Brood parasitism and nest survival of Brown-headed Cowbird hosts at high-elevation riparian sites in the eastern Sierra Nevada, California

Deciduous riparian ecosystems in the western United States provide habitat for a higher density of breeding birds than reported for any other avian habitat type and provide habitat for more breeding bird species than adjacent uplands. On the east slope of the Sierra Nevada, riparian ecosystems make up Molothrus ater )—an obligate brood parasite that forages on bare ground and feedlots but typically commutes to distinct shrubland or woodland habitats for breeding. We examined nest survival, brood parasitism, breeding phenology, and causes of nest failure for birds at North Lake and Rock Creek: 2 high-elevation (>2500 m) riparian breeding habitats adjacent to recreational development and within cowbird commuting distance to additional potential foraging sites. Nest survival tended to be higher for host species at Rock Creek than for those at North Lake, but parasitism rates were not significantly different between plots. Of 21 open-cup nesting species, 12 were parasitized. We found the highest rate of parasitism (92%) for Warbling Vireos ( Vireo gilvus ) at North Lake, and parasitism contributed to lower total nest survival there (14%). For nearly all species, parasitized nests were less successful and produced fewer young than nonparasitized nests. However, predation was the leading cause of complete nest failure across all species and contributed to the lowest total nest survival estimates for Western Wood-Pewees ( Contopus sordidulus, 11%) and Dusky Flycatchers ( Empidonax oberholseri, 15%) at North Lake and for Dark-eyed Juncos ( Junco hyemalis, 15%) at Rock Creek. Nest survival was relatively high for Western Wood-Pewees (41%) at Rock Creek and for Yellow Warblers ( Dendroica petechia, 47%) at North Lake. We noted whether the arrival of pack animals at pack-station corrals contributed to variation in cowbird numbers at corrals or in parasitism rates at the 2 sites. Cowbirds occupied corrals before and after pack-stock arrival, and most host clutches were completed prior to pack-stock arrival at nearby corrals, suggesting that the presence of pack animals did not directly affect cowbird host species.     

Silicon nanowires as efficient thermoelectric materials

Thermoelectric materials interconvert thermal gradients and electric fields for power generation or for refrigeration. Thermoelectrics currently find only niche applications because of their limited efficiency, which is measured by the dimensionless parameter ZT-a function of the Seebeck coefficient or thermoelectric power, and of the electrical and thermal conductivities. Maximizing ZT is challenging because optimizing one physical parameter often adversely affects another. Several groups have achieved significant improvements in ZT through multi-component nanostructured thermoelectrics, such as Bi(2)Te(3)/Sb(2)Te(3) thin-film superlattices, or embedded PbSeTe quantum dot superlattices. Here we report efficient thermoelectric performance from the single-component system of silicon nanowires for cross-sectional areas of 10 nm x 20 nm and 20 nm x 20 nm. By varying the nanowire size and impurity doping levels, ZT values representing an approximately 100-fold improvement over bulk Si are achieved over a broad temperature range, including ZT approximately 1 at 200 K. Independent measurements of the Seebeck coefficient, the electrical conductivity and the thermal conductivity, combined with theory, indicate that the improved efficiency originates from phonon effects. These results are expected to apply to other classes of semiconductor nanomaterials.     

DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Acute myeloid leukaemia is a highly malignant haematopoietic tumour that affects about 13,000 adults in the United States each year. The treatment of this disease has changed little in the past two decades, because most of the genetic events that initiate the disease remain undiscovered. Whole-genome sequencing is now possible at a reasonable cost and timeframe to use this approach for the unbiased discovery of tumour-specific somatic mutations that alter the protein-coding genes. Here we present the results obtained from sequencing a typical acute myeloid leukaemia genome, and its matched normal counterpart obtained from the same patient's skin. We discovered ten genes with acquired mutations; two were previously described mutations that are thought to contribute to tumour progression, and eight were new mutations present in virtually all tumour cells at presentation and relapse, the function of which is not yet known. Our study establishes whole-genome sequencing as an unbiased method for discovering cancer-initiating mutations in previously unidentified genes that may respond to targeted therapies.     

Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing

Most patients with acute myeloid leukaemia (AML) die from progressive disease after relapse, which is associated with clonal evolution at the cytogenetic level. To determine the mutational spectrum associated with relapse, we sequenced the primary tumour and relapse genomes from eight AML patients, and validated hundreds of somatic mutations using deep sequencing; this allowed us to define clonality and clonal evolution patterns precisely at relapse. In addition to discovering novel, recurrently mutated genes (for example, WAC, SMC3, DIS3, DDX41 and DAXX) in AML, we also found two major clonal evolution patterns during AML relapse: (1) the founding clone in the primary tumour gained mutations and evolved into the relapse clone, or (2) a subclone of the founding clone survived initial therapy, gained additional mutations and expanded at relapse. In all cases, chemotherapy failed to eradicate the founding clone. The comparison of relapse-specific versus primary tumour mutations in all eight cases revealed an increase in transversions, probably due to DNA damage caused by cytotoxic chemotherapy. These data demonstrate that AML relapse is associated with the addition of new mutations and clonal evolution, which is shaped, in part, by the chemotherapy that the patients receive to establish and maintain remissions.     

Human gut microbiome viewed across age and geography

Gut microbial communities represent one source of human genetic and metabolic diversity. To examine how gut microbiomes differ among human populations, here we characterize bacterial species in fecal samples from 531 individuals, plus the gene content of 110 of them. The cohort encompassed healthy children and adults from the Amazonas of Venezuela, rural Malawi and US metropolitan areas and included mono- and dizygotic twins. Shared features of the functional maturation of the gut microbiome were identified during the first three years of life in all three populations, including age-associated changes in the genes involved in vitamin biosynthesis and metabolism. Pronounced differences in bacterial assemblages and functional gene repertoires were noted between US residents and those in the other two countries. These distinctive features are evident in early infancy as well as adulthood. Our findings underscore the need to consider the microbiome when evaluating human development, nutritional needs, physiological variations and the impact of westernization.     

Peptide-dependent recognition of H-2Kb by alloreactive cytotoxic T lymphocytes

Antigen-specific T lymphocytes appear to recognize foreign antigens in the form of peptide fragments presented within the antigen-binding groove of class I or class II molecules encoded by the major histocompatibility complex (MHC). Alloreactive T cells also show specificity for MHC molecules, and various reports suggest that residues of the MHC molecules constitute at least part of the ligand to which alloreactive T-cell receptors bind. The X-ray crystal structure of the human MHC class I molecule, HLA-A2, has provided evidence to strengthen the argument that MHC-bound self-peptide might also contribute to such recognition. We now provide direct evidence for this, showing that at least some alloreactive cytotoxic T lymphocyte clones recognize peptide fragments derived from cytoplasmic proteins. We reasoned that if self-peptides were involved in allorecognition, then the sequence of some of these peptides could vary between species, resulting in species-restricted distribution of the relevant ligand(s). Several alloreactive cytotoxic T lymphocyte clones specific for H-2Kb, expressed by the murine cell line EL4, did not lyse a human-cell transfectant expressing the H-2Kb molecule (Jurkat-Kb cells). However, these clones were able to lyse Jurkat-Kb cells sensitized by preincubation with an EL4 cytoplasmic extract cleaved by cyanogen bromide. The sensitizing activity from this extract was destroyed by protease and appeared to be due to a peptide consisting of 10 to 15 amino acids.     

Effects of light,temperature and nutrients on the production of conidia and sclerotia by forms ofAspergillus japonicus

Zusammenfassung Aspergillus japonicus bildet je nach den Belichtungs-, Temperatur- und Ernährungsbedingungen, unter denen er wächst, entweder nur Konidien oder nur Sklerotien oder beide zusammen.