Biology subjects

Faber, J.

Publications and source records attributed to Faber, J..

18 recordsLinked to original sources

bioRxiv2026

Tuning the mechanical properties of polymer-based surrogate materials for articular cartilage and vocal fold repair

The macroscopic biomechanical characteristics of soft and ultrasoft tissues, such as articular cartilage and vocal folds, significantly determine their physiological function. Treatments of widespread tissue degradations due to osteoarthritis in the knee or vocal fold impairment remain an unresolved challenge. For the design of implants for tissue repair after injury or disease, it is key to thoroughly understand the unique biomechanical properties of native tissues and potential substitute materials. We use multimodal mechanical testing methods combined with hyperelastic nonlinear continuum mechanics modeling, and finite element simulations to determine the macroscopic behavior of surrogate materials for human articular cartilage in the knee and human vocal folds. Our cyclic loading experiments reveal qualitative similarities for both tissues and their surrogates, including a nonlinear stress-strain behavior, hysteresis, and conditioning. We demonstrate the tunability of biomimetic and biosimilar stiffnesses of synthetic articular cartilage and vocal fold surrogates through tissue-specific process-material combinations. Our results demonstrate the feasibility of synthetic metamaterials in replicating essential passive biomechanical functions with great potential for future treatment options.

bioengineering↗

bioRxiv2025

Distortion rules: audibility creation in the mosquito ear

Hearing begins when ears convert sound into neuronal excitation. The hearing organs of male Anopheles mosquitoes rank amongst the most sensitive ears evolved. Males use them to detect faint female flight tones within noisy mating swarms, but female flight tones largely lie above the males hearing range. We report a mechanism by which inaudible higher-frequency primary tones become audible through intrinsically generated, lower-frequency distortion tones. Distortion-evoked responses show [~]10-times greater sensitivity and 45% higher temporal precision than those of same-frequency primary tones. Moreover, self-sustained oscillations of the males ear dramatically reshape auditory frequency tuning and neuronal recruitment. By one mechanism, mosquito ears thus create audible signals and isolate these from the most salient frequencies of background noise. In audiology, distortions are used for diagnostics; their biological relevance, however, is unknown. Our results suggest that distortions are not mere by-products of the auditory process, but integral to its signaling logic.

neuroscience↗

bioRxiv2025

A Core Pattern of Cerebellar and Brainstem Degeneration and Reduced Cerebrocerebellar Structural Covariance in Spinocerebellar Ataxia Type 3 (SCA3): MRI Volumetrics from ENIGMA-Ataxia

ObjectiveSpinocerebellar ataxia type 3 (SCA3) is a rare, inherited neurodegenerative disease. Here, we profile the spatial spread of atrophy across the whole brain, determine whether brain degeneration preferentially maps onto specific functional networks, and investigate the relationship between cerebellar and cerebral anatomical changes. MethodsWhole-brain grey and white matter (GM and WM) voxel-based morphometry was performed on 408 individuals with SCA3 (82 pre-ataxic) and 293 controls. The SCA3 cohort was stratified by ataxia severity to investigate disease progression, with cerebellar GM atrophy mapped onto a task-based functional atlas. Volume was correlated with disease duration and intensity. Cerebrocerebellar volumetric covariance was assessed to determine whether atrophy was coupled between infra- and supratentorial regions. ResultsThe pattern of atrophy is spatially consistent but progressive in magnitude across the disease course. The greatest atrophy was found in the pons, cerebellar WM, and cerebellar peduncles; correlations with disease severity and duration were also strongest in these regions. Cerebellar GM atrophy was greatest in functional regions associated with motor execution and planning, attention, and emotional processing. Sparse cerebral cortical atrophy appears only in the most severe disease subgroup, while striatal atrophy begins in the earliest stages. Reduced cerebrocerebellar structural covariance is observed in SCA3 participants versus controls. InterpretationWhile cerebellar and brainstem atrophy become more severe, the pattern of atrophy remains largely consistent as SCA3 progresses. Cerebellar GM degeneration occurs in regions associated with motor, cognitive, and affective control, in line with clinical presentation. Cerebellar atrophy is not directly mirrored by cerebral changes.

