bluuebunny/crossref_metadata_2025 huggingface dataset:
Epigenetic variations are accompanying landmarks of freshwater adaptation in threespine sticklebacks
Authors: Golden Artemiy , Starshin Alexey , Mazur Alexandr , Mugue Nikolai , Kaplun Daria , Artemov Artem , Khrameeva Ekaterina , Prokhortchouk Egor
Published: August 2022

For evolutionary biology, the phenotypic consequences of epigenetic variations and their potential contribution to adaptation and diversification are pressing issues. Marine and freshwater sticklebacks represent an ideal model for studying both genetic and epigenetic components of phenotypic plasticity that allow fish to inhabit water with different salinity. Here, we applied single-cell genomics (scRNA-seq and scATAC-seq) and whole-genome bisulfite sequencing to characterize intercellular variability in transcription, the abundance of open chromatin regions, and CpG methylation level in gills of marine and freshwater stickleback morphs. We found little difference in overall transcriptional variance between the morphs but observed significant changes in chromatin openness variance. In addition, genomic divergence islands (DIs) coincided with regions of increased methylation entropy in freshwater fish. Moreover, analysis of transcription factor binding sites within DIs revealed that СTCF motifs around marker SNPs were significantly enriched within the region. Altogether, our data show that increased epigenetic variance accompanies the adaptation of marine sticklebacks to freshwater.
VIRify: an integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models
Authors: Rangel-Pineros Guillermo , Almeida Alexandre , Beracochea Martin , Sakharova Ekaterina , Marz Manja , Muñoz Alejandro Reyes , Hölzer Martin , Finn Robert D.
Published: August 2022

The study of viral communities has revealed the enormous diversity and impact these biological entities have on a range of different ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterization of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterization of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities and a large metagenomics study. The results showed that VIRify was able to identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an accuracy of at least 95.5%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.
Age-associated reduction of nuclear shape dynamics in excitatory neurons of the visual cortex
Authors: Frey Tanita , Murakami Tomonari , Maki Koichiro , Kawaue Takumi , Sugai Ayaka , Nakazawa Naotaka , Adachi Taiji , Kengaku Mineko , Ohki Kenichi , Gotoh Yukiko , Kishi Yusuke
Published: August 2022

Neurons decline in their functionality over time, and age-related neuronal alterations are associated with phenotypes of neurodegenerative diseases. In non-neural tissues, an infolded nuclear shape has been proposed as a hallmark of aged cells and neurons with infolded nuclei have also been reported to be associated with neuronal activity. Here, we perform time-lapse imaging in the visual cortex ofNex-Cre;SUN1-GFPmice. Nuclear infolding was observed within 15 minutes of stimulation in young nuclei, while the aged nuclei were already infolded pre-stimulation and showed reduced dynamics of the morphology. In young nuclei, the depletion of the stimuli restored the nucleus to a spherical shape and reduced the dynamic behavior, suggesting that nuclear infolding is a reversible process. We also found the aged nucleus to be stiffer than the young one, further relating to the age-associated loss of nuclear shape dynamics. We reveal temporal changes in the nuclear shape upon external stimulation and observe that these morphological dynamics decrease with age.
Growth hormone remodels the 3D-structure of the mitochondria of inflammatory macrophages and promotes metabolic reprogramming
Authors: Palacios Blanca Soler , Villares Ricardo , Lucas Pilar , Miguel-Rodríguez-Frade José , Cayuela Ana , Piccirillo Jonathan G , Lombardía Manuel , Gestoso David Delgado , Risco Cristina , Corrales Fernando , Sorzano Carlos Oscar S. , Martínez Nuria , Conesa José Javier , Iborra Francisco J. , Mellado Mario
Published: August 2022

Macrophages are a heterogeneous population of innate immune cells that support tissue homeostasis through their involvement in tissue development and repair, and pathogen defense. Emerging data reveal that metabolism may control macrophage polarization and function and, conversely, phenotypic polarization may drive metabolic reprogramming. Here, using biochemical analysis, correlative cryogenic fluorescence microscopy and cryo-focused ion-beam scanning electron microscopy, we demonstrate that growth hormone (GH) functions as a metabolic modulator to reprogram inflammatory GM-CSF-primed monocyte-derived macrophages (GM-MØ). We found that exogenous treatment of GM-MØ with recombinant human GH suppressed glycolysis, lactate production and non-mitochondrial respiration, and enhanced mitochondrial oxidative phosphorylation. Likewise, GH treatment augmented mitochondrial volume and altered mitochondrial dynamics, including the remodeling of the inner membrane to increase the density of cristae. Our data demonstrate that GH likely serves a modulatory role in the metabolism of inflammatory macrophages and suggest that metabolic reprogramming of macrophages should be considered a new target to intervene in multiple inflammatory diseases.
No evidence for cognitive impairment in an experimental rat model of knee osteoarthritis and associated chronic pain
Authors: Gonçalves Sara , Hathway Gareth J. , Woodhams Stephen G. , Chapman Victoria , Bast Tobias
Published: August 2022

Although chronic pain states have been associated with impaired cognitive functions, including memory and cognitive flexibility, the cognitive effects of osteoarthritis (OA) pain remain to be clarified. The aim of this study was to measure cognitive function in the mono-iodoacetate (MIA) rat model of chronic OA-like knee pain.

