Excited States of Nucleic Acids Probed by Proton Relaxation Dispersion NMR Spectroscopy

In this work an improved stable isotope labeling protocol for nucleic acids is introduced. The novel building blocks eliminate/minimize homonuclear 13C and 1H scalar couplings thus allowing proton relaxation dispersion (RD) experiments to report accurately on the chemical exchange of nucleic acids. Using site-specific 2H and 13C labeling, spin topologies are introduced into DNA and RNA that make 1H relaxation dispersion experiments applicable in a straightforward manner. The novel RNA/DNA building blocks were successfully incorporated into two nucleic acids. The A-site RNA was previously shown to undergo a two site exchange process in the micro- to millisecond time regime. Using proton relaxation dispersion experiments the exchange parameters determined earlier could be recapitulated, thus validating the proposed approach. We further investigated the dynamics of the cTAR DNA, a DNA transcript that is involved in the viral replication cycle of HIV-1. Again, an exchange process could be characterized and quantified. This shows the general applicablility of the novel labeling scheme for 1H RD experiments of nucleic acids

DNA-Based Diet Analysis for Any Predator

Background: Prey DNA from diet samples can be used as a dietary marker; yet current methods for prey detection require a priori diet knowledge and/or are designed ad hoc, limiting their scope. I present a general approach to detect diverse prey in the feces or gut contents of predators. Methodology/Principal Findings: In the example outlined, I take advantage of the restriction site for the endonuclease Pac I which is present in 16S mtDNA of most Odontoceti mammals, but absent from most other relevant non-mammalian chordates and invertebrates. Thus in DNA extracted from feces of these mammalian predators Pac I will cleave and exclude predator DNA from a small region targeted by novel universal primers, while most prey DNA remain intact allowing prey selective PCR. The method was optimized using scat samples from captive bottlenose dolphins (Tursiops truncatus) fed a diet of 6–10 prey species from three phlya. Up to five prey from two phyla were detected in a single scat and all but one minor prey item (2% of the overall diet) were detected across all samples. The same method was applied to scat samples from free-ranging bottlenose dolphins; up to seven prey taxa were detected in a single scat and 13 prey taxa from eight teleost families were identified in total. Conclusions/Significance: Data and further examples are provided to facilitate rapid transfer of this approach to any predator. This methodology should prove useful to zoologists using DNA-based diet techniques in a wide variety of study systems

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Analysing the diets of invertebrate predators using terminal restriction fragments

Analysing food webs in agricultural habitats is essential for the development of natural control strategies. Several molecular tools to investigate trophic interactions on a species-specific level have been developed in recent years and their advantages and limitations have been discussed. With this study we introduce another tool, terminal restriction fragment length polymorphism (tRFLP). Generalist predators found in Australian brassica crops, their prey and abundant parasitoids were chosen as a model system to adapt and evaluate the tRFLP approach. Using general primers and selecting six restriction enzymes, we obtained species-specific tRF patterns for 21 of the most abundant arthropods in brassica crops. We detected up to three prey species in the gut contents of laboratory-fed predators. Detection rates differed among predators, ranging between 28 and 100%. The identification of a species-specific tRF pattern was strongly affected by the presence and concentrations of DNA from other species. In a preliminary field study, prey could be identified from 20% of the collected brown lacewings. The advantage of the tRFLP method is the possibility of identifying multiple species at once. This advantage is counterbalanced by methodological limitations, among which the most critical one is the fact that it will be difficult to maintain specificity in highly diverse ecosystems. However, if species diversity is limited and the target sequence and the primers are chosen to increase detection success, the tRFLP method can be used to study trophic interactions in the field.Anita Juen, Katja Hogendoorn, Gang Ma, Otto Schmidt and Michael A. Kellerhttp://link.springer.com/article/10.1007%2Fs10340-011-0406-x?LI=tru