MoRFpred, a computational tool for sequence-based prediction and characterization of short disorder-to-order transitioning binding regions in proteins

Motivation: Molecular recognition features (MoRFs) are short binding regions located within longer intrinsically disordered regions that bind to protein partners via disorder-to-order transitions. MoRFs are implicated in important processes including signaling and regulation. However, only a limited number of experimentally validated MoRFs is known, which motivates development of computational methods that predict MoRFs from protein chains.

Results: We introduce a new MoRF predictor, MoRFpred, which identifies all MoRF types (α, β, coil and complex). We develop a comprehensive dataset of annotated MoRFs to build and empirically compare our method. MoRFpred utilizes a novel design in which annotations generated by sequence alignment are fused with predictions generated by a Support Vector Machine (SVM), which uses a custom designed set of sequence-derived features. The features provide information about evolutionary profiles, selected physiochemical properties of amino acids, and predicted disorder, solvent accessibility and B-factors. Empirical evaluation on several datasets shows that MoRFpred outperforms related methods: α-MoRF-Pred that predicts α-MoRFs and ANCHOR which finds disordered regions that become ordered when bound to a globular partner. We show that our predicted (new) MoRF regions have non-random sequence similarity with native MoRFs. We use this observation along with the fact that predictions with higher probability are more accurate to identify putative MoRF regions. We also identify a few sequence-derived hallmarks of MoRFs. They are characterized by dips in the disorder predictions and higher hydrophobicity and stability when compared to adjacent (in the chain) residues.

Availability:http://biomine.ece.ualberta.ca/MoRFpred/; http://biomine.ece.ualberta.ca/MoRFpred/Supplement.pdf

Contact:lkurgan@ece.ualberta.ca

Supplementary information:Supplementary data are available at Bioinformatics online.

The structural and functional signatures of proteins that undergo multiple events of post-translational modification

The structural, functional, and mechanistic characterization of several types of post-translational modifications (PTMs) is well-documented. PTMs, however, may interact or interfere with one another when regulating protein function. Yet, characterization of the structural and functional signatures of their crosstalk has been hindered by the scarcity of data. To this end, we developed a unified sequence-based predictor of 23 types of PTM sites that, we believe, is a useful tool in guiding biological experiments and data interpretation. We then used experimentally determined and predicted PTM sites to investigate two particular cases of potential PTM crosstalk in eukaryotes. First, we identified proteins statistically enriched in multiple types of PTM sites and found that they show preferences toward intrinsically disordered regions as well as functional roles in transcriptional, posttranscriptional, and developmental processes. Second, we observed that target sites modified by more than one type of PTM, referred to as shared PTM sites, show even stronger preferences toward disordered regions than their single-PTM counterparts; we explain this by the need for these regions to accommodate multiple partners. Finally, we investigated the influence of single and shared PTMs on differential regulation of protein-protein interactions. We provide evidence that molecular recognition features (MoRFs) show significant preferences for PTM sites, particularly shared PTM sites, implicating PTMs in the modulation of this specific type of macromolecular recognition. We conclude that intrinsic disorder is a strong structural prerequisite for complex PTM-based regulation, particularly in context-dependent protein-protein interactions related to transcriptional and developmental processes.

AVAILABILITY

www.modpred.org.

High-efficiency broadband meta-hologram with polarization-controlled dual images

Holograms, the optical devices to reconstruct predesigned images, show many applications in our daily life. However, applications of hologram are still limited by the constituent materials and therefore their working range is trapped at a particular electromagnetic region. In recent years, the metasurfaces, an array of subwavelength antenna with varying sizes, show the abilities to manipulate the phase of incident electromagnetic wave from visible to microwave frequencies. Here, we present a reflective-type and high-efficiency meta-hologram fabricated by metasurface for visible wavelength. Using gold cross nanoantennas as building blocks to construct our meta-hologram devices with thickness ∼ λ/4, the reconstructed images of meta-hologram show polarization-controlled dual images with high contrast, functioning for both coherent and incoherent light sources within a broad spectral range and under a wide range of incidence angles. The flexibility demonstrated here for our meta-hologram paves the road to a wide range of applications related to holographic images at arbitrary electromagnetic wave region.

