Optimizing DNA Extraction Methods for Nanopore Sequencing of Neisseria gonorrhoeae Directly from Urine Samples

Empirical gonorrhea treatment at initial diagnosis reduces onward transmission. However, increasing resistance to multiple antibiotics may necessitate waiting for culture-based diagnostics to select an effective treatment. There is a need for same-day culture-free diagnostics that identify infection and detect antimicrobial resistance. We investigated if Nanopore sequencing can detect sufficient Neisseria gonorrhoeae DNA to reconstruct whole genomes directly from urine samples. We used N. gonorrhoeae-spiked urine samples and samples from gonorrhea infections to determine optimal DNA extraction methods that maximize the amount of N. gonorrhoeae DNA sequenced while minimizing contaminating host DNA. In simulated infections, the Qiagen UCP pathogen mini kit provided the highest ratio of N. gonorrhoeae to human DNA and the most consistent results. Depletion of human DNA with saponin increased N. gonorrhoeae yields in simulated infections but decreased yields in clinical samples. In 10 urine samples from men with symptomatic urethral gonorrhea, ≥92.8% coverage of an N. gonorrhoeae reference genome was achieved in all samples, with ≥93.8% coverage breath at ≥10-fold depth in 7 (70%) samples. In simulated infections, if ≥104 CFU/ml of N. gonorrhoeae was present, sequencing of the large majority of the genome was frequently achieved. N. gonorrhoeae could also be detected from urine in cobas PCR medium tubes and from urethral swabs and in the presence of simulated Chlamydia coinfection. Using Nanopore sequencing of urine samples from men with urethral gonorrhea, sufficient data can be obtained to reconstruct whole genomes in the majority of samples without the need for culture

Rotation and Spin in Physics

We delineate the role of rotation and spin in physics, discussing in order Newtonian classical physics, special relativity, quantum mechanics, quantum electrodynamics and general relativity. In the latter case, we discuss the generalization of the Kepler formula to post-Newtonian order $(c^{-2}$) including spin effects and two-body effects. Experiments which verify the theoretical results for general relativistic spin-orbit effects are discussed as well as efforts being made to verify the spin-spin effects

A cluster randomized trial evaluating electronic prescribing in an ambulatory care setting

<p>Abstract</p> <p>Background</p> <p>Medication errors, adverse drug events and potential adverse drug events are common and serious in terms of the harms and costs that they impose on the health system and those who use it. Errors resulting in preventable adverse drug events have been shown to occur most often at the stages of ordering and administration. This paper describes the protocol for a pragmatic trial of electronic prescribing to reduce prescription error. The trial was designed to overcome the limitations associated with traditional study design.</p> <p>Design</p> <p>This study was designed as a 65-week, cluster randomized, parallel study.</p> <p>Methods</p> <p>The trial was conducted within ambulatory outpatient clinics in an academic tertiary care centre in Ontario, Canada. The electronic prescribing software for the study is a Canadian electronic prescribing software package which provides physician prescription entry with decision support at the point of care. Using a handheld computer (PDA) the physician selects medications using an error minimising menu-based pick list from a comprehensive drug database, create specific prescription instructions and then transmit the prescription directly and electronically to a participating pharmacy via facsimile or to the physician's printer using local area wireless technology. The unit of allocation and randomization is by 'week', i.e. the system is "on" or "off" according to the randomization scheme and the unit of analysis is the prescription, with adjustment for clustering of patients within practitioners.</p> <p>Discussion</p> <p>This paper describes the protocol for a pragmatic cluster randomized trial of point-of-care electronic prescribing, which was specifically designed to overcome the limitations associated with traditional study design.</p> <p>Trial Registration</p> <p>This trial has been registered with clinicaltrials.gov (ID: NCT00252395)</p

Do Mismatches between Pre- and Post-Natal Environments Influence Adult Physiological Functioning?

