| 1. |
- Loftsdottir, Heidur, et al.
(författare)
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Dynamics of insertion sequence element IS629 inactivation of verotoxin 2 genes in Escherichia coli O157:H7
- 2017
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Ingår i: FEMS Microbiology Letters. - : Oxford University Press. - 0378-1097 .- 1574-6968. ; 364:8
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Tidskriftsartikel (refereegranskat)abstract
- There are several anecdotal reports of insertion sequence (IS) element inactivation of verotoxin genes among enterohaemorrhagic Escherichia coli of the serotype O157:H7, a pathogen causing severe gastrointestinal disease in infected humans. These insertions can be expected to drastically reduce the virulence of the bacteria. IS element inactivation has been shown to be reversible in model systems, suggesting the possibility of spontaneous restoration of virulence. In this study, traditional and high-throughput sequencing was used to characterise three patterns of IS629 inactivation of verotoxin 2 genes in EHEC O157:H7, caused by insertion or insertion followed by partial deletion. At least one of the patterns of inactivation appears to have persisted several years among cattle O157:H7, indicating it has no major effect on fitness in the animal reservoir. Digital PCR was used to directly quantify the reversal rates of the insertional inactivation of a selected isolate under laboratory conditions. Inserts were found to be absent from in the order of 1/10(5) of individual genomes, with significantly higher loss frequencies observed in cultures under nutrient-poor conditions. We conclude that strains with this type of inactivation found in food or animal samples should be considered a threat to human health, and may pose a challenge for PCR-based detection methods.
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| 2. |
- Bongcam Rudloff, Erik
(författare)
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2016 EMBnet Annual General Meeting – Executive Board Report
- 2017
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Ingår i: EMBnet.journal. - : EMBnet Stichting. - 2226-6089. ; 22
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- During the past year, the Executive Board (EB) held regular monthly meetings either via Skype or using Adobe Connect. These meetings were carried out with the Interim Board (IB), comprising members of the EB and Teresa Attwood and Etienne de Villiers. The IB was established during the 2015 Annual General Meeting (AGM) both to support the new EB in its first steps forward (as three of its members were new), and to help oversee implementation and delivery of the investment strategy. The EB also regularly invited Special Interest Group (SIG) Chairs to participate at EB-IB meetings. Additional monthly meetings open to the full EMBnet constituency were also convened. In this report, we provide a brief overview of activities and achievements from June 2015 to October 2016.
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| 3. |
- Bongcam Rudloff, Erik
(författare)
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Correction: GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
- 2015
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Ingår i: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 11
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Annan publikation (refereegranskat)abstract
- In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy-paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.
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| 4. |
- Bongcam Rudloff, Erik
(författare)
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GOBLET: The Global Organisation for Bioinformatics Learning, Education and Training
- 2015
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Ingår i: PLoS Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 11
-
Tidskriftsartikel (refereegranskat)abstract
- In recent years, high-throughput technologies have brought big data to the life sciences. The march of progress has been rapid, leaving in its wake a demand for courses in data analysis, data stewardship, computing fundamentals, etc., a need that universities have not yet been able to satisfy-paradoxically, many are actually closing "niche" bioinformatics courses at a time of critical need. The impact of this is being felt across continents, as many students and early-stage researchers are being left without appropriate skills to manage, analyse, and interpret their data with confidence. This situation has galvanised a group of scientists to address the problems on an international scale. For the first time, bioinformatics educators and trainers across the globe have come together to address common needs, rising above institutional and international boundaries to cooperate in sharing bioinformatics training expertise, experience, and resources, aiming to put ad hoc training practices on a more professional footing for the benefit of all.
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| 5. |
- Bongcam Rudloff, Erik
(författare)
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Standardization and Quality Assurance in Life-Science Research - Crucially Needed or Unnecessary and Annoying Regulation?
- 2018
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Ingår i: Communications in Computer and Information Science. - Cham : Springer International Publishing. - 1865-0929 .- 1865-0937. ; 940, s. 13-20
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Konferensbidrag (refereegranskat)abstract
- Open Science describes the ongoing transitions in the way research is performed, i.e. researchers collaborate, knowledge is shared, and science is organized. It is driven by digital technologies and by the enormous growth of data, globalization, enlargement of the scientific community and the need to address societal challenges [23]. It has now widely been recognized that making research results more accessible to all societal actors contributes to better and more efficient science, as well as to innovation in the public and private sectors [1, 17]. However, the reuse of research results can only be achieved reliably and efficiently, if these data are valorized in a specific manner. Data are to be generated, formatted and stored according to Standard Operating Procedures (SOPs) and according to sophisticated Data Management Plans [23]. Hence, to generate accurate and reproducible data sets, to allow interlaboratory comparisons as well as further and future use of research data it is mandatory to work in line with good laboratory practices and well-defined and validated methodologies. Within this article, members of the Cost Action CHARME [10] will discuss aspects of quality management and standardization in context with Open Access (OA) efforts. We will address the question: Are Standardization and Quality Management measures in life-science research crucially needed or introduce further unwanted means of regulation?
