bluuebunny/crossref_metadata_2025_split huggingface dataset:
Wheel running, but not home cage activity in Digital Ventilated Cages® is impaired in a mouse model of breast cancer-induced bone pain
Authors: Hopkins Chelsea , Kanneworff Ida Buur , Kornum Birgitte Rahbek , Heegaard Anne-Marie 
Published: November 2024

AbstractIntroductionCancer-induced bone pain (CIBP) due to metastatic breast cancer is common and debilitating. Effective, long-term treatment options have side effects that reduce patients’ quality of life. Preclinical models are a valuable tool to test novel analgesics, but new methods that are translationally and clinically relevant are necessary. This study aimed to assess spontaneous pain-like behaviour of home cage activity and wheel running in Digital Ventilated Cages®.MethodTwenty BALB/cAnNHsd mice were housed in Digital Ventilated Cages® from Tecniplast® with GYM500 home cage running wheels. Mice were assessed by limb use analysis and static weight bearing to determine the development of CIBP and this was compared to the dark-phase home cage activity and wheel running in the Digital Ventilated Cages®. Ten mice underwent 4T1-Luc2 mammary gland adenocarcinoma cell inoculation into the right femur to establish CIBP and another ten mice underwent a sham surgical procedure.ResultsThe 4T1-inoculated mice displayed pain-like behaviour in limb use and weight bearing tests, demonstrating a preference for the contralateral limb. The limb use scores were compared with home cage activity and wheel running. A reduced wheel running distance corresponded to reduced limb use scores, with the shortest wheel running distances corresponding to the lowest limb use scores. However, this behavioural pattern was not observed in home cage activity, which remained consistent over the study period.DiscussionReduced wheel running corresponded with reduced limb use scores. This suggests that wheel running behaviour is affected by the development of metastatic breast cancer. However, the home cage activity was not influenced by disease development. Digital Ventilated Cage® wheel running may be a useful behavioural assessment of spontaneous pain-like behaviour of CIBP and may be useful to assess analgesic efficacy.
Vincristine treatment reverses podocyte damage in focal segmental glomerulosclerosis
Authors: Mason William J , Chandler Jennifer C , Pomeranz Gideon , Price Karen L , Antonelou Marilina , Henderson Scott R , Perin Laura , Da Sacco Stefano , Salama Alan D , Long David A , Pepper Ruth J 
Published: November 2024

AbstractIntroductionFocal segmental glomerulosclerosis (FSGS) is a significant cause of chronic kidney disease and triggered by podocyte damage which can result in cytoskeletal alterations leading to foot process effacement. Vincristine is a chemoprotective drug which alters cytoskeletal microtubules and has been used clinically to reverse FSGS. However, the mechanisms underlying the beneficial effect of vincristine are not understood.MethodsWe exposed immortalised human podocytes to serum obtained from an FSGS patient before, during, and after vincristine treatment. Using RNA-sequencing we determined the effect on the podocyte transcriptome alongside impacts on cytoskeletal structure and filtration barrier integrity using a glomerulus-on-a-chip model.ResultsWe describe an adult index FSGS patient successfully treated on multiple occasions by vincristine. Podocytes exposed to serum obtained during or after vincristine treatment contained lower levels of genes associated with microtubule function compared with cells stimulated with serum collected before treatment during disease presentation. Presentation serum altered the patterning of two key podocyte cytoskeletal components, tubulin and F-actin and increased albumin permeability, changes prevented by vincristine treatment. Immunoglobulin depletion experiments revealed that the podocyte damage initiated by the presentation serum was not due to circulating autoantibodies. Defects in tubulin patterning were observed when podocytes were exposed to serum from other FSGS patients, suggestive of a common disease mechanism.ConclusionVincristine therapy produces a milieu that protects against pathological changes induced by FSGS serum, associated with preservation of tubulin and F-actin organisation. The functional role of vincristine warrants further investigation, to advance our understanding of this alternative FSGS therapeutic.
Targeted degradation of endogenous condensation-prone proteins improves crop performance
Authors: Luo Ming , Wen Qing , Zhu Sitao , Dang Hua , Niu Ruixia , Long Jiawei , Wang Zhao , Tong Yongjia , Ning Yuese , Yuan Meng , Xu Guoyong 
Published: November 2024

AbstractEffective methods, such as CRISPR and RNA interference, exist for modulating gene expression at DNA and RNA levels, but approaches for directly modifying endogenous proteins remain lacking in plants. Here, we develop a targeted condensation-prone-protein degradation (TCD) strategy to eliminate endogenous proteins, particularly those prone to condensation. We identify an E3 ligase, E3TCD1, that degrades itself but selectively targets other proteins when fused to them. In rice, transgenic E3TCD1 fusions with Teosinte branched 1 and Early flowering 3 (OsELF3) modulate tiller numbers and flowering times, respectively. The TCD system is also controllable. Using the ProTBF1-uORFsTBF1expression control cassette, we can conditionally degrade the negative defense regulator OsELF3 upon pathogen invasion, enhancing rice resistance without interfering with rice flowering time. This method, unlike animal-targeting strategies, does not rely on small molecules, antibodies, or genetic knock-ins, showing promise as a gene therapeutic avenue for optimizing crop performance and potentially addressing human diseases.
Type I interferon signaling enhances kainic acid-induced seizure severity
Authors: Ma Jeong-Hwa , Eo Jun-Cheol , Lee Changjun , Hwang Inhwa , Choi Jihye , Shin Sung Jae , Kim Chul Hoon , Yu Je-Wook 
Published: November 2024

AbstractEpilepsy is a chronic neurological disorder characterized by recurrent seizures, yet the role and mechanisms of type I interferon (IFN) signaling in seizure conditions remain elusive. In this study, we demonstrate that type I IFN signaling exacerbates seizure phenotypes in a kainic acid-induced seizure mouse model. We found that the absence of type I IFN signaling inIfnar1-/-mice led to decreased neuronal excitability and microglial activation in response to kainic acid stimulation. Conversely, intracerebroventricular injection of IFN-β heightened the severity of kainic acid-induced seizures.In vitrocalcium imaging revealed that IFN-β treatment amplified both basal and kainic acid-induced neuronal excitability, though no significant difference was observed in basal neuronal excitability between wild-type andIfnar1-/-neurons. Furthermore,Ifnar1-/-mice exhibited reduced mTOR activation in the brain following kainic acid administration. Consistent with this finding, IFN-β treatment induced mTOR activation, as indicated by S6 phosphorylation inin vitromixed glial cultures. Taken together, these results demonstrate the critical role of type I IFN signaling in seizure pathogenesis and suggest that targeting type I IFNs could be a promising therapeutic strategy for reducing seizure severity and mitigating epilepsy.
Exploring large protein sequence space through homology- and representation-based hierarchical clustering
Authors: Chen JZ , Gall B , Tokuriki N , Jackson CJ 
Published: November 2024

AbstractExploration of protein sequence space can offer insight into protein sequence-function relationships, benefitting both basic science and industrial applications. The use of sequence similarity networks (SSNs) is a standard method for exploring large sequence datasets, but is currently limited when scaling to very large datasets and when viewing more than one level (hierarchy) of homology. Here, we present a sequence analysis pipeline with a number of innovations that address some limitations of traditional SSNs. First, we develop a hierarchical visualization approach that captures the full range of homologies across protein superfamilies. Second, we leverage representations embedded by protein language models as an alternative homology metric to the basic local alignment search tool (BLAST), showing that they produce comparable results when identifying isofunctional protein families. Finally, we demonstrate that unbiased representative sampling of sequences from genetic neighborhoods can be achieved through the use of hidden Markov models (HMMs) or vector representations. The utility of these methods is exemplified by updating the sequence-function analysis of the FMN/F420-binding split barrel superfamily and improving phylogenetic analyses. We provide our sequence exploration pipeline as publicly available code (ProteinClusterTools) and show it to be scalable to large datasets (∼300k sequences) using desktop computers.
Thanzi La Mawa (TLM) datasets: health worker time and motion, patient exit interview and follow-up, and health facility resources, perceptions and quality in Malawi
Authors: Nkhoma Dominic , Chitsulo Precious , Mulwafu Watipaso , Mnjowe Emmanuel , Tafesse Wiktoria , Mohan Sakshi , Hallet Timothy B , Collins Joseph H , Revill Paul , Chalkley Martin , Mwapasa Victor , Mfutso-Bengo Joseph , Colbourn Tim 
Published: November 2024

