bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-varying stimuli that prolong IKK activation promote nuclear remodeling and mechanistic switching of NF-κB dynamics
Authors: Smeal Steven W. , Mokashi Chaitanya S. , Kim A. Hyun , Chiknas P. Murdo , Lee Robin E. C. 
Published: September 2024

AbstractTemporal properties of molecules within signaling networks, such as sub-cellular changes in protein abundance, encode information that mediate cellular responses to stimuli. How dynamic signals relay and process information is a critical gap in understanding cellular behaviors. In this work, we investigate transmission of information about changing extracellular cytokine concentrations from receptor-level supramolecular assemblies of IκB kinases (IKK) downstream to the nuclear factor κB (NF-κB) transcription factor (TF). In a custom robot-controlled microfluidic cell culture, we simultaneously measure input-output (I/O) encoding of IKK-NF-κB in dual fluorescent-reporter cells. When compared with single cytokine pulses, dose-conserving pulse trains prolong IKK assemblies and lead to disproportionately enhanced retention of nuclear NF-κB. Using particle swarm optimization, we demonstrate that a mechanistic model does not recapitulate this emergent property. By contrast, invoking mechanisms for NF-κB-dependent chromatin remodeling to the model recapitulates experiments, showing how temporal dosing that prolongs IKK assemblies facilitates switching to permissive chromatin that sequesters nuclear NF-κB. Remarkably, using simulations to resolve single-cell receptor data accurately predicts same-cell NF-κB time courses for more than 80% of our single cell trajectories. Our data and simulations therefore suggest that cell-to-cell heterogeneity in cytokine responses are predominantly due to mechanisms at the level receptor-associated protein complexes.
Comparative Analysis of AAV Serotypes for Transduction of Olfactory Sensory Neurons
Authors: Belfort Benjamin D.W. , Jia Johnathan D. , Garza Alexandra , Insalaco Anthony M. , McGinnis JP , Pekarek Brandon T. , Ortiz-Guzman Joshua , Tepe Burak , Chen Hu ,   aSCENT-PD Investigators, Liu Zhandong , Arenkiel Benjamin R. 
Published: September 2024

AbstractOlfactory sensory neurons within the nasal epithelium detect volatile odorants and relay odor information to the central nervous system. Unlike other sensory inputs, olfactory sensory neurons interface with the external environment and project their axons directly into the central nervous system. The use of adeno-associated viruses to target these neurons has garnered interest for applications in gene therapy, probing olfactory sensory neuron biology, and modeling disease. To date, there is no consensus on the optimal AAV serotype for efficient and selective transduction of olfactory sensory neuronsin vivo. Here we utilized serial confocal imaging and single-nucleus RNA sequencing to evaluate the efficacy of 11 different AAV serotypes in transducing murine olfactory sensory neurons via non-invasive nasal inoculation. Our results reveal that AAV1, while highly effective, exhibited broad tropism, whereas AAV-DJ/8 showed the greatest specificity for olfactory sensory neurons.
EmbedSimScore: Advancing Protein Similarity Analysis with Structural and Contextual Embeddings
Authors: Saha Gourab , Tahmid Md Toki , Bayzid Md. Shamsuzzoha 
Published: September 2024

AbstractAccurately computing protein similarity is challenging due to the intricate interplay between local substructures and the global structure within protein molecules. Traditional metrics like TM-score often focus on aligning the global structures of the proteins in a rather geometry-based algorithmic way, potentially overlooking critical local-global relations and contextual comparisons. We introduce Embed-SimScore, a novel self-supervised method that generates structural and contextual embeddings by jointly considering both local substructures and global proteins’ structures. Utilizing contrastive language-structure pre-training (CLSP) and structural contrastive learning, EmbedSimScore captures comprehensive features across different scales of protein structure. These embeddings provide a more precise and holistic means of computing protein similarities, resulting in the identification of intrinsic relations among proteins that traditional approaches overlook.
ABA-regulated JAZ1 Proteins Bind NAC42 Transcription Factors to Suppress the Activation of Phytoalexin Biosynthesis in Plants
Authors: Lin Jie , Monsalvo Ivan , Jahan Md Asraful , Ly Melissa , Wi Dasol , Martirosyan Izabella , Jahan Israt , Kovinich Nik 
Published: September 2024

SUMMARYPhytoalexins are plant defense metabolites whose biosynthesis remains suppressed until elicited by a pathogen or stress, yet the mechanism of their suppression has remained elusive. The transcription factor GmNAC42-1 is an important and direct activator of the biosynthesis of glyceollin phytoalexins in soybean. Yet, without elicitation, overexpressing GmNAC42-1 is insufficient to activate the expression of glyceollin biosynthetic genes, suggesting that the activity of GmNAC42-1 may be suppressed by a negative regulator. JAZ1 proteins are negative regulators of the canonical jasmonic acid (JA) signaling pathway. JAZ protein degradation and JAZ gene transcription comprise antagonistic mechanisms that activate and suppress JA signaling, respectively. In search for negative regulators of glyceollin biosynthesis, we identified by RNA-seq analysis abscisic acid (ABA) signaling and GmJAZ1 genes that are oppositely regulated compared to glyceollin biosynthesis. Long-term ABA treatment upregulated GmJAZ1 transcripts, whereas its biosynthesis inhibitor fully suppressed their upregulation by dehydration stress. Opposite patterns were observed for glyceollin biosynthesis. RNAi silencing of GmJAZ1s prevented the suppression of glyceollin biosynthesis by dehydration and derepressed glyceollin synthesis in non-elicited tissues. Overexpressing GmJAZ1-9 in hairy roots elicited with Phytophthora sojae wall glucan elicitor partially suppressed glyceollin biosynthesis. The GmJAZ1-9 protein physically interacted with GmNAC42-1 and inhibited its transactivation and DNA binding activities in promoter-luciferase and yeast-three hybrid systems. Silencing JAZ1s in Arabidopsis and grapevine has been reported to derepress camalexin and stilbene phytoalexin biosynthesis. Here, we found that JAZ1 and NAC42 proteins from all three plant species physically interact, suggesting a conserved mechanism negatively regulates phytoalexin biosynthesis in plants.Abstract Figure
Overestimation of sex differences in psychostimulant activity via comparisons of males and females from different behavioral groups
Authors: Tigano Anthony M. , Job Martin O 
Published: September 2024

AbstractBackgroundThere are inconsistencies in the observation of sex differences in baseline activity and psychostimulant activity. To address this, we have developed the MISSING (Mapping Intrinsic Sex Similarities as an Integral quality of Normalized Groups) model. MISSING model proposes that sex similarities are observed when we compare similar behavioral groups of males and females, with sex differences occurring when we compare distinct groups of sexes, but this model has not been tested.MethodsTo test this model, we identified within-sex groups of Sprague Dawley rats (male n = 22, female n = 23) by conducted normal mixtures clustering of baseline activity, cocaine activity (as distance traveled in cm over 90 min) and cocaine activity normalized-to-baseline activity (NBA) of all subjects. We employed 2-way ANOVA to determine the impact of within-sex heterogeneity on sex differences. We compared our cluster-based method to current median-split approaches.ResultsOur new cluster-based method revealed three distinct clusters, each consisting of both males and females. We determined there were no sex differences in any of the variables when males and females from the same clusters were compared. The within-sex clusters for females were not defined by estrous phase. Median split analysis was ineffective in accurately identifying within-sex groups.ConclusionsOur results validate the MISSING model: there are no sex differences in psychostimulant activity except when we compare males and females from different behavioral groups. This has significant implications for how we proceed with research towards understanding the mechanism governing sex differences in psychostimulant activity.
Anatomically and Physiologically Accurate Engineered Neurovascular Unit and Blood-Brain Barrier Model Using Microvessels Isolated from Postmortem Human Brain Tissue
Authors: O’Grady Brian J. , McCall A. Scott , Cullison Samuel , Chavarria Daniel , Kjar Andrew , Schrag Matthew S. , Lippmann Ethan S. 
Published: September 2024

AbstractBrain vasculature is a complex and heterogeneous physiological structure that serves specialized roles in maintaining brain health and homeostasis. There is substantial interest in developing representative human models of the brain vasculature for drug screening and disease modeling applications. Many contemporary strategies have focused on culturing neurovascular cell types in hydrogels and microdevices, but it remains challenging to achieve anatomically relevant vascular structures that have physiologically similar function to theirin vivocounterparts. Here, we present a strategy for isolating microvessels from cryopreserved human cortical tissue and culturing these vessels in a biomimetic gelatin-based hydrogel contained in a microfluidic device. We provide histological evidence of arteriole and capillary architectures within hydrogels, as well as anastomosis to the hydrogel edges allowing lumen perfusion. In capillaries, we demonstrate restricted diffusion of a 10 kDa dextran, indicating intact passive blood-brain barrier function. We anticipate this bona fide human brain vasculature-on-a-chip will be useful for various biotechnology applications.
Benchmarking copy number aberrations inference tools using single-cell multi-omics datasets
Authors: Song Minfang , Ma Shuai , Wang Gong , Wang Yukun , Yang Zhenzhen , Xie Bin , Guo Tongkun , Huang Xingxu , Zhang Liye 
Published: September 2024

AbstractCopy number aberrations (CNAs) are an important type of genomic variation which play a crucial role in the initiation and progression of cancer. With the explosion of single-cell RNA sequencing (scRNA-seq), several computational methods have been developed to infer CNAs from scRNA-seq studies. However, to date, no independent studies have comprehensively benchmarked their performance. Herein, we evaluated five state-of-the-art methods based on their performance in tumor vs normal cell classification, CNAs profile accuracy, tumor subclone inference and aneuploidy identification in non-malignant cells. Our results showed that Numbat outperformed others across most evaluation criteria, while CopyKAT excelled in scenarios when expression matrix alone was used as input. In specific tasks, SCEVAN showed the best performance in clonal breakpoint detection and Numbat showed high sensitivity in copy number neutral LOH (cnLOH) detection. Additionally, we investigated how referencing settings, inclusion of tumor microenvironment cells, tumor type, and tumor purity impact the performance of these tools. This study provides a valuable guideline for researchers in selecting the appropriate methods for their datasets.
AMPK agonism optimizes thein vivopersistence and anti-leukemia efficacy of chimeric antigen receptor T cells
Authors: Braverman Erica L , Qin Mengtao , Schuler Herbert , Brown Harrison , Wittmann Christopher , Ramgopal Archana , Kemp Felicia , Mullet Steven J , Yang Aaron , Poholek Amanda C , Gelhaus Stacy L , Byersdorfer Craig A. 
Published: September 2024

ABSTRACTBACKGROUNDChimeric antigen receptor T cell (CART) therapy has seen great clinical success. However, up to 50% of leukemia patients relapse and long-term survivor data indicate that CART cell persistence is key to enforcing relapse-free survival. Unfortunately, ex vivo expansion protocols often drive metabolic and functional exhaustion, reducing in vivo efficacy. Preclinical models have demonstrated that redirecting metabolism ex vivo can improve in vivo T cell function and we hypothesized that exposure to an agonist targeting the metabolic regulator AMP-activated protein kinase (AMPK), would create CARTs capable of both efficient leukemia clearance and increased in vivo persistence.METHODSCART cells were generated from healthy human via lentiviral transduction. Following activation, cells were exposed to either Compound 991 or DMSO for 96 hours, followed by a 48-hour washout. During and after agonist treatment, T cells were harvested for metabolic and functional assessments. To test in vivo efficacy, immunodeficient mice were injected with luciferase+ NALM6 leukemia cells, followed one week later by either 991- or DMSO-expanded CARTs. Leukemia burden and anti-leukemia efficacy was assessed via radiance imaging and overall survival.RESULTSHuman T cells expanded in Compound 991 activated AMPK without limiting cellular expansion and gained both mitochondrial density and improved handling of reactive oxygen species (ROS). Importantly, receipt of 991-exposed CARTs significantly improved in vivo leukemia clearance, prolonged recipient survival, and increased CD4+ T cell yields at early times post-injection. Ex vivo, 991 agonist treatment mimicked nutrient starvation, increased autophagic flux, and promoted generation of mitochondrially-protective metabolites.DISCUSSIONEx vivo expansion processes are necessary to generate sufficient cell numbers, but often promote sustained activation and differentiation, negatively impacting in vivo persistence and function. Here, we demonstrate that promoting AMPK activity during CART expansion metabolically reprograms cells without limiting T cell yield, enhances in vivo anti-leukemia efficacy, and improves CD4+ in vivo persistence. Importantly, AMPK agonism achieves these results without further modifying the expansion media, changing the CART construct, or genetically altering the cells. Altogether, these data highlight AMPK agonism as a potent and readily translatable approach to improve the metabolic profile and overall efficacy of cancer-targeting T cells.
MirGeneDB 3.0: Improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families, and updated covariance models
Authors: Clarke Alexander W. , Høye Eirik , Hembrom Anju Angelina , Paynter Vanessa Molin , Vinther Jakob , Wyrożemski Łukasz , Biryukova Inna , Formaggioni Alessandro , Ovchinnikov Vladimir , Herlyn Holger , Pierce Alexandra , Wu Charles , Aslanzadeh Morteza , Cheneby Jeanne , Martinez Pedro , Friedländer Marc R. , Hovig Eivind , Hackenberg Michael , Umu Sinan Uğur , Johansen Morten , Peterson Kevin J. , Fromm Bastian 
Published: September 2024

AbstractWe present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate species, including representatives of 5 previously unsampled phyla, and 6 mammal species. MirGeneDB now contains entries for 21, 822 microRNA genes (5, 160 of these from the new species) belonging to