A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms ( SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds ( a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines - in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases

Adaptive hard and tough mechanical response in single-crystal B1 VNx ceramics via control of anion vacancies

High hardness and toughness are generally considered mutually exclusive properties for single-crystal ceramics. Combining experiments and ab initio molecular dynamics (AIMD) atomistic simulations at room temperature, we demonstrate that both the hardness and toughness of single-crystal NaCl-structure VNx/MgO(001) thin films are simultaneously enhanced through the incorporation of anion vacancies. Nanoindentation results show that VN0.8, here considered as representative understoichiometric VNx system, is ~20% harder, as well as more resistant to fracture than stoichiometric VN samples. AIMD modeling of VN and VN0.8 supercells subjected to [001] and [110] elongation reveal that the tensile strengths of the two materials are similar. Nevertheless, while the stoichiometric VN phase systematically cleaves in a brittle manner at tensile yield points, the understoichiometric compound activates transformation-toughening mechanisms that dissipate accumulated stresses. AIMD simulations also show that VN0.8 exhibits an initially greater resistance to both {110} and {111} shear deformation than VN. However, for progressively increasing shear strains, the VN0.8 mechanical behavior gradually evolves from harder to more ductile than VN. The transition is mediated by anion vacancies, which facilitate {110} and {111} lattice slip by reducing activation shear stresses by as much as 35%. Electronic-structure analyses show that the two-regime hard/tough mechanical response of VN0.8 primarily stems from its intrinsic ability to transfer d electrons between 2nd-neighbor and 4th-neighbor (i.e., across vacancy sites) V-V metallic states. Our work offers a route for electronic-structure design of hard materials in which a plastic mechanical response is triggered with loading

