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Biology subjects

Kaiser, M.

Publications and source records attributed to Kaiser, M..

At least 19 recordsLinked to original sources

Polychrome activity profiling distinguishes Cys proteases and their isoforms in plants

Activity-based profiling with fluorescent probes is a powerful tool for the functional characterization of whole enzyme classes in crude proteomes. Here, we discovered that probe cocktails consisting of the E-64 warhead carrying different fluorophores via short linkers distinguishes the labeling of papain-like cysteine proteases and their isoforms because of their differential affinity to these probes. This causes polychrome labeling with specific apparent colors for different protease families and isoforms. Polychrome labeling revealed differential labeling of isoforms of RD21-like proteases carrying C-terminal granulin domains. Molecular modeling of the RD21 isoforms revealed that the C-terminal granulin may create a fluorophore-binding pocket with the substrate-binding groove, implying that the granulin domain influences substrate selectivity. The concept of polychrome labeling may be widely applicable to other chemical probes for the characterization of protein families in all kingdoms of life.

Plant Biology↗

Multi-centre laboratory study to determine discriminating concentrations for broflanilide and isocycloseram resistance monitoring in mosquitoes

1In 2024-2025 a multi-centre study involving seven international laboratories was conducted with the support of the World Health Organization (WHO). The aim of the study was to establish and validate discriminating concentrations (DCs) in WHO bottle bioassays for monitoring susceptibility to broflanilide and isocycloseram in Anopheles gambiae s.s., An. funestus, An. stephensi and Aedes aegypti. The following values are recommended for adoption as DCs for broflanilide: 10 {micro}g/bottle for An. gambiae and Ae. aegypti, 15 {micro}g/bottle for An. funestus, and 25 {micro}g/bottle for An. stephensi. The recommended DCs for isocycloseram are 15 {micro}g/bottle for Ae. aegypti, 30 {micro}g/bottle for An. gambiae, 50 {micro}g/bottle for An. stephensi, and 60 {micro}g/bottle for An. funestus. Based on the experiences of conducting this study, which represents the application of a generic protocol for establishing discriminating concentrations produced by the WHO, technical recommendations are made on the generation and analysis of DC data for insecticides in future.

zoology↗

Differences in substrate engagement and Retinoblastoma protein (RB) binding of human KDM5A and KDM5B

Trimethylation of lysine 4 of histone H3 (H3K4me3) is a post-translational modification (PTM) enriched at promoters of actively transcribed genes. H3K4me3 is removed by the human histone demethylases of the KDM5 family. KDM5 demethylases act as transcriptional repressors through their catalytic activity in addition to more complex roles that depend on their interactions with other chromatin regulators and may be independent of demethylase activity. To better understand the mechanistic differences of the closely related paralogs KDM5A and KDM5B as well as their interactions with Retinoblastoma protein (RB), we systematically analyzed and compared their demethylase activities, nucleosome engagement, and RB binding. We used recombinant nucleosome binding and demethylase activity assays, as well as an integrative structural biology approach using negative-stain electron microscopy (EM), AlphaFold predictions, and cross-linking mass spectrometry for a comprehensive in vitro analysis of these critical and largely non-redundant enzymes. KDM5A and KDM5B showed differences in enzyme kinetics using peptide substrates, as well as in nucleosome binding. Furthermore, KDM5A interacts with RB, mainly mediated by its canonical LxCxE RB binding motif. KDM5B, on the other hand, lacks an LxCxE binding motif and does not stably bind to RB under the conditions tested here. RB directly interacts with nucleosomes, and its nucleosome binding does not measurably affect KDM5A demethylase activity or nucleosome interactions. Our findings provide a biochemical framework for the differences between KDM5A and KDM5B regarding RB interactions and nucleosome engagement.

biochemistry↗

NbRD21 protease controls receptor kinase homeostasis in Nicotiana benthamiana

RD21-like proteases are papain-like cysteine proteases with a C-terminal granulin domain that are abundant and ubiquitous in angiosperms and have often been implicated in immunity. We previously found that the activity of RD21 in Nicotiana benthamiana (NbRD21) is suppressed during infection with Pseudomonas syringae. Here, we studied the role of NbRD21 in immunity and proteome processing. NbRD21 was disrupted by genome editing and rd21 mutants were subjected to disease assays and shot-gun proteomics. Dipeptide substrate zLR-AMC was used in protease assays and agroinfiltration was used to transiently express NbRD21 and candidate substrates. Genome edited lines lacking NbRD21 develop normally but have drastically reduced zLRase activity and are significantly more susceptible to P. syringae. Shot gun proteomics revealed an increased accumulation of [~]20 diverse receptor-like kinases (RLKs) in untreated rd21 knockout lines, but their transcript levels are unaltered when compared to wild-type plants. 35S-driven GFP-tagged RLKs accumulate more upon transient expression in rd21 plants than in wild- type plants. These data indicate that NbRD21 post-translationally controls RLK homeostasis, either by directly degrading RLKs, or indirectly by regulating endocytic RLK recycling.

plant biology↗

Rewiring the Human Brain: On the Fabric of Associative Thinking

Concept cells are neurons in the medial temporal lobe that represent an abstract concept, such as a familiar person, in a context-independent way. They are activated by heterogeneous and potentially multi-modal sensory input related to the concept, such as viewing a photo of the person, reading the persons name, or hearing the persons voice. Learning the concept implies connecting the cortical cells that are triggered when such features are perceived with the cells of the concept, resulting in an associative memory engram. Traditional models explain the formation of such an engram with Hebbian learning through synaptic plasticity, the strengthening of existing synapses in response to co-stimulation. However, the low edge density of the brain suggests that direct connections in the form of preexisting synapses between these cells are relatively unlikely, rendering such constructs inefficient and volatile. Instead, it is plausible that more persistent concept engrams rely on structural plasticity, involving the creation of synapses de novo. Yet, it has still been unclear how neurons can project their axons across such a considerable distance, finding a target they do not know in advance. In this paper, we simulate the formation of such structural engrams in the connectomes of healthy subjects, offering a model hypothesis of how such engrams can be formed on a structural level. Based on our model, we further demonstrate how activating a concept can trigger related concepts through overlapping sensory associations, in a process we call a percept-concept loop.

neuroscience↗

Transcutaneous auricular Vagus nerve stimulation for working memory enhancement: A comparative study of electrical and ultrasound stimulation

ObjectivesTranscutaneous auricular vagus nerve stimulation (taVNS) is a non-invasive neuromodulation technique that has shown potential to enhance cognitive function, including working memory. This study investigated the acute effects of both electrical (E-taVNS) and ultrasound (U-taVNS) modalities on working memory using a 3-back task in healthy young adults. We hypothesized that active taVNS would enhance working memory performance relative to sham, and that both stimulation modalities would engage similar neuromodulatory mechanisms. Materials and MethodsFifty-nine participants underwent a single-blind, sham-controlled, within-subject design study, with working memory performance assessed using a 3-back task before and after stimulation. Primary performance measures included correct rejection rate, error false alarm, and sensitivity (d'). Statistical analyses compared pre- and post-stimulation performance across modalities. ResultsE-taVNS significantly enhanced working memory performance through an increase in correct rejection rate and sensitivity (measured by d), alongside a reduction in error of false alarm. U-taVNS showed a similar directional trend across performance measures, although these effects did not reach statistical significance. Baseline anxiety levels significantly predicted individual responsiveness to taVNS. In terms of tolerability, a higher proportion of participants receiving E-taVNS reported skin irritation compared to those receiving U-taVNS. ConclusionsE-taVNS can acutely enhance working memory performance, while U-taVNS may offer a comparable, better tolerated alternative. Our findings highlight the potential of taVNS to support memory function, while showing the importance of further research to clarify modality-specific effects and optimize stimulation parameters.

neuroscience↗

Comparing Electrical and Ultrasound Transcutaneous Vagus Nerve Stimulation (taVNS) on Associative Memory

