bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine Learning Elucidates Design Features of Plasmid DNA Lipid Nanoparticles for Cell Type-Preferential Transfection
Authors: Cheng Leonardo , Zhu Yining , Ma Jingyao , Aggarwal Ataes , Toh Wu Han , Shin Charles , Sangpachatanaruk Will , Weng Gene , Kumar Ramya , Mao Hai-Quan 
Published: December 2023

AbstractFor cell and gene therapies to become more broadly accessible, it is critical to develop and optimize non-viral cell type-preferential gene carriers such as lipid nanoparticles (LNPs).Despite the effectiveness of high throughput screening (HTS) approaches in expediting LNP discovery, they are often costly, labor-intensive, and often do not provide actionable LNP design rules that focus screening efforts on the most relevant chemical and formulation parameters. Here we employed a machine learning (ML) workflow using well-curated plasmid DNA LNP transfection datasets across six cell types to maximize chemical insights from HTS studies and has achieved predictions with 5–9% error on average depending on cell type. By applying Shapley additive explanations to our ML models, we unveiled composition-function relationships dictating cell type-preferential LNP transfection efficiency. Notably, we identified consistent LNP composition parameters that enhancein vitrotransfection efficiency across diverse cell types, such as ionizable to helper lipid ratios near 1:1 or 10:1 and the incorporation of cationic/zwitterionic helper lipids. In addition, several parameters were found to modulate cell type-preferentiality, including the ionizable and helper lipid total molar percentage, N/P ratio, cholesterol to PEGylated lipid ratio, and the chemical identity of the helper lipid. This study leverages HTS of compositionally diverse LNP libraries and ML analysis to understand the interactions between lipid components in LNP formulations; and offers fundamental insights that contribute to the establishment of unique sets of LNP compositions tailored for cell type-preferential transfection.
Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues
Authors: Wang Huan , Huang Ruixu , Nelson Jack , Gao Ce , Tran Miles , Yeaton Anna , Felt Kristen , Pfaff Kathleen L. , Bowman Teri , Rodig Scott J. , Wei Kevin , Goods Brittany A. , Farhi Samouil L. 
Published: December 2023

AbstractEmerging imaging spatial transcriptomics (iST) platforms and coupled analytical methods can recover cell-to-cell interactions, groups of spatially covarying genes, and gene signatures associated with pathological features, and are thus particularly well-suited for applications in formalin fixed paraffin embedded (FFPE) tissues. Here, we benchmarked the performance of three commercial iST platforms on serial sections from tissue microarrays (TMAs) containing 23 tumor and normal tissue types for both relative technical and biological performance. On matched genes, we found that 10x Xenium shows higher transcript counts per gene without sacrificing specificity, but that all three platforms concord to orthogonal RNA-seq datasets and can perform spatially resolved cell typing, albeit with different false discovery rates, cell segmentation error frequencies, and with varying degrees of sub-clustering for downstream biological analyses. Taken together, our analyses provide a comprehensive benchmark to guide the choice of iST method as researchers design studies with precious samples in this rapidly evolving field.
Movement-related increases in subthalamic activity optimize locomotion
Authors: Callahan Joshua W. , Morales Juan Carlos , Atherton Jeremy F. , Wang Dorothy , Kostic Selena , Bevan Mark D. 
Published: December 2023

SummaryThe subthalamic nucleus (STN) is traditionally thought to restrict movement. Lesion or prolonged STN inhibition increases movement vigor and propensity, while optogenetic excitation typically has opposing effects. Subthalamic and motor activity are also inversely correlated in movement disorders. However, most STN neurons exhibit movement-related increases in firing. To address this paradox, STN activity was recorded and manipulated in head-fixed mice at rest and during self-initiated and -paced treadmill locomotion. The majority of STN neurons (type 1) exhibited locomotion-dependent increases in activity, with half encoding the locomotor cycle. A minority of neurons exhibited dips in activity or were uncorrelated with movement. Brief optogenetic inhibition of the dorsolateral STN (where type 1 neurons are concentrated) slowed and prematurely terminated locomotion. In Q175 Huntington’s disease mice abnormally brief, low-velocity locomotion was specifically associated with type 1 hypoactivity. Together these data argue that movement-related increases in STN activity contribute to optimal locomotor performance.
Atlas of nascent RNA transcripts reveals enhancer to gene linkages
Authors: Sigauke Rutendo F. , Sanford Lynn , Maas Zachary L. , Jones Taylor , Stanley Jacob T. , Townsend Hope A. , Allen Mary A. , Dowell Robin D. 
Published: December 2023

