bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel role of TRIM28 B box domain in L1 retrotransposition and ORF2p-mediated cDNA synthesis
Authors: Du Qianhui , Stow Emily C , LaCoste Dawn , Freeman Benjamin , Baddoo Melody , Shareef Afzaal M , Miller Kyle M , Belancio Victoria P 
Published: April 2023

Abstract
The long interspersed element 1 (LINE-1 or L1) integration is affected by many cellular factors through various mechanisms. Some of these factors are required for L1 amplification, while others either suppress or enhance specific steps during L1 propagation. Previously, TRIM28 has been identified to suppress transposable elements, including L1 expression via its canonical role in chromatin remodeling. Here, we report that TRIM28 through its B box domain increases L1 retrotransposition and facilitates shorter cDNA and L1 insert generation in cultured cells. Consistent with the latter, we observe that tumor specific L1 inserts are shorter in endometrial, ovarian, and prostate tumors with higher TRIM28 mRNA expression than in those with lower TRIM28 expression. We determine that three amino acids in the B box domain that are involved in TRIM28 multimerization are critical for its effect on both L1 retrotransposition and cDNA synthesis. We provide evidence that B boxes from the other two members in the Class VI TRIM proteins, TRIM24 and TRIM33, also increase L1 retrotransposition. Our findings could lead to a better understanding of the host/L1 evolutionary arms race in the germline and their interplay during tumorigenesis.
RecA and SSB genome-wide distribution in ssDNA gaps and ends in Escherichia coli
Authors: Pham Phuong , Wood Elizabeth A , Cox Michael M , Goodman Myron F 
Published: April 2023

Abstract
Single-stranded DNA (ssDNA) gapped regions are common intermediates in DNA transactions. Using a new non-denaturing bisulfite treatment combined with ChIP-seq, abbreviated ‘ssGap-seq’, we explore RecA and SSB binding to ssDNA on a genomic scale in E. coli in a wide range of genetic backgrounds. Some results are expected. During log phase growth, RecA and SSB assembly profiles coincide globally, concentrated on the lagging strand and enhanced after UV irradiation. Unexpected results also abound. Near the terminus, RecA binding is favored over SSB, binding patterns change in the absence of RecG, and the absence of XerD results in massive RecA assembly. RecA may substitute for the absence of XerCD to resolve chromosome dimers. A RecA loading pathway may exist that is independent of RecBCD and RecFOR. Two prominent and focused peaks of RecA binding revealed a pair of 222 bp and GC-rich repeats, equidistant from dif and flanking the Ter domain. The repeats, here named RRS for replication risk sequence, trigger a genomically programmed generation of post-replication gaps that may play a special role in relieving topological stress during replication termination and chromosome segregation. As demonstrated here, ssGap-seq provides a new window on previously inaccessible aspects of ssDNA metabolism.
PAXIP1 and STAG2 converge to maintain 3D genome architecture and facilitate promoter/enhancer contacts to enable stress hormone-dependent transcription
Authors: Mayayo-Peralta Isabel , Gregoricchio Sebastian , Schuurman Karianne , Yavuz Selçuk , Zaalberg Anniek , Kojic Aleksandar , Abbott Nina , Geverts Bart , Beerthuijzen Suzanne , Siefert Joseph , Severson Tesa M , van Baalen Martijn , Hoekman Liesbeth , Lieftink Cor , Altelaar Maarten , Beijersbergen Roderick L , Houtsmuller Adriaan B , Prekovic Stefan , Zwart Wilbert 
Published: April 2023

AbstractHow steroid hormone receptors (SHRs) regulate transcriptional activity remains partly understood. Upon activation, SHRs bind the genome together with a co-regulator repertoire, crucial to induce gene expression. However, it remains unknown which components of the SHR-recruited co-regulator complex are essential to drive transcription following hormonal stimuli. Through a FACS-based genome-wide CRISPR screen, we functionally dissected the Glucocorticoid Receptor (GR) complex. We describe a functional cross-talk between PAXIP1 and the cohesin subunit STAG2, critical for regulation of gene expression by GR. Without altering the GR cistrome, PAXIP1 and STAG2 depletion alter the GR transcriptome, by impairing the recruitment of 3D-genome organization proteins to the GR complex. Importantly, we demonstrate that PAXIP1 is required for stability of cohesin on chromatin, its localization to GR-occupied sites, and maintenance of enhancer-promoter interactions. In lung cancer, where GR acts as tumor suppressor, PAXIP1/STAG2 loss enhances GR-mediated tumor suppressor activity by modifying local chromatin interactions. All together, we introduce PAXIP1 and STAG2 as novel co-regulators of GR, required to maintain 3D-genome architecture and drive the GR transcriptional programme following hormonal stimuli.
Selective translational control of cellular and viral mRNAs by RPS3 mRNA binding
Authors: Havkin-Solomon Tal , Itzhaki Elad , Joffe Nir , Reuven Nina , Shaul Yosef , Dikstein Rivka 
Published: April 2023

Abstract
RPS3, a universal core component of the 40S ribosomal subunit, interacts with mRNA at the entry channel. Whether RPS3 mRNA-binding contributes to specific mRNA translation and ribosome specialization in mammalian cells is unknown. Here we mutated RPS3 mRNA-contacting residues R116, R146 and K148 and report their impact on cellular and viral translation. R116D weakened cap-proximal initiation and promoted leaky scanning, while R146D had the opposite effect. Additionally, R146D and K148D displayed contrasting effects on start-codon fidelity. Translatome analysis uncovered common differentially translated genes of which the downregulated set bears long 5’UTR and weak AUG context, suggesting a stabilizing role during scanning and AUG selection. We identified an RPS3-dependent regulatory sequence (RPS3RS) in the sub-genomic 5’UTR of SARS-CoV-2 consisting of a CUG initiation codon and a downstream element that is also the viral transcription regulatory sequence (TRS). Furthermore, RPS3 mRNA-binding residues are essential for SARS-CoV-2 NSP1-mediated inhibition of host translation and for its ribosomal binding. Intriguingly, NSP1-induced mRNA degradation was also reduced in R116D cells, indicating that mRNA decay occurs in the ribosome context. Thus, RPS3 mRNA-binding residues have multiple translation regulatory functions and are exploited by SARS-CoV-2 in various ways to influence host and viral mRNA translation and stability.
Saccharomyces cerevisiae DNA polymerase IV overcomes Rad51 inhibition of DNA polymerase δ in Rad52-mediated direct-repeat recombination
Authors: Cerqueira Paula G , Meyer Damon , Zhang Lilin , Mallory Benjamin , Liu Jie , Hua Fu Becky Xu , Zhang Xiaoping , Heyer Wolf-Dietrich 
Published: April 2023

Abstract
Saccharomyces cerevisiae DNA polymerase IV (Pol4) like its homolog, human DNA polymerase lambda (Polλ), is involved in Non-Homologous End-Joining and Microhomology-Mediated Repair. Using genetic analysis, we identified an additional role of Pol4 also in homology-directed DNA repair, specifically in Rad52-dependent/Rad51-independent direct-repeat recombination. Our results reveal that the requirement for Pol4 in repeat recombination was suppressed by the absence of Rad51, suggesting that Pol4 counteracts the Rad51 inhibition of Rad52-mediated repeat recombination events. Using purified proteins and model substrates, we reconstituted in vitro reactions emulating DNA synthesis during direct-repeat recombination and show that Rad51 directly inhibits Polδ DNA synthesis. Interestingly, although Pol4 was not capable of performing extensive DNA synthesis by itself, it aided Polδ in overcoming the DNA synthesis inhibition by Rad51. In addition, Pol4 dependency and stimulation of Polδ DNA synthesis in the presence of Rad51 occurred in reactions containing Rad52 and RPA where DNA strand-annealing was necessary. Mechanistically, yeast Pol4 displaces Rad51 from ssDNA independent of DNA synthesis. Together our in vitro and in vivo data suggest that Rad51 suppresses Rad52-dependent/Rad51-independent direct-repeat recombination by binding to the primer-template and that Rad51 removal by Pol4 is critical for strand-annealing dependent DNA synthesis.
GeoBind: segmentation of nucleic acid binding interface on protein surface with geometric deep learning
Authors: Li Pengpai , Liu Zhi-Ping 
Published: April 2023

Abstract
Unveiling the nucleic acid binding sites of a protein helps reveal its regulatory functions in vivo. Current methods encode protein sites from the handcrafted features of their local neighbors and recognize them via a classification, which are limited in expressive ability. Here, we present GeoBind, a geometric deep learning method for predicting nucleic binding sites on protein surface in a segmentation manner. GeoBind takes the whole point clouds of protein surface as input and learns the high-level representation based on the aggregation of their neighbors in local reference frames. Testing GeoBind on benchmark datasets, we demonstrate GeoBind is superior to state-of-the-art predictors. Specific case studies are performed to show the powerful ability of GeoBind to explore molecular surfaces when deciphering proteins with multimer formation. To show the versatility of GeoBind, we further extend GeoBind to five other types of ligand binding sites prediction tasks and achieve competitive performances.
The Dictyostelium discoideum genome lacks significant DNA methylation and uncovers palindromic sequences as a source of false positives in bisulfite sequencing
Authors: Drewell Robert A , Cormier Tayla C , Steenwyk Jacob L , Denis James St , Tabima Javier F , Dresch Jacqueline M , Larochelle Denis A 
Published: April 2023

Abstract
DNA methylation, the addition of a methyl (CH3) group to a cytosine residue, is an evolutionarily conserved epigenetic mark involved in a number of different biological functions in eukaryotes, including transcriptional regulation, chromatin structural organization, cellular differentiation and development. In the social amoeba Dictyostelium, previous studies have shown the existence of a DNA methyltransferase (DNMA) belonging to the DNMT2 family, but the extent and function of 5-methylcytosine in the genome are unclear. Here, we present the whole genome DNA methylation profile of Dictyostelium discoideum using deep coverage replicate sequencing of bisulfite-converted gDNA extracted from post-starvation cells. We find an overall very low number of sites with any detectable level of DNA methylation, occurring at significant levels in only 303–3432 cytosines out of the ∼7.5 million total cytosines in the genome depending on the replicate. Furthermore, a knockout of the DNMA enzyme leads to no overall decrease in DNA methylation. Of the identified sites, significant methylation is only detected at 11 sites in all four of the methylomes analyzed. Targeted bisulfite PCR sequencing and computational analysis demonstrate that the methylation profile does not change during development and that these 11 cytosines are most likely false positives generated by protection from bisulfite conversion due to their location in hairpin-forming palindromic DNA sequences. Our data therefore provide evidence that there is no significant DNA methylation in Dictyostelium before fruiting body formation and identify a reproducible experimental artifact from bisulfite sequencing.
Paying forward to future generations: how infrastructure can do more
Authors: Bowditch Garry 
Published: April 2023

Abstract
When infrastructure is done well, it forms the fabric beneath us that enables individuals, businesses and communities to experience more prosperous and inclusive living for current and future generations. In this brief commentary paper, I offer arguments and case examples from my recent book BIG FIXES: Building Bridges to an Inclusive Future. Unfortunately, as an infrastructure practitioner for over 30 years, I have observed a global shift among policymakers to exaggerate the benefits of investing in infrastructure without accountability and a framework for governance to assure positive long-term outcomes. In essence, infrastructure has fallen victim to short-termism. The central thesis of my book for readers and future contributors of Oxford Open Infrastructure and Health (OOIH) aligns well with the journal’s mission for infrastructure and health scholarship that fosters ‘Big Connections’. My argument is as follows. Is your vision of infrastructure about physical assets like roads, bridges, tunnels, power lines, water pipes, schools and hospitals? If so, then it is too narrow. There is an urgent need for policymakers, investors and scholars to widen their perspective to consider infrastructure as a gift that current generations pay forward to future generations. The infrastructure decisions of our forebearers act like ripples on a lake, radiating out in time and space. These ripples can amplify benefits into the future, like favorable tailwinds. But equally, where short-sightedness has taken root in the past, the consequences of earlier infrastructure decisions (or none at all) can saddle future generations with the burden of headwinds—slowing, dragging upon efforts to improve. When a society invests in infrastructure, they express hope and optimism for the future. However, that aspiration implies a big bundle of expectations, including health and economic well-being and sustaining and building trust between people and the institutions created to serve them. Moreover, as environmental and social issues grow in importance, society has less room to be complacent with nonresponsive infrastructure blocking adaptation and innovation to support new growth. These are examples of the lens to view ‘Big Connections’ referred to by OOIH.
Update: on selected ROP cell polarity mechanisms in plant cell morphogenesis
Authors: Müller Sabine 
Published: April 2023

AbstractThe unequal (asymmetric) distribution of cell structures and proteins within a cell is designated as cell polarity. Cell polarity is a crucial prerequisite for morphogenetic processes such as oriented cell division and directed cell expansion. Rho-related GTPase from plants (ROPs) are required for cellular morphogenesis through the reorganization of the cytoskeleton and vesicle transport in various tissues. Here, I review recent advances in ROP-dependent tip growth, vesicle transport, and tip architecture. I report on the regulatory mechanisms of ROP upstream regulators found in different cell types. It appears that these regulators assemble in nanodomains with specific lipid compositions and recruit ROPs for activation in a stimulus-dependent manner. Current models link mechanosensing/mechanotransduction to ROP polarity signaling involved in feedback mechanisms via the cytoskeleton. Finally, I discuss ROP signaling components that are upregulated by tissue-specific transcription factors and exhibit specific localization patterns during cell division, clearly suggesting ROP signaling in division plane alignment.
Visual policy narrative messaging improves COVID-19 vaccine uptake
Authors: Shanahan Elizabeth A , DeLeo Rob A , Albright Elizabeth A , Li Meng , Koebele Elizabeth A , Taylor Kristin , Crow Deserai Anderson , Dickinson Katherine L , Minkowitz Honey , Birkland Thomas A , Zhang Manli 
Published: April 2023

Abstract
In the face of vaccine hesitancy, public health officials are seeking more effective risk communication approaches to increase vaccination rates. We test the influence of visual policy narratives on COVID-19 vaccination behavior through a panel survey experiment conducted in early 2021 (n = 3,900) and then 8 weeks later (n = 2,268). We examine the effects of three visual policy narrative messages that test the narrative mechanism of character selection (yourself, your circle, and your community) and a nonnarrative control on COVID-19 vaccine behavior. Visual risk messages that use narratives positively influence COVID-19 vaccination through serial mediation of affective response to the messages and motivation to get the COVID-19 vaccination. Additionally, character selection matters, as messages focusing on protecting others (i.e. your circle and your community) perform stronger than those of yourself. Political ideology moderated some of the effects, with conservative respondents in the nonnarrative control condition having a higher probability of vaccination in comparison to the protect yourself condition. Taken together, these results suggest that public health officials should use narrative-based visual communication messages that emphasize communal benefits of vaccinations.
Dimension matters when modeling network communities in hyperbolic spaces
Authors: Désy Béatrice , Desrosiers Patrick , Allard Antoine 
Published: April 2023

Abstract
Over the last decade, random hyperbolic graphs have proved successful in providing geometric explanations for many key properties of real-world networks, including strong clustering, high navigability, and heterogeneous degree distributions. These properties are ubiquitous in systems as varied as the internet, transportation, brain or epidemic networks, which are thus unified under the hyperbolic network interpretation on a surface of constant negative curvature. Although a few studies have shown that hyperbolic models can generate community structures, another salient feature observed in real networks, we argue that the current models are overlooking the choice of the latent space dimensionality that is required to adequately represent clustered networked data. We show that there is an important qualitative difference between the lowest-dimensional model and its higher-dimensional counterparts with respect to how similarity between nodes restricts connection probabilities. Since more dimensions also increase the number of nearest neighbors for angular clusters representing communities, considering only one more dimension allows us to generate more realistic and diverse community structures.
A simple, dual direct expression plasmid system in prokaryotic and mammalian cells
Authors: Murakami Manabu , Murakami Agnieszka M , Yonekura Manabu , Miyoshi Ichiro , Itagaki Shirou , Niwa Yasutaka 
Published: April 2023

Abstract
We introduce a simple, dual direct cloning plasmid system (pgMAX-II) for gene expression analysis in both prokaryotic (Escherichia coli) and mammalian cells. This system, which uses a prokaryotic expression unit adapted from the pgMAX system and a mammalian promoter, is effective for subcloning using the DNA topoisomerase II toxin CcdB. Given that molecular biological cloning systems broadly rely on E. coli for rapid growth, the proposed concept may have wide applicability beyond mammalian cells.
Aircraft and satellite observations reveal historical gap between top–down and bottom–up CO2 emissions from Canadian oil sands
Authors: Wren Sumi N , McLinden Chris A , Griffin Debora , Li Shao-Meng , Cober Stewart G , Darlington Andrea , Hayden Katherine , Mihele Cristian , Mittermeier Richard L , Wheeler Michael J , Wolde Mengistu , Liggio John 
Published: April 2023

AbstractMeasurement-based estimates of greenhouse gas (GHG) emissions from complex industrial operations are challenging to obtain, but serve as an important, independent check on inventory-reported emissions. Such top–down estimates, while important for oil and gas (O&G) emissions globally, are particularly relevant for Canadian oil sands (OS) operations, which represent the largest O&G contributor to national GHG emissions. We present a multifaceted top–down approach for estimating CO2 emissions that combines aircraft-measured CO2/NOx emission ratios (ERs) with inventory and satellite-derived NOx emissions from Ozone Monitoring Instrument (OMI) and TROPOspheric Ozone Monitoring Instrument (TROPOMI) and apply it to the Athabasca Oil Sands Region (AOSR) in Alberta, Canada. Historical CO2 emissions were reconstructed for the surface mining region, and average top–down estimates were found to be &gt;65% higher than facility-reported, bottom–up estimates from 2005 to 2020. Higher top–down vs. bottom–up emissions estimates were also consistently obtained for individual surface mining and in situ extraction facilities, which represent a growing category of energy-intensive OS operations. Although the magnitudes of the measured discrepancies vary between facilities, they combine such that the observed reporting gap for total AOSR emissions is ≥(31 ± 8) Mt for each of the last 3 years (2018–2020). This potential underestimation is large and broadly highlights the importance of continued review and refinement of bottom–up estimation methodologies and inventories. The ER method herein offers a powerful approach for upscaling measured facility-level or regional fossil fuel CO2 emissions by taking advantage of satellite remote sensing observations.
Nonuse and hypocritical use of strategic narratives in Megaprojects: the case of the Florence high-speed railway
Authors: Coticchia Fabrizio , Di Giulio Marco 
Published: April 2023

Abstract
Since megaprojects are costly, impactful, and often contentious policymaking processes, scholars have started to look at policy narratives as instruments that actors use strategically to justify their preferences and achieve their goals. But is this really the case? Do actors always adopt a narrative to support their goals? Do they develop arguments that are consistent with their official goals and in a timely manner? This paper suggests that, when megaprojects are not salient, narratives are likely to be strategically nonused or used in a hypocritical way, as such strategies better fit the process-related goals of significant actors. Such a claim is illustrated by a case study on the construction of a new high-speed railway line and station in the city of Florence (Italy). Relying on content and discourse analysis of official documents, and experts’ interviews, the paper shows that, despite favorable premises for the emergence of a battle of narratives, this never took place, as some of the proponents choose to nonuse a strategic narrative, while others occasionally publicly used arguments to jeopardize the whole project. In turn, opponents effectively developed a strategic narrative that, differently from other similar cases, mostly relied on technical arguments and emplotment. Hence, the case study generates hypotheses that could be tested in further studies on the conditions under which a coalitional dynamic emerges and the role played by policy narratives in the process.
Genome Sequence Resource of Pseudofabraea citricarpa: A Fungus Causing Citrus Target Spot
Authors: Chen Li , Liu Saifei , Ren Jiequn , Li Li , Sun Haijun , Zhang Xin , Qiao Xinghua , Yang Yuheng 
Published: April 2023

Citrus target spot disease caused by Pseudofabraea citricarpa poses a major threat to citrus production worldwide. Here, we report a high-quality genome assembly and annotation of a strain isolated from Chongqing, China. We have provided valuable insights into the evolution and pathogenicity of this fungus. The genome of P. citricarpa spans 44,005,176 bp with a G+C content of 44.71%, and its coding genes have been extensively annotated in various databases, such as GO and KEGG. Notably, we have predicted important proteins, such as secreted proteins, transmembrane proteins, and carbohydrate-active enzymes. Our findings serve as a key resource for understanding the global spread of this pathogen, enabling better control measures to be implemented. In conclusion, this study enriches our understanding of P. citricarpa and provides a foundation for future research in the field. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .