Dataset Information

A beginner's guide to radiation damage.

ABSTRACT: Many advances in the understanding of radiation damage to protein crystals, particularly at cryogenic temperatures, have been made in recent years, but with this comes an expanding literature, and, to the new breed of protein crystallographer who is not really interested in X-ray physics or radiation chemistry but just wants to solve a biologically relevant structure, the technical nature and breadth of this literature can be daunting. The purpose of this paper is to serve as a rough guide to radiation damage issues, and to provide references to the more exacting and detailed work. No attempt has been made to report precise numbers (a factor of two is considered satisfactory), and, since there are aspects of radiation damage that are demonstrably unpredictable, the 'worst case scenario' as well as the 'average crystal' are discussed in terms of the practicalities of data collection.

SUBMITTER: Holton JM

PROVIDER: S-EPMC2651760 | biostudies-literature | 2009 Mar

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

A beginner's guide to radiation damage.

Holton James M JM

Journal of synchrotron radiation 20090225 Pt 2

Many advances in the understanding of radiation damage to protein crystals, particularly at cryogenic temperatures, have been made in recent years, but with this comes an expanding literature, and, to the new breed of protein crystallographer who is not really interested in X-ray physics or radiation chemistry but just wants to solve a biologically relevant structure, the technical nature and breadth of this literature can be daunting. The purpose of this paper is to serve as a rough guide to ra ...[more]

PMID: 19240325

Similar Datasets

Project description:BackgroundDNA methylation is a conserved epigenetic mark that controls genome stability, development and environmental responses in many eukaryotes. DNA methylation can be guided by non-coding RNAs that include small interfering RNAs and scaffold RNAs. Although measurement of DNA methylation and regulatory non-coding RNAs is desirable for many biologists who are interested in exploring epigenetic regulation in their areas, conventional methods have limitations and are technically challenging. For instance, traditional siRNA detection through RNA hybridization requires relatively large amount of small RNAs and involves radioactive isotopes. An alternative approach is RT-qPCR that employs stem loop primers during reverse transcription; however, it requires a prerequisite that the exact sequences of siRNAs should be known.ResultsBy using the model organism Arabidopsis thaliana, we developed an easy-to-follow, integrative procedure for time-efficient, quantitative measurement of DNA methylation, small interfering RNAs, and scaffold RNAs. Starting with simplified nucleic acid manipulation, we examined DNA methylation levels by using Chop PCR (methylation-sensitive enzyme digestion followed by PCR), which allowed for fast screening for DNA methylation mutants without the need of transgenic reporters. We deployed a simple bioinformatics method for mining published small RNA databases, in order to obtain the nucleotide (nt) sequences of individual 24nt siRNAs within the regions of interest. The protocol of commercial TaqMan Small RNA Assay was subsequently optimized for reliable quantitative detection of individual siRNAs. We used nested qPCR to quantify scaffold RNAs that are of low abundance and without Poly-A tails. In addition, nuclei fraction enables separation of chromatin-associated scaffold RNAs from their cognate non-scaffold transcripts that have been released from chromatin.ConclusionsWe have developed a procedure for quantitative investigations on nucleic acids that are core components of RNA-directed DNA methylation. Our results not only demonstrated the efficacy of this procedure, but also provide lists of methylation-sensitive restriction enzymes, novel DNA methylation marker loci, and related siRNA sequences, all of which can be valuable for future epigenetic studies. Importantly, step-by-step protocols are provided in details such that the approaches can be easily followed by biologists with little experience in epigenetics.

Project description:Introduction Writing a case report increases one's knowledge about a particular disease condition, demonstrates intellectual curiosity and commitment to scientific inquiry and the ability to follow through on scholarly projects. Despite several articles and journal-specific instructions published concerning case report writing, none have been evaluated by their intended audience. The aim of this study was to get junior doctors to evaluate an online presentation as part of the process of developing a beginner's guide to writing a clinical case report. Materials and methods In response to our previous studies an online presentation concerning how to write a clinical case report was provided for junior doctors. Junior doctors were invited by email to look at the online presentation and complete an online evaluation form thereafter. The questions were adapted from the Evaluation Form for Teaching and Presentations provided by the Joint Royal Colleges of Physicians Training Board. Data was analysed both quantitatively and qualitatively. Results Sixty-five doctors looked at the presentation and completed the online evaluation form. All agreed that the objectives of the presentation were identified and met. Sixty-four (98.5%) agreed that it was effective and clear. Sixty percent indicated that they found the information and instructions useful. An additional 13.85% found the whole presentation useful without specifying any aspect. Eight percent found the summary slide useful, 4.62% found the case selection criteria slide to be useful and 4.62% found the permission and patient consenting slide useful. Twenty percent would like the inclusion of examples of good abstracts and case reports, 13.85% would like more teaching sessions, and 13.85% would like improvements to the slide-presentation format. Overall, 64 junior doctors (98.46%) remarked that the presentation was good, very good or excellent. Conclusions This study has demonstrated the importance of evaluation of teaching material by junior doctors while developing a beginner's guide to writing a clinical case report. Once the above action points and limitations have been taken into account, further repeat evaluations by junior doctors need to be undertaken while developing a robust beginner's guide to writing a clinical case report.

Dataset Information

A beginner's guide to radiation damage.

Publications

A beginner's guide to radiation damage.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets