bluuebunny/crossref_metadata_2025_split huggingface dataset:
TCF3::HLF Orchestrates an Enhancer-Promoter Network with Activation of MEF2C to Promote Immature HSC gene Expression in Leukemia
Authors: Priebe Valdemar , Drakul Aneta , Galvan Bartimée , Aguadé-Gorgorió Júlia , Mikkola Hanna K. A. , Bornhauser Beat , Santoro Raffaella , Bourquin Jean-Pierre 
Published: November 2024

AbstractOncogenic fusion transcription factors (TFs) frequently drive hematopoietic malignancies by altering gene expression in key developmental programs. TCF3::HLF is a fusion TF that characterizes a rare, treatment-resistant subtype of B-cell acute lymphoblastic leukemia (t(17;19) TCF3::HLF-positive B-ALL). Despite its clinical significance, the mechanisms by which TCF3::HLF induces leukemia are unclear. We used HiChIP mapping and genetic interference to analyze TCF3::HLF at the 3D-genome level, revealing enhancer-promoter interactions that control gene activation or repression. Notably, TCF3::HLF directly regulatesMEF2Cexpression through its enhancer, as interference disruptedMEF2Ctranscription and inhibited leukemia propagation. This disruption also diminished embryonal hematopoietic stem cell (HSC) gene signatures and restored mature HSC and B-lymphoid markers. These findings highlightMEF2Cas a critical component of the transcriptional network reprogrammed by TCF3::HLF. Our study provides insight into how TCF3::HLF rewires the 3D genome to drive leukemia and serves as a resource for further exploration of the TCF3::HLF regulome.TeaserUnraveling the 3D genomic interactions mediated by TCF3::HLF fusion protein in t(17;19) positive acute lymphoblastic leukemia.
Compositional Flexibility of the ER-Mitochondria Encounter Structure
Authors: Covill-Cooke Christian , Hirashima Takashi , Kawano Shin , Ganellin Joe , Moody Andrew , van Schie Sabine N.S. , John Peter Arun T. , Saito Chika , Endo Toshiya , Kornmann Benoît 
Published: November 2024

AbstractYeast mitochondria receive the majority of their lipids from the endoplasmic reticulum (ER) via the heterotetrameric ERMES lipid transport complex. This complex is thought to establish a lipid transporting tube of fixed composition spanning the space between both organelles. Intriguingly, however, some of the lipid-transporting components of the complex can be replaced by an artificial ER-mitochondria tether without lipid transport activity, indicating that ERMES subunits are not all of equal importance for lipid transport. Here, we propose a model whereby lipid transfer by the ERMES complex can occur with various sub-ensembles of ERMES, and minimally with only one of the four members, namely Mmm1. Our results imply flexibility in the composition of the ERMES complex, which might help it accommodate various interorganelle distances.
Limited impact of the siRNA pathway on transposable element expression inAedes aegypti
Authors: Bergman Alexander , Crist Anna B. , Lopez-Maestre Hélène , Blanc Hervé , Castelló-Sanjuán Mauro , Frangeul Lionel , Varet Hugo , Daron Josquin , Merkling Sarah H. , Saleh Maria-Carla , Lambrechts Louis 
Published: November 2024

AbstractTransposable elements (TEs) are DNA sequences that can change their position within a genome. In the germline of arthropods, post-transcriptional regulation of TE expression is mainly mediated by the Piwi-interacting RNA (piRNA) pathway. piRNAs are small RNAs of 24-30 nucleotides (nt) in length produced from genomic precursor transcripts as well as through a ‘ping-pong’ amplification cycle. In somatic tissues, certain insects, such asDrosophila, instead rely on the small interfering RNA (siRNA) pathway as a key regulator of TE expression. siRNAs are 21nt small RNAs produced from double-stranded RNA by the endonuclease Dicer2, which guides an RNA-induced silencing complex to degrade a complementary RNA. However, whether the siRNA pathway also regulates TE expression in the mosquitoAedes aegypti, a medically significant vector species with abundant somatic piRNAs, is unknown. To address this question, we investigated the expression of TEs and small RNAs in both somatic and gonadal tissues of aDicer2mutant line ofAe. aegyptiand its wild-type counterpart. Our results show a modified pattern of TE expression and a decrease in TE-derived 21nt small RNAs in theDicer2mutant, but no major shift of TE transcript abundance. The lack of a functional siRNA pathway also causes perturbations in piRNA ping-pong signatures and the expression of certain piRNA-associated genes, but without clear evidence for compensation by increased piRNA pathway activity. We conclude that the mosquitoAe. aegyptiproduces siRNAs targeting TEs but these lack a critical role in the regulation of TE expression both in somatic and in gonadal tissues.
Enhancedin vivogene knockout with undetectable off-targets using multiplexed Cas12a sgRNAs
Authors: Port Fillip , Buhmann Martha A. , Zhou Jun , Stricker Mona , Vaughan-Brown Alexander , Michalsen Ann-Christin , Roßmanith Eva , Pöltl Amélie , Großkurth Lena , Huber Julia , Menendez Kury Laura B. , Weberbauer Bea , Hübl Maria , Heigwer Florian , Boutros Michael 
Published: November 2024

AbstractCRISPR nuclease-mediated gene knock-out is limited by suboptimal sgRNAs, inaccessible target sites, and silent mutations. Here, we present a Cas12a-based system that targets each gene with four sgRNAs to overcome these limitations, usingDrosophilaas a tractablein vivomodel. We show that multiplexed sgRNAs act synergistically to create deletions between target sites, substantially increasing the fraction of loss-of-function mutations. To systematically assess off-target effects, we developed a novel screening assay that visualizes CRISPR-induced chromosomal alterations in living animals. This enabled comprehensive screening of more than 2000 sgRNAs clustered in 525 quadruple arrays across 21 megabases of genomic DNA, revealing remarkably high on-target activity (100%, 82/82) and undetectable off-target cutting (0%, 0/443). Quantitative side-by-side comparisons with a current Cas9-based system targeting over 100 genes demonstrates that multiplexed Cas12a-mediated gene targeting achieves superior performance and reveals phenotypes missed by established methods. This highly efficient and specific system provides a framework for reliable functional genomics studies across diverse organisms.
Unveiling the native architecture of adult cardiac tissue using the 3D-NaissI method
Authors: Pataluch Nicolas , Guilbeau-Frugier Céline , Pons Véronique , Wahart Amandine , Karsenty Clément , Sénard Jean-Michel , Galés Céline 
Published: November 2024

AbstractAccurately imaging adult cardiac tissue in its native state is essential for regenerative medicine and understanding heart disease. Current fluorescence methods encounter challenges with tissue fixation. Here, we introduce the 3D-NaissI (3D-Native Tissue Imaging) method, enabling rapid, cost-effective imaging of fresh cardiac tissue samples in their closest native state, that we also extended to other tissues.We validated 3D-NaissI’s efficacy in preserving cardiac tissue integrity using small biopsies under hypothermic conditions in phosphate-buffered saline, offering unparalleled resolution in confocal microscopy for imaging fluorescent-small molecules/-antibodies. Compared to conventional histology, 3D-NaissI preserves cardiac tissue architecture and native protein epitopes, facilitating the use of a wide range of commercial antibodies without unmasking strategies. We successfully identified specific cardiac protein expression patterns in cardiomyocytes (CMs) from rodents and humans, including for the first time ACE2 localization in the lateral membrane/T-Tubules and SGTL2 in the sarcoplasmic reticulum. These findings shed light on COVID-19-related cardiac complications and suggest novel explanations for iSGLT2 therapeutic benefits in HFpEF patients. Additionally, we challenge the notion of "connexin-43 lateralization” in heart pathology, suggesting it may be an artifact of cardiac fixation, as 3D-NaissI clearly revealed native connexin-43 expression at the lateral membrane of healthy CMs. We also discovered previously undocumented periodic ring-like 3D structures formed by pericytes covering CMs’ lateral surfaces. These structures, positive for laminin-2, delineate a specific spatial architecture of laminin-2 receptors at the CM surface, highlighting the pivotal role of pericytes in CM function. Lastly, 3D-NaissI facilitates mapping native human protein expression in fresh cardiac autopsies, providing insights into both pathological and non-pathological contexts.Hence, 3D-NaissI offers unparalleled insights into native cardiac tissue biology and promises to advance our understanding of physiology and pathophysiology, surpassing standard histology in resolution and accuracy.
Drone-Based Identification of Flood-Tolerant Maize via Multispectral Imaging: A Real-World Case Study
Authors: Mitchell Madison , Sidberry Grace , Mathison Morgan , DeSalvio Aaron J. , Kick Daniel , Washburn Jacob D. 
Published: November 2024

