Biology subjects

Kraus, A.

Publications and source records attributed to Kraus, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Deletion of the gene for a cyanobacterial ribosome-associated protein affects the carbon/nitrogen metabolism

In contrast to their important structural and regulatory functions, such as in the metabolism of cyanobacteria, genes encoding small proteins are often not well characterized. Cyanobacteria use redox equivalents and energy from oxygenic photosynthesis to produce organic carbon compounds from inorganic carbon (Ci) and organic nitrogen compounds from inorganic nitrogen sources. Therefore, the assimilation and metabolism of carbon and nitrogen are coordinated at multiple levels in cyanobacteria. Here, we analyzed the Synechocystis sp. PCC 6803 gene ssr3189 encoding a 55 amino acids protein. Orthologs were detected in 665 cyanobacterial genomes defining COG5794 in the Database of Clusters of Orthologous Genes. Homologs in several eukaryotic algae suggest that Ssr3189 is an important protein that originated in cyanobacteria, was retained in algae after endosymbiosis, but was lost in plants. Polynucleotide kinase assays validated Ssr3189 as an RNA-binding protein. Deletion of ssr3189 resulted in lower pigmentation, delayed growth, and alterations in the expression of genes encoding transporters for nitrogen and Ci, and metabolic enzymes. Metabolomic analysis revealed a substantial overaccumulation of glutamine and tricarboxylic acid cycle intermediates in the deletion mutant, and further differences in the amino acid and organic acid pools compared to the wild type. Co-immunoprecipitation analysis yielded ribosomal protein S21, enolase and the Cas6-1 endoribonuclease as the most strongly co-enriched proteins, together with all other ribosomal proteins and a small set of metabolic enzymes. These findings are consistent with observations that ssr3189 encodes the ribosome-associated protein cS24 and suggest that it connects translation with metabolic control, and, potentially, RNA decay. IMPACT STATEMENTDespite considerable progress in analyzing microbial genomes, there are still substantial numbers of uncharacterized gene functions. Here, we analyzed a mutant lacking gene ssr3189 that is widely conserved, but phenotypically uncharacterized in cyanobacteria. This gene is important for growth at the optimum temperature and essential at lower temperatures. In its absence, important metabolites were overaccumulated, while genes involved in nitrogen and Ci uptake were dysregulated. The encoded protein binds RNA and interacts with proteins involved in translation and metabolism. The findings are consistent with a function as a ribosomal protein bridging protein synthesis and the regulation of metabolism.

microbiology↗

bioRxiv2025

Live longitudinal imaging of meningeal cerebrovascular injury and its sequelae in adult zebrafish

Nearly 1.4 million people in the United States sustain a traumatic brain injury (TBI) each year, with almost half of those hospitalized for TBI developing long-term disability. For many patients, prolonged bleeding and inflammation from damaged vessels in the meninges result in long-lasting sequelae. Although their injured blood vessels regrow, the site of injury is full of inflammatory immune cells that may influence vascular function. Adult zebrafish have a thin, translucent skull and a mammalian-like meninges that is easily imaged in living animals. We have established a novel adult zebrafish model to investigate vessel-immune cell interactions after meningeal cerebrovascular injury (mCVI). We use carefully calibrated sonication to rupture meningeal blood vessels without breaching the skull or causing damage to the underlying brain. By performing longitudinal live imaging of intubated adult fish we observe vascular regrowth and immune responses to mCVI over time in the same animal with unprecedented resolution allowing measurement of blood flow, dynamics of vessel regrowth, and interactions between individual immune and vascular cells. This newly developed zebrafish model provides a powerful tool for longitudinal live imaging of meningeal immune cell-vascular interactions after cerebrovascular injury, opening the door to new insights into chronic neuroinflammatory disease.

neuroscience↗

bioRxiv2025

The fibrocystin C-terminal domain inhibits Src/STAT3 signal induced cystogenesis of kidney epithelia.

