Draft Genome Sequence of Kocuria sp. Strain UCD-OTCP (Phylum Actinobacteria).

Here, we present the draft genome of Kocuria sp. strain UCD-OTCP, a member of the phylum Actinobacteria, isolated from a restaurant chair cushion. The assembly contains 3,791,485 bp (G+C content of 73%) and is contained in 68 scaffolds.

Phylogeny of bacterial and archaeal genomes using conserved genes: supertrees and supermatrices.

Over 3000 microbial (bacterial and archaeal) genomes have been made publically available to date, providing an unprecedented opportunity to examine evolutionary genomic trends and offering valuable reference data for a variety of other studies such as metagenomics. The utility of these genome sequences is greatly enhanced when we have an understanding of how they are phylogenetically related to each other. Therefore, we here describe our efforts to reconstruct the phylogeny of all available bacterial and archaeal genomes.

Longitudinal course of pharmacotherapy in obsessive-compulsive disorder.

Background: Although data fully support the use of serotonin reuptake inhibitors (SRIs) in the treatment of obsessive-compulsive disorder (OCD), investigations on pharmacotherapy discontinuation during the course of OCD are lacking. This 5-year prospective study sought to better understand the long-term course of SRI utilization among individuals with OCD.

Methods: A total of 252 adult outpatients with Diagnostic and Statistical Manual of Mental Disorders, 4th ed.

Five-year course of obsessive-compulsive disorder: predictors of remission and relapse.

Background: Obsessive-compulsive disorder (OCD) is a heterogeneous and disabling condition; however, no studies have examined symptom categories or subtypes as predictors of long-term clinical course in adults with primary OCD.

Method: A total of 213 adults with DSM-IV OCD were recruited from several mental health treatment sites between July 2001 and February 2006 as part of the Brown Longitudinal Obsessive Compulsive Study, a prospective, naturalistic study of treatment-seeking adults with primary OCD. OCD symptoms were assessed annually over the 5-year follow-up period using the Longitudinal Interval Follow-Up Evaluation.

Draft Genome Sequence of Microbacterium sp. Strain UCD-TDU (Phylum Actinobacteria).

Here, we present the draft genome sequence of Microbacterium sp. strain UCD-TDU, a member of the phylum Actinobacteria. The assembly contains 3,746,321 bp (in 8 scaffolds).

Draft genome sequence of an Actinobacterium, Brachybacterium muris strain UCD-AY4.

Here we present the draft genome of an actinobacterium, Brachybacterium muris UCD-AY4. The assembly contains 3,257,338 bp and has a GC content of 70%. This strain was isolated from a residential bath towel and has a 16S rRNA gene 99.

Genome sequence of the orange-pigmented seawater bacterium Owenweeksia hongkongensis type strain (UST20020801(T)).

Owenweeksia hongkongensis Lau et al. 2005 is the sole member of the monospecific genus Owenweeksia in the family Cryomorphaceae, a poorly characterized family at the genome level thus far. This family comprises seven genera within the class Flavobacteria.

Genome sequence of the Antarctic rhodopsins-containing flavobacterium Gillisia limnaea type strain (R-8282(T)).

Gillisia limnaea Van Trappen et al. 2004 is the type species of the genus Gillisia, which is a member of the well characterized family Flavobacteriaceae. The genome of G.

Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8(T)).

Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N.

Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NAL(T)).

Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which comprises five species of the order Clostridiales. Sulfobacillus species are of interest for comparison to other sulfur and iron oxidizers and also have biomining applications.

Insights into the evolution of Darwin's finches from comparative analysis of the Geospiza magnirostris genome sequence.

Background: A classical example of repeated speciation coupled with ecological diversification is the evolution of 14 closely related species of Darwin's (Galápagos) finches (Thraupidae, Passeriformes). Their adaptive radiation in the Galápagos archipelago took place in the last 2-3 million years and some of the molecular mechanisms that led to their diversification are now being elucidated. Here we report evolutionary analyses of genome of the large ground finch, Geospiza magnirostris.

Characterization of enteric neurons in wild-type and mutant zebrafish using semi-automated cell counting and co-expression analysis.

To characterize fluorescent enteric neurons labeled for expression of cytoplasmic markers in zebrafish mutants, we developed a new MATLAB-based program that can be trained by user input. We used the program to count enteric neurons and to analyze co-expression of the neuronal marker, Elavl, and the neuronal subtype marker, serotonin, in 3D confocal image stacks of dissected whole-mount zebrafish intestines. We quantified the entire population of enteric neurons and the serotonergic subpopulation in specific regions of the intestines of gutwrencher mutant and wild-type sibling larvae.

Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing.

The cyanobacterial phylum encompasses oxygenic photosynthetic prokaryotes of a great breadth of morphologies and ecologies; they play key roles in global carbon and nitrogen cycles. The chloroplasts of all photosynthetic eukaryotes can trace their ancestry to cyanobacteria. Cyanobacteria also attract considerable interest as platforms for "green" biotechnology and biofuels.

Pilot Study of Implementation of an Internet-Based Depression Prevention Intervention (CATCH-IT) for Adolescents in 12 US Primary Care Practices: Clinical and Management/Organizational Behavioral Perspectives.

