Peakhood: individual site context extraction for CLIP-seq peak regions.

Motivation: CLIP-seq is by far the most widely used method to determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). The binding site locations are identified from CLIP-seq read data by tools termed peak callers. Many RBPs bind to a spliced RNA (i.

RNAProt: an efficient and feature-rich RNA binding protein binding site predictor.

Background: Cross-linking and immunoprecipitation followed by next-generation sequencing (CLIP-seq) is the state-of-the-art technique used to experimentally determine transcriptome-wide binding sites of RNA-binding proteins (RBPs). However, it relies on gene expression, which can be highly variable between conditions and thus cannot provide a complete picture of the RBP binding landscape. This creates a demand for computational methods to predict missing binding sites.

Lessons learned from a corporate manufacturer on driving the adoption of nature-based solutions.

Companies are increasingly focused on driving the adoption of nature-based solutions across their organizations. Yet, implementing nature-based solutions within existing regulatory frameworks poses a unique set of challenges. In this paper, we present three nature-based solution case studies from The Dow Chemical Company and The Nature Conservancy's nearly 10-year collaboration.

Improving CLIP-seq data analysis by incorporating transcript information.

Background: Current peak callers for identifying RNA-binding protein (RBP) binding sites from CLIP-seq data take into account genomic read profiles, but they ignore the underlying transcript information, that is information regarding splicing events. So far, there are no studies available that closer observe this issue.

Results: Here we show that current peak callers are susceptible to false peak calling near exon borders.

Analysis of factors influencing the productivity of hammer drilling - user forces, human fatigue, drilling direction, and drill bit.

In order to be able to develop a hammer drill with which the user can work as ergonomically and productively as possible, the relevant influencing factors must be known. In addition to the unknown influence of the drilling direction, there is a lack of understanding of the relations between user forces, human fatigue, and productivity. To analyze these relations, an experiment was carried out with 15 professional users.

Galaxy CLIP-Explorer: a web server for CLIP-Seq data analysis.

Background: Post-transcriptional regulation via RNA-binding proteins plays a fundamental role in every organism, but the regulatory mechanisms lack important understanding. Nevertheless, they can be elucidated by cross-linking immunoprecipitation in combination with high-throughput sequencing (CLIP-Seq). CLIP-Seq answers questions about the functional role of an RNA-binding protein and its targets by determining binding sites on a nucleotide level and associated sequence and structural binding patterns.

CopomuS-Ranking Compensatory Mutations to Guide RNA-RNA Interaction Verification Experiments.

In silico RNA-RNA interaction prediction is widely applied to identify putative interaction partners and to assess interaction details in base pair resolution. To verify specific interactions, in vitro evidence can be obtained via compensatory mutation experiments. Unfortunately, the selection of compensatory mutations is non-trivial and typically based on subjective ad hoc decisions.

Analysis of the androgen receptor-regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression.

The androgen receptor (AR) plays a critical role in the development of the normal prostate as well as prostate cancer. Using an integrative transcriptomic analysis of prostate cancer cell lines and tissues, we identified ARLNC1 (AR-regulated long noncoding RNA 1) as an important long noncoding RNA that is strongly associated with AR signaling in prostate cancer progression. Not only was ARLNC1 induced by the AR protein, but ARLNC1 stabilized the AR transcript via RNA-RNA interaction.

Determination of hydroxy metabolites of cocaine from hair samples and comparison with street cocaine samples.

Drugs which are commonly smoked or sniffed (e.g. cocaine), can contaminate hair through smoke or dust; therefore testing for metabolites, especially hydroxy metabolites, is highly recommended.

hnRNP R and its main interactor, the noncoding RNA 7SK, coregulate the axonal transcriptome of motoneurons.

Disturbed RNA processing and subcellular transport contribute to the pathomechanisms of motoneuron diseases such as amyotrophic lateral sclerosis and spinal muscular atrophy. RNA-binding proteins are involved in these processes, but the mechanisms by which they regulate the subcellular diversity of transcriptomes, particularly in axons, are not understood. Heterogeneous nuclear ribonucleoprotein R (hnRNP R) interacts with several proteins involved in motoneuron diseases.

RIP-Seq Suggests Translational Regulation by L7Ae in .

L7Ae is a universal archaeal protein that recognizes and stabilizes kink-turn (k-turn) motifs in RNA substrates. These structural motifs are widespread in nature and are found in many functional RNA species, including ribosomal RNAs. Synthetic biology approaches utilize L7Ae/k-turn interactions to control gene expression in eukaryotes.

Computational analysis of CLIP-seq data.

CLIP-seq experiments are currently the most important means for determining the binding sites of RNA binding proteins on a genome-wide level. The computational analysis can be divided into three steps. In the first pre-processing stage, raw reads have to be trimmed and mapped to the genome.

Catalytic competence, structure and stability of the cancer-associated R139W variant of the human NAD(P)H:quinone oxidoreductase 1 (NQO1).

The human NAD(P)H:quinone oxidoreductase 1 (NQO1; EC1.6.99.

Mechanism of β-actin mRNA Recognition by ZBP1.

Zipcode binding protein 1 (ZBP1) is an oncofetal RNA-binding protein that mediates the transport and local translation of β-actin mRNA by the KH3-KH4 di-domain, which is essential for neuronal development. The high-resolution structures of KH3-KH4 with their respective target sequences show that KH4 recognizes a non-canonical GGA sequence via an enlarged and dynamic hydrophobic groove, whereas KH3 binding to a core CA sequence occurs with low specificity. A data-informed kinetic simulation of the two-step binding reaction reveals that the overall reaction is driven by the second binding event and that the moderate affinities of the individual interactions favor RNA looping.

The lncRNA landscape of breast cancer reveals a role for DSCAM-AS1 in breast cancer progression.

Molecular classification of cancers into subtypes has resulted in an advance in our understanding of tumour biology and treatment response across multiple tumour types. However, to date, cancer profiling has largely focused on protein-coding genes, which comprise <1% of the genome. Here we leverage a compendium of 58,648 long noncoding RNAs (lncRNAs) to subtype 947 breast cancer samples.

Structural and kinetic studies on RosA, the enzyme catalysing the methylation of 8-demethyl-8-amino-d-riboflavin to the antibiotic roseoflavin.

Unlabelled: N,N-8-demethyl-8-amino-d-riboflavin dimethyltransferase (RosA) catalyses the final dimethylation of 8-demethyl-8-amino-d-riboflavin (AF) to the antibiotic roseoflavin (RoF) in Streptomyces davawensis. In the present study, we solved the X-ray structure of RosA, and determined the binding properties of substrates and products. Moreover, we used steady-state and rapid reaction kinetic studies to obtain detailed information on the reaction mechanism.

RC3H1 post-transcriptionally regulates A20 mRNA and modulates the activity of the IKK/NF-κB pathway.

The RNA-binding protein RC3H1 (also known as ROQUIN) promotes TNFα mRNA decay via a 3'UTR constitutive decay element (CDE). Here we applied PAR-CLIP to human RC3H1 to identify ∼ 3,800 mRNA targets with >16,000 binding sites. A large number of sites are distinct from the consensus CDE and revealed a structure-sequence motif with U-rich sequences embedded in hairpins.

The crystal structure of D-threonine aldolase from Alcaligenes xylosoxidans provides insight into a metal ion assisted PLP-dependent mechanism.

Threonine aldolases catalyze the pyridoxal phosphate (PLP) dependent cleavage of threonine into glycine and acetaldehyde and play a major role in the degradation of this amino acid. In nature, L- as well as D-specific enzymes have been identified, but the exact physiological function of D-threonine aldolases (DTAs) is still largely unknown. Both types of enantio-complementary enzymes have a considerable potential in biocatalysis for the stereospecific synthesis of various β-hydroxy amino acids, which are valuable building blocks for the production of pharmaceuticals.

Structure and stability of an unusual zinc-binding protein from Bacteroides thetaiotaomicron.

The crystal structure of a putative protease from Bacteroides thetaiotaomicron (ppBat) suggested the presence of a zinc ion in each protomer of the dimer as well as a flavin in the dimer interface. Since the chemical identity of the flavin and the exact mode of binding remained unclear, we have determined the crystal structure of ppBat in complex with riboflavin. The obtained structure revealed that the isoalloxazine ring is sandwiched between two tryptophan residues (Trp164) from both chains and adopts two alternate orientations with the N(10)-ribityl side chain protruding from the binding site in opposite directions.

Collapse of the native structure caused by a single amino acid exchange in human NAD(P)H:quinone oxidoreductase(1.).

Unlabelled: Human

Nad(p)h: quinone oxidoreductase 1 (NQO1) is essential for the antioxidant defense system, stabilization of tumor suppressors (e.g. p53, p33, and p73), and activation of quinone-based chemotherapeutics.

Differentiation of heroin and cocaine using dual-energy CT-an experimental study.

Objective: To evaluate if heroin and cocaine can be distinguished using dual-energy CT.

Materials And Methods: Twenty samples of heroin and cocaine at different concentrations and standardized compression (SC) were scanned in dual-energy mode on a newest generation Dual Energy 64-row MDCT scanner. CT number, spectral graphs, and dual-energy index (DEI) were evaluated.

Low-dose CT in body-packers: delineation of body packs and radiation dose in a porcine model.

Purpose: To compare low-dose computed tomography (CT) with standard CT and conventional radiography (CR) regarding delineation of body packs and radiation dose.

Methods: Nine samples of illicit drugs including cocaine, heroin, and hashish were positioned in the rectum of a 121.5 kg pig cadaver.

Proof of cannabis administration by sensitive detection of 11-nor-Delta(9)-tetrahydrocannabinol-9-carboxylic acid in hair using selective methylation and application of liquid chromatography- tandem and multistage mass spectrometry.

The identification of 11-nor-Δ9-tetrahydrocannabinol-9-carboxylic acid (THCCOOH) in hair represents an exceptional forensic analytical challenge due to low target concentrations in a complex matrix. Several dedicated techniques [gas chromatography-negative chemical ionization-tandem mass spectrometry (GC-NCI-MS/MS) or GC-GC-MS couplings] were specifically introduced into forensic toxicology aiming to a selective and sensitive identification of THCCOOH in hair. The combination of liquid-chromatography (LC) and MS/MS gained an outstanding relevance in forensic toxicology (including the detection of cannabinoids).