Autosomal recessive polycystic kidney disease (ARPKD) is caused by impaired function of fibrocystin/polyductin (FPC) in collecting duct epithelia resulting in cyst formation. We hypothesized that the membrane-bound C-terminal FPC domain (FPCct) is necessary to suppress cystogensis and facilitate epithelial homeostasis. In ARPKD, cystic kidney epithelia are characterized by a secretory phenotype associated with high intracellular cAMP levels and enhanced STAT3-dependent transcription. Moreover, impaired FPC function may lead to enhanced activation of Src tyrosine kinase, thereby activating STAT3 signaling and its downstream transcriptional activity. To investigate the effects of FPC loss on the cystic epithelial cell phenotype, we used an established principal-like MDCK cell line (pl-MDCK) and studied monolayers in both two and three-dimensional culture. In this in vitro model of collecting duct epithelia, FPC-deficient cells showed two-fold elevated basal cAMP levels and enhanced apical secretion leading to three-fold higher luminal pressure. Forskolin-stimulated elevation of cAMP levels triggered enhanced Src-dependent activation of STAT3 resulting in a pronounced cystic phenotype. Notably, expression of wildtype FPCct reduced both STAT3-dependent transcription and the secretory phenotype in knockout epithelial cells. Our data suggest that FPCct interacts with Src kinase at the plasma membrane, thereby reducing Src-mediated STAT3 phosphorylation and limiting STAT3-dependent transcription. Thus, FPCct appears to act like a physiological suppressor of cystogenic signaling, as found in healthy kidney epithelia, that is essential for maintaining epithelial homeostasis. Protein constructs that restore FPC C-terminal function may offer a therapeutic lead to mitigate epithelial dysfunction and slow disease progression in ARPKD.

cell biology↗

bioRxiv2025

Lifestyle, Early-life, and Genetic Health Risk Factors Underlying the Brain Age Gap: A Mega-Analysis Across 3,934 Individuals from the ENIGMA MDD Consortium

BackgroundLarge-scale studies show that adults with major depressive disorder (MDD) generally have a higher imaging-predicted age relative to their chronological age (i.e., positive brain age gap) compared to controls, though considerable within-group variation exists. This study examines lifestyle, early-life, and genetic health risk factors contributing to the brain age gap. Identifying risk and resilience factors could help protect brain and mental health. MethodsUsing an established model trained on FreeSurfer-derived brain regions (www.photon-ai.com/enigma_brainage), we generated brain age predictions for 1,846 controls and 2,088 individuals with MDD (aged 18-75) from 12 international cohorts. Polygenic risk scores (PRS) were calculated for major depression, C-reactive protein, and body mass index (BMI) using large-scale GWAS results. Linear mixed models were applied to assess lifestyle (BMI, smoking, education), early-life childhood trauma, and genetic (PRS) health risk associations with the brain age gap. Additionally, we evaluated the link between the brain age gap and peripheral biological age indicators (epigenetic clocks). ResultsHigher brain age gaps were significantly associated with BMI ({beta}=0.01, PFDR=0.02) and smoking ({beta}=0.11, PFDR=0.02), while lower brain age gaps were linked to higher education ({beta}=-0.02, PFDR=0.02). Higher childhood trauma scores predicted a higher brain age gap ({beta}=0.04, P=0.01). Higher brain age gaps were positively associated with all PRS ({beta}s=0.04-0.16, PsFDR=0.02-0.03). There were no significant interactions between diagnosis and assessed factors on the brain age gap. In a multivariable model, only modifiable health factors--BMI, smoking, and education--remained uniquely associated with brain age gaps. ConclusionsGenetic liability for depression and related traits is linked to poorer brain health, but health behaviors potentially offer a key opportunity for intervention. This study underscores the importance of targeting modifiable lifestyle factors to mitigate poor brain health in depressed individuals, an approach perhaps under-recognized in clinical practice.