Purpose: Mismatches between pre- and post-natal environments have implications for disease in adulthood. However, less is known about how this mismatch can affect physiological systems more generally, especially at younger ages. We hypothesised that mismatches between pre- and post-natal environments, as measured by the measures of birthweight and adult leg length, would be associated with poorer biomarker levels across five key physiological systems in young adults. Methods: Data were collected from 923, 36 year-old respondents from the West of Scotland Twenty-07 Study. The biomarkers were: systolic blood pressure (sBP); forced expiratory volume (FEV1); glycated haemoglobin (HbA1c); glomerular filtration rate (eGFR); and gamma- glutamyltransferase (GGT). These biomarkers were regressed against pre-natal conditions (birthweight), post-natal conditions (leg length) and the interaction between pre- and post-natal measures. Sex, childhood socioeconomic position and adult lifestyle characteristics were adjusted for as potential effect modifiers and confounders, respectively. Results: There were no associations between birthweight and leg length and sBP, FEV1, HbA1c, or GGT. Higher birthweight and longer leg length were associated with better kidney function (eGFR). However, there was no evidence for mismatches between birthweight and leg length to be associated with worse sBP, FEV1, HbA1c, eGFR or GGT levels (P>0.05). Conclusions: Our hypothesis that early signs of physiological damage would be present in young adults given mismatches in childhood environments, as measured by growth markers, was not proven. This lack of association could be because age 36 is too young to identify significant trends for future health, or the associations simply not being present. © 2014 Robertson, Benzeval

A study of association between common variation in the growth hormone-chorionic somatomammotropin hormone gene cluster and adult fasting insulin in a UK Caucasian population

BACKGROUND: Reduced growth during infancy is associated with adult insulin resistance. In a UK Caucasian cohort, the CSH1.01 microsatellite polymorphism in the growth hormone-chorionic somatomammotropin hormone gene cluster was recently associated with increases in adult fasting insulin of approximately 23 pmol/l for TT homozygote males compared to D1D1 or D2D2 homozygotes (P = 0.001 and 0.009; n = 206 and 92, respectively), but not for females. TT males additionally had a 547-g lower weight at 1 year (n = 270; P = 0.008) than D2D2 males. We sought to replicate these data in healthy UK Caucasian subjects. We genotyped 1396 subjects (fathers, mothers and children) from a consecutive birth study for the CSH1.01 marker and analysed genotypes for association with 1-year weight in boys and fasting insulin in fathers. RESULTS: We found no evidence for association of CSH1.01 genotype with adult male fasting insulin concentrations (TT/D1D1 P = 0.38; TT/D2D2 P = 0.18) or weight at 1 year in boys (TT/D1D1 P = 0.76; TT/D2D2 P = 0.85). For fasting insulin, our data can exclude the previously observed effect sizes as the 95 % confidence intervals for the differences observed in our study exclude increases in fasting insulin of 9.0 and 12.6 pmol/l for TT relative to D1D1 and D2D2 homozygotes, respectively. Whilst we have fewer data on boys' 1-year weight than the original study, our data can exclude a reduction in 1-year weight greater than 557 g for TT relative to D2D2 homozygotes. CONCLUSION: We have not found association of the CSH1.01 genotype with fasting insulin or weight at 1 year. We conclude that the original study is likely to have over-estimated the effect size for fasting insulin, or that the difference in results reflects the younger age of subjects in this study relative to those in the previous study

Interactions between the Nse3 and Nse4 Components of the SMC5-6 Complex Identify Evolutionarily Conserved Interactions between MAGE and EID Families

The SMC5-6 protein complex is involved in the cellular response to DNA damage. It is composed of 6-8 polypeptides, of which Nse1, Nse3 and Nse4 form a tight sub-complex. MAGEG1, the mammalian ortholog of Nse3, is the founding member of the MAGE (melanoma-associated antigen) protein family and Nse4 is related to the EID (E1A-like inhibitor of differentiation) family of transcriptional repressors.Using site-directed mutagenesis, protein-protein interaction analyses and molecular modelling, we have identified a conserved hydrophobic surface on the C-terminal domain of Nse3 that interacts with Nse4 and identified residues in its N-terminal domain that are essential for interaction with Nse1. We show that these interactions are conserved in the human orthologs. Furthermore, interaction of MAGEG1, the mammalian ortholog of Nse3, with NSE4b, one of the mammalian orthologs of Nse4, results in transcriptional co-activation of the nuclear receptor, steroidogenic factor 1 (SF1). In an examination of the evolutionary conservation of the Nse3-Nse4 interactions, we find that several MAGE proteins can interact with at least one of the NSE4/EID proteins.We have found that, despite the evolutionary diversification of the MAGE family, the characteristic hydrophobic surface shared by all MAGE proteins from yeast to humans mediates its binding to NSE4/EID proteins. Our work provides new insights into the interactions, evolution and functions of the enigmatic MAGE proteins

Genomic network analysis of environmental and livestock F-type 1 plasmid populations

F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation

Systemic multicompartmental effects of the gut microbiome on mouse metabolic phenotypes

To characterize the impact of gut microbiota on host metabolism, we investigated the multicompartmental metabolic profiles of a conventional mouse strain (C3H/HeJ) (n=5) and its germ-free (GF) equivalent (n=5). We confirm that the microbiome strongly impacts on the metabolism of bile acids through the enterohepatic cycle and gut metabolism (higher levels of phosphocholine and glycine in GF liver and marked higher levels of bile acids in three gut compartments). Furthermore we demonstrate that (1) well-defined metabolic differences exist in all examined compartments between the metabotypes of GF and conventional mice: bacterial co-metabolic products such as hippurate (urine) and 5-aminovalerate (colon epithelium) were found at reduced concentrations, whereas raffinose was only detected in GF colonic profiles. (2) The microbiome also influences kidney homeostasis with elevated levels of key cell volume regulators (betaine, choline, myo-inositol and so on) observed in GF kidneys. (3) Gut microbiota modulate metabotype expression at both local (gut) and global (biofluids, kidney, liver) system levels and hence influence the responses to a variety of dietary modulation and drug exposures relevant to personalized health-care investigations

Pulmonary cystic disease in HIV positive individuals in the Democratic Republic of Congo: three case reports

Pulmonary emphysema and bronchiectasis in HIV seropositive patients has been described in the presence of injection drug use, malnutrition, repeated opportunistic infections, such as Pneumocytis jirovici pneumonia and Mycobacterium tuberculosis infection, and has been linked to the presence of HIV virus in lung tissue. Given the high burden of pulmonary infections and malnutrition among people living with HIV in resource poor settings, these individuals may be at increased risk of developing pulmonary emphysema, potentially reducing the long term benefit of antiretroviral therapy (ART) if initiated late in the course of HIV infection

Psychiatric disorder in early adulthood and risk of premature mortality in the 1946 British Birth Cohort

<p>Abstract</p> <p>Background</p> <p>Few studies of the association between psychiatric disorder and premature death have adjusted for key confounders and used structured psychiatric interviews. We aimed to investigate if psychiatric disorder was associated with a higher risk of mortality and whether any excess mortality was due to suicide, or explained by other health or socioeconomic risk factors.</p> <p>Methods</p> <p>We used data from the MRC National Survey of Health and Development, a nationally representative UK birth cohort. 3283 men and women completed the Present State Examination at age 36. The main outcome measure was all-cause mortality before age 60.</p> <p>Results</p> <p>Those with psychiatric disorder at age 36 had a higher risk of death even after adjusting for potential confounders (Hazard ratio = 1.84, 95% C.I. 1.22-2.78). Censoring violent deaths and suicides led to similar results.</p> <p>Conclusions</p> <p>Psychiatric disorder was associated with excess premature mortality not explained by suicide or other health or socioeconomic risk factors.</p