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Interleukin 12 (IL-12) family cytokines are secreted proteins that regulate immune responses. Each family member is a heterodimer and nature uses shared building blocks to assemble the functionally distinct IL-12 cytokines. In recent years we have gained insights into the molecular principles and cellular regulation of IL-12 family biogenesis. For each of the family members, generally one subunit depends on its partner to acquire its native structure and be secreted from immune cells. If unpaired, molecular chaperones retain these subunits in cells. This allows cells to regulate and control secretion of the highly potent IL-12 family cytokines. Molecular insights gained into IL-12 family biogenesis, structure, and function now allow us to engineer IL-12 family cytokines to develop novel immunotherapeutic approaches.

Heat stress events during flowering in Brassica crops reduce grain yield and are expected to increase in frequency due to global climate change. We evaluated heat stress tolerance and molecular genetic diversity in a global collection of Brassica rapa accessions, including leafy, rooty and oilseed morphotypes with spring, winter and semi-winter flowering phenology. Tolerance to transient daily heat stress during the early reproductive stage was assessed on 142 lines in a controlled environment. Well-watered plants of each genotype were exposed to the control (25/15 °C day/night temperatures) or heat stress (35/25 °C) treatments for 7 d from the first open flower on the main stem. Bud and leaf temperature depression, leaf conductance and chlorophyll content index were recorded during the temperature treatments. A large genetic variation for heat tolerance and sensitivity was found for above-ground biomass, whole plant seed yield and harvest index and seed yield of five pods on the main stem at maturity. Genetic diversity was assessed on 212 lines with 1602 polymorphic SNP markers with a known location in the B. rapa physical map. Phylogenetic analyses confirmed two major genetic populations: one from East and South Asia and one from Europe. Heat stress-tolerant lines were distributed across diverse geographic origins, morphotypes (leafy, rooty and oilseed) and flowering phenologies (spring, winter and semi-winter types). A genome-wide association analysis of heat stress-related yield traits revealed 57 SNPs distributed across all 10 B. rapa chromosomes, some of which were associated with potential candidate genes for heat stress tolerance.

Many structural aspects of music, such as tonality, can be expressed using hierarchical representations. In music analysis, so-called keyscapes can be used to map a key estimate (e.g., C major, F minor) to each subsection of a piece of music, thus providing an intuitive visual representation of its tonality, in particular of the hierarchical organization of local and global keys. However, that approach is limited in that the mapping relies on assumptions that are specific to common-practice tonality, such as the existence of 24 major and minor keys. This limitation can be circumvented by applying the discrete Fourier transform (DFT) to the tonal space. The DFT does not rely on style-specific theoretical assumptions but only presupposes an encoding of the music as pitch classes in 12-tone equal temperament. We introduce wavescapes, a novel visualization method for tonal hierarchies that combines the visual representation of keyscapes with music analysis based on the DFT. Since wavescapes produce visual analyses deterministically, a number of potential subjective biases are removed. By concentrating on one or more Fourier coefficients, the role of the analyst is thus focused on the interpretation and contextualization of the results. We illustrate the usefulness of this method for computational music theory by analyzing eight compositions from different historical epochs and composers (Josquin, Bach, Liszt, Chopin, Scriabin, Webern, Coltrane, Ligeti) in terms of the phase and magnitude of several Fourier coefficients. We also provide a Python library that allows such visualizations to be easily generated for any piece of music for which a symbolic score or audio recording is available.

Additional file 18. Demographic models created with Phylogeographic Inference Using Approximate Likelihoods (PHRAPL) to test the evolution of Psammolestes. (A) Divergence with no migration (B) Divergence with bidirectional migration between P. coreodes and P. tertius. (C) Divergence with bidirectional migration between P. tertius and P. arthuri. (D) divergence with bidirectional migration between P. tertius with P. coreodes, and P. tertius with P. arthuri. (E) Divergence with bidirectional migration between P. coreodes and P. arthuri. (F) Divergence with bidirectional migration between P. tertius with P. coreodes, and P. coreodes with P. arthuri. (G) Divergence with bidirectional migration between P. tertius with P. arthuri, and P. arthuri with P. coreodes (H) Divergence with bidirectional migration between the three Psammolestes species. Starting from this point, all of the demographic models include bidirectional migration between P. arthuri and the MRCA (most recent common ancestor) of P. tertius and P. coreodes. (I) Divergence with bidirectional migration between P. arthuri and the MRCA of P. tertius and P. coreodes. (J) Divergence with bidirectional migration between P. coreodes and P. tertius. (K) Divergence with bidirectional migration between P. tertius and P. arthuri. (L) divergence with bidirectional migration between P. tertius with P. coreodes and P. arthuri. (M) Divergence with bidirectional migration between P. coreodes and P. arthuri. (N) divergence with bidirectional migration between P. coreodes with P. tertius and P. arthuri. (O) Divergence with bidirectional migration between P. arthuri with P. coreodes and P. tertius. (P) Divergence with bidirectional migration between the three Psammolestes species. Support values for the demographic scenarios are shown under each figure.

Additional file 1: Supplementary Figure S1. Genome coverage plot of B.intestinalis reported by Wochenende. Wochenende did not misclassify B. subtilis in the mock community by Sui et al (SRSRR11207337) [29], but rather detected B. intestinalis with a high and evenly distributed coverage. Indeed all the other tools also reported B. intestinalis instead of B. subtilis. Supplementary Figure S2. Wochenende analysis of an alternative long-read Zymo Even DNA mock community. The mock community was sequenced on an Oxford Nanopore GridION sequencer by the laboratory of Nick Loman (https://github.com/LomanLab/mockcommunity). To our knowledge, the other tested tools are not able to analyze these long reads appropriately. The dataset and analysis is plausible yet suboptimal, as none of the species was found within their expected range, though Enterococcus faecalis, Staphylococcus aureus and Listeria monocytogenes come close. Lactobacillus fermentum is present at higher abundance than the expected range. B.subtilis is again underrepresented, similarly to the results from short read data presented in Figure 2 [29]. Supplementary Figure S3. A heat tree automatically produced by our tool Haybaler using the R package metacoder. The taxonomy of this fairly typical airway metagenome is illustrated succinctly and is useful for rapid initial comparative analyses across samples. Rothia mucilaginosa and Haemophilus influenzae dominate, though diverse Streptococcus and several Veillonella and Prevotella species are also present. Supplementary Figure S4. Reads from a skin swab were mapped to a fungus from the Wochenende reference genome. These reads were mapped with high mapping quality to all Candida tropicalis supercontigs, providing a rare example of a fungus in this metagenome. Fungi are generally difficult to reliably locate in metagenomes because of low abundance, poor reference genomes and wet lab sampling bias due to their highly resistant physical structures. Fungi remain rare in our experience of hundreds of particularly airway metagenomes, despite frequent reanalysis. It is not unexpected to find C. tropicalis at higher biomass in a skin sample, as opposed to our usual lung samples, but demonstrates our pipeline’s utility in locating eukaryotes. Supplementary Table S1. Results from Kaiju on the same mock community dataset SRR11207337 analyzed in Figure 2. Eight bacteria should be present at 12%, with two fungi at 2% each. Results were only at genus level and are therefore reported here.

Additional file 22. Individuals of Psammolestes species collected in this study.

Additional file 6. TRNA Phylogenetic reconstruction and Barrier test. (A) Phylogenetic reconstruction with the ML algorithm based on the nuclear marker TRNA (B) Barrier test algorithm based on molecular and geographical arrays. Bootstrap values on the internal nodes are shown in the following order: SH-aLRT/aBayes/ultrafast bootstrap support. Only nodes with bootstrap values higher than 60 are shown.

Additional file 5. LSM Phylogenetic reconstruction and Barrier test. (A) Phylogenetic reconstruction wit the ML algorithm based on the nuclear marker LSM (B) Barrier test algorithm based on molecular and geographical arrays. Bootstrap values on the internal nodes are shown in the following order: SH-aLRT/aBayes/ultrafast bootstrap support. Only nodes with bootstrap values higher than 60 are shown.

Additional file 9. Bayesian inference phylogenetics tree for the locus CYTB obtained in *BEAST. Horizontal purple bars illustrate the 95% HPD for the nodes��� divergence time. Branch with a posterior probability above 0.95 are show

Additional file 8. Bayesian inference of species tree based on multilocus data (A) Maximum clade credibility tree based on Bayesian inference of the seven genes used in this study. The values observed represent posterior probabilities. (B) Bayesian species tree from multilocus data.

