Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

Visualizing genome and systems biology: technologies, tools, implementation techniques and trends, past, present and future.

"Α picture is worth a thousand words." This widely used adage sums up in a few words the notion that a successful visual representation of a concept should enable easy and rapid absorption of large amounts of information. Although, in general, the notion of capturing complex ideas using images is very appealing, would 1000 words be enough to describe the unknown in a research field such as the life sciences? Life sciences is one of the biggest generators of enormous datasets, mainly as a result of recent and rapid technological advances; their complexity can make these datasets incomprehensible without effective visualization methods. Here we discuss the past, present and future of genomic and systems biology visualization. We briefly comment on many visualization and analysis tools and the purposes that they serve. We focus on the latest libraries and programming languages that enable more effective, efficient and faster approaches for visualizing biological concepts, and also comment on the future human-computer interaction trends that would enable for enhancing visualization further

Metagenomics : tools and insights for analyzing next-generation sequencing data derived from biodiversity studies

Advances in next-generation sequencing (NGS) have allowed significant breakthroughs in microbial ecology studies. This has led to the rapid expansion of research in the field and the establishment of “metagenomics”, often defined as the analysis of DNA from microbial communities in environmental samples without prior need for culturing. Many metagenomics statistical/computational tools and databases have been developed in order to allow the exploitation of the huge influx of data. In this review article, we provide an overview of the sequencing technologies and how they are uniquely suited to various types of metagenomic studies. We focus on the currently available bioinformatics techniques, tools, and methodologies for performing each individual step of a typical metagenomic dataset analysis. We also provide future trends in the field with respect to tools and technologies currently under development. Moreover, we discuss data management, distribution, and integration tools that are capable of performing comparative metagenomic analyses of multiple datasets using well-established databases, as well as commonly used annotation standards

Comparative antilipidemic effect of N-acetylcysteine and sesame oil administration in diet-induced hypercholesterolemic mice

<p>Abstract</p> <p>Background</p> <p>There is an increasing number of novel antilipidemic therapies under consideration. The putative hypolipidemic effect of N-acetylcysteine (NAC) and sesame oil was studied in a mouse model of dietary-induced hypercholesterolemia.</p> <p>Methods</p> <p>Male C57bl/6 mice were assigned to the following groups: (NC) control group, (HC) group receiving test diet supplemented with 2% cholesterol and 0.5% cholic acid for 8 weeks, (HCN) group receiving the test diet with NAC supplementation (230 mg/kg p.o.) and (HCS) group fed the test diet enriched with 10% sesame oil. Total serum cholesterol, LDL-cholesterol, HDL-cholesterol and triglycerides were assayed at the beginning and at the end of the experiment. Total peroxides and nitric oxide (NO) levels were measured in the serum at the end of the experiment. Hepatic and aortic lesions were evaluated by haematoxylin-eosin staining.</p> <p>Results</p> <p>Higher serum levels of total and LDL-cholesterol were recorded in all groups fed the high cholesterol diet. The HCN group presented reduced lipid levels compared to HC and HCS groups. No differences were observed between HCS and HC groups. Peroxide content in serum was markedly increased in mice consuming high cholesterol diet. NAC and sesame oil administration led to a significant decrease of serum lipid peroxidation in the levels of control group, whereas only NAC restored NO bioavailability. In terms of liver histology, the lesions observed in HCN group were less severe than those seen in the other high cholesterol groups.</p> <p>Conclusion</p> <p>Co-administration of NAC, but not sesame oil, restored the disturbed lipid profile and improved hepatic steatosis in the studied diet-induced hypercholesterolemic mice. Both agents appear to ameliorate serum antioxidant defense.</p

Cancer rate of Bethesda category II thyroid nodules

Aim Thyroid nodules are very common and may be found in more than 50% of the population. Fine-needle aspiration cytology (FNAC) of thyroid nodules is a very useful diagnostic tool with high sensitivity and predictive value for diagnosis. The Bethesda System for Reporting Thyroid Cytopathology (BSRTC) uses six categories for thyroid cytology reporting (I-nondiagnostic, IIbenign, III-atypia of undetermined significance (AUS)/ follicular lesion of undetermined significance (FLUS), IV-follicular neoplasm/suspicious for follicular neoplasm (SFN), V-suspicious for malignancy, and VI-malignant. Our objective was to determine the malignancy rate in Bethesda II nodules. Methods From June 2010 to May 2020 a retrospective analysis was performed among 1166 patients who underwent thyroid surgery for benign thyroid diseases in our institution. Thyroid cytopathological slides and Ultrasound (US) reports were reviewed and classified according to the BSRTC. Data collected included age, gender, cytological features, and histological type of thyroid cancer. Results During the study period, 44.77% (522/1166) of patients with an FNA categorized as Bethesda II underwent thyroid surgery. Incidental malignancy was found in 1.53% (8/522) cases of Bethesda II. The most common malignant tumour type was papillary thyroid carcinoma. Conclusion The current study demonstrates that incidental thyroid carcinoma can be diagnosed after thyroidectomy even in patients with an FNA categorized as Bethesda II

Genome sequences and great expectations

To assess how automatic function assignment will contribute to genome annotation in the next five years, we have performed an analysis of 31 available genome sequences. An emerging pattern is that function can be predicted for almost two-thirds of the 73,500 genes that were analyzed. Despite progress in computational biology, there will always be a great need for large-scale experimental determination of protein function