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| 6. |
- Bongcam Rudloff, Erik
(författare)
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The GOBLET training portal: a global repository of bioinformatics training materials, courses and trainers
- 2015
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 31, s. 140-142
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Tidskriftsartikel (refereegranskat)abstract
- A Summary: Rapid technological advances have led to an explosion of biomedical data in recent years. The pace of change has inspired new collaborative approaches for sharing materials and resources to help train life scientists both in the use of cutting-edge bioinformatics tools and databases and in how to analyse and interpret large datasets. A prototype platform for sharing such training resources was recently created by the Bioinformatics Training Network (BTN). Building on this work, we have created a centralized portal for sharing training materials and courses, including a catalogue of trainers and course organizers, and an announcement service for training events. For course organizers, the portal provides opportunities to promote their training events; for trainers, the portal offers an environment for sharing materials, for gaining visibility for their work and promoting their skills; for trainees, it offers a convenient one-stop shop for finding suitable training resources and identifying relevant training events and activities locally and worldwide.
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| 7. |
- Bongcam Rudloff, Erik, et al.
(författare)
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The identification and classification of endogenous retroviruses in the horse genome
- 2018
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Ingår i: Mongolian Journal of Agricultural Science. - : Mongolian Journals Online. - 2310-6212 .- 2524-0722. ; 23, s. 3-8
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Tidskriftsartikel (refereegranskat)abstract
- Endogenous retroviruses (ervs) are sequences that derived from ancient retroviral infections of germ cells and integrated in humans, mammals and other vertebrates millions years ago. These ervs are inherited according to Mendelian expectations as all other genes in the genome. Coding sequences are flanked by two ltrs (long terminal repeat sequences). Most ervs are defective however some ervs still have open reading frames in their genome. These ervs settle close to functional genes or within the genes and can influence or control functions of the host genes using their ltrs. Most integration has deleterious effects. However some integration could be example of positive co-adaptation as syncitin. The first equine endogenous beta retrovirus which is ecerv-beta1 has been found in 2011 by Antoinette C.van der Kuyl1. The first known beta retrovirus and few pol gene similar to foamy retrovirus were only known endogenous retroviruses fixed in the domestic horse (equuscaballus) genome. Our aim of the study was to identify other endogenous retrovirus sequences in an equine genome and classify them into groups. Based on the high number of sines (equine repetitive element) in the horse genome we hypothesized that certain ervs will be located sufficiently close to sines that they will be amplified using an unbiased sine-pcr approach with degenerate primers. The nearest sine element was located 5.5 kbp upstream at the 5’of the ecerv-beta1. Pan-pol pcr was also used to find novel ervs based on 640 bp long region of pol gene which is the most conserved region of ervs. 27 complete and novel ervs that are 13 beta, 13 gamma, 1 spuma and 249 candidate endogenous retroviruses have been revealed using ltr_struc tool and double checked by retrotector online tool and ncbi-blast tool. It was proven that ecerv-beta1, which has 2 ltrs with 1% divergence between ltrs has a polymorphism among 13 different breeds.
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| 8. |
- Dahlö, Martin, et al.
(författare)
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BioImg.org : A catalog of virtual machine images for the life sciences
- 2015
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Ingår i: Bioinformatics and Biology Insights. - 1177-9322. ; 9, s. 125-128
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Tidskriftsartikel (refereegranskat)abstract
- Virtualization is becoming increasingly important in bioscience, enabling assembly and provisioning of complete computer setups, including operating system, data, software, and services packaged as virtual machine images (VMIs). We present an open catalog of VMIs for the life sciences, where scientists can share information about images and optionally upload them to a server equipped with a large file system and fast Internet connection. Other scientists can then search for and download images that can be run on the local computer or in a cloud computing environment, providing easy access to bioinformatics environments. We also describe applications where VMIs aid life science research, including distributing tools and data, supporting reproducible analysis, and facilitating education.
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| 9. |
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| 10. |
- Gourlé, Hadrien, et al.
(författare)
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Simulating Illumina metagenomic data with InSilicoSeq
- 2019
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 35, s. 521-522
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Tidskriftsartikel (refereegranskat)abstract
- Motivation: The accurate in silico simulation of metagenomic datasets is of great importance for benchmarking bioinformatics tools as well as for experimental design. Users are dependant on large-scale simulation to not only design experiments and new projects but also for accurate estimation of computational needs within a project. Unfortunately, most current read simulators are either not suited for metagenomics, out of date or relatively poorly documented. In this article, we describe InSilicoSeq, a software package to simulate metagenomic Illumina sequencing data. InsilicoSeq has a simple command-line interface and extensive documentation.Results: InSilicoSeq is implemented in Python and capable of simulating realistic Illumina (meta) genomic data in a parallel fashion with sensible default parameters.
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