The human gutome: nutrigenomics of the host-microbiome interactions

Demonstrating the importance of the gut microbiota in human health and well-being represents a major transformational task in both medical and nutritional research. Owing to the high-throughput -omics methodologies, the complexity, evolution with age, and individual nature of the gut microflora have been more thoroughly investigated. The balance between this complex community of gut bacteria, food nutrients, and intestinal genomic and physiological milieu is increasingly recognized as a major contributor to human health and disease. This article discusses the "gutome," that is, nutritional systems biology of gut microbiome and host-microbiome interactions. We examine the novel ways in which the study of the human gutome, and nutrigenomics more generally, can have translational and transformational impacts in 21st century practice of biomedicine. We describe the clinical context in which experimental methodologies, as well as data-driven and process-driven approaches are being utilized in nutrigenomics and microbiome research. We underscore the pivotal importance of the gutome as a common platform for sharing data in the emerging field of the integrated metagenomics of gut pathophysiology. This vision needs to be articulated in a manner that recognizes both the omics biotechnology nuances and the ways in which nutrigenomics science can effectively inform population health and public policy, and vice versa.     

Temporal encoding in a nervous system

We examined the extent to which temporal encoding may be implemented by single neurons in the cercal sensory system of the house cricket Acheta domesticus. We found that these neurons exhibit a greater-than-expected coding capacity, due in part to an increased precision in brief patterns of action potentials. We developed linear and non-linear models for decoding the activity of these neurons. We found that the stimuli associated with short-interval patterns of spikes (ISIs of 8 ms or less) could be predicted better by second-order models as compared to linear models. Finally, we characterized the difference between these linear and second-order models in a low-dimensional subspace, and showed that modification of the linear models along only a few dimensions improved their predictive power to parity with the second order models. Together these results show that single neurons are capable of using temporal patterns of spikes as fundamental symbols in their neural code, and that they communicate specific stimulus distributions to subsequent neural structures.     

Estimate of M-wave changes in human biceps brachii during continuous stimulation.

The purpose of the present study was to validate the capability of new fatigue indexes (in the time and frequency domain) applied to experimental recordings and thus, to test some assumptions made in previous simulations. The indexes were applied to M-waves detected non-invasively from human m.biceps brachii during repetitive slightly above threshold stimulations. It was found that distance between the motor point and middle of the end-plate region could be relatively large. Under identical conditions (signals detected by monopolar electrodes and high-pass filtered at 1 Hz), the relative changes of the indexes obtained in electrophysiological experiments and simulations were similar. Changes of the intracellular action potential profile during fatigue used in the simulations were consequently supposed to be close to the actual ones for the muscle analyzed. When the high-pass cut-off frequency was higher than 1 Hz, the sensitivity of the index in the time domain was higher, while that in the frequency domain was lower. If the normalizing spectral moment was of higher order, the sensitivity of the spectral index could be even 150-times greater than that of the fatigue indexes traditionally used. Thus, the spectral index promises high capability to assess fatigue during functional electrical stimulation.     

Internodal sodium channels ensure active processes under myelin manifesting in depolarizing afterpotentials

The current opinion about processes in myelinated axon is that action potential saltatorially propagates between nodes of Ranvier and passively charges internodal axolemma thus causing depolarizing afterpotentials (DAP). Demyelination blocks the conduction that gives additional argument in favor of hypothesis that internode is not able to be activated by the existing internodal sodium channels. The results of our modeling study shows that, when periaxonal space is sufficiently narrow, saltatorial action potential is able to activate internodes. Low density of internodal sodium channels is sufficient to generate active internodal waves that slowly propagate from nodes towards corresponding midinternodes where they collide. The periaxonal width that stops internodal wave propagation (about 400 nm) is significantly larger than the highest value of the physiological range for this parameter (30 nm). Internodal activation is directly manifested as transmembrane internodal potential or as a full-sized action potential in periaxonal space where it can hardly be detected, and only as a small deflection in intracellular space. However, changes in the periaxonal potential cause transmyelin currents that lead to significant DAP. The shape and amplitude of DAP depends on myelin parameters and densities of internodal channels. Several technical parameters affect the results of calculations. Internodal spatial segmentation has to be sufficiently fine (at most 20 microm) for the model to be able to simulate internodal activation. We employ 338 internodal segments as compared with up to 21 used in previous models. Ionic accumulation together with related diffusive and electrical processes alter the calculated DAP amplitude. Inclusion of these processes in calculations demands such increase in the total number of segments that the numerical methods used up to now become unapplicable. To overcome the problem, an iterative implicit approach is proposed. It reduces a matrix of general type in multi-cable models to tridiagonal one and accelerates calculations considerably.     

