Biology subjects

Baumann, A.

Publications and source records attributed to Baumann, A..

13 recordsLinked to original sources

bioRxiv2026

Disagreement between demultiplexing methods reveals structured cell quality gradients in multiplexed single-cell data

BackgroundSingle-cell multi-omics profiling of hematopoietic malignancies frequently involves pooling of patient samples before library preparation to reduce costs. Demultiplexing and quality control of the resulting sequencing data depend on experimental design, sequencing depth, and computational methods. Existing approaches benchmark individual tools, auto-select a single best method, or apply majority voting. However, none systematically exploit disagreement patterns among orthogonal strategies as a diagnostic signal for cell quality. ResultsWe introduce Split-flow, a modular Nextflow pipeline that runs hashing-based and SNP-based demultiplexing, and transcriptome-based doublet detection in parallel. It classifies cells into quality strata through a concordance-based decision framework. Validation on multiplexed CITE-seq data from 14 multiple myeloma patients across eight Chromium channels demonstrates high reproducibility and shows that discordant cells cluster within specific cell types and quality strata. TCR clonotype cross-referencing against VDJdb confirms that concordance-based classification enriches for biologically genuine immune receptor sequences, with a 5.3-fold enrichment of confirmed public TCR sequences in the high-confidence stratum. Downsampling analysis reveals that SNP-based methods are more depth-sensitive than hash-based approaches, supporting the recommendation to combine both strategies. The framework transfers to AML samples across three assay types (snMultiome-seq, scRNA-seq, scATAC-seq), where ATAC-based demultiplexing resolves donor assignment discordance under low hashing efficiency. ConclusionsSplit-flow demonstrates that combining of orthogonal preprocessing methods yields structured information about cell quality and offers a concordance-based framework that transforms this disagreement into a diagnostic signal. It introduces a preprocessing approach that can be exploited beyond hematopoietic malignancies in multiplexed single-cell applications. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/724135v1_ufig1.gif" ALT="Figure 1"> View larger version (26K): org.highwire.dtl.DTLVardef@1f36dbcorg.highwire.dtl.DTLVardef@a9799forg.highwire.dtl.DTLVardef@6fca94org.highwire.dtl.DTLVardef@15cc1f3_HPS_FORMAT_FIGEXP M_FIG C_FIG Highlights and main findingsO_LIIntroduces Split-flow, a modular Nextflow DSL2 pipeline for preprocessing of multiplexed single-cell multi-omics sequencing data from hematopoietic malignancy samples via a post hoc concordance-based decision framework. C_LIO_LIProvides practical guidance for the experimental design of multiplexed single-cell multi-omics experiments, including the recommendation to combine antibody-based hashing with a SNP genotype reference for orthogonal demultiplexing. C_LIO_LIReveals that SNP-based demultiplexing is more sensitive to sequencing depth than hash-based approaches, and that the combined strategy mitigates depth-dependent biases in cell-type recovery. C_LIO_LIDemonstrates that disagreement between demultiplexing methods contains structured diagnostic information about cell quality, with concordance categories reflecting genuine quality gradients in multiple myeloma CITE-seq samples. C_LIO_LIValidates the concordance framework using T cell receptor sequences as an orthogonal biological readout, with a 5.3-fold enrichment of confirmed public TCR sequences in the high-confidence stratum. C_LIO_LIApplies the preprocessing framework to AML patient samples across three assay types (snMultiome-seq, scRNA-seq, and scATAC-seq) and demonstrates that ATAC-based demultiplexing can resolve donor-assignment discordance. C_LI

bioinformatics↗

bioRxiv2026

Evolutionary optimization of allosteric activation by Cl- and Cl- conduction in vesicular glutamate transporters

Vesicular glutamate transporters harness proton gradients to load glutamate into synaptic vesicles, while mediating luminal chloride efflux through a channel-like conductance. We combined heterologous expression in mammalian cells, whole-cell patch-clamp recordings and mathematical modeling to functionally characterize the Drosophila melanogaster vesicular glutamate transporter DVGLUT and to compare it to a rat counterpart, rVGLUT1. As in mammalian VGLUTs, DVGLUT glutamate transport is coupled to proton exchange, in a 1:1 stoichiometry. In both, luminal Cl- is necessary as allosteric activator, however, the allosteric affinity is higher in fly than in rat transporters. DVGLUT anion channels exhibit lower unitary currents, but higher anion channel open probabilities, resulting in larger Cl- currents for the fly transporter in the presence of cytoplasmic glutamate. The higher allosteric affinity together with the enhanced anion channel activity may serve as evolutionary adaptation of VGLUTs to lower ion concentrations in Drosophila, illustrating the impact of these particular features for synaptic vesicle filling.

