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1.  Whole-Genome Sequences of 80 Environmental and Clinical Isolates of Burkholderia pseudomallei 
Genome Announcements  2015;3(1):e01282-14.
Here, we present the draft genome sequences of 80 isolates of Burkholderia pseudomallei. The isolates represent clinical cases of melioidosis and environmental isolates from regions in Australia and Papua New Guinea where B. pseudomallei is endemic. The genomes provide further context for the diversity of the pathogen.
doi:10.1128/genomeA.01282-14
PMCID: PMC4333647  PMID: 25676747
2.  Finished Genome Sequence of Bacillus cereus Strain 03BB87, a Clinical Isolate with B. anthracis Virulence Genes 
Genome Announcements  2015;3(1):e01446-14.
Bacillus cereus strain 03BB87, a blood culture isolate, originated in a 56-year-old male muller operator with a fatal case of pneumonia in 2003. Here we present the finished genome sequence of that pathogen, including a 5.46-Mb chromosome and two plasmids (209 and 52 Kb, respectively).
doi:10.1128/genomeA.01446-14
PMCID: PMC4299909  PMID: 25593267
3.  Draft Genome Sequence of Enterobacter cloacae Strain S611 
Genome Announcements  2014;2(6):e00710-14.
We report draft genomes of Enterobacter cloacae strain S611, an endophytic bacterium isolated from surface-sterilized germinating wheat seeds. We present the assembly and annotation of its genome, which may provide insights into the metabolic pathways involved in adaptation.
doi:10.1128/genomeA.00710-14
PMCID: PMC4263822  PMID: 25502660
4.  The Path to Triacylglyceride Obesity in the sta6 Strain of Chlamydomonas reinhardtii 
Eukaryotic Cell  2014;13(5):591-613.
When the sta6 (starch-null) strain of the green microalga Chlamydomonas reinhardtii is nitrogen starved in acetate and then “boosted” after 2 days with additional acetate, the cells become “obese” after 8 days, with triacylglyceride (TAG)-filled lipid bodies filling their cytoplasm and chloroplasts. To assess the transcriptional correlates of this response, the sta6 strain and the starch-forming cw15 strain were subjected to RNA-Seq analysis during the 2 days prior and 2 days after the boost, and the data were compared with published reports using other strains and growth conditions. During the 2 h after the boost, ∼425 genes are upregulated ≥2-fold and ∼875 genes are downregulated ≥2-fold in each strain. Expression of a small subset of “sensitive” genes, encoding enzymes involved in the glyoxylate and Calvin-Benson cycles, gluconeogenesis, and the pentose phosphate pathway, is responsive to culture conditions and genetic background as well as to boosting. Four genes—encoding a diacylglycerol acyltransferase (DGTT2), a glycerol-3-P dehydrogenase (GPD3), and two candidate lipases (Cre03.g155250 and Cre17.g735600)—are selectively upregulated in the sta6 strain. Although the bulk rate of acetate depletion from the medium is not boost enhanced, three candidate acetate permease-encoding genes in the GPR1/FUN34/YaaH superfamily are boost upregulated, and 13 of the “sensitive” genes are strongly responsive to the cell's acetate status. A cohort of 64 autophagy-related genes is downregulated by the boost. Our results indicate that the boost serves both to avert an autophagy program and to prolong the operation of key pathways that shuttle carbon from acetate into storage lipid, the combined outcome being enhanced TAG accumulation, notably in the sta6 strain.
doi:10.1128/EC.00013-14
PMCID: PMC4060482  PMID: 24585881
5.  Assessing an Intervention to Improve Clinical Trial Perceptions Among Predominately African-American Communities in South Carolina 
Background
African Americans (AA) are not well-represented in cancer clinical trials despite having significantly higher cancer mortality rates than their European-American (EA) counterparts.
Objectives
The purpose of this study was to evaluate a program to improve perceptions of cancer clinical trials among AA.
Methods
The program was conducted in a convenience sample of 195 participants (75.4% AA) who lived in counties with high racial disparities in cancer mortality rates and who were recruited by community partners. The 30-minute program, part of a larger 3.5-hour cancer education program, was developed by the National Institutes of Health (NIH)/ National Cancer Institute (NCI). It was modified to include additional pictures of AA, AA-specific cancer mortality data, and information about the Tuskegee Syphilis Study and the resulting improved participant protection measures.
Measures
The seven-item Attitudes to Randomized Trial Questionnaire (ARTQ) was used to evaluate changes in trial perceptions from pre- to posttest. Additional survey items assessed general demographic characteristics.
Results
Slightly more than half of the participants had at least a college diploma (54.4%), 45.1% were married/living as married, 53.3% were female, and 45.6% had an annual household income of less than $40,000. For each ARTQ item, most participants who had less favorable perceptions of trials at pretest changed to more positive perceptions at posttest (p < .001).
Conclusions
Providing cancer clinical trial information led to more positive perceptions of cancer clinical trials. In future studies, the program could be used to help potential trial participants make informed decisions about participation; trial enrollment rates could then be evaluated.
doi:10.1353/cpr.2012.0038
PMCID: PMC4180673  PMID: 22982839
Clinical trials; African Americans; underrepresentation; perceptions; knowledge
6.  Genome Sequencing of 15 Clinical Vibrio Isolates, Including 13 Non-O1/Non-O139 Serogroup Strains 
Genome Announcements  2014;2(5):e00893-14.
We present draft genome sequences of 15 clinical Vibrio isolates of various serogroups. These are valuable data for use in studying Vibrio cholerae genetic diversity, epidemic potential, and strain attribution.
doi:10.1128/genomeA.00893-14
PMCID: PMC4161747  PMID: 25212618
7.  Draft Genome Assembly of Acinetobacter baumannii ATCC 19606 
Genome Announcements  2014;2(4):e00832-14.
Acinetobacter baumannii is an emerging nosocomial pathogen, and therefore high-quality genome assemblies for this organism are needed to aid in detection, diagnostic, and treatment technologies. Here we present the improved draft assembly of A. baumannii ATCC 19606 in two scaffolds. This 3,953,621-bp genome contains 3,750 coding regions and has a 39.1% G+C content.
doi:10.1128/genomeA.00832-14
PMCID: PMC4153487  PMID: 25146140
8.  Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates 
Genome Announcements  2014;2(3):e00558-14.
Klebsiella pneumoniae, an ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogen, has acquired multiple antibiotic resistance genes and is becoming a serious public health threat. Here, we report the genome sequences of two representative strains of K. pneumoniae from the emerging K. pneumoniae carbapenemase (KPC) outbreak in northeast Ohio belonging to sequence type 258 (ST258) (isolates Kb140 and Kb677, which were isolated from blood and urine, respectively). Both isolates harbor a blaKPC gene, and strain Kb140 carries blaKPC-2, while Kb677 carries blaKPC-3.
doi:10.1128/genomeA.00558-14
PMCID: PMC4064024  PMID: 24948759
9.  Characterization of TEM-1 β-Lactamase-Producing Kingella kingae Clinical Isolates 
Kingella kingae is a human pathogen that causes pediatric osteoarticular infections and infective endocarditis in children and adults. The bacterium is usually susceptible to β-lactam antibiotics, although β-lactam resistance has been reported in rare isolates. This study was conducted to identify β-lactam-resistant strains and to characterize the resistance mechanism. Screening of a set of 90 K. kingae clinical isolates obtained from different geographic locations revealed high-level resistance to penicillins among 25% of the strains isolated from Minnesota and Iceland. These strains produced TEM-1 β-lactamase and were shown to contain additional ≥50-kb plasmids. Ion Torrent sequencing of extrachromosomal DNA from a β-lactamase-producing strain confirmed the plasmid location of the blaTEM gene. An identical plasmid pattern was demonstrated by multiplex PCR in all β-lactamase producers. The porin gene's fragments were analyzed to investigate the relatedness of bacterial strains. Phylogenetic analysis revealed 27 single-nucleotide polymorphisms (SNPs) in the por gene fragment, resulting in two major clusters with 11 allele types forming bacterial-strain subclusters. β-Lactamase producers were grouped together based on por genotyping. Our results suggest that the β-lactamase-producing strains likely originate from a single plasmid-bearing K. kingae isolate that traveled from Europe to the United States, or vice versa. This study highlights the prevalence of penicillin resistance among K. kingae strains in some regions and emphasizes the importance of surveillance for antibiotic resistance of the pathogen.
doi:10.1128/AAC.00318-13
PMCID: PMC3754283  PMID: 23796935
10.  Characterization of the Asian Citrus Psyllid Transcriptome 
Journal of Genomics  2014;2:54-58.
The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447].
doi:10.7150/jgen.7692
PMCID: PMC3914308  PMID: 24511328
Asian Citrus Psyllid; Diaphorina citri Kuwayama
11.  Characterization of the Asian Citrus Psyllid Transcriptome 
Journal of genomics  2014;2:54-58.