We used young adult male Lister hooded rats, which are well suited for cognitive testing. Rats received either a unilateral knee injection of MIA (3mg/50µL) or saline as control. Joint pain at rest was assessed for up to 12 weeks using weight-bearing asymmetry, and referred pain at a distal site using determination of hindpaw withdrawal thresholds (PWT). The watermaze delayed-matching-to-place (DMP) test of rapid place learning, novel object recognition (NOR) memory assay and an operant response-shift and -reversal task were used to measure memory and behavioural flexibility. Open field locomotor activity, startle response, and prepulse inhibition (PPI) were also measured for comparison.

MIA-injected rats showed markedly reduced weight-bearing on the injured limb, as well as pronounced cartilage damage and synovitis, but interestingly no changes in PWT. Rearing was reduced, but otherwise locomotor activity was normal and no changes in startle and PPI were detected. MIA-injected rats had intact watermaze DMP performance, suggesting no substantial change in hippocampal function, and there were no changes in NOR memory or performance on the operant task of behavioural flexibility. Our finding that OA-like pain does not alter hippocampal function, unlike other chronic pain conditions, is consistent with human neuroimaging findings.
Bayesian inference reveals a complex evolutionary history of belemnites
Authors: Stevens Kevin , Pohle Alexander , Hoffmann René , Immenhauser Adrian
Published: August 2022

Belemnites are an extinct group of Mesozoic coleoid cephalopods, common in Jurassic and Cretaceous marine sedimentary rocks. Despite their significance, their total group phylogeny has rarely been considered in recent decades. In contrast, most researchers restricted the assignment of families to one of the two usually recognized subgroups, the Belemnitina and the Belemnopseina. As for many fossil cephalopods, researchers have been reluctant to employ modern phylogenetic methods to illuminate belemnites’ evolutionary history.

To overcome the “dead end” of belemnite systematics, we performed the first tip-dated Bayesian analysis of belemnite phylogeny. In our analysis, the Aulacoceratida are found as the monophyletic sister group to belemnites. The Sinobelemnitidae are resolved as paraphyletic and fall outside the Belemnitina and Belemnopseina, which make up the remaining belemnites. Belemnitina is restricted to Jurassic species with generally no or apical furrows. Holcobelidae are the earliest branching Belemnopseina. Cylindroteuthidssensu lato(including Oxyteuthidae) are nested within Belemnopseina, contrary to the common hypothesis placing them within the Belemnitina. Duvaliidae and Dicoelitidae are recovered as members of the Belemnopseina, but their precise relationship has to be evaluated based on more taxa and additional characters. We introduce the well-supported unranked clade Pseudoalveolata, which includes Dimitobelidae, Belemnitellidae, and members of the paraphyletic “Belemnopseidae”.

The phylogeny presented here, based on reproducible and quantitative methods, contrasts with the usually applied authoritative “stratophenetic” approach to belemnite systematics, based on the overemphasis of single characters. This result is considered the basis for future studies on belemnite phylogeny, allowing for a rigorous testing of evolutionary hypotheses.

PLAIN LANGUAGE SUMMARY

Belemnites were common extinct cephalopods that were closely related to today’s squid and cuttlefish. The most common fossil remains of belemnites are bullet-shaped calcitic “cones” (rostrum) that cover their internal shells. Belemnites’ evolutionary history is not well known. Our study revealed an evolutionary tree of belemnites based on the statistical analysis of morphological features of the rostrum and calibrated to the known geological ages of the studied belemnite species. This approach was for the first time applied to belemnites and changed several aspects that were believed about their evolution.
Immunohistochemical diagnosis of Trypanosoma vivax in experimentally infected sheep tissues
Authors: do Nascimento Luiz Flávio Nepomuceno , de Cristo Thierry Grima , Franco Cintia , Salbego Fabiano Zanini , Tamanho Renato Batista , Casagrande Renata Assis , Bittar Joely Ferreira Figueiredo , Miletti Luiz Claudio
Published: August 2022

Trypanosoma vivax is one of the main species responsible for animal African trypanosomiasis in West Africa and has a marked economic impact on livestock in Sub-Saharan Africa and South America endemic countries. In this work, T. vivax was demonstrated by immunohistochemical technique in formalin-fixed paraffin-embedded in tissues of experimentally infected sheep using polyclonal antibodies produced against formalin-fixed trypomastigotes. T. vivax was observed within multiple small and medium-size vessels from multiple organs, including the liver and kidneys. The immunostaining was evidenced in an intense cherry red. This is the first immunohistochemical experiment that shows T. vivax in fixed tissues.
Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA cluster biogenesis in mosquitoes
Authors: Qu Jieqiong , Betting Valerie , van Iterson Ruben , Kwaschik Florence M. , van Rij Ronald P.
Published: August 2022

The piRNA pathway in mosquitoes differs substantially from other model organisms, with an expanded PIWI gene family and functions in antiviral defense. Here, we defined core piRNA clusters as small RNA source loci that showed ubiquitous expression in both somatic and germline tissues. These core piRNA clusters were enriched for non-retroviral endogenous viral elements (nrEVEs) in antisense orientation and depended on key biogenesis factors, Nxf1, Veneno, Tejas, Yb, and Shutdown. Combined transcriptome and chromatin state analyses identified transcriptional readthrough as a conserved mechanism for piRNA cluster biogenesis in Aedes aegypti, Aedes albopictus, Culex quinquefasciatus, and Anopheles gambiae. Comparative analyses between two Aedes mosquitoes suggested that piRNA clusters function as traps for nrEVEs, allowing adaptation to environmental challenges such as virus infection. Our systematic transcriptome and chromatin state analyses lay the foundation for studies of gene regulation, genome evolution and piRNA functions in these important vector species.