neuroscience↗

bioRxiv2025

Legacy effects of European colonialism on hotspots of biocultural diversity threat

Patterns of biological diversity have been shaped by cultural practices in the past, while in turn, cultures and languages have evolved in close interaction with local species and ecosystems. However, in the Anthropocene, humans are putting increasingly more and diverse pressures on ecosystems and cultures resulting in accelerating threat levels on both. Understanding where biological and linguistic diversity (a common measure of cultural diversity) is threatened globally, and which drivers shape their distribution is crucial for pinpointing hotspots and prioritizing efforts to counter these threats. We find that the spatial patterns of the erosion of biological and cultural diversity are weakly congruent on a global scale and that they are driven by differential sets of mechanisms. However, our results also indicate that particularly large-scale historic socio-political events like the European colonial expansion have left long-lasting imprints on both biological and cultural diversity. The duration of European colonialism (i.e., the time a specific region was occupied by Europeans powers) significantly increases contemporary observed threat levels of biological and linguistic diversity. Significance StatementBiological and cultural diversity are closely intertwined. However, in an increasingly changing world where anthropogenic drivers put increasing pressures on ecosystems and cultures, both are threatened. Understanding how these threats to both, biological and linguistic diversity, are organized in space and where their individual and combined threat hotspots are is crucial for prioritization efforts to safeguard both. We also show what drivers affect their threat level globally and pinpoint that particularly large-scale socio-political events like the European colonial expansion have left long-lasting imprints on both biological and cultural diversity.

ecology↗

bioRxiv2024

Personal Mastery Attenuates the Association between Greater Perceived Discrimination and Lower Amygdala and Anterior Hippocampal Volume in a Diverse Sample of Older Adults

There is limited research investigating whether perceived discrimination influences brain structures that subserve episodic memory, namely the hippocampus and amygdala. Our rationale for examining these regions build on their known sensitivity to stress and functional differences along the long-axis of the hippocampus, with the anterior hippocampus and amygdala implicated in emotional and stress regulation. We defined perceived discrimination as the unfair treatment of one group by a dominant social group without the agency to respond to the event. A potential moderator of perceived discrimination is personal mastery, which we operationally defined as personal agency. Our primary goals were to determine whether perceived discrimination correlated with amygdala and anterior hippocampal volume, and if personal mastery moderated these relationships. Using FreeSurfer 7.1.0, we processed T1-weighted images to extract bilateral amygdala and hippocampal volumes. Discrimination and personal mastery were assessed via self-report (using the Experiences of Discrimination and Sense of Control questionnaires, respectively). Using multiple regression, greater perceived discrimination correlated with lower bilateral amygdala and anterior hippocampal volume, controlling for current stress, sex, education, age, and intracranial volume. Exploratory subfield analyses showed these associations were localized to the anterior hippocampal CA1 and subiculum. As predicted, using a moderation analysis, personal mastery attenuated the relationship between perceived discrimination and amygdala and anterior hippocampal volume. Here, we extend our knowledge on perceived discrimination as a salient psychosocial stressor with a neurobiological impact on brain systems implicated in stress, memory, and emotional regulation, and provide evidence for personal mastery as a moderating factor of these relationships.

neuroscience↗

bioRxiv2023

Revealing the Oligomerization of Channelrhodopsin-2 in the Cell Membrane using Photo-Activated Localization Microscopy

