Reliable First-Principles Alloy Thermodynamics via Truncated Cluster Expansions

In alloys cluster expansions (CE) are increasingly used to combine first-principles electronic-structure and Monte Carlo methods to predict thermodynamic properties. As a basis-set expansion in terms of lattice geometrical clusters and effective cluster interactions, the CE is exact if infinite, but is tractable only if truncated. Yet until now a truncation procedure was not well-defined and did not guarantee a reliable truncated CE. We present an optimal truncation procedure for CE basis sets that provides reliable thermodynamics. We then exemplify its importance in Ni$_3$V, where the CE has failed unpredictably, and now show agreement to a range of measured values, predict new low-energy structures, and explain the cause of previous failures.Comment: 4 pages, 2 figure

Kinetics of coherent order-disorder transition in Al3ZrAl_3 Zr

Within a phase field approach which takes the strain-induced elasticity into account, the kinetics of the coherent order-disorder transition is investigated for the specific case of $Al_3 Zr$ alloy. It is shown that a microstructure with cubic $L1_2$ precipitates appears as a transient state during the decomposition of a homogeneous disordered solid solution into a microstructure with tetragonal $DO_{23}$ precipitates embedded into a disordered matrix. At low enough temperature, favored by a weak internal stress, only $L1_2$ precipitates grow in the transient microstructure preceding nucleation of the $DO_{23}$ precipitates that occurs exclusively at the interface of the solid solution with the $L1_2$ precipitates. Analysis of microstructures at nanoscopic scale shows a characteristic rod shape for the $DO_{23}$ precipitates due to the combination of their tetragonal symmetry and their large internal stress.Comment: 2 postscript figures and 1 JPG pag

Confinement Effects in Antiferromagnets

Phase equilibrium in confined Ising antiferromagnets was studied as a function of the coupling (v) and a magnetic field (h) at the surfaces, in the presence of an external field H. The ground state properties were calculated exactly for symmetric boundary conditions and nearest-neighbor interactions, and a full zero-temperature phase diagram in the plane v-h was obtained for films with symmetry-preserving surface orientations. The ground-state analysis was extended to the H-T plane using a cluster-variation free energy. The study of the finite-T properties (as a function of v and h) reveals the close interdependence between the surface and finite-size effects and, together with the ground-state phase diagram, provides an integral picture of the confinement in anisotropic antiferromagnets with surfaces that preserve the symmetry of the order parameter.Comment: 10 pages, 8 figures, Accepted in Phys. Rev.

The First Aspartic Acid of the DQxD Motif for Human UDP-Glucuronosyltransferase 1A10 Interacts with UDP-Glucuronic Acid during Catalysis

All UDP-glucuronosyltransferase enzymes (UGTs) share a common cofactor, UDP-glucuronic acid (UDP-GlcUA). The binding site for UDP-GlcUA is localized to the C-terminal domain of UGTs on the basis of amino acid sequence homology analysis and crystal structures of glycosyltransferases, including the C-terminal domain of human UGT2B7. We hypothesized that the 393DQMD-NAK399 region of human UGT1A10 interacts with the glucuronic acid moiety of UDP-GlcUA. Using site-directed mutagenesis and enzymatic analysis, we demonstrated that the D393A mutation abolished the glucuronidation activity of UGT1A10 toward all substrates. The effects of the alanine mutation at Q394, D396, and K399 on glucuronidation activities were substrate-dependent. Previously, we examined the importance of these residues in UGT2B7. Although D393 (D398 in UGT2B7) is similarly critical for UDP-GlcUA binding in both enzymes, the effects of Q394 (Q399 in UGT2B7) to Ala mutation on activity were significant but different between UGT1A10 and UGT2B7. A model of the UDP-GlcUA binding site suggests that the contribution of other residues to cosubstrate binding may explain these differences between UGT1A10 and UGT2B7. We thus postulate that D393 is critical for the binding of glucuronic acid and that proximal residues, e.g., Q394 (Q399 in UGT2B7), play a subtle role in cosubstrate binding in UGT1A10 and UGT2B7. Hence, this study provides important new information needed for the identification and understanding of the binding sites of UGTs, a major step forward in elucidating their molecular mechanism

The Evolution of Respiratory Chain Complex I from a Smaller Last Common Ancestor Consisting of 11 Protein Subunits

The NADH:quinone oxidoreductase (complex I) has evolved from a combination of smaller functional building blocks. Chloroplasts and cyanobacteria contain a complex I-like enzyme having only 11 subunits. This enzyme lacks the N-module which harbors the NADH binding site and the flavin and iron–sulfur cluster prosthetic groups. A complex I-homologous enzyme found in some archaea contains an F420 dehydrogenase subunit denoted as FpoF rather than the N-module. In the present study, all currently available whole genome sequences were used to survey the occurrence of the different types of complex I in the different kingdoms of life. Notably, the 11-subunit version of complex I was found to be widely distributed, both in the archaeal and in the eubacterial kingdoms, whereas the 14-subunit classical complex I was found only in certain eubacterial phyla. The FpoF-containing complex I was present in Euryarchaeota but not in Crenarchaeota, which contained the 11-subunit complex I. The 11-subunit enzymes showed a primary sequence variability as great or greater than the full-size 14-subunit complex I, but differed distinctly from the membrane-bound hydrogenases. We conclude that this type of compact 11-subunit complex I is ancestral to all present-day complex I enzymes. No designated partner protein, acting as an electron delivery device, could be found for the compact version of complex I. We propose that the primordial complex I, and many of the present-day 11-subunit versions of it, operate without a designated partner protein but are capable of interaction with several different electron donor or acceptor proteins

Genetic Variations and Haplotype Diversity of the UGT1 Gene Cluster in the Chinese Population

Vertebrates require tremendous molecular diversity to defend against numerous small hydrophobic chemicals. UDP-glucuronosyltransferases (UGTs) are a large family of detoxification enzymes that glucuronidate xenobiotics and endobiotics, facilitating their excretion from the body. The UGT1 gene cluster contains a tandem array of variable first exons, each preceded by a specific promoter, and a common set of downstream constant exons, similar to the genomic organization of the protocadherin (Pcdh), immunoglobulin, and T-cell receptor gene clusters. To assist pharmacogenomics studies in Chinese, we sequenced nine first exons, promoter and intronic regions, and five common exons of the UGT1 gene cluster in a population sample of 253 unrelated Chinese individuals. We identified 101 polymorphisms and found 15 novel SNPs. We then computed allele frequencies for each polymorphism and reconstructed their linkage disequilibrium (LD) map. The UGT1 cluster can be divided into five linkage blocks: Block 9 (UGT1A9), Block 9/7/6 (UGT1A9, UGT1A7, and UGT1A6), Block 5 (UGT1A5), Block 4/3 (UGT1A4 and UGT1A3), and Block 3′ UTR. Furthermore, we inferred haplotypes and selected their tagSNPs. Finally, comparing our data with those of three other populations of the HapMap project revealed ethnic specificity of the UGT1 genetic diversity in Chinese. These findings have important implications for future molecular genetic studies of the UGT1 gene cluster as well as for personalized medical therapies in Chinese

PTCy-based haploidentical vs matched related or unrelated donor reduced-intensity conditioning transplant for DLBC

This study retrospectively compared long-term outcomes of nonmyeloablative/reduced intensity conditioning (NMC/RIC) allogeneic hematopoietic cell transplantation (allo-HCT) from a haploidentical family donor (haplo-HCT) using posttransplant cyclophosphamide (PTCy) with those of matched sibling donor (MSD) and matched unrelated donor (MUD) with or without T-cell depletion (TCD+/TCD-) in patients with relapsed diffuse large B-cell lymphoma (DLBCL). Adult patients with DLBCL who had undergone their first NMC/RIC allo-HCT between 2008 and 2015 were included. Recipients of haplo-HCT were limited to those receiving graft-versus-host disease (GVHD) prophylaxis with PTCy. GVHD prophylaxis in MSD was limited to calcineurin inhibitor (CNI)-based approaches without in vivo TCD, while MUD recipients received CNI-based prophylaxis with or without TCD. Outcome analyses for overall survival (OS) and progression-free survival (PFS), nonrelapse mortality (NRM), and disease relapse/progression were calculated. A total of 1438 patients (haplo, 132; MSD, 525; MUD TCD+, 403; and MUD TCD-, 378) were included. Patients with haplo donors were significantly older, had a better performance status and had more frequently received total body irradiation-based conditioning regimens and bone marrow grafts than MSD and MUD TCD+ or TCD-. 3-year OS, PFS, NRM and relapse/progression incidence after haplo-HCT was 46%, 38%, 22%, and 41%, respectively, and not significantly different from outcomes of matched donor transplants on multivariate analyses. Haplo-HCT was associated with a lower cumulative incidence of chronic GVHD compared with MSD, MUD TCD+/TCD-. NMC/RIC haplo-HCT with PTCy seems to be a valuable alternative for patients with DLBCL considered for allo-HCT but lacking a matched donor