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The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94 % and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.
Serafeim C. Chaintoutis; Taxiarchis Chassalevris; George Tsiolas; Sofia Balaska; Ioannis Vlatakis; Evangelia Mouchtaropoulou; Victoria I. Siarkou; Areti Tychala; Dimitris Koutsioulis; Lemonia Skoura; Anagnostis Argiriou; Chrysostomos I. Dovas. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. Journal of Virological Methods 2021, 296, 114242 -114242.
AMA StyleSerafeim C. Chaintoutis, Taxiarchis Chassalevris, George Tsiolas, Sofia Balaska, Ioannis Vlatakis, Evangelia Mouchtaropoulou, Victoria I. Siarkou, Areti Tychala, Dimitris Koutsioulis, Lemonia Skoura, Anagnostis Argiriou, Chrysostomos I. Dovas. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. Journal of Virological Methods. 2021; 296 ():114242-114242.
Chicago/Turabian StyleSerafeim C. Chaintoutis; Taxiarchis Chassalevris; George Tsiolas; Sofia Balaska; Ioannis Vlatakis; Evangelia Mouchtaropoulou; Victoria I. Siarkou; Areti Tychala; Dimitris Koutsioulis; Lemonia Skoura; Anagnostis Argiriou; Chrysostomos I. Dovas. 2021. "A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions." Journal of Virological Methods 296, no. : 114242-114242.
Olives are among the main components of the Mediterranean diet, rich in micronutrients and powerful antioxidants; their unique organoleptic properties and high nutritional value have increased table olive consumption worldwide. The purpose of this work was to study the microbiological and biochemical changes in Greek-style ‘Kalamata’ table olives, throughout different time-points of the shelf life of the product, packaged under modified atmosphere. Results revealed the prevalence of lactic acid bacteria (Lactobacillus spp.) from T0 and after the end of the product's shelf life, with L. parafarraginis being the dominant species, ranging from 37.8% to 49.8%. Concerning the eukaryotic populations, antagonistic interactions were observed among the dominant genera i.e. Pichia, Cladosporium and Saccharomyces. While Candida pseudolambica was the most abundant species up to T6, it was gradually displaced by Brettanomyces custersianus at T12 and T18. The significant decrease of total phenol content and a-tocopherol at T12, reflected the increment of Lactobacillus and yeast populations. The dominance of Lactobacillus spp. And B. custersianus at T18 was also depicted on the significant increase of hydroxytyrosol. The content of some fatty acids was shown to be affected by the yeast populations while the concentration of maslinic and oleanolic acid remained intact throughout storage. The combined approach of amplicon metabarcoding and biochemical analyses of naturally fermented olives packaged under modified atmosphere, enabled us to better understand the microbial competitions and interactions and the biochemical changes that accompany these transitions, hence, defining the quality of the end product offered to the consumer.
Sofia Michailidou; Fotini Trikka; Konstantinos Pasentsis; George Economou Petrovits; Mary Kyritsi; Anagnostis Argiriou. Insights into the evolution of Greek style table olives microbiome stored under modified atmosphere: Biochemical implications on the product quality. Food Control 2021, 130, 108286 .
AMA StyleSofia Michailidou, Fotini Trikka, Konstantinos Pasentsis, George Economou Petrovits, Mary Kyritsi, Anagnostis Argiriou. Insights into the evolution of Greek style table olives microbiome stored under modified atmosphere: Biochemical implications on the product quality. Food Control. 2021; 130 ():108286.
Chicago/Turabian StyleSofia Michailidou; Fotini Trikka; Konstantinos Pasentsis; George Economou Petrovits; Mary Kyritsi; Anagnostis Argiriou. 2021. "Insights into the evolution of Greek style table olives microbiome stored under modified atmosphere: Biochemical implications on the product quality." Food Control 130, no. : 108286.
The emergence of SARS-CoV-2 mutations resulting in the S protein amino-acid substitutions N501Y and E484K, which have been associated with enhanced transmissibility and immune escape, respectively, necessitates immediate actions, for which their rapid identification is crucial. For the simultaneous typing of both of these mutations of concern (MOCs), a one-step real-time RT-PCR assay employing four locked nucleic acid (LNA) modified TaqMan probes was developed. The assay is highly sensitive with a LOD of 117 copies/reaction, amplification efficiencies >94% and a linear range of over 5 log10 copies/reaction. Validation of the assay using known SARS-CoV-2-positive and negative samples from human and animals revealed its ability to correctly identify wild type strains, and strains possessing either one or both targeted amino-acid substitutions, thus comprising a useful pre-screening tool for rapid MOC identification. The basic principles of the methodology for the development of the assay are explained in order to facilitate the rapid design of similar assays able to detect emerging MOCs.
Serafeim C. Chaintoutis; Taxiarchis Chassalevris; George Tsiolas; Sofia Balaska; Ioannis Vlatakis; Evangelia Mouchtaropoulou; Victoria I. Siarkou; Areti Tychala; Dimitris Koutsioulis; Lemonia Skoura; Anagnostis Argiriou; Chrysostomos I. Dovas. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. 2021, 1 .
AMA StyleSerafeim C. Chaintoutis, Taxiarchis Chassalevris, George Tsiolas, Sofia Balaska, Ioannis Vlatakis, Evangelia Mouchtaropoulou, Victoria I. Siarkou, Areti Tychala, Dimitris Koutsioulis, Lemonia Skoura, Anagnostis Argiriou, Chrysostomos I. Dovas. A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions. . 2021; ():1.
Chicago/Turabian StyleSerafeim C. Chaintoutis; Taxiarchis Chassalevris; George Tsiolas; Sofia Balaska; Ioannis Vlatakis; Evangelia Mouchtaropoulou; Victoria I. Siarkou; Areti Tychala; Dimitris Koutsioulis; Lemonia Skoura; Anagnostis Argiriou; Chrysostomos I. Dovas. 2021. "A one-step real-time RT-PCR assay for simultaneous typing of SARS-CoV-2 mutations associated with the E484K and N501Y spike protein amino-acid substitutions." , no. : 1.
V3-V4 16S rRNA sequences from mice gut microbiome.
Konstantinos Axarlis; Maria G. Daskalaki; Sofia Michailidou; Nikolais Androulaki; Antiopi Tsoureki; Evangelia Mouchtaropoulou; Ourania Kolliniati; Ioanna Lapi; Eirini Dermitzaki; Maria Venihaki; Katerina Kousoulaki; Anagnostis Argiriou; Zouhir El Marsni; Christos Tsatsanis. Dataset from: Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity. 2021, 1 .
AMA StyleKonstantinos Axarlis, Maria G. Daskalaki, Sofia Michailidou, Nikolais Androulaki, Antiopi Tsoureki, Evangelia Mouchtaropoulou, Ourania Kolliniati, Ioanna Lapi, Eirini Dermitzaki, Maria Venihaki, Katerina Kousoulaki, Anagnostis Argiriou, Zouhir El Marsni, Christos Tsatsanis. Dataset from: Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity. . 2021; ():1.
Chicago/Turabian StyleKonstantinos Axarlis; Maria G. Daskalaki; Sofia Michailidou; Nikolais Androulaki; Antiopi Tsoureki; Evangelia Mouchtaropoulou; Ourania Kolliniati; Ioanna Lapi; Eirini Dermitzaki; Maria Venihaki; Katerina Kousoulaki; Anagnostis Argiriou; Zouhir El Marsni; Christos Tsatsanis. 2021. "Dataset from: Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity." , no. : 1.
V3-V4 16S rRNA sequences from mice gut microbiome.
Konstantinos Axarlis; Maria G. Daskalaki; Sofia Michailidou; Nikolais Androulaki; Antiopi Tsoureki; Evangelia Mouchtaropoulou; Ourania Kolliniati; Ioanna Lapi; Eirini Dermitzaki; Maria Venihaki; Katerina Kousoulaki; Anagnostis Argiriou; Zouhir El Marsni; Christos Tsatsanis. Dataset from: Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity. 2021, 1 .
AMA StyleKonstantinos Axarlis, Maria G. Daskalaki, Sofia Michailidou, Nikolais Androulaki, Antiopi Tsoureki, Evangelia Mouchtaropoulou, Ourania Kolliniati, Ioanna Lapi, Eirini Dermitzaki, Maria Venihaki, Katerina Kousoulaki, Anagnostis Argiriou, Zouhir El Marsni, Christos Tsatsanis. Dataset from: Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity. . 2021; ():1.
Chicago/Turabian StyleKonstantinos Axarlis; Maria G. Daskalaki; Sofia Michailidou; Nikolais Androulaki; Antiopi Tsoureki; Evangelia Mouchtaropoulou; Ourania Kolliniati; Ioanna Lapi; Eirini Dermitzaki; Maria Venihaki; Katerina Kousoulaki; Anagnostis Argiriou; Zouhir El Marsni; Christos Tsatsanis. 2021. "Dataset from: Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity." , no. : 1.
Metabolic syndrome-related diseases affect millions of people worldwide. It is well established that changes in nutritional habits and lifestyle can improve or prevent metabolic-related pathologies such as type-2 diabetes and obesity. Previous reports have shown that nutritional supplements have the capacity to limit glucose intolerance and suppress diabetes development. In this study, we investigated the effect of dietary supplementation with fish-derived extracts on obesity and type 2 diabetes and their impact on gut microbial composition. We showed that nutritional supplements containing Fish Complex (FC), Fish Complex combined with Cod Powder (FC + CP), or Cod Powder combined with Collagen (CP + C) improved glucose intolerance, independent of abdominal fat accumulation, in a mouse model of diet-induced obesity and type 2 diabetes. In addition, collagen-containing supplements distinctly modulate the gut microbiome in high-fat induced obesity in mice. Our results suggest that fish-derived supplements suppress diet-induced type 2 diabetes, which may be partly mediated through changes in the gut microbiome. Thus, fish-derived supplements and particularly the ones containing fish collagen have potential beneficial properties as dietary supplements in managing type 2 diabetes and metabolic syndrome via modulation of the gut microbiome.
Konstantinos Axarlis; Maria Daskalaki; Sofia Michailidou; Nikolais Androulaki; Antiopi Tsoureki; Evangelia Mouchtaropoulou; Ourania Kolliniati; Ioanna Lapi; Eirini Dermitzaki; Maria Venihaki; Katerina Kousoulaki; Anagnostis Argiriou; Zouhir Marsni; Christos Tsatsanis. Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity. Marine Drugs 2021, 19, 268 .
AMA StyleKonstantinos Axarlis, Maria Daskalaki, Sofia Michailidou, Nikolais Androulaki, Antiopi Tsoureki, Evangelia Mouchtaropoulou, Ourania Kolliniati, Ioanna Lapi, Eirini Dermitzaki, Maria Venihaki, Katerina Kousoulaki, Anagnostis Argiriou, Zouhir Marsni, Christos Tsatsanis. Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity. Marine Drugs. 2021; 19 (5):268.
Chicago/Turabian StyleKonstantinos Axarlis; Maria Daskalaki; Sofia Michailidou; Nikolais Androulaki; Antiopi Tsoureki; Evangelia Mouchtaropoulou; Ourania Kolliniati; Ioanna Lapi; Eirini Dermitzaki; Maria Venihaki; Katerina Kousoulaki; Anagnostis Argiriou; Zouhir Marsni; Christos Tsatsanis. 2021. "Diet Supplementation with Fish-Derived Extracts Suppresses Diabetes and Modulates Intestinal Microbiome in a Murine Model of Diet-Induced Obesity." Marine Drugs 19, no. 5: 268.
