Assembling large, complex environmental metagenomes

The large volumes of sequencing data required to sample complex environments deeply pose new challenges to sequence analysis approaches. De novo metagenomic assembly effectively reduces the total amount of data to be analyzed but requires significant computational resources. We apply two pre-assembly filtering approaches, digital normalization and partitioning, to make large metagenome assemblies more comput\ ationaly tractable. Using a human gut mock community dataset, we demonstrate that these methods result in assemblies nearly identical to assemblies from unprocessed data. We then assemble two large soil metagenomes from matched Iowa corn and native prairie soils. The predicted functional content and phylogenetic origin of the assembled contigs indicate significant taxonomic differences despite similar function. The assembly strategies presented are generic and can be extended to any metagenome; full source code is freely available under a BSD license.Comment: Includes supporting informatio

The Breast Cancer and the Environment Research Centers: Transdisciplinary Research on the Role of the Environment in Breast Cancer Etiology

ObjectivesWe introduce and describe the Breast Cancer and the Environment Research Centers (BCERC), a research network with a transdisciplinary approach to elucidating the role of environmental factors in pubertal development as a window on breast cancer etiology. We describe the organization of four national centers integrated into the BCERC network.Data sourcesInvestigators use a common conceptual framework based on multiple levels of biologic, behavioral, and social organization across the life span. The approach connects basic biologic studies with rodent models and tissue culture systems, a coordinated multicenter epidemiologic cohort study of prepubertal girls, and the integration of community members of breast cancer advocates as key members of the research team to comprise the network.Data extractionRelevant literature is reviewed that describes current knowledge across levels of organization. Individual research questions and hypotheses in BCERC are driven by gaps in our knowledge that are presented at genetic, metabolic, cellular, individual, and environmental (physical and social) levels.Data synthesisAs data collection on the cohort, animal experiments, and analyses proceed, results will be synthesized through a transdisciplinary approach.ConclusionCenter investigators are addressing a large number of specific research questions related to early pubertal onset, which is an established risk factor for breast cancer. BCERC research findings aimed at the primary prevention of breast cancer will be disseminated to the scientific community and to the public by breast cancer advocates, who have been integral members of the research process from its inception

A New Chicken Genome Assembly Provides Insight into Avian Genome Structure

The importance of the Gallus gallus (chicken) as a model organism and agricultural animal merits a continuation of sequence assembly improvement efforts. We present a new version of the chicken genome assembly (Gallus_gallus-5.0; GCA_000002315.3), built from combined long single molecule sequencing technology, finished BACs, and improved physical maps. In overall assembled bases, we see a gain of 183 Mb, including 16.4 Mb in placed chromosomes with a corresponding gain in the percentage of intact repeat elements characterized. Of the 1.21 Gb genome, we include three previously missing autosomes, GGA30, 31, and 33, and improve sequence contig length 10-fold over the previous Gallus_gallus-4.0. Despite the significant base representation improvements made, 138 Mb of sequence is not yet located to chromosomes. When annotated for gene content, Gallus_gallus-5.0 shows an increase of 4679 annotated genes (2768 noncoding and 1911 protein-coding) over those in Gallus_gallus-4.0. We also revisited the question of what genes are missing in the avian lineage, as assessed by the highest quality avian genome assembly to date, and found that a large fraction of the original set of missing genes are still absent in sequenced bird species. Finally, our new data support a detailed map of MHC-B, encompassing two segments: one with a highly stable gene copy number and another in which the gene copy number is highly variable. The chicken model has been a critical resource for many other fields of study, and this new reference assembly will substantially further these efforts

Comparison of 6q25 Breast Cancer Hits from Asian and European Genome Wide Association Studies in the Breast Cancer Association Consortium (BCAC)

Peer reviewe

Gender Differences in Victimization Among Youths with and Without Hearing Loss Admitted to Substance Abuse Treatment

The purpose of this study is to examine gender differences in the victimization profiles of deaf and hard of hearing youths presenting to substance abuse treatment and compare them with parallel profiles from their hearing peers. Intake data on 111 deaf and hard of hearing youths (42% female) was analyzed and compared with that from a weighted gender matched sample of hearing youths. Results indicate the victimization histories of the deaf and hard of hearing girls were more severe than those of their male peers. Although the same pattern was observed in the hearing group, the strength of the difference was greater for youths with hearing loss. Girls with hearing loss were the most severely victimized of all youths, with 75% reporting any abuse, 60% reporting two to four types of abuse, and 70% experiencing high severity victimization. Both groups of girls reported a significantly greater prevalence of sexual and emotional abuse, abuse by a trusted person, abuse that resulted in sex, and worry about future emotional abuse. Substance abuse treatment for deaf and hard of hearing youths should include routine screening of victimization and trauma-informed methods

Adolescent community reinforcement approach for adolescent cannabis use.

[Note. The Cannabis Youth Treatment Series is no longer available on the SAMHSA website. It is here as an archival record]. This manual is part of a series detailing a range of interventions for adolescents with cannabis use problems. They were developed for use in the US. This is Vol 4 of 5 and details a version of Community Reinforcement Approach (CRA) for adolescents with cannabis use problems. The intervention comprises:- •10 Individual sessions with the young person •2 sessions with a family member(s)/carer(s) •2 session with both the young person and the family member(s) The intervention can be carried out by drug workers with additional relevant competences and receiving specialist supervision. For other reports in the series, click on related publication links below

Satisfaction With Life Scale in American Sign Language: Validation and Normative Data

The Satisfaction With Life Scale (SWLS) is a brief instrument that assesses a person’s global life satisfaction. Using state-of-the-science techniques, the SWLS was translated into American Sign Language (ASL). A national sample of 350 deaf and hard of hearing individuals who preferentially use ASL completed the ASL version of the SWLS (SWLS-ASL) online. The individuals in this sample had a mean SWLS score of 23.4, well within the range of mean scores reported for samples from general populations of hearing individuals. No significant differences were identified in SWLS-ASL scores due to gender, cultural identification (identified as culturally Deaf or not), race, ethnicity, education, or employment status