TREMSUCS-TCGA - an integrated workflow for the identification of biomarkers for treatment success.

Many publicly available databases provide disease related data, that makes it possible to link genomic data to medical and meta-data. The cancer genome atlas (TCGA), for example, compiles tens of thousand of datasets covering a wide array of cancer types. Here we introduce an interactive and highly automatized TCGA-based workflow that links and analyses epigenomic and transcriptomic data with treatment and survival data in order to identify possible biomarkers that indicate treatment success.

Sweet syndrome: an update on clinical aspects, pathophysiology, and treatment.

Sweet syndrome is a neutrophilic dermatosis characterized by an autoinflammatory nature and a sterile neutrophilic infiltrate. It presents with tender, erythematous, edematous papules or plaques, often accompanied by fever. Aim of this review is to summarize the most meaningful aspects of Sweet syndrome, critically discussing old paradigms and novel findings.

Diverse prehistoric cattle husbandry strategies in the forests of Central Europe.

During the sixth millennium BCE, the first farmers of Central Europe rapidly expanded across a varied mosaic of forested environments. Such environments would have offered important sources of mineral-rich animal feed and shelter, prompting the question: to what extent did early farmers exploit forests to raise their herds? Here, to resolve this, we have assembled multi-regional datasets, comprising bulk and compound-specific stable isotope values from zooarchaeological remains and pottery, and conducted cross-correlation analyses within a palaeo-environmental framework. Our findings reveal a diversity of pasturing strategies for cattle employed by early farmers, with a notable emphasis on intensive utilization of forests for grazing and seasonal foddering in some regions.

Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution.

Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern changes with regard to mitochondrial tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mitochondrial tRNAs with a uniform workflow.

Evolution of neuropeptide Y/RFamide-like receptors in nematodes.

The Neuropeptide Y/RFamide-like receptors belong to the Rhodopsin-like G protein-coupled receptors G protein-coupled receptors (GPCRs) and are involved in functions such as locomotion, feeding and reproduction. With 41 described receptors they form the best-studied group of neuropeptide GPCRs in . In order to understand the expansion of the Neuropeptide Y/RFamide-like receptor family in nematodes, we started from the sequences of selected receptor paralogs in as query and surveyed the corresponding orthologous sequences in another 159 representative nematode target genomes.

Reaction rebalancing: a novel approach to curating reaction databases.

Purpose: Reaction databases are a key resource for a wide variety of applications in computational chemistry and biochemistry, including Computer-aided Synthesis Planning (CASP) and the large-scale analysis of metabolic networks. The full potential of these resources can only be realized if datasets are accurate and complete. Missing co-reactants and co-products, i.

Comprehensive survey of conserved RNA secondary structures in full-genome alignment of Hepatitis C virus.

Hepatitis C virus (HCV) is a plus-stranded RNA virus that often chronically infects liver hepatocytes and causes liver cirrhosis and cancer. These viruses replicate their genomes employing error-prone replicases. Thereby, they routinely generate a large 'cloud' of RNA genomes (quasispecies) which-by trial and error-comprehensively explore the sequence space available for functional RNA genomes that maintain the ability for efficient replication and immune escape.

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.

Mechanistic insights into G-protein coupling with an agonist-bound G-protein-coupled receptor.

G-protein-coupled receptors (GPCRs) activate heterotrimeric G proteins by promoting guanine nucleotide exchange. Here, we investigate the coupling of G proteins with GPCRs and describe the events that ultimately lead to the ejection of GDP from its binding pocket in the Gα subunit, the rate-limiting step during G-protein activation. Using molecular dynamics simulations, we investigate the temporal progression of structural rearrangements of GDP-bound G protein (G·GDP; hereafter G) upon coupling to the β-adrenergic receptor (βAR) in atomic detail.

Comparative RNA Genomics.

Over the last quarter of a century it has become clear that RNA is much more than just a boring intermediate in protein expression. Ancient RNAs still appear in the core information metabolism and comprise a surprisingly large component in bacterial gene regulation. A common theme with these types of mostly small RNAs is their reliance of conserved secondary structures.

The Theory of Gene Family Histories.

Most genes are part of larger families of evolutionary-related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene family histories, i.

Assessing the Quality of Cotranscriptional Folding Simulations.

Structural changes in RNAs are an important contributor to controlling gene expression not only at the posttranscriptional stage but also during transcription. A subclass of riboswitches and RNA thermometers located in the 5' region of the primary transcript regulates the downstream functional unit - usually an ORF - through premature termination of transcription. Not only such elements occur naturally, but they are also attractive devices in synthetic biology.

Cavity approach for the approximation of spectral density of graphs with heterogeneous structures.

Graphs have become widely used to represent and study social, biological, and technological systems. Statistical methods to analyze empirical graphs were proposed based on the graph's spectral density. However, their running time is cubic in the number of vertices, precluding direct application to large instances.

The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.

Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C.

BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.

The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification.

Taking identity-by-descent analysis into the wild: Estimating realized relatedness in free-ranging macaques.

Biological relatedness is a key consideration in studies of behavior, population structure, and trait evolution. Except for parent-offspring dyads, pedigrees capture relatedness imperfectly. The number and length of DNA segments that are identical-by-descent (IBD) yield the most precise estimates of relatedness.

Proteinortho6: pseudo-reciprocal best alignment heuristic for graph-based detection of (co-)orthologs.

Proteinortho is a widely used tool to predict (co)-orthologous groups of genes for any set of species. It finds application in comparative and functional genomics, phylogenomics, and evolutionary reconstructions. With a rapidly increasing number of available genomes, the demand for large-scale predictions is also growing.

Immune checkpoint inhibitor-induced epidermal necrolysis: A narrative review evaluating demographics, clinical features, and culprit medications.

Immune checkpoint inhibitors (ICIs) have transformed cancer treatment but can cause immune-related adverse events (irAEs). Severe cutaneous irAEs, including epidermal necrolysis, are rare but potentially life-threatening. There is limited understanding of the clinical features and management of ICI-induced Stevens-Johnson syndrome (SJS)/toxic epidermal necrolysis (TEN), so we aimed to analyze 95 cases of ICI-induced SJS/TEN (35 cases of SJS, 26 cases of TEN, two cases of SJS/TEN overlap, and 32 cases of unspecified) to increase knowledge of this condition among oncologists and dermatologists.

MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy.

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination.

Experience with German Research Consortia in the Field of Chemical Biology of Native Nucleic Acid Modifications.

The chemical biology of native nucleic acid modifications has seen an intense upswing, first concerning DNA modifications in the field of epigenetics and then concerning RNA modifications in a field that was correspondingly rebaptized epitranscriptomics by analogy. The German Research Foundation (DFG) has funded several consortia with a scientific focus in these fields, strengthening the traditionally well-developed nucleic acid chemistry community and inciting it to team up with colleagues from the life sciences and data science to tackle interdisciplinary challenges. This Perspective focuses on the genesis, scientific outcome, and downstream impact of the DFG priority program SPP1784 and offers insight into how it fecundated further consortia in the field.

Cryopreserved amniotic membrane in chronic nonhealing wounds: a series of case reports.

A case series of the use of amniotic membrane (AM) for treating chronic nonhealing wounds. It presents five cases of polymorbid patients with a total of nine chronic nonhealing wounds. The patient group consisted of four men and one woman with various comorbidities, aged 45-72 years.