Biology subjects

Scholz, M.

Publications and source records attributed to Scholz, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Lateral organization of cytochrome b6f in thylakoid membranes controls photosynthetic electron transfer efficiency

Photosynthetic electron transfer relies on the coordinated function and spatial organization of large protein complexes within the thylakoid membrane. The cytochrome b6f complex (b6f) functionally interconnects photosystem (PS) II and PSI in photosynthetic electron transfer and is equally distributed between appressed and non-appressed thylakoid membranes. Here, we investigate the functional link between the lateral distribution of b6f and efficient photosynthetic electron flow in Chlamydomonas reinhardtii. We engineered strains with stromal fusions between PetA of b6f and two fluorescent proteins (FPs) of different molecular mass: Clover and ATeam. Under oxic conditions, these strains exhibited significantly slower electron transfer rates (ETR), lower PSII quantum yields, and increased donor-side limitation of PSI. State transitions were diminished in the fusion strains, accompanied by a strong impairment of STT7-dependent function, suggesting that the presence of fused FPs at b6f interfere with STT7 function. Yet, ETR phenotypes were STT7-independent and FP fusion did not impact intrinsic b6f function. In situ cryogenic electron tomography revealed a significant depletion of b6f from appressed thylakoid membranes in the ATeam strains, while the overall membrane protein concentration remained unchanged. Overall, our data indicate that a balanced distribution of b6f between appressed and non-appressed thylakoid membranes is essential for regulating photosynthetic electron transfer, highlighting the functional importance of thylakoid molecular architecture in vivo.

plant biology↗

bioRxiv2026

The C. elegans nervous system reads the internal state of the hydrogen peroxide-detoxification machinery to trigger escape from this common reactive chemical

Hydrogen peroxide (H2O2) is the most common reactive chemical threat faced by organisms. Here, we map the neural circuit that drives chemotactic escape from environmental H2O2 in the nematode C. elegans. Twenty-four neuron classes with sensory endings at the mouth and nose of the animal detect H2O2. Their response dynamics encode stimulus intensity and exposure history, and their partial redundancy makes avoidance resilient to the loss of individual inputs. Sensing begins when H2O2 oxidizes the peroxidatic and resolving cysteines of the cytosolic peroxiredoxin PRDX-2, which relays this oxidative signal to cysteines on the LITE-1 and GUR-3 ion channels, triggering calcium influx in sensory neurons that drive escape. Most of these neurons release glutamate to drive H2O2-dependent excitation of AIA interneurons, whereas others signal through non-glutamatergic routes, providing multiple routes for signal transmission. Thus, the C. elegans nervous system acts as a hydrogen peroxide sentinel that monitors H2O2-induced changes in the intracellular H2O2-detoxification machinery and relays them to interneurons driving organism-wide escape. This raises the possibility that circuit defects in aging and neurodegenerative disease arise from altered peroxiredoxin-mediated H2O2 signaling rather than primarily from direct macromolecular damage.

neuroscience↗

bioRxiv2025

Chloroplast cpHsc70-1 interacts with VIPP1 C-terminal tail and controls VIPP1 oligomer disassembly in thylakoid membrane remodeling

Oxygenic photosynthetic organisms depend on the thylakoid membranes (TMs) for light-driven energy conversion. Recent studies on TM homeostasis (thylakostasis) have highlighted the essential role of the TM remodeling protein VIPP1 (Vesicle Inducing Protein in Plastids 1). As a member of the ESCRT-III/PspA/VIPP1 superfamily, VIPP1 forms large ring- and filament-like homo-oligomeric structures that exhibit a membrane remodeling activity. The oligomerization status was proposed to be modulated by the intrinsically disordered C-terminal tail (Vc), whereas its functional role remained unclear. Notably, this Vc region is conserved not only in photosynthetic VIPP1 but also in the PspA proteins of extremophilic species, implicating its role in membrane stress responses. To investigate the role of the Vc region in VIPP1 assembly, we performed co-immunoprecipitation assays in Arabidopsis chloroplasts and identified chloroplast-localized HSP70 proteins as major interactors. Among the two isoforms, cpHsc70-1 was found to be specifically required for modulating VIPP1 oligomeric assembly and dynamics in response to heat stress. Genetic analyses revealed that cpHsc70-1 facilitates the disassembly of VIPP1 oligomers, similarly to Vps4 ATPase in ESCRT-III; loss of either the Vc region or cpHsc70-1 impaired VIPP1 disassembly, resulting in more static oligomeric structures. Furthermore, cpHsc70-1 exhibited a broader role in chloroplast proteostasis, as the cphsc70-1 mutant showed impaired accumulation of GFP-fusion proteins. Together, our findings uncover a crucial crosstalk between proteostasis and thylakostasis in chloroplasts, coordinated by cpHsc70-1 and VIPP1 in response to membrane stress. Significance StatementOrganisms performing oxygen-evolving photosynthesis rely on the thylakoid membranes (TMs) for light-driven energy conversion. We reveal that VIPP1, a membrane remodeling protein forming dynamic oligomeric structures, is crucial for TM maintenance. Its intrinsically disordered C-terminal region (Vc) and the heat shock protein cpHsc70-1 coordinate VIPP1 disassembly during stress in Arabidopsis chloroplasts. Loss of either component causes defects in membrane remodeling and proteostasis. Our findings uncover a fundamental mechanism connecting membrane integrity and protein quality control, ensuring chloroplast resilience against environmental stress.

plant biology↗

bioRxiv2025

FLP-15 functions through the GPCR NPR-3 to regulate local and global search behaviours in Caenorhabditis elegans

Foraging is essential for sustenance and well-being of all organisms. The transition from well-fed to food-deprived conditions in C. elegans triggers a localized exploration of the environment characterized by frequent reorientations. However, over time the cumulative frequency of these reorientations decreases, facilitating the transition to global search behaviour. To investigate the genetic regulation of foraging in C. elegans, we conducted a screen of neuropeptide mutants and identified several candidates involved in modulating this behaviour. Among these, neuropeptide FLP-15 emerged as a key regulator of both local and global search behaviours. Our observations revealed that FLP-15 regulates the frequency and duration of reversals during foraging. Further investigation indicated that FLP-15 is expressed in and functions through the I2 pharyngeal neuron via the G-protein coupled receptor NPR-3. Mutants lacking either flp-15 or npr-3 displayed a significant decrease in reversal frequency during local search behaviours. Interestingly, unlike wild-type animals, the reversal frequency in flp-15 and npr-3 mutants did not decrease over time. This study also describes the expression pattern of NPR-3, in a subset of head neurons, predominantly comprising of dopaminergic neurons. This expression pattern highlights a potential link between neuropeptide signalling and dopaminergic modulation of behaviour. Finally, exogenous dopamine supplementation assays revealed that FLP-15 may regulate foraging by modulating dopamine transmission, highlighting a novel neuropeptide-dopamine interaction involved in the control of foraging behaviours.

neuroscience↗

bioRxiv2025

A modular multi-color fluorescence microscope for simultaneous tracking of cellular activity and behavior

We present a modular epifluorescence tracking microscope which enables ratiometric imaging of muscles, neurons, and other structures in moving animals. The microscope is assembled entirely from commercial parts within 3 hours, making the system broadly accessible. Leveraging the improved brightness and bleaching characteristics of recent genetically-encoded indicators and fluorophores, the simple microscope is even suitable for simultaneous calcium imaging of neurons and behavior as we demonstrate in C. elegans. We also show how muscle dynamics in D. melanogaster larvae can be analyzed and how dual color fluorescence tracking elucidates inter-species interactions by visualizing both predatory nematodes and their prey. Finally, we showcase a configuration for bright-field imaging, by tracking tardigrade gait as an example of utility for non-model species. The affordability of the hardware and ease of use of the accompanying software make this a suitable tool for education in addition to its use in research.

animal behavior and cognition↗

bioRxiv2025

Evolution of sensory systems underlies the emergence of predatory feeding behaviours in nematodes

Understanding how animal behaviour evolves remains a major challenge, with few studies linking genetic changes to differences in neural function and behaviour across species. Here, we identify specific sensory adaptations associated with the emergence of predatory feeding behaviours in the nematode Pristionchus pacificus. While Caenorhabditis elegans uses contact-dependent sensing primarily to avoid threats, Pristionchus pacificus has co-opted this modality to support both avoidance and prey detection, enabling context-dependent predatory behaviour. To uncover a potential mechanism underlying the evolution of P. pacificus prey perception, we mutated 27 canonical mechanosensory genes and assessed their function using behavioural assays, automated behavioural tracking, and a machine learning analysis of behavioural states. While several mutants showed mechanosensory defects, Ppa-mec-6 mutants specifically also impaired prey detection, indicating the emergence of a novel mechanosensory module linked to predatory behaviour. Furthermore, disrupting both mechanosensation alongside chemosensation revealed a synergistic influence for these modalities. Crucially, both mechanosensation and chemosensation pathways converge in the same environmentally exposed IL2 neurons, and silencing these cells induced severe predation defects validating their importance for prey sensing. Thus, predation evolved through the co-option of mechanosensory and chemosensory systems that act together to shape the evolution of complex behavioural traits.

