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Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

ABSTRACT: With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analysis. To reach that goal, a practical course has been set up for master students at the University of Lausanne: the "Sequence a genome" class. At the beginning of the academic year, a few bacterial species whose genome is unknown are provided to the students, who sequence and assemble the genome(s) and perform manual annotation. Here, we report the progress of the first class from September 2010 to June 2011 and the results obtained by seven master students who specifically assembled and annotated the genome of Estrella lausannensis, an obligate intracellular bacterium related to Chlamydia. The draft genome of Estrella is composed of 29 scaffolds encompassing 2,819,825 bp that encode for 2233 putative proteins. Estrella also possesses a 9136 bp plasmid that encodes for 14 genes, among which we found an integrase and a toxin/antitoxin module. Like all other members of the Chlamydiales order, Estrella possesses a highly conserved type III secretion system, considered as a key virulence factor. The annotation of the Estrella genome also allowed the characterization of the metabolic abilities of this strictly intracellular bacterium. Altogether, the students provided the scientific community with the Estrella genome sequence and a preliminary understanding of the biology of this recently-discovered bacterial genus, while learning to use cutting-edge technologies for sequencing and to perform bioinformatics analyses.

SUBMITTER: Bertelli C

PROVIDER: S-EPMC4333871 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

Bertelli Claire C Aeby Sébastien S Chassot Bérénice B Clulow James J Hilfiker Olivier O Rappo Samuel S Ritzmann Sébastien S Schumacher Paolo P Terrettaz Céline C Benaglio Paola P Falquet Laurent L Farinelli Laurent L Gharib Walid H WH Goesmann Alexander A Harshman Keith K Linke Burkhard B Miyazaki Ryo R Rivolta Carlo C Robinson-Rechavi Marc M van der Meer Jan Roelof JR Greub Gilbert G

Frontiers in microbiology 20150219

With the widespread availability of high-throughput sequencing technologies, sequencing projects have become pervasive in the molecular life sciences. The huge bulk of data generated daily must be analyzed further by biologists with skills in bioinformatics and by "embedded bioinformaticians," i.e., bioinformaticians integrated in wet lab research groups. Thus, students interested in molecular life sciences must be trained in the main steps of genomics: sequencing, assembly, annotation and analy ...[more]

PMID: 25745418

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Project description:BackgroundEncouraging professional integrity is vital for providing a standard of excellence in quality medical care and education and in promoting a culture of respect and responsibility. The primary objective of this work consisted of studying the relationship of medical students to the right to patient privacy in Spain, specifically by analysing the conditions for accessing patient clinical histories (CHs).MethodsA cross-sectional study was conducted based on a questionnaire sent by e-mail to final-year students at 41 Spanish universities. It had 14 multiple choice and closed questions framed in 3 large blocks. The first question addressed basic general knowledge issues on the right to privacy and the obligation for confidentiality. The two remaining blocks were made up of questions directed towards evaluating the frequency with which certain requirements and action steps related to students attending patients were performed and regarding the guarantees associated with accessing and handling patient CHs both on paper and in the Electronic Medical Record.ResultsA total of 245 valid replies were considered. A total of 67.8 % of participants were women, with an average age of 24.05 ± 3.49 years. Up to 90.6 % were aware that confidentiality affected the data in CHs, although 43.3 % possessed non-anonymized photocopies of patient clinical reports outside the healthcare context, and only 49.8 % of the students were always adequately identified. A total of 59.2 % accessed patient CHs on some occasions by using passwords belonging to healthcare professionals, 77.2 % of them did not have the patients' express consent, and 71.9 % accessed a CH that was not anonymised.ConclusionsThe role of healthcare institutions and universities is considered to be fundamental in implementing educational measures regarding the risks and ethical and legal problems arising from the use of CHs among professionals and students. A thorough study of medical ethics is needed through the analysis of clinical cases and direct exposure to situations in which the patient's confidentiality is questioned.

Project description:Background: The current study evaluated whether a new digitized scaling training program (DTP: n?=?30; supervisor-student-ratio 1:10) improves the performance of undergraduate dental student during a preclinical course in regard to two different instruments [sonic scalers (AIR) and Gracey curettes (GRA)] compared to a conventional training program (CTP: n?=?19; supervisor-student-ratio 1:4).Methods: All the participants received a two-hour lecture on both instruments, followed by a 12-week period with a weekly training program lasting 45 min (10 sessions); one group was supported by DTP. At the end of the training phase, all the participants performed the subgingival scaling of six equivalent test teeth using GRA and AIR. Treatment time, proportion of removed simulated biofilm (relative cleaning efficacy, RCE-b) and hard deposits (RCE-d) were recorded. By using a pseudonymized questionnaire with a 5-point Likert scale, self-assessment of scaling effort, handling, root surface roughness/destruction and effectiveness were evaluated. In addition, personal data such as age, gender, handedness, regularity of playing computer games/consoles and previous dental/technical or medical education were elevated and correlated with cleaning efficacy.Results: The DTP participants showed higher effectiveness in RCE-b compared to those who used the CTP with GRA (71.54% vs. 67.23%, p?=?0.004) and AIR (71.75% vs. 62.63%, p???0.001), and the DTP students were faster with both instruments (p???0.001). For RCE-d, there was no significant difference between the DTP and CTP groups (GRA p?=?0.471; AIR p?=?0.158), whereas DTP showed better RCE-d results with GRA versus AIR (84.68% vs. 77.85%, p?<?0.001). According to the questionnaire, no significant differences were detected between the training groups in terms of self-assessment, handling, treatment time, root surface roughness/destruction or effectiveness of the instruments. The CTP group favored AIR compared to GRA regarding the fatigue effect. The CTP and playing computer games/consoles regularly was correlated with lower RCE-b, whereas previous education in medicine/dentistry was correlated with higher RCE-b values.Conclusions: Within the limitations of the study, the DTP with a reduced supervision effort compared to the CTP resulted in higher effectiveness and lower instrumentation time for removing simulated biofilms.

Dataset Information

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

Publications

Sequencing and characterizing the genome of Estrella lausannensis as an undergraduate project: training students and biological insights.

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