Patome: a database server for biological sequence annotation and analysis in issued patents and published patent applications

With the advent of automated and high-throughput techniques, the number of patent applications containing biological sequences has been increasing rapidly. However, they have attracted relatively little attention compared to other sequence resources. We have built a database server called Patome, which contains biological sequence data disclosed in patents and published applications, as well as their analysis information. The analysis is divided into two steps. The first is an annotation step in which the disclosed sequences were annotated with RefSeq database. The second is an association step where the sequences were linked to Entrez Gene, OMIM and GO databases, and their results were saved as a gene–patent table. From the analysis, we found that 55% of human genes were associated with patenting. The gene–patent table can be used to identify whether a particular gene or disease is related to patenting. Patome is available at ; the information is updated bimonthly

Altered expression of norepinephrine transporter and norepinephrine in human placenta cause pre-eclampsia through regulated trophoblast invasion

Objective: We investigated the norepinephrine transporter (NET) expression in normal and pre-eclamptic placentas and analyzed the invasion activity of trophoblastic cells based on norepinephrine (NE)-NET regulation. Methods: NET and NE expression levels were examined by western blot and enzyme-linked immunosorbent assay, respectively. Trophoblast invasion activity, depending on NE-NET regulation, was determined by NET-small interfering RNA (siRNA) and NET transfection into the human extravillous trophoblast cells with or without NE treatment and invasion rates were analyzed by zymography and an invasion assay. Results: NET mRNA was expressed at a low level in pre-eclamptic placentas compared with normal placentas and NE concentration in maternal plasma increased significantly in pre-eclamptic women compared to normal pregnant women (p<0.05). NET gene upregulation and NE treatment stimulated trophoblast cell invasion up to 2.5-fold (p<0.05) by stimulating matrix metalloproteinase-9 activity via the phosphoinositol-3-kinase/AKT signaling pathway, whereas NET-siRNA with NE treatment reduced invasion rates. Conclusion: NET expression is reduced by inadequate regulation of NE levels during placental development. This suggests that a complementary balance between NET and NE regulates trophoblast cell invasion activities during placental development

Synergistic multi-doping effects on the Li7La3Zr2O12 solid electrolyte for fast lithium ion conduction.

Here, we investigate the doping effects on the lithium ion transport behavior in garnet Li7La3Zr2O12 (LLZO) from the combined experimental and theoretical approach. The concentration of Li ion vacancy generated by the inclusion of aliovalent dopants such as Al(3+) plays a key role in stabilizing the cubic LLZO. However, it is found that the site preference of Al in 24d position hinders the three dimensionally connected Li ion movement when heavily doped according to the structural refinement and the DFT calculations. In this report, we demonstrate that the multi-doping using additional Ta dopants into the Al-doped LLZO shifts the most energetically favorable sites of Al in the crystal structure from 24d to 96 h Li site, thereby providing more open space for Li ion transport. As a result of these synergistic effects, the multi-doped LLZO shows about three times higher ionic conductivity of 6.14 × 10(-4) S cm(-1) than that of the singly-doped LLZO with a much less efforts in stabilizing cubic phases in the synthetic condition

Efficient electron dynamics with the planewave-based real-time time-dependent density functional theory: Absorption spectra, vibronic electronic spectra, and coupled electron-nucleus dynamics

The electron dynamics with complex third-order Suzuki-Trotter propagator (ST(3)) has been implemented into a planewave (PW) based density functional theory program, and several applications including linear absorption spectra and coupled electron-nucleus dynamics have been calculated. Since the ST(3) reduces the number of Fourier transforms to less than half compared to the fourth-order Suzuki-Trotter propagator (ST(4)), more than twice faster calculations are possible by exploiting the ST(3). We analyzed numerical errors of both the ST(3) and the ST(4) in the presence/absence of an external field for several molecules such as Al(2), N(2), and C(2)H(4). We obtained that the ST(3) gives the same order of numerical errors (10(-5) Ry after 100 fs) as the ST(4). Also, the time evolution of dipole moments, hence the absorption spectrum, is equivalent for both ST(3) and ST(4). As applications, the linear absorption spectrum for an ethylene molecule was studied. From the density difference analysis, we showed that the absorption peaks at 6.10 eV and 7.65 eV correspond to the pi -&gt; 4a(g) and pi -&gt; pi* excitation bands, respectively. We also investigated the molecular vibrational effect to the absorption spectra of an ethylene molecule and the dynamics of a hydrogen molecule after the sigma -&gt; sigma* transition by formulating coupled electron-nucleus dynamics within the Ehrenfest regime. The trajectory of nuclei follows the excited state potential energy curve exactly. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3671952close

Tetrathiomolybdate sensitizes ovarian cancer cells to anticancer drugs doxorubicin, fenretinide, 5-fluorouracil and mitomycin C

