Biology subjects

Strube, C.

Publications and source records attributed to Strube, C..

3 recordsLinked to original sources

bioRxiv2025

Scalable Assembly of Ascaris Mitogenomes from Whole-Genome Data Reveals a Novel Clade

The genus Ascaris is an important group of giant parasitic roundworms, infecting over 700 million people globally, with substantial economic losses in domestic pigs. Whilst species of Ascaris are morphologically indistinguishable, analysis of mitochondrial and selected nuclear DNA loci has revealed three clades (A, B, C), which may inflate with the addition of genomic data. Here, we present a bioinformatic pipeline for de novo assembly of complete mitochondrial genomes (mtDNA) from low-coverage whole-genome data through host-read depletion or mtDNA read enrichment, followed by mtDNA-specific assembly. Our approach yielded 149 high-quality Ascaris mtDNA assemblies, enabling the study of population-level diversity, including the identification of a novel clade (Clade D, designated here) associated with human samples from Ethiopia. Our analysis further revealed Clade C to comprise of pig-derived samples from Europe based on characterisation of worms isolated in Germany. Furthermore, genetic diversity across all mitochondrial loci was high (concatenated dataset: S = 1261; h = 94; {pi} = 0.0224), indicating substantial intraspecies variation. Our methods described here provide a scalable framework for mtDNA genome reconstruction with insights into roundworm population-genomic and phylogenetic studies.

genomics↗

bioRxiv2024

HvNotch coordinates two independent pattern forming systems during head regeneration in Hydra by supporting a lateral inhibition process restricting the tentacle system

Hydra polyps regenerate lost body parts, including the head. In addition, Hydra head tissue has organizer properties thus being able to recruit body column tissue from a host polyp to produce ectopic hydranths after transplantation. These pattern forming processes involve Notch- and Wnt/{beta}-catenin-signaling. Hydra head regeneration consists of two parts, hypostome/organizer and tentacle development. Previous work had shown that the Notch inhibitor DAPT blocks hypostome regeneration and organizer formation, but not the appearance of tentacle genes and tentacle tissue. Here we show that the {beta}-catenin inhibitor iCRT14 blocks tentacle regeneration, but not regeneration of hypostome and organizer tissue. Using RT-qPCR gene expression analyzes during head regeneration we found that DAPT inhibits HyWnt3- and HyBMP2/4 expression and expression of transcriptional repressor genes including CnGsc, Sp5 and HyHes, while increasing expression of HyBMP5/8b and the c-fos-related gene HyKayak. ICRT14 blocks expression of the tentacle specification factor HyAlx, but not expression of HyWnt3. Thus, in accordance with regeneration of two head structures we find two signaling and gene expression modules with HyWnt3 and HyBMP4 part of a hypostome/organizer module, and BMP5/8, HyAlx and {beta}-catenin part of a tentacle module. We conclude that Notch functions as an inhibitor of tentacle production to allow regeneration of hypostome/head organizer. Furthermore, with HyKayak we present a candidate target gene for HvNotch induced repressor genes. Using siRNA and the Fos/Jun-inhibitor T5224 we show that HyKayak attenuates the expression of HyWnt3. Finally, Notch signaling was not required for head regeneration of fresh water polyps of Craspedacusta. Polyps of Craspedacusta do not have tentacles and thus, after head removal only regenerate a hypostome with a crescent of nematocytes around the mouth opening. This corroborates the idea that Notch-signaling mediates between two pattern forming processes during Hydra head regeneration.

developmental biology↗

bioRxiv2017

Variability of quantal NMDA to AMPA current ratio in nucleus tractus solitarii neurons

The ratio between AMPA and NMDA receptors is a key factor governing integrative and plastic properties of excitatory glutamatergic synapses. To determine whether the respective proportions of AMPA and NMDA receptors are similar or vary across a neuron's synapse, we analyzed the variability of NMDA and AMPA currents in quantal responses recorded from neurons located in the nucleus tractus solitarii. We found that the average NMDA to AMPA current ratio strongly differed between recorded neurons and that most of the intra-neuronal current ratio variability was attributable to fluctuations in NMDA current. We next performed computer simulations with a Monte Carlo model of a glutamatergic synapse to estimate the part of AMPA and NMDA currents fluctuations induced by stochastic factors. We found that NMDA current variability mainly resulted from strong channel noise with few influence of release variations. On the contrary, partly because of the presence of subconductance states, AMPA receptor channel noise was low and AMPA current fluctuations tightly reflected changes in the amount of glutamate released. We next showed that these two factors, channel noise and fluctuations in glutamate release, were sufficient to explain the observed variability of the NMDA to AMPA current ratio in quantal events recorded from the same neuron. We therefore concluded that the proportion of AMPA and NMDA receptors was similar, or roughly similar, across synapses onto the same target cell.

neuroscience↗