Graphical abstract

Highlights

Core piRNA clusters showed ubiquitous expression in both somatic and germline tissues in four vector mosquitoes.

Chromatin profiling identifies transcriptional readthrough as a conserved mechanism for piRNA biogenesis.

Biogenesis of cluster-derived piRNAs depends on key factors, Nxf1, Veneno, Tejas, Yb, and Shutdown.

piRNA clusters function as traps for viral elements downstream of conserved set of genes in Aedes mosquitoes
Multinucleation resets human macrophages for specialized functions at the expense of mononuclear phagocyte identity
Authors: Ahmadzadeh Kourosh , Pereira Marie , Vanoppen Margot , Bernaerts Eline , Ko Jeong-Hun , Mitera Tania , Maksoudian Christy , Manshian Bella B , Soenen Stefaan , Rose Carlos D , Matthys Patrick , Wouters Carine , Behmoaras Jacques
Published: August 2022

Macrophages undergo plasma membrane fusion and cell multinucleation to form multinucleated giant cells (MGCs) such as osteoclasts in bone, Langhans giant cells (LGCs) as part of granulomas or foreign-body giant cells (FBGCs) in reaction to exogenous material. While osteoclast multinucleation is a prerequisite for vertebrate bone homeostasis, the effector function resulting from LGC and FBGC multinucleation is less well-defined. More generally, how multinucleation per se contributes to functional specialization of mature mononuclear macrophages remains poorly understood in humans. Here, we integrated comparative transcriptomics with functional assays in purified mature mononuclear and multinucleated human osteoclasts, LGCs and FBGCs. Strikingly, in all three types of MGCs, multinucleation causes a pronounced down-regulation of mononuclear phagocyte identity. We show enhanced lysosome-mediated intracellular iron homeostasis promoting MGC formation. The transition from mononuclear to multinuclear state is accompanied by cell specialization specific to each polykaryon. Enhanced phagocytic and mitochondrial function associate with FBGCs and osteoclasts, respectively. Moreover, only B7-H3 (CD276)-expressing human LGCs can form granuloma-like clusters in vitro, suggesting that LGC multinucleation potentiates T cell activation. These findings demonstrate how cell-cell fusion and multinucleation reset human macrophage identity as part of an advanced maturation step that confers MGC-specific functionality.
Virtual drug screen reveals context-dependent inhibition of cardiomyocyte hypertrophy
Authors: Eggertsen Taylor G. , Saucerman Jeffrey J.
Published: August 2022

Background and Purpose

Pathological cardiomyocyte hypertrophy is a response to cardiac stress that typically leads to heart failure. Despite being a primary contributor to pathological cardiac remodeling, the therapeutic space that targets hypertrophy is limited. Here, we apply a network model to virtually screen for FDA-approved drugs that induce or suppress cardiomyocyte hypertrophy.

Experimental Approach

A logic-based differential equation model of cardiomyocyte signaling was used to predict drugs that modulate hypertrophy. These predictions were validated against curated experiments from the prior literature. The actions of midostaurin were validated in new experiments using TGFβ- and NE-induced hypertrophy in neonatal rat cardiomyocytes.

Key Results

Model predictions were validated in 60 out of 70 independent experiments from the literature and identify 38 inhibitors of hypertrophy. We additionally predict that the efficacy of drugs that inhibit cardiomyocyte hypertrophy is often context dependent. We predicted that midostaurin inhibits cardiomyocyte hypertrophy induced by TGFβ, but not NE, exhibiting context dependence. We further validated this prediction byin vitroexperimentation. Network analysis predicted critical roles for the PI3K and RAS pathways in the activity of celecoxib and midostaurin, respectively. We further investigated the polypharmacology and combinatorial pharmacology of drugs. Brigatinib and irbesartan in combination were predicted to synergistically inhibit cardiomyocyte hypertrophy.

Conclusion and Implications

This study provides a well-validated platform for investigating the efficacy of drugs on cardiomyocyte hypertrophy, and identifies midostaurin for consideration as an antihypertrophic drug.

‘What is already known’

- Cardiac hypertrophy is a leading predictor of heart failure.

- Cardiomyocyte hypertrophy is driven by intracellular signaling pathways that are not targeted by current drugs

‘What this study adds’

- Computational model integrates 69 unique drugs to predict cardiomyocyte hypertrophy

- Drug-induced inhibition of cardiomyocyte hypertrophy is context-dependent

- Midostaurin inhibits TGFβ-induced cardiomyocyte hypertrophy

‘Clinical significance’

- Midostaurin is identified as a candidate antihypertrophic drug

- Several FDA approved drugs are predicted to inhibit cardiomyocyte hypertrophy either individually or in combination.
Photophysical studies at cryogenic temperature reveal a novel photoswitching mechanism of rsEGFP2
Authors: Mantovanelli Angela M. R. , Glushonkov Oleksandr , Adam Virgile , Wulffele Jip , Thédié Daniel , Byrdin Martin , Gregor Ingo , Nevskyi Oleksii , Enderlein Jörg , Bourgeois Dominique
Published: August 2022

Single-molecule-localization-microscopy (SMLM) at cryogenic temperature opens new avenues to investigate intact biological samples at the nanoscale and perform cryo-correlative studies. Genetically encoded fluorescent proteins (FPs) are markers of choice for cryo-SMLM, but their reduced conformational flexibility below the glass transition temperature hampers efficient photoswitching at low temperature. We investigated cryo-switching of rsEGFP2, one of the most efficient reversibly switchable fluorescent protein at ambient temperature due to facile cis-trans isomerization of the chromophore. UV-visible microspectrophotometry and X-ray crystallography revealed a completely different switching mechanism at ∼110 K. At this cryogenic temperature, on-off photoswitching involves the formation of 2 dark states with blue shifted absorption relative to that of the trans protonated chromophore populated at ambient temperature. Only one of these dark states can be switched back to the fluorescent state by 405 nm light, while both of them are sensitive to UV light at 355 nm. The rsEGFP2 photoswitching mechanism discovered in this work adds to the panoply of known switching mechanisms in fluorescent proteins. It suggests that employing 355 nm light in cryo-SMLM experiments using rsEGFP2 or possibly other FPs could improve the achievable effective labeling efficiency in this technique.

Table of Contents artwork
Visuomotor skill learning in young adults with Down syndrome
Authors: Munk Højberg Laurits , Lundbye-Jensen Jesper , Wienecke Jacob
Published: August 2022

Background

Individuals with Down syndrome (DS) have impaired general motor skills compared to typically developed (TD) individuals.

Aims

To gain knowledge on how young adults with DS learn and retain new motor skills.

Methods and Procedures

A DS-group (mean age = 23.9 ± 3 years, N = 11), and an age- matched TD-group (mean age 22.8 ± 1.8, N= 14) were recruited. The participants practiced a sequence visuomotor accuracy tracking task (VATT). Online and offline effects of practice were assessed in immediate and 7-day retention tests. Participants practiced the task in seven blocks (10.6 minutes).

Outcomes and Results

The TD-group performed better than the DS-group in all blocks (all P < 0.001). Both groups improved VATT-performance online from baseline to immediate retention (all P < 0.001). The DS-groups’ performance at 7-day retention was at the same level as the immediate retention tests (ΔDS). An offline decrease in performance was found in the TD-group (ΔTD, P < 0.001). A between-group difference was observed in the offline effect on the sequence task (ΔTD - ΔDS, P = 0.04).

Conclusions and Implications

The motor performance of adults with DS is lower compared to their TD peers. However, adults with DS display significant online performance improvement during training, and offline consolidation following motor learning.

What this paper adds

Learning new motor skills is fundamental throughout our lifespan. Persons with Down syndrome have other prerequisites for learning new tasks, related to psychological, physiological, and anatomical factors imposed by the syndrome. This study is the first to investigate online and offline learning effects of a single motor skill training session in adults with DS. Our results show generally lower motor performance in DS individuals compared to the typically developed population, but with equal online learning effects. Both groups demonstrate retention, i.e., offline stabilisation but while TD demonstrate negative offline effects, this was not the case for DS. These results should be taken into consideration when planning training of motor and general life skills for adults with DS. This work lays the ground for further investigations of the trajectory of the early learning processes and the mechanisms involved when this target group acquires new skills.
Temporally multiplexed imaging of dynamic signaling networks in living cells
Authors: Qian Yong , Celiker Orhan T. , Wang Zeguan , Guner-Ataman Burcu , Boyden Edward S.
Published: August 2022

Molecular signals interact to mediate diverse biological computations. Ideally one would be able to image many signals at once, in the same living cell, to reveal how they work together. Here we report temporally multiplexed imaging (TMI), which uses the clocklike properties of fluorescent proteins to enable different cellular signals to be represented by different temporal fluorescence codes. Using different photoswitchable fluorescent proteins to represent different cellular signals, we can linearly decompose a brief movie of the fluorescence fluctuations in a given cell, into a sum of the fluctuation traces of each individual fluorophore, each weighted by its respective signal amplitude. We demonstrate the power of TMI to report relationships amongst a diversity of second messenger, kinase, and cell cycle signals, using ordinary microscopes.

One-Sentence Summary

Imaging of many dynamic signals in a living cell is possible by using distinct clocklike fluorophores to represent the activity of each signal.
The Role of Objecthood and Animacy in Apparent Movement Processing
Authors: Cracco Emiel , Linthout Tilia , Orgs Guido
Published: August 2022

Movement perception involves both motion and form processing. Previous research has shown that processing along the motion pathway requires a familiar but not necessarily a human shape. However, the role of objecthood and animacy in the form pathway is less clear. Here, we used EEG frequency tagging to study how objecthood and animacy influence both posture processing and the integration of postures into movements. Specifically, we measured brain responses to repeating sequences of well-defined or pixelated images (objecthood) of human or corkscrew agents (animacy) performing fluent or non-fluent movements (movement fluency). The results revealed that movement processing was sensitive to objecthood but not to animacy, whereas posture processing was sensitive to both. Thus, our results indicate that movement processing in the form pathway requires a familiar shape, but not necessarily a human shape. Instead, stimulus animacy appears to be relevant only for posture processing.
Dynamic applicability domain (dAD) for compound-target binding affinity prediction task with confidence guarantees
Authors: Oršolić Davor , Šmuc Tomislav
Published: August 2022

Abstract

Increasing efforts are being made in the field of machine learning to advance the learning of robust and accurate models from experimentally measured data and enable more efficient drug discovery processes. The prediction of binding affinity is one of the most frequent tasks of compound bioactivity modelling. Learned models for binding affinity prediction are assessed by their average performance on unseen samples, but point predictions are typically not provided with a rigorous confidence assessment. Approaches such as conformal predictor framework equip conventional models with more rigorous assessment of confidence for individual point predictions. In this paper, we extend the inductive conformal prediction (ICP) framework for the dyadic data, such as compound-target binding affinity prediction task. The new framework is based on dynamically defined calibration sets that are specific for each testing interaction pair and provides prediction assessment in the context of calibration pairs from its compound-target neighbourhood, enabling improved guarantees based on local properties of the prediction model. The effectiveness of the approach is benchmarked on several publicly available datasets and through testing in more realistic scenarios with increasing levels of difficulty on a bespoke, complex compound-target binding affinity space. We demonstrate that in such scenarios, novel approach combining applicability domain paradigm with conformal prediction framework, produces superior confidence assessment with informative prediction regions compared to other state-of-the-art conformal prediction approaches.
Can growth in captivity alter the calcaneal microanatomy of a wild ungulate?
Authors: Cottereau Romain , Ortiz Katia , Locatelli Yann , Houssaye Alexandra , Cucchi Thomas
Published: August 2022

Abstract

Reduced mobility associated with captivity induces changes in biomechanical stress on the skeleton of domesticated animals. Due to bone plasticity, bone’s morphology and internal structure can respond to these new biomechanical stresses over individuals’ lifetime. In a context where documenting early process of animal domestication is challenging, this study will test the hypothesis that change in mobility patterns during a wild ungulate’s life will alter the internal structure of its limb bones and provide a proof of concept for the application of this knowledge in Zooarchaeology. Using the calcaneus as a phenotypic marker through qualitative and quantitative 3D microanatomical analyses, we relied on a comparative study across wild boars (Sus scrofa) populations from controlled experimental conditions with different mobility patterns (natural habitat, large pen, and stall) and archaeological specimens collected from middle and late Mesolithic as surrogate for the norm of reaction in European wild boar phenotype before the spread of agriculture and domestic pigs. Results provide evidence for compressive and tensile forces as the main elements affecting the variation in the cortical thickness along the calcaneus. Furthermore, changes in the internal structure of the calcaneus between mobility patterns are observed but their intensity is not directly associated with the degree of mobility restriction and only weakly impacted by the size or weight of the individuals. Despite having greater bone volume, the calcaneus of the Mesolithic wild boars displays a very similar microanatomy compared to the present-day hunted or captive wild boars. These results suggest that calcaneal microanatomy is more affected by population differences than by locomotor variation. For all these reasons, this preliminary study doesn’t support the use of microanatomy of the calcaneus as an indicator of change in locomotor behaviour induced by captivity in the archaeological record.
Predicting scale-dependent chromatin polymer properties from systematic coarse-graining
Authors: Kadam Sangram , Kumari Kiran , M Vinoth , Dutta Shuvadip , Mitra Mithun K. , Padinhateeri Ranjith
Published: August 2022

Simulating chromatin is crucial for predicting genome organization and dynamics. Even though coarse-grained bead-spring polymer models are commonly used to describe chromatin, the relevant bead dimensions, elastic properties, and the nature of inter-bead potentials are unknown. Using publicly available nucleosome-resolution contact probability (Micro-C) data, we systematically coarse-grain chromatin and predict quantities essential for polymer representation of chromatin. We compute size distributions of chromatin beads for different coarse-graining scales, quantify fluctuations and distributions of bond lengths between neighboring regions, and derive effective spring constant values. Unlike the prevalent notion, our findings argue that coarse-grained chromatin beads must be considered as soft particles that can overlap, and we derive an effective inter-bead soft potential and quantify an overlap parameter. We also compute angle distributions between neighboring bonds giving insights into intrinsic folding and local bendability of chromatin. While the nucleosome-linker DNA bond angle naturally emerges from our work, we show that there are two populations of local structural states. The bead sizes, bond lengths, and bond angles show different mean behavior at Topologically Associating Domain (TAD) boundaries and TAD interiors. We integrate our findings into a coarse-grained polymer model and provide quantitative estimates of all model parameters, which can serve as a foundational basis for all future coarse-grained chromatin simulations.
Peripheral Myeloid-Derived Suppressor Cells are good biomarkers of the efficacy of Fingolimod in Multiple Sclerosis
Authors: Camacho-Toledano Celia , Machín-Díaz Isabel , Calahorra Leticia , Cabañas María , Otaegui David , Castillo-Triviño Tamara , Villar Luisa María , Costa-Frossard Lucienne , Comabella Manuel , Midaglia Luciana , García-Domínguez José Manuel , García-Arocha Jennifer , Ortega María Cristina , Clemente Diego
Published: August 2022

The increasing number of treatments that are now available to manage patients with multiple sclerosis (MS) highlights the need to develop biomarkers that can be used within the framework of individualized medicine. Fingolimod is a disease-modifying treatment that belongs to the sphingosine-1-phosphate receptor modulators. In addition of inhibiting T cell egression from lymph nodes, fingolimod promotes the immunosuppressive activity of Myeloid-Derived Suppressor Cells (MDSCs), a cell type that can be used as a biomarker of disease severity, and of the degree of demyelination and extent of axonal damage in MS. In the present study, we have assessed whether the abundance of circulating monocytic-MDSCs (M-MDSCs) may represent a useful biomarker of fingolimod efficacy. As such, blood immune cells were analyzed at disease onset in the experimental autoimmune encephalomyelitis (EAE) MS mouse model. Fingolimod treated animals presented a milder EAE course with less demyelination and axonal damage, although a few animals did not respond well to treatment and they invariably had fewer M-MDSCs prior to initiating the treatment. Remarkably, M-MDSC abundance was also found to be an important and specific parameter to distinguish EAE mice prone to better fingolimod efficacy. Finally, in a translational effort, M-MDSCs were quantified in MS patients at baseline and correlated with different clinical parameters after 12 months of fingolimod treatment. The data obtained indicated that the M-MDSCs at baseline were highly representative of a good therapeutic response to fingolimod, i.e. patients who met at least two of the criteria used to define non-evidence of disease activity (NEDA-3) 12 months after treatment, providing relevant information of intention-to-treat MS patients. Collectively, our data indicate that M-MDSCs might be a useful predictive biomarker of the response of MS patients to fingolimod.
16p11.2 locus decelerates subpallial maturation and limits variability in human iPSC-derived ventral telencephalic organoids
Authors: Fetit Rana , Theil Thomas , Pratt Thomas , Price David J.
Published: August 2022

Inhibitory interneurons regulate the activity of cortical circuitry, and their dysfunction has been implicated in Autism Spectrum Disorder (ASD). 16p11.2 microdeletions are genetically linked to 1% of ASD. However, there have been few studies of the effects of this microdeletion on interneuron development. Using ventral telencephalic organoids derived from human induced pluripotent stem cells, we investigated the effect of this microdeletion on organoid size, progenitor proliferation and organisation into neural rosettes, ganglionic eminence (GE) marker expression at early developmental timepoints and expression of the neuronal marker, NEUN at later stages. Early deletion organoids exhibited significantly greater variations in size with concomitant increases in relative neural rosette area and the expression of the ventral telencephalic marker, COUPTFII, with significantly increased variability in these properties. Cell cycle analysis revealed a significant increase in total cell cycle length caused primarily by an elongated G1-phase, the duration of which also varied significantly more than normal. Late deletion organoids increased their expression of the neuronal marker NEUN. We propose that 16p11.2 microdeletions increase developmental variability and may contribute to ASD aetiology by lengthening the cell cycle of ventral progenitors, promoting premature differentiation into interneurons.

Summary Statement

Using 3D-region-specific organoids, we demonstrate that 16p11.2 deletion increases variability and prolongs the cell cycle of human subpallial progenitors by lengthening their G1 phase.
Predicting Dementia Severity by Merging Anatomical and Diffusion MRI with Deep 3D Convolutional Neural Networks
Authors: Chattopadhyay Tamoghna , Singh Amit , Joshy Neha Ann , Thomopoulos Sophia I. , Nir Talia M. , Zheng Hong , Nourollahimoghadam Elnaz , Gupta Umang , Steeg Greg Ver , Jahanshad Neda , Thompson Paul M. ,   the Alzheimer’s Disease Neuroimaging Initiative
Published: August 2022

Machine learning methods have been used for over a decade for staging and subtyping a variety of brain diseases, offering fast and objective methods to classify neurodegenerative diseases such as Alzheimer’s disease (AD). Deep learning models based on convolutional neural networks (CNNs) have also been used to infer dementia severity and predict future clinical decline. Most CNN-based deep learning models use T1-weighted brain MRI scans to identify predictive features for these tasks. In contrast, we examine the added value of diffusion-weighted MRI (dMRI) - a variant of MRI, sensitive to microstructural tissue properties - as an additional input in CNN-based models of dementia severity. dMRI is sensitive to microstructural brain abnormalities not evident on standard anatomical MRI. By training CNNs on combined anatomical and diffusion MRI, we hypothesize that we could boost performance when predicting widely-used clinical assessments of dementia severity, such as individuals’ scores on the ADAS11, ADAS13, and MMSE (mini-mental state exam) clinical scales. For benchmarking, we evaluate CNNs that use T1-weighted MRI and dMRI to estimate “brain age” - the task of predicting a person’s chronological age from their neuroimaging data. To assess which dMRI-derived maps were most beneficial, we computed DWI-derived diffusion tensor imaging (DTI) maps of mean and radial diffusivity (MD/RD), axial diffusivity (AD) and fractional anisotropy (FA) for 1198 elderly subjects (age: 74.35 +/- 7.74 yrs.; 600 F/598 M, with a distribution of 636 CN/421 MCI/141 AD) from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). We tested both 2D Slice CNN and 3D CNN neural network models for the above predictive tasks. Our results suggest that for at least some deep learning architectures, diffusion-weighted MRI may enhance performance for several AD-relevant deep learning tasks relative to using T1-weighted images alone.
Protective effects of different doses of MitoQ separately and combined with trehalose on sperm function and antioxidative status of cryopreserved Markhoz goat semen
Authors: Rezaei Ako , Bahmani Hamid Reza , Mafakheri Shiva , Farshad Abbas , Nazari Parisa
Published: August 2022

The mitochondria-targeted antioxidant MitoQ has been regarded as an effective antioxidant agent against cryo-induced oxidative cellular damage. This study aimed to evaluate the use of different doses of MitoQ combined with trehalose to minimize mitochondrial impairment and oxidative stress during sperm cryopreservation of Markhoz goat. For this, semen collection was performed every 5 days from 5 bucks (10 ejaculates per buck). The ejaculates were pooled and then diluted in eight different Tris-based extenders as follows: no additives (control), 20, 200, 2000 nM of MitoQ (MT20, MT200, MT 2000, respectively), 150 mM of trehalose (Tr), MT20+Tr, MT200+Tr, MT2000+Tr. Each semen sample was frozen using a standard protocol, and sperm function and antioxidative status were evaluated after thawing. Results indicated higher total and progressive motility, acrosome and membrane integrity, superoxide dismutase, glutathione peroxidase, total antioxidant capacity, and lower DNA fragmentation and malondialdehyde in MT200+Tr than for all other groups except MT200; meanwhile, MT200 was also greater in these parameters than in the control group (P < 0.05). Furthermore, MT200 and MT200+Tr showed higher (P < 0.05) percentages of live cryopreserved sperm with high membrane mitochondrial potential than other groups. However, abnormality percentage and catalase activity of frozen-thawed sperm were not affected by treatments (P > 0.05). To conclude, we have found that supplementation of 200 nM MitoQ alone or in combination with 150 mM trehalose to semen extender improves the quality of cryopreserved sperm in goats, which is associated with enhanced antioxidant enzymatic defense and mitochondrial activity and reduced DNA fragmentation.
A layered, hybrid machine learning analytic workflow for mouse risk assessment behavior
Authors: Wang Jinxin , Karbasi Paniz , Wang Liqiang , Meeks Julian P.
Published: August 2022

Accurate and efficient quantification of animal behavior facilitates the understanding of the brain. An emerging approach within machine learning (ML) field is to combine multiple ML-based algorithms to quantify animal behavior. These so-called hybrid models have emerged because of limitations associated with supervised (e.g., random forest, RF) and unsupervised (e.g., hidden Markov model, HMM) ML classifiers. For example, RF models lack temporal information across video frames, and HMM latent states are often difficult to interpret. We sought to develop a hybrid model, and did so in the context of a study of mouse risk assessment behavior. We utilized DeepLabCut to estimate the positions of mouse body parts. Positional features were calculated using DeepLabCut outputs and were used to train RF and HMM models with equal number of states, separately. The per-frame predictions from RF and HMM models were then passed to a second HMM model layer (“reHMM”). The outputs of the reHMM layer showed improved interpretability over the initial HMM output. Finally, we combined predictions from RF and HMM models with selected positional features to train a third HMM model (“reHMM+”). This reHMM+ layered hybrid model unveiled distinctive temporal and human-interpretable behavioral patterns. We applied this workflow to investigate risk assessment to trimethylthiazoline and snake feces odor, finding unique behavioral patterns to each that were separable from attractive and neutral stimuli. We conclude that this layered, hybrid machine learning workflow represents a balanced approach for improving the depth and reliability of ML classifiers in chemosensory and other behavioral contexts.

