Macromolecular recognition: Structural aspects of the origin of the genetic system

Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique

The Impact of a Supernova Explosion in a Very Massive Binary

We consider the effect of a supernova (SN) explosion in a very massive binary that is expected to form in a portion of Population III stars with the mass higher than 100$M_\odot$. In a Population III binary system, a more massive star can result in the formation of a BH and a surrounding accretion disc. Such BH accretion could be a significant source of the cosmic reionization in the early universe. However, a less massive companion star evolves belatedly and eventually undergoes a SN explosion, so that the accretion disc around a BH might be blown off in a lifetime of companion star. In this paper, we explore the dynamical impact of a SN explosion on an accretion disc around a massive BH, and elucidate whether the BH accretion disc is totally demolished or not. For the purpose, we perform three-dimensional hydrodynamic simulations of a very massive binary system, where we assume a BH of $10^3 M_{\odot}$ that results from a direct collapse of a very massive star and a companion star of $100 M_{\odot}$ that undergoes a SN explosion. We calculate the remaining mass of a BH accretion disc as a function of time. As a result, it is found that a significant portion of gas disc can survive through three-dimensional geometrical effects even after the SN explosion of a companion star. Even if the SN explosion energy is higher by two orders of magnitude than the binding energy of gas disc, about a half of disc can be left over. The results imply that the Population III BH accretion disc can be a long-lived luminous source, and therefore could be an important ionizing source in the early universe.Comment: 12 pages, 9 figures, accepted for publication in MNRAS, for high resolution figures, see http://www.rccp.tsukuba.ac.jp/Astro/Members/junichi/sus2008.pd

Mechanism of strong quenching of photosystem II chlorophyll fluorescence under drought stress in a lichen, Physciella melanchla, studied by subpicosecond fluorescence spectroscopy

AbstractThe mechanism of the severe quenching of chlorophyll (Chl) fluorescence under drought stress was studied in a lichen Physciella melanchla, which contains a photobiont green alga, Trebouxia sp., using a streak camera and a reflection-mode fluorescence up-conversion system. We detected a large 0.31 ps rise of fluorescence at 715 and 740 nm in the dry lichen suggesting the rapid energy influx to the 715–740 nm bands from the shorter-wavelength Chls with a small contribution from the internal conversion from Soret bands. The fluorescence, then, decayed with time constants of 23 and 112 ps, suggesting the rapid dissipation into heat through the quencher. The result confirms the accelerated 40 ps decay of fluorescence reported in another lichen (Veerman et al., 2007 [36]) and gives a direct evidence for the rapid energy transfer from bulk Chls to the longer-wavelength quencher. We simulated the entire PS II fluorescence kinetics by a global analysis and estimated the 20.2 ns−1 or 55.0 ns−1 energy transfer rate to the quencher that is connected either to the LHC II or to the PS II core antenna. The strong quenching with the 3–12 times higher rate compared to the reported NPQ rate, suggests the operation of a new type of quenching, such as the extreme case of Chl-aggregation in LHCII or a new type of quenching in PS II core antenna in dry lichens

Preventive and therapeutic effects of imatinib in Wistar-Kyoto rats with anti-glomerular basement membrane glomerulonephritis

Imatinib is a selective tyrosine kinase inhibitor that can block activity of the platelet-derived growth factor receptor (PDGFR) and that has immunomodulatory effects on various cell types. Here we measured the protective effects of imatinib in Wistar-Kyoto rats with nephrotoxic serum nephritis, a kidney disease model where CD8+ T cells and macrophages play pathogenetic roles. Groups of animals were given imatinib from one day before up to 13 days following induction of nephritis and from day 7 to 20 following disease induction. Compared to control rats, at each time point imatinib treatment caused significantly less proteinuria, lowered serum blood urea nitrogen and creatinine, and decreased the number of glomeruli with necrosis, crescents, and fibrin deposits. Imatinib-treated rats had a significant reduction in glomerular macrophage accumulation and reduced renal cortical PDGFR-β and M-CSF receptor mRNA expression. Using colocalization we found that glomerular macrophages had reduced IL-1β and MCP-1 protein expression. Late imatinib treatment significantly reduced proteinuria, serum blood urea nitrogen, and creatinine, and reversed renal histopathological changes. We show that imatinib has renoprotective and therapeutic properties and provide pre-clinical work that will need to be confirmed in patients with crescentic glomerulonephritis

