bluuebunny/crossref_metadata_2025 huggingface dataset:
ST6GAL1-mediated sialyl linkage switching in tumor-associated macrophages drives cancer-promoting nanotubes carrying α2,6-sialylation in anti-inflammatory cells
Authors: Dipta Priya , Bansal Naaz , Sumer-Bayraktar Zeynep , Chien Arthur , Ugonotti Julian , Chau The Huong , Anugraham Merrina , Kolarich Daniel , Tirosh Boaz , Kawahara Rebeca , Thaysen-Andersen Morten
Published: December 2024

Tumor-associated macrophages (TAMs) form functionally diverse populations of innate immune cells in the tumor microenvironment (TME). Pro- and anti-inflammatory TAMs are central to cancer progression by shaping inflammation and immune (im)balance, but it remains unknown if polarization-induced remodeling of the TAM glycocalyx critical for cellular communication occurs within the TME. Taking a systems glycobiology approach, we here firstly used cell surface-focused glycomics and lectin flow cytometry ofex vivopolarized monocyte-derived macrophages to demonstrate profound sialyl linkage switching of the surfaceN-glycome in pro-inflammatory (α2,3-sialo-favored) and anti-inflammatory (α2,6-sialo-dominant) macrophages. In contrast, no polarization-induced alterations in sialylation were observed in the surfaceO-glycome. ST6GAL1 that modifiesN-glycans with α2,6-sialylation was elevated in anti-inflammatory compared to levels in pro-inflammatory macrophages providing a mechanistic basis for the sialyl linkage switching, which was supported byST6GAL1silencing. Interestingly, SNA-focused lectin cytochemistry of anti-inflammatory macrophages revealed dense networks of dynamic α2,6-sialylated protein-based nanotubules forming inter-connecting cellular structures that were absent in pro-inflammatory macrophages. TemporalST6GAL1silencing in anti-inflammatory macrophages caused nanotubule disintegration as evidenced by SNA and biotin fluorescence microscopy. Moreover, live cell recordings of anti-inflammatory macrophages cultured with and without colorectal cancer (CRC) cells showed reduced macrophage motility, attenuated inter-macrophage and macrophage-CRC cell interactions and diminished CRC cell proliferation upon ST6GAL1 disruption indicating functional roles of the α2,6-sialylated nanotubules. Finally, sialyl linkage switching was recapitulated in pro- and anti-inflammatory TAMs from tumor tissues of patients with advanced CRC. We report on the mechanistic basis for and functional consequences of glycocalyx remodeling accompanying TAM polarization.
microRNA-544a as a new modulator of the Wnt-signalling network in the articular cartilage and osteoarthritis
Authors: Heluany Cintia Scucuglia , Day Nicholas J , Santos Keemo Delos , De Palma Anna , Swingler Tracey E , Sochart David , Clark Ian M , Kapoor Mohit , Nalesso Giovanna
Published: December 2024

Objective

Determining the effect of microRNA-544a (miR-544a) in articular chondrocytes isolated from patients affected by osteoarthritis (OA) and its role in the modulation of the Wnt signalling.

Methods

Articular chondrocytes were isolated from patients undergoing joint replacement because of OA. Expression levels of miR-544a were measured by PCR and by in situ hybridization. Putative targets of miR-544a were confirmed by reporter assay and by qPCR in cells stimulated with a miR-544a mimic. The effect of miR-544a on chondrocyte metabolism was monitored by qPCR for phenotypic markers, protein expression levels of aggrecan neoepitopes/MMP-13 and modulation of alcian blue content in micromass cultures, upon stimulation with a miR-544a mimic. The expression levels of MMP-13 and Aggrecan neoepitopes in response to miR-544a stimulation was also measured in co-stimulation with Xav-939 and KN93, which are respectively β-catenin and CaMKII inhibitors.

Results

Our results suggest that miR-544a enhances the activation of the Wnt-signalling in the articular chondrocytes, by downregulating the expression of components of the Wnt/β-catenin destruction complex. The expression of miR-544a is higher in chondrocytes isolated from damaged areas of the articular cartilage removed from OA patients, and can be upregulated by pro-inflammatory and pro-fibrotic cytokines. miR-544a exerts a pro-catabolic effect of articular chondrocytes, which is rescued both by the inhibition of the Wnt/β-catenin and Wnt/CaMKII signalling pathways.

Conclusion

our results point to miR-544a as a new, important modulator of the Wnt signalling network within the articular cartilage suggesting a key role for microRNAs in regulating how the multiple branches of the network and their interaction modulate cartilage homeostasis.
Dynamic remodeling of mechano-sensing complexes in suspended fibroblast cell-sheets under external mechanical stimulus
Authors: Suzuki Madoka , Kawauchi Keiko , Machiyama Hiroaki , Hirata Hiroaki , Ishiwata Shin’ichi , Fujita Hideaki
Published: December 2024

Freestanding cell-sheets are valuable bio-materials for use in regenerative medicine and tissue engineering. Because cell-sheets experience various mechanical stimulations during handling, it is important to understand the responses of cells to these stimulations. Here, we demonstrate changes in the localization of various proteins during the stretching of fibroblast cell-sheets. These proteins are known to be involved in mechano-sensing. Upon stretching, actin filaments appear parallel to the stretching direction. At cell-cell junctions, β-catenin forms clusters that co-localize with accumulated vinculin and zyxin as well as the actin filaments. The p130 Crk-associated substrate, known to be present in focal adhesions, is also recruited to these clusters and phosphorylated. Our results suggest that mechano-sensing machinery is formed at cell-cell junctions when the cell-sheets are stretched.
The MultiMusic multidomain intervention including choral practice in community-dwelling older people: A study protocol for Brain-Derived Neurotrophic Factor (BDNF) salivary biomarkers, audiometric and neuropsychological parameters
Authors: Lippolis M. , Lenti R. , Mantuano P. , De Luca A. , Pantaleo A. , Quaranta N. , Pilotto A. , Solfrizzi V. , Vuust P. , Brattico E.
Published: December 2024

Brain-Derived Neurotrophic Factor (BDNF) plays a crucial role in neuroplasticity, supporting brain health along life and even during aging. This longitudinal study investigates the impact of a 9-month multidomain intervention, including choral practice, on BDNF levels, audiometric and neuropsychological outcomes, in older adults, assessed also for their multidimensional frailty, based on their physical, cognitive and nutritional conditions. BDNF levels, along with geriatric, neuropsychological, audiometric and neurophysiological measures, are taken, via saliva samples, both pre- and post-intervention. For BDNF longitudinal analyses, up to 80 elderly will be randomly assigned to an experimental group participating in a 9 month long multidomain program of activities including choir, physical, intellectual and manual activities or to an active control group participating in physical, intellectual or manual non-musical activities for 9 months or to a passive control group. Participation in daily activities for all groups will be monitored via diaries. Our primary goal is to investigate whether engaging in physical, cognitive and social multidomain activities can enhance neuroplasticity as measured by BDNF levels, to contrast aspects of multidimensional frailty (as assessed by the multidimensional prognostic score, MPI) in the aging population. Secondly, we aim to relate changes in BDNF levels to the perceptual and cognitive domains and psychosocial well-being. Although previous studies point out the positive effects of musical training and active aging on brain health, the scarcity of longitudinal research on effects on BDNF for older individuals keeps the issue open. Moreover, we aim to test whether non-invasive, accessible saliva-based BDNF measurements, despite some reliability limitations, could offer indications of neuroprotection in aging.
A unified model of gene expression control by cohesin and CTCF
Authors: Narita Takeo , Kilic Sinan , Higashijima Yoshiki , Pappas Georgios , Maskey Elina , Choudhary Chunaram
Published: December 2024

Cohesin and CTCF fold vertebrate genomes into loops and topologically associating domains (TADs). The genome folding by cohesin and CTCF is considered crucial for enhancer-promoter communication and gene regulation. However, the extent of cohesin and CTCF-dependent looping in global enhancer function and their potential non-architectural roles in gene activation have remained unclear. Here, we demonstrate that the acute removal of cohesin or CTCF in mouse cells dysregulates hundreds of genes, albeit subtly. Among various possible enhancer types, cohesin almost exclusively facilitates gene activation by one enhancer type—the CBP/p300-dependent enhancers. Interestingly, CTCF plays a dual role, operating both with and without cohesin, and promoting gene activation both in an enhancer-dependent and independent manner. By anchoring cohesin loops, CTCF directs enhancers to specific target genes and prevents their mistargeting. Independently of cohesin and enhancers, CTCF acts as a transcriptional activator or repressor, depending on its precise binding position near promoters. Acting as a canonical transcription activator, CTCF directly activates hundreds of housekeeping genes, including those essential for mammalian cell proliferation. Mechanistically, promoter-bound CTCF controls DNA accessibility and RNA polymerase II recruitment. The transcriptional activator function of CTCF appears unique to vertebrates and is shared by its vertebrate-specific paralog, CTCFL, despite CTCFL’s inability to anchor cohesin loops. These findings reveal the scope of cohesin and CTCF in gene regulation, delineate their shared and unique functions, define a specific class of enhancers using cohesin-mediated looping, and establish a crucial function of CTCF in gene regulation independent of its architectural role. The work reconciles conflicting views and provides a unified model for gene regulation by cohesin and CTCF.
Motor unit discharge properties of the vastii muscles and their modulation with contraction level depend on the knee-joint angle
Authors: Valenčič Tamara , Maeo Sumiaki , Kluzek Stefan , Holobar Aleš , Škarabot Jakob , Folland Jonathan P
Published: December 2024

This study examined the effect of the knee-joint angle on motor unit (MU) discharge properties of the vastii muscles and their modulation with contraction level. Twelve young adults performed unilateral isometric knee-extension contractions during three experimental sessions at either 25, 55, and 85° of knee flexion (full extension: 0°) in a randomised order. Each session involved maximal voluntary contractions (MVCs) followed by submaximal trapezoidal and triangular contractions at different levels relative to maximal voluntary torque (MVT). High-density surface electromyograms were recorded from vastus lateralis and medialis muscles and, subsequently, decomposed to obtain discharge timings of individual MUs. MVT was the greatest, whereas MU discharge rate (DR) during MVCs and submaximal contraction levels (≥30% MVT) was the lowest at the intermediate joint angle (55°). The highest DR during MVCs and high-level contractions (70% MVT), however, was at the most flexed knee position (85°), which was due to a greater DR increase 50-70% MVT compared to 25° and 55°. The onset-offset DR hysteresis (ΔF), an estimate of persistent inward current contribution to motoneuron discharge, decreased with knee flexion and increased with contraction level, whereas the degree of motoneuron input-output nonlinearity (brace height) did not vary with joint angle but decreased with contraction level. At 85°, ΔF increased more and brace height decreased less with contraction level compared to 25° and 55°. These findings indicate that vastii MU DR and its modulation with contraction level vary with knee-joint angle, which could be partly explained by the modulation of motoneuron intrinsic electrical properties.

NEW & NOTEWORTHY

This study explored the relationship between motoneuron output to the vastii muscles at different knee-joint angles (quadriceps lengths) and isometric contraction levels. We showed that the motor unit discharge rate was lowest at the angle of the greatest absolute torque capacity, whereas the contraction-level-induced increases in discharge rate and motoneuron excitability were the greatest in the flexed position. These findings suggest that joint-angle-dependent adjustments in sensory feedback modulate motor control of the knee-extensor muscles.
Using animal tracking for early detection of mass poisoning events
Authors: Curk T. , Santangeli A. , Rast W. , Portas R. , Shatumbu G. , Cloete C. , Beytell P. , Aschenborn O. , Melzheimer J.
Published: December 2024

1 Amidst the sixth mass extinction, some groups, such as vultures, the only obligate scavengers among vertebrates, are disappearing at an unprecedented rate. Vulture populations worldwide are largely threatened by poisoning. As many vulture species are social foragers, they can congregate in large numbers to scavenge at a carcass, potentially increasing their exposure to poisoning risk. Current anti-poisoning prevention and mitigation measures are insufficient to tackle this threat. There is an urgent need for new effective strategies to prevent mass vulture mortality.

2 In this study, we used agent-based modeling to: (1) quantify the impact of different foraging strategies on vulture poisoning risk, and (2) evaluate the cost-effectiveness of using vultures as sentinels for poisoning detection. This approach involves GPS tracking of various numbers of vultures and using the data to quickly detect poisoning incidents and decontaminate carcasses. These actions help mitigate further vulture mortality and prevent mass poisoning.

3 Our results indicate that social foraging significantly elevates the risk of vultures being poisoned. Vulture tracking contributes substantially to the early detection of poisoning events, which results in reduced mortality. Poisoning can be mitigated by tracking more vultures and responding faster, with an optimal cost-effectiveness achieved by tracking 5% of the vulture population (25 individuals in our system) and a budget of 58,728 USD. This approach could potentially prevent 45% of poisoning-related mortalities if interventions occur within 2 hours.

4Synthesis and applications: Our results suggest that, in order to reduce mortality incidences from poisoning, it is sufficient to track a small proportion of the vulture population, which would act as sentinels for the rest. By evaluating the costs and ecological benefits of these mitigation strategies, we provide evidence-based solutions that practitioners can use to design conservation plans. These findings are therefore instrumental in supporting vulture and scavenger conservation policy and practice.
PlantRing: A high-throughput wearable sensor system for decoding plant growth, water relations and innovating irrigation
Authors: Sun Ting , Lu Chenze , Shi Zheng , Zou Mei , Bi Peng , Xu Xiaodong , Xie Qiguang , Jiang Rujia , Liu Yunxiu , Cheng Rui , Xu Wenzhao , Zhang Yingying , Xu Pei
Published: December 2024

The combination of flexible electronics and plant science has generated various plant-wearable sensors, yet challenges persist in their applications in real-world agriculture, particularly in high-throughput settings. Overcoming the trade-off between sensing sensitivity and range, adapting them to a wide range of crop types, and bridging the gap between sensor measurements and biological understandings remain the primary obstacles. Here we introduce PlantRing, an innovative, nano-flexible sensing system designed to address the aforementioned challenges. PlantRing employs bio-sourced carbonized silk georgette as the strain sensing material, offering exceptional resolution (tensile deformation: < 100 μm), stretchability (tensile strain up to 100 %), and remarkable durability (season long), exceeding existing plant strain sensors. PlantRing effectively monitors plant growth and water status, by measuring organ circumference dynamics, performing reliably under harsh conditions and being adaptable to a wide range of plants. Applying PlantRing to study fruit cracking in tomato and watermelon reveals novel hydraulic mechanism, characterized by genotype-specific excess sap flow within the plant to fruiting branches. Its high-throughput application enabled large-scale quantification of stomatal sensitivity to soil drought, a traditionally difficult-to-phenotype trait, facilitating drought tolerant germplasm selection. Combing PlantRing with soybean mutant led to the discovery of a potential novel function of theGmLNK2circadian clock gene in stomatal regulation. More practically, integrating PlantRing into feedback irrigation achieves simultaneous water conservation and quality improvement, signifying a paradigm shift from experience- or environment-based to plant-based feedback control. Collectively, PlantRing represents a groundbreaking tool ready to revolutionize botanical studies, agriculture, and forestry.
Functional insights intoPlasmodiumactin depolymerizing factor interactions with phosphoinositides
Authors: Lasiwa Devaki , Kursula Inari
Published: December 2024

Malaria is caused by protozoan parasites,Plasmodiumspp., that belong to the phylum Apicomplexa. The life cycle of these parasites depends on two different hosts; the definitive host, or vector, is a mosquito, and the intermediate host is a vertebrate, such as human. Malaria parasites use a unique form of substrate-dependent motility for host cell invasion and egress, which is dependent on an actomyosin motor complex called the glideosome. Apicomplexa have a small set of actin regulators, which are poorly conserved compared to their equivalents in higher eukaryotes. Actin depolymerizing factors (ADFs) are key regulators responsible for accelerating actin turnover in eukaryotic cells. The activity of ADFs is regulated by membrane phosphoinositides. Malaria parasites express two ADF isoforms at different life stages. ADF1 differs substantially from canonical ADF/cofilins and fromPlasmodiumADF2 in terms of both structure and function. Here, we studied the interaction of bothPlasmodiumADFs with phosphoinositides using biochemical and biophysical methods and mapped their binding sites on ADF1. BothPlasmodiumADFs bind to different phosphoinositides, and bindingin vitrorequires the formation of vesicles or micelles. Interaction with phosphoinositides increases the α-helical content of the parasite ADFs, and the affinities are in the micromolar range. The binding site for PI(4,5)P2 inPfADF1 involves a small, positively charged surface patch.
Industrialization of three-dimensional hiPSC-cardiac microtissues for high-throughput cardiac safety and drug discovery screening
Authors: de Korte Tessa , Johnson Benjamin B. , Kosmidis Georgios , Samson-Couterie Benoit , Mol Mervyn P. H. , van Helden Ruben W. J. , François Louise , Meraviglia Viviana , Yiangou Loukia , Kuipers Tom , Mei Hailiang , Bellin Milena , Braam Stefan R. , Jain Shushant , Mummery Christine L. , Davis Richard P.
Published: December 2024

Current cardiac cell models for drug screening often face a trade-off between cellular maturity and achieving high throughput. While three-dimensional human induced pluripotent stem cell-based heart models typically exhibit more adult-like features, their application is hindered by the need for large cell numbers or complex equipment. Here, we developed cost-effective methods to scale up production of three-dimensional cardiac microtissues (cMTs) containing three cardiac cell types, and assess calcium transients and action potential metrics for high-throughput screening (HTS). Automating the procedure revealed reproducible drug responsiveness and predictive accuracy in a reference compound screen. Furthermore, an arrhythmic phenotype was reliably triggered in cMTs containing cardiomyocytes with a RYR2 mutation. A screen of FDA-approved drugs identified 17 drugs that rescued the arrhythmic phenotype. Our findings underscore the scalability of cMTs and their utility in disease modelling and HTS. The advanced “technology-readiness-level” of cMTs supports their regulatory uptake and acceptance within the pharmaceutical industry.
Adaptation of the tetracycline-repressible system for modulating the expression of essential genes inCryptococcus neoformans
Authors: Fu Ci , Robbins Nicole , Cowen Leah E.
Published: December 2024

The opportunistic human fungal pathogenCryptococcus neoformanshas an enormous impact on human health as the causative agent of cryptococcal meningitis, an AIDS-defining illness that results in significant human mortality. To combatC. neoformansinfections, there is a dire need to expand our current antifungal arsenal. Essential gene products often serve as ideal targets for antimicrobials, and thus identifying and characterizing essential genes in a pathogen of interest is critical for drug development. Unfortunately, characterization of essential genes inC. neoformansis limited due to its haploid nature and lack of genetic tools for generating effective conditional-expression mutants. To date, the copper-repressible promoterpCTR4is the mostly widely used system to regulate essential gene expression, however, its expression is leaky and copper has pleiotropic effects. In diverse fungal species, includingSaccharomyces cerevisiae, Candida albicans, andCandida auris, the tetracycline-repressible promoter system is a powerful tool to regulate gene expression, however, it has yet to be adapted forC. neoformans. In this study, we successfully implemented the tetracycline-repressible system inC. neoformansto regulate the expression of the essential geneHSP90. Supplementation of cultures with the tetracycline analog doxycycline efficiently depletedHSP90at both transcript and protein levels and inhibitedC. neoformansgrowth and viability. Thus, this work unveils a novel approach to generate conditional-expression mutants inC. neoformans, providing unprecedented potential to systematically study essential gene function in this important human fungal pathogen.
Concordance between upper and lower airway microbiota in children with Cystic Fibrosis
Authors: Nassirnia Sedreh , Scherz Valentin , Greub Gilbert , Caruana Giorgia , Taffé Patrick , Jaton Katia , Papis Sebastien , Posfay-Barbe Klara M. , Mornand Anne , Rochat-Guignard Isabelle , Bertelli Claire , Asner Sandra A.
Published: December 2024

Background

Sputum is the sample to monitor the lower respiratory tract microbiota in cystic fibrosis (CF), but young patients often cannot expectorate. We hypothesized that throat swabs could reflect lower airway colonization and assessed the concordance of bacterial community composition between paired sputum and throat swab samples from children with CF.

Methods

The prospective longitudinal multicenter MUCOVIB cohort included 379 samples from 61 CF children. Using V3-V4 16S rRNA amplicon metagenomics, we compared bacterial community diversity and composition between sputum and throat swabs in the full cohort and in 11 patients with paired samples from the same visit.

Results

Sputum and Throat swabs exhibited similar bacterial diversity, regardless of the exacerbation status, and presented a substantial agreement for detecting pathogens (Cohen’s Kappa: 0.6). Differences in bacterial abundance were observed (p=0.001), but not presence/absence (p=0.098). Community typing revealed three distinct community types, with 86% of paired samples falling into the same cluster, highlighting the homogeneity between sputum and throat swabs microbiota. Network analysis demonstrated slight, non-random similarities in microbial interactions between sample types (ARI = 0.08 and 0.10). The average distance between samples collected from the same visit was shorter (0.505, ± 0.056 95%CI), compared to sputum (0.695, ± 0.017) or throat swab (0.704, ± 0.045) from the same patient collected during different visits.

