A prospective, randomized, blinded, placebo-controlled pilot study on the effect of Enterococcus faecium on clinical activity and intestinal gene expression in canine food-responsive chronic enteropathy

Background

Canine chronic enteropathies (CE) are believed to be caused by an aberrant immune response towards the intestinal microbiome. Administration of probiotics can alleviate colitis in people. In vitro effects of the probiotic Enterococcus faecium NCIMB 10415 E1707 (EF) previously have been evaluated using canine cells (e.g., whole blood, intestinal biopsies), but data on in vivo efficacy are lacking.

Hypothesis/Objectives

Administration of EF to dogs with food‐responsive CE will improve clinical outcome and decrease the intestinal inflammatory profile.

Animals

Dogs diagnosed with CE were prospectively recruited to receive a hydrolyzed elimination diet plus either a synbiotic product containing EF or placebo for 6 weeks. Both veterinary staff and owners were blinded to the treatment.

Methods

Clinical severity index (CCECAI), clinicopathological data and gene expression using intestinal biopsies (TLR2/4/5/9, IL‐17A, IL‐22, IL‐23p19, RORC, IL‐2, IL‐12p35, TNFα, IL‐4, IFNy, IL‐10, TGFβ, IL‐1β, IL‐18, NLRP3, casp‐1, TFF1, TFF3 and PPARy) before and after 6 weeks of treatment were analyzed using linear mixed modeling.

Results

Of the 45 cases recruited, 12 finished the clinical trial. Seven received the synbiotic and 5 the placebo product. There was no difference between groups or treatments regarding clinical efficacy, histology scores or expression of any of the investigated genes.

Conclusions and clinical importance

Standard dietary treatment induced rapid clinical response in all cases. Because the study was underpowered, it was not possible to determine whether or not EF had an additional effect within the time period of 6 weeks.

Interactive augmented reality using Scratch 2.0 to improve physical activities for children with developmental disabilities

This study uses a body motion interactive game developed in Scratch 2.0 to enhance the body strength of children with disabilities. Scratch 2.0, using an augmented-reality function on a program platform, creates real world and virtual reality displays at the same time. This study uses a webcam integration that tracks movements and allows participants to interact physically with the project, to enhance the motivation of children with developmental disabilities to perform physical activities. This study follows a single-case research using an ABAB structure, in which A is the baseline and B is the intervention. The experimental period was 2 months. The experimental results demonstrated that the scores for 3 children with developmental disabilities increased considerably during the intervention phrases. The developmental applications of these results are also discussed.

The modulation effect of transverse, antibonding, and higher-order longitudinal modes on the two-photon photoluminescence of gold plasmonic nanoantennas

Plasmonic nanoantennas exhibit various resonant modes with distinct properties. Upon resonant excitation, plasmonic gold nanoantennas can generate strong two-photon photoluminescence (TPPL). The TPPL from gold is broadband and depolarized, and may serve as an ideal local source for the investigation of antenna eigenmodes. In this work, TPPL spectra of three arrays of single-crystalline gold nanoantennas are comprehensively investigated. We carefully compare the TPPL spectra with dark-field scattering spectra and numerically simulated spectra. We show the modulation effect of the transverse resonant mode and the nonfundamental longitudinal mode on the TPPL spectrum. We also demonstrate suppression of TPPL due to the subradiant antibonding modes and study the influence of antenna resonant modes on the overall TPPL yield. Our work provides direct experimental evidence on nanoantenna-mediated near-to-far-field energy coupling and gains insight into the emission spectrum of the TPPL from gold nanoantennas.

Increase in physical activities in kindergarten children with cerebral palsy by employing MaKey-MaKey-based task systems

In this study, we employed Flash- and Scratch-based multimedia by using a MaKey-MaKey-based task system to increase the motivation level of children with cerebral palsy to perform physical activities. MaKey MaKey is a circuit board that converts physical touch to a digital signal, which is interpreted by a computer as a keyboard message. In this study, we used conductive materials to control this interaction. This study followed single-case design using ABAB models in which A indicated the baseline and B indicated the intervention. The experiment period comprised 1 month and a half. The experimental results demonstrated that in the case of two kindergarten children with cerebral palsy, their scores were considerably increased during the intervention phrases. The developmental applications of the results are also discussed.

Does stress induce bowel dysfunction?

Psychological stress is known to induce somatic symptoms. Classically, many gut physiological responses to stress are mediated by the hypothalamus-pituitary-adrenal axis. There is, however, a growing body of evidence of stress-induced corticotrophin-releasing factor (CRF) release causing bowel dysfunction through multiple pathways, either through the HPA axis, the autonomic nervous systems, or directly on the bowel itself. In addition, recent findings of CRF influencing the composition of gut microbiota lend support for the use of probiotics, antibiotics, and other microbiota-altering agents as potential therapeutic measures in stress-induced bowel dysfunction.

Tryptophan catabolism restricts IFN-γ-expressing neutrophils and Clostridium difficile immunopathology

The interplay between Clostridium difficile and the host's metabolome is believed to influence the severity of infection. However, the mechanism for this phenomenon remains unclear. In this study, we model one of these metabolic pathways by focusing on tryptophan metabolism in the host. We found that inhibition of tryptophan catabolism in IDO1-knockout mice led to increased mucosal destruction, cecal hemorrhage, and increased production of IFN-γ in response to C. difficile infection, but no significant change in mucosal effector or regulatory T cell numbers or IL-10 mRNA expression. The increased immunopathology in infected IDO1-knockout mice was associated with a lower C. difficile burden and an increased percentage of IFN-γ-expressing neutrophils. We further demonstrated the ability of kynurenine to induce apoptosis in bone marrow-derived neutrophils, whereas the presence of tryptophan reversed this effect, providing a possible mechanism for the increased neutrophil accumulation in IDO1(-/-) mice. We conclude that C. difficile induces tryptophan catabolism in cecal lamina propria cells, which restricts C. difficile-associated immunopathology and the accumulation of IFN-γ-expressing neutrophils. This might represent a self-regulatory mechanism for neutrophils, via the IFN-γ-IDO1 pathway, to restrict their own accumulation during infection. These findings have important clinical implications because IDO inhibitors are used to treat cancer in clinical trials (in patients particularly susceptible to getting C. difficile infection), and treatment with IDO1 inhibitors may exacerbate the severity of C. difficile colitis.

Application of polycolloid-releasing substrate to remediate trichloroethylene-contaminated groundwater: a pilot-scale study

The objectives of this pilot-scale study were to (1) evaluate the effectiveness of bioremediation of trichloroethylene (TCE)-contaminated groundwater with the supplement of slow polycolloid-releasing substrate (SPRS) (contained vegetable oil, cane molasses, surfactants) under reductive dechlorinating conditions, (2) apply gene analyses to confirm the existence of TCE-dechlorinating genes, and (3) apply the real-time polymerase chain reaction (PCR) to evaluate the variations in TCE-dechlorinating bacteria (Dehalococcoides spp.). Approximately 350L of SPRS solution was supplied into an injection well (IW) and groundwater samples were collected and analyzed from IW and monitor wells periodically. Results show that the SPRS caused a rapid increase of the total organic carbon concentration (up to 5794mg/L), and reductive dechlorination of TCE was significantly enhanced. TCE dechlorination byproducts were observed and up to 99% of TCE removal (initial TCE concentration=1872μg/L) was observed after 50 days of operation. The population of Dehalococcoides spp. increased from 4.6×10(1) to 3.41×10(7)cells/L after 20 days of operation. DNA sequencing results show that there were 31 bacterial species verified, which might be related to TCE biodegradation. Results demonstrate that the microbial analysis and real-time PCR are useful tools to evaluate the effectiveness of TCE reductive dechlorination.

Structural basis for the identification of the N-terminal domain of coronavirus nucleocapsid protein as an antiviral target

Coronaviruses (CoVs) cause numerous diseases, including Middle East respiratory syndrome and severe acute respiratory syndrome, generating significant health-related and economic consequences. CoVs encode the nucleocapsid (N) protein, a major structural protein that plays multiple roles in the virus replication cycle and forms a ribonucleoprotein complex with the viral RNA through the N protein’s N-terminal domain (N-NTD). Using human CoV-OC43 (HCoV-OC43) as a model for CoV, we present the 3D structure of HCoV-OC43 N-NTD complexed with ribonucleoside 5′-monophosphates to identify a distinct ribonucleotide-binding pocket. By targeting this pocket, we identified and developed a new coronavirus N protein inhibitor, N-(6-oxo-5,6-dihydrophenanthridin-2-yl)(N,N-dimethylamino)acetamide hydrochloride (PJ34), using virtual screening; this inhibitor reduced the N protein’s RNA-binding affinity and hindered viral replication. We also determined the crystal structure of the N-NTD–PJ34 complex. On the basis of these findings, we propose guidelines for developing new N protein-based antiviral agents that target CoVs.

TcaR-ssDNA complex crystal structure reveals new DNA binding mechanism of the MarR family proteins

The teicoplanin-associated locus regulator (TcaR) regulates gene expression of proteins on the intercellular adhesion (ica) locus involved in staphylococci poly-N-acetylglucosamine biosynthesis. The absence of TcaR increases poly-N-acetylglucosamine production and promotes biofilm formation. Until recently, the mechanism of multiple antibiotic resistance regulator family protein members, such as TcaR, was restricted to binding double-stranded DNA. However, we recently found that TcaR strongly interacts with single-stranded DNA, which is a new role for this family of proteins. In this study, we report Staphylococcus epidermidis TcaR–single-stranded DNA complex structures. Our model suggests that TcaR and single-stranded DNA form a 6₁-symmetry polymer composed of TcaR dimers with single-stranded DNA that wraps outside the polymer and 12 nt per TcaR dimer. Single-stranded DNA binding to TcaR involves a large conformational change at the DNA binding lobe. Several point mutations involving the single-stranded DNA binding surface validate interactions between single-stranded DNA and TcaR. Our results extend the novel role of multiple antibiotic resistance regulator family proteins in staphylococci.

Control of trichloroethylene plume migration using a biobarrier system: a field-scale study

The objective of this field-scale study was to evaluate the effectiveness of controlling trichloroethylene (TCE) plume migration using the polycolloid substrate (PS) biobarrier. The developed PS (containing soybean oil, lactate and surfactants) could release substrate to enhance the TCE dechlorination. In this study, a biobarrier comprising PS injection wells was installed. Injection wells were installed at 5-m intervals, and approximately 15 L of PS was injected into each well. Results show that TCE concentrations in the injection wells dropped from an average of 87 μg/L to below 1 μg/L after 35 days of PS injection. The total organic carbon concentrations in the injection wells increased from an average of 2.1-543 mg/L after 30 days of PS injection. The dissolved oxygen (DO) concentrations and oxidation-reduction potential (ORP) values dropped from an average of 1.6 mg/L to below 0.1 mg/L and from 124 mv to -14 mv after 20 days of injection, respectively. The DO and ORP remained in anaerobic conditions during the remaining 100 days of the operational period. TCE degradation by-products were observed in groundwater samples during the operational period. This reveals that the addition of PS could effectively enhance the reductive dechlorinating of TCE.

Depth-resolved confocal micro-Raman spectroscopy for characterizing GaN-based light emitting diode structures

In this work, we demonstrate that depth-resolved confocal micro-Raman spectroscopy can be used to characterize the active layer of GaN-based LEDs. By taking the depth compression effect due to refraction index mismatch into account, the axial profiles of Raman peak intensities from the GaN capping layer toward the sapphire substrate can correctly match the LED structural dimension and allow the identification of unique Raman feature originated from the 0.3 μm thick active layer of the studied LED. The strain variation in different sample depths can also be quantified by measuring the Raman shift of GaN A1(LO) and E2(high) phonon peaks. The capability of identifying the phonon structure of buried LED active layer and depth-resolving the strain distribution of LED structure makes this technique a potential optical and remote tool for in operando investigation of the electronic and structural properties of nitride-based LEDs.

Tunable and stable UV-NIR photoluminescence from annealed SiOx with Si nanoparticles

We demonstrate stable and tunable light emission in ultraviolet to near infrared regime by using annealed SiOx sample. By adjusting the ratio of Si and O of SiOx, different wavelengths such as ultraviolet, visible and near infrared photoluminescence can be tuned. From the results of transmission electron microscope, various sizes (1~4 nm) of the embedded Si nanoparticles were formed. Nanoparticles with smaller sizes were indeed formed for UV-blue emitting samples and the origin of light emission may be misattributed to the quantum confinement effects. However, we found the efficient and stable light emission in UV-blue regime, with lifetime on the order of nanoseconds, is dominantly from the defects.

Clean-lifting transfer of large-area residual-free graphene films

A unique "clean-lifting transfer" (CLT) technique that applies a controllable electrostatic force to transfer large-area and high-quality CVD-grown graphene onto various rigid or flexible substrates is reported. The CLT technique without using any organic support or adhesives can produce residual-free graphene films with large-area processability, and has great potential for future industrial production of graphene-based electronics or optoelectronics.

Stress-induced corticotropin-releasing hormone-mediated NLRP6 inflammasome inhibition and transmissible enteritis in mice

BACKGROUND & AIMS

Stress alters brain-gut interactions and could exacerbate intestinal disorders, including irritable bowel syndrome. Alterations in the intestinal microbiota have been associated with irritable bowel syndrome. Maintenance of healthy microbiota requires nucleotide-binding oligomerization domain protein-like receptors, pyrin-domain containing (NLRP)-6 inflammasomes. We investigated the involvement of NLRP6 in water-avoidance stress (WAS)-induced intestinal disorders in mice.

METHODS

B57BL6 mice were subjected to WAS for 1 hour each day for 10 days; body weights and intestinal inflammation and permeability were analyzed. We investigated signaling via the NLRP3 and NLRP6 inflammasomes, and the role of corticotropin-releasing hormone (CRH) in WAS-associated inflammation and NLRP6 inhibition. Mice that were not exposed to stress were co-housed with mice subjected to WAS to determine the effects of WAS-induced dysbiosis, measured by sequencing bacterial 16S ribosomal RNA. We also assessed the effects of a peroxisome proliferator-activated receptor-γ agonist and probiotics.

RESULTS

WAS-induced small-bowel inflammation (enteritis) was associated with inhibition of NLRP6, but not NLRP3, and was prevented by a peroxisome proliferator-activated receptor-γ agonist, which induced epithelial expression of NLRP6. CRH was released during WAS and inhibited NLRP6 expression. WAS induced alterations in the gut microbiota of mice; co-housed nonstressed mice developed enteritis associated with increased CRH and decreased levels of NLRP6. Probiotic therapy reduced intestinal inflammation in mice with WAS-induced enteritis.

CONCLUSIONS

Exposure of mice to stress inhibits NLRP6 and alters the composition of the gut microbiota, leading to intestinal inflammation. These findings might explain the benefits of probiotics for patients with stress-associated gastrointestinal disorders.

Crystal structure-based exploration of the important role of Arg106 in the RNA-binding domain of human coronavirus OC43 nucleocapsid protein

Human coronavirus OC43 (HCoV-OC43) is a causative agent of the common cold. The nucleocapsid (N) protein, which is a major structural protein of CoVs, binds to the viral RNA genome to form the virion core and results in the formation of the ribonucleoprotein (RNP) complex. We have solved the crystal structure of the N-terminal domain of HCoV-OC43 N protein (N-NTD) (residues 58 to 195) to a resolution of 2.0Å. The HCoV-OC43 N-NTD is a single domain protein composed of a five-stranded β-sheet core and a long extended loop, similar to that observed in the structures of N-NTDs from other coronaviruses. The positively charged loop of the HCoV-OC43 N-NTD contains a structurally well-conserved positively charged residue, R106. To assess the role of R106 in RNA binding, we undertook a series of site-directed mutagenesis experiments and docking simulations to characterize the interaction between R106 and RNA. The results show that R106 plays an important role in the interaction between the N protein and RNA. In addition, we showed that, in cells transfected with plasmids that encoded the mutant (R106A) N protein and infected with virus, the level of the matrix protein gene was decreased by 7-fold compared to cells that were transfected with the wild-type N protein. This finding suggests that R106, by enhancing binding of the N protein to viral RNA plays a critical role in the viral replication. The results also indicate that the strength of N protein/RNA interactions is critical for HCoV-OC43 replication.

Interactions between fluorescence of atomically layered graphene oxide and metallic nanoparticles

Graphene oxide (GO) demonstrates interesting photoluminescence (PL) because of its unique heterogeneous atomic structure, which consists of variable sp(2)- and sp(3)-bonded carbons. In this study, we report the interaction between the luminescence of GO ranging from a single atomic layer to few-layered thin films and localized surface plasmon resonance (LSPR) from silver nanoparticles (Ag NPs). The photoluminescence of GO in the vicinity of the Ag NPs is enhanced significantly due to the near-field plasmonic effect by coupling electron-hole pairs of GO with oscillating electrons in Ag NPs, leading to an increased PL intensity and a decreased PL decay lifetime. The maxima 30-fold enhancement in PL intensity is obtained with an optimized film thickness of GO, and the luminescence image from a single atomic layer GO sheet is successfully observed with the assistance of the LSPR effect. The results provide an ideal platform for exploring the interactions between the fluorescence of two-dimensional layered materials and the LSPR effect.

Functional studies of ssDNA binding ability of MarR family protein TcaR from Staphylococcus epidermidis

The negative transcription regulator of the ica locus, TcaR, regulates proteins involved in the biosynthesis of poly-N-acetylglucosamine (PNAG). Absence of TcaR increases PNAG production and promotes biofilm formation in Staphylococci. Previously, the 3D structure of TcaR in its apo form and its complex structure with several antibiotics have been analyzed. However, the detailed mechanism of multiple antibiotic resistance regulator (MarR) family proteins such as TcaR is unclear and only restricted on the binding ability of double-strand DNA (dsDNA). Here we show by electrophoretic mobility shift assay (EMSA), electron microscopy (EM), circular dichroism (CD), and Biacore analysis that TcaR can interact strongly with single-stranded DNA (ssDNA), thereby identifying a new role in MarR family proteins. Moreover, we show that TcaR preferentially binds 33-mer ssDNA over double-stranded DNA and inhibits viral ssDNA replication. In contrast, such ssDNA binding properties were not observed for other MarR family protein and TetR family protein, suggesting that the results from our studies are not an artifact due to simple charge interactions between TcaR and ssDNA. Overall, these results suggest a novel role for TcaR in regulation of DNA replication. We anticipate that the results of this work will extend our understanding of MarR family protein and broaden the development of new therapeutic strategies for Staphylococci.

Conformational changes in DNA upon ligand binding monitored by circular dichroism

Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also shows its potential to be a drug-screening platform in the future.

A set of polymorphic trinucleotide and tetranucleotide microsatellite markers for silver crucian carp (Carassius auratus gibelio) and cross-amplification in crucian carp

Silver crucian carp (Carassius auratus gibelio Bloch), as a gynogenetic fish, is a promising model for the study of the evolutionary genetics of vertebrates. We have developed 59 polymorphic trinucleotide and tetranucleotide markers for the silver crucian carp through the biotin capture method and radioactive-labeling hybridization. The number of alleles ranged from 2 to 12 in the population, and the average proportion of heterozygotes (including tri- and diallelic) at polymorphic loci was 76.8%. In addition, these loci were successfully applied to a close relative, the crucian carp (Carassius auratus), by cross-amplification, as shown by the range of alleles (2-19), observed heterozygosity (0.1765-0.9706), expected heterozygosity (0.2392-0.9421), and polymorphism information content (0.2186-0.9236).

Salinity effects on the expression of osmoregulatory genes in the euryhaline black porgy Acanthopagrus schlegeli

Black porgy is a marine euryhaline species with a capacity to cope with demands in a wide range of salinities and thus is a perfect model-fish to study osmoregulatory responses to salinity-acclimated processes and their hormonal control. The present study was performed to understand the regulatory changes in hormone, hormone receptors and important osmoregulatory genes in pituitary, gill, intestine and kidney in response to acute salinity stress. Transcript levels were analyzed by quantitative real-time PCR following acute salinity challenge by direct transfer of seawater (SW) acclimatized fish to fresh water (FWBP) and vice versa (SWBP). SW acclimation significantly increased plasma osmolality and intestine Na+/K+-ATPase (NKA) activity while FW acclimation increased plasma cortisol and branchial NKA activity. Plasma osmolality and chloride concentration decreased in FWBP whereas GH levels remained unchanged in both FWBP and SWBP. Comparative analysis of gene profiles between FWBP and SWBP showed that pituitary prolactin transcript increased significantly in FWBP. Prolactin receptor (PRLR) transcripts increased in gill of FWBP while it decreased in gill and kidney of SWBP. NKA transcripts increased in gill of both FWBP and SWBP, while it decreased in intestine of FWBP and increased in intestine and kidney of SWBP. Glucocorticoid receptor (GR) transcripts decreased in intestine and kidney of FWBP while it increased in gill and intestine of SWBP. No significant changes were observed in growth hormone receptor (GHR) transcripts of both FWBP and SWBP in pituitary, gill, intestine and kidney. Our current data demonstrated the correlation between PRLR gene expression in relation to FW adaptation, and GR gene expression in relation to SW adaptation in euryhaline black porgy. The results indicate that black porgy has an excellent osmoregulatory capacity and is capable of withstanding large variations in salinity.

Functional four-base A/T gap core sequence CATTAG of P53 response elements specifically bound tetrameric P53 differently than two-base A/T gap core sequence CATG bound both dimeric and tetrameric P53

The consensus sequence of p53 is repeated half sites of PuPuPuC(A/T)(A/T)GPyPyPy. GtAGCAttAGCCCAGACATGTCC is a 14-3-3sigma promoter p53 regulation site; the first core sequence is CAttAG, and the second is CATG. Both mutants GtAGgAttAGCCCAGACATGTCC and GtAGCAttAGCCCAGACATcTCC can be activated by p53 as a 1.5-fold half site. The original p53 regulated site on the 14-3-3sigma promoter is a whole site, and CATTAG is a functional core sequence. The p53-binding affinity and the activity of CATTAG were lower than for the mutant CATATG core sequence. Wild-type p53 acts as a tetramer to bind to the whole site; however, it also can bind to a half site by one of its dimers. Wild-type p53 can only bind to a half site with core sequence CATG but not to CATATG. The 1.5-fold half site or whole site with core sequence CATATG can be bound by wild-type p53. A p53 mutant, A344, forms dimeric p53; it can only bind to CATG, and not to CATATG. Therefore, tetrameric and dimeric p53 can bind to a two-base A/T gap core sequence, but only tetrameric p53 can bind to a four-base A/T gap core sequence.