Coded-MPMC: One-to-Many Transfer Using Multipath Multicast With Sender Coding

One-to-many transfers in a fast and efficient manner are essential to meet the growing need for duplicating, migrating, or sharing bulk data among servers in a datacenter and across geographically distributed datacenters. Some existing works utilize multiple multicast trees for a one-to-many transfer request to increase network link utilization and its transfer throughput. However, since those schemes do not fully utilize the max-flow value of transmission from a single sender to each recipient, there is room for each recipient to retrieve data more quickly. Therefore, assuming fully-controlled networks with full-duplex links, we pose a problem to find a set of multicast flows with an allocation of block-wise transmissions by which each of multiple recipients with diverse max-flow values from the sender can utilize its own max-flow value. Based on that, assuming a sender-side coding capability on file blocks, we design a schedule of block transmissions over multiple phases by which each recipient can achieve a lower-bound of its file retrieval completion time, i.e., the file size divided by its own max-flow value. This paper presents the coded Multipath Multicast (Coded-MPMC) for one-to-many transfers with heuristic procedures to find a desired set of multicast flows on which block transmissions are scheduled. Through extensive simulations on large-scale real-world network topologies and different types of randomly-generated synthetic topologies, the proposed method is shown to design a desired schedule efficiently. A preliminary implementation on OpenFlow is also reported to show the fundamental feasibility of Coded-MPMC

Experiments of Multipath Multicast One-to-many Transfer with RS coding over Wide-Area OpenFlow Testbed Network

The importance of fast and efficient one-to-many transfers of a large file is increasing to replicate, move, or share bulk data not only intra a datacenter but also inter geographically distributed datacenters. We previously proposed the Coded Multipath Multicast (Coded-MPMC) one-to-many file transfer method in which the multicast transfer, the multipath transfer, and Reed-Solomon (RS) coding are integrated. This method aims to minimize the retrieval completion time of each recipient by simultaneously transmitting blocks of a file on multiple paths from a single sender to each recipient to maximize the aggregated flow value, i.e., to realize the max-flow to the recipient. We preliminarily implemented Coded-MPMC with OpenFlow protocol; however we only tested its feasibility over a small homogeneous in-lab OpenFlow network. In this paper, through experiments on a wide-area OpenFlow testbed network, we show that Coded-MPMC correctly works in a heterogeneous and geographically-distributed network. The results suggest the practicability and potential benefits of Coded-MPMC in real networks.2020 International Conference on Emerging Technologies for Communications (ICETC2020), December 2-4, 2020, Online, Virtual Conferenc

Coherent-Incoherent Crossover of Charge and Neutral Mode Transport as Evidence for the Disorder-Dominated Fractional Edge Phase

Couplings between topological edge channels open electronic phases possessing nontrivial eigenmodes far beyond the noninteracting-edge picture. However, inelastic scatterings mask the eigenmodes' inherent features, often preventing us from identifying the phases, as is the case for the quintessential Landau-level filling factor v = 2/3 edge composed of the counter-propagating v = 1/3 and 1 (1/3-1) channels. Here, we study the coherent-incoherent crossover of the 1/3-1 channels by tuning the channel length in-situ using a new device architecture comprising a junction of v = 1/3 and 1 systems, the particle-hole conjugate of the 2/3 edge. We successfully observed the concurrence of the fluctuating electrical conductance and the quantized thermal conductance in the crossover regime, the definitive hallmark of the eigenmodes in the disorder-dominated edge phase left experimentally unverified

A macroscopic anatomical study of the appropriate palpation zone of the gluteus medius muscle

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