Conclusions

Throat swabs can provide representative information on lower respiratory microbiota. Clinicians should collect throat swabs rather than relying on sputum samples from previous visits to guide antibiotic prescriptions in CF children unable to expectorate.
Genome-wide mapping of EBV-induced genomic variations identifies the role of MUC19 in EBV latency
Authors: Yu Jingwen , Wang Yaohao , Liu Qirong , Zhou Xiaohui , Robertson Erle S , Pei Yonggang
Published: December 2024

Epstein-Barr virus (EBV) infects over 95% of the world’s population and is tightly associated with multiple human malignant diseases. As the first discovered human oncovirus, EBV is known to induce genomic instability by promoting various types of genomic modifications in host chromosomes. However, the mechanisms through which EBV interacts with the host genome and regulates cellular gene expression in genomic modifications are not yet fully elucidated. In this study, we conducted primary EBV infection in B cells and performed the analyses of copy number variants using whole genome sequencing. After comparing to other distinct B cells with varying EBV infection backgrounds, we identified susceptible regions and unveiled critical host factors induced by EBV infection on chromosomes. Combined with the genome-wide transcriptomic analyses, we found that the mucin geneMUC19is distinctively activated by EBV infection and MUC19 promotes oncogenesis through the activation of mTOR signaling in lymphoblastoid cell lines (LCLs). Further results indicate that EBV nuclear antigen 1 (EBNA1) binds to multiple regions withinMUC19and enhances the expression ofMUC19. Moreover, sequence alignment has shown intriguing motif homology between the basic repeat unit ofMUC19and EBV genome, suggesting the potential of EBV-specific integration. To conclude, our study maps the genomic perturbations induced by EBV primary infection and offers new insights into the oncogenic roles of MUC19 during EBV latency.
Rhizobium rhizogenesA4-derived strains mediate hyper-efficient transient gene expression inNicotiana benthamianaand other solanaceous plants
Authors: Lopez-Agudelo Juan Carlos , Goh Foong-Jing , Tchabashvili Sopio , Huang Yu-Seng , Huang Ching-Yi , Lee Kim-Teng , Wang Yi-Chieh , Wu Yu , Chang Hao-Xun , Kuo Chih-Horng , Lai Erh-Min , Wu Chih-Hang
Published: December 2024

Agroinfiltration, a method utilizing agrobacteria to transfer DNA into plant cells, is widely used for transient gene expression in plants. Besides the commonly usedAgrobacteriumstrains,Rhizobium rhizogenescan also introduce foreign DNA into host plants for gene expression. While manyR. rhizogenesstrains have been known for inducing hairy root symptoms, their use for transient expression has not been fully explored. Here, we showed thatR. rhizogenesA4 outperformed all other tested agrobacterial strains in agroinfiltration experiments on leaves ofNicotiana benthamianaand other solanaceous plants. By conducting an agroinfiltration screening inN. benthamianaleaves using various agrobacterial strains carrying the RUBY reporter gene cassette, we discovered that A4 mediates the strongest and fastest transient expression. Utilizing the genomic information, we developed a collection of disarmed and modified strains derived from A4. By performing vacuum infiltration assays, we demonstrated that these A4-derived strains efficiently transiently transform 6-week-oldN. benthamianaleaves, showing less sensitivity to the age of plants compared to the laboratory strain GV3101. Furthermore, we performed agroinfiltration using AS109, an A4-derived disarmed strain, on the leaves of tomato, pepper, and eggplant. Remarkably, AS109 mediated transient gene expression on tested solanaceous plants more effectively than all the tested commonly used agrobacterial strains. This discovery paves the way for establishingR. rhizogenesA4-derived strains as a new option for enhancing transient expression inN. benthamianaand facilitating the functional study of plant genes in other solanaceous species.
Functional, Biotinylproteomic and Bioinformatic Analysis of Both Cytoskeletal and Plastoskeletal Proteins in Plant Mechanoresponse
Authors: Wu Kebin , Yang Nan , Ren Jia , Liu Shichang , Wang Kai , Dai Shuaijian , Lu Yinglin , An Yuxing , Tian Fuyun , Gao Zhaobing , Yang Zhu , Zhang Yage , Yu Weichuan , Li Ning
Published: December 2024

To investigate the early signaling components of skeletal proteins in mediating Arabidopsis thigmomorphogenesis, both microscopic and proximity labeling (PL)-based quantitative biotinylproteomics were applied to investigate the subcellular location and putative interactors of a touch-responsive WPRa4 protein. These experiments have demonstrated that the cytoskeletal protein WPRa4 is localized nearby the plastid. Several cytosolic Plastid Movement-Impaired (PMI) proteins and a member of the plastidic translocon were identified as putative interactors of WPRa4, suggesting an integrated network of skeletal proteins linking the cytoskeleton with the plastid membrane. Further bioinformatic analysis of both Proximity Labeling- and XL-MS-based proteomic results suggested that Plastid Movement-Impaired 4 (PMI4) protein may serve as a candidate in mediating the plant touch response. The loss-of-functionpmi4mutant showed neither the touch-induced bolting delay nor the rosette size reduction upon repetitive touches, suggesting thatpmi4is a unique type of mutant of Arabidopsis thigmomorphogenesis. Moreover, the null mutantpmi4displayed a severe defect in the touch-induced Ca2+oscillation. Further transcriptomic analysis performed on both the wild-type Arabidopsis andpmi4mutant indicated that the mutatedpmi4gene suppressed the expression of a number of touch rapidly induced transcripts and a JA-responsive gene,LOX2. These findings led us to propose a revised touch force-sensing theory, in which the interconnected cytosolic and plastidic skeletal proteins serve as the early mechano-sensing components mediating Arabidopsis thigmomorphogenesis and the retrograde calcium signaling in response to touch.
Defining and Controlling Axial Nephron Patterning in Human Kidney Organoids with Synthetic Wnt-Secreting Organizers
Authors: Fausto Connor C. , Glykofrydis Fokion , Kumar Navneet , Schnell Jack , Csipan Reka L. , De Kuyper Faith , Grubbs Brendan , Thornton Matthew , Achieng MaryAnne , Morsut Leonardo , Lindström Nils O.
Published: December 2024

Current human pluripotent stem cell-derived kidney organoids contain nephron-like structures that lack organotypic patterning. It is thought that during human development, nephrons form their proximal-distal axial polarity in response to collecting duct-derived signals that are absent in kidney organoids. To delineate how nephron polarities establish, we profiled human kidney development by spatial transcriptomic approaches. Our analyses describe a new axial polarity in the nephron and demonstrate that the nephron proximal-distal polarity develops adjacent to a transcriptional boundary in the collecting duct where non-canonicalWNT11is downregulated and canonicalWNT9Bligand is upregulated. The nephron region closest to this boundary in turn activates a series of canonical WNT target genes inferring positional nephron identities. To establish whether a canonical WNT source can improve organoid patterning to anin vivo-like state, we bioengineered self-organizing WNT-secreting synthetic organizers. Organizer-coupled kidney organoids respond to WNT ligands by forming expression gradients and developing distal cell identities. Tuning the WNT dose produced nephrons with continuous patterning along the proximal-distal axis. Strikingly, polarized iPSC-derived nephrons directed their distal tubules towards the WNT-source, indicating axial patterning and morphogenetic programs are tuned by WNTs from the synthetic organizers. Our data present a strategy to control organ patterning, build an artificial kidney, and highlights the power of synthetic organizer systems for advancing organoid models.
Impact of Temporal Uncertainty on Sign-tracking Behavior
Authors: Kaneko Rie , Simpson Eleanor H , Balsam Peter D
Published: December 2024

Sign-tracking behavior, also known as “autoshaping”, is defined as approach and interaction with reward-predictive cues. It is associated with addiction-related phenotypes and compulsive behavior. Several previous studies have demonstrated that when there is uncertainty about reward properties (e.g. probability, size), sign-tracking is increased. However, the effect of cue-uncertainty on sign-tracking behavior is not known. Here, using a Pavlovian conditioning paradigm, we manipulated the temporal uncertainty about the appearance of cues by implementing either fixed or variable inter-trial intervals (ITIs) of different durations across groups of mice. We found that temporal uncertainty during acquisition significantly enhances sign-tracking, which persists during extinction, even when ITI variability was different in the extinction session than in the acquisition session. This suggests that the effects of temporal uncertainty are learned and retained, rather than performance-based. Our results demonstrate that sign-tracking behavior is not only modified by the characteristic of the reward, but it can also be modified by the uncertainty regarding cues. These findings highlight how temporal predictability shapes cue-directed behaviors and has implications for understanding reward-related behavioral responses including sign-tracking behaviors.
Optimizing femtosecond laser fabricating strategy of Nitinol hypotube for vascular interventional surgery
Authors: Song Yunfeng , Yang Zhiwei , Xu Tiangang , Xie Hao , Wang Depeng , Chen Lan , Yang Xusan
Published: December 2024

Guidewires and catheters are essential in minimally invasive procedures, particularly in accessing targets within the vascular system for neuron surgery. Femtosecond lasers can precisely cut nickel-titanium micro tubes, known as Nitinol hypotubes, serving as the heads of micro guidewires while protecting their core tips. The quality and geometry of these hypotubes depend on the focus of the laser cutting system. We evaluated the cutting efficiency and quality of Nitinol hypotubes using objective lenses with three numerical apertures (NA). Quantitative analysis indicated that higher NA objectives yield better surface quality, resulting in lower debris. Additionally, cutting with high NA objectives produced significantly lower arithmetic mean surface roughness and enhanced mechanical properties. Using a two-temperature model, we simulated the interaction between femtosecond lasers and Nitinol, showing that higher NA objectives increase electron temperatures, thus improving material removal efficiency. This study also tested the optimized Nitinol hypotube prformance in simulations of invasive neuron surgery.
The ALS-associated co-chaperone DNAJC7 mediates neuroprotection against proteotoxic stress by modulating HSF1 activity
Authors: Fleming Andrew C. , Rao Nalini R. , Wright Matthew , Savas Jeffrey N. , Kiskinis Evangelos
Published: December 2024

The degeneration of neurons in patients with amyotrophic lateral sclerosis (ALS) is commonly associated with accumulation of misfolded, insoluble proteins. Heat shock proteins (HSPs) are central regulators of protein homeostasis as they fold newly synthesized proteins and refold damaged proteins. Heterozygous loss-of- function mutations in theDNAJC7gene that encodes an HSP co-chaperone were recently identified as a cause for rare forms of ALS, yet the mechanisms underlying pathogenesis remain unclear. Using mass spectrometry, we found that the DNAJC7 interactome in human motor neurons (MNs) is enriched for RNA binding proteins (RBPs) and stress response chaperones. MNs generated from iPSCs with the ALS-associated mutation R156X inDNAJC7exhibit increased insolubility of its client RBP HNRNPU and associated RNA metabolism alterations. Additionally, DNAJC7 haploinsufficiency renders MNs increasingly susceptible to proteotoxic stress and cell death as a result of an ablated HSF1 stress response pathway. Critically, expression of HSF1 in mutant DNAJC7 MNs is sufficient to rescue their sensitivity to proteotoxic stress, while postmortem ALS patient cortical neurons exhibit a reduction in the expression of HSF1 pathway genes. Taken together, our work identifies DNAJC7 as a crucial mediator of HNRNPU function and stress response pathways in human MNs and highlights HSF1 as a therapeutic target in ALS.
The effects of varying intensities of unilateral handgrip fatigue on bilateral movement
Authors: Knorz Adrian L. , Andrushko Justin W. , Sporn Sebastian , Stagg Charlotte J. , Zich Catharina
Published: December 2024

The human ability to maintain adequate movement quality despite muscle fatigue is of critical importance to master physically demanding activities of daily life and for retaining independence following motor impairments. Many real-life situations call for asymmetrical activation of extremity muscles leading to unilateral manifestations of muscle fatigue. Repeated unilateral handgrip contractions at submaximal force have been shown to be associated with neural dynamics in both contralateral and ipsilateral cortical motor areas and improved response times of the contralateral, unfatigued homologue in a button-press task. However, it remains unclear whether the observed improvement in contralateral response latency translates into higher-level benefits in movement quality.

To investigate this, 30 healthy participants underwent unilateral handgrip fatiguing tasks at 5%, 50%, and 75% of maximum voluntary contraction (MVC) force. Subsequently, bimanual movement quality was assessed in an object-hit task using a Kinarm robot.

The protocol at 50% and 75% of MVC elicited clear signs of muscle fatigue compared to the control condition (5%) measured by a decline in force, post-exercise deterioration in MVC, characteristic changes in surface electromyography magnitudes, and increases in ratings of perceived exertion. No change was observed on kinematic measures in the object-hit task for both arms indicating that unilateral handgrip fatigue did not elicit measurable effects on higher-level movement quality on the ipsilateral or contralateral homologue. Previously reported improvements on contralateral response latency were not found to translate into advanced movement quality benefits.
Early prediction of preeclampsia using the first trimester vaginal microbiome
Authors: Kindschuh William F. , Austin George I. , Meydan Yoli , Park Heekuk , Urban Julia A. , Watters Emily , Pollak Susan , Saade George R. , Chung Judith , Mercer Brian M. , Grobman William A. , Haas David M. , Silver Robert M. , Serrano Myrna , Buck Gregory A. , McNeil Rebecca , Nandakumar Renu , Reddy Uma , Wapner Ronald J. , Kav Aya Brown , Uhlemann Anne-Catrin , Korem Tal
Published: December 2024

Preeclampsia is a severe obstetrical syndrome which contributes to 10-15% of all maternal deaths. Although the mechanisms underlying systemic damage in preeclampsia—such as impaired placentation, endothelial dysfunction, and immune dysregulation—are well studied, the initial triggers of the condition remain largely unknown. Furthermore, although the pathogenesis of preeclampsia begins early in pregnancy, there are no early diagnostics for this life-threatening syndrome, which is typically diagnosed much later, after systemic damage has already manifested. Here, we performed deep metagenomic sequencing and multiplex immunoassays of vaginal samples collected during the first trimester from 124 pregnant individuals, including 62 who developed preeclampsia with severe features. We identified multiple significant associations between vaginal immune factors, microbes, clinical factors, and the early pathogenesis of preeclampsia. These associations vary with BMI, and stratification revealed strong associations between preeclampsia andBifidobacteriumspp.,Prevotella timonensis, andSneathia vaginalis. Finally, we developed machine learning models that predict the development of preeclampsia using this first trimester data, collected ~5.7 months prior to clinical diagnosis, with an auROC of 0.78. We validated our models using data from an independent cohort (MOMS-PI), achieving an auROC of 0.80. Our findings highlight robust associations among the vaginal microbiome, local host immunity, and early pathogenic processes of preeclampsia, paving the way for early detection, prevention and intervention for this devastating condition.
Optogenetically Induced Microtubule Acetylation Unveils the Molecular Dynamics of Actin-Microtubule Crosstalk in Directed Cell Migration
Authors: Deb Roy Abhijit , Saez Gonzalez Cristian , Shahid Farid , Yadav Eesha , Inoue Takanari
Published: December 2024

Microtubule acetylation is implicated in regulating cell motility, yet its physiological role in directional migration and the underlying molecular mechanisms have remained unclear. This knowledge gap has persisted primarily due to a lack of tools capable of rapidly manipulating microtubule acetylation in actively migrating cells. To overcome this limitation and elucidate the causal relationship between microtubule acetylation and cell migration, we developed a novel optogenetic actuator, optoTAT, which enables precise and rapid induction of microtubule acetylation within minutes in live cells. Using optoTAT, we observed striking and rapid responses at both molecular and cellular level. First, microtubule acetylation triggers release of the RhoA activator GEF-H1 from sequestration on microtubules. This release subsequently enhances actomyosin contractility and drives focal adhesion maturation. These subcellular processes collectively promote sustained directional cell migration. Our findings position GEF-H1 as a critical molecular responder to microtubule acetylation in the regulation of directed cell migration, revealing a dynamic crosstalk between the actin and microtubule cytoskeletal networks.
From Stability to Complexity: A Systematic Review Protocol on Long-term Divergence Exponents in Gait Analysis
Authors: Terrier Philippe
Published: December 2024

Long-term divergence exponents derived from nonlinear gait analysis (maximum Lyapunov exponent method) have recently been reinterpreted as measures of gait complexity rather than stability. This shift necessitates a comprehensive review of existing literature. This systematic review protocol aims to critically examine studies using long-term divergence exponents in gait analysis. The focus will be on reconciling previous findings with current understanding, evaluating methodological approaches, and synthesizing comparable results. We will search Web of Science (including MEDLINE) for peer-reviewed articles published between 2001 and 2024 that report long-term divergence exponents calculated using Rosenstein’s algorithm in human gait studies. Two independent reviewers will screen articles and extract data on study characteristics, methodological specifications, and result interpretations. Primary outcomes will include tracking how result interpretations have evolved over time and identifying potential reinterpretations based on current knowledge. Secondary outcomes will address methodological standardization. Data synthesis will primarily be narrative. Where possible, meta-analyses will be conducted for studies with comparable methods and objectives. Given the expected exploratory nature of many included studies, a narrative assessment of methodological quality will be performed instead of a formal risk of bias evaluation. This review will consolidate understanding of long-term divergence exponents as measures of gait complexity and automaticity, establish standardized computational methods, and inform future research and clinical applications in gait analysis.
DNA methylation in primary myelofibrosis is partly associated with driver mutations and distinct from other myeloid malignancies
Authors: Torlak Esra Dursun , Tharmapalan Vithurithra , Kricheldorf Kim , Schifflers Joelle , Caduc Madeline , Zenke Martin , Koschmieder Steffen , Wagner Wolfgang
Published: December 2024

Primary myelofibrosis (PMF) is a clonal blood disorder characterized by mutually exclusive driver mutations inJAK2,CALR, orMPLgenes. To explore the epigenetic impact of these mutations, we analyzed DNA methylation (DNAm) profiles from PMF patients. Notably, no differences were found in DNAm betweenJAK2andCALRmutated cases, whereasMPLmutations displayed slightly distinct patterns. Furthermore, induced pluripotent stem cell (iPSC) models withJAK2mutations indicated only a moderate association with PMF-related epigenetic changes, suggesting that these alterations may not be directly driven by the mutations themselves. Additionally, PMF-associated epigenetic changes showed minimal correlation with allele burden and were largely influenced by shifts in the cellular composition. PMF DNAm profiles compared with those from other myeloid malignancies - such as acute myeloid leukemia, juvenile myelomonocytic leukemia, and myelodysplastic syndrome – showed numerous overlapping changes, making it difficult to distinguish PMF based on individual CpGs. However, a PMF score created by combining five CpGs was able to discern PMF from other diseases in both training and validation datasets. These findings demonstrate that PMF driver mutations do not directly evoke epigenetic changes. While PMF shares certain epigenetic alterations with other myeloid malignancies, epigenetic signatures can distinguish between PMF and related diseases.
Adherence to Life’s Essential 8 is associated with delayed white matter aging
Authors: Feng Li , Ye Zhenyao , Pan Yezhi , McCoy Rozalina G. , Mitchell Braxton D. , Kochunov Peter , Thompson Paul M. , Chen Jie , Liang Menglu , Nguyen Thu T. , Shenassa Edmond , Li Yan , Canida Travis , Ke Hongjie , Lee Hwiyoung , Liu Song , Hong L. Elliot , Chen Chixiang , Lei David K.Y. , Chen Shuo , Ma Tianzhou
Published: December 2024

Importance

The American Heart Association introduced Life’s Essential 8 (LE8) as a checklist of healthy lifestyle factors to help older individuals maintain and improve cardiovascular health and live longer. How LE8 can foster healthy brain aging and interact with genetic risk factors to render the aging brain less vulnerable to dementia is not well understood.

Objective

To investigate the impact of LE8 on the white matter brain aging and the moderating effects of theAPOE4allele.

Design, Setting, and Participants

This cross-sectional study uses genetic, imaging, and other health-related data collected in the UK Biobank cohort. Participants included non-pregnant whites with LE8 variables, diffusion tensor imaging data, and genetic data onAPOE4available, and excluded the extreme white matter hyperintensities. The baseline assessment was performed from 2006 to 2010. The diffusion tensor imaging data were collected since 2014.

Exposures

LE8 variables, encompassing diet, physical activity, smoking, sleep, body mass index, lipids, hemoglobin, and blood pressure.

Main Outcomes and Measures

The white matter brain age was predicted from regional fractional anisotropy measures derived from diffusion tensor imaging data using the random forest regression method. The outcome white matter brain age gap was calculated by subtracting individuals’ chronological age from their predicted brain age.

Results

The analysis included 9,430 women and 9,387 men (mean age 55.45 [SD: 7.46] years). Higher LE8 scores were associated with lower white matter brain age gap, indicating delayed brain aging. The findings are consistent for each of the individual LE8 variables. The effect was stronger among non-APOE4carriers (124 days younger per 10-point increase, 95% CI, 102 to 146 days; P<0.001) thanAPOE4carriers (84 days younger per 10-point increase, 95% CI, 47 to 120 days; P<0.001). Notably, early middle-aged women withAPOE4showed significant interactions between LE8 scores and brain aging (P interaction = 0.048), not observed in men.

Conclusions and Relevance

Adherence to LE8 is associated with delayed brain aging, moderated by genetic factors such asAPOE4. These findings highlight the potential of behavioral and lifestyle interventions in reducing dementia risk, emphasizing tailored prevention plans for those with different genetic predispositions to dementia and sex.