The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447].
doi:10.7150/jgen.7692
PMCID: PMC3914308  PMID: 24511328
Asian Citrus Psyllid; Diaphorina citri Kuwayama
12.  Draft Genome Sequence of Pseudomonas putida Strain S610, a Seed-Borne Bacterium of Wheat 
Genome Announcements  2013;1(6):e01048-13.
We report the genome sequence of a seed-borne bacterium, Pseudomonas putida strain S610. The size of the draft genome sequence is approximately 4.6 Mb, which is the smallest among all P. putida strains sequenced to date.
doi:10.1128/genomeA.01048-13
PMCID: PMC3873609  PMID: 24371199
13.  Draft Genome Sequences of Two Alginate-Overproducing Variants of Pseudomonas aeruginosa, PAO1-VE2 and PAO1-VE13 
Genome Announcements  2013;1(6):e01031-13.
The small envelope protein MucE and the sensor kinase KinB are a positive and negative alginate regulator, respectively. Here, we announce the draft genome sequences of the alginate-overproducing variants Pseudomonas aeruginosa PAO1-VE2 (PAO1 with constitutive expression of mucE) and PAO1-VE13 (PAO1 with kinB inactivated). Both mutants were generated from a transposon mutagenesis screen.
doi:10.1128/genomeA.01031-13
PMCID: PMC3861424  PMID: 24336371
14.  Complete Genome Sequence of Bacillus thuringiensis Serovar Israelensis Strain HD-789 
Genome Announcements  2013;1(6):e01023-13.
Bacillus thuringiensis is an important microbial insecticide for controlling agricultural pests. We report the finished genome sequence of Bacillus thuringiensis serovar israelensis strain HD-789, which contains genes encoding 7 parasporal crystals consisting of Cry4Aa3, Cry4Ba5 (2 genes), Cry10Aa3, Cry11Aa3, Cry60Ba3, and Cry60Aa3, plus 3 Cyt toxin genes and 1 hemagglutinin gene.
doi:10.1128/genomeA.01023-13
PMCID: PMC3853066  PMID: 24309743
15.  Draft Genome Sequence of a Stable Mucoid Strain of Pseudomonas aeruginosa PAO581 with a mucA25 Mutation 
Genome Announcements  2013;1(5):e00834-13.
A mutation in the mucA gene, which encodes a negative regulator of alginate production in Pseudomonas aeruginosa, is the main mechanism underlying the conversion to mucoidy in clinical isolates from patients with cystic fibrosis (CF). Here, we announce the draft genome sequence of the stable alginate-overproducing mucoid strain P. aeruginosa PAO581 with a mucA25 mutation, a derivative from the nonmucoid strains P. aeruginosa PAO381 and PAO1.
doi:10.1128/genomeA.00834-13
PMCID: PMC3795219  PMID: 24115549
16.  Draft Genome Sequence of a Mucoid Isolate of Pseudomonas aeruginosa Strain C7447m from a Patient with Cystic Fibrosis 
Genome Announcements  2013;1(5):e00837-13.
Alginate overproduction by Pseudomonas aeruginosa, or mucoidy, plays an important role in the pathogenesis of chronic lung infections in cystic fibrosis (CF) patients. Here we report the draft genome sequence of a clinical isolate of mucoid P. aeruginosa strain C7447m from a CF patient with chronic lung infection.
doi:10.1128/genomeA.00837-13
PMCID: PMC3795222  PMID: 24115552
17.  Complete Genome Sequence of the Encephalomyelitic Burkholderia pseudomallei Strain MSHR305 
Genome Announcements  2013;1(4):e00656-13.
We describe the complete genome sequence of Burkholderia pseudomallei MSHR305, a clinical isolate taken from a fatal encephalomyelitis case, a rare form of melioidosis. This sequence will be used for comparisons to identify the genes that are involved in neurological cases.
doi:10.1128/genomeA.00656-13
PMCID: PMC3751613  PMID: 23969058
18.  Systems Factorial Technology provides new insights on global–local information processing in autism spectrum disorders 
Previous studies of global–local processing in autism spectrum disorders (ASDs) have indicated mixed findings, with some evidence of a local processing bias, or preference for detail-level information, and other results suggesting typical global advantage, or preference for the whole or gestalt. Findings resulting from this paradigm have been used to argue for or against a detail focused processing bias in ASDs, and thus have important theoretical implications. We applied Systems Factorial Technology, and the associated Double Factorial Paradigm (both defined in the text), to examine information processing characteristics during a divided attention global–local task in high-functioning individuals with an ASD and typically developing controls. Group data revealed global advantage for both groups, contrary to some current theories of ASDs. Information processing models applied to each participant revealed that task performance, although showing no differences at the group level, was supported by different cognitive mechanisms in ASD participants compared to controls. All control participants demonstrated inhibitory parallel processing and the majority demonstrated a minimum-time stopping rule. In contrast, ASD participants showed exhaustive parallel processing with mild facilitatory interactions between global and local information. Thus our results indicate fundamental differences in the stopping rules and channel dependencies in individuals with an ASD.
