Human body numerical simulation: An accurate model for a thigh subjected to a cold treatment

This article presents the development of a digital twin model of a thigh portion subjected to various thermal treatments. Two scenarios are investigated: cold water immersion (CWI) and whole body cryotherapy (WBC), for which the comparison of numerical results with experimental measurements validates the consistency of the developed model. The use of real geometry on a first subject demonstrates the high heterogeneity of the temperature field and the need for accurate geometry. A second subject with thicker adipose tissue highlights the impact of the subject's actual morphology on the validity of the treatment and the necessity to work with real geometry in order to optimize cold modalities and develop personalized treatments.

A precise swaying map for how promiscuous cellobiose-2-epimerase operate bi-reaction

Promiscuous enzymes play a crucial role in organism survival and new reaction mining. However, comprehensive mapping of the catalytic and regulatory mechanisms hasn't been well studied due to the characteristic complexity. The cellobiose 2-epimerase from Caldicellulosiruptor saccharolyticus (CsCE) with complex epimerization and isomerization was chosen to comprehensively investigate the promiscuous mechanisms. Here, the catalytic frame of ring-opening, cis-enediol mediated catalysis and ring-closing was firstly determined. To map the full view of promiscuous CE, the structure of CsCE complex with the isomerized product glucopyranosyl-β1,4-fructose was determined. Combined with computational calculation, the promiscuity was proved a precise cooperation of the double subsites, loop rearrangement, and intermediate swaying. The flexible loop was like a gear, whose structural reshaping regulates the sway of the intermediates between the two subsites of H377-H188 and H377-H247, and thus regulates the catalytic directions. The different protonated states of cis-enediol intermediate catalyzed by H188 were the key point for the catalysis. The promiscuous enzyme tends to utilize all elements at hand to carry out the promiscuous functions.

Threshold of 25(OH)D and consequently adjusted parathyroid hormone reference intervals: data mining for relationship between vitamin D and parathyroid hormone

PURPOSE

By recruiting reference population, we aimed to (1): estimate the 25(OH)D threshold that maximally inhibits the PTH, which can be defined as the cutoff value for vitamin D sufficiency; (2) establish the PTH reference interval (RI) in population with sufficient vitamin D.

METHODS

Study data were retrieved from LIS (Laboratory Information Management System) under literature suggested criteria, and outliers were excluded using Tukey fence method. Locally weighted regression (LOESS) and segmented regression (SR) were conducted to estimate the threshold of 25(OH)D. Multivariate linear regression was performed to evaluate the associations between PTH concentration and variables including 25(OH)D, gender, age, estimated glomerular filtration rate (EGFR), body mass index (BMI), albumin-adjusted serum calcium (aCa), serum phosphate(P), serum magnesium(Mg), and blood collection season. Z test was adopted to evaluate whether the reference interval should be stratified by determinants such as age and gender.

RESULTS

A total of 64,979 apparently healthy subjects were recruited in this study, with median (Q1, Q3) 25(OH)D of 45.33 (36.15, 57.50) nmol/L and median (Q1, Q3) PTH of 42.19 (34.24, 52.20) ng/L. The segmented regression determined the 25(OH)D threshold of 55 nmol/L above which PTH would somewhat plateau and of 22 nmol/L below which PTH would rise steeply. Multivariate linear regression suggested that gender, EGFR, and BMI were independently associated with PTH concentrations. The PTH RI was calculated as 22.17-72.72 ng/L for subjects with 25(OH)D ≥ 55 nmol/L with no necessity of stratification according to gender, age, menopausal status nor season.

CONCLUSION

This study reported 25(OH)D thresholds of vitamin D sufficiency at 55 nmol/L and vitamin D deficiency at 22 nmol/L, and consequently established PTH RIs in subjects with sufficient vitamin D for northern China population for the first time.

Combined Antibodies Evusheld against the SARS-CoV-2 Omicron Variants BA.1.1 and BA.5: Immune Escape Mechanism from Molecular Simulation

The Omicron lineage of SARS-CoV-2, which was first reported in November 2021, has spread globally and become dominant, splitting into several sublineages. Experiments have shown that Omicron lineage has escaped or reduced the activity of existing monoclonal antibodies, but the origin of escape mechanism caused by mutation is still unknown. This work uses molecular dynamics and umbrella sampling methods to reveal the escape mechanism of BA.1.1 to monoclonal antibody (mAb) Tixagevimab (AZD1061) and BA.5 to mAb Cilgavimab (AZD8895), both mAbs were combined to form antibody cocktail, Evusheld (AZD7442). The binding free energy of BA.1.1-AZD1061 and BA.5-AZD8895 has been severely reduced due to multiple-site mutated Omicron variants. Our results show that the two Omicron variants, which introduce a substantial number of positively charged residues, can weaken the electrostatic attraction between the receptor binding domain (RBD) and AZD7442, thus leading to a decrease in affinity. Additionally, using umbrella sampling along dissociation pathway, we found that the two Omicron variants severely impaired the interaction between the RBD of SARS-CoV-2's spike glycoprotein (S protein) and complementary determining regions (CDRs) of mAbs, especially in CDR3H. Although mAbs AZD8895 and AZD1061 are knocked out by BA.5 and BA.1.1, respectively, our results confirm that the antibody cocktail AZD7442 retains activity against BA.1.1 and BA.5 because another antibody is still on guard. The study provides theoretical insights for mAbs interacting with BA.1.1 and BA.5 from both energetic and dynamic perspectives, and we hope this will help in developing new monoclonals and combinations to protect those unable to mount adequate vaccine responses.

Binding of berberine derivates to G-quadruplex: insight from a computational study

Human telomerase exhibits significant activity in cancer cells relative to normal cells, which contributes to the immortal proliferation of cancer cells. To counter this, the stabilization of G-quadruplexes formed in the guanine-rich sequence of the cancer cell chromosome has emerged as a promising avenue for anti-cancer therapy. Berberine (BER), an alkaloid that is derived from traditional Chinese medicines, has shown potential for stabilizing G-quadruplexes. To investigate the atomic interactions between G-quadruplexes and BER and its derivatives, molecular dynamics simulations were conducted. Modeling the interactions between G-quadruplexes and ligands accurately is challenging due to the strong negative charge of nucleic acids. Thus, various force fields and charge models for the G-quadruplex and ligands were tested to obtain precise simulation results. The binding energies were calculated by a combination of molecular mechanics/generalized Born surface area and interaction entropy methods, and the calculated results correlated well with experimental results. B-factor and hydrogen bond analyses demonstrated that the G-quadruplex was more stable in the presence of ligands than in the absence of ligands. Calculation of the binding free energy showed that the BER derivatives bind to a G-quadruplex with higher affinity than that of BER. The breakdown of the binding free energy to per-nucleotide energies suggested that the first G-tetrad played a primary role in binding. Additionally, energy and geometric properties analyses indicated that van der Waals interactions were the most favorable interactions between the derivatives and the G-quadruplexes. Overall, these findings provide crucial atomic-level insights into the binding of G-quadruplexes and their inhibitors.