neuroscience↗

bioRxiv2025

New Insights into Plastocyanin-Cytochrome b6f Formation: the Role of Plastocyanin Phosphorylation

In this work we investigated the role of plastocyanin (PC) phosphorylation in photosynthetic electron transfer, focusing on interactions with both cytochrome-b6f (Cytb6f) and Photosystem-I (PSI) in Chlamydomonas reinhardtii. While the binding and electron transfer between PC and PSI are well characterized, the interaction between PC and Cytf remains less clear. Using chemical cross-linking combined with mass spectrometry, we identified two potential binding models for PC and Cytf: "Side-on" and "Head-on". To evaluate electron transfer, we developed an in vitro system that allowed oxidized PC, formed via light-driven electron transfer at PSI, to re-oxidize Cytf. Our data shows that a phosphomimetic variant of PC, where phosphorylated PC S49 residue interacts with PetA-K188, displays faster Cytf oxidation, likely optimizing binding and electron transfer between PC and Cytf. Additionally, PC phosphomimetic variants exhibited slower transfer rates than wild type, suggesting that phosphorylation modulates PCs interaction with PSI. This regulation likely optimizes Cytf oxidation and electron transfer under conditions of low PC availability, such as during high light stress. Overall, PC phosphorylation appears to play a role in fine-tuning electron transfer between PSI, Cytb6f, and PC, thereby ensuring efficient photosynthesis in dynamic environmental conditions.

plant biology↗

bioRxiv2025

N-terminal region of PetD is essential for cytochrome b6f function and controls STT7 kinase activity via STT7-dependent feedback loop phosphorylation

The cytochrome b6f complex (b6f) links photosystem I (PSI) and photosystem II (PSII) in the photosynthetic electron transport chain and is distributed across appressed and non-appressed thylakoid membranes. The b6f also activates the state-transition 7 kinase (STT7), which phosphorylates light-harvesting complex proteins, triggering their migration to enable energy redistribution between PSII and PSI. STT7-dependent phosphorylation has also been observed at T4 in the N-terminal domain of the b6f subunit-IV (PetD), though its functional significance has remained unclear. To investigate its role, we generated several chloroplast mutants. The phosphomimic mutation PetD T4E - but not T4A - inhibited STT7 kinase activity, as indicated by the absence of STT7-dependent phosphorylation and a State 1-locked phenotype. This reveals a novel feedback mechanism regulating STT7-dependent phosphorylation. Deletion of the first five N-terminal amino acids similarly inhibited STT7 activity and additionally disrupted electron transfer, underscoring a crucial role of the PetD N-terminus in b6f function.

plant biology↗

bioRxiv2024

ConvexGating infers gating strategies from clusters in single cell cytometry data

Manual expert gating remains common practice for the definition of specific cell populations in the analysis of flow cytometry data. The increasing number of measured parameters per individual cell and high inter-rater variability makes manual gating inconsistent in many scenarios such as multi-center studies. Here, we propose ConvexGating, an AI tool that automatically learns gating strategies in an unbiased, fully data-driven, yet interpretable manner. ConvexGating scales efficiently with increasing parameter space, creating proficient strategies with low-contamination in the extracted population for previously known and so far unknown or ill-defined cell populations. The inferred strategies are independent of parent populations, for instance, plasmacytoid dendritic cells (pDCs) can be fully identified as CD45RA- CD123+. In addition to flow cytometry data, ConvexGating derives gating strategies for cyTOF (Cytometry by Time of Flight) and CITEseq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) data and supports optimal design of marker panels for cell sorting.

immunology↗

bioRxiv2024

Unwrapping the ciliary coat: high-resolution structure and function of the ciliary glycocalyx