Exploring the binding diversity of intrinsically disordered proteins involved in one-to-many binding

Molecular recognition features (MoRFs) are intrinsically disordered protein regions that bind to partners via disorder-to-order transitions. In one-to-many binding, a single MoRF binds to two or more different partners individually. MoRF-based one-to-many protein-protein interaction (PPI) examples were collected from the Protein Data Bank, yielding 23 MoRFs bound to 2-9 partners, with all pairs of same-MoRF partners having less than 25% sequence identity. Of these, 8 MoRFs were bound to 2-9 partners having completely different folds, whereas 15 MoRFs were bound to 2-5 partners having the same folds but with low sequence identities. For both types of partner variation, backbone and side chain torsion angle rotations were used to bring about the conformational changes needed to enable close fits between a single MoRF and distinct partners. Alternative splicing events (ASEs) and posttranslational modifications (PTMs) were also found to contribute to distinct partner binding. Because ASEs and PTMs both commonly occur in disordered regions, and because both ASEs and PTMs are often tissue-specific, these data suggest that MoRFs, ASEs, and PTMs may collaborate to alter PPI networks in different cell types. These data enlarge the set of carefully studied MoRFs that use inherent flexibility and that also use ASE-based and/or PTM-based surface modifications to enable the same disordered segment to selectively associate with two or more partners. The small number of residues involved in MoRFs and in their modifications by ASEs or PTMs may simplify the evolvability of signaling network diversity.

Motor equivalent control of the center of mass in response to support surface perturbations

To claim that the center of mass (CM) of the body is a controlled variable of the postural system is difficult to verify experimentally. In this report, a new variant of the method of the uncontrolled manifold (UCM) hypothesis was used to evaluate CM control in response to an abrupt surface perturbation during stance. Subjects stood upright on a support surface that was displaced in the posterior direction. Support surface translations between 0.03 and 0.12 m, each lasting for 275 ms, were presented randomly. The UCM corresponding to all possible combinations of joints that are equivalent with respect to producing the average pre-perturbation anterior-posterior position of the center of mass (CM(AP)) were linearly estimated for each trial. At each point in time thereafter, the difference between the current joint configuration and the average pre-perturbation joint configuration was computed. This joint difference vector was then projected onto the pre-perturbation UCM as a measure of motor equivalence, and onto its complementary subspace, which represents joint combinations that lead to a different CM(AP) position. A similar analysis was performed related to control of the trunk's spatial orientation. The extent to which the joint velocity vector acted to stabilize the CM(AP) position was also examined. Excursions of the hip and ankle joints both increased linearly with perturbation magnitude. The configuration of joints at each instance during the perturbation differed from the mean configuration prior to the perturbation, as evidenced by the joint difference vector. Most of this joint difference vector was consistent, however, with the average pre-perturbation CM(AP) position rather than leading to a different CM(AP )position. This was not the case, however, when performing this analysis with respect to the UCM corresponding to the control of the pre-perturbation trunk orientation. The projection of the instantaneous joint velocity vector also was found to lie primarily in the UCM corresponding to the pre-perturbation CM(AP) position, indicating that joint motion was damped in directions leading to a change away from the pre-perturbation CM(AP) position. These results provide quantitative support for the argument that the CM position is a planned variable of the postural system and that its control is achieved through selective, motor equivalent changes in the joint configuration in response to support surface perturbations. The results suggest that the nervous system accomplishes postural control by a control strategy that considers all DOFs. This strategy presumably resists combinations of DOFs that affect the stability of important task-relevant variables (CM(AP) position) while, to a large extent, freeing from control combinations of those DOFs that have no effect on the task-relevant variables (Schöner in Ecol Psychol 8:291-314, 1995).

A dynamic connection between centromeres and ND10 proteins

ND10, otherwise known as nuclear dots, PML nuclear bodies or PODs, are punctate foci in interphase nuclei that contain several cellular proteins. The functions of ND10 have not been well defined, but they are sensitive to external stimuli such as stress and virus infection, and they are disrupted in malignant promyelocytic leukaemia cells. Herpes simplex virus type 1 regulatory protein Vmw110 induces the proteasome-dependent degradation of ND10 component proteins PML and Sp100, particularly the species of these proteins which are covalently conjugated to the ubiquitin-like protein SUMO-1. We have recently reported that Vmw110 also induces the degradation of centromere protein CENP-C with consequent disruption of centromere structure. These observations led us to examine whether there were hitherto undetected connections between ND10 and centromeres. In this paper we report that hDaxx and HP1 (which have been shown to interact with CENP-C and Sp100, respectively) are present in a proportion of both ND10 and interphase centromeres. Furthermore, the proteasome inhibitor MG132 induced an association between centromeres and ND10 proteins PML and Sp100 in a significant number of cells in the G(2) phase of the cell cycle. These results imply that there is a dynamic, cell cycle regulated connection between centromeres and ND10 proteins which can be stabilised by inhibition of proteasome-mediated proteolysis.

Proportion of solvent-exposed amino acids in a protein and rate of protein evolution

Translational selection, including gene expression, protein abundance, and codon usage bias, has been suggested as the single dominant determinant of protein evolutionary rate in yeast. Here, we show that protein structure is also an important determinant. Buried residues, which are responsible for maintaining protein structure or are located on a stable interaction surface between 2 subunits, are usually under stronger evolutionary constraints than solvent-exposed residues. Our partial correlation analysis shows that, when whole proteins are included, the variance of evolutionary rate explained by the proportion of solvent-exposed residues (P(exposed)) can reach two-thirds of that explained by translational selection, indicating that P(exposed) is the most important determinant of protein evolutionary rate next only to translational selection. Our result suggests that proteins with many residues under selective constraint (e.g., maintaining structure or intermolecular interaction) tend to evolve slowly, supporting the "fitness (functional) density" hypothesis.

