CPT Evaluation of Liquefaction Potential Using Neural Networks

The increasing popularity of the cone penetration test (CPT) for site investigations has led to several methods for predicting liquefaction potential from CPT data. This paper describes a feed-forward neural network model trained by back-propagation for predicting liquefaction potential. The model requires the following seven input variables: cone resistance, total vertical stress, effective vertical stress, earthquake magnitude, maximum horizontal acceleration at ground surface, the mean grain size D50, and the seismic shear-stress ratio. A total of ninety-six data sets from different sites around the world were used for training, and eighty-two data sets were used for testing and validating the neural network model. The model gave an overall success rate of 96% for correctly predicting the liquefaction potential

Effect of Multimeric Structure of CaMKII in the GluN2B-Mediated Modulation of Kinetic Parameters of ATP

<div><p>Interaction of GluN2B subunit of N-methyl-D-aspartate receptor with calcium/calmodulin dependent protein kinase II (CaMKII) is critical for the induction of long term potentiation at hippocampal CA3-CA1 synapses. We have previously reported that CaMKII binding to GluN2B increases its affinity but abolishes the cooperativity for ATP. In the present study, we demonstrate that the reduction in S_0.5 for ATP of an individual CaMKII subunit seems to be directly induced by the binding of GluN2B to the same subunit, while any GluN2B induced effects on the cooperativity and maximal velocity would additionally require the CaMKII holoenzyme structure. We measured the apparent kinetic parameters for ATP using an association domain truncated monomeric CaMKII and a heteromultimeric CaMKII (having subunits that are either GluN2B binding defective or ATP binding defective), in the presence of GluN2A or GluN2B substrates. The S_0.5 value for ATP of monomeric CaMKII is reduced ∼ 3 fold by the presence of GluN2B suggesting that the induced change in affinity for ATP is independent of the holoenzyme structure. The heteromultimeric mutant of CaMKII, did not exhibit cooperativity of ATP binding probably because of the interspersing of ATP binding defective subunits in the holoenzyme. In contrast to the wild type holoenzyme, presence of GluN2B increased the V_max of monomeric CaMKII which resulted in an approximately 4.0 fold increase in the apparent catalytic constant (V_max/S_0.5) as compared to GluN2A. The kinetic parameter values of the heteromultimeric CaMKII for ATP, on the other hand, did not show any significant difference between the phosphorylation of GluN2B and GluN2A suggesting that modulation requires binding of GluN2B to the same subunit. Overall, our present study provides insights into the role of multimeric structure of CaMKII in GluN2B-mediated regulation.</p> </div

GST-pull down assay shows that α-I205K-CaMKII and β-K43R-CaMKII can form heteromultimers.

<p>The mutants, α-I205K-CaMKII and β-K43R-CaMKII, when expressed from a single vector, form heteromultimers and are pulled down by GST-GluN2B. <b>A: Western blot of (α-I205K)-(β-K43R)-CaMKII expressed in insect cell line.</b> The heteromeric CaMKII was prepared by coexpressing GluN2B binding defective α-subunits (I205K) with β-subunit defective in nucleotide binding (K43R) using pFastBac^TMDual vector. Both the CaMKII mutants were His-tagged at their N-terminii. Lane 2, 3 and 5: Molecular weight marker; Lane 1: Lysate (50 µg) expressing heteromer probed with anti-α-CaMKII antibody; Lane 4: Lysate (50 µg) expressing heteromer probed with anti-β-CaMKII antibody; Lane 6: Lysate (50 µg) expressing heteromer probed with anti-(poly) His antibody. The arrows indicate the positions of α and β subunits in each lane. <b>B: Heteromeric CaMKII binds specifically to GST-GluN2B.</b> Western blot following GST pull down assay of the heteromeric CaMKII mutant is shown. GST-Pull down assays were done with crude cell lysates of fusion proteins and heteromeric CaMKII. Upper panel was probed with anti-(poly) His antibody and lower panel was probed with anti-GST antibody. Lane 1: Pull down with GST-GluN2A; Lane 2: Pull down with GST-GluN2B. Data represents 4 experiments. <b>C: GluN2B binding of heteromeric CaMKII is calcium dependent.</b> Western blot following GST pull down assay of the heteromeric CaMKII mutant with GST- GluN2B is shown. GST-Pull down assays were done with crude cell lysates of fusion proteins and heteromeric CaMKII. Upper panel was probed with anti-(poly) His Antibody and lower panel was probed with anti- GST antibody. Lane 1: Pull down in presence of Ca²⁺; Lane 2: Pull down in the absence of Ca²⁺. Data represents 3 experiments.</p

Kinetic parameters of WT, Monomeric and Heteromultimeric CaMKII for ATP.