The SARS-CoV-2 pandemic represents an unprecedented global crisis necessitating novel approaches for, amongst others, early detection of emerging variants relating to the evolution and spread of the virus. Recently, the detection of SARS-CoV-2 RNA in wastewater has emerged as a useful tool to monitor the prevalence of the virus in the community. Here, we propose a novel methodology, called lineagespot , for the detection of SARS-CoV-2 lineages in wastewater samples using next-generation sequencing. Our proposed method was tested and evaluated using NGS data produced by the sequencing of three wastewater samples from the municipality of Thessaloniki, Greece, covering three distinct time periods. The results showed a clear identification of trends in the presence of SARS-CoV-2 mutations in sewage data, and allowed for a robust inference between the variants evident through our approach and the variants observed in patients from the same area time periods. Lineagespot is an open-source tool, implemented in R, and is freely available on GitHub.
Nikolaos Pechlivanis; Maria Tsagiopoulou; Maria Christina Maniou; Anastasis Togkousidis; Evangelia Mouchtaropoulou; Taxiarchis Chassalevris; Serafeim Chaintoutis; Chrysostomos Dovas; Maria Petala; Margaritis Kostoglou; Thodoris Karapantsios; Stamatia Laidou; Elisavet Vlachonikola; Anastasia Chatzidimitriou; Agis Papadopoulos; Nikolaos Papaioannou; Anagnostis Argiriou; Fotis Psomopoulos. Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece. 2021, 1 .
AMA StyleNikolaos Pechlivanis, Maria Tsagiopoulou, Maria Christina Maniou, Anastasis Togkousidis, Evangelia Mouchtaropoulou, Taxiarchis Chassalevris, Serafeim Chaintoutis, Chrysostomos Dovas, Maria Petala, Margaritis Kostoglou, Thodoris Karapantsios, Stamatia Laidou, Elisavet Vlachonikola, Anastasia Chatzidimitriou, Agis Papadopoulos, Nikolaos Papaioannou, Anagnostis Argiriou, Fotis Psomopoulos. Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece. . 2021; ():1.
Chicago/Turabian StyleNikolaos Pechlivanis; Maria Tsagiopoulou; Maria Christina Maniou; Anastasis Togkousidis; Evangelia Mouchtaropoulou; Taxiarchis Chassalevris; Serafeim Chaintoutis; Chrysostomos Dovas; Maria Petala; Margaritis Kostoglou; Thodoris Karapantsios; Stamatia Laidou; Elisavet Vlachonikola; Anastasia Chatzidimitriou; Agis Papadopoulos; Nikolaos Papaioannou; Anagnostis Argiriou; Fotis Psomopoulos. 2021. "Detecting SARS-CoV-2 lineages and mutational load in municipal wastewater; a use-case in the metropolitan area of Thessaloniki, Greece." , no. : 1.
In the present study, both yeast leavened bread (YLB) and artisanal sourdough wheat bread (SDB) were prepared. The physico-chemical, microbiological, and sensory properties of breads were monitored as a function of storage time (T = 25 °C). As expected, the titratable acidity (TA) values of SDB were higher than those of YLB. The aroma profile of SDB was similar to that of YLB, including classes of compounds such as alcohols, aldehydes, ketones, esters, organic acids, terpenes, and sulfur compounds; however, the concentrations between the two were different. Aroma deterioration of bread during storage was partly related to the loss of several volatiles. Texture and sensory analysis showed that SDB was harder, less elastic, but richer in aroma and light sour taste than YLB. Mold growth was apparent when the population of yeasts/molds reached approximately 4 log cfu/g. This yeast/mold count was reached on days 4–5 for YLB and day 18 + for SDB. A 16S amplicon meta-barcoding analysis showed that the bacterial profile of SDB was dominated by a single genus, (Lactobacillus). Analysis of the eukaryotic load showed that at the genus level, Saccharomyces and Alternaria were the most abundant genera, independently of the gene sequenced (18S or ITS). Based primarily on mold growth and texture data, which proved to be the most sensitive quality parameters, the shelf life was ca. 4–5 days for YLB and 10 days for SDB.
Pavlina Katsi; Ioanna Kosma; Sofia Michailidou; Anagnostis Argiriou; Anastasia Badeka; Michael Kontominas. Characterization of Artisanal Spontaneous Sourdough Wheat Bread from Central Greece: Evaluation of Physico-Chemical, Microbiological, and Sensory Properties in Relation to Conventional Yeast Leavened Wheat Bread. Foods 2021, 10, 635 .
AMA StylePavlina Katsi, Ioanna Kosma, Sofia Michailidou, Anagnostis Argiriou, Anastasia Badeka, Michael Kontominas. Characterization of Artisanal Spontaneous Sourdough Wheat Bread from Central Greece: Evaluation of Physico-Chemical, Microbiological, and Sensory Properties in Relation to Conventional Yeast Leavened Wheat Bread. Foods. 2021; 10 (3):635.
Chicago/Turabian StylePavlina Katsi; Ioanna Kosma; Sofia Michailidou; Anagnostis Argiriou; Anastasia Badeka; Michael Kontominas. 2021. "Characterization of Artisanal Spontaneous Sourdough Wheat Bread from Central Greece: Evaluation of Physico-Chemical, Microbiological, and Sensory Properties in Relation to Conventional Yeast Leavened Wheat Bread." Foods 10, no. 3: 635.
Niki Mougiou; Foteini Trikka; Sofia Michailidou; Mariana Pantoura; Anagnostis Argiriou. Molecular and Biochemical Characterization of the Greek Pepper (Capsicum annuum) Cultivars ‘Florinis’ and ‘Karatzova’. Polish Journal of Food and Nutrition Sciences 2021, 71, 89 -96.
AMA StyleNiki Mougiou, Foteini Trikka, Sofia Michailidou, Mariana Pantoura, Anagnostis Argiriou. Molecular and Biochemical Characterization of the Greek Pepper (Capsicum annuum) Cultivars ‘Florinis’ and ‘Karatzova’. Polish Journal of Food and Nutrition Sciences. 2021; 71 (1):89-96.
Chicago/Turabian StyleNiki Mougiou; Foteini Trikka; Sofia Michailidou; Mariana Pantoura; Anagnostis Argiriou. 2021. "Molecular and Biochemical Characterization of the Greek Pepper (Capsicum annuum) Cultivars ‘Florinis’ and ‘Karatzova’." Polish Journal of Food and Nutrition Sciences 71, no. 1: 89-96.
Under the current and future climate crisis, a significant rise in soil salinity will likely affect vine productivity in several Mediterranean regions. During the present research, the rootstock effects on salinity tolerance of Merlot and Cabernet Franc grapevine cultivars were studied. In a pot hydroponic culture, own-rooted Merlot and Cabernet Franc grapevine cultivars or grafted onto the rootstocks 1103 P and 101-14 Mgt were drip-irrigated with saline water. A completely randomized 3 × 2 × 2 factorial experiment was designed with two vine rootstocks or own-rooted vines, two scion cultivars, and 100 mM NaCl salinity or control treatments, with six replications. A significant effect of scion cultivar, rootstock, and salinity was observed for most of the measured parameters. At the end of salinity stress period, leaf, shoot, root, and trunk nutrient concentrations were measured. Salinity stress increased Chloride (Cl) and Sodium (Na) concentrations in all parts of the vines and decreased leaf concentrations of Potassium (K), Calcium (Ca), Magnesium (Mg), Nitrogen (N), and Iron (Fe). In contrast, salinity stress increased leaf Boron (B) concentrations, whereas that of Manganese (Mn) remained unaffected. Leaf chlorophyll concentration decreased from 42% to 40% after thirty and sixty days of salt treatment, respectively. A similar trend was observed for the CCM-200 relative chlorophyll content. Salinity significantly decreased steam water potential (Ws), net CO2 assimilation rate (A), and stomatal conductance (gs) in all cases of grafted or own-rooted vines. Sixty days after the beginning of salt treatment, total Phenolics and PSII maximum quantum yield (Fv/Fm) decreased significantly. The rootstock 1103 P seems to be a better excluder for Na and Cl and more tolerant to salinity compared to 101-14 Mgt rootstock.
Kleopatra-Eleni Nikolaou; Theocharis Chatzistathis; Serafeim Theocharis; Anagnostis Argiriou; Stefanos Koundouras; Elefteria Zioziou. Effects of Salinity and Rootstock on Nutrient Element Concentrations and Physiology in Own-Rooted or Grafted to 1103 P and 101-14 Mgt Rootstocks of Merlot and Cabernet Franc Grapevine Cultivars under Climate Change. Sustainability 2021, 13, 2477 .
AMA StyleKleopatra-Eleni Nikolaou, Theocharis Chatzistathis, Serafeim Theocharis, Anagnostis Argiriou, Stefanos Koundouras, Elefteria Zioziou. Effects of Salinity and Rootstock on Nutrient Element Concentrations and Physiology in Own-Rooted or Grafted to 1103 P and 101-14 Mgt Rootstocks of Merlot and Cabernet Franc Grapevine Cultivars under Climate Change. Sustainability. 2021; 13 (5):2477.
Chicago/Turabian StyleKleopatra-Eleni Nikolaou; Theocharis Chatzistathis; Serafeim Theocharis; Anagnostis Argiriou; Stefanos Koundouras; Elefteria Zioziou. 2021. "Effects of Salinity and Rootstock on Nutrient Element Concentrations and Physiology in Own-Rooted or Grafted to 1103 P and 101-14 Mgt Rootstocks of Merlot and Cabernet Franc Grapevine Cultivars under Climate Change." Sustainability 13, no. 5: 2477.
Goats play an important role in the livestock sector in Greece. The national herd consists mainly of two indigenous breeds, the Eghoria and Skopelos. Here, we report the population structure and genomic profiles of these two native goat breeds using Illumina’s Goat SNP50 BeadChip. Moreover, we present a panel of candidate markers acquired using different genetic models for breed discrimination. Quality control on the initial dataset resulted in 48,841 SNPs kept for downstream analysis. Principal component and admixture analyses were applied to assess population structure. The rate of inbreeding within breed was evaluated based on the distribution of runs of homozygosity in the genome and respective coefficients, the genomic relationship matrix, the patterns of linkage disequilibrium, and the historic effective population size. Results showed that both breeds exhibit high levels of genetic diversity. Level of inbreeding between the two breeds estimated by the Wright’s fixation index FST was low (Fst = 0.04362), indicating the existence of a weak genetic differentiation between them. In addition, grouping of farms according to their geographical locations was observed. This study presents for the first time a genome-based analysis on the genetic structure of the two indigenous Greek goat breeds and identifies markers that can be potentially exploited in future selective breeding programs for traceability purposes, targeted genetic improvement schemes and conservation strategies.
S. Michailidou; G. Th. Tsangaris; A. Tzora; I. Skoufos; Georgios Banos; A. Argiriou; Georgios Arsenos. Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds. PLOS ONE 2019, 14, e0226179 .
AMA StyleS. Michailidou, G. Th. Tsangaris, A. Tzora, I. Skoufos, Georgios Banos, A. Argiriou, Georgios Arsenos. Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds. PLOS ONE. 2019; 14 (12):e0226179.
Chicago/Turabian StyleS. Michailidou; G. Th. Tsangaris; A. Tzora; I. Skoufos; Georgios Banos; A. Argiriou; Georgios Arsenos. 2019. "Analysis of genome-wide DNA arrays reveals the genomic population structure and diversity in autochthonous Greek goat breeds." PLOS ONE 14, no. 12: e0226179.
Biological treatment of table olive processing wastewater (TOPW) may be problematic due to its high organic and polyphenolic compound content. Biomass acclimatization is a necessary, yet sensitive, stage for efficient TOPW biological treatment. Next-generation sequencing technologies can provide valuable insights into this critical process step. An aerobic membrane bioreactor (MBR) system, initially inoculated with municipal activated sludge, was acclimatized to treat TOPW. Operational stability and bioremediation efficiency were monitored for approx. three months, whereas microbial community dynamics and metabolic adaptation were assessed through metagenomic and metatranscriptomic analysis. A swift change was identified in both the prokaryotic and eukaryotic bio-community after introduction of TOPW in the MBR, and a new diverse bio-community was established. Thauera and Paracoccus spp. are dominant contributors to the metabolic activity of the stable bio-community, which resulted in over 90% and 85% removal efficiency of total organic carbon and total polyphenols, respectively. This is the first study assessing the microbial community dynamics in a well-defined MBR process treating TOPW, offering guidance in the start-up of large-scale applications.
Sotiris I. Patsios; Sofia Michailidou; Konstantinos Pasentsis; Antonios M. Makris; Anagnostis Argiriou; Anastasios J. Karabelas. Analysis of Microbial Community Dynamics during the Acclimatization Period of a Membrane Bioreactor Treating Table Olive Processing Wastewater. Applied Sciences 2019, 9, 3647 .
AMA StyleSotiris I. Patsios, Sofia Michailidou, Konstantinos Pasentsis, Antonios M. Makris, Anagnostis Argiriou, Anastasios J. Karabelas. Analysis of Microbial Community Dynamics during the Acclimatization Period of a Membrane Bioreactor Treating Table Olive Processing Wastewater. Applied Sciences. 2019; 9 (18):3647.
Chicago/Turabian StyleSotiris I. Patsios; Sofia Michailidou; Konstantinos Pasentsis; Antonios M. Makris; Anagnostis Argiriou; Anastasios J. Karabelas. 2019. "Analysis of Microbial Community Dynamics during the Acclimatization Period of a Membrane Bioreactor Treating Table Olive Processing Wastewater." Applied Sciences 9, no. 18: 3647.
Bacterial communities composition using 16S Next Generation Sequencing (NGS) and Volatile Organic Compounds (VOCs) profile of whole blue crabs (Callinectes sapidus) stored at 4 and 10 °C (proper and abuse temperature) simulating real storage conditions were performed. Conventional microbiological and chemical analyses (Total Volatile Base-Nitrogen/TVB-N and Trimethylamine-Nitrogen/TMA-N) were also carried out. The rejection time point was 10 and 6 days for the whole crabs stored at 4 and 10 °C, respectively, as determined by development of unpleasant odors, which coincided with crabs death. Initially, the Aerobic Plate Count (APC) was 4.87 log cfu/g and increased by 3 logs at the rejection time. The 16S NGS analysis of DNA extracted directly from the crab tissue (culture-independent method), showed that the initial microbiota of the blue crab mainly consisted of Candidatus Bacilloplasma, while potential pathogens e.g. Listeria monocytogenes, Pseudomonas aeruginosa and Acinetobacter baumannii, were also found. At the rejection point, bacteria of Rhodobacteraceae family (52%) and Vibrio spp. (40.2%) dominated at 4 and 10 °C, respectively. TVB-N and TMA-N also increased, reaching higher values at higher storage temperature. The relative concentrations of some VOCs such as 1-octen-3-ol, trans-2-octenal, trans,trans-2,4-heptadienal, 2-butanone, 3-butanone, 2-heptanone, ethyl isobutyrate, ethyl acetate, ethyl-2-methylbutyrate, ethyl isovalerate, hexanoic acid ethyl ester and indole, exhibited an increasing trend during crab storage, making them promising spoilage markers. The composition of microbial communities at different storage temperatures was examined by 16S amplicon meta-barcoding analysis. This kind of analysis in conjugation with the volatile profile can be used to explore the microbiological quality and further assist towards the application of the appropriate strategies to extend crab shelf-life and protect consumer's health.
F.F. Parlapani; S. Michailidou; D.A. Anagnostopoulos; S. Koromilas; K. Kios; K. Pasentsis; F. Psomopoulos; A. Argiriou; S.A. Haroutounian; I.S. Boziaris. Bacterial communities and potential spoilage markers of whole blue crab (Callinectes sapidus) stored under commercial simulated conditions. Food Microbiology 2019, 82, 325 -333.
AMA StyleF.F. Parlapani, S. Michailidou, D.A. Anagnostopoulos, S. Koromilas, K. Kios, K. Pasentsis, F. Psomopoulos, A. Argiriou, S.A. Haroutounian, I.S. Boziaris. Bacterial communities and potential spoilage markers of whole blue crab (Callinectes sapidus) stored under commercial simulated conditions. Food Microbiology. 2019; 82 ():325-333.
Chicago/Turabian StyleF.F. Parlapani; S. Michailidou; D.A. Anagnostopoulos; S. Koromilas; K. Kios; K. Pasentsis; F. Psomopoulos; A. Argiriou; S.A. Haroutounian; I.S. Boziaris. 2019. "Bacterial communities and potential spoilage markers of whole blue crab (Callinectes sapidus) stored under commercial simulated conditions." Food Microbiology 82, no. : 325-333.
Diatoms are eukaryotic, unicellular algae that are responsible for c. 20% of the Earth's primary production. Their dominance and success in contemporary oceans have prompted investigations on their distinctive metabolism and physiology. One metabolic pathway that remains largely unexplored in diatoms is isoprenoid biosynthesis, which is responsible for the production of numerous molecules with unique features. We selected the diatom species Haslea ostrearia because of its characteristic isoprenoid content and carried out a comprehensive transcriptomic analysis and functional characterization of the genes identified. We functionally characterized one farnesyl diphosphate synthase, two geranylgeranyl diphosphate synthases, one short‐chain polyprenyl synthase, one bifunctional isopentenyl diphosphate isomerase – squalene synthase – and one phytoene synthase. We inferred the phylogenetic origin of these genes and used a combination of functional analysis and subcellular localization predictions to propose their physiological roles. Our results provide insight into isoprenoid biosynthesis in H. ostrearia and propose a model of the central steps of the pathway. This model will facilitate the study of metabolic pathways of important isoprenoids in diatoms, including carotenoids, sterols and highly branched isoprenoids. This article is protected by copyright. All rights reserved.
Anastasia Athanasakoglou; Emilia Grypioti; Sofia Michailidou; Codruta Ignea; Antonios M. Makris; Kriton Kalantidis; Guillaume Massé; Anagnostis Argiriou; Frederic Verret; Sotirios C. Kampranis. Isoprenoid biosynthesis in the diatom Haslea ostrearia. New Phytologist 2018, 222, 230 -243.
AMA StyleAnastasia Athanasakoglou, Emilia Grypioti, Sofia Michailidou, Codruta Ignea, Antonios M. Makris, Kriton Kalantidis, Guillaume Massé, Anagnostis Argiriou, Frederic Verret, Sotirios C. Kampranis. Isoprenoid biosynthesis in the diatom Haslea ostrearia. New Phytologist. 2018; 222 (1):230-243.
Chicago/Turabian StyleAnastasia Athanasakoglou; Emilia Grypioti; Sofia Michailidou; Codruta Ignea; Antonios M. Makris; Kriton Kalantidis; Guillaume Massé; Anagnostis Argiriou; Frederic Verret; Sotirios C. Kampranis. 2018. "Isoprenoid biosynthesis in the diatom Haslea ostrearia." New Phytologist 222, no. 1: 230-243.
Bacterial diversity of whole gilt-head sea bream (Sparus aurata L. 1758) originating from Ionian and Aegean Sea aquaculture farms and stored at 0 (ice), 4 and 8 °C was determined by 16S rRNA gene amplicon sequencing method using the Illumina's MiSeq platform. The composition of Aerobic Plate Counts (APC) was also monitored by 16S rRNA gene sequencing. The rejection time point of sea bream from either area, as determined by sensory evaluation, was about 14, 6 and 3 days at 0, 4 and 8 °C, respectively. APC was approximately 4.5 log cfu/g at day 0 and ranged from 7.5 to 8.5 log cfu/g at sensory rejection. Culture-depended analysis showed that Pseudomonas and Shewanella were the most abundant microorganisms grown on plates for both seas. Moreover, culture-independent analysis of DNA extracted directly from fish flesh showed that sea bream originating from different geographical areas exhibited different bacterial diversity. Pseudomonas and Psychrobacter were the dominant microorganisms of chill-stored fish from Ionian (apart from 8 °C, where Carnobacterium dominated) and Aegean Sea, respectively. In addition, small changes of storage temperature greatly affected bacterial microbiota of stored fish. Various bacterial species, not detected by conventional microbiological methods, were also revealed through 16S amplicon sequencing. In conclusion, the use of NGS approach is a promising methodology for assessing bacterial diversity of sea bream originating from different geographical areas and stored at various temperatures.
Foteini F. Parlapani; Sofia Michailidou; Konstantinos Pasentsis; Anagnostis Argiriou; Grigorios Krey; Ioannis S. Boziaris. A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream ( Sparus aurata ) originating from fish farms from two geographically distinct areas of Greece. International Journal of Food Microbiology 2018, 278, 36 -43.
AMA StyleFoteini F. Parlapani, Sofia Michailidou, Konstantinos Pasentsis, Anagnostis Argiriou, Grigorios Krey, Ioannis S. Boziaris. A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream ( Sparus aurata ) originating from fish farms from two geographically distinct areas of Greece. International Journal of Food Microbiology. 2018; 278 ():36-43.
Chicago/Turabian StyleFoteini F. Parlapani; Sofia Michailidou; Konstantinos Pasentsis; Anagnostis Argiriou; Grigorios Krey; Ioannis S. Boziaris. 2018. "A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream ( Sparus aurata ) originating from fish farms from two geographically distinct areas of Greece." International Journal of Food Microbiology 278, no. : 36-43.
Olive tree is one of the most valuable crops cultivated for its oil that is rich in antioxidants. The beneficial effects of oleuropein and hydroxytyrosol (HT), the most abundant and the most powerful antioxidant respectively, as well as tyrosol, HT's precursor molecule, are well studied however their biosynthetic pathways are not yet clarified. The transcriptome analysis of the young olive fruit, cultivar "Koroneiki", revealed transcripts of all the enzymes used to reconstitute the biosynthetic pathway of tyrosol and HT in other organisms. We also identified transcripts of the genes that encode for enzymes involved in the secologanin biosynthesis, oleuropein's precursor molecule. Following the transcriptome analysis, the relative expression of the transcripts was monitored during fruit development and compared to the concentration of the 3 metabolites they synthesize at the same developmental stages. The highest expression levels, accompanied by the maximum concentration of the three metabolites, was found in the young olive fruit. The correlation between the expression profile and the metabolites' concentration indicates that the transcripts were correctly identified and the synthesis of the compounds is regulated at a transcriptional level. Interestingly, HT showed a sudden increment in the final developmental stage of the black mature fruit that is attributed to oleuropein catabolism.
Niki Mougiou; Fotini Trikka; Emmanouil Trantas; Filippos Ververidis; Antonios Makris; Anagnostis Argiriou; Konstantinos E. Vlachonasios. Expression of hydroxytyrosol and oleuropein biosynthetic genes are correlated with metabolite accumulation during fruit development in olive, Olea europaea , cv. Koroneiki. Plant Physiology and Biochemistry 2018, 128, 41 -49.
AMA StyleNiki Mougiou, Fotini Trikka, Emmanouil Trantas, Filippos Ververidis, Antonios Makris, Anagnostis Argiriou, Konstantinos E. Vlachonasios. Expression of hydroxytyrosol and oleuropein biosynthetic genes are correlated with metabolite accumulation during fruit development in olive, Olea europaea , cv. Koroneiki. Plant Physiology and Biochemistry. 2018; 128 ():41-49.
Chicago/Turabian StyleNiki Mougiou; Fotini Trikka; Emmanouil Trantas; Filippos Ververidis; Antonios Makris; Anagnostis Argiriou; Konstantinos E. Vlachonasios. 2018. "Expression of hydroxytyrosol and oleuropein biosynthetic genes are correlated with metabolite accumulation during fruit development in olive, Olea europaea , cv. Koroneiki." Plant Physiology and Biochemistry 128, no. : 41-49.
In the present study, genome-wide genotyping was applied to characterize the genetic diversity and population structure of three autochthonous Greek breeds: Boutsko, Karagouniko and Chios. Dairy sheep are among the most significant livestock species in Greece numbering approximately 9 million animals which are characterized by large phenotypic variation and reared under various farming systems. A total of 96 animals were genotyped with the Illumina's OvineSNP50K microarray beadchip, to study the population structure of the breeds and develop a specialized panel of single-nucleotide polymorphisms (SNPs), which could distinguish one breed from the others. Quality control on the dataset resulted in 46,125 SNPs, which were used to evaluate the genetic structure of the breeds. Population structure was assessed through principal component analysis (PCA) and admixture analysis, whereas inbreeding was estimated based on runs of homozygosity (ROHs) coefficients, genomic relationship matrix inbreeding coefficients (FGRM) and patterns of linkage disequilibrium (LD). Associations between SNPs and breeds were analyzed with different inheritance models, to identify SNPs that distinguish among the breeds. Results showed high levels of genetic heterogeneity in the three breeds. Genetic distances among breeds were modest, despite their different ancestries. Chios and Karagouniko breeds were more genetically related to each other compared to Boutsko. Analysis revealed 3802 candidate SNPs that can be used to identify two-breed crosses and purebred animals. The present study provides, for the first time, data on the genetic background of three Greek indigenous dairy sheep breeds as well as a specialized marker panel that can be applied for traceability purposes as well as targeted genetic improvement schemes and conservation programs.
S. Michailidou; G. Tsangaris; G. C. Fthenakis; A. Tzora; I. Skoufos; S. C. Karkabounas; Georgios Banos; A. Argiriou; Georgios Arsenos. Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays. Molecular and General Genetics MGG 2018, 293, 753 -768.
AMA StyleS. Michailidou, G. Tsangaris, G. C. Fthenakis, A. Tzora, I. Skoufos, S. C. Karkabounas, Georgios Banos, A. Argiriou, Georgios Arsenos. Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays. Molecular and General Genetics MGG. 2018; 293 (3):753-768.
Chicago/Turabian StyleS. Michailidou; G. Tsangaris; G. C. Fthenakis; A. Tzora; I. Skoufos; S. C. Karkabounas; Georgios Banos; A. Argiriou; Georgios Arsenos. 2018. "Genomic diversity and population structure of three autochthonous Greek sheep breeds assessed with genome-wide DNA arrays." Molecular and General Genetics MGG 293, no. 3: 753-768.
Epidermal cell differentiation is a paramount and conserved process among plants. In Arabidopsis, a ternary complex formed by MYB, bHLH transcription factors and TTG1 modulates unicellular trichome morphogenesis. The formation of multicellular glandular trichomes of the xerophytic shrub Cistus creticus that accumulate labdane-type diterpenes, has attained much attention renowned for its medicinal properties. Here, we show that C. creticus TTG1 (CcTTG1) interacts with the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE (SPLA/B) proteins, putative homologs of AtSPL4/5 that in turn interact with AtTTG1. These interactions occur between proteins from evolutionarily distant species supporting the conserved function of TTG1-SPL complex. Overexpression of AtSPL4 and AtSPL5 decreased the expression of GLABRA2 (AtGL2), the major regulator of trichome morphogenesis, resulting in trichome reduction on the adaxial surface of cauline leaves, thereby illuminating the significance of TTG1-SPLs interactions in trichome formation control. AtGL2 and AtSPL4 have opposite expression patterns during early stages of leaf development. We postulate an antagonistic effect between SPLs and the heterogeneous MYB-bHLH factors binding to TTG1. Hence, the SPLs potentially rearrange the complex, attenuating its transcriptional activity to control trichome distribution.
Eugenia Ioannidi; Stamatis Rigas; Dikran Tsitsekian; Gerasimos Daras; Anastasios Alatzas; Antonis Makris; Georgia Tanou; Anagnostis Argiriou; Dimitrios Alexandrou; Scott Poethig; Polydefkis Hatzopoulos; Angelos K. Kanellis. Trichome patterning control involves TTG1 interaction with SPL transcription factors. Plant Molecular Biology 2016, 92, 675 -687.
AMA StyleEugenia Ioannidi, Stamatis Rigas, Dikran Tsitsekian, Gerasimos Daras, Anastasios Alatzas, Antonis Makris, Georgia Tanou, Anagnostis Argiriou, Dimitrios Alexandrou, Scott Poethig, Polydefkis Hatzopoulos, Angelos K. Kanellis. Trichome patterning control involves TTG1 interaction with SPL transcription factors. Plant Molecular Biology. 2016; 92 (6):675-687.
Chicago/Turabian StyleEugenia Ioannidi; Stamatis Rigas; Dikran Tsitsekian; Gerasimos Daras; Anastasios Alatzas; Antonis Makris; Georgia Tanou; Anagnostis Argiriou; Dimitrios Alexandrou; Scott Poethig; Polydefkis Hatzopoulos; Angelos K. Kanellis. 2016. "Trichome patterning control involves TTG1 interaction with SPL transcription factors." Plant Molecular Biology 92, no. 6: 675-687.
Salvia diterpenes have been found to have health promoting properties. Among them, carnosic acid and carnosol, tanshinones and sclareol are well known for their cardiovascular, antitumor, antiinflammatory and antioxidant activities. However, many of these compounds are not available at a constant supply and developing biotechnological methods for their production could provide a sustainable alternative. The transcriptome of S.pomifera glandular trichomes was analysed aiming to identify genes that could be used in the engineering of synthetic microbial systems. In the present study, a thorough metabolite analysis of S. pomifera leaves led to the isolation and structure elucidation of carnosic acid-family metabolites including one new natural product. These labdane diterpenes seem to be synthesized through miltiradiene and ferruginol. Transcriptomic analysis of the glandular trichomes from the S. pomifera leaves revealed two genes likely involved in miltiradiene synthesis. Their products were identified and the corresponding enzymes were characterized as copalyl diphosphate synthase (SpCDS) and miltiradiene synthase (SpMilS). In addition, several CYP-encoding transcripts were identified providing a valuable resource for the identification of the biosynthetic mechanism responsible for the production of carnosic acid-family metabolites in S. pomifera. Our work has uncovered the key enzymes involved in miltiradiene biosynthesis in S. pomifera leaf glandular trichomes. The transcriptomic dataset obtained provides a valuable tool for the identification of the CYPs involved in the synthesis of carnosic acid-family metabolites.
Fotini A. Trikka; Alexandros Nikolaidis; Codruta Ignea; Aphrodite Tsaballa; Leto-Aikaterini Tziveleka; Efstathia Ioannou; Vassilios Roussis; Eleni A. Stea; Dragana Božić; Anagnostis Argiriou; Angelos K. Kanellis; Sotirios C. Kampranis; Antonios M. Makris. Combined metabolome and transcriptome profiling provides new insights into diterpene biosynthesis in S. pomifera glandular trichomes. BMC Genomics 2015, 16, 1 -19.
AMA StyleFotini A. Trikka, Alexandros Nikolaidis, Codruta Ignea, Aphrodite Tsaballa, Leto-Aikaterini Tziveleka, Efstathia Ioannou, Vassilios Roussis, Eleni A. Stea, Dragana Božić, Anagnostis Argiriou, Angelos K. Kanellis, Sotirios C. Kampranis, Antonios M. Makris. Combined metabolome and transcriptome profiling provides new insights into diterpene biosynthesis in S. pomifera glandular trichomes. BMC Genomics. 2015; 16 (1):1-19.
Chicago/Turabian StyleFotini A. Trikka; Alexandros Nikolaidis; Codruta Ignea; Aphrodite Tsaballa; Leto-Aikaterini Tziveleka; Efstathia Ioannou; Vassilios Roussis; Eleni A. Stea; Dragana Božić; Anagnostis Argiriou; Angelos K. Kanellis; Sotirios C. Kampranis; Antonios M. Makris. 2015. "Combined metabolome and transcriptome profiling provides new insights into diterpene biosynthesis in S. pomifera glandular trichomes." BMC Genomics 16, no. 1: 1-19.
Solanum elaeagnifolium, an invasive weed of the Solanaceae family, is poorly studied although it poses a significant threat to crops. Here the analysis of the transcriptome of S. elaeagnifolium is presented, as a means to explore the biology of this species and to identify genes related to its adaptation to environmental stress. One of the basic mechanisms by which plants respond to environmental stress is through the synthesis of specific secondary metabolites that protect the plant from herbivores and microorganisms, or serve as signaling molecules. One important such group of secondary metabolites are terpenes. By next-generation sequencing, the flower/leaf transcriptome of S. elaeagnifolium was sequenced and de novo assembled into 75,618 unigenes. Among the unigenes identified, several corresponded to genes involved in terpene biosynthesis; these included terpene synthases (TPSs) and genes of the mevalonate (MVA) and the methylerythritol phosphate (MEP) pathways. Functional characterization of two of the TPSs showed that one produced the sesquiterpene (E)-caryophyllene and the second produced the monoterpene camphene. Analysis of wounded S. elaeagnifolium leaves has shown significant increase of the concentration of (E)-caryophyllene and geranyl linalool, two terpenes implicated in stress responses. The increased production of (E)-caryophyllene was matched to the induced expression of the corresponding TPS gene. Wounding also led to the increased expression of the putative 1-deoxy-D-xylulose-5-phosphate synthase 2 (DXS2) gene, a key enzyme of the MEP pathway, corroborating the overall increased output of terpene biosynthesis. The reported S. elaeagnifolium de novo transcriptome provides a valuable sequence database that could facilitate study of this invasive weed and contribute to our understanding of the highly diverse Solanaceae family. Analysis of genes and pathways involved in the plant's interaction with the environment will help to elucidate the mechanisms that underly the intricate features of this unique Solanum species.
Aphrodite Tsaballa; Alexandros Nikolaidis; Foteini Trikka; Codruta Ignea; Sotirios C. Kampranis; Antonios M. Makris; Anagnostis Argiriou. Use of the de novo transcriptome analysis of silver-leaf nightshade (Solanum elaeagnifolium) to identify gene expression changes associated with wounding and terpene biosynthesis. BMC Genomics 2015, 16, 504 .
AMA StyleAphrodite Tsaballa, Alexandros Nikolaidis, Foteini Trikka, Codruta Ignea, Sotirios C. Kampranis, Antonios M. Makris, Anagnostis Argiriou. Use of the de novo transcriptome analysis of silver-leaf nightshade (Solanum elaeagnifolium) to identify gene expression changes associated with wounding and terpene biosynthesis. BMC Genomics. 2015; 16 (1):504.
Chicago/Turabian StyleAphrodite Tsaballa; Alexandros Nikolaidis; Foteini Trikka; Codruta Ignea; Sotirios C. Kampranis; Antonios M. Makris; Anagnostis Argiriou. 2015. "Use of the de novo transcriptome analysis of silver-leaf nightshade (Solanum elaeagnifolium) to identify gene expression changes associated with wounding and terpene biosynthesis." BMC Genomics 16, no. 1: 504.