Phylogenetic and Chemical Probing Information as Soft Constraints in RNA Secondary Structure Prediction.

Extrinsic, experimental information can be incorporated into thermodynamics-based RNA folding algorithms in the form of pseudo-energies. Evolutionary conservation of RNA secondary structure elements is detectable in alignments of phylogenetically related sequences and provides evidence for the presence of certain base pairs that can also be converted into pseudo-energy contributions. We show that the centroid base pairs computed from a consensus folding model such as RNAalifold result in a substantial improvement of the prediction accuracy for single sequences. Evidence for specific base pairs turns out to be more informative than a position-wise profile for the conservation of the pairing status. A comparison with chemical probing data, furthermore, strongly suggests that phylogenetic base pairing data are more informative than position-specific data on (un)pairedness as obtained from chemical probing experiments. In this context we demonstrate, in addition, that the conversion of signal from probing data into pseudo-energies is possible using thermodynamic structure predictions as a reference instead of known RNA structures.

Led-Seq: ligation-enhanced double-end sequence-based structure analysis of RNA.

Structural analysis of RNA is an important and versatile tool to investigate the function of this type of molecules in the cell as well as in vitro. Several robust and reliable procedures are available, relying on chemical modification inducing RT stops or nucleotide misincorporations during reverse transcription. Others are based on cleavage reactions and RT stop signals. However, these methods address only one side of the RT stop or misincorporation position. Here, we describe Led-Seq, a new approach based on lead-induced cleavage of unpaired RNA positions, where both resulting cleavage products are investigated. The RNA fragments carrying 2', 3'-cyclic phosphate or 5'-OH ends are selectively ligated to oligonucleotide adapters by specific RNA ligases. In a deep sequencing analysis, the cleavage sites are identified as ligation positions, avoiding possible false positive signals based on premature RT stops. With a benchmark set of transcripts in Escherichia coli, we show that Led-Seq is an improved and reliable approach based on metal ion-induced phosphodiester hydrolysis to investigate RNA structures in vivo.

LazyB: fast and cheap genome assembly.

BACKGROUND: Advances in genome sequencing over the last years have lead to a fundamental paradigm shift in the field. With steadily decreasing sequencing costs, genome projects are no longer limited by the cost of raw sequencing data, but rather by computational problems associated with genome assembly. There is an urgent demand for more efficient and and more accurate methods is particular with regard to the highly complex and often very large genomes of animals and plants. Most recently, "hybrid" methods that integrate short and long read data have been devised to address this need. RESULTS: LazyB is such a hybrid genome assembler. It has been designed specificially with an emphasis on utilizing low-coverage short and long reads. LazyB starts from a bipartite overlap graph between long reads and restrictively filtered short-read unitigs. This graph is translated into a long-read overlap graph G. Instead of the more conventional approach of removing tips, bubbles, and other local features, LazyB stepwisely extracts subgraphs whose global properties approach a disjoint union of paths. First, a consistently oriented subgraph is extracted, which in a second step is reduced to a directed acyclic graph. In the next step, properties of proper interval graphs are used to extract contigs as maximum weight paths. These path are translated into genomic sequences only in the final step. A prototype implementation of LazyB, entirely written in python, not only yields significantly more accurate assemblies of the yeast and fruit fly genomes compared to state-of-the-art pipelines but also requires much less computational effort. CONCLUSIONS: LazyB is new low-cost genome assembler that copes well with large genomes and low coverage. It is based on a novel approach for reducing the overlap graph to a collection of paths, thus opening new avenues for future improvements. AVAILABILITY: The LazyB prototype is available at https://github.com/TGatter/LazyB .

Pentraxin-3 detected in human saliva shows limited correlation with biomarkers associated with systemic inflammation.