Associative memory, the ability to bind and retrieve relationships between unrelated elements, is a cornerstone of human cognition and a primary target for neurorehabilitation. Vagus nerve stimulation (VNS) has emerged as a promising method to modulate the locus coeruleus-norepinephrine (LC-NE) system and hippocampal-prefrontal circuits essential for memory. However, the comparative efficacy of non-invasive modalities such as electrical (E-taVNS) and the emerging field of ultrasound (U-taVNS) remains poorly understood in the context of active recall. In this study, participants performed a crossmodal video-word associative memory task before and after receiving either E-taVNS or U-taVNS in active and sham conditions. We investigated whether these modalities enhance cued recall accuracy and retrieval reaction time. Our results revealed that neither E-taVNS nor U-taVNS significantly improved recall accuracy. However, E-taVNS significantly accelerated response times specifically for correctly recalled items. These findings suggest that while taVNS may not increase the likelihood of recalling associative memories, electrical stimulation may enhances the efficiency in which we do so. These findings suggest that electrical taVNS is a viable tool for facilitating memory search processes, though further research is required to optimize ultrasound parameters and validate mechanistic pathways through physiological monitoring.

neuroscience↗

Ultrasound transcutaneous auricular vagus nerve stimulation enhances semantic processing

Efficient access to conceptual knowledge is central to everyday cognition, yet the effects of non-invasive neuromodulation on semantic retrieval remain insufficiently characterised. Transcutaneous auricular vagus nerve stimulation (taVNS) offers a mechanistically distinct route to modulate distributed cognitive systems via ascending vagal afferent pathways, but its effects on semantic processing has not been explored. Here, we tested whether ultrasound-based taVNS delivered to the right cymba conchae can acutely enhance semantic retrieval efficiency in healthy adults. Twenty-seven participants completed a single blind, sham-controlled study comprising two counterbalanced sessions (active vs. sham) in a within-subject design, separated by at least five days. In each session, participants performed a semantic association task and a number-judgement control task before and immediately after 30 minutes of stimulation. Active taVNS produced selective post-stimulation improvements in semantic retrieval performance relative to sham and baseline, while performance on the control task remained unchanged. Adverse effects were minimal and did not differ between active and sham conditions. These findings provide causal evidence that ultrasound-based taVNS can acutely improve the efficiency of semantic processing, expanding the cognitive profile of taVNS beyond predominantly episodic and emotional memory domains and supporting its feasibility as a scalable approach for memory enhancement.

neuroscience↗

Selective proteasomal degradation from the Golgi apparatus membrane

To maintain cellular homeostasis, protein quality control (PQC) machineries target damaged proteins for degradation. However, the PQC machinery, operating at the major protein sorting and processing site of mammalian cells, the Golgi, has remained largely elusive. Here we used a chemical biology tool to induce misfolding and ubiquitination of Golgi-localized model substrates. Our tool recruits a Cullin-RING ubiquitin ligase complex by exposure of a degron, recognized by the substrate receptor KLHDC2. Using this tool, we found that ubiquitinated Golgi membrane proteins are targeted for proteasomal degradation, a process that is critical to avoid Golgi fragmentation. This process is facilitated by the p97-unfoldase, which assembles with its adaptors UFD1-NPL4 and FAF2 at the Golgi. We further identified the rhomboid pseudo-protease RHBDD2 as an important contributor to Golgi homeostasis as it binds misfolded, ubiquitinated Golgi membrane proteins and regulates Golgi morphology. Our findings establish a molecular framework for Golgi-PQC in mammalian cells. O_LIThe accumulation of misfolded Golgi proteins causes Golgi fragmentation. C_LIO_LIUbiquitinated Golgi membrane proteins are degraded by the proteasome. C_LIO_LIThe p97 unfoldase operates at the Golgi with its adaptors UFD1-NPL4 and FAF2. C_LIO_LIThe rhomboid pseudo-protease RHBDD2 contributes to Golgi protein quality control. C_LI

cell biology↗

Transcranial ultrasound stimulation selectively enhances fronto-temporal context-guided memory

