Biology subjects

Becker, L.

Publications and source records attributed to Becker, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Joining Two Perspectives of the Proteome with the Trypsin+HTA Protease Workflow

Proteolysis can be completed in a single-step, rapid (5-30 minutes) reaction using hyperthermoacidic archaeal (HTA) proteases. Protocol simplicity and stability of HTA proteases in ambient storage conditions removes many logistical barriers to widespread deployment of proteomic analysis. HTA protease cleavage selectivity is complicated but quantitatively reproducible and generates peptides that negligibly overlap with trypsin. Tryptic and HTA protease peptides emphasize different proteins and provide complementary coverage of amino acid sequence and post-translational modification (PTM) sites. Digestion of a sample's separate aliquot with HTA protease is a minor addition to trypsin-based workflows, but LC-MS analysis of both sets of peptides is not practical for large cohorts. This manuscript evaluates the identifications and reproducibility of LC-MS analysis of tryptic and HTA protease peptide mixtures. Adding HTA protease peptides to 20% increased total protein identifications by 24% on average in neat plasma and identified 216 additional non-artifact modifications compared to conventional trypsin-only bottom-up proteomic analysis. This approach is reproducible and does not increase sample preparation or analysis time. Peptides from each protease present independent opportunities to quantify overlapping proteins and a quantification model was developed in which the protease with the most complete data is selected for each protein while the second protease is used to infer missing values. This cross-protease inference is more accurate than the alternative minimum, mean, or nearest neighbor imputations. Finally, biomarkers discovered through HTA protease peptides are amenable to rapid HTA protease only proteomic workflows thus streamlining translation from discovery to fieldable applications.

biochemistry↗

bioRxiv2025

Extracellular Polymeric Substances Drive Curvibacter Host Adaptation and Co-Speciation with Hydra

The interactions between hosts and their microbial symbionts play a crucial role in shaping biological diversity and ecosystem function. Bacteria can adapt to specific host environments over evolutionary timescales, leading to co-speciation and the formation of specialized host-microbe relationships. Understanding the molecular mechanisms underlying these adaptations provides key insights into the evolution of symbiosis and the stability of microbial communities. This study investigates the co-speciation and molecular adaptations of Curvibacter to its host Hydra, a well-established model for the study of host-microbe interactions. We provide strong evidence of co-speciation, as demonstrated by phylogenetic congruence between different Hydra species and their corresponding Curvibacter symbionts, along with preferential recolonization of germ-free Hydra by their native Curvibacter strains. Comparative genomic analyses reveal that host-associated Curvibacter strains exhibit distinct metabolic and biosynthetic adaptations compared to their free-living relatives. Specifically, the enrichment of proteins involved in sugar metabolism and transport, as well as the selective purification of proteins linked to macromolecule biosynthesis, highlights the specialization of Curvibacter symbionts within the Hydra glycocalyx. Functional experiments identify a symbiont-specific extracellular polymeric substances (EPS) operon as key factor for microbial adhesion and host colonization, underscoring its role in facilitating symbiont specificity and stability. These findings provide insights into the molecular mechanisms driving host-microbe co-evolution and highlight the evolutionary forces shaping microbial specialization within host-symbiont relationships. Significant StatementThe vast majority of animal and plant species are associated with microbial organisms that offer a wide range of benefits for development, physiology, and health. Understanding the evolutionary forces that shape these symbiotic interactions is crucial for elucidating the mechanisms through which organisms mitigate environmental stress and enhance their resilience, particularly in response to rapidly changing environmental conditions. Using advanced bioinformatic, bioanalytical, and genetic approaches, this study demonstrates that Curvibacter symbionts have evolved specific extracellular polymeric substances to enhance their ability to form a specific symbiosis with Hydra.

microbiology↗

bioRxiv2025

Marker-independent imaging reveals a correlation of fibrotic and epigenetic alterations in endometriosis