Significance Statement

In this study, we integrate two widely-adopted machine learning (ML) classifiers, random forest and hidden Markov model, to develop a layered, hybrid ML-based workflow. Our workflow not only overcomes the intrinsic limitations of each model alone, but also improves the depth and reliability of ML models. Implementing this analytic workflow unveils distinctive and dynamic mouse behavioral patterns to chemosensory cues in the context of mouse risk assessment behavioral experiments. This study provides an efficient and interpretable analytic strategy for the quantification of animal behavior in diverse experimental settings.
Mitochondrial iron transport via MFRN1 is required for erythroid cell cycle progression
Authors: Perfetto Mark , Danoff Aidan , Ishfaq Muhammad , Monroe Heidi , Mohideen Aiden , Chen Meilin , Stratman Amber , Okawa Satoshi , Yien Yvette
Published: August 2022

Iron metabolism drives key erythropoietic processes, including hemoglobinization, survival, and proliferation. Here, we developedin vivomethods to interrogate how iron regulates erythropoiesis and report that mitochondrial iron transport via MFRN1 is essential for erythroid cell cycle progression.mfrn1embryos had severely decreased erythroid cell number caused by cell cycle arrest at G2/M. They had enlarged nuclei, suggesting a mitotic defect. Iron supplementation rescued the cell cycle defect, implicating mitochondrial iron deficiency as its cause. In contrast,fpn1mutants, anemic from systemic iron deficiency, had less severe decreases in erythroid mitochondrial iron thanmfrn1mutants and no proliferative defects. scRNAseq and FACS analyses forcd41(thrombocytic) andgata1reporters indicated that developmental defects inmfrn1mutants were largely erythroid restricted.mfrn1mutantgata1+erythroid progenitors were severely decreased at 3 dpf, and a further decrease inglobin-expressing terminally differentiating erythroid cells. While wild-type erythroid cells mostly lost expression of thegata1progenitor marker by 3 dpf,mfrn1mutant erythroid cells retainedgata1expression. These data are consistent with a model where mitochondrial iron transport facilitates development ofgata1+erythroid progenitors and is required for the completion of erythropoiesis by facilitating mitosis in the terminal cell cycles.
When do we become more prone to distraction? Progressive evolution of the different components of distractibility from early to late adulthood
Authors: Hoyer R.S. , Abdoun O. , Riedinger M. , Bouet R. , Elshafei H. , Bidet-Caulet A.
Published: August 2022

Life expectancy has steadily increased for over a century; we thus live longer and are more likely to experience cognitive difficulties such as increased distractibility which can hamper autonomy. This cross-sectional behavioral study aimed to characterize the decline of the cognitive components of distractibility during typical aging, and the onset of this decline. 191 participants from 21 to 86 years old, distributed within seven age groups, were tested using the Competitive Attention Test. Results indicate that cognitive components contributing to distractibility follow different trajectories with aging: voluntary orienting remains stable from 21 to 86 years old, sustained attention decreases while distraction increases between 26 and 86 years old, finally, impulsivity is lower in older compared to younger adults. Increased distractibility in older adults thus seems to result from a dominance of involuntary over voluntary attention processes, whose detrimental effect on performance is partly compensated by enhanced recruitment of motor control.
SPEX: A modular end-to-end platform for high-plex tissue spatial omics analysis
Authors: Li Xiao , Pechuan-Jorge Ximo , Risom Tyler , Foo Conrad , Prilipko Alexander , Zubkov Artem , Chan Caleb , Chang Patrick , Peale Frank , Ziai James , Rost Sandra , Hibar Derrek , McGinnis Lisa , Tabatsky Evgeniy , Ye Xin , Bravo Hector Corrada , Shi Zhen , Nowicka Malgorzata , Scherdin Jon , Cowan James , Giltnane Jennifer , Orlova Darya , Jesudason Rajiv
Published: August 2022

Recent advancements in transcriptomics and proteomics have opened the possibility for spatially resolved molecular characterization of tissue architecture with the promise of enabling a deeper understanding of tissue biology in either homeostasis or disease. The wealth of data generated by these technologies has recently driven the development of a wide range of computational methods. These methods have the requirement of advanced coding fluency to be applied and integrated across the full spatial omics analysis process thus presenting a hurdle for widespread adoption by the biology research community. To address this, we introduce SPEX (Spatial Expression Explorer), a web-based analysis platform that employs modular analysis pipeline design, accessible through a user-friendly interface. SPEX’s infrastructure allows for streamlined access to open source image data management systems,analysis modules, and fully integrated data visualization solutions. Analysis modules include essential steps covering image processing, single-cell and spatial analysis. We demonstrate SPEX’s ability to facilitate the discovery of biological insights in spatially resolved omics datasets from healthy tissue to tumor samples.
SREBP1 activation contributes to fatty acid accumulations in necroptosis
Authors: Lu Daniel , Parisi Laura R. , Gokcumen Omer , Atilla-Gokcumen G. Ekin
Published: August 2022

Necroptosis is a type of programmed cell death. It is characterized by membrane permeabilization and is associated with a strong inflammatory response due to the release of intracellular components due to compromised membrane integrity. We recently showed that the accumulation of very long chain fatty acids (VLCFAs) contributes to membrane permeabilization during necroptosis. However, the mechanisms that result in the accumulation of these cytotoxic lipids remain unknown. Using comparative transcriptomics, we found that sterol regulatory element-binding protein 1 (SREBP1) is activated and that its downstream gene targets result in the accumulation of VLCFAs during necroptosis. We demonstrated that activation of SREBP1 during necroptosis exacerbates cell death. On the contrary, inactivation of SREBP1 reversed the accumulation of VLCFAs, and restored cell death and membrane permeabilization during necroptosis. Collectively, our results highlight a role for SREBP1 in regulating lipid changes during necroptosis and suggest SREBP1 as a potential target for therapeutics to reduce membrane permeabilization during necroptosis.