Galectin-3 promotes Aβ oligomerization and Aβ toxicity in a mouse model of Alzheimer's disease

Amyloid-β (Aβ) oligomers largely initiate the cascade underlying the pathology of Alzheimer's disease (AD). Galectin-3 (Gal-3), which is a member of the galectin protein family, promotes inflammatory responses and enhances the homotypic aggregation of cancer cells. Here, we examined the role and action mechanism of Gal-3 in Aβ oligomerization and Aβ toxicities. Wild-type (WT) and Gal-3-knockout (KO) mice, APP/PS1;WT mice, APP/PS1;Gal-3^+/- mice and brain tissues from normal subjects and AD patients were used. We found that Aβ oligomerization is reduced in Gal-3 KO mice injected with Aβ, whereas overexpression of Gal-3 enhances Aβ oligomerization in the hippocampi of Aβ-injected mice. Gal-3 expression shows an age-dependent increase that parallels endogenous Aβ oligomerization in APP/PS1 mice. Moreover, Aβ oligomerization, Iba1 expression, GFAP expression and amyloid plaque accumulation are reduced in APP/PS1;Gal-3^+/- mice compared with APP/PS1;WT mice. APP/PS1;Gal-3^+/- mice also show better acquisition and retention performance compared to APP/PS1;WT mice. In studying the mechanism underlying Gal-3-promoted Aβ oligomerization, we found that Gal-3 primarily co-localizes with Iba1, and that microglia-secreted Gal-3 directly interacts with Aβ. Gal-3 also interacts with triggering receptor expressed on myeloid cells-2, which then mediates the ability of Gal-3 to activate microglia for further Gal-3 expression. Immunohistochemical analyses show that the distribution of Gal-3 overlaps with that of endogenous Aβ in APP/PS1 mice and partially overlaps with that of amyloid plaque. Moreover, the expression of the Aβ-degrading enzyme, neprilysin, is increased in Gal-3 KO mice and this is associated with enhanced integrin-mediated signaling. Consistently, Gal-3 expression is also increased in the frontal lobe of AD patients, in parallel with Aβ oligomerization. Because Gal-3 expression is dramatically increased as early as 3 months of age in APP/PS1 mice and anti-Aβ oligomerization is believed to protect against Aβ toxicity, Gal-3 could be considered a novel therapeutic target in efforts to combat AD.

Enrichment enhances the expression of sgk, a glucocorticoid-induced gene, and facilitates spatial learning through glutamate AMPA receptor mediation

We have previously demonstrated that the serum and glucocorticoid-inducible kinase (sgk) gene plays a causal role in facilitating memory performance in rats. Environment enrichment is known to facilitate spatial learning. We therefore examined the effect of enrichment on sgk expression. We also examined the role of sgk in spatial and nonspatial learning and the regulation of sgk expression by activation of different glutamate receptors. Both real-time polymerase chain reaction and Western blot analyses revealed that enrichment training preferentially increased sgk mRNA and protein levels in the hippocampus. Transfection of sgk mutant DNA to the hippocampal CA1 area markedly impaired spatial learning, fear-conditioning learning and novel object-recognition learning in rats, but enrichment training effectively reversed these learning deficits. Meanwhile, S422A mutant DNA transfection prevented enrichment-induced spatial learning facilitation. In studying glutamate receptor regulation of sgk expression, we found that blockade of N-methyl-d-aspartate (NMDA) receptors in general, and the NR2B subunit in particular both effectively blocked enrichment-induced spatial learning facilitation, but they did not block enrichment-induced sgk expression. Upon various glutamate agonist infusions, only alpha-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA) increased sgk mRNA levels significantly in the hippocampus. Furthermore, blockade of AMPA receptors effectively blocked both enrichment-induced spatial learning facilitation and sgk expression. These results indicate that there is a dissociation between NMDA receptor activation and sgk expression. Enrichment enhanced spatial learning through both NMDA and AMPA receptor activation, whereas enrichment-induced sgk expression is specifically mediated through AMPA receptors. These results suggest that sgk could serve as a novel molecular mechanism, in addition to the NMDA receptor NR2B, underlying enrichment-induced learning facilitation.

Expression of leukemia inhibitory factor and its receptor in preimplantation embryos

OBJECTIVE

To examine the expression of leukemia inhibitory factor (LIF) and its receptor (LIF-R) transcripts in human and murine preimplantation embryos.

DESIGN

Prospective study.

SETTING

University medical center.

PATIENT(S)

Human oocytes were obtained from patients undergoing IVF treatment. Two-cell murine embryos were obtained from ICR strain mice.