Pentraxin-3 (PTX3) is a conserved protein of the innate immune system which has been less studied than the pentraxin C-reactive protein (CRP), but it is of relevance in, for example, vascular pathology and pregnancy morbidities. Since the interest in salivary biomarkers in general is increasing, we asked whether PTX3 could be detected in saliva and if any substantial diurnal variation occurs. In addition, we evaluated association with biomarkers of systemic inflammation (interleukin (IL)-1ß, IL-6, and IL-8 and CRP), body mass index (BMI), smoking, and age. PTX3 in morning and evening saliva from 106 middle-aged participants of the general population was investigated by ELISA and total protein levels by spectrophotometry. PTX3 was detectable in saliva, and concentrations varied over the day with higher morning concentrations, but the PTX3 relative protein levels (percentage of total protein) were significantly higher in the evening. Sex and age did not impact salivary PTX3, but smoking was associated with lower PTX3 levels. BMI correlated positively with PTX3 in evening saliva. There was no general association with biomarkers of systemic inflammation, except for IL-6. Salivary PTX3 likely reflects the local inflammatory milieu, and adjustments for sampling time, smoking habits, and BMI are needed to adequately interpret PTX3 in saliva.

Pronounced Diurnal Pattern of Salivary C-Reactive Protein (CRP) With Modest Associations to Circulating CRP Levels.

C-reactive protein (CRP), a humoral component of the innate immune system with important functions in host-defense, is extensively used as a sensitive biomarker of systemic inflammation. During inflammation, hepatocyte-derived CRP rises dramatically in the blood due to increased interleukin-6 (IL-6) levels. Reliable detection of CRP in saliva, instead of blood, would offer advantages regarding sampling procedure and availability but using saliva as a diagnostic body fluid comes with challenges. The aims of this study were to evaluate associations between salivary CRP, total protein levels in saliva and serum CRP. Furthermore, we examined associations with plasma IL-6, body mass index (BMI), tobacco smoking and age. Salivary CRP was investigated by ELISA in 107 middle-aged participants from the general population. We employed spectrophotometric determination of total protein levels. Correlation analyses were used for associations of salivary CRP with serum CRP (turbidimetry), plasma IL-6 (Luminex®), BMI and smoking habits. Salivary median CRP was 68% higher (p=0.009), and total protein levels were 167% higher (p<0.0001), in morning compared to evening saliva. The correlation coefficients between serum and salivary CRP were low to moderate, but stronger for evening than morning saliva. Plasma IL-6 correlated significantly with serum CRP (rs =0.41, p<0.01), but not with morning or evening salivary CRP. Non-smokers showed 103% higher salivary CRP levels (p=0.015), whereas serum CRP was independent of smoking status. As opposed to CRP in serum, salivary CRP was not associated with BMI. Salivary CRP was 90% higher among the age interval 60-69 years compared to subjects aged 45-59 (p=0.02) while serum CRP levels did not differ between the age groups. In conclusion, CRP in saliva did not straightforwardly reflect serum concentrations. This raises questions regarding adequate reflection of biological events. The pronounced diurnal salivary CRP pattern accentuates the importance of standardizing the time-point of sampling.

Elevated Hedgehog activity contributes to attenuated DNA damage responses in aged hematopoietic cells.

Accumulation of DNA damage and myeloid-skewed differentiation characterize aging of the hematopoietic system, yet underlying mechanisms remain incompletely understood. Here, we show that aging hematopoietic progenitor cells particularly of the myeloid branch exhibit enhanced resistance to bulky DNA lesions-a relevant type of DNA damage induced by toxins such as cancer drugs or endogenous aldehydes. We identified aging-associated activation of the Hedgehog (Hh) pathway to be connected to this phenotype. Inhibition of Hh signaling reverts DNA damage tolerance and DNA damage-resistant proliferation in aged hematopoietic progenitors. Vice versa, elevating Hh activity in young hematopoietic progenitors is sufficient to impair DNA damage responses. Altogether, these findings provide experimental evidence for aging-associated increases in Hh activity driving DNA damage tolerance in myeloid progenitors and myeloid-skewed differentiation. Modulation of Hh activity could thus be explored as a therapeutic strategy to prevent DNA damage tolerance, myeloid skewing, and disease development in the aging hematopoietic system.