bluuebunny/crossref_metadata_2025_split huggingface dataset:
High-throughput optimized prime editing mediated endogenous protein tagging for pooled imaging of protein localization
Authors: Sanchez Henry M. , Lapidot Tomer , Shalem Ophir 
Published: September 2024

AbstractThe subcellular organization of proteins carries important information on cellular state and gene function, yet currently there are no technologies that enable accurate measurement of subcellular protein localizations at scale. Here we develop an approach for pooled endogenous protein tagging using prime editing, which coupled with an optical readout and sequencing, provides a snapshot of proteome organization in a manner akin to perturbation-based CRISPR screens. We constructed a pooled library of 17,280 pegRNAs designed to exhaustively tag 60 endogenous proteins spanning diverse localization patterns and explore a large space of genomic and pegRNA design parameters. Pooled measurements of tagging efficiency uncovered both genomic and pegRNA features associated with increased efficiency, including epigenetic states and interactions with transcription. We integrate pegRNA features into a computational model with predictive value for tagging efficiency to constrain the design space of pegRNAs for large-scale peptide knock-in. Lastly, we show that combining in-situ pegRNA sequencing with high-throughput deep learning image analysis, enables exploration of subcellular protein localization patterns for many proteins in parallel following a single pooled lentiviral transduction, setting the stage for scalable studies of proteome dynamics across cell types and environmental perturbations.
Quantitative Comparison of Monomeric StayGold Variants Using Protein Nanocages in Living Cells
Authors: Viola Giulia , Jacobs Kyle A. , Lemière Joël , Kutys Matthew L. , Wittmann Torsten 
Published: September 2024

AbstractTo standardize comparison of fluorescent proteins and independently determine which monomeric StayGold variant is best for live microscopy, we analyzed fluorescent protein tagged I3-01 peptides that self-assemble into stable sixty subunit dodecahedrons inside live cells. We find mStayGold is 3-fold brighter and 3-fold more photostable compared with EGFP and superior to other monomeric variants in mammalian cytoplasm. In addition, analysis of intracellular nanocage diffusion confirms the monomeric nature of mStayGold.
An integrated view of the structure and function of the human 4D nucleome
Authors:   4D Nucleome Consortium, Dekker Job , Oksuz Betul Akgol , Zhang Yang , Wang Ye , Minsk Miriam K. , Kuang Shuzhen , Yang Liyan , Gibcus Johan H. , Krietenstein Nils , Rando Oliver J. , Xu Jie , Janssens Derek H. , Henikoff Steven , Kukalev Alexander , Willemin Andréa , Winick-Ng Warren , Kempfer Rieke , Pombo Ana , Yu Miao , Kumar Pradeep , Zhang Liguo , Belmont Andrew S , Sasaki Takayo , van Schaik Tom , Brueckner Laura , Peric-Hupkes Daan , van Steensel Bas , Wang Ping , Chai Haoxi , Kim Minji , Ruan Yijun , Zhang Ran , Quinodoz Sofia A. , Bhat Prashant , Guttman Mitchell , Zhao Wenxin , Chien Shu , Liu Yuan , Venev Sergey V. , Plewczynski Dariusz , Irastorza Azcarate Ibai , Szabó Dominik , Thieme Christoph J. , Szczepińska Teresa , Chiliński Mateusz , Sengupta Kaustav , Conte Mattia , Esposito Andrea , Abraham Alex , Zhang Ruochi , Wang Yuchuan , Wen Xingzhao , Wu Qiuyang , Yang Yang , Liu Jie , Boninsegna Lorenzo , Yildirim Asli , Zhan Yuxiang , Chiariello Andrea Maria , Bianco Simona , Lee Lindsay , Hu Ming , Li Yun , Barnett R. Jordan , Cook Ashley L. , Emerson Daniel J. , Marchal Claire , Zhao Peiyao , Park Peter , Alver Burak H. , Schroeder Andrew , Navelkar Rahi , Bakker Clara , Ronchetti William , Ehmsen Shannon , Veit Alexander , Gehlenborg Nils , Wang Ting , Li Daofeng , Wang Xiaotao , Nicodemi Mario , Ren Bing , Zhong Sheng , Phillips-Cremins Jennifer E. , Gilbert David M. , Pollard Katherine S. , Alber Frank , Ma Jian , Noble William S. , Yue Feng 
Published: September 2024