doi:10.1016/j.jmp.2009.06.006
PMCID: PMC3676313  PMID: 23750050
Autism spectrum disorders; Information processing; Mathematical modeling; Serial; Parallel; Double factorial; Parallel interactive processing; Global and local perception; Divided attention; Weak Central Coherence
19.  Draft Genome Sequence for Pseudomonas aeruginosa Strain PAO579, a Mucoid Derivative of PAO381 
Journal of Bacteriology  2012;194(23):6617.
Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cystic fibrosis. Here, we announce the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing derivative of strain PAO381.
doi:10.1128/JB.01406-12
PMCID: PMC3497492  PMID: 23144378
20.  Addiction and “Generation Me:” Narcissistic and Prosocial Behaviors of Adolescents with Substance Dependency Disorder in Comparison to Normative Adolescents 
Alcoholism treatment quarterly  2012;30(2):163-178.
The purpose of this study is to explore narcissistic and prosocial behaviors as reported by adolescents with and without substance dependency disorder (SDD). This study employs a quasi-experimental design using SDD adolescents compared with two normative samples of adolescents. In comparison to normative adolescents, adolescents with SDD were strongly distinguished by overt narcissistic behaviors and less monetary giving. Levels of narcissistic and prosocial behaviors among adolescents with SDD suggest a connection between self-centeredness and addiction. Results also suggest volunteerism as a potential option to counter narcissism in substance dependent adolescents.
doi:10.1080/07347324.2012.663286
PMCID: PMC3335730  PMID: 22544995
narcissism; altruism; generation me; adolescents; addiction; substance dependence disorder
21.  Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands 
The ISME Journal  2011;6(4):886-897.
The impact of 10 years of annual foot trampling on soil biocrusts was examined in replicated field experiments at three cold desert sites of the Colorado Plateau, USA. Trampling detrimentally impacted lichens and mosses, and the keystone cyanobacterium, Microcoleus vaginatus, resulting in increased soil erosion and reduced C and N concentrations in surface soils. Trampled biocrusts contained approximately half as much extractable DNA and 20–52% less chlorophyll a when compared with intact biocrusts at each site. Two of the three sites also showed a decline in scytonemin-containing, diazotrophic cyanobacteria in trampled biocrusts. 16S rRNA gene sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses of soil bacteria from untrampled and trampled biocrusts demonstrated a reduced proportion (23–65% reduction) of M. vaginatus and other Cyanobacteria in trampled plots. In parallel, other soil bacterial species that are natural residents of biocrusts, specifically members of the Actinobacteria, Chloroflexi and Bacteroidetes, became more readily detected in trampled than in untrampled biocrusts. Replicate 16S rRNA T-RFLP profiles from trampled biocrusts at all three sites contained significantly more fragments (n=17) than those of untrampled biocrusts (n⩽6) and exhibited much higher variability among field replicates, indicating transition to an unstable disturbed state. Despite the dramatic negative impacts of trampling on biocrust physical structure and composition, M. vaginatus could still be detected in surface soils after 10 years of annual trampling, suggesting the potential for biocrust re-formation over time. Physical damage of biocrusts, in concert with changing temperature and precipitation patterns, has potential to alter performance of dryland ecosystems for decades.
doi:10.1038/ismej.2011.153
PMCID: PMC3309361  PMID: 22113374
chlorophyll a; cyanobacteria; Microcoleus vaginatus; soil biocrust; scytonemin; 16S rRNA
22.  Alcoholics Anonymous-Related Helping and the Helper Therapy Principle 
Alcoholism treatment quarterly  2011;29(1):23-34.
The helper therapy principle (HTP) observes the helper’s health benefits derived from helping another with a shared malady. The HTP is embodied by the program of Alcoholics Anonymous as a method to diminish egocentrism as a root cause of addiction. This article reviews recent evidence of the HTP in alcohol populations, extends to populations with chronic conditions beyond addiction, and concludes with new directions of empirical inquiry.
doi:10.1080/07347324.2011.538320
PMCID: PMC3603139  PMID: 23525280
Service; AA-related helping; substance use disorders; 12-Step programs
23.  Alveolar hydatid disease (Echinococcus multilocularis) in the liver of a Canadian dog in British Columbia, a newly endemic region 
The Canadian Veterinary Journal  2012;53(8):870-874.