Microbial rhodopsins are retinal membrane proteins that found a broad application in optogenetics. The oligomeric state of rhodopsins is important for their functionality and stability. Of particular interest is the oligomeric state in the cellular native membrane environment. Fluorescence microscopy provides powerful tools to determine the oligomeric state of membrane proteins directly in cells. Among these methods is quantitative photoactivated localization microscopy (qPALM) allowing the investigation of molecular organization at the level of single protein clusters. Here, we apply qPALM to investigate the oligomeric state of the first and most used optogenetic tool Channelrhodopsin-2 (ChR2) in the plasma membrane of eukaryotic cells. ChR2 appeared predominantly as a dimer in the cell membrane and did not form higher oligomers. The disulfide bonds between Cys34 and Cys36 of adjacent ChR2 monomers were not required for dimer formation and mutations disrupting these bonds resulted in only partial monomerization of ChR2. The monomeric fraction increased when the total concentration of mutant ChR2 in the membrane was low. The dissociation constant was estimated for this partially monomerized mutant ChR2 as 2.2{+/-}0.9 proteins/m2. Our findings are important for understanding the mechanistic basis of ChR2 activity as well as for improving existing and developing future optogenetic tools.

biophysics↗

bioRxiv2022

Lipid metabolism dysfunction following symbiont elimination is linked to altered Kennedy pathway homeostasis

Lipid metabolism is critical for insect reproduction, especially for species that invest heavily into early developmental stages of their offspring. The role of symbiotic bacteria during this process is unknown but likely essential, especially in the case of obligate microbes that fulfill key biological functions in the host. Using a combined lipidomics, functional genomics and biochemical strategy, we examined the role of lipid metabolism in the interaction between the viviparous tsetse fly (Glossina morsitans morsitans) and its obligate endosymbiotic bacteria (Wigglesworthia glossinidia) during tsetse pregnancy. We observed increased CTP:phosphocholine cytidylyltransferase (cct1) expression during pregnancy. This gene codes for the enzyme that functions as the rate limiting step in phosphatidylcholine biosynthesis in the Kennedy pathway which is critical for stored lipid metabolism and progeny development. Experimental removal of Wigglesworthia impaired lipid metabolism via disruption of the Kennedy pathway, yielding obese mothers whose developing progeny ultimately starve. Functional validation via experimental cct1 suppression revealed a phenotype similar to females lacking obligate Wigglesworthia symbionts. These results indicate that, in Glossina, symbiont-derived factors, likely B vitamins, are critical for proper function of both lipid biosynthesis and lipolysis. Loss of the symbiosis has a dramatic impact on Glossina fecundity, and may be broadly applicable to other insect systems, particularly to species that require symbiotic partners to maximize lipolysis and reproductive output.

physiology↗

bioRxiv2022

An Epitope-Focused Trypanosome-Derived Vaccine Platform Elicits High-Affinity Antibodies and Immunity Against Fentanyl Effects

Poorly antigenic small molecules pose challenges for the production of clinically efficacious antibodies. To address this, we have developed an immunization platform derived from the antigenic surface coat of the African trypanosome. Through sortase-based conjugation of antigens to the trypanosome surface coat protein variant surface glycoprotein (VSG), we created the VAST (VSG-immunogen Array by Sortase Tagging). We used VAST to elicit protective immunity to the effects fentanyl. Immunizing mice with fentanyl-VAST generated serological memory and protection from fentanyl challenge. Employing single-cell RNAseq, we then developed a streamlined method that synergizes with the VAST to identify immunization-elicited memory B cells and the antibodies they encode. All antibodies selected by this method displayed picomolar affinities for fentanyl. Passive immunization protected animals from fentanyl, while crystallography revealed that the mAbs bind fentanyl in an unusually deep pocket suited to small molecules, demonstrating the ability of the VAST to elicit high-quality therapeutic antibodies.

immunology↗

bioRxiv2021

Metabolically-Incorporated Deuterium in Myelin Localized by Neutron Diffraction and Identified by Mass Spectrometry