neuroscience↗

bioRxiv2025

Anatomical and Molecular Characterization of the Zebrafish Meninges

The meninges are a set of connective tissue layers that surround the central nervous system, protecting the brain from mechanical shock, supporting its buoyancy, guarding it from infection and injury, and maintaining brain homeostasis. Despite their critical role, the molecular identity, developmental origins, and functional properties of the cell types populating the meninges remain poorly characterized. This is in large part due to lack of cell type specific markers and difficulty in visualizing and studying these structures through the thick mammalian skull. Here, we show that the zebrafish, a genetically and experimentally accessible vertebrate, possesses an easily imaged mammalian-like meninges. Anatomical and cellular characterization of its composition via histology, electron microscopy, and confocal imaging shows that the adult zebrafish possesses complex multilayered meninges with double-layered dura mater and intricate leptomeningeal layers. Using single cell transcriptomics, we define the molecular identities of meningeal cell populations, including a unique ependymin (epd)-expressing cell population that constitutes the major cellular component of the leptomeningeal barrier and is essential for brain development and survival. These findings support the use of zebrafish as a useful comparative model for studying the meninges, provide a foundational description for future zebrafish meningeal research, and identify a new Leptomeningeal Barrier Cell that serves as the primary epithelial cell component of the leptomeninges.

developmental biology↗

bioRxiv2025

Network-based framework for studying etiology and phenotype diversity in primary ciliopathies

Recent advances in sequencing technologies have increasingly enabled the identification of genetic causes for human monogenic diseases. However, systematic understanding remains limited due to the rarity, genetic heterogeneity, and complex genotype-phenotype relationships of these diseases. Primary ciliopathies are a diverse group of rare disorders caused by variants in genes associated with the cilium, a cellular organelle involved in signaling during development and cell homeostasis. These genetic variants result in a wide spectrum of clinical phenotypes involving the brain, eye, kidney and skeleton. It remains unclear to what extent this phenotypic diversity can be attributed to the disease-causing genes and their specific roles in ciliary function. Here, we systematically compared human primary ciliopathies with each other and with mouse phenotypes by propagating known disease genes through a network of protein interactions. Network propagation improved the clustering of primary ciliopathies with shared clinical phenotypes and facilitated the identification of mouse phenotypes closely related to primary ciliopathies due to shared groups of proteins in the interaction network. By leveraging this phenotype-specific approach, we prioritized candidate genes for ciliopathies and identified likely pathogenic variants in CEP43, a novel candidate gene for human primary ciliopathies in three previously unsolved cases. This study demonstrates that network propagation enhances the genetic and phenotypic understanding of primary ciliopathies, aiding in the prioritization of candidate genes and identification of relevant mouse models for these rare disorders, and providing a framework for unraveling shared underlying mechanisms for other rare genetic diseases.

genetics↗

bioRxiv2024

Gray matter correlates of childhood maltreatment in the context of major depression: searching for replicability in a multi-cohort brain-wide association study of 3225 adults

Childhood maltreatment effects on cerebral gray matter have been frequently discussed as a neurobiological pathway for depression. However, localizations are highly heterogeneous, and recent reports have questioned the replicability of mental health neuroimaging findings. Here, we investigate the replicability of gray matter correlates of maltreatment (measured retrospectively via the Childhood Trauma Questionnaire) across three large adult cohorts (total N=3225). Pooling cohorts revealed maltreatment-related gray matter reductions, with most extensive effects when not controlling for depression diagnosis (maximum partial R2=.022). However, none of these effects significantly replicated across cohorts. Non-replicability was consistent across a variety of maltreatment subtypes and operationalizations, as well as subgroup analyses with and without depression, and stratified by sex. In this work we show that there is little evidence for the replicability of gray matter correlates of childhood maltreatment, when adequately controlling for psychopathology. This underscores the need to focus on replicability research in mental health neuroimaging.

neuroscience↗

bioRxiv2024

The axillary lymphoid organ - an external, experimentally accessible immune organ in the zebrafish

Lymph nodes and other secondary lymphoid organs play critical roles in immune surveillance and immune activation in mammals, but the deep internal locations of these organs make it challenging to image and study them in living animals. Here, we describe a previously uncharacterized external immune organ in the zebrafish ideally suited for studying immune cell dynamics in vivo, the axillary lymphoid organ (ALO). This small, translucent organ has an outer cortex teeming with immune cells, an inner medulla with a mesh-like network of fibroblastic reticular cells along which immune cells migrate, and a network of lymphatic vessels draining to a large adjacent lymph sac. Noninvasive high-resolution imaging of transgenically marked immune cells can be carried out in the lobes of living animals, and the ALO is readily accessible to external treatment. This newly discovered tissue provides a superb model for dynamic live imaging of immune cells and their interaction with pathogens and surrounding tissues, including blood and lymphatic vessels. TeaserA newly characterized external zebrafish lymphoid organ provides a powerful model for live imaging of immune cell dynamics

developmental biology↗

bioRxiv2024

Brain Structural Correlates of an Impending Initial Major Depressive Episode

BackgroundNeuroimaging research has yet to elucidate, whether reported gray matter volume (GMV) alterations in major depressive disorder (MDD) exist already before the onset of the first episode. Recruitment of presently healthy individuals with a known future transition to MDD (converters) is extremely challenging but crucial to gain insights into neurobiological vulnerability. Hence, we compared converters to patients with MDD and sustained healthy controls (HC) to distinguish pre-existing neurobiological markers from those emerging later in the course of depression. MethodsCombining two clinical cohorts (n=1709), voxel-wise GMV of n=45 converters, n=748 patients with MDD, and n=916 HC were analyzed in regions-of-interest approaches. By contrasting the subgroups and considering both remission state and reported recurrence at a 2-year clinical follow-up, we stepwise disentangled effects of 1) vulnerability, 2) the acute depressive state, and 3) an initial vs. a recurrent episode. ResultsAnalyses revealed higher amygdala GMV in converters relative to HC (pTFCE-FWE=.037, d=0.447) and patients (pTFCE-FWE=.005, d=0.508), remaining significant when compared to remitted patients with imminent recurrence. Lower GMV in the dorsolateral prefrontal cortex (pTFCE-FWE<.001, d=0.188) and insula (pTFCE-FWE=.010, d=0.186) emerged in patients relative to HC but not to converters, driven by patients with acute MDD. ConclusionBy examining one of the largest available converter samples in psychiatric neuroimaging, this study allowed a first determination of neural markers for an impending initial depressive episode. Our findings suggest a temporary vulnerability, which in combination with other common risk factors might facilitate prediction and in turn improve prevention of depression.

neuroscience↗

bioRxiv2023

Nitrite secretion by cyanobacteria is controlled by the small protein NirP1

When the supply of inorganic carbon is limiting, photosynthetic cyanobacteria excrete nitrite, a toxic intermediate in the ammonia assimilation pathway from nitrate. While it has been hypothesized that the secreted nitrite represents excess nitrogen that could not be further assimilated due to the missing carbon, the underlying molecular mechanism has remained enigmatic. Here, we characterized a hitherto unannotated gene with homologs in the genomes of 485 different cyanobacteria that is upregulated under low carbon conditions and controlled by the transcription factor NtcA, a central regulator of nitrogen homeostasis. To understand its function, we ectopically overexpressed it in Synechocystis sp. PCC 6803, which resulted in a chlorotic phenotype, delayed growth, severe changes in amino acid pools, and nitrite excretion. Coimmunoprecipitation experiments revealed that this protein targets nitrite reductase, a central enzyme in the assimilation of ammonia from nitrate/nitrite, and was re-named to nitrite reductase regulator protein 1 (NirP1). Our results reveal that NirP1 is widely conserved in cyanobacteria and plays a crucial role in the coordination of C/N primary metabolism by targeting one of the central enzymes. In natural environments, the excreted nitrite will be utilized by other microorganisms; therefore, NirP1 ultimately impacts the activities and composition of the surrounding microbiome.

