The dynamic genetic determinants of increased transcriptional divergence in spermatids.

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify allele-specific expression during spermatogenic differentiation at single-cell resolution in an F1 hybrid mouse system, allowing for the comprehensive characterisation of cis- and trans-genetic effects, including their dynamics across cellular differentiation. Collectively, almost half of the genes subject to genetic regulation show evidence for dynamic cis-effects that vary during differentiation. Our system also allows us to robustly identify dynamic trans-effects, which are less pervasive than cis-effects. In aggregate, genetic effects were strongest in round spermatids, which parallels their increased transcriptional divergence we identified between species. Our approach provides a comprehensive quantification of the variability of genetic effects in vivo, and demonstrates a widely applicable strategy to dissect the impact of regulatory variants on gene regulation in dynamic systems.

Exceptionally Stable And Super-Efficient Electrocatalysts Derived From Semiconducting Metal Phosphonate Frameworks.

Two new isostructural semiconducting metal-phosphonate frameworks are reported. Co2 [1,4-NDPA] and Zn2 [1,4-NDPA] (1,4-NDPA4- is 1,4-naphthalenediphosphonate) have optical bandgaps of 1.7 eV and 2.5 eV, respectively. The electrocatalyst derived from Co2 [1,4-NPDA] as a precatalyst generated a low overpotential of 374 mV in the oxygen evolution reaction (OER) with a Tafel slope of 43 mV dec-1 at a current density of 10 mA cm-2 in alkaline electrolyte (1 mol L-1 KOH), which is indicative of remarkably superior reaction kinetics. Benchmarking of the OER of Co2 [1,4-NPDA] material as a precatalyst coupled with nickel foam (NF) showed exceptional long-term stability at a current density of 50 mA cm-2 for water splitting compared to the state-of-the-art Pt/C/RuO2 @NF after 30 h in 1 mol L-1 KOH. In order to further understand the OER mechanism, the transformation of Co2 [1,4-NPDA] into its electrocatalytically active species was investigated.

Halogen Bonding in Sulphonamide Co-Crystals: X···π Preferred over X···O/N?

Sulphonamides have been one of the major pharmaceutical compound classes since their introduction in the 1930s. Co-crystallisation of sulphonamides with halogen bonding (XB) might lead to a new class of pharmaceutical-relevant co-crystals. We present the synthesis and structural analysis of seven new co-crystals of simple sulphonamides N-methylbenzenesulphonamide (NMBSA), N-phenylmethanesulphonamide (NPMSA), and N-phenylbenzenesulphonamide (BSA), as well as of an anti-diabetic agent Chlorpropamide (CPA), with the model XB-donors 1,4-diiodotetrafluorobenzene (14DITFB), 1,4-dibromotetrafluorobenzene (14DBTFB), and 1,2-diiodotetrafluorobenzene (12DITFB). In the reported co-crystals, X···O/N bonds do not represent the most common intermolecular interaction. Against our rational design expectations and the results of our statistical CSD analysis, the normally less often present X···π interaction dominates the crystal packing. Furthermore, the general interaction pattern in model sulphonamides and the CPA multicomponent crystals differ, mainly due to strong hydrogen bonds blocking possible interaction sites.

Microwave-assisted synthesis of iridium oxide and palladium nanoparticles supported on a nitrogen-rich covalent triazine framework as superior electrocatalysts for the hydrogen evolution and oxygen reduction reaction.

Iridium oxide (IrOx-NP) and palladium nanoparticles (Pd-NP) were supported on a 2,6-dicyanopyridine-based covalent-triazine framework (DCP-CTF) by energy-saving and sustainable microwave-assisted thermal decomposition reactions in propylene carbonate and in the ionic liquid [BMIm][NTf2]. Transmission electron microscopy (TEM), scanning electron microscopy (SEM), and X-ray photoelectron spectroscopy (XPS) confirm well-distributed NPs with sizes from 2 to 13 nm stabilized on the CTF particles. Metal contents between 10 and 41 wt% were determined by flame atomic absorption spectroscopy (AAS). Nitrogen sorption measurements of the metal-loaded CTFs revealed Brunauer-Emmett-Teller (BET) surface areas between 904 and 1353 m2 g-1. The composites show superior performance toward the hydrogen evolution reaction (HER) with low overpotentials from 47 to 325 mV and toward the oxygen reduction reaction (ORR) with high half-wave potentials between 810 and 872 mV. IrOx samples in particular show high performances toward HER while the Pd samples show better performance toward ORR. In both reactions, electrocatalysts can compete with the high performance of Pt/C. Exemplary cyclic voltammetry durability tests with 1000 cycles and subsequent TEM analyses show good long-term stability of the materials. The results demonstrate the promising synergistic effects of NP-decorated CTF materials, resulting in a high electrocatalytic activity and stability.

CellRegMap: a statistical framework for mapping context-specific regulatory variants using scRNA-seq.

Single-cell RNA sequencing (scRNA-seq) enables characterizing the cellular heterogeneity in human tissues. Recent technological advances have enabled the first population-scale scRNA-seq studies in hundreds of individuals, allowing to assay genetic effects with single-cell resolution. However, existing strategies to analyze these data remain based on principles established for the genetic analysis of bulk RNA-seq. In particular, current methods depend on a priori definitions of discrete cell types, and hence cannot assess allelic effects across subtle cell types and cell states. To address this, we propose the Cell Regulatory Map (CellRegMap), a statistical framework to test for and quantify genetic effects on gene expression in individual cells. CellRegMap provides a principled approach to identify and characterize genotype-context interactions of known eQTL variants using scRNA-seq data. This model-based approach resolves allelic effects across cellular contexts of different granularity, including genetic effects specific to cell subtypes and continuous cell transitions. We validate CellRegMap using simulated data and apply it to previously identified eQTL from two recent studies of differentiating iPSCs, where we uncover hundreds of eQTL displaying heterogeneity of genetic effects across cellular contexts. Finally, we identify fine-grained genetic regulation in neuronal subtypes for eQTL that are colocalized with human disease variants.

Simultaneous cellular and molecular phenotyping of embryonic mutants using single-cell regulatory trajectories.

Developmental progression and cellular diversity are largely driven by transcription factors (TFs); yet, characterizing their loss-of-function phenotypes remains challenging and often disconnected from their underlying molecular mechanisms. Here, we combine single-cell regulatory genomics with loss-of-function mutants to jointly assess both cellular and molecular phenotypes. Performing sci-ATAC-seq at eight overlapping time points during Drosophila mesoderm development could reconstruct the developmental trajectories of all major muscle types and reveal the TFs and enhancers involved. To systematically assess mutant phenotypes, we developed a single-nucleus genotyping strategy to process embryo pools of mixed genotypes. Applying this to four TF mutants could identify and quantify their characterized phenotypes de novo and discover new ones, while simultaneously revealing their regulatory input and mode of action. Our approach is a general framework to dissect the functional input of TFs in a systematic, unbiased manner, identifying both cellular and molecular phenotypes at a scale and resolution that has not been feasible before.

scDALI: modeling allelic heterogeneity in single cells reveals context-specific genetic regulation.

While it is established that the functional impact of genetic variation can vary across cell types and states, capturing this diversity remains challenging. Current studies using bulk sequencing either ignore this heterogeneity or use sorted cell populations, reducing discovery and explanatory power. Here, we develop scDALI, a versatile computational framework that integrates information on cellular states with allelic quantifications of single-cell sequencing data to characterize cell-state-specific genetic effects. We apply scDALI to scATAC-seq profiles from developing F1 Drosophila embryos and scRNA-seq from differentiating human iPSCs, uncovering heterogeneous genetic effects in specific lineages, developmental stages, or cell types.

Capture and Separation of SO2 Traces in Metal-Organic Frameworks via Pre-Synthetic Pore Environment Tailoring by Methyl Groups.

Herein, we report a pre-synthetic pore environment design strategy to achieve stable methyl-functionalized metal-organic frameworks (MOFs) for preferential SO2 binding and thus enhanced low (partial) pressure SO2 adsorption and SO2 /CO2 separation. The enhanced sorption performance is for the first time attributed to an optimal pore size by increasing methyl group densities at the benzenedicarboxylate linker in [Ni2 (BDC-X)2 DABCO] (BDC-X=mono-, di-, and tetramethyl-1,4-benzenedicarboxylate/terephthalate; DABCO=1,4-diazabicyclo[2,2,2]octane). Monte Carlo simulations and first-principles density functional theory (DFT) calculations demonstrate the key role of methyl groups within the pore surface on the preferential SO2 affinity over the parent MOF. The SO2 separation potential by methyl-functionalized MOFs has been validated by gas sorption isotherms, ideal adsorbed solution theory calculations, simulated and experimental breakthrough curves, and DFT calculations.

Evolution of a New Testis-Specific Functional Promoter Within the Highly Conserved Map2k7 Gene of the Mouse.