Myelin is a natural and dynamic multilamellar membrane structure that continues to be of significant biological and neurological interest, especially with respect to its biosynthesis and assembly during its normal formation, maintenance, and pathological breakdown. To explore the usefulness of neutron diffraction in the structural analysis of myelin, we investigated the use of in vivo labeling by metabolically incorporating non-toxic levels of deuterium (2H; D) via drinking water into a pregnant dam (D-dam) and her developing embryos. All of the mice were sacrificed when the pups (D-pups) were 55 days old. Myelinated sciatic nerves were dissected, fixed in glutaraldehyde and examined by neutron diffraction. Parallel samples that were unfixed (trigeminal nerves) were frozen for mass spectrometry (MS). The diffraction patterns of the nerves from deuterium-fed mice (D-mice) vs. the controls (H-mice) had major differences in the intensities of the Bragg peaks but no appreciable differences in myelin periodicity. Neutron scattering density profiles showed an appreciable increase in density at the center of the lipid-rich membrane bilayer. This increase was greater in D-pups than in D-dam, and its localization was consistent with deuteration of lipid hydrocarbon, which predominates over transmembrane protein in myelin. MS analysis of the lipids isolated from the trigeminal nerves demonstrated that in the pups the percentage of lipids that had one or more deuterium atoms was uniformly high across lipid species (97.6% {+/-} 2.0%), whereas in the mother the lipids were substantially less deuterated (60.6% {+/-} 26.4%) with levels varying among lipid species and subspecies. The mass distribution pattern of deuterium-containing isotopologues indicated the fraction (in %) of each lipid (sub-)species having one or more deuteriums incorporated: in the D-pups, the pattern was always bell-shaped, and the average number of D atoms ranged from a low of [~]4 in fatty acid to a high of [~]9 in cerebroside. By contrast, in D-dam most lipids had more complex, overlapping distributions that were weighted toward a lower average number of deuteriums, which ranged from a low of [~]3-4 in fatty acid and in one species of sulfatide to a high of 6-7 in cerebroside and sphingomyelin. The consistently high level of deuteration in D-pups can be attributed to their de novo lipogenesis during gestation and rapid, postnatal myelination. The widely varying levels of deuteration in D-dam, by contrast, likely depends on the relative metabolic stability of the particular lipid species during myelin maintenance. Our current findings demonstrate that stably-incorporated D label can be detected and localized using neutron diffraction in a complex tissue such as myelin; and moreover, that MS can be used to screen a broad range of deuterated lipid species to monitor differential rates of lipid turnover. In addition to helping to develop a comprehensive understanding of the de novo synthesis and turnover of specific lipids in normal and abnormal myelin, our results also suggest application to studies on myelin proteins (which constitute only 20-30% by dry mass of the myelin, vs. 70-80% for lipid), as well as more broadly to the molecular constituents of other biological tissues.

neuroscience↗

bioRxiv2021

Kazrin C entraps early endosomes at the pericentriolar region and facilitates endocytic recycling

Kazrin is a protein widely expressed in vertebrates whose depletion causes a myriad of developmental defects, in part derived from altered cell adhesion, impaired cell migration and failure to undergo Epidermal to Mesenchymal Transition (EMT). However, the primary molecular role of kazrin, which might contribute to all these functions, has not been elucidated yet. We previously identified one of its isoforms, kazrin C, as a protein that potently inhibits clathrin-mediated endocytosis when overexpressed. We now generated kazrin knock out Mouse Embryonic Fibroblasts (MEFs) to investigate its endocytic function. We found that kazrin depletion delays perinuclear enrichment of internalized material, indicating a role in endocytic traffic from Early (EE) to Recycling Endosomes (REs). Consistently, we found that the C-terminal domain of kazrin C, predicted to be an Intrinsically Disordered Region (IDR), directly interacts with several components of the EEs, and that kazrin depletion impairs centripetal motility of EEs. Further, we noticed that the N-terminus of kazrin C shares homology with dynein/dynactin adaptors and that it directly interacts with the dynactin complex and the dynein Light Intermediate Chain 1 (LIC1). Altogether, the data indicate that one of the primary kazrin functions is to facilitate endocytic recycling via the perinuclear endocytic compartment, by promoting microtubule and dynein/dynactin-dependent transport of EEs or EE-derived transport intermediates to the RE.

cell biology↗

bioRxiv2020

GADL1 is a multifunctional decarboxylase with tissue specific roles in β-alanine and carnosine production

Carnosine and related {beta}-alanine-containing peptides are believed to be important antioxidants, pH-buffers and neuromodulators. However, their biosynthetic routes and therapeutic potential are still being debated. This study describes the first animal model lacking the enzyme glutamic acid decarboxylase-like 1 (GADL1). We show that Gadl1-/-mice are deficient in {beta}-alanine, carnosine and anserine, particularly in the olfactory bulb, cerebral cortex, and skeletal muscle. Gadl1-/-mice also exhibited decreased anxiety, increased levels of oxidative stress markers, alterations in energy and lipid metabolism, and age-related changes. Examination of the GADL1 active site indicated that the enzyme may have multiple physiological substrates, including aspartate and cysteine sulfinic acid, compatible with organ-specific functions. Human genetic studies show strong associations of the GADL1 locus with plasma levels of carnosine, subjective well-being, and muscle strength, also indicating a role for {beta}-alanine and its peptide derivatives in these traits. Together, this shows the multifaceted and organ specific roles of carnosine peptides and establishes Gadl1 knockout mice as a versatile model to explore carnosine biology and its therapeutic potential.