neuroscience↗

bioRxiv2025

Integration of customizable 3D printed mixing printheads for controlled and tuneable material and stiffness gradient fabrication with high cell viability in extrusion-based bioprinting

The fabrication of native tissue-like structures with gradual transitions in material properties, cell types and growth factors remains a major challenge in biofabrication. Particularly the complex hierarchical organization, present in living tissues, has to be mimicked as close as possible for the created models to fulfil the desired function. However, the fabrication of gradual structures incorporating several materials ensuring high cell survival and subsequent unaffected tissue maturation is highly challenging. To get a step closer to the goal of generating tissue models containing controlled gradient structures, here we show a novel approach combining extrusion- based 3D bioprinting with static mixing, using self-designed Digital Light Processing (DLP) printed mixing units to fabricate defined gradual structures. Two passive mixing geometries, sinusoidal and obstacle-based, are designed and fabricated and benchmarked against commercially available static mixers. The mixing performance is assessed pixelwise using dyed alginate solutions that are extruded through the mixers using an adapted 3D printer equipped with cavity pumps. The obstacle structure exhibits the highest mixing rate compared to the sinusoidal design and commercially available static mixers. Beyond mixing efficiency, the biological compatibility of the systems is assessed by evaluating the viability of U87 and NIH3T3 cells after extrusion. Two distinct polymer solutions of differing viscosities, composed of allyl-modified gelatin (gelAGE), polyethylene glycol dithiol (PEG-2-SH), and Matrigel, are extruded through the static mixer, revealing significantly higher cell viability in the self-designed printheads compared to commercial mixers. Subsequently, graded structures mimicking the mechanical profile of native brain tissue are fabricated and mechanically characterized using nanoindentation, confirming the successful generation of continuous stiffness gradients. In summary, this study demonstrates that combining extrusion-based 3D printing with customizable mixing units enables the controlled fabrication of tissue-like gradient structures with enhanced mixing rates and cell viability. The design flexibility and rapid fabrication of DLP-printed printheads enable the adaptation to specific tissue requirements, providing a robust platform for future developments in biofabrication and tissue engineering. This work serves as foundation for the creation of increasingly complex and functional tissue models.

bioengineering↗

bioRxiv2025

Predicting GD2 expression across cancer types by the integration of pathway topology and transcriptome data

The disialoganglioside GD2 is a key cancer therapy target due to its overexpression in several cancer types and limited expression in normal tissues. We developed a computational framework integrating reaction activity scores derived from transcriptomic data with glycosphingolipid biosynthesis pathway to predict GD2 expression. We labeled specific reactions as GD2-promoting or -mitigating, and used their cumulative activity as features to distinguish neuroblastoma from normal tissue. Predicted GD2 scores were validated by comparing them with literature-reported values and by assessing GD2 expression through flow cytometry in clear cell sarcoma of the kidney, which express GD2 at high level according to the GD2 scores. GD2 expression heterogeneity across cancer subtypes indicated patient subgroups potentially suitable for targeted therapy, and a role of B4GALNT1 amplification as a GD2 promoting factor. We offer our approach via the R package GD2Viz including also an interactive Shiny application and enable an enhanced processing of custom datasets.

cancer biology↗

bioRxiv2024

Inhibition of nitric oxide synthase transforms carotid occlusion-mediated benign oligemia into de novo large cerebral infarction

It remains unclear why unilateral proximal carotid artery occlusion (UCAO) causes benign oligemia, without progressing to cerebral infarction, in mice, yet leads to a wide variety of outcomes (ranging from asymptomatic to death) in humans. We hypothesized that inhibition of NOS both transforms UCAO-mediated oligemia into full infarction and expands pre-existing infarction. In support, intraperitoneal administration of N{omega}-nitro-L-arginine methyl ester (L-NAME) followed by UCAO induced large-arterial infarction in mice, unlike UCAO alone. Six-hour laser-speckle-contrast imaging detected spreading ischemia in mice with infarction as assessed at 24h. In agreement with vasoconstriction/microthrombus formation shown by intravital microscopy, the NO-donor, molsidomine and the endothelial-NOS- activating antiplatelet, cilostazol, attenuated or prevented progression to infarction. Moreover, UCAO without L-NAME caused infarction in mice with hyperglycemia and hyperlipidemia, which, in turn, were associated with greater symmetric dimethylarginine (SDMA) levels. Further, increased levels of glucose and cholesterol associated with significantly larger infarct volumes in 438 consecutive patients with UCAO-mediated infarction. Lastly, Mendelian randomization identified a causative role of NOS inhibition, particularly in elevated SDMA concentration, in ischemic stroke risk. Therefore, NOS activity is a key factor determining the fate of hypoperfused brain following acute carotid occlusion, where SDMA could be a potential risk predictor.

