bluuebunny/crossref_metadata_2025 huggingface dataset:
FGF2 promotes the expansion of parietal mesothelial progenitor pools and inhibits BMP4-mediated smooth muscle cell differentiation
Authors: Hwang Youngmin , Shimamura Yuko , Tanaka Junichi , Miura Akihiro , Sawada Anri , Sarmah Hemanta , Shimizu Dai , Kondo Yuri , Ninish Zurab , Yamada Kazuhiko , Mori Munemasa
Published: February 2024

Mesothelial cells, in the outermost layer of internal organs, are essential for both organ development and homeostasis. Although the parietal mesothelial cell is the primary origin of mesothelioma that may highjack developmental signaling, the signaling pathways that orchestrate developing parietal mesothelial progenitor cell (MPC) behaviors, such as MPC pool expansion, maturation, and differentiation, are poorly understood. To address it, we established a robust protocol for culturing WT1+MPCs isolated from developing pig and mouse parietal thorax. Quantitative qPCR and immunostaining analyses revealed that BMP4 facilitated MPC differentiation into smooth muscle cells (SMCs). In contrast, FGF2 significantly promoted MPC progenitor pool expansion but blocked the SMC differentiation. BMP4 and FGF2 counterbalanced these effects, but FGF2 had the dominant impact in the long-term culture. A Wnt activator, CHIR99021, was pivotal in MPC maturation to CALB2+mesothelial cells, while BMP4 or FGF2 was limited. Our results demonstrated central pathways critical for mesothelial cell behaviors.
Notch is Required for Neural Progenitor Proliferation During Embryonic Eye Regrowth
Authors: Guerin Dylan J. , Gutierrez Belen , Zhang Baoyi , Tseng Kelly Ai-Sun
Published: February 2024

The ability of an organism to regrow tissues is regulated by various signaling pathways. One such pathway that has been studied widely both in the context of regeneration and development is the Notch signaling pathway. Notch signaling is required for development of the eye and regeneration of tissues in multiple organisms but it is unknown if Notch plays a role in the regulation ofXenopus laevisembryonic eye regrowth. We found that Notch1 is required for eye regrowth and regulates retinal progenitor cell proliferation. Chemical and molecular inhibition of Notch1 significantly decreased eye regrowth through reducing retinal progenitor cell proliferation without affecting retinal differentiation. Temporal inhibition studies showed that Notch function is required during the first day of regrowth. Interestingly, Notch1 loss-of-function phenocopied the effects of the inhibition of the proton pump, V-ATPase, where retinal proliferation but not differentiation was blocked during eye regrowth. Overexpression of a form of activated Notch1, the Notch intracellular domain (NICD) was sufficient to rescue loss of eye regrowth due to V-ATPase inhibition, suggesting that Notch acts downstream of V-ATPase. These findings highlight the importance of the Notch signaling pathway in eye regeneration and its role in inducing retinal progenitor cell proliferation in response to injury.
HSP60 chaperone deficiency disrupts the mitochondrial matrix proteome and dysregulates cholesterol synthesis
Authors: Cömert Cagla , Kjær-Sørensen Kasper , Hansen Jakob , Carlsen Jasper , Just Jesper , Meaney Brandon F. , Østergaard Elsebet , Luo Yonglun , Oxvig Claus , Schmidt-Laursen Lisbeth , Palmfeldt Johan , Fernandez-Guerra Paula , Bross Peter
Published: February 2024

Mitochondrial proteostasis is critical for cellular function and survival. HSP60 is a molecular chaperone that interacts with more than 260 mitochondrial matrix proteins to assist in their folding and few genetic variants of HSP60 are compatible with life. The few reported human patients with HSP60 variants show phenotypes of neurodevelopmental delay associated with brain hypomyelination. It is currently unknown how deficiency of the HSP60 links to hypomyelination. Here, we studied the onset and progression of HSP60 deficiency in: (1) a HSP60 mutation-inducible cell system, (2) skin fibroblasts from patients with disease-associated HSP60 variants, and (3) zebrafish HSP60 knockout larvae. Collectively, we show how HSP60 deficiency leads to pervasive dysfunctions: (1) downregulated mitochondrial matrix proteome, (2) transcriptional activation of cytosolic stress responses, (3) and lipid accumulation with dysregulated cholesterol biosynthesis. In zebrafish larvae HSP60 deficiency induced early developmental abnormalities. Our comprehensive data identifies HSP60 as a master regulator of mitochondrial proteostasis and suggests a pivotal effect of HSP60 dysfunction on myelination through dysregulation of cholesterol biosynthesis.

Highlights

HSP60 deficiency disrupts mitochondrial matrix proteins activating stress responses

Disrupted matrix proteome impairs catabolism causing acetyl-CoA shortage

HSP60 deficiency dysregulates cytosolic cholesterol synthesis

Hsp60 deficiency causes developmental abnormalities in zebrafish larvae

Dysregulated cholesterol synthesis links HSP60 deficiency to hypomyelination

Graphical abstract
Quantification of beta cell carrying capacity in prediabetes
Authors: Woller Aurore , Tamir Yuval , Bar Alon , Mayo Avi , Rein Michal , Godneva Anastasia , Cohen Netta Mendelson , Segal Eran , Toledano Yoel , Shilo Smadar , Gonze Didier , Alon Uri
Published: February 2024

Prediabetes, a subclinical state of high glucose, carries a risk of transition to diabetes. One cause of prediabetes is insulin resistance, which impairs the ability of insulin to control blood glucose. However, many individuals with high insulin resistance retain normal glucose due to compensation by enhanced insulin secretion by beta cells. Individuals seem to differ in their maximum compensation level, termed beta cell carrying capacity, such that low carrying capacity is associated with a higher risk of prediabetes and diabetes. Carrying capacity has not been quantified using a mathematical model and cannot be estimated directly from measured glucose and insulin levels in patients, unlike insulin resistance and beta cell function which can be estimated using HOMA-IR and HOMA-B formula.

