Human gut microbiota analysis of cystic fibrosis infants using metaproteomics.

We report a metaproteomic analysis of the gut microbiota of eight infants with cystic fibrosis, during the first year of life. This is the first study in this disease that uses metaproteomics to analyze stool samples from patients at such a young age.

Enhanced covalent p-phenylenediamine crosslinked graphene oxide membranes: Towards superior contaminant removal from wastewaters and improved membrane reusability.

The increasing depletion of freshwater necessitates the re-use and purification of wastewaters. Among the existing separation membrane materials, graphene oxide (GO) is a promising candidate, owing to its tunable physicochemical properties. However, the widening of GO membranes pore gap in aqueous environments is a major limitation. Crosslinking agents can be incorporated to alleviate this problem. This study describes a comparative analysis of uncrosslinked and p-Phenylenediamine (PPD) crosslinked GO membranes' water purification performance. Dip-coating and dip-assisted layer-by-layer methods were used to fabricate the uncrosslinked and crosslinked membranes respectively. The covalent interaction between GO and PPD was confirmed by Fourier Transform Infra-Red and X-ray Photoelectron Spectroscopy. The excellent membrane topographical continuity and intactness was assessed by means of Scanning Electron Microscopy, while water contact angle measurements were undertaken to evaluate and confirm membrane hydrophilicity. The improvement impact of the crosslinker was manifested on the enhancement of the stability and performance of the membranes during nanofiltration tests of aqueous solutions of methylene blue in a homemade nanofiltration cell operated at 1 bar.

CROMqs: an infinitesimal successive refinement lossy compressor for the quality scores.

Massive amounts of sequencing data are being generated thanks to advances in sequencing technology and a dramatic drop in the sequencing cost. Much of the data are comprised of nucleotides and the corresponding quality scores that indicate their reliability. The latter are more difficult to compress and are themselves noisy. As a result, lossy compression of the quality scores has recently been proposed to alleviate the storage costs. Further, it has been shown that lossy compression, at some specific rates, can achieve a performance on variant calling similar to that achieved with the lossless compressed data. We propose CROMqs, a new lossy compressor for the quality scores with the property of "infinitesimal successive refinability". This property allows the decoder to decompress the data iteratively without the need of agreeing with the encoder on a specific rate prior to compression. This characteristic is particularly amenable in practice, as in most cases the appropriate rate at which the lossy compressor should operate can not be established prior to compression. Further, this property can be of interest in scenarios involving streaming of genomic data. CROMqs is the first infinitesimal successive refinement lossy compressor for the quality scores in the literature, and we show that it obtains a comparable rate-distortion performance to previously proposed algorithms. Moreover, we also show that CROMqs achieves a comparable performance on variant calling to that of the lossless compressed data.

Optical fiber refractometers based on indium tin oxide coatings fabricated by sputtering.

This Letter presents the fabrication of optical fiber refractometers based on indium tin oxide (ITO) coatings deposited by sputtering with response in the visible region. ITO thin films have been sputtered by means of a rotating mechanism that enables the fabrication of smooth and homogeneous coatings onto the optical fiber core. The ITO coating acts as a resonance supporting layer. This permits us to couple light from the waveguide to the ITO-coating/external medium region at specific wavelength ranges. The device is sensitive to external medium refractive index, which allows its utilization as a refractometer. The sensitivity is dependent on the coating thickness, ranging from 523.21 to 1221 nm/refractive index unit in the explored sensors. The sensor development process is time effective compared to other techniques such as dip coating or layer-by-layer self-assembly, which is interesting in terms of mass production.

Proteomic analysis by two-dimensional differential gel electrophoresis (2D DIGE) of a high-pressure effect in Bacillus cereus.

High hydrostatic pressure (HHP) is a new method used to reduce or eliminate microorganisms that are present in food. Proteins are known to be the most important target of high pressure in living organisms. The main goal of this investigation was focused on the changes that occur on the proteins of Bacillus cereus under HHP stress conditions. The two-dimensional differential gel electrophoresis (2D DIGE) technique allows for a simultaneous resolution of thousands of proteins based on fluorescent prelabeling of the samples with spectrally resolvable fluorescent CyDyes. The results of proteomics profiling show an average of 1300 spots being detected. The analysis revealed 75 spot proteins whose abundance is modified after the application of high pressure, of which 66 were decreased after the HHP treatment. Among them, flagellin was the protein that changed the most. The differential expression of some proteins after HHP treatment at 700 MPa may suggest a reduction of virulence and protective response against oxidative stress in flagellated Bacillus .

Identification of a hydratase and a class II aldolase involved in biodegradation of the organic solvent tetralin.

Two new genes whose products are involved in biodegradation of the organic solvent tetralin were identified. These genes, designated thnE and thnF, are located downstream of the previously identified thnD gene and code for a hydratase and an aldolase, respectively. A sequence comparison of enzymes similar to ThnE showed the significant similarity of hydratases involved in biodegradation pathways to 4-oxalocrotonate decarboxylases and established four separate groups of related enzymes. Consistent with the sequence information, characterization of the reaction catalyzed by ThnE showed that it hydrated a 10-carbon dicarboxylic acid. The only reaction product detected was the enol tautomer, 2,4-dihydroxydec-2-ene-1,10-dioic acid. The aldolase ThnF showed significant similarity to aldolases involved in different catabolic pathways whose substrates are dihydroxylated dicarboxylic acids and which yield pyruvate and a semialdehyde. The reaction products of the aldol cleavage reaction catalyzed by ThnF were identified as pyruvate and the seven-carbon acid pimelic semialdehyde. ThnF and similar aldolases showed conservation of the active site residues identified by the crystal structure of 2-dehydro-3-deoxy-galactarate aldolase, a class II aldolase with a novel reaction mechanism, suggesting that these similar enzymes are class II aldolases. In contrast, ThnF did not show similarity to 4-hydroxy-2-oxovalerate aldolases of other biodegradation pathways, which are significantly larger and apparently are class I aldolases.

Identification of a serine hydrolase which cleaves the alicyclic ring of tetralin.

A gene designated thnD, which is required for biodegradation of the organic solvent tetralin by Sphingomonas macrogoltabidus strain TFA, has been identified. Sequence comparison analysis indicated that thnD codes for a carbon-carbon bond serine hydrolase showing highest similarity to hydrolases involved in biodegradation of biphenyl. An insertion mutant defective in ThnD accumulates the ring fission product which results from the extradiol cleavage of the aromatic ring of dihydroxytetralin. The gene product has been purified and characterized. ThnD is an octameric thermostable enzyme with an optimum reaction temperature at 65 degrees C. ThnD efficiently hydrolyzes the ring fission intermediate of the tetralin pathway and also 2-hydroxy-6-oxo-6-phenylhexa-2,4-dienoic acid, the ring fission product of the biphenyl meta-cleavage pathway. However, it is not active towards the equivalent intermediates of meta-cleavage pathways of monoaromatic compounds which have small substituents in C-6. When ThnD hydrolyzes the intermediate in the tetralin pathway, it cleaves a C-C bond comprised within the alicyclic ring of tetralin instead of cleaving a linear C-C bond, as all other known hydrolases of meta-cleavage pathways do. The significance of this activity of ThnD for the requirement of other activities to mineralize tetralin is discussed.

Identification of an extradiol dioxygenase involved in tetralin biodegradation: gene sequence analysis and purification and characterization of the gene product.

A genomic region involved in tetralin biodegradation was recently identified in Sphingomonas strain TFA. We have cloned and sequenced from this region a gene designated thnC, which codes for an extradiol dioxygenase required for tetralin utilization. Comparison to similar sequences allowed us to define a subfamily of 1, 2-dihydroxynaphthalene extradiol dioxygenases, which comprises two clearly different groups, and to show that ThnC clusters within group 2 of this subfamily. 1,2-Dihydroxy-5,6,7, 8-tetrahydronaphthalene was found to be the metabolite accumulated by a thnC insertion mutant. The ring cleavage product of this metabolite exhibited behavior typical of a hydroxymuconic semialdehyde toward pH-dependent changes and derivatization with ammonium to give a quinoline derivative. The gene product has been purified, and its biochemical properties have been studied. The enzyme is a decamer which requires Fe(II) for activity and shows high activity toward its substrate (V(max), 40.5 U mg(-1); K(m), 18. 6 microM). The enzyme shows even higher activity with 1, 2-dihydroxynaphthalene and also significant activity toward 1, 2-dihydroxybiphenyl or methylated catechols. The broad substrate specificity of ThnC is consistent with that exhibited by other extradiol dioxygenases of the same group within the subfamily of 1, 2-dihydroxynaphthalene dioxygenases.

Genetic analysis of biodegradation of tetralin by a Sphingomonas strain.

A strain designated TFA which very efficiently utilizes tetralin has been isolated from the Rhine river. The strain has been identified as Sphingomonas macrogoltabidus, based on 16S rDNA sequence similarity. Genetic analysis of tetralin biodegradation has been performed by insertion mutagenesis and by physical analysis and analysis of complementation between the mutants. The genes involved in tetralin utilization are clustered in a region of 9 kb, comprising at least five genes grouped in two divergently transcribed operons.

Induced expression of the Candida albicans multidrug resistance gene CDR1 in response to fluconazole and other antifungals.

The Candida albicans CDR1 gene encodes a member of the ABC-type family of multidrug transporters which has been shown to be involved in azole resistance. Using an in-frame gene fusion between the CDR1 open reading frame and the green fluorescent protein allele yEGFP3, an optimized derivative for its use in C. albicans, we show here how the CDR1-yEGFP3 gene expression is induced in response to azoles as well as to other structurally unrelated drugs like cycloheximide. Moderate increases were observed for calcofluor, canavanine, 5'-fluorcytosine, cilofungin and caffeine, while no induction was found for the antifungals benomyl and amphotericin B or hydrogen peroxide at subinhibitory concentrations. The use of confocal microscopy enabled us to localize the Cdr1p fusion protein at the cell periphery, thus suggesting a cytoplasmic membrane localization. These results suggest deregulation of CDR1 gene as a putative mechanism for the generation of azole resistance in this clinically important pathogenic fungus.

Analysis of the leaching and toxicity of new amine activators for the curing of acrylic bone cements and composites.

The comparative reactivity of new tertiary amine activators with the basic chemical structure of N,N-dimethyl-4-toluidine, but reduced toxicity, is analysed. The leaching of the amine compounds from cured cements was studied by analysis of the concentration of the corresponding amine in a physiological saline solution after 3 months of immersion, giving lower values for the new amine compounds as compared to N,N-dimethyl-4-toluidine. The acute toxicity was determined by intravenous injection of saline solutions of the corresponding chlorhydrates in mice and the cytotoxicity by the evolution of specific culture media. The results obtained demonstrate a lower acute toxicity and cytotoxicity of the new activators, even with a noticeable antiseptic action, which makes these materials very interesting from a practical point of view as activators of the curing process of acrylic bone cements for orthopaedic surgery and dentistry.

[Molecular and genetic aspects of resistance to azoles in Candida albicans]. / Aspectos moleculares y genéticos de la resistencia a azoles en Candida albicans.

Fluconazole is one of the most useful drugs in the treatment of fungal systemic infections which frequently affect non immunocompetent individuals. However, the emergence of resistant strains in recent years may severely limit its usefulness in future. Although there are several described mechanisms involved in resistance to azoles, recent genetic studies demonstrate the role of specific genes in clinical resistance. Currently, the best characterized are the MDR1 and CDR1 genes, which code members of the MFS or ABC family of drug transporters, respectively. These proteins respond to the membrane potential (MFS) or hydrolyse ATP (ABC) thus promoting drug efflux and therefore reducing its intracellular accumulation. It has been shown that the mRNA from these genes is frequently increased in some Candida albicans resistant strains from patients receiving long term azole treatment. The development of molecular genetic tools in C. albicans is allowing characterization of their role in this and other important processes in the fungal cell.

Intra- and interobserver concordance in scoring Harris lines: a test on bone sections and radiographs.

Little attention has been devoted to assessing the reproducibility of (paleo) pathological observations. Harris lines (HL) are among the markers most used to determine chronology of stresses suffered during growth. Nevertheless, their scoring entails remarkable methodological difficulty. Bone sections (S) and radiographs (R) of 29 adult tibiae of archeological provenance (medieval) were scored for HL by five observers. At regular intervals of time, each observer gave two independent counts on both series. Results show a) a substantial interobserver disagreement of HL estimates for both sectional and radiographic records, and b) a high level of intraobserver error.