neuroscience↗

bioRxiv2019

An open resource of structural variation for medical and population genetics

Structural variants (SVs) rearrange large segments of the genome and can have profound consequences for evolution and human diseases. As national biobanks, disease association studies, and clinical genetic testing grow increasingly reliant on genome sequencing, population references such as the Genome Aggregation Database (gnomAD) have become integral for interpreting genetic variation. To date, no large-scale reference maps of SVs exist from high-coverage sequencing comparable to those available for point mutations in protein-coding genes. Here, we constructed a reference atlas of SVs across 14,891 genomes from diverse global populations (54% non-European) as a component of gnomAD. We discovered a rich landscape of 433,371 distinct SVs, including 5,295 multi-breakpoint complex SVs across 11 mutational subclasses, and examples of localized chromosome shattering, as in chromothripsis. The average individual harbored 7,439 SVs, which accounted for 25-29% of all rare protein-truncating events per genome. We found strong correlations between constraint against damaging point mutations and rare SVs that both disrupt and duplicate protein-coding sequence, suggesting intolerance to reciprocal dosage alterations for a subset of tightly regulated genes. We also uncovered modest selection against noncoding SVs in cis-regulatory elements, although selection against protein-truncating SVs was stronger than any effect on noncoding SVs. Finally, we benchmarked carrier rates for medically relevant SVs, finding very large ([≥]1Mb) rare SVs in 3.8% of genomes (~1:26 individuals) and clinically reportable incidental SVs in 0.18% of genomes (~1:556 individuals). These data have been integrated directly into the gnomAD browser (https://gnomad.broadinstitute.org) and will have broad utility for population genetics, disease association, and diagnostic screening.

genomics↗

bioRxiv2018

Molecular structure and function of myelin protein P0 in membrane stacking

Compact myelin forms the basis of nerve insulation essential for higher vertebrates. Dozens of myelin membrane bilayers undergo tight stacking, and in the peripheral nervous system, this is partially enabled by myelin protein zero (P0). Consisting of an immunoglobulin (Ig)-like extracellular domain, a single transmembrane helix, and a cytoplasmic extension (P0ct), P0 harbours an important task in ensuring the integrity of compact myelin in the extracellular compartment, referred to as the intraperiod line. Several disease mutations resulting in peripheral neuropathies have been identified for P0, reflecting its physiological importance, but the arrangement of P0 within the myelin ultrastructure remains obscure. We performed a biophysical characterization of recombinant P0ct. P0ct contributes to the binding affinity between apposed cytoplasmic myelin membrane leaflets, which not only results in fluidity changes of the bilayers themselves, but also potentially involves the rearrangement of the Ig-like domains in a manner that stabilizes the intraperiod line. Transmission electron cryomicroscopy of native full-length P0 showed that P0 stacks lipid membranes by forming antiparallel dimers between the extracellular Ig-like domains. The zipper-like arrangement of the P0 extracellular domains between two membranes explains the double structure of the myelin intraperiod line. Our results contribute to the understanding of PNS myelin, the role of P0 therein, and the underlying molecular foundation of compact myelin stability in health and disease.

biochemistry↗

bioRxiv2017

FireCloud, a scalable cloud-based platform for collaborative genome analysis: Strategies for reducing and controlling costs

FireCloud, one of three NCI Cloud Pilots, is a collaborative genome analysis platform built on a cloud computing infrastructure. FireCloud aims to solve the many challenges presented by the increasingly large data sets and computing requirements employed in cancer research. However, cost uncertainty associated with cloud computings pay-as-you-go model is proving to be a barrier to adoption of cloud computing. In this paper we present guidelines for optimizing workflows to minimize cost and reduce latency. Our guidelines include: (i) dynamic disk sizing to efficiently utilize virtual disks; (ii) tuned provisioning of virtual machines (VMs) using a performance monitoring tool; (iii) taking advantage of steep price discounts of preemptible VMs; and (iv) utilizing the optimal parallelization of a tasks workload.

bioinformatics↗