Genetic structuring of remnant forest patches in an endangered medicinal tree in North-western Ethiopia.

Background: Habitat loss and fragmentation may have detrimental impacts on genetic diversity, population structure and overall viability of tropical trees. The response of tropical trees to fragmentation processes may, however, be species, cohort or region-specific. Here we test the hypothesis that forest fragmentation is associated with lower genetic variability and higher genetic differentiation in adult and seedling populations of Prunus africana in North-western Ethiopia.

A genome-wide association study of early-onset breast cancer identifies PFKM as a novel breast cancer gene and supports a common genetic spectrum for breast cancer at any age.

Early-onset breast cancer (EOBC) causes substantial loss of life and productivity, creating a major burden among women worldwide. We analyzed 1,265,548 Hapmap3 single-nucleotide polymorphisms (SNP) among a discovery set of 3,523 EOBC incident cases and 2,702 population control women ages ≤ 51 years. The SNPs with smallest P values were examined in a replication set of 3,470 EOBC cases and 5,475 control women.

Visualization of the magnetic structure of sculpted three-dimensional cobalt nanospirals.

In this work, we report on the direct visualization of magnetic structure in sculpted three-dimensional cobalt (Co) nanospirals with a wire diameter of 20 nm and outer spiral diameter of 115 nm and on the magnetic interactions between the nanospirals, using aberration-corrected Lorentz transmission electron microscopy. By analyzing the magnetic domains in three dimensions at the nanoscale, we show that magnetic domain formation in the Co nanospirals is a result of the shape anisotropy dominating over the magnetocrystalline anisotropy of the system. We also show that the strong dipolar magnetic interactions between adjacent closely packed nanospirals leads to their magnetization directions adopting alternating directions to minimize the total magnetostatic energy of the system.

Low interbasin connectivity in a facultatively diadromous fish: evidence from genetics and otolith chemistry.

Southern smelts (Retropinna spp.) in coastal rivers of Australia are facultatively diadromous, with populations potentially containing individuals with diadromous or wholly freshwater life histories. The presence of diadromous individuals is expected to reduce genetic structuring between river basins due to larval dispersal via the sea.

A fully genetically encoded protein architecture for optical control of peptide ligand concentration.

Ion channels are among the most important proteins in biology, regulating the activity of excitable cells and changing in diseases. Ideally it would be possible to actuate endogenous ion channels, in a temporally precise and reversible manner, and without requiring chemical cofactors. Here we present a modular protein architecture for fully genetically encoded, light-modulated control of ligands that modulate ion channels of a targeted cell.

Molecular signatures of antibody responses derived from a systems biology study of five human vaccines.

Many vaccines induce protective immunity via antibodies. Systems biology approaches have been used to determine signatures that can be used to predict vaccine-induced immunity in humans, but whether there is a 'universal signature' that can be used to predict antibody responses to any vaccine is unknown. Here we did systems analyses of immune responses to the polysaccharide and conjugate vaccines against meningococcus in healthy adults, in the broader context of published studies of vaccines against yellow fever virus and influenza virus.

Identification of new genetic susceptibility loci for breast cancer through consideration of gene-environment interactions.

Genes that alter disease risk only in combination with certain environmental exposures may not be detected in genetic association analysis. By using methods accounting for gene-environment (G × E) interaction, we aimed to identify novel genetic loci associated with breast cancer risk. Up to 34,475 cases and 34,786 controls of European ancestry from up to 23 studies in the Breast Cancer Association Consortium were included.

Explaining variance in the cumulus mammographic measures that predict breast cancer risk: a twins and sisters study.

Background: Mammographic density, the area of the mammographic image that appears white or bright, predicts breast cancer risk. We estimated the proportions of variance explained by questionnaire-measured breast cancer risk factors and by unmeasured residual familial factors.

Methods: For 544 MZ and 339 DZ twin pairs and 1,558 non-twin sisters from 1,564 families, mammographic density was measured using the computer-assisted method Cumulus.

Indirect estimates of natal dispersal distance from genetic data in a stream-dwelling fish (Mogurnda adspersa).