microbiology↗

bioRxiv2023

Cross-validation for the estimation of effect size generalizability in mass-univariate brain-wide association studies

IntroductionStatistical effect sizes are systematically overestimated in small samples, leading to poor generalizability and replicability of findings in all areas of research. Due to the large number of variables, this is particularly problematic in neuroimaging research. While cross-validation is frequently used in multivariate machine learning approaches to assess model generalizability and replicability, the benefits for mass-univariate brain analysis are yet unclear. We investigated the impact of cross-validation on effect size estimation in univariate voxel-based brain-wide associations, using body mass index (BMI) as an exemplary predictor. MethodsA total of n=3401 adults were pooled from three independent cohorts. Brain-wide associations between BMI and gray matter structure were tested using a standard linear mass-univariate voxel-based approach. First, a traditional non-cross-validated analysis was conducted to identify brain-wide effect sizes in the total sample (as an estimate of a realistic reference effect size). The impact of sample size (bootstrapped samples ranging from n=25 to n=3401) and cross-validation on effect size estimates was investigated across selected voxels with differing underlying effect sizes (including the brain-wide lowest effect size). Linear effects were estimated within training sets and then applied to unseen test set data, using 5-fold cross-validation. Resulting effect sizes (explained variance) were investigated. ResultsAnalysis in the total sample (n=3401) without cross-validation yielded mainly negative correlations between BMI and gray matter density with a maximum effect size of R2p=.036 (peak voxel in the cerebellum). Effects were overestimated exponentially with decreasing sample size, with effect sizes up to R2p=.535 in samples of n=25 for the voxel with the brain-wide largest effect and up to R2p=.429 for the voxel with the brain-wide smallest effect. When applying cross-validation, linear effects estimated in small samples did not generalize to an independent test set. For the largest brain-wide effect a minimum sample size of n=100 was required to start generalizing (explained variance >0 in unseen data), while n=400 were needed for smaller effects of R2p =.005 to generalize. For a voxel with an underlying null effect, linear effects found in non-cross-validated samples did not generalize to test sets even with the maximum sample size of n=3401. Effect size estimates obtained with and without cross-validation approached convergence in large samples. DiscussionCross-validation is a useful method to counteract the overestimation of effect size particularly in small samples and to assess the generalizability of effects. Train and test set effect sizes converge in large samples which likely reflects a good generalizability for models in such samples. While linear effects start generalizing to unseen data in samples of n>100 for large effect sizes, the generalization of smaller effects requires larger samples (n>400). Cross-validation should be applied in voxel-based mass-univariate analysis to foster accurate effect size estimation and improve replicability of neuroimaging findings. We provide open-source python code for this purpose (https://osf.io/cy7fp/?view_only=a10fd0ee7b914f50820b5265f65f0cdb).

neuroscience↗

bioRxiv2023

Peripheral detection of viruses shapes brain immunity and behavior in zebrafish

Olfactory sensory neurons (OSNs) are constantly exposed to pathogens, including viruses. However, serious brain infection via the olfactory route rarely occurs. When OSNs detect a virus, they coordinate local antiviral immune responses to stop virus progression to the brain. Despite effective immune control in the olfactory periphery, pathogen-triggered neuronal signals reach the CNS via the olfactory bulb (OB). We hypothesized that neuronal detection of a virus by OSNs initiates neuroimmune responses in the OB that prevent pathogen invasion. Using zebrafish (Danio rerio) as a model, we demonstrate viral-specific neuronal activation of OSNs projecting into the OB, indicating that OSNs are electrically activated by viruses. Further, behavioral changes are seen in both adult and larval zebrafish after viral exposure. By profiling the transcription of single cells in the OB after OSNs are exposed to virus, we found that both microglia and neurons enter a protective state. Microglia and macrophage populations in the OB respond within minutes of nasal viral delivery followed decreased expression of neuronal differentiation factors and enrichment of genes in the neuropeptide signaling pathway in neuronal clusters. Pituitary adenylate-cyclase-activating polypeptide (pacap), a known antimicrobial, was especially enriched in a neuronal cluster. We confirm that PACAP is antiviral in vitro and that PACAP expression increases in the OB 1 day post-viral treatment. Our work reveals how encounters with viruses in the olfactory periphery shape the vertebrate brain by inducing antimicrobial programs in neurons and by altering host behavior.

immunology↗

bioRxiv2022

Peyers Patch B cells undergo cell death via neutrophil-released toxic DNA following sterile tissue injury

Lymphocyte contraction (LC) in central immune organs is a concomitant of sterile tissue injury, for example after stroke. Intestinal Peyers patches (PP) harbor large numbers of B cells, but how sterile tissue injury leads to LC in PP has not been explored. We observed rapid and macroscopically evident shrinkage of PP after stroke and myocardial infarction. Light-sheet fluorescence microscopy and flow cytometry revealed a strong reduction in the number of PP-resident B cells. Mechanistically, tissue injury triggered the activation of neutrophils that released B cell-toxic neutrophil extracellular traps (NETs) decorated with citrullinated histone-H3. Antibody-mediated or genetically induced neutrophil-loss, NETs-degradation or blockade of their generation completely reversed B cell loss and preserved the tissue architecture of PP. We also found NET-like elements in human post-stroke plasma. Hence, we propose that targeting NET-generation or -function counteracts post-injury B cell contraction in PP and thereby maintains immune homeostasis at mucosal barriers. In briefHigh numbers of B cells reside in the intestinal Peyers patches. Tuz et al. revealed that in response to sterile tissue injury, activated neutrophils release histone-decorated DNA into the circulation which induces B cell death. The loss of B cells results in the shrinkage of Peyers patches and reduced amounts of secretory IgA. HighlightsO_LIStroke and myocardial infarction induce the melting of Peyers patch C_LIO_LILight-sheet microscopy and cytometry revealed B cell loss in Peyers patch C_LIO_LIPost-injury activated neutrophils release NETs and trigger B cell death C_LIO_LIInhibition of NETs rescues B cell loss and degeneration of Peyers patch C_LI

immunology↗

bioRxiv2022

Cryo-EM of prion strains from the same genotype of host identifies conformational determinants

Prion strains in a given type of mammalian host are distinguished by differences in clinical presentation, neuropathological lesions, survival time, and characteristics of the infecting prion protein (PrP) assemblies. Near-atomic structures of prions from two host species with different PrP sequences have been determined but comparisons of distinct prion strains of the same amino acid sequence are needed to identify purely conformational determinants of prion strain characteristics. Here we report a 3.2 [A] resolution cryogenic electron microscopy-based structure of the 22L prion strain purified from the brains of mice engineered to express only PrP lacking glycophosphatidylinositol anchors (a22L). Comparison of this near-atomic structure to our recently determined structure of the aRML strain propagated in the same inbred mouse reveals that these two mouse prion strains have distinct conformational templates for growth via incorporation of PrP molecules of the same sequence. Both a22L and aRML are assembled as stacks of PrP molecules forming parallel in-register intermolecular {beta}-sheets and intervening loops, with single monomers spanning the ordered fibril core. Each monomer shares an N-terminal steric zipper, three major {beta}-arches, and an overall V-shape, but the details of these and other conformational features differ markedly. Thus, variations in shared conformational motifs within a parallel in-register {beta}-stack fibril architecture provide a structural basis for prion strain differentiation within a single host genotype.