INTERVENTION(S)

Second-day intracytoplasmic sperm injection procedures were performed on oocytes that failed to be fertilized by IVF. Embryos were cultured to various stages and collected for study.

MAIN OUTCOME MEASURE(S)

The transcript levels of LIF and LIF-R in these embryos were examined and semiquantitated using single-cell reverse transcription-polymerase chain reaction methodology.

RESULT(S)

Leukemia inhibitory factor and LIF-R transcripts were detectable in most human preimplantation embryos (30 of 34 and 31 of 34 embryos showed LIF and LIF-R messenger RNA, respectively). There was a trend toward decreased expression of both transcripts in embryos at the four-cell stage and in embryos in which growth had been arrested for 24-48 hours. The expression of LIF and LIF-R genes in murine embryos was inconsistent.

CONCLUSION(S)

Preimplantation human embryos express LIF and LIF-R messenger RNA. It is suggested that LIF may be able to affect embryo development through its action at stages before implantation in an autocrine or paracrine manner.

Improving protein order-disorder classification using charge-hydropathy plots

Background

The earliest whole protein order/disorder predictor (Uversky et al., Proteins, 41: 415-427 (2000)), herein called the charge-hydropathy (C-H) plot, was originally developed using the Kyte-Doolittle (1982) hydropathy scale (Kyte & Doolittle., J. Mol. Biol, 157: 105-132(1982)). Here the goal is to determine whether the performance of the C-H plot in separating structured and disordered proteins can be improved by using an alternative hydropathy scale.

Results

Using the performance of the CH-plot as the metric, we compared 19 alternative hydropathy scales, with the finding that the Guy (1985) hydropathy scale (Guy, Biophys. J, 47:61-70(1985)) was the best of the tested hydropathy scales for separating large collections structured proteins and intrinsically disordered proteins (IDPs) on the C-H plot. Next, we developed a new scale, named IDP-Hydropathy, which further improves the discrimination between structured proteins and IDPs. Applying the C-H plot to a dataset containing 109 IDPs and 563 non-homologous fully structured proteins, the Kyte-Doolittle (1982) hydropathy scale, the Guy (1985) hydropathy scale, and the IDP-Hydropathy scale gave balanced two-state classification accuracies of 79%, 84%, and 90%, respectively, indicating a very substantial overall improvement is obtained by using different hydropathy scales. A correlation study shows that IDP-Hydropathy is strongly correlated with other hydropathy scales, thus suggesting that IDP-Hydropathy probably has only minor contributions from amino acid properties other than hydropathy.

Conclusion

We suggest that IDP-Hydropathy would likely be the best scale to use for any type of algorithm developed to predict protein disorder.

A comparative study on cannabidiol-induced apoptosis in murine thymocytes and EL-4 thymoma cells

It has been shown that leukemia and glioma cells are sensitive to cannabidiol (CBD)-induced apoptosis, whereas primary monocytes and glia cells are relatively insensitive. In the current study, the cellular events and sensitivity to CBD-induced apoptosis between murine thymocytes and EL-4 thymoma cells were compared. Cannabidiol markedly induced apoptosis in a time- and concentration-related manner in both cells. The efficacy of CBD to induce apoptosis was comparable between the 2 types of T cells, whereas CBD induced apoptosis in thymocytes with a slightly greater potency than in EL4 cells. Time-course analyses revealed CBD-mediated apoptosis occurred earlier in EL-4 cells than that in thymocytes. An increased level of cellular reactive oxygen species (ROS) was detected in both cells with the peak response at 2 h post CBD treatment. Concordantly, CBD triggered a gradual diminishment in the cellular thiols. The presence of N-acetyl-L-cysteine (NAC), a precursor of glutathione, markedly attenuated the induction of apoptosis, and restored the diminished levels of cellular thiols. The results demonstrated that both thymocytes and EL-4 thymoma cells were susceptible to CBD-induced apoptosis and that ROS played a critical role in the apoptosis induction.

Thermal dependence of nanofluidic energy conversion by reverse electrodialysis

The thermal dependence of salinity-gradient-driven energy conversion by reverse electrodialysis using a mesoporous silica thin film with pores ca. 2-3 nm in diameter was studied in a temperature range of 293-333 K. As the temperature increases, the surface charge density of mesopores increases owing to an increase in the zeta potential of the pore walls, which in turn increases the concentration of counter-ions in the electrical double layer. The ion mobility also increases with increasing temperature owing to a decrease in the liquid viscosity. As a result, the temperature increase improves the ion conductance of mesopores both in the surface-charge-governed regime at low ion concentrations and in the bulk regime at high ion concentrations. However, further increases in temperature induce bubble nucleation. In particular, in highly concentrated salt solutions, hydrophobic patches appear on the pore surfaces because of the salting-out effect and mask the surface charge. The weakened polarity in mesopores allows more co-ions to enter them, decreasing the potential difference across the film, resulting in a serious deterioration of the energy conversion efficiency. The thermal dependence of the performance characteristics of mesoporous-silica-based nanofluidic devices was also evaluated.

