bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid iPSC inclusionopathy models shed light on formation, consequence and molecular subtype of α-synuclein inclusions
Authors: Lam Isabel , Ndayisaba Alain , Lewis Amanda J. , Fu YuHong , Sagredo Giselle T. , Zaccagnini Ludovica , Sandoe Jackson , Sanz Ricardo L. , Vahdatshoar Aazam , Martin Timothy D. , Morshed Nader , Ichihashi Toru , Tripathi Arati , Ramalingam Nagendran , Oettgen-Suazo Charlotte , Bartels Theresa , Schäbinger Max , Hallacli Erinc , Jiang Xin , Verma Amrita , Tea Challana , Wang Zichen , Hakozaki Hiroyuki , Yu Xiao , Hyles Kelly , Park Chansaem , Theunissen Thorold W. , Wang Haoyi , Jaenisch Rudolf , Lindquist Susan , Stevens Beth , Stefanova Nadia , Wenning Gregor , Luk Kelvin C. , Pernaute Rosario Sanchez , Gómez-Esteban Juan Carlos , Felsky Daniel , Kiyota Yasujiro , Sahni Nidhi , Yi S. Stephen , Chung Chee-Yeun , Stahlberg Henning , Ferrer Isidro , Schöneberg Johannes , Elledge Stephen J. , Dettmer Ulf , Halliday Glenda M. , Bartels Tim , Khurana Vikram
Published: November 2022

Intracellular inclusions accompanying neurodegeneration are histopathologically and ultrastructurally heterogeneous but the significance of this heterogeneity is unclear. iPSC models, while promising for disease modeling, do not form inclusions in a reasonable timeframe and suffer from limited tractability. Here, we developed an iPSC toolbox utilizing piggyBac-based or targeted transgenes to rapidly induce CNS cells with concomitant expression of aggregation-prone proteins. This system is amenable to screening and longitudinal tracking at single-cell and single-inclusion resolution. For proof-of-principle, cortical neuron α-synuclein “inclusionopathy” models were engineered to form inclusions through exogenous seeding or α-synuclein mutation. These models recapitulated known fibril- and lipid-rich inclusion subtypes, uncovering dynamic interactions between them, and refined the classification of inclusions in postmortem brain. Genetic-modifier and protein-interaction screens pinpointed proteins like RhoA whose sequestration into specific inclusion subtypes is likely to be toxic. This iPSC platform should enhance our understanding of proteinaceous pathologies in neurodegeneration and facilitate therapeutics development.
Asymmetric cell division safeguards memory CD8 T cell development
Authors: Gräbnitz Fabienne , Stark Dominique , Shlesinger Danielle , Petkidis Anthony , Borsa Mariana , Yermanos Alexander , Carr Andreas , Barandun Niculò , Wehling Arne , Balaz Miroslav , Schroeder Timm , Oxenius Annette
Published: November 2022

The strength of T cell receptor (TCR) stimulation and asymmetric distribution of fate determinants are both implied to affect T cell differentiation. Here, we uncovered asymmetric cell division (ACD) as a safeguard mechanism for memory CD8 T cell generation specifically upon strong TCR stimulation. Using live imaging approaches, we found that strong TCR stimulation induced elevated ACD rates and subsequent single cell derived colonies comprised both effector and memory precursor cells. The abundance of memory precursor cells emerging from a single activated T cell positively correlated with first mitosis ACD. Accordingly, preventing ACD by inhibition of PKCζ during the first mitosis upon strong TCR stimulation markedly curtailed the formation of memory precursor cells. Conversely, no effect of ACD on fate commitment was observed upon weak TCR stimulation. Our data provide new mechanistic insights into the role of ACD for CD8 T cell fate regulation upon different activation conditions.
Human Nucleolar Protein 7 (NOL7) is required for pre-rRNA transcription and pre-18S rRNA processing
Authors: McCool Mason A. , Bryant Carson J. , Huang Hannah , Ogawa Lisa M. , Farley-Barnes Katherine I. , Sondalle Samuel B. , Abriola Laura , Surovtseva Yulia V. , Baserga Susan J.
Published: November 2022

The main components of the essential cellular process of eukaryotic ribosome biogenesis are highly conserved from yeast to humans. Among these, the transcription-U3 Associated Proteins (t-UTPs) are a small subunit processome subcomplex that coordinate the first two steps of ribosome biogenesis in transcription and pre-18S processing. While we have identified the human counterparts of most of the yeast Utps, the homologs of yeast Utp9 and Bud21 (Utp16) have remained elusive. In this study, we find NOL7 is the likely ortholog of Bud21. Previously described as a tumor suppressor through regulation of antiangiogenic transcripts, we now show that NOL7 is required for early pre-rRNA stability and pre-18S processing in human cells. These roles lead to decreased protein synthesis, induction of the nucleolar stress response, and defects in cell cycle progression upon NOL7 depletion. Beyond Bud21’s nonessential role in yeast, we establish human NOL7 as an essential UTP that is necessary for both pre-rRNA transcription and processing.
Autonomous behaviour and the limits of human volition
Authors: Ota Keiji , Charles Lucie , Haggard Patrick
Published: November 2022

Humans and some other animals can autonomously generate action choices that contribute to solving complex problems. However, experimental investigations of the cognitive bases of human autonomy are challenging, because experimental paradigms typically constrain behaviour using controlled contexts, and elicit behaviour by external triggers. In contrast, autonomy and freedom imply unconstrained behaviour initiated by endogenous triggers. Here we propose a new theoretical construct of adaptive autonomy, meaning the capacity to make behavioural choices that are free from constraints of both immediate external triggers and of routine response patterns, but nevertheless show appropriate coordination with the environment. Participants (N = 152) played a competitive game in which they had to choose the right time to act, in the face of an opponent who punished (in separate blocks) either choice biases (such as always responding early), sequential patterns of action timing across trials (such as early, late, early, late…), or predictable action-outcome dependence (such as win-stay, lose-shift). Adaptive autonomy was quantified as the ability to maintain performance when each of these influences on action selection was punished. We found that participants could become free from habitual choices regarding when to act and could also become free from sequential action patterns. However, they were not able to free themselves from influences of action-outcome dependence, even when these resulted in poor performance. These results point to a new concept of autonomous behaviour as flexible adaptation of voluntary action choices in a way that avoids stereotypy. In a sequential analysis, we also demonstrated that participants increased their reliance on belief learning in which they attempt to understand the competitor’s beliefs and intentions, when transition bias and reinforcement bias were punished. Taken together, our study points to a cognitive mechanism of adaptive autonomy in which competitive interactions with other agents could promote both social cognition and volition in the form of non-stereotyped action choices.
The genome of the brackish-water malaria vectorAnopheles aquasalis
Authors: Sepulveda Cesar C. P. , Alencar Rodrigo M. , Martinez-Villegas Luiz , Bahia Ana Cristina , Santana Rosa A. , de Souza Igor B. , D’Elia Gigliola M. A. , Duarte Ana Paula M. , de Lacerda Marcus V. G. , Monteiro Wuelton M. , F. Costa Secundino Nágila , Koerich Leonardo B. , Pimenta Paulo F. P.
Published: November 2022

Anopheles aquasalisis a primary malaria vector in coastal South America that grows in brackish waters of mangroves. Its importance has increased in recent years as it has been established as a model for parasite-vector studies for non-modelPlasmodiumspecies, such asP. yoelli. In this study, we present the complete genome ofAn. aquasalisand offer some insights into evolution and physiology. With a 162Mb and 12,446 coding proteins, theAn. aquasalisgenome is similar in size and gene content as other neotropical anophelines. 1,038 single-copy orthologs are present inAn. aquasalisand all Diptera and it was possible to infer thatAn. aquasalisdiverged fromAn. darlingi(the main malaria vector in inland South America) nearly 14 million years ago (mya). Ion transport and metabolism proteins is one the major gene families inAn. aquasaliswith 660 genes. Amongst these genes, important gene families relevant for osmosis control (e.g., aquaporins, vacuolar-ATPases, Na+/K+-ATPases and carbonic anhydrases) were identified in one-to-one orthologs with other anophelines. Evolutionary analysis suggests that all osmotic regulation genes are under strong purifying selection. We also observed low copy number variation in immunity-related genes (for which all classical pathways were described) and insecticide resistance genes. This is the third genome of a neotropical anopheline published so far. The data provided by this study may offer candidate genes for further studies on parasite-vector interactions and for studies on how brackish water anophelines deals with high fluctuation in water salinity.

Significance Statement

The brackish water mosquitoAnopheles aquasalisis a primary malaria vector in coastal South America. Besides its peculiar ecological features (it is one of the few anopheline mosquitoes that survives high fluctuation of water salinity),An. aquasalishas gained relevance in recent years as a model for parasite-vector studies for non-modelPlasmodiumparasites. Still, the physiology and genetics ofAn. aquasalisare poorly understood. Here we present the genome ofAn. aquasaliswith more than 12,000 annotated genes, offering insights in genome evolution, osmoregulation related, immunity, chemosensory and insecticide resistance genes. The data presented here will help to further advance the studies onAn. aquasalisgenetics and physiology to better understand parasite-vector interactions in non-model organisms.
Clinical PARP inhibitors allosterically induce PARP2 retention on DNA
Authors: Langelier Marie-France , Lin Xiaohui , Zha Shan , Pascal John M.
Published: November 2022

PARP1 and PARP2 detect DNA breaks, which activates their catalytic production of poly(ADP-ribose) that recruits repair factors and releases PARP1/2 from DNA. PARP inhibitors (PARPi) are used in cancer treatment and target PARP1/2 catalytic activity, interfering with repair and increasing PARP1/2 persistence on DNA damage. Additionally, certain PARPi exert allosteric effects that increase PARP1 retention on DNA. However, no clinical PARPi exhibit this allosteric behavior toward PARP1. In contrast, we show that certain clinical PARPi exhibit an allosteric effect that retains PARP2 on DNA breaks in a manner that depends on communication between the catalytic and DNA-binding regions. Using a PARP2 mutant that mimics an allosteric inhibitor effect, we observed increased PARP2 retention at cellular damage sites. The new PARPi AZD5305 also exhibited a clear reverse allosteric effect on PARP2. Our results can help explain the toxicity of clinical PARPi and suggest ways to improve PARPi moving forward.
Dissecting the cell cycle regulation, DNA damage sensitivity and lifespan effects of caffeine in fission yeast
Authors: Alao John-Patrick , Kumar Juhi , Stamataki Despina , Rallis Charalampos
Published: November 2022

