Biology subjects

Wacker, A.

Publications and source records attributed to Wacker, A..

6 recordsLinked to original sources

bioRxiv2026

Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution

Protein interactions with DNA often result in rotational movements. These movements underlie many genetic processes such as DNA transcription by RNA polymerase (RNAP). To illuminate these movements, we previously developed Origami Rotor-Based Imaging and Tracking (ORBIT), a fluorescence-based method that enables high-speed tracking of DNA rotation. When used to track DNA rotation during transcription by E. coli RNAP, ORBIT enabled detection of single base-pair steps. However, the duration of ORBIT experiments was limited due to fluorescence photobleaching. To overcome this limitation and extend the total possible observation time, we here introduce dye-cycling ORBIT (dcORBIT), a method that enables observation of protein-DNA interactions for over 10 minutes at 20 Hz while maintaining single base-pair precision. dcORBIT thereby opens new possibilities to study the fundamental rotational movements underlying gene expression.

biophysics↗

bioRxiv2024

Winter temperature effects in a cold-adapted northern population of a range-expanding spider: survival, energy stores, and differential gene expression

Species expand their spatial distribution when environmental conditions are favorable or when mutations arise that allow them to live in previously unfavorable conditions. The European wasp spider, Argiope bruennichi, is known to have expanded its range poleward faster than climate change would predict. Northern edge populations show higher cold tolerance and are genetically differentiated from core populations, suggesting local adaptation to colder winter conditions. To investigate the degree and limits of plasticity in a cold-adapted population, we exposed overwintering juveniles (spiderlings) from Estonia - the northern edge of the distribution - to three winter regimes: two with a strong difference in day/night temperatures and an overall 10 degrees difference (warm and cold treatment) and one with moderate temperatures and less difference between day and night (moderate). We investigated if survival, lipid content, metabolites, and gene expression patterns differ depending on these temperature regimes. The survival probability of the spiderlings and their overall lipid content decreased over winter, with no difference between treatments, suggesting high resilience of the spiderlings towards very different temperature regimes at the edge of the distribution. At the end of winter, the content of saturated and monounsaturated fatty acids per spiderling also did not differ between treatments. However, omega-3 polyunsaturated fatty acids (PUFAs) levels were significantly lower in spiders exposed to the warm winter suggesting increased metabolic activity. We identified 4096 significant differentially expressed genes (DEGs) across the treatments, of which 1389 were specific for the moderate treatment, and 832 specific for the warm treatment, while 69 were unique for the cold treatment, showing a stronger temperature stress response to the moderate and warmer than to the cold treatment. Taken together, our results show that A. bruennichi has physiological plasticity and the ability to cope with very different winter temperature regimes despite being cold adapted. However, warmer winters might come with metabolic costs that could impact on the spiderling[s] survival and foraging success when they emerge from the egg sac in spring.

ecology↗

bioRxiv2024

Onco-fetal protein Nogo-A restricts human and mouse glioma vascularization and growth via VEGF-Notch-hippo-metabolic signaling

Glioblastoma is one of the most deadly human cancers characterized by high degrees of vascularization, but targeting its vasculature has resulted in very limited success so far. Angiogenesis, the growth of new blood vessels, is highly dynamic during brain development, enters a mostly quiescent state in the adult homeostatic brain, and is reactivated in vascular-dependent CNS diseases including brain tumors. In consequence, a better understanding of the relevance of the onco-fetal axis - describing the reactivation of fetal signaling programs in tumors - in endothelial- and perivascular cells of the human brain tumor vasculature harbors great translational potential, yet remains poorly defined. In development, neurovascular link (NVL) molecules guide both neuronal growth cones as well as capillary endothelial tip cells. Nogo-A is an NVL molecule known to inhibit axonal growth in the developing and adult CNS and to restrict angiogenesis during brain development, but its role in the mouse and human brain tumor vasculature along the onco-fetal axis remains unknown. Here, we characterize Nogo-A as an onco-fetal protein expressed in the neurovascular unit (NVU) in human fetal brains and human gliomas in vivo that negatively regulates sprouting angiogenesis and endothelial tip cells in glioma vascularization. The Nogo-A-specific Delta 20 domain restricts angiogenic sprouting and branching and promotes vascular normalization while inhibiting glioma growth in experimental gliomas. Moreover, Nogo-A expression in tumor cells negatively correlate/s with glioma malignancy in vivo. In vitro, Nogo-A Delta 20 reduced human brain- and brain tumor endothelial cell (HBMVEC, HBTMVEC) and human umbilical vein endothelial cell (HUVEC) spreading, migration, and sprouting, in a dose-dependent manner and inhibited filopodia extension glucose metabolism. Mechanistically, RNA sequencing of Nogo-A Delta 20-treated HBMVECs and HBTMVECs revealed Nogo-A Delta 20-induced positive regulation of the angiogenesis-inhibiting Dll4-Notch-pathway and inhibition of the angiogenesis-promoting VEGF-VEGFR and Hippo-YAP-TAZ pathways, whereas metabolomics and functional metabolic assays revealed Nogo-A Delta 20-induced negative regulation of endothelial glycolysis in HBMVECs and HBTMVECs. These findings characterize Nogo-A as an onco-fetal protein in the human glial brain tumor vasculature and identify Nogo-A Delta 20 signaling as an important negative regulator of human glioma vascularization and growth. Enhancing Nogo-A signaling may be an attractive alternative or combinatorial anti-angiogenic therapy to restrict human glioma/glioblastoma vascularization and growth.

