bluuebunny/crossref_metadata_2025_split huggingface dataset:
mt-LAF3 is a pseudouridine synthase ortholog required for mitochondrial rRNA and mRNA gene expression inTrypanosoma brucei
Authors: McDermott Suzanne M , Pham Vy , Lewis Isaac , Tracy Maxwell , Stuart Kenneth 
Published: February 2023

AbstractTrypanosoma bruceiand related kinetoplastid parasites possess unique RNA processing pathways, including in their mitochondria, that regulate metabolism and development. Altering RNA composition or conformation through nucleotide modifications is one such pathway, and modifications including pseudouridine regulate RNA fate and function in many organisms. We surveyed pseudouridine synthase (PUS) orthologs in Trypanosomatids, with a particular interest in mitochondrial enzymes due to their potential importance for mitochondrial function and metabolism.T. bruceimt-LAF3 is an ortholog of human and yeast mitochondrial PUS enzymes, and a mitoribosome assembly factor, but structural studies differ in their conclusion as to whether it has PUS catalytic activity. Here, we generatedT. bruceicells that are conditionally null for mt-LAF3 and showed that mt-LAF3 loss is lethal and disrupts mitochondrial membrane potential (ΔΨm). Addition of a mutant gamma-ATP synthase allele to the conditionally null cells permitted ΔΨm maintenance and cell survival, allowing us to assess primary effects on mitochondrial RNAs. As expected, these studies showed that loss of mt-LAF3 dramatically decreases levels of mitochondrial 12S and 9S rRNAs. Notably, we also observed decreases in mitochondrial mRNA levels, including differential effects on edited vs. pre-edited mRNAs, indicating that mt-LAF3 is required for mitochondrial rRNA and mRNA processing, including of edited transcripts. To assess the importance of PUS catalytic activity in mt-LAF3 we mutated a conserved aspartate that is necessary for catalysis in other PUS enzymes and showed it is not essential for cell growth, or maintenance of ΔΨm and mitochondrial RNA levels. Together, these results indicate that mt-LAF3 is required for normal expression of mitochondrial mRNAs in addition to rRNAs, but that PUS catalytic activity is not required for these functions. Instead, our work, combined with previous structural studies, suggests thatT. bruceimt-LAF3 acts as a mitochondrial RNA-stabilizing scaffold.
The histone demethylase KDM5C controls female bone mass by promoting energy metabolism in osteoclasts
Authors: Liu Huadie , Zhai Lukai , Liu Ye , Lu Di , VanderArk Alexandra , Yang Tao , Krawczyk Connie M. 
Published: February 2023

AbstractWomen experience osteoporosis at higher rates than men. Aside from hormones, the mechanisms driving sex-dependent bone mass regulation are not well-understood. Here, we demonstrate that the X-linked H3K4me2/3 demethylase KDM5C regulates sex-specific bone mass. Loss of KDM5C in hematopoietic stem cells or bone marrow monocytes (BMM) increases bone mass in female but not male mice. Mechanistically, loss of KDM5C impairs the bioenergetic metabolism resulting in impaired osteoclastogenesis. Treatment with the KDM5 inhibitor reduces osteoclastogenesis and energy metabolism of both female mice and human monocytes. Our report details a novel sex-dependent mechanism for bone homeostasis, connecting epigenetic regulation to osteoclast metabolism, and positions KDM5C as a target for future treatment of osteoporosis in women.One-Sentence SummaryKDM5C, an X-linked epigenetic regulator, controls female bone homeostasis by promoting energy metabolism in osteoclasts.
Balancing grain yield trade-offs in ‘Miracle-Wheat’
Authors: Abbai Ragavendran , Golan Guy , Longin C. Friedrich H. , Schnurbusch Thorsten 
Published: February 2023

