Creation of Golden Gate constructs for gene doctoring

Background: Gene doctoring is an efficient recombination-based genetic engineering approach to mutagenesis of the bacterial chromosome that combines the λ-Red recombination system with a suicide donor plasmid that is cleaved in vivo to generate linear DNA fragments suitable for recombination. The use of a suicide donor plasmid makes Gene Doctoring more efficient than other recombineering technologies. However, generation of donor plasmids typically requires multiple cloning and screening steps. Results: We constructed a simplified acceptor plasmid, called pDOC-GG, for the assembly of multiple DNA fragments precisely and simultaneously to form a donor plasmid using Golden Gate assembly. Successful constructs can easily be identified through blue-white screening. We demonstrated proof of principle by inserting a gene for green fluorescent protein into the chromosome of Escherichia coli. We also provided related genetic parts to assist in the construction of mutagenesis cassettes with a tetracycline-selectable marker. Conclusions: Our plasmid greatly simplifies the construction of Gene Doctoring donor plasmids and allows for the assembly of complex, multi-part insertion or deletion cassettes with a free choice of target sites and selection markers. The tools we developed are applicable to gene editing for a wide variety of purposes in Enterobacteriaceae and potentially in other diverse bacterial families

rPinecone : Define sub-lineages of a clonal expansion via a phylogenetic tree

The ability to distinguish different circulating pathogen clones from each other is a fundamental requirement to understand the epidemiology of infectious diseases. Phylogenetic analysis of genomic data can provide a powerful platform to identify lineages within bacterial populations, and thus inform outbreak investigation and transmission dynamics. However, resolving differences between pathogens associated with low-variant (LV) populations carrying low median pairwise single nucleotide variant (SNV) distances remains a major challenge. Here we present rPinecone, an R package designed to define sub-lineages within closely related LV populations. rPinecone uses a root-to-tip directional approach to define sub-lineages within a phylogenetic tree according to SNV distance from the ancestral node. The utility of this software was demonstrated using both simulated outbreaks and real genomic data of two LV populations: a hospital outbreak of methicillin-resistant Staphylococcus aureus and endemic Salmonella Typhi from rural Cambodia. rPinecone identified the transmission branches of the hospital outbreak and geographically confined lineages in Cambodia. Sub-lineages identified by rPinecone in both analyses were phylogenetically robust. It is anticipated that rPinecone can be used to discriminate between lineages of bacteria from LV populations where other methods fail, enabling a deeper understanding of infectious disease epidemiology for public health purposes.Peer reviewe

Giant flagellins form thick flagellar filaments in two species of marine γ-proteobacteria

Flagella, the primary means of motility in bacteria, are helical filaments that function as microscopic propellers composed of thousands of copies of the protein flagellin. Here, we show that many bacteria encode “giant” flagellins, greater than a thousand amino acids in length, and that two species that encode giant flagellins, the marine γ-proteobacteria Bermanella marisrubri and Oleibacter marinus, produce monopolar flagellar filaments considerably thicker than filaments composed of shorter flagellin monomers. We confirm that the flagellum from B. marisrubri is built from its giant flagellin. Phylogenetic analysis reveals that the mechanism of evolution of giant flagellins has followed a stepwise process involving an internal domain duplication followed by insertion of an additional novel insert. This work illustrates how “the” bacterial flagellum should not be seen as a single, idealised structure, but as a continuum of evolved machines adapted to a range of niches

Forage grasses with lower uptake of casesium and strontium could provide 'safer' crops for radiologically contaminated areas

Substitution of a species or cultivar with higher uptake of an element by one with lower uptake has been proposed as a remediation strategy following accidental releases of radioactivity. However, despite the importance of pasture systems for radiological dose, species/cultivar substitution has not been thoroughly investigated for forage grasses. 397 cultivars from four forage grass species; hybrid ryegrass (Lolium perenne L. x Lolium multiflorum Lam.), perennial ryegrass (Lolium perenne L.), Italian ryegrass (Lolium multiflorum Lam.) and tall fescue (Festuca arundinacea Shreb.); were sampled from 19 field-based breeding experiments in Aberystwyth and Edinburgh (UK) in spring 2013 and analysed for caesium (Cs) and strontium (Sr) concentrations. In order to calculate concentration ratios (CRs; the concentration of an element in a plant in relation to the concentration in the soil), soils from the experiments were also analysed to calculate extractable concentrations of Cs and Sr. To test if cultivars have consistently low Cs and Sr concentration ratios, 17 hybrid ryegrass cultivars were sampled from both sites again in summer 2013 and spring and summer 2014. Tall fescue cultivars had lower Cs and Sr CRs than the other species. Three of the selected 17 hybrid ryegrass cultivars had consistently low Cs CRs, two had consistently low Sr CRs and one had consistently low Cs and Sr CRs. Cultivar substitution could reduce Cs CRs by up to 14-fold and Sr CRs by 4-fold in hybrid ryegrass. The identification of species and cultivars with consistently low CRs suggests that species or cultivar substitution could be an effective remediation strategy for contaminated areas

Amikacin use and therapeutic drug monitoring in adults : do dose regimens and drug exposures affect either outcome or adverse events? A systematic review

Objectives To identify the amikacin dosage regimens and drug concentrations consistent with good outcomes and to determine the drug exposures related to nephrotoxicity and ototoxicity. Methods A literature review was conducted in Medline, EMBASE and the Cochrane Central Register of Controlled Trials. Full journal articles of randomised controlled trials, controlled clinical trials, interrupted time series trials and controlled before and after studies involving amikacin TDM and dose adjustment were considered for inclusion. Results Seventeen included studies were identified, comprising 1677 participants. Amikacin doses ranged from 11-15 mg/kg/day with thirteen studies using 15 mg/kg/day. Studies were generally designed to compare different aminoglycosides rather than to assess concentration-effect relationships. Only eleven papers presented data on target concentrations, rate of clinical cure and toxicity. Target peak concentrations ranged from 15 – 40 mg/L and target troughs were typically <10 mg/L or <5 mg/L. It was not clear whether these targets were achieved. Measured peaks averaged 28 mg/L for twice daily dosing and 40-45 mg/L for once daily dosing; troughs averaged 5 mg/L and 1-2 mg/L, respectively. Fifteen of the included studies reported rates of nephrotoxicity; auditory and vestibular toxicities were reported in twelve and eight studies. Conclusions This systematic review found little published evidence to support an optimal dosage regimen or TDM targets for amikacin therapy. The use of alternative approaches, such as consensus opinion and a review of current practice, will be required to develop guidelines to maximise therapeutic outcomes and minimise toxicity with amikacin

A putative, novel coli surface antigen 8B (CS8B) of enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) strains harbor multiple fimbriae and pili to mediate host colonization, including the type IVb pilus, colonization factor antigen III (CFA/III). Not all colonization factors are well characterized or known in toxin positive ETEC isolates, which may have an impact identifying ETEC isolates based on molecular screening of these biomarkers. We describe a novel coli surface antigen (CS) 8 subtype B (CS8B), a family of CFA/III pilus, in a toxin producing ETEC isolate from a Kenyan collection. In highlighting the existence of this putative CS, we provide the sequence and specific primers, which can be used alongside other ETEC primers previously described

Skin Conductance Responses to a Discrete Threat in Virtual Reality: Associations with Psychopathy and Anxiety

People with high levels of psychopathic traits are often described as fearless and lacking in emotional depth, particularly when evaluating threats in their environments. Skin conductance responsivity (SCR) to negative emotional stimuli represents a robust autonomic correlate of conduct problem behavior in children (Fanti et al., in Neuroscience and Biobehavioral Reviews, 100, 98–107, 2019). However, studies that have examined threat-related processing in youth with conduct problems have tended to use a variety of negative stimuli that might induce various and unspecific negative emotions. Few studies have taken in to account the moderating effects of anxiety on the relationship of distinct psychopathic traits (e.g., narcissism, callousness, impulsivity) with SCR to a fear inducing stimulus. In this study, we examined SCR to a virtual reality rollercoaster drop – that is, a discrete fear inducing event – in a sample of 75 youths (61 males; M = 14 years, SD = 1.4) enrolled in a non-mainstream school. The rollercoaster drop was used to more clearly examine an event-related response to a discrete threat, rather than examining SCR throughout the rollercoaster ride. We used the teacher-reported Antisocial Process Screening Device (Frick & Hare, in Antisocial process screening device: APSD. Toronto: Multi-Health Systems, 2001) to examine the relations of distinct psychopathic traits with SCR and self-reported anxiety. Lower anxiety was associated with higher callousness, but only in youths with low SCR to discrete threat. These findings suggest that fear and anxiety show complex and interactive relations with distinct psychopathic traits

Autonomous metabolic reprogramming and oxidative stress characterize endothelial dysfunction in acute myocardial infarction

