Smart network solutions in an amoeboid organism

We present evidence that the giant amoeboid organism, the true slime mold, constructs a network appropriate for maximizing nutrient uptake. The body of the plasmodium of Physarum polycephalum contains a network of tubular elements by means of which nutrients and chemical signals circulate through the organism. When food pellets were presented at different points on the plasmodium it accumulated at each pellet with a few tubes connecting the plasmodial concentrations. The geometry of the network depended on the positions of the food sources. Statistical analysis showed that the network geometry met the multiple requirements of a smart network: short total length of tubes, close connections among all the branches (a small number of transit food-sites between any two food-sites) and tolerance of accidental disconnection of the tubes. These findings indicate that the plasmodium can achieve a better solution to the problem of network configuration than is provided by the shortest connection of Steiner's minimum tree.     

SynArfGEF is a guanine nucleotide exchange factor for Arf6 and localizes preferentially at post-synaptic specializations of inhibitory synapses

SynArfGEF, also known as BRAG3 or IQSEC3, is a member of the brefeldin A-resistant Arf-GEF/IQSEC family and was originally identified by screening for mRNA species associated with the post-synaptic density fraction. In this study, we demonstrate that synArfGEF activates Arf6, using Arf pull down and transferrin incorporation assays. Immunohistochemical analysis reveals that synArfGEF is present in somata and dendrites as puncta in close association with inhibitory synapses, whereas immunoelectron microscopic analysis reveals that synArfGEF localizes preferentially at post-synaptic specializations of symmetric synapses. Using yeast two-hybrid and pull down assays, we show that synArfGEF is able to bind utrophin/dystrophin and S-SCAM/MAGI-2 scaffolding proteins that localize at inhibitory synapses. Double immunostaining reveals that synArfGEF co-localizes with dystrophin and S-SCAM in cultured hippocampal neurons and cerebellar cortex, respectively. Both β-dystroglycan and S-SCAM were immunoprecipitated from brain lysates using anti-synArfGEF IgG. Taken together, these findings suggest that synArfGEF functions as a novel regulator of Arf6 at inhibitory synapses and associates with the dystrophin-associated glycoprotein complex and S-SCAM.     

Postmortem changes of uric acid in various rat tissues: Determination of uric acid by reversed-phase high-performance liquid chromatography with electrochemical detection

As a function of time after decapitation, postmortem changes of uric acid in various rat tissues have been studied by reversed-phase high-performance liquid chromatography with electrochemical detection. The chromatographic examination revealed that uric acid in rat tissues such as brain, liver, musculus rectus abdominis, and femoral muscle tends to increase after decapitation as a function of time between the sacrifice and homogenization in a 2.0% metaphosphoric acid solution.     

Xanthine and Uric Acid Levels in Rat Brain Following Focal Ischemia

Changes of the xanthine and uric acid (UA) levels in rat forebrain following focal cerebral ischemia were studied by reversed-phase HPLC with electrochemical detection. Focal ischemia was induced by occluding the left middle cerebral artery in the rat. The xanthine level in the normal group was 11.50 nmol/g tissue. In the ischemic group, the xanthine concentration in the ischemic hemisphere progressively increased after occlusion and reached a maximum value of 59.42 nmol/g tissue 4 h after operation. The UA level in the normal group was 2.20 nmol/g tissue, whereas in the ischemic group the UA concentration in the ischemic hemisphere gradually increased after occlusion, reaching a value of 38.53 nmol/g tissue 24 h after ischemia. The concentration of UA remained elevated in the ischemic hemisphere until 48 h after occlusion, and reached a maximum value of 38.98 nmol/g tissue. The xanthine and UA levels in the contralateral hemisphere remained unchanged. The xanthine and UA concentrations in the sham-operated group did not show a significant increase after operation. The time course of xanthine and UA levels suggests that in ischemic forebrain UA is formed from xanthine as a product of purine metabolism.     

