FRANz: reconstruction of wild multi-generation pedigrees

Summary: We present a software package for pedigree reconstruction in natural populations using co-dominant genomic markers such as microsatellites and single nucleotide polymorphisms (SNPs). If available, the algorithm makes use of prior information such as known relationships (sub-pedigrees) or the age and sex of individuals. Statistical confidence is estimated by Markov Chain Monte Carlo (MCMC) sampling. The accuracy of the algorithm is demonstrated for simulated data as well as an empirical dataset with known pedigree. The parentage inference is robust even in the presence of genotyping errors

IFLA Special Interest Group (SIG) on Library Publishing. 2019 Midterm Meeting (Dublin, February 28–March 1, 2019)

Von 28. Februar bis 1. März 2019 fand in Dublin/IRL eine von der International Federation of Library Associations and Institutions veranstaltete Konferenz zum Thema „Library Publishing“ statt. Vortragende aus Europa und Nordamerika sprachen an der Dublin Business School (DBS) zu Publikationsprojekten, Herausforderungen und Perspektiven von Bibliotheken als Verleger und Herausgeber von Publikationen.On the 28th of February and 1th of March the International Federation of Library Associations and Institutions organized a conference about “Library Publishing“ in Dublin, Ireland. Hosted by Dublin Business School (DBS) lecturers from Europe and North America discussed publication projects, challenges and perspectives of library publishing

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures

BACKGROUND: Large RNA molecules are often composed of multiple functional domains whose spatial arrangement strongly influences their function. Pre-mRNA splicing, for instance, relies on the spatial proximity of the splice junctions that can be separated by very long introns. Similar effects appear in the processing of RNA virus genomes. Albeit a crude measure, the distribution of spatial distances in thermodynamic equilibrium harbors useful information on the shape of the molecule that in turn can give insights into the interplay of its functional domains. RESULT: Spatial distance can be approximated by the graph-distance in RNA secondary structure. We show here that the equilibrium distribution of graph-distances between a fixed pair of nucleotides can be computed in polynomial time by means of dynamic programming. While a naïve implementation would yield recursions with a very high time complexity of O(n(6)D(5)) for sequence length n and D distinct distance values, it is possible to reduce this to O(n(4)) for practical applications in which predominantly small distances are of of interest. Further reductions, however, seem to be difficult. Therefore, we introduced sampling approaches that are much easier to implement. They are also theoretically favorable for several real-life applications, in particular since these primarily concern long-range interactions in very large RNA molecules. CONCLUSIONS: The graph-distance distribution can be computed using a dynamic programming approach. Although a crude approximation of reality, our initial results indicate that the graph-distance can be related to the smFRET data. The additional file and the software of our paper are available from http://www.rna.uni-jena.de/RNAgraphdist.html

Learning to solve ill-defined statistics problems: does self-explanation quality mediate the worked example effect?

Extensive research has established that successful learning from an example is conditional on an important learning activity: self-explanation. Moreover, a model for learning from examples suggests that self-explanation quality mediates effects of examples on learning outcomes (Atkinson et al. in Rev Educ Res 70:181–214, 2000). We investigated self-explanation quality as mediator in a worked examples—problem-solving paradigm. We developed a coding scheme to assess self-explanation quality in the context of ill-defined statistics problems and analyzed self-explanation data of a study by Schwaighofer et al. (J Educ Psychol 108: 982–1000, 2016). Schwaighofer et al. (J Educ Psychol 108: 982–1000, 2016) investigated whether the worked example effect depends on prior knowledge, working memory capacity, shifting ability, and fluid intelligence. In our study, we included these variables to jointly explore mediating and moderating factors when individuals learn with worked examples versus through problem-solving. Seventy-four university students (mean age = 23.83, SD = 5.78) completed an open item pretest, self-explained while either studying worked examples or solving problems, and then completed a post-test. We used conditional process analysis to test whether the effect of worked examples on learning gains is mediated by self-explanation quality and whether any effect in the mediation model depends on the suggested moderators. We reproduced the interaction effects reported by Schwaighofer et al. (J Educ Psychol 108: 982–1000, 2016) but did not detect a mediation effect. This might indicate that worked examples are directly effective because they convey a solution strategy, which might be particularly important when learning to solve problems that have no algorithmic solution procedure

The Effect of RNA Secondary Structures on RNA-Ligand Binding and the Modifier RNA Mechanism: A Quantitative Model

RNA-ligand binding often depends crucially on the local RNA secondary structure at the binding site. We develop here a model that quantitatively predicts the effect of RNA secondary structure on effective RNA-ligand binding activities based on equilibrium thermodynamics and the explicit computations of partition functions for the RNA structures. A statistical test for the impact of a particular structural feature on the binding affinities follows directly from this approach. The formalism is extended to describing the effects of hybridizing small \modifier RNAs' to a target RNA molecule outside its ligand binding site. We illustrate the applicability of our approach by quantitatively describing the interaction of the mRNA stabilizing protein HuR with AU-rich elements [Meisner et al. (2004), Chem. Biochem. in press]. We discuss our model and recent experimental findings demonstrating the ffectivity of modifier RNAs in vitro in the context of the current research activities in the field of non-coding RNAs. We speculate that modifier RNAs might also exist in nature; if so, they present an additional regulatory layer for fine-tuning gene expression that could evolve rapidly, leaving no obvious traces in the genomic DNA sequences

Phylogenetics from paralogs

Motivation: Sequence-based phylogenetic approaches heavily rely on initial data sets to be composed of orthologous sequences only. Paralogs are treated as a dangerous nuisance that has to be detected and removed. Recent advances in mathematical phylogenetics, however, have indicated that gene duplications can also convey meaningful phylogenetic information provided orthologs and paralogs can be distinguished with a degree of certainty. Results: We demonstrate that plausible phylogenetic trees can be inferred from paralogy information only. To this end, tree-free estimates of orthology, the complement of paralogy, are first corrected to conform cographs and then translated into equivalent event-labeled gene phylogenies. A certain subset of the triples displayed by these trees translates into constraints on the species trees. While the resolution is very poor for individual gene families, we observe that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees of several groups of eubacteria. The novel method introduced here relies on solving three intertwined NP-hard optimization problems: the cograph editing problem, the maximum consistent triple set problem, and the least resolved tree problem. Implemented as Integer Linear Program, paralogy-based phylogenies can be computed exactly for up to some twenty species and their complete protein complements. Availability:The ILP formulation is implemented in the Software ParaPhylo using IBM ILOG CPLEX (TM) Optimizer 12.6 and is freely available from http://pacosy.informatik.uni-leipzig.de/paraphyl

Transmission Dynamics of Extended-Spectrum β-lactamase-Producing Enterobacteriaceae in the Tertiary Care Hospital and the Household Setting

Transmission of extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae in households outweighs nosocomial dissemination in the non-outbreak setting. Importation of ESBL producers into the hospitals is as frequent as transmission during hospital stay. ESBL-Klebsiella pneumoniae might be more efficiently transmitted within the hospital than ESBL-Escherichia col

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis

Small non-protein-coding RNAs (ncRNAs) have systematically been studied in various model organisms from Escherichia coli to Homo sapiens. Here, we analyse the small ncRNA transcriptome from the pathogenic filamentous fungus Aspergillus fumigatus. To that aim, we experimentally screened for ncRNAs, expressed under various growth conditions or during specific developmental stages, by generating a specialized cDNA library from size-selected small RNA species. Our screen revealed 30 novel ncRNA candidates from known ncRNA classes such as small nuclear RNAs (snRNAs) and C/D box-type small nucleolar RNAs (C/D box snoRNAs). Additionally, several candidates for H/ACA box snoRNAs could be predicted by a bioinformatical screen. We also identified 15 candidates for ncRNAs, which could not be assigned to any known ncRNA class. Some of these ncRNA species are developmentally regulated implying a possible novel function in A. fumigatus development. Surprisingly, in addition to full-length tRNAs, we also identified 5′- or 3′-halves of tRNAs, only, which are likely generated by tRNA cleavage within the anti-codon loop. We show that conidiation induces tRNA cleavage resulting in tRNA depletion within conidia. Since conidia represent the resting state of A. fumigatus we propose that conidial tRNA depletion might be a novel mechanism to down-regulate protein synthesis in a filamentous fungus