Direction Detector on an Excitable Field: Field Computation with Coincidence Detection

Living organisms process information without any central control unit and without any ruling clock. We have been studying a novel computational strategy that uses a geometrically arranged excitable field, i.e., "field computation." As an extension of this research, in the present article we report the construction of a "direction detector" on an excitable field. Using a numerical simulation, we show that the direction of a input source signal can be detected by applying the characteristic as a "coincidence detector" embedded on an excitable field. In addition, we show that this direction detection actually works in an experiment using an excitable chemical system. These results are discussed in relation to the future development of "field computation."Comment: 6 pages, 3 figure

The protective role of the 3-mercaptopyruvate sulfurtransferase (3-MST)-hydrogen sulfide (H₂S) pathway against experimental osteoarthritis.

Osteoarthritis (OA) is characterized by the formation and deposition of calcium-containing crystals in joint tissues, but the underlying mechanisms are poorly understood. The gasotransmitter hydrogen sulfide (H <sub>2</sub> S) has been implicated in mineralization but has never been studied in OA. Here, we investigated the role of the H <sub>2</sub> S-producing enzyme 3-mercaptopyruvate sulfurtransferase (3-MST) in cartilage calcification and OA development. 3-MST expression was analyzed in cartilage from patients with different OA degrees, and in cartilage stimulated with hydroxyapatite (HA) crystals. The modulation of 3-MST expression in vivo was studied in the meniscectomy (MNX) model of murine OA, by comparing sham-operated to MNX knee cartilage. The role of 3-MST was investigated by quantifying joint calcification and cartilage degradation in WT and 3-MST <sup>-/-</sup> meniscectomized knees. Chondrocyte mineralization in vitro was measured in WT and 3-MST <sup>-/-</sup> cells. Finally, the effect of oxidative stress on 3-MST expression and chondrocyte mineralization was investigated. 3-MST expression in human cartilage negatively correlated with calcification and OA severity, and diminished upon HA stimulation. In accordance, cartilage from menisectomized OA knees revealed decreased 3-MST if compared to sham-operated healthy knees. Moreover, 3-MST <sup>-/-</sup> mice showed exacerbated joint calcification and OA severity if compared to WT mice. In vitro, genetic or pharmacologic inhibition of 3-MST in chondrocytes resulted in enhanced mineralization and IL-6 secretion. Finally, oxidative stress decreased 3-MST expression and increased chondrocyte mineralization, maybe via induction of pro-mineralizing genes. 3-MST-generated H <sub>2</sub> S protects against joint calcification and experimental OA. Enhancing H <sub>2</sub> S production in chondrocytes may represent a potential disease modifier to treat OA

Electronic Structure of Isolated Graphene Nanoribbons in Solution Revealed by Two-Dimensional Electronic Spectroscopy

Structurally well-defined graphene nanoribbons (GNRs) are nanostructures with unique optoelectronic properties. In the liquid phase, strong aggregation typically hampers the assessment of their intrinsic properties. Recently we reported a novel type of GNRs, decorated with aliphatic side chains, yielding dispersions consisting mostly of isolated GNRs. Here we employ two-dimensional electronic spectroscopy to unravel the optical properties of isolated GNRs and disentangle the transitions underlying their broad and rather featureless absorption band. We observe that vibronic coupling, typically neglected in modeling, plays a dominant role in the optical properties of GNRs. Moreover, a strong environmental effect is revealed by a large inhomogeneous broadening of the electronic transitions. Finally, we also show that the photoexcited bright state decays, on the 150 fs time scale, to a dark state which is in thermal equilibrium with the bright state, that remains responsible for the emission on nanosecond time scales

Structures of the Ets Protein DNA-binding Domains of Transcription Factors Etv1, Etv4, Etv5, and Fev: Determinants of DNA Binding and Redox Regulation by Disulfide Bond Formation.

Ets transcription factors, which share the conserved Ets DNA-binding domain, number nearly 30 members in humans and are particularly involved in developmental processes. Their deregulation following changes in expression, transcriptional activity, or by chromosomal translocation plays a critical role in carcinogenesis. Ets DNA binding, selectivity, and regulation have been extensively studied; however, questions still arise regarding binding specificity outside the core GGA recognition sequence and the mode of action of Ets post-translational modifications. Here, we report the crystal structures of Etv1, Etv4, Etv5, and Fev, alone and in complex with DNA. We identify previously unrecognized features of the protein-DNA interface. Interactions with the DNA backbone account for most of the binding affinity. We describe a highly coordinated network of water molecules acting in base selection upstream of the GGAA core and the structural features that may account for discrimination against methylated cytidine residues. Unexpectedly, all proteins crystallized as disulfide-linked dimers, exhibiting a novel interface (distant to the DNA recognition helix). Homodimers of Etv1, Etv4, and Etv5 could be reduced to monomers, leading to a 40-200-fold increase in DNA binding affinity. Hence, we present the first indication of a redox-dependent regulatory mechanism that may control the activity of this subset of oncogenic Ets transcription factors