neuroscience↗

bioRxiv2021

New fossil wasp species from the earliest Eocene Fur Formation has its closest relatives in late Eocene ambers (Hymenoptera, Ichneumonidae, Pherhombinae)

Darwin wasps (Ichneumonidae) are one of the most species-rich insect families, but also one of the most understudied ones, both in terms of their extant and extinct diversity. We here use morphometrics of wing veins and an integrative Bayesian analysis to place a new rock fossil species from the Danish Fur Formation ([~]54 Ma) in the tree of Darwin wasps. The new species, Pherhombus parvulus n. sp., is placed firmly in Pherhombinae, an extinct subfamily so far only known from Baltic and Rovno-Ukranian ambers, which are estimated to be 34-48 Ma and 34-38 Ma, respectively. Our phylogenetic analysis recovers a subfamily clade within the higher Ophioniformes formed by Pherhombinae, Townesitinae and Hybrizontinae, in accordance with previous suggestions. Due to the placement of the new species as sister to the remaining members of Pherhombinae, we argue that our finding is not at odds with a much younger, late Eocene age ([~]34-41 Ma) of Baltic amber and instead demonstrates that Pherhombus existed over a much longer period than previously thought. Our results also exemplify the power of wing vein morphometrics and integrative phylogenetic analyses in resolving the placement even of poorly preserved fossil specimens.

paleontology↗

bioRxiv2018

Resource co-limited growth in fluctuating environments

Variability in the supply of limiting resources determines consumer-resource interactions. Yet, how consumers are affected by variability when multiple resources co-limit growth remains unknown. We use a two-resource DEB model to predict how consumer somatic growth rate responds to the temporal structure (i.e. fluctuation frequency, phase and covariance) of single and co-limiting resources supply. Subsequently, we experimentally test the model predictions using Daphnia magna (co-)limited by dietary phosphorus and cholesterol supply. Both model and experiments indicate that for certain fluctuation frequencies, resource fluctuation phase and (co)variance can heavily affect somatic growth. The model suggests that dynamic resource storage and assimilation efficiency adjustment are key for predicting the frequencies at which the growth rate is mostly affected by (co)variance and phase. In a context of ongoing anthropogenic landscape homogenization, our results offer novel insights on how co-occurring perturbations to the temporal structure of resource supply can affect consumer performance.

ecology↗

bioRxiv2018

One man’s trash is another man’s treasure - the effect of bacteria on phytoplankton-zooplankton interactions in chemostat systems

Chemostat experiments are employed to study predator-prey and other trophic interactions, frequently using phytoplankton-zooplankton systems. These experiments often use population dynamics as fingerprints of ecological and evolutionary processes, assuming that the contributions of all major actors to these dynamics are known. However, bacteria are often neglected although they are frequently present. We argue that even without external carbon sources bacteria may affect the experimental outcomes depending on experimental conditions and the physiological traits of bacteria, phytoplankton and zooplankton. Using a static carbon flux model and a dynamic simulation model we predict the minimum and maximum impact of bacteria on phytoplankton-zooplankton population dynamics. Under bacteria-suppressing conditions, we find that the effect of bacteria is indeed negligible and their omission justified. Under bacteria-favouring conditions, however, bacteria may strongly affect average biomasses. Furthermore, the population dynamics may become highly complex resulting in wrong conclusions if bacteria are not considered. Our model results provide suggestions to reduce the bacterial impact experimentally. Next to optimizing experimental conditions (e.g. the dilution rate) the appropriate choice of the zooplankton predator is decisive. Counterintuitively, bacteria have a larger impact if they are not ingested by the predator as high bacterial biomasses and complex population dynamics arise via competition for nutrients with the phytoplankton. Only if the predator is at least partly bacterivorous the impact of bacteria is minimized. Our results help to improve both the design of chemostat experiments and their interpretation and thus advance the study of ecological and evolutionary processes in aquatic food webs.

ecology↗