There is substantial scientific interest in advancing knowledge on the control mechanisms supporting adaptive memory and improving approaches that can enhance cognition through brain stimulation. We implemented a non-invasive focal Transcranial Ultrasound Stimulation (TUS) approach with known longer-lasting post-stimulation effects in two rhesus macaques performing a novel context-dependent memory-sequencing task implemented on multiple touchscreens within their home units. Consistently in both monkeys, TUS to the anterior, but not posterior, medial temporal lobe enhanced performance under stable memory-sequencing contexts. TUS to the medial prefrontal cortex, on the other hand, selectively improved performance when contexts were unstable and the monkey needed to adapt to both a change in context and temporal sequence. These findings provide positive causal evidence of a functional dissociation within fronto-temporal memory circuits and pave the way for advancing non-invasive approaches to improve cognitive function and the study of neural circuits under focal enhancement across species. IMPACT STATEMENTTranscranial ultrasound stimulation of the prefrontal-hippocampal network selectively enhances context-guided memory in macaques, demonstrating that non-invasive brain stimulation can causally improve, rather than only disrupt, memory circuits.

neuroscience↗

Transcutaneous auricular vagus nerve stimulation enhances emotional bias towards happiness in healthy young adults: A comparative study of electrical and ultrasound stimulation

Transcutaneous auricular vagus nerve stimulation (taVNS) is an emerging neuromodulation technique demonstrating promise in emotional regulation. This study investigated the acute effects of both electrical (E-taVNS) and ultrasound (U-taVNS) modalities on emotional bias using a facial emotion categorization task in healthy young adults. Fifty-nine participants underwent a single-blind, sham-controlled, within-subject design, with emotional bias assessed at pre-, during-, and post-stimulation phases. Our findings revealed that both E-taVNS and U-taVNS significantly enhanced emotional bias scores, shifting the perception of neutral and ambiguous faces towards positive interpretations and reducing negative emotional bias. No significant differences in efficacy were observed between the two stimulation modalities. Furthermore, individual differences in interoceptive awareness were found to be associated with the observed taVNS effects. These results suggest that both electrical and ultrasound taVNS can acutely modulate emotional regulation, highlighting the potential of taVNS as a non-invasive, well-tolerated alternative for interventions targeting emotional bias and mood disorders. HighlightsO_LItaVNS reduces negative emotional bias toward ambiguous stimuli. C_LIO_LIBoth electrical and ultrasound taVNS shifted emotional bias toward more positive interpretations of ambiguous facial expressions. C_LIO_LIUltrasound taVNS (U-taVNS) demonstrated comparable efficacy to electrical taVNS (E-taVNS). C_LIO_LIThe subscale of the Multidimensional Assessment of Interoceptive Awareness predicted individual variability in taVNS-induced emotional bias change. C_LI

neuroscience↗

TPS Proteins coordinate plant growth with sugar availability via the SnRK1 Kinase

The ability to sense and respond to nutrients determines adaptation and survival in all organisms. In plants, sucrose stimulates growth and developmental progression via the signalling sugar trehalose 6-phosphate (T6P) which reflects sucrose availability. T6P acts, at least partly, by inhibiting the protein kinase SUCROSE NON-FERMENTING 1 (SNF1)-RELATED KINASE 1 (SnRK1) but the underlying mechanisms are poorly understood. Here, we identify a group of catalytically inactive T6P synthase (TPS) proteins, TPS5/6/7, as important factors for coupling the T6P signal to SnRK1 activity. In Arabidopsis thaliana, lack of TPS5/6/7 causes severe growth defects, particularly in roots. This is accompanied by a metabolic signature that is suggestive of T6P insensitivity and impaired sucrose utilization. Using a combination of genetics, SnRK1 activity assays, and imaging, we demonstrate that the growth defects of the tps5/6/7 mutant are due to SnRK1 misregulation and are reverted by knocking-down SnRK1 in this background. Co-immunoprecipitation assays further show that T6P promotes the interaction of TPS proteins with SnRK1 in a highly specific and dose-dependent manner. Our results support a model where TPS proteins act as T6P sensors, inhibiting non-nuclear SnRK1 activity when sucrose is abundant to promote biosynthetic processes and growth.

plant biology↗

Atovaquone-venturicidin A combination is synergistic against Plasmodium falciparum

We report the synergistic interaction between the complex III inhibitor atovaquone and an ATP synthase inhibitor, venturicidin A, against Plasmodium falciparum. Our results suggest the simultaneous inhibition of the parasites primary and alternative pathways for generating the mitochondrial membrane potential to be responsible for this phenomenon, whereby the alternative pathway relies on ATP synthase running in reverse mode. We hypothesize that the synergistic interaction between atovaquone and proguanil could follow a similar mechanism.

microbiology↗

Targeted degradation of USP7 in solid cancer cells reveals disparate effects of deubiquitinase inhibition vs. acute protein depletion

Proteolysis-targeting chimeras (PROTACs) co-op the ubiquitin system for targeted protein degradation, creating opportunities to interrogate cellular functions of proteins through "chemical knockdown". However, matched pairs of protein degraders and inhibitors, that possess high specificity and chemical complementarity, for individual components of the ubiquitin system have remained scarce. This includes reagents to modulate activity and abundance of deubiquitinases (DUBs), which critically regulate ubiquitin-mediated signaling. Here, using an integrated chemical biology approach, we explored the cellular function of the DUB USP7 as a case study comparing inhibition and degradation of this DUB in melanoma and pancreatic cancer cells. Through the synthesis of a degrader library, we identified potent USP7 PROTACs for each cancer type, established BRET-based ternary complex formation and quantified degradation efficiency. USP7 degraders and their cognate inhibitor were subsequently employed to characterize treatment-induced phenotypic alterations. Proteomic and cellular analyses revealed that highly specific degradation of USP7 modulated both shared and distinct protein sets across cancer cell types, without impacting cell growth. Notably, cellular responses to USP7 degradation differed markedly from those to USP7 inhibition. Moreover, our data uncovered broad proteomic and metabolic changes induced by prolonged USP7 inhibitor treatment. Collectively, our work provides a chemical toolbox of comprehensively characterized reagents to distinguish on-target phenotypes which will aid the understanding of the role of USP7 in malignant diseases. More broadly, our data emphasize the importance of increased specificity via PROTAC-mediated degradation and the potential of this modality to distinguish catalytic from non-catalytic as well as cell-line specific functions of DUBs.

biochemistry↗

MTBP allosterically activates Cdk8-CycC kinase activity

How the approximately 300 human protein kinases identify their dedicated substrates despite the significant overlap of their phosphorylation consensus sequences is relevant for nearly all cellular processes. We show here that the Cdk8/19-CycC kinase uses mutually exclusive targeting and activation factors to facilitate distinct cellular roles. The Med12 protein is known to target Cdk8/19-CycC to the mediator of transcription complex to control the transcription of specific gene sets upon respective stimuli. We describe that a second Cdk8/19-CycC targeting factor exists, the replication origin firing regulator MTBP that targets the kinase to Med12-independent cellular roles. Both Med12 and MTBP constitute allosteric activators of the enzymatic Cdk8/19-CycC kinase activity in vitro. We describe the structural basis of this activation that involves distinct mechanisms how Med12 and MTBP reposition the T-loop of the kinase independently of T-loop phosphorylation - the canonical mechanism of CDK kinase activation. Our results support the following model: the Cdk8/19-CycC dimer alone has low enzymatic activity, which may help avoid off-target phosphorylation. Med12, MTBP and potentially other as yet unidentified accessory factors, target the kinase to distinct molecular environments, at the same time activating kinase activity for efficient substrate phosphorylation. Our work establishes an unusual mechanism of CDK kinase control and change the current paradigm how Cdk8/19-CycC selects its substrates. Substrate selection of the kinase may be relevant for cancer biology and therapy because Cdk8 is a well-established colorectal cancer promoting factor.

biochemistry↗

ATXN3 regulates lysosome regeneration after damage by targeting K48-K63-branched ubiquitin chains

The cellular response to lysosomal damage involves fine-tuned mechanisms of membrane repair, lysosome regeneration and lysophagy, but how these different processes are coordinated is not fully understood. Here we show in human cells that the deubiquitinating enzyme ATXN3 helps restore integrity of the lysosomal system after damage by targeting K48-K63-linked branched ubiquitin chains on regenerating lysosomes. We find that ATXN3 translocates to lysosomes after different types of damage and there colocalizes with its partner, VCP/p97. ATXN3 recruitment occurs late after the initial repair of a subset of lysosomes and after phagophore formation on terminally damaged lysosomes. Of note, inactivation of ATXN3 by induced degradation, depletion or knock-out impairs clearance of damaged lysosomes and full restoration of lysosomal capacity. Mechanistically, ATXN3, along with VCP/p97, turns over K48-K63-branched ubiquitin conjugates on LAMP1-positive, phosphatidylinositol-(4,5)-bisphosphate-decorated compartments that are not yet fully re-acidified indicating involvement in lysosome regeneration. Our findings identify a key role of ATXN3 in restoring lysosomal function after lysosomal membrane damage and uncover K48-K63-branched ubiquitin chain-regulated regeneration as a critical element of the lysosomal damage stress response.

