Publications & Projects

Affiliated scientific publications

  2023
  1. Katsiari, M., Mavroidi, A., Kesesidis, N., Palla, E., Zourla, K., Ntorlis, K., Konstantinidis, K., et al. (2023). ‘Emergence of Clonally-Related South Asian Clade I Clinical Isolates of Candida auris in a Greek COVID-19 Intensive Care Unit’, Journal of Fungi, 9/2. MDPI. DOI: 10.3390/jof9020243
  2. Mpekoulis, G., Kalliampakou, K. I., Milona, R. S., Lagou, D., Ioannidis, A., Jahaj, E., Chasapis, C. T., et al. (2023). ‘Significance of Catecholamine Biosynthetic/Metabolic Pathway in SARS-CoV-2 Infection and COVID-19 Severity’, Cells, 12/1. MDPI. DOI: 10.3390/cells12010012
  3. Pliakou, E., Lampropoulou, D. I., Dovrolis, N., Chrysikos, D., Filippou, D., Papadimitriou, C., Vezakis, A., et al. (2023). ‘Circulating miRNA Expression Profiles and Machine Learning Models in Association with Response to Irinotecan-Based Treatment in Metastatic Colorectal Cancer’, International Journal of Molecular Sciences, 24/1. MDPI. DOI: 10.3390/ijms24010046
  4. Rezasoltani, S., Aghdaei, H. A., Jasemi, S., Gazouli, M., Dovrolis, N., Sadeghi, A., Schlüter, H., et al. (2023). ‘Oral Microbiota as Novel Biomarkers for Colorectal Cancer Screening’, Cancers, 15/1. MDPI. DOI: 10.3390/cancers15010192
   2022
  1. Bampali, M., Konstantinidis, K., Kellis, E. E., Pouni, T., Mitroulis, I., Kottaridi, C., Mathioudakis, A. G., et al. (2022). ‘West Nile Disease Symptoms and Comorbidities: A Systematic Review and Analysis of Cases’, Tropical Medicine and Infectious Disease, 7/9. MDPI. DOI: 10.3390/tropicalmed7090236
  2. Beka, A. A., Papadopoulos, V., Mylopoulou, T., Panopoulou, M., Karakasiliotis, I., Mavromara, P., Mimidis, K., et al. (2022). ‘Association between vitamin D receptor gene polymorphisms and fibrosis susceptibility in Greek patients with HCV infection’, GERMS, 12/3: 384–93. European Academy of HIV/AIDS and Infectious Diseases. DOI: 10.18683/germs.2022.1342
  3. Dovrolis, N., Filidou, E., Tarapatzi, G., Kokkotis, G., Spathakis, M., Kandilogiannakis, L., Drygiannakis, I., et al. (2022). ‘Co-expression of fibrotic genes in inflammatory bowel disease; A localized event?’, Frontiers in Immunology, 13. Frontiers Media S.A. DOI: 10.3389/fimmu.2022.1058237
  4. Evangelou, K., Veroutis, D., Paschalaki, K., Foukas, P. G., Lagopati, N., Dimitriou, M., Papaspyropoulos, A., et al. (2022). ‘Pulmonary infection by SARS-CoV-2 induces senescence accompanied by an inflammatory phenotype in severe COVID-19: possible implications for viral mutagenesis’, European Respiratory Journal, 60/2. European Respiratory Society. DOI: 10.1183/13993003.02951-2021
  5. Konstantinidis, K., Dovrolis, N., Kouvela, A., Kassela, K., Rosa Freitas, M. G., Nearchou, A., De Courcy Williams, M., et al. (2022). ‘Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem’, Virus Evolution, 8/1. Oxford University Press. DOI: 10.1093/ve/veac036
  6. Konstantinidis, K., Bampali, M., de Courcy Williams, M., Dovrolis, N., Gatzidou, E., Papazilakis, P., Nearchou, A., et al. (2022). ‘Dissecting the Species-Specific Virome in Culicoides of Thrace’, Frontiers in Microbiology, 13. Frontiers Media S.A. DOI: 10.3389/fmicb.2022.802577
  7. Ridgway, H., Moore, G. J., Mavromoustakos, T., Tsiodras, S., Ligielli, I., Kelaidonis, K., Chasapis, C. T., et al. (2022). ‘Discovery of a new generation of angiotensin receptor blocking drugs: Receptor mechanisms and in silico binding to enzymes relevant to SARS-CoV-2’, Computational and Structural Biotechnology Journal, 20: 2091–111. Elsevier B.V. DOI: 10.1016/j.csbj.2022.04.010
  8. Stefanou, I. K., Dovrolis, N., Gazouli, M., Theodorou, D., Zografos, G. K., & Toutouzas, K. G. (2022). ‘MiRNAs expression pattern and machine learning models elucidate risk for gastric GIST’, Cancer Biomarkers, 33/2: 237–47. IOS Press BV. DOI: 10.3233/CBM-210173
  9. Talli, I., Dovrolis, N., Oulas, A., Stavrakaki, S., Makedou, K., Spyrou, G. M., & Maroulakou, I. (2022). ‘Novel clinical, molecular and bioinformatics insights into the genetic background of autism’, Human Genomics, 16/1. BioMed Central Ltd. DOI: 10.1186/s40246-022-00415-x
  10. Vrazas, V., Moustafa, S., Makridakis, M., Karakasiliotis, I., Vlahou, A., Mavromara, P., & Katsani, K. R. (2022). ‘A Proteomic Approach to Study the Biological Role of Hepatitis C Virus Protein Core+1/ARFP’, Viruses, 14/8. MDPI. DOI: 10.3390/v14081694
  2021
  1. Mpekoulis, G., Frakolaki, E., Taka, S., Ioannidis, A., Vassiliou, A. G., Kalliampakou, K. I., Patas, K., et al. (2021). ‘Alteration of L-Dopa decarboxylase expression in SARS-CoV-2 infection and its association with the interferon-inducible ACE2 isoform’, PLoS ONE, 16/6 June. Public Library of Science. DOI: 10.1371/journal.pone.0253458
  2. Ntolios, P., Tzilas, V., Bouros, E., Avdoula, E., Karakasiliotis, I., Bouros, D., & Steiropoulos, P. (2021). ‘The role of microbiome and virome in idiopathic pulmonary fibrosis’, Biomedicines, 9/4. MDPI AG. DOI: 10.3390/biomedicines9040442
  3. Andreou, N.-P., Legaki, E., Dovrolis, N., Boyanov, N., Georgiou, K., Gkouskou, K., & Gazouli, M. (2021). ‘B-cell activating factor (BAFF) expression is associated with Crohn’s disease and can serve as a potential prognostic indicator of disease response to Infliximab treatment’, Digestive and Liver Disease, 53/5: 574–80. Elsevier B.V. DOI: 10.1016/j.dld.2020.11.030
  4. Dovrolis, N., Kassela, K., Konstantinidis, K., Kouvela, A., Veletza, S., & Karakasiliotis, I. (2021). ‘ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach’, PLoS Computational Biology, 17/8. Public Library of Science. DOI: 10.1371/journal.pcbi.1009304
  5. Spanakis, N., Kassela, K., Dovrolis, N., Bampali, M., Gatzidou, E., Kafasi, A., Froukala, E., et al. (2021). ‘A main event and multiple introductions of SARS-CoV-2 initiated the COVID-19 epidemic in Greece’, Journal of Medical Virology, 93/5: 2899–907. John Wiley and Sons Inc. DOI: 10.1002/jmv.26778
  6. Konstantinidis, K., Karakasiliotis, I., Anagnostopoulos, K., & Boulougouris, G. C. (2021). ‘On the estimation of the molecular inaccessible volume and the molecular accessible surface of a ligand in protein-ligand systems’, Molecular Systems Design and Engineering, 6/11: 946–63. Royal Society of Chemistry. DOI: 10.1039/d1me00053e
  7. Karakasiliotis, I., Lagopati, N., Evangelou, K., & Gorgoulis, V. G. (2021). ‘Cellular senescence as a source of SARS-CoV-2 quasispecies’, FEBS Journal. John Wiley and Sons Inc. DOI: 10.1111/febs.16230
  8. Kofidou, M., Williams, M. C., Nearchou, A., Veletza, S., Gemitzi, A., & Karakasiliotis, I. (2021). ‘Applying remotely sensed environmental information to model mosquito populations’, Sustainability (Switzerland), 13/14. MDPI AG. DOI: 10.3390/su13147655
  2019
  1. Kassela, K., Karakasiliotis, I., Kokkiou, E., Souvalidou, F., Mimidis, P., Veletza, S., Panopoulou, M., et al. (2019). ‘Intergenotypic 2k/1b hepatitis C virus recombinants in the east macedonia and thrace region of Greece’, Annals of Gastroenterology, 32/1: 88–92. Hellenic Society of Gastroenterology. DOI: 10.20524/aog.2018.0322
  2018
  1. Christodoulou-Vafeiadou, E., Ioakeimidis, F., Andreadou, M., Giagkas, G., Stamatakis, G., Reczko, M., Samiotaki, M., et al. (2018). ‘Divergent innate and epithelial functions of the RNA-binding protein HuR in intestinal inflammation’, Frontiers in Immunology, 9/NOV. Frontiers Media S.A. DOI: 10.3389/fimmu.2018.02732
  2. Moustafa, S., Karakasiliotis, I., & Mavromara, P. (2018). ‘Hepatitis C virus core+1/ARF protein modulates the cyclin D1/pRb pathway and promotes carcinogenesis’, Journal of Virology, 92/9. American Society for Microbiology. DOI: 10.1128/JVI.02036-17
  3. Mylopoulou, T., Papadopoulos, V., Kassela, K., Karakasiliotis, I., Souvalidou, F., Mimidis, P., Veletza, S., et al. (2018). ‘Relationship between antibodies to hepatitis C virus core+1 protein and treatment outcome’, Annals of Gastroenterology, 31/5: 593–7. Hellenic Society of Gastroenterology. DOI: 10.20524/aog.2018.0290
  2017
  1. Kassela, K., Karakasiliotis, I., Charpantidis, S., Koskinas, J., Mylopoulou, T., Mimidis, K., Sarrazin, C., et al. (2017). ‘High prevalence of antibodies to core+1/ARF protein in HCV-infected patients with advanced cirrhosis’, Journal of General Virology, 98/7: 1713–9. Microbiology Society. DOI: 10.1099/jgv.0.000851

Projects

The Laboratory of Biology focuses on genomic and metagenomic studies, which mainly include analyses of viruses and other significant pathogens, originating from patients, cultured cells and various insects. These studies are greatly supported by the incorporated BSL-3 (Bio-Safety Level 3) and Next Generation Sequencing (NGS, Ion Torrent S5) facilities, which are essential for handling potentially lethal infectious agents or toxins as well as identifying novel viruses and pathogens in clinical or environmental samples. The Laboratory of Biology is also open to the public providing a number of services, such as molecular diagnostics, molecular genetics of multifactorial diseases and PCR/Real time PCR.

1) INSEQT

The modern facilities and equipment of the Laboratory of Biology laid the foundation for studying mosquitoes and other hematophagous insects via metagenomics technology, in an attempt to analyse the composition and seasonal population changes of insects within the region of north-eastern Greece, which constitute some of the most significant factors in vector-borne diseases. The above concept was part of the research project titled INSEQT, which was co-financed by the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation under the call RESEARCH – CREATE – INNOVATE (ESPA 2014-2020, project code: T1EDK-5000) and involved collaboration between the Democritus University of Thrace, the Oswaldo Cruz-Fiocruz Institute of Brazil as well as Geotechnoygeionomiki G.P. and Campus S.A. dairy farm. The innovative methodologies and interesting findings of this research project are summarised below, while more detailed information can be retrieved via the respective scientific article hyperlinks.

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Observed and predicted mosquito population from the MLP ANN, as an ensemble mean of the 100-fold cross validation exercise.

Relative importance for each input variable in the MLP NN.

Number of reported cases with laboratory diagnosed WNV disease (WNF with WNND and without WNND) with mean LST at municipalities within and close to the study area. Data are retrieved from the National Organization of Public Health of Greece (EODY) and are reported per suspected municipality of exposure.

Applying Remotely Sensed Environmental Information to Model Mosquito Populations

Maria Kofidou1, Michael de Courcy Williams2, Andreas Nearchou2, Stavroula Veletza2, Alexandra Gemitzi1, Ioannis Karakasiliotis2 1 Department of Environmental Engineering, Democritus University of Thrace, PC 67100 Xanthi, Greece 2 Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Dragana, PC 68100 Alexandroupolis, Greece

Vector borne diseases have been related to various environmental parameters and environmental changes like climate change, which impact their propagation in time and space. Remote sensing data have been used widely for monitoring environmental conditions and changes. We hypothesized that changes in various environmental parameters may be reflected in changes in mosquito population size, thus impacting the temporal and spatial patterns of vector diseases. The aim of this study was to analyze the effect of environmental variables on mosquito populations using the remotely sensed Normalized Difference Vegetation Index (NDVI) and Land Surface Temperature (LST) obtained from Landsat 8, along with other factors, such as altitude and water covered areas surrounding the examined locations. Therefore, a Multilayer Perceptron (MLP) Artificial Neural Network (ANN) model was developed and tested for its ability to predict mosquito populations. The model was applied in north-eastern Greece using mosquito population data from 17 locations where mosquito traps were placed from June to October 2019. All performance metrics indicated a high predictive ability of the model. LST was proved to be the factor with the highest relative importance in the prediction of mosquito populations, whereas the developed model can predict mosquito populations 13 days ahead to allow a substantial window for appropriate control measures.

From qualitative to quantitative insect metabarcoding: an in tandem multilocus mosquito identification methodology

Nikolas Dovrolis1, Katerina Kassela1, Adamantia Kouvela1, Konstantinos Konstantinidis1, Andreas Nearchou2, Michael De Courcy Williams1, Stavroula Veletza1, Ioannis Karakasiliotis1 1 Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Dragana, PC 68100 Alexandroupolis, Greece 2 Geotechnoygeionomiki O.E, Konstantinou Mpeni 49, PC 67100 Xanthi, Greece

High throughput trap-based insect monitoring is essential for the study of insect populations and the identification of invasive species. Insect DNA metabarcoding technology has emerged as a highly promising methodology for unbiased and largescale surveillance. Although significant attempts have been made to apply DNA metabarcoding within mosquito or other insect surveillance, the combined application of qualitative and quantitative metabarcoding has remained a challenge. In the present study, we developed a bioinformatic method of in-tandem identification and quantification of environmental mosquito samples, implementing custom computational tools mainly based on sequence alignment algorithms and software. The proposed approach includes initial detection of the examined mosquito species using cytochrome c oxidase subunit I (COI) combined with a secondary multilocus identification and quantification involving three loci of 28S ribosomal DNA. Using the methodology developed here, we were able to identify individual species in sample pools of mosquitoes with 95.94% accuracy and resolve with high accuracy (p = 1, χ2 = 2.55) mosquito population composition species by species, thus providing a technology capable of revolutionizing mosquito surveillance through metabarcoding. The results obtained here show that the methodology has the potential to be applied widely, including to various invertebrate and non-invertebrate populations made up of small-sized individuals.

CLUSTAL OMEGA multiple alignment heatmap of 28S and 18S rRNAs coloured according to similarity percentage (1-100 %) per 60 bp of multiple alignment length. The first species in each group was used as reference. Indicators (1,2 and 3) correspond to the three 28S regions used in the study (n=24 species).

Stack bars representing the diversity of each pool as predicted [P] by the metabarcoding pipeline compared to the actual [R] composition of the pool as determined through morphological and single-specimen COI barcoding. Numbers 1-27 represent the trap numbers while colour coding depicts species variation only between P and R of the same trap.

List of detected viruses within Culicoides samples. Black filled squares indicate presence of the corresponding viral genes or segments

Virus-carrier/host Chord Diagram network in the ecosystem of Eastern Macedonia and Thrace region. Variants of assembled viruses detected in multiple mosquito species, which presented high aa sequence similarity (>95 per cent) to each other, were plotted as links, highlighting the interconnectedness between mosquito species and viruses in the habitat.

Sankey diagram of the global virus-carrier/host network involving viruses with >20 per cent aa similarity to the viruses identified in the study. On the left side are the virus families and on the right side are the respective carrier/host mosquito genera. Grey chords represent links reported in the literature. Orange chords represent links identified in this study.

Defining virus-carrier networks that shape the composition of mosquito core virome of a local ecosystem Dissecting the species-specific virome in Culicoides of Thrace

Konstantinos Konstantinidis1, Nikolas Dovrolis1, Adamantia Kouvela1, Katerina Kassela1, Maria Goreti Rosa Freitas2, Maria Bampali1, Elisavet Gatzidou1, Andreas Nearchou3, Michael de Courcy Williams1, Stavroula Veletza1 and Ioannis Karakasiliotis1* 1 Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Dragana, PC 68100 Alexandroupolis, Greece 2 Laboratório de Mosquitoes Transmissores de Hematozoários, Instituto Oswaldo Cruz-Fiocruz, Pavilhão Carlos Chagas, Avenida Brasil, 4365, Manguinhos-Rio de Janeiro, Brazil 3 Geotechnoygeionomiki O.E, Konstantinou Mpeni 49, PC 67100 Xanthi, Greece

Viruses transmitted via blood-feeding insects (arboviruses), such as West Nile virus, Zika virus, bluetongue virus and lumpy skin disease virus, pose a significant threat to public health and animal husbandry worldwide, potentially causing epidemics with considerable and multifaceted – if not detrimental - repercussions for the infected host organisms. Undoubtedly, tropical, rural and agricultural areas are plagued by arboviruses, while climate change, urbanisation and globalisation, contribute to more efficient reproduction of blood-feeding insects and the pathogens they may carry. A considerable increase of arthropod-borne diseases has been reported over the past few years and pest-control of those blood-feeding insects is a top priority to prevent future outbreaks of viruses. Mosquitoes and biting midges constitute major vectors of these emerging virus diseases. In spite of the diversity of viruses they may carry, most of them infect exclusively insect species and are considered insect-specific. Significant efforts have been made to elucidate the core virome of these insects in their natural habitats, although the vast majority of metagenomics approaches has focused on specific or only a few species. However, in most ecosystems, multiple species may participate in virus emergence and circulation, while there is lack of understanding on the viruses carrier/host network for both vector-borne and insect-specific viruses.

In this study, the core virome of 24 mosquito species and 10 Culicoides (Latreille) (Diptera: Ceratopogonidae) midges species was defined, which were all field-collected from the diverse ecosystem of the Eastern Macedonia and Thrace region on north-eastern Greece, an important path of various arboviruses. Utilising the Ion Torrent Next Generation Sequencing (NGS) platform for total RNA sequencing and custom bioinformatics pipelines resulted in identifying and assembling 48 viruses, including 29 novel viruses according to the respective families’ species demarcation criteria. More specifically, comparison of the viromes of all blood-feeding insect species revealed a complex interconnected virus-carrier network in the ecosystem and novel relationships between mosquito genera and virus families, as most of the mosquito species had never been analysed in the past. Sample analyses of mosquitoes of variable composition as per species not only showed a stable core virome for each species but also a relationship between mosquito population and virome composition. The proposed study emphasized on the importance of a holistic approach regarding insect viromes in rich and diverse ecosystems. The results further supported the idea of a stable core virome, characteristic of each blood-feeing insect species. The remarkable stability of the core virome seemed to determine the composition of the total core virome in a local ecosystem as it is directly related to the population of the respective species.

ZWA: Viral genome assembly and characterization hindrances from virus-host chimeric reads; a refining approach

Nikolas Dovrolis, Katerina Kassela, Konstantinos Konstantinidis, Adamantia Kouvela, Stavroula Veletza, Ioannis Karakasiliotis Laboratory of Biology, Department of Medicine, Democritus University of Thrace, Dragana, PC 68100 Alexandroupolis, Greece

Viral metagenomics, also known as virome studies, have yielded an unprecedented number of novel sequences, essential in recognizing and characterizing the etiological agent and the origin of emerging infectious diseases. Several tools and bioinformatic pipelines have been developed to date for the identification and assembly of viral genomes. Assembly pipelines however often result in viral genomes contaminated with host genetic material, some of which are currently deposited into public databases. In the current report, we present a group of deposited viral sequences that encompass ribosomal RNA (rRNA) contamination. We highlight the detrimental role of chimeric next generation sequencing (NGS) reads, between host rRNA sequences and viral sequences, in virus genome assembly and the hindrances these reads may pose to current methodologies. We have further developed a refining pipeline, the Zero Waste Algorithm (ZWA) which performs context-depended trimming of chimeric reads, precisely removing their rRNA moiety, for the construction of larger and cleaner virus contigs. ZWA pipeline may significantly enhance virus genome assembly from low abundance samples and virus metagenomics approaches in which a small number of reads determine genome quality and integrity.

ZWA pipeline.

Example of visualization, in Integrative Genomics Viewer, of NGS reads aligned on rRNA-viral chimeric contigs generated via de novo assembly. Dark grey reads indicate chimeric that serve as bridges in the assembly between rRNA and viral sequences. Coloured lines represent gaps and mutations against reference sequence. Reads have been reduced for illustration purposes.

Venn diagrams depicting (A) the initial sorting of rRNA reads and non-rRNA reads with numbers referring to rRNA reads and virus reads in the two bins. The intersection are rRNA-virus chimeric reads. (B) The rRNA reads recognized as chimeric (less than 90% rRNA) and the resulted cured virus reads after ZWA. The intersection are the remaining rRNA-virus chimeric reads. (C) The rRNA reads recognized in the second round as chimeric ( less than 90% rRNA) and the resulted cured virus reads after ZWA. The intersection are the discarded remaining rRNA-virus chimeric reads.

Partnerships