The genome sequence of Trypanosoma cruzi, etiologic agent of chagas disease

Whole-genome sequencing of the protozoan pathogen Trypanosoma cruzi revealed that the diploid genome contains a predicted 22,570 proteins encoded by genes, of which 12,570 represent allelic pairs. Over 50% of the genome consists of repeated sequences, such as retrotransposons and genes for large families of surface molecules, which include trans-sialidases, mucins, gp63s, and a large novel family (>1300 copies) of mucin-associated surface protein (MASP) genes. Analyses of the T. cruzi, T. brucei, and Leishmania major (Tritryp) genomes imply differences from other eukaryotes in DNA repair and initiation of replication and reflect their unusual mitochondrial DNA. Although the Tritryp lack several classes of signaling molecules, their kinomes contain a large and diverse set of protein kinases and phosphatases; their size and diversity imply previously unknown interactions and regulatory processes, which may be targets for intervention.Fil: El-Sayed, Najib M.. The George Washington University; Estados Unidos. The Institute for Genomic Research; Estados UnidosFil: Myler, Peter J.. University of Washington; Estados Unidos. Seattle Biomedical Research Institute; Estados Unidos. University Of Washington School Of Public Health And Community Medicine; Estados UnidosFil: Bartholomeu, Daniella C.. The Institute for Genomic Research; Estados UnidosFil: Nilsson, Daniel. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Aggarwal, Gautam. Seattle Biomedical Research Institute; Estados UnidosFil: Tran, Anh-Nhi. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Ghedin, Elodie. The George Washington University; Estados Unidos. The Institute for Genomic Research; Estados UnidosFil: Worthey, Elizabeth A.. Seattle Biomedical Research Institute; Estados UnidosFil: Delcher, Arthur L.. The Institute for Genomic Research; Estados UnidosFil: Blandin, Gaëlle. The Institute for Genomic Research; Estados UnidosFil: Westenberger, Scott J.. The Institute for Genomic Research; Estados Unidos. University of California at Los Angeles; Estados UnidosFil: Caler, Elisabet. The Institute for Genomic Research; Estados UnidosFil: Cerqueira, Gustavo C.. The Institute for Genomic Research; Estados Unidos. Universidade Federal de Minas Gerais; BrasilFil: Branche, Carole. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Haas, Brian. The Institute for Genomic Research; Estados UnidosFil: Anupama, Atashi. Seattle Biomedical Research Institute; Estados UnidosFil: Arner, Erik. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Åslund, Lena. Uppsala Universitet; SueciaFil: Attipoe, Philip. Seattle Biomedical Research Institute; Estados UnidosFil: Bontempi, Esteban. Karolinska Huddinge Hospital. Karolinska Institutet; Suecia. Dirección Nacional de Instituto de Investigación. Administración Nacional de Laboratorio e Instituto de Salud “Dr. C. G. Malbrán”; ArgentinaFil: Bringaud, Frédéric. Centre National de la Recherche Scientifique; FranciaFil: Burton, Peter. University of Glasgow; Reino UnidoFil: Cadag, Eithon. Seattle Biomedical Research Institute; Estados UnidosFil: Campbell, David A.. University of California at Los Angeles; Estados UnidosFil: Carrington, Mark. University of Cambridge; Estados UnidosFil: Crabtree, Jonathan. The Institute for Genomic Research; Estados UnidosFil: Darban, Hamid. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Da Silveira, Jose Franco. Universidade Federal de Sao Paulo; BrasilFil: De Jong, Pieter. Children's Hospital Oakland Research Institute; Estados UnidosFil: Edwards, Kimberly. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Englund, Paul T.. The Johns Hopkins School Of Medicine; Estados UnidosFil: Fazelina, Gholam. Seattle Biomedical Research Institute; Estados UnidosFil: Feldblyum, Tamara. The Institute for Genomic Research; Estados UnidosFil: Ferella, Marcela. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Frasch, Alberto Carlos C.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Gull, Keith. University of Oxford; Reino UnidoFil: Horn, David. London School of Hygiene and Tropical Medicine; Reino UnidoFil: Hou, Lihua. The Institute for Genomic Research; Estados UnidosFil: Huang, Yiting. Seattle Biomedical Research Institute; Estados UnidosFil: Kindlund, Ellen. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Klingbeil, Michele. University Of Massachusetts; Estados UnidosFil: Kluge, Sindy. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Koo, Hean. The Institute for Genomic Research; Estados UnidosFil: Lacerda, Daniela. Fundación Oswaldo Cruz; Brasil. The Institute for Genomic Research; Estados UnidosFil: Levin, Mariano Jorge. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Lorenzi, Hernan. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Louie, Tin. Seattle Biomedical Research Institute; Estados UnidosFil: Machado, Carlos Renato. Universidade Federal de Minas Gerais; BrasilFil: McCulloch, Richard. University of Glasgow; Reino UnidoFil: McKenna, Alan. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Mizuno, Yumi. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Mottram, Jeremy C.. University of Glasgow; Reino UnidoFil: Nelson, Siri. Seattle Biomedical Research Institute; Estados UnidosFil: Ochaya, Stephen. Karolinska Huddinge Hospital. Karolinska Institutet; SueciaFil: Osoegawa, Kazutoyo. Children's Hospital Oakland Research Institute; Estados UnidosFil: Pai, Grace. The Institute for Genomic Research; Estados UnidosFil: Parsons, Marilyn. Seattle Biomedical Research Institute; Estados Unidos. University Of Washington School Of Public Health And Community Medicine; Estados UnidosFil: Pentony, Martin. Seattle Biomedical Research Institute; Estados UnidosFil: Pettersson, Ulf. Uppsala Universitet; SueciaFil: Pop, Mihai. The Institute for Genomic Research; Estados UnidosFil: Ramirez, Jose Luis. Universidad Central de Venezuela, Facultad de Ciencias; VenezuelaFil: Rinta, Joel. Seattle Biomedical Research Institute; Estados UnidosFil: Robertson, Laura. Seattle Biomedical Research Institute; Estados UnidosFil: Salzberg, Steven L.. The Institute for Genomic Research; Estados UnidosFil: Sanchez, Daniel Oscar. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; ArgentinaFil: Seyler, Amber. Seattle Biomedical Research Institute; Estados UnidosFil: Sharma, Reuben. University of Cambridge; Estados UnidosFil: Shetty, Jyoti. The Institute for Genomic Research; Estados UnidosFil: Simpson, Anjana J.. The Institute for Genomic Research; Estados UnidosFil: Sisk, Ellen. Seattle Biomedical Research Institute; Estados UnidosFil: Tammi, Martti T.. Karolinska Huddinge Hospital. Karolinska Institutet; Suecia. National University Of Singapore; SingapurFil: Tarleton, Rick. University of Georgia; Estados UnidosFil: Teixeira, Santuza. Universidade Federal de Minas Gerais; BrasilFil: Van Aken, Susan. The Institute for Genomic Research; Estados UnidosFil: Vogt, Christy. Seattle Biomedical Research Institute; Estados UnidosFil: Ward, Pauline N.. University of Glasgow; Reino UnidoFil: Wickstead, Bill. Sir William Dunn School Of Pathology; Reino UnidoFil: Wortman, Jennifer. The Institute for Genomic Research; Estados UnidosFil: White, Owen. The Institute for Genomic Research; Estados UnidosFil: Fraser, Claire M.. The Institute for Genomic Research; Estados UnidosFil: Stuart, Kenneth D.. Seattle Biomedical Research Institute; Estados Unidos. University Of Washington School Of Public Health And Community Medicine; Estados UnidosFil: Andersson, Björn. Karolinska Huddinge Hospital. Karolinska Institutet; Sueci