Species with large distributions provide unique opportunities to test how geography has influenced biotic diversification. In this work, we aimed to explore the effect of geographic barriers on the distribution of the phenotypic and genetic variation of a spider species that is widespread in continental and insular America. We obtained an alignment of the mitochondrial locus Cytochrome Oxidase I (COI) for 408 individuals across the geographic range of Gasteracantha cancriformis. We used phylogenetics, population genetics, and morphology to explore the genetic and phenotypic variation of this species. We found five genetically differentiated and geographically structured populations. Three of them are distributed in continental America, separated by the Andes mountains, and two are in the Caribbean and Galapagos Islands. Some of these geographic clades shared haplotypes between them, which may be a consequence of dispersal. We detected at least 20 phenotypes of G. cancriformis, some of which were exclusive to a geographic region, while others occurred in multiple regions. We did not observe well-defined morphological differences across male genitalia. This evidence suggests that G. cancriformis is a widespread species with high phenotypic variation that should be explored in more depth.

Additional file 3. 28S Phylogenetic reconstruction and Barrier test (A) Phylogenetic reconstruction with the ML algorithm based on the nuclear marker 28S (B) Barrier test algorithm based on molecular and geographical arrays (B). Bootstrap values on the internal nodes are shown in the following order: SH-aLRT/aBayes/ultrafast bootstrap support. Only nodes with bootstrap values higher than 60 are shown.

Additional file 4. CISP Phylogenetic reconstruction and Barrier test (A) Phylogenetic reconstruction with the ML algorithm based on the nuclear marker CISP (B) Barrier test algorithm based on molecular and geographical arrays. Bootstrap values on the internal nodes are shown in the following order: SH-aLRT/aBayes/ultrafast bootstrap support. Only nodes with bootstrap values higher than 60 are shown.

Metal-organic frameworks (MOFs) have been used to improve vaccine formulations by stabilizing proteins and protecting them against thermal degradation. This has led to increased 2 immunogenicity of these proteinaceous therapeutics. In this work we show that MOFs can also be used to protect the ssDNA oligomer, CpG, to increase its immunoadjuvancy. By encapsulating phosphodiester CpG in the zinc-based MOF, ZIF-8, the DNA oligomer is protected from nuclease degradation and exhibits improved cellular uptake. As a result, we have been able to achieve drastically enhanced B-cell activation in splenocyte cultures comparable to the current state-of-the-art, phosphorothioate CpG. Furthermore, we have made a direct comparison of micro- and nano-sized MOF for the optimization of particulate delivery of immunoadjuvants to maximize immune activation.

In continuation of the search for new anthelmintic natural products, the study at hand investigated the nematicidal effects of the two naturally occurring quassinoids ailanthone and bruceine A against the reproductive system of the model nematode 'Caenorhabditis elegans' to pinpoint their anthelmintic mode of action by the application of various microscopic techniques. Differential Interference Contrast (DIC) and the epifluorescence microscopy experiments used in the presented study indicated the genotoxic effects of the tested quassinoids (c ailanthone = 50 µM, c bruceine A = 100 µM) against the nuclei of the investigated gonadal and spermathecal tissues, leaving other morphological key features such as enterocytes or body wall muscle cells unimpaired. In order to gain nanoscopic insight into the morphology of the gonads as well as the considerably smaller spermathecae of 'C. elegans', an innovative protocol of polyethylene glycol embedding, ultra-sectioning, acridine orange staining, tissue identification by epifluorescence, and subsequent AFM-based ultrastructural data acquisition was applied. This sequence allowed the facile and fast assessment of the impact of quassinoid treatment not only on the gonadal but also on the considerably smaller spermathecal tissues of 'C. elegans'. These first-time ultrastructural investigations on 'C. elegans' gonads and spermathecae by AFM led to the identification of specific quassinoid-induced alterations to the nuclei of the reproductive tissues (e.g., highly condensed chromatin, impaired nuclear membrane morphology, as well as altered nucleolus morphology), altogether implying an apoptosis-like effect of ailanthone and bruceine A on the reproductive tissues of 'C. elegans'., Finanziert durch den Open-Access-Publikationsfonds der Westfälischen Wilhelms-Universität Münster (WWU Münster).

The parasite Trypanosoma brucei (T. brucei) is responsible for human African trypanosomiasis (HAT) and the cattle disease “Nagana” which to this day cause severe medical and socio-economic issues for the affected areas in Africa. So far, most of the available treatment options are accompanied by harmful side effects and are constantly challenged by newly emerging drug resistances. Since trypanosomatids are auxotrophic for folate, their pteridine metabolism provides a promising target for an innovative chemotherapeutic treatment. They are equipped with a unique corresponding enzyme system consisting of the bifunctional dihydrofolate reductase-thymidylate synthase (TbDHFR-TS) and the pteridine reductase 1 (TbPTR1). Previously, gene knockout experiments with PTR1 null mutants have underlined the importance of these enzymes for parasite survival. In a search for new chemical entities with a dual inhibitory activity against the TbPTR1 and TbDHFR, a multi-step in silico procedure was employed to pre-select promising candidates against the targeted enzymes from a natural product database. Among others, the sesquiterpene lactones (STLs) cynaropicrin and cnicin were identified as in silico hits. Consequently, an in-house database of 118 STLs was submitted to an in silico screening yielding 29 further virtual hits. Ten STLs were subsequently tested against the target enzymes in vitro in a spectrophotometric inhibition assay. Five compounds displayed an inhibition over 50% against TbPTR1 as well as three compounds against TbDHFR. Cynaropicrin turned out to be the most interesting hit since it inhibited both TbPTR1 and TbDHFR, reaching IC50 values of 12.4 µM and 7.1 µM, respectively.

The use of the subarachnoid space to drug release on neural axis is an important therapeutic alternative for managing patients with chronic pain and spasticity. Intrathecal drug delivery system (IDDS) provides direct access to the central nervous system, for small and large molecules, leading to the exact site, bypassing the blood-brain barrier. The main advantage is to provide lower drug dosages near the spinal cord receptors and powerful effect compared to different administration routes, minimizing side effects. In this chapter, we are going to discuss the main aspects of IDDS and review its use in chronic pain conditions, with focus on surgical technique.

Two dimensional covalent organic frameworks (2D-COFs) are a class of crystalline porous organic polymers that consist of covalently linked, two dimensional sheets that can stack together through non-covalent interactions. Here we report the synthesis of a novel COF, called PyCOFamide, which has an experimentally observed pore size that is greater than 6 nm in diameter. This is among the largest pore size reported to date for a 2D-COF. PyCOFamide exhibits permanent porosity and high crystallinity as evidenced by the nitrogen adsorption, powder X-ray diffraction, and high-resolution transmission electron microscopy. We show that the pore size of PyCOFamide is large enough to accommodate fluorescent proteins such as Superfolder green fluorescent protein and mNeonGreen. This work demonstrates the utility of non-covalent structural reinforcement in 2D-COFs to produce larger, persistent pore sizes than previously possible.

The creation and curation of labeled datasets can be an arduous, expensive, and time-consuming task. We introduce a workflow paradigm for remote consensus-building between expert annotators, while considerably reducing the associated administrative overhead through automation. Most music annotation tasks rely heavily on human interpretation and therefore defy the concept of an objective and indisputable ground truth. Thus, our paradigm invites and documents inter-annotator controversy based on a transparent set of analytical criteria, and aims at putting forth the consensual solutions emerging from such deliberations. The workflow that we suggest traces the entire genesis of annotation data, including the relevant discussions between annotators, reviewers, and curators. It adopts a well-proven pattern from collaborative software development, namely distributed version control, and allows for the automation of repetitive maintenance tasks, such as validity checks, message dispatch, or updates of meta- and paradata. To demonstrate the workflow's effectiveness, we introduce one possible implementation through GitHub Actions and showcase its success in creating cadence, phrase, and harmony annotations for a corpus of 36 trio sonatas by Arcangelo Corelli. Both code and annotated scores are freely available and the implementation can be readily used in and adapted for other MIR projects.

Studying how the environment shapes current biodiversity patterns in species rich regions is a fundamental issue in biogeography, ecology, and conservation. However, in the Neotropics, the study of the forces driving species distribution and richness, is mostly based on vertebrates and plants. In this study, we used 54,392 georeferenced records for 46 species and 1,012 georeferenced records for 38 interspecific hybrids of the Neotropical Heliconius butterflies to investigate the role of the environment in shaping their distribution and richness, as well as their geographic patterns of phylogenetic diversity and phylogenetic endemism. We also evaluated whether niche similarity promotes hybridization in Heliconius. We found that these insects display five general distribution patterns mostly explained by precipitation and isothermality, and to a lesser extent, by altitude. Interestingly, altitude plays a major role as a predictor of species richness and phylogenetic diversity, while precipitation explains patterns of phylogenetic endemism. We did not find evidence supporting the role of the environment in facilitating hybridization because hybridizing species do not necessarily share the same climatic niche despite some of them having largely overlapping geographic distributions. Overall, we confirmed that, as in other organisms, high annual temperature, a constant supply of water, and spatio-topographic complexity are the main predictors of diversity in Heliconius. However, future studies at large scale need to investigate the effect of microclimate variables and ecological interactions.