60. "Frequent gene fissions associated with human pathogenic bacteria."
I. Karamichali, V.L. Koumandou, A.D. Karagouni, S. Kossida.
Genomics, doi:10.1016/j.ygeno.2014.02.001, (2014).  View at publisher's site  Request copy
Abstract: Gene fusion and fission events are important for evolutionary studies and for predicting protein-protein interactions. Previous studies have shown that fusion events always predominate over fission events and, in their majority, they represent singular events throughout evolution. In this project, the role of fusion and fission events in the genome evolution of 104 human bacterial pathogens was studied. 141 protein pairs were identified to be involved in gene fusion or fission events. Surprisingly, we find that, in the species analyzed, gene fissions prevail over fusions. Moreover, while most events appear to have occurred only once in evolution, 23% of the gene fusion and fission events identified are deduced to have occurred independently multiple times. Comparison of the analyzed bacteria with non-pathogenic close relatives indicates that this impressive result is associated with the recent evolutionary history of the human bacterial pathogens, and thus is probably caused by their pathogenic lifestyle.

59. "Pipelines for New Chemicals: a strategy to create new value chains and stimulate innovation-based economic revival in Southern European countries."
K. Timmis, V. de Lorenzo, W. Verstraete, J.L. Garcia, J.L. Ramos, H. Santos, I. Economidis, B. Nogales, J.K. Timmis, C. Fonseca, C. Pruzzo, A. Karagouni, N. Panopoulos, B. Dixon.
Environmental Microbiology, doi: 10.1111/1462-2920.12337, (2014).  View at publisher's site  Request copy
Abstract: Countries of Southern Europe are currently suffering from severe socio-economic pain resulting from high debt levels and austerity measures which constrain investment in innovation-based recovery strategies that are essential for entry into a long-term sustainable period of increasing employment and wealth creation. Young university-educated people are particularly innovative, and hence vital to the development of such strategies, but employment opportunities are poor and many are forced to seek employment that neither profits from their training nor satisfies their justified career expectations, or to emigrate. They are the 'lost generation'. A strategy is proposed here for the creation of Pipelines for New Chemicals, national centre-network partnerships for the discovery-synthesis of new chemicals obtained though harvesting new biological diversity, and their exploitation to develop new medicines, agrochemicals, materials, and other products and applications. The goal is to create new regional motors of economic growth and development, by harnessing the knowledge, motivation and innovation potential of the excellently educated young people of Europe to catalyse the development of new small, medium and large enterprises centred around novel chemicals, and the value chains that will evolve with them, and thereby develop a powerful sector of sustainable growth in employment and social and economic prosperity in Southern Europe.

58. "Carbapenemase-producing Pseudomonas aeruginosa from central Greece: molecular epidemiology and genetic analysis of class I integrons."
A. Liakopoulos, A. Mavroidi, E.A. Katsifas, A. Theodosiou, A.D. Karagouni, V. Miriagou, E. Petinaki.
BMC Infectious Diseases, doi: 10.1186/1471-2334-13-505, (2013).  View at publisher's site  Request copy
Abstract: BACKGROUND: Multidrug-resistant Pseudomonas aeruginosa is a serious challenge for antimicrobial therapy of nosocomial infections, as it possesses several mechanisms of antimicrobial resistance. In Central Greece, a sudden increase of infections caused by carbapenem-resistant P. aeruginosa was observed during 2011, indicating the need for further analysis. METHODS: Five-hundred and sixty-eight P. aeruginosa isolates were collected consecutively during an 8-month period in 2011 from inpatients treated in three hospitals in the Thessaly region (1,000,000 habitants) of Greece. Carbapenem-resistant P. aeruginosa (n = 284) were characterized by antimicrobial susceptibility testing and β-lactamase content, and the genetic relatedness of carbapenemase-producing isolates was assessed by BOX-PCR, multilocus sequence typing, and eBURST analysis. Mapping of the class I integrons of Verona integron-encoded metallo-β-lactamase (VIM)-carrying isolates was also performed, and clinical data of the VIM producers were reviewed. RESULTS: Eighty (14.1%) out of the 568 P. aeruginosa isolates recovered from clinical specimens were VIM producers. Multilocus sequence typing revealed high prevalence of the international clones ST111 and ST235 among blaVIM-2- and blaVIM-4-positive isolates, respectively. blaVIM-17 was identified in an isolate of a novel sequence type (ST1457). blaVIM gene cassettes were carried by five distinct class I integrons, including two novel ones. CONCLUSIONS: Since the first report of VIM-producing P. aeruginosa in 2000, this microorganism still remains among the most prevalent multidrug resistant pathogens in Greece. The spread of VIM-producers belonging to the most common international clones (ST111 and ST235), the spread of integrons of divergent structures, and the emergence of novel integrons underscore their ongoing evolution.

57. "Streptomyces rochei ACTA1551, an indigenous Greek isolate studied as a potential biocontrol agent against Fusarium oxysporum f.sp. lycopersici."
G.S. Kanini, E.A. Katsifas, A.L. Savvides, and Karagouni AD.
BioMed Research International, doi: 10.1155/2013/387230, (2013).  View at publisher's site  Request copy
Abstract: Many studies have shown that several Greek ecosystems inhabit very interesting bacteria with biotechnological properties. Therefore Streptomyces isolates from diverse Greek habitats were selected for their antifungal activity against the common phytopathogenic fungus Fusarium oxysporum. The isolate encoded ACTA1551, member of Streptomyces genus, could strongly suppress the fungal growth when examined in antagonistic bioassays in vitro. The isolate was found phylogenetically relative to Streptomyces rochei after analyzing its 16S rDNA sequence. The influence of different environmental conditions, such as medium composition, temperature, and pH on the expression of the antifungal activity was thoroughly examined. Streptomyces rochei ACTA1551 was able to protect tomato seeds from F. oxysporum infection in vivo while it was shown to promote the growth of tomato plants when the pathogen was absent. In an initial effort towards the elucidation of the biochemical and physiological nature of ACTA1551 antifungal activity, extracts from solid streptomycete cultures under antagonistic or/and not antagonistic conditions were concentrated and fractionated. The metabolites involved in the antagonistic action of the isolate showed to be more than one and produced independently of the presence of the pathogen. The above observations could support the application of Streptomyces rochei ACTA1551 as biocontrol agent against F. oxysporum.

56. "Unraveling the lipolytic activity of thermophilic bacteria isolated from a volcanic environment."
P.M. Stathopoulou, A.L. Savvides, A.D. Karagouni, D.G. Hatzinikolaou.
BioMed Research International, doi: 10.1155/2013/703130, (2013).  View at publisher's site  Request copy
Abstract: In a bioprospecting effort towards novel thermostable lipases, we assessed the lipolytic profile of 101 bacterial strains isolated from the volcanic area of Santorini, Aegean Sea, Greece. Screening of lipase activity was performed both in agar plates and liquid cultures using olive oil as carbon source. Significant differences were observed between the two screening methods with no clear correlation between them. While the percentage of lipase producing strains identified in agar plates was only 17%, lipolytic activity in liquid culture supernatants was detected for 74% of them. Nine strains exhibiting elevated extracellular lipase activities were selected for lipase production and biochemical characterization. The majority of lipase producers revealed high phylogenetic similarity with Geobacillus species and related genera, whilst one of them was identified as Aneurinibacillus sp. Lipase biosynthesis strongly depended on the carbon source that supplemented the culture medium. Olive oil induced lipase production in all strains, but maximum enzyme yields for some of the strains were also obtained with Tween-80, mineral oil, and glycerol. Partially purified lipases revealed optimal activity at 70-80°C and pH 8-9. Extensive thermal stability studies revealed marked thermostability for the majority of the lipases as well as a two-step thermal deactivation pattern.

55. "Granulomatous infection of the hand and wrist due to Azospirillum spp."
J. Serelis, J. Papaparaskevas, A. Stathi, A.L. Sawides, A.D. Karagouni, A. Tsakris, A. Pangalis.
Diagnostic Microbiology and Infectious Disease, Vol. 76, pages 513-515, (2013).  View at publisher's site  Request copy
Abstract: We report a case of Azospirillum infection manifestating as granulomatous tenosynovitis of the right hand, in an immunocompetent middle-aged female. We highlight the unusual source of the infection, the diagnostic workup, as well as the treatment approach.

54. "Greek indigenous streptomycetes as biocontrol agents against the soil-borne fungal plant pathogen Rhizoctonia solani."
G.S. Kanini, E.A. Katsifas, A.L. Savvides, D.G. Hatzinikolaou and Karagouni AD.
Journal of Applied Microbiology, Vol. 114, pages 1468-1479, (2013).  View at publisher's site  Request copy
Abstract: AIMS: To examine the biocontrol potential of multiactive Greek indigenous Streptomyces isolates carrying antifungal activity against Rhizoctonia solani that causes damping-off symptoms on beans. METHODS AND RESULTS: A total of 605 Streptomyces isolates originated from 12 diverse Greek habitats were screened for antifungal activity against R. solani DSM843. Almost one-third of the isolates proved to be antagonistic against the fungus. From the above isolates, six were selected due to their higher antifungal activity, identified by analysing their 16S rRNA gene sequence and studied further. The obtained data showed the following: firstly, the isolates ACTA1383 and ACTA1557 exhibited the highest antagonistic activity, and therefore, they were selected for in vivo experiments using bean seeds as target; secondly, in solid and liquid culture experiments under optimum antagonistic conditions, the medium extracts from the isolates OL80, ACTA1523, ACTA1551 and ACTA1522 suppressed the growth of the fungal mycelium, while extracts from ACTA 1383 and ACTA1557 did not show any activity. CONCLUSIONS: These results corresponded important indications for the utility of two Greek indigenous Streptomyces isolates (ACTA1557 and ACTA1383) for the protection of the bean crops from R. solani damping-off symptoms, while four of them (isolates OL80, ACTA1523, ACTA1551 and ACTA1522) seem to be promising producers of antifungal metabolites. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study on the biocontrol of R. solani using multiactive Streptomyces isolates originated from ecophysiologically special Greek habitats. Our study provides basic information to further explore managing strategies to control this critical disease.

53. "Assessment of the biomass hydrolysis potential in bacterial isolates from a volcanic environment: biosynthesis of the corresponding activities."
P.M. Stathopoulou, A.P. Galanopoulou, G.E. Anasontzis, A.D. Karagouni AD, and D.G. Hatzinikolaou.
World Journal of Microbiology and Biotechnology, Vol. 28, pages 2889-2892, (2012).  View at publisher's site  Request copy
Abstract: The biomass degrading enzymatic potential of 101 thermophilic bacterial strains isolated from a volcanic environment (Santorini, Aegean Sea, Greece) was assessed. 80 % of the strains showed xylanolytic activity in Congo Red plates, while only eight could simultaneously hydrolyze cellulose. Fifteen isolates were selected on the basis of their increased enzyme production, the majority of which was identified as Geobacilli through 16S rDNA analysis. In addition, the enzymatic profile was evaluated in liquid cultures using various carbon sources, a procedure that revealed lack of correlation on xylanase levels between the two cultivation modes and the inability of solid CMC cultures to fully unravel the cellulose degrading potential of the isolates. Strain SP24, showing more than 99 % 16S DNA similarity with Geobacillus sp. was further studied for its unique ability to simultaneously exhibit cellulase, xylanase, β-glucosidase and β-xylosidase activities. The first two enzymes were produced mainly extracellularly, while the β-glycosidic activities were primarily detected in the cytosol. Maximum enzyme production by this strain was attained using a combination of wheat bran and xylan in the growth medium. Bioreactor cultures showed that aeration was necessary for both enhanced growth and enzyme production. Aeration had a strong positive effect on cellulase production while it negatively affected expression of β-glucosidase. Xylanase and β-xylosidase production was practically unaffected by aeration levels.

52. "Xanthan production by Xanthomonas campestris using whey permeate medium."
A.L. Savvides, E.A. Katsifas, D.G. Hatzinikolaou, and A.D. Karagouni.
World Journal of Microbiology and Biotechnology, Vol. 28, pages 2759-2764, (2012).  View at publisher's site  Request copy
Abstract: Xanthan gum is a polysaccharide that is widely used as stabilizer and thickener with many industrial applications in food industry. Our aim was to estimate the ability of Xanthomonas campestris ATCC 13951 for the production of xanthan gum by using whey as a growth medium, a by-product of dairy industry. X. campestris ATCC 13951 has been studied in batch cultures using a complex medium for the determination of the optimal concentration of glucose, galactose and lactose. In addition, whey was used under various treatment procedures (de-proteinated, partially hydrolyzed by β-lactamase and partially hydrolyzed and de-proteinated) as culture medium, to study the production of xanthan in a 2 l bioreactor with constant stirring and aeration. A production of 28 g/l was obtained when partially hydrolysed β-lactamase was used, which proved to be one of the highest xanthan gum production reported so far. At the same time, an effort has been made for the control and selection of the most appropriate procedure for the preservation of the strain and its use as inoculant in batch cultures, without loss of its viability and its capability of xanthan gum production. The pre-treatment of whey (whey permeate medium hydrolyzed, WPH) was very important for the production of xanthan by the strain X. campestris ATCC 13951 during batch culture conditions in a 2 l bioreactor. Preservation methods such as lyophilization, cryopreservation at various glycerol solution and temperatures have been examined. The results indicated that the best preservation method for the producing strain X. campestris ATCC 13951 was the lyophilization. Taking into account that whey permeate is a low cost by-product of the dairy industry, the production of xanthan achieved under the studied conditions was considered very promising for industrial application.

51. "Protein increase and lysine production by a Paecilomyces variotii strain grown on two-phase olive mill waste."
E.P. Giannoutsou, E.A. Katsifas, A. Geli and A.D. Karagouni.
World Journal of Microbiology and Biotechnology, Vol. 28, pages 849-856, (2012).  View at publisher's site  Request copy
Abstract: Two-phase olive-mill waste, the so-called "ecological", has been treated with a Paecilomyces variotii isolate in solid state fermentation experiments. The growth of the microorganism was estimated by measuring the production of carbon dioxide, using gas chromatography. A 46% increase of the protein content was achieved at the fermented product, after molasses addition at the initial mixture. The amino acid profile of the produced protein, as far as the essential amino acids are concerned, was significantly improved, resulting in a product that has the potential to be used as animal feed. Furthermore, it contains lysine, one of the essential amino acids that did not exist at the original product and is produced during fermentation. This is the first report on solid state fermentation of the two-phase olive mill waste (TPOMW) as a substrate, using a Paecilomyces variotii strain.

50. "Identification of OXA-23-producing Acinetobacter baumannii in Greece, 2010 to 2011."
A. Liakopoulos, V. Miriagou, E. Katsifas, A. Karagouni, G. Daikos, L. Tzouvelekis and E. Petinaki.
Euro Surveillance, Vol. 17, pii 20117, (2012).  View at publisher's site  Request copy
Abstract: We report on the sequence type and beta-lactamase content of 174 carbapenem-resistant Acinetobacter baumannii isolates recovered from clinical specimens during 2010 and 2011 in a tertiary care hospital in central Greece. Carbapenem resistance was associated mainly with carriage of the blaOXA-23 gene (in 72.4% of the isolates). To our knowledge, this is the first description of A. baumannii strains producing OXA-23 in Greece. During 2011, in our hospital they rapidly ‘replaced’ the previously predominant OXA-58-positive A. baumannii strains.

49. "SAFE Software and FED Database to Uncover protein-protein Interactions using Gene Fusion Analysis."
D. Tsagrasoulis, V. Danos, M. Kissa, P. Trimpalis, L. Koumandou, A.D. Karagouni, A. Tsakalidis and S. Kossida.
Evolutionary Bioinformatics Online, Vol. 8, pages 47-60, (2012).  View at publisher's site  Request copy
Abstract: Domain Fusion Analysis takes advantage of the fact that certain proteins in a given proteome A, are found to have statistically significant similarity with two separate proteins in another proteome B. In other words, the result of a fusion event between two separate proteins in proteome B is a specific full-length protein in proteome A. In such a case, it can be safely concluded that the protein pair has a common biological function or even interacts physically. In this paper, we present the Fusion Events Database (FED), a database for the maintenance and retrieval of fusion data both in prokaryotic and eukaryotic organisms and the Software for the Analysis of Fusion Events (SAFE), a computational platform implemented for the automated detection, filtering and visualization of fusion events (both available at: http://www.bioacademy.gr/bioinformatics/projects/ProteinFusion/index.htm). Finally, we analyze the proteomes of three microorganisms using these tools in order to demonstrate their functionality.

48. "Protein increase and lysine production by a Paecilomyces variotii strain grown on two-phase olive mill waste."
E.P. Gianoutsou, E.A. Katsifas, A. Geli A.D. Karagouni.
World Journal of Microbiology and Biotechnology, Vol. 28, pages 849-856, (2012).  View at publisher's site  Request copy
Abstract: Two-phase olive-mill waste, the so-called ‘‘ecological’’, has been treated with a Paecilomyces variotii isolate in solid state fermentation experiments. The growth of the microorganism was estimated by measuring the production of carbon dioxide, using gas chromatography. A 46% increase of the protein content was achieved at the fermented product, after molasses addition at the initial mixture. The amino acid profile of the produced protein, as far as the essential amino acids are concerned, was significantly improved, resulting in a product that has the potential to be used as animal feed. Furthermore, it contains lysine, one of the essential amino acids that did not exist at the original product and is produced during fermentation. This is the first report on solid state fermentation of the two-phase olive mill waste (TPOMW) as a substrate, using a Paecilomyces variotii strain.

47. "Variability of prokaryotic community structure in a drinking water reservoir (Marathonas, Greece)."
D.S. Lymperopoulou, K.A. Kormas and A.D. Karagouni.
Microbes and Environments, Vol. 27, pages 1-8, (2011).  View at publisher's site  Request copy
Abstract: The structure of the Bacteria and Archaea community in a large drinking water reservoir (Marathonas, Greece; MR) was investigated in October 2007 and September 2008, using 16S rRNA gene clone libraries. The bacterial communities were more diverse than archaeal communities (Shannon diversity index H' 0.81-3.28 and 1.36-1.77, respectively). The overall bacterial community composition was comparable to bacterioplankton community described in other freshwater habitats. Within the Bacteria, Betaproteobacteria dominated, while representatives of Alpha-, Gamma- and Deltaproteobacteria also occurred. Other important phyla were Actinobacteria and Bacteroidetes, while representatives of Acidobacteria, Cyanobacteria, Chloroflexi, Planctomycetes and Verrucomicrobia were also retrieved. Several phylotypes in Alpha- and Betaproteobacteria and Bacteroidetes were related to bacteria capable of cyanotoxin degradation and with aromatic compounds/iron oxidizers or polymer degraders. Euryarchaeota dominated (60.5%) the Archaea community mostly with phylotypes related to Methanobacteriales and Methanosarcinales. Among the Thaumarchaeota, the two most abundant phylotypes were affiliated (97% similarity) with the only cultivated mesophilic thaumarchaeote of marine origin, Nitrosopumilus maritimus. Temporal and spatial comparison of the prokaryotic community structure revealed that three of the most abundant prokaryotic phylotypes, belonging to Actinobacteria, were recovered from all sites both years, suggesting that these Actinobacteria could be important key players in MR ecosystem functioning.

46. "Homologous overexpression of xylanase in Fusarium oxysporum increases ethanol productivity during consolidated bioprocessing (CBP) of lignocellulosics."
G.E. Anasontzis, A. Zerva, P.M. Stathopoulou, K. Haralampidis, G. Diallinas, A.D. Karagouni and D.G. Hatzinikolaou.
Journal of Biotechnology, Vol. 152, pages 16-23, (2011).  View at publisher's site  Request copy
Abstract: In an effort to increase ethanol productivity during the consolidated bioprocessing (CBP) of lignocellulosics by Fusarium oxysporum, we attempted the constitutive homologous overexpression of one of the key process enzymes, namely an endo-xylanase. The endo-β-1,4-xylanase 2 gene, was incorporated into the F. oxysporum genome under the regulation of the gpdA promoter of Aspergillus nidulans. The transformation was effected through Agrobacterium tumefaciens and resulted in 12 transformants, two of which were selected for their high extracellular xylanase activities under normally repressing conditions (glucose as sole carbon source). During natural induction conditions (growth on xylan) though, the extracellular enzyme levels of the transformants were only marginally higher (5–10%) compared to the wild type despite the significantly stronger xylanase 2 mRNA signals. SDS-PAGE verified enzyme assay results that there was no intracellular xylanase 2 accumulation in the transformants, suggesting the potential regulation in a post transcriptional or translation level. The fermentative performance of the transformants was evaluated and compared to that of the wild type in simple CBP systems using either corn cob or wheat bran as sole carbon sources. Both transformants produced approximately 60% more ethanol compared to the wild type on corn cob, while for wheat bran this picture was repeated for only one of them. This result is attributed to the high extracellular xylanase activities in the transformants’ fermentation broths that were maintained 2–2.5 fold higher compared to the wild type.

45. "Selective isolation of indigenous Pseudomonas syringae strains with ice nucleation activity properties from a ski resort."
A.L. Savvides, C.P. Andriopoulos, K.A. Kormas, D.G. Hatzinikolaou, E.A. Katsifas and A.D. Karagouni.
Journal of Biological Research, vol. 15, pages 67-73, (2011).  View at publisher's site  Request copy
Abstract: Four sampling sites were selected in the area of Velouhi mountain, Greece in order to screen for Pseudomonas syringae isolates with high ice nucleation activity from a ski resort environment. Bacterial isolates (n=147) were obtained from soil and phyllosphere samples. Seven isolates exhibited morphological, biochemical and physiological profile similar to P. syringae. Phylogenetic relationships of the seven isolates were determined by 16S rRNA gene sequencing. Two isolates were phylogenetically affiliated to P. syringae, three to P. viridiflava, one to P. avellanae, and one Pseudomonas strain could not be assigned to a known species. The seven isolates were examined for their ice-nucleation activity properties. Three out of the seven studied isolates exhibited ice nucleation activity from –4.67 to –4.35 ice nuclei per cell, values similar to those obtained from a known ice-nucleation protein producer P. syringae strain and therefore could be used for the production of artificial snow in ski resort areas with short snow periods.

44. "Diversity of cyanobacterial phylotypes in a Mediterranean drinking water reservoir (Marathonas, Greece)."
D.S. Lymperopoulou, K.A. Kormas, M. Moustaka-Gouni and A. D. Karagouni.
Environmental Monitoring and Assessment, vol. 173, pages 155-165, (2011).  View at publisher's site  Request copy
Abstract: The structure of the cyanobacterial community in a large drinking water reservoir (Marathonas, Greece) was investigated in October 2007 and September 2008. Cyanobacteria-specific primers were used for the PCR amplification of cyanobacterial 16S rDNAs from three water column sites and the water collection tank. In total, 199 clones were sequenced representing 52 unique cyanobacterial, including chloroplast-related, and 11 non-cyanobacterial phylotypes. All cyanobacterial phylotypes belonged to the order Chroococcales. Cluster analysis showed that the cyanobacterial communities in 2007 in the three water column sites showed high similarity between the stations and low diversity (H=1.17-1.44), due to the occurring common phylotypes, while all sites in 2008 had very low similarities between them and higher diversity (H=1.56-2.40). Some of the most abundant phylotypes were closely related (>98%) to members of the genus Gloeocapsa and a potentially toxin-producing strain of Microcystis aeruginosa. The non-cyanobacterial phylotypes were either unaffiliated or belonged to the Verrucomicrobia, and were related with sequences originating from lake water habitats.