Biology subjects

Schaefer, M.

Publications and source records attributed to Schaefer, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

A phosphate-binding pocket in cyclin B3 is essential for XErp1/Emi2 degradation in meiosis I

To ensure the correct euploid state of embryos, it is essential that vertebrate oocytes await fertilization arrested at metaphase of meiosis II. This MII arrest is mediated by XErp1/Emi2, which inhibits the ubiquitin ligase APC/C (anaphase-promoting complex/cyclosome). Cyclin B3 in complex with Cdk1 (cyclin-dependent kinase 1) is essential to prevent an untimely arrest of vertebrate oocytes in meiosis I by targeting XErp1/Emi2 for degradation. Yet, the molecular mechanism of XErp1/Emi2 degradation in MI is not well understood. Here, by combining TRIM-Away in oocytes with egg extract and in vitro studies, we demonstrate that a hitherto unknown phosphate-binding pocket in cyclin B3 is essential for efficient XErp1/Emi2 degradation in meiosis I. This pocket enables Cdk1/cyclin B3 to bind pre-phosphorylated XErp1/Emi2 facilitating further phosphorylation events, which ultimately target XErp1/Emi2 for degradation in a Plk1 (Polo-like kinase 1) dependent manner. Key elements of this degradative mechanism are conserved in frog and mouse. Our studies identify a novel, evolutionarily conserved determinant of Cdk/cyclin substrate specificity essential to prevent an untimely oocyte arrest at meiosis I with catastrophic consequences upon fertilization.

molecular biology↗

bioRxiv2023

The how, when, and what of odor valence communication between the olfactory bulb and piriform cortex

A core function of the olfactory system is to determine an odors valence. The central processing of odor valence is initiated in the olfactory bulb, but the neural mechanisms by which this important information is communicated to, and from, the olfactory cortex (piriform cortex) in humans are not known. To assess communication between the two nodes, we simultaneously measured odor-dependent neural activity in the olfactory bulb and piriform cortex from human participants while obtaining trial-by-trial valence ratings. We determined when valence information was communicated, what kind of information was transferred, and how the information was transferred (i.e., in which frequency band). Support vector machine learning on the coherence spectrum and frequency-resolved Granger causality were used to identify valence-dependent differences in functional and effective connectivity between the olfactory bulb and piriform cortex. We found that the olfactory bulb communicates odor valence to the piriform cortex in the gamma band shortly after odor onset, while the piriform cortex subsequently feeds valence-related information back to the olfactory bulb in the beta band. Decoding accuracy was better for negative than positive valence, suggesting negative valence superiority. Critically, we replicated these findings in an independent dataset using other odors across a larger perceived valence range. Combined, these results demonstrate that the olfactory bulb and piriform cortex communicate levels of odor pleasantness across multiple frequencies, at specific time-points and in a direction-dependent pattern in accordance with the two-stage model of odor processing. It also provides further evidence that odor valence should be viewed as two perceptual dimensions and not one continuous.

neuroscience↗

bioRxiv2023

Large language models are universal biomedical simulators

Computational simulation of biological processes can be a valuable tool in accelerating biomedical research, but usually requires extensive domain knowledge and manual adaptation. Recently, large language models (LLMs) such as GPT-4 have proven surprisingly successful for a wide range of tasks by generating human language at a very large scale. Here we explore the potential of leveraging LLMs as simulators of biological systems. We establish proof-of-concept of a text-based simulator, SimulateGPT, that uses LLM reasoning. We demonstrate good prediction performance for various biomedical applications, without requiring explicit domain knowledge or manual tuning. LLMs thus enable a new class of versatile and broadly applicable biological simulators. This text-based simulation paradigm is well-suited for modeling and understanding complex living systems that are difficult to describe with physics-based first-principles simulation, but for which extensive knowledge and context is available as written text.

bioinformatics↗

bioRxiv2023

Persistent biofluid small molecule alterations induced by Trypanosoma cruzi infection are not restored by antiparasitic treatment

