Adaptative biochemical pathways and regulatory networks in Klebsiella oxytoca BAS-10 producing a biotechnologically relevant exopolysaccharide during Fe(III)-citrate fermentation.

Abstract Background A bacterial strain previously isolated from pyrite mine drainage and named BAS-10 was tentatively identified as Klebsiella oxytoca. Unlikely other enterobacteria, BAS-10 is able to grow on Fe(III)-citrate as sole carbon and energy source, yielding acetic acid and CO2 coupled with Fe(III) reduction to Fe(II) and showing unusual physiological characteristics. In fact, under this growth condition, BAS-10 produces an exopolysaccharide (EPS) having a high rhamnose content and metal-binding properties, whose biotechnological applications were proven as very relevant. Results Further phylogenetic analysis, based on 16S rDNA sequence, definitively confirmed that BAS-10 belongs t…

Cyclodextrin‐Calixarene Nanosponges as Potential Platforms for pH‐Dependent Delivery of Tetracycline

Four mixed cyclodextrin-calixarene nanosponges were tested as possible Drug Delivery Systems, using Tetracycline antibiotic as a suitable model drug. The selected nanosponges featured a different composition ratio between the two host co-monomer components, and the possible presence of ionisable amine or carboxyl groups deriving from chemical post-modification. The pH-dependent absorption and release abilities of the materials were verified; in particular release kinetics showed the occurrence of a simple first-order profile. The antibacterial activity of nanosponge-tetracycline composites suitably prepared under sterile conditions was assayed towards both Gram-positive and Gram-negative ty…

Modification of halloysite lumen with dopamine derivatives as filler for antibiofilm coating

Hypothesis: Development of nanocomposite coating with antibiofilm properties is of fundamental importance to efficient fight biofilm formation preventing infections in biomedical area. In this context, halloysite nanotubes (HNTs), biocompatible and low-cost clay mineral, have been efficiently used as filler for different polymeric matrices affording several nanocomposites with appealing antimicrobial properties. The modification of HNTs surfaces represents a valuable strategy to improve the utilization of the clay for biological purposes. Experiments: Herein, the covalent modification of the HNTs lumen with properly designed dopamine derivatives with different perfluoroalkyl chain length is…

The NUMEN project @ LNS: Status and perspectives

The NUMEN project aims at accessing experimentally driven information on Nuclear Matrix Elements (NME) involved in the half-life of the neutrinoless double beta decay (0νββ), by high-accuracy measurements of Heavy Ion (HI) induced Double Charge Exchange (DCE) reaction cross sections. In particular, the (18O,18Ne) and (20Ne,20O) reactions are used as tools for β+β+ and β−β− decays, respectively. In the experiments, performed at INFN - Laboratory Nazionali del Sud (LNS) in Catania, the beams are accelerated by the Superconducting Cyclotron (CS) and the reaction ejectiles are detected the MAGNEX magnetic spectrometer. The measured cross sections are challengingly low (a few nb), being the tota…

Development and characterization of antimicrobial PCL fibres for surgical suture applications

Additional file 4: of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Supplementary Results section. (PDF 123 kb)

Architettura e second digital turn, l’evoluzione degli strumenti informatici e il progetto

La condizione digitale che ha gradualmente ibridato le nostre esistenze, trasformando atomi in bit, si è oggi cementificata sulla nostra società, arricchendone la postmodernità e determinando una nuova liquidità acuitasi con l’avvento di internet. Un momento storico segnato da una nuova maturità del digitale, evidente nel nostro diverso rapporto con i dati, e nella diffusione di metodi di machine learning avanzato, che promettono una nuova capacità di comprensione della complessità contemporanea e nel frattempo contribuiscono alla propagazione dell’apparato tecnico sul mondo. Questi cambiamenti, tanto profondi da toccare la nostra cultura, stanno modificando il nostro modo di interpretare e…

Recent results on heavy-ion induced reactions of interest for neutrinoless double beta decay at INFN-LNS

Abstract The NUMEN project aims at accessing experimentally driven information on Nuclear Matrix Elements (NME) involved in the half-life of the neutrinoless double beta decay (0νββ). In this view measurements of Heavy Ion (HI) induced Double Charge Exchange (DCE) reaction cross sections are performed with high-accuracy. In particular, the (18O,18Ne) and (20Ne,20O) reactions are used as tools for β+β+ and β-β- decays, respectively. In the experiments, performed at INFN - Laboratory Nazionali del Sud (LNS) in Catania, the beams are accelerated by the Superconducting Cyclotron (CS) and the reaction ejectiles are detected the MAGNEX magnetic spectrometer. The measured cross sections are challe…

Bacterial Community Structure of an IFAS-MBRs Wastewater Treatment Plant

TIn this work, the bacterial community putatively involved in BNR events of a UCT-MBMBR pilot plant was elucidated by both culture-dependent and metagenomics DNA analyses. The presence of bacterial isolates belonging to Bacillus (in the anoxic compartment) and to Acinetobacter, Stenotrophomonas, Rhodococcus, Escherichia and Aeromonas (in the aerobic compartment) is in agreement with the nitrification/denitrification processes observed in the plant. Moreover, the study of bacterial community structure by NGS revealed a microbial diversity suggesting a biochemical complexity which can be further explored and exploited to improve UCT-MBMBR plant performance.

LAPTOP: Lantibiotic production, Technology, optimization and improved process

Influence of volatile solids and pH for the production of volatile fatty acids: batch fermentation tests using sewage sludge

The aim of this work was to study the effect of volatile suspended solid (VSS) and pH on volatile fatty acids (VFA) production from waste activated sludge (WAS) fermentation by means of batch tests. The final goal was to gain insights to enhance VFA stream quality, with the novelty of using WAS with high sludge retention time. Results revealed that the optimum conditions to maximize VFAs and minimize nutrients and non-VFA sCOD are a VSS concentration of 5.9 g/L and initial pH adjustment to pH 10. The WAS bacterial community structures were analysed according to Next Generation Sequencing (NGS) of 16S rDNA amplicons. The results revealed changes of bacterial phyla abundance in comparison wit…

Additional file 4: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Figure S1. K. oxytoca DSM 29614 grown in NaC (left) and in FeC medium (right) after 7 day of incubation at 30 °C. Figure S2. a,b) Production of ortorhomboidal struvite in the presence of Hg2+ (a) and Ag+ (b); both crystals precipitated in aerobic cultures of K. oxytoca DSM 29614. c,d) Micrographs of microcrystal of struvite by K. oxytoca DSM 29614 cells, grown in aerobic conditions in the presence of Pd2+ in transmission mode (c) and in fluorescence mode (d) with cells stained with DAPI. e) Micrographs of TEM of microcrystals of struvite coated by Pd2+. (PDF 527 kb)

The effects of structural changes on the anti-microbial and anti-proliferative activities of diimidazolium salts

An array of diimidazolium salts has been synthesized and used to investigate their anti-microbial and anti-proliferative activities. In particular, salts based on the 3,30-di-n-alkyl-1,10-(1,n-phenylenedimethylene)- diimidazolium cation and differing in the alkyl chain length on the imidazolium ion, the isomeric substitution on the aromatic spacer and in the anion nature were used. The anti-proliferative activity was evaluated against cervical (HeLa), colon adenocarcinoma (HT-29) and breast (SKBR3) cancer cell lines. In the latter case, also a morphological assessment after treatment with salts was performed. All salts were tested for their hemolytic activity against human erythrocytes. On …

Omic-based strategies reveal novel links between primary metabolism and antibiotic production

Preparazione e caratterizzazione di fibre a base di PCL con proprietà antimicrobiche per applicazioni chirurgiche

Proteomics for milk proteins characterization in Girgentana goat breed

Proteomics has been widely used to characterize milk protein content in livestock species and unravel protein biological functions. The aim of this work was to characterize the Girgentana goat breed whole milk and milk fraction proteins by two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry. Bulk milk samples from two farms locate in Palermo and Agrigento (Sicily) areas were collected during the early stage of lactation. Initially, 2D-PAGE and protein detection protocols were set-up. In particular, 2D-PAGE analyses were carried out on whole milk using 18-cm IPG strips ranging from pH 3-10 and 4-7 and 12.5% polyacrylamide gel for first and the second dimension …

A new p65 isoform that bind the glucocorticoid hormone and is expressed in inflammation liver diseases and COVID-19

AbstractInflammation is a physiological process whose deregulation causes some diseases including cancer. Nuclear Factor kB (NF-kB) is a family of ubiquitous and inducible transcription factors, in which the p65/p50 heterodimer is the most abundant complex, that play critical roles mainly in inflammation. Glucocorticoid Receptor (GR) is a ligand-activated transcription factor and acts as an anti-inflammatory agent and immunosuppressant. Thus, NF-kB and GR are physiological antagonists in the inflammation process. Here we show that in mice and humans there is a spliced variant of p65, named p65 iso5, which binds the corticosteroid hormone dexamethasone amplifying the effect of the glucocorti…

Proteomics highlights metabolic changes associated with n-hexadecane utilization in a Streptomyces coelicolor engineered strain.

biotecnologiche di batteri del suolo

Differential proteomic analysis highlights metabolic strategies associated with balhimycin production in Amycolatopsis balhimycina chemostat cultivations

Abstract Background Proteomics was recently used to reveal enzymes whose expression is associated with the production of the glycopeptide antibiotic balhimycin in Amycolatopsis balhimycina batch cultivations. Combining chemostat fermentation technology, where cells proliferate with constant parameters in a highly reproducible steady-state, and differential proteomics, the relationships between physiological status and metabolic pathways during antibiotic producing and non-producing conditions could be highlighted. Results Two minimal defined media, one with low Pi (0.6 mM; LP) and proficient glucose (12 g/l) concentrations and the other one with high Pi (1.8 mM) and limiting (6 g/l; LG) glu…

Supramolecular Hydro- and Ionogels: A Study of Their Properties and Antibacterial Activity.

Diimidazolium-based organic salts, bearing peptides or amino acids as anions have been synthesised and tested for their gelling ability in biocompatible solvents. These low molecular weight salts were successfully used as gelators in phosphate buffered saline (PBS) solution and ionic liquids. Then, the properties of the obtained soft materials were analysed in terms of melting temperature and gel strength as accounted for by rheological investigations. The gel-phase formation was studied by using UV/Vis and resonance light scattering measurements, whereas the morphology of the soft materials was analysed by using polarised optical microscopy and scanning electron microscopy. To get informat…

Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024.

Background The filamentous actinomycete Microbispora ATCC-PTA-5024 produces the lantibiotic NAI-107, which is an antibiotic peptide effective against multidrug-resistant Gram-positive bacteria. In actinomycetes, antibiotic production is often associated with a physiological differentiation program controlled by a complex regulatory and metabolic network that may be elucidated by the integration of genomic, proteomic and bioinformatic tools. Accordingly, an extensive evaluation of the proteomic changes associated with NAI-107 production was performed on Microbispora ATCC-PTA-5024 by combining two-dimensional difference in gel electrophoresis, mass spectrometry and gene ontology approaches. R…

Inorganic phosphate is a trigger factor for Microbispora sp. ATCC-PTA-5024 growth and NAI-107 production

Synthesis, characterization and antimicrobial activity of polyaminocyclodextrin-capped Ag Nanoparticles

Biocompatible Ag nanocomposites were prepared by photoreduction of ammoniacal silver acetate in the presence of a polyaminocyclodextrin, namely the poly-{6-[3-(2-(3-aminopropylamino)-ethylamino)-propylamino]}-(6-deoxy)-b-CD (amCD, figure 1). The obtained Ag-amCD systems, which possess an oniontype structure [1] with a metal core surrounded by several layers of the capping agent, were characterized by means of various complementary techniques. In particular, FT-IR spectroscopy confirmed the presence of the amCD scaffold in the composite, and evidenced a partial oxidative degradation of the polyamine branches,due to the fact that these groups function as sacrificial reducing agents in the pho…

Expression in Streptomyces lividans of Nonomuraea genes cloned in an artificial chromosome

A bacterial artificial chromosomal library of Nonomuraea sp. ATCC39727 was constructed using Escherichia coli-Streptomyces artificial chromosome (ESAC) and screened for the presence of dbv genes known to be involved in the biosynthesis of the glycopeptide A40926. dbv genes were cloned as two large, partially overlapping, fragments and transferred into the host Streptomyces lividans, thus generating strains S. lividansColon, two colonsNmESAC50 and S. lividansColon, two colonsNmESAC57. The heterologous expression of Nonomuraea genes in S. lividans was successfully demonstrated by using combined RT-PCR and proteomic approaches. MALDI-TOF analysis revealed that a Nonomuraea ABC transporter is e…

Novel Sortase A Inhibitors to Counteract Gram-Positive Bacterial Biofilms

Sortase A (SrtA) is a membrane enzyme responsible for the covalent anchoring of surface proteins on the cell wall of Gram-positive bacteria. Nowadays it is considered an interesting target for the development of new anti-infective drugs which aim to interfere with important Gram-positive virulence mechanisms. Along the years, we studied the anti-staphylococcal and anti-biofilm activity of some natural and synthetic polyhalogenated pyrrolic compounds, called pyrrolomycins. Some of them were active on Gram-positive pathogens at a μg/mL range of concentration (1.5-0.045 μg/mL) and showed a biofilm inhibition in the range of 50-80%. [1-3] In light of these encouraging results, herein we present…

Chemo-enzymatic Conversion of Glucose in 5-Hydroxymethylfurfural: The Joint Effect of Ionic Liquids and Ultrasound

For the valorization of lignocellulosic biomass, a key step is unlocking the conversion of glucose to suitable chemical platforms. To this aim, we herein describe the sequential chemo-enzymatic conversion of glucose into 5-hydroxymethylfurfural (5-HMF), in two steps: glucose isomerization to fructose, catalyzed by glucose isomerase (GI) and fructose dehydration to 5-HMF promoted by Amberlyst 15. The novelty of our approach lies in the use of crude cell extracts of Streptomyces coelicolor showing GI activity, as isomerization catalysts, along with a commercial immobilized GI. Under optimized reaction conditions, we obtained a conversion to 5-HMF (C5‑HMF) from glucose of 50% in the H2O/[bmim]…

Applicazioni biotecnologiche di batteri del suolo

Feasibility in routine clinical setting of combined resting-state fMRI and DTI-tractography for surgical planning of brain tumors

Purpose Methods and materials Results Conclusion Personal information and conflict of interest References

Proteomic study of the antibiotic producing Amycolatopsis balhimycina

PLA graphene nanoplatelets nanocomposites: Physical properties and release kinetics of an antimicrobial agent

Abstract Graphene nanoplatelets (GnP) as filler and ciprofloxacin (CFX) as biocide were incorporated via melt-compounding into poly(lactic acid) (PLA) to obtain biopolymer-based nanocomposites with antimicrobial properties. GnP were added with the aim of improving the mechanical properties of the antimicrobial system and tuning the drug release. The obtained systems were mechanically characterized in tensile mode by quasi-static and dynamic mechanical tests. Furthermore, rheological measurements were performed. The morphology of the samples was analyzed through scanning electron microscopy (SEM). Moreover, a mathematical model, i.e. power law model, was used to fit the release data in order…

Differential Proteomics Based on 2D-Difference In-Gel Electrophoresis and Tandem Mass Spectrometry for the Elucidation of Biological Processes in Antibiotic-Producer Bacterial Strains

Proteomics based on 2D-Difference In Gel Electrophoresis (2D-DIGE) coupled with mass spectrometry (MS) procedures can be considered a “gold standard” to determine quantitatively and comparatively protein abundances in cell extracts from different biological sources/conditions according to a gel-based approach. In particular, 2D-DIGE is used for protein specie separation, detection, and relative quantification, whenever tandem MS is used to obtain peptide sequence information that is managed according to bioinformatic procedures to identify the differentially represented protein species. The proteomic results consist of a dynamic portray of over- and down-represented protein species that…

Spoilage of oat bran by sporogenic microorganisms revived from soil buried 4000 years ago in Iranian archaeological site

Abstract The Bronze Age archaeological site of Shahr-i Sokhta (30° 39′ N; 61° 24’ E), located today in southeastern Iran, Sistan region, is a special archaeological deposit in which the exceptional preservation of human, plant and animal remains, due to the dry climate of the region, can provide detailed information on one of the first complex proto-urban societies. In recent years, there has been growing interest in changes in local climate and environment as major reasons why the settlement was abandoned about 4000 years ago. Food shortage has been regarded as a direct effect of these changes. No attention has been paid to the potential health hazards associated with ancient urban/domesti…

Regulation of antibiotic biosynthesis in Actinomycetes.

NovelAmycolatopsis balhimycinabiochemical abilities unveiled by proteomics

Amycolatopsis balhimycina DSM5908 is an actinomycete producer of balhimycin, an analogue of vancomycin, the antibiotic of ‘last resort’ against multidrug-resistant Gram-positive pathogens. Most knowledge on glycopeptide biosynthetic pathways comes from studies on A. balhimycina as this strain, among glycopeptide producers, is genetically more amenable. The recent availability of its genome sequence allowed to perform differential proteomic analyses elucidating key metabolic pathways leading to antibiotic production in different growth conditions. To implement proteomic data on A. balhimycina derived from 2-DE approaches and to identify novel components, a combined approach based on protein …

Diimidazolium organic salts and supramolecular gels exerting antimicrobial activity

Streptomyces coelicolor Vesicles: Many Molecules To Be Delivered

ABSTRACT Streptomyces coelicolor is a model organism for the study of Streptomyces, a genus of Gram-positive bacteria that undergoes a complex life cycle and produces a broad repertoire of bioactive metabolites and extracellular enzymes. This study investigated the production and characterization of membrane vesicles (MVs) in liquid cultures of S. coelicolor M145 from a structural and biochemical point of view; this was achieved by combining microscopic, physical and -omics analyses. Two main populations of MVs, with different sizes and cargos, were isolated and purified. S. coelicolor MV cargo was determined to be complex, containing different kinds of proteins and metabolites. In particul…

Anticancer activity of biogenerated silver nanoparticles: an integrated proteomic investigation

Silver nanoparticles (AgNPs), embedded into a specific polysaccharide (EPS), were biogenerated by Klebsiella oxytoca DSM 29614 under aerobic (AgNPs-EPSaer) and anaerobic conditions (AgNPs-EPSanaer). Both AgNPs-EPS matrices were tested by MTT assay for cytotoxic activity against human breast (SKBR3 and 8701-BC) and colon (HT-29, HCT 116 and Caco-2) cancer cell lines, revealing AgNPs-EPSaer as the most active, in terms of IC50, with a more pronounced efficacy against breast cancer cell lines. Therefore, colony forming capability, morphological changes, generation of reactive oxygen species (ROS), induction of apoptosis and autophagy, inhibition of migratory and invasive capabilities and prote…

Assessment and characterization of the bacterial community structure in advanced activated sludge systems

Abstract The present study is aimed to assess and characterize the structure of bacterial community in advanced activated sludge systems. In particular, activated sludge samples were collected from an Integrated Fixed-film Activated Sludge – Membrane Bioreactor pilot plant under a University of Cape Town configuration with in-series anaerobic (Noair)/anoxic (Anox)/aerobic (Oxy) reactors – and further analyzed. The achieved results – based on Next Generation Sequencing (NGS) of 16S rDNA amplicons – revealed that the bacterial biofilm (bf) communities on plastic carriers of Oxy and Anox reactors had a greater diversity compared to suspended (sp) bacterial flocs of Oxy, Anox and Noair. Indeed,…

Dbv4 is a DNA-binding protein regulating the expression of OxyA during A40926 biosynthesis

New Results from the NUMEN Project

International audience; NUMEN aims at accessing experimentally driven information on Nuclear Matrix Elements (NME) involved in the half-life of the neutrinoless double beta decay (0νββ), by high-accuracy measurements of the cross sections of Heavy Ion (HI) induced Double Charge Exchange (DCE) reactions. First evidence about the possibility to get quantitative information about NME from experiments is found for the (^18O,^18Ne) and (^20Ne,^20O) reactions. Moreover, to infer the neutrino average masses from the possible measurement of the half-life of 0νββ decay, the knowledge of the NME is a crucial aspect. The key tools for this project are the high resolution Superconducting Cyclotron beam…

Influence of Drawing on the Antimicrobial and Physical Properties of Chlorhexidine-Compounded Poly(caprolactone) Monofilaments

In this work, we prepared poly(caprolactone) (PCL) monofilaments incorporating different amounts of the antiseptic chlorhexidine diacetate (CHX) and evaluated the effect of “online” drawing during the melt spinning or of an “offline” cold drawing on the antimicrobial and physical properties of PCL/CHX monofilaments. The results showed that the drawing conditions strongly affected the properties of the threads. In particular, the filaments exhibited antimicrobial activity for all the draw ratios (DR) adopted, but on increasing DR the antibacterial efficiency reduced. These results were correlated with the CHX surface concentration and with the release kinetics.

Enhancing a Transition to a Circular Economy in the Water Sector: The EU Project WIDER UPTAKE

A novel approach for resource recovery includes forward osmosis (FO) as a concentration step in municipal wastewater treatment. The current study investigates different pre-treatment strategies including biological treatment with a moving-bed bioreactor (MBBR) at different loading rates and particle removal by filtration and sedimentation. Membrane performance and recovery potential for energy and nutrients were investigated in laboratory-scale FO experiments in batch mode using pre-treated municipal wastewater as feed and 35 g/L NaCl as a draw solution. Initial water fluxes were in the range of 6.3 to 8.0 L/(m2·h). The baseline fluxes were modelled to account for flux decline due to concen…

Reactivation of aerobic granular sludge for the treatment of industrial shipboard slop wastewater: Effects of long-term storage on granules structure, biofilm activity and microbial community

Abstract This work reports on reactivation of aerobic granular sludge (AGS) for the treatment of industrial recalcitrant wastewater (slop wastewater) characterized by high salinity and hydrocarbons. AGS were reactivated in two reactors, R1 and R2, to treat industrial slop wastewater after a long-term storage for 12-months at 4 °C. In R1, salt-adapted mature aerobic granules were previously subjected to a step-wise increase of hydrocarbons, whereas in R2 aerobic granules were previously cultivated in presence of salinity and hydrocarbons. After a short-term reactivation period, the slop dosage caused a simultaneous decrease of granules dimensions and proteins/polysaccharides (PN/PS) ratio do…

Additional file 5: of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Figure S1-S6 with corresponding figure legends. (PDF 511 kb)

Tryptophan promotes morphological and physiological differentiation in Streptomyces coelicolor.

The molecular mechanisms regulating tryptophan biosynthesis in actinomycetes are poorly understood; similarly, the possible roles of tryptophan in the differentiation program of microorganism life-cycle are still underexplored. To unveil the possible regulatory effect of this amino acid on gene expression, an integrated study based on quantitative teverse transcription-PCR (qRT-PCR) and proteomic approaches was performed on the actinomycete model Streptomyces coelicolor. Comparative analyses on the microorganism growth in a minimal medium with or without tryptophan supplementation showed that biosynthetic trp gene expression in S. coelicolor is not subjected to a negative regulation by the …

Artificial Chromosomes to Explore and to Exploit Biosynthetic Capabilities of Actinomycetes

Actinomycetes are an important source of biologically active compounds, like antibiotics, antitumor agents, and immunosuppressors. Genome sequencing is revealing that this class of microorganisms has larger genomes relative to other bacteria and uses a considerable fraction of its coding capacity (5–10%) for the production of mostly cryptic secondary metabolites. To access actinomycetes biosynthetic capabilities or to improve the pharmacokinetic properties and production yields of these chemically complex compounds, genetic manipulation of the producer strains can be performed. Heterologous expression in amenable hosts can be useful to exploit and to explore the genetic potential of actinom…

Digital and quarantine

The epidemic we are facing denies our contemporary liquid world, freezing and expanding its physical distances again. The global city, distributed beyond its geographical borders, interconnected and shared, is now being questioned, as the role of our houses, previous part of a city-ecosystem, now isolated refuges. It is not the first time we face an epidemic, but it is the first time a pandemic hits a global digital world. Digital has offered us a novel way to face the epidemic, transforming IT possibilities in an obligation. This aspect showed us the limits of the digital paradigm, and we are all hit regardless our level of computer literacy: not just some parents who must now deal with e-…

Additional file 5: of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Figure S1-S6 with corresponding figure legends. (PDF 511 kb)

Influence of Drawing on the Antimicrobial and Physical Properties of Chlorhexidine-Compounded Poly(caprolactone) Monofilaments

In this work, we prepared poly(caprolactone) (PCL) monofilaments incorporating different amounts of the antiseptic chlorhexidine diacetate (CHX) and evaluated the effect of "online" drawing during the melt spinning or of an "offline" cold drawing on the antimicrobial and physical properties of PCL/CHX monofilaments. The results showed that the drawing conditions strongly affected the properties of the threads. In particular, the filaments exhibited antimicrobial activity for all the draw ratios (DR) adopted, but on increasing DR the antibacterial efficiency reduced. These results were correlated with the CHX surface concentration and with the release kinetics.

Thymus vulgaris Essential Oil and Hydro-Alcoholic Solutions to Counteract Wooden Artwork Microbial Colonization

Aromatic plants represent a source of natural products with medicinal properties, and are also utilized in the food and pharmaceutical industries. Recently, the need for eco-compatible and non-toxic products, safe for both the environment and human health, have been proposed for the sustainable conservation of historic–artistic artifacts. In this study, in order to counteract microbial colonization (Aspergillus sp., Streptomyces sp., Micrococcus sp.) on wooden artwork surfaces, Thymus vulgaris L. (Lamiaceae) essential oil (EO) and hydro-alcoholic (HA) solutions were applied in a polyphasic approach. The antimicrobial activities of EO and HA solutions were preliminarily assessed by agar disc…

Polysaccharide-based silver nanoparticles synthesized by Klebsiella oxytoca DSM 29614 cause DNA fragmentation in E-coli cells

Silver nanoparticles (AgNPs), embedded into a specific exopolysaccharide (EPS), were produced by Klebsiella oxytoca DSM 29614 by adding AgNO3 to the cultures during exponential growth phase. In particular, under aerobic or anaerobic conditions, two types of silver nanoparticles, named AgNPs-EPS(aer) and the AgNPs-EPS(anaer), were produced respectively. The effects on bacterial cells was demonstrated by using Escherichia coli K12 and Kocuria rhizophila ATCC 9341 (ex Micrococcus luteus) as Gram-negative and Gram-positive tester strains, respectively. The best antimicrobial activity was observed for AgNPs-EPS(aer), in terms of minimum inhibitory concentrations and minimum bactericidal concentr…

Draft Genome Sequence of the Microbispora sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107.

ABSTRACT We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that produces NAI-107, a new lantibiotic with the potential to treat life-threatening infections caused by multidrug-resistant Gram-positive pathogens. The draft genome of strain Microbispora sp. ATCC-PTA-5024 consists of 8,543,819 bp, with a 71.2% G+C content and 7,860 protein-coding genes.

Differential proteomic analysis reveals novel links between primary metabolism and antibiotic production in Amycolatopsis balhimycina.

A differential proteomic analysis, based on 2-DE and MS procedures, was performed on Amycolatopsis balhimycina DSM5908, the actinomycete producing the vancomycin-like antibiotic balhimycin. A comparison of proteomic profiles before and during balhimycin production characterized differentially and constitutively expressed protein isoforms, which were associated to 203 ORFs in the A. balhimycina genome. These data, providing insights on the major metabolic pathways/molecular processes operating in this organism, were used to compile 2-DE reference maps covering 3-10, 4-7 and 4.5-5.5 pH gradients available over the World Wide Web as interactive web pages (http://www.unipa.it/ampuglia/Abal-prot…

Enzymatic Synthesis and Antimicrobial Activity of Oligomer Analogues of Medicinal Biopolymers from Comfrey and Other Species of the Boraginaceae Family

This study reports the first enzymatic synthesis leading to several oligomer analogues of poly[3-(3,4-dihydroxyphenyl)glyceric acid]. This biopolymer, extracted from plants of the Boraginaceae family has shown a wide spectrum of pharmacological properties, including antimicrobial activity. Enzymatic ring opening polymerization of 2-methoxycarbonyl-3-(3,4-dibenzyloxyphenyl)oxirane (MDBPO) using lipase from Candida rugosa leads to formation of poly[2-methoxycarbonyl-3-(3,4-dibenzyloxyphenyl)oxirane] (PMDBPO), with a degree of polymerization up to 5. Catalytic debenzylation of PMDBPO using H2 on Pd/C yields poly[2-methoxycarbonyl-3-(3,4-dihydroxyphenyl)oxirane] (PMDHPO) without loss in molecul…

Differential proteomic analysis of an engineered Streptomyces coelicolor strain reveals metabolic pathways supporting growth on n-hexadecane

The alkB gene, encoding an alkane monooxygenase in the actinomycete Gordonia sp. SoCg, was expressed in the non-alkane-degrading actinomycete Streptomyces coelicolor M145. The resulting engineered strain, M145-AH, can grow on n-hexadecane as sole carbon source. To unravel proteins associated with growth on n-alkanes, proteome of M145-AH after 6, 24, and 48 h of incubation in the Bushnell-Haas (BH) mineral medium containing n-hexadecane as sole carbon source (H condition) and in BH without any carbon source (0 condition) were compared using 2D-differential gel electrophoresis. Proteome analysis revealed significant changes only at 48 h, showing 48 differentially abundant proteins identified …

Luigi Moretti, from history to parametric architecture

In this article we aim to give new light on the thinking of Luigi Moretti, first to have formulated the concept of parametric architecture, comparing it with those of some contemporary architectural theorists and designers. The latest researches on materials and form-finding experiences have shown a new relationship between form and structure, Moretti understood it before the advent of the internet. Moretti's parameter stems from the architectural tradition, as Carpo sees relations between parametric design and history. Moretti’s Parametric architecture is interdisciplinary, open to science in ways that we are only now understanding. We, therefore, believe that recovering Moretti’s methods …

Photosynthesized silver-polyaminocyclodextrin nanocomposites as promising antibacterial agents with improved activity

Ag nanocomposites were prepared by photoreduction of ammoniacal silver acetate in the presence of poly-{6-[3-(2-(3-aminopropylamino)ethylamino)propylamino]}-(6-deoxy)-β-CD (amCD). The obtained systems were characterized by means of various complementary techniques (UV-vis, FT-IR, TEM, SAED). In particular, FT-IR spectroscopy evidenced a partial oxidative degradation of the polyamine branches of the capping auxiliary, due to the fact that these groups function as a sacrificial reducing agent in the photoinduced formation of the Ag metal core. TEM and SAED micrographs showed that the Ag cores possess a relatively low polydispersity and a significantly crystalline character. The Ag–amCD system…

Amycolatopsis proteomic analysis to reveal primary metabolism genes involved in balhimycin production

Differential proteomics highlights metabolic changes associated with n-hexadecane utilization in a Streptomyces coelicolor strain expressing Gordonia sp. SoCg n-alkane monooxigenase.

Introduction: Alkanes are biodegraded to generate the corresponding primary alcohol trough alkane hydroxylases (AHs) consisting on an integral membrane alkane monooxygenase (AlkB) and two soluble proteins, rubredoxin and rubredoxin reductase. Recently, an alkB gene was reported to be involved in degradation of long chain n-alkanes in the actinobacterium Gordonia sp. SoCg. This gene was expressed in Streptomyces coelicolor M145 which is unable to degrade n-alkanes. Results: The engineered strain, M145-AH, can biotransform n-hexadecane into the corresponding 1-hexadecanol and it is able to grow on n-hexadecane as sole carbon source. Changes in global protein expression associated with n-hexad…

An extended catalogue of ncRNAs in Streptomyces coelicolor reporting abundant tmRNA, RNase-P RNA and RNA fragments derived from pre-ribosomal RNA leader sequences

Streptomyces coelicolor is a model organism for studying streptomycetes. This genus possesses relevant medical and economical roles, because it produces many biologically active metabolites of pharmaceutical interest, including the majority of commercialized antibiotics. In this bioinformatic study, the transcriptome of S. coelicolor has been analyzed to identify novel RNA species and quantify the expression of both annotated and novel transcripts in solid and liquid growth medium cultures at different times. The major characteristics disclosed in this study are: (i) the diffuse antisense transcription; (ii) the great abundance of transfer-messenger RNAs (tmRNA); (iii) the abundance of rnpB…

TrpM, a Small Protein Modulating Tryptophan Biosynthesis and Morpho-Physiological Differentiation in Streptomyces coelicolor A3(2).

In the model actinomycete Streptomyces coelicolor A3(2), small open reading frames encoding proteins with unknown functions were identified in several amino acid biosynthetic gene operons, such as SCO2038 (trpX) in the tryptophan trpCXBA locus. In this study, the role of the corresponding protein in tryptophan biosynthesis was investigated by combining phenotypic and molecular analyses. The 2038KO mutant strain was characterized by delayed growth, smaller aerial hyphae and reduced production of spores and actinorhodin antibiotic, with respect to the WT strain. The capability of this mutant to grow on minimal medium was rescued by tryptophan and tryptophan precursor (serine and/or indole) su…

Gordonia sp. SoCg alkB gene confers the ability to degrade and use n-alkanes as carbon source in Gram positive bacteria

Gordonia sp. SoCg, a Gram positive strain able to grow on long chain n-alkanes1, possess a single copy of alkB2 gene, whose product is required for n-alkane hydroxylation3. An analysis of alkB flanking regions revealed five ORFs which were designed as orf1, rubA3, rubA4, rubB and alkU, according to the sequence 14 homology with that of known alk clusters3. In G. sp. SoCg the transcription of these genes was induced by long-chain and solid n-alkanes as revealed by quantitative RT-PCR, and the essential role of alkB in nalkane degradation was demonstrated by the construction of an alkB disruption mutant strain3. The SoCg alkB gene was successfully expressed in Streptomyces coelicolor M145 (M1…

PROTEOMIC ANALYSIS OF AMYCOLATOPSIS BALHIMYCINA TO REVEAL NOVEL LINKS BETWEEN PRIMARY AND SECONDARY METABOLISM.

Bacterial metal nanoparticles to develop new weapons against bacterial biofilms and infections

The widespread use of antibiotics has resulted in the outbreak and spread of antibiotic-resistant pathogens. Bacterial antibiotic resistance may develop at cellular and community levels. In the latter case, it is based on tolerance which implicates the shift from a free-living form of life (i.e., planktonic) to a sessile multi-stratified community (i.e., biofilm). Metal nanoparticles (MNPs) have been shown to be promising candidates as antimicrobial agents. MNPs are able to interact with and penetrate bacterial biofilms, thus, resulting effective antibiofilm compounds. Another interesting aspect is the possibility of using plants, fungi, yeasts, and bacteria to obtain biogenic MNPs (BMNP). …

The role of Artificial intelligence in architectural design: conversation with designer and researchers

The proliferation of data together with the increase of computing power in the last decade has triggered a new interest in artificial intelligence methods. Machine learning and in particular deep learning techniques, inspired by the topological structure of neurons network in brains, are omnipresent in the IT discourse, and generated new enthusiasms and fears in our society. These methods have already shown great effectiveness in fields far from architecture and have long been exploited in software that we use every day. Many computing libraries are available for anyone with some programming skills and allow them to "train" a neural network based on several types of data. The world of archi…

Photo-oxidative degradation of poly(ethylene-co-vinyl acetate)/nisin antimicrobial films

The photo-oxidative behaviour of different antimicrobial blown films based on poly (ethylene-co-vinyl acetate) (EVA) was studied. In particular, two samples of EVA containing different level of vinyl acetate comonomer (namely 14% and 28%) were used as matrices while nisin at different concentrations was used as antimicrobial agent. The degradation was followed by analyzing the changes in the spectroscopic behaviour and of the elongation at break measured in tensile tests. Moreover, changes in the antimicrobial activity of the films were followed by measuring the inhibition halo in agar diffusion tests. The results indicate that nisin acts as an excellent UV stabilizer for both samples of EV…

Regulation of the biosynthesis of the glycopeptide antibiotic A40926 in Nonomuraea ATCC39727

The actinomycete Nonomuraea produces the glycopeptide A40926, precursor of dalbavancin. Dalbavancin is a novel lipoglycopeptide agent against emerging resistant Gram-positive cocci with superior pharmacodynamics properties compared to vancomycin. Chemically, a glycopeptide antibiotic consists of a heptapeptide core constituted by proteinogenic and nonproteinogenic amino acids such as 3,5-dihydroxyphenylglycine (DPG) and 4-hydroxyphenylglycine (HPG). The heptapeptide is assembled by a nonribosomal peptide synthetase and modified by oxidative cross-linking of the electron-rich aromatic side chains, halogenation, sulfation, methylation, acylation, and glycosylation. The A40926 biosynthetic gen…

Incorporation of an antibiotic in poly(lactic acid) and polypropylene by melt processing

Purpose In this work an antibiotic, ciprofloxacin (CFX), was incorporated into 2 different polymeric matrices, poly(lactic acid) (PLA) and polypropylene (PP), to provide them with antimicrobial properties. The influence of CFX content on release kinetics and on antimicrobial and mechanical properties was evaluated. Methods CFX was incorporated into both the polymers by melt mixing. Results The effect of CFX incorporation was found to strongly depend on which polymer matrix was used. In particular, the antimicrobial tests revealed that PLA samples containing CFX produced no inhibition zone and only a slight antibacterial activity was observed when the highest concentration of CFX was added t…

Coupling Proteomics and Fermentation Technology for the Improvement of Bioactive Molecule Production Yield in Actinomycetes

Copyright: © 2013 Gallo. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Most bioactive molecules (like anticancers, antitumors, antibiotics, immunosuppressants, insecticidals, antivirals, herbicidals, antifungals) with valuable industrial and market value are naturally produced by actinomycetes [1-4], Gram-positive filamentous bacteria widespread in both terrestrial and aquatic environments [5,6]. Out of thousands of bioactive molecules, also known as secondary metabolites since they are not essential for…

Effetto dello stiro sulle proprietà fisiche e antimicrobiche di fibre a base di PCL contenenti clorexidina

Amycolatopsis balhimycina gene expression under inorganic phosphate limitation

Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Background Klebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM 29614 strain is multi metal resistant and produces metal nanoparticles that are embedded in its very peculiar capsular exopolysaccharide. These metal nanoparticles were effective as antimicrobial and anticancer compounds, chemical catalysts and nano-fertilizers. Results The DSM 29614 strain genome was sequenced and analysed by a combination of in silico procedures. Comparative genomics, performed between 85 K. oxytoca representatives and K. oxytoca DSM 29614, revealed th…

Proteomic investigations to unravel molecular physiology of the lantibiotic producer Microbispora sp. ATCC‐PTA‐5024

Antimicrobial and antioxidant supramolecular ionic liquid gels from biopolymer mixtures

In this work, we describe the preparation and characterization of supramolecular ionic liquid gels based on binary mixtures of biopolymers, comprising chitosan, chitin, cellulose and lignin. The gels were obtained in ionic liquids differing in the cation or the anion, with no need for a cross-linking agent or acid treatment. The materials obtained were characterized for the minimum gelation concentration, porosity, swelling and rheological properties, finding a prominent influence of the nature of the ionic liquid anion. Then, we investigated the ability of the gels to scavenge free radicals, finding that the gels exhibit a higher antioxidant ability than their individual components. Moreov…

Proteomic analysis of the antibiotic producer Amycolatopsis balhimycina

DICATIONIC IMIDAZOLIUM SALTS: TUNABLE ANTIMICROBIAL AND ANTITUMORAL CHEMIOTHERAPEUTIC LEADS

The chemical synthesis of novel chemotherapeutical leads is evolving thanks to possibility to design molecules with desired physical-chemical and, thus, biological properties. The imidazolium salts, recently proven effective to inhibit bacterial and/or cancer cell growth, posses an amphiphilic nature that is conferred by the imidazolium cation having a polar head generally coupled with aliphatic side chains. Thus, biological properties of imidazolium salts can be tuned through modifications involving the cation structure and/or the anion nature. By covalently linking two imidazolium rings, di-imidazolium salts were obtainedobtain differing in: i) kind of anions; ii) geometric isomerization …

Additional file 4: of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Supplementary Results section. (PDF 123 kb)

Artificial Chromosomes to Explore and to Exploit Biosynthetic Capabilities of Actinomycetes

Actinomycetes are an important source of biologically active compounds, like antibiotics, antitumor agents, and immunosuppressors. Genome sequencing is revealing that this class of microorganisms has larger genomes relative to other bacteria and uses a considerable fraction of its coding capacity (5–10%) for the production of mostly cryptic secondary metabolites. To access actinomycetes biosynthetic capabilities or to improve the pharmacokinetic properties and production yields of these chemically complex compounds, genetic manipulation of the producer strains can be performed. Heterologous expression in amenable hosts can be useful to exploit and to explore the genetic potential of actinom…

In vitro effects of AGNPs exopolysaccharide from Klebsiella Oxytoca DSM29614 on breast cancer cells

Recent results on Heavy-Ion induced reactions of interest for 0νββ decay

An updated overview of recent results on Heavy-Ion induced reactions of interest for neutrinoless double beta decay is reported in the framework of the NUMEN project. The NUMEN idea is to study heavy-ion induced Double Charge Exchange (DCE) reactions with the aim to get information on the nuclear matrix elements for neutrinoless double beta (0νββ) decay. Moreover, to infer the neutrino average masses from the possible measurement of the half- life of 0νββ decay, the knowledge of the nuclear matrix elements is a crucial aspect. Uma visão geral atualizada dos resultados recentes sobre reações induzidas por íons pesados ​​de interesse para o decaimento beta duplo sem neutrinos é relatada na es…

Antibiotics and Resistance: A Fatal Attraction

When penicillin and other classes of antibiotics were discovered and used to treat infectious diseases human morbidity and mortality due to infective microorganisms were successfully contrasted. However, almost as soon as antibacterial drugs were introduced in clinics, bacterial resistance spread. From a biological and microbiological viewpoint, antibacterial drug resistance is a fascinating aspect of molecular evolution, and resistome concept has been introduced to shed light on driving forces that control the spreading and maintenance of resistance genes within microbial populations. Despite the wide range of chemical complexity of antibiotics, there is a restricted number of modes of act…

Changes in surgicaL behaviOrs dUring the CoviD-19 pandemic. The SICE CLOUD19 Study

Abstract Background The spread of the SARS-CoV2 virus, which causes COVID-19 disease, profoundly impacted the surgical community. Recommendations have been published to manage patients needing surgery during the COVID-19 pandemic. This survey, under the aegis of the Italian Society of Endoscopic Surgery, aims to analyze how Italian surgeons have changed their practice during the pandemic. Methods The authors designed an online survey that was circulated for completion to the Italian departments of general surgery registered in the Italian Ministry of Health database in December 2020. Questions were divided into three sections: hospital organization, screening policies, and safety profile of…

Effect of PCL/PEG-Based Membranes on Actinorhodin Production in Streptomyces coelicolor Cultivations

The actinomycetes, Gram-positive filamentous bacteria, are the most prolific source of natural occurring antibiotics. At an industrial level, antibiotics from actinomycete strains are produced by means of submerged fermentations, where one of the major factors negatively affecting bioproductivity is the pellet-shaped biomass growth. The immobilization of microorganisms on properly chosen supports prevents cell-cell aggregation resulting in improving the biosynthetic capability. Thus, novel porous biopolymer-based devices are developed by combining melt mixing and particulate leaching. In particular, polycaprolactone (PCL), polyethylene glycol (PEG), and sodium chloride (NaCl) with different…

Proteomic analysis of Amycolatopsis balhimycina to reveal primary metabolism proteins involved in balhimycin production

Unravelling the DNA sequences carried by Streptomyces coelicolor membrane vesicles

AbstractMembrane vesicles (MVs) are spherical particles with nanoscale dimensions and characterized by the presence of diverse cargos, such as nucleic acids, proteins, lipids, and cellular metabolites. Many examples of (micro)organisms producing MVs are reported in literature. Among them, bacterial MVs are of particular interest because they are now considered as the fourth mechanism of horizontal gene transfer. Streptomyces bacteria are well-known for their ecological roles and ability to synthesize bioactive compounds, with Streptomyces coelicolor being the model organism. It was previously demonstrated that it can produce distinct populations of MVs characterized by different protein and…

Measuring nuclear reaction cross sections to extract information on neutrinoless double beta decay

Neutrinoless double beta decay (0v\b{eta}\b{eta}) is considered the best potential resource to access the absolute neutrino mass scale. Moreover, if observed, it will signal that neutrinos are their own anti-particles (Majorana particles). Presently, this physics case is one of the most important research "beyond Standard Model" and might guide the way towards a Grand Unified Theory of fundamental interactions. Since the 0v\b{eta}\b{eta} decay process involves nuclei, its analysis necessarily implies nuclear structure issues. In the NURE project, supported by a Starting Grant of the European Research Council (ERC), nuclear reactions of double charge-exchange (DCE) are used as a tool to extr…

A proteomic investigation to explore biochemical capabilities of a lantibiotic producer Microbispora strain

Initial pH Conditions Shape the Microbial Community Structure of Sewage Sludge in Batch Fermentations for the Improvement of Volatile Fatty Acid Production

Conversion of wastewater treatment plants into biorefineries is a sustainable alternative for obtaining valuable compounds, thus reducing pollutants and costs and protecting the environment and human health. Under specific operating conditions, microbial fermentative products of sewage sludge are volatile fatty acids (VFA) that can be precursors of polyhydroxyalkanoate thermoplastic polyesters. The role of various operating parameters in VFA production has yet to be elucidated. This study aimed to correlate the levels of VFA yields with prokaryotic microbiota structures of sewage sludge in two sets of batch fermentations with an initial pH of 8 and 10. The sewage sludge used to inoculate th…

Plasma modified PLA electrospun membranes for actinorhodin production intensification in Streptomyces coelicolor immobilized-cell cultivations

Most of industrially relevant bioproducts are produced by submerged cultivations of actinomycetes. The immobilization of these Gram-positive filamentous bacteria on suitable porous supports may prevent mycelial cell-cell aggregation and pellet formation which usually negatively affect actinomycete submerged cultivations, thus, resulting in an improved biosynthetic capability. In this work, electrospun polylactic acid (PLA) membranes, subjected or not to O2-plasma treatment (PLA-plasma), were used as support for immobilized-cell submerged cultivations of Streptomyces coelicolor M145. This strain produces different bioactive compounds, including the blue-pigmented actinorhodin (ACT) and red-p…

The evolution of the digital curve: from shipbuilding spline to the diffusion of NURBS, subdivision surface and t-splines as tools for architectural design

In this article, we will follow the history of splines, digital methods that have characterized the architectural design process since the last decade of the twentieth century. We will describe their evolutions since the beginning as analogical tools for boat construction in the eighteenth century, to its passage to digital within the automotive industry. Then the relationship with the aerospace industry, and the evolution which from digital animation, have led nurbs, subdivision surfaces and t-splines to become everyday computational tools within architecture workflow. Recent developments on t-splines, following their acquisition by Autodesk, will lead us to a reflection on the relationshi…

Biogenic iron-silver nanoparticles inhibit bacterial biofilm formation due to Ag+ release as determined by a novel phycoerythrin-based assay

Silver nanoparticles (Ag-NPs) can be considered as a cost-effective alternative to antibiotics. In the presence of Fe(III)-citrate and Ag+, Klebsiella oxytoca DSM 29614 produces biogenic Ag-NPs embedded in its peculiar exopolysaccharide (EPS). K. oxytoca DSM 29614 was cultivated in a defined growth medium–containing citrate (as sole carbon source) and supplemented with Ag+ and either low or high Fe(III) concentration. As inferred from elemental analysis, transmission and scanning electron microscopy, Fourier transform infrared spectrometry and dynamic light scattering, Ag-EPS NPs were produced in both conditions and contained also Fe. The production yield of high-Fe/Ag-EPS NPs was 12 times …

Synergistic effect with antibiotics and inhibition of bacterial biofilm formation by polyaminocyclodextrin-silver nanoparticles

Stategie metaboliche indotte dal triptofano in Streptomyces coelicolor

A Genomic, Transcriptomic and Proteomic Look at the GE2270 Producer Planobispora rosea, an Uncommon Actinomycete.

We report the genome sequence of Planobispora rosea ATCC 53733, a mycelium-forming soil-dweller belonging to one of the lesser studied genera of Actinobacteria and producing the thiopeptide GE2270. The P. rosea genome presents considerable convergence in gene organization and function with other members in the family Streptosporangiaceae, with a significant number (44%) of shared orthologs. Patterns of gene expression in P. rosea cultures during exponential and stationary phase have been analyzed using whole transcriptome shotgun sequencing and by proteome analysis. Among the differentially abundant proteins, those involved in protein metabolism are particularly represented, including the G…

Antimicrobial thermoplastic materials for biomedical applications prepared by melt processing

In this work thermoplastic polymers with antimicrobial properties were prepared by incorporating an antibiotic, i.e., ciprofloxacin (CFX), by melt processing. Two different polymers were used as matrices, i.e., polypropylene (PP) and poly(lactid acid) (PLA) and different concentrations of CFX have been incorporated. The antimicrobial properties, the release kinetic and the mechanical performances of the prepared materials were evaluated.

Pirin: A novel redox-sensitive modulator of primary and secondary metabolism in Streptomyces

Pirins are evolutionarily conserved iron-containing proteins that are found in all kingdoms of life, and have been implicated in diverse molecular processes, mostly associated with cellular stress. In the present study, we started from the evidence that the insertional inactivation of pirin-like gene SAM23877_RS18305 (pirA) by Phi C31 Att/Int system-based vectors in spiramycin-producing strain Streptomyces ambofaciens ATCC 23877 resulted in marked effects on central carbon and energy metabolism gene expression, high sensitivity to oxidative injury and repression of polyketide antibiotic production. By using integrated transcriptomic, proteomic and metabolite profiling, together with genetic…

Additional file 5: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Supporting Information. (PDF 130 kb)

Effect of osmotic and heat shock on the biosynthesis of glycopeptide antibiotics in actinomycetes

The chemical composition of the flowers essential oil of Inula crithmoides (Asteraceae) growing in aeolian islands, Sicily (Italy) and its biocide properties on microorganisms affecting historical art crafts

Essential oils have been used for a long time in several fields of interest. Recently, they have also been applied in the conservation of Cultural Heritage to contrast biodeterioration replacing the most current biocides toxic for humans and environment. Inula crithmoides L. (syn. Limbarda crithmoides (L.) Dumort) is a halophyte species distributed along the Mediterranean coasts and it is used as an edible vegetable since the young leaves or shoots are eaten raw or cooked. Several biological properties have been determined for this plant including antimicrobial activities. In this study the volatile composition of the aerial part of an accession from the Aeolian Islands, Sicily (Italy) is d…

Combining in the melt physical and biological properties of poly(caprolactone) and chlorhexidine to obtain antimicrobial surgical monofilaments.

Bacterial infections on a sutured wound represent a critical problem, and the preparation of suture threads possessing antimicrobial properties is valuable. In this work, poly(caprolactone) (PCL) monofilaments were compounded at the concentration of 1, 2 and 4 % (w/w), respectively, to the antiseptic chlorhexidine diacetate (CHX). The incorporation was carried out in the melt by a single-step methodology, i.e. “online” approach. Mechanical tests revealed that the incorporation of CHX does not significantly change tensile properties of PCL fibres as the thermal profile adopted to prepare the compounded fibres does not compromise the antibacterial activity of CHX. In fact, CHX confers to comp…

Inorganic phosphate is a trigger factor for Microbispora sp. ATCC-PTA-5024 growth and NAI-107 production

Background NAI-107, produced by the actinomycete Microbispora sp. ATCC-PTA-5024, is a promising lantibiotic active against Gram-positive bacteria and currently in late preclinical-phase. Lantibiotics (lanthionine-containing antibiotics) are ribosomally synthesized and post-translationally modified peptides (RiPPs), encoded by structural genes as precursor peptides. The biosynthesis of biologically active compounds is developmentally controlled and it depends upon a variety of environmental stimuli and conditions. Inorganic phosphate (Pi) usually negatively regulates biologically-active molecule production in Actinomycetes, while it has been reported to have a positive control on lantibiotic…

The Streptomyces coelicolor Small ORF trpM Stimulates Growth and Morphological Development and Exerts Opposite Effects on Actinorhodin and Calcium-Dependent Antibiotic Production

In actinomycetes, antibiotic production is often associated with a morpho-physiological differentiation program that is regulated by complex molecular and metabolic networks. Many aspects of these regulatory circuits have been already elucidated and many others still deserve further investigations. In this regard, the possible role of many small open reading frames (smORFs) in actinomycete morpho-physiological differentiation is still elusive. In Streptomyces coelicolor, inactivation of the smORF trpM (SCO2038) – whose product modulates L-tryptophan biosynthesis – impairs production of antibiotics and morphological differentiation. Indeed, it was demonstrated that TrpM is able to interact w…

Draft genome sequence of the Microbispora sp. strain ATCC-PTA-5024, producing the lantibiotic NAI-107

We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that produces NAI-107, a new lantibiotic with the potential to treat life-threatening infections caused by multidrug-resistant Gram-positive pathogens. The draft genome of strain Microbispora sp. ATCC-PTA-5024 consists of 8,543,819 bp, with a 71.2% G+C content and 7,860 proteincoding genes.

The endophytic microbiota of Citrus limon is transmitted from seed to shoot highlighting differences of bacterial and fungal community structures

AbstractCitrus limon (L.) Burm. F. is an important evergreen fruit crop whose rhizosphere and phyllosphere microbiota  have been characterized, while seed microbiota is still unknown. Bacterial and fungal endophytes were isolated from C. limon surface-sterilized seeds. The isolated fungi—belonging to Aspergillus, Quambalaria and Bjerkandera genera—and bacteria—belonging to Staphylococcus genus—were characterized for indoleacetic acid production and phosphate solubilization. Next Generation Sequencing based approaches were then used to characterize the endophytic bacterial and fungal microbiota structures of surface-sterilized C. limon seeds and of shoots obtained under aseptic conditions fr…

Effect of cold drawing on the antimicrobial and physical properties of PCL/CHX monofilaments

From genome to phenome and back: understanding the high metabolic veratility of Bulkholderia cepacia complex

Pyrrolomycins as antimicrobial agents. Microwave-assisted organic synthesis and insights into their antimicrobial mechanism of action

Abstract New compounds able to counteract staphylococcal biofilm formation are needed. In this study we investigate the mechanism of action of pyrrolomycins, whose potential as antimicrobial agents has been demonstrated. We performed a new efficient and easy method to use microwave organic synthesis suitable for obtaining pyrrolomycins in good yields and in suitable amount for their in vitro in-depth investigation. We evaluate the inhibitory activity towards Sortase A (SrtA), a transpeptidase responsible for covalent anchoring in Gram-positive peptidoglycan of many surface proteins involved in adhesion and in biofilm formation. All compounds show a good inhibitory activity toward SrtA, havi…

Microbispora sp. proteomic analysis to study metabolic pathway changes during lantibiotic production

Regulation of the biosynthesis of dalbavancin

Having a look at Microbispora sp. ATCC-PTA-5024, a lantibiotic producer, "from the cradle to the grave" at the proteome level

Isolation and characterization of sea urchin P. lividus microbiota from coelomic fluid

The role of Plant Growth Promoting (PGP) bacteria in the growth of Mediterranean diet plants producing high-value compounds

Loss of fertility, together with drought and aridity, results in soil unproductivity and eventually desertification. Unsustainable agricultural practices are currently stressing the soil: an undervalued resource that, in addition to food, provides a multitude of invaluable services such as regulating the microclimate, reducing contaminants, and capturing CO2. Hence, there is an increasing need to resort to sustainable approaches toward agricultural systems. Although Sicily is one of those regions most affected by water shortages, it is at the same time a reservoir of drought-resistant Mediterranean plants with high nutritional value and a rich microbiota. This project aims to promote agricu…

An integrated proteomic and metabolomic study to evaluate the effect of nucleus-cytoplasm interaction in a diploid citrus cybrid between sweet orange and lemon.

Key message: Our results provide a comprehensive overview how the alloplasmic condition might lead to a significant improvement in citrus plant breeding, developing varieties more adaptable to a wide range of conditions. Abstract: Citrus cybrids resulting from somatic hybridization hold great potential in plant improvement. They represent effective products resulting from the transfer of organelle-encoded traits into cultivated varieties. In these cases, the plant coordinated array of physiological, biochemical, and molecular functions remains the result of integration among different signals, which derive from the compartmentalized genomes of nucleus, plastids and mitochondria. To dissect …

Composition and geographic variation of the bacterial microbiota associated with the coelomic fluid of the sea urchin Paracentrotus lividus

AbstractIn the present work, culture-based and culture-independent investigations were performed to determine the microbiota structure of the coelomic fluid of Mediterranean sea urchin Paracentrotus lividus individuals collected from two distinct geographical sites neighboring a high-density population bay and a nature reserve, respectively. Next Generation Sequencing analysis of 16S rRNA gene (rDNA) showed that members of the Proteobacteria, Bacteroidetes and Fusobacteria phyla, which have been previously reported to be commonly retrieved from marine invertebrates, dominate the overall population of microorganisms colonizing this liquid tissue, with minority bacterial genera exhibiting rem…

Streptomyces coelicolor extracellular vesicles

This study may reveal the importance of extracellular vesicles in the physiology of S. coelicolor and may also have important biotechnological implications.

Proteomic profiling of vesicles released by 8701-bc cells

8701-BC cells were shown to release “membrane vesicles” playing a role in tumor progression mechanisms. On the other hand, production of “exosomes”, smaller vesicles known to be involved in immune response activation, had not been revealed. The first goal of this study was to separate different vesicle populations from 8701-BC cell conditioned medium. To this aim, the medium was differentially centrifuged. Western analysis revealed that the 15,000xg pelletted fraction contains β1-integrin, which had been shown to be clustered in membrane vesicles shed by 8701-BC cells, but not Hsc70, a protein found in exosomes. On the contrary, Hsc70 is detectable while β1-integrin is not present in the fr…

Antimicrobial effect of cyclodextrin-based nanodevices capable of antibiotic release

Additional file 5: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Supporting Information. (PDF 130 kb)

Phosphate control of balhimycin biosynthesis in Amycolatopsis balhimycina

Additional file 4: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Figure S1. K. oxytoca DSM 29614 grown in NaC (left) and in FeC medium (right) after 7 day of incubation at 30 °C. Figure S2. a,b) Production of ortorhomboidal struvite in the presence of Hg2+ (a) and Ag+ (b); both crystals precipitated in aerobic cultures of K. oxytoca DSM 29614. c,d) Micrographs of microcrystal of struvite by K. oxytoca DSM 29614 cells, grown in aerobic conditions in the presence of Pd2+ in transmission mode (c) and in fluorescence mode (d) with cells stained with DAPI. e) Micrographs of TEM of microcrystals of struvite coated by Pd2+. (PDF 527 kb)

NURE: An ERC project to study nuclear reactions for neutrinoless double beta decay

Neutrinoless double beta decay (0{\nu}\b{eta}\b{eta}) is considered the best potential resource to determine the absolute neutrino mass scale. Moreover, if observed, it will signal that the total lepton number is not conserved and neutrinos are their own anti-particles. Presently, this physics case is one of the most important research beyond Standard Model and might guide the way towards a Grand Unified Theory of fundamental interactions. Since the \b{eta}\b{eta} decay process involves nuclei, its analysis necessarily implies nuclear structure issues. The 0{\nu}\b{eta}\b{eta} decay rate can be expressed as a product of independent factors: the phase-space factors, the nuclear matrix elemen…

Water Resource Recovery Facilities (WRRFs): The Case Study of Palermo University (Italy)

The wastewater sector paradigm is shifting from wastewater treatment to resource recovery. In addition, concerns regarding sustainability during the operation have increased. In this sense, there is a need to break barriers (i.e., social, economic, technological, legal, etc.) for moving forward towards water resource recovery facilities and demonstration case studies can be very effective and insightful. This paper presents a new water resource recovery case study which is part of the Horizon 2020 EU Project “Achieving wider uptake of water-smart solutions—Wider Uptake”. The final aim is to demonstrate the importance of a resource recovery system based on the circular economy concept. The r…

Primary and secondary metabolism gene expression in Amycolatopsis balhimycina

Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy)

: The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bon…

The seed endosphere of Anadenanthera colubrina is inhabited by a complex microbiota, including Methylobacterium spp. and Staphylococcus spp. with potential plant-growth promoting activities

Background and aims: Plant seeds are emerging micro–habitats, whose importance as reservoir and vector of beneficial microbes just begins to be recognized. Here we aimed to characterize the bacterial microbiota of the Anadenanthera colubrina seed endosphere, with special focus to beneficial traits and to the colonization pattern. Methods: Cultivation–dependent (isolation from surface–sterilized seeds) and cultivation–independent (pyrosequencing of 16S rRNA gene from metagenomic seed DNA) analyses, functional tests and microscopical investigations (fluorescence in situ hybridization coupled with confocal laser scanning microscopy (FISH-CLSM) were performed. Results: We isolated several Methy…

Microbispora sp. ATCC-PTA-5024 proteomic analysis to study metabolic pathway changes before and during lantibiotic production

Heterologous expression of Nonomuraea sp. ATCC39727 genes in Streptomyces lividans

CONVERSIONE CHEMO-ENZIMATICA DI GLUCOSIO IN 5-HMF IN MISCELE IL/H2O, PROMOSSA DA ESTRATTO CELLULARE BATTERICO E ULTRASUONI

Antimicrobial properties and release profile of monofilaments incorporating chlorhexidine for surgical applications

Architects as tool consumers: discovering trends in software and programming languages for Architecture with Google Trends

Architect professional figure and skills have undergone innumerable evolutions throughout human history, and although the architect's task is always substantially to design buildings and spaces, the use of digital tools has undoubtedly marked the greatest change in architectural design since the Renaissance, if not since the time of Vitruvius (Sacchi 2018). However, when we talk about the relationship between architecture and digital tools, we immediately think about projects of some contemporary architects and researches of some important academics come to mind. Digital tools are now everywhere within the fragmented world of architecture: from multinationals firm with offices in the major …

Additional file 2: Table S2. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from global proteome analysis at D substages. (XLS 107 kb)

Additional file 6: Table S5. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, abundance profile and mass spectrometry identification parameters of differentially represented spots containing multiple protein components. (XLS 45 kb)

Additional file 6: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Table S4. List of genes associate with cps1 cluster in DSM 29614 strain. (XLSX 10 kb)

Additional file 3: Table S3. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from membrane proteome analysis at A substages. (XLSX 37 kb)

Additional file 2: Table S2. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from global proteome analysis at D substages. (XLS 107 kb)

Additional file 6: Table S5. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, abundance profile and mass spectrometry identification parameters of differentially represented spots containing multiple protein components. (XLS 45 kb)

Additional file 2: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Table S2. List of differentially abundant proteins in DSM 29614 strain used for protein functional enrichment analysis. (XLSX 17 kb)

Additional file 7: Table S4. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented proteins due to NAI-107 exposure in Microbispora ATCC-PTA-5024 RP0 strain. (XLSX 32 kb)

Additional file 1: Table S1. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from global proteome analysis at A substages. (XLSX 48 kb)

Additional file 1: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Table S1. List of genomes of K. oxytoca strains used for comparative genomics. (XLSX 10 kb)

Additional file 3: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Table S3. List of metal resistance genes identified in the DSM 29614 strain genome. (XLSX 48 kb)

Additional file 8: Table S6. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Numbers of KEGG orthology groups participating in molecular and metabolic processes as inferred from genome and proteome analyses, respectively. (XLS 24 kb)

Additional file 6: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Table S4. List of genes associate with cps1 cluster in DSM 29614 strain. (XLSX 10 kb)

Additional file 3: Table S3. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from membrane proteome analysis at A substages. (XLSX 37 kb)

Additional file 3: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Table S3. List of metal resistance genes identified in the DSM 29614 strain genome. (XLSX 48 kb)

Additional file 2: of Genomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages

Table S2. List of differentially abundant proteins in DSM 29614 strain used for protein functional enrichment analysis. (XLSX 17 kb)

Additional file 7: Table S4. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented proteins due to NAI-107 exposure in Microbispora ATCC-PTA-5024 RP0 strain. (XLSX 32 kb)

Additional file 8: Table S6. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Numbers of KEGG orthology groups participating in molecular and metabolic processes as inferred from genome and proteome analyses, respectively. (XLS 24 kb)

Additional file 1: Table S1. of Elucidating the molecular physiology of lantibiotic NAI-107 production in Microbispora ATCC-PTA-5024

Description, functional classification, abundance profile and mass spectrometry identification parameters of differentially represented Microbispora ATCC-PTA-5024 proteins identified from global proteome analysis at A substages. (XLSX 48 kb)