Going Deeper: Metagenome of a Hadopelagic Microbial Community

The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above

Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25–1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition

Photography-based taxonomy is inadequate, unnecessary, and potentially harmful for biological sciences

The question whether taxonomic descriptions naming new animal species without type specimen(s) deposited in collections should be accepted for publication by scientific journals and allowed by the Code has already been discussed in Zootaxa (Dubois & Nemésio 2007; Donegan 2008, 2009; Nemésio 2009a–b; Dubois 2009; Gentile & Snell 2009; Minelli 2009; Cianferoni & Bartolozzi 2016; Amorim et al. 2016). This question was again raised in a letter supported by 35 signatories published in the journal Nature (Pape et al. 2016) on 15 September 2016. On 25 September 2016, the following rebuttal (strictly limited to 300 words as per the editorial rules of Nature) was submitted to Nature, which on 18 October 2016 refused to publish it. As we think this problem is a very important one for zoological taxonomy, this text is published here exactly as submitted to Nature, followed by the list of the 493 taxonomists and collection-based researchers who signed it in the short time span from 20 September to 6 October 2016

Multilevel Confirmatory Factor Analysis of the System of Care Implementation Survey (SOCIS)

A major impediment to obtaining national information on systems of care implementation has been the lack of a psychometrically sound large-scale survey instrument. The present study provided information on the factorial and concurrent validity of the Systems of Care Implementation Survey scales. Multilevel confirmatory factor analysis and multilevel regression analysis were used to test these indicators of internal and external validity. Two hundred twenty-five counties were randomly selected and stratified by population size and poverty level. Nine hundred ten informants responded to the survey questionnaire, M = 4.04 informants per county (SD = 3.17). Results indicated that all models had at least adequate fit to the data, with nine of the 14 factor models having excellent fit. Overall, 11 of the 14 factors had some indication that receiving federal funding to create systems of care was associated with higher scores on the factors. Implications for future research were discussed

System of Care Implementation

For almost 25 years now, a major policy emphasis in children’s mental health at the federal level and within most states has been the development of community-based systems of care. There have been many meetings and conferences about this, training and technical assistance material has been provided, and written material has been prepared, and a federal grant program, the Children’s Mental Health Initiative (CMHI) has now provided funding to over 100 grantees for the development of such systems of care

Untangling the Web: An Approach to Analyzing the Impacts of Individually Tailored, Multi-Component Treatment Interventions

In this paper the use of a maximum individualized change score is proposed as an analytic alternative to the more traditional MANOVA and latent variable approaches in studies examining the use of individually tailored interventions. This strategy offers a number of significant advantages when multiple indicators are used to assess a broad array of potential outcomes that might result from client-specific treatments. Data on 146 children from a study examining the effectiveness of 3 short-term intensive in-home services were used to contrast the results of our proposed analytic strategy with those from the MANOVA and latent variable approaches. Results indicate that the maximum individualized change score approach improves the outcome comparisons among the 3 treatment interventions and eliminates some concerns regarding subjectivity that exists with procedures such as goal-attainment scaling. A simulation study suggests the maximum change score statistics is a nonbiased estimate for assessing between-group differences in program effectiveness and has more power than MANOVA to produce significant differences when smaller program effects exist. Suggestions for strengthening this analytic approach as well as examples regarding use of this technique in other research contexts are also provided

Outcomes Associated with Clinical Profiles of Children in Psychiatric Crisis Enrolled in Intensive, In-Home Interventions

Little is known about the characteristics of children and youth presenting at emergency settings in psychiatric crisis, and virtually nothing is known about their outcomes. The purpose of this study is to describe the clinical profiles of 238 children presenting at two psychiatric emergency settings and enrolled in a randomized controlled trial of three intensive in-home interventions. A second purpose is to examine child mental health outcomes, based on clinical profile and to suggest the utility of using a clinical-profiles approach