bluuebunny/crossref_metadata_2025 huggingface dataset:
Rats Chasing the Dragon: A new heroin inhalation method
Authors: Gutierrez Arnold , Taffe Michael A.
Published: August 2023

Rationale

Despite extensive human use of the inhalation route for ingesting opioids, models in rodents have mostly been limited to parenteral injection and oral dosing. Methods using electronic drug delivery systems (EDDS; “e-cigarettes”) have shown efficacy in rodent models but these do not faithfully mimic the most popular human inhalation method of heating heroin to the point of vaporization.

Objective

This study was designed to determine if direct volatilization of heroin hydrochloride delivers effective heroin doses to rodents.

Methods

Middle aged rats were exposed to vapor created by direct heating of heroin HCl powder in a ceramic e-cigarette type atomizer. Efficacy was determined with a warm water tail withdrawal nociception assay, rectal temperature and self-administration.

Results

Ten minutes of inhalation of vaporized heroin slowed response latency in a warm water tail withdrawal assay and increased rectal temperature in male rats, in a dose-dependent manner. Similar antinociceptive effects in female rats were attenuated by the opioid antagonist naloxone (1.0 mg/kg, s.c.). Female rats made operant responses for heroin vapor in 15-minute sessions, increased their response rate when the reinforcement ratio increased from FR1 to FR5, and further increased their responding when vapor delivery was omitted. Anti-nociceptive effects of self-administered volatilized heroin were of a similar magnitude as those produced by the 10-minute non-contingent exposure.

Conclusions

This study shows that “chasing the dragon” methods of inhalation of heroin can be modeled successfully in the rat. Inhalation techniques may be particularly useful for longer term studies deep into middle age of rat species.
Epigenetic Regulation of Endothelial Extracellular Matrix Components is Critical for Murine Lung Development
Authors: Wu Meng-Ling , Wheeler Kate , Silasi-Mansat Robert , Lupu Florea , Griffin Courtney T.
Published: August 2023

Background

The chromatin remodeling enzymes BRG1 (brahma-related gene 1) and CHD4 (chromodomain helicase DNA binding protein 4) independently regulate transcription of genes critical for vascular development, but their coordinated impact on vessels in late- stage embryos has not been explored.

Methods

In this study we genetically deleted endothelialBrg1andChd4in mixed background mice (Brg1fl/fl;Chd4fl/fl;VE-Cadherin-Cre+), and littermates that were negative for Cre recombinase were used as controls. Perinatal lung tissue was analyzed by immunostaining, immunoblots, and flow cytometry. Quantitative reverse transcription PCR was used to determine gene expression, and chromatin immunoprecipitation revealed gene targets of BRG1 and CHD4 in cultured endothelial cells (ECs).

Results

We found thatBrg1/Chd4double mutants died soon after birth with small and compact lungs. Despite having normal cellular composition, distal air sacs of the mutant lungs displayed diminished ECM (extracellular matrix) components and TGFβ (transforming growth factor beta) signaling, which typically promotes matrix synthesis. Transcripts for collagen- and elastin-related genes and the TGFβ ligandTgfb1were decreased in mutant lung ECs, but genetic deletion of endothelialTgfb1failed to recapitulate the small lungs and ECM defects seen inBrg1/Chd4mutants. We instead found several ECM genes to be direct targets of BRG1 and CHD4 in cultured ECs.

Conclusions

Collectively, our data highlight essential roles for ECs in promoting ECM deposition at late stages of embryonic lung development. Moreover, this endothelial ECM production is epigenetically regulated.

Abstract Figure

HIGHLIGHTS

Genetic deletion of the chromatin remodeling enzymes BRG1 and CHD4 in endothelial cells of late-stage mouse embryos (Brg1/Chd4-ECdko) results in small and compact lungs at birth.

Mutant embryos display reduced collagen IV deposition, dysregulated elastin fibers, and diminished TGFβ1 in the distal air sacs.

Our combined in vitro and in vivo analyses indicate that BRG1 and CHD4 epigenetically regulate collagen IV- and elastin-related gene expression in embryonic ECs to promote proper lung development.
Video gaming, but not reliance on GPS, is associated with spatial navigation performance
Authors: Yavuz Emre , He Chuanxiuyue , Goodroe Sarah , Ganstrom Chris , Coutrot Antoine , Hornberger Michael , Hegarty Mary , Spiers Hugo J.
Published: August 2023

Recent evidence suggests that greater reliance on GPS-assisted devices is associated with poorer navigation ability. Contrastingly, studies have shown that video gaming can enhance navigation ability. While gender differences in navigation ability in favour of men are well-reported, it remains unclear if the effects of reliance on GPS and video gaming on navigation performance are influenced by gender. We investigated whether gender would influence the effect of gaming experience and reliance on GPS on navigation ability using the mobile app Sea Hero Quest, which has been shown to predict real-world wayfinding performance. Alongside navigation performance assessment we asked a series of self-report questions relating to reliance on GPS, navigation strategies and gaming experience with a group of US-based participants (n = 822, 280 men, 542 women, mean age = 26.3 years, range = 18-52 years). A multivariate linear regression model found no significant association between reliance on GPS and navigation performance for either gender. There was a significant association between weekly hours of video gaming and navigation performance which was not moderated by gender. After accounting for video game experience, gender was no longer significantly associated with navigation performance. These findings have implications for which daily activities may enhance or disrupt specific cognitive abilities. Future studies applying an interventional design and real-world navigation testing would be useful to determine whether video games playing increases navigation skill, or whether those who are good at navigating tend to play more video games.
A multi-channel TMS system enabling accurate stimulus orientation control during concurrent ultra-high-field MRI for preclinical applications
Authors: Souza Victor H. , Sinisalo Heikki , Korhonen Juuso T. , Paasonen Jaakko , Nyrhinen Mikko , Nieminen Jaakko O. , Koponen Maria , Kettunen Mikko , Gröhn Olli , Ilmoniemi Risto J.
Published: August 2023