Caffeine is a widely consumed neuroactive substance. It can modulate cell cycle progression, override DNA damage checkpoint signalling and increase chronological lifespan (CLS) in various model systems. Early studies suggested that caffeine inhibits the phosphatidylinositol 3-kinase-related kinase (PIKK) Rad3 to override DNA damage-induced cell cycle arrest in fission yeast. We have previously suggested that caffeine modulates cell cycle progression and lifespan by inhibiting the Target of Rapamycin Complex 1 (TORC1). Nevertheless, whether this inhibition is direct or not, has remained elusive. TORC1 controls metabolism and mitosis timing by integrating nutrients and environmental stress response (ESR) signalling. Nutritional or other stresses activate the Sty1-Ssp1-Ssp2 (AMP-activated protein kinase complex, AMPK) pathway, which inhibits TORC1 and accelerates mitosis through Sck2 inhibition. Additionally, activation of the ESR pathway can extend lifespan in fission yeast. Here, we demonstrate that caffeine activates Ssp1, Ssp2 and the AMPKβ regulatory subunit Amk2 to advance mitosis. Ssp2 is phosphorylated in an Ssp1-dependent manner following exposure to caffeine. Furthermore, Ssp1 and Amk2, are required for resistance to caffeine under conditions of prolonged genotoxic stress. The effects of caffeine on DNA damage sensitivity are uncoupled from mitosis in AMPK pathway mutants. We propose that caffeine interacts synergistically with other genotoxic agents to increase DNA damage sensitivity. Our findings suggest that caffeine accelerates mitotic division and is beneficial for CLS through AMPK. Direct pharmacological targeting of AMPK may serve towards health span and lifespan benefits beyond yeasts, given the highly conserved nature of this key regulatory cellular energy sensor.
Automated model discovery for human brain using Constitutive Artificial Neural Networks
Authors: Linka Kevin , Pierre Sarah St. , Kuhl Ellen
Published: November 2022

The brain is our softest and most vulnerable organ, and understanding its physics is a challenging but significant task. Massive efforts have been dedicated at testing the human brain, and various competing models have emerged to characterize its response to mechanical loading. However, selecting the best constitutive model remains a heuristic process that strongly depends on user experience and personal preference. Here we challenge the conventional wisdom to first select a constitutive model and then fit its parameters to experimental data. Instead, we propose a new strategy that simultaneously discovers both model and parameters that best describe the data. Towards this goal, we integrate more than a century of knowledge in thermodynamics and state-of-the-art machine learning to build a family of Constitutive Artificial Neural Networks that enable automated model discovery for human brain tissue. Our overall design paradigm is to reverse engineer a Constitutive Artificial Neural Network from a set of functional building blocks that are, by design, a generalization of widely used and commonly accepted constitutive models, including the neo Hooke, Blatz Ko, Mooney Rivlin, Demiray, Gent, and Holzapfel models. By constraining the input, output, activation functions, and architecture, our network a priori satisfies thermodynamic consistency, material objectivity, material symmetry, physical constrains, and polyconvexity. We demonstrate that our network autonomously discovers both model and parameters that best characterize the behavior of human gray and white matter under tension, compression, and shear. Importantly, our network weights translate naturally into physically meaningful material parameters, e.g., shear moduli of 1.82kPa, 0.88kPa, 0.94kPa, and 0.54kPa for the cortex, basal ganglia, corona radiata, and corpus callosum. Our results suggest that Constitutive Artificial Neural Networks have the potential to induce a paradigm shift in soft tissue modeling, from user-defined model selection to automated model discovery. Our source code, data, and examples are available athttps://github.com/LivingMatterLab/CANN.
The photosystem I supercomplex from a primordial green algaOstreococcus tauriharbors three light-harvesting complex trimers
Authors: Ishii Asako , Shan Jianyu , Sheng Xin , Kim Eunchul , Watanabe Akimasa , Yokono Makio , Noda Chiyo , Song Chihong , Murata Kazuyoshi , Liu Zhenfeng , Minagawa Jun
Published: November 2022