Here we present a mathematical model of beta cell compensation and carrying capacity, and develop a new formula called HOMA-C to estimate it from glucose and insulin measurements. HOMA-C estimates the maximal potential beta cell function of an individual, rather than the current beta cell function. We test this approach using longitudinal cohorts of prediabetic people, finding 10-fold variation in carrying capacity. Low carrying capacity is associated with higher risk of transitioning to diabetes. We estimate the timescales of beta cell compensation and insulin resistance using large datasets, showing that, unlike previous mathematical models, the new model can explain the slow rise in glucose over decades. Our mathematical understanding of beta cell carrying capacity may help to assess the risk of prediabetes in each individual.
NMDtxDB: Data-driven identification and annotation of human NMD target transcripts
Authors: Britto-Borges Thiago , Gehring Niels , Boehm Volker , Dieterich Christoph
Published: February 2024

The nonsense-mediated RNA decay (NMD) pathway is a crucial mechanism of mRNA quality control. Current annotations of NMD substrate RNAs are rarely data-driven, but use general established rules. We introduce a dataset with 4 cell lines and combinations for SMG5, SMG6 and SMG7 knockdowns or SMG7 knockout. Based on this dataset, we implemented a workflow that combines Nanopore and Illumina sequencing to assemble a transcriptome, which is enriched for NMD target transcripts. Moreover, we use coding sequence information from Ensembl, Gencode consensus RiboSeq ORFs and OpenProt to enhance the CDS annotation of novel transcript isoforms. 302,889 transcripts were obtained from the transcriptome assembly process, out of which, 48,213 contain a premature stop codon and 6,433 are significantly up regulated in three or more comparisons of NMD active vs deficient cell lines.

We present an in-depth view on these results through the NMDtxDB database, which is available athttps://shiny.dieterichlab.org/app/NMDtxDB, and supports the study of NMD-sensitive transcripts. We open sourced our implementation of the respective web-application and analysis workflow athttps://github.com/dieterich-lab/NMDtxDBandhttps://github.com/dieterich-lab/nmd-wf.
Chromosome segment scanning for gain- or loss-of-function screening (CHASING) and its application in metabolic engineering
Authors: Xia Yan , Sun Lichao , Liang Zeyu , Han ZhongRao , Li Jing , Guo Yingjie , Dong Pengyu , Huo Yi-Xin , Guo Shuyuan
Published: February 2024

Constructing a library of thousands of single-gene knockout or interference strains is a powerful tool to understand the relation between genotype and phenotype, but it is labor and cost intensive. Powered by the computer-aided gene annotation and functional grouping of non-essential genes, we showed that targeting a single gene directly to a specific observed phenotype could be quickly achieved for a specific microorganism via constructing a library of strains containing single chromosome-segment-deletion per strain. As a proof-of-concept, a genome-scale library consisting of 70 chromosome-segment-deletion strains forB. subtiliswas constructed by CRISPR-based methods and strains with six loss-of- and gain-of-function phenotypes were screened out. To facilitate the rapid genotyping, we developed a web tool to visualize the potential targets of each chromosome segment associated with a particular function, successfully identifying the genes for valuable representative phenotypes. To apply the library to metabolic engineering, the hosts with improved production capacity of acetoin and lycopene were screened in the presence of pathway genes. This work demonstrated the significance of our strategy ofchromosome segment scanning for gain- or loss-of-function screening(CHASING)on functional genomics investigation, robust chassis engineering, and chemical overproduction.

Abstract Figure

TOC
Label-free and reference region-free X-ray cross-β index for quantifying protein aggregates of neurodegenerative diseases
Authors: Suresh Karthika , Dahal Eshan , Badano Aldo
Published: February 2024

Background and objectives

Recent advancements in therapies targeting various protein aggregates, ranging from oligomers to fibrils, in neurodegenerative diseases exhibit considerable promise. This underscores the imperative for robust quantitative methods capable of accurately detecting and quantifying these biomarker aggregates across different structural states, even when present in sparse quantities during the early stages of the disease continuum. In response to this exigency, we propose and assess an X-ray-based quantitative metric designed for the global and region-specific detection and quantification of oligomers and fibrils within tissues. This methodology proves applicable to a broad spectrum of neurodegenerative diseases, including Alzheimer’s and Parkinson’s. Notably, unlike positron emission tomography (PET)-based biomarker quantification methods, our approach obviates the need for a contrast agent or a reference region.

Methods

We assessed the proposed metric, termed X-ray cross-β aggregate index (XβAI), in a sheep brain model and brain tissue phantoms, incorporating synthetic oligomers and fibrils characterized against amyloid β-42 and α-synuclein aggregates. Detection of these biomarkers utilized laboratory-based monochromatic, and polychromatic X-ray sources, specifically targeting the cross-β substructure of protein aggregates. We employed a peak-location, knowledge-based material decomposition approach to extract target signals from the complex X-ray scattering spectrum originating from a mixture of tissue, water, and aggregate signals.