Psychopathology and personality trait in subgroups of functional dyspepsia based on Rome III criteria

OBJECTIVES

Functional dyspepsia is a heterogeneous symptom complex that may be subdivided into postprandial distress syndrome and epigastric pain syndrome. We aimed to investigate differences among these subgroups in psychopathological factors and personality traits.

METHODS

We enrolled 187 consecutive outpatients (72.2% female patients, mean age 42.6 years) with functional dyspepsia based on the Rome III criteria. Patients were interviewed and evaluated by the Brief Symptom Rating Scale and the short-form Maudsley personality inventory for severity of psychopathology and personality traits. Multiple linear regression models were built for each psychopathological dimension and personality trait to assess the independent association with each subclass diagnosis of functional dyspepsia.

RESULTS

There was an overlap (n=64, 34.2%) between the patients diagnosed with epigastric pain syndrome (n=157, 84.0%) and those with postprandial distress syndrome (n=94, 50.3%). Patients with symptoms compatible with both syndromes were psychopathologically more severe than either subgroup without overlapping. Multiple linear regression analysis demonstrated that the diagnosis of postprandial distress syndrome was independently associated with higher scores in overall psychopathological stress, and specifically in somatization (P=0.034), depression (P=0.028), phobia (P=0.044), and additional symptoms (P<0.001). However, epigastric pain syndrome was not associated with psychopathology. Postprandial distress was univariately associated with neuroticism, but the association was insignificant in the multivariate analysis (P=0.136).

CONCLUSIONS

The Rome III subgroups of functional dyspepsia significantly overlap. Patients fulfilling criteria for both subgroups had symptoms that were psychopathologically more severe than those of patients without overlapping. Diagnosis of postprandial distress syndrome, but not epigastric pain syndrome, is independently associated with psychopathological factors.

Vertical split-ring resonator based anomalous beam steering with high extinction ratio

Metasurfaces created artificially with metal nanostructures that are patterned on surfaces of different media have shown to possess “unusual” abilities to manipulate light. Limited by nanofabrication difficulties, so far most reported works have been based on 2D metal structures. We have recently developed an advanced e-beam process that allowed for the deposition of 3D nanostructures, namely vertical split-ring resonators (VSRRs), which opens up another degree of freedom in the metasurface design. Here we explore the functionality of beam steering with phase modulation by tuning only the vertical dimension of the VSRRs and show that anomalous steering reflection of a wide range of angles can be accomplished with high extinction ratio using the finite-difference-time-domain simulation. We also demonstrate that metasurfaces made of 3D VSRRs can be made with roughly half of the footprint compared to that of 2D nano-rods, enabling high density integration of metal nanostructures.

Recurrent Intussusception: when Should Surgical Intervention be performed?

OBJECTIVE

To determine the optimal timing of surgery for recurrent intussusception.

METHODS

We retrospectively reviewed medical records of patients aged from 0 to 18 years old with diagnosis of intussusception in the Pediatric Department at Mackay Memorial Hospital between January 1995 and May 2010.

RESULTS

During the study period, there were 686 children (divided into three age groups: 367 < 2 years, 289 aged 2 to 5 years, 30 > 5 years) with diagnoses of intussusception. Eighty-five of the 686 patients had recurrent intussusception, of whom 56 had two, 16 had three, 11 had four, and 2 had five episodes. The recurrence rate after the first, second, third, and fourth barium enema reductions were 15.7%, 37.7%, 68.4%, and 100.0%, respectively. The incidence of recurrence and failure rate of barium enema reduction did not differ significantly among these three age groups. Surgery was performed in 177 children (146 during the first episode and 31 in recurrent cases). The probability of eventual surgery after first enema reduction was 21.8%, after the second 35.7%, and after the third 70.0%. Lead points were found in 15 children, and all of them were found during surgery for the first episode of intussusception.

CONCLUSION

The probability of recurrence was 100% after the fourth episode of intussusception in our study. After the third episode of intussusception, the probability of recurrence and eventual surgery were 68% and 70%, respectively. From this study, surgical intervention should be considered at the third episode of intussusception.

Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations

The significant work that has been invested toward understanding protein-protein interaction has not translated into significant advances in structure-based predictions. In particular redesigning protein surfaces to bind to unrelated receptors remains a challenge, partly due to receptor flexibility, which is often neglected in these efforts. In this work, we computationally graft the binding epitope of various small proteins obtained from the RCSB database to bind to barnase, lysozyme, and trypsin using a previously derived and validated algorithm. In an effort to probe the protein complexes in a realistic environment, all native and designer complexes were subjected to a total of nearly 400 ns of explicit-solvent molecular dynamics (MD) simulation. The MD data led to an unexpected observation: some of the designer complexes were highly unstable and decomposed during the trajectories. In contrast, the native and a number of designer complexes remained consistently stable. The unstable conformers provided us with a unique opportunity to define the structural and energetic factors that lead to unproductive protein-protein complexes. To that end we used free energy calculations following the MM-PBSA approach to determine the role of nonpolar effects, electrostatics and entropy in binding. Remarkably, we found that a majority of unstable complexes exhibited more favorable electrostatics than native or stable designer complexes, suggesting that favorable electrostatic interactions are not prerequisite for complex formation between proteins. However, nonpolar effects remained consistently more favorable in native and stable designer complexes reinforcing the importance of hydrophobic effects in protein-protein binding. While entropy systematically opposed binding in all cases, there was no observed trend in the entropy difference between native and designer complexes. A series of alanine scanning mutations of hot-spot residues at the interface of native and designer complexes showed less than optimal contacts of hot-spot residues with their surroundings in the unstable conformers, resulting in more favorable entropy for these complexes. Finally, disorder predictions revealed that secondary structures at the interface of unstable complexes exhibited greater disorder than the stable complexes.

CREB SUMOylation by the E3 ligase PIAS1 enhances spatial memory

cAMP-responsive element binding protein (CREB) phosphorylation and signaling plays an important role in long-term memory formation, but other posttranslational modifications of CREB are less known. Here, we found that CREB1Δ, the short isoform of CREB, could be sumoylated by the small ubiquitin-like modifier (SUMO) E3 ligase protein inhibitor of activated STAT1 (PIAS1) at Lys271 and Lys290 and PIAS1 SUMOylation of CREB1Δ increased the expression level of CREB1Δ. CREB1Δ could also be sumoylated by other PIAS family proteins, but not by the E3 ligases RanBP2 and Pc2 or by the E2 ligase Ubc9. Furthermore, water maze training increased the level of endogenous CREB SUMOylation in rat CA1 neurons determined by in vitro SUMOylation assay, but this effect was not observed in other brain areas. Moreover, transduction of Lenti-CREBWT to rat CA1 area facilitated, whereas transduction of Lenti-CREB double sumo-mutant (CREBK271RK290R) impaired, spatial learning and memory performance. Transduction of Lenti-CREBWT-SUMO1 fusion vector to rat CA1 area showed a more significant effect in enhancing spatial learning and memory and CREB SUMOylation. Lenti-CREBWT transduction increased, whereas Lenti-CREBK271RK290R transduction decreased, CREB DNA binding to the brain-derived neurotrophic factor (bdnf) promoter and decreased bdnf mRNA expression. Knock-down of PIAS1 expression in CA1 area by PIAS1 siRNA transfection impaired spatial learning and memory and decreased endogenous CREB SUMOylation. In addition, CREB SUMOylation was CREB phosphorylation dependent and lasted longer. Therefore, CREB phosphorylation may be responsible for signal transduction during the early phase of long-term memory formation, whereas CREB SUMOylation sustains long-term memory.

Proton pump inhibitor versus prokinetic therapy in patients with functional dyspepsia: is therapeutic response predicted by Rome III subgroups?

BACKGROUND

The comparative effectiveness of proton pump inhibitor versus prokinetic therapy in relieving the symptoms of patients with functional dyspepsia remains unknown. Whether the Rome III subgroups predict therapeutic response has not been investigated.

METHODS

This was an open-label, parallel randomized controlled trial. A total of 329 adult outpatients fulfilling the Rome III criteria for functional dyspepsia were randomly allocated to receive either lansoprazole 30 mg once daily (n = 166) or mosapride 5 mg thrice daily (n = 163) for 2 weeks. Enrolled patients were evaluated with the validated Hong Kong Index questionnaire for symptom severity at baseline and at the end of the trial. The primary outcome was symptom relief as defined by the Hong Kong Index, and the secondary outcome was decrease of symptom scores. Post-hoc multivariate logistic regression analysis was conducted to identify independent predictors for therapeutic response.

RESULTS

After 2-week therapy, 50.6% (84/166) and 47.85% (78/163) of the patients treated with lansoprazole and mosapride, respectively, achieved significant symptom relief (odds ratio 1.12, 95% confidence interval 0.72-1.72, p = 0.62). Differences in decreases of symptom scores between lansoprazole and mosapride receivers were also insignificant (-0.08, 95% confidence interval -1.25 to 1.09, p = 0.89). Therapeutic responses to either pharmacotherapy did not differ in the subgroup of patients fulfilling the criteria for epigastric pain syndrome (n = 256) or in those fulfilling the criteria for postprandial distress syndrome (n = 161). Multivariate logistic regression confirmed that the treatment allocation and Rome III subgroup were unrelated to treatment outcome.