Table of contents graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/543565v1_figu1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@10c3a0aorg.highwire.dtl.DTLVardef@1b69d6dorg.highwire.dtl.DTLVardef@199867org.highwire.dtl.DTLVardef@64b20b_HPS_FORMAT_FIGEXP M_FIG C_FIG Chagas Disease (CD), caused by Trypanosoma cruzi (T. cruzi) protozoa, is a complicated parasitic illness with inadequate medical measures for diagnosing infection and monitoring treatment success. To address this gap, we analyzed changes in the metabolome of T. cruzi-infected mice via liquid chromatography tandem mass spectrometry analysis of clinically-accessible biofluids: saliva, urine, and plasma. Urine was the most indicative of infection status, across mouse and parasite genotypes. Metabolites perturbed by infection in the urine include kynurenate, acylcarnitines, and threonylcarbamoyladenosine. Based on these results, we sought to implement urine as a tool for assessment of CD treatment success. Strikingly, it was found that mice with parasite clearance following benznidazole antiparasitic treatment had comparable overall urine metabolome to mice that failed to clear parasites. These results match with clinical trial data in which benznidazole treatment did not improve patient outcomes in late-stage disease. Overall, this study provides insights into new small molecule-based CD diagnostic methods and a new approach to assess functional treatment response.

microbiology↗

bioRxiv2022

Precision RNAi using synthetic shRNAmir target sites

Loss-of-function genetic tools are widely applied for validating therapeutic targets, but their utility remains limited by incomplete on- and uncontrolled off-target effects. We describe artificial RNA interference (ARTi) based on synthetic, ultra-potent, off-target-free shRNAs that enable efficient and inducible suppression of any gene upon introduction of a synthetic target sequence into non-coding transcript regions. ARTi establishes a scalable loss-of-function tool with full control over on- and off-target effects.

genetics↗

bioRxiv2022

HUWE1 controls tristetraprolin proteasomal degradation by regulating its phosphorylation

Tristetraprolin (TTP) is a critical negative immune regulator. It binds AU-rich elements in the untranslated-regions of many mRNAs encoding pro-inflammatory mediators, thereby accelerating their decay. A key but poorly understood mechanism of TTP regulation is its timely proteolytic removal: TTP is degraded by the proteasome through yet unidentified phosphorylation-controlled drivers. In this study, we set out to identify factors controlling TTP stability. Cellular assays showed that TTP is strongly lysine-ubiquitinated, which is required for its turnover. A genetic screen identified the ubiquitin E3 ligase HUWE1 as a strong regulator of TTP proteasomal degradation, which we found to control TTP stability indirectly by regulating its phosphorylation. Pharmacological assessment of multiple kinases revealed that HUWE1-regulated TTP phosphorylation and stability was independent of the previously characterized effects of MAPK-mediated S52/S178 phosphorylation. HUWE1 function was dependent on phosphatase and E3 ligase binding sites identified in the TTP C-terminus. Our findings indicate that while phosphorylation of S52/S178 is critical for TTP stabilization at earlier times after pro-inflammatory stimulation, phosphorylation of the TTP C-terminus controls its stability at later stages.

cell biology↗

bioRxiv2022

Evidence of active oviposition avoidance to systemically applied imidacloprid in the Colorado Potato Beetle (Leptinotarsa decemlineata)

Agricultural pests can develop behavioral resistance to insecticides via choosing to feed or oviposit on non-toxic hosts. As young larvae have relatively low mobility, oviposition preferences from female adults may play a critical role in shaping the evolutionary trajectory of pest populations. While oviposition avoidance of toxic hosts was found in different agriculture pests, it remains unclear whether such preferences can be learned from female adults. To address this question, we investigated feeding and oviposition preferences to imidacloprid in the Colorado Potato Beetle (CPB, Leptinotarsa decemlineata), a major potato pest. We first identified two CPB strains that have different levels of resistance to imidacloprid. Then, we performed choice assays in the two strains and found that both strains did not have an innate feeding avoidance to systemically applied imidacloprid at both larval and adult stages. Further oviposition choice assays showed that the susceptible strain preferred to lay eggs on insecticide-free plants while the resistant strain did not. Analysing moving patterns of the two strains suggested that the oviposition preference is likely due to active learning by the female adults. Together, these results indicate that CPB can have active oviposition avoidance, which might have contributed to the rapid global invasion of this agricultural pest.

animal behavior and cognition↗

bioRxiv2021

ARGONAUTE proteins regulate a specific network of genes through KLF4 in mouse embryonic stem cells