Results

Clinically relevant quantities of oligomers and fibrils were detected in tissues from different brain regions using the laboratory-based X-ray scattering method, without the need for a contrast agent. The signals from protein aggregates were successfully recovered from composite X-ray scattering spectra through material decomposition, eliminating the need for a reference region. The area under the peak of the decomposed inter-β-strand signal correlated well with aggregate burden in synthetically diseased brain tissues. The X-ray cross-β aggregate index (XβAI) accurately quantified aggregate burden in heterogeneous tissues across various brain regions and effectively tracked the deposition increments in specific tissue regions.

Conclusion

Our study introduces a novel metric, for both regional and global quantification of protein aggregates linked to various protein misfolding diseases, including synucleinopathies.
No cardiac phase bias for threat perception under naturalistic conditions in immersive virtual reality
Authors: Klotzsche Felix , Motyka Paweł , Molak Aleksander , Sahula Václav , Darmová Barbora , Byrnes Conor , Fajnerová Iveta , Gaebler Michael
Published: February 2024

Previous studies have found that threatening stimuli are more readily perceived and more intensely experienced when presented during cardiac systole compared to diastole. Also, threatening stimuli are judged as physically closer than neutral ones. In a pre-registered study, we tested these effects and their interaction using a naturalistic (interactive, 3D) experimental design in immersive virtual reality: We briefly displayed threatening and non-threatening animals (four each) at varying distances (1.5–5.5 meters) to a group of young, healthy participants (n = 41), while recording their ECGs (electrocardiograms). Participants then pointed to the location where they had seen the animal (ca. 29k trials in total). Our pre-registered analyses indicated that perceived distances to both threatening and non-threatening animals did not differ significantly between cardiac phases – with Bayesian analysis supporting the null hypothesis. There was also no evidence for an association between subjective fear and perceived proximity to threatening animals. These results contrast with previous findings that used verbal or declarative distance measures in less naturalistic experimental conditions. Furthermore, our findings suggest that the cardiac phase-related variation in threat processing may not generalize across different paradigms and may be less relevant in naturalistic scenarios than under more abstract experimental conditions.

Impact statement

To our knowledge, this is the first study to assess the influence of interoceptive cardiac signals on visual perception using naturalistic stimuli in immersive virtual reality. We based the design of our experiment on previous reports about threat processing biases and the role of the cardiac cycle but did not observe the expected effects. This poses the question of their generalizability from abstract settings to more naturalistic setups, featuring greater behavioral engagement and a richer sensory environment.
Histological comparison of repeated mild weight drop and lateral fluid percussion injury models of traumatic brain injury (TBI) in female and male rats
Authors: Vita Sydney M. , Cruise Shealan C. , Gilpin Nicholas W. , Molina Patricia E.
Published: February 2024

Traumatic brain injury (TBI) heterogeneity has led to the development of several preclinical models, each modeling a distinct subset of outcomes. Selection of an injury model should be guided by the research question and the specific outcome measures of interest. Consequently, there is a need for conducting direct comparisons of different TBI models. Here, we used immunohistochemistry to directly compare the outcomes from two common models, lateral fluid percussion (LFP) and repeat mild weight drop (rmWD), on neuropathology in adult female and male Wistar rats. Specifically, we used immunohistochemistry to measure the effects of LFP and rmWD on cerebrovascular and tight junction disruption, inflammatory markers, mature neurons and perineuronal nets in the cortical site of injury, cortex adjacent to injury, dentate gyrus, and the CA2/3 area of the hippocampus. Animals were randomized into either LFP or rmWD groups. The LFP group received a craniotomy prior to LFP (or corresponding sham procedure) three days later, while rmWD animals underwent either weight drop or sham (isoflurane only) on each of those four days. After a recovery period of 7 days, animals were euthanized, and brains were harvested for analysis of RECA-1, claudin-5, GFAP, Iba-1, CD-68, NeuN, and wisteria floribunda lectin. Overall, our observations revealed that the most significant disruptions were evident in response to LFP, followed by craniotomy-only, while rmWD animals showed the least residual changes compared to isoflurane-only controls. These findings support consideration of rmWD as a mild, transient injury. LFP leads to longer-lasting disruptions that are more closely associated with a moderate TBI. We further show that both craniotomy and LFP produced greater disruptions in females relative to males at 7 days post-injury. These findings support the inclusion of a time-matched experimentally-naïve or anesthesia-only control group in preclinical TBI research to enhance the validity of data interpretation and conclusions.
The Switchmaze: an open-design device for measuring motivation and drive switching in mice
Authors: Hartmann Clara , Mahajan Ambika , Borges Vinicius , Razenberg Lotte , Thönnes Yves , Karnani Mahesh M.
Published: February 2024

Animals need to switch between motivated behaviours, like drinking, feeding or social interaction, to meet environmental availability, internal needs and more complex ethological needs such as hiding future actions from competitors. Inflexible, repetitive behaviours are a hallmark of many neuropsychiatric disorders. However, how the brain orchestrates switching between the neural mechanisms controlling motivated behaviours, or drives, is unknown. This is partly due to a lack of appropriate measurement systems. We designed an automated extended home-cage, the Switchmaze, using open-source hardware and software. In this study, we use it to establish a behavioural assay of motivational switching in mice. Individual animals access the Switchmaze from the home-cage and choose between entering one of two chambers containing different goal objects or returning to the home-cage. Motivational switching is measured as a ratio of switching between chambers and continuous exploitation of one chamber. Behavioural transition analysis is used to further dissect altered motivational switching. As proof-of-concept, we show environmental manipulation, and targeted brain manipulation experiments which altered motivational switching without effect on traditional behavioural parameters. Chemogenetic inhibition of the prefrontal-hypothalamic axis increased the rate of motivation switching, highlighting the involvement of this pathway in drive switching. This work demonstrates the utility of open-design in understanding animal behaviour and its neural correlates.
A Cell Cycle-aware Network for Data Integration and Label Transferring of Single-cell RNA-seq and ATAC-seq
Authors: Liu Jiajia , Ma Jian , Wen Jianguo , Zhou Xiaobo
Published: February 2024

In recent years, the integration of single-cell multi-omics data has provided a more comprehensive understanding of cell functions and internal regulatory mechanisms from a non-single omics perspective, but it still suffers many challenges, such as omics-variance, sparsity, cell heterogeneity and confounding factors. As we know, cell cycle is regarded as a confounder when analyzing other factors in single-cell RNA-seq data, but it’s not clear how it will work on the integrated single-cell multi-omics data. Here, we developed a Cell Cycle-Aware Network (CCAN) to remove cell cycle effects from the integrated single-cell multi-omics data while keeping the cell type-specific variations. This is the first computational model to study the cell-cycle effects in the integration of single-cell multi-omics data. Validations on several benchmark datasets show the out-standing performance of CCAN in a variety of downstream analyses and applications, including removing cell cycle effects and batch effects of scRNA-seq datasets from different protocols, integrating paired and unpaired scRNA-seq and scATAC-seq data, accurately transferring cell type labels from scRNA-seq to scATAC-seq data, and characterizing the differentiation process from hematopoietic stem cells to different lineages in the integration of differentiation data.
MYBL2 drives prostate cancer plasticity and identifies CDK2 as a therapeutic vulnerability in RB1-loss and neuroendocrine prostate cancer
Authors: German Beatriz , Singh Jagpreet N. , Fonseca Marcos AdS , Burkhart Deborah L. , Sheahan Anjali , Bergom Hannah , Morel Katherine L. , Beltran Himisha , Hwang Justin H. , Lawrenson Kate , Ellis Leigh
Published: February 2024

Phenotypic plasticity is a recognized mechanism driving therapeutic resistance in prostate cancer (PCa) patients. While underlying molecular causations driving phenotypic plasticity have been identified, therapeutic success is yet to be achieved. To identify putative master regulator transcription factors (MR-TF) driving phenotypic plasticity in PCa, this work utilized a multiomic approach using genetically engineered mouse models of prostate cancer combined with patient data to identify MYBL2 as a significantly enriched transcription factor in PCa exhibiting phenotypic plasticity. Genetic inhibition ofMybl2using independent murine PCa cell lines representing phenotypic plasticity demonstratedMybl2loss significantly decreased in vivo growth as well as cell fitness and repressed gene expression signatures involved in pluripotency and stemness. Because MYBL2 is currently not druggable, a MYBL2 gene signature was employed to identify cyclin-dependent kinase-2 (CDK2) as a potential therapeutic target. CDK2 inhibition phenocopied genetic loss ofMybl2and significantly decreased in vivo tumor growth associated with enrichment of DNA damage. Together, this work demonstrates MYBL2 as an important MR-TF driving phenotypic plasticity in PCa. Further, high MYBL2 activity identifies PCa that would be responsive to CDK2 inhibition.

Significance

PCa that escapes therapy targeting the androgen receptor signaling pathways via phenotypic plasticity are currently untreatable. Our study identifies MYBL2 as a MR-TF in phenotypic plastic PCa and implicates CDK2 inhibition as novel therapeutic target for this most lethal subtype of PCa.
Disruption of DLL4/NOTCH1 Causes Dysregulated PPARγ/AKT Signaling in Pulmonary Arterial Hypertension
Authors: Awad Keytam S. , Wang Shuibang , Dougherty Edward J. , Keshavarz Ali , Demirkale Cumhur Y. , Yu Zu Xi , Miller Latonia , Elinoff Jason M. , Danner Robert L.
Published: February 2024

Pulmonary arterial hypertension (PAH) is a progressive cardiopulmonary disease characterized by vascular remodeling of small pulmonary arteries. Endothelial dysfunction in advanced PAH is associated with proliferation, apoptosis resistance, and endothelial to mesenchymal transition (EndoMT) due to aberrant signaling. DLL4, a cell membrane associated NOTCH ligand, activates NOTCH1 signaling and plays a pivotal role maintaining vascular integrity. Inhibition of DLL4 has been associated with the development of pulmonary hypertension, but the mechanism is incompletely understood. Here we report thatBMPR2silencing in PAECs activated AKT and decreased DLL4 expression. DLL4 loss was also seen in lungs of patients with IPAH and HPAH. Over-expression of DLL4 in PAECs inducedBMPR2promoter activity and exogenous DLL4 increasedBMPR2mRNA through NOTCH1 activation. Furthermore, DLL4/NOTCH1 signaling blocked AKT activation, decreased proliferation and reversed EndoMT inBMPR2– silenced PAECs and ECs from IPAH patients. PPARγ, suppressed by BMPR2 loss, was induced and activated by DLL4/NOTCH1 signaling in bothBMPR2-silenced and IPAH PAECs, reversing aberrant phenotypic changes, in part through AKT inhibition. Finally, leniolisib, a well-tolerated oral PI3K8/AKT inhibitor, decreased cell proliferation, induced apoptosis and reversed markers of EndoMT inBMPR2-silenced PAECs. Restoring DLL4/NOTCH1/PPARγ signaling and/or suppressing AKT activation may be beneficial in preventing or reversing the pathologic vascular remodeling of PAH.
Reactive oxygen species suppress phagocyte surveillance by oxidizing cytoskeletal regulators
Authors: Ferling Iuliia , Pfalzgraf Steffen , Moutounet Lea , Qiu Lanhui , Li Iris , Zhou Yuhuan , Grinstein Sergio , Freeman Spencer A.
Published: February 2024

Despite their superficial similarities, the phagocytosis of pathogens differs from that of apoptotic cells in their recognition mechanisms and downstream signaling pathways. While the initial stages of these processes have been studied, the cytoskeletal reorganization that follows particle uptake is not well understood. By comparing the uptake of phosphatidylserine (PS)- coated targets versus IgG-opsonized targets of identical size, shape, and rigidity, we noted remarkable differences in the accompanying changes in cell morphology, adhesion and migration that persisted long after phagocytosis. While myeloid cells continued to survey their microenvironment after engulfing PS-coated targets, the uptake of IgG-opsonized targets caused phagocytes to round up, decreased their membrane ruffling, and led to the complete disassembly of podosomes. These changes were associated with increased activation of Rho and a concomitant decrease of Rac activity that collectively resulted in the thickening and compaction of the cortical F-actin cytoskeleton. Rho/formin-induced actin polymers were fastened to the membrane by their preferential interaction with Ezrin-Radixin-Moesin (ERM) proteins, which were necessary for cell compaction and podosome disassembly following ingestion of IgG-coated particles. The source of the distinct responses to PS- versus IgG-targets was the differential activation of the respiratory burst mediated by the NADPH oxidase: reactive oxygen species (ROS), emanating from phagosomes containing IgG-opsonized targets – but not those containing PS-coated ones – directly led to the activation of Rho. Similar findings were made with phagocytes that encountered pathogens or microbial-associated molecular patterns (MAMPS) that instigate the activation of the NADPH oxidase. These results implicate a connection between sensing of harmful particulates, the oxidation of cytoskeletal regulators, and the immune surveillance by myeloid cells that have potentially important consequences for the containment of pathogens.
The correlation between Rate of Force Development Maximal Strength and Electromyography Variables of Basketball Athletes
Authors: Pinheiro Brandão Hiury Caio , de Andrade Marcelino Monteiro , do Carmo Jake Carvalho
Published: February 2024

The rate of force development (RFD), is seen as a determining characteristic in fast actions present in basketball. However, we observed different relationships between RFD and maximum strength, as well as different relationships between RFD and neuromuscular variables according to the evaluated population. The aim of the present study is to evaluate the degree of determination of maximum strength (Tmax) and neuromuscular recruitment variables (RMS), Absolute Energy (AE) and the motor units firing frequencies (MPF) in rate of force development (RFD) for basketball athletes. Nine basketball athletes from the same team (mean ± SD; age: 20.8 ± 2.08 years; body mass: 84.33 ± 8.80kg; height: 1.86 ± 0.095 meters; practice time: 11.67 ± 1.65 years) were evaluated through maximum isometric contraction with highest value of maximum force among 3 attempts. The RFD were evaluated and correlated with the RMS and AE values and the MPF values of the electromyographic signal at instants 0-50; 50-100, 100-150 and 150-200 milliseconds. The results show a reduction in RFD and MPF over the evaluated time windows and also a correlation between MPF and TDF in the 0-50ms time window (R20.67p<0.05). The results show no relationship between RFD and RMS and AE, in addition to these variables not showing significant reductions in the evaluated time windows. The levels of RFD show to be more related to the firing frequency of the motor units than the maximum force and the level of recruitment of the motor units.
Hypothalamic dopamine neuron activity is modulated by caloric states and amphetamine abuse in zebrafish larvae
Authors: Bansal Pushkar , Jung Erica E.
Published: February 2024

Dopaminergic (DA) neuron activity is affected by reward and stress-inducing entities such as food and drugs of abuse, and different DA neuron populations can respond distinctly to these stimuli. Interaction between both stimuli significantly alters the dynamics of DA release in different DA populations. Additionally, these stimulating entities can affect the interconnections among different DA populations by impairing their correspondence with each other. However, limited studies have been performed that could point to the effect of interaction between AMPH and caloric states on DA neurons and their inter-correlation. This study explores the individual and interactive effect of two caloric states, ad-libitum fed (AL) and food deprived (FD), and acute exposure to a stimulant drug (amphetamine) in two different DA neurons in the hypothalamus of zebrafish larvae. We used a transgenic zebrafish line Tg(th2:GCaMP7s), which expresses a calcium indicator (GCaMP7s) in A11(Posterior Tuberculum) and a part of A14 (Caudal Hypothalamus and Intermediate Hypothalamus) DA populations located in the hypothalamus of the larval zebrafish. The larvae were subjected to acute FD and ad AL feeding followed by acute treatment with 0.7uM and 1.5uM doses of AMPH. We recorded calcium activity and quantified fluorescence change, activity duration, peak rise/fall time, and latency in the spikes of the DA neurons. Our results show that baseline DA neuron activity amplitude, spike duration, and correlation between inter- and intra-DA neurons were higher in the FD than in the AL state. Dose-dependent AMPH treatment further increased the activity intensity of the aforementioned parameters in the neuron spikes in the FD state. The DA activity correlation and spike latency were dose-dependently impaired in both DA populations. These results suggest that different DA populations in the brain exhibit a similar activity trend in response to caloric states and AMPH, where the AMPH-mediated intensity change in the activity was dose-dependent.
ALS-Associated TDP-43 Dysfunction Compromises UPF1-Dependent mRNA Metabolism Pathways Including Alternative Polyadenylation and 3’UTR Length
Authors: Alessandrini Francesco , Wright Matthew , Kurosaki Tatsuaki , Maquat Lynne E. , Kiskinis Evangelos
Published: February 2024

UPF1-mediated decay entails several mRNA surveillance pathways that play a crucial role in cellular homeostasis. However, the precise role of UPF1 in postmitotic neurons remains unresolved, as does its activity in amyotrophic lateral sclerosis (ALS), a devastating neurodegenerative disease characterized by TDP-43 pathology and disrupted mRNA metabolism. Here, we used human iPSC-derived spinal motor neurons (MNs) to identify mRNAs subject to UPF1 degradation by integrating RNA-seq before and after UPF1 knockdown with RIP-seq to identify RNAs that co-immunoprecipitate with the active form of phosphorylated UPF1. We define a stringent set ofbona fideUPF1 targets in MNs that are functionally enriched for autophagy and structurally enriched for GC-rich and long 3’ UTRs but not for premature termination codon (PTC)-containing transcripts. TDP-43 depletion in iPSC-derived MNs reduces UPF1 phosphorylation and consequently post-transcriptional upregulation of UPF1 targets, suggesting that TDP-43 dysfunction compromises UPF1-mediated mRNA surveillance. Intriguingly, our datasets reveal that UPF1 and TDP-43 regulate alternative polyadenylation and 3’UTR length of mRNAs associated with synaptic and axonal function, a process that we find to be compromised in ALS modelsin vitroand ALS patient tissue. Our study provides a comprehensive description of UPF1-mediated mRNA decay activity in neurons, reveals overlapping roles between UPF1 and TDP-43 in regulating 3’UTR length, and offers novel insight into the intricate interplay between RNA metabolism and neurodegeneration in ALS.
AAV-based delivery of RNAi targeting Ataxin-2 improves survival, strength, and pathology in mouse models of rapidly and slowly progressive sporadic ALS
Authors: Amado Defne A. , Robbins Ashley B. , Smith Alicia R. , Whiteman Katherine R. , Chillon Bosch Guillem , Chen Yonghong , Fuller Joshua A. , Izda Aleksandar , Nelson Shareen , Dichter Abigail I. , Monteys Alex Mas , Davidson Beverly L.
Published: February 2024

Amyotrophic lateral sclerosis (ALS) is characterized by motor neuron death due to nuclear loss and cytoplasmic aggregation of the splice factor TDP-43. Pathologic TDP-43 associates with stress granules (SGs) and downregulating the SG-associated protein Ataxin-2 (Atxn2) using antisense oligonucleotides (ASO) prolongs survival in the TAR4/4 sporadic ALS mouse model, a strategy now in clinical trials. Here, we used AAV-mediated RNAi delivery to achieve lasting and targetedAtxn2knockdown after a single injection. To achieve this, a novel AAV with improved transduction potency of our target cells was used to deliverAtxn2-targeting miRNAs. Mouse dosing studies demonstrated 55%Atxn2knockdown in frontal cortex and 25% knockdown throughout brainstem and spinal cord after intracerebroventricular injection at a dose 40x lower than used in other recent studies. In TAR4/4 mice, miAtxn2 treatment increased mean and median survival by 54% and 45% respectively (p<0.0003). Mice showed robust improvement across strength-related measures ranging from 24-75%. Interestingly, treated mice showed increased vertical activity above wildtype, suggesting unmasking of an FTD phenotype with improved strength. Histologically, lower motor neuron survival improved with a concomitant reduction in CNS inflammatory markers. Additionally, phosphorylated TDP-43 was reduced to wildtype levels. Bulk RNA sequencing revealed correction of 153 genes in the markedly dysregulated transcriptome of mutant mice, several of which are described in the human ALS literature. In slow progressing hemizygous mice, treatment rescued weight loss and improved gait at late time points. Cumulatively the data support the utility of AAV-mediated RNAi againstAtxn2as a robust and translatable treatment strategy for sporadic ALS.
A machine-learning model to harmonize brain volumetric data for quantitative neuro-radiological assessment of Alzheimer’s disease
Authors: Archetti Damiano , Venkatraghavan Vikram , Weiss Béla , Bourgeat Pierrick , Auer Tibor , Vidnyánszky Zoltán , Durrleman Stanley , van der Flier Wiesje M. , Barkhof Frederik , Alexander Daniel C. , Altmann Andre , Redolfi Alberto , Tijms Betty M. , Oxtoby Neil P. ,   Australian Imaging Biomarkers and Lifestyle Study,   Alzheimer’s Disease Neuroimaging Initiative,   the E-DADS Consortium
Published: February 2024

Background

Structural MRI plays a pivotal role in the radiological workup for assessing neurodegeneration. Scanner-related differences hinder quantitative neuroradiological assessment of Alzheimer’s disease (QNAD). This study aims to train a machine-learning model to harmonize brain volumetric data of patients not encountered during model training.

