Serodiagnosis and Bacterial Genome of Helicobacter pylori Infection

The infection caused by Helicobacter pylori is associated with several diseases, including gastric cancer. Several methods for the diagnosis of H. pylori infection exist, including endoscopy, the urea breath test, and the fecal antigen test, which is the serum antibody titer test that is often used since it is a simple and highly sensitive test. In this context, this study aims to find the association between different antibody reactivities and the organization of bacterial genomes. Next-generation sequences were performed to determine the genome sequences of four strains of antigens with different reactivity. The search was performed on the common genes, with the homology analysis conducted using a genome ring and dot plot analysis. The two antigens of the highly reactive strains showed a high gene homology, and Western blots for CagA and VacA also showed high expression levels of proteins. In the poorly responsive antigen strains, it was found that the inversion occurred around the vacA gene in the genome. The structure of bacterial genomes might contribute to the poor reactivity exhibited by the antibodies of patients. In the future, an accurate serodiagnosis could be performed by using a strain with few gene mutations of the antigen used for the antibody titer test of H. pylori

A case of Falciparum malaria without getting serious by early therapeutic intervention

A １７years old man studying in Nigeria came back to Japan three days before hospitalization date. He came to our emergency department with fever, headache and epigastric pain from the day before. At first, I couldn’t diagnose with physical examination, blood test and image inspection. But my leader suggested that possibility of malaria because of his travel history. Then we checked his peripheral blood smear and found a malaria parasite. Immediately, we hospitalized him and started antimalarial drug. ３ days after admission, fever went down, and malaria parasite disappeared in peripheral blood smear. He discharged in ７ days after admission. A polymerase chain reaction of Plasmodium falciparum was positive at a later date. Plasmodium falciparum is often to become severe, and it is important to diagnose early onset. Our case suggests that rapid diagnostic kit and peripheral blood smear are useful to diagnose malaria, and early therapeutic intervention may prevent severe malaria and complications

Feasibility study of immediate pharyngeal cooling initiation in cardiac arrest patients after arrival at the emergency room

AIM: Cooling the pharynx and upper oesophagus would be more advantageous for rapid induction of therapeutic hypothermia since the carotid arteries run in their vicinity. The aim of this study was to determine the effects of pharyngeal cooling on brain temperature and the safety and feasibility for patients under resuscitation. METHODS: Witnessed non-traumatic cardiac arrest patients (n=108) were randomized to receive standard care with (n=53) or without pharyngeal cooling (n=55). In the emergency room, pharyngeal cooling was initiated before or shortly after return of spontaneous circulation by perfusing physiological saline (5 °C) into a pharyngeal cuff for 120 min. RESULTS: There was a significant decrease in tympanic temperature at 40 min after arrival (P=0.02) with a maximum difference between the groups at 120 min (32.9 ± 1.2°C, pharyngeal cooling group vs. 34.1 ± 1.3°C, control group; P<0.001). The return of spontaneous circulation (70% vs. 65%, P=0.63) and rearrest (38% vs. 47%, P=0.45) rates were not significantly different based on the initiation of pharyngeal cooling. No post-treatment mechanical or cold-related injury was observed on the pharyngeal epithelium by macroscopic observation. The thrombocytopaenia incidence was lower in the pharyngeal cooling group (P=0.001) during the 3-day period after arrival. The cumulative survival rate at 1 month was not significantly different between the two groups. CONCLUSIONS: Initiation of pharyngeal cooling before or immediately after the return of spontaneous circulation is safe and feasible. Pharyngeal cooling can rapidly decrease tympanic temperature without adverse effects on circulation or the pharyngeal epithelium

Flow‐To‐Fracture Transition of Linear Maxwell‐Type Versus Yield Strength Fluids by Air Injection—Implications for Magma Fracturing

Abstract To illuminate brittle and ductile fracturing of magma, we investigated bubble expansion and fracturing in two contrasting fluids: a Maxwell‐type viscoelastic fluid and a Bingham‐type yield‐strength fluid. Measurements of the complex shear modulus, G′ + iG″ (i is the imaginary unit), under small‐strain oscillation showed that both fluids are elastic (G′ > G″) with similar rigidity. Viscous behavior (G′  G″ condition is insufficient to infer that brittle fracturing can occur. Brittle fracturing of the Maxwell fluid occurred not at a critical strain rate but under decreasing strain rate and increasing stress

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method

Abstract Background The reliable and robust estimation of ligand binding affinity continues to be a challenge in drug design. Many current methods rely on molecular mechanics (MM) calculations which do not fully explain complex molecular interactions. Full quantum mechanical (QM) computation of the electronic state of protein-ligand complexes has recently become possible by the latest advances in the development of linear-scaling QM methods such as the ab initio fragment molecular orbital (FMO) method. This approximate molecular orbital method is sufficiently fast that it can be incorporated into the development cycle during structure-based drug design for the reliable estimation of ligand binding affinity. Additionally, the FMO method can be combined with approximations for entropy and solvation to make it applicable for binding affinity prediction for a broad range of target and chemotypes. Results We applied this method to examine the binding affinity for a series of published cyclin-dependent kinase 2 (CDK2) inhibitors. We calculated the binding affinity for 28 CDK2 inhibitors using the ab initio FMO method based on a number of X-ray crystal structures. The sum of the pair interaction energies (PIE) was calculated and used to explain the gas-phase enthalpic contribution to binding. The correlation of the ligand potencies to the protein-ligand interaction energies gained from FMO was examined and was seen to give a good correlation which outperformed three MM force field based scoring functions used to appoximate the free energy of binding. Although the FMO calculation allows for the enthalpic component of binding interactions to be understood at the quantum level, as it is an in vacuo single point calculation, the entropic component and solvation terms are neglected. For this reason a more accurate and predictive estimate for binding free energy was desired. Therefore, additional terms used to describe the protein-ligand interactions were then calculated to improve the correlation of the FMO derived values to experimental free energies of binding. These terms were used to account for the polar and non-polar solvation of the molecule estimated by the Poisson-Boltzmann equation and the solvent accessible surface area (SASA), respectively, as well as a correction term for ligand entropy. A quantitative structure-activity relationship (QSAR) model obtained by Partial Least Squares projection to latent structures (PLS) analysis of the ligand potencies and the calculated terms showed a strong correlation (r2 = 0.939, q2 = 0.896) for the 14 molecule test set which had a Pearson rank order correlation of 0.97. A training set of a further 14 molecules was well predicted (r2 = 0.842), and could be used to obtain meaningful estimations of the binding free energy. Conclusions Our results show that binding energies calculated with the FMO method correlate well with published data. Analysis of the terms used to derive the FMO energies adds greater understanding to the binding interactions than can be gained by MM methods. Combining this information with additional terms and creating a scaled model to describe the data results in more accurate predictions of ligand potencies than the absolute values obtained by FMO alone.</p

TECHNOLOGIES DRUG DISCOVERY Fragments: past, present and future

Fragment-based drug discovery has come a long way in a short period of time and is now being used throughout the biopharmaceutical industry. Here we review the origin of the approach, discuss how it is being applied and the prospects for future development. We illustrate this with examples from our own projects where we have found that information from fragments can inform the optimisation of hits identified by other means (e.g. HTS and/or virtual screening) and vice versa. We further discuss that fragment information can also be applied to the discovery of ligands for targets that are not readily amenable to structural analysis by experimentation such as GPCRs, particularly through the application of computational modelling methods