ABSTRACTExcess moisture (flooding, water logging, etc.) is a major source of crop damage causing catastrophic monetary losses to farmers around the world. Losses from excess water are often more common and costly than those from too little water (i.e., drought). Extreme weather patterns are predicted to increase, increasing the expected frequency of excess moisture events to farmers across the Midwest. Despite its importance, studying the impacts of flooding in the field is challenging due to unpredictability of flooding and fields being rendered inaccessible during flooding. Here, we took advantage of a natural flood experiment to examine the responses, damage, and recovery of diverse maize hybrids. Using drones, we monitored the hybrids before, during, and after flooding and examined the spatial and genetic components associated with post-flood survival.
Successful establishment of an exogenous gene expression system inChlamydomnaschloroplast based on viral replication elements
Authors: Jiang Yanan , Zhang Guiying , Wang Song , Raza Ali , Liu Xiang , Guo Chunli , Wu Sha , Luo Jixu , Lie Yihao , Liu Yingqi , Jia Bin , Hu Zhangli 
Published: November 2024

AbstractCurrently, transformation in unicellular green alga (Chlamydomonas reinhardtii) chloroplast is hindered by a low yield of target products, possibly due to the heterogeneity of the chloroplast genome. In this study, an expression platform was established inC. reinhardtiiby leveraging replicative elements from beet curly top geminivirus, which led to a high level of heterologous gene expression, as previously reported inNicotiana tabacum. Platform performance was verified by the successful expression of a linearizedmvenuscassette, achieving a higher expression level than that obtained using the homologous-recombination-based approach. This study provides a new strategy in microalgae synthetic biology and opens new avenue for accumulating valuable bioproducts at high concentrations.
Degradation of intrinsically disordered proteins using proteolysis targeting nanobody conjugate
Authors: Sun Xiaofeng , Wu Donglian , Zhou Chengjian , Xia Simin , Chen Xi 
Published: November 2024

AbstractIntrinsically disordered proteins (IDPs) play crucial roles in diverse cellular processes and are implicated in numerous diseases. However, due to the inherently unstructured nature, it is challenging to modulate their function using small molecule degraders or inhibitors. To address this, we introduced proteolysis targeting nanobody conjugate (PROTNC) composed of a nanobody that binds to an IDP, an E3 ligase ligand, and a cyclic cell-penetrating peptide for efficient intracellular delivery. We first showed a general-purpose PROTNC system capable to degrade different endogenous IDPs based on a co-condensate formation mechanism. We also introduced a straightforward strategy to degrade individual IDPs using specific PROTNCs equipped with a nanobody recognizing that particular IDP. Notably, we demonstrated the degradation of TPX2 which is an undruggable oncogenic IDP responsible for microtubule nucleation. This targeted degradation effectively inhibited cancer cell proliferation by disrupting bipolar mitotic spindle assembly in metaphase and directed cells to apoptotic pathway.
Ciliopathy interacts with neonatal anesthesia to cause non-apoptotic caspase-mediated motor deficits
Authors: Sarić Nemanja , Atak Zeynep , Sade Courtni Foster , Reddy Nikita , Bell Gabrielle , Tolete Christina , Rajtboriraks May T. , Hashimoto-Torii Kazue , Jevtović-Todorović Vesna , Haydar Tarik F. , Ishibashi Nobuyuki 
Published: November 2024

AbstractIncreasing evidence suggests that anesthesia may induce developmental neurotoxicity, yet the influence of genetic predispositions associated with congenital anomalies on this toxicity remains largely unknown. Children with congenital heart disease often exhibit mutations in cilia-related genes and ciliary dysfunction, requiring sedation for their catheter or surgical interventions during the neonatal period. Here we demonstrate that briefly exposing ciliopathic neonatal mice to ketamine causes motor skill impairments, which are associated with a baseline deficit in neocortical layer V neuron apical spine density and their altered dynamics during motor learning.. These neuromorphological changes were linked to augmented non-apoptotic neuronal caspase activation. Neonatal caspase suppression rescued the spine density and motor deficits, confirming the requirement for sublethal caspase signaling in appropriate spine formation and motor learning. Our findings suggest that ciliopathy interacts with ketamine to induce motor impairments, which is reversible through caspase inhibition. Furthermore, they underscore the potential for ketamine- induced sublethal caspase responses in shaping neurodevelopmental outcomes.
Piezo2 in sensory neurons influences systemic and adipose tissue metabolism
Authors: Passini Fabian S. , Bornstein Bavat , Rubin Sarah , Kuperman Yael , Krief Sharon , Masschelein Evi , Mehlman Tevie , Brandis Alexander , Addadi Yoseph , Shalom Shira Huri-Ohev , Richter Erik A. , Yardeni Tal , Tirosh Amir , De Bock Katrien , Zelzer Elazar 
Published: November 2024

SummarySystemic metabolism ensures energy homeostasis through inter-organ crosstalk regulating thermogenic adipose tissue. Unlike the well-described inductive role of the sympathetic system, the inhibitory signal ensuring energy preservation remains poorly understood. Here, we show that, via the mechanosensor Piezo2, sensory neurons regulate morphological and physiological properties of brown and beige fat and prevent systemic hypermetabolism. Targeting Runx3/PV sensory neurons in independent genetic mouse models resulted in a systemic metabolic phenotype characterized by reduced body fat and increased insulin sensitivity and glucose tolerance. Deletion of Piezo2 in PV sensory neurons reproduced the phenotype, protected against high-fat diet-induced obesity and caused adipose tissue browning and beiging, likely driven by elevated norepinephrine levels. Finding that brown and beige fat are innervated by Runx3/PV sensory neurons expressing Piezo2, suggests a model where mechanical signals sensed by Piezo2 in sensory neurons protect energy storages and prevent a systemic metabolic phenotype.HighlightsLack of Runx3/PV sensory neurons reduces body fat and fasting glucose levels and increases glucose tolerance in miceMechanosensitive ion channel PIEZO2 in PV sensory neurons plays an important role in systemic metabolism under physiological and pathological conditionsPIEZO2 in PV sensory neurons regulates thermogenic programs and glucose uptake in brown and beige adipose tissuesBrown and beige adipose tissues are innervated by Runx3/PV sensory neurons
Glycocalyx-induced formation of membrane tubes
Authors: Xiao Ke , Rangamani Padmini 
Published: November 2024

AbstractTubular membrane structures are ubiquitous in cells and in the membranes of intracellular organelles such as the Golgi complex and the endoplasmic reticulum. Tubulation plays essential roles in numerous biological processes, including filopodia growth, trafficking, ion transport, and cellular motility. Understanding the fundamental mechanism of the formation of membrane tubes is thus an important problem in the fields of biology and biophysics. Though extensive studies have shown that tubes can be formed due to localized forces acting on the membrane or by the curvature induced by membrane-bound proteins, little is known about how membrane tubes are induced by glycocalyx, a sugar-rich layer at the cell surface. In this work, we develop a biophysical model that combines polymer physics theory and the Canham-Helfrich membrane theory to investigate how the glycocalyx generates cylindrical tubular protrusions on the cell membrane. Our results show that the glycocalyx alone can induce the formation of tubular membrane structures. This tube formation involves a first-order shape transition without any externally applied force or other curvature-inducing mechanisms. We also find that critical values of glycocalyx grafting density and glycopolymer length are needed to induce the formation of tubular structures. The presence of vertical actin force, line tension, and spontaneous curvature reduces the critical grafting density and length of polymer that triggers the formation of membrane tube, which suggests that the glycocalyx makes tube formation energetically more favorable when combined with an actin force, line tension, and spontaneous curvature.Significance StatementIn many cells, the existence of glycocalyx, a thick layer of polymer meshwork comprising proteins and complex sugar chains coating the outside of the cell membrane, regulates the formation of membrane tubes. Here, we propose a theoretical model that combines polymer physics theory and the Canham-Helfrich membrane theory to study the formation of cylindrical tubular protrusions induced by the glycocalyx. Our findings indicate that glycocalyx plays an important role in the formation of membrane tubes. We find that there exists critical grafting density and length of polymer that triggers the formation of membrane tubes, and the glycocalyx-induced tube formation is facilitated when combined with actin forces, line tension, and spontaneous curvature. Our theoretical model has implications for understanding how biological membranes may form tubular structures.
Disordered Hippocampal Reactivations Predict Spatial Memory Deficits in a Mouse Model of Alzheimer’s Disease
Authors: Shipley S. , Abrate M.P. , Hayman R. , Chan D. , Barry C. 
Published: November 2024

