Cellular dynamic simulator: an event driven molecular simulation environment for cellular physiology.

In this paper, we present the Cellular Dynamic Simulator (CDS) for simulating diffusion and chemical reactions within crowded molecular environments. CDS is based on a novel event driven algorithm specifically designed for precise calculation of the timing of collisions, reactions and other events for each individual molecule in the environment. Generic mesh based compartments allow the creation / importation of very simple or detailed cellular structures that exist in a 3D environment. Multiple levels of compartments and static obstacles can be used to create a dense environment to mimic cellular boundaries and the intracellular space. The CDS algorithm takes into account volume exclusion and molecular crowding that may impact signaling cascades in small sub-cellular compartments such as dendritic spines. With the CDS, we can simulate simple enzyme reactions; aggregation, channel transport, as well as highly complicated chemical reaction networks of both freely diffusing and membrane bound multi-protein complexes. Components of the CDS are generally defined such that the simulator can be applied to a wide range of environments in terms of scale and level of detail. Through an initialization GUI, a simple simulation environment can be created and populated within minutes yet is powerful enough to design complex 3D cellular architecture. The initialization tool allows visual confirmation of the environment construction prior to execution by the simulator. This paper describes the CDS algorithm, design implementation, and provides an overview of the types of features available and the utility of those features are highlighted in demonstrations

Structural Plasticity within the Postsynaptic Density

The postsynaptic density (PSD) is a large protein complex that clusters neurotransmitter receptors at the synapse and organizes the intracellular signaling molecules responsible for altering the efficiency of synaptic transmission – termed synaptic plasticity. We propose that synapses from different parts of the brain place unique demands on the process of synaptic transmission and that the structure and composition of the PSD play a role in providing these distinctive properties. To begin to address this question, PSDs were isolated from adult rat cerebella, hippocampi and cortices, three brain areas amenable to straightforward isolation that contain unique distributions of neuronal cell types. Electron-tomography (ET) was used to visualize the fine morphology of the isolated PSDs and calculate total protein occupancy within the PSD structure. Immunogold labeling was utilized to quantify protein composition and distribution of key signaling and scaffold molecules. Although the mean surface area did not significantly differ between PSD types, the PSD thickness, as measured from Cryo ET reconstructions, differed significantly between PSD types. Labeling densities for PSD-95 and αCaMKII were found to differ dramatically among the PSD types, while all regions had moderate to high labeling for βCaMKII, illustrating the importance of βCaMKII to the PSD structure. PSD-95, a scaffold protein, was absent from a fraction of cerebellar PSDs, unlike hippocampal and cortical PSDs, showing that protein composition varies between PSD types. Ripley's K function analysis of immunogold labeled PSDs showed that PSD-95 was clustered in cerebellar PSDs, unlike other PSD types, suggesting a different function for PSD-95 in cerebellar PSDs. In contrast, βCaMKII was found to have similar non-random organization in all PSD types. These results support the idea that the composition and structure of the PSD are modified to achieve the specific synaptic functions required of each brain region

Isotopic evidence of plutonium release into the environment from the Fukushima DNPP accident

The Fukushima Daiichi nuclear power plant (DNPP) accident caused massive releases of radioactivity into the environment. The released highly volatile fission products, such as 129mTe, 131I, 134Cs, 136Cs and 137Cs were found to be widely distributed in Fukushima and its adjacent prefectures in eastern Japan. However, the release of non-volatile actinides, in particular, Pu isotopes remains uncertain almost one year after the accident. Here we report the isotopic evidence for the release of Pu into the atmosphere and deposition on the ground in northwest and south of the Fukushima DNPP in the 20–30 km zones. The high activity ratio of 241Pu/239+240Pu (> 100) from the Fukushima DNPP accident highlights the need for long-term 241Pu dose assessment, and the ingrowth of 241Am. The results are important for the estimation of reactor damage and have significant implication in the strategy of decontamination

Mirtazapine exerts astrocyte-mediated dopaminergic neuroprotection

Mirtazapine, a noradrenergic and specific serotonergic antidepressant (NaSSA), is known to activate serotonin (5-HT) 1A receptor. Our recent study demonstrated that stimulation of astrocytic 5-HT1A receptors promoted astrocyte proliferation and upregulated antioxidative property in astrocytes to protect dopaminergic neurons against oxidative stress. Here, we evaluated the neuroprotective effects of mirtazapine against dopaminergic neurodegeneration in models of Parkinson's disease (PD). Mirtazapine administration attenuated the loss of dopaminergic neurons in the substantia nigra and increased the expression of the antioxidative molecule metallothionein (MT) in the striatal astrocytes of 6-hydroxydopamine (6-OHDA)-injected parkinsonian mice via 5-HT1A receptors. Mirtazapine protected dopaminergic neurons against 6-OHDA-induced neurotoxicity in mesencephalic neuron and striatal astrocyte cocultures, but not in enriched neuronal cultures. Mirtazapine-treated neuron-conditioned medium (Mir-NCM) induced astrocyte proliferation and upregulated MT expression via 5-HT1A receptors on astrocytes. Furthermore, treatment with medium from Mir-NCM-treated astrocytes protected dopaminergic neurons against 6-OHDA neurotoxicity, and these effects were attenuated by treatment with a MT-1/2-specific antibody or 5-HT1A antagonist. Our study suggests that mirtazapine could be an effective disease-modifying drug for PD and highlights that astrocytic 5-HT1A receptors may be a novel target for the treatment of PD

Experimental model for irradiating a restricted region of the rat brain using heavy-ion beams