<p>Abstract</p> <p>Background</p> <p>Our recent study showed that tetrathiomolybdate (TM), a drug to treat copper overload disorders, can sensitize drug-resistant endometrial cancer cells to reactive oxygen species (ROS)-generating anticancer drug doxorubicin. To expand these findings in the present study we explore TM efficacy in combination with a spectrum of ROS-generating anticancer drugs including mitomycin C, fenretinide, 5-fluorouracil and doxorubicin in ovarian cancer cells as a model system.</p> <p>Methods</p> <p>The effects of TM alone or in combination with doxorubicin, mitomycin C, fenretinide, or 5-fluorouracil were evaluated using a sulforhodamine B assay. Flow cytometry was used to detect the induction of apoptosis and ROS generation. Immunoblot analysis was carried out to investigate changes in signaling pathways.</p> <p>Results</p> <p>TM potentiated doxorubicin-induced cytotoxicity and modulated key regulators of apoptosis (PARP, caspases, JNK and p38 MAPK) in SKOV-3 and A2780 ovarian cancer cell lines. These effects were linked to the increased production of ROS, as shown in SKOV-3 cells. ROS scavenging by ascorbic acid blocked the sensitization of cells by TM. TM also sensitized SKOV-3 to mitomycin C, fenretinide, and 5-fluorouracil. The increased cytotoxicity of these drugs in combination with TM was correlated with the activity of ROS, loss of a pro-survival factor (e.g. XIAP) and the appearance of a pro-apoptotic marker (e.g. PARP cleavage).</p> <p>Conclusions</p> <p>Our data show that TM increases the efficacy of various anticancer drugs in ovarian cancer cells in a ROS-dependent manner.</p

High-resolution crystal structure of the non-specific lipid-transfer protein from maize seedlings

AbstractBackground: The movement of lipids between membranes is aided by lipid-transfer proteins (LTPs). Some LTPs exhibit broad specificity, transferring many classes of lipids, and are termed non-specific LTPs (ns-LTPs). Despite their apparently similar mode of action, no sequence homology exists between mammalian and plant ns-LTPs and no three-dimensional structure has been reported for any plant ns-LTP.Results We have determined the crystal structure of ns-LTP from maize seedlings by multiple isomorphous replacement and refined the structure to 1.9 å resolution. The protein comprises a single compact domain with four α-helices and a long C-terminal region. The eight conserved cysteines form four disulfide bridges (assigned as Cys4–Cys52, Cys14–Cys29, Cys30–Cys75, and Cys50–Cys89) resolving the ambiguity that remained from the chemical determination of pairings in the homologous protein from castor bean. Two of the bonds, Cys4–Cys52 and Cys50–Cys89, differ from what would have been predicted from sequence alignment with soybean hydrophobic protein. The complex between maize ns-LTP and hexadecanoate (palmitate) has also been crystallized and its structure refined to 1.8 å resolution.Conclusion The fold of maize ns-LTP places it in a new category of all-α-type structure, first described for soybean hydrophobic protein. In the absence of a bound ligand, the protein has a tunnel-like hydrophobic cavity, which is large enough to accommodate a long fatty acyl chain. In the structure of the complex with palmitate, most of the acyl chain is buried inside this hydrophobic cavity

Role of Staphylococcal Superantigen in Atopic Dermatitis: Influence on Keratinocytes

Staphylococcus aureus may perform an crucial function in atopic dermatitis (AD), via the secretion of superantigens, including staphylococcal enterotoxins (SE) A or B, and toxic shock syndrome toxin-1 (TSST-1). Dysregulated cytokine production by keratinocytes (KCs) upon exposure to staphylococcal superantigens (SsAgs) may be principally involved in the pathophysiology of AD. We hypothesized that lesional KCs from AD may react differently to SsAgs compared to nonlesional skin or normal skin from nonatopics. We conducted a comparison of HLA-DR or CD1a expression in lesional skin as opposed to that in nonlesional or normal skin by immunohistochemistry (IHC). We also compared, using ELISA, the levels of IL-1α, IL-1β, and TNF-α secreted by cultured KCs from lesional, nonlesional, and normal skin, after the addition of SEA, SEB and TSST-1. IHC revealed that both HLA-DR and CD1a expression increased significantly in the epidermis of lesional skin versus nonlesional or normal skin in quite a similar manner. IL-1α, IL-1β, and TNF-α secretion was also significantly elevated in the cultured KCs from lesional skin after the addition of SsAgs. Our results indicated that KCs from lesional skin appear to react differently to SsAgs and increased proinflammatory cytokine production in response to SsAgs may contribute to the pathogenesis of AD

Is the Molecular Berry Phase an Artifact of the Born-Oppenheimer Approximation?

We demonstrate that the molecular Berry phase and the corresponding nonanalyticity in the electronic Born-Oppenheimer wave function is, in general, not a true topological feature of the exact solution of the full electron-nuclear Schrodinger equation. For a numerically exactly solvable model we show that a nonanalyticity, and the associated geometric phase, only appear in the limit of infinite nuclear mass, while a perfectly smooth behavior is found for any finite nuclear mass.open

Structure and spectral features of H+(H2O)(7): Eigen versus Zundel forms

The two dimensional (2D) to three dimensional (3D) transition for the protonated water cluster has been controversial, in particular, for H+(H2O)(7). For H+(H2O)(7) the 3D structure is predicted to be lower in energy than the 2D structure at most levels of theory without zero-point energy (ZPE) correction. On the other hand, with ZPE correction it is predicted to be either 2D or 3D depending on the calculational levels. Although the ZPE correction favors the 3D structure at the level of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using the aug-cc-pVDZ basis set, the result based on the anharmonic zero-point vibrational energy correction favors the 2D structure. Therefore, the authors investigated the energies based on the complete basis set limit scheme (which we devised in an unbiased way) at the resolution of the identity approximation Moller-Plesset second order perturbation theory and CCSD(T) levels, and found that the 2D structure has the lowest energy for H+(H2O)(7) [though nearly isoenergetic to the 3D structure for D+(D2O)(7)]. This structure has the Zundel-type configuration, but it shows the quantum probabilistic distribution including some of the Eigen-type configuration. The vibrational spectra of MP2/aug-cc-pVDZ calculations and Car-Parrinello molecular dynamics simulations, taking into account the thermal and dynamic effects, show that the 2D Zundel-type form is in good agreement with experiments. (c) 2006 American Institute of Physics.open353