An adult dog that lived in central British Columbia was examined because of a history of lethargy and vomiting. Histology, immunohistochemistry, and polymerase chain reaction (PCR) examination of a hepatic mass confirmed the presence of an alveolar hydatid cyst, the first description of Echinococcus multilocularis in British Columbia. We provide recommendations for case management and remind practitioners in endemic areas of western Canada that dogs can serve as definitive and, rarely, intermediate hosts for E. multilocularis.
PMCID: PMC3398525  PMID: 23372195
24.  A hybrid zone between Bathymodiolus mussel lineages from eastern Pacific hydrothermal vents 
Background
The inhabitants of deep-sea hydrothermal vents occupy ephemeral island-like habitats distributed sporadically along tectonic spreading-centers, back-arc basins, and volcanically active seamounts. The majority of vent taxa undergo a pelagic larval phase, and thus varying degrees of geographical subdivision, ranging from no impedance of dispersal to complete isolation, often exist among taxa that span common geomorphological boundaries. Two lineages of Bathymodiolus mussels segregate on either side of the Easter Microplate, a boundary that separates the East Pacific Rise from spreading centers connected to the Pacific-Antarctic Ridge.
Results
A recent sample from the northwest flank of the Easter Microplate contained an admixture of northern and southern mitochondrial haplotypes and corresponding alleles at five nuclear gene loci. Genotypic frequencies in this sample did not fit random mating expectation. Significant heterozygote deficiencies at nuclear loci and gametic disequilibria between loci suggested that this transitional region might be a ‘Tension Zone’ maintained by immigration of parental types and possibly hybrid unfitness. An analysis of recombination history in the nuclear genes suggests a prolonged history of parapatric contact between the two mussel lineages. We hereby elevate the southern lineage to species status as Bathymodiolus antarcticus n. sp. and restrict the use of Bathymodiolus thermophilus to the northern lineage.
Conclusions
Because B. thermophilus s.s. exhibits no evidence for subdivision or isolation-by-distance across its 4000 km range along the EPR axis and Galápagos Rift, partial isolation of B. antarcticus n. sp. requires explanation. The time needed to produce the observed degree of mitochondrial differentiation is consistent with the age of the Easter Microplate (2.5 to 5.3 million years). The complex geomorphology of the Easter Microplate region forces strong cross-axis currents that might disrupt self-recruitment of mussels by removing planktotrophic larvae from the ridge axis. Furthermore, frequent local extinction events in this tectonically dynamic region might produce a demographic sink rather than a source for dispersing mussel larvae. Historical changes in tectonic rates and current patterns appear to permit intermittent contact and introgression between the two species.
doi:10.1186/1471-2148-13-21
PMCID: PMC3740784  PMID: 23347448
Bathymodiolus antarcticus n. sp; Hybridization; Recombination; Linkage disequilibrium; Deep-sea; Hydrothermal vent; Bathymodiolus thermophilus
25.  φX216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity 
BMC Microbiology  2012;12:289.
Background
Burkholderia pseudomallei and B. mallei are closely related Category B Select Agents of bioterrorism and the causative agents of the diseases melioidosis and glanders, respectively. Rapid phage-based diagnostic tools would greatly benefit early recognition and treatment of these diseases. There is extensive strain-to-strain variation in B. pseudomallei genome content due in part to the presence or absence of integrated prophages. Several phages have previously been isolated from B. pseudomallei lysogens, for example φK96243, φ1026b and φ52237.
Results
We have isolated a P2-like bacteriophage, φX216, which infects 78% of all B. pseudomallei strains tested. φX216 also infects B. mallei, but not other Burkholderia species, including the closely related B. thailandensis and B. oklahomensis. The nature of the φX216 host receptor remains unclear but evidence indicates that in B. mallei φX216 uses lipopolysaccharide O-antigen but a different receptor in B. pseudomallei. The 37,637 bp genome of φX216 encodes 47 predicted open reading frames and shares 99.8% pairwise identity and an identical strain host range with bacteriophage φ52237. Closely related P2-like prophages appear to be widely distributed among B. pseudomallei strains but both φX216 and φ52237 readily infect prophage carrying strains.
Conclusions
The broad strain infectivity and high specificity for B. pseudomallei and B. mallei indicate that φX216 will provide a good platform for the development of phage-based diagnostics for these bacteria.
doi:10.1186/1471-2180-12-289
PMCID: PMC3548686  PMID: 23217012
Bacteriophage; Burkholderia pseudomallei; B. mallei; P2; Prophage distribution; Phage-based diagnostics

Results 1-25 (40)