IntroductionEndometriosis describes the presence of endometrial glands outside of the uterus and can cause various symptoms such as chronic pelvic pain, hypermenorrhea and infertility. These complications pose an extreme burden on the patients, especially as up to date, the average time until diagnosis can consume several years and requires invasive laparoscopy. ObjectivesThe aim of this study is to molecularly characterize endometrium and endometriosis using marker-independent Raman microspectroscopy to identify potential biomarkers and validate its diagnostic potential. MethodsAfter histopathological characterization of tissue sections of human endometrium and endometriosis, Raman microspectroscopy was performed on the gland region. Multivariate analysis of the hyperspectral maps was used to localize major subcellular structures and further decipher their molecular composition. Samples from different anatomical regions and throughout all menstrual cycle phases were analyzed. ResultsRaman imaging enabled label-free visualization of tissue morphology and submolecular tissue characterization. Distinct differences between endometrium and endometriosis were found for collagen type I and nuclear signatures. Spectral deconvolution allowed identification of a Raman biomarker indicative of fibrotic changes in endometriosis samples. Additionally, a significant increase in epigenetic 5mC foci and an increased signal intensity relevant for methylations was detected in nuclei of endometriosis. Furthermore, a neural network-based classification of Raman data resulted in high accuracies in discriminating endometrial and peritoneal tissue from endometriosis. ConclusionThe non-destructive approach by hyperspectral Raman imaging enabled for molecular sensitive characterization of endometriotic lesions which could not only be an asset in complementing histopathological tissue evaluation but combined with data-driven classification models support in situ tissue diagnosis.

biophysics↗

bioRxiv2025

Paralemmin-3 sustains the integrity of the lateral plasma membrane and subsurface cisternae of auditory hair cells

In the mammalian inner ear, cochlear inner hair cells (IHCs) enable accurate and faithful synaptic sound encoding, while outer hair cells (OHCs) perform frequency-specific sound amplification and fine-tuning through their intrinsic voltage-dependent somatic electromotility. This latter process is facilitated by the unique trilaminate structure of the OHC lateral wall, which consists of the plasma membrane that is densely occupied by the transmembrane motor protein Prestin, the submembrane actin- and spectrin-based cytoskeleton, and the endomembranous subsurface cisternae. This complex system provides mechanical resilience while allowing for cell expansion and contraction during electromotility. Whereas the ultrastructure of the lateral wall is well described, its molecular architecture remains largely elusive. Here, we identified Paralemmin-3 (Palm3) as a novel protein specifically localized to the lateral walls of auditory HCs to play a crucial role in connecting the plasma membrane to the underlying cytoskeleton and subsurface cisternae. Palm3-KO mice display early-onset and progressive hearing impairment that results from diminished cochlear amplification. Subsequent multiscale morphological analyses revealed structural collapse of OHCs that led to progressive and extensive OHC loss along the tonotopic axis. Palm3-KO OHCs exhibited disrupted expression and distribution of several membrane-associated proteins - including spectrin isoforms and Prestin - suggesting an essential role of Palm3 in plasma membrane scaffolding. Electron tomography of OHC lateral walls revealed significantly fewer and structurally perturbed subsurface cisternae. Finally, adeno-associated virus (AAV)-mediated rescue of Palm3 during early postnatal development partly restored hearing function, enhanced OHC survival, and restored OHC cell shape as well as membrane protein expression levels. In summary, Palm3 is a key component of the submembrane cytoskeleton in cochlear hair cells, playing a fundamental role in hair cell biology and hearing, and emerges as an attractive candidate for the long-elusive "pillar" component of the hair cell lateral wall ultrastructure.

cell biology↗

bioRxiv2025

Dynamic neural representations of scene beauty are relatively unaffected by stimulus timing and task

Understanding the neural correlates of aesthetic experiences in natural environments is a central question in neuroaesthetics. A previous EEG study (Kaiser, 2022) identified early and temporally sustained neural representations of visual scene beauty. These results were obtained with long presentation durations (1,450 ms) and with explicit beauty judgments, rendering it unclear how presentation time and task demands shape the neural correlates of scene beauty. In two EEG experiments, we replicated this study while varying presentation time and task. Experiment 1 tested whether reducing stimulus presentation time from 1,450 ms to 100 ms altered neural representations of beauty. Experiment 2 examined whether beauty-related representations prevailed when participants performed an orthogonal task instead of explicitly judging beauty. Representational similarity analysis revealed that beauty-related neural representations emerged early (within 150 - 200 ms post-stimulus) and were sustained over time, in line with previous findings. Critically, we found that neither reduced presentation time nor the absence of an explicit beauty judgment significantly altered beauty-related neural dynamics. These results suggest that the neural correlates of scene beauty are relatively robust to stimulus presentation and task regimes, providing a potential correlate of the spontaneous perception of beauty in natural environments.

neuroscience↗

bioRxiv2025

Multi-lineage transcriptional and cell communication signatures define pathways in individuals at-risk for developing rheumatoid arthritis that initiate and perpetuate disease

Rheumatoid arthritis (RA) is a systemic autoimmune disease arising from loss of tolerance and autoantibody development in at-risk individuals. Targeted therapies yield variable responses and current preventive strategies delay but do not stop disease onset. We propose that a set of transcription factors (TFs) and their downstream pathways regulate inflammatory cell communication networks in at-risk populations and RA. These networks enable multiple pathogenic cell types and mediators and could account for variable responses to targeted agents. To test this hypothesis, we identified anti-citrullinated protein antibody (ACPA)-positive at-risk individuals, patients with early and established RA and healthy controls. Single cell chromatin accessibility and transcriptomic profiles from blood mononuclear r cells were integrated and identified share pathogenic mechanisms, especially SUMOylation, RUNX2, YAP1, NOTCH3, and {beta}-Catenin Pathways. Surprisingly, this signature was found in multiple cell types. Individualized gene expression patterns were then confirmed in RA synovium. Cell communication analysis revealed that multiple lineages can deliver a core set of pro-inflammatory mediators to receiver cells. Longitudinal analysis showed that the signature cell types evolve in individual at-risk participants. Cell-type-specific signature pathways could contribute to the differing clinical responses to targeted therapies. This study describes how a common clinical phenotype could arise from multiple pathogenic mechanisms.

systems biology↗

bioRxiv2024

Capturing the Conformational Heterogeneity of HSPB1 Chaperone Oligomers at Atomic Resolution

Small heat shock proteins (sHSPs), including HSPB1, are essential regulators of cellular proteostasis that interact with unfolded and partially folded proteins to prevent aberrant misfolding and aggregation. These proteins fulfill a similar role in biological condensates, where they interact with intrinsically disordered proteins to modulate their liquid-liquid and liquid-to-solid phase transitions. Characterizing sHSP structure, dynamics, and client interactions is challenging due to their partially disordered nature, their tendency to form polydisperse oligomers, and their diverse range of clients. In this work, we leverage various biophysical methods, including fast 1H-based magic angle spinning (MAS) NMR spectroscopy, molecular dynamics (MD) simulations and modeling, to shed new light on the structure and dynamics of HSPB1 oligomers. Using split-intein mediated segmental labeling, we provide unambiguous evidence that in the oligomer context the N-terminal domain (NTD) of HSPB1 is rigid and adopts an ensemble of heterogenous conformations, the -crystallin domain (ACD) forms dimers and experiences multiple distinct local environments, while the C-terminal domain (CTD) remains highly dynamic. Our computational models suggest that the NTDs participate in extensive NTD-NTD and NTD-ACD interactions and are sequestered within the oligomer interior. We further demonstrate that HSPB1 higher order oligomers disassemble into smaller oligomeric species in the presence of a client protein and that an accessible NTD is essential for HSPB1 partitioning into condensates and interactions with client proteins. Our integrated approach provides a high-resolution view of the complex oligomeric landscape of HSPB1 and sheds light on the elusive network of interactions that underly HSPB1 function in biological condensates. Significance statementHSPB1 is a ubiquitous cellular chaperone that helps prevent the aberrant aggregation of intrinsically disordered proteins involved in biological condensates and neurodegenerative diseases. Despite its central role in this process, many aspects of HSPB1s structure and interactions with clients are not well understood due to its tendency to form polydisperse oligomeric structures and to function in heterogeneous condensate environments. Here, we present an integrated approach that includes segmental labeling, fast MAS NMR spectroscopy, and computational tools to characterize the structure and dynamics of HSPB1 in its oligomeric form and within client condensates at high resolution. Our approach, which is applicable to other complex biological systems, highlights the important role of HSPB1s N-terminal domain in oligomeric assembly and interactions with clients.

biophysics↗

bioRxiv2024

Context-dependent roles for autophagy in myeloid cells in tumor progression

Autophagy is known to suppress tumor initiation by removing genotoxic stresses in normal cells. Conversely, autophagy is also known to support tumor progression by alleviating metabolic stresses in neoplastic cells. Centered on this pro-tumor role of autophagy, there have been many clinical trials to treat cancers through systemic blocking of autophagy. Such systemic inhibition affects both tumor cells and non-tumor cells, and the consequence of blocked autophagy in non-tumor cells in the context of tumor microenvironment is relatively understudied. Here, we examined the effect of autophagy-deficient myeloid cells on the progression of autophagy-competent tumors. We found that blocking autophagy only in myeloid cells modulated tumor progression markedly but such effects were context dependent. In a tumor implantation model, the growth of implanted tumor cells was substantially reduced in mice with autophagy-deficient myeloid cells; T cells infiltrated deeper into the tumors and were responsible for the reduced growth of the implanted tumor cells. In an oncogene-driven tumor induction model, however, tumors grew faster and metastasized more in mice with autophagy- deficient myeloid cells. These data demonstrate that the autophagy status of myeloid cells plays a critical role in tumor progression, promoting or suppressing tumor growth depending on the context of tumor-myeloid cell interactions. This study indicates that systemic use of autophagy inhibitors in cancer therapy may have differential effects on rates of tumor progression in patients due to effects on myeloid cells and that this warrants more targeted use of selective autophagy inhibitors in a cancer therapy in a clinical setting.

cancer biology↗

bioRxiv2024

Oligonucleotide Library Assisted Sequence Mining Reveals Promoter Sequences With Distinct Temporal Expression Dynamics For Applications In Curvibacter SP. AEP1-3

AO_SCPLOWBSTRACTC_SCPLOWThe {beta}-proteobacterial species Curvibacter sp. AEP1-3 is a model organism for the study of symbiotic interactions as it is the most abundant bacterial colonizer of the basal metazoan Hydra vulgaris. Yet, genetic tools for Curvibacter are still in an infancy: few promoters have been characterized for Curvibacter. Here we employ an oligonucleotide based strategy to find potential expression systems derived from the genome of Curvibacter. Potential promoters were systematically mined from the genome in silico. The sequences were cloned as a mixed library into a mCherry reporter gene expression vector and single positive candidates were selected through Flow Cytometry based sorting to be further analyzed through bulk measurements. From 500 candidate sequences, 25 were identified as active promoters of varying expression strength levels. Bulk measurements revealed unique activity profiles for these sequences across growth phases. The expression levels of these promoters ranged over two orders of magnitudes and showed distinct temporal expression dynamics over the growth phases: while 3 sequences showed higher expression levels in the exponential phase than in the stationary phase, we found 12 sequences saturating expression during stationary phase and 10 that showed little discrimination between growth phases. From our library, promoters the genes encoding for DnaK, RpsL and an AHL synthase stood out as the most interesting candidates as their expression profiles fit a variety of applications. Examining the expression levels of successful candidates in relation to RNAseq read counts revealed only weak correlation between the two datasets. This underscores the importance of employing comprehensive high-throughput strategies when establishing expression systems for newly introduced model organisms.

synthetic biology↗

bioRxiv2024

Stability of the Wheat Seed Mycobiome Across North Carolina's Longitudinal Gradient