CONCLUSIONS

The effectiveness of proton pump inhibitor therapy and that of prokinetic therapy in functional dyspepsia are not different, and cannot be predicted by Rome III subgroups (ClinicalTrials.gov number, NCT00663897).

Effects of the dietary phytoestrogen biochanin A on cell growth in the mammary carcinoma cell line MCF-7

Studies of the dietary phytoestrogen biochanin A on cell proliferation of the cultured estrogen responsive cells human breast carcinoma MCF-7 showed that biochanin A exhibits biphasic regulation on MCF-7 cells. At concentrations of less than 10 microg/mL, cells respond to biochanin A by increasing cell growth and de novo DNA synthesis. The addition of biochanin A at concentrations of greater than 30 microg/mL significantly inhibited cell growth and DNA synthesis in a dose-dependent fashion, resulting in an IC(50) value of 40 microg/mL. The reversibility of these inhibitory effects by biochanin A appears also to be concentration dependent. Cells previously treated with high concentrations (>60 microg/mL) of biochanin A did not regain normal growth after treatment ceased. Biochanin A was cytostatic at low concentrations (<40 microg/mL) and cytotoxic at higher concentrations. Upon exposure to 100 microg/mL of biochanin A, cell morphology was severely altered, cell volume decreased, and condensation of cell components was clearly noticeable. In addition, biochanin A damaged cell membranes by increasing membrane permeability. These results suggest possible molecular and cellular mechanisms of the action of dietary phytoestrogens on estrogen target cells.

Glutamate Stimulates Local Protein Synthesis in the Axons of Rat Cortical Neurons by Activating α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptors and Metabotropic Glutamate Receptors

Glutamate is the principal excitatory neurotransmitter in the mammalian CNS. By analyzing the metabolic incorporation of azidohomoalanine, a methionine analogue, in newly synthesized proteins, we find that glutamate treatments up-regulate protein translation not only in intact rat cortical neurons in culture but also in the axons emitting from cortical neurons before making synapses with target cells. The process by which glutamate stimulates local translation in axons begins with the binding of glutamate to the ionotropic AMPA receptors and metabotropic glutamate receptor 1 and members of group 2 metabotropic glutamate receptors on the plasma membrane. Subsequently, the activated mammalian target of rapamycin (mTOR) signaling pathway and the rise in Ca(2+), resulting from Ca(2+) influxes through calcium-permeable AMPA receptors, voltage-gated Ca(2+) channels, and transient receptor potential canonical channels, in axons stimulate the local translation machinery. For comparison, the enhancement effects of brain-derived neurotrophic factor (BDNF) on the local protein synthesis in cortical axons were also studied. The results indicate that Ca(2+) influxes via transient receptor potential canonical channels and activated the mTOR pathway in axons also mediate BDNF stimulation to local protein synthesis. However, glutamate- and BDNF-induced enhancements of translation in axons exhibit different kinetics. Moreover, Ca(2+) and mTOR signaling appear to play roles carrying different weights, respectively, in transducing glutamate- and BDNF-induced enhancements of axonal translation. Thus, our results indicate that exposure to transient increases of glutamate and more lasting increases of BDNF would stimulate local protein synthesis in migrating axons en route to their targets in the developing brain.

Different risks of symptomatic brain necrosis in NPC patients treated with different altered fractionated radiotherapy techniques

PURPOSE

To report our observation of excessive temporal lobe necrosis in nasopharyngeal carcinoma (NPC) patients treated with 160 cGy b.i.d. radiotherapy technique. During the same period, patients treated with 120 cGy b.i.d. have not shown a similar tendency. Our experience may be useful for designing unconventional radiotherapy regimens for NPC patients.

METHODS AND MATERIALS

During the period from October 1991 to January 1998, 81 M0, previously untreated NPC patients completed altered fractionated radiotherapy. Seventy patients were treated with the hyperfractionated technique, and 11 were treated using the accelerated-hyperfractionated scheme. Hyperfractionated radiotherapy was delivered using 120 cGy b.i.d. separated by 6-h intervals throughout the course. A minimum tumor dose of 8000 cGy was the standard dose over an 8-week period. With the accelerated-hyperfractionated scheme, 160 cGy was given twice daily, also with an interval of 6 h. The minimum tumor dose ranged between 6840 and 7640 cGy, with 7 of the 11 patients receiving 7000 cGy. The arrangement of portals was the same for both regimens. The follow-up period for patients alive was from 32 to 102 months with a median of 61 months for the hyperfractionated patients. For the accelerated-hyperfractionated group, it ranged from 67 to 82 months with a median of 72 months. No patient was lost to follow-up.