As a ubiquitous picophytoplankton in the ocean and an early-branching green alga,Ostreococcus tauriis a model prasinophyte species for studying the functional evolution of the light-harvesting systems in photosynthesis. Here, we report the structure and function of theO. tauriphotosystem I (PSI) supercomplex in the low light, where it expands its photon-absorbing capacity by assembling with the light-harvesting complexes I (LHCI) and a prasinophyte-specific light-harvesting complex (Lhcp). Its architecture exhibits hybrid features of the plant-type and the green algal-type PSI supercomplexes, consisting of a PSI core, a Lhca1-Lhca4-Lhca2-Lhca3 belt attached on one side and a Lhca5-Lhca6 heterodimer associated on the other side between PsaG and PsaH. Interestingly, nine Lhcp subunits, including one Lhcp1 monomer with a phosphorylated amino-terminal threonine and eight Lhcp2 monomers, oligomerize into three trimers and associate with PSI on the third side between Lhca6 and PsaK. The Lhcp1 phosphorylation and the light-harvesting capacity of PSI were subjected to reversible photoacclimation, suggesting that the formation ofOtPSI–LHCI–Lhcp supercomplex is likely due to a state transition-like mechanism induced by light intensity change. Notably, this supercomplex did not exhibit far-red peaks in the 77 K fluorescence spectra, which is possibly due to weak coupling of the chlorophylla603-a609 pair inOtLhca1-4.
Subsensory stochastic electrical stimulation targeting muscle afferents alters gait control during locomotor adaptations to haptic perturbations
Authors: Severini Giacomo , Koenig Alexander , Cajigas Iahn , Lesniewski-Laas Nicholas , Niemi Jim , Bonato Paolo
Published: November 2022

Subsensory noise stimulation targeting sensory receptors has been shown to improve balance control in healthy and impaired individuals. However, the potential for application of this technique in other contexts is still unknown. Gait control and adaptation rely heavily on the input from proprioceptive organs in the muscles and joints. Here we investigated the use of subsensory noise stimulation as a means to influence motor control by “boosting” proprioception during locomotor adaptations to forces delivered by a robot. The forces increase step length unilaterally and trigger an adaptive response that restores the original symmetry. Healthy participants performed two adaptation experiments, one with stimulation applied to the hamstring muscles and one without. We found that participants adapted faster but to a lesser extent when undergoing subsensory stimulation. We argue that this behaviour is due to the dual effect that the stimulation has on the afferents encoding position and velocity that are present in the muscle spindles.
Prediction of Transport, Deposition, and Resultant Immune Response of Nasal Spray Vaccine Droplets using a CFPD-HCD Model in a 6-Year-Old Upper Airway Geometry to Potentially Prevent COVID-19
Authors: Hayati Hamideh , Feng Yu , Chen Xiaole , Kolewe Emily , Fromen Catherine
Published: November 2022

This study focuses on the transport, deposition, and triggered immune response of intranasal vaccine droplets to the Angiotensin-converting enzyme 2-rich region (i.e., the olfactory region (OR)) in the nasal cavity of a 6-year-old female to possibly prevent COVID-19. To investigate how administration strategy can influence nasal vaccine efficiency, a validated multiscale model (i.e., computational fluid-particle dynamics (CFPD) and host-cell dynamics (HCD) model) was employed. Droplet deposition fraction, size change, residence time, and the area percentage of OR covered by the vaccine droplets and triggered immune system response were predicted with different spray cone angles, initial droplet velocities, and compositions. Numerical results indicate that droplet initial velocity and composition have negligible influences on the vaccine delivery efficiency to OR. In contrast, the spray cone angle can significantly impact the vaccine delivery efficiency. The triggered immunity was not significantly influenced by the administration investigated in this study, due to the low percentage of OR area covered by the droplets. To enhance the effectiveness of the intranasal vaccine to prevent COVID-19 infection, it is necessary to optimize the vaccine formulation and administration strategy so that the vaccine droplets can cover more epithelial cells in OR to minimize the available receptors for SARS-CoV-2.
Endometrial decidualization status modulates endometrial perivascular complexity and trophoblast outgrowth in gelatin hydrogels
Authors: Zambuto Samantha G. , Theriault Hannah , Jain Ishita , Crosby Cody O. , Pintescu Ioana , Chiou Noah , Zoldan Janet , Underhill Gregory H. , Clancy Kathryn B.H. , Harley Brendan A.C.
Published: November 2022

The endometrium undergoes rapid cycles of vascular growth, remodeling, and breakdown during the menstrual cycle and pregnancy. Decidualization is an endometrial differentiation process driven by steroidal sex hormones that is critical for blastocyst-uterine interfacing and blastocyst implantation. Certain pregnancy disorders may be linked to decidualization processes. However, much remains unknown regarding the role of decidualization and reciprocal trophoblast-endometrial interactions on endometrial angiogenesis and trophoblast invasion. Here, we report an artificial endometrial perivascular niche embedded in gelatin methacrylol hydrogels that displays morphological and functional patterns of decidualization. We show vessel complexity and soluble factor secretion are sensitive to decidualization and affect trophoblast motility. Importantly, we demonstrate the engineered perivascular niche can be combined with epithelial cultures to form a stratified endometrial model. This artificial perivascular niche provides a well-characterized platform to investigate dynamic changes in angiogenesis in response to pathological and physiological endometrial states.

Teaser

We describe an endometrial vessel model to understand endometrial vasculature in the menstrual cycle and pregnancy.
Knockdown of mitochondrialatp1mRNA by a custom-designed pentatricopeptide repeat protein alters F1FoATP synthase
Authors: Yang Fei , Vincis Pereira Sanglard Lilian , Lee Chun-Pong , Ströher Elke , Singh Swati , Oh Glenda Guec Khim , Millar A. Harvey , Small Ian , Colas des Francs-Small Catherine
Published: November 2022

We show that a custom-designed RNA-binding protein binds and specifically induces cleavage ofatp1RNA in mitochondria, significantly decreasing the abundance of the Atp1 protein and the assembled F1FoATP synthase inArabidopsis thaliana. The transformed plants are characterized by delayed vegetative growth and reduced fertility. Five-fold depletion of Atp1 level was accompanied by a decrease in abundance of other ATP synthase subunits, lowered ATP synthesis rate of isolated mitochondria, but no change to mitochondrial electron transport chain complexes, adenylates or energy chargein planta. Transcripts for amino acid transport and a variety of stress response processes were differentially expressed in lines containing the PPR protein, indicating changes to achieve cellular homeostasis when ATP synthase was highly depleted. Leaves of ATP-synthase-depleted lines showed higher respiratory rates and elevated levels of most amino acids at night, most notably serine family amino acids. The results show the value of using custom-designed PPR proteins to influence expression of specific mitochondrial transcripts to carry out reverse genetics studies on mitochondrial gene functions and the consequences of ATP synthase depletion on cellular functions inArabidopsis.

One sentence Summary

Knockdown of mitochondrialatp1mRNA by a custom-designed pentatricopeptide repeat protein alters F1Fo ATP synthase, plant growth and amino acid metabolism and ATP synthesis inArabidopsis thaliana
Individual differences in volitional social motivation in male and female mice following social stress
Authors: Navarrete Jovana , Schneider Kevin N. , Smith Briana M. , Goodwin Nastacia L. , Zhang Yizhe Y. , Gross Ethan , Tsai Valerie S. , Heshmati Mitra , Golden Sam A.
Published: November 2022

Background

A key challenge in developing new treatments for neuropsychiatric illness is the disconnect between preclinical models and the complexity of human social behavior. We aimed to integrate voluntary social self-administration into a preclinical rodent stress model, as a platform for the identification of basic brain and behavior mechanisms underlying stress-induced individual differences in social motivation. Here, we introduce an operant social stress (OSS) procedure with male and female mice, where lever presses are reinforced by freely moving social interaction with a familiar social partner across social stress exposure.

Methods

OSS is composed of three phases: (i) social self-administration training, (ii) social stress concurrent with daily reinforced social self-administration testing, and (iii) post-stress operant social reward testing under both non-reinforced and reinforced conditions. We resolve social stress-induced changes to social motivation behaviors using hierarchical clustering and aggregated z-scores, capturing the spectrum of individual differences that we describe with a social index score.

Results

OSS captures a range of stress-related dynamic social motivation behaviors inclusive of sex as a biological variable. Both male and female mice lever press for access to a social partner, independent of social partner coat color or familiarity. Social stress attenuates social self-administration in males and promotes social reward seeking behavior in females. Hierarchical clustering does not adequately describe the relative distributions of social motivation following stress, which we find is better described as a non-binary behavioral distribution that we define by introducing the social index score. This index is stable across individual mice.

Conclusion

We demonstrate that OSS can be used to detect stable individual differences in stress-induced changes to social motivation in male and female mice. These differences may reflect unique neurobiological, cellular and circuit mechanisms not captured by preclinical models that omit voluntary social behaviors. The inclusion of volitional social procedures may enhance the understanding of behavioral adaptations promoting stress resiliency and their mechanisms under more naturalistic conditions.
GABAergic neuron-to-glioma synapses in diffuse midline gliomas
Authors: Barron Tara , Yalçın Belgin , Mochizuki Aaron , Cantor Evan , Shamardani Kiarash , Tlais Dana , Franson Andrea , Lyons Samantha , Mehta Vilina , Jahan Samin Maleki , Taylor Kathryn R. , Keough Michael B. , Xu Haojun , Su Minhui , Quezada Michael A. , Woo Pamelyn J , Fisher Paul G. , Campen Cynthia J. , Partap Sonia , Koschmann Carl , Monje Michelle
Published: November 2022

Pediatric high-grade gliomas are the leading cause of brain cancer-related death in children. High-grade gliomas include clinically and molecularly distinct subtypes that stratify by anatomical location into diffuse midline gliomas (DMG) such as diffuse intrinsic pontine glioma (DIPG) and hemispheric high-grade gliomas. Neuronal activity drives high-grade glioma progression both through paracrine signaling1,2and direct neuron-to-glioma synapses3–5. Glutamatergic, AMPA receptor-dependent synapses between neurons and malignant glioma cells have been demonstrated in both pediatric3and adult high-grade gliomas4, but neuron-to-glioma synapses mediated by other neurotransmitters remain largely unexplored. Using whole-cell patch clamp electrophysiology,in vivooptogenetics and patient-derived glioma xenograft models, we have now identified functional, tumor-promoting GABAergic neuron-to-glioma synapses mediated by GABAAreceptors in DMGs. GABAergic input has a depolarizing effect on DMG cells due to NKCC1 expression and consequently elevated intracellular chloride concentration in DMG tumor cells. As membrane depolarization increases glioma proliferation3, we find that the activity of GABAergic interneurons promotes DMG proliferationin vivo. Increasing GABA signaling with the benzodiazepine lorazepam – a positive allosteric modulator of GABAAreceptors commonly administered to children with DMG for nausea or anxiety - increases GABAAreceptor conductance and increases glioma proliferation in orthotopic xenograft models of DMG. Conversely, levetiracetam, an anti-epileptic drug that attenuates GABAergic neuron-to-glioma synaptic currents, reduces glioma proliferation in patient-derived DMG xenografts and extends survival of mice bearing DMG xenografts. Concordant with gene expression patterns of GABAAreceptor subunit genes across subtypes of glioma, depolarizing GABAergic currents were not found in hemispheric high-grade gliomas. Accordingly, neither lorazepam nor levetiracetam influenced the growth rate of hemispheric high-grade glioma patient-derived xenograft models. Retrospective real-world clinical data are consistent with these conclusions and should be replicated in future prospective clinical studies. Taken together, these findings uncover GABAergic synaptic communication between GABAergic interneurons and diffuse midline glioma cells, underscoring a tumor subtype-specific mechanism of brain cancer neurophysiology with important potential implications for commonly used drugs in this disease context.
Differential bending stiffness of the bacterial flagellar hook under counterclockwise and clockwise rotations
Authors: Zhang Xinwen , Zhang Chi , Zhang Rongjing , Yuan Junhua
Published: November 2022

The bacterial hook, as a universal joint coupling rotation of the flagellar motor and the filament, is an important component of the flagellum that propels the bacteria to swim. The mechanical properties of the hook are essential for the flagellum to achieve normal functions. In multi-flagellated bacteria such as Escherichia coli, the hook must be compliant so that it can bend for the filaments to form a coherently rotating bundle to generate the thrust when the motor rotates counterclockwise (CCW), yet it also must be rigid so that the bundle can disrupt for the bacteria to tumble to change swimming direction when the motor rotates clockwise (CW). Here, by combining an elastic rod model with high-resolution bead assay to accurately measure the bending stiffness of the hook under CCW or CW rotationin vivo, we elucidate how the hook accomplishes this dual functionality: the hook stiffens under CW rotation, with bending stiffness under CW rotation twice as large as that under CCW rotation. This enables a robust run-and-tumble swimming motility for multi-flagellated bacteria.
Flap-enabled next-generation capture (FENGC): precision targeted single-molecule profiling of epigenetic heterogeneity, chromatin dynamics, and genetic variation
Authors: Zhou Mingqi , Nabilsi Nancy H. , Wang Anqi , Gauthier Marie-Pierre L. , Murray Kevin O. , Azari Hassan , Owens William S. , Newman Jeremy R. B. , Pardo-Palacios Francisco J. , Conesa Ana , Riva Alberto , Clanton Thomas L. , Reynolds Brent A. , Concannon Patrick , Brant Jason O. , Bacher Rhonda , Kladde Michael P.
Published: November 2022

Targeted sequencing is an increasingly sought technology. Available methods, however, are often costly and yield high proportions of off-target reads. Here, we present FENGC, a scalable, multiplexed method in which target sequences are assembled into 5′ flaps for precise excision by flap endonuclease. Recovery of length-matched sequences, amplification with universal primers, and exonucleolytic removal of non-targeted genomic regions mitigate amplification biases and consistently yield ≥ 80% on-target sequencing. Furthermore, optimized sequential reagent addition and purifications minimize sample loss and facilitate rapid processing of sub-microgram quantities of DNA for detection of genetic variants and DNA methylation. Treatment of cultured human glioblastoma cells and primary murine monocytes with GC methyltransferase followed by FENGC and high-coverage enzymatic methyl sequencing provides single-molecule, long-read detection of differential endogenous CG methylation, dynamic nucleosome repositioning, and transcription factor binding. FENGC provides a versatile and cost-effective platform for targeted sequence enrichment for analysis of genetic and/or epigenetic heterogeneity.
Reliable and accurate gene expression quantification with subpopulation structure-aware constraints for single-cell RNA sequencing
Authors: Tu Ching-Chih , Hung Jui-Hung
Published: November 2022

Background

Single-cell RNA sequencing (scRNA-seq) analysis analyzes the type and state of individual cells by estimating the gene expression of each cell and enables researchers to study the biological phenomena that cannot be observed in bulk RNA sequencing.

Motivation

However, the current scRNA-seq quantification tools estimate the gene expression profile of each cell independently, ignoring the fact that there are multiple cell types in the scRNA-seq data and the expression level should be highly correlated with the cell type. Since scRNA-seq suffers from a low sequencing depth, the conventional strategy leads to a high proportion of missing values in the gene expression profile, obscuring the biological characteristics of cell subpopulations and further impacting the correctness of the subsequent downstream analysis.

Results

In this study, we proposed Quasic, a novel scRNA-seq quantification pipeline which examines the potential cell subpopulation information during quantification, and uses the information to calculate the gene expression level. Using the human peripheral blood mononuclear cells and the simulated doublet dataset, we verified that Quasic not only correctly reinforced the cell signatures, but also identified the corresponding cell subpopulations and biological pathways more accurately. In addition, we also applied Quasic to the breast cancer cell line dataset (MCF-7), and successfully identified more potentially therapeutic resistant cells of which characteristics are consistent with that from previous studies.

Conclusions

The proposed pipeline can let the gene expression profile of each cell be more consistent with the corresponding subpopulation, making the biological features unique to the subpopulation more apparent and convenient for analysis. By using Quasic, researchers can effectively extract the desired cell subpopulation information from their sampled cells, enable them to perform cell subpopulation-related studies more accurately.
Whole-Brain fMRI Functional Connectivity Signatures Predict Sustained Emotional Experience in Naturalistic Contexts
Authors: Xu Shuyue , Zhang Zhiguo , Li Linling , Zhou Yongjie , Lin Danyi , Zhang Li , Huang Gan , Liu Xiqin , Becker Benjamin , Liang Zhen
Published: November 2022

Determining and decoding emotional brain processes under ecologically valid conditions remains a key challenge in affective neuroscience. The current functional magnetic resonance imaging (fMRI) based emotion decoding studies are mainly based on brief and isolated episodes of emotion induction, while sustained emotional experience in naturalistic environments that mirror daily life experiences are scarce. Here we use 10-minute movie clips as ecologically valid emotion-evoking procedures in n=52 individuals to explore emotion-specific fMRI functional connectivity (FC) profiles on the whole-brain level at high spatial resolution (400 atlas based parcels). Employing machine-learning based decoding and cross validation procedures allowed to develop predictive FC profiles that can accurately distinguish sustained happiness and sadness and that generalize across movies and subjects. Both functional brain network-based and subnetwork-based emotion prediction results suggest that emotion manifests as distributed representation of multiple networks, rather than a single functional network or subnetwork. Further, the results show that the Visual Network (VN) and Default Mode Network (DMN) associated functional networks, especially VN-DMN, exhibit a strong contribution to emotion prediction. To further estimate the cumulative effect of naturalistic long-term movie-based video-evoking emotions, we divide the 10-min episode into three stages: early stimulation (1 ~ 200 s), middle stimulation (201 ~ 400 s), and late stimulation (401 ~ 600 s) and examine the emotion prediction performance at different stimulation stages. We found that the late stimulation has a stronger predictive ability (accuracy=85.32%, F1-score=85.62%) compared to early and middle stimulation stages, implying that continuous exposure to emotional stimulation can lead to more intense emotions and further enhance emotion-specific distinguishable representations. The present work demonstrates that sustained sadness and happiness under naturalistic conditions are presented in emotion-specific network profiles and these expressions may play different roles in the generation and modulation of emotions. These findings elucidate the importance of network level adaptations for sustained emotional experiences during naturalistic contexts and open new venues for imaging network level contributions under naturalistic conditions.
Systematic transcriptome analysis associated with physiological and chronological aging inCaenorhabditis elegans
Authors: Ham Seokjin , Kim Sieun S. , Park Sangsoon , Kim Eun Ji E. , Kwon Sujeong , Park Hae-Eun H. , Jung Yoonji , Lee Seung-Jae V.
Published: November 2022

Aging is associated with changes in a variety of biological processes at the transcriptomic level, including gene expression. Two types of aging occur during a lifetime: chronological and physiological aging. However, dissecting the difference between chronological and physiological ages at the transcriptomic level has been a challenge because of its complexity. We analyzed the transcriptomic features associated with physiological and chronological aging usingCaenorhabditis elegansas a model. Many structural and functional transcript elements, such as noncoding RNAs and intron-derived transcripts, were up-regulated with chronological aging. In contrast, mRNAs with many biological functions, including RNA processing, were down-regulated with physiological aging. We also identified an age-dependent increase in the usage of distal 3′ splice sites in mRNA transcripts as a biomarker of physiological aging. Our study provides crucial information for dissecting chronological and physiological aging at the transcriptomic level.
Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
Authors: Hénault Mathieu , Marsit Souhir , Charron Guillaume , Landry Christian R.
Published: November 2022

Mitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. Although uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. mtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation, and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we useSaccharomycesyeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates ofSaccharomyces paradoxusandSaccharomyces cerevisiae. Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but the recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which led to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism, and the emergence of reproductive isolation.
Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
Authors: Zee Alexander , Deng Dori Z.Q. , Adams Matthew , Schimke Kayla D. , Corbett-Detig Russell , Russell Shelbi L. , Zhang Xuan , Schmitz Robert J. , Vollmers Christopher
Published: November 2022

High-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short-read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the ONT MinION by using the rolling circle to concatemeric consensus (R2C2) method to circularize and amplify the short library molecules. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, and regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.
Genetic exchange with an outcrossing sister species causes severe genome-wide dysregulation in a selfingCaenorhabditisnematode
Authors: Xie Dongying , Ye Pohao , Ma Yiming , Li Yongbin , Liu Xiao , Sarkies Peter , Zhao Zhongying
Published: November 2022

