Michler's hydrol blue elucidates structural differences in prion strains.

Yeast prions provide self-templating protein-based mechanisms of inheritance whose conformational changes lead to the acquisition of diverse new phenotypes. The best studied of these is the prion domain (NM) of Sup35, which forms an amyloid that can adopt several distinct conformations (strains) that confer distinct phenotypes when introduced into cells that do not carry the prion. Classic dyes, such as thioflavin T and Congo red, exhibit large increases in fluorescence when bound to amyloids, but these dyes are not sensitive to local structural differences that distinguish amyloid strains.

Near-infrared nerve-binding fluorophores for buried nerve tissue imaging.

Nerve-binding fluorophores with near-infrared (NIR; 650 to 900 nm) emission could reduce iatrogenic nerve injury rates by providing surgeons precise, real-time visualization of the peripheral nervous system. Unfortunately, current systemically administered nerve contrast agents predominantly emit at visible wavelengths and show nonspecific uptake in surrounding tissues such as adipose, muscle, and facia, thus limiting detection to surgically exposed surface-level nerves. Here, a focused NIR fluorophore library was synthesized and screened through multi-tiered optical and pharmacological assays to identify nerve-binding fluorophore candidates for clinical translation.

Rationale and design of a randomized controlled trial examining oral administration of bisphenol A on hepatic glucose production and skeletal muscle insulin sensitivity in adults.

Previous observational studies have shown that the endocrine disrupting chemical bisphenol A (BPA) is associated with type 2 diabetes, but few studies have examined direct effects of BPA on human health. The purpose of this study is to determine whether orally administered BPA at the US Environmental Protection Agency (EPA) safe dose of 50 μg/kg body weight has an adverse effect on hepatic glucose production and skeletal muscle insulin sensitivity. Forty, non-habitually active, healthy adults of normal weight will be enrolled.

Dysregulated FXR-FGF19 signaling and choline metabolism are associated with gut dysbiosis and hyperplasia in a novel pig model of pediatric NASH.

To investigate the role of bile acids (BAs) in the pathogenesis of diet-induced nonalcoholic steatohepatitis (NASH), we fed a "Western-style diet" [high fructose, high fat (HFF)] enriched with fructose, cholesterol, and saturated fat for 10 wk to juvenile Iberian pigs. We also supplemented probiotics with in vitro BA deconjugating activity to evaluate their potential therapeutic effect in NASH. Liver lipid and function, cytokines, and hormones were analyzed using commercially available kits.

Enumeration of industrial Bacillus assemblages in commercial products with customized plate-counting assays.

The aerobic plate count assay remains among the most widespread methods for enumerating industrial Bacillus assemblages, as growth-independent methods are either cost prohibitive or unavailable in some areas. However, the standard plating assays used to verify the CFU count of Bacillus-based products are not tailored to Bacillus species and thus may not produce the most accurate possible estimations. Standard plating assays assume that established limits of quantification are applicable to Bacillus species whose colonies swarm on solid media, and that colonies of each species in a mixed-species assemblage form independently of one another on agar plates.

A comparison of methods for enumerating bacteria in direct fed microbials for animal feed.

Aerobic plate counts are the standard enumeration method for probiotic-containing products. This counting method is limited by the ability of many cells to enter a viable but non-culturable (VBNC) state upon exposure to stressful conditions like dehydration and heating commonly used in probiotic product preparation. Alternative enumeration methods are available including flow cytometry (FC) which counts total live/dead cells by assessing cellular integrity and/or metabolic activity, and quantitative polymerase chain reaction (qPCR) in which enumeration is correlated with the quantity of a nucleic acid target.

Altering Fundamental Trends in the Emission of Xanthene Dyes.

Fluorescent small molecules enable researchers and clinicians to visualize biological events in living cells, tissues, and organs in real time. Herein, the focus is on the structure and properties of the relatively rare benzo[ a]xanthenes that exhibit enhanced steric and electronic interactions due to their annulated structures. Three types of fluorophores were synthesized: (i) pH- and solvent-dependent seminaphthorhodafluors, (ii) pH- and solvent-independent seminaphthorhodafluors, and (iii) pH-independent but solvent-sensitive seminaphthorhodamines.

Effect of the Specific Carbohydrate Diet on the Microbiome of a Primary Sclerosing Cholangitis and Ulcerative Colitis Patient.

A 20-year-old female was diagnosed with ulcerative colitis (UC) at age 14 and primary sclerosing cholangitis (PSC) at age 16. The PSC was successfully treated with high doses of oral vancomycin; however, the UC was more difficult to manage. After many drug treatments failed to treat the UC, the patient began following the specific carbohydrate diet (SCD).

Short communication: Typing and tracking Bacillaceae in raw milk and milk powder using pyroprinting.

Contamination of fluid and processed milk products with endospore-forming bacteria, such as Bacillaceae, affect milk quality and longevity. Contaminants come from a variety of sources, including the dairy farm environment, transportation equipment, or milk processing machinery. Tracking the origin of bacterial contamination to allow specifically targeted remediation efforts depends on a reliable strain-typing method that is reproducible, fast, easy to use, and amenable to computerized analysis.

Orientation of aromatic residues in amyloid cores: structural insights into prion fiber diversity.

Structural conversion of one given protein sequence into different amyloid states, resulting in distinct phenotypes, is one of the most intriguing phenomena of protein biology. Despite great efforts the structural origin of prion diversity remains elusive, mainly because amyloids are insoluble yet noncrystalline and therefore not easily amenable to traditional structural-biology methods. We investigate two different phenotypic prion strains, weak and strong, of yeast translation termination factor Sup35 with respect to angular orientation of tyrosines using polarized light spectroscopy.

Pyroprinting: a rapid and flexible genotypic fingerprinting method for typing bacterial strains.

Bacterial strain typing is commonly employed in studies involving epidemiology, population ecology, and microbial source tracking to identify sources of fecal contamination. Methods for differentiating strains generally use either a collection of phenotypic traits or rely on some interrogation of the bacterial genotype. This report introduces pyroprinting, a novel genotypic strain typing method that is rapid, inexpensive, and discriminating compared to the most sensitive methods already in use.

The O/OREOS mission: first science data from the space environment viability of organics (SEVO) payload.

We report the first science results from the Space Environment Viability of Organics (SEVO) payload aboard the Organism/Organic Exposure to Orbital Stresses (O/OREOS) free-flying nanosatellite, which completed its nominal spaceflight mission in May 2011 but continues to acquire data biweekly. The SEVO payload integrates a compact UV-visible-NIR spectrometer, utilizing the Sun as its light source, with a 24-cell sample carousel that houses four classes of vacuum-deposited organic thin films: polycyclic aromatic hydrocarbon (PAH), amino acid, metalloporphyrin, and quinone. The organic films are enclosed in hermetically sealed sample cells that contain one of four astrobiologically relevant microenvironments.

The O/OREOS mission: first science data from the Space Environment Survivability of Living Organisms (SESLO) payload.

We report the first telemetered spaceflight science results from the orbiting Space Environment Survivability of Living Organisms (SESLO) experiment, executed by one of the two 10 cm cube-format payloads aboard the 5.5 kg Organism/Organic Exposure to Orbital Stresses (O/OREOS) free-flying nanosatellite. The O/OREOS spacecraft was launched successfully to a 72° inclination, 650 km Earth orbit on 19 November 2010.

Spectroscopic characterization of Coomassie blue and its binding to amyloid fibrils.

Coomassie brilliant blue G-250 (CB) is the dye used frequently in the Bradford assay for protein concentration determination. In this study, we investigated how the solvent polarity and viscosity affect the CB absorption and fluorescence spectra and apply this understanding to investigate the binding of CB to lysozyme and insulin in the native and amyloid fibril states. Coomassie blue binds both to the native protein and to amyloid fibrils but gives distinctly different spectral responses.

A new highly adaptable design of shear-flow device for orientation of macromolecules for Linear Dichroism (LD) measurement.

This article presents a new design of flow-orientation device for the study of bio-macromolecules, including DNA and protein complexes, as well as aggregates such as amyloid fibrils and liposome membranes, using Linear Dichroism (LD) spectroscopy. The design provides a number of technical advantages that should make the device inexpensive to manufacture, easier to use and more reliable than existing techniques. The degree of orientation achieved is of the same order of magnitude as that of the commonly used concentric cylinders Couette flow cell, however, since the device exploits a set of flat strain-free quartz plates, a number of problems associated with refraction and birefringence of light are eliminated, increasing the sensitivity and accuracy of measurement.

Michler's hydrol blue: a sensitive probe for amyloid fibril detection.

Michler's hydrol blue (MHB) is investigated with respect to photophysical properties in varied solvent environment and when bound to insulin and lysozyme fibrils. The MHB chromophore is shown to act like a molecular rotor and bind well to amyloid fibrils, where it exhibits a characteristic red-shift in its excitation spectrum and an increase in the emission quantum yield upon binding. MHB is more sensitive to environmental changes than Thioflavin T (ThT) and furthermore, in contrast to the latter amyloid probe, can differentiate between insulin and lysozyme fibrils by a more red-shifted excitation spectrum for insulin fibrils.

Intestinal alkaline phosphatase preserves the normal homeostasis of gut microbiota.

Background And Aims: The intestinal microbiota plays a critical role in maintaining human health; however, the mechanisms governing the normal homeostatic number and composition of these microbes are largely unknown. Previously it was shown that intestinal alkaline phosphatase (IAP), a small intestinal brush border enzyme, functions as a gut mucosal defence factor limiting the translocation of gut bacteria to mesenteric lymph nodes. In this study the role of IAP in the preservation of the normal homeostasis of the gut microbiota was investigated.

Distinct microbiome in pouchitis compared to healthy pouches in ulcerative colitis and familial adenomatous polyposis.

Background: Pouchitis occurs in up to 50% of patients with ulcerative colitis (UC) undergoing ileal pouch anal anastomosis (IPAA). Pouchitis rarely occurs in patients with familial adenomatous polyposis (FAP) who undergo IPAA. Our aim was to compare mucosal and luminal flora in patients with UC-associated pouchitis (UCP), healthy UC pouches (HUC), and healthy FAP pouches (FAP).

A spectroscopic study of 2-[4'-(dimethylamino)phenyl]-benzothiazole binding to insulin amyloid fibrils.

The spectroscopic properties of 2-[4'-(dimethylamino)phenyl]-benzothiazole (BTA-2) in solution and in the presence of amyloid fibrils were investigated using absorption and fluorescence spectroscopy. Solution studies show that BTA-2 forms micelles in aqueous solutions, but that the dye can be solvated upon the addition of acetonitrile (CH(3)CN). BTA-2 binds to amyloid fibrils in solution leading to a characteristic blue-shift in the emission spectrum and an increase in fluorescence intensity.

Near-field scanning optical microscopy measurements of fluorescent molecular probes binding to insulin amyloid fibrils.

The binding of two amyloid fibril stain dyes, thioflavin T (ThT) and its neutral analog 2-[4'-(dimethylamino)phenyl]-benzothiazole (BTA-2), are measured using near-field scanning optical microscopy (NSOM), which is able to image individual amyloid fibrils. Polarized NSOM images reveal that both dyes bind to the fibrils with the long axis of the molecule aligned parallel to the long axis of the fibrils. This indicates that the dyes bind along the surface of the beta-sheet within the grooves of the fibril that run parallel to the fibril axis.

Probiotics to minimize the disruption of faecal microbiota in healthy subjects undergoing antibiotic therapy.

A novel combination of culturing and DNA-based terminal restriction fragment length polymorphism (TRFLP) analysis was used to investigate the effect of probiotics on antibiotic-induced gut microbiota alterations to determine if a probiotic preparation containing bifidobacteria and lactobacilli, taken during and after antibiotic therapy, can minimize antibiotic disturbance of faecal microbiota. Healthy subjects administered amoxicillin/clavulanate were randomized and concomitantly received a placebo or probiotic mixture. The primary end point was similarity of faecal microbiota as determined by culturing and TRFLP from subjects taking probiotics compared to those taking a placebo measured by comparing data from baseline to post-treatment for each subject.

Biological breakdown of RDX in slurry reactors proceeds with multiple kinetically distinguishable paths.

Biotransformation of RDX (hexahydro-1,3,5-trinitro-1,3,5-triazine) in slurry reactors was studied to determine the importance of supplementation of known biodegraders and the type of nutrient source required. Although addition of bacteria to the system increased the biotransformation rates, the increase may not justify the additional work and cost needed to grow the organisms in a laboratory and mix them into the soil. An inexpensive, rich nutrient source, corn steep liquor, was shown to provide sufficient nutrients to allow for the cometabolic biotransformation of RDX.

Analysis of treatment effects on the microbial ecology of the human intestine.

A large number of studies have investigated gastrointestinal microbiota and changes in the gastrointestinal community. However, a concern in these studies is how best to assess changes in gastrointestinal community structure. This paper presents two different human trials where the fecal terminal restriction fragment length polymorphism data sets were analyzed to search for treatment effects.

The use of ribotyping and antibiotic resistance patterns for identification of host sources of Escherichia coli strains.

Aims: To compare antibiotic resistance and ribotyping patterns ability to identify triplicate isolates sent from a group of 40 Escherichia coli taken from seven host sources.

Methods And Results: Of the 120 isolates, 22 isolates were resistant to ampicillin, streptomycin, tetracycline and trimethoprim and 98 isolates were susceptible. Antibiotic patterns identified 33 of the triplicates and three of the six groups had isolates from multiple hosts.