AbstractGene transcription is controlled and modulated by regulatory regions, including enhancers and promoters. These regions are abundant in unstable, non-coding bidirectional transcription. Using nascent RNA transcription data across hundreds of human samples, we identified over 800,000 regions containing bidirectional transcription. We then identify highly correlated transcription between bidirectional and gene regions. The identified correlated pairs, a bidirectional region and a gene, are enriched for disease associated SNPs and often supported by independent 3D data. We present these resources as an SQL database which serves as a resource for future studies into gene regulation, enhancer associated RNAs, and transcription factors.
Direct stimulation of anterior insula and ventromedial prefrontal cortex disrupts economic choices
Authors: Cecchi Romane , Collomb-Clerc Antoine , Rachidi Inès , Minotti Lorella , Kahane Philippe , Pessiglione Mathias , Bastin Julien 
Published: December 2023

AbstractNeural activities within the ventromedial prefrontal cortex and anterior insula are associated with economic choices. However, whether these brain regions are causally related to these processes remains unclear. To address this issue, we leveraged rare intracerebral electrical stimulation (iES) data in epileptic patients. We show that opposite effects of iES on choice depend on the location of stimulation on a dorso-ventral axis within each area, thus demonstrating dissociable neural circuits causally involved in accepting versus avoiding challenges.
Adaptive Regularized Tri-Factor Non-Negative Matrix Factorization for Cell Type Deconvolution
Authors: Liu Tianyi , Liu Chuwen , Li Quefeng , Zheng Xiaojing , Zou Fei 
Published: December 2023

AbstractAccurate deconvolution of cell types from bulk gene expression is crucial for understanding cellular compositions and uncovering cell-type specific differential expression and physiological states of diseased tissues. Existing deconvolution methods have limitations, such as requiring complete cellular gene expression signatures or neglecting partial biological information. Moreover, these methods often overlook varying cell-type mRNA amounts, leading to biased proportion estimates. Additionally, they do not effectively utilize valuable reference information from external studies, such as means and ranges of population cell-type proportions. To address these challenges, we introduce an Adaptive Regularized Tri-factor non-negative matrix factorization approach for deconvolution (ARTdeConv). We rigorously establish the numerical convergence of our algorithm. Through benchmark simulations, we demonstrate the superior performance of ARTdeConv compared to state-of-the-art semi-reference-based and reference-free methods. In a real-world application, our method accurately estimates cell proportions, as evidenced by the nearly perfect Pearson’s correlation between ARTdeConv estimates and flow cytometry measurements in a dataset from a trivalent influenza vaccine study. Moreover, our analysis of ARTdeConv estimates in COVID-19 patients reveals patterns consistent with important immunological phenomena observed in other studies. The proposed method, ARTdeConv, is implemented as an R package and can be accessed on GitHub for researchers and practitioners.
Variations in cellular unfolded protein response, respiratory capacity, and stress tolerance in skin and lung fibroblasts of deer mice (Peromyscus maniculatus)
Authors: Yap Kang Nian , Yamada KayLene , Zikeli Shelby L , Zhang Yufeng , Zhang Youwen , Naderi Asieh , Soltanmohammadi Elham , Kavazis Andreas N , Roberts Michael D , Kiaris Hippokratis , Hood Wendy R 
Published: December 2023