<p>The ATP kinetic parameters of WT-CaMKII, Δ317-α-CaMKII and heteromeric (α-I205K)-(β-K43R) CaMKII are given. The quantity of CaMKII used for the assays was: WT-CaMKII-0.01–0.017 µg; Monomeric Δ317-α-CaMKII- (0.15 µg); Heteromeric (α-I205K)-(β-K43R) CaMKII-1.9 µg. For heteromeric CaMKII assay, saturating concentrations of purified preparations of GST-GluN2A (6.5 µM) and GST-GluN2B (9.4 µM) were used. For the rest of the assays saturating concentrations of fusion proteins in bacterial lysates were used. p values were calculated in comparison with corresponding GluN2A data in each set of experiments. p<0.05 was considered significant which are indicated with asterisk (*). Representative data used for estimation of kinetic parameters is shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0045064#pone.0045064.s001" target="_blank">Fig. S1</a>.</p

Prenatal drug exposure to illicit drugs alters working memory-related brain activity and underlying network properties in adolescence

The persistence of effects of prenatal drug exposure (PDE) on brain functioning during adolescence is poorly understood. We explored neural activation to a visuospatial working memory (VSWM) versus a control task using functional magnetic resonance imaging (fMRI) in adolescents with PDE and a community comparison group (CC) of non-exposed adolescents. We applied graph theory metrics to resting state data using a network of nodes derived from the VSWM task activation map to further explore connectivity underlying WM functioning. Participants (ages 12-15 years) included 47 adolescents (27 PDE and 20 CC). All analyses controlled for potentially confounding differences in birth characteristics and postnatal environment. Significant group by task differences in brain activation emerged in the left middle frontal gyrus (BA 6) with the CC group, but not the PDE group, activating this region during VSWM. The PDE group deactivated the culmen, whereas the CC group activated it during the VSWM task. The CC group demonstrated a significant relation between reaction time and culmen activation, not present in the PDE group. The network analysis underlying VSWM performance showed that PDE group had lower global efficiency than the CC group and a trend level reduction in local efficiency. The network node corresponding to the BA 6 group by task interaction showed reduced nodal efficiency and fewer direct connections to other nodes in the network. These results suggest that adolescence reveals altered neural functioning related to response planning that may reflect less efficient network functioning in youth with PDE

Influence of a mutation in the ATP-binding region of Ca<SUP>2+</SUP>/calmodulindependent protein kinase II on its interaction with peptide substrates

CaMKII (Ca<SUP>2+</SUP>/calmodulin-dependent protein kinase II) is expressed in high concentrations in the brain and is found enriched in the postsynaptic densities. The enzyme is activated by the binding of calmodulin to the autoregulatory domain in the presence of high levels of intracellular Ca<SUP>2+</SUP>, which causes removal of auto-inhibition from the N-terminal catalytic domain. Knowledge of the 3D (three-dimensional) structure of this enzyme at atomic resolution is restricted to the association domain, a region at the extreme C-terminus. The catalytic domain of CaMKII shares high sequence similarity with CaMKI. The 3D structure of the catalytic core of CaMKI comprises ATP-and substrate-binding regions in a cleft between two distinct lobes, similar to the structures of all protein kinases solved to date. Mutation of Glu-60, a residue in the ATP-binding region of CaMKII, to glycine exerts different effects on phosphorylation of two peptide substrates, syntide and NR2B (N-methyl-D-aspartate receptor subunit 2B) 17-mer. Although the mutation caused increases in the K<SUB>m</SUB> values for phosphorylation for both the peptide substrates, the effect on the k<SUB>cat</SUB> values for each was different. The kcat value decreased in the case of syntide, whereas it increased in the case of the NR2B peptide as a result of the mutation. This resulted in a significant decrease in the apparent k<SUB>cat</SUB>/K<SUB>m</SUB> value for syntide, but the change was minimal for the NR2B peptide. These results indicate that different catalytic mechanisms are employed by the kinase for the two peptides. Molecular modelling suggests structural changes are likely to occur at the peptide-binding pocket in the active state of the enzyme as a consequence of the Glu-60Gly mutation