RESULTS

At the time of analysis, 49 of the 70 patients in the hyperfractionated group were alive. In the accelerated group, 8 of the 11 patients were alive. The estimated radiation dose to the temporal lobe for the hyperfractionated group was 6000-7440 cGy with a median of 7080 cGy. For the accelerated-hyperfractionated group, the dose range was 4480-6700 cGy with a median of 6400 cGy. Of the 70 patients treated with hyperfractionated radiotherapy, none developed symptomatic brain necrosis, despite the higher total dose to the temporal lobe in general. In contrast, 3 of the 11 (27%) patients irradiated using the accelerated-hyperfractionated regimen suffered from temporal lobe necrosis at 16, 19, and 40 months after completion of radiotherapy.

CONCLUSION

An excessive incidence of temporal lobe necrosis was noted when an accelerated-hyperfractionated regimen with 160 cGy b.i.d. was used in NPC patients with a median brain dose of 6400 cGy. There has been no such event in patients treated using a hyperfractionated regimen with 120 cGy and a median brain dose of 7000 cGy. The real causes of this discrepancy are not known. However, a high sensitivity of the human brain to a change in fraction size may play a role.

A three-dimensional flexible microprobe array for neural recording assembled through electrostatic actuation

We designed, fabricated and tested a novel three-dimensional flexible microprobe to record neural signals of a lateral giant nerve fiber of the escape circuit of an American crayfish. An electrostatic actuation folded planar probes into three-dimensional neural probes with arbitrary orientations for neuroscientific applications. A batch assembly based on electrostatic forces simplified the fabrication and was non-toxic. A novel fabrication for these three-dimensional flexible probes used SU-8 and Parylene technology. The mechanical strength of the neural probe was great enough to penetrate into a bio-gel. A flexible probe both decreased the micromotion and alleviated tissue encapsulation of the implant caused by chronic inflammation of tissue when an animal breathes or moves. The cortex consisted of six horizontal layers, and the neurons of the cortex were arranged in vertical structures; the three-dimensional microelectrode arrays were suitable to investigate the cooperative activity for neurons in horizontal separate layers and in vertical cortical columns. With this flexible probe we recorded neural signals of a lateral giant cell from an American crayfish. The response amplitude of action potentials was about 343 µV during 1 ms period; the average recorded data had a ratio of signal to noise as great as 30.22 ± 3.58 dB. The improved performance of this electrode made feasible the separation of neural signals according to their distinct shapes. The cytotoxicity indicated a satisfactory biocompatibility and non-toxicity of the flexible device fabricated in this work.

Mosapride as an adjunct to lansoprazole for symptom relief of reflux oesophagitis

WHAT IS ALREADY KNOWN ABOUT THIS SUBJECT Reflux oesophagitis is a common clinical disorder associated with significant morbidity. Proton pump inhibitors are the current pharmacotherapy of choice, but not all treated patients achieve symptom relief. Little is known about the efficacy of mosapride, a prokinetic agent which decreases episodes of gastro-oesophageal reflux, as an adjunct to proton pump inhibitors in improving the symptoms of reflux oesophagitis. WHAT THIS STUDY ADDS Mosapride was generally not more effective than placebo as an adjunct therapy to a standard dose of lansoprazole in decreasing the symptom burden of patients with reflux oesophagitis. However, in a subgroup with more severe symptoms, combination therapy with lansoprazole and mosapride was possibly superior to monotherapy with lansoprazole. AIMS To investigate if mosapride, a prokinetic agent, was an effective adjunct to acid suppression in improving the symptoms of reflux oesophagitis. METHODS Patients (n= 96) with reflux oesophagitis were randomly assigned to either mosapride (5 mg three times daily) or placebo for 4 weeks. Symptom severity was assessed by a validated questionnaire at enrolment, 4 and 8 weeks after medication. The primary outcome for the first 4 weeks was decrease in symptom scores. After a 3 day washout period, patients initially allocated to mosapride crossed over to placebo and vice versa for the next 4 weeks. The outcome of the second phase was maintenance of symptom control. All patients received lansoprazole (30 mg once daily) throughout study. RESULTS The decreased symptom score after 4 weeks of treatment with lansoprazole and mosapride (n= 50) was 13.42 +/- 1.16 (mean +/- SEM), similar to that of lansoprazole plus placebo (10.85 +/- 1.03, n= 46), with an insignificant difference of 2.57 (95% CI -0.53, 5.67, P= 0.103). However, a sub-group analysis for patients with pre-treatment scores of >18 points (n= 48) revealed that lansoprazole plus mosapride achieved a greater reduction of symptom score than lansoprazole plus placebo (18.22 +/- 1.91 vs. 12.88 +/- 1.65; mean difference of 5.34, 95% CI 0.28, 10.40, P= 0.039). In the second phase, there was no difference between lansoprazole with mosapride or placebo in maintaining symptom control (39/44 or 86.64% vs. 41/50 or 82%, P= 0.401). Subgroup analysis for those with substantial residual symptoms revealed similar results. CONCLUSION Compared with placebo, mosapride generally does not provide additional benefit to a standard dose of lansoprazole in patients with reflux oesophagitis, except possibly in the subgroup of severely symptomatic patients.