Kinetic Engineering of Wurtzite and Zinc-Blende AlSb Shells on InAs Nanowires

Using AlSb as the model system, we demonstrate that kinetic limitations can lead to the preferential growth of wurtzite (WZ) AlSb shells rather than the thermodynamically stable zinc-blende (ZB) AlSb and that the WZ and ZB relative thickness can be tuned by a careful control of the deposition parameters. We report selective heteroepitaxial radial growth of AlSb deposited by metal-organic vapor phase epitaxy (MOVPE) on InAs nanowire core templates with engineered lengths of axial WZ and ZB segments. AlSb shell thickness, crystal phase, nanostructure, and composition are investigated as a function of the shell growth temperature, Ts, using scanning electron microscopy, transmission electron microscopy, electron tomography, and energy-dispersive X-ray spectroscopy. We find that ZB- and WZ-structured AlSb shells grow heteroepitaxially around the ZB and WZ segments of the InAs core, respectively. Surprisingly, at 390 < Ts < 450 °C, the WZ-AlSb shells are thicker than the ZB-AlSb shells, and their thickness increases with decreasing Ts. In comparison, the ZB-AlSb shell thicknesses increase slightly with increasing Ts. We find that the increased thickness of the WZ-AlSb shells is due to the formation and enhanced deposition on {112-0} facets rather than on the more commonly grown {101-0} sidewall facets. Overall, these results, which are in direct contrast with previous reports suggesting that heteroepitaxial radial growth of III-antimonides is always favored on the ZB-structure facets, indicate that the growth of WZ-AlSb is preferred over the thermodynamically stable ZB-AlSb at lower growth temperatures. We attribute this behavior to kinetic limitations of MOVPE of AlSb on ZB and WZ phases of InAs

Function and recruitment of mucosal regulatory T cells in human chronic Helicobacter pylori infection and gastric adenocarcinoma.

CD4(+)CD25(high) FOXP3-expressing regulatory T cells (Treg) can suppress immune responses to infections and tumors, thereby promoting microbial persistence and tumor progression. However, little is known about the phenotype and function of human mucosal Treg. Therefore, we analyzed the suppressive activity and homing phenotype of Treg in gastric mucosa of Helicobacter pylori-infected gastric adenocarcinoma patients. We found increased numbers of CD4(+)FOXP3(+) Treg in the tumor compared to tumor-free gastric mucosa. Gastric Treg cells were able to suppress H. pylori-induced T cell proliferation and IFN-gamma production. Furthermore, gastric Treg expressed increased levels of l-selectin and CCR4, compared to non-Treg cells, suggesting that these receptors contribute to Treg recruitment. The presence of functional antigen-specific Treg in H. pylori-infected gastric mucosa supports an important role for these cells in suppression of mucosal effector T cell responses, which probably contribute to bacterial persistence and possibly also to gastric tumor progression