AbstractEvolutionary physiologists have long been interested in physiological mechanisms underpinning variation in life-history performance. Recent efforts to elucidate these mechanisms focused on bioenergetics and oxidative stress. One underappreciated area that could play a role in mediating variation in performance is the unfolded protein response (UPR), a cellular stress response that reduces secretory protein load, enhances endoplasmic reticulum (ER) protein folding and clearance capacity during stress and during its adaptive phase. Given that the ER and mitochondria interact to regulate cellular homeostasis, it seems intuitive that UPR phenotype would correlate strongly with mitochondrial physiology, which in turn would contribute to variations in whole-organism metabolism. One way researchers have been studying cellular controls of life-history traits is by assessing stress resistance and bioenergetic properties of primary dermal fibroblasts. However, it is unclear if findings from dermal fibroblasts can be generalized to other cell and tissue types, and if fibroblasts’ phenotypes are repeatable across different life-history stages. This study aimed to explore the relationships between UPR profile, cellular respiration, and stress resistance using primary dermal fibroblasts isolated at puberty and primary lung fibroblasts isolated at adulthood. Specifically, we tested if 1) UPR profile of dermal fibroblasts isolated at puberty corresponds to UPR profile of lung fibroblasts isolated at adulthood, 2) UPR profile of dermal fibroblasts isolated at puberty and lung fibroblasts isolated at adulthood correspond to cellular bioenergetics of lung fibroblasts isolated at adulthood, and 3) UPR profile of dermal fibroblasts isolated at puberty corresponds to multiplex stress resistance (ER stress, oxidative stress, DNA damage) of lung fibroblasts isolated at adulthood. We found that only tunicamycin induced BiP expression was repeatable in skin and lung fibroblasts. Tunicamycin induced expressions of BiP, GRP94, and CNX in skin fibroblasts predicted resistance of lung fibroblasts to tunicamycin, (but not thapsigargin and other inducers of lethal stress), which is indicative for the pro-survival role of UPR during stress. Tunicamycin induced BiP expression in skin and lung fibroblasts also predicted multiple cellular bioenergetics parameters in lung fibroblasts.Statements and DeclarationsNo competing interests declared. This work was supported by National Science Foundation grants IOS1453784 and OIA1736150 to W.R.H., IOS1755670 to the PGSC, and a National Science Foundation EPSCoR pilot grant to K.N.Y. The funders did not have any input into the content of the manuscript nor require approval prior to submission.
CRISPR Spacers Acquired from Plasmids Primarily Target Backbone Genes, Making Them Valuable for Predicting Potential Hosts and Host Range
Authors: Androsiuk Lucy , Maane Sivan , Tal Shay 
Published: December 2023

ABSTRACTIn recent years, there has been a surge in metagenomic studies focused on identifying plasmids in environmental samples. While these studies have unearthed numerous novel plasmids, enriching our understanding of their environmental roles, a significant gap remains: the scarcity of information regarding the bacterial hosts of these newly discovered plasmids. Furthermore, even when plasmids are identified within bacterial isolates, the reported host is typically limited to the original isolate, with no insight into alternative hosts or the plasmid’s potential host range. Given that plasmids depend on hosts for their existence, investigating plasmids without knowledge of potential hosts offers only a partial perspective.This study introduces a method for identifying potential hosts and host ranges for plasmids through alignment with CRISPR spacers. To validate the method, we compared the PLSDB plasmids database with the CRISPR spacers database, yielding host predictions for 46% of the plasmids. When compared to reported hosts, our predictions achieved an 84% concordance at the family level and 99% concordance at the phylum level. Moreover, the method frequently identified multiple potential hosts for a plasmid, thereby enabling predictions of alternative hosts and the host range.Notably, we found that CRISPR spacers predominantly target plasmid backbone genes while sparing functional genes, such as those linked to antibiotic resistance, aligning with our hypothesis that CRISPR spacers are acquired from plasmid-specific regions rather than insertion elements from diverse sources. Lastly, we illustrate the network of connections among different bacterial taxa through plasmids, revealing potential pathways for horizontal gene transfer.IMPORTANCEPlasmids are notorious for their role in distributing antibiotic resistance genes, but they may also carry and distribute other environmentally important genes. Since plasmids are not free-living entities and rely on host bacteria for survival and propagation, predicting their hosts is essential. This study presents a method for predicting potential hosts for plasmids and offers insights into the potential paths for spreading functional genes between different bacteria. Understanding plasmid-host relationships is crucial for comprehending the ecological and clinical impact of plasmids and implications for various biological processes.
CytoSimplex: Visualizing Single-cell Fates and Transitions on a Simplex
Authors: Liu Jialin , Wang Yichen , Li Chen , Gu Yichen , Ono Noriaki , Welch Joshua D. 
Published: December 2023

AbstractSummaryCells differentiate to their final fates along unique trajectories, often involving multi-potent progenitors that can produce multiple terminally differentiated cell types. Recent developments in single-cell transcriptomic and epigenomic measurement provide tremendous opportunities for mapping these trajectories. The visualization of single-cell data often relies on dimension reduction methods such as UMAP to simplify high-dimensional single-cell data down into an understandable two-dimensional (2D) form. However, these visualization methods can be misleading and often do not effectively represent the direction of cell differentiation. To address these limitations, we developed a new approach that places each cell from a single-cell dataset within a simplex whose vertices correspond to terminally differentiated cell types. Our approach can quantify and visualize current cell fate commitment and future cell potential. We developed CytoSimplex, a standalone open-source package implemented in R and Python that provides simple and intuitive visualizations of cell differentiation in 2D ternary and three-dimensional (3D) quaternary plots. We believe that CytoSimplex can help researchers gain a better understanding of cell type transitions in specific tissues and characterize developmental processes.Availability and implementationThe R version of CytoSimplex is available on Github athttps://github.com/welch-lab/CytoSimplex. The Python version of CytoSimplex is available on Github athttps://github.com/welch-lab/pyCytoSimplex.
Tail Length and E525K Dilated Cardiomyopathy Mutant Alter Human β-Cardiac Myosin Super-Relaxed State
Authors: Duno-Miranda Sebastian , Nelson Shane R. , Rasicci David V. , Bodt Skylar L.M. , Cirilo Joseph A. , Vang Duha , Sivaramakrishnan Sivaraj , Yengo Christopher M. , Warshaw David M. 
Published: December 2023

AbstractDilated cardiomyopathy (DCM) is characterized by impaired cardiac function due to myocardial hypo-contractility and is associated with point mutations in β-cardiac myosin, the molecular motor that powers cardiac contraction. Myocardial function can be modulated through sequestration of myosin motors into an auto-inhibited "super relaxed" state (SRX), which is further stabilized by a structural state known as the "Interacting Heads Motif" (IHM). Therefore, hypo-contractility of DCM myocardium may result from: 1) reduced function of individual myosin, and/or; 2) decreased myosin availability due to increased IHM/SRX stabilization. To define the molecular impact of an established DCM myosin mutation, E525K, we characterized the biochemical and mechanical activity of wild-type (WT) and E525K human β-cardiac myosin constructs that differed in the length of their coiled-coil tail, which dictates their ability to form the IHM/SRX state. Single-headed (S1) and a short-tailed, double-headed (2HEP) myosin constructs exhibited low (∼10%) IHM/SRX content, actin-activated ATPase activity of ∼5s-1and fast velocities in unloaded motility assays (∼2000nm/s). Double-headed, longer-tailed (15HEP, 25HEP) constructs exhibited higher IHM/SRX content (∼90%), and reduced actomyosin ATPase (<1s-1) and velocity (∼800nm/s). A simple analytical model suggests that reduced velocities may be attributed to IHM/SRX-dependent sequestration of myosin heads. Interestingly, the E525K 15HEP and 25HEP mutants showed no apparent impact on velocity or actomyosin ATPase at low ionic strength. However, at higher ionic strength, the E525K mutation stabilized the IHM/SRX state. Therefore, the E525K-associated DCM human cardiac hypo-contractility may be attributable to reduced myosin head availability caused by enhanced IHM/SRX stability.SummaryThis research investigates the E525K mutation in human β-cardiac myosin, crucial for heart contraction, and its role in causing Dilated Cardiomyopathy (DCM). It demonstrates that the length of the myosin tail influences its self-inhibition, and the E525K mutation strengthens this effect, potentially reducing heart contractility in DCM.
Nodule organogenesis inMedicago truncatularequires local stage-specific auxin biosynthesis and transport
Authors: Xiao TT , Shen D , Müller S , Liu J , van Seters A , Franssen H , Bisseling T , Kulikova O , Kohlen W 
Published: December 2023

ABSTRACTThe importance of auxin in plant organ development including root nodule formation is well established. Using auxin reporter constructs the spatiotemporal auxin distribution pattern during nodule development has previously been illustrated. However, our understanding of how this pattern is built-up and maintained still remains elusive.To this end, we studied how the auxin gradient visualized by DR5 expression patterns at different stages of nodule development in Medicago truncatula (Medicago), is correlated with the spatiotemporal expression patterns of known auxin biosynthesis and auxin transport genes. In addition, we record the MtPIN10-GFP expression pattern and polar positioning on the cell plasma membranes during nodule primordium development to investigate the auxin flux. RNA interference and the application of auxin synthesis blockers were used to demonstrate the relevance of biosynthesis and transport at the initial stages of the nodulation process.Our results show that upon rhizobium inoculation, preceding the first mitotic activity, a specific set of MtYUCs and MtPINs as well as MtLAX2 are expressed in the pericycle contributing to the creation of an auxin maximum. Overall, we demonstrate that dynamic spatiotemporal expression of both, MtYUCs and MtPINs, result in specific auxin outputs in subsequent stages of nodule primordia and nodule meristem formation.
OsUVR8b, rather than OsUVR8a, plays a predominant role in rice UVR8-mediated UV-B response
Authors: Chen Yu-long , Zhong You-bin , Leung David W. M. , Yan Xiao-Yu , Ouyang Meng-ni , Ye Yu-zhen , Li Shi-mei , Peng Xin-xiang , Liu E-e 
Published: December 2023

AbstractUV RESISTANCE LOCUS 8 (UVR8) has been identified inArabidopsis thalianaas the receptor for UV-B radiation mediating photomorphogenic responses and acclimation to UV-B radiation. However, UVR8-mediated UV-B signaling pathways in rice, that has two proteins (UVR8a and UVR8b) with homology to AtUVR8, remain largely unknown. In this study,UVR8aandUVR8bwere found to be expressed mainly in rice leaves and leaf sheaths, while the level of UVR8b was higher than that of UVR8a. In agreement with prior studies on AtUVR8,uvr8banduvr8a uvr8brice mutants exposed to UV-B showed reduced UVB-induced growth inhibition and upregulation ofCHSandHY5transcripts along with acclimation to UV-B, overexpressing UVR8a or UVR8b enhanced UV-B-induced growth inhibition and acclimation to UV-B, compared to wild-type plants. UV-B was able to enhance the interaction between CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) with UVR8a/UVR8b, whereas the interaction intensity of REPRESSOR OF UV-B PHOTOMORPHOGENESIS2 (RUP2) with UVR8a was significantly higher than that with UVR8b. In addition, UVR8a and UVR8b were also found in the nucleus and cytoplasm, but OsUVR8 proteins were localized in nucleus in the absence of UV-B. The level of OsUVR8 monomer showed an invisible change in the leaves of rice seedlings transferred from white light to white light supplemented with UV-B, even UV-B can weaken the interactions of UVR8a or/and UVR8b. Therefore, both UVR8a and UVR8b, that have different location and response modes with Arabidopsis UVR8, function in the response of rice to UV-B radiation, whereas UVR8b plays a predominant role in this process.
Haplo-pheno association forOsNRT1.1paralog in rice reveals superior haplogroup with high nitrate uptake efficiency
Authors: Elangovan Dharani , Pandey Renu , Sharma Sandeep , Balamurugan Balaji , Anand Neha , Das Adhip , Kumar Tarun , Ellur Ranjith Kumar , Kalia Sanjay , Rane Jagadish 
Published: December 2023

AbstractHaplotype-based breeding approaches hold promise for enhancing crop improvement strategies, allowing for targeted selection of superior genetic combinations to develop high-yielding and resilient varieties. The current study aimed at identification ofNRT1.1nitrate transporter haplotype that could serve as “donors” in haplotype-based breeding. We phenotyped 272 rice accessions in hydroponics with sufficient and low nitrogen (N) for nitrate uptake efficiency. By employing principal component and hierarchical cluster analysis, the accessions were grouped into N efficient, intermediate, and inefficient clusters. Haplotype analysis unveiled the presence of two haplogroups forOsNRT1.1A, three forOsNRT1.1B, and five forOsNRT1.1C. Through haplo-pheno association, the comparison of mean trait values revealed H2 and H3 as the superior haplotypes (SH) for OsNRT1.1A and OsNRT1.1B, respectively. In the case of OsNRT1.1C, H3 and H1 emerged as SH within the N-efficient cluster. Conversely, the inferior haplotypes (IH) consisted of H1 in OsNRT1.1A, H3 in OsNRT1.1B, and H3 and H2 in OsNRT1.1C within the N-inefficient cluster. However, relative expression ofOsNRT1.1(with specific paralogs) in contrasting rice accessions revealed that a few of the inferior accession exhibited higher expression levels in the root but lower in the shoot, which might have contributed to their N-inefficiency. Furthermore, amino acid change at position 403 (Isoleucine to Valine) in inferior accessions influences the active site OsNRT1.1C protein causing N-inefficiency. Ours is the first report on haplotype analysis ofNRT1.1gene demonstrating its genetic diversity, as well as its association with phenotype will have potential implications for improving nitrate uptake efficiency.