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Schiavone M.,University of Catanzaro | Schiavone M.,University of Naples Federico II | Schiavone M.,University of Padua | Fiume G.,University of Catanzaro | And 28 more authors.
International Journal of Molecular Sciences | Year: 2012

The Bridging Sheet domain of HIV-1 gp120 is highly conserved among the HIV-1 strains and allows HIV-1 binding to host cells via the HIV-1 coreceptors. Further, the bridging sheet domain is a major target to neutralize HIV-1 infection. We rationally designed four linear peptide epitopes that mimic the three-dimensional structure of bridging sheet by using molecular modeling. Chemically synthesized peptides BS3 and BS4 showed a fair degree of antigenicity when tested in ELISA with IgG purified from HIV+ broadly neutralizing sera while the production of synthetic peptides BS1 and BS2 failed due to their high degree of hydrophobicity. To overcome this limitation, we linked all four BS peptides to the COOH-terminus of GST protein to test both their antigenicity and immunogenicity. Only the BS1 peptide showed good antigenicity; however, no envelope specific antibodies were elicited upon mice immunization. Therefore we performed further analyses by linking BS1 peptide to the NH2-terminus of the E2 scaffold from the Geobacillus Stearothermophylus PDH complex. The E2-BS1 fusion peptide showed good antigenic results, however only one immunized rabbit elicited good antibody titers towards both the monomeric and oligomeric viral envelope glycoprotein (Env). In addition, moderate neutralizing antibodies response was elicited against two HIV-1 clade B and one clade C primary isolates. These preliminary data validate the peptide mimotope approach as a promising tool to obtain an effective HIV-1 vaccine. © 2012 by the authors; licensee MDPI, Basel, Switzerland. Source

Mesquita N.,University of Coimbra | Portugal A.,University of Coimbra | Pinar G.,Institute of Applied Microbiology | Loureiro J.,University of Coimbra | And 5 more authors.
International Biodeterioration and Biodegradation | Year: 2013

Flow cytometry is often used for viability and vitality assessment in bacteria and yeasts. However, its application to the study of fungal spore development is uncommon, probably due to the difficulties in successfully staining these cells.In the current study, we used flow cytometry for the first time to assess the effects of a disinfection treatment on the survival, growth and metabolic activity of fungal spores (Penicillium chrysogenum, Aspergillus nidulans and Aspergillus niger) submitted to gamma radiation (0-15kGy). The Forward and Side-Scatter parameters of the cytometer were used to assess the differences in size and complexity of particles. Furthermore, two fluorescent dyes were used: Propidium Iodide to assess the membrane integrity and spore viability, in a culture-independent procedure; and Dihydroethidium to measure the changes in metabolic activity of irradiated spores in their first 10h of growth in a liquid culture medium.Our results support that flow cytometry is a valuable tool in assessing different biological parameters and biocide effects, as it allowed accurate determination of the viability, growth and metabolic activity of gamma-irradiated spores. The fluorescence of Propidium Iodide was 5-7× more intense in unviable spores. The Dihydroethidium fluorescence increase was associated with faster growth. Control and low radiation doses allowed the germination and growth of spores, while higher doses led to growth inhibition and lower fluorescence. © 2012 Elsevier Ltd. Source

Krempl P.M.,ACIB | Krempl P.M.,University of Graz | Mairhofer J.,ACIB | Mairhofer J.,Institute of Applied Microbiology | And 4 more authors.
Bioinformatics | Year: 2012

We present a plug-in for Pathway Tools, an integrated systems biology software to create, maintain and query Pathway/Genome Databases. Fully integrated into the graphical user interface and menu, this plug-in extends the application's functionality by the ability to create multiple sequence alignments, systematically annotate insertion sequence (IS) elements and analyse their activity by cross-species comparison tools. Microarray probes can be automatically mapped to target genes, and expression data obtained with these arrays can be transformed into input formats needed to visualize them in the various omics viewers of Pathway Tools. The plug-in API itself allows developers to integrate their own functions into the Pathway Tools menu. © The Author 2012. Published by Oxford University Press. All rights reserved. Source

Pinar G.,Institute of Applied Microbiology | Garcia-Valles M.,University of Barcelona | Gimeno-Torrente D.,University of Barcelona | Fernandez-Turiel J.L.,CSIC - Institute of Earth Sciences Jaume Almera | And 2 more authors.
International Biodeterioration and Biodegradation | Year: 2013

We investigated the decayed historical church window glasses of two Catalonian churches, both under Mediterranean climate. Glass surfaces were studied by scanning electron microscopy (SEM), energy dispersive spectrometry (EDS), and X-ray diffraction (XRD). Their chemical composition was determined by wavelength-dispersive spectrometry (WDS) microprobe analysis. The biodiversity was investigated by molecular methods: DNA extraction from glass, amplification by PCR targeting the16S rRNA and ITS regions, and fingerprint analyses by denaturing gradient gel electrophoresis (DGGE). Clone libraries containing either PCR fragments of the bacterial 16S rDNA or the fungal ITS regions were screened by DGGE. Clone inserts were sequenced and compared with the EMBL database. Similarity values ranged from 89 to 100% to known bacteria and fungi. Biological activity in both sites was evidenced in the form of orange patinas, bio-pitting, and mineral precipitation. Analyses revealed complex bacterial communities consisting of members of the phyla Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria. Fungi showed less diversity than bacteria, and species of the genera Cladosporium and Phoma were dominant. The detected Actinobacteria and fungi may be responsible for the observed bio-pitting phenomenon. Moreover, some of the detected bacteria are known for their mineral precipitation capabilities. Sequence results also showed similarities with bacteria commonly found on deteriorated stone monuments, supporting the idea that medieval stained glass biodeterioration in the Mediterranean area shows a pattern comparable to that on stone. © 2012 Elsevier Ltd. Source

Ettenauer J.,Institute of Applied Microbiology | Pinar G.,Institute of Applied Microbiology | Sterflinger K.,Institute of Applied Microbiology | Gonzalez-Munoz M.T.,University of Granada | Jroundi F.,University of Granada
Science of the Total Environment | Year: 2011

Microbially Induced Carbonate Precipitation is proposed as an environmentally friendly method to protect decayed ornamental stone and introduced in the field of preservation of Cultural Heritage. Recent conservation studies performed under laboratory conditions on non-sterile calcarenite stones have successfully reported on the application of a suitable nutritional solution, inoculated and non-inoculated with Myxococcus xanthus, as a bioconsolidation treatment. Furthermore, this procedure has been applied in situ, very recently, to selected historical buildings in Granada, Spain. For the first time, we evaluate the efficiency and risks of the in situ application of the above mentioned treatments onto two historical buildings in Granada. The evaluation consists of a detailed investigation of the micro-biota actively growing during the seven days of the treatments - short-term monitoring and of that remaining on the stones after six and twelve months of the application - long-term monitoring. A molecular strategy, including DNA extraction, PCR amplification of 16S rRNA sequences, construction of clone libraries and fingerprinting by DGGE (Denaturing Gradient Gel Electrophoresis) analysis followed by sequencing was used to gain insight into the microbial diversity present on the differentially treated stones. The monitoring of M. xanthus was performed by PCR using species-specific primers. Similar dynamics were triggered on both buildings by the application of the nutritional solution (inoculated or non-inoculated). 16S rDNA sequencing revealed the dominant occurrence of members belonging to the Firmicutes and Proteobacteria during the seven days of the treatment, whereas after one year the order Bacillales of the phylum Firmicutes was the predominantly detected microorganisms. M. xanthus could be detected only during the seven days of the treatment. The treatments seem to activate no dangerous microorganisms and furthermore, to select the remainder of a homogeneous group of carbonatogenic bacteria on the stones after a long period of time. © 2011 Elsevier B.V. Source

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