Monitoring cortical responses to neuromodulation protocols on preclinical models can elucidate fundamental mechanisms of brain function. Concurrent brain stimulation and imaging is challenging, usually compromising spatiotemporal resolution, accuracy, and versatility. Here we report a non-invasive brain stimulation system with electronic control of neuromodulation parameters in a 9.4-T magnetic resonance imaging (MRI) environment. In the imaging scanner, transcranial magnetic stimulation is delivered with a set of two coils and the MRI signals are recorded with a radiofrequency coil. The coil set provides millisecond-scale electronic control of the stimulus orientation with 1° resolution. Without physically rotating the coils, we evoked orientation-specific muscle responses after cortical stimulation on an anesthetized rat. We show that the stimulation pulses do not affect the anatomical imaging quality, and imaging signals are disrupted only if recorded before 10 ms after pulse delivery. Concurrent electronically targeted brain stimulation and neuroimaging sets the stage for the causal investigation of whole-brain network functions, endorsing more efficient treatment protocols.
Comparative Analysis of Cameras and Software Tools for Skeleton Tracking
Authors: Aharony Naama , Meshurer Amir , Krakovski Maya , Parmet Yisrael , Melzer Itshak , Edan Yael
Published: August 2023

Background

Skeleton tracking is a valuable tool for monitoring user performance and has been performed with different sensors and software tools. It enables to quantify 3D motion accurately. We present a comparative analysis of cameras and software tools utilized in skeleton tracking. We describe an experimental design and analysis methods with four steps. Specifically, we conducted an analysis comparing two ZED-2i cameras with a RealSense camera using commercial skeleton tracking algorithms.

Methods

The comparative analysis methodology describes the experimental design and analysis methods for comparing kinematic data from both upper and lower extremities. An experiment to evaluate the performance of three different cameras (RealSense, ZED2mm, and ZED4mm) and three skeleton tracking algorithms (PyZED, Nuitrack, and MediaPipe) was performed with 16 participants. The participants were required to walk along a 6-meter-long path while moving their hands up and down horizontally. Ground truth was measured by a Vicon 3D motion analysis system. Two groups of features corresponding to the upper and lower extremities were derived from the raw data and compared using two methods. In the first method, the RMSE values were compared to the data from the Vicon system. The RMSE results were also combined using two grading techniques with different feature importance weights to determine the camera with the lowest RMSE. In the second method, a linear mix model with a Wald statistical test was applied.

Results

The ZED-2i cameras outperformed the RealSense camera across upper- and lower-extremity features and different weights. The ZED2mm camera showed better average median grading, lower standard deviation, and superior performance in the model analysis.

Conclusion

The comparative analysis methodology provides a systematic method to compare software tools and cameras for skeleton tracking. The ranking enables to prioritize different features. Skeleton tracking with the ZED cameras yielded better performances for both upper and lower extremities features.
Model integration of circadian and sleep-wake driven contributions to rhythmic gene expression reveals novel regulatory principles
Authors: Jan Maxime , Jimenez Sonia , Hor Charlotte N. , Dijk Derk-Jan , Skeldon Anne C. , Franken Paul
Published: August 2023

Transcriptome studies aim at gaining insight into the molecular pathways underlying biological processes. Analyses of gene-expression dynamics in research on circadian rhythms and sleep homeostasis describe these two processes independently, using separate models such as sinusoidal oscillations and exponential saturating functions. Rhythmically expressed genes are, however, influenced by both processes. We therefore implemented a driven, damped harmonic oscillator model which can accommodate both types of dynamics by varying the degree of damping. This makes it possible to estimate the contribution of circadian and sleep-wake driven influences on the expression of a gene within the framework of a single model. We applied the model to cortex, liver, and blood data obtained in mice and humans. The model reliably captured a wide range of rhythmic dynamics under various experimental conditions, including the long-term amplitude reduction of cortical clock-gene rhythms observed after sleep deprivation. Cortical gene expression was generally influenced more by sleep-wake driven than circadian factors, while the opposite was observed in liver and blood. Importantly, the model suggested that sleep-wake state can alter gene expression with a delayed, long-lasting response not previously considered. Our model further predicted that, perhaps paradoxically, the gain in sleep time after sleep deprivation, delayed re-establishing baseline expression rhythms of intrinsically oscillatory transcripts indicating that similar to insufficient sleep, also excess sleep can impact rhythmic gene expression. Because of the tissue- and gene-specific responses, sleep deprivation led to a profound intra- and inter-tissue desynchronization which in the cortex lasted well beyond phenotypic sleep-wake recovery. The results demonstrate that analyzing rhythmic gene expression must take the complex interactions between circadian and sleep-wake influences into account. The model is a versatile tool with a low number of free parameters to fit and predict gene expression under a variety of conditions relevant to society.
Combining molecular dynamics simulations and X-ray scattering techniques for the accurate treatment of protonation degree and packing of ionizable lipids in monolayers
Authors: Grava Miriam , Ibrahim Mohd , Sudarsan Akhil , Pusterla Julio , Philipp Julian , Rädler Joachim O. , Schwierz Nadine , Schneck Emanuel
Published: August 2023

