Biology subjects

Berger, M.

Publications and source records attributed to Berger, M..

26 records · Page 2Linked to original sources

bioRxiv2022

S6K1 phosphorylates Cdk1 and MSH6 to regulate DNA repair.

The mTORC1 substrate, S6 Kinase 1 (S6K1), is involved in the regulation of cell growth, ribosome biogenesis, glucose homeostasis and adipogenesis. Accumulating evidence has suggested a role for mTORC1 signaling in the DNA damage response. This is mostly based on the findings that mTORC1 inhibitors sensitized cells to DNA damage. However, a direct role of the mTORC1-S6K1 signaling pathway in DNA repair and the mechanism by which this signaling pathway regulates DNA repair is unknown. In this study, we discovered a novel role for S6K1 in regulating DNA repair through the coordinated regulation of the cell cycle, homologous recombination (HR) DNA repair (HRR) and mismatch DNA repair (MMR) mechanisms. Here we show that S6K1 orchestrates DNA repair by phosphorylation of Cdk1 at serine 39, causing G2/M cell cycle arrest enabling homologous recombination and by phosphorylation of MSH6 at serine 309, enhancing MMR. Moreover, breast cancer cells harboring RPS6KB1 gene amplification show increased resistance to several DNA damaging agents and S6K1 expression is associated with poor survival of breast cancer patients treated with chemotherapy. Our findings reveal an unexpected function of S6K1 in the DNA repair pathway, serving as a tumorigenic barrier by safeguarding genomic stability.

cancer biology↗

bioRxiv2022

Universal guide for skull extraction and custom-fitting of implants to continuous and discontinuous skulls

Intracranial neurophysiological recordings require chronic implants to provide transcranial access to the brain. Especially in larger animals, which participate in experiments over extended periods of time, implants should match the skull curvature to promote osseointegration and avoid tissue and bacterial ingress over time. Proposed CAD methods for designing implants to date have focused on naive animals with continuous and even skull surfaces and calculate Boolean differences between implant and skull surface to fit the implant to the skull curvature. However, custom-fitting by calculating the difference fails, if a discontinuous skull surface needs to be matched. Also, the difference method does not allow designs with constant material thickness along the skull curvature, e.g. to allow fixed screw lengths. We present a universal step-by-step guide for custom-fitting implants which overcomes these limitations. It is suited for unusual skull conditions, like surface discontinuities or irregularities and includes virtual bending as a process to match skull surfaces while maintaining implant thickness. We demonstrate its applicability for a wide spectrum of scenarios, ranging from complex-shaped single-pieced implants to detailed multi-component implant systems built on even or discontinuous skull. The guide uses only a few software tools and the final virtual product can be manufactured using CNC milling or 3D printing. A detailed description of this process is available on GitHub including step-by-step video instructions suitable for users without any prior knowledge in CAD programming. We report the experience with these implants over several years in 11 rhesus monkeys. Significance StatementChronic implants are essential for intracranial neurophysiological recordings. In this study we show how to custom-design and -fit such implants for rhesus monkeys (Macacca mulatta). Different to existing approaches, our procedure is not limited to even skull surfaces but can be applied to discontinuous or irregular surfaces. It furthermore presents a description of virtual implant bending to match the skull curvature while maintaining implant thickness. The final virtual product can be manufactured using CNC milling or 3D printing. In contrast to previous studies, this guide is suited for users without any prior expertise in CAD programming using our step-by-step video instructions.

neuroscience↗

bioRxiv2021

Ethanol-guided behavior in Drosophila larvae

Chemosensory signals allow vertebrates and invertebrates not only to orient in its environment toward energy-rich food sources to maintain nutrition but also to avoid unpleasant or even poisonous substrates. Ethanol is a substance found in the natural environment of Drosophila melanogaster. Accordingly, D. melanogaster has evolved specific sensory systems, physiological adaptations, and associated behaviors at its larval and adult stage to perceive and process ethanol. To systematically analyze how D. melanogaster larvae respond to naturally occurring ethanol, we examined ethanol-induced behavior in great detail by parametrically reevaluating existing approaches and comparing them with new experiments. Using behavioral assays, we confirm that larvae are attracted to different concentrations of ethanol in their environment. This behavior is controlled both by olfactory and contact cues. It is independent of previous exposure to ethanol in their food. Moreover, moderate, naturally occurring ethanol concentration of 4% results in increased larval fitness. On the contrary, higher concentrations of 10% and 20% ethanol, which rarely or never appear in nature, increase larval mortality. Finally, ethanol also serves as a positive teaching signal in learning and memory and updates valence associated with simultaneously processed odor information. Since information on how larvae perceive and process ethanol at the genetic and neuronal level is limited, the establishment of standardized assays described here is an important step towards their discovery.

animal behavior and cognition↗

bioRxiv2020

Single-dose ethanol intoxication causes acute and lasting neuronal changes in the brain

Alcohol intoxication at early ages is a risk factor for development of addictive behavior. To uncover neuronal molecular correlates of acute ethanol intoxication, we used stable-isotope labeled mice combined with quantitative mass spectrometry to screen over 2000 hippocampal proteins of which 72 changed synaptic abundance up to two-fold after ethanol exposure. Among those were mitochondrial proteins and proteins important for neuronal morphology, including MAP6 and Ankyrin-G. Based on these candidate proteins, we found acute and lasting molecular, cellular, and behavioral changes following a single intoxication in alcohol-naive mice. Immunofluorescence analysis revealed a shortening of axon initial segments. Longitudinal two-photon in vivo imaging showed increased synaptic dynamics and mitochondrial trafficking in axons. Knockdown of mitochondrial trafficking in dopaminergic neurons abolished conditioned alcohol preference in Drosophila. This introduces mitochondrial trafficking as a process implicated in reward learning, and highlights the potential of high-resolution proteomics to identify cellular mechanisms relevant for addictive behavior.

neuroscience↗

bioRxiv2020

Cellular water analysis in T cells reveals a switch from metabolic water gain to water influx

Cell growth is driven by the acquisition and synthesis of dry biomass and water mass. This study examines the increase of water in T cells biomass during cell growth. We found that T cell growth is initiated by a phase of slow increase of cellular water, followed by a second phase of rapid increase in water content. To study the origin of the water gain, we developed a novel method, Cold Aqua Trap - Isotope Ratio Mass Spectrometry (CAT-IRMS), which allows analysis of intracellular water isotope composition. Applying CAT-IRMS, we discovered that glycolysis-coupled metabolic water accounts on average for 11 femtoliter (fL) out of the 20 fL of water gained per cell during the slow phase. At the end of the rapid phase, before initiation of cell division, a water influx occurs, increasing the water level by three-fold. Thus, activated T cells switch from acquiring metabolic water to incorporating water from the extracellular medium. Our work provides a method to analyze cell water content and an insight into the way cells regulate their water mass.

biochemistry↗

bioRxiv2020

Systemic hypoxia inhibits T cell response by limiting mitobiogenesis via matrix substrate-level phosphorylation arrest

Systemic oxygen restriction (SOR) is prevalent in numerous clinical conditions including chronic obstructive pulmonary disease (COPD). However, the influence of SOR on T cell protective immunity remains uncharacterized. Here we show the detrimental effect of hypoxia on mitochondrial biogenesis in activated CD8+ T cells. We find that low oxygen diminishes CD8+ T cell viral response in vivo. Using genetic and pharmacological models, we demonstrate that respiratory restriction inhibits ATP dependent matrix processes, all critical for mitochondrial biogenesis. The effect mediated by respiratory restriction could be rescued by TCA cycle re-stimulation, which led to increased mitochondrial matrix localized ATP via substrate-level phosphorylation. Finally, we demonstrate that short exposure to atmospheric oxygen pressure rescues the CD8+ viral response under systemic oxygen restriction in vivo. Our findings reveal the detrimental effect of hypoxia on mitochondrial biogenesis in activated CD8+ T cells and provide a new approach for reducing viral infections in COPD. HighlightsO_LISystemic chronic hypoxia compromises CD8+ T cell activation C_LIO_LIShortly upon activation, T cells cytoplasmic activity becomes independent of mitochondrial ATP outflux C_LIO_LIRespiratory-blockade arrests mitochondrial remodeling due to energy depletion C_LIO_LIUncoupler-based TCA stimulation rescues respiratory-restricted activated CD8+ T cells by stimulating matrix localized substrate-level phosphorylation C_LIO_LICD8+ T cell arrest due to hypoxia in vivo can be rescued by short exposure to atmospheric oxygen pressure. C_LI

immunology↗

bioRxiv2018

Differential expression of PKCα and -β in the zebrafish retina

The retina is a complex neural circuit in which visual information is transmitted and processed from light perceiving photoreceptors to projecting retinal ganglion cells. Much of the computational power of the retina rests on signal integrating interneurons, such as bipolar cells in the outer retina. While mammals possess about 10 different bipolar cell types, zebrafish (Danio rerio) has at least six ON-type, seven OFF-type, and four mixed-input bipolar cells. Commercially available antibodies against bovine and human conventional protein kinase C (PKC) and -{beta} are frequently used as markers for retinal ON-bipolar cells in different species, despite the fact that it is not known which bipolar cell subtype(s) they actually label.\n\nMoreover, the expression pattern of the five prkc genes (coding for PKC proteins) has not been systematically determined. While prkcg is not expressed in retinal tissue, the other four prkc (prkcaa, prkcab, prkcba, prkcbb) transcripts were found in different parts of the inner nuclear layer and some as well in the retinal ganglion cell layer.\n\nImmunohistochemical analysis in adult zebrafish retina using PKC and PKC{beta} antibodies showed an overlapping immunolabeling of ON-bipolar cells that are most likely of the BON s6L or RRod type and of the BON s6 type. However, comparison of transcript expression with immunolabling, implies that these antibodies are not specific for one single zebrafish conventional PKC, but rather detect a combination of PKC - and -{beta} variants.

neuroscience↗

bioRxiv2018

The Reach Cage environment for wireless neural recordings during structured goal-directed behavior of unrestrained monkeys

System neuroscience of motor cognition regarding the space beyond immediate reach mandates free, yet experimentally controlled movements. We present an experimental environment (Reach Cage) and a versatile visuo-haptic interaction system (MaCaQuE) for investigating goal-directed whole-body movements of unrestrained monkeys. Two rhesus monkeys conducted instructed walk-and-reach movements towards targets flexibly positioned in the cage. We tracked 3D multi-joint arm and head movements using markerless motion capture. Movements show small trial-to-trial variability despite being unrestrained. We wirelessly recorded 192 broad-band neural signals from three cortical sensorimotor areas simultaneously. Single unit activity is selective for different reach and walk-and-reach movements. Walk-and-reach targets could be decoded from premotor and parietal but not motor cortical activity during movement planning. The Reach Cage allows systems-level sensorimotor neuroscience studies with full-body movements in a configurable 3D spatial setting with unrestrained monkeys. We conclude that the primate frontoparietal network encodes reach goals beyond immediate reach during movement planning.

neuroscience↗