ABSTRACTIntroducing variations in inflorescence architecture, such as the ‘Miracle-Wheat’ (Triticum turgidumconvar.compositum(L.f.) Filat.) with a branching spike, has relevance for enhancing wheat grain yield. However, in the spike-branching genotypes, the increase in spikelet number is generally not translated into grain yield advantage because of reduced grains per spikelet and grain weight. Here, we investigated if such trade-offs might be a function of source-sink strength by using 385 RILs developed by intercrossing the spike-branching landrace TRI 984 and CIRNO C2008, an elite durum (T. durumL.) cultivar; they were genotyped using the 25K array. Various plant and spike architectural traits, including flag leaf, peduncle and spike senescence rate, were phenotyped under field conditions for two consecutive years. On Chr 5AL, we found a new modifier QTL for spike-branching,branched headt3(bht-A3), which was epistatic to the previously knownbht-A1locus. Besides,bht-A3was associated with more grains per spikelet and a delay in flag leaf senescence rate. Importantly, favourable allelesviz., bht-A3andgrain protein content(gpc-B1) that delayed senescence are required to improve grain number and grain weight in the spike-branching RILs. In summary, achieving a balanced source-sink relationship might minimise grain yield trade-offs in Miracle-Wheat.HIGHLIGHTGenetic interplay between sink number and post-anthesis source activity limits grain yield in the spike-branching ‘Miracle-Wheat’.
The Multidrug Resistance Transporter P-glycoprotein Confers Resistance to Ferroptosis Inducers
Authors: Frye William J. E. , Huff Lyn M. , González Dalmasy José M. , Salazar Paula , Carter Rachel M. , Gensler Ryan T. , Esposito Dominic , Robey Robert W. , Ambudkar Suresh V. , Gottesman Michael M. 
Published: February 2023

ABSTRACTFerroptosis is a form of cell death caused by direct or indirect inhibition of glutathione peroxidase 4 that leads to lethal lipid peroxidation. Several small molecule ferroptosis inducers (FINs) have been reported, yet little information is available regarding resistance mechanisms, particularly their interaction with the ATP-binding cassette (ABC) transporters P-glycoprotein (P-gp, ABCB1) and ABCG2. Given the role that ABC transporters play in absorption, distribution, and excretion of many drugs, characterizing these interactions could provide information regarding oral bioavailability and brain penetration and may predict drug-drug interactions. Using ferroptosis-sensitive A673 cells transfected to express P-gp or ABCG2, we found that P-gp overexpression was able to confer resistance to FIN56 and the erastin derivatives imidazole ketone erastin and piperazine erastin. Results were confirmed with OVCAR8-derived NCI/ADR-RES cells that overexpress P-gp, where the P-gp inhibitor valspodar completely inhibited resistance to the FINs. P-gp-mediated resistance to imidazole ketone erastin and piperazine erastin was also reversed in UO-31 renal cancer cells by CRISPR-mediated knockout ofABCB1. At a concentration of 10 μM, the FINs ML-162, GPX inhibitor 26a, and PACMA31 were able to increase intracellular rhodamine 123 fluorescence over 10-fold in P-gp-expressing MDR-19 cells and GPX inhibitor 26a was able to increase intracellular purpurin-18 fluorescence over 4-fold in ABCG2-expressing R-5 cells. Expression of P-gp may reduce the efficacy of these FINs in cancers that express the transporter and may prevent access to sanctuary sites such as the brain. The ability of some FINs to inhibit P-gp and ABCG2 suggests potential drug-drug interactions.SIGNIFICANCE STATEMENTWhile several small-molecule ferroptosis inducers have been described, little work has addressed potential interactions with ABC transporters such as P-glycoprotein or ABCG2 that might limit bioavailability or brain penetration. We find that the ferroptosis inducers FIN56, imidazole ketone erastin, and piperazine erastin are substrates of P-glycoprotein. ML-162, GPX inhibitor 26a, and PACMA31 were found to inhibit P-glycoprotein, while GPX inhibitor 26a was additionally able to inhibit ABCG2, suggesting the potential for drug-drug interactions.
Spatial and Temporal Dynamics at an Actively Silicifying Hydrothermal System
Authors: Rasmussen Kalen L. , Stamps Blake W. , Vanzin Gary F. , Ulrich Shannon M. , Spear John R. 
Published: February 2023

AbstractSteep Cone Geyser is a unique geothermal feature in Yellowstone National Park, Wyoming (YNP), actively gushing silicon rich fluids along outflow channels possessing living and actively silicifying microbial biomats. To assess the geomicrobial dynamics occurring temporally and spatially at Steep Cone, samples were collected at discrete locations along one of Steep Cone’s outflow channels for both microbial community composition and aqueous geochemistry analysis during field campaigns in 2010, 2018, 2019, and 2020. Geochemical analysis characterized Steep Cone as an oligotrophic, surface boiling, silicious, alkaline-chloride thermal feature with consistent dissolved inorganic carbon and total sulfur concentrations down the outflow channel ranging from 4.59 ± 0.11 to 4.26 ± 0.07 mM and 189.7 ± 7.2 to 204.7 ± 3.55 μM respectively. Furthermore, geochemistry remained relatively stable temporally with consistently detectable analytes displaying a relative standard deviation < 32%. A thermal gradient decrease of ~55°C was observed from the sampled hydrothermal source to the end of the sampled outflow transect (90.34°C ± 3.38 to 35.06°C ± 7.24). The thermal gradient led to temperature-driven divergence and stratification of the microbial community along the outflow channel. The hyperthermophileThermocrinisdominates the hydrothermal source biofilm community, and the thermophilesMeiothermusandLeptococcusdominate along the outflow before finally giving way to more diverse and even microbial communities at the end of the transect. Beyond the hydrothermal source, phototrophic taxa such asLeptococcus, Chloroflexus, andChloracidobacteriumact as primary producers for the system supporting heterotrophic growth of taxa such asRaineya, Tepidimonas, andMeiothermus. Community dynamics illustrate large changes yearly driven by abundance changes of the dominant taxa in the system. Results indicate Steep Cone possesses dynamic outflow microbial communities despite stable geochemistry. These findings improve our understanding of thermal geomicrobiological dynamics and inform how we can interpret the silicified rock record.
Candida albicansstimulates the formation of a multi-receptor complex that mediates epithelial cell invasion during oropharyngeal infection
Authors: Phan Quynh T. , Solis Norma V. , Cravener Max V. , Swidergall Marc , Lin Jianfeng , Huang Manning Y. , Liu Hong , Singh Shakti , Ibrahim Ashraf S. , Mazzone Massimiliano , Mitchell Aaron P. , Filler Scott G. 
Published: February 2023

SummaryFungal invasion of the oral epithelium is central to the pathogenesis of oropharyngeal candidiasis (OPC).Candida albicansinvades the oral epithelium by receptor-induced endocytosis but this process is incompletely understood. We found thatC. albicansinfection of oral epithelial cells induces c-Met to form a multi-protein complex with E-cadherin and the epidermal growth factor receptor (EGFR). E-cadherin is necessary forC. albicansto activate both c-Met and EGFR and to induce the endocytosis ofC. albicans. Proteomics analysis revealed that c-Met interacts withC. albicansHyr1, Als3 and Ssa1. Both Hyr1 and Als3 were required forC. albicansstimulation of c-Met and EGFR in oral epithelial cells in vitro and for full virulence during OPC in mice. Treating mice with small molecule inhibitors of c-Met and EGFR ameliorated OPC, demonstrating the potential therapeutic efficacy of blocking these host receptors forC. albicans.Graphical abstractHighlightsc-Met is an oral epithelial cell receptor forCandida albicansC. albicansinfection causes c-Met and the epidermal growth factor receptor (EGFR) to form a complex with E-cadherin, which is required for c-Met and EGFR functionC. albicansHyr1 and Als3 interact with c-Met and EGFR, inducing oral epithelial cell endocytosis and virulence during oropharyngeal candidiasisDual blockade of c-Met and EGFR ameliorates oropharyngeal candidiasis
Epilepsy-associatedSCN2A(NaV1.2) Variants Exhibit Diverse and Complex Functional Properties
Authors: Thompson Christopher H. , Potet Franck , Abramova Tatiana V. , DeKeyser Jean-Marc , Ghabra Nora F. , Vanoye Carlos G. , Millichap John , George Alfred L. 
Published: February 2023

ABSTRACTPathogenic variants in neuronal voltage-gated sodium (NaV) channel genes includingSCN2A, which encodes NaV1.2, are frequently discovered in neurodevelopmental disorders with and without epilepsy.SCN2Ais also a high confidence risk gene for autism spectrum disorder (ASD) and nonsyndromic intellectual disability (ID). Previous work to determine the functional consequences ofSCN2Avariants yielded a paradigm in which predominantly gain-of-function (GoF) variants cause epilepsy whereas loss-of-function (LoF) variants are associated with ASD and ID. However, this framework is based on a limited number of functional studies conducted under heterogenous experimental conditions whereas most disease-associatedSCN2Avariants have not been functionally annotated. We determined the functional properties of more than 30SCN2Avariants using automated patch clamp recording to assess the analytical validity of this approach and to examine whether a binary classification of variant dysfunction is evident in a larger cohort studied under uniform conditions. We studied 28 disease-associated variants and 4 common population variants using two distinct alternatively spliced forms of NaV1.2 that were heterologously expressed in HEK293T cells. Multiple biophysical parameters were assessed on 5,858 individual cells. We found that automated patch clamp recording provided a valid high throughput method to ascertain detailed functional properties of NaV1.2 variants with concordant findings for a subset of variants that were previously studied using manual patch clamp. Additionally, many epilepsy-associated variants in our study exhibited complex patterns of gain- and loss-of-function properties that are difficult to classify overall by a simple binary scheme. The higher throughput achievable with automated patch clamp enables study of a larger number of variants, greater standardization of recording conditions, freedom from operator bias, and enhanced experimental rigor valuable for accurate assessment of NaVchannel variant dysfunction. Together, this approach will enhance our ability to discern relationships between variant channel dysfunction and neurodevelopmental disorders.
In vitroandin vivoeffects of zoledronate on senescence and senescence-associated secretory phenotype markers
Authors: Samakkarnthai Parinya , Saul Dominik , Zhang Lei , Aversa Zaira , Doolittle Madison L. , Sfeir Jad G. , Kaur Japneet , Atkinson Elizabeth J , Edwards James R. , Russell R. Graham G. , Pignolo Robert J. , Kirkland James L. , Tchkonia Tamar , Niedernhofer Laura J. , Monroe David G. , LeBrasseur Nathan K. , Farr Joshua N. , Robbins Paul D. , Khosla Sundeep 
Published: February 2023