cell biology↗

Expanding and applying reactivity-based protein profiling (RBPP) in Arabidopsis

Chemical probes that label surface-exposed amino acid residues in native proteomes serve as powerful tools for studying native reactivities, yet their use has primarily been limited to drug discovery. In this study, we expand the application of reactivity proteomics by monitoring ATP-induced changes over 21,000 reactive lysine, serine, threonine, and tyrosine residues across native Arabidopsis proteomes using biotinylated N-hydroxysuccinimide (BioNHS) ester probes. ATP caused significant differential labelling. Labelling was reduced in ATP-binding pockets, consistent with ligand occupancy, whereas many sites outside ATP-binding regions showed either reduced or increased labelling in response to ATP. Structural modelling revealed that these differentially labelled sites are associated with ATP-induced conformational changes, altering lysine exposure. Notable examples of ATP-driven structural shifts include adenylate kinase ADK4, acyl-activating enzyme AAE3, cell division control protein CDC48A and its interacting partner PUX1, and ATP-induced 26S proteasome assembly. Furthermore, we show that reactivity proteomics using phosphonic acid-NHS (PhoNHS) followed by IMAC enrichment offers a complementary and expanded list of labelling sites. Our findings establish reactivity proteomics as a versatile and powerful platform for exploring protein conformational dynamics, metabolite-protein interactions, and regulatory mechanisms directly in native proteomes.

plant biology↗

Induced pluripotent stem cell-derived human macrophages as an infection model for Trypanosoma cruzi

Chagas disease, caused by the parasite Trypanosoma cruzi, affects millions of people globally. Unfortunately, the available treatment options, especially for the chronic stage of the disease, are suboptimal. Given the chronic nature of the disease and the elusive nature of the parasite, there is a high need for new and safer drugs that deliver sterile cure. Posaconazole was a promising lead in the drug discovery pipeline but ultimately failed in clinical trials due to patient relapses. This failure illustrates the need for a drug screening assay that can predict sterile cure by assessing recrudescence after treatment. Here, we used human induced pluripotent stem cell (iPSC)-derived macrophages (iMACs) as host cells for T. cruzi. The iMACs were highly susceptible to infection by the parasites. By combining red fluorescent protein (RFP)-expressing iMACs with mNeonGreen-expressing T. cruzi, we were able to monitor the dynamics of the infection through live cell imaging. The activity of the compounds benznidazole and posaconazole was consistent with the results of an established infection system using mouse primary macrophages. The post-mitotic nature of iMACs makes them suitable host cells for long-term assays needed to assess recrudescence of parasites. Moreover, their human origin, stable genetic background, and capacity for genetic modification make the iMACs excellent host cells for studying host-pathogen interaction. Author summaryThe parasite Trypanosoma cruzi, the causative agent of Chagas disease, is a global health concern affecting millions each year. Infection with T. cruzi can cause chronic disease, often remaining asymptomatic for decades before resulting in severe cardiac or gastro-intestinal pathologies. To date, only benznidazole and nifurtimox are used for treatment of the infection, but both drugs are suboptimal for curing the chronic stage. Posaconazole showed great promise in preclinical studies but failed to achieve sterile cure in clinical trials, causing patient relapses. These disappointing results underline the need for drug screening assays able to predict sterile cure by evaluating recrudescence post-treatment. We used human induced pluripotent stem cell derived macrophages as host cells for T. cruzi and testing of trypanocidal compounds. This model can be used for long-term in vitro screening assays to find new drug candidates against Chagas disease. The human origin of these cells combined with the possibility of upscaling their production make them great host cells for drug screening campaigns.

microbiology↗