A model for the study of Helicobacter pylori interaction with human gastric acid secretion

Use of Individual-Based Mathematical Modelling to Understand More About Antibiotic Resistance Within-Host

To model complex systems, individual-based models (IBMs), sometimes called "agent-based models" (ABMs), describe a simplification of the system through an adequate representation of the elements. IBMs simulate the actions and interaction of discrete individuals/agents within a system in order to discover the pattern of behavior that comes from these interactions. Examples of individuals/agents in biological systems are individual immune cells and bacteria that act independently with their own unique attributes defined by behavioral rules. In IBMs, each of these agents resides in a spatial environment and interactions are guided by predefined rules. These rules are often simple and can be easily implemented. It is expected that following the interaction guided by these rules we will have a better understanding of agent-agent interaction as well as agent-environment interaction. Stochasticity described by probability distributions must be accounted for. Events that seldom occur such as the accumulation of rare mutations can be easily modeled.Thus, IBMs are able to track the behavior of each individual/agent within the model while also obtaining information on the results of their collective behaviors. The influence of impact of one agent with another can be captured, thus allowing a full representation of both direct and indirect causation on the aggregate results. This means that important new insights can be gained and hypotheses tested.

Extra precision glide docking, free energy calculation and molecular dynamics studies of 1,2-diarylethane derivatives as potent urease inhibitors

For the latter half of the twentieth century, most medical professionals considered bacterial infection to be a primary cause of gastrointestinal ulcers in human beings. In 1994, the World Health Organization (WHO) recognized Helicobacter pylori, the bacterium most closely linked to ulcer development, as a type I carcinogen. Biological research has shown that there is a positive correlation between the number of species in the Helicobacter genus and the number of medical conditions associated with Helicobacter infection, both of which are increasing rapidly. N-Benzylaniline derivatives, frequently used in industrial manufacturing, are being considered as a strong candidate for ongoing drug modeling in search of novel therapies. The basic goal behind this study was to determine the potency of experimentally proved data, and to determine favorable substituents to enhance potency, and thereafter to support this finding through theoretical modification of the existing base skeleton by addition of suitable substituents. Ligands were investigated thoroughly by paying attention to the urease-inhibitory properties present in the selected series. Initially, docking was performed on ligands with protein to produce efficient docking poses. Molecular dynamics (MD) simulations were also performed to precisely understand the interactions between ligands and proteins. Thereafter, MM-GBSA was used in order to validate the methods and results. Good interaction was observed with amino acids Arg338, Ala169, Asp223, His322, and Asn168. This study also revealed that the electron rich hydroxyl group (-OH) substituent plays an important role during bond formation. In addition, various hydrogen bonds, ionic bonds, and pi-pi stacking bonds make significant contributions towards urease inhibition. Therefore, further research utilizing electron-rich moieties may lead to novel and efficacious urease inhibitors.

Analysis of the Relationship between Helicobacter pylori Infection and Diabetic Gastroparesis

Background:

Whether Helicobacter pylori infection is associated with diabetic gastroparesis (DGP) is unclear. This study aimed to investigate the potential correlation between H. pylori infection and DGP.

Methods:

In this study, 163 patients with type 2 diabetes mellitus and 175 nondiabetic patients who were treated in our department were divided into DGP, simple diabetes, non-DGP (NDG), and normal groups based on their conditions. The H. pylori infection rate in each group was calculated. H. pylori eradication therapy was performed for patients with H. pylori infection in each group. The eradication rates were compared between the groups, and the improvements in gastroparesis-associated symptoms were compared before and after treatment in patients with DGP.

Results:

The H. pylori infection rate was 74.6% in the DGP group, which was significantly higher than that in the simple diabetes (51.1%, P < 0.01), NDG (57.7%, P < 0.05), and normal groups (48.0%, P < 0.01). With increased disease course, the incidence of DGP and the H. pylori infection rate gradually increased (P < 0.05). In the DGP group, the incidences of upper abdominal pain and distention, early satiety, and anorexia were 75.5%, 66.0%, and 67.9%, respectively, before eradication treatment; and 43.4%, 35.8%, and 39.6%, respectively, after eradication treatment, and the difference was statistically significant (P < 0.01). In patients with DGP with successful H. pylori eradication, the number of barium strips discharged after eradication was 5.9 ± 1.0, which was significantly larger than that before treatment (4.1 ± 0.7, P < 0.01). In addition, the number of barium strips discharged was significantly larger in patients with DGP with successful H. pylori eradication than those with failed H. pylori eradication (P < 0.01).

Conclusions:

DGP development might be associated with H. pylori infection. H. pylori eradication can effectively improve dyspepsia-associated symptoms and delayed gastric emptying in patients with DGP.

Multiscale positive feedbacks contribute to unidirectional gastric disease progression induced by helicobacter pylori infection

Background

Helicobacter Pylori (HP) is the most common risk factor for gastric cancer. Nearly half the world’s population is infected with HP, but only a small percentage of those develop significant pathology. The bacteria itself does not directly cause cancer; rather it promotes an environment that is conducive to tumor formation. Upon infection, HP induces transcriptional changes in the host, leading to enhanced proliferation and host immune response. In addition, HP causes direct damage to gastric epithelial cells.

Results

We present a multiscale mechanistic model of HP induced changes. The model includes four modules representing the host transcriptional changes in response to infection, gastric atrophy, the Hedgehog pathway response, and the restriction point that controls cell cycle. This model was able to recapture a number of literature reported observations and was used as an “in silico” representation of the biological system for further analysis. Dynamical analysis of the model revealed that HP might induce the activation of multiple interplayed positive feedbacks, which in turn might result in a “ratchet ladder” system that promotes a unidirectional progression of gastric disease.

Conclusions

The current multiscale model is able to recapitulate the observed experimental features of HP host interactions and provides dynamic insights on the epidemiologically observed heterogeneity in disease progression. This model provides a solid framework that can be further expanded and validated to include additional experimental evidence, to understand the complex multi-pathway interactions characterizing HP infection, and to design novel treatment protocols for HP induced diseases.

Electronic supplementary material

The online version of this article (10.1186/s12918-017-0497-y) contains supplementary material, which is available to authorized users.

A Multiphase Flow in the Antroduodenal Portion of the Gastrointestinal Tract: A Mathematical Model

A group of authors has developed a multilevel mathematical model that focuses on functional disorders in a human body associated with various chemical, physical, social, and other factors. At this point, the researchers have come up with structure, basic definitions and concepts of a mathematical model at the "macrolevel" that allow describing processes in a human body as a whole. Currently we are working at the "mesolevel" of organs and systems. Due to complexity of the tasks, this paper deals with only one meso-fragment of a digestive system model. It describes some aspects related to modeling multiphase flow in the antroduodenal portion of the gastrointestinal tract. Biochemical reactions, dissolution of food particles, and motor, secretory, and absorbing functions of the tract are taken into consideration. The paper outlines some results concerning influence of secretory function disorders on food dissolution rate and tract contents acidity. The effect which food density has on inflow of food masses from a stomach to a bowel is analyzed. We assume that the future development of the model will include digestive enzymes and related reactions of lipolysis, proteolysis, and carbohydrates breakdown.

What a Dinner Party! Mechanisms and Functions of Interkingdom Signaling in Host-Pathogen Associations

Chemical signaling between cells is an effective way to coordinate behavior within a community. Although cell-to-cell signaling has mostly been studied in single species, it is now appreciated that the sensing of chemical signals across kingdoms can be an important regulator of nutrient acquisition, virulence, and host defense. In this review, we focus on the role of interkingdom signaling in the interactions that occur between bacterial pathogens and their mammalian hosts. We discuss the quorum-sensing (QS) systems and other mechanisms used by these bacteria to sense, respond to, and modulate host signals that include hormones, immune factors, and nutrients. We also describe cross talk between these signaling pathways and strategies used by the host to interfere with bacterial signaling, highlighting the complex bidirectional signaling networks that are established across kingdoms.

Use of selected lactic acid bacteria in the eradication of Helicobacter pylori infection

Helicobacter pylori is among the major pathogenic bacteria that cause chronic gastritis and peptic ulcer disease and is related to the development of gastric cancer. Several chemicals, including antibiotics, have been used to eradicate H. pylori; however, they do not always curb the infection. Ten representative type strains of lactic acid bacteria (LAB) were screened for antagonism toward H. pylori via inhibition of urease activity. Strains inhibiting the binding of H. pylori to human gastric cell line cells and suppressing H. pylori-induced interleukin-8 (IL-8) production were also screened. Of these, Pediococcus pentosaseus (SL4), which inhibited the adhesion of H. pylori to MKN-45 gastric cancer cells, Bifidobacterium longum (BG7), with urease inhibiting activity, and Lactococcus lactis (SL3), and Enterococcus faecalis (SL5), which suppressed H. pylori-induced IL-8 production within MKN-45 and AGS cells, were selected. In mouse model, these LAB stains in combination significantly suppressed IL-8 levels in serum. Gastric pH also recovered to normal values after the administration of these LAB. These stains effectively suppressed H. pylori viability, although not to the extent of antibiotic treatment. When used as probiotics, LAB may help decrease the occurrence of gastritis and reduce the risk of H. pylori infection without, inducing side effects.

A mathematical model representing cellular immune development and response to Salmonella of chicken intestinal tissue

The aim of this study was to create a dynamic mathematical model of the development of the cellular branch of the intestinal immune system of poultry during the first 42 days of life and of its response towards an oral infection with Salmonella enterica serovar Enteritidis. The system elements were grouped in five important classes consisting of intra- and extracellular S. Enteritidis bacteria, macrophages, CD4+, and CD8+ cells. Twelve model variables were described by ordinary differential equations, including 50 parameters. Parameter values were estimated from literature or from own immunohistochemistry data. The model described the immune development in non-infected birds with an average R² of 0.87. The model showed less accuracy in reproducing the immune response to S. Enteritidis infection, with an average R² of 0.51, although model response did follow observed trends in time. Evaluation of the model against independent data derived from several infection trials showed strong/significant deviations from observed values. Nevertheless, it was shown that the model could be used to simulate the effect of varying input parameters on system elements response, such as the number of immune cells at hatch. Model simulations allowed one to study the sensitivity of the model outcome for varying model inputs. The initial number of immune cells at hatch was shown to have a profound impact on the predicted development in the number of systemic S. Enteritidis bacteria after infection. The theoretical contribution of this work is the identification of responses in system elements of the developing intestinal immune system of poultry obtaining a mathematical representation which allows one to explore the relationships between these elements under contrasting environmental conditions during different stages of intestinal development.

H. pylori acutely inhibits gastric secretion by activating CGRP sensory neurons coupled to stimulation of somatostatin and inhibition of histamine secretion

Acute Helicobacter pylori infection produces hypochlorhydria. The decrease in acid facilitates survival of the bacterium and its colonization of the stomach. The present study was designed to identify the pathways in oxyntic mucosa by which acute H. pylori infection inhibits acid secretion. In rat fundic sheets in an Ussing chamber, perfusion of the luminal surface with H. pylori in spent broth (10(3)-10(8) cfu/ml) or spent broth alone (1:10(5) to 1:10(0) final dilution) caused a concentration-dependent increase in somatostatin (SST; maximal: 200 ± 20 and 194 ± 9% above basal; P < 0.001) and decrease in histamine secretion (maximal: 45 ± 5 and 48 ± 2% below basal; P < 0.001); the latter was abolished by SST antibody, implying that changes in histamine secretion reflected changes in SST secretion. Both responses were abolished by the axonal blocker tetrodotoxin (TTX), the sensory neurotoxin capsaicin, or the CGRP antagonist CGRP8-37, implying that the reciprocal changes in SST and histamine secretion were due to release of CGRP from sensory neurons. In isolated rabbit oxyntic glands, H. pylori inhibited basal and histamine-stimulated acid secretion in a concentration-dependent manner; the responses were not affected by TTX or SST antibody, implying that H. pylori can directly inhibit parietal cell function. In conclusion, acute administration of H. pylori is capable of inhibiting acid secretion directly as well as indirectly by activating intramural CGRP sensory neurons coupled to stimulation of SST and inhibition of histamine secretion. Activation of neural pathways provides one explanation as to how initial patchy colonization of the superficial gastric mucosa by H. pylori can acutely inhibit acid secretion.

The roles of immune memory and aging in protective immunity and endogenous reactivation of tuberculosis

Finding more effective vaccines against tuberculosis (TB) and improved preventive treatments against endogenous reactivation of latent TB is strategic to block transmission and reach the WHO goal of eliminating TB by 2050. Key related open questions in TB research include: i) what are the determinants of a strong memory response upon primary infection? ii) what is the role of cytokines towards protective memory response against a secondary infection? iii) what are the mechanisms responsible for the increased risk of reactivation in elderly individuals? To address these questions, we explored a computational model of the immune response to Mycobacterium tuberculosis including a mathematical description of immunosenescence and the generation and maintenance of immune memory. Sensitivity analysis techniques, together with extensive model characterization and in silico experiments, were applied to identify key mechanisms controlling TB reactivation and immunological memory. Key findings of this study are summarized by the following model predictions: i) increased strength and duration of memory protection is associated with higher levels of Tumor Necrosis Factor- (TNF) during primary infection; ii) production of TNF, but not of interferon-, by memory T cells during secondary infection is a major determinant of effective protection; iii) impaired recruitment of CD4+ T cells may promote reactivation of latent TB infections in aging hosts. This study is a first attempt to consider the immune dynamics of a persistent infection throughout the lifetime of the host, taking into account immunosenescence and memory. While the model is TB specific, the results are applicable to other persistent bacterial infections and can aid in the development, evaluation and refinement of TB treatment and/or vaccine protocols.

A model for Vibrio cholerae colonization of the human intestine

Vibrio cholerae is a strict human pathogen that causes the disease cholera. It is an old-world pathogen that has re-emerged as a new threat since the early 1990s. V. cholerae colonizes the upper, small intestine where it produces a toxin that leads to watery diarrhea, characterizing the disease (Kahn et al., 1988). The dynamics of colonization by the bacteria of the intestines are largely unknown. Although a large initial infectious dose is required for infection, data suggests that only a smaller sub-population colonizes a portion of the small bowel leading to disease. There are many barriers to colonization in the intestines including peristalsis, fluid wash-out, viscosity of the mucus layer, and pH. We are interested in identifying the mechanisms that allow this sub-population of bacteria to survive and colonize the intestines when faced with these barriers. To elaborate the dynamics of V. cholerae infection, we have developed a mathematical model based on a convection-diffusion-reaction-swimming equation capturing bacterial dynamics coupled with Stokes equations governing fluid velocity where we developed a novel non-local boundary condition. Our results indicate that both host and bacterial factors contribute to bacterial density in the gut. Host factors include intestinal diffusion and convection rates while bacterial factors include adherence, motility and growth rates. This model can ultimately be used to test therapeutic strategies against V. cholerae.

Relationship among Helicobacter pylori infection, gut hormones and diabetic gastroparesis

AIM: To investigate the relationship among serum gastrin (GAS) and somatostatin (SS) and Helicobacter pylori (H.pylori) in patients with diabetic gastroparesis (DGP).

METHODS: Fifty-six patients with type 2 diabetes mellitus were divided into simple diabetes mellitus group and DGP group. Forty-seven non-diabetes mellitus patients were divided into control group and simple gastroparesis group. H.pylori infection in the mucosa of sinus ventriculi was evaluated by rapid urease test and Giemsa staining. The contents of serum GAS and SS were measured by radioimmunoassay.

RESULTS: There was no significant difference between the rapid urease test and Giemsa staining in detecting H.pylori. The detection rate of H.pylori was comparable between the simple diabetes mellitus group and the control group. The detection rate of H.pylori was higher in the simple gastroparesis group than in the control group (rapid urease test: 73.3% vs 47.1%, P < 0.05), and in the DGP group than in the control group (rapid urease test: 87.8% vs 47.1%, P < 0.01; Giemsa staining: 81.9% vs 41.2%, P < 0.01), the simple diabetes mellitus group (rapid urease test: 87.8% vs 47.8%, P < 0.01; Giemsa staining: 81.9 % vs 43.5%, P < 0.05) and the simple gastroparesis group (rapid urease test: 87.8% vs 73.3%, P < 0.01; Giemsa staining: 81.9% vs 66.7%, P < 0.01). In H.pylori-positive patients, the level of serum GAS in the DGP group was higher than that in the control group (147.58 ± 16.68 vs 80.91 ± 15.23, P < 0.01), and the level of serum SS in the DGP group was lower than that in the control group (16.29 ± 4.27 vs 47.81 ± 16.88, P < 0.01). In H.pylori-negative patients, there was no significant differences in serum GAS and SS levels between different groups.

CONCLUSION: H.pylori infection can increase serum GAS level but decrease serum SS level. The pathological alterations in the gastric mucosa induced by H.pylori infection are closely related with the development of DGP.

Phenylphosphonate transport by Helicobacter pylori

BACKGROUND

Helicobacter pylori can utilize phenylphosphonate as a sole source of phosphorus, and it is able to transport the phosphonate N-phosphonoacetyl-L-aspartate. However, H. pylori does not have any genes homologous to those of the known pathways for phosphonate degradation in bacteria, indicating that it must have novel pathways for the transport and metabolism of phosphonates.

METHODS

Phenylphosphonate transport by H. pylori was studied in strains LC20, J99 and N6 by the centrifugation through oil method using [(14)C]-labeled phenylphosphonate.

RESULTS

The Michaelis constants of transport K(t) and V(max) for phenylphosphonate showed similar kinetics in the three strains. The Arrhenius plot for phenylphosphonate transport rates at permeant concentrations of 50 micromol/L was linear over the temperature range 10-40 degrees C with an activation energy of 3.5 kJ/mol, and a breakpoint between 5 and 10 degrees C. Transport rates increased with monovalent cation size. The effects of various inhibitors were investigated: iodoacetamide, amiloride, valinomycin, and nigericin reduced the rate of phenylphosphonate transport; sodium azide and sodium cyanide increased the transport rate; and monensin had no effect.

CONCLUSIONS

The kinetics and properties of H. pylori phenylphosphonate transport were characterized, and the data suggested a carrier-mediated transport mechanism.

The potential influence of gastric acid secretion during fasting on digestion time in leopard sharks (Triakis semifasciata)

Vertebrates are known to differ in their response of gastric acid secretion during periods of fasting, yet the reasons for these differences remain unclear. Previously, continuous measurements of gastric pH in leopard sharks (Triakis semifasciata) had determined that acid secretion in this species is continuous. In order to determine if maintaining an empty acidic stomach may reduce digestion time of a subsequent meal, a simple descriptive model based on acid secretion rates was developed. In vivo gastric acid secretion rates were measured using an auto-titration technique. Acid secretion rates were pH dependent, with rates of 6.1+/-3.0 (+/-1 SD) mmol/h when gastric pH was >2.5, and 1.7+/-0.8 mmol/h when pH was 2.0-2.5. Analysis by Western blots suggests that pepsin secretion occurs within 1 h of feeding, and that there is a de-coupling of acid and pepsin secretion. The model estimates that digestion time can be reduced by 5.7+/-1.3 h and pepsin activity increased by 10-100% during that time if the stomach is acidic before feeding. Gastric acid secretion during fasting is hypothesized to reduce digestion time of a subsequent meal in frequently feeding sharks, which may be advantageous for exploiting resources that are spatially and temporally unpredictable.

Gastric secretion

PURPOSE OF REVIEW

The purpose of this review is to summarize the pertinent literature published in the past year regarding the regulation of gastric exocrine and endocrine secretion.

RECENT FINDINGS

Gastric acid aids protein digestion; facilitates the absorption of iron, calcium, and vitamin B12; thwarts enteric infection; and prevents bacterial overgrowth. When levels of acid and proteolytic enzymes overwhelm the mucosal defense mechanisms, ulcers occur. To avoid damage under these harsh conditions, gastric acid must be finely regulated by overlapping neural (e.g. orexin, pituitary adenylate cyclase-activating polypeptide, nitric oxide, and galanin), hormonal (e.g. gastrin, cholecystokinin, and ghrelin), paracrine (e.g. histamine and somatostatin), and autocrine (e.g. transforming growth factor-alpha) pathways. The precise mechanisms whereby Helicobacter pylori induces perturbations in acid secretion are not known, but they seem to involve changes in somatostatin and perhaps ghrelin secretion. Acid secretion by parietal cells involves intracellular elevation of calcium and/or cyclic AMP, followed by a cascade that triggers translocation of the proton pump, HK-adenosine triphosphatase, from cytoplasmic tubulovesicles to the secretory canaliculi.

SUMMARY

An improved understanding of the pathways and mechanisms regulating gastric acid secretion may lead to the development of new strategies to prevent and treat acid peptic disorders as well as circumvent the adverse effects of currently prescribed antisecretory medications.

Variations in gastric acid secretion during periods of fasting between two species of shark

Vertebrates differ in their regulation of gastric acid secretion during periods of fasting, yet it is unknown why these differences occur. Elasmobranch fishes are the earliest known vertebrates to develop an acid secreting stomach and as such may make a good comparative model for determining the causative factors behind these differences. We measured gastric pH and temperature continuously during periods of fasting in captive free-swimming nurse sharks (Ginglymostoma cirratum) using autonomous pH/temperature data-loggers. All nurse sharks secreted strong gastric acids (minimum pH 0.4) after feeding; however, for most of the sharks, pH increased to 8.2-8.7, 2-3 days after feeding. Half of the sharks also exhibited periodic oscillations in pH when the stomach was empty that ranged from 1.1 to 8.7 (acid secretion ceased for 11.3 +/- 4.3 h day(-1)). This is in contrast to the gastric pH changes observed from leopard sharks (Triakis semifasciata) in a previous study, where the stomach remains acidic during fasting. The leopard shark is a relatively active, more frequently feeding predator, and continuous acid secretion may increase digestive efficiency. In contrast, the nurse shark is less active and is thought to feed less frequently. Periodic cessation of acid secretion may be an energy conserving mechanism used by animals that feed infrequently and experience extended periods of fasting.

Clinical endocrinology and metabolism. The somatostatin neuroendocrine system: physiology and clinical relevance in gastrointestinal and pancreatic disorders

Somatostatin is produced in enteroendocrine D cells and intrinsic neurons of the stomach, intestines and pancreas. Its physiologic actions are mediated primarily by somatostatin receptors type 2 and 5, and include the inhibition of secretion of most endocrine and exocrine factors. Diseases directly attributable to somatostatin excess or deficiency are rare, although there is a complex pathogenic relationship between persistent Helicobacter pylori infection and reduced somatostatin in chronic gastritis. Abundant somatostatin receptors on many neoplastic and inflammatory cells are the basis for sensitive in vivo imaging with radiolabeled somatostatin analogs and provide a therapeutic target. Current indications for somatostatin therapy include hormone-expressing neuroendocrine tumors, intractable diarrhea and variceal bleeding secondary to portal hypertension. Exciting advances are being made in the development of high-affinity nonpeptide analogs with receptor-subtype selectivity and increased bioavailability. Somatostatin analogs coupled to high-energy radionuclides show promise as novel cytotoxic agents for certain metastatic tumors.