Characterization and cloning of plasmids from the iron-oxidizing bacteriumThiobacillus ferrooxidans

More than 100 independent strains ofThiobacillus ferrooxidans were isolated from six different domestic mining sites. Although there was some variation according to sampling site, about 73% of all strains carried more than one plasmid ranging in size from about 2.0 to 30 kilobase-pairs(kb). Among these, four plasmids of 2.4, 4.7, 5.1, and 8.9 kb, designated pTNA33, pTSY91, pTSB121, and pTSB122, respectively, were cloned intoEscherichia coli plasmids. pTSB121 and pTSB122, originated from the sameT. ferrooxidans strain, showed weak homology by Southern blotting, whereas pTSB121 showed high homology with pTSY91 from a different strain. It seems that the occurrence of the plasmid homologous to pTSB121 or pTSB122 is more ubiquitous inThiobacillus. On the other hand, pTNA33 is a unique plasmid because it showed no significant homology with other plasmids.     

Analysis of the rice mutant dwarf and gladius leaf 1. Aberrant katanin-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling

Molecular genetic studies of plant dwarf mutants have indicated that gibberellin (GA) and brassinosteroid (BR) are two major factors that determine plant height; dwarf mutants that are caused by other defects are relatively rare, especially in monocot species. Here, we report a rice (Oryza sativa) dwarf mutant, dwarf and gladius leaf 1 (dgl1), which exhibits only minimal response to GA and BR. In addition to the dwarf phenotype, dgl1 produces leaves with abnormally rounded tip regions. Positional cloning of DGL1 revealed that it encodes a 60-kD microtubule-severing katanin-like protein. The protein was found to be important in cell elongation and division, based on the observed cell phenotypes. GA biosynthetic genes are up-regulated in dgl1, but the expression of BR biosynthetic genes is not enhanced. The enhanced expression of GA biosynthetic genes in dgl1 is not caused by inappropriate GA signaling because the expression of these genes was repressed by GA3 treatment, and degradation of the rice DELLA protein SLR1 was triggered by GA3 in this mutant. Instead, aberrant microtubule organization caused by the loss of the microtubule-severing function of DGL1 may result in enhanced expression of GA biosynthetic genes in that enhanced expression was also observed in a BR-deficient mutant with aberrant microtubule organization. These results suggest that the function of DGL1 is important for cell and organ elongation in rice, and aberrant DGL1-mediated microtubule organization causes up-regulation of gibberellin biosynthetic genes independently of gibberellin signaling.     

Selective reduction of a PDZ protein,SAP-97, in the prefrontal cortex of patients with chronic schizophrenia

Many postsynaptic density proteins carrying postsynaptic density-95/discs large/zone occludens-1 (PDZ) domain(s) interact with glutamate receptors to control receptor dynamics and synaptic plasticity. Here we examined the expression of PDZ proteins, synapse-associated protein (SAP) 97, postsynaptic density (PSD)-95, chapsyn-110, GRIP1 and SAP102, in post-mortem brains of schizophrenic patients and control subjects, and evaluated their contribution to schizophrenic pathology. Among these PDZ proteins, SAP97 exhibited the most marked change: SAP97 protein levels were decreased to less than half that of the control levels specifically in the prefrontal cortex of schizophrenic patients. In parallel, its binding partner, GluR1, similarly decreased in the same brain region. The correlation between SAP97 and GluR1 levels in control subjects was, however, altered in schizophrenic patients. SAP102 levels were also significantly reduced in the hippocampus of schizophrenic patients, but this reduction was correlated with sample storage time and post-mortem interval. There were no changes in the levels of the other PDZ proteins in any of the regions examined. In addition, neuroleptic treatment failed to mimic the SAP97 change. These findings suggest that a phenotypic loss of SAP97 is associated with the postsynaptic impairment in prefrontal excitatory circuits of schizophrenic patients.