Formation of an Ultracarbonaceous Antarctic Micrometeorite through Minimum Aqueous Alteration in a Small Porous Icy Body

A comprehensive study of the organic chemistry and mineralogy of an ultracarbonaceous micrometeorite (UCAMM D05IB80) collected from near the Dome Fuji Station, Antarctica, was carried out to understand the genetic relationship among organic materials, silicates, and water. The micrometeorite is composed of a dense aggregate of ∼5 µm-sized hollow ellipsoidal organic material containing submicrometer-sized phases such as glass with embedded metal and sulfides (GEMS) and mineral grains. There is a wide area of organic material (∼15 × 15 μm) in its interior. Low-Ca pyroxene is much more abundant than olivine and shows various Mg/(Mg + Fe) ratios ranging from ∼1.0 to 0.78, which is common to previous works on UCAMMs. By contrast, GEMS grains in this UCAMM have unusual chemical compositions. They are depleted in both Mg and S, which suggests that these elements were leached out from the GEMS grains during very weak aqueous alteration, without the formation of phyllosilicates. The organic materials have two textures—smooth and globular with an irregular outline—and these are composed of imine, nitrile and/or aromatic nitrogen heterocycles, and amide. The ratio of nitrogen to carbon (N/C) in the smooth region of the organics is ∼0.15, which is five times higher than that of insoluble organic macromolecules in types 1 and 2 carbonaceous chondritic meteorites. In addition, the UCAMM organic materials are soluble in epoxy and are thus hydrophilic; this polar nature indicates that they are very primitive. The surface of the material is coated with an inorganic layer, a few nanometers thick, that consists of C, O, Si, S, and Fe. Sulfur is also contained in the interior, implying the presence of organosulfur moieties. There are no isotopic anomalies of D, 13C, or 15N in the organic material. Interstellar photochemistry alone would not be sufficient to explain the N/C ratio of the UCAMM organics; therefore, we suggest that a very small amount of fluid on a comet must have been necessary for the formation of the UCAMM. The GEMS grains depleted in Mg and S in the UCAMM prove a very weak degree of aqueous alteration; weaker than that of carbonaceous chondrites. Short-duration weak alteration probably caused by planetesimal shock locally melted cometary ice grains and released water that dissolved the organics; the fluid would likely have not mobilized because of the very low thermal conductivity of the porous icy body. This event allowed the formation of the large organic puddle of the UCAMM, as well as organic matter sulfurization, formation of thin membrane-like layers of minerals, and deformation of organic nanoglobules.アクセプト後にタイトル・アブストラクト等変更あり、著者最終稿は変更前のタイトル"Formation of an Ultracarbonaceous Antarctic Micrometeorite through Minimum Aqueous Alteration in a Small Porous Icy Body"This work was supported by a Grant-in-Aid for Scientific Research from the Japanese Ministry of Education, Culture, Sports, Science and Technology (No. 22224010, PI: H. Nagahara). The STXM facility at the beamline 5.3.2.2, ALS, is supported by the Department of Energy, Basic Energy Sciences Program

Transduction of artificial transcriptional regulatory proteins into human cells

Protein transduction (PT) is a method for delivering proteins into mammalian cells. PT is accomplished by linking a small peptide tag—called a PT domain (PTD)—to a protein of interest, which generates a functional fusion protein that can penetrate efficiently into mammalian cells. In order to study the functions of a transcription factor (TF) of interest, expression plasmids that encode the TF often are transfected into mammalian cells. However, the efficiency of DNA transfection is highly variable among different cell types and is usually very low in primary cells, stem cells and tumor cells. Zinc-finger transcription factors (ZF-TFs) can be tailor-made to target almost any gene in the human genome. However, the extremely low efficiency of DNA transfection into cancer cells, both in vivo and in vitro, limits the utility of ZF-TFs. Here, we report on an artificial ZF-TF that has been fused to a well-characterized PTD from the human immunodeficiency virus-1 (HIV-1) transcriptional activator protein, Tat. This ZF-TF targeted the endogenous promoter of the human VEGF-A gene. The PTD-attached ZF-TF was delivered efficiently into human cells in vitro. In addition, the VEGF-A-specific transcriptional repressor retarded the growth rate of tumor cells in a mouse xenograft experiment

Evaluation of Cell Cycle Arrest in Estrogen Responsive MCF-7 Breast Cancer Cells: Pitfalls of the MTS Assay

