Biology subjects

Schaefer, I.

Publications and source records attributed to Schaefer, I..

12 recordsLinked to original sources

bioRxiv2026

Loss of either RASSF1A alone or in combination with Caveolin-1 inhibition is associated with different premalignant histopathological alterations in the mammary glands of transgenic mice

Analyses of human breast carcinomas (BCs) and premalignant breast lesions show that the loss of RASSF1A is an early event in the development of ER+ BCs, which correlates linearly with malignant progression. This observation suggests that RASSF1A inhibition is important for the development and progression of ER+ BCs. In addition to RASSF1A, concurrent caveolin-1 (Cav-1) inhibition may further promote ER+ breast carcinogenesis. In the present study, transgenic Rassf1a-/- and Cav-1(-/-) single as well as Rassf1a-/-, Cav-1(-/-) double knockout mice were used to investigate the impact of single or combined Rassf1a and Cav-1 inactivation on BC initiation. Loss of either one or both proteins led to different, pre-malignant histopathological alterations within the mammary glands of the mice, but not to fully developed BC, confirming that Rassf1a and Cav-1 are both important for maintaining the integrity of mammary gland epithelial structure, but suggesting that further intracellular changes or extracellular factors are required for the development of luminal BC when both genes are lost.

cancer biology↗

bioRxiv2026

A little feat in translation: miniaturized tRNAs in nematode and arachnid mitochondria

Transfer RNAs carry a highly conserved, cloverleaf-like secondary structure, which is essential to fulfill their task as adaptor molecules in translation. However, in mitochondria of metazoans, tRNA molecules were identified that deviate from this consensus structure and lack either the D- or T-arm, or, in some extreme cases, even both arms. These deviations are predominantly found in nematodes and arachnids, where in many cases the entire set of 22 mt tRNA genes are predicted to encode for such aberrant tRNAs or where even the complete loss of tRNA genes is proposed. Due to this unusual composition, we analyzed and characterized the mt tRNA pool of one representative of both groups. We identified the whole set of mt tRNAs and reannotated several tRNAs that differ significantly from previous genome-based predictions. In some cases, the sequence reads indicate putative tRNA editing events, showing that predictions exclusively based on mitogenome data have only a limited reliability. Our data also provide first insights into the modification pattern of such hairpin-like tRNAs.

Molecular Biology↗

bioRxiv2025

Genomes of ancient asexual mites appear streamlined in their architecture

The long-term persistence of obligate asexual lineages represents one of the most enduring and critical paradoxes in evolutionary biology. Sexual reproduction, through meiotic recombination and segregation, enables the efficient removal of deleterious mutations and facilitates rapid adaptation to shifting environmental pressures. Lineages that lose sex are therefore classically predicted to experience genomic decay and face rapid extinction. Oribatid mites (Acari, Sarcoptiformes) represent a unique system for testing these predictions, as they feature multiple, ancient, and independent transitions to asexuality, providing a natural experiment on the evolutionary fate of asexual genomes. We compared four sets of sister sexual and asexual species using high-quality nuclear genome assemblies to investigate the genomic consequences of long-term asexuality. Our study revealed a profound, reproductive-mode-dependent dichotomy in the evolution of genome architecture. Contrary to their expected genomic decay, asexual species have mostly streamlined genomes with less novel genes than their sexual sister species. In contrast, sexual species have acquired genetic innovations, encompassing both gene and transposable element content. These results challenge classical expectations of genomic deterioration in asexual species and might explain the long-term evolutionary persistence of oribatid mites.

genomics↗

bioRxiv2025

Targeted ortholog search in unannotated genome assemblies with fDOG-Assembly

Whole genome shotgun sequencing and assembly is routine. However, identifying protein-coding genes in newly assembled genomes remains complex, time-consuming, and labour-intensive. Therefore, most eukaryotic genome assemblies in public databases lack gene annotations reducing their value for evolutionary and functional genomics. Here, we present fDOG-Assembly, a novel tool for targeted, feature architecture-aware ortholog searches directly in unannotated genome assemblies. Benchmarking shows that fDOG-Assembly performs similarly to BUSCO and Compleasm in ortholog identification while offering the advantage of not being restricted to universal single-copy genes. Applied to identify orthologs of 5,000 human genes in rat and Nematostella vectensis, fDOG-Assembly approaches the performance of traditional ortholog search tools that rely on pre-annotated proteomes. Importantly, it can recover orthologs missed by conventional methods because of incomplete gene annotations, helping to fill gaps in phylogenetic profiles. As a case study, we screened 176 soil invertebrate genome assemblies for genes involved in antibacterial compound production. We found that orthologs of {beta}-lactam biosynthesis genes are widespread in springtails, with individual species possessing nearly complete cephamycin biosynthetic gene sets, suggesting they may represent previously unrecognized natural producers of {beta}-lactam antibiotics. Overall, fDOG-Assembly is a powerful resource for orthology-based analyses of the rapidly growing collection of unannotated genome assemblies.

bioinformatics↗

bioRxiv2022

Population structure and genetic variance among local populations of an non-native earthworm species in Minnesota, USA

A variety of human activities have been identified as driving factors for the release and spread of invasive earthworm species in North America. Population genetic markers can help to identify locally relevant anthropogenic vectors and provide insights into the processes of population dispersal and establishment. We sampled the invasive European earthworm species Lumbricus terrestris at nine sites and several bait shops within the metropolitan area of Minneapolis-St. Paul in Minnesota, USA. We used microsatellite markers to infer genetic diversity and population structure, and 16S rDNA to address multiple introduction events, including bait dumping, which is a common source of L. terrestris introductions into the wild. Our results indicate multiple introductions but not from current bait dumping. Overall, genetic structure was low and earthworms >5000 m apart were genetically differentiated, except for one sampling location, indicating jump-dispersal followed by population establishment. Further, earthworms at one location north of Minneapolis established from one or few founder individuals, suggesting that earthworm invasions are ongoing. We therefore encourage further monitoring of earthworm populations using molecular markers, in order to disentangle the different human-related vectors contributing to the spread of earthworms and their establishment, which is essential to develop adequate management strategies.

molecular biology↗

bioRxiv2022

The molecular mechanism and physiological role of silent nociceptor activation

Silent nociceptors are sensory afferents that are insensitive to noxious mechanical stimuli under normal conditions but become sensitized to such stimuli during inflammation. Using RNA-sequencing and quantitative RT-PCR we demonstrate that inflammation selectively upregulates the expression of the transmembrane protein TMEM100 in silent nociceptors and electrophysiology revealed that over-expression of TMEM100 is required and sufficient to un-silence silent nociceptors. Moreover, we show that mice lacking TMEM100 do not develop secondary allodynia - i.e. pain hypersensitivity that spreads beyond the site of inflammation - in a mouse model of knee joint inflammation and that AAV-mediated overexpression of TMEM100 in articular afferents in the absence of inflammation is sufficient to induce allodynia in remote skin regions without causing knee joint pain. Thus, our work identifies TMEM100 as a key regulator of silent nociceptor un-silencing and reveals a physiological role for this hitherto enigmatic afferent subclass in triggering spatially remote secondary allodynia during inflammation.

neuroscience↗

bioRxiv2021

Nse5/6 inhibits the Smc5/6 ATPase to facilitate DNA substrate selection.

Eukaryotic cells employ three SMC complexes to control DNA folding and topology. The Smc5/6 complex plays roles in DNA repair and in preventing the accumulation of deleterious DNA junctions. To elucidate how specific features of Smc5/6 govern these functions, we reconstituted the yeast holo-complex. We found that the Nse5/6 sub-complex strongly inhibited the Smc5/6 ATPase by preventing productive ATP binding. This inhibition was relieved by plasmid DNA binding but not by short linear DNA, while opposing effects were observed without Nse5/6. We uncovered two binding sites for Nse5/6 on Smc5/6, based on an Nse5/6 crystal structure and cross-linking mass spectrometry data. One binding site is located at the Smc5/6 arms and one at the heads, the latter likely exerting inhibitory effects on ATP hydrolysis. Cysteine cross-linking demonstrated that the interaction with Nse5/6 anchored the ATPase domains in a non-productive state, which was destabilized by ATP and DNA. Under similar conditions, the Nse4/3/1 module detached from the ATPase. Altogether, we show how DNA substrate selection is modulated by direct inhibition of the Smc5/6 ATPase by Nse5/6.

biochemistry↗

bioRxiv2021

An intrinsically disordered intracellular domain of PIEZO2 is required for force-from-filament activation of the channel

A central question in mechanobiology is how mechanical forces acting in or on a cell are transmitted to mechanically-gated PIEZO channels that convert these forces into biochemical signals. Here we show that PIEZO2 is sensitive to force-transmission via the membrane (force-from-lipids) as well as force transmission via the cytoskeleton (force-from-filament) and demonstrate that the latter requires the intracellular linker between the transmembrane helices nine and ten (IDR5). Moreover, we show that rendering PIEZO2 insensitive to force-from-filament by deleting IDR5 abolishes PIEZO2-mediated inhibition of neurite outgrowth, which relies on the detection of cellgenerated traction forces, while it only partially affects its sensitivity to cell indentation and does not at all alter its sensitivity to membrane stretch. Hence, we propose that PIEZO2 is a polymodal mechanosensor that detects different types of mechanical stimuli via different force transmission pathways, which highlights the importance of utilizing multiple complementary assays when investigating PIEZO channel function.

