Bioconversion of soy isoflavones daidzin and daidzein by <Emphasis Type="Italic">Bifidobacterium</Emphasis> strains

Twenty-two strains of Bifidobacterium, representative of eight major species of human origin, were screened for their ability to transform the isoflavones daidzin and daidzein. Most of the strains released the aglycone from daidzin and 12 gave yields higher than 90%. The kinetics of growth, daidzin consumption, and daidzein production indicated that the hydrolytic activity occurred during the growth. The supernatant of the majority of the strains did not release the aglycone from daidzin, suggesting that cell-associated β-glucosidases (β-Glu) are mainly responsible for the metabolism of soybean glyco-conjugates. Cell-associated β-Glu was mainly intracellular and significantly varied among the species and the strains. The lack of β-Glu was correlated with the inability to hydrolyze daidzin. Although S-equol production by anaerobic intestinal bacteria has been established, information on S-equol-producing bifidobacteria is contradictory. In this study, 22 bifidobacteria failed to transform daidzein into reduced metabolites under all the experimental conditions, excluding any role in the reductive pathway of daidzein toward the production of S-equol. These results suggest that selected probiotic strains of Bifidobacterium can be used to speed up the release of daidzein, improving its bioavailability for absorption by colonic mucosa and/or biotransformation to S-equol by other intestinal microorganisms.     

Statistical Assessment of Variability of Terminal Restriction Fragment Length Polymorphism Analysis Applied to Complex Microbial Communities

The variability of terminal restriction fragment polymorphism analysis applied to complex microbial communities was assessed statistically. Recent technological improvements were implemented in the successive steps of the procedure, resulting in a standardized procedure which provided a high level of reproducibility.Terminal restriction fragment length polymorphism (T-RFLP) analysis is a robust, high-resolution, high-throughput, rapid, and cost-effective method for studying the structures of microbial communities (3, 10). T-RFLP analysis is based on group-specific variations in the restriction patterns of molecular markers essential to all life forms (i.e., rRNA genes) or unique to a particular physiological group (e.g., ammonia-oxidizing and sulfate-reducing bacteria) which generate specific and characteristic terminal restriction fragment (T-RF) patterns from mixed fluorescently labeled amplicon pools of environmental nucleic acid extracts. This analysis has developed recently into one of the favorite techniques for the rapid assessment of the structures of bacterial communities. Refinements of the technique and data analysis have been introduced (5, 8, 11, 14, 20-22). Improvements have been made to the sampling procedure (16), to the DNA extraction and amplification steps (17, 19, 26), and to enzymatic restriction digestion (2, 6). Statistical analysis has also been improved in the treatment of the raw data and the selection of logical binning and clustering algorithms resulting, for instance, in the alignment of replicate profiles into a single consensus profile (1, 13). Finally, recent developments have been proposed for the statistical analysis of the profiles using multivariate techniques from numerical ecology (4, 7, 9, 23-25, 27).Both the resolution and reproducibility of T-RFLP analysis have already been assessed using artificially created bacterial communities (12) comprising up to 30 different clones or bacterial species. However, to the best knowledge of the authors, so far no study has been conducted to assess statistically the dissimilarities obtained in the electropherogram profiles when more complex bacterial communities from natural samples have been analyzed. The main purpose of this report is then to assess statistically the resolution and reproducibility of a standardized T-RFLP protocol, as applied to the analysis of 16S rRNA gene pools from complex communities. The statistical analysis was carried out at successive steps of the procedure, from the initial PCR amplification to the sizing of the obtained T-RFs.The samples used for this study were taken from a sequencing batch bubble column reactor inoculated with activated sludge from a municipal wastewater treatment plant and operated in such a way as to produce aerobic granular sludge able to remove carbon, nitrogen, and phosphate from an artificial wastewater sample containing acetate, ammonium, and phosphate. Samples were taken at different steps of operation of the reactor systems. The standardized protocol used in the present report is presented in detail in the supplemental material. Note that the methodology implied in the extraction of the total bacterial DNA is not discussed in the context of this work. The T-RFLP protocol was conceived on the basis of recent developments made in the protocol at various stages of the T-RFLP analysis and was implemented with optimized procedures allowing us to minimize potential biases and to ensure a high degree of reproducibility. Whenever possible, technological advances in instrumentation were included, as for instance with the application of optimized electrophoresis conditions and the use of more complex sizing standards and brighter fluorochromes. The use of relatively large and precise amounts of digested PCR fragments (200 ng per replica) also contributed to a drastic reduction of the background noise, which was usually observed to be equal to only about 10 relative fluorescence units (RFU).Numerical treatment and analysis of the data were carried out with R (R Development Core Team) and the Vegan library (18). We used asymmetric dissimilarity indices to compare T-RFLP profiles using the Jaccard formula, so that the double absence of a T-RF was not considered a resemblance between two profiles (15). The Jaccard dissimilarity was applied to binary data, i.e., the presence/absence of T-RFs. Moreover, to take into account the relative intensity of T-RF areas within each profile in the comparison, we used Ruzicka dissimilarity, which is the Jaccard index applied to quantitative data. Both dissimilarity measures range from 0 (identical profiles) to 1 (different profiles with no T-RF in common). Numerical treatment of the data was also carried out on the modified results, so as to reduce potential biases induced by the inconsistent presence of T-RFs showing very small amounts of fluorescence. T-RF signals just above the detection threshold (low signal-to-noise ratio) can be a cause of suboptimal fingerprinting reproducibility. For this reason, small-area T-RFs (<300 RFU) were suppressed when they were not present in all replicate profiles of a sample.     

Synthesis, characterization of strontium-bile acid salts and their bioactivity vs. the anti-osteoporosis drug strontium ranelate

The strontium salts Sr(cholate)₂, (Compound 1), Sr(dehydrocholate)₂, (Compound 2) and Sr₃(3-dehydrocholanoyliden-l-tartrate)₂, (Compound 3) have been prepared and characterized. The potential anti-osteoporotic activity of these compounds was tested on human primary osteoblasts (hOBs) and human primary osteoclasts (hOCs) in comparison with the bioactivity of strontium ranelate, previously registered as drug in the treatment of post-menopausal osteoporosis. Our results led to the hypothesis that the tested compounds, particularly Compound 2, may have requirements for modulating skeletal tissue regeneration or at least down regulating the loss of bone mass. In fact, all tested compounds have been shown to induce maturation in human primary osteoblasts (hOBs) and apoptosis of human primary osteoclasts (hOCs) at the same time.     

Species identity, diversity and microbial carbon flow in reassembling macrobenthic communities

Intense disturbance may locally destroy patches of habitat and shape the landscape into a mosaic of reassembling communities. The development of ecosystem properties during such community reassembly is poorly understood. In intertidal bare sediments, trophic relations between microphytobenthos or heterotrophic bacteria and macrofauna invertebrates may guarantee fundamental ecosystem properties such as carbon flow through the food web. We studied the dynamic relation between reassembling macrofauna communities and such microbial carbon flow during recovery after severe disturbance. We deliberately induced prolonged hypoxia in winter and early summer and allowed recolonisation for periods of two and five months. Carbon flow was quantified from basal resources (microphytobenthos and bacteria) to intermediate consumers using ¹³C as a tracer. Within the period of study (5 months), microbial carbon flow fully recovered, although macrofauna diversity was still very low compared to the natural communities (ranging from 6 to 17 species). More than 90% of microbial carbon flow to macrofauna was due to the consumers that recolonised within two months. Two of these species were dominant contributors to microphytobenthos carbon transfer to fauna. Furthermore, at an early stage of reassembly, this ecosystem property was remarkably similar when disturbance took place at different times of the year (winter or early summer), although there were differences in assemblage composition and functional diversity. We conclude that species assemblages and ecosystem function developed relatively independently in this benthic system. We discuss which ecological factors may have caused such non-parallel development of macrofaunal communities and carbon flow.     

Prediction of <Emphasis Type="Italic">Alternaria</Emphasis> and <Emphasis Type="Italic">Pleospora</Emphasis> concentrations from the meteorological forecast and artificial neural network in L’Aquila,Abruzzo (Central Italy)

In a previous work a 1-year time series of fungal spore concentrations was used to calibrate an artificial neural network for the estimation of Alternaria and Pleospora concentrations associated with observed meteorological variables in the atmosphere of L’Aquila, Italy. In this article the possibility to use the neural model calibrated with observed meteorological variables to predict the future fungal spore concentration from meteorological forecast is investigated. The results show that the proposed technique appears to be a suitable device to operationally predict the Alternaria and Pleospora concentrations a few days in advance. Emphasis is given to the actual use of these predictions for establishing a preventive strategy for allergy sufferers and for an appropriate use of fungicide treatments in agricultural activities, avoiding unsafe and useless pollution of the atmosphere, crops and fields.     

Skin blood flowmotion and microvascular reactivity investigation in hypercholesterolemic patients without clinically manifest arterial diseases

Fourier spectral analysis of forearm skin laser Doppler flowmetry (LDF) signal was performed in fifteen hypercholesterolemic patients (HP), without clinically manifest arterial diseases, and in fifteen age-matched healthy control subjects (CS), in order to investigate skin blood flowmotion (SBF). The LDF frequency intervals studied were: 0.01-1.6 Hz total spectrum, as well as 0.01-0.02 Hz (endothelial), 0.02-0.06 Hz (sympathetic), 0.06-0.2 Hz (myogenic), 0.2-0.6 Hz (respiratory) and 0.6-1.6 Hz (cardiac). Skin microvascular reactivity (MVR) to acetylcholine (ACh) and to sodium nitroprusside (SNP) iontophoresis was also investigated. HP showed a lower post-ACh increase in power spectral density (PSD) of the 0.01-0.02 Hz SBF subinterval compared to CS (1.80+/-1.73 PU(2)/Hz vs 3.59+/-1.78 PU(2)/Hz, respectively; p<0.005), while they did not differ in MVR from CS. In eleven HP the 0.01-0.02 Hz SBF subinterval showed a higher post-ACh PSD increase near to the statistical significance after 10 weeks of rosuvastatin therapy (10 mg/day) compared to pretreatment test (3.04+/-2.95 PU(2)/Hz vs 1.91+/-1.94 PU(2)/Hz; p=0.07). The blunted post-ACh increase in PSD of the 0.01-0.02 Hz SBF subinterval in HP suggests a skin endothelial dysfunction in these patients. This SBF abnormality showed a tendency to improve after rosuvastatin therapy in eleven treated patients.     

Construct optimization for protein NMR structure analysis using amide hydrogen/deuterium exchange mass spectrometry

Disordered or unstructured regions of proteins, while often very important biologically, can pose significant challenges for resonance assignment and three‐dimensional structure determination of the ordered regions of proteins by NMR methods. In this article, we demonstrate the application of ¹H/²H exchange mass spectrometry (DXMS) for the rapid identification of disordered segments of proteins and design of protein constructs that are more suitable for structural analysis by NMR. In this benchmark study, DXMS is applied to five NMR protein targets chosen from the Northeast Structural Genomics project. These data were then used to design optimized constructs for three partially disordered proteins. Truncated proteins obtained by deletion of disordered N‐ and C‐terminal tails were evaluated using ¹H‐¹⁵N HSQC and ¹H‐¹⁵N heteronuclear NOE NMR experiments to assess their structural integrity. These constructs provide significantly improved NMR spectra, with minimal structural perturbations to the ordered regions of the protein structure. As a representative example, we compare the solution structures of the full length and DXMS‐based truncated construct for a 77‐residue partially disordered DUF896 family protein YnzC from Bacillus subtilis, where deletion of the disordered residues (ca. 40% of the protein) does not affect the native structure. In addition, we demonstrate that throughput of the DXMS process can be increased by analyzing mixtures of up to four proteins without reducing the sequence coverage for each protein. Our results demonstrate that DXMS can serve as a central component of a process for optimizing protein constructs for NMR structure determination. Proteins 2009. © 2009 Wiley‐Liss, Inc.     

A recombinant MnSOD is radioprotective for normal cells and radiosensitizing for tumor cells

Organisms exposed to ionizing radiation are mainly damaged by free radicals, which are generated by the radiolysis of water contained in the cells. Recently a significant reduction of tissue injury from irradiation damage was demonstrated by using MnSOD-plasmid/liposome treatments in the protection of murine lung. In this study we show that a new active recombinant human MnSOD (rMnSOD), easily administered in vivo, not only exerts the same radioprotective effect on normal cells and organisms as any MnSOD, but it is also radiosensitizing for tumor cells. In addition, we show how healthy animals, exposed to lethal doses of ionizing radiation and daily injections with rMnSOD, were protected from radiodamage and were still alive 30 days after the irradiation, while animals treated with only PBS solution, in the absence of rMnSOD, died after 7-8 days from the radiotreatments. The molecular analysis of all irradiated tissues revealed that the antiapoptotic AVEN gene appeared activated only in the animals treated in the presence of rMnSOD. The data suggest that rMnSOD deserves to be considered as a pharmaceutical tool for making radiotherapy more selective on cancer cells and to prevent and/or cure the accidental damage derived from exposure to ionizing radiation.