neuroscience↗

bioRxiv2024

Small non-coding RNA content in plasma-derived extracellular vesicles distinguish ataxic SCA3 mutation carriers from pre-ataxic and control subjects

Spinocerebellar ataxia type 3 (SCA3), a neurodegenerative disorder caused by a CAG expansion in the ATXN3 gene, is the most common spinocerebellar ataxia subtype worldwide. Currently, there is no therapy to stop or prevent disease progression. Promising therapeutic strategies are emerging, but their translation into clinical practice requires sensitive and reliable biomarkers. Blood circulating extracellular vesicles constitute a promising source of biomarkers with potential to track alterations of the central nervous system due to their ability to cross the blood brain barrier. Here, we perform sequencing analysis of small RNAs from plasma-derived extracellular vesicles from SCA3 mutation carriers (10 pre-ataxic and 10 ataxic) and 12 control subjects to identify potential RNA biomarker candidates for this disease. Data showed that plasma-derived extracellular vesicles from ataxic SCA3 mutation carriers are enriched in mitochondrial, nuclear, and nucleolar RNA biotypes compared to pre-ataxic and control subjects. Moreover, ataxic mutation carriers could be discriminated from control and pre-ataxic subjects based on the miRNAs or piRNAs content, but not tRNA. Furthermore, we identified a subset of differentially expressed miRNAs and piRNAs that clearly differentiate ataxic mutation carriers from pre-ataxic and control subjects. These findings open new avenues for further investigation on the role of these RNAs in the pathogenesis of SCA3 and their potential as biomarkers for this disease.

neuroscience↗

bioRxiv2023

Blood and cerebellar abundance of ATXN3 splice variants in spinocerebellar ataxia type 3/Machado-Joseph disease

BackgroundSpinocerebellar ataxia type 3 (SCA3)/Machado-Joseph disease (MJD) is an autosomal dominant polyglutamine disease. SCA3/MJD causative gene, ATXN3, is known to undergo alternative splicing (AS) and 54 transcripts are currently annotated. Differences in the toxicity of ataxin-3 protein isoforms, harbouring on its C-terminus two or three ubiquitin interacting motifs (UIMs), were previously uncovered, raising the hypothesis that specific ATXN3 splice variants play key roles in promoting the selective toxicity displayed in SCA3/MJD. MethodsUsing RNA-seq datasets we identified and determined the abundance of annotated ATXN3 transcripts in blood (n=60) and cerebellum (n=12) of SCA3/MJD subjects and controls. ResultsGlobally, the number and the abundance of individual ATXN3 transcripts were higher in the cerebellum than in the blood. While the most abundant transcript in the cerebellum was a protein with a coding sequence not defined of unknown function (ATXN3-208), the transcript with the highest abundance in blood was the reference transcript (ATXN3-251) which translates into an ataxin-3 isoform harboring three UIMs. Noteworthy, the abundance of ATXN3-251 and ATXN3-214, two out of the four transcripts that encode full-length ataxin-3 protein isoforms but differ in the C-terminus were strongly related with tissue expression specificity: ATXN3-251 (3UIM) was expressed in blood 50-fold more than in cerebellum, whereas ATXN3-214 (2UIM) was expressed in the cerebellum 20-fold more than in blood. ConclusionsThese findings provide new insights into the elucidation of ATXN3 AS in different tissues, contributing for a better understanding of SCA3/MJD pathogenesis and providing information for the development of future effective ATXN3 mRNA-lowering therapies.

genetics↗

bioRxiv2023

Frequency-coded patterns of sympathetic vasomotor activity are differentially evoked by the paraventricular nucleus of the hypothalamus in the Goldblatt hypertension model

The activation of specific brain areas involved in regulating the vasomotor sympathetic activity can lead to distinct effects in the postganglionic nerves in both physiological and pathological conditions, suggesting that the sympathetic vasomotor activity is differentially coded depending on the nerve outflow and the target organs. Previous studies investigating such patterns have mostly focused on the global energy of the signal. However, recent evidence has suggested that relevant information is coded in the power distribution along the frequency range. Disturbing the sympathoexcitatory vasomotor tone in the paraventricular nucleus of the hypothalamus (PVN) allows to investigate the sympathetic nerve activity in overloaded conditions in both hypertensive and control animals. By disinhibiting the PVN through the microinjection of bicuculline, an antagonist of {gamma}-aminobutyric acid type A (GABAa) receptors, in the Goldblatt (2K1C) rat model of hypertension we addressed the territorially differential changes in the frequency parameters of the renal and splanchnic sympathetic nerve activity (rSNA and sSNA, respectively). We also tested the effect of the systemic administration of losartan, an antagonist of the angiotensin II type 1 receptors (AT1), in the attenuation of the increased rSNA and sSNA in 2K1C rats, once these changes are reported to be dependent on the AT1 activation in the Goldblatt model. Our results revealed that each nerve activity presents its own electrophysiological pattern of frequency-coded rhythm in each group, in basal condition and after bicuculline microinjection, but with no significant differences regarding total power comparison among groups. Additionally, the 2K1C animals treated with losartan showed no decrease in the hypertensive response triggered by the GABAa antagonism when compared to the non-treated 2K1C group. However, their spectral patterns of sympathetic nerve activity were different from the other two groups, suggesting that the systemic blockade of AT1 receptors does not totally recover the basal levels of neither the autonomic symptoms nor the electrophysiological patterns in the Goldblatt model, but act on their spectral frequency distribution. These results suggest that the differential responses evoked by the PVN were preferentially coded in frequency of vasomotor sympathetic responses, indicating that the PVN distinctly modulated each rhythmic activity. Financial Support - FAPESP (2019/25295-0)

neuroscience↗

bioRxiv2023

Epileptic seizure suppression: a computational approach for identification and control using real data

Epilepsy affects millions of people worldwide every year and remains an open subject for research. Current development on this field has focused on obtaining computational models to better understand its triggering mechanisms, attain realistic descriptions and study seizure suppression. Controllers have been successfully applied to mitigate epileptiform activity in dynamic models written in state-space notation, whose applicability is, however, restricted to signatures that are accurately described by them. Alternatively, autoregressive modeling (AR), a typical data-driven tool related to system identification (SI), can be directly applied to signals to generate more realistic models, and since it is inherently convertible into state-space, it can thus be used for the artificial reconstruction and attenuation of seizures as well. Considering this, the first objective of this work is to propose an SI approach using AR models to describe real epileptiform activity. The second objective is to provide a strategy for reconstructing and mitigating such activity artificially, considering non-hybrid and hybrid controllers - designed from ictal and interictal events, respectively. The results show that AR models of relatively low order represent epileptiform activities fairly well and both controllers are effective in attenuating the undesired activity while simultaneously driving the signal to an interictal stage. These findings may lead to customized models based on each signal, brain region or patient, from which it is possible to better define shape, frequency and duration of external stimuli that are necessary to attenuate seizures. Author summaryEpilepsy is perhaps one of the most studied brain disorders and it is still not sufficiently well understood. The use of computational models is useful in this case since several simulations can be run using them, such that experience and insight about seizures can be gained without necessarily carrying out experiments. These models are usually designed with or without some knowledge about the brain region or phenomenon. Seizure attenuation approaches have been proposed for the first case, but they are limited to the type of seizure correctly described by the model. The present work proposes a similar procedure for the second one (where only the data are available and nothing else is assumed), which is regarded as more realistic due to its direct application on the signals and can lead to customized models for each activity, brain region or patient, defining important information such as the shape, frequency and duration of the external stimuli that must be applied to mitigate a seizure.

bioinformatics↗

bioRxiv2022

Phase of firing does not reflect temporal order in sequence memory of humans and recurrent neural networks

A prominent theory proposes that the temporal order of a sequence of items held in memory is reflected in ordered firing of neurons at different phases of theta oscillations 1. We probe this theory by directly measuring single neuron activity (1420 neurons) and local field potentials (LFP, 921 channels) in the medial temporal lobe of 16 epilepsy patients performing a working memory task for temporal order. We observe theta oscillations and preferential firing of single neurons at theta phase during memory maintenance. We find that - depending on memory performance - phase of firing is related to item position within a sequence. However, in contrast to the theory, phase order did not match item order. To investigate underlying mechanisms, we subsequently trained recurrent neural networks (RNNs) to perform an analogous task. Similar to recorded neural activity, we show that RNNs generate theta oscillations during memory maintenance. Importantly, model neurons exhibit theta phase-dependent firing related to item position, where phase of firing again did not match item order. Instead, we observed a mechanistic link between phase order, stimulus timing and oscillation frequency - a relationship we subsequently confirmed in our neural recordings. Taken together, in both biological and artificial neural networks we provide validating evidence for the role of phase-of-firing in memory processing while at the same time challenging a long-held theory about the functional role of spiking and oscillations in sequence memory.

neuroscience↗

bioRxiv2022

A key role of the hippocampal P3 in the attentional blink

The attentional blink (AB) refers to an impaired identification of target stimuli (T2), which are presented shortly after a prior target (T1) within a rapid serial visual presentation (RSVP) stream. It has been suggested that the AB is related to a failed transfer of T2 into working memory and that hippocampus (HC) and entorhinal (EC) cortex are regions crucial for this transfer. Since the event-related P3 component has been linked to inhibitory processes, we hypothesized that the hippocampal P3 elicited by T1 may impact on T2 processing within HC and EC. To test this hypothesis, we reanalyzed microwire data from 21 patients, who performed an RSVP task, during intracranial recordings for epilepsy surgery assessment (Reber et al., 2017). We identified T1-related hippocampal P3 components in the local field potentials (LFPs) and determined the temporal onset of T2 processing in HC/EC based on single-unit response onset activity. In accordance with our hypothesis, T1-related single-trial P3 amplitudes at the onset of T2 processing were clearly larger for unseen compared to seen T2-stimuli. Moreover, increased T1-related single-trial P3 peak latencies were found for T2[unseen] versus T2[seen] trials in case of lags 1 to 3, which was in line with our predictions. In conclusion, our findings support inhibition models of the AB and indicate that the hippocampal P3 elicited by T1 plays a central role in the AB.

neuroscience↗

bioRxiv2021

Self-organization of in vitro neuronal assemblies drives to complex network topology

Activity-dependent self-organization plays an important role in the formation of specific and stereotyped connectivity patterns in neural circuits. By combining neuronal cultures, tools with approaches from network neuroscience and information theory, we can study how complex network topology emerges from local neuronal interactions. We constructed effective connectivity networks using a transfer entropy analysis of electrophysiological signals recorded from rat embryo dissociated hippocampal neuron cultures between 6 and 35 days in vitro to investigate how the neuronal network topology evolves during maturation. The methodology for constructing the networks considered the synapse delay and addressed the influence of firing rate and population bursts as well as spurious effects on the inference of connections. We found that the number of links in the networks grew over the course of development, shifting from a segregated to a more integrated architecture. As part of this progression, three significant aspects of complex network topology emerged. In agreement with previous in silico and in vitro studies, a small-world architecture was detected, largely due to strong clustering among neurons. Additionally, the networks developed in a modular community topology, with most modules comprising nearby neurons. Finally, highly active neurons acquired topological characteristics that made them important nodes to the network and integrators of communities. These findings leverage new insights into how neuronal effective network topology relates to neuronal assembly self-organization mechanisms.

neuroscience↗

bioRxiv2021

High-throughput mutagenesis identifies mutations and RNA binding proteins controlling CD19 splicing and CART-19 therapy resistance

During CART-19 immunotherapy for B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the cognate CD19 epitope. Since epitope loss can be caused by aberrant CD19 exon 2 processing, we herein investigate the regulatory code that controls CD19 splicing. We combine high-throughput mutagenesis with mathematical modelling to quantitatively disentangle the effects of all mutations in the region comprising CD19 exons 1-3. Thereupon, we identify ~200 single point mutations that alter CD19 splicing and thus could predispose B-ALL patients to CART-19 resistance. Furthermore, we report almost 100 previously unknown splice isoforms that emerge from cryptic splice sites and likely encode non-functional CD19 proteins. We further identify cis-regulatory elements and trans-acting RNA-binding proteins that control CD19 splicing (e.g., PTBP1 and SF3B4) and validate that loss of these factors leads to enhanced CD19 mis-splicing. Our dataset represents a comprehensive resource for potential prognostic factors predicting success of CART-19 therapy. HighlightsO_LIMutations in relapsed CART-19 patients lead to CD19 mis-splicing C_LIO_LIHigh-throughput mutagenesis uncovers ~200 single point mutations with a potential role in CART-19 therapy resistance C_LIO_LIMany mutations generate non-functional CD19 proteins by activating cryptic splice sites C_LIO_LIRNA-binding proteins such as PTBP1 are key to the expression of properly spliced, CART-19 immunotherapy-sensitive isoforms C_LI

molecular biology↗

bioRxiv2020

Dynamics of mechanically coupled hair-cell bundles of the inner ear

The high sensitivity and effective frequency discrimination of sound detection performed by the auditory system rely on the dynamics of a system of hair cells. In the inner ear, these acoustic receptors are primarily attached to an overlying structure which provides mechanical coupling between the hair bundles. While the dynamics of individual hair bundles have been extensively investigated, the influence of mechanical coupling on the motility of the system of bundles remains underdetermined. We developed a technique of mechanically coupling two active hair bundles, enabling us to probe the dynamics of the coupled system experimentally. We demonstrated that the coupling could enhance the coherence of hair bundles spontaneous oscillation as well as their phase-locked response to sinusoidal stimuli, at the calcium concentration in the surrounding fluid near the physiological level. The empirical data were consistent with numerical results from a model of two coupled nonisochronous oscillators, each displaying a supercritical Hopf bifurcation. The model revealed that weak coupling can poise the system of unstable oscillators closer to the bifurcation by a shift in the critical point. In addition, the dynamics of strongly coupled oscillators far from criticality suggested that individual hair bundles may be regarded as nonisochronous oscillators. An optimal degree of nonisochronicity was required for the observed tuning behavior in the coherence of autonomous motion of the coupled system. STATEMENT OF SIGNIFICANCEHair cells of the inner ear transduce acoustic energy into electrical signals via a deflection of hair bundles. Unlike a passive mechanical antenna, a free-standing hair bundle behaves as an active oscillator that can sustain autonomous oscillations, as well as amplify a low-level stimulus. Hair bundles under physiological conditions are elastically coupled to each other via an extracellular matrix. Therefore, the dynamics of coupled nonlinear oscillators underlie the performance of the peripheral auditory system. Despite extensive theoretical investigations, there are limited experimental evidence that support the significance of coupling on hair bundle motility. We develop a technique to mechanically couple hair bundles and demonstrate the benefits of coupling on hair bundle spontaneous motility.

biophysics↗

bioRxiv2020

The MNK1/2-eIF4E axis contributes to phenotype switching, melanoma progression, and resistance to immunotherapy.

Melanomas commonly undergo a phenotype switch, from a proliferative to an invasive state. Melanoma plasticity exhibited as phenotype switching contributes to immunotherapy resistance, however the mechanisms are not completely understood and thus therapeutically unexploited. Here, using a transgenic melanoma mouse model, we demonstrated a critical role of the MNK1/2-eIF4E axis in melanoma plasticity and resistance to immunotherapy. We showed that phospho-eIF4E deficient murine melanomas express high levels of melanocytic antigens, with similar results verified in patient melanomas. Mechanistically, we identified that phospho-eIF4E controls the translation of NGFR, a critical effector of phenotype switching. In patients with melanoma, the expression of MKNK1, the kinase for eIF4E, positively correlated with markers of immune exhaustion. Genetic ablation of phospho-eIF4E reprogrammed the immunosuppressive microenvironment, exemplified by lowered production of inflammatory factors and increased CD8+ T cell infiltrates. Blocking phospho-eIF4E, using MNK1/2 inhibitors, offers a new strategy to inhibit melanoma plasticity and improve the survival response to anti-PD-1 immunotherapy.

cancer biology↗

bioRxiv2020

Content and performance of the MiniMUGA genotyping array, a new tool to improve rigor and reproducibility in mouse research

The laboratory mouse is the most widely used animal model for biomedical research, due in part to its well annotated genome, wealth of genetic resources and the ability to precisely manipulate its genome. Despite the importance of genetics for mouse research, genetic quality control (QC) is not standardized, in part due to the lack of cost effective, informative and robust platforms. Genotyping arrays are standard tools for mouse research and remain an attractive alternative even in the era of high-throughput whole genome sequencing. Here we describe the content and performance of a new Mouse Universal Genotyping Array (MUGA). MiniMUGA, an array-based genetic QC platform with over 11,000 probes. In addition to robust discrimination between most classical and wild-derived laboratory strains, MiniMUGA was designed to contain features not available in other platforms: 1) chromosomal sex determination, 2) discrimination between substrains from multiple commercial vendors, 3) diagnostic SNPs for popular laboratory strains, 4) detection of constructs used in genetically engineered mice, and 5) an easy to interpret report summarizing these results. In-depth annotation of all probes should facilitate custom analyses by individual researchers. To determine the performance of MiniMUGA we genotyped 6,899 samples from a wide variety of genetic backgrounds. The performance of MiniMUGA compares favorably with three previous iterations of the MUGA family of arrays both in discrimination capabilities and robustness. We have generated publicly available consensus genotypes for 241 inbred strains including classical, wild-derived and recombinant inbred lines. Here we also report the detection of a substantial number of XO and XXY individuals across a variety of sample types, the extension of the utility of reduced complexity crosses to genetic backgrounds other than C57BL/6, and the robust detection of 17 genetic constructs. There is preliminary but striking evidence that the array can be used to identify both partial sex chromosome duplication and mosaicism, and that diagnostic SNPs can be used to determine how long inbred mice have been bred independently from the main stock for a significant action of the genotyped inbred samples. We conclude that MiniMUGA is a valuable platform for genetic QC and important new tool to the increase rigor and reproducibility of mouse research.

genetics↗

bioRxiv2018

Little variation in the morphology of the atria across 13 orders of birds

Mammals and birds acquired high performance hearts and endothermy during their independent evolution from amniotes with many reptile characters. A literature review shows that the variation in atrial morphology is greater in mammals than in ectothermic reptiles. We therefore hypothesized that the transition from ectothermy to endothermy associated with greater variation in cardiac structure. We tested the hypothesis in birds, by assessing the variation in 15 characters in hearts from 13 orders of birds. Hearts were assessed by gross morphology and histology, and we focused on the atria as they have multiple features that lend themselves to quantification. We found bird hearts to have multiple features in common with ectothermic reptiles (synapomorphies), for instance the presence of three sinus horns. Convergent features were shared with crocodylians and mammals, such as the cranial offset of the left atrioventricular junction. Other convergent features like the compact organization of the atrial walls were shared with mammals only. Sinus myocardium expressing Isl1 was node-like (Mallard), thickened (chicken), or anatomically indistinct from surrounding myocardium (Lesser redpoll). Some features were distinctively avian (apomorphies), including the presence of a left atrial antechamber, and the ventral merger of the left and right atrium, which was found in parrots and passerine birds. Most features, however, exhibited little variation. For instance, there were always three systemic veins and two pulmonary veins, whereas among mammals there are 2-3 and 1-7, respectively. Our findings suggest that the transition to high cardiac performance does not necessarily lead to greater variation in cardiac structure.

evolutionary biology↗