Identification of inulin-responsive bacteria in the gut microbiota via multi-modal activity-based sorting.

Prebiotics are defined as non-digestible dietary components that promote the growth of beneficial gut microorganisms. In many cases, however, this capability is not systematically evaluated. Here, we develop a methodology for determining prebiotic-responsive bacteria using the popular dietary supplement inulin. We first identify microbes with a capacity to bind inulin using mesoporous silica nanoparticles functionalized with inulin. 16S rRNA gene amplicon sequencing of sorted cells revealed that the ability to bind inulin was widespread in the microbiota. We further evaluate which taxa are metabolically stimulated by inulin and find that diverse taxa from the phyla Firmicutes and Actinobacteria respond to inulin, and several isolates of these taxa can degrade inulin. Incubation with another prebiotic, xylooligosaccharides (XOS), in contrast, shows a more robust bifidogenic effect. Interestingly, the Coriobacteriia Eggerthella lenta and Gordonibacter urolithinfaciens are indirectly stimulated by the inulin degradation process, expanding our knowledge of inulin-responsive bacteria.

Linear Interval Approximation of Sensor Characteristics with Inflection Points.

The popularity of smart sensors and the Internet of Things (IoT) is growing in various fields and applications. Both collect and transfer data to networks. However, due to limited resources, deploying IoT in real-world applications can be challenging. Most of the algorithmic solutions proposed so far to address these challenges were based on linear interval approximations and were developed for resource-constrained microcontroller architectures, i.e., they need buffering of the sensor data and either have a runtime dependency on the segment length or require the sensor inverse response to be analytically known in advance. Our present work proposed a new algorithm for the piecewise-linear approximation of differentiable sensor characteristics with varying algebraic curvature, maintaining the low fixed computational complexity as well as reduced memory requirements, as demonstrated in a test concerning the linearization of the inverse sensor characteristic of type K thermocouple. As before, our error-minimization approach solved the two problems of finding the inverse sensor characteristic and its linearization simultaneously while minimizing the number of points needed to support the characteristic.

Three-Dimensional Scanning Applied for Flexible and In Situ Calibration of Galvanometric Scanner Systems.

Galvanometric laser scanner (GLS) systems are widely used for materials processing due to their high precision, processing velocity, and repeatability. However, GLS systems generally suffer from scan field distortions due to joint and task space relationship errors. The problem is further pronounced in robotic applications, where the GLS systems are manipulated in space, as unknown errors in the relative pose of the GLS can be introduced. This paper presents an in situ, data-driven methodology for calibrating GLS systems using 3D scanning, emphasising the flexibility, generalisation, and automated industrial integration. Three-dimensional scanning serves two primary purposes: (1) determining the relative pose between the GLS system and the calibration plate to minimise calibration errors and (2) supplying an image processing algorithm with dense and accurate data to measure the scan field distortion based on the positional deviations of marked fiducials. The measured deviations are used to train a low-complexity Radial Basis Function (RBF) network to predict and correct the distorted scan field. The proposed method shows promising results and significantly reduces the scan field distortion without the use of specialised calibration tools and with limited knowledge of the optical design of the GLS system.

Nutrient niche specificity for glycosaminoglycans is reflected in polysaccharide utilization locus architecture of gut Bacteroides species.

Introduction: Glycosaminoglycans (GAGs) present in the mucosal layer can be used as nutrients by certain intestinal bacteria, particularly members of the Bacteroides. GAG abundances are altered in some diseases such as inflammatory bowel diseases, which may affect microbial composition and activity, and it is therefore important to understand GAG utilization by members of the gut microbiota. Methods: We used growth assays, transcriptomics, and comparative genomics to evaluate chondroitin sulfate (CS) and hyaluronan (HA) degradation ability by multiple gut Bacteroides species. Results and discussion: We found that not all Bacteroides species able to degrade CS could also degrade HA, despite having lyases which act on both compounds. We propose that in the model organism Bacteroides thetaiotaomicron, the lyase BT_3328 in combination with surface binding proteins BT_3329 and BT_3330 and potentially BT_4411 are involved in HA breakdown. Furthermore, degradation of both compounds provides public goods for other Bacteroides, including non-degraders, suggesting that cooperative degradation as well as cross-feeding may be widespread in the mucosal glycan utilization clade.

Impaired Mucosal Homeostasis in Short-Term Fiber Deprivation Is Due to Reduced Mucus Production Rather Than Overgrowth of Mucus-Degrading Bacteria.

The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders.

Linear Interval Approximation for Smart Sensors and IoT Devices.

In this work, we introduce and use an innovative approach for adaptive piecewise linear interval approximation of sensor characteristics, which are differentiable functions. The aim is to obtain a discreet type of inverse sensor characteristic, with a predefined maximum approximation error, with minimization of the number of points defining the characteristic, which in turn is related to the possibilities for using microcontrollers with limited energy and memory resources. In this context, the results from the study indicate that to overcome the problems arising from the resource constraints of smart devices, appropriate "lightweight" algorithms are needed that allow efficient connectivity and intelligent management of the measurement processes. The method has two benefits: first, low-cost microcontrollers could be used for hardware implementation of the industrial sensor devices; second, the optimal subdivision of the measurement range reduces the space in the memory of the microcontroller necessary for storage of the parameters of the linearized characteristic. Although the discussed computational examples are aimed at building adaptive approximations for temperature sensors, the algorithm can easily be extended to many other sensor types and can improve the performance of resource-constrained devices. For prescribed maximum approximation error, the inverse sensor characteristic is found directly in the linearized form. Further advantages of the proposed approach are: (i) the maximum error under linearization of the inverse sensor characteristic at all intervals, except in the general case of the last one, is the same; (ii) the approach allows non-uniform distribution of maximum approximation error, i.e., different maximum approximation errors could be assigned to particular intervals; (iii) the approach allows the application to the general type of differentiable sensor characteristics with piecewise concave/convex properties.

Analysis and evaluation of correlation between DNA polymorphism in the genes MTHFR, PAI-1 and serum creatinine, creatinine clearance and albumin/creatinine ratio in morning urine of patients with type 2 diabetes mellitus and diabetic nephropathy.

INTRODUCTION: Diabetic nephropathy is a major microangiopathic complication of type 2 diabetes and a leading cause of chronic kidney disease (CKD).

Allergen-Specific IgE and IgG4 as Biomarkers for Immunologic Changes during Subcutaneous Allergen Immunotherapy.

(1) Background: Biomarkers of efficacy for subcutaneous immunotherapy (SCIT) on allergic rhinitis have not been evaluated in details. The present study aims to assess the relevance of measuring of sIgE, sIgG4 and IgE/IgG4 ratio during SCIT in patients with allergic rhinitis; (2) Methods: 20 patients, 13 men and 7 women aged 19 to 58 years, with clinically manifested seasonal and perennial allergic rhinitis were studied. At the initiation and in the end of the three-year course of SCIT serum allergen-specific IgE and IgG4 were measured with ImmunoCAP system. The sIgE/sIgG4 ratio was calculated as a biomarker for immunologic effectiveness; (3) Results: There was a significant increase of sIgG4 antibodies (p < 0.05), while at the end of SCIT for the sIgE levels no significant changes were seen (p > 0.05). Moreover, 90% of patients showed a decrease of the IgE/IgG4 ratio; (4) Conclusions: In most of treated patients with AR, SCIT with Bulgarian allergen products leads to clear immunological changes. After a 3-year of SCIT there is a significant increase in allergen specific IgG4 levels and both decrease of sIgE and IgE/IgG4 ratio. sIgE, sIgG4 and IgE/IgG4 ratio can be used as a substantial biomarker for predicting immunological effectiveness of SCIT.

Transparent soil microcosms for live-cell imaging and non-destructive stable isotope probing of soil microorganisms.

Microscale processes are critically important to soil ecology and biogeochemistry yet are difficult to study due to soil's opacity and complexity. To advance the study of soil processes, we constructed transparent soil microcosms that enable the visualization of microbes via fluorescence microscopy and the non-destructive measurement of microbial activity and carbon uptake in situ via Raman microspectroscopy. We assessed the polymer Nafion and the crystal cryolite as optically transparent soil substrates. We demonstrated that both substrates enable the growth, maintenance, and visualization of microbial cells in three dimensions over time, and are compatible with stable isotope probing using Raman. We applied this system to ascertain that after a dry-down/rewetting cycle, bacteria on and near dead fungal hyphae were more metabolically active than those far from hyphae. These data underscore the impact fungi have facilitating bacterial survival in fluctuating conditions and how these microcosms can yield insights into microscale microbial activities.

Late Postpregnancy Modifications in the Subset of Peripheral Natural T Regulatory Cells in Healthy Women.

The establishment of a relevant regulatory T cell (Treg) pool in the periphery is of importance to ensure immune homoeostasis. Finely tuned signaling pathways in Tregs control the immune response during extreme endocrine changes in pregnancy and afterward. In this study, we investigate the population of Tregs and, in particular, the natural Tregs (nTregs) in healthy women divided into three groups according to the number of previous pregnancies, if any (Gr.1-one pregnancy, Gr.2-≥2 pregnancies, and Gr.0-no pregnancy). The overall analysis showed similar proportions in the entire Treg pool and nTregs (FoxP3+CD45RA+) in all the three groups (p > 0.05). However, the age-related trend of CD25+ nTregs was found to be different in parous and nonparous women. Analysis of phosphorylated ERK1/2, an important signaling molecule in T cell maintenance, showed a significantly higher percentage in CD25+ nTregs in the group of nonparous compared with parous women (p < 0.05). Thus, our results provide evidence that pregnancy may exert a long-lasting impact on the subset of nTregs due to the extreme changes in the hormonal status, which in turn, influences pre- and post-thymic maturation.

Suppression of allergen-specific B lymphocytes by chimeric protein-engineered antibodies.

House dust mites Dermatophagoides pteronyssinus (Dpt) are among the most frequent causes of allergy symptoms in Europe. Der p 1 is one of the major allergenic compounds of Dpt and the pathological Der p 1-specific B cells play a key role as producers of allergen-binding antibodies. The selective elimination of these cells by artificial protein molecules which inhibit the production of Dpt-recognizing IgE antibodies is a perspective therapeutic goal of allergy. A protein engineered chimeric molecule has been constructed, which binds Der p 1-specific B cells via their BCR and suppresses selectively the production of anti-Der p 1 antibodies via CR1. The synthetic peptide Der p 1 p52-71 and an anti-CD35 monoclonal antibody were used for the construction of Der p 1 chimera. The functional effects of engineered antibodies were analyzed in vitro using PBMCs from allergy patients. Significant inhibition of allergen-specific proliferation and reduction of Der p 1-IgE antibody production were observed after treatment of PBMCs from allergic patients with Der p 1-peptide chimera. Culturing of these PBMCs in the presence of the chimeric molecule increased the percentage of apoptotic (Annexin V-positive) B lymphocytes, but not T lymphocytes.

Nitric oxide stimulates the production of atrial natriuretic peptide and progesterone by human granulosa luteinized cells with an antiapoptotic effect.

OBJECTIVE: To study the effect of nitric oxide (NO) on atrial natriuretic peptide (ANP) and progesterone (P) production by human granulose luteinized cells (GLC) in vitro and to elucidate their role on the survival of cultured cells. METHODS: Human GLCs were cultured in HAM's F10/10% FCS as monolayers for 24 h. Subsequently GLCs were treated for 24 h with 0.5 mM Sodium Nitroprusside (SNP, NO donor) and 0.5 mM Aminoglutethimide (AG , P450scc inhibitor). The levels of ANP and P were measured in supernatants of cultured cells by proANP(1-98) kit and RIA, respectively. Caspase-3 activity was determined by Ac-DEVD-pNA as substrate. RESULTS: The production of ANP and P was increased by NO as compared to control cells (p<0.05). AG diminished the production of P compared to SNP (p<0.05). The caspase-3 activity was significantly lower in SNP treated cells (p<0.05) and increased significantly after AG treatment compared to control cells (p<0.05). CONCLUSION: NO generated by SNP in human GLCs culture stimulated the production of ANP and P. The higher levels of ANP and P were closely related to significantly lower caspase-3 activity thus showing the role of ANP, P and NO on the survival of preovulatory human follicle.

Electronic structure of oxide, peroxide, and superoxide clusters of the 3d elements: a comparative density functional study.

The 3d-element transition metal dioxide MO(2), peroxide M(O(2)), and superoxide MOO clusters (M=Sc-Zn), are studied by density functional theory with the B1LYP functional. The reliability of the methods and basis sets employed was tested by a reinvestigation of the monoxides, for which a database of experimental data is available. The global minima on the M+O(2) potential energy surfaces correspond to dioxide structure, the only exception being CuOO, with a superoxide structure. All Zn dioxygen clusters are thermodynamically unstable-their ground states lie higher than the dissociation limit to Zn+O(2). Our calculations are in favor of the high-spin configurations for the FeO(2), CoO(2), and NiO(2) ground states, which are still a subject of extensive theoretical and experimental studies. These assignments are confirmed by the coupled-cluster method, CCSD(T), except for NiO(2). Based on the existence of a stable NiO(2) monoanion in a (4)B(1) state, however, it can be concluded that NiO(2) in its (5)A(1) state should also be stable. The vibrational frequencies are calculated for clusters entrapped in the cubic cell of solid Ar matrix and compared with those obtained for gas-phase clusters. The matrix has no influence on the vibrations of the monoxides and most of the dioxides; however, Co and Ni-dioxoclusters interact strongly with the atoms from the noble gas matrix. The most intense frequencies in the IR spectra are shifted to lower energies and the ordering of the low-lying electronic states by stability is also reversed. According to the electrostatic potential maps, the oxygen atoms in the peroxides are more nucleophilic than those in the dioxides and superoxides. The terminal oxygen atom in superoxides is more nucleophilic than its M-bonded oxygen atom, though charge distribution analysis predicts a smaller negative charge on the terminal oxygen. TiO(2) is the only dioxide in which nucleophilic character in the vicinity of the metal cation is induced.

Interaction of molecular nitrogen and oxygen with extraframework cations in zeolites with double six-membered rings of oxygen-bridged silicon and aluminum atoms: a DFT study.

The interaction of N(2) and O(2) with extraframework cations of zeolite frameworks was studied by DFT, using the B3LYP method. The extraframework cation sites located in the vicinity of the double six-member rings (D6R) of FAU zeolites (SI, SI', SIII') were considered and clusters with composition (M(n)(+))(2/)(n)()H(12)Si(10)Al(2)O(18), M = Li(+), Na(+), K(+), Ca(2+), were selected to represent the adsorption centers. The cation sites SII in the center of single six-membered rings (S6R) were modeled by [M(I)H(12)Si(4)Al(2)O(6)](-) and M(II)H(12)Si(4)Al(2)O(6) clusters. The adsorption energy of N(2) and O(2) is the highest for Li(+) cations at the SIII' cation sites, while for the SI' and SII sites the adsorption energies decrease in the order Ca(2+) > Na(+) > Li(+). The calculated small N(2) adsorption energy for Li(+) cations at SII sites suggests that these sites do not take part in the sorption process in agreement with results of NMR studies and Monte Carlo simulations. The N(2) adsorption complexes with the extraframework cations are linear, while those of O(2) are bent regardless of the extraframework cation location. The SIII' cation sites are the most favorable ones with respect to N(2) adsorption capacity and N(2)/O(2) selectivity; the SII sites are less selective and the SI sites are not accessible.

Manganese, iron, cobalt, and nickel oxo-, peroxo-, and superoxoclusters: a density functional theory study.

The 3d-transition-metal dioxo-, peroxo-, and superoxoclusters with the general composition MO2, M(O2), and MOO (M = Mn, Fe, Co, and Ni) were studied by DFT by the B1LYP functional. The dioxides in their ground states represent the global minima for the M + O2 system. Both ground-state dioxides and the lowest-energy peroxides are in their (d-only) highest spin states. The 6A1 state of Co(O2) exceeds the d-only spin-multiplicity value (quartet), being nearly isoenergetic with the 4A1 state of Co(O2). The energy gain on transforming the peroxides to the corresponding dioxides decreases in the order Mn(O2) > Fe(O2) > Co(O2) > Ni(O2) and varies in the range 0.27-1.8 eV. The dissociation energy to M + O2 for all studied peroxides is less than 1 eV being the lowest (0.47 eV) for Mn(O2). The Mn and Fe peroxides need less than 0.3 eV to rupture one of the MO bonds to form the corresponding superoxide. Mn and Fe superoxides are less stable than the corresponding peroxides; the superoxide of Co is more stable than its peroxide, while Ni superoxide is unstable--its energy is above the limit of dissociation to Ni + O2. According to the electrostatic potential maps, the oxygen atoms in the peroxides are more nucleophilic than those in the dioxides and superoxides, in which the terminal oxygen atom is more nucleophilic than the M-bonded oxygen atom. This result differs from the expectations based on charge-distribution analysis.