Different modes of reproduction evolve rapidly, with important consequences for genome composition. Selfing species often occupy a similar niche as their outcrossing sister species with which they are able to mate and produce viable hybrid progeny, raising the question of how they maintain genomic identity. Here, we investigate this issue by using the nematodeCaenorhabditis briggsae, which reproduces as a hermaphrodite, and its outcrossing sister speciesCaenorhabditis nigoni. We hypothesize that selfing species might develop some barriers to prevent gene intrusions through gene regulation. We therefore examined gene regulation in the hybrid F2 embryos resulting from reciprocal backcrosses between F1 hybrid progeny andC. nigoniorC. briggsae. F2 hybrid embryos with ∼75% of their genome derived fromC. briggsae(termed as bB2) were inviable, whereas those with ∼75% of their genome derived fromC. nigoni(termed as nB2) were viable. Misregulation of transposable elements, coding genes, and small regulatory RNAs was more widespread in the bB2 compared with the nB2 hybrids, which is a plausible explanation for the differential phenotypes between the two hybrids. Our results show that regulation of theC. briggsaegenome is strongly affected by genetic exchanges with its outcrossing sister species,C. nigoni, whereas regulation of theC. nigonigenome is more robust on genetic exchange withC. briggsae. The results provide new insights into how selfing species might maintain their identity despite genetic exchanges with closely related outcrossing species.
Synthesis and structural characterization of a new dinuclear platinum(III) complex, [Pt2Cl4(NH3)2{μ-HN=C(O)But}2]
Authors: Vinci Doriana , Chateigner Daniel
Published: November 2022

Cisplatin plays an important role in treating many tumors. However, its pharmacological potential is limited by several side effects (nephrotoxicity, neurotoxicity, hair loss) and the resistance of many cancer types. In the effort of overcome resistance to cisplatin, more than 3000 platinum complexes have been synthesized in the past 45 years, but only about 30 have demonstrated adequate pharmacological platinum(III) complexes have been synthesized and their structure determined, because some of these exhibit antitumor and catalytic activity for the oxidation of olefins. Herein the synthesis of a new dinuclear platinum(III) complex with two butyl(amidato) bridging ligands, namely [Pt2Cl4(NH3)2{μ-HN=C(O)Bu
t
}2], is reported. The complex was characterized by means of nuclear magnetic resonance (1H and 195Pt NMR) and infrared spectroscopy, and the crystal structure determined using X-ray single-crystal diffraction. This complex, to the best of our knowledge, is the first dinuclear complex of PtIII with two butyl(amidato) bridging ligands with a head-to-tail configuration.
Evolution of intermolecular contacts with temperature and pressure in bromoethane and iodoethane – a comparative study
Authors: Bujak Maciej , Olejniczak Anna , Podsiadło Marcin
Published: November 2022

At ambient conditions two liquids, bromoethane, C2H5Br (MBE, m.p. 154.6 K) and iodoethane, C2H5I (MIE, m.p. 162.1 K), have been crystallized under both isobaric and isochoric conditions using in situ low-temperature and high-pressure techniques. The single-crystal X-ray diffraction studies, supported by the isothermal compressibility and isobaric differential scanning calorimetry measurements, allowed the monitoring and analysis at low temperature and high pressure of the effects of externally induced changes in MBE and MIE. The monoclinic MBE and MIE crystals are found to be isostructural. They are stable, in the investigated regimes, i.e. down to 100 K/0.1 MPa and up to ∼295 K/3.7 GPa, without undergoing any symmetry or phase change. Both the contraction and compression is mainly noted for the intermolecular separation distances. The Hirshfeld surface analysis of intermolecular contacts clearly shows the nature of occurrence and hierarchy of interactions pointing out the role played by Br/I...Br/I contacts, in particular at ambient temperature and high-pressure conditions. The preferences for the formation of intermolecular contacts in MIE are more pronounced and do not require such extreme conditions as in the case of MBE. It is notable that the Br/I...Br/I and Br/I...H contacts could be basically classified as type-I interactions.
Using deep-learning predictions of inter-residue distances for model validation
Authors: Sánchez Rodríguez Filomeno , Chojnowski Grzegorz , Keegan Ronan M. , Rigden Daniel J.
Published: November 2022

Determination of protein structures typically entails building a model that satisfies the collected experimental observations and its deposition in the Protein Data Bank. Experimental limitations can lead to unavoidable uncertainties during the process of model building, which result in the introduction of errors into the deposited model. Many metrics are available for model validation, but most are limited to consideration of the physico-chemical aspects of the model or its match to the experimental data. The latest advances in the field of deep learning have enabled the increasingly accurate prediction of inter-residue distances, an advance which has played a pivotal role in the recent improvements observed in the field of protein ab initio modelling. Here, new validation methods are presented based on the use of these precise inter-residue distance predictions, which are compared with the distances observed in the protein model. Sequence-register errors are particularly clearly detected and the register shifts required for their correction can be reliably determined. The method is available in the ConKit package (https://www.conkit.org).