The glycocalyx, a highly heterogeneous glycoprotein layer of cilia regulates adhesion and force transduction, and is involved in signalling. The high-resolution molecular architecture of this layer is currently not understood. We describe the structure of the ciliary coat in the green alga Chlamydomonas reinhardtii by cryo-electron tomography and proteomic approaches and present the high-resolution cryoEM structure of the main component, FMG1B. We describe FMG1B as a mucin orthologue which lacks the major O-glycosylation of mammalian mucins, but is N-glycosylated. FMG1A, a previously undescribed isoform of FMG1B is expressed in C. reinhardtii. By microflow-based adhesion assays we observe increased surface adhesion in the glycocalyx deficient double-mutant fmg1a-fmg1b. We find this mutant to be capable of surface-gliding, with neither isoform required for extracellular force transduction by intraflagellar transport. Our results find FMG1 to form a protective layer with adhesion-regulative instead of adhesion-conferring properties and an example of an undescribed class of mucins.

cell biology↗

bioRxiv2024

Predicting chemotherapy-induced thrombotoxicity by NARX neural networks and transfer learning

BackgroundThrombocytopenia is a common side effect of cytotoxic chemotherapies, which is often dose-limiting. Predicting an individuals risk is of high clinical importance, as otherwise, a small subgroup of patients limits dosages for the overall population for safety reasons. MethodsWe aim to predict individual platelet dynamics using non-linear auto-regressive networks with exogenous inputs (NARX). We consider different architectures of the NARX networks, namely feed-forward networks (FNN) and gated recurrent units (GRU). To cope with the relative sparsity of individual patient data, we employ transfer learning (TL) approaches based on a semi-mechanistic model of hematotoxicity. We use a large data set of patients with high-grade non-Hodgkins lymphoma to learn the respective models on an individual scale and to compare prediction performances with that of the semi-mechanistic model. ResultsOf the examined network models, the NARX with GRU architecture performs best. In comparison to the semi-mechanistic model, the network model can result in a substantial improvement of prediction accuracy for patients with irregular dynamics, given well-spaced measurements. TL improves individual prediction performances. ConclusionNARX networks can be utilized to predict an individuals thrombotoxic response to cytotoxic chemotherapy treatment. For reasonable model learning, we recommend at least three well-spaced measurements per cycle: at baseline, during the nadir phase and during the recovery phase. We aim at generalizing our approach to other treatment scenarios and blood lineages in the future.

systems biology↗

bioRxiv2024

Predatory aggression evolved through adaptations to noradrenergic circuits

Behaviors are adaptive traits evolving through natural selection. Crucially, the genetic, molecular, and neural modifications that shape behavioral innovations are poorly understood. Here, we identify specialized adaptations linked to the evolution of aggression in the predatory nematode Pristionchus pacificus. Using machine learning, we identified robust behavioral states associated with aggressive episodes. These depend on modifications to the invertebrate noradrenergic pathway, with octopamine promoting predatory bouts, and tyramine antagonistically suppressing predation. Strikingly, aggression coincides with rewiring of key circuits across nematode evolution. We find additional octopaminergic neurons with morphological adaptations, including neurites extending to teeth-like structures, and expanded receptor expression throughout head sensory neurons gating prey detection. Thus, evolutionary adaptations in noradrenergic circuits facilitated the emergence of aggressive behavioral states associated with complex predatory traits.

animal behavior and cognition↗

bioRxiv2024

Diminished Immune Cell Adhesion in Hypoimmune ICAM-1 Knockout Pluripotent Stem Cells

Hypoimmune gene edited human pluripotent stem cells (hPSCs) are a promising platform for developing reparative cellular therapies that evade immune rejection. Existing first-generation hypoimmune strategies have used CRISPR/Cas9 editing to modulate genes associated with adaptive (e.g., T cell) immune responses, but have largely not addressed the innate immune cells (e.g., monocytes, neutrophils) that mediate inflammation and rejection processes occurring early after graft transplantation. We identified the adhesion molecule ICAM-1 as a novel hypoimmune target that plays multiple critical roles in both adaptive and innate immune responses post-transplantation. In a series of studies, we found that ICAM-1 blocking or knock-out (KO) in hPSC-derived cardiovascular therapies imparted significantly diminished binding of multiple immune cell types. ICAM-1 KO resulted in diminished T cell proliferation responses in vitro and in longer in vivo retention/protection of KO grafts following immune cell encounter in NeoThy humanized mice. The ICAM-1 KO edit was also introduced into existing first-generation hypoimmune hPSCs and prevented immune cell binding, thereby enhancing the overall hypoimmune capacity of the cells. This novel hypoimmune editing strategy has the potential to improve the long-term efficacy and safety profiles of regenerative therapies for cardiovascular pathologies and a number of other diseases. HighlightsO_LIAntibody blocking of ICAM-1 on human pluripotent stem cell-derived cells inhibits immune cell adhesion C_LIO_LICRISPR/Cas9 knock-out of ICAM-1 ablates surface and secreted ICAM-1 protein and inhibits immune adhesion C_LIO_LIICAM-1 knock-out results in decreased T cell proliferative responses to human pluripotent stem cell-derived grafts in vitro, and resistance to immune-mediated graft loss in vivo C_LIO_LIAddition of ICAM-1 knock-out to first generation MHC knock-out human pluripotent stem cells confers protection against immune adhesion C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=129 SRC="FIGDIR/small/597791v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@890b56org.highwire.dtl.DTLVardef@147449borg.highwire.dtl.DTLVardef@1e94f08org.highwire.dtl.DTLVardef@43c55c_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO ICAM-1 Knock-out in Transendothelial Migration and at the Immune Synapse. Abbreviations: PSC-EC - pluripotent stem cell-derived endothelial cells; KO - knock-out; dSMAC - distal supramolecular activation complex; pSMAC - peripheral supramolecular activation complex; cSMAC - central supramolecular activation complex. C_FIG

immunology↗

bioRxiv2024

Adapting and optimizing GCaMP8f for use in C. elegans

Improved genetically-encoded calcium indicators (GECIs) are essential for capturing intracellular dynamics of both muscle and neurons. A novel set of GECIs with ultra-fast kinetics and high sensitivity was recently reported by Zhang et al. (Nature, 2023). While these indicators, called jGCaMP8, were demonstrated to work in Drosophila and mice, data for Caenorhabditis elegans was not reported. Here, we present an optimized plasmid for C. elegans and use this to generate several strains expressing GCaMP8f. Utilizing the myo-2 promoter, we compare pharyngeal muscle activity measured with GCaMP7f and GCaMP8f and find that GCaMP8f is brighter, shows faster kinetics and is less disruptive to the intrinsic contraction dynamics of the pharynx. Additionally, we validate its application for detecting neuronal activity in touch receptor neurons which reveals robust calcium transients at 25 ms time resolution. As such, we establish GCaMP8f as a potent tool for C. elegans research which is capable of extracting fast calcium dynamics at very low magnifications across multiple cell types.

neuroscience↗

bioRxiv2024

Neural Network-Assisted Humanization of COVID-19 Hamster scRNAseq Data Reveals Matching Severity States in Human Disease

Translating findings from animal models to human disease is essential for dissecting disease mechanisms, developing and testing precise therapeutic strategies. The coronavirus disease 2019 (COVID-19) pandemic has highlighted this need, particularly for models showing disease severity-dependent immune responses. Single-cell transcriptomics (scRNAseq) is well poised to reveal similarities and differences between species at the molecular and cellular level with unprecedented resolution. However, computational methods enabling detailed matching are still scarce. Here, we provide a structured scRNAseq-based approach that we applied to scRNAseq from blood leukocytes originating from humans and hamsters affected with moderate or severe COVID-19. Integration of COVID-19 patient data with two hamster models that develop moderate (Syrian hamster, Mesocricetus auratus) or severe (Roborovski hamster, Phodopus roborovskii) disease revealed that most cellular states are shared across species. A neural network-based analysis using variational autoencoders quantified the overall transcriptomic similarity across species and severity levels, showing highest similarity between neutrophils of Roborovski hamsters and severe COVID-19 patients, while Syrian hamsters better matched patients with moderate disease, particularly in classical monocytes. We further used transcriptome-wide differential expression analysis to identify which disease stages and cell types display strongest transcriptional changes. Consistently, hamsters response to COVID-19 was most similar to humans in monocytes and neutrophils. Disease-linked pathways found in all species specifically related to interferon response or inhibition of viral replication. Analysis of candidate genes and signatures supported the results. Our structured neural network-supported workflow could be applied to other diseases, allowing better identification of suitable animal models with similar pathomechanisms across species. Key PointsO_LINeural networks can successfully match disease states between animal models and humans using single-cell data as shown for COVID-19 C_LIO_LIModerately diseased patients best matched Syrian hamster cells; severely diseased patients best matched Roborovski hamster neutrophils C_LI

immunology↗

bioRxiv2023

Characterization of Tryptophan Oxidation Affecting D1 Degradation by FtsH in the Photosystem II Quality Control of Chloroplasts

Photosynthesis is one of the most important reactions for sustaining our environment. Photosystem II (PSII) is the initial site of photosynthetic electron transfer by water oxidation. Light in excess, however, causes the simultaneous production of reactive oxygen species (ROS), leading to photo-oxidative damage in PSII. To maintain photosynthetic activity, the PSII reaction center protein D1, which is the primary target of unavoidable photo-oxidative damage, is efficiently degraded by FtsH protease. In PSII subunits, photo-oxidative modifications of several amino acids such as Trp have been indeed documented, whereas the linkage between such modifications and D1 degradation remains elusive. Here, we show that an oxidative post-translational modification of Trp residue at the N-terminal tail of D1 is correlated with D1 degradation by FtsH during high-light stress. We revealed that Arabidopsis mutant lacking FtsH2 had increased levels of oxidative Trp residues in D1, among which an N-terminal Trp-14 was distinctively localized in the stromal side. Further characterization of Trp-14 using chloroplast transformation in Chlamydomonas indicated that substitution of D1 Trp-14 to Phe, mimicking Trp oxidation enhanced FtsH-mediated D1 degradation under high light, although the substitution did not affect protein stability and PSII activity. Molecular dynamics simulation of PSII implies that both Trp-14 oxidation and Phe substitution cause fluctuation of D1 N-terminal tail. Furthermore, Trp-14 to Phe modification appeared to have an additive effect in the interaction between FtsH and PSII core in vivo. Together, our results suggest that the Trp oxidation at its N-terminus of D1 may be one of the key oxidations in the PSII repair, leading to processive degradation by FtsH. Competing Interest StatementThe authors have no conflict of interest, financial or otherwise, in relation to this study Impact StatementOxidative modification of Tryptophan residues in the reaction center protein D1 may be a key to drive the Photosystem II repair, likely enhancing accessibility of FtsH protease to D1.

plant biology↗

bioRxiv2022

Calredoxin regulates the chloroplast NADPH-dependent thioredoxin reductase in Chlamydomonas reinhardtii

Calredoxin (CRX) is a calcium (Ca2+)-dependent thioredoxin (TRX) in the chloroplast of Chlamydomonas reinhardtii with largely unclear physiological role. We elucidated the CRX functionality by performing in-depth quantitative proteomics of wild type cells in comparison with crx insertional mutant (IMcrx), two CRISPR/Cas9 KO mutants and CRX rescues. These analyses revealed that the chloroplast NADPH-dependent TRX reductase (NTRC) is co-regulated with CRX. Electron transfer measurements revealed that CRX inhibits NADPH-dependent reduction of oxidized chloroplast 2-Cys peroxiredoxin (PRX1) via NTRC and that the function of the NADPH-NTRC complex is under strict control of CRX. Via non-reducing SDS-PAGE assays and mass spectrometry, our data also demonstrated that PRX1 is more oxidized under high light (HL) conditions in the absence of CRX. The redox tuning of PRX1 and control of the NADPH-NTRC complex via CRX interconnects redox control with active photosynthetic electron transport and metabolism as well as Ca2+ signaling. In this way, an economic use of NADPH for PRX1 reduction is ensured. The finding, that the absence of CRX under HL conditions severely inhibited light-driven CO2 fixation underpins the importance of CRX for redox tuning as well as for efficient photosynthesis. One-sentence summaryCalredoxin dependent redox regulation ensures efficient photosynthesis.

plant biology↗

bioRxiv2022

vcferr: Development, Validation, and Application of a SNP Genotyping Error Simulation Framework

MotivationGenotyping error can impact downstream SNP-based analyses. Simulating various modes and and levels of error can help investigators better understand potential biases caused by miscalled genotypes. ResultsWe have developed and validated vcferr, a tool to probabilistically simulate genotyping error and missigness in VCF files. We demonstrate how vcferr could be used to address a research question by introducing varying levels of error of different type into a sample in a simulated pedigree, and assessed how kinship analysis degrades as a function of kind and type of error. Software Availabilityvcferr is available for installation via PyPi (https://pypi.org/project/vcferr/) or conda (https://anaconda.org/bioconda/vcferr). The software is released under the MIT license with source code available on GitHub (https://github.com/signaturescience/vcferr).

bioinformatics↗