Background: Compelling evidence has accumulated on the role of oxidative stress on the endothelial cell (EC) dysfunction underlying acute coronary syndrome. However, unveiling the underlying metabolic determinants has been hampered by the scarcity of appropriate cell models to address cell-autonomous mechanisms of ED dysfunction. Methods: We have generated endothelial cells derived from thrombectomy specimens from patients affected with acute myocardial infarction (AMI) and conducted phenotypical and metabolic characterization, focused on central carbon metabolism. Results: AMI-derived endothelial cells (AMIECs), but not control healthy coronary endothelial cells, display impaired growth, migration and tubulogenesis. Metabolically, AMIECs displayed augmented reactive oxygen species (ROS) and glutathione intracellular content, along with a diminished glucose consumption coupled to high lactate production. Consistent with diminished glycolysis in AMIECs, the protein levels of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase type 3, PFKFB3, were downregulated. In contrast, PFKFB4 levels were upregulated, suggesting a shunting of glycolysis towards the pentose phosphate pathway (PPP), supported by upregulation in AMIECs of G6PD, the key enzyme in the oxidative branch of the PPP. Further, the glutaminolytic enzyme GLS was upregulated in AMIECs, providing a mechanistic explanation for the observed increase in glutathione content. Finally, AMIECs displayed a significantly higher mitochondrial membrane potential than control ECs, which, together with high ROS levels, suggest a highly coupled mitochondrial activity in patient ECs. Conclusions: We suggest high mitochondrial proton coupling underlies the abnormally high production of ROS, balanced by PPP- and glutaminolysis-driven synthesis of glutathione, as a primary, cell-autonomous abnormality driving EC dysfunction in AMI. Funding: European Commission Horizon 2020; CIBER- Carlos III National Institute of Health, Spain; Ministerio de Economia y Competitividad (MINECO) and Ministerio de Ciencia e Innovación, Spain; Generalitat de Catalunya-AGAUR, Catalonia; Plataforma Temática Interdisciplinar Salud Global (PTI-SG), Spain; British Heart Foundation, UK. </p

Genetic parameters of color phenotypes of black tiger shrimp (Penaeus monodon)

Black tiger shrimp (Penaeus monodon) is the second most important aquaculture species of shrimp in the world. In addition to growth traits, uncooked and cooked body color of shrimp are traits of significance for profitability and consumer acceptance. This study investigated for the first time, the phenotypic and genetic variances and relationships for body weight and body color traits, obtained from image analyses of 838 shrimp, representing the progeny from 55 sires and 52 dams. The color of uncooked shrimp was subjectively scored on a scale from 1 to 4, with “1” being the lightest/pale color and “4” being the darkest color. For cooked shrimp color, shrimp were graded firstly by subjective scoring using a commercial grading score card, where the score ranged from 1 to 12 representing light to deep coloration which was subsequently found to not be sufficiently reliable with poor repeatability of measurement (r = 0.68–0.78) Therefore, all images of cooked color were regraded on a three-point scale from brightest and lightest colored cooked shrimp, to darkest and most color-intense, with a high repeatability (r = 0.80–0.92). Objective color of both cooked and uncooked color was obtained by measurement of RGB intensities (values range from 0 to 255) for each pixel from each shrimp. Using the “convertColor” function in “R”, the RGB values were converted to L*a*b* (CIE Lab) systems of color properties. This system of color space was established in 1976, by the International Commission of Illumination (CIE) where “L*” represents the measure of degree of lightness, values range from 0 to 100, where 0 = pure black and 100 = pure white. The value “a*” represents red to green coloration, where a positive value represents the color progression towards red and a negative value towards green. The value “b*” represents blue to yellow coloration, where a positive value refers to more yellowish and negative towards the blue coloration. In total, eight color-related traits were investigated. An ordinal mixed (threshold) model was adopted for manually (subjectively) scored color phenotypes, whereas all other traits were analyzed by linear mixed models using ASReml software to derive variance components and estimated breeding values (EBVs). Moderate to low heritability estimates (0.05–0.35) were obtained for body color traits. For subjectively scored cooked and uncooked color, EBV-based selection would result in substantial genetic improvement in these traits. The genetic correlations among cooked, uncooked and body weight traits were high and ranged from −0.88 to 0.81. These suggest for the first time that 1) cooked color can be improved indirectly by genetic selection based on color of uncooked/live shrimp, and 2) intensity of coloration is positively correlated with body weight traits and hence selection for body weight will also improve color traits in this population

Contrasting patterns of longitudinal population dynamics and antimicrobial resistance mechanisms in two priority bacterial pathogens over 7 years in a single center

Abstract: Background: Two of the most important pathogens contributing to the global rise in antimicrobial resistance (AMR) are Klebsiella pneumoniae and Enterobacter cloacae. Despite this, most of our knowledge about the changing patterns of disease caused by these two pathogens is based on studies with limited timeframes that provide few insights into their population dynamics or the dynamics in AMR elements that they can carry. Results: We investigate the population dynamics of two priority AMR pathogens over 7 years between 2007 and 2012 in a major UK hospital, spanning changes made to UK national antimicrobial prescribing policy in 2007. Between 2006 and 2012, K. pneumoniae showed epidemiological cycles of multi-drug-resistant (MDR) lineages being replaced approximately every 2 years. This contrasted E. cloacae where there was no temporally changing pattern, but a continuous presence of the mixed population. Conclusions: The differing patterns of clonal replacement and acquisition of mobile elements shows that the flux in the K. pneumoniae population was linked to the introduction of globally recognized MDR clones carrying drug resistance markers on mobile elements. However, E. cloacae carries a chromosomally encoded ampC conferring resistance to front-line treatments and shows that MDR plasmid acquisition in E. cloacae was not indicative of success in the hospital. This led to markedly different dynamics in the AMR populations of these two pathogens and shows that the mechanism of the resistance and its location in the genome or mobile elements is crucial to predict population dynamics of opportunistic pathogens in clinical settings