AbstractThe Thanzi La Mawa (TLM) study aims to enhance understanding of healthcare delivery and resource allocation in Malawi by capturing real-world data across a range of health facilities. To inform the Thanzi La Onse (TLO) model, which is the first comprehensive health system model developed for any country, this study uses a cross-sectional, mixed-methods approach to collect data on healthcare worker productivity, patient experiences, facility resources, and care quality. The TLM dataset includes information from 29 health facilities sampled across Malawi, covering facility audits, patient exit interviews, follow-ups, time and motion studies, and healthcare worker interviews, conducted from January to May 2024.Through these data collection tools, the TLM study gathers insights into critical areas such as time allocation of health workers, healthcare resource availability, patient satisfaction, and overall service quality. This data is crucial for enhancing the TLO model’s capacity to answer complex policy questions related to health resource allocation in Malawi. The study also offers a structured framework that other countries in East, Central, and Southern Africa can adopt to improve their healthcare systems.By documenting methods and protocols, this paper provides valuable guidance for researchers and policymakers interested in healthcare system evaluation and improvement. Given the formal adoption of the TLO model in Malawi, the TLM dataset serves as a foundation for ongoing analyses into quality of care, healthcare workforce efficiency, and patient outcomes. This study seeks to support informed decision-making and future implementation of comprehensive healthcare system models in similar settings.
A Dual Role for the PP2A Phosphatase in Hippo Signalling Regulation
Authors: Sekar Aashika , Rizzo Alberto , Sins Elodie , Fulford Alexander D. , Ribeiro Paulo S. 
Published: November 2024

AbstractHippo signalling is an evolutionarily conserved pathway that regulates tissue growth. The FERM domain protein Expanded plays a crucial role in integrating polarity cues to activate the Hippo pathway. Previous work has shown that the apicobasal polarity protein Crumbs can limit Hippo activity by promoting the phosphorylation and degradation of Expanded. Here, we provide evidence that PP2AWrdcan counteract the effects of Crumbs, by dephosphorylating and stabilising Expanded. Indeed, we demonstrate that the PP2AWrdholoenzyme can increase Hippo signalling activity, in contrast to the previously established Hippo pathway inhibitory role of the PP2ACka-containing STRIPAK complex. We also uncover a role for PP2AWrdand PP2ATwsin the regulation of Expanded proteostasis. Remarkably, the upstream Hippo regulator, Kibra interacts with PP2AWrdand prevents Expanded degradation. However, Kibra is unable to antagonise Crumbs-mediated Expanded regulation, in agreement with the previously established role of Crumbs in inhibiting Kibra function. Overall, our work characterises a novel Hippo-activating role for PP2A in the stabilisation of Expanded and provides new insights into how PP2A tightly controls Hippo activity in response to polarity stimuli.
Decrypting the complex phenotyping traits of plants by machine learning
Authors: Zdrazil Jan , Kong Lingping , Klimeš Pavel , Jasso-Robles Francisco Ignacio , Saiz-Fernández Iñigo , Güder Firat , Spíchal Lukaš , Snášel Václav , De Diego Nuria 
Published: November 2024

AbstractPhenotypes, defining an organism’s behaviour and physical attributes, arise from the complex, dynamic interplay of genetics, development, and environment, whose interactions make it enormously challenging to forecast future phenotypic traits of a plant at a given moment. This work reports AMULET, a modular approach that uses imaging-based high-throughput phenotyping and machine learning to predict morphological and physiological plant traits hours to days before they are visible. AMULET streamlines the phenotyping process by integrating plant detection, prediction, segmentation, and data analysis, enhancing workflow efficiency and reducing time. The machine learning models used data from over 30,000 plants, using theArabidopsis thaliana-Pseudomonas syringaepathosystem. AMULET also demonstrated its adaptability by accurately detecting and predicting phenotypes ofin vitropotato plants after minimal fine-tuning with a small dataset. The general approach implemented through AMULET streamlines phenotyping and will improve breeding programs and agricultural management by enabling pre-emptive interventions optimising plant health and productivity.
PYR1 biosensor-driven genome-wide CRISPR screens for improved monoterpenoid production inKluyveromyces marxianus
Authors: Robertson Nicholas R. , Lenert-Mondou Chase , Leonard Alison C. , Tafrishi Aida , Carrera Stephanie , Lee Sangcheon , Aguilar Yuna , Zamora Leonardo Sanchez , Nguyen Trinity , Beltrán Jesús , Li Mengwan , Cutler Sean R. , Whitehead Timothy A. , Wheeldon Ian 
Published: November 2024