Heavy-ion beams have the feature to administer a large radiation dose in the vicinity of the endpoint in the beam range, its irradiation system and biophysical characteristics are different from ordinary irradiation instruments like X-rays or gamma-rays. In order to get clarify characteristic effects of heavy-ion beams on the brain, we have developed an experimental system for irradiating a restricted region of the rat brain using heavy-ion beams. The left cerebral hemispheres of the adult rat brain were irradiated at dose of 50Gy charged carbon particles (290MeV/nucleon 5mmspread-out Bragg peak). After irradiation, the characteristics of the heavy-ion beams and the animal model were studied. Histological examination and measurement showed that extensive necrosis was observed between 2.5mmand7.5mmdepth from the surface of the rat head, suggesting a relatively high dose and uniform dose was delivered among designed depths and the spread-out bragg peak used here successfully and satisfactorily retained its high-dose localization in the defined region. We believe that our experimental model for irradiating a restricted region of the rat brain using heavy-ion beams is a good model for analyzing regional radiation susceptibility of the brain

Expression of neural cell adhesion molecule L1 in the brain of rats exposed to X-irradiation in utero

To gain insight to the cellular and molecular mechanisms involved abnormal neuronal migration induced by irradiation, we investigated expression of neuronal cell adhesion molecule L 1 and neuronal migration in the brains through comparison between rats prenatally exposed to X-ray and controls. To observe the pattern of neuronal migration, bromodeoxyuridine (BrdU) was chosen as a marker to label migrating cells. The results showed some of the labeled cells remained in the lower of the cortical plate in the irradiated rats, suggesting that neuronal migration was disrupted by X-ray. To study change of expressing neural cell molecule L1, rat brains were analyzed by SDS-PAGE after isolation of L1 by immunoaffinity chromatography. In the all brain membrane fraction, immunoaffinity purified L1 had bands at 200, 180, 140 and 80 kDa. However, the bands in the irradiated group were very weak when compared with the control. Taking these results into account, abnormal neuronal migration and reduction of expression L1 found in their radiated brain indicated that migration of neural cells may be largely dependent on radial glial fiber as well as neural cell molecules like L1. A decrease in L1 expressionmay be one of reasons of abnormal neuronal migration

Lobe Specific Ca2+-Calmodulin Nano-Domain in Neuronal Spines: A Single Molecule Level Analysis

Calmodulin (CaM) is a ubiquitous Ca2+ buffer and second messenger that affects cellular function as diverse as cardiac excitability, synaptic plasticity, and gene transcription. In CA1 pyramidal neurons, CaM regulates two opposing Ca2+-dependent processes that underlie memory formation: long-term potentiation (LTP) and long-term depression (LTD). Induction of LTP and LTD require activation of Ca2+-CaM-dependent enzymes: Ca2+/CaM-dependent kinase II (CaMKII) and calcineurin, respectively. Yet, it remains unclear as to how Ca2+ and CaM produce these two opposing effects, LTP and LTD. CaM binds 4 Ca2+ ions: two in its N-terminal lobe and two in its C-terminal lobe. Experimental studies have shown that the N- and C-terminal lobes of CaM have different binding kinetics toward Ca2+ and its downstream targets. This may suggest that each lobe of CaM differentially responds to Ca2+ signal patterns. Here, we use a novel event-driven particle-based Monte Carlo simulation and statistical point pattern analysis to explore the spatial and temporal dynamics of lobe-specific Ca2+-CaM interaction at the single molecule level. We show that the N-lobe of CaM, but not the C-lobe, exhibits a nano-scale domain of activation that is highly sensitive to the location of Ca2+ channels, and to the microscopic injection rate of Ca2+ ions. We also demonstrate that Ca2+ saturation takes place via two different pathways depending on the Ca2+ injection rate, one dominated by the N-terminal lobe, and the other one by the C-terminal lobe. Taken together, these results suggest that the two lobes of CaM function as distinct Ca2+ sensors that can differentially transduce Ca2+ influx to downstream targets. We discuss a possible role of the N-terminal lobe-specific Ca2+-CaM nano-domain in CaMKII activation required for the induction of synaptic plasticity

Abnormally High Levels of Virus-Infected IFN-γ+CCR4+CD4+CD25+ T Cells in a Retrovirus-Associated Neuroinflammatory Disorder

BACKGROUND:Human T-lymphotropic virus type 1 (HTLV-1) is a human retrovirus associated with both HTLV-1-associated myelopathy/tropical spastic paraparesis (HAM/TSP), which is a chronic neuroinflammatory disease, and adult T-cell leukemia (ATL). The pathogenesis of HAM/TSP is known to be as follows: HTLV-1-infected T cells trigger a hyperimmune response leading to neuroinflammation. However, the HTLV-1-infected T cell subset that plays a major role in the accelerated immune response has not yet been identified. PRINCIPAL FINDINGS:Here, we demonstrate that CD4(+)CD25(+)CCR4(+) T cells are the predominant viral reservoir, and their levels are increased in HAM/TSP patients. While CCR4 is known to be selectively expressed on T helper type 2 (Th2), Th17, and regulatory T (Treg) cells in healthy individuals, we demonstrate that IFN-gamma production is extraordinarily increased and IL-4, IL-10, IL-17, and Foxp3 expression is decreased in the CD4(+)CD25(+)CCR4(+) T cells of HAM/TSP patients as compared to those in healthy individuals, and the alteration in function is specific to this cell subtype. Notably, the frequency of IFN-gamma-producing CD4(+)CD25(+)CCR4(+)Foxp3(-) T cells is dramatically increased in HAM/TSP patients, and this was found to be correlated with disease activity and severity. CONCLUSIONS:We have defined a unique T cell subset--IFN-gamma(+)CCR4(+)CD4(+)CD25(+) T cells--that is abnormally increased and functionally altered in this retrovirus-associated inflammatory disorder of the central nervous system