The pH-dependent change in protonation of ionizable lipids is crucial for the success of lipid-based nanoparticles as mRNA delivery systems. Despite their widespread application in vaccines, the structural changes upon acidification are not well understood. Molecular dynamics simulations support structure prediction but require an a-priori knowledge of the lipid packing and protonation degree. The presetting of the protonation degree is a challenging task in the case of ionizable lipids since it depends on pH and on the local lipid environment and often lacks experimental validation. Here, we introduce a methodology of combining all-atom molecular dynamics simulations with experimental total-reflection X-ray fluorescence and scattering measurements for the ionizable lipid Dlin-MC3-DMA (MC3) in POPC monolayers. This joint approach allows us to simultaneously determine the lipid packing and the protonation degree of MC3. The consistent parameterization is expected to be useful for further predictive modeling of the action of MC3-based lipid nanoparticles.
Pleistocene glaciation advances the younger temporal dimension of species diversification in a major biodiversity hotspot
Authors: Rana Santosh Kumar , Rana Hum Kala , Landis Jacob B. , Kuang Tianhui , Chen Juntong , Wang Hengchang , Deng Tao , Davis Charles C. , Sun Hang
Published: August 2023

The expansive Himalayan-Hengduan Mountains (HM) and Qinghai-Tibet Plateau (QTP) form a biodiversity hotspot imperiled by global change. The species diversity, resulting from myriad factors led to plant diversification from 10 million years ago till now. However, despite understanding speciation timing better, a lack of in-depth population-level studies and a dearth of organismal sampling among closely related species and populations leaves an incomplete view of diversification trends and biotic influences.

We delve into the complex factors influencing diversification through genomic and eco-morphological analysis within theStellera chamaejasmeL. complex, known for its significant floral diversity.

Our results uncover four cryptic species, indicating a more recent and younger diversification period (∼2.67–0.9 Mya), driven by Pleistocene glaciation and a complex set of interacting biotic factors. These factors prompted allopatric speciation and advocated cyclical warming–cooling episodes along latitudinal and altitudinal gradients throughout the Pleistocene.

The study emphasizes the existence of cryptic species within these mountains, broadening our understanding of species diversification to more recent than previously recognized. This novel perspective may reshape evolutionary paradigms in plant science. Additionally, it also brings to light concerns over future warming’s possible impacts on alpine species distribution and speciation, underlining the urgency for increased conservation efforts.
A multigenerational Turing model reproduces transgressive petal spot phenotypes in hybridMimulus
Authors: Simmons Emily S. G. , Cooley Arielle M. , Puzey Joshua R. , Conradi Smith Gregory D.
Published: August 2023

The origin of phenotypic novelty is a perennial question of genetics and evolution. To date, few studies of biological pattern formation specifically address multi-generational aspects of inheritance and phenotypic novelty. For quantitative traits influenced by many segregating alleles, offspring phenotypes are often intermediate to parental values. In other cases, offspring phenotypes can be transgressive to parental values. For example, in the model organismMimulus(monkeyflower), the offspring of parents with solid-colored petals exhibit novel spotted petal phenotypes. These patterns are controlled by an activator-inhibitor gene regulatory network with a small number of loci. Here we develop and analyze a model of hybridization and pattern formation that accounts for inheritance in diploid gene regulatory networks composed of either homozygous or heterozygous alleles. We find that the resulting model of multi-generational Turing-type pattern formation can reproduce the transgressive petal phenotypes observed inMimulus. The model gives insight into how non-patterned parent phenotypes can yield phenotypically transgressive, patterned offspring, aiding in the development of empirically testable hypotheses.
Amyloidosis and ageing have differential effects on microglial Ca2+activity in the mouse brain
Authors: Izquierdo Pablo , Jolivet Renaud B. , Attwell David , Madry Christian
Published: August 2023

In microglia, changes in intracellular calcium concentration ([Ca2+]i) may regulate process motility, inflammasome activation, and phagocytosis. However, while neurons and astrocytes exhibit frequent spontaneous Ca2+activity, microglial Ca2+signals are much rarer and poorly understood. Here, we studied [Ca2+]ichanges of microglia in acute brain slices using Fluo-4–loaded cells and mice expressing GCaMP5g in microglia. Spontaneous Ca2+transients occurred ∼5 times more frequently in individual microglial processes than in their somata. We assessed whether microglial Ca2+responses change in Alzheimer’s disease (AD) usingAppNL-G-Fknock-in mice. Proximity to Aβ plaques strongly affected microglial Ca2+activity. Although spontaneous Ca2+transients were unaffected in microglial processes, they were 5-fold more frequent in microglial somata near Aβ plaques than in wild-type microglia. Microglia away from Aβ plaques in AD mice showed intermediate properties for morphology and Ca2+responses, partly resembling those of wild-type microglia. By contrast, somatic Ca2+responses evoked by tissue damage were less intense in microglia near Aβ plaques than in wild-type microglia, suggesting different mechanisms underlying spontaneous vs. damage-evoked Ca2+signals. Finally, as similar processes occur in neurodegeneration and old age, we studied whether ageing affected microglial [Ca2+]i. Somatic damage-evoked Ca2+responses were greatly reduced in microglia from old mice, as in the AD mice. In contrast to AD, however, old age did not alter the occurrence of spontaneous Ca2+signals in microglial somata but reduced the rate of events in processes. Thus, we demonstrate distinct compartmentalised Ca2+activity in microglia from healthy, aged and AD-like brains.
Plug-and-play protein biosensors using aptamer-regulated in vitro transcription
Authors: Lee Heonjoon , Xie Tian , Yu Xinjie , Schaffter Samuel W. , Schulman Rebecca
Published: August 2023

Molecular biosensors that accurately measure protein concentrations without external equipment are critical for solving numerous problems in diagnostics and therapeutics. Modularly transducing the binding of protein antibodies, protein switches or aptamers into a useful output remains challenging. Here, we develop a biosensing platform based on aptamer-regulated transcription in which aptamers integrated into transcription templates serve as inputs to molecular circuits that can be programmed to a produce a variety of responses. We modularly design molecular biosensors using this platform by swapping aptamer domains for specific proteins and downstream domains that encode different RNA transcripts. By coupling aptamer-regulated transcription with diverse transduction circuits, we rapidly construct analog protein biosensors or digital protein biosensors with detection ranges that can be tuned over two orders of magnitude. Aptamer-regulated transcription is a straightforward and inexpensive approach for constructing programmable protein biosensors suitable for diverse research and diagnostic applications.

One sentence summary

We develop a modular platform for biosensing across a wide dynamic range using aptamer-regulated transcription to detect different proteins and molecular circuits to process the RNA transcript outputs.
Interareal synaptic inputs underlying whisking-related activity in the primary somatosensory barrel cortex
Authors: Kawatani Masahiro , Horio Kayo , Ohkuma Mahito , Li Wan-Ru , Yamashita Takayuki
Published: August 2023

Body movements, especially orofacial movements, are known to influence brain-wide neuronal activity. In the sensory cortex, thalamocortical bottom-up inputs and motor-sensory top-down inputs are thought to affect the dynamics of membrane potentials (Vm) of neurons and change their processing of sensory information during movements. However, direct perturbation of the axons projecting to the sensory cortex from other remote areas during movements has remained unassessed, and therefore the interareal circuits generating motor-related signals in sensory cortices are still unclear. Using a Gi-coupled opsin, eOPN3, we here inhibited interareal signals incoming to the whisker primary somatosensory cortex (wS1) of awake behaving mice and tested their effects on whisking-related changes in neuronal activities in wS1. Spontaneous whisking in air induced the changes in spike rates of a fraction of wS1 neurons which were accompanied by depolarization and substantial reduction of slow-wave oscillatory fluctuations of Vm. Despite an extensive innervation, inhibition of inputs from the whisker primary motor cortex (wM1) to wS1 did not alter the spike rates and Vmdynamics of wS1 neurons during whisking. In contrast, inhibition of axons from the whisker-related thalamus (wTLM) and the whisker secondary somatosensory cortex (wS2) to wS1 largely attenuated the whisking-related supra- and sub-threshold Vmdynamics of wS1 neurons. Our findings thus suggest that sensorimotor integration in wS1 during spontaneous whisking is mediated by direct synaptic inputs from wTLM and wS2 rather than from wM1.

Significance statement

The traditional viewpoint underscores the importance of motor-sensory projections in shaping movement-induced neuronal activity within sensory cortices. However, this study challenges such established views. We reveal that the synaptic inputs from the whisker primary motor cortex do not alter the dynamics of neuronal activity in the whisker primary somatosensory cortex (wS1) during spontaneous whisker movements. Furthermore, we make a novel observation that inhibiting inputs from the whisker secondary somatosensory cortex (wS2) substantially curtails movement-related activities in wS1. These findings provoke a reconsideration of the role of motor-sensory projections in sensorimotor integration and bring to light a new function for wS2-to-wS1 projections.
Cryopreservation of cerebrospinal fluid cells preserves transcriptomics integrity for single-cell analysis
Authors: Kodali Mahesh , Antone Jerry , Alsop Eric , Jayakumar Rojashree , Parikh Khushi , Sanchez-Molina Paula , Ajami Bahareh , Arnold Steven , Jensen Kendall , Das Sudeshna , Weinberg Marc S.
Published: August 2023