Improving wheat yield and performance involves selecting varieties that are well adapted for a regional area. Although host genotype and environment are major factors that impact crop performance and resilience, less is known about the relative contribution and occurrence of wheat seed endophytic fungal communities across spatial and temporal scales. An increased understanding of composition and assembly of beneficial endophytic fungal communities across regional scales provides valuable insight into the stability of the endophytic seed mycobiome. Our aim in this study was to examine the relative contribution and impact of latitude and longitude gradients within North Carolina (NC) on wheat seed fungal community structure of two regionally adapted soft red winter wheat cultivars, Hilliard and USG 3640. We examined the endophytic wheat seed microbiome of the two winter wheat cultivars planted in official variety trials at five geographic locations across NC in 2021 and two geographic locations in 2022. ITS1 sequence-based analysis of surface disinfested wheat seeds was conducted to determine alpha and beta diversity. Species richness is influenced by geographical location, however wheat seed mycobiome community structure is stable across cultivars and years. Latitude and longitude contributed to the observed variation in wheat seed mycobiome structure, in addition to yield, seed moisture, and leaf nutrients. When surveying taxa present within all cultivars, geographical sites and years, Alternaria and Epicoccum spp. exhibited high relative abundance in the wheat seed mycobiome. Our results provide a comprehensive catalog of core fungal taxa well-adapted to diverse environments and conserved across wheat cultivars.

microbiology↗

bioRxiv2023

Comparative phenotyping of mice reveals canonical and noncanonical physiological functions of TRα and TRβ

Thyroid hormone (TH) effects are mediated through TH receptors (TRs) TR1, TR{beta}1, and TR{beta}2. The TRs bind to thyroid hormone responsive elements on the DNA and regulate expression of TH target genes as ligand dependent transcription factors (canonical signaling). In addition, the TRs and {beta} mediate activation of signaling pathways, e.g. the PI3K/AKT and MAPK/ERK pathways (noncanonical signaling). Whether such DNA-binding independent TR action contributes to the spectrum of physiological TH effects is largely unknown. The aim of this study was to attribute physiological effects to the two TR isoforms and {beta} and their canonical and noncanonical signaling. We conducted multi-parameter phenotyping in male and female TR knockout mice (TRKO, TR{beta}KO), mice with disrupted canonical signaling due to a mutation in the TR DNA-binding domain (TRGS, TR{beta}GS) and their respective wild-type littermates. Perturbations in senses, especially hearing (mainly TR{beta} with a lesser impact of TR), visual acuity and retinal thickness (TR and TR{beta}), in muscle metabolism (TR) and in heart rate (TR) highlighted the role of canonical TR action. Strikingly, selective abrogation of canonical TR action often had little to no phenotypic consequence, suggesting that noncanonical TR action sufficed to maintain the wild-type phenotype for specific effects. For instance, macrocytic anemia, reduced retinal vascularization or increased anxiety related behavior were only observed in TRKO, but not TRGS mice. Noncanonical TR action increased the efficiency of energy utilization and prevented hyperphagia observed in TRKO mice. In summary, by examining the phenotypes of TR and TR{beta} knockout models alongside their DNA-binding-deficient GS mutants and wildtype counterparts, we could establish that the independent noncanonical actions of TR and TR{beta} play a crucial role in modulating sensory, behavioral, and metabolic functions. This comparison underscores the significance of the TRs in orchestrating a spectrum of physiological processes beyond their traditional genomic pathways.

physiology↗

bioRxiv2023

CATHI: An interactive platform for comparative genomics and homolog identification

AO_SCPLOWBSTRACTC_SCPLOWBioinformatics has established itself as a central pillar of modern biology. Specifically, comparative genomics enables scientists to study a vast number of genomes efficiently. These comparative analyses shed light on the evolution and potential function of genomes and genes, but are also increasingly used as a key tool for metabolic engineering and synthetic biology by identifying appropriate targets for modification. While numerous sophisticated tools for comparative genomics and homolog identification exist, those tools predominantly target highly skilled bioinformatics users. Consequently, many biologists either defer such analyses to their more versed bioinformatic collaborators or resort to suboptimal tools. Here, we present an intuitive solution available on all major operating systems, easily accessed through common web browsers. CATHI - Comparative Analysis Tool for Homolog Identification - integrates a suite of best-practice bioinformatic tools, encompassing BLAST for homology searches, MAFFT for multiple sequence alignment, FastTree2 for phylogeny reconstruction, and clinker for synteny analysis. Specifically tailored to biologists, CATHI orchestrates predefined settings and automated pipelines, obviating the need for programming expertise. This platform empowers researchers to confidently engage in detailed comparative genomics studies by streamlining the analytical process. The interactive framework provides users with a plethora of options. This includes real-time execution and progress monitoring, facilitates dynamic result tracking, and a set of search functions across NCBI databases like CDD or ProtFam. Users can interactively engage in data exploration, filtering, and visualization through CATHIs intuitive interface. Furthermore, the seamless export of project data in standard formats (FASTA, Newick, CSV, and HTML) facilitates the integration with further third-party tools such as TreeViewer and Jalview. To benchmark CATHI, we revisited the comparative analysis of cyanobacterial circadian clock proteins conducted by Schmelling et al. in 2017, revealing consistent global patterns among identified homologs, while also highlighting individual variations attributed to the expansion of available databases.