neuroscience↗

bioRxiv2020

Haplotype divergence supports ancient asexuality in the oribatid mite Oppiella nova

Sex strongly impacts genome evolution via recombination and segregation. In the absence of these processes, haplotypes within lineages of diploid organisms are predicted to accumulate mutations independently of each other and diverge over time. This so-called Meselson effect is regarded as a strong indicator of the long-term evolution under obligate asexuality. Here, we present genomic and transcriptomic data of three populations of the asexual oribatid mite species Oppiella nova and its sexual relative Oppiella subpectinata. We document strikingly different patterns of haplotype divergence between the two species, strongly supporting Meselson effect like evolution and ancient asexuality in O. nova: (I) Variation within individuals exceeds variation between populations in O. nova but vice versa in O. subpectinata. (II) Two O. nova sub-lineages feature a high proportion of heterozygous genotypes and lineage-specific haplotypes, indicating that haplotypes diverged independently within the two lineages after their split. (III) The deepest split in gene trees generally separates haplotypes in O. nova, but populations in O. subpectinata. (IV) Tree topologies of the two haplotypes match each other. Our findings provide positive evidence for the absence of sex over evolutionary time in O. nova and suggest that asexual oribatid mites can escape the dead-end fate usually associated with asexual lineages.

evolutionary biology↗

bioRxiv2019

Cryo-EM structure of the complete and ligand-saturated insulin receptor ectodomain

Glucose homeostasis and growth essentially depend on the peptide hormone insulin engaging its receptor. Despite biochemical and structural advances, a fundamental contradiction has persisted in the current understanding of insulin ligand-receptor interactions. While biochemistry predicts two distinct insulin binding sites, 1 and 2, recent structural analyses have only resolved site 1. Using a combined approach of cryo-EM and atomistic molecular dynamics simulation, we determined the structure of the entire dimeric insulin receptor ectodomain saturated with four insulin molecules. Complementing the previously described insulin-site 1 interaction, we present the first view of insulin bound to the discrete insulin receptor site 2. Insulin binding stabilizes the receptor ectodomain in a T-shaped conformation wherein the membrane-proximal domains converge and contact each other. These findings expand the current models of insulin binding to its receptor and of its regulation. In summary, we provide the structural basis enabling a comprehensive description of ligand-receptor interactions that ultimately will inform new approaches to structure-based drug design.\n\nIn briefA cryo-EM structure of the complete insulin receptor ectodomain saturated with four insulin ligands is reported. The structural model of the insulin-insulin receptor complex adopts a T-shaped conformation, reveals two additional insulin-binding sites potentially involved in the initial interaction of insulin with its receptor, and resolves the membrane proximal region.

biochemistry↗

bioRxiv2018

Radial F-actin Organization During Early Neuronal Development

The centrosome is thought to be the major neuronal microtubule-organizing center (MTOC) in early neuronal development, producing microtubules with a radial organization. In addition, albeit in vitro, recent work showed that isolated centrosomes could serve as an actin-organizing center (Farina et al., 2016), raising the possibility that neuronal development may, in addition, require a centrosome-based actin radial organization. Here we report, using super-resolution microscopy and live-cell imaging, F-actin organization around the centrosome with dynamic F-actin aster-like structures with F-actin fibers extending and retracting actively. Photoconversion/photoactivation experiments and molecular manipulations of F-actin stability reveal a robust flux of somatic F-actin towards the cell periphery. Finally, we show that somatic F-actin intermingles with centrosomal PCM-1 satellites. Knockdown of PCM-1 and disruption of centrosomal activity not only affect F-actin dynamics near the centrosome but also in distal growth cones. Collectively the data show a radial F-actin organization during early neuronal development, which might be a cellular mechanism for providing peripheral regions with a fast and continuous source of actin polymers; hence sustaining initial neuronal development.

neuroscience↗

bioRxiv2017

Effective purifying selection in ancient asexual oribatid mites

Sex is beneficial in the long-term, because it can prevent mutational meltdown through increased effectiveness of selection. This idea is supported by empirical evidence of deleterious mutation accumulation in species with a recent transition to asexuality. Here, we studied the effectiveness of purifying selection in oribatid mites, which have lost sex millions of years ago and diversified into different families and species while reproducing asexually. We compared the accumulation of deleterious coding and non-coding mutations between three asexual and three sexual lineages using transcriptome data. Contrasting studies of young asexual lineages, we find evidence for strong purifying selection that is more effective in asexual compared to sexual oribatid mite lineages. Our results suggest that large populations likely sustain effective purifying selection and facilitate the escape of mutational meltdown in the absence of sex. Thus, sex per se is not a prerequisite for the long-term persistence of animal lineages.

evolutionary biology↗