Map2k7 (synonym Mkk7) is a conserved regulatory kinase gene and a central component of the JNK signaling cascade with key functions during cellular differentiation. It shows complex transcription patterns, and different transcript isoforms are known in the mouse (Mus musculus). We have previously identified a newly evolved testis-specific transcript for the Map2k7 gene in the subspecies M. m. domesticus. Here, we identify the new promoter that drives this transcript and find that it codes for an open reading frame (ORF) of 50 amino acids. The new promoter was gained in the stem lineage of closely related mouse species but was secondarily lost in the subspecies M. m. musculus and M. m. castaneus. A single mutation can be correlated with its transcriptional activity in M. m. domesticus, and cell culture assays demonstrate the capability of this mutation to drive expression. A mouse knockout line in which the promoter region of the new transcript is deleted reveals a functional contribution of the newly evolved promoter to sperm motility and the spermatid transcriptome. Our data show that a new functional transcript (and possibly protein) can evolve within an otherwise highly conserved gene, supporting the notion of regulatory changes contributing to the emergence of evolutionary novelties.

Prediction of single-cell gene expression for transcription factor analysis.

BACKGROUND: Single-cell RNA sequencing is a powerful technology to discover new cell types and study biological processes in complex biological samples. A current challenge is to predict transcription factor (TF) regulation from single-cell RNA data. RESULTS: Here, we propose a novel approach for predicting gene expression at the single-cell level using cis-regulatory motifs, as well as epigenetic features. We designed a tree-guided multi-task learning framework that considers each cell as a task. Through this framework we were able to explain the single-cell gene expression values using either TF binding affinities or TF ChIP-seq data measured at specific genomic regions. TFs identified using these models could be validated by the literature. CONCLUSION: Our proposed method allows us to identify distinct TFs that show cell type-specific regulation. This approach is not limited to TFs but can use any type of data that can potentially be used in explaining gene expression at the single-cell level to study factors that drive differentiation or show abnormal regulation in disease. The implementation of our workflow can be accessed under an MIT license via https://github.com/SchulzLab/Triangulate.

Emergence of a new gene from an intergenic region.

It is generally assumed that new genes would arise by gene duplication mechanisms, because the signals for regulation and transcript processing would be unlikely to evolve in parallel with a new gene function. We have identified here a transcript in the house mouse (Mus musculus) that has arisen within the past 2.5-3.5 million years in a large intergenic region. The region is present in many mammals, including humans, allowing us to exclude the involvement of gene duplication, transposable elements, or other genome rearrangements, which are typically found for other cases of newly evolved genes. The gene has three exons, shows alternative splicing, and is specifically expressed in postmeiotic cells of the testis. The transcript is restricted to species within the genus Mus and its emergence correlates with indel mutations in the 5' regulatory region of the transcript. A recent selective sweep is associated with the transcript region in M. m. musculus populations. A knockout in the laboratory strain BL6 results in reduced sperm motility and reduced testis weight. Our results show that cryptic signals for transcript regulation and processing exist in intergenic regions and can become the basis for the evolution of a new functional gene.

Tolerance without clonal expansion: self-antigen-expressing B cells program self-reactive T cells for future deletion.

B cells have been shown in various animal models to induce immunological tolerance leading to reduced immune responses and protection from autoimmunity. We show that interaction of B cells with naive T cells results in T cell triggering accompanied by the expression of negative costimulatory molecules such as PD-1, CTLA-4, B and T lymphocyte attenuator, and CD5. Following interaction with B cells, T cells were not induced to proliferate, in a process that was dependent on their expression of PD-1 and CTLA-4, but not CD5. In contrast, the T cells became sensitive to Ag-induced cell death. Our results demonstrate that B cells participate in the homeostasis of the immune system by ablation of conventional self-reactive T cells.

A Cre-inducible diphtheria toxin receptor mediates cell lineage ablation after toxin administration.

A new system for lineage ablation is based on transgenic expression of a diphtheria toxin receptor (DTR) in mouse cells and application of diphtheria toxin (DT). To streamline this approach, we generated Cre-inducible DTR transgenic mice (iDTR) in which Cre-mediated excision of a STOP cassette renders cells sensitive to DT. We tested the iDTR strain by crossing to the T cell- and B cell-specific CD4-Cre and CD19-Cre strains, respectively, and observed efficient ablation of T and B cells after exposure to DT. In MOGi-Cre/iDTR double transgenic mice expressing Cre recombinase in oligodendrocytes, we observed myelin loss after intraperitoneal DT injections. Thus, DT crosses the blood-brain barrier and promotes cell ablation in the central nervous system. Notably, we show that the developing DT-specific antibody response is weak and not neutralizing, and thus does not impede the efficacy of DT. Our results validate the use of iDTR mice as a tool for cell ablation in vivo.