Endocrine resistance is a major problem with anti-estrogen treatments and how to overcome resistance is a major concern in the clinic. Reliable measurement of cell viability, proliferation, growth inhibition and death is important in screening for drug treatment efficacy in vitro. This report describes and compares commonly used proliferation assays for induced estrogen-responsive MCF-7 breast cancer cell cycle arrest including: determination of cell number by direct counting of viable cells; or fluorescence SYBR®Green (SYBR) DNA labeling; determination of mitochondrial metabolic activity by 3-(4,5-dimethylthiazol-2-yl)-5-(3-carboxymethoxyphenyl)-2-(4-sulfophenyl)-2H-tetrazolium (MTS) assay; assessment of newly synthesized DNA using 5-ethynyl-2′-deoxyuridine (EdU) nucleoside analog binding and Alexa Fluor® azide visualization by fluorescence microscopy; cell-cycle phase measurement by flow cytometry. Treatment of MCF-7 cells with ICI 182780 (Faslodex), FTY720, serum deprivation or induction of the tumor suppressor p14ARF showed inhibition of cell proliferation determined by the Trypan Blue exclusion assay and SYBR DNA labeling assay. In contrast, the effects of treatment with ICI 182780 or p14ARF-induction were not confirmed using the MTS assay. Cell cycle inhibition by ICI 182780 and p14ARF-induction was further confirmed by flow cytometric analysis and EdU-DNA incorporation. To explore this discrepancy further, we showed that ICI 182780 and p14ARF-induction increased MCF-7 cell mitochondrial activity by MTS assay in individual cells compared to control cells thereby providing a misleading proliferation readout. Interrogation of p14ARF-induction on MCF-7 metabolic activity using TMRE assays and high content image analysis showed that increased mitochondrial activity was concomitant with increased mitochondrial biomass with no loss of mitochondrial membrane potential, or cell death. We conclude that, whilst p14ARF and ICI 182780 stop cell cycle progression, the cells are still viable and potential treatments utilizing these pathways may contribute to drug resistant cells. These experiments demonstrate how the combined measurement of metabolic activity and DNA labeling provides a more reliable interpretation of cancer cell response to treatment regimens

Analysis of Sulfur Poisoning on a PEM Fuel Cell Electrode

The extent of irreversible deactivation of Pt towards hydrogen oxidation reaction (HOR) due to sulfur adsorption and subsequent electrochemical oxidation is quantified in a functional PEM fuel cell. At 70 {\deg}C, sequential hydrogen sulfide (H2S) exposure and electrochemical oxidation experiments indicate that as much as 6% of total Pt sites are deactivated per monolayer sulfur adsorption at open circuit potential of a PEM fuel cell followed by its removal. The extent of such deactivation is much higher when the electrode is exposed to H2S when the fuel cell is operating at a finite load, and is dependent on the local overpotential and the duration of exposure. Regardless of this deactivation, the H2/O2 polarization curves obtained on post-recovery electrodes do not show performance losses suggesting that such performance curves alone cannot be used to assess the extent of recovery due to sulfur poisoning. A concise mechanism for the adsorption and electro-oxidation of H2S on Pt anode is presented. H2S dissociatively adsorbs onto Pt as two different sulfur species and at intermediate oxidation potentials, undergoes electro-oxidation to sulfur and then to sulfur dioxide (SO2). This mechanism is validated by charge balances between hydrogen desorption and sulfur electro-oxidation on Pt. The ignition potential for sulfur oxidation decreases with increase in temperature, which coupled with faster electro-oxidation kinetics result in the easier removal of adsorbed sulfur at higher temperatures. Furthermore, the adsorption potential is found to influence sulfur coverage of an electrode exposed to H2S. As an implication, the local potential of a PEM fuel cell anode exposed to H2S contaminated fuel should be kept below the equilibrium potential for sulfur oxidation to prevent irreversible loss of Pt sites.Comment: 28 pages, 15 figure

The Potential Role of ORM2 in the Development of Colorectal Cancer

Colorectal cancer (CRC) is the third most common malignancy in the world. The risk of death is closely correlated to the stage of CRC at the time of primary diagnosis. Therefore, there is a compelling need for the identification of blood biomarkers that can enable early detection of CRC. We used a quantitative proteomic approach with isobaric labeling (iTRAQ) to examine changes in the plasma proteome of 10 patients with CRC compared to healthy volunteers. Enzyme-Linked Immunosorbnent Assay (ELISA) and Western blot were used for further validation. In our quantitative proteomics analysis, we detected 75 human plasma proteins with more than 95% confidence using iTRAQ labeling in conjunction with microQ-TOF MS. 9 up-regulated and 4 down-regulated proteins were observed in the CRC group. The ORM2 level in plasma was confirmed to be significantly elevated in patients suffering from CRC compared with the controls. ORM2 expression in CRC tissues was significantly increased compared with that in corresponding adjacent normal mucous tissues (P<0.001). ITRAQ together with Q-TOF/MS is a sensitive and reproducible technique of quantitative proteomics. Alteration in expression of ORM2 suggests that ORM2 could be used as a potential biomarker in the diagnosis of CRC