Method

Neuroharmony is a recently developed method that uses image quality metrics (IQM) as predictors to remove scanner-related effects in brain-volumetric data using random forest regression. To account for the interactions between AD-pathology and IQM during harmonization, we developed a multi-class extension of Neuroharmony. We performed cross-validation experiments to benchmark performance against existing approaches using data from 20,864 participants comprising cognitively unimpaired (CU) and impaired (CI) individuals, spanning 11 cohorts and 43 scanners. Evaluation metrics assessed ability to remove scanner-related variations in brain volumes (biomarker concordance), while retaining the ability to delineate different diagnostic groups (preserving disease-related signal).

Results

For each strategy, biomarker concordances between scanners were significantly better (p < 10−6) compared to pre-harmonized data. The proposed multi-class model achieved significantly higher concordance than the Neuroharmony model trained on CU individuals (CI: p < 10−6, CU: p = 0.02) and preserved disease-related signal better than the Neuroharmony model trained on all individuals without our proposed extension (ΔAUC= −0.09). The biomarker concordance was better in scanners seen during training (concordance > 97%) than unseen (concordance < 79%), independent of cognitive status.

Conclusion

In a large-scale multi-center dataset, our proposed multi-class Neuroharmony model outperformed other strategies available for harmonizing brain-volumetric data in a clinical setting. This paves the way for enabling QNAD in the future.
Does Education Sculpt Healthcare Choices? Exploring Factors Influencing Healthcare Utilization Among Female Youths in Eight Low and Lower-Middle-Income Countries
Authors: Nishan Nahid Hassan , Akter Khadiza , Sharmin Afroza , Tithi Tazmin Akter , Ahmed M Z E M Naser Uddin
Published: February 2024

Abstracts

Introduction

Emphasizing the global commitment to universal health coverage, this research addresses geographical variations and challenges faced by young females across low and lower-middle-income countries. Therefore, the objective of this study is to determine the factors that influence the decision-making of young females when it comes to seeking healthcare services in low or lower-middle-income countries.

Methodology

We examined healthcare usage among female youth across eight countries. We used data from the DHS and employed regression and Chi2tests for our analysis. Our focus was on females aged 15 to 24 and their visits to healthcare facilities. To ensure the validity of our findings, we used weighted sampling to represent the population.

Results

We had a total sample of 51,298 female youth groups between the ages of 15 and 24 who participated in our study. When it comes to the demographics of the participants, most of those in the 15-19 age group were from Burkina Faso (54.26%), while most of those in the 20-24 age group were from Ghana (50.19%). The impact of education varied across countries; primary education led to increased healthcare utilization in Kenya, Tanzania, and Cambodia, but unexpected trends were observed in Burkina Faso.

Conclusions

Education significantly influences healthcare utilization, both primary and secondary education positively impacting this. Rural residents face challenges accessing timely healthcare. Geographical challenges, like diseases and limited accessibility, contribute to varied healthcare usage in Kenya and the Philippines. Addressing infrastructure issues is critical, emphasizing education and promoting transparency to enhance healthcare equity.
VAL-1221 FOR THE TREATMENT OF PATIENTS WITH LAFORA DISEASE: STUDY PROTOCOL FOR A SINGLE-ARM, OPEN-LABEL CLINICAL TRIAL
Authors: Muccioli Lorenzo , Vignatelli Luca , Tappatà Maria , Mazzone Serena , Zenesini Corrado ,   DEFEAT-LD study group, Armstrong Dustin , Michelucci Roberto , Bisulli Francesca
Published: February 2024

Introduction

Lafora Disease (LD) is an ultrarare fatal progressive myoclonic epilepsy, causing drug-resistant epilepsy, myoclonus, and psychomotor deterioration. LD is caused by mutations in EPM2A or NHLRC1, which lead to the accumulation of polyglucosans in the brain and neurodegeneration. There are no approved treatments for LD. VAL-1221 is a fusion protein comprised of the Fab portion of a cell-penetrating antibody and recombinant human acid alpha glucosidase, and has demonstrated an ability to clear polyglucosans. We hypothesize that intravenous infusion of VAL-1221 might be able to degrade cerebral polyglucosans and stabilize or improve disease outcomes. The aim of this study is to assess the safety and preliminary efficacy of VAL-1221 in patients with LD.

Methods and analysis

The study is a phase 2, single-arm, open-label, baseline-controlled clinical trial which will be conducted in a single investigational study center in Italy, namely the sponsor “IRCCS Istituto delle Scienze Neurologiche di Bologna - Azienda USL di Bologna”. The study will enroll 6 genetically-confirmed patients with mid- to late stage LD. The global duration of the study for each participant will be 18 months, including screening period, open-label treatment (12 months), and follow-up period. VAL-1221 20 mg/kg will be administered as an intravenous infusion every week for 3 weeks, then every other week. Patients will undergo full clinical assessments at baseline, at an intermediate and at the end-of-treatment visit. The primary objective is to evaluate the safety. The exploratory efficacy endpoints will be related to epilepsy, neuropsychological and motor functions, global assessment and disease burden, in addition to biomarkers. Statistical analyses will be primarily descriptive.

Ethics and dissemination

The study protocol was approved by the local ethics committee (number 232-2023-FARM-AUSLBO–23020, 22-Mar-2023). The results of this study will be disseminated by the investigators through presentations at international scientific conferences and reported in peer-reviewed scientific journals.

Trial Registration

European Union Clinical Trials Register (EudraCT number 2023-000185-34).

ARTICLE SUMMARY

Strengths And Limitations Of This Study

This was the first approved study protocol developed for a potential disease-modifying drug in Lafora disease

The study will be open label due to the serious and life-threatening nature of the disease and its rarity

Given the lack of a control group in this study, the exploratory endpoints observed will be baseline-controlled and compared with natural history studies

The rationale for VAL-1221 dose and schedule comes from experience in Pompe disease clinical trials and expanded access programs
ETHICAL CONSIDERATIONS FOR CLINICAL CARE ON SHORT TERM MEDICAL MISSIONS IN LOW- AND MIDDLE-INCOME COUNTRIES: A SCOPING REVIEW
Authors: Smith M. , Graham R. , Vance C. , Coburn W. , Richards D. , Whitfield J.
Published: February 2024

Intro

Despite short term medical missions (STMMs) to low- and middle-income countries (LMIC) becoming increasingly popular, ethical considerations for the provision of clinical care on STMMs are poorly defined. Clinicians are often unprepared to adapt care and ethical precepts to resource limited environments. There may be discord in interpretation of ethical principles between visiting providers and hosts. Clinical care provision has direct impact on the health of patients and communities and there is a need for guidelines regarding ethical clinical care.

Methods

Scoping review of the literature published from 2001-2021 restricted to English language identified 3072 records discussing ethical considerations of provision of clinical care on STMMs. Records were screened by title, abstract and finally full text by independent reviewers resulting in 40 records for inclusion.

Results

Thirteen themes were identified as important considerations for provision of ethical clinical care on STMMs. These themes included: collaboration/longitudinal relationship, education, lack of follow up, cultural barriers, needs assessment/goal setting, capacity building, outcome evaluation, pre-departure preparation, scope of practice, resources allocation, detriment to local systems, bidirectionality, and formal ethical review. From these themes a list of guidelines is outlined.

Conclusion

While ideally clinical care on STMMs would be regulated by formal ethical review boards this is difficult to develop and enforce. Independent STMMs must evaluate their approach to clinical care in LMICs. Care should be given to focusing on collaboration, education, follow up, cultural barriers, and performing a needs assessment/goal setting. These efforts may be guided by the checklist included within.
Botryococcus brauniireduces algal grazing losses toDaphniaandPoterioochromonasthrough both chemical and physical interference
Authors: Thomas Patrick , Arn Finn , Freiermuth Micha , Narwani Anita
Published: February 2024

Crop protection from algal grazers is a key area of concern, as grazing zooplankton and flagellates can decimate algal crops and impede economic viability of cultivation for biofuels and bioproducts. Inhibition of grazing by chemical and physical interference is one promising solution; however, there have been few empirical tests of this approach that use defense traits innate to algal crop species. Here we conduct an experiment to test whether the hydrocarbon excreting algaBotryococcus brauniican mitigate losses to grazing by two distinct grazers,Daphnia magnaandPoterioochromonas malhamensis, due to both chemical inhibition and physical interference linked to large/inedible colonies. We show that chemical and physical defenses interactively reduce the total effect of grazing, thus significantly increasing the biomass of cultures ofB. brauniiandNannochloropsis limneticawhen either grazer is present. Specifically,B. brauniifiltrate alone inhibits grazing and thus weakens top-down control ofN. limneticagrowth rates and final biomass by both grazers;B. brauniicolonies alone also inhibit biomass losses; and the combination of filtrate andB. brauniicolonies reveals an interactive effect of both chemical and physical defenses on grazing. Our study demonstrates how community engineering can identify synergies arising from algal cocultivation (e.g., by using industrially relevant strains for crop protection). Such ecological discoveries may help to reduce the costs of large-scale deployment of algal cultivation for sustainable foods, fuels, bioproducts (e.g., bioplastics), and carbon capture.
Development of a cell-based DIFF-rGFP assay system for generalized discovery of viral protease Inhibitors
Authors: Xiaoyan Wu , Yan Feng , Ruiting Chen , Chenjie Fang , Shuai Wang , huimin Sun , shuling Jian , jiiasheng Song , Beibei Wu
Published: February 2024

1.

Viral protease is an attractive target for antiviral therapeutics, but current viral protease inhibitor screening methods still need to be improved. Here, we systematically investigated the sites that may accommodate exogenous short peptides within Enhanced Green Fluorescent Protein (EGFP) and constructed a series of recombinant green fluorescent proteins (rGFPs). Meanwhile, a cell-based, simple and reliable assay system named DIFF-rGFP was developed relying on the co-expression of rGFP and the protease for protease inhibitor screening with the example of 3CLpro, in which the fluorescence intensity increases with the action of the inhibitor. The DIFF-rGFP assay avoided the requirement of a higher biosafety lab and can be performed in a high-throughput manner. For proof of concept, we demonstrated this method to discover novel inhibitors against SARS-CoV-2. We believe the proposed method, in combination with available drug libraries, may accelerate the identification of novel antivirals.