Engaging teenagers with genetics and genomics through a school-based competition: Pilot evaluation

As part of a university outreach programme, the authors ran an interschool competition encouraging youngpeople (year 10, age 14–15) to explore their ideas about the likely social impacts of whole genome screening. Schoolsparticipating in the competition selected teams of 4–5 young people who participated in a one day workshop. Thisworkshop provided an introduction to whole genome screening, what it is and what it might (and might not) be able totell us about our future health. The workshop also included sessions on communicating scientific ideas through film (e.g.storyboarding and basic editing). Students were then instructed to create a 4–6 minute film about genomics and whatissues it might present for individuals and/or society. Students reconvened for a second workshop to view and discuss thefilms created. This paper focuses on a thematic analysis of the films entered in the competition, exploring the issues thatstudents raise. In addition to the thematic analysis, quantitative and qualitative data were collected that enable apreliminary exploration of student learning. This will be explored in the context of what students of this age already knowand how they have built upon this learning during the competition

An Empirical Study of Dynamic Scheduling on Rings of Processors

The authors empirically analyze and compare two distributed low-overhead policies for scheduling dynamic tree-structured computations on rings of identical PEs. The experiments show that both policies give significant parallel speedup on large classes of computations, and that one yields almost optimal speedup on moderate size rings. They believe that the methodology of experiment design and analysis will prove useful in other such studies

Chromosomal ampC mutations in cefpodoxime-resistant ESBL-negative uropathogenic escherichia coli

AmpC beta-lactamase is an enzyme commonly produced by Escherichia coli that causes resistance to cephalosporins and penicillins. Enzyme production is controlled by the strength of the promoter encoded by the chromosomal ampC gene, with the level of production affected by the presence of certain mutations in this region. This study sets out to determine the prevalence of ampC promoter mutations present in a group of uropathogenic E. coli strains. A total of 50 clinical strains of E. coli were collected from urine samples between June 2011 and November 2011. Strains were investigated for the presence of mutations in the chromosomal ampC promoter region by amplification and sequencing of a 271 bp product. The presence of ampC-carrying plasmids derived from other species was also determined, to exclude these from further analysis. ampC-carrying plasmids were found in 10 of the 50 strains, all of which were of the CIT-type. Analysis of the chromosomal ampC promoter region in the 40 remaining strains showed mutations at 16 different positions, with 18 different genotype patterns detected overall. The most common ampC chromosomal mutation, present in 25 of 40 strains, was a T→A transition at position -32. This mutation has been shown by others to increase enzyme production by up to 46-fold. Altogether, three separate mutations (-32, -42 and -13ins) were present in 90% of the 40 non-plasmid strains, indicating a strong association with the resistance observed. It appears, therefore, that the majority of AmpC-mediated resistance in E. coli can be accounted for by just three point mutations in the chromosome

Multi-locus sequence typing of Escherichia coli isolates with acquired ampC genes and ampC promoter mutations

© 2016 Elsevier Inc. Multi-locus sequence typing was used to reveal a high degree of diversity amongst the E. coli isolates with AmpC plasmid genes, and a high prevalence of the −32 mutation present

Genotypic and phenotypic analyses reveal distinct population structures and ecotypes for sugar beet-associated Pseudomonas in Oxford and Auckland

Fluorescent pseudomonads represent one of the largest groups of bacteria inhabiting the surfaces of plants, but their genetic composition in planta is poorly understood. Here, we examined the population structure and diversity of fluorescent pseudomonads isolated from sugar beet grown at two geographic locations (Oxford, United Kingdom and Auckland, New Zealand). To seek evidence for niche adaptation, bacteria were sampled from three types of leaves (immature, mature, and senescent) and then characterized using a combination of genotypic and phenotypic analysis. We first performed multilocus sequence analysis (MLSA) of three housekeeping genes (gapA, gltA, and acnB) in a total of 152 isolates (96 from Oxford, 56 from Auckland). The concatenated sequences were grouped into 81 sequence types and 22 distinct operational taxonomic units (OTUs). Significant levels of recombination were detected, particularly for the Oxford isolates (rate of recombination to mutation (r/m) = 5.23 for the whole population). Subsequent ancestral analysis performed in STRUCTURE found evidence of six ancestral populations, and their distributions significantly differed between Oxford and Auckland. Next, their ability to grow on 95 carbon sources was assessed using the Biolog™ GN2 microtiter plates. A distance matrix was generated from the raw growth data (A660) and subjected to multidimensional scaling (MDS) analysis. There was a significant correlation between substrate utilization profiles and MLSA genotypes. Both phenotypic and genotypic analyses indicated presence of a geographic structure for strains from Oxford and Auckland. Significant differences were also detected for MLSA genotypes between strains isolated from immature versus mature/senescent leaves. The fluorescent pseudomonads thus showed an ecotypic population structure, suggestive of adaptation to both geographic conditions and local plant niches

