the controls and CD patients with ten FDRs that their parameters matched those of CD patients and significantly different from other FDRs. This group was defined as high-risk relatives (HRRs). Conclusions. Analysis of the hematological profile and CRP level might be proven as a fast, reliable, and less money-consuming tool to identify FDRs with a probable increased risk to develop the disease.
doi:10.1155/MI/2006/74785
PMCID: PMC1592587  PMID: 16883067

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