Objective: To explore the implementation of CATCH-IT (Competent Adulthood Transition with Cognitive-behavioral Humanistic and Interpersonal Training), an Internet-based depression intervention program in 12 primary care sites, occurring as part of a randomized clinical trial comparing 2 versions of the intervention (motivational interview + Internet program versus brief advice + Internet program) in 83 adolescents aged 14 to 21 years recruited from February 1, 2007, to November 31, 2007.

Method: The CATCH-IT intervention model consists of primary care screening to assess risk, a primary care physician interview to encourage participation, and 14 online modules of Internet training to teach adolescents how to reduce behaviors that increase vulnerability to depressive disorders. Specifically, we evaluated this program from both a management/organizational behavioral perspective (provider attitudes and demonstrated competence) and a clinical outcomes perspective (depressed mood scores) using the RE-AIM model (Reach, Efficacy, Adoption, Implementation, and Maintenance of the intervention).

Incorporating 16S gene copy number information improves estimates of microbial diversity and abundance.

The abundance of different SSU rRNA ("16S") gene sequences in environmental samples is widely used in studies of microbial ecology as a measure of microbial community structure and diversity. However, the genomic copy number of the 16S gene varies greatly - from one in many species to up to 15 in some bacteria and to hundreds in some microbial eukaryotes. As a result of this variation the relative abundance of 16S genes in environmental samples can be attributed both to variation in the relative abundance of different organisms, and to variation in genomic 16S copy number among those organisms.

Gene conservation among endospore-forming bacteria reveals additional sporulation genes in Bacillus subtilis.

The capacity to form endospores is unique to certain members of the low-G+C group of Gram-positive bacteria (Firmicutes) and requires signature sporulation genes that are highly conserved across members of distantly related genera, such as Clostridium and Bacillus. Using gene conservation among endospore-forming bacteria, we identified eight previously uncharacterized genes that are enriched among endospore-forming species. The expression of five of these genes was dependent on sporulation-specific transcription factors.

Zebrafish Mnx proteins specify one motoneuron subtype and suppress acquisition of interneuron characteristics.

Background: Precise matching between motoneuron subtypes and the muscles they innervate is a prerequisite for normal behavior. Motoneuron subtype identity is specified by the combination of transcription factors expressed by the cell during its differentiation. Here we investigate the roles of Mnx family transcription factors in specifying the subtypes of individually identified zebrafish primary motoneurons.

Sifting through genomes with iterative-sequence clustering produces a large, phylogenetically diverse protein-family resource.

Background: New computational resources are needed to manage the increasing volume of biological data from genome sequencing projects. One fundamental challenge is the ability to maintain a complete and current catalog of protein diversity. We developed a new approach for the identification of protein families that focuses on the rapid discovery of homologous protein sequences.

Functional biogeography of ocean microbes revealed through non-negative matrix factorization.

The direct "metagenomic" sequencing of genomic material from complex assemblages of bacteria, archaea, viruses and microeukaryotes has yielded new insights into the structure of microbial communities. For example, analysis of metagenomic data has revealed the existence of previously unknown microbial taxa whose spatial distributions are limited by environmental conditions, ecological competition, and dispersal mechanisms. However, differences in genotypes that might lead biologists to designate two microbes as taxonomically distinct need not necessarily imply differences in ecological function.

An integrated pipeline for de novo assembly of microbial genomes.

Remarkable advances in DNA sequencing technology have created a need for de novo genome assembly methods tailored to work with the new sequencing data types. Many such methods have been published in recent years, but assembling raw sequence data to obtain a draft genome has remained a complex, multi-step process, involving several stages of sequence data cleaning, error correction, assembly, and quality control. Successful application of these steps usually requires intimate knowledge of a diverse set of algorithms and software.

Yeast communities of diverse Drosophila species: comparison of two symbiont groups in the same hosts.

The combination of ecological diversity with genetic and experimental tractability makes Drosophila a powerful model for the study of animal-associated microbial communities. Despite the known importance of yeasts in Drosophila physiology, behavior, and fitness, most recent work has focused on Drosophila-bacterial interactions. In order to get a more complete understanding of the Drosophila microbiome, we characterized the yeast communities associated with different Drosophila species collected around the world.

Sequencing of seven haloarchaeal genomes reveals patterns of genomic flux.

We report the sequencing of seven genomes from two haloarchaeal genera, Haloferax and Haloarcula. Ease of cultivation and the existence of well-developed genetic and biochemical tools for several diverse haloarchaeal species make haloarchaea a model group for the study of archaeal biology. The unique physiological properties of these organisms also make them good candidates for novel enzyme discovery for biotechnological applications.

A comparison of insight in body dysmorphic disorder and obsessive-compulsive disorder.

Insight/delusionality of beliefs is an important dimension of psychopathology across psychiatric disorders. This construct is of increasing interest in obsessive-compulsive and related disorders, including obsessive-compulsive disorder (OCD) and body dysmorphic disorder (BDD). Even though OCD and BDD are considered closely related, no prior study has compared these disorders across a range of categories of global insight (excellent, good, fair, poor, absent/delusional), and only one study has compared these disorders on individual components of insight.

Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)).

Deinococcus proteolyticus (ex Kobatake et al. 1973) Brook and Murray 1981 is one of currently 47 species in the genus Deinococcus within the family Deinococcaceae. Strain MRP(T) was isolated from feces of Lama glama and possesses extreme radiation resistance, a trait is shares with various other species of the genus Deinococcus, with D.