Electronic structure and carrier transfer in B-DNA monomer polymers and dimer polymers: Stationary and time-dependent aspects of wire model vs. extended ladder model

We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site energies of base pairs and the hopping integrals between successive base pairs, i.e., a wire model and (II) at the single-base level, using the on-site energies of the bases and the hopping integrals between neighboring bases, i.e., an \textit{extended} ladder model since we also include diagonal hoppings. We solve a system of $MD$ ("matrix dimension") coupled equations [(I) $MD$ = $N$, (II) $MD$ = $2N$] for the time-independent problem, and a system of $MD$ coupled $1^\text{st}$ order differential equations for the time-dependent problem. We study the HOMO and the LUMO eigenspectra, the occupation probabilities, the Density of States (DOS) and the HOMO-LUMO gap as well as the mean over time probabilities to find the carrier at each site [(I) base pair or (II) base)], the Fourier spectra, which reflect the frequency content of charge transfer (CT) and the pure mean transfer rates from a certain site to another. The two TB approaches give coherent, complementary aspects of electronic properties and charge transfer in B-DNA monomer polymers and dimer polymers.Comment: 20 pages, 23 figure

Coronavirus Gene 7 Counteracts Host Defenses and Modulates Virus Virulence

Transmissible gastroenteritis virus (TGEV) genome contains three accessory genes: 3a, 3b and 7. Gene 7 is only present in members of coronavirus genus a1, and encodes a hydrophobic protein of 78 aa. To study gene 7 function, a recombinant TGEV virus lacking gene 7 was engineered (rTGEV-Δ7). Both the mutant and the parental (rTGEV-wt) viruses showed the same growth and viral RNA accumulation kinetics in tissue cultures. Nevertheless, cells infected with rTGEV-Δ7 virus showed an increased cytopathic effect caused by an enhanced apoptosis mediated by caspase activation. Macromolecular synthesis analysis showed that rTGEV-Δ7 virus infection led to host translational shut-off and increased cellular RNA degradation compared with rTGEV-wt infection. An increase of eukaryotic translation initiation factor 2 (eIF2α) phosphorylation and an enhanced nuclease, most likely RNase L, activity were observed in rTGEV-Δ7 virus infected cells. These results suggested that the removal of gene 7 promoted an intensified dsRNA-activated host antiviral response. In protein 7 a conserved sequence motif that potentially mediates binding to protein phosphatase 1 catalytic subunit (PP1c), a key regulator of the cell antiviral defenses, was identified. We postulated that TGEV protein 7 may counteract host antiviral response by its association with PP1c. In fact, pull-down assays demonstrated the interaction between TGEV protein 7, but not a protein 7 mutant lacking PP1c binding motif, with PP1. Moreover, the interaction between protein 7 and PP1 was required, during the infection, for eIF2α dephosphorylation and inhibition of cell RNA degradation. Inoculation of newborn piglets with rTGEV-Δ7 and rTGEV-wt viruses showed that rTGEV-Δ7 virus presented accelerated growth kinetics and pathology compared with the parental virus. Overall, the results indicated that gene 7 counteracted host cell defenses, and modified TGEV persistence increasing TGEV survival. Therefore, the acquisition of gene 7 by the TGEV genome most likely has provided a selective advantage to the virus