Comprehensive Evaluation of End-Point Free Energy Techniques in Carboxylated-Pillar[6]arene Host–Guest Binding: III. Force-Field Comparison, Three-Trajectory Realization and Further Dielectric Augmentation

Host–guest binding, despite the relatively simple structural and chemical features of individual components, still poses a challenge in computational modelling. The extreme underperformance of standard end-point methods in host–guest binding makes them practically useless. In the current work, we explore a potentially promising modification of the three-trajectory realization. The alteration couples the binding-induced structural reorganization into free energy estimation and suffers from dramatic fluctuations in internal energies in protein–ligand situations. Fortunately, the relatively small size of host–guest systems minimizes the magnitude of internal fluctuations and makes the three-trajectory realization practically suitable. Due to the incorporation of intra-molecular interactions in free energy estimation, a strong dependence on the force field parameters could be incurred. Thus, a term-specific investigation of transferable GAFF derivatives is presented, and noticeable differences in many aspects are identified between commonly applied GAFF and GAFF2. These force-field differences lead to different dynamic behaviors of the macrocyclic host, which ultimately would influence the end-point sampling and binding thermodynamics. Therefore, the three-trajectory end-point free energy calculations are performed with both GAFF versions. Additionally, due to the noticeable differences between host dynamics under GAFF and GAFF2, we add additional benchmarks of the single-trajectory end-point calculations. When only the ranks of binding affinities are pursued, the three-trajectory realization performs very well, comparable to and even better than the regressed PBSA_E scoring function and the dielectric constant-variable regime. With the GAFF parameter set, the TIP3P water in explicit solvent sampling and either PB or GB implicit solvent model in free energy estimation, the predictive power of the three-trajectory realization in ranking calculations surpasses all existing end-point methods on this dataset. We further combine the three-trajectory realization with another promising modified end-point regime of varying the interior dielectric constant. The combined regime does not incur sizable improvements for ranks and deviations from experiment exhibit non-monotonic variations.

Molecular Modelling of Ionic Liquids: Situations When Charge Scaling Seems Insufficient

Charge scaling as an effective solution to the experiment-computation disagreement in molecular modelling of ionic liquids (ILs) could bring the computational results close to the experimental reference for various thermodynamic properties. According to the large-scale benchmark calculations of mass density, solvation, and water-ILs transfer-free energies in our series of papers, the charge-scaling factor of 0.8 serves as a near-optimal option generally applicable to most ILs, although a system-dependent parameter adjustment could be attempted for further improved performance. However, there are situations in which such a charge-scaling treatment would fail. Namely, charge scaling cannot really affect the simulation outcome, or minimally perturbs the results that are still far from the experimental value. In such situations, the vdW radius as an additional adjustable parameter is commonly tuned to minimize the experiment-calculation deviation. In the current work, considering two ILs from the quinuclidinium family, we investigate the impacts of this vdW-scaling treatment on the mass density and the solvation/partition thermodynamics in a fashion similar to our previous charge-scaling works, i.e., scanning the vdW-scaling factor and computing physical properties under these parameter sets. It is observed that the mass density exhibits a linear response to the vdW-scaling factor with slopes close to -1.8 g/mL. By further investigating a set of physiochemically relevant temperatures between 288 K and 348 K, we confirm the robustness of the vdW-scaling treatment in the estimation of bulk properties. The best vdW-scaling parameter for mass density would worsen the computation of solvation/partition thermodynamics, and a marginal decrease in the vdW-scaling factor is considered as an intermediate option balancing the reproductions of bulk properties and solvation thermodynamics. These observations could be understood in a way similar to the charge-scaling situation. i.e., overfitting some properties (e.g., mass density) would degrade the accuracy of the other properties (e.g., solvation free energies). Following this principle, the general guideline for applying this vdW-tuning protocol is by using values between the density-derived choice and the solvation/partition-derived solution. The charge and current vdW scaling treatments cover commonly encountered ILs, completing the protocol for accurate modelling of ILs with fixed-charge force fields.

Rational Design of a Highly Specific Prolyl Endopeptidase To Activate the Antihypertensive Effect of Peptides

Enzymatic hydrolysis of food-derived proteins to produce bioactive peptides could activate food functions such as antihypertension. However, the diversity of enzymatic hydrolysis products can reduce bioactive peptides' efficacy. Highly specific proteases can homogenize the hydrolysis products to reduce the production of impotent peptides. In this study, we successfully obtained M. xanthus prolyl endopeptidase mutant Y451M by constraint/free molecular dynamics simulations and binding energy calculations. The specificity of Y451M for proline was increased by 286 % compared to WT, while its activity was almost unchanged. Milk-derived substrates processed with Y451M showed an antihypertensive effect that was 567 % higher than without enzymes. The ability to activate food antihypertension increased 152 % and the use of enzyme by 192 % compared with WT. Specific proteases are thus valuable tools in the processing of complex substrates to obtain bioactive peptides.

Comprehensive evaluation of end-point free energy techniques in carboxylated-pillar[6]arene host-guest binding: II. regression and dielectric constant

End-point free energy calculations as a powerful tool have been widely applied in protein-ligand and protein-protein interactions. It is often recognized that these end-point techniques serve as an option of intermediate accuracy and computational cost compared with more rigorous statistical mechanic models (e.g., alchemical transformation) and coarser molecular docking. However, it is observed that this intermediate level of accuracy does not hold in relatively simple and prototypical host-guest systems. Specifically, in our previous work investigating a set of carboxylated-pillar[6]arene host-guest complexes, end-point methods provide free energy estimates deviating significantly from the experimental reference, and the rank of binding affinities is also incorrectly computed. These observations suggest the unsuitability and inapplicability of standard end-point free energy techniques in host-guest systems, and alteration and development are required to make them practically usable. In this work, we consider two ways to improve the performance of end-point techniques. The first one is the PBSA_E regression that varies the weights of different free energy terms in the end-point calculation procedure, while the second one is considering the interior dielectric constant as an additional variable in the end-point equation. By detailed investigation of the calculation procedure and the simulation outcome, we prove that these two treatments (i.e., regression and dielectric constant) are manipulating the end-point equation in a somehow similar way, i.e., weakening the electrostatic contribution and strengthening the non-polar terms, although there are still many detailed differences between these two methods. With the trained end-point scheme, the RMSE of the computed affinities is improved from the standard ~ 12 kcal/mol to ~ 2.4 kcal/mol, which is comparable to another altered end-point method (ELIE) trained with system-specific data. By tuning PBSA_E weighting factors with the host-specific data, it is possible to further decrease the prediction error to ~ 2.1 kcal/mol. These observations along with the extremely efficient optimized-structure computation procedure suggest the regression (i.e., PBSA_E as well as its GBSA_E extension) as a practically applicable solution that brings end-point methods back into the library of usable tools for host-guest binding. However, the dielectric-constant-variable scheme cannot effectively minimize the experiment-calculation discrepancy for absolute binding affinities, but is able to improve the calculation of affinity ranks. This phenomenon is somehow different from the protein-ligand case and suggests the difference between host-guest and biomacromolecular (protein-ligand and protein-protein) systems. Therefore, the spectrum of tools usable for protein-ligand complexes could be unsuitable for host-guest binding, and numerical validations are necessary to screen out really workable solutions in these 'prototypical' situations.

Immune Escape Mechanisms of SARS-CoV-2 Delta and Omicron Variants against Two Monoclonal Antibodies That Received Emergency Use Authorization

Multiple-site mutated SARS-CoV-2 Delta and Omicron variants may trigger immune escape against existing monoclonal antibodies. Here, molecular dynamics simulations combined with the interaction entropy method reveal the escape mechanism of Delta/Omicron variants to Bamlanivimab/Etesevimab. The result shows the significantly reduced binding affinity of the Omicron variant for both antibodies, due to the introduction of positively charged residues that greatly weaken their electrostatic interactions. Meanwhile, significant structural deflection induces fewer atomic contacts and an unstable binding mode. As for the Delta variant, the reduced binding affinity for Bamlanivimab is owing to the alienation of the receptor-binding domain to the main part of this antibody, and the binding mode of the Delta variant to Etesevimab is similar to that of the wild type, suggesting that Etesevimab could still be effective against the Delta variant. We hope this work will provide timely theoretical insights into developing antibodies to prevalent and possible future variants of SARS-CoV-2.

A fast-slow method to treat solute dynamics in explicit solvent

Aiming to reduce the computational cost in the current explicit solvent molecular dynamics (MD) simulation, this paper proposes a fast-slow method for the fast MD simulation of biomolecules in explicit solvent. This fast-slow method divides the entire system into two parts: a core layer (typically solute or biomolecule) and a peripheral layer (typically solvent molecules). The core layer is treated using standard MD method but the peripheral layer is treated by a slower dynamics method to reduce the computational cost. We compared four different simulation models in testing calculations for several small proteins. These include gas-phase, implicit solvent, fast-slow explicit solvent and standard explicit solvent MD simulations. Our study shows that gas-phase and implicit solvent models do not provide a realistic solvent environment and fail to correctly produce reliable dynamic structures of proteins. On the other hand, the fast-slow method can essentially reproduce the same solvent effect as the standard explicit solvent model while gaining an order of magnitude in efficiency. This fast-slow method thus provides an efficient approach for accelerating the MD simulation of biomolecules in explicit solvent.

Computational Insights into the Binding Mechanism of OxyS sRNA with Chaperone Protein Hfq

Under the oxidative stress condition, the small RNA (sRNA) OxyS that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in the defection of gene regulation. However, how the Hfq protein interacts with sRNA OxyS and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result was correlated with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly came from the increased van der Waals interactions (vdW). This research explored the binding mechanism between Oxys and chaperone protein Hfq and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights into the mechanism of gene expression regulation affected by protein mutations.

Anchor-Locker Binding Mechanism of the Coronavirus Spike Protein to Human ACE2: Insights from Computational Analysis

COVID-19 has emerged as the most serious international pandemic in early 2020 and the lack of comprehensive knowledge in the recognition and transmission mechanisms of this virus hinders the development of suitable therapeutic strategies. The specific recognition during the binding of the spike glycoprotein (S protein) of coronavirus to the angiotensin-converting enzyme 2 (ACE2) in the host cell is widely considered the first step of infection. However, detailed insights on the underlying mechanism of dynamic recognition and binding of these two proteins remain unknown. In this work, molecular dynamics simulation and binding free energy calculation were carried out to systematically compare and analyze the receptor-binding domain (RBD) of six coronavirus' S proteins. We found that affinity and stability of the RBD from SARS-CoV-2 under the binding state with ACE2 are stronger than those of other coronaviruses. The solvent-accessible surface area (SASA) and binding free energy of different RBD subunits indicate an "anchor-locker" recognition mechanism involved in the binding of the S protein to ACE2. Loop 2 (Y473-F490) acts as an anchor for ACE2 recognition, and Loop 3 (G496-V503) locks ACE2 at the other nonanchoring end. Then, the charged or long-chain residues in the β-sheet 1 (N450-F456) region reinforce this binding. The proposed binding mechanism was supported by umbrella sampling simulation of the dissociation process. The current computational study provides important theoretical insights for the development of new vaccines against SARS-CoV-2.

Inhibition mechanism and hot-spot prediction of nine potential drugs for SARS-CoV-2 Mpro by large-scale molecular dynamic simulations combined with accurate binding free energy calculations

Coronavirus disease 2019 (COVID-19), which is caused by a new coronavirus known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is spreading around the world. However, a universally effective treatment regimen has not been developed to date. The main protease (M^pro), a key enzyme of SARS-CoV-2, plays a crucial role in the replication and transcription of this virus in cells and has become the ideal target for rational antiviral drug design. In this study, we performed molecular dynamics simulations three times for these complexes of M^pro (monomeric and dimeric) and nine potential drugs that have a certain effect on the treatment of COVID-19 to explore their binding mechanism. In addition, a total of 12 methods for calculating binding free energy were employed to determine the optimal drug. Ritonavir, Arbidol, and Chloroquine consistently showed an outstanding binding ability to monomeric M^pro under various methods. Ritonavir, Arbidol, and Saquinavir presented the best performance when binding to a dimer, which was independent of the protonated state of Hie41 (protonated at N_ε) and Hid41 (protonated at N_δ), and these findings suggest that Chloroquine may not effectively inhibit the activity of dimeric M^proin vivo. Furthermore, three common hot-spot residues of Met165, Hie41, and Gln189 of monomeric M^pro systems dominated the binding of Ritonavir, Arbidol, and Chloroquine. In dimeric M^pro, Gln189, Met165, and Met49 contributed significantly to binding with Ritonavir, Arbidol, and Saquinavir; therefore, Gln189 and Met165 might serve as the focus in the discovery and development of anti-COVID-19 drugs. In addition, the van der Waals interaction played a significant role in the binding process, and the benzene ring of the drugs showed an apparent inhibitory effect on the normal function of M^pro. The binding cavity had great flexibility to accommodate these different drugs. The results would be notably helpful for enabling a detailed understanding of the binding mechanisms for these important drug-M^pro interactions and provide valuable guidance for the design of potent inhibitors.

Engineering the biomimetic cofactors of NMNH for cytochrome P450 BM3 based on binding conformation refinement

Cytochrome P450 BM3 (BM3) is an important oxidoreductase that is widely used in drug synthesis, chemical synthesis, and other industries. However, as BM3 unquestionably increases costs by consuming a natural cofactor that unstably provides electrons, an alternative biomimetic cofactor with simpler structures represented by nicotinamide mononucleotide (NMNH) has been utilized. Currently, few reports exist on artificially modified BM3 enzymes using NMNH, especially regarding theoretical simulation and calculation. With the cognition of the mechanism in mind, we propose a strategy that optimizes and refines catalytic conformation. Based on constrained molecular dynamics simulation, the distance between N-5 of FAD flavin and C-4 of NMNH is used as a cue for the determination of improved conformation, and the potential positive mutants are subsequently screened virtually in accordance with binding free energy requirements. As a result, the K_cat/K_M values of the favorable mutant S848R increased to 205.38% compared to the wild-type BM3 with NMNH. These data indicate that our strategy can be applied for the specific utilization of biomimetic cofactors by oxidoreductases represented by BM3.

A rational design strategy was proposed to improve the efficient utilization of alternative biomimetic cofactor by P450 BM3 enzyme.

Computational analysis of binding free energies, hotspots and the binding mechanism of Bcl-xL/Bcl-2 binding to Bad/Bax

Hierarchical clustering tree of residues providing contributions to system binding based on the binding free energy of specific residues for (A) Bcl-xL systems (B) Bcl-2 systems.

An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein-ligand binding affinity

The molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) method is constantly used to calculate the binding free energy of protein-ligand complexes, and has been shown to effectively balance computational cost against accuracy. The relative binding affinities obtained by the MM/PBSA approach are acceptable, while it usually overestimates the absolute binding free energy. This paper proposes four free energy estimators based on the MM/PBSA for enthalpy change combined with interaction entropy (IE) for entropy change using different weights for individual energy terms. The ΔG_{PBSA_IE} method is determined to be an optimal estimator based on its performance in terms of the correlation between experimental and theoretical values and error estimations. This approach is optimized using high-quality experimental values from a training set containing 84 protein-ligand systems, and the coefficients for the sum of electrostatic energy and polar solvation free energy, van der Waals (vdW) energy, non-polar solvation energy and entropy change are obtained by multivariate linear fitting to the corresponding experimental values. A comparison between the traditional MM/PBSA method and this method shows that the correlation coefficient is improved from 0.46 to 0.72 and the slope of the regression line increases from 0.10 to 1.00. More importantly, the mean absolute error (MAE) is significantly reduced from 22.52 to 1.59 kcal mol^-1. Furthermore, the numerical stability of this method is validated on a test set with a similar correlation coefficient, slope and MAE to those of the training set. Based on the above advantages, the ΔG_{PBSA_IE} method can be a powerful tool for a reliable and accurate estimation of binding free energy and plays a significant role in a detailed energetic investigation of protein-ligand interaction.

An Energy Optimization Strategy Based on the Perfect Conformation of Prolyl Endopeptidase for Improving Catalytic Efficiency

Prolyl endopeptidases (PEPs) hydrolyze proteins to yield bioactive peptides and are effective in the treatment of celiac disease. However, the catalytic efficiency of PEPs still has the potential to be improved, which could further strengthen their industrial and therapeutic applications. Herein, a novel rational design strategy based on a "near-attack conformation" of the catalytic state of PEP was adopted. Constrained dynamic simulations were applied, followed by the virtual screening of potentially favorable mutants according to their binding free energy. We redesigned Sphaerobacter thermophiles PEP with high-temperature activity/stability, a wide range of pH stabilities, and high proline specificity. As a result, the k_cat value of two PEP mutants (I462W and Q560Y) increased by 208.2 and 150.1%, respectively, and the k_cat/K_M increased by 32.7 and 6.3%, respectively. These data revealed that the PEP mutants had improved catalytic efficiency and that our strategy can be applied for enzyme engineering.

Upholding ethical values and human rights at the frontier of TB research

Until recently, human rights have played a minor role in the fight against tuberculosis (TB), even less so in TB research. This is changing, however. The WHO's End TB Strategy and Ethics Guidance stress respect for human rights and ethical principles in every area of TB care, including research. The desired reductions in TB incidence and mortality are impossible without new tools and strategies to fight the disease. Yet, little suggests that the current state of TB research-including funding levels, evidence being produced, and community involvement-will alleviate concerns related to the availability, accessibility, and acceptability of TB diagnostics, drugs, and prevention in the near future. In this article, we consider these ethics concerns in relation to the right to enjoy the benefits of scientific progress and the right to health. We also reflect on community involvement in research and offer recommendations in the spirit of the rights to health and science, such as involving affected communities in all aspects of research planning, execution, and dissemination. Finally, we argue that states have a responsibility under international law for the continued realization of the right to health. This realization rests, in part, on the realization of the right to science.

Molecular Mechanism of Selective Binding of NMS-P118 to PARP-1 and PARP-2: A Computational Perspective

The nuclear protein poly (ADP-ribose) polymerase-1 (PARP-1) inhibitors have been proven effective to potentiate both chemotherapeutic agents and radiotherapy. However, a major problem of most current PARP inhibitors is their lack of selectivity for PARP-1 and its closest isoform PARP-2. NMS-P118 is a highly selective PARP inhibitor that binds PARP-1 stronger than PARP-2 and has many advantages such as excellent pharmacokinetic profiles. In this study, molecular dynamics (MD) simulations of NMS-P118 in complex with PARP-1 and PARP-2 were performed to understand the molecular mechanism of its selectivity. Alanine scanning together with free energy calculation using MM/GBSA and interaction entropy reveal key residues that are responsible for the selectivity. Although the conformation of the binding pockets and NMS-P118 are very similar in PARP-1 and PARP-2, most of the hot-spot residues in PARP-1 have stronger binding free energy than the corresponding residues in PARP-2. Detailed analysis of the binding energy shows that the 4′4-difluorocyclohexyl ring on NMS-P118 form favorable hydrophobic interaction with Y889 in PARP-1. In addition, the H862 residue in PARP-1 has stronger binding free energy than H428 in PARP-2, which is due to shorter distance and stronger hydrogen bonds. Moreover, the negatively charged E763 residue in PARP-1 forms stronger electrostatic interaction energy with the positively charged NMS-P118 than the Q332 residue in PARP-2. These results rationalize the selectivity of NMS-P118 and may be useful for designing novel selective PARP inhibitors.

Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin-biotin binding

Molecular dynamics (MD) simulations were performed employing the polarized protein-specific charge (PPC) to explore the origin of the cooperativity in streptavidin-biotin systems (wild type, two single mutations and one double-mutation). The results of the experiment found that the existence of cooperativity is mainly the result of the entropic effect. In this study, the entropic contribution to the binding free energy was calculated using the recently developed interaction entropy (IE) method, and computational results are in excellent agreement with the experimental observations and are further verified by the calculation of the thermodynamic integration. Comparison of different force fields in terms of predicted binding strength ordering, cooperativity of energy and the stability of hydrogen bonding suggests that the PPC force field combined IE method is a suitable choice. In addition, the IE method enables us to obtain the residue-specific entropic contributions to the streptavidin-biotin binding affinity and identify ten hot-spot residues providing the dominant contribution to the cooperative binding. Importantly, the overall cooperativity obtained from the ten residues also comes mainly from the entropic effect in our study. The calculation of the potential of mean force shows that the unbinding of streptavidin-biotin is a multi-step process, and each step corresponds to the formation and rupture of the hydrogen bond network. And S45A mutation may increase the rigidity of the linker region, making the flap region relatively difficult to open. The present study provides significant molecular insight into the binding cooperativity of the streptavidin-biotin complex.

Accelerated Molecular Dynamics Simulation for Helical Proteins Folding in Explicit Water

In this study, we examined the folding processes of eight helical proteins (2I9M, TC5B, 1WN8, 1V4Z, 1HO2, 1HLL, 2KFE, and 1YYB) at room temperature using the explicit solvent model under the AMBER14SB force field with the accelerated molecular dynamics (AMD) and traditional molecular dynamics (MD), respectively. We analyzed and compared the simulation results obtained by these two methods based on several aspects, such as root mean square deviation (RMSD), native contacts, cluster analysis, folding snapshots, free energy landscape, and the evolution of the radius of gyration, which showed that these eight proteins were successfully and consistently folded into the corresponding native structures by AMD simulations carried out at room temperature. In addition, the folding occurred in the range of 40~180 ns after starting from the linear structures of the eight proteins at 300 K. By contrast, these stable folding structures were not found when the traditional molecular dynamics (MD) simulation was used. At the same time, the influence of high temperatures (350, 400, and 450 K) is also further investigated. Study found that the simulation efficiency of AMD is higher than that of MD simulations, regardless of the temperature. Of these temperatures, 300 K is the most suitable temperature for protein folding for all systems. To further investigate the efficiency of AMD, another trajectory was simulated for eight proteins with the same linear structure but different random seeds at 300 K. Both AMD trajectories reached the correct folded structures. Our result clearly shows that AMD simulation are a highly efficient and reliable method for the study of protein folding.

Bacillus coagulans and its applications in medicine

Bacillus coagulans is a probiotic bacterium that produces spores. Due to its excellent stability, it has been widely used in medicine, food and chemical industry. Recent studies have shown that B. coagulans has therapeutic effects on intestinal diseases, such as acute diarrhoea, irritable bowel syndrome, antibiotic-related diarrhoea, constipation and colitis via modulation of the microbiota composition, host immunity and metabolism. Additionally, toxicological experiments and a large number of clinical observations have showed that B. coagulans is safe and has no effect of mutagenicity, teratogenicity or genotoxicity. This review summarises the latest advances associated with B. coagulans, from its biological features, probable action mechanisms, toxicity, and medical applications.

Bacillus coagulans and its applications in medicine

Bacillus coagulans is a probiotic bacterium that produces spores. Due to its excellent stability, it has been widely used in medicine, food and chemical industry. Recent studies have shown that B. coagulans has therapeutic effects on intestinal diseases, such as acute diarrhoea, irritable bowel syndrome, antibiotic-related diarrhoea, constipation and colitis via modulation of the microbiota composition, host immunity and metabolism. Additionally, toxicological experiments and a large number of clinical observations have showed that B. coagulans is safe and has no effect of mutagenicity, teratogenicity or genotoxicity. This review summarises the latest advances associated with B. coagulans, from its biological features, probable action mechanisms, toxicity, and medical applications.

Insight Into the Binding Mechanism of p53/pDIQ-MDMX/MDM2 With the Interaction Entropy Method

The study of the p53-MDMX/MDM2 binding sites is a research hotspot for tumor drug design. The inhibition of p53-targeted MDMX/MDM2 has become an effective approach in anti-tumor drug development. In this paper, a theoretically rigorous and computationally accurate method, namely, the interaction entropy (IE) method, combined with the polarized protein-specific charge (PPC) force field, is used to explore the difference in the binding mechanism between p53-MDMX and p53-MDM2. The interaction of a 12mer peptide inhibitor (pDIQ), which is similar to p53 in structure, with MDMX/MDM2 is also studied. The results demonstrate that p53/pDIQ with MDM2 generates a stronger interaction than with MDMX. Compared to p53, pDIQ has larger binding free energies with MDMX and MDM2. According to the calculated binding free energies, the differences in the binding free energy among the four complexes that are obtained from the combination of PPC and IE are more consistent with the experimental values than with the results from the combination of the non-polarizable AMBER force field and IE. In addition, according to the decomposition of the binding free energy, the van der Waals (vdW) interactions are the main driving force for the binding of the four complexes. They are also the main source of the weaker binding affinity of p53/pDIQ-MDMX relative to p53/pDIQ-MDM2. Compared with p53-MDMX/MDM2, according to the analysis of the residue decomposition, the predicated total residue contributions are higher in pDIQ-MDMX/MDM2 than in p53-MDMX/MDM2, which explains why pDIQ has higher binding affinity than p53 with MDMX/MDM2. The current study provides theoretical guidance for understanding the binding mechanisms and designing a potent dual inhibitor that is targeted to MDMX/MDM2.

Drug-resistance mechanisms of three mutations in anaplastic lymphoma kinase against two inhibitors based on MM/PBSA combined with interaction entropy

As a promising drug target in the treatment of lung cancer, anaplastic lymphoma kinase (ALK) and its mutations have been studied widely. This work explored the origin of the resistance mechanism of the ALK mutants again two inhibitors.

The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction

At present, the calculated binding free energy obtained using the molecular mechanics/Poisson-Boltzmann (Generalized-Born) surface area (MM/PB(GB)SA) method is overestimated due to the lack of knowledge of suitable interior dielectric constants in the simulation on the interaction of Human Immunodeficiency Virus (HIV-1) protease systems with inhibitors. Therefore, the impact of different values of the interior dielectric constant and the entropic contribution when using the MM/PB(GB)SA method to calculate the binding free energy was systemically evaluated. Our results show that the use of higher interior dielectric constants (1.4-2.0) can clearly improve the predictive accuracy of the MM/PBSA and MM/GBSA methods, and computational errors are significantly reduced by including the effects of electronic polarization and using a new highly efficient interaction entropy (IE) method to calculate the entropic contribution. The suitable range for the interior dielectric constant is 1.4-1.6 for the MM/PBSA method; within this range, the correlation coefficient fluctuates around 0.84, and the mean absolute error fluctuates around 2 kcal/mol. Similarly, an interior dielectric constant of 1.8-2.0 produces a correlation coefficient of approximately 0.76 when using the MM/GBSA method. In addition, the entropic contribution of each individual residue was further calculated using the IE method to predict hot-spot residues, and the detailed binding mechanisms underlying the interactions of the HIV-1 protease, its inhibitors, and bridging water molecules were investigated. In this study, the use of a higher interior dielectric constant and the IE method can improve the calculation accuracy of the HIV-1 system.

Exploring the Reasons for Decrease in Binding Affinity of HIV-2 Against HIV-1 Protease Complex Using Interaction Entropy Under Polarized Force Field

In this study, the differences of binding patterns between two type HIV (HIV-1 and HIV-2) protease and two inhibitors (darunavir and amprenavir) are analyzed and compared using the newly developed interaction entropy (IE) method for the entropy change calculation combined with the polarized force field. The functional role of protonation states in the two HIV-2 complexes is investigated and our study finds that the protonated OD1 atom of Asp25' in B chain is the optimal choice. Those calculated binding free energies obtained from the polarized force field combined with IE method are significantly consistent with the experimental observed. The bridging water W301 is favorable to the binding of HIV-1 complexes; however, it is unfavorable to the HIV-2 complexes in current study. The volume of pocket, B-factor of Cα atoms and the distance of flap tip in HIV-2 complexes are smaller than that of HIV-1 consistently. These changes may cause localized rearrangement of residues lining their surface and finally result in the different binding mode for the two types HIV. Predicated hot-spot residues (Ala28/Ala28', Ile50/Ile50', and Ile84/Ile84') are nearly same in the four systems. However, the contribution to the free energy of Asp30 residue is more favorable in HIV-1 system than in HIV-2 system. Current study, to some extent, reveals the origin for the decrease in binding affinity of inhibitors against HIV-2 compared with HIV-1 and will provides theoretical guidance for future design of potent dual inhibitors targeting two type HIV protease.

Smad nuclear interacting protein 1 (SNIP1) inhibits intestinal inflammation through regulation of epithelial barrier function

Smad nuclear interacting protein 1 (SNIP1) has been implicated in the pathogenesis of inflammatory bowel disease (IBD). However, the mechanisms involved are still largely unknown. Our results demonstrated that SNIP1 was markedly decreased in intestinal epithelial cells (IEC) from IBD patients compared with healthy controls. Impaired expression of SNIP1 caused a significant decrease of transepithelial electrical resistance but an increase of fluorescein isothiocyanate-dextran flux in Caco-2 monolayers, whereas overexpression of SNIP1 reversed such effects. Overexpression of SNIP1 also inhibited the activity of NF-κB p65 and proinflammatory cytokine production (e.g., TNF-α, IL-1β, and IL-8) by IEC. Importantly, supplementation of exogenous SNIP1 significantly ameliorated intestinal mucosal inflammation in experimental colitis, characterized by less-severe intestinal epithelial barrier damage and decreased proinflammatory cytokine production. Our data thus demonstrated a novel mechanism whereby SNIP1 regulates intestinal inflammation through modulating intestinal epithelial barrier function. Targeting SNIP1 may provide a therapeutic approach for the treatment of IBD.

Hypoxia inducible factor-1α-induced interleukin-33 expression in intestinal epithelia contributes to mucosal homeostasis in inflammatory bowel disease

Intestinal epithelial cells (IECs), an important barrier to gut microbiota, are subject to low oxygen tension, particularly during intestinal inflammation. Hypoxia inducible factor-1α (HIF-1α) is expressed highly in the inflamed mucosa of inflammatory bowel disease (IBD) and functions as a key regulator in maintenance of intestinal homeostasis. However, how IEC-derived HIF-1α regulates intestinal immune responses in IBD is still not understood completely. We report here that the expression of HIF-1α and IL-33 was increased significantly in the inflamed mucosa of IBD patients as well as mice with colitis induced by dextran sulphate sodium (DSS). The levels of interleukin (IL)-33 were correlated positively with that of HIF-1α. A HIF-1α-interacting element was identified in the promoter region of IL-33, indicating that HIF-1α activity regulates IL-33 expression. Furthermore, tumour necrosis factor (TNF) facilitated the HIF-1α-dependent IL-33 expression in IEC. Our data thus demonstrate that HIF-1α-dependent IL-33 in IEC functions as a regulatory cytokine in inflamed mucosa of IBD, thereby regulating the intestinal inflammation and maintaining mucosal homeostasis.

Regulatory immune cells in regulation of intestinal inflammatory response to microbiota

The intestinal lumen harbors nearly 100 trillion commensal bacteria that exert crucial function for health. An elaborate balance between immune responses and tolerance to intestinal microbiota is required to maintain intestinal homeostasis. This process depends on diverse regulatory mechanisms, including both innate and adaptive immunity. Dysregulation of the homeostasis between intestinal immune systems and microbiota has been shown to be associated with the development of inflammatory bowel diseases (IBD) in genetically susceptible populations. In this review, we discuss the recent progress reported in studies of distinct types of regulatory immune cells in the gut, including intestinal intraepithelial lymphocytes, Foxp3(+) regulatory T cells, regulatory B cells, alternatively activated macrophages, dendritic cells, and innate lymphoid cells, and how dysfunction of this immune regulatory system contributes to intestinal diseases such as IBD. Moreover, we discuss the manipulation of these regulatory immune cells as a potential therapeutic method for management of intestinal inflammatory disorders.

Self-reported lactose intolerance in clinic patients with functional gastrointestinal symptoms: prevalence, risk factors, and impact on food choices

BACKGROUND

Many patients complain of abdominal symptoms with dairy products; however, clinical and psychosocial factors associated with self-reported lactose intolerance (SLI) have not been assessed in large studies. In particular, data are lacking from lactase deficient populations. This prospective cohort study assessed the prevalence of, and risk factors for, SLI in Chinese patients attending a gastroenterology clinic.

METHODS

Consecutive patients completed questionnaires to assess digestive health (Rome III), psychological state (HADS), life event stress (LES), food intake, and quality-of-life (SF-8). A representative sample completed genetic studies and hydrogen breath testing (HBT) at the clinically relevant dose of 20 g lactose.

KEY RESULTS

SLI was present in 411/910 (45%) clinic patients with functional abdominal symptoms. The genotype in all subjects was C/C-13910. A small number of novel SNPs in lactase promoter region were identified, including C/T-13908 which appeared to confer lactase persistence. Over half of the patients (54%) completed the 20 g lactose HBT with 58% (285/492) reporting typical symptoms. Positive and negative predictive values of SLI for abdominal symptoms during HBT were 60% and 44%, respectively. Psychological state and stress were not associated with SLI in clinic patients. SLI impacted on physical quality-of-life and was associated with reduced ingestion of dairy products, legumes, and dried fruit (p ≤ 0.05).

CONCLUSIONS & INFERENCES

In a lactase deficient population, approximately half of patients attending clinic with functional gastrointestinal symptoms reported intolerance to dairy products; however, SLI did not predict findings on 20 g lactose HBT. Independent of psychosocial factors, SLI impacted on quality-of-life and impacted on food choices with restrictions not limited to dairy products.

Development of biodegradable Zn-1X binary alloys with nutrient alloying elements Mg, Ca and Sr

Biodegradable metals have attracted considerable attentions in recent years. Besides the early launched biodegradable Mg and Fe metals, Zn, an essential element with osteogenic potential of human body, is regarded and studied as a new kind of potential biodegradable metal quite recently. Unfortunately, pure Zn is soft, brittle and has low mechanical strength in the practice, which needs further improvement in order to meet the clinical requirements. On the other hand, the widely used industrial Zn-based alloys usually contain biotoxic elements (for instance, ZA series contain toxic Al elements up to 40 wt.%), which subsequently bring up biosafety concerns. In the present work, novel Zn-1X binary alloys, with the addition of nutrition elements Mg, Ca and Sr were designed (cast, rolled and extruded Zn-1Mg, Zn-1Ca and Zn-1Sr). Their microstructure and mechanical property, degradation and in vitro and in vivo biocompatibility were studied systematically. The results demonstrated that the Zn-1X (Mg, Ca and Sr) alloys have profoundly modified the mechanical properties and biocompatibility of pure Zn. Zn-1X (Mg, Ca and Sr) alloys showed great potential for use in a new generation of biodegradable implants, opening up a new avenue in the area of biodegradable metals.

A study of the methodological and clinical validity of the combined lactulose hydrogen breath test with scintigraphic oro-cecal transit test for diagnosing small intestinal bacterial overgrowth in IBS patients

BACKGROUND

Small intestinal bacterial overgrowth (SIBO) may be a cause of irritable bowel syndrome (IBS); however, current investigations have important limitations. We aimed to identify clinically relevant diagnostic criteria for SIBO based on lactulose hydrogen breath test (LHBT) alone and combined with scintigraphic measurement of oro-cecal transit (SOCT).

METHODS

Results of LHBT/SOCT investigation from 89 IBS patients and 13 healthy volunteers were included in a systematic analysis of six published criteria for SIBO diagnosis. Clinical relevance of competing criteria was determined by assessing (i) prevalence of SIBO in IBS patients and healthy volunteers (ii) if SIBO diagnosis predicted improvement in IBS symptoms in a prospective, pilot therapeutic trial of a non-absorbable antibiotic (rifaximin 600 mg b.d.) in IBS patients.

KEY RESULTS

Reproducibility of SIBO diagnosis by combined LHBT/SOCT was near perfect. A ≥5 ppm H2 increase prior to appearance of cecal contrast was detected in more IBS patients than healthy volunteers (35/89 vs 1/13; p = 0.026), but not for other diagnostic criteria. IBS patients with SIBO, compared to those without SIBO, reported significantly greater improvement in abdominal symptoms following rifaximin therapy (p < 0.002 overall IBS symptom severity). This improvement was most marked in D-IBS patients in whom all symptoms improved, including stool frequency and consistency (all p < 0.004).

CONCLUSIONS & INFERENCES

Combined LHBT/SOCT testing using a H2 5 ppm cutoff may identify a subgroup of IBS patients with SIBO. Pilot data examining the clinical response to rifaximin suggest that this subset of IBS patients may benefit more than those with a normal test.

Lactose intolerance in irritable bowel syndrome patients with diarrhoea: the roles of anxiety, activation of the innate mucosal immune system and visceral sensitivity

BACKGROUND

Irritable bowel syndrome patients with diarrhoea (IBS-D) often report intolerance to milk; however, the mechanism underlying these symptoms is unknown.

AIM

To assess the role of psychological factors, immune activation and visceral sensitivity on the development of lactose intolerance (LI) in IBS-D patients.

METHODS

Fifty-five IBS-D patients and 18 healthy controls (HCs) with lactase deficiency underwent a 20-g lactose hydrogen breath test (LHBT). Patients were categorised as lactose malabsorption (LM; malabsorption only) or LI [malabsorption plus increase in total symptom score (TSS). Measurements included (i) psychological status; (ii) enteric biopsies with quantification of mast cells (MCs), T-lymphocytes and enterochromaffin cells; (iii) serum cytokines; (iv) rectal sensitivity before and after lactose ingestion.

RESULTS

LI was more prevalent in IBS-D patients than HCs [25/55 (46%) vs. 3/18 (17%), P = 0.029]. IBS-D patients with LI had (i) higher levels of anxiety than those with LM (P = 0.017) or HCs (P = 0.006); (ii) increased mucosal MCs compared with LM (P = 0.006) and HCs (P < 0.001); (iii) raised serum TNF-α compared with LM (P = 0.034) and HCs (P < 0.001) and (iv) increased rectal sensitivity after lactose ingestion compared with LM (P < 0.001) or HCs (P < 0.001). Severity of abdominal symptoms after lactose ingestion was associated with the increase in visceral sensitivity after lactose intake (r = 0.629, P < 0.001), MCs (r = 0.650, P < 0.001) and anxiety (r = 0.519, P < 0.001).

CONCLUSIONS

IBS-D patients with lactose intolerence are characterised by anxiety, mucosal immune activation and increased visceral sensitivity after lactose ingestion. The presence of these biomarkers may indicate an IBS phenotype that responds to dietary therapy and/or mast cell stabilisers.

Anti-tumour necrosis factor therapy enhances mucosal healing through down-regulation of interleukin-21 expression and T helper type 17 cell infiltration in Crohn's disease

Anti-tumour necrosis factor (TNF) monoclonal antibody (mAb) (infliximab, IFX) has been shown to be highly effective in the management of Crohn's disease (CD). Herein we investigated the potential role of IFX in inducing clinical remission and regulating interleukin (IL)-21 expression and T helper type 17 (Th17) cell infiltration in the intestinal mucosa of CD patients. Twenty-six CD patients were treated with IFX at weeks 0, 2 and 6. Clinical response, mucosal healing, serum C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) were evaluated at week 10 after IFX administration. Expression of IL-21, IL-17A and retinoic acid-related orphan receptor C (RORC) in intestinal mucosa were analysed by quantitative real-time polymerase chain reaction (PCR) and immunohistochemistry. Peripheral blood and lamina propria CD4(+) T cells were stimulated with anti-CD3 and anti-CD28 mAbs in the presence of IFX. Cytokine profiles and RORC were determined with enzyme-linked immunosorbent assay (ELISA) and real-time PCR. IL-21 and Th17 cells were found to be expressed highly in inflamed mucosa of active CD patients compared with healthy controls. Ten weeks after IFX infusion, CD activity index, ESR, CRP and intestinal mucosal healing were improved markedly in CD patients, and IL-21 expression and Th17 cell infiltration were decreased significantly compared with those before IFX therapy. In-vitro study demonstrated that IFX treatment could suppress IL-21, IL-17A and RORC expression in cultured CD biopsies. Moreover, IFX was also observed to down-regulate markedly IL-17A, IL-21 and RORC expression by CD CD4(+) T cells. IFX is highly effective in inducing clinical remission and promoting intestinal mucosal healing in CD patients through down-regulation of IL-21 expression and Th17 cell infiltration in intestinal mucosa.

Lactose intolerance in patients with chronic functional diarrhoea: the role of small intestinal bacterial overgrowth

BACKGROUND

Many studies report a high prevalence of lactose intolerance in patients with functional, gastrointestinal disease.

AIM

To evaluate the role of small intestinal bacterial overgrowth (SIBO) in condition of lactose intolerance and the mechanism by which SIBO may impact lactose tolerance in affected patients.

METHODS

Consecutive out-patients with chronic functional diarrhoea (CFD) and healthy controls underwent a validated 20 g lactose hydrogen breath test (HBT). Patients completed also a 10 g lactulose HBT with concurrent assessment of small bowel transit by scintigraphy.

RESULTS

Lactose malabsorption was present in 27/31 (87%) patients with CFD and 29/32 (91%) healthy controls (P = 0.708). From the patient group 14/27 (52%) had lactose intolerance and 13/27 (48%) experienced no symptoms (lactose malabsorption controls). Only 5 (17%) healthy controls reported symptoms (P < 0.01). The oro-caecal transit time was similar between patient groups with or without symptoms (P = 0.969). SIBO was present in 11 (41%) subjects and was more prevalent in lactose intolerance than in lactose malabsorption [9/14 (64%) vs. 2/13 (15%), P = 0.018]. Symptom severity was similar in lactose intolerance patients with and without SIBO (P = 0.344).

CONCLUSIONS

Small intestinal bacterial overgrowth increases the likelihood of lactose intolerance in patients with CFD as a direct result of lactose fermentation in the small intestine, independent of oro-caecal transit time and visceral sensitivity.

Distribution and enumeration of attractors in probabilistic Boolean networks

Many mathematical models for gene regulatory networks have been proposed. In this study, the authors study attractors in probabilistic Boolean networks (PBNs). They study the expected number of singleton attractors in a PBN and show that it is (2 - (1/2)(L-1))(n), where n is the number of nodes in a PBN and L is the number of Boolean functions assigned to each node. In the case of L=2, this number is simplified into 1.5(n). It is an interesting result because it is known that the expected number of singleton attractors in a Boolean network (BN) is 1. Then, we present algorithms for identifying singleton and small attractors and perform both theoretical and computational analyses on their average case time complexities. For example, the average case time complexities for identifying singleton attractors of a PBN with L=2 and L=3 are O(1.601(n)) and O(1.763(n)), respectively. The results of computational experiments suggest that these algorithms are much more efficient than the naive algorithm that examines all possible 2(n) states.

Prevalence of irritable bowel syndrome among undergraduates in Southeast China

BACKGROUND

There is a wide range in reported prevalence of irritable bowel syndrome worldwide. From the data appeared recently in medical literatures in China, it seems that the incidence of irritable bowel syndrome in young adults is not dissimilar to the one in the Western countries.

AIMS

To explore the prevalence and epidemiological variations of irritable bowel syndrome in an undergraduate student population in Southeast China on the basis of the Rome II and Rome III criteria.

METHODS

All the undergraduate student participants were administered self-report diagnostic measures for irritable bowel syndrome.

RESULTS

The sex-adjusted prevalence rate of irritable bowel syndrome was 4.7% (Rome II) and 10.4% (Rome III), respectively. When we combined irritable bowel syndrome mixed and irritable bowel syndrome unsubtyped in the Rome III subgroups into one group considering the counterpart in the Rome II subgroups was alternative irritable bowel syndrome, the agreement between the two ways to subdivide these 54 patients who were identified with irritable bowel syndrome by both the two criteria was 81%, with a kappa value of 0.67. By the Rome III criteria, we found a female predominance which was especially attributed to the subtypes of irritable bowel syndrome with constipation and unsubtyped.

CONCLUSIONS

Our study suggests that, in young adults in Southeast China, changing diagnostic criteria for irritable bowel syndrome from Rome II to Rome III may affect women more than men on not only the overall prevalence rate but also the sex-difference present or not, especially in irritable bowel syndrome with constipation and irritable bowel syndrome unsubtyped subgroups.

Early upregulation of T cell IL-10 production plays an important role in oral tolerance induction

Early in oral tolerance induction, IL-10-producing CD4(+) T cells were increased, and adoptive transfer of IL-10-deficient CD4(+) T cells failed induction of oral tolerance, suggesting a key role of IL-10 production in such a process.

Immunostimulatory activity of CpG oligonucleotides containing non-ionic methylphosphonate linkages

Bacterial DNA and synthetic oligodeoxynucleotides containing unmethylated CpG-motifs in a particular sequence context activate vertebrate immune cells. We examined the significance of negatively charged internucleoside linkages in the flanking sequences 5' and 3' to the CpG-motif on immunostimulatory activity. Cell proliferation and secretion of IL-12 and IL-6 in mouse spleen cell cultures, and spleen weights of mice increased significantly when a non-ionic linkage was placed at least four or more internucleoside linkages away from the CpG-motif in the 5'-flanking sequence. When the non-ionic linkage was placed closer than three internucleoside linkages in the 5'-flanking sequence to the CpG-motif, immunostimulatory activity was suppressed compared with that observed with the unmodified parent oligo. In general, the placement of non-ionic linkage in the 3'-flanking sequence to the CpG-motif either did not affect or slightly increased immunostimulatory activity compared with the parent oligo. These results have significance in understanding CpG oligonucleotide-receptor interactions and the development of potent immunomodulatory agents.

Modulation of immunostimulatory activity of CpG oligonucleotides by site-specific deletion of nucleobases

The effect of nucleobase deletion in the 3'- or the 5'-flanking sequence to a CpG-motif on immunostimulatory activity of CpG-containing oligonucleotides was examined by cell proliferation, secretion of IL-12 and IL-6 in mouse spleen cell cultures, and by spleen enlargement in mice. Deletion of one or two nucleobases in the 3'-flanking sequence to a CpG-motif at certain positions did not affect immunostimulatory activity, while similar deletions in the 5'-flanking sequence increased immunostimulatory activity compared with the parent oligo.

Immuno-bacterial homeostasis in the gut: new insights into an old enigma

The intestinal mucosa is the interface between the immune system and the massive antigenic load represented by the commensal enteric bacteria. These commensal bacteria drive the development of the mucosal immune system, and in turn most of the lymphocytes in the intestinal mucosa appear to be specific for enteric bacteria antigens. Proper regulation of the responses of these anti-bacterial lymphocytes are extremely important because T cell effectors reactive to enteric bacterial antigens have been shown to cause chronic intestinal inflammation in an adoptive transfer system. The cells and molecules important in regulating mucosal immune response are now being identified. Insights into the mechanisms of mucosal regulation have come from a number of genetically manipulated mouse strains which develop inflammatory bowel disease in response to the enteric bacterial flora. CD4(+)T cells with regulatory function in the mucosa are being identified; other cell types such as CD8(+)T cells. NK cells, and B cells may also have a role in mucosal immune regulation. A model for T cell-immune homeostasis in the intestinal mucosa is presented.