The Argonaute proteins (AGO) are well-known for their essential role in post-transcriptional gene silencing in the microRNA (miRNA) biogenesis pathway. Only two AGOs (AGO1 and AGO2) are expressed in mouse embryonic stem cells (mESCs). The transcriptome of Ago mutant mESCs revealed a large and specific set of misregulated genes, compared to other miRNA biogenesis factor mutant cells, suggesting additional functions for the AGOs in stem cells. In this study, we endeavored to understand miRNA-independent roles of the AGOs in gene expression regulation through the integration of multiple datasets. Correlation of Ago mutant differential gene expression with ENCODE histone modification data of WT mESCs revealed that affected genes were regulated by the repressive histone modification H3K27me3. We validated this observation by performing chromatin immunoprecipitation followed by sequencing and observed a global loss of H3K27me3 in Ago mutant cells. Nevertheless, this reduction explains only a small part of the specific differential gene expression observed in Ago mutant mESCs. By integrating chromatin accessibility data in conjunction with prediction of transcription factor binding sites, we identified differential binding for five transcription factors, including KLF4 as a key modulator of more than half of the specific misregulation of gene expression in the absence of AGO proteins. Our findings illustrate that in addition to chromatin state, information about transcription factor binding is more revelatory in understanding the multi-layered mechanism adopted by cells to regulate gene expression. These data also highlight the importance of an integrative approach to unravel the variety of noncanonical functions of AGOs in mESCs.

molecular biology↗

bioRxiv2021

Integrative analysis allows a global and precise identification of functional miRNA target genes in mESCs

MicroRNA (miRNA) loaded Argonaute (AGO) complexes regulate gene expression via direct base pairing with their mRNA targets. Current prediction approaches identified that between 20 to 60% of mammalian transcriptomes are regulated by miRNAs, but it remains largely unknown which fraction of these interactions are functional in a specific cellular context. Here, we integrated transcriptome data from a set of miRNA-depleted mouse embryonic stem cell (mESC) lines with published miRNA interaction predictions and AGO-binding profiles. This integrative approach, combined with molecular validation data, identified that only 6% of expressed genes are functionally and directly regulated by miRNAs in mESCs. In addition, analyses of the stem cell-specific miR-290-295 cluster target genes identified TFAP4 as an important transcription factor for early development. The extensive datasets developed in this study will support the development of improved predictive models for miRNA-mRNA functional interactions.

systems biology↗

bioRxiv2021

AGO1 regulates major satellite transcripts and H3K9me3 distribution at pericentromeric regions in mESCs

Argonaute proteins (AGOs), that play an essential role in cytosolic post-transcriptional gene silencing, have been also reported to function in nuclear processes like transcriptional activation or repression, alternative splicing and, chromatin organization. As most of these studies have been conducted in human cancer cell lines, the relevance of AGOs nuclear functions in the context of mouse early embryonic development remains uninvestigated. Here, we examined a possible role of the AGO1 protein on the distribution of constitutive heterochromatin in mouse Embryonic Stem Cells (mESCs). We observed a specific redistribution of the repressive histone mark H3K9me3 and the heterochromatin protein HP1, away from pericentromeric regions upon Ago1 depletion. Furthermore, we demonstrated that major satellite transcripts are strongly upregulated in Ago1_KO mESCs and that their levels are partially restored upon AGO1 rescue. We also observed a similar redistribution of H3K9me3 and HP1 in Drosha_KO mESCs, suggesting a role for microRNAs (miRNAs) in the regulation of heterochromatin distribution in mESCs. Finally, we showed that specific miRNAs with complementarity to major satellites can partially regulate the expression of these transcripts. Summary blurbDepletion of AGO1 in mESCs leads to a redistribution of H3K9me3 and HP1 away from pericentromeric regions and is accompanied by an upregulation of major satellites transcripts.

cell biology↗

bioRxiv2021

NECAB2 orchestrates an endosomal pathway of mitochondrial quality control at striatal synapses

Synaptic signaling depends on ATP generated by mitochondria. Due to extensive connectivity, the striatum is especially vulnerable to mitochondrial dysfunction and thus requires efficient mitochondrial quality control and repair. We found that global knockout of the neuronal calcium-binding protein 2 (NECAB2) in the mouse causes loss of striatal synapses and behavioral phenotypes related to striatal dysfunction such as reduced motivation and altered sensory gating. Striatal mitochondria from Necab2 knockout mice are more abundant and smaller. They are characterized by increased respiration and superoxide production resulting in oxidative stress. This accumulation of dysfunctional mitochondria is caused by a defective assembly of mitochondria with early endosomes in a pathway that involves the small GTPase Rab5 and its guanine nucleotide exchange factor Alsin/ALS2. NECAB2 therefore participates in an endosomal pathway of mitochondrial stress response and repair important for striatal function.

neuroscience↗

bioRxiv2021

The human olfactory bulb process odor valence representation and initiate motor avoidance behavior

Determining the valence of an odor to provide information to guide rapid approach-avoidance behavior is thought to be one of the core tasks of the olfactory system, yet little is known of its initial neural mechanisms or subsequent behavioral manifestation in humans. In two experiments, we measured the functional processing of odor valence perception in the human olfactory bulb (OB)--the first processing stage of the olfactory system--using a non-invasive method as well as assessed subsequent motor avoidance response. We demonstrate that odor valence perception is associated with both gamma and beta activity in the human OB. Moreover, we show that negative, but not positive, odors initiate an early beta response in the OB, a response that is linked to a preparatory neural motor response in motor cortex. Finally, in a separate experiment we show that negative odors trigger a full-body motor avoidance response, manifested as a rapid leaning away from the odor, in the time period predicted by the OB results. Taken together, these results demonstrate that the human OB processes odor valence in a sequential manner in both the gamma and beta frequency bands and suggest that early processing of unpleasant odors in the OB might underlie rapid approach-avoidance decisions.

neuroscience↗

bioRxiv2020

Specific decorations of 17-hydroxygeranyllinalool diterpene glycosides solve the autotoxicity problem of chemical defense in Nicotiana attenuata

17-hydroxygeranyllinalool diterpene glycosides (HGL-DTGs) are abundant and potent anti-herbivore defense metabolites in Nicotiana attenuata whose glycosylation and malonylation biosynthetic steps are regulated by jasmonate signaling. To characterize the biosynthetic pathway of HGL-DTGs, we conducted a genome-wide analysis of uridine diphosphate glycosyltransferases (UGTs) and identified 107 members of family-1 UGTs. Tissue-specific time-course transcriptional profiling revealed that the transcripts of three UGTs were highly correlated with two HGL-DTG key biosynthetic genes: geranylgeranyl diphosphate synthase (NaGGPPS) and geranyllinalool synthase (NaGLS). NaGLSs role in HGL-DTG biosynthesis was confirmed by virus-induced gene-silencing. Silencing the UDP-rhamnosyltransferase, UGT91T1, indicated its role in the rhamnosylation of HGL-DTGs. In vitro enzyme assays revealed that UGT74P3 and UGT74P4 use UDP-glucose for the glucosylation of 17-hydroxygeranyllinalool (17-HGL) to lyciumoside I. UGT74P3 and UGT74P5 stably silenced plants were severely developmentally deformed, suggesting a phytotoxic effect of 17-HGL. Applications of synthetic 17-HGL and silencing of these UGTs in HGL-DTG-free plants confirmed the phytotoxic effect of 17-HGL. Feeding assays with Manduca sexta larvae revealed the defensive functions of the glucosylation and rhamnosylation steps in HGL-DTG biosynthesis. Glucosylation is a critical step that contributes to the metabolites defensive function and solves the autotoxicity problem of this potent chemical defense.

plant biology↗

bioRxiv2020

Landscape management for grassland multifunctionality

Land-use intensification has contrasting effects on different ecosystem services, often leading to land-use conflicts. While multiple studies have demonstrated how landscape-scale strategies can minimise the trade-off between agricultural production and biodiversity conservation, little is known about which land-use strategies maximise the landscape-level supply of multiple ecosystem services (landscape multifunctionality), a common goal of stakeholder communities. We combine comprehensive data collected from 150 German grassland sites with a simulation approach to identify landscape compositions, with differing proportions of low-, medium-, and high-intensity grasslands, that minimise trade-offs between the six main grassland ecosystem services prioritised by local stakeholders: biodiversity conservation, aesthetic value, productivity, carbon storage, foraging, and regional identity. Results are made accessible through an online tool that provides information on which compositions best meet any combination of user-defined priorities (https://neyret.shinyapps.io/landscape_composition_for_multifunctionality/). Results show that an optimal landscape composition can be identified for any pattern of ecosystem service priorities. However, multifunctionality was similar and low for all landscape compositions in cases where there are strong trade-offs between services (e.g. aesthetic value and fodder production), where many services were prioritised, and where drivers other than land use played an important role. We also found that if moderate service levels are deemed acceptable, then strategies in which both high and low intensity grasslands are present can deliver landscape multifunctionality. The tool presented can aid informed decision-making by predicting the impact of future changes in landscape composition, and by allowing for the relative roles of stakeholder priorities and biophysical trade-offs to be understood by scientists and practitioners alike. HighlightsO_LIAn online tool identifies optimal landscape compositions for desired ecosystem services C_LIO_LIWhen the desired services are synergic, the optimum is their common best landscape composition C_LIO_LIWhen the desired services trade-off, a mix of grassland intensity is most multifunctional C_LIO_LISuch tools could support decision-making processes and aid conflict resolution C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/208199v5_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@3273f6org.highwire.dtl.DTLVardef@5b3a5aorg.highwire.dtl.DTLVardef@153f526org.highwire.dtl.DTLVardef@103cbea_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2020

Translational adaptation of human viruses to the tissues they infect

Viruses need to hijack the translational machinery of the host cell for a productive infection to happen. However, given the dynamic landscape of tRNA pools among tissues, it is unclear whether different viruses infecting different tissues have adapted their codon usage toward their tropism. Here, we collect the coding sequences of over 500 human-infecting viruses and determine that tropism explains changes in codon usage. Using an in silico model of translational efficiency, we validate the correspondence of the viral codon usage with the translational machinery of their tropism. In particular, we propose that the improved translational adaptation to the upper respiratory airways of the pandemic agent SARS-CoV-2 coronavirus could enhance its transmissibility. Furthermore, this correspondence is specifically defined in early viral proteins, as upon infection cells undergo reprogramming of tRNA pools that favors the translation of late counterparts.

systems biology↗

bioRxiv2018

Bumetanide prevents brain trauma-induced depressive-like behavior.

Brain trauma triggers a cascade of deleterious events leading to enhanced incidence of drug resistant epilepsies, depression and cognitive dysfunctions. The underlying mechanisms leading to these alterations are poorly understood and treatment that attenuates those sequels not available. Using controlled-cortical impact (CCI) as experimental model of brain trauma in adult mouse we found a strong suppressive effect of the sodium-potassium-chloride importer (NKCC1) specific antagonist bumetanide on appearance of depression-like behavior. We demonstrate that this alteration in behavior is associated with a block of CCI-induced decrease in parvalbumin-positive interneurons and impairment of post-traumatic secondary neurogenesis within the dentate gyrus of the hippocampus. The mechanism mediating the effect of bumetanide involves early transient changes in expression of chloride regulatory proteins and qualitative changes in GABA(A) mediated transmission after brain trauma. This work opens new perspectives in the early treatment of human post-traumatic induced depression. Our results strongly suggest that bumetanide might constitute an efficient prophylactic treatment to reduce neurological and psychiatric consequences of brain trauma.

neuroscience↗

bioRxiv2018

PCF11 connects alternative polyadenylation to formation and spontaneous regression of neuroblastoma

Diversification at the transcriptome 3end is an important and evolutionarily conserved layer of gene regulation associated with differentiation and dedifferentiation processes. However the underlying mechanisms and functional consequences are poorly defined. Here, we identify extensive transcriptome-3end-alterations in neuroblastoma, a tumour entity with a paucity of recurrent somatic mutations and an unusually high frequency of spontaneous regression. Utilising extensive RNAi-screening we reveal the landscape and drivers of transcriptome-3end-diversification, discovering PCF11 as critical regulator, directing alternative polyadenylation (APA) of hundreds of transcripts including a differentiation RNA-operon. PCF11 shapes inputs converging on WNT-signalling, and governs cell cycle, proliferation, apoptosis and neurodifferentiation. Postnatal PCF11 down-regulation induces a neurodifferentiation program, and low-level PCF11 in neuroblastoma associates with favourable outcome and spontaneous tumour regression. Our findings document a critical role for APA in tumourigenesis and describe a novel mechanism for cell fate reprogramming in neuroblastoma with important clinical implications. An interactive data repository of transcriptome-wide APA covering >170 RNAis, and an APA-network map with regulatory hubs is provided.

developmental biology↗

bioRxiv2018

PAVOOC: Designing CRISPR sgRNAs using 3D protein structures and functional domain annotation

Summary: sgRNAs targeting the same gene can significantly vary in terms of efficacy and specificity. PAVOOC (Prediction And Visualization of On- and Off-targets for CRISPR) is a web-based CRISPR sgRNA design tool that employs state-of-the art machine learning models to prioritize most effective candidate sgRNAs. In contrast to other tools, it maps sgRNAs to functional domains and protein structures and visualizes cut sites on corresponding protein crystal structures. Furthermore, PAVOOC supports HDR template generation for gene editing experiments and the visualization of the mutated amino acids in 3D.\n\nAvailability and Implementation: PAVOOC is available under https://pavooc.me and accessible using current browsers (Chrome/Chromium recommended). The source code is hosted at github.com/moritzschaefer/pavooc under the MIT License. The backend, including data processing steps, and the frontend is implemented in Python 3 and ReactJS respectively. All components run in a simple Docker environment.\n\nContact: mail@moritzs.de

bioinformatics↗