bioinformatics↗

bioRxiv2022

The basolateral amygdala-anterior cingulate pathway contributes to depression and its comorbidity with chronic pain

While depression and chronic pain are frequently comorbid, underlying neuronal circuits, and their relevance for the understanding of psychopathology, remain poorly defined. Here we show in mice that hyperactivity of the neuronal pathway linking the basolateral amygdala to the anterior cingulate cortex is essential for chronic pain-induced depression. In naive animals, we demonstrate that activation of this pathway is sufficient to trigger depressive-like behaviors, as well as transcriptomic alterations that recapitulate core molecular features of depression in the human brain. These alterations notably impact gene modules related to myelination and the oligodendrocyte lineage. Among these, we show that Sema4a, a hub gene significantly upregulated in both mice and humans in the context of altered mood, is necessary for the emergence of depressive-like behaviors. Overall, these results place the BLA-ACC pathway at the core of pain and depression comorbidity, and unravel the role of impaired myelination and Sema4a in mood control.

neuroscience↗

bioRxiv2022

Deep Phenotyping and Lifetime Trajectories Reveal Limited Effects of Longevity Regulators on the Aging Process in C57BL/6J Mice

Current concepts regarding the biology of aging are based on studies aimed at identifying factors regulating natural lifespan. However, lifespan as a sole proxy measure for aging can be of limited value because it may be restricted by specific sets of pathologies, rather than by general physiological decline. Here, we employed large-scale phenotyping to analyze hundreds of phenotypes and thousands of molecular markers across tissues and organ systems in a single study of aging male C57BL/6J mice. For each phenotype, we established lifetime profiles to determine when age-dependent phenotypic change is first detectable relative to the young adult baseline. We examined central genetic and environmental lifespan regulators (putative anti-aging interventions, PAAIs; the following PAAIs were examined: mTOR loss-of-function, loss-of-function in growth hormone signaling, dietary restriction) for a possible countering of the signs and symptoms of aging. Importantly, in our study design, we included young treated groups of animals, subjected to PAAIs prior to the onset of detectable age-dependent phenotypic change. In parallel to our studies in mice, we assessed genetic variants for their effects on age-sensitive phenotypes in humans. We observed that, surprisingly, many PAAI effects influenced phenotypes long before the onset of detectable age-dependent changes, rather than altering the rate at which these phenotypes developed with age. Accordingly, this subset of PAAI effects does not reflect a targeting of age-dependent phenotypic change. Overall, our findings suggest that comprehensive phenotyping, including the controls built in our study, is critical for the investigation of PAAIs as it facilitates the proper interpretation of the mechanistic mode by which PAAIs influence biological aging. HighlightsO_LIPhenotyping at scale defines lifetime trajectories of age-dependent changes in C57BL/6J mice C_LIO_LICentral genetic and environmental lifespan regulators (putative anti-aging interventions; PAAIs) influence age-sensitive phenotypes (ASPs) often long before the appearance of age-dependent changes in these ASPs C_LIO_LICorresponding genetic variants in humans also have age-independent effects C_LIO_LIMany PAAI effects shift the baseline of ASPs rather than slowing their rate of change C_LI

physiology↗

bioRxiv2020

Tubular lysosomes harbor active ion gradients and poise macrophages for phagocytosis

Lysosomes adopt dynamic, tubular states that regulate antigen presentation, phagosome resolution and autophagy. To date, tubular lysosomes have been studied either by inducing autophagy or by activating immune cells, both of which lead to cell states where lysosomal gene expression differs from the resting state. Therefore, it has been challenging to pinpoint the specific biochemical properties lysosomes acquire upon tubulation that could drive their functionality. We describe a DNA-based assembly that tubulates lysosomes in macrophages without activating them. Lumenal proteolytic activity maps at single lysosome resolution revealed that tubular lysosomes were less degradative. Further, they showed striking proximal to distal lumenal pH and Ca2+ gradients. Such gradients had been predicted, but never previously observed. We now identify a role for tubular lysosomes whereby they poise resting macrophages for phagocytosis. The ability to tubulate lysosomes without having to starve or activate immune cells may help reveal new roles for tubular lysosomes.

cell biology↗

bioRxiv2020

Multiscale and multimodal reconstruction of cortical structure and function

We present a semi-automated reconstruction of L2/3 mouse primary visual cortex from 3 million cubic microns of electron microscopic images, including pyramidal and inhibitory neurons, astrocytes, microglia, oligodendrocytes and precursors, pericytes, vasculature, mitochondria, and synapses. Visual responses of a subset of pyramidal cells are included. The data are being made publicly available, along with tools for programmatic and 3D interactive access. The density of synaptic inputs onto inhibitory neurons varies across cell classes and compartments. We uncover a compartment-specific correlation between mitochondrial coverage and synapse density. Frequencies of connectivity motifs in the graph of pyramidal cells are predicted quite accurately from node degrees using the configuration model of random graphs. Cells receiving more connections from nearby cells exhibit stronger and more reliable visual responses. These example findings illustrate the resources utility for relating structure and function of cortical circuits as well as for neuronal cell biology.

neuroscience↗

bioRxiv2020

Schistosoma haematobium extracellular vesicle proteins confer protection in a heterologous model of schistosomiasis

Helminth parasites release extracellular vesicles which interact with the surrounding host tissues, mediating host-parasite communication and other fundamental processes of parasitism. As such, vesicle proteins present attractive targets for the development of novel intervention strategies to control these parasites and the diseases they cause. Herein, we describe the first proteomic analysis by LC-MS/MS of two types of extracellular vesicles (exosome-like, 120k pellet vesicles and microvesicle-like, 15k pellet vesicles) from adult Schistosoma haematobium worms. A total of 57 and 330 proteins were identified in the 120k pellet vesicles and larger 15k pellet vesicles, respectively, and some of the most abundant molecules included homologues of known helminth vaccine and diagnostic candidates such as Sm-TSP2, Sm23, glutathione S-tranferase, saposins and aminopeptidases. Tetraspanins were highly represented in the analysis and found in both vesicle types. Vaccination of mice with recombinant versions of three of these tetraspanins induced protection in a heterologous challenge (S. mansoni) model of infection, resulting in significant reductions (averaged across two independent trials) in liver (47%, 38% and 41%) and intestinal (47%, 45% and 41%) egg burdens. These findings offer insight into the mechanisms by which anti-tetraspanin antibodies confer protection and highlight the potential that extracellular vesicle surface proteins offer as anti-helminth vaccines.

microbiology↗

bioRxiv2020

Titan Mice are Unique Short-Lived Mammalian Model of Metabolic Syndrome and Aging

Suitable animal models are essential for translational research, especially in the case of complex, multifactorial conditions, such as obesity. The outbred mouse line Titan (DU6) results from the worlds longest selection experiment for high body mass and was previously described as a model for metabolic healthy (benign) obesity. The present study deeper characterized the geno- and phenotypes of this outbred mouse line and tested its suitability as an interventional obesity model. In contrast to previous findings, our data suggests that Titan mice are metabolically unhealthy obese and short-lived. Line-specific patterns of genetic invariability are in accordance with observed phenotypic traits. Titan mice show modifications in the liver transcriptome, proteome and epigenome that are linked to metabolic (dys)regulations. However, dietary intervention partially reversed the metabolic phenotype in Titan mice and significantly extended their life expectancy. Therefore, the Titan mouse line is a valuable resource for translational and interventional obesity research.

biochemistry↗