Recent work has highlighted the need to account for hierarchical patterns of genetic structure when estimating evolutionary and ecological parameters of interest. This caution is particularly relevant to studies of riverine organisms, where hierarchical structure appears to be commonplace. Here, we indirectly estimate dispersal distance in a hierarchically structured freshwater fish, Mogurnda adspersa.

Synthesis and characterization of pullulan-polycaprolactone core-shell nanospheres encapsulated with ciprofloxacin.

Nanosphere-encapsulated drugs offer a means to overcome many drug delivery limitations by localizing the site of delivery and providing controlled release. This research details the synthesis and encapsulation of ciprofloxacin in pullulan-polycaprolactone (PCL) core shell nanospheres and the characterization of these materials by 1H-NMR, UV spectroscopy, dynamic light scattering (DLS) and scanning electron microscopy (SEM).1H-NMR results confirm that the pullulan-PCL grafted copolymer was successfully synthesized.

Evidence of gene-environment interactions between common breast cancer susceptibility loci and established environmental risk factors.

Various common genetic susceptibility loci have been identified for breast cancer; however, it is unclear how they combine with lifestyle/environmental risk factors to influence risk. We undertook an international collaborative study to assess gene-environment interaction for risk of breast cancer. Data from 24 studies of the Breast Cancer Association Consortium were pooled.

Genome-wide association studies identify four ER negative-specific breast cancer risk loci.

Estrogen receptor (ER)-negative tumors represent 20-30% of all breast cancers, with a higher proportion occurring in younger women and women of African ancestry. The etiology and clinical behavior of ER-negative tumors are different from those of tumors expressing ER (ER positive), including differences in genetic predisposition. To identify susceptibility loci specific to ER-negative disease, we combined in a meta-analysis 3 genome-wide association studies of 4,193 ER-negative breast cancer cases and 35,194 controls with a series of 40 follow-up studies (6,514 cases and 41,455 controls), genotyped using a custom Illumina array, iCOGS, developed by the Collaborative Oncological Gene-environment Study (COGS).

Large-scale genotyping identifies 41 new loci associated with breast cancer risk.

Breast cancer is the most common cancer among women. Common variants at 27 loci have been identified as associated with susceptibility to breast cancer, and these account for ∼9% of the familial risk of the disease. We report here a meta-analysis of 9 genome-wide association studies, including 10,052 breast cancer cases and 12,575 controls of European ancestry, from which we selected 29,807 SNPs for further genotyping.

Mapping the biological oxidative damage of engineered nanomaterials.

Novel engineered nanomaterials (ENMs) are being introduced into the market rapidly with little understanding of their potential toxicity. Each ENM is a complex combination of diverse sizes, surface chemistries, crystallinity, and metal impurities. Variability in physicochemical properties is poorly understood but is critically important in revealing adverse effects of ENMs.

Evaluation of environmental filtration control of engineered nanoparticles using the Harvard Versatile Engineered Nanomaterial Generation System (VENGES).

Applying engineering controls to airborne engineered nanoparticles (ENPs) is critical to prevent environmental releases and worker exposure. This study evaluated the effectiveness of two air sampling and six air cleaning fabric filters at collecting ENPs using industrially relevant flame-made engineered nanoparticles generated using a versatile engineered nanomaterial generation system (VENGES), recently designed and constructed at Harvard University. VENGES has the ability to generate metal and metal oxide exposure atmospheres while controlling important particle properties such as primary particle size, aerosol size distribution, and agglomeration state.

Evolutionary and ecological implications of sexual parasitism.

Sexual parasites offer unique insights into asexual and sexual reproduction. They mate with a 'host' whose genetic contribution is discarded either immediately (in androgenesis or gynogenesis) or after a delay of one generation (in hybridogenesis). The discarded genome can be maternal or paternal, implying that not only females but also males can reproduce asexually.

Supercomputing enabling exhaustive statistical analysis of genome wide association study data: Preliminary results.

Most published GWAS do not examine SNP interactions due to the high computational complexity of computing p-values for the interaction terms. Our aim is to utilize supercomputing resources to apply complex statistical techniques to the world's accumulating GWAS, epidemiology, survival and pathology data to uncover more information about genetic and environmental risk, biology and aetiology. We performed the Bayesian Posterior Probability test on a pseudo data set with 500,000 single nucleotide polymorphism and 100 samples as proof of principle.

Variants in the VEGFA gene and treatment outcome after anti-VEGF treatment for neovascular age-related macular degeneration.

Purpose: To determine the association of genetic variants of the VEGFA gene with outcome of anti-vascular endothelial growth factor (VEGF) treatment in neovascular age-related macular degeneration (AMD).

Design: A prospective cohort study.

Participants: We included 201 consecutive patients receiving anti-VEGF injections for neovascular AMD.

Sequence variation in the melanocortin-1 receptor (MC1R) does not explain continent-wide plumage color differences in the Australian Magpie (Cracticus tibicen).

The genetic basis of plumage color variation has already been determined for many model species; however, the genetic mechanisms responsible for intraspecific color variation in the majority of wild-bird species are yet to be uncovered. The Australian magpie (Cracticus tibicen) is a large black and white passerine which is widely distributed across the Australian continent. The proportion of melanized back plumage varies between regionally delineated subspecies; where back-color forms overlap, intermediate color phenotypes are produced.

A silk-based scaffold platform with tunable architecture for engineering critically-sized tissue constructs.

In the field of tissue engineering and regenerative medicine there is significant unmet need for critically-sized, fully degradable biomaterial scaffold systems with tunable properties for optimizing tissue formation in vitro and tissue regeneration in vivo. To address this need, we have developed a silk-based scaffold platform that has tunable material properties, including localized and bioactive functionalization, degradation rate, and mechanical properties and that provides arrays of linear hollow channels for delivery of oxygen and nutrients throughout the scaffold bulk. The scaffolds can be assembled with dimensions that range from millimeters to centimeters, addressing the need for a critically-sized platform for tissue formation.

A meta-analysis of genome-wide association studies of breast cancer identifies two novel susceptibility loci at 6q14 and 20q11.

Genome-wide association studies (GWAS) of breast cancer defined by hormone receptor status have revealed loci contributing to susceptibility of estrogen receptor (ER)-negative subtypes. To identify additional genetic variants for ER-negative breast cancer, we conducted the largest meta-analysis of ER-negative disease to date, comprising 4754 ER-negative cases and 31 663 controls from three GWAS: NCI Breast and Prostate Cancer Cohort Consortium (BPC3) (2188 ER-negative cases; 25 519 controls of European ancestry), Triple Negative Breast Cancer Consortium (TNBCC) (1562 triple negative cases; 3399 controls of European ancestry) and African American Breast Cancer Consortium (AABC) (1004 ER-negative cases; 2745 controls). We performed in silico replication of 86 SNPs at P ≤ 1 × 10(-5) in an additional 11 209 breast cancer cases (946 with ER-negative disease) and 16 057 controls of Japanese, Latino and European ancestry.

Tumour morphology of early-onset breast cancers predicts breast cancer risk for first-degree relatives: the Australian Breast Cancer Family Registry.

Introduction: We hypothesised that breast cancer risk for relatives of women with early-onset breast cancer could be predicted by tumour morphological features.

Methods: We studied female first-degree relatives of a population-based sample of 452 index cases with a first primary invasive breast cancer diagnosed before the age of 40 years. For the index cases, a standardised tumour morphology review had been conducted for all; estrogen (ER) and progesterone receptor (PR) status was available for 401 (89%), and 77 (17%) had a high-risk mutation in a breast cancer susceptibility gene or methylation of the BRCA1 promoter region in peripheral blood DNA.

Measuring cation dependent DNA polymerase fidelity landscapes by deep sequencing.

High-throughput recording of signals embedded within inaccessible micro-environments is a technological challenge. The ideal recording device would be a nanoscale machine capable of quantitatively transducing a wide range of variables into a molecular recording medium suitable for long-term storage and facile readout in the form of digital data. We have recently proposed such a device, in which cation concentrations modulate the misincorporation rate of a DNA polymerase (DNAP) on a known template, allowing DNA sequences to encode information about the local cation concentration.