Origin and development of oligoadenylate synthetase immune system

Abstract Background Oligoadenylate synthetases (OASs) are widely distributed in Metazoa including sponges, fish, reptiles, birds and mammals and show large variation, with one to twelve members in any given species. Upon double-stranded RNA (dsRNA) binding, avian and mammalian OASs generate the second messenger 2'-5'-linked oligoadenylate (2-5A), which activates ribonuclease L (RNaseL) and blocks viral replication. However, how Metazoa shape their OAS repertoires to keep evolutionary balance to virus infection is largely unknown. We performed comprehensive phylogenetic and functional analyses of OAS genes from evolutionarily lower to higher Metazoa to demonstrate how the OAS repertoires have developed anti-viral activity and diversified their functions. Results Ancient Metazoa harbor OAS genes, but lack both upstream and downstream genes of the OAS-related pathways, indicating that ancient OASs are not interferon-induced genes involved in the innate immune system. Compared to OASs of ancient Metazoa (i.e. sponge), the corresponding ones of higher Metazoa present an increasing number of basic residues on the OAS/dsRNA interaction interface. Such an increase of basic residues might improve their binding affinity to dsRNA. Moreover, mutations of functional residues in the active pocket might lead to the fact that higher Metazoan OASs lose the ability to produce 3'-5'-linked oligoadenylate (3-5A) and turn into specific 2-5A synthetases. In addition, we found that multiple rounds of gene duplication and domain coupling events occurred in the OAS family and mutations at functionally critical sites were observed in most new OAS members. Conclusions We propose a model for the expansion of OAS members and provide comprehensive evidence of subsequent neo-functionalization and sub-functionalization. Our observations lay the foundation for interrogating the evolutionary transition of ancient OAS genes to host defense genes and provide important information for exploring the unknown function of the OAS gene family

Intermolecular Phosphite-Mediated Radical Desulfurative Alkene Alkylation Using Thiols.

We report herein the development of a S atom transfer process using triethyl phosphite as the S atom acceptor that allows thiols to serve as precursors of C-centered radicals. A range of functionalized and electronically unbiased alkenes including those containing common heteroatom-based functional groups readily participate in this reductive coupling. This process is driven by the exchange of relatively weak S-H and C-S bonds of aliphatic thiols for C-H, C-C, and S-P bonds of the products formed

Intermolecular Phosphite-Mediated Radical Desulfurative Alkene Alkylation Using Thiols.

We report herein the development of a S atom transfer process using triethyl phosphite as the S atom acceptor that allows thiols to serve as precursors of C-centered radicals. A range of functionalized and electronically unbiased alkenes including those containing common heteroatom-based functional groups readily participate in this reductive coupling. This process is driven by the exchange of relatively weak S-H and C-S bonds of aliphatic thiols for C-H, C-C, and S-P bonds of the products formed

Electric Railway Signal.

Patent for an electric railway signal, which is attached to train engines and signals that a train is stopped to other trains by a light reflecting forwards and lights the platform for passengers by having a light reflecting backwards behind the engine

PHARMACOLOGICAL PROPERTIES OF MM-706, A NEW PROSTACYCLIN DERIVATIVE

. 1. In human platelet-rich plasma, platelet aggregation induced in vitro by collagen (10 \u3bcg/ml) or thrombin (50 mU/ml) was dose-dependently inhibited by increasing concentrations of prostacyclin or of the new derivative (\ub1)(5E)-13,14-didehydro-\u3c9-hexanor(1-hydroxycyclohexyl)-9a-carbaprostacyclin (MM-706) with an IC50 of 20\u201350 nM and 250\u2013500 nM, respectively. In human platelets loaded with fura-2, the intracellular rise of [Ca2+] induced by thrombin was dose-dependently inhibited by MM-706 with an approximate IC50 of 100 \u3bcM. 2. 2. In rabbit isolated femoral artery, MM-706 (10nM\u201310\u3bcM) was completely ineffective in relaxing the vessel, which was different to prostacyclin which was able to relax vessels at the same concentrations. 3. 3. In in vitro guinea-pig ileum, prostacyclin produced a contractile effect in the concentration range 1 nM-10\u3bcM, but the derivative MM-706 was ineffective at the same concentrations. Preventive addition of MM-706 did not inhibit prostacyclin contraction. 4. 4. On isolated guinea-pig tracheal preparation, prostacyclin induced a concentration-dependent contraction but the new compound MM-706 showed a lower activity, in the concentration range 10nM\u201310\u3bcM. The activity of prostacyclin was not affected by the contemporary presence of MM-706. 5. 5. It is concluded that MM-706 is a prostacyclin analogue with antiaggregating properties but without evident effects on smooth muscle of different regions