Immobilization of cells with nitrilase activity from a thermophilic bacterial strain

Cells of the moderately thermophilic Bacillus sp. UG-5B strain, producing nitrilase (EC3.5.5.1), which converts nitriles directly to the corresponding acid and ammonia, were immobilized using different types of matrices and techniques. A variety of sol-gel silica hybrids were tested for entrapment and adsorption of bacterial cells as well as chemical binding on polysulphone membranes. Activation of the matrix surface with formaldehyde led to an increase in immobilization efficiency and operational stability of the biocatalysts. Among the supports screened, membranes gave the best results for enzyme activity and especially operational stability, with retention of 100% activity after eight reaction cycles.     

Augmentation of T(H)-1 type response by immunoactive AT oligonucleotide from lactic acid bacteria via Toll-like receptor 9 signaling

Toll-like receptor 9, which is expressed on the surface of antigen presenting cells and which was recently identified in the cytoplasmic follicle, recognizes bacterial CpG oligodeoxynucleotides (ODNs), resulting in the induction of a potent immune response. However, in our previous study, we found that TLR9 potentially recognizes not only CpG ODN but also non-CpG ODN such as AT ODN. Therefore, in the present study, to investigate this possibility, we elucidated the effects of AT ODN on T(H)-1, T(H)-2 type cytokine induction via TLR9 by real-time quantitative PCR analysis and ELISA of the swine TLR9 transfectant. The results demonstrated that the T(H)-1 type cytokines such as interleukin (IL)-12p70 and interferon (IFN)-gamma were strongly induced by AT ODN compared to the unexposed controls, while T(H)-2 type cytokines were not induced. These results indicate that the AT ODN can augment the T(H)-1 immune response, which plays an important role in prevention of allergic responses. Moreover, the swine TLR9 transfectant demonstrated its usefulness for evaluation of immunostimulation by bacterial DNA through the detection of T(H)-1, T(H)-2 type cytokine induction via TLR9 signaling.     

Comparative study of the stability of poplar plastocyanin isoforms

The stability of the two isoforms of poplar plastocyanin (PCa and PCb) was studied with differential scanning calorimetry (DSC) technique. It was shown that the thermal unfolding of both isoforms is an irreversible process with two endothermic and one exothermic peaks. The melting temperature of PCb was found to be 1.3+/-0.2 K degrees higher than of PCa, which indicates that PCb is more stable. The enthalpy of unfolding was estimated from the heat capacity curves and was found to be significantly higher for PCb at salt concentration I=0.1 M. In addition, PCb unfolding enthalpy and melting temperature are much more sensitive to the changes in the salt concentration as found in the experiments done at different ionic strength. The experiments were complemented with numerical calculations. The salt effect on the stability was modeled using the X-ray structure of PCa and a homology modeled structure of PCb. It was found, in agreement with the experimental data, that the stability of PCb changes by 4.7 kJ more than PCa, as the salt concentration increases from zero to 0.1 M. Thus, the differences in only 12 amino acid positions between "a" and "b" isoforms result in a measurable difference in the folding enthalpy and a significant difference in the salt dependence. The optimization of the electrostatic energies of PCa and PCb were studied and it was shown that PCb is better electrostatically optimized.     

Seasonal environmental changes regulate the expression of the histone variant macroH2A in an eurythermal fish

Adaptation to cold and warm conditions requires dramatic change in gene expression. The acclimatization process of the common carp Cyprinus carpio L. in its natural habitat has been used to study how organisms respond to natural environmental changes. At the cellular level, adaptation to cold condition is accompanied by a dramatic alteration in nucleolar structure and a down regulation of the expression of ribosomal genes. We show that the enrichment of condensed chromatin in winter adapted cells is not correlated with an increase of the heterochromatin marker trimethyl and monomethyl K20H4. However, the expression of the tri methyl K4 H3 and of the variant histone macroH2A is significantly increased during the winter season together with a hypermethylation of CpG residues. Taking into account the properties of macroH2A toward chromatin structure and dynamics and its role in gene repression our data suggest that the increased expression of macroH2A and the hypermethylation of DNA which occurs upon winter-acclimatization plays a major role for the reorganization of chromatin structure and the regulation of gene expression during the physiological adaptation to a colder environment.