biophysics↗

bioRxiv2022

The extracellular matrix protein fibronectin modulates metanephric kidney development

Complex interactions of the branching ureteric bud and surrounding mesenchymal cells during metanephric kidney development determine the final number of nephrons. Alterations that result in impaired nephron endowment predispose to arterial hypertension and chronic kidney disease. In the kidney, extracellular matrix (ECM) proteins are usually regarded as acellular scaffolds or as the common histological end-point of chronic kidney diseases. Only little is known about their physiological role in kidney development. The ECM protein fibronectin is expressed at early time points of kidney growth. Therefore, we were interested in the characterization of its expression and role in kidney development. In mouse, fibronectin was expressed during all stages of kidney development with significant changes over time. At embryonic day (E) 12.0 and E13.5 fibronectin lined the ureteric bud epithelium, which was less pronounced at E16.5 and then switched to a glomerular expression in the postnatal and adult kidneys. Similar results were obtained in human kidneys. Deletion of fibronectin at E13.5 in cultured metanephric mouse kidneys resulted in reduced kidney sizes, impaired branching morphogenesis and decreased glomerulogenesis. In line with these findings, fibronectin deletion led to reduced cell proliferation of the branching epithelial cells. Fibronectin colocalized with alpha8 integrin and fibronectin loss caused a reduction in alpha8 integrin-dependent formation of glial cell line-derived factor and expression of Wnt11, both of which are essentially involved in promoting ureteric bud branching. In conclusion, the ECM protein fibronectin acts as a regulator of metanephric kidney development and is a determinant of nephron number.

developmental biology↗

bioRxiv2021

Structure of anchorless RML prion reveals motif variation between strains

Little is known about the structural basis of prion strains. Here we provide a high (3.0 [A]) resolution cryo-electron microscopy-based structure of brain-derived fibrils of the mouse anchorless RML scrapie strain which, like the recently determined hamster 263K strain, has a parallel in-register {beta}-sheet-based core. However, detailed comparisons reveal that variations in shared structural motifs provide a basis for prion strain determination. One-sentence summaryCryo-electron microscopy reveals a near-atomic structure of an infectious, brain-derived murine prion fibril and strain differences.

biochemistry↗

bioRxiv2021

Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing

Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. We find that no single method is best for all cases. Instead, the optimal storage and extraction methods vary by taxa, by tissue, and by down-stream application. Therefore, we provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for Phase 1 of the Vertebrate Genomes Project (VGP), whose ultimate mission is to generate chromosome-level reference genome assemblies of all [~]70,000 extant vertebrate species.

genomics↗

bioRxiv2021

Structure of an infectious mammalian prion

Classical mammalian prions are assemblies of prion protein molecules that are extraordinarily transmissible, with a microgram of protein containing up to 108 lethal doses of infectivity1,2. Unlike most other pathologic and amyloidogenic proteins, prions typically contain glycolipid anchors 3 and abundant asparagine-linked glycans4-6. The infectious nature, complexity, and biophysical properties of prions have complicated structural analyses and stymied any prior elucidation of 3D conformation at the polypeptide backbone level7. Here we have determined the structure of the core of a fully infectious, brain-derived prion by cryo-electron microscopy with [~]3.1 [A] resolution. The purified prions are amyloid fibrils comprised of monomers assembled with parallel in-register intermolecular beta sheets and connecting chains. Residues [~]95-227 of each monomer provide one rung of the ordered fibril core, with the glycans and glycolipid anchor projecting from the lateral surfaces of the fibril. The fibril ends, where prion growth occurs, are formed by single monomers in an extended serpentine combination of {beta}- arches, a Greek key, and loops that presumably template the refolding of incoming monomers. Our results describe an atomic model to underpin detailed molecular hypotheses of how pathologic prion proteins can propagate as infectious agents, and how such propagation and associated pathogenesis might be impeded.

biochemistry↗