AbstractThe dynamic three-dimensional (3D) organization of the human genome (the “4D Nucleome”) is closely linked to genome function. Here, we integrate a wide variety of genomic data generated by the 4D Nucleome Project to provide a detailed view of human 3D genome organization in widely used embryonic stem cells (H1-hESCs) and immortalized fibroblasts (HFFc6). We provide extensive benchmarking of 3D genome mapping assays and integrate these diverse datasets to annotate spatial genomic features across scales. The data reveal a rich complexity of chromatin domains and their sub-nuclear positions, and over one hundred thousand structural loops and promoter-enhancer interactions. We developed 3D models of population-based and individual cell-to-cell variation in genome structure, establishing connections between chromosome folding, nuclear organization, chromatin looping, gene transcription, and DNA replication. We demonstrate the use of computational methods to predict genome folding from DNA sequence, uncovering potential effects of genetic variants on genome structure and function. Together, this comprehensive analysis contributes insights into human genome organization and enhances our understanding of connections between the regulation of genome function and 3D genome organization in general.
INVESTIGATION OF SECONDARY METABOLITES PRESENT IN METHANOLIC AND ALKALOIDAL EXTRACTS OF HUNTERIA UMBELLATA LEAVES USING COMPUTATIONAL MOLECULAR NETWORKING TOOL
Authors: Adedeji Rukayat A. , Opemipo Musibau , Babalola Oluwabukunmi , Julius Solomon O. , Alaribe Stephenie C. 
Published: September 2024

AbstractBackgroundPlants have long served as a vital source of therapeutic agents in both traditional and orthodox medicine. However, with the shift in drug discovery towards synthetic laboratory compounds, there has also been a decline in the exploration of natural sources for drug development. Research attention needs to be diverted toward natural drug discovery and more importantly, towards the development of new and improved methods of isolating, analyzing, identifying, and characterizing chemical moieties obtained from plants.ObjectivesTo investigate the secondary metabolites present in the methanolic and alkaloidal extracts ofHunteria umbellata, a medicinally significant plant, and explore potential links between the identified compounds and the plant’s pharmacological uses.MethodsMetabolomic technique was employed, utilizing liquid chromatography-tandem mass spectrometry (LC-MS/MS) to separate the components within the extracts. The isolated compounds were then identified based on their mass-to-charge (m/z) ratios. The resulting chromatograms and spectra were analyzed using a computational molecular networking tool to match the m/z values to known compounds in mass spectrometry libraries.ResultEighteen compounds were successfully isolated from the methanolic and alkaloidal extracts, including Yohimbine; (-)-Epicatechin; Picrinine; Tubotaiwine; Quercetin-3-O-robinobioside; and Pheophorbide A. Many of these compounds have been previously studied for their clinical relevance, such as antidiabetic, antioxidant, and anti-inflammatory activities, supporting the medicinal uses traditionally attributed to Hunteria umbellata. Notably, the identification of Pheophorbide A, a compound with potential photodynamic therapy applications, opens new avenues for further investigation.ConclusionThese findings provide significant insight into the bioactive components of Hunteria umbellata, supporting its traditional medicinal uses. The identification of clinically relevant compounds not only validates traditional practices but also highlights the plant’s potential for contributing to modern drug discovery efforts.
High-throughput robotic isolation of human iPS cell clones reveals frequent homozygous induction of identical genetic manipulations by CRISPR-Cas9
Authors: Takahashi Gou , Maeda Minato , Shinozaki Kayoko , Harada Gakuro , Ito Saburo , Miyaoka Yuichiro 
Published: September 2024

SUMMARYGenome editing in human iPS cells is a powerful approach in regenerative medicine. CRISPR-Cas9 is the most common genome editing tool, but it often induces byproduct insertions and deletions in addition to the desired edits. Therefore, genome editing of iPS cells produces diverse genotypes. Existing assays mostly analyze genome editing results in cell populations, but not in single cells. However, systematic profiling of genome editing outcomes in single iPS cells was lacking. In this study, we developed a method for high-throughput iPS cell clone isolation based on the precise robotic picking of cell clumps derived from single cells grown in extracellular matrices. We analyzed over 1,000 genome-edited iPS cell clones and found that homozygous editing was much more frequent than heterozygous editing. We also observed frequent homozygous induction of identical genetic manipulations, including insertions and deletions. Our new cloning method and findings will facilitate the application of genome editing to human iPS cells.
Visualizing nuclear pore complex plasticity with Pan-Expansion Microscopy
Authors: Morgan Kimberly J. , Carley Emma , Coyne Alyssa N. , Rothstein Jeffrey D. , Lusk C. Patrick , King Megan C. 
Published: September 2024

AbstractCell-type specific and environmentally-responsive plasticity in nuclear pore complex (NPC) composition and structure is an emerging area of investigation, but its molecular underpinnings remain ill defined. To understand the cause and consequence of NPC plasticity requires technologies to visualize differences within individual NPCs across the thousands in a given nucleus. We evaluate the utility of Pan Expansion Microscopy (Pan-ExM), which enables 16-20 fold isotropic cell enlargement while preserving the proteome, to reveal NPC plasticity. NPCs are robustly identified by deep learning-facilitated segmentation as tripartite structures corresponding to the nucleoplasmic ring, inner ring with central transport channel, and cytoplasmic ring, as confirmed by immunostaining. We demonstrate a range of NPC diameters with a bias for dilated NPCs at the basal nuclear surface, often in local clusters. These diameter biases are eliminated by disrupting linker of nucleoskeleton and cytoskeleton (LINC) complex-dependent connections between the nuclear envelope (NE) and the cytoskeleton, supporting that they reflect local variations in NE tension. Pan-ExM further reveals that the transmembrane nucleoporin/nup POM121 resides specifically at the nuclear ring in multiple model cell lines, surprising given the expectation that it would be a component of the inner ring like other transmembrane nups. Remarkably, however, POM121 shifts from the nuclear ring to the inner ring specifically in aged induced pluripotent stem cell derived neurons (iPSNs) from a patient withC9orf72amyotrophic lateral sclerosis (ALS). Thus, Pan-ExM allows the visualization of changes in NPC architecture that may underlie early steps in an ALS pathomechanism. Taken together, Pan-ExM is a powerful and accessible tool to visualize NPC plasticity in physiological and pathological contexts at single NPC resolution.
Central Presynapses Regulate Spontaneous Synaptic Vesicle Exocytosis Rate by Constraining Recycling Pool Density
Authors: Wilson P. , Kim N. , Cotter R. , Parkes M. , Reed M.N. , Gramlich M.W. 
Published: September 2024

AbstractSynapses represent a fundamental unit of information transfer during cognition. They accomplish this via presynaptic vesicle exocytosis, which can occur either spontaneously or by an action potential leading to evoked release. It has been well established that evoked release is probabilistic in nature, but it has been less clear what mechanisms mediate spontaneous release. Understanding spontaneous release is important because it is an essential maintenance mechanism for synaptic connections. We propose a mechanistic framework and model of spontaneous release based on immobile vesicles in the reserve pool geometrically constraining mobile vesicles in the recycling pool, which provides a force leading to a spontaneous release rate. We experimentally support this framework using a combination of Scanning Electron Microscopy (SEM), high-resolution fluorescence microscopy techniques using pHluorin-VGlut1 and a single vesicle SGC5 reporter, and a computational model. We observe that the spontaneous release rate increases linearly with the number of vesicles but is constant in the absence of presynaptic actin. We then use an acute agent, Forskolin, to further constrain the volume of the recycling pool, leading to an increased spontaneous release rate. We show that our framework predicts the increasing spontaneous release rate experimentally observed. These results suggest that synapses constrain the density of the recycling pool to mediate spontaneous release rate via the entropic force.
Floral Reversion based micropropagation of Day-NeutralCannabis sativaL
Authors: Tabatabaei Darya Sadat , Abiri Rambod , Jones A.M.P. 
Published: September 2024

AbstractMicropropagation systems have been developed for photoperiod sensitive cultivars of cannabis, but there are currently no published methods for day-neutral genotypes. Most established cannabis micropropagation systems rely on shoot proliferation using modal explants that need them to be maintained in vegetative growth, which is not possible for day-neutral genotypes. Floral reversion, the process by which plants revert to vegetative growth from the generative stage, has been demonstrated as an alternative and potentially more efficient approach to the micropropagation of photoperiodic cannabis. The current study investigated if this process could be adapted to facilitate the micropropagation of day-neutral genotypes and overcome existing barriers. During the process, various factors such as photoperiod and light intensity may influence the efficiency of floral reversion. To evaluate this approach in day-neutral cultivars, various photoperiods were compared to assess the impact on reversion rate and subsequent growth. Excised florets obtained fromin vitroday-neutralC. sativacv. “Blue Auto Mazar x auto Blueberry” seedlings were subjected to five photoperiods including 12.0, 16.0, 18.0, 20.0, and 24.0 hours of light per day for four weeks. Reversion rates and time, shoot length, shoot number, and node number were measured. Statistical analyses revealed significant differences (p-values < 0.05) in terms of reversion time among photoperiod treatments. The highest reversion rate happened under the 16.0 hr photoperiod with 72% success. The highest shoot lengths were observed under 20.0 hr of photoperiods with a mean of 10.1 mm and the lowest shoot length belonged to 12.0 hr of photoperiods with a mean of 5.6 mm, respectively. Reverted shoots developed vegetatively for some time before initiating new flowers. However, during this period the shoots were successfully rooted in vitro and then acclimated to the growth chamber where they completed their life cycle, including seed production. This process was also successfully achieved from a 2-year old culture ofC. sativacv. “Blue Auto Mazar”, demonstrating that it is feasible to use this approach for long term culture maintenance and multiplication. This study demonstrates that floral reversion can successfully be used to clonally propagate day-neutral cannabis plants and serves as a basis for developing large-scale clonal propagation and breeding strategies.
Mineral fertilization reduces the drought resistance of soil multifunctionality in a mountain grassland system through plant-soil interactions
Authors: Piton Gabin , Foulquier Arnaud , Bernard Lionel , Bonin Aurélie , Pommier Thomas , Lavorel Sandra , Geremia Roberto , Clement Jean Christophe 
Published: September 2024

AbstractIncreasing droughts threaten soil microbial communities and the multiple functions they control in agricultural soils. These soils are often fertilized with mineral nutrients, but it remains unclear how this fertilization may alter the capacity of soil multifunctionality (SMF) to be maintained under drought, and how plant-soil interactions shape these effects. In this study, we used a mountain grassland soil to test the interactive effect of mineral nutrient (Nitrogen and Phosphorous) addition and drought on SMF with and without plants (Lolium perenne) in a mesocosm experiment. We calculated SMF based on 8 microbial properties associated with the capacity of soil microbes to store carbon (C), nitrogen (N) and phosphorous (P) in their biomass, and to process these elements through organic matter depolymerization, mineralization, nitrification and denitrification processes. To investigate mechanisms underlying the SMF response we characterized the associated changes in soil stoichiometry and microbial community composition using 16S and 18S rRNA amplicon sequencing. Our results showed that fertilization decreased the SMF drought resistance when plants were present, but the opposite was observed in the unplanted mountain grassland soil. Our analysis suggested this was due to the interaction of plants, fertilization and drought in influencing four coupled properties related to high SMF: high soil moisture, low microbial C limitation, high bacterial diversity and low bacteria gram positive:gram negative ratio. Altogether, our results suggested that reducing the use of mineral fertilizer for plant production in mountain grassland could improve the ability of their soils to maintain their multifunctionality during drought period. Finally, our study clearly further demonstrated the importance of plant in the complex responses of SMF to global changes and showed that combining stoichiometric and microbial diversity assessment represents a powerful approach to disentangle the underlying mechanisms.
Polarized dipole scattering amplitudes meet the valence quark model
Authors: Dumitru Adrian , Mäntysaari Heikki , Tawabutr Yossathorn 
Published: September 2024

The recently revised small-x helicity evolution [], resumming the double-logarithmic factor, αsln2(1/x), allows for the study of helicity distributions of quarks and gluons at small Bjorken x, corresponding to high center-of-mass energy. In this work, we calculate the moderate-x initial conditions in the regime, αsln2(1/x)∼1, for the small-x helicity evolution using a light-front valence quark model of the proton, which provides additional physical information about the target. The perturbative emission and absorption of a gluon by the valence quarks are also included. The results, given in Eqs. (35), provide a new set of initial conditions with a significantly reduced number of free parameters than conventional models []. Consequently, the predictive power of small-x helicity evolution is expected to improve once the initial conditions from this work are incorporated.

Published by the American Physical Society
2024
Pressure-Tuned Quantum Criticality in the Locally Noncentrosymmetric Superconductor
CeRh2As2
Authors: Pfeiffer M. , Semeniuk K. , Landaeta J. F. , Borth R. , Geibel C. , Nicklas M. , Brando M. , Khim S. , Hassinger E. 
Published: September 2024

The unconventional superconductor CeRh2As2 (critical temperature Tc≈0.4  K) displays an exceptionally rare magnetic-field-induced transition between two distinct superconducting (SC) phases, proposed to be states of even and odd parity of the SC order parameter, which are enabled by a locally noncentrosymmetric structure. The superconductivity is preceded by a phase transition of unknown origin at T0=0.5  K. Electronic low-temperature properties of CeRh2As2 show pronounced non-Fermi-liquid behavior, indicative of a proximity to a quantum critical point (QCP). The role of quantum fluctuations and normal state orders for the superconductivity in a system with staggered Rashba interaction is currently an open question, pertinent to explaining the occurrence of the two-phase superconductivity. In this work, using measurements of resistivity and specific heat under hydrostatic pressure, we show that the T0 order vanishes completely at a modest pressure of P0≈0.5  GPa, revealing a QCP. In line with the quantum criticality picture, the linear temperature dependence of the resistivity at P0 evolves into a Fermi-liquid quadratic dependence as quantum critical fluctuations are suppressed by increasing pressure. Furthermore, the domelike behavior of Tc around P0 implies that the fluctuations of the T0 order are involved in the SC pairing mechanism.

Published by the American Physical Society
2024
Persuasion for protection: an analysis of online safety videos on YouTube
Authors: Huang Liuyu , Goh Dion Hoe-Lian , Yin Stella Xin 
Published: September 2024

PurposePublic service announcements (PSAs) have been shown to be effective instruments that raise awareness, educate society, and change behaviors and attitudes. Many governments and organizations have utilized PSAs on social media to promote online safety among children and youth. However, we have limited understanding of the range of topics that these PSAs address and how they present their content to audiences. This study provides an inventory of the types of online safety topics that current PSAs address and a catalogue of the types of persuasive features employed by PSAs.Design/methodology/approachA content analysis of 220 YouTube PSA videos on online safety was conducted. Various topics under the umbrella of online safety were identified. Guided by the prospect theory and exemplification theory, different persuasive features employed in the PSAs were sought.FindingsThe findings highlight that the primary focus of these PSAs is on online safety behaviors and general instructions on online hygiene. Interestingly, nearly half of the videos employ a neutral frame, while a significant portion provides no evidential support. Additionally, video length was associated with the number of views and likes it gathered but not with the number of comments.Originality/valueThe inventory of PSAs can help researchers, practitioners, and policymakers better understand the type of content being produced and disseminated online as well as identify topics that are either over or under-represented. Further, the catalogue of the types of persuasive features employed by PSAs would be helpful in guiding research, practice, and policymaking in the context of creating effective online safety videos.