Cerebrospinal fluid (CSF) matrix biomarkers have become increasingly valuable surrogate markers of neuropsychiatric diseases in research and clinical practice. In contrast, CSF cells have been rarely investigated due to their relative scarcity and fragility, and lack of common collection and cryopreservation protocols, with limited exceptions for neurooncology and primary immune-based diseases like multiple sclerosis. the advent of a microfluidics-based multi-omics approaches to studying individual cells has allowed for the study of cellular phenotyping, intracellular dynamics, and intercellular relationships that provide multidimensionality unable to be obtained through acellular fluid-phase analyses. challenges to cell-based research include site-to-site differences in handling, storage, and thawing methods, which can lead to inaccuracy and inter-assay variability. In the present study, we performed single-cell RNA sequencing (10x Genomics) on fresh or previously cryopreserved human CSF samples from three alternative cryopreservation methods: Fetal Bovine Serum with Dimethyl sulfoxide (FBS/DMSO), FBS/DMSO after a DNase step (a step often included in epigenetic studies), and cryopreservation using commercially available Recovery© media. In comparing relative differences between fresh and cryopreserved samples, we found little effect of the cryopreservation method on being able to resolve donor-linked cell type proportions, markers of cellular stress, and overall gene expression at the single-cell level, whereas donor-specific differences were readily discernable. We further demonstrate the compatibility of fresh and cryopreserved CSF immune cell sequencing using biologically relevant sexually dimorphic gene expression differences by donor. Our findings support the utility and interchangeability of FBS/DMSO and Recovery cryopreservation with fresh sample analysis, providing a methodological grounding that will enable researchers to further expand our understanding of the CSF immune cell contributions to neurological and psychiatric disease.
Gaze tracking of large-billed crows (Corvus macrorhynchos) in a motion-capture system
Authors: Itahara Akihiro , Kano Fumihiro
Published: August 2023

The visually guided behaviors of corvids (Corvidae) are often examined in previous studies because they provide important clues about their perception, attention, and cognition. However, the details regarding how they orient their heads toward the visual targets (or how they use their visual fields when attending to the visual targets) remain largely unclear. This study used a newly established motion capture system to examine the visual field use of large-billed crows (Corvus macrorhynchos). Study 1 employed an established ophthalmoscopic reflex technique to identify the visual field configuration, including the binocular width and optic axes, as well as the degree of eye movement. Study 2 used the motion capture system to track the head movements of freely moving crows and examined how they oriented their reconstructed visual fields toward attention-getting objects. When visual targets were moving, the crows used their binocular visual fields, particularly around the projection of the beak-tip. When the visual targets stopped moving, crows frequently used non-binocular visual fields, particularly around the regions where their optic axes were found in Study 1 (close to their visual axes). On such occasions, the crows slightly preferred the right eye. Overall, the visual field use of crows is clearly predictable. Thus, while the untracked eye movements could introduce some level of uncertainty (typically within 15 degrees), we demonstrated the feasibility of inferring a crow’s attentional focus by 3D tracking of their heads. Our system represents a promising initial step towards establishing gaze tracking methods for studying corvid behavior and cognition.
Measuring and monitoring skill learning in closed-loop myoelectric hand prostheses using speed-accuracy tradeoffs
Authors: Mamidanna Pranav , Gholinezhad Shima , Farina Dario , Dideriksen Jakob Lund , Dosen Strahinja
Published: August 2023

Objective

Closed-loop myoelectric prostheses, which combine supplementary sensory feedback and electromyography (EMG) based control, hold the potential to narrow the divide between natural and bionic hands. The use of these devices, however, requires dedicated training. Therefore, it is crucial to develop methods that quantify how users acquire skilled control over their prostheses to effectively monitor skill progression and inform the development of interfaces that optimize this process.

Approach

Building on theories of skill learning in human motor control, we measured speed-accuracy tradeoff functions (SAFs) to comprehensively characterize learning-induced changes in skill – as opposed to merely tracking changes in task success across training – facilitated by a closed-loop interface that combined proportional control and EMG feedback. Sixteen able-bodied and one amputee participated in a 3-day experiment where they were instructed to perform the box-and-blocks task using a timed force-matching paradigm at four specified speeds to reach two target force levels, such that the SAF could be determined.

Main results

We found that the participants’ accuracy increased in a similar way across all speeds we tested. Consequently, the shape of the SAF remained similar across days, at both force levels. Further, we observed that EMG feedback enabled participants to improve their motor execution in terms of reduced trial-by-trial variability, a hallmark of skilled behavior. We then fit a power law model of the SAF, and demonstrated how the model parameters could be used to identify and monitor changes in skill.

Significance

We comprehensively characterized how an EMG feedback interface enabled skill acquisition, both at the level of task performance and movement execution. More generally, we believe that the proposed methods are effective for measuring and monitoring user skill progression in closed-loop prosthesis control.
A new experimental evidence-weighted signaling pathway resource in FlyBase
Authors: Attrill Helen , Antonazzo Giulia , Goodman Joshua L. , Thurmond Jim , Strelets Victor B , Brown Nicholas H. ,   the FlyBase Consortium
Published: August 2023

Research in model organisms is central to the characterization of signaling pathways in multicellular organisms. Here, we present the systematic curation of 17 Drosophila signaling pathways using the Gene Ontology framework to establish a comprehensive and dynamic resource that has been incorporated into FlyBase, providing visualization and data integration tools to aid research projects. By restricting to experimental evidence reported in the research literature and quantifying the amount of such evidence for each gene in a pathway, we captured the landscape of empirical knowledge of signaling pathways inDrosophila.

Summary statement

Comprehensive curation of Drosophila signaling pathways and new visual displays of the pathways provides a new FlyBase resource for researchers, and new insights into signaling pathway architecture.
Studies on the International Space Station to assess the effects of microgravity on iPSC-derived neural organoids
Authors: Marotta Davide , Ijaz Laraib , Barbar Lilianne , Nijsure Madhura , Stein Jason , Clements Twyman , Stoudemire Jana , Grisanti Paula , Noggle Scott A. , Loring Jeanne F. , Fossati Valentina
Published: August 2023

Exposure to microgravity in low-Earth orbit (LEO) has been shown to affect human cardiovascular, musculoskeletal, and immune systems. Post-flight brain imaging indicates that reports about astronauts and mouse models suggest that microgravity may cause intracranial fluid shifts and possibly alter white and gray matter of the brain [1]. To focus on the effects of microgravity on the brain, we used induced pluripotent stem cells (iPSCs) to produce three-dimensional (3D) human neural organoids as models of the nervous system. We studied iPSCs derived from four individuals, including people with the neurological diseases primary progressive multiple sclerosis (PPMS) and Parkinson’s disease (PD) and non-symptomatic controls. We patterned the organoids toward cortical and dopaminergic fates representing regions of the brain affected by MS and PD, respectively. Microglia were generated from the same cell lines and integrated into a portion of the organoids. The organoids were maintained for 30 days in a novel static culture system on the International Space Station (ISS) and live samples were returned to Earth. The post-flight samples were evaluated using histology, transcriptome and secretome analysis. Microglia-specific genes and secreted proteins were detectable in the microglia-containing organoid cultures. The gene expression analyses of individual organoids cultured in LEO and on Earth suggest that cell proliferation was lower and neural cells were more mature in samples that were cultured in LEO. These experiments lay the groundwork for further studies, including long term studies to investigate the effects of microgravity on the brain. With two more missions using similar cells, we are determining whether this effect of microgravity is consistent in separate experiments. Such studies may ultimately aid in developing countermeasures for the effects of microgravity on the nervous systems of astronauts during space exploration and suggest novel therapeutic interventions for neurological diseases on Earth.
Nuclear Transformation In Metalloenzyme. A Novel And High Potential Cancer Treatment Research
Authors: Van Luyen Tran , Tuan Truong Hoang
Published: August 2023

In this study, we have introduced a novel approach to cancer treatment involving the deactivation of metalloenzymes through the utilization of radioisotopes. The concept of leveraging radioisotopes to interact with metalloenzymes represents a groundbreaking theoretical advancement. Through simulations utilizing the MIRD code and based on the consistent concentration of stable Mg within stage 2A cancerous tissue, we have quantified the potential success rates.

To conduct these simulations, we employed 0.1 nanograms (ng) of stable Mg, which corresponds to an activity of 19.7 MBq of Mg-28. This data was input into the MIRD calculations to estimate the absorbed doses within various organs, employing diverse methods of radioisotope administration into the body. Remarkably, even with a mere 1‰ probability of effectively reaching the intended cancerous tissues, this quantity of Mg-28 demonstrates the capability to render billions of Mg-containing metalloenzymes inactive.

The remarkable efficiency achieved through precise radioisotope targeting underscores the promise of this methodology. Nevertheless, the findings underscore the necessity of undertaking both in vitro and in vivo research initiatives prior to embarking on clinical trials.
Meningeal CSF transport is primarily mediated by the arachnoid and pia maters during development
Authors: Pan Shelei , Koleske Joshua , Koller Gretchen M. , Halupnik Grace L. , Alli Abdul-Haq O. , Koneru Shriya , DeFreitas Dakota , Ramagiri uthi , Strahle Jennifer M.
Published: August 2023

Background

The recent characterization of the glymphatic system and meningeal lymphatics has re-emphasized the role of the meninges in facilitating CSF transport and clearance. Here, we characterize small and large CSF solute distribution patterns along the intracranial and surface meninges in neonatal rodents and compare our findings to a rodent model of intraventricular hemorrhage-posthemorrhagic hydrocephalus. We also examine CSF interactions with the tela choroidea and its pial invaginations into the choroid plexuses of the lateral, third, and fourth ventricles.

Methods

1.9-nm gold nanoparticles, 15-nm gold nanoparticles, or 3 kDa Red Dextran Tetramethylrhodamine constituted in aCSF were infused into the right lateral ventricle of P7 rats to track CSF circulation. 10 minutes post-1.9-nm gold nanoparticle and Red Dextran Tetramethylrhodamine injection and 4 hours post-15-nm gold nanoparticle injection, animals were sacrificed and brains harvested for histologic analysis to identify CSF tracer localization in the cranial and spine meninges and choroid plexus. Spinal dura and leptomeninges (arachnoid and pia) wholemounts were also performed.

Results

There was significantly less CSF tracer distribution in the dura compared to the arachnoid and pia maters in neonatal rodents. Both small and large CSF tracers were transported intracranially to the arachnoid and pia mater of the perimesencephalic cisterns and tela choroidea, but not the dura mater of the falx cerebri. CSF tracers followed a similar distribution pattern in the spinal meninges. In the choroid plexus, there was large CSF tracer distribution in the apical surface of epithelial cells, and small CSF tracer along the basolateral surface. There were no significant differences in tracer intensity in the intracranial meninges of control vs. intraventricular hemorrhage-posthemorrhagic hydrocephalus (PHH) rodents, indicating preserved meningeal transport in the setting of PHH.

Conclusions

Differential CSF tracer handling by the leptomeninges suggests that there are distinct roles for CSF handling between the arachnoid-pia and dura maters in the developing brain. Similarly, differences in apical vs. luminal choroid plexus CSF handling may provide insight into particle-size dependent CSF transport at the CSF-choroid plexus border.
Long-Term Exposure of Cells to Cdk4 Inhibitor Palbociclib Leads to Chromosomal Aberrations
Authors: Kaulich Manuel , Dowdy Steven F.
Published: August 2023

Breast cancers are often driven by mutations, alterations and activation of cell cycle regulatory proteins, including the retinoblastoma tumor suppressor protein (Rb), cyclin E and cyclin-dependent kinases (Cdks), especially cyclin D:Cdk4/6 complexes. There are currently three FDA approved Cdk4/6 inhibitors (Cdk4i) for treating breast cancer. The standard treatment protocol is 21 days of continuous Cdk4i treatment, followed by a 7 day cessation period and then repeating the 28 day protocol. We asked the question of what happens to cells that reenter the cell cycle during the 7 day Cdk4i cessation period. Using RPE1 cells containing visual reporter endogenous histone 2B and p27 genes tagged with eGFP and mCherry, we treated the cells with a Cdk4i, Palbociclib for 1 to 42 days that spanned the clinical exposure, followed by drug release (washout) and video microscopic analysis. Surprisingly, we found that as little as 4 days of Cdk4i treatment and release resulted in a significant increase in micronuclei and multinucleated cells that had reentered the cell cycle. The peak chromosomal aberration occurred between 14 and 35 days, a timing that spans the clinical dosing regimen.These observations raise questions concerning the potential that cycling patients on and off of Cdk4 inhibitors may generate gross chromosomal changes to tumor cells that reenter the cell cycle during the 7 day clinical cessation (washout) period and thereby increase the potential to initiate secondary oncogenic events.
Probing for Intentions: The Early Readiness Potential Does Not Reflect Awareness of Motor Preparation
Authors: Gavenas Jake , Schurger Aaron , Maoz Uri
Published: August 2023

Voluntary actions are typically preceded by the Readiness Potential (RP), a negative midfrontal EEG deflection that begins ∼2 seconds before movement. What cognitive and neural process the RP reflects and how it relates to conscious intention remain unclear due to conflicting findings. We investigated the neural basis and cognitive significance of the RP in a novel probe-based paradigm. Contrary to prior reports, we found that pre-probe RP buildups were not related to reported awareness of motor preparation. Computational modeling suggested that the best explanation for these results is via metacognitive access to stochastic accumulation. Reported preparation was also related to beta desynchronization over contralateral motor cortex shortly before probe onset. We conclude that the RP may be metacognitively accessible in response to external task demands but does not reflect the onset of a conscious intention. We discuss implications of these findings for voluntary action initiation and intention awareness.

Highlights

We investigate the mechanisms underlying voluntary action initiation in a new probe paradigm.

Contrary to prior results, the readiness does not reflect reported awareness of motor preparation.

Computational modeling supports stochastic accumulation over linear ballistic accumulation and classic RP models.

Reported awareness of motor preparation may emerge from metacognitive access to stochastic accumulation.

Time-frequency analysis suggests reported awareness may also relate to pre-probe beta desynchronization.
Modulation of Viability, Proliferation, and Stemness by Rosmarinic Acid in Medulloblastoma Cells: Involvement of HDACs and EGFR
Authors: Herlinger Alice Laschuk , Michaelsen Gustavo Lovatto , Sinigaglia Marialva , Fratini Lívia , Debom Gabriela Nogueira , Braganhol Elizandra , de Farias Caroline Brunetto , Brunetto Algemir Lunardi , Brunetto André Tesainer , Jaeger Mariane da Cunha , Roesler Rafael
Published: August 2023

Medulloblastoma (MB) is a heterogeneous group of malignant pediatric brain tumors, divided into molecular groups with distinct biological features and prognosis. Currently available therapy often results in poor long-term quality of life for patients, which will be afflicted by neurological, neuropsychiatric, and emotional sequelae. Identifying novel therapeutic agents capable of targeting the tumors without jeopardizing patients’ quality of life is imperative. Rosmarinic acid (RA) is a plant-derived compound whose action against a series of diseases including cancer has been investigated, with no side effects reported so far. Previous studies have not examined whether RA has effects in MB. Here, we show RA is cytotoxic against human Daoy (IC50= 168 μM) and D283 (IC50= 334 μM) MB cells. Exposure to RA for 48 h reduced histone deacetylase 1 (HDAC1) expression while increasing H3K9 hyperacetylation, reduced epidermal growth factor (EGFR) expression, and inhibited EGFR downstream targets extracellular-regulated kinase (ERK)1/2 and AKT in Daoy cells. These modifications were accompanied by increased expression ofCDKN1A/p21, reduced expression ofSOX2, and a decrease in proliferative rate. Treatment with RA also reduced cancer stem cell markers expression and neurosphere size. Taken together, our findings indicate that RA can reduce cell proliferation and stemness and induce cell cycle arrest in MB cells. Mechanisms mediating these effects may include targeting HDAC1, EGFR, and ERK signaling, and promoting p21 expression, possibly through an increase in H3K9ac and AKT deactivation. RA should be further investigated as a potential anticancer agent in experimental MB.
IL-1Ra and CCL5, but not IL-10, are promising targets for treating SMA astrocyte-driven pathology
Authors: Allison Reilly L. , Suneja Mya , LaCroix Megan , Harmelink Matthew , Ebert Allison D.
Published: August 2023

Spinal muscular atrophy (SMA) is a pediatric genetic disorder characterized by the loss of spinal cord motor neurons. Although the mechanisms underlying motor neuron loss are not clear, current data suggest that glial cells contribute to disease pathology. We have previously found that SMA astrocytes drive microglial activation and motor neuron loss potentially through the upregulation of NFkB-mediated pro-inflammatory cytokines. In this study, we tested the ability of increasing either interleukin 10 (IL-10) or IL-1 receptor antagonist (IL-1ra) while neutralizing C-C motif chemokine ligand 5 (CCL5) to reduce the pro-inflammatory phenotype of SMA astrocytes. While IL-10 was ineffective, IL-1ra ameliorated SMA astrocyte-driven glial activation and motor neuron loss in iPSC-derived culturesin vitro.In vivoAAV5 delivered IL-1ra overexpression and miR-30 shRNA knockdown of CCL5 had modest but significant improvements on lifespan, weight gain, and motor function of SMNΔ7 mice. Together these data identify IL-1ra and CCL5 as possible therapeutic targets for SMA and highlight the importance of glial-targeted therapeutics for neurodegenerative disease.
NUCLEOPORIN1 mediates proteasome-based degradation of ABI5 to regulateArabidopsisseed germination
Authors: Thapa Raj K , Tian Gang , Lu Qing Shi Mimmie , Yu Yaoguang , Shu Jie , Chen Chen , Song Jingpu , Xie Xin , Shan Binghui , Nguyen Vi , Li Chenlong , Bian Shaomin , Liu Jun , Kohalmi Susanne E , Cui Yuhai
Published: August 2023

NUCLEOPORIN1 (NUP1), a member of the Nuclear Pore Complex (NPC), is located on the inner side of the nuclear membrane. It is highly expressed in seeds; however, its role in seeds including germination has not been explored yet. Here, we identified an abscisic acid (ABA) hypersensitive phenotype ofnup1during germination. ABA treatment drastically changes the expression pattern of thousands of genes innup1, including the major transcription factors (TFs) involved in germination,ABI3,ABI4, andABI5. Double mutant analysis ofNUP1and these ABA-related genes showed that mutations inABI5can rescue the phenotype ofnup1, suggesting thatNUP1acts upstream ofABI5to regulate seed germination. ABI5, a key negative regulator of germination, is abundant in dry seeds and rapidly degrades during germination. However, its spatiotemporal regulation and interaction with other molecular players during degradation remained to be fully elucidated. We found that NUP1 is physically associated with ABI5 and the 26S proteasome. Mutation inNUP1delayed ABI5 degradation through its post-translational retention in nucleolus under abiotic stress. Taken together, our findings suggest that NUP1 anchors the proteasome to NPC and modulates seed germination through proteasome-mediated degradation of ABI5 in the vicinity of NPC in the nucleoplasm.
Sex differences in seizure presentation in Dravet syndrome model mice,Scn1a+/-
Authors: Vermudez Sheryl Anne D. , Lin Rui , McGinty Gabrielle , Liebhardt Amanda , Choe Yongho , Hui Benjamin , Lubbers Ella , Dhamne Sameer C. , Hameed Mustafa Q. , Rotenberg Alexander
Published: August 2023

Dravet syndrome (DS) is an epileptic encephalopathy mostly due to haploinsufficiency of theSCN1Avoltagegated sodium channel subunit. Disease presentation (i.e., severe seizures and early life mortality) is highly recapitulated in mice haploinsufficient inScn1a(Scn1a+/-). However, phenotypic characterization inScn1a+/-mice in a sex and temporal manner is limited. Given the reliance of mouse models for studying disease pathophysiology and for the development of novel treatments, we tested whether mortality and seizure morbidity differed among young and adult male and femaleScn1a+/-animals in the F1 hybrid C57×129S6 background. We found increased mortality in femaleScn1a+/-mice regardless of age compared to their male counterparts (n = 120-125 mice/sex;p < 0.05). Interestingly, long-term video EEG recordings revealed the opposite for morbidity as seizure frequency and severity were escalated in adult maleScn1a+/-animals (n = 21-30 mice/sex;p < 0.05orp < 0.01). Adult femaleScn1a+/-mice, however, are more hyperactive (p < 0.05), which could be related to sleep impairment and contribute to the increased mortality despite decreased seizure morbidity. Overall, the phenotypic presentation ofScn1a+/-mice is sex-dependent and may have translational implications for therapeutic drug discovery and basic biology understanding in DS.

Short Summary

Sex differences in mortality and seizure morbidity are discovered inScn1ahaploinsufficient mice,Scn1a+/-, which faithfully model the epileptic encephalopathy disorder, Dravet syndrome (DS). FemaleScn1a+/-mice die more across all ages, whereas adult maleScn1a+/-mice have more seizures that are of greater severity. Hyperactivity, as a proxy for sleep disruption, may contribute to the increased mortality in femaleScn1a+/-mice despite decreased seizure incidence and severity. These sex-specific findings may have considerable impact in therapeutic discovery and development for DS and otherSCN1A-related disorders.