AbstractMonoterpenoids are valued for their roles as flavors, fragrances, insecticides, and energy-dense fuels. Microbial biosynthesis offers sustainable biosynthesis routes for these important molecules, but production levels remain limited. Here, we introduce a biosensor-driven microbial engineering strategy to enhance monoterpenoid production, specifically targeting geraniol. Using mutagenized libraries of the PYR1 receptor—a versatile biosensor from plant ABA signaling pathways with a malleable binding pocket—we screened 24 monoterpenoids and identified PYR1 variants responsive to eight, including geraniol. A low background, highly selective geraniol-sensitive PYR1 variant was expressed in the thermotolerant yeastKluyveromyces marxianusas a growth-based biosensor circuit, allowing for rapid strain engineering. By coupling the geraniol-sensitive PYR1 sensor with a genome-wide CRISPR-Cas9 mutagenesis approach, we identified six gene knockouts that enhance geraniol production, achieving up to a 2-fold increase in titer. This study demonstrates the power of the PYR1 biosensor platform to enable rapid strain engineering and the identification of mutants that improve titer of a desired metabolite.
Sulfatide deficiency-induced astrogliosis and myelin lipid dyshomeostasis are independent of Trem2-mediated microglial activation
Authors: Mittra Namrata , He Sijia , Bao Hanmei , Bhattacharjee Anindita , Dodds Sherry G , Dupree Jeffrey L , Han Xianlin 
Published: November 2024

AbstractDisrupted lipid homeostasis and neuroinflammation often co-exist in neurodegenerative disorders including Alzheimer’s disease (AD). However, the intrinsic connection and causal relationship between these deficits remain elusive. Our previous studies show that the loss of sulfatide (ST), a class of myelin-enriched lipids, causes AD-like neuroinflammatory responses, cognitive impairment, bladder enlargement, as well as lipid dyshomeostasis. To better understand the relationship between neuroinflammation and lipid disruption induced by ST deficiency, we established a ST-deficient mouse model with constitutiveTrem2knockout and studied the impact of Trem2 in regulating ST deficiency-induced microglia-mediated neuroinflammation, astrocyte activation and lipid disruption. Our study demonstrates that Trem2 regulates ST deficiency-induced microglia-mediated neuroinflammatory pathways and astrogliosis at the transcriptomic level, but not astrocyte activation at the protein level, suggesting that Trem2 is indispensable for ST deficiency-induced microglia-mediated neuroinflammation but not astrogliosis. Meanwhile, ST loss-induced lipidome disruption and free water retention were consistently observed in the absence ofTrem2. Collectively, these results emphasize the essential role of Trem2 in mediating lipid loss-associated microglia-mediated neuroinflammation, but not both astrogliosis and myelin lipid disruption. Moreover, we demonstrated that attenuating neuroinflammation has a limited impact on brain ST loss-induced lipidome alteration or AD-like peripheral disorders. Our findings suggest that preserving lipidome and astrocyte balance may be crucial in decelerating the progression of AD.
Naturally-occurring, strain-specific defects in the retraction ofAcinetobacter baumanniitype IV pili promote biofilm formation
Authors: Yu Yafan , Mahdi Rabab , Leon Ahmad Al-Hilfy , Vo Nam , Lofgren Reese , Mutabazi Jean Luc , Piepenbrink Kurt H. 
Published: November 2024

AbstractType IV pili are helical filaments composed of protein subunits which are produced by numerous taxa of bacteria, includingAcinetobacter. Type IV pili are extended out from the cell by extension enzyme complexes, which extract subunits from the membrane and insert them into the base of the filament, but can also be retracted by reverse rotation catalyzed by a retraction enzyme. Type IV pili have diverse functions, and some (twitching motility, DNA-uptake) require retraction while others (host adhesion, bacterial aggregation) do not.Acinetobacterbacteria, including International Clone I (IC-I) and International Clone II (IC-II) strains, show variable phenotypes in assays of type IV pilus-dependent functions. We show this variation is the result of variable efficiency in pilus retraction between pilus subtypes, and from that, a differential balance between retraction-dependent and retraction-independent functions. We define type IV pilus subtypes based on the sequence of the major subunit, PilA. In both naturally-occurringpilAvariants from the IC-I and IC-II groups and isogenic strains complemented with IC-I or IC-IIpilA, the IC-I pilus subtype promotes greater twitching motility and DNA-uptake while the IC-II pilus subtype promotes biofilm formation while showing reduced capacity for DNA-uptake and twitching motility, similar to a retraction-deficient mutant and consistent with the hypothesis that pilus retraction of the IC-II pilus is naturally deficient. Testing the hypothesis that this defect in retraction was sufficient to increase the level of piliation on the cell surface, we compared the yields of T4P sheared from the cell surface and found that in an isogenic background, complementation with IC-IIpilAresults in greater levels of surface PilA per cell than equivalent complementation with an IC-IpilAgene.
Opposing action of photosystem II assembly factors RBD1 and HCF136 underlies light-regulatedpsbAtranslation in plant chloroplasts
Authors: Rojas Margarita , Chotewutmontri Prakitchai , Williams-Carrier Rosalind , Belcher Susan , Boyce Emily , Barkan Alice 
Published: November 2024

ABSTRACTThe D1 reaction center protein of photosystem II (PSII) is subject to light-induced damage. In plants, D1 photodamage activates translation of the chloroplastpsbAmRNA encoding D1, providing D1 for PSII repair. Genetic data have implicated three D1 assembly factors in the regulatory mechanism: HCF244 and RBD1 activatepsbAtranslation whereas HCF136 repressespsbAtranslation in the dark. To clarify the regulatory circuit, we analyzedpsbAribosome occupancy in dark-adapted and illuminatedrbd1andhcf136;rbd1double mutants in Arabidopsis, and in Zm-hcf244and Zm-hcf136;Zm-hcf244double mutants in maize. The results show that RBD1 is required for the light-induced recruitment of ribosomes topsbAmRNA but has little effect onpsbAribosome occupancy in the dark. Furthermore, RBD1 is dispensable forpsbAtranslation when HCF136 is absent, indicating that RBD1 activatespsbAtranslation indirectly, by inhibiting HCF136’s repressive effect. By contrast, HCF244 is required to recruit ribosomes topsbAmRNA in light, dark, and in the absence of HCF136. These results demonstrate that the step in D1 assembly that is mediated by RBD1 is central to the perception of the D1 photodamage that triggers D1 synthesis, that RBD1 activatespsbAtranslation in the light by relieving the repressive effect of an HCF136-dependent assembly intermediate, and that HCF244 acts independently of these events to activatepsbAtranslation. The results implicate a feature of nascent D1 that is affected by both HCF136 and RBD1 as the signal that reports D1 photodamage to regulatepsbAtranslation rate as needed for PSII repair.Significance StatementThe D1 subunit of photosystem II (PSII) is damaged by light and must be replaced with nascent D1 to maintain photosynthesis. In plants, D1 photodamage triggers D1 synthesis by activating translation of chloroplastpsbAmRNA encoding D1. Our results demonstrate that an antagonistic interplay between two photosystem II assembly factors, HCF136 and RBD1, is at the core of the signal transduction process that senses light-induced D1 damage to regulatepsbAtranslation. These findings implicate a feature of nascent D1 that is affected by both HCF136 and RBD1 as the signal that reports D1 photodamage to tunepsbAtranslation as needed for PSII repair. The results elucidate an assembly-coupled translational rheostat that maintains photosynthesis in the face of PSII photodamage.