bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequences at gene segment termini inclusive of untranslated regions and partial open reading frames play a critical role in mammalian orthoreovirus S gene packaging
Authors: Dhar Debarpan , Mehanovic Samir , Moss Walter , Miller Cathy L. 
Published: May 2023

ABSTRACTMammalian orthoreovirus (MRV) is a prototypic member of theSpinareoviridaefamily and has ten double-stranded RNA segments. One copy of each segment must be faithfully packaged into the mature virion, and prior literature suggests that nucleotides (nts) at the terminal ends of each gene likely facilitate their packaging. However, little is known about the precise packaging sequences required or how the packaging process is coordinated. Using a novel approach, we have determined that 200 nts at each terminus, inclusive of untranslated regions (UTR) and parts of the open reading frame (ORF), are sufficient for packaging each S gene segment (S1-S4) individually and together into replicating virus. Further, we mapped the minimal sequences required for packaging the S1 gene segment to 25 5′ nts and 50 3′ nts. The S1 UTRs alone are not sufficient, but are necessary for packaging, as mutations of the 5′ or 3′ UTRs led to a complete loss of virus recovery. Using a second novel assay, we determined that 50 5′nts and 50 3′ nts of S1 are sufficient to package a non-viral gene segment into MRV. The 5′ and 3′ termini of the S1 gene are predicted to form a panhandle structure and specific mutations within the predicted stem of the panhandle region led to a significant decrease in viral recovery. Additionally, mutation of six nts that are conserved in the three major serotypes of MRV and are predicted to form an unpaired loop in the S1 3′UTR, led to a complete loss of viral recovery. Overall, our data provide strong experimental proof that MRV packaging signals lie at the terminal ends of the S gene segments and offer support that the sequence requirements for efficient packaging of the S1 segment include a predicted panhandle structure and specific sequences within an unpaired loop in the 3′ UTR.
Structure-Activity Relationship Study Identifies a Novel Lipophilic Amiloride Derivative that Efficiently Kills Chemoresistant Breast Cancer Cells
Authors: Hu Michelle , Liu Ruiwu , Castro Noemi , Sanchez Liliana Loza , Learn Julie , Huang Ruiqi , Lam Kit S. , Carraway Kermit L. 
Published: May 2023

AbstractDerivatives of the potassium-sparing diuretic amiloride are preferentially cytotoxic toward tumor cells relative to normal cells, and have the capacity to target tumor cell populations resistant to currently employed therapeutic agents. However, a major barrier to clinical translation of the amilorides is their modest cytotoxic potency, with estimated IC50values in the high micromolar range. Here we report the synthesis of ten novel amiloride derivatives and the characterization of their cytotoxic potency toward MCF7 (ER/PR-positive), SKBR3 (HER2-positive) and MDA-MB-231 (triple negative) cell line models of breast cancer. Comparisons of derivative structure with cytotoxic potency toward these cell lines underscore the importance of an intact guanidine group, and uncover a strong link between drug-induced cytotoxicity and drug lipophilicity. We demonstrate that our most potent derivative called LLC1 is preferentially cytotoxic toward mouse mammary tumor over normal epithelial organoids, acts in the single digit micromolar range on breast cancer cell line models representing all major subtypes, acts on cell lines that exhibit both transient and sustained resistance to chemotherapeutic agents, but exhibits limited anti-tumor effects in a mouse model of metastatic breast cancer. Nonetheless, our observations offer a roadmap for the future optimization of amiloride-based compounds with preferential cytotoxicity toward breast tumor cells.
Mapping memories: pulse-chase labeling reveals AMPA receptor dynamics during memory formation
Authors: Kim Doyeon , Park Pojeong , Li Xiuyuan , Campos J. David Wong , Tian He , Moult Eric M. , Grimm Jonathan B. , Lavis Luke , Cohen Adam E. 
Published: May 2023

AbstractA tool to map changes in synaptic strength during a defined time window could provide powerful insights into the mechanisms governing learning and memory. We developed a technique, Extracellular Protein Surface Labeling in Neurons (EPSILON), to map α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) insertionin vivoby pulse-chase labeling of surface AMPARs with membrane-impermeable dyes. This approach allows for single-synapse resolution maps of plasticity in genetically targeted neurons during memory formation. We investigated the relationship between synapse-level and cell-level memory encodings by mapping synaptic plasticity and cFos expression in hippocampal CA1 pyramidal cells upon contextual fear conditioning (CFC). We observed a strong correlation between synaptic plasticity and cFos expression, suggesting a synaptic mechanism for the association of cFos expression with memory engrams. The EPSILON technique is a useful tool for mapping synaptic plasticity and may be extended to investigate trafficking of other transmembrane proteins.
DNA replication is not a limiting factor for rapid growth ofVibrio natriegens
Authors: Ramming Lea , Stukenberg Daniel , Sánchez Olmos María del Carmen , Becker Anke , Schindler Daniel 
Published: May 2023

AbstractDNA replication prior to cell division is essential for the proliferation of all cells. Bacterial chromosomes are replicated bidirectionally from a single origin of replication, with replication proceeding at about 1000 bp per second. For the best-studied model organism,Escherichia coli, this translates into a replication time of about 40 min for its 4.6 Mb chromosome. Nevertheless,E. colican propagate by overlapping replication cycles with a maximum short doubling time of 20 min. The fastest growing bacterium known today,Vibrio natriegens, is able to replicate with a generation time of less than 10 min. It has a bipartite genome with chromosome sizes of 3.2 and 1.9 Mb. Is simultaneous replication from two origins a prerequisite for its rapid growth? We fused the two chromosomes ofV. natriegensto create a strain carrying a 5.2 Mb chromosome with a single origin of replication. Compared to the wild-type, this strain showed little deviation in growth rate. This suggests that the split genome is not a prerequisite for rapid growth, and that DNA replication is not an important growth rate-limiting factor.
MINI-AC: Inference of plant gene regulatory networks using bulk or single-cell accessible chromatin profiles
Authors: Manosalva Pérez Nicolás , Ferrari Camilla , Engelhorn Julia , Depuydt Thomas , Nelissen Hilde , Hartwig Thomas , Vandepoele Klaas 
Published: May 2023

AbstractGene regulatory networks (GRNs) represent the interactions between transcription factors (TF) and their target genes. GRNs control transcriptional programs involved in growth, development and stress responses, ultimately affecting diverse agricultural traits. While recent developments in accessible chromatin (AC) profiling technologies make it possible to identify context-specific regulatory DNA, learning the underlying GRNs remains a major challenge. We developed MINI-AC (Motif-Informed Network Inference based on Accessible Chromatin), a method that combines AC data from bulk or single-cell experiments with TF binding site information to learn GRNs in plants. We benchmarked MINI-AC using bulk AC datasets from differentArabidopsis thalianatissues and showed that it outperforms other methods to identify correct TFs binding sites. In maize, a crop with a complex genome and abundant distal AC regions, MINI-AC successfully inferred leaf GRNs with experimentally confirmed, both proximal and distal, TF-target gene interactions. Furthermore, we showed that both AC regions and footprints are valid alternatives to infer AC-based GRNs with MINI-AC. Finally, we combined MINI-AC predictions from bulk and single-cell AC datasets to identify general and cell-type specific maize leaf regulators. Focusing on C4 metabolism, we identified diverse regulatory interactions in specialized cell types for this photosynthetic pathway. MINI-AC represents a powerful tool for inferring accurate AC-derived GRNs in plants and identifying known and novel candidate regulators, improving our understanding of gene regulation in plants.
Low soil moisture induces recruitment of Actinobacteria in the rhizosphere of a drought-sensitive and Rhizobiales in a drought-tolerant potato cultivar
Authors: Martins Benoit R. , Siani Roberto , Treder Krzysztof , Michałowska Dorota , Radl Viviane , Pritsch Karin , Schloter Michael 
Published: May 2023

AbstractGrowing evidence suggests that soil microbes can improve plant fitness under drought. However, in potato, the world’s most important non-cereal crop, the role of the rhizosphere microbiome under drought has been poorly studied. Using a cultivation independent metabarcoding approach, we examined the rhizosphere microbiome of two potato cultivars with different drought tolerance as a function of water regime (continuous versus reduced watering) and manipulation of soil microbial diversity (i.e., natural (NSM), vs. disturbed (DSM) soil microbiome). Water regime and soil pre-treatment showed a significant interaction with bacterial community composition of the drought-sensitive (HERBST) but not the drought-resistant cultivar (MONI). Depending on the cultivar, different taxa responded to reduced watering. Under NSM conditions, these were mostly rhizobiales order representative in MONI, andStreptomyces,Glycomyces,Marmoricola,Aeromicrobium,Mycobacterium, amongst Actinobacteriota, and the root endophytic fungusFalciphorain HERBST. Under DSM conditions and reduced watering,Bradyrhizobium,Ammoniphilus,Symbiobacteriumand unclassified Hydrogenedensaceae responded in the rhizosphere of MONI compared to the continuous, while in HERBST, fewer taxa of Actinobacteriota and no fungi responded to reduced vs. continuous watering. Overall, our results indicate a strong cultivar specific relationship between potato and their associated rhizosphere microbiomes under reduced soil moisture.
Histone lactylation antagonizes senescence and skeletal muscle aging via facilitating gene expression reprogramming
Authors: Zhang Xuebin , Meng Fanju , Lyu Wencong , He Jianuo , Wei Ran , Du Zhehao , Zhang Chao , Guan Yiting , Huang Xiaoke , Lyu Guoliang , Tian Xiao-Li , Zhang Lijun , Tao Wei 
Published: May 2023

AbstractOne of the prominent drivers of cellular senescence and/or aging is epigenetic alteration, through which orchestrated regulation of gene expression is achieved during the processes. Accumulating endeavors have been devoted to identifying histone modifications-related mechanisms underlying senescence and aging. Here, we show that histone lactylation, a recently identified histone modification bridging metabolism, epigenetic regulation of gene expression and cellular activities in response to internal and external cues, plays a crucial role in counteracting senescence as well as mitigating dysfunctions of skeletal muscle in aged mice. Mechanistically, the abundance of histone lactylation is markedly decreased during senescence and aging but restored following manipulation of the metabolic environment. Genome-wide distribution profiling and gene expression network analysis uncover that the maintenance of histone lactylation level is critical for suppressing senescence and aging programs via targeting of proliferation- and homeostasis-related pathways. We also confirmed that the level of histone lactylation is not only controlled by glycolysis but also regulated by NAD+contentin vivo. More intriguingly, running exercise enhances the level of histone lactylation and reconstructs the cell landscape and communications of mouse skeletal muscle, leading to rejuvenation and functional improvement. Our study highlights the role of histone lactylation in regulating senescence as well as aging-related tissue function, implying that this modification could be used as a novel marker of senescence, and provides a potential target for aging intervention via metabolic manipulation.
Pan-tissue Transcriptome Analysis Reveals Sex-dimorphic Human Aging
Authors: Wang Siqi , Dong Danyue , Li Xin , Wang Zefeng 
Published: May 2023

AbstractComplex diseases often exhibit sex-dimorphism in morbidity and prognosis, many of which are age-related. However, the underlying mechanisms of the sex-dimorphic aging remain foggy, with limited studies across multiple tissues. We systematically analyzed ∼17,000 transcriptomes from 35 human tissues to quantitatively evaluate the individual and combined contributions of sex and age to transcriptomic variations. We discovered extensive sex-dimorphisms during aging with distinct patterns of change in gene expression and alternative splicing (AS). Intriguingly, the male-biased age-associated AS events have a stronger association with Alzheimer’s disease, and the females-biased events are often regulated by several sex-biased splicing factors that may be controlled by estrogen receptors. Breakpoint analysis showed sex-dimorphic aging rates that are significantly associated with decline of sex hormones, with males having a larger and earlier transcriptome change. Collectively, this study uncovered an essential role of sex during aging at the molecular and multi-tissue levels, providing insight into sex-dimorphic regulatory patterns.
Elucidating human ageing-related phenotypic abnormalities with a novel hierarchical feature selection-based knowledge discovery framework
Authors: Wan Cen , Barton Carl 
Published: May 2023

ABSTRACTAgeing is a complex biological process involving multiple genes that are also related to phenotypic abnormalities. However, the micro view of the associations between ageing and human phenotypic abnormalities is still under-studied. We propose a new hierarchical feature selection method namely HIP+, which selects positive hierarchical information-preserving features according to pre-defined hierarchical ontology information. The experimental results confirm that HIP+obtained better performance than the state-of-the-art hierarchical feature selection method in predicting human phenotypic abnormalities annotations. We further propose a HIP+-based knowledge discovery framework that also successfully highlights some important associations between biological processes and human phenotypic abnormalities.
Viral modulation of type II interferon increases T cell adhesion and virus spread
Authors: Jürgens Carina , Ssebyatika George , Beyer Sarah , Plückebaum Nina , Kropp Kai A. , González-Motos Víctor , Ritter Birgit , Böning Heike , Nikolouli Eirini , Kinchington Paul R. , Lachmann Nico , Depledge Daniel Pearce , Krey Thomas , Viejo-Borbolla Abel 
Published: May 2023

AbstractDuring primary infection, varicella zoster virus (VZV) infects epithelial cells in the respiratory lymphoid organs and mucosa. Subsequent infection of lymphocytes, T cells in particular, causes primary viremia allowing systemic spread throughout the host, including the skin. This results in the expression of cytokines, including interferons (IFNs) which partly limit primary infection. VZV also spreads from skin keratinocytes to lymphocytes prior to secondary viremia. How VZV infects lymphocytes from epithelial cells while evading the cytokine response has not been fully established. Here, we show that VZV glycoprotein C (gC) binds IFN-γ and modifies its activity. Transcriptomic analysis revealed that gC in combination with IFN-γ increased the expression of a small subset of IFN-stimulated genes (ISGs), including intercellular adhesion molecule 1 (ICAM1), as well as several chemokines and immunomodulatory genes. The higher ICAM1 protein level at the plasma membrane of epithelial cells resulted in lymphocyte function-associated antigen 1 (LFA-1)-dependent T cell adhesion. This gC activity required a stable interaction with IFN-γ and signalling through the IFN-γ receptor. Finally, the presence of gC during infection increased VZV spread from epithelial cells to peripheral blood mononuclear cells. This constitutes the discovery of a novel strategy to modulate the activity of IFN-γ, inducing the expression of a subset of ISGs, leading to enhanced T cell adhesion and virus spread.
KMT2C knockout generates ASD-like behaviors in mice
Authors: Brauer Bastian , Merino-Veliz Nicolas , Ahumada Constanza , Arriagada Gloria , Bustos Fernando J 
Published: May 2023

ABSTRACTNeurodevelopmental disorders have been associated with genetic mutations that affect cellular function, including chromatin regulation and epigenetic modifications. Recent studies in humans have identified mutations in KMT2C, an enzyme responsible for modifying histone tails and depositing H3K4me1 and H3K4me3, as being associated with Kleefstra syndrome 2 and autism spectrum disorder (ASD). However, the precise role of KMT2C mutations in brain disorders remains poorly understood. Here we employed CRISPR/Cas9 gene editing to analyze the effects of KMT2C knockout on animal behavior. Knocking out KMT2C expression in cortical neurons and the mouse brain resulted in decreased KMT2C levels. Importantly, KMT2C knockout animals exhibited repetitive behaviors, social deficits, and intellectual disability resembling ASD. Our findings shed light on the involvement of KMT2C in neurodevelopmental processes and establish a valuable model for elucidating the cellular and molecular mechanisms underlying KMT2C mutations and their relationship to Kleefstra syndrome 2 and ASD.
Sequence-independent, site-specific incorporation of chemical modifications to generate light-activated plasmids
Authors: Chung Khoa , Booth Michael J. 
Published: May 2023

AbstractPlasmids are ubiquitous in biology, where they are used to study gene-function relationships and intricate molecular networks, and hold potential as therapeutic devices. Developing methods to control their function will advance their application in research and may also expedite their translation to clinical settings. Light is an attractive stimulus to conditionally regulate plasmid expression as it is non-invasive, and its properties such as wavelength, intensity, and duration can be adjusted to minimise cellular toxicity and increase penetration. Herein, we have developed a method to site-specifically introduce photocages into plasmids, by resynthesizing one strand in a manner similar to Kunkel mutagenesis. Unlike alternative approaches to chemically-modify plasmids, this method is sequence independent at the site of modification and uses commercially available phosphoramidites. To generate our light-activated (LA) plasmids, photocleavable biotinylated nucleobases were introduced at specific sites across the T7 and CMV promoters on plasmids and bound to streptavidin to sterically block access. These LA-plasmids were then successfully used to control expression in both cell-free systems (T7 promoter) and mammalian cells (CMV promoter). These light-activated plasmids might be used to remotely-control cellular activity and reduce off-target toxicity for future medical use. Our simple approach to plasmid modification might also be used to introduce novel chemical moieties for advanced function.Abstract Figure
The protein-bound uremic solute 3-carboxy-4-methyl-5-propyl-2-furanpropionate (CMPF) increases erythrocyte osmotic fragility through interaction with the mechanosensitive channel Piezo1
Authors: Kondo Van Spitzenbergen Beatriz Akemi , Bohnen Gabriela , Dias Erika Sousa , Monte Alegre Júlia B. , Ferreira Dias Gabriela , Grobe Nadja , Moreno-Amaral Andrea Novais , Kotanko Peter 
Published: May 2023

AbstractJedi1, a chemical activator of the mechanosensitive cation channel Piezo1, shares structural similarities with the uremic solute 3-carboxy-4-methyl-5-propyl-2-furanpropionate (CMPF). We explored the hypothesis that CMPF at a concentration seen in uremia activates Piezo1 located on red blood cells (RBC). We incubated RBC from five healthy individuals with either Jedi1 or CMPF (both 87 μM), with or without the Piezo1 inhibitor GsMTx-4 (2 μM), and quantified the cells’ osmotic fragility. Our results indicate that compared to controls (i.e., RBC incubated with buffer), both Jedi1 and CMPF increase the osmotic fragility of RBC (i.e., reduce their resistance to osmotic stress). Effects of Jedi1 and CMPF were reversed to the control level by GsMTx-4. These results indicate a role of Piezo1 in augmenting RBC osmotic fragility and modulation of this effect by Jedi1 and CMPF. Our findings open the possibility that CMPF may act as an endogenous chemical activator of Piezo1.
Self-Assembly of a Repeatable DNA Nanohinge System Supporting Higher Order Structure Formation
Authors: Law Melanie , Susham Charlie , Mackay David , Nguyen Stephanie , Nicholas Rachael , Tsai Miguel Roberto G. , Rajkumar Ethan , Inaba Fumiya , Maheden Kieran , Abdi Immanuel , Ho Joe C.H. , Kieft Brandon , Hallam Steven J. 
Published: May 2023

ABSTRACTDNA base pairs can both encode biological information and be used as a programmable material to build nanostructures with potential application in nanofabrication, data processing and storage, biosensing and drug delivery. Over several decades development of these DNA origami nanostructures has led to increasingly advanced self-assembling nanostructures and molecular machines actuated by various mechanisms such as toehold-mediated strand displacement (TMSD), magnetism and even light. However, scalability remains challenging as using larger scaffold strands can increase the likelihood of kinetic traps and misfolded conformations. Here we describe a repeatable DNA nanohinge system to increase the scalability of existing nanohinge designs for hierarchical assembly of more complex structures with greater degrees of mobility and functionality. The components of this system, comprising two distinct nanohinges, were designed in caDNAno. Structure conformation and stability were simulated using CanDo and MrDNA, and hinge assembly was validated by TEM. Electron micrographs revealed hinge-shaped nanostructures capable of self-assembly into more complex structures, as well as actuation using TMSD through a reversible locking mechanism incorporated into the design. Our work expands the existing utility of DNA nanohinges as building blocks for scalable DNA nanostructures and demonstrates the feasibility of polymerizing hinges in a novel manner for higher order assembly. The enhanced functionality of our dual hinge systems can be employed in future applications requiring greater control and mobility of DNA nanostructures.
Super-resolution imaging of neuronal structure with structured illumination microscopy
Authors: Paul Tristan C. , Johnson Karl A. , Hagen Guy M. 
Published: May 2023

AbstractSuper-resolution structured illumination microscopy (SR-SIM) is a method in optical fluorescence microscopy which is suitable for imaging a wide variety of cells and tissues in biological and biomedical research. Typically, SIM methods use high spatial frequency illumination patterns generated by laser interference. This approach provides high resolution but is limited to thin samples such as cultured cells. Using a different strategy for processing the raw data and coarser illumination patterns, we imaged through a 150 µm thick coronal section of a mouse brain expressing GFP in a subset of neurons. The resolution reached 144 nm, an improvement of 1.7 fold beyond conventional widefield imaging.