Syntheses and characterizations of the in vivo replicative bypass and mutagenic properties of the minor-groove O2-alkylthymidine lesions.

Endogenous metabolism, environmental exposure, and treatment with some chemotherapeutic agents can all give rise to DNA alkylation, which can occur on the phosphate backbone as well as the ring nitrogen or exocyclic nitrogen and oxygen atoms of nucleobases. Previous studies showed that the minor-groove O(2)-alkylated thymidine (O(2)-alkyldT) lesions are poorly repaired and persist in mammalian tissues. In the present study, we synthesized oligodeoxyribonucleotides harboring seven O(2)-alkyldT lesions, with the alkyl group being a Me, Et, nPr, iPr, nBu, iBu or sBu, at a defined site and examined the impact of these lesions on DNA replication in Escherichia coli cells. Our results demonstrated that the replication bypass efficiencies of the O(2)-alkyldT lesions decreased with the chain length of the alkyl group, and these lesions directed promiscuous nucleotide misincorporation in E. coli cells. We also found that deficiency in Pol V, but not Pol II or Pol IV, led to a marked drop in bypass efficiencies for most O(2)-alkyldT lesions. We further showed that both Pol IV and Pol V were essential for the misincorporation of dCMP opposite these minor-groove DNA lesions, whereas only Pol V was indispensable for the T→A transversion introduced by these lesions. Depletion of Pol II, however, did not lead to any detectable alterations in mutation frequencies for any of the O(2)-alkyldT lesions. Thus, our study provided important new knowledge about the cytotoxic and mutagenic properties of the O(2)-alkyldT lesions and revealed the roles of the SOS-induced DNA polymerases in bypassing these lesions in E. coli cells

A Hybridized Weak Galerkin Finite Element Scheme for the Stokes Equations

In this paper a hybridized weak Galerkin (HWG) finite element method for solving the Stokes equations in the primary velocity-pressure formulation is introduced. The WG method uses weak functions and their weak derivatives which are defined as distributions. Weak functions and weak derivatives can be approximated by piecewise polynomials with various degrees. Different combination of polynomial spaces leads to different WG finite element methods, which makes WG methods highly flexible and efficient in practical computation. A Lagrange multiplier is introduced to provide a numerical approximation for certain derivatives of the exact solution. With this new feature, HWG method can be used to deal with jumps of the functions and their flux easily. Optimal order error estimate are established for the corresponding HWG finite element approximations for both {\color{black}primal variables} and the Lagrange multiplier. A Schur complement formulation of the HWG method is derived for implementation purpose. The validity of the theoretical results is demonstrated in numerical tests.Comment: 19 pages, 4 tables,it has been accepted for publication in SCIENCE CHINA Mathematics. arXiv admin note: substantial text overlap with arXiv:1402.1157, arXiv:1302.2707 by other author

Introduction for the Special Issue on Beyond the Hypes of Geospatial Big Data: Theories, Methods, Analytics, and Applications

We live in the era of ‘Big Data’. In particular, Geospatial data, whether captured through remote sensors (e.g., satellite imagery) or generated from large-scale simulations (e.g., climate change models) have always been significantly large in size. Over the last decade however, advances in instrumentation and computation has seen the volume, variety, velocity, and veracity of this data increase exponentially. Of the 2.5 quintillion (1018) bytes of data that are generated on a daily basis across the globe, a large portion (arguably as much as 80%) is found to be geo-referenced. Therefore, this special issue is dedicated to the innovative theories, methods, analytics, and applications of geospatial big data

Nodes in the Gap Function of LaFePO, the Gap Function of the Fe(Se,Te) Systems, and the STM Signature of the s±_{\pm} Pairing

We reiterate, in more details, our previous proposal of using quasi-particle interference to determine the pairing form factor in iron-based superconductors. We also present our functional renormalization group(FRG) results on LaFePO and Fe(Se,Te) superconductors. In particular we found that the leading pairing channel in LaFePO is nodal s$_{\pm}$, with nodes on electron Fermi surfaces. For Fe(Se,Te) system we found fully gapped s$_{\pm}$ pairing, with substantial gap anisotropy on electron Fermi surfaces, and large gap is concentrated in regions with dominant $xy$ orbital character. We further fit the form factor obtained by FRG to real space orbital basis pairing picture, which shows more clearly the differences between different iron-based superconductors.Comment: 8 pages, 6 figures, 1 table, RevTex4, references update