AbstractAlzheimer’s disease (AD) is characterised by progressive memory decline associated with hippocampal degeneration. However, the specific physiological mechanisms underlying hippocampal dysfunction in AD remain poorly understood and improved knowledge may aid both diagnosis and help identify new avenues for therapeutic intervention. We investigated how disruptions in hippocampal reactivations relate to place cell stability and spatial memory deficits in an AD mouse model. Using the APP knock-in mouse model ‘NL-G-F’, we conducted simultaneous behavioural and electrophysiological recordings in a radial arm maze. NL-G-F mice exhibited significant impairments in memory performance, demonstrated by an increased propensity to revisit arms, compared to wild-type controls. These memory deficits were associated with a reduction in the stability of hippocampal place cells, which occurred over short timescales and was accentuated across rest. While the rate of hippocampal reactivation events during rest was unchanged, the structure of these events was significantly degraded in NL-G-F mice. The decreased structure of reactivations was predictive of decreased stability in place cell firing. These findings suggest that disrupted reactivation sequences may act as a mechanism of memory disorder in AD.
Visuo-Vestibular Integration for Self-Motion: Human Cortical Area V6 Prefers Forward and Congruent Stimuli
Authors: Marchand Sarah , Balcou Marine , Picher Philippine , Rosito Maxime , Mateo Damien , Vayssiere Nathalie , Durand Jean-Baptiste , Severac Cauquil Alexandra 
Published: November 2024

AbstractBACKGROUNDThe integration of visual and vestibular input is crucial for self-motion. Information from both sensory systems merges early in the central nervous system. Among the numerous cortical areas involved in processing this information, some (V6 and VIP) respond specifically to vestibular anteroposterior information.OBJECTIVETo further understand the involvement of these and other areas in self-motion processing when vestibular and visual information are combined with varying congruence and direction parameters.METHODSFifteen subjects underwent an MRI session while receiving visual (optic flow patterns) and galvanic vestibular stimuli mimicking six conditions: (1) visual forward, (2) visual backward, visual forward with (3) congruent or (4) incongruent vestibular information, visual backward with (5) congruent or (6) incongruent vestibular information.RESULTSThe combination of concurrent vestibular stimulation and fully consistant optic flow patterns activated several bilateral cortical areas found predominantly in the insula. Among these vestibular areas and those previously defined in our initial study, the large majority do not show any specifity for the forward/backward direction or for the visuo-vestibular congruency. A notable exception was the parieto-occipital area V6, which showed a marked preference for congruent visuo-vestibular signals and for cues signaling forward motion.CONCLUSIONSBy showing that V6 is more active when visuo-vestibular signals are more ecological (i.e.when both signals specify the most common self-motion direction), our results support the view that this area plays a crucial role in visuo-vestibular integration during self-motion.
Optimized directed evolution ofE. colileucyl-tRNA synthetase adds many noncanonical amino acids into the eukaryotic genetic code including ornithine and Nε-acetyl-methyllysine
Authors: Ficaretta Elise D. , Yared Tarah J. , Bhattacharjee Subrata , Voss Lena A. , Huang Rachel L. , Chatterjee Abhishek 
Published: November 2024

AbstractSite-specific incorporation of noncanonical amino acids (ncAAs) into proteins in eukaryotes has predominantly relied on the pyrrolysyl-tRNA synthetase/tRNA pair. However, access to additional easily engineered pairs is crucial for expanding the structural diversity of the ncAA toolbox in eukaryotes. TheEscherichia coli-derived leucyl-tRNA synthetase (EcLeuRS)/tRNA pair presents a particularly promising alternative. This pair has been engineered to charge a small yet structurally diverse group of ncAAs in eukaryotic cells. However, expanding the substrate scope of EcLeuRS has been difficult due to the suboptimal yeast-based directed evolution platform used for its engineering. In this study, we address this limitation by optimizing the yeast-based directed evolution platform for efficient selection of ncAA-selective EcLeuRS mutants. Using the optimized selection system, we demonstrate rapid isolation of many novel EcLeuRS mutants capable of incorporating various ncAAs in mammalian cells, including ornithine and Nε-acetyl-methyllysine, a recently discovered post-translational modification in mammalian cells.