ABSTRACTIn addition to reducing fracture risk, zoledronate has been found in some studies to decrease mortality in humans and extend lifespan and healthspan in animals. Because senescent cells accumulate with aging and contribute to multiple co-morbidities, the non-skeletal actions of zoledronate could be due to senolytic (killing of senescent cells) or senomorphic (inhibition of the secretion of the senescence-associated secretory phenotype [SASP]) actions. To test this, we first performedin vitrosenescence assays using human lung fibroblasts and DNA repair-deficient mouse embryonic fibroblasts, which demonstrated that zoledronate killed senescent cells with minimal effects on non-senescent cells. Next, in aged mice treated with zoledronate or vehicle for 8 weeks, zoledronate significantly reduced circulating SASP factors, including CCL7, IL-1β, TNFRSF1A, and TGFβ1 and improved grip strength. Analysis of publicly available RNAseq data from CD115+ (CSF1R/c-fms+) pre-osteoclastic cells isolated from mice treated with zoledronate demonstrated a significant downregulation of senescence/SASP genes (SenMayo). To establish that these cells are potential senolytic/senomorphic targets of zoledronate, we used single cell proteomic analysis (cytometry by time of flight [CyTOF]) and demonstrated that zoledronate significantly reduced the number of pre-osteoclastic (CD115+/CD3e-/Ly6G-/CD45R-) cells and decreased protein levels of p16, p21, and SASP markers in these cells without affecting other immune cell populations. Collectively, our findings demonstrate that zoledronate has senolytic effectsin vitroand modulates senescence/SASP biomarkersin vivo. These data point to the need for additional studies testing zoledronate and/or other bisphosphonate derivatives for senotherapeutic efficacy.
Desmosome-anchored intermediate filaments facilitate tension-sensitive RhoA signaling for epithelial homeostasis
Authors: Nanavati Bageshri Naimish , Noordstra Ivar , Verma Suzie , Duszyc Kinga , Green Kathleen J. , Yap Alpha S. 
Published: February 2023

SummaryEpithelia are subject to diverse forms of mechanical stress during development and post-embryonic life. They possess multiple mechanisms to preserve tissue integrity against tensile forces, which characteristically involve specialized cell-cell adhesion junctions coupled to the cytoskeleton. Desmosomes connect to intermediate filaments (IF) via desmoplakin (DP)1,2, while the E-cadherin complex links to the actomyosin cytoskeleton in adherens junctions (AJ)3. These distinct adhesion-cytoskeleton systems support different strategies to preserve epithelial integrity, especially against tensile stress. IFs coupled to desmosomes can passively respond to tension by strain-stiffening4–10, whereas for AJs a variety of mechanotransduction mechanisms associated with the E-cadherin apparatus itself11,12, or proximate to the junctions13, can modulate the activity of its associated actomyosin cytoskeleton by cell signaling. We now report a pathway where these systems collaborate for active tension-sensing and epithelial homeostasis. We found that DP was necessary for epithelia to activate RhoA at AJ on tensile stimulation, an effect that required its capacity to couple IF to desmosomes. DP exerted this effect by facilitating the association of Myosin VI with E-cadherin, the mechanosensor for the tension-sensitive RhoA pathway at AJ12. This connection between the DP-IF system and AJ-based tension-sensing promoted epithelial resilience when contractile tension was increased. It further facilitated epithelial homeostasis by allowing apoptotic cells to be eliminated by apical extrusion. Thus, active responses to tensile stress in epithelial monolayers reflect an integrated response of the IF- and actomyosin-based cell-cell adhesion systems.
Trophic flexibility and hydrology structure alpine stream food webs: Implications for a fading cryosphere
Authors: Jorgenson Karen L. , Hotaling Scott , Tronstad Lusha M. , Finn Debra S. , Collins Sarah M. 
Published: February 2023

AbstractUnderstanding biotic interactions and how they vary across habitats is important for assessing the vulnerability of communities to climate change. Receding glaciers in high mountain areas can lead to the hydrologic homogenization of streams and reduce habitat heterogeneity, which are predicted to drive declines in regional diversity and imperil endemic species. However, little is known about food web structure in alpine stream habitats, particularly among streams fed by different hydrologic sources (e.g., glaciers or snowfields). We used gut content and stable isotope analyses to characterize food web structure of alpine macroinvertebrate communities in streams fed by glaciers, subterranean ice, and seasonal snowpack in the Teton Range, Wyoming, USA. Specifically, we sought to: (1) assess community resource use among streams fed by different hydrologic sources; (2) explore how variability in resource use relates to feeding strategies; and (3) identify which environmental variables influenced resource use within communities. Average taxa diet differed among all hydrologic sources, and food webs in subterranean ice-fed streams were largely supported by the gold algaHydrurus. This finding bolsters a hypothesis that streams fed by subterranean ice may provide key habitat for cold-water species under climate change by maintaining a longer growing season for this high-quality food resource. While a range of environmental variables associated with hydrologic source (e.g., stream temperature) were related to diet composition, hydrologic source categories explained the most variation in diet composition models. Less variable diets within versus among streams suggests high trophic flexibility, which was further supported by high levels of omnivory. This inherent trophic flexibility may bolster alpine stream communities against future changes in resource availability as the mountain cryosphere fades. Ultimately, our results expand understanding of the habitat requirements for imperiled alpine taxa while empowering predictions of their vulnerability under climate change.
Exon 44 skipping in Duchenne muscular dystrophy: NS-089/NCNP-02, an antisense oligonucleotide with a novel connected-sequence design
Authors: Watanabe Naoki , Tone Yuichiro , Nagata Tetsuya , Masuda Satoru , Saito Takashi , Motohashi Norio , Takagaki Kazuchika , Aoki Yoshitsugu , Takeda Shin’ichi 
Published: February 2023

ABSTRACTExon-skipping therapy mediated by antisense oligonucleotides (ASOs) is expected to provide a therapeutic option for Duchenne muscular dystrophy (DMD). ASOs for exon skipping reported so far target a single continuous sequence in or around the target exon. In the present study, we investigated ASOs for exon 44 skipping (applicable to approximately 6% of all DMD patients) to improve activity by using a novel ASO design incorporating two connected sequences. Phosphorodiamidate morpholino oligomers targeting two separate sequences in exon 44 were created to simultaneously target two splicing regulators in exon 44, and their exon 44 skipping was measured. NS-089/NCNP-02 showed the highest skipping activity among the oligomers. NS-089/NCNP-02 also induced exon 44 skipping and dystrophin protein expression in cells from a DMD patient to whom exon 44 skipping is applicable. We also assessed thein vivoactivity of NS-089/NCNP-02 by intravenous administration to cynomolgus monkeys. NS-089/NCNP-02 induced exon 44 skipping in skeletal and cardiac muscle of cynomolgus monkeys. In conclusion, NS-089/NCNP-02, an ASO with a novel connected-sequence design, showed bothin vitroandin vivoexon-skipping activity.
Mouse Embryonic Stem Cell Pluripotency Factors Regulate RNA Methylation
Authors: Sedivy Laura J. , Brandt Gabrielle , Martin Aspen L. , Abroe Hannah M. , Phiel Christopher J. 
Published: February 2023

AbstractThe pluripotency of embryonic stem cells (ESCs) is actively promoted by a diverse set of factors, including leukemia inhibitory factor (LIF), glycogen synthase kinase-3 (Gsk-3) and mitogen-activated protein kinase kinase (MEK) inhibitors, ascorbic acid, and α-ketoglutarate. Strikingly, several of these factors intersect with the post-transcriptional methylation of RNA (m6A), which has also been shown to play a role in ESC pluripotency. Therefore, we explored the possibility that these factors converge on this biochemical pathway to promote the retention of ESC pluripotency. Mouse ESCs were treated with various combinations of small molecules, and the relative levels of m6A RNA were measured, as well as the expression of genes marking naïve and primed ESCs. The most surprising result was the discovery that replacing glucose with high levels of fructose pushed ESCs to a more naïve state and reduced m6A RNA abundance. Our results suggest a correlation between molecules previously shown to promote the retention of ESC pluripotency and m6A RNA levels, strengthening a molecular connection between reduced m6A RNA and the pluripotent state, and provides a foundation for future mechanistic studies on the role of m6A and ESC pluripotency.