Serum Zinc Correlates with Parent- and Teacher-Rated Inattention in Children with Attention-Deficit/Hyperactivity Disorder

Objective: The aim of this study was to explore the relationship of zinc nutrition to the severity of attentiondeficit/ hyperactivity disorder (ADHD) symptoms in a middle-class American sample with well-diagnosed ADHD. Previous reports of zinc in ADHD, including two positive clinical trials of supplementation, have come mainly from countries and cultures with different diets and/or socioeconomic realities. Method: Children 5–10 years of age with DISC- and clinician-diagnosed ADHD had serum zinc determinations and parent and teacher ratings of ADHD symptoms. Zinc levels were correlated (Pearson’s and multiple regression) with ADHD symptom ratings. Results: Forty-eight children (37 boys, 11 girls; 33 combined type, 15 inattentive) had serum zinc levels with a median/mode at the lowest 30% of the laboratory reference range; 44 children also had parent/teacher ratings. Serum magnesium levels were normal. Nutritional intake by a parent-answered food frequency questionnaire was unremarkable. Serum zinc correlated at r = -0.45 (p = 0.004) with parent-teacher-rated inattention, even after controlling for gender, age, income, and diagnostic subtype, but only at r = -0.20 (p = 0.22) with CPT omission errors. In contrast, correlation with parent-teacher-rated hyperactivity-impulsivity was nonsignificant in the opposite direction. Conclusion: These findings add to accumulating evidence for a possible role of zinc in ADHD, even for middle-class Americans, and, for the first time, suggest a special relationship to inattentive symptoms. They do not establish either that zinc deficiency causes ADHD nor that ADHD should be treated with zinc. Hypothesis-testing clinical trials are needed

Vestibular Stimulation for ADHD: Randomized Controlled Trial of Comprehensive Motion Apparatus

Objective: This research evaluates effects of vestibular stimulation by Comprehensive Motion Apparatus (CMA) in ADHD. Method: Children ages 6 to 12 (48 boys, 5 girls) with ADHD were randomized to thrice-weekly 30-min treatments for 12 weeks with CMA, stimulating otoliths and semicircular canals, or a single-blind control of equal duration and intensity, each treatment followed by a 20-min typing tutorial. Results: In intent-to-treat analysis (n = 50), primary outcome improved significantly in both groups (p = .0001, d = 1.09 to 1.30), but treatment difference not significant (p = .7). Control children regressed by follow-up (difference p = .034, d = 0.65), but overall difference was not significant (p = .13, d = .47). No measure showed significant treatment differences at treatment end, but one did at follow-up. Children with IQ-achievement discrepancy ≥ 1 SD showed significantly more CMA advantage on three measures. Conclusion: This study illustrates the importance of a credible control condition of equal duration and intensity in trials of novel treatments. CMA treatment cannot be recommended for combined-type ADHD without learning disorder

Pseudomonas syringae Differentiates into Phenotypically Distinct Subpopulations During Colonization of a Plant Host

Bacterial microcolonies with heterogeneous sizes are formed during colonization of Phaseolus vulgaris by Pseudomonas syringae. Heterogeneous expression of structural and regulatory components of the P. syringae type III secretion system (T3SS), essential for colonization of the host apoplast and disease development, is likewise detected within the plant apoplast. T3SS expression is bistable in the homogeneous environment of nutrient-limited T3SS-inducing medium, suggesting that subpopulation formation is not a response to different environmental cues. T3SS bistability is reversible, indicating a non-genetic origin, and the T3SSHIGH and T3SSLOW subpopulations show differences in virulence. T3SS bistability requires the transcriptional activator HrpL, the double negative regulatory loop established by HrpV and HrpG, and may be enhanced through a positive feedback loop involving HrpA, the main component of the T3SS pilus. To our knowledge, this is the first example of phenotypic heterogeneity in the expression of virulence determinants during colonization of a non-mammalian host.Ministerio de Ciencia e Innovación BIO2009-11516, AGL2010-22287-C02-2Ministerio de Economía y Competitividad BIO2012-35641, BIO2015-64391-

The stealth episome: suppression of gene expression on the excised genomic island PPHGI-1 from Pseudomonas syringae pv. phaseolicola

Pseudomonas syringae pv. phaseolicola is the causative agent of halo blight in the common bean, Phaseolus vulgaris. P. syringae pv. phaseolicola race 4 strain 1302A contains the avirulence gene avrPphB (syn. hopAR1), which resides on PPHGI-1, a 106 kb genomic island. Loss of PPHGI-1 from P. syringae pv. phaseolicola 1302A following exposure to the hypersensitive resistance response (HR) leads to the evolution of strains with altered virulence. Here we have used fluorescent protein reporter systems to gain insight into the mobility of PPHGI-1. Confocal imaging of dual-labelled P. syringae pv. phaseolicola 1302A strain, F532 (dsRFP in chromosome and eGFP in PPHGI-1), revealed loss of PPHGI-1::eGFP encoded fluorescence during plant infection and when grown in vitro on extracted leaf apoplastic fluids. Fluorescence-activated cell sorting (FACS) of fluorescent and non-fluorescent PPHGI-1::eGFP F532 populations showed that cells lost fluorescence not only when the GI was deleted, but also when it had excised and was present as a circular episome. In addition to reduced expression of eGFP, quantitative PCR on sub-populations separated by FACS showed that transcription of other genes on PPHGI-1 (avrPphB and xerC) was also greatly reduced in F532 cells harbouring the excised PPHGI-1::eGFP episome. Our results show how virulence determinants located on mobile pathogenicity islands may be hidden from detection by host surveillance systems through the suppression of gene expression in the episomal state

Rahnella perminowiae sp. nov., Rahnella bonaserana sp. nov., Rahnella rivi sp. nov. and Rahnella ecdela sp. nov., isolated from diverse environmental sources, and emended description of the genus Rahnella

Bacteria isolated from onion bulbs suffering from bacterial decay in the United States and Norway were previously shown to belong to the genus Rahnella based on partial housekeeping gene sequences and/or fatty acid analysis. However, many strains could not be assigned to any existing Rahnella species. Additionally, strains isolated from creek water and oak as well as a strain with bioremediation properties were assigned to Rahnella based on partial housekeeping gene sequences. The taxonomic status of these 21 strains was investigated using multilocus sequence analysis, whole genome analyses, phenotypic assays and fatty acid analysis. Phylogenetic and phylogenomic analyses separated the strains into five clusters, one of which corresponded to Rahnella aceris. The remaining four clusters could be differentiated both genotypically and phenotypically from each other and existing Rahnella species. Based on these results, we propose the description of four novel species: Rahnella perminowiae sp. nov. (type strain SL6T=LMG 32257T=DSM 112609T), Rahnella bonaserana sp. nov. (H11bT=LMG 32256T=DSM 112610T), Rahnella rivi sp. nov. (FC061912-KT=LMG 32259T=DSM 112611T) and Rahnella ecdela sp. nov. (FRB 231T=LMG 32255T=DSM 112612T).This research was supported by the UK Research and Innovation’s (UKRI) Strategic Priorities Fund (SPF) programme on Bacterial Plant Diseases (grant BB/T010886/1) funded by the Biotechnology and Biological Sciences Research Council (BBSRC), the Department for Environment, Food and Rural Affairs (Defra), the Natural Environment Research Council (NERC) and the Scottish Government. CB received additional funding from Woodland Heritage, BC and SD received funding from the Forestry Commission.https://www.microbiologyresearch.org/content/journal/ijsemBiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog