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

Ten simple rules for organizing a bioinformatics training course in low- And middle-income countries

© 2021 Moore et al.Bioinformatics training is required at every stage of a scientist’s research career. Continual bioinformatics training allows exposure to an ever-changing and growing repertoire of techniques and databases, and so biologists, computational scientists, and healthcare practitioners are all seeking learning opportunities in the use of computational resources and tools designed for data storage, retrieval, and analysis. There are abundant opportunities for accessing bioinformatics training for scientists in high-income countries (HICs), with well-equipped facilities and participants and trainers requiring minimal travel and financial costs alongside a range of general advice for developing short bioinformatics training courses [1–3]. However, regionally targeted bioinformatics training in low- and middle-income countries (LMICs) often requires more extensive local and external support, organization, and travel. Due to the limited expertise in bioinformatics in LMICs in general, most bioinformatics training requires a fair amount of collaboration with experts beyond the local community, country, or region. A common model of training, used as the basis of this article, includes a local host collaborating with local, regional, and international experts gathering to train local or regional participants. Recently, there has been a growth of capacity strengthening initiatives in LMICs, such as the Pan African Bioinformatics Network for Human Heredity and Health in Africa (H3ABioNet) Initiative [4–6], the Capacity Building for Bioinformatics in Latin America (CABANA) Project [7], the Asia Pacific BioInformatics Network (APBioNet) [8], and the Wellcome Connecting Science Courses and Conferences program [9]. One of the important strands of these initiatives is a drive to organize and deliver valuable bioinformatics training, but organizing and delivering short bioinformatics training workshops in an LMIC present a unique set of challenges. This paper attempts to build upon the sage advice for organizing bioinformatics workshops with specific guidance for organizing and delivering them in LMICs. It describes the processes to follow in organizing courses taking into consideration the low-resource setting. We should also note that LMICs are not a monolithic group and that setting, context, temporality, and specific location matters. LMICs are a complex regional grouping [10] and should be treated as such; however, we will present some common lessons that we hope will help organizers and trainers of bioinformatics training events in LMICs to navigate the often different, challenging, and rewarding experience.The authors who contributed to this manuscript are funded as follows: BM receives salary support from Wellcome Trust grants [WT108749/Z/15/Z, WT108749/Z/15/A], PC, VR, NM, AG’s salaries are funded in whole, or in part, by the NIH Common Fund H3ABioNet grant [U24HG006941], MC, SLFV, AR, PG, PCL’s salaries were partly funded by the UKRI-BBSRC ‘Capacity building for bioinformatics in Latin America’ (CABANA) grant, on behalf of the Global Challenges Research Fund [BB/P027849/1], JDLR is funded by ISCiii AES [ref. PI18/00591] at the CSIC/USAL (Spain) and by CYTED, RIABIO (Red Iberoamericana 521RT0118), AM’s salary is funded by [WT206194/Z/17/Z], GO is funded by the CABANA grant and SM is funded by the EMBL-EBI

Analyses of the genomic variation to study cork oak evolution and adaptation : from past to future climatic changes

Tese de doutoramento, Biologia e Ecologia das Alterações Globais (Biologia do Genoma e Evolução), Universidade de Lisboa, Faculdade de Ciências, 2018Current scientific literature indicates that climate change will cause an average world temperature increase between 1 and 4ºC, along with changes in precipitation patterns and extreme weather events in the next 50 years. These are likely to have a negative impact for biodiversity in general, and forest ecosystems should be particularly affected, especially those in Mediterranean areas, like the cork oak (Quercus suber L.) “montados”. In order to understand how species can respond to such alterations, it is important to know their evolutionary history and genetic architecture of adaptive traits. Advances in sequencing technologies have relatively recently brought down the cost of sequencing per base pair to a point where even small research facilities can obtain genomic information of non-model organisms. These advances made SNP markers become the most abundant type of genetic variation in eukaryotic genomes, especially with the advent of Reduced Representation libraries such as RAD-Seq and GBS. Yet, despite their widespread use, SNP data analyses still bore its own set of bioinformatics challenges. While most of these are related with the practical aspects of the process, such as being able to handle very large datasets, or discriminate between neutral and non-neutral markers, some fundamental problems, like reproducibility are also important issues affecting research in this area. In this thesis, genomic and transcriptomic data from Q. suber was used to assess the evolutionary history of the species, detect the effects of natural selection across the cork oak’s distribution range and find any associations between the obtained markers and environmental variables. The main methodological contributions of this thesis are in the form of three software suites: (1) 4Pipe4, a software for automatically mining SNP markers from NGS data when no reference genome nor strain information is present, (2) NCBI Mass Sequence Downloader, a program to automate the downloading of large datasets from the NCBI databases, and (3) Structure_threader, a software to automate and parallelize analyses using several popular clustering analyses programs. All of these programs were developed with the intent to improve the automation and reproducibility value of the analysis processes they are meant to be part of. The main findings of this thesis are that (1) the evolutionary history and population structure of Q. suber is not as neatly structured as chloroplastidial markers indicate, (2) local adaptation plays and important role in the distribution of the species’ genetic variability, and (3) the cork oak may be better equipped, from a genetic point of view, to adapt to climate change than what previous studies based solely on ecological modelling indicated

ISOLASI DAN IDENTIFIKASI HOUSEKEEPING GENE PADA IKAN SIDAT (Anguilla bicolor)

ISOLASI DAN IDENTIFIKASI HOUSEKEEPING GENE PADA IKAN SIDAT (Anguilla bicolor) ABSTRAK Housekeeping gene adalah gen kosntitutif yang diperlukan dalam pemeliharaan fungsi sel dan sering digunakan sebagai kontrol internal pada normalisasi ekspresi gen. Akan tetapi informasi genetik dari housekeeping gene khususnya pada ikan sidat (Anguilla bicolor) masih minim dan banyak yang belum diketahui. Berhubungan dengan hal tersebut maka penelitian ini bertujuan untuk mensikuensing hasil isolasi housekeeping gene pada ikan sidat (Anguilla bicolor), guna mendapatkan sikuen spesifik dengan cara melakukan perancangan primer degenerate pada housekeeping gene 18s ribosomal RNA (18S rRNA), Beta Actin (ACTB), Elongation Factor 1-Alpha (EF1A) dan Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH). Primer degenerate yang terdiri dari dua set primer (outer dan inner) dirancang dengan cara: (1) Pengumpulan sikuen housekeeping gene pada ikan class Actinopterygii; (2) Pensejajaran sikuen; (3) Pengunggahan sikuen ke laman Primaclade; (4) Pemilihan pasangan primer. Primer yang terpilih selanjutnya digunakan untuk mengamplifikasi housekeeping gene DNA Anguilla bicolor dengan menggunakan metode Nested PCR. Adapun DNA Anguilla bicolor didapat dari hasil isolasi DNA menggunakan protokol Sambrook. Kemudian hasil amplifikasi housekeeping gene dilakukan sikuensing secara langsung (direct PCR) untuk menentukan urutan nukleotida dari sikuen gen. Selanjutnya dilakukan contig dan analisis BLAST pada sikuen gen yang didapat untuk memastikan bahwa sikuen tersebut sesuai dengan gen target. Hasil analisis BLAST menunjukkan dari keempat sikuen gen, diperoleh tiga sikuen yang sesuai dengan gen target yaitu gen 18s ribosomal RNA (18S rRNA), Beta Actin (ACTB) dan Elongation Factor 1-Alpha (EF1A) dan identifikasi pengelompokan menggunakan dendrogram menunjukkan bahwa ketiga sikuen gen tersebut berkelompok dengan gen target. Kesimpulan dari penelitian ini adalah diperoleh tiga sikuen spesifik pada tiga housekeeping gene target yang dapat digunakan sebagai sumber untuk merancang primer spesifik pada penelitian selanjutnya. Kata Kunci : Anguilla bicolor, Housekeeping gene, Primer degenerate, Nested PCR, Primer spesifik. ISOLATION AND IDENTIFICATION OF HOUSEKEEPING GENE IN EEL FISH (Anguilla bicolor) ABSTRACT Housekeeping gene are effective genes needed in cell maintenance and often used as internal controls in gene expression normalization because of their stable nature. However, genetic information from housekeeping genes, especially in Anguilla bicolor is still minimal and much is unknown. In relation to that, this study aims to sequencing the isolation results of housekeeping gene in Anguilla bicolor in order to get specific sequences by designing degenerate primer on 18s ribosomal RNA (18S rRNA), Beta Actin (ACTB), Elongation Factor 1-Alpha (ef1a) and Glyceraldehyde-3-Phosphate Dehydrogenase (GAPDH). The degenerate primer consists of two primer sets (outer and inner) were designed by: (1) Collection fish sequences of Actinopterygii class; (2) Aligment sequences; (3) Uploading sequences to the Primaclade web; (4) Selection of primary pairs. The selected primers were then used to amplify housekeeping gene of Anguilla bicolor using the Nested PCR method. DNA of Anguilla bicolor was obtained from DNA isolation using the Sambrook protocol. The result of housekeeping gene amplification was then sequenced directly to determine the nucleotide sequences of the gene. Next, contig and BLAST analysis were performed on the gene sequences obtained to ensure that the sequences match the target genes. The results of BLAST analysis showed that the three of four genes sequences were corresponding to the target gene, which are ribosome RNA 18s (18S rRNA), Beta Actin (ACTB) and Elongation Factor 1-Alpha (ef1a). The general grouping of dendrograms showed that the three gene sequences were in groups with gene target. The conclusion of this study is the discovery of three specific sequences in three housekeeping gene targets which can be used as a source for designing specific primers in subsequent studies. Keywords: Anguilla bicolor, Housekeeping gene, Degenerate Primer, Nested PCR, Specific Primer

Simple identification tools in FishBase

Simple identification tools for fish species were included in the FishBase information system from its inception. Early tools made use of the relational model and characters like fin ray meristics. Soon pictures and drawings were added as a further help, similar to a field guide. Later came the computerization of existing dichotomous keys, again in combination with pictures and other information, and the ability to restrict possible species by country, area, or taxonomic group. Today, www.FishBase.org offers four different ways to identify species. This paper describes these tools with their advantages and disadvantages, and suggests various options for further development. It explores the possibility of a holistic and integrated computeraided strategy

Africa–Europe Cooperation and Digital Transformation

Africa–Europe Cooperation and Digital Transformation explores the opportunities and challenges for cooperation between Africa and Europe in the digital sphere. Digitalisation and digital technologies are not only essential for building competitive and dynamic economies; they transform societies, pose immense challenges for policymakers, and increasingly play a pivotal role in global power relations. Digital transformations have had catalytic effects on African and European governance, economies, and societies, and will continue to do so. The COVID-19 pandemic has already accelerated the penetration of digital tools all over the globe and is likely to be perceived as a critical juncture in how and to what purpose the world accepts and uses new and emerging technologies. This book offers a holistic analysis of how Africa and Europe can manage and harness digital transformation as partners in a globalised world. The authors shed light on issues ranging from economic growth, youth employment, and gender, to regulatory frameworks, business environments, entrepreneurship, and interest-driven power politics. They add much-needed perspectives to the debates that shape the two continents’ digital transformation and innovation environments. This book will interest practitioners working in the areas of innovation, digital technologies, and digital entrepreneurship, as well as students and scholars of international relations. It will also be relevant for policymakers, regulators, decision-makers, and leaders in Africa and Europe

Generating genomic resources for two crustacean species and their application to the study of White Spot Disease

Over the last decades the crustacean aquaculture sector has been steadily growing, in order to meet global demands for its products. A major hurdle for further growth of the industry is the prevalence of viral disease epidemics that are facilitated by the intense culture conditions. A devastating virus impacting on the sector is the White Spot Syndrome Virus (WSSV), responsible for over US $ 10 billion in losses in shrimp production and trade. The Pathogenicity of WSSV is high, reaching 100 % mortality within 3-10 days in penaeid shrimps. In contrast, the European shore crab Carcinus maenas has been shown to be relatively resistant to WSSV. Uncovering the basis of this resistance could help inform on the development of strategies to mitigate the WSSV threat. C. maenas has been used widely in studies on ecotoxicology and host-pathogen interactions. However, like most aquatic crustaceans, the genomic resources available for this species are limited, impairing experimentation. Therefore, to facilitate interpretations of the exposure studies, we first produced a C. maenas transcriptome and genome scaffold assembly. We also produced a transcriptome for the European lobster (Homarus gammarus), an ecologically and commercially important crustacean species in United Kingdom waters, for use in comparing WSSV responses in this, a susceptible species, and C. maenas. For the C. maenas transcriptome assembly we isolated and pooled RNA from twelve different tissues and sequenced RNA on an Illumina HiSeq 2500 platform. After de novo assembly a transcriptome encompassing 212,427 transcripts was produced. Similar, the H. gammarus transcriptome was based on RNA from nine tissues and contained 106,498 transcripts. The transcripts were filtered and annotated using a variety of tools (including BLAST, MEGAN and RSEM) and databases (including GenBank, Gene Ontology and KEGG). The annotation rate for transcripts in both transcriptomes was around 20-25 % which appears to be common for aquatic crustacean species, as a result of the lack of well annotated gene sequences for this clade. Since it is likely that the host immune system would play an important role in WSSV infection we characterized the IMD, JAK/STAT, Toll-like receptor and other innate immune system pathways. We found a strong overlap between the immune system pathways in C. maenas and H. gammarus. In addition we investigated the sequence diversity of known WSSV interacting proteins amongst susceptible penaeid shrimp/lobster and the more resistant C. maenas. There were differences in viral receptor sequences, like Rab7, that correlate with a less efficient infection by WSSV. To produce the genome scaffold assembly for C. maenas we isolated DNA from muscle tissue and produced both paired-end and mate pair libraries for processing on the Illumina HiSeq 2500 platform. A de novo draft genome assembly consisting of 338,980 scaffolds and covering 362 Mb (36 % of estimated genome size) was produced, using SOAP-denovo2 coupled with the BESST scaffolding system. The generated assembly was highly fragmented due to the presence of repetitive areas in the C. maenas genome. Using a combination of ab initio predictors, RNA-sequencing data from the transcriptome datasets and curated C. maenas sequences we produced a model encompassing 10,355 genes. The gene model for C. maenas Dscam, a gene potentially involved in (pan)crustacean immune memory, was investigated in greater detail as manual curation can improve on the results of ab initio predictors. The scaffold containing C. maenas Dscam was fragmented, thus only contained the latter exons of the gene. The assembled draft genome and transcriptomes for C. maenas and H. gammarus are valuable molecular resources for studies involving these and other aquatic crustacean species. To uncover the basis of their resistance to WSSV, we infected C. maenas with WSSV and measured mRNA and miRNA expression for 7 time points spread over a period of 28 days, using RNA-Seq and miRNA-Seq. The resistance of C. maenas to WSSV infection was confirmed by the fact that no mortalities occurred. In these animals replicating WSSV was latent and detected only after 7 days, and this occurred in five of out 28 infected crabs only. Differential expression of transcripts and miRNAs were identified for each time point. In the first 12 hours post exposure we observed decreased expression of important regulators in endocytosis. Since it is established that WSSV enters the host cells through endocytosis and that interactions between the viral protein VP28 and Rab7 are important in successful infection, it is likely that changes in this process could impact WSSV infection success. Additionally we observed an increased expression of transcripts involved in RNA interference pathways across many time points, indicating a longer term response to initial viral exposure. miRNA sequencing showed several miRNAs that were differentially expressed. The most striking finding was a novel C. maenas miRNA that we found to be significantly downregulated in every WSSV infected individual, suggesting that it may play an important role in mediating the response of the host to the virus. In silico target prediction pointed to the involvement of this miRNA in endocytosis regulation. Taken together we hypothesize that C. maenas resistance to WSSV involves obstruction of viral entry by endocytosis, a process probably regulated through miRNAs, resulting in inefficient uptake of virions.Cefa