H. pylori predictors and outcomes among adults undergoing upper endoscopy at a Jamaican teaching hospital: A cross-sectional study.

BACKGROUND: Recent data on the prevalence of H. pylori infection in Jamaica are lacking. It is postulated that there has been a decline in the prevalence of H. pylori infection and its associated complications. We determined sociodemographic characteristics, prevalence of H. pylori infection and clinical outcomes among adults undergoing esophagogastroduodenoscopy (EGD) and histology at the University Hospital of the West Indies (UHWI) between May 2018 and December 2020. MATERIALS AND METHODS: A cross-sectional study of patients (≥18 years old), who underwent EGD and histological evaluation for H. pylori infection, was conducted. Associations of H. pylori positivity and gastric cancer with sociodemographic/clinical variables and endoscopic findings were determined by stepwise logistic regression using backward selection. Unadjusted and adjusted odds ratios with related 95% confidence intervals (Cis) were calculated for H. pylori positivity and gastric cancer status. RESULTS: There were 323 participants (mean age 58.6 ± 17.8 years, 54.2% females). H. pylori prevalence was 22.2% (n = 70 of 315), 5.6% had gastric neoplasia (GN), 15.5% gastric atrophy, 11.4% intestinal metaplasia and 3.7% dysplasia on histology. Mucositis (64.5%), gastric ulcer (14.9%), and duodenal ulcer (13.9%) were the most common endoscopic findings. Participants with peptic ulcer disease (PUD) (unOR = 4.0; p = .017), gastric cancer (unOR = 9.5; p = .003), gastric atrophy (unOR = 12.8; p < .001), and intestinal metaplasia (unOR = 5.0; p < .001) had a significantly higher odds of being H. pylori positive, but after multivariable analyses only gastric atrophy remained significant (aOR = 27.3; p < .001). Participants with mucositis had a significantly lower odds of gastric cancer (unOR 0.1; p = .035) while participants with dysplasia had significantly higher odds (unOR 8.0; p = .042), but these were no longer significant after multivariable analyses (aOR = 0.2; p = .156 and aOR = 18.9; p = .070, respectively). CONCLUSIONS: Histology based prevalence of H. pylori infection is lower than previously reported in Jamaica. Gastric atrophy is a significant predictor of H. pylori positivity.

Who moves in vulnerable Caribbean neighborhoods? Positive deviance for physical activity: Findings from the Jamaica health and Lifestyle Survey 2017 (JHLS III).

Decreased physical activity (PA) has been associated with residents living in neighborhoods perceived as being disordered or having high crime levels. What is unknown are the characteristics of individuals who engage in moderate to vigorous levels of PA (MVPA) despite living in these vulnerable neighborhoods, or who may be referred to as positive deviants (PD). We examined the factors associated with PD for PA among Jamaicans. Between 2016 and 2017 the Jamaica Health and Lifestyle Survey, a cross-sectional nationally representative survey (n = 2807), was conducted on individuals aged 15 years and older. Regression analyses were performed to identify associations with PD, defined using engagement in MVPA among persons living in vulnerable neighborhoods (N = 1710). Being female (odds ratio [OR]a = 0.64 (0.48, 0.86); p = 0.003), obese while living in an urban area (ORa = 0.39; 95 % CI = 0.26, 0.59; p < 0.0001), unemployed (ORa = 0.53; 95 % CI = 0.39, 0.73; p < 0.0001), or a student (ORa = 0.62; 95 % CI = 0.39, 0.98); p = 0.041) was associated with a significantly lower likelihood of PD, while having a personal medical history of at least one chronic disease significantly increased likelihood (ORa = 1.43; 95 % CI = 1.08, 1.90; p = 0.014). Taking a PD approach may be one angle to consider in trying to determine what is working and for whom, so that this may be harnessed in policy, prevention and intervention programming to increase PA.

Systematic Evaluation of Genetic and Environmental Factors Affecting Performance of Translational Riboswitches.

Since their discovery, riboswitches have been attractive tools for the user-controlled regulation of gene expression in bacterial systems. Riboswitches facilitate small molecule mediated fine-tuning of protein expression, making these tools of great use to the synthetic biology community. However, the use of riboswitches is often restricted due to context dependent performance and limited dynamic range. Here, we report the drastic improvement of a previously developed orthogonal riboswitch achieved through in vivo functional selection and optimization of flanking coding and noncoding sequences. The behavior of the derived riboswitches was mapped under a wide array of growth and induction conditions, using a structured Design of Experiments approach. This approach successfully improved the maximal protein expression levels 8.2-fold relative to the original riboswitches, and the dynamic range was improved to afford riboswitch dependent control of 80-fold. The optimized orthogonal riboswitch was then integrated downstream of four endogenous stress promoters, responsive to phosphate starvation, hyperosmotic stress, redox stress, and carbon starvation. These responsive stress promoter-riboswitch devices were demonstrated to allow for tuning of protein expression up to ∼650-fold in response to both environmental and cellular stress responses and riboswitch dependent attenuation. We envisage that these riboswitch stress responsive devices will be useful tools for the construction of advanced genetic circuits, bioprocessing, and protein expression.

The E. coli DNA Replication Fork.

DNA replication in Escherichia coli initiates at oriC, the origin of replication and proceeds bidirectionally, resulting in two replication forks that travel in opposite directions from the origin. Here, we focus on events at the replication fork. The replication machinery (or replisome), first assembled on both forks at oriC, contains the DnaB helicase for strand separation, and the DNA polymerase III holoenzyme (Pol III HE) for DNA synthesis. DnaB interacts transiently with the DnaG primase for RNA priming on both strands. The Pol III HE is made up of three subassemblies: (i) the αɛθ core polymerase complex that is present in two (or three) copies to simultaneously copy both DNA strands, (ii) the ß2 sliding clamp that interacts with the core polymerase to ensure its processivity, and (iii) the seven-subunit clamp loader complex that loads ß2 onto primer-template junctions and interacts with the α polymerase subunit of the core and the DnaB helicase to organize the two (or three) core polymerases. Here, we review the structures of the enzymatic components of replisomes, and the protein-protein and protein-DNA interactions that ensure they remain intact while undergoing substantial dynamic changes as they function to copy both the leading and lagging strands simultaneously during coordinated replication.

The treatment of uncertainties in reactive pollution dispersion models at urban scales.

The ability to predict NO2 concentrations ([NO2]) within urban street networks is important for the evaluation of strategies to reduce exposure to NO2. However, models aiming to make such predictions involve the coupling of several complex processes: traffic emissions under different levels of congestion; dispersion via turbulent mixing; chemical processes of relevance at the street-scale. Parameterisations of these processes are challenging to quantify with precision. Predictions are therefore subject to uncertainties which should be taken into account when using models within decision making. This paper presents an analysis of mean [NO2] predictions from such a complex modelling system applied to a street canyon within the city of York, UK including the treatment of model uncertainties and their causes. The model system consists of a micro-scale traffic simulation and emissions model, and a Reynolds averaged turbulent flow model coupled to a reactive Lagrangian particle dispersion model. The analysis focuses on the sensitivity of predicted in-street increments of [NO2] at different locations in the street to uncertainties in the model inputs. These include physical characteristics such as background wind direction, temperature and background ozone concentrations; traffic parameters such as overall demand and primary NO2 fraction; as well as model parameterisations such as roughness lengths, turbulent time- and length-scales and chemical reaction rate coefficients. Predicted [NO2] is shown to be relatively robust with respect to model parameterisations, although there are significant sensitivities to the activation energy for the reaction NO + O3 as well as the canyon wall roughness length. Under off-peak traffic conditions, demand is the key traffic parameter. Under peak conditions where the network saturates, road-side [NO2] is relatively insensitive to changes in demand and more sensitive to the primary NO2 fraction. The most important physical parameter was found to be the background wind direction. The study highlights the key parameters required for reliable [NO2] estimations suggesting that accurate reference measurements for wind direction should be a critical part of air quality assessments for in-street locations. It also highlights the importance of street scale chemical processes in forming road-side [NO2], particularly for regions of high NOx emissions such as close to traffic queues.

The role of deep convection and nocturnal low-level jets for dust emission in summertime West Africa: Estimates from convection-permitting simulations.

[1] Convective cold pools and the breakdown of nocturnal low-level jets (NLLJs) are key meteorological drivers of dust emission over summertime West Africa, the world's largest dust source. This study is the first to quantify their relative contributions and physical interrelations using objective detection algorithms and an off-line dust emission model applied to convection-permitting simulations from the Met Office Unified Model. The study period covers 25 July to 02 September 2006. All estimates may therefore vary on an interannual basis. The main conclusions are as follows: (a) approximately 40% of the dust emissions are from NLLJs, 40% from cold pools, and 20% from unidentified processes (dry convection, land-sea and mountain circulations); (b) more than half of the cold-pool emissions are linked to a newly identified mechanism where aged cold pools form a jet above the nocturnal stable layer; (c) 50% of the dust emissions occur from 1500 to 0200 LT with a minimum around sunrise and after midday, and 60% of the morning-to-noon emissions occur under clear skies, but only 10% of the afternoon-to-nighttime emissions, suggesting large biases in satellite retrievals; (d) considering precipitation and soil moisture effects, cold-pool emissions are reduced by 15%; and (e) models with parameterized convection show substantially less cold-pool emissions but have larger NLLJ contributions. The results are much more sensitive to whether convection is parameterized or explicit than to the choice of the land-surface characterization, which generally is a large source of uncertainty. This study demonstrates the need of realistically representing moist convection and stable nighttime conditions for dust modeling. Citation: Heinold, B., P. Knippertz, J. H. Marsham, S. Fiedler, N. S. Dixon, K. Schepanski, B. Laurent, and I. Tegen (2013), The role of deep convection and nocturnal low-level jets for dust emission in summertime West Africa: Estimates from convection-permitting simulations, J. Geophys. Res. Atmos., 118, 4385-4400, doi:10.1002/jgrd.50402.

Binding assays of inhibitors towards selected V-ATPase domains.

The macrolide antibiotic bafilomycin and the related synthetic compound SB 242784 are potent inhibitors of the vacuolar H+ -ATPases (V-ATPase). It is currently believed that the site of action of these inhibitors is located on the membrane bound c-subunits of V-ATPases. To address the identification of the critical inhibitors binding domain, their specific binding to a synthetic peptide corresponding to the putative 4th transmembrane segment of the c-subunit was investigated using fluorescence resonance energy transfer (FRET), and for this purpose a specific formalism was derived. Another peptide of the corresponding domain of the c' isoform, was checked for binding of bafilomycin, since it is not clear if V-ATPase inhibition can also be achieved by interaction of the inhibitor with the c'-subunit. It was concluded that bafilomycin binds to the selected peptides, whereas SB 242784 was unable to interact, and in addition for bafilomycin, its interaction with the peptides either corresponding to the c- or the c'-subunit isoforms is identical. Since the observed interactions are however much weaker as compared to the very efficient binding of both bafilomycin and SB 242784 to the whole protein, it can be concluded that assembly of all V-ATPase transmembrane segments is required for an efficient interaction.

Interaction of the indole class of vacuolar H(+)-ATPase inhibitors with lipid bilayers.

The selective inhibitor of osteoclastic V-ATPase (2Z,4E)-5-(5,6-dichloro-2-indolyl)-2-methoxy-N-(1,2,2,6,6-pentamethylpiperidin-4-yl)-2,4-pentadienamide (SB 242784), member of the indole class of V-ATPase inhibitors, is expected to target the membrane-bound domain of the enzyme. A structural study of the interaction of this inhibitor with the lipidic environment is an essential step in the understanding of the mechanism of inhibition. In this work, a comprehensive study of the relevant features of this interaction was performed. Inhibitor partition coefficients to lipid vesicles as well as its transverse location, orientation (order parameters), and dynamics while bound to bilayers were determined through photophysical techniques, taking advantage of the intrinsic fluorescence of the molecule. To better evaluate the functionally relevant features of SB 242784, a second inhibitor, INH-1, from the same class and having a reduced activity was also examined. It is shown that regarding membrane interaction their properties remain very similar for both molecules, suggesting that the differences in inhibition efficiencies are solely a consequence of the molecular recognition processes within the inhibition site in the V-ATPase.

Molecular cloning and expression of the dihydrofolate reductase (DHFR) gene from adult buffalo fly (Haematobia irritans exigua): effects of antifolates.

The folate analogues methotrexate, aminopterin and pyrimethamine were toxic when fed in a blood meal to adult buffalo flies (Haematobia irritans exigua), but aminopterin caused greater mortality than methotrexate, while trimethoprim was not toxic to adult flies. This is the first recorded instance of mortality in adult insects caused by ingestion of folate analogues. In order to investigate the mechanism of this toxicity, the dihydrofolate reductase (DHFR) gene was cloned from adult buffalo fly cDNA using a PCR-based approach. The full-length DHFR coding sequence (BF-DHFR) was 887 bp and contained an open reading frame encoding a protein of 188 amino acids. The deduced protein sequence identities between BF-DHFR and the other known insect DHFR sequences were: Drosophila melanogaster, 75%; Aedes albopictus, 54%; Heliothis virescens, 43%. The BF-DHFR gene has a single 52 bp intron, an organization more similar to Dipteran species (Drosophila and Aedes). The cDNA encoding BF-DHFR was inserted into an Escherichia coli expression vector and the recombinant protein was expressed to levels representing about 25% of total cell protein. The active enzyme was purified by affinity chromatography on methotrexate-agarose and displayed a relatively low affinity (IC50 = 30 nm) for methotrexate.

The impact of bowel cancer awareness week.

OBJECTIVES: To assess knowledge of Bowel Cancer Awareness Week (BCAW) amongst patients attending their general practice surgery and to identify whether BCAW could increase knowledge of colorectal cancer symptoms. METHOD: Questionnaire study with ethics committee approval. Patients attending non-emergency clinics in a single general practice during the week following BCAW were given a questionnaire. Respondents were asked for knowledge of colorectal cancer symptoms, sources of this information and awareness of BCAW compared to similar knowledge of breast cancer. RESULTS: Seventy-seven patients responded (96% response rate, median age 42, 40% male). Eighty-five percent could name a breast cancer symptom compared to only 44% who could name a colorectal cancer symptom (McNemar's chi2, P < 0.0001). Respondents identified more sources of information for breast than colorectal cancer. Only 21% had heard of BCAW and none could name any symbol for bowel cancer awareness whereas 69% were aware of Breast Cancer Awareness Month and 28% could name its symbol (McNemar's chi2, P < 0.0001). Multivariate analysis demonstrated that patients who were aware of BCAW were 4.6 times more likely to have knowledge of colorectal cancer symptoms (95% CI 1.25-17.1). CONCLUSIONS: Despite their similar incidence, knowledge of colorectal cancer is much less than breast cancer. In part this may be due to the greater publicity given to breast cancer. BCAW can increase knowledge of colorectal cancer symptoms but currently, too few people are aware of it.

Writing for publication--a guide for new authors.

Health care practitioners who are inexperienced in writing for publication are sometimes daunted by the publication process and fail to submit their work on quality improvement to a journal. New authors can acquire experience in writing a paper by working through a systematic thought process that includes consideration of what journal readers and editors want and if the work is ready for publication. The most important part of writing a paper is to think through the key ideas and messages for readers and then to organize the ideas into a logical structure. Writing clear answers to 10 key questions may be one way to start the process.

A universal protein-protein interaction motif in the eubacterial DNA replication and repair systems.

The interaction between DNA polymerases and sliding clamp proteins confers processivity in DNA synthesis. This interaction is critical for most DNA replication machines from viruses and prokaryotes to higher eukaryotes. The clamp proteins also participate in a variety of dynamic and competing protein-protein interactions. However, clamp-protein binding sequences have not so far been identified in the eubacteria. Here we show from three lines of evidence, bioinformatics, yeast two-hybrid analysis, and inhibition of protein-protein interaction by modified peptides, that variants of a pentapeptide motif (consensus QL[SD]LF) are sufficient to enable interaction of a number of proteins with an archetypal eubacterial sliding clamp (the beta subunit of Escherichia coli DNA polymerase III holoenzyme). Representatives of this motif are present in most sequenced members of the eubacterial DnaE, PolC, PolB, DinB, and UmuC families of DNA polymerases and the MutS1 mismatch repair protein family. The component tripeptide DLF inhibits the binding of the alpha (DnaE) subunit of E. coli DNA polymerase III to beta at microM concentration, identifying key residues. Comparison of the eubacterial, eukaryotic, and archaeal sliding clamp binding motifs suggests that the basic interactions have been conserved across the evolutionary landscape.

Disproportionation of a model chromium(V) complex causes extensive chromium(III)-DNA binding in vitro.

The first direct evidence for the role of Cr(V) complexes in the formation of potentially mutagenic Cr(III)-DNA adducts has been obtained. A model complex for the stabilized Cr(V) species formed in Cr(VI)-treated cells, [Cr(V)O(ehba)(2)]-[ehba = 2-ethyl-2-hydroxybutanoato(2-)], rapidly disproportionates in HEPES buffers at pH 7.4 [3 Cr(V) --> 2 Cr(VI) + Cr(III)], and the formed Cr(III) species undergo efficient ionic binding to DNA, followed by slower covalent binding. The extent of Cr(III)-DNA binding significantly exceeds that caused by [Cr(III)(OH(2))(6)](3+) or by the Cr(III) products of Cr(VI) reductions under similar conditions. The Cr(III)-DNA binding can be dramatically reduced by the ability of the reaction medium (e.g., phosphate buffer) to form complexes with Cr(III) during and after the disproportionation reaction. A mechanism of Cr(III)-DNA binding caused by Cr(V) disproportionation has been proposed on the basis of stoichiometric and kinetic studies.

Chromium(VI) reduction by catechol(amine)s results in DNA cleavage in vitro: relevance to chromium genotoxicity.

Catechols are found extensively in nature both as essential biomolecules and as the byproducts of normal oxidative damage of amino acids and proteins. They are also present in cigarette smoke and other atmospheric pollutants. Here, the interactions of reactive species generated in Cr(VI)/catechol(amine) mixtures with plasmid DNA have been investigated to model a potential route to Cr(VI)-induced genotoxicity. Reduction of Cr(VI) by 3,4-dihydroxyphenylalanine (DOPA) (1), dopamine (2), or adrenaline (3) produces species that cause extensive DNA damage, but the products of similar reactions with catechol (4) or 4-tert-butylcatechol (5) do not damage DNA. The Cr(VI)/catechol(amine) reactions have been studied at low added H(2)O(2) concentrations, which lead to enhanced DNA cleavage with 1 and induce DNA cleavage with 4. The Cr(V) and organic intermediates generated by the reactions of Cr(VI) with 1 or 4 in the presence of H(2)O(2) were characterized by EPR spectroscopy. The detected signals were assigned to Cr(V)-catechol, Cr(V)-peroxo, and mixed Cr(V)-catechol-peroxo complexes. Oxygen consumption during the reactions of Cr(VI) with 1, 2, 4, and 5 was studied, and H(2)O(2) production was quantified. Reactions of Cr(VI) with 1 and 2, but not 4 and 5, consume considerable amounts of dissolved O(2), and give extensive H(2)O(2) production. Extents of oxygen consumption and H(2)O(2) production during the reaction of Cr(VI) with enzymatically generated 1 and N-acetyl-DOPA (from the reaction of Tyr and N-acetyl-Tyr with tyrosinase, respectively) were correlated with the DNA cleaving abilities of the products of these reactions. The reaction of Cr(VI) with enzymatically generated 1 produced significant amounts of H(2)O(2) and caused significant DNA damage, but the N-acetyl-DOPA did not. The extent of in vitro DNA damage is reduced considerably by treatment of the Cr(VI)/catechol(amine) mixtures with catalase, which shows that the DNA damage is H(2)O(2)-dependent and that the major reactive intermediates are likely to be Cr(V)-peroxo and mixed Cr(V)-catechol-peroxo complexes, rather than Cr(V)-catechol intermediates.

The DnaB.DnaC complex: a structure based on dimers assembled around an occluded channel.

Replicative helicases are motor proteins that unwind DNA at replication forks. Escherichia coli DnaB is the best characterized member of this family of enzymes. We present the 26 A resolution three-dimensional structure of the DnaB hexamer in complex with its loading partner, DnaC, obtained from cryo-electron microscopy. Analysis of the volume brings insight into the elaborate way the two proteins interact, and provides a structural basis for control of the symmetry state and inactivation of the helicase by DnaC. The complex is arranged on the basis of interactions among DnaC and DnaB dimers. DnaC monomers are observed for the first time to arrange as three dumb-bell-shaped dimers that interlock into one of the faces of the helicase. This could be responsible for the freezing of DnaB in a C(3) architecture by its loading partner. The central channel of the helicase is almost occluded near the end opposite to DnaC, such that even single-stranded DNA could not pass through. We propose that the DnaB N-terminal domain is located at this face.

pH-controlled quaternary states of hexameric DnaB helicase.

DnaB is the major helicase in the Escherichia coli replisome. It is a homohexameric enzyme that interacts with many other replisomal proteins and cofactors. It is usually loaded onto a single strand of DNA at origins of replication from its complex with its loading partner DnaC, then translocates in the 5' to 3' direction, unwinding duplex DNA in an NTP-driven process. Quaternary polymorphism has been described for the DnaB oligomer, a feature it has in common with some other hexameric helicases. In the present work, electron microscopy and in- depth rotational analysis studies of negatively stained specimens has allowed the establishment of conditions that govern the transition between the two different rotational symmetry states (C(3) and C(6)) of DnaB. It is shown: (a) that the pH value of the sample buffer, within the physiological range, dictates the quaternary organisation of the DnaB oligomer; (b) that the pH-induced transition is fully reversible; (c) that the type of adenine nucleotide complexed to DnaB, whether hydrolysable or not, does not affect its quaternary architecture; (d) that the DnaB.DnaC complex exists only as particles with C(3) symmetry; and (e) that DnaC interacts only with DnaB particles that have C(3) symmetry. Structural consequences of this quaternary polymorphism, as well as its functional implications for helicase activity, are discussed.

Preliminary X-ray crystallographic and NMR studies on the exonuclease domain of the epsilon subunit of Escherichia coli DNA polymerase III.

The structured core of the N-terminal 3'-5' exonuclease domain of epsilon, the proofreading subunit of Escherichia coli DNA polymerase III, was defined by multidimensional NMR experiments with uniformly (15)N-labeled protein: it comprises residues between Ile-4 and Gln-181. A 185-residue fragment, termed epsilon(1-185), was crystallized by the hanging drop vapor diffusion method in the presence of thymidine-5'-monophosphate, a product inhibitor, and Mn(2+) at pH 5.8. The crystals are tetragonal, with typical dimensions 0.2 mm x 0.2 mm x 1.0 mm, grow over about 2 weeks at 4 degrees C, and diffract X-rays to 2.0 A. The space group was determined to be P4(n)2(1)2 (n = 0, 1, 2, 3), with unit cell dimensions a = 60.8 A, c = 111.4 A.

Interaction of the Escherichia coli replication terminator protein (Tus) with DNA: a model derived from DNA-binding studies of mutant proteins by surface plasmon resonance.

The Escherichia coli replication terminator protein (Tus) binds tightly and specifically to termination sites such as TerB in order to halt DNA replication. To better understand the process of Tus-TerB interaction, an assay based on surface plasmon resonance was developed to allow the determination of the equilibrium dissociation constant of the complex (K(D)) and association and dissocation rate constants for the interaction between Tus and various DNA sequences, including TerB, single-stranded DNA, and two nonspecific sequences that had no relationship to TerB. The effects of factors such as the KCl concentration, the orientation and length of the DNA, and the presence of a single-stranded tail on the binding were also examined. The K(D) measured for the binding of wild type and His(6)-Tus to TerB was 0.5 nM in 250 mM KCl. Four variants of Tus containing single-residue mutations were assayed for binding to TerB and the nonspecific sequences. Three of these substitutions (K89A, R198A, and Q250A) increased K(D) by 200-300-fold, whereas the A173T substitution increased K(D) by 4000-fold. Only the R198A substitution had a significant effect on binding to the nonspecific sequences. The kinetic and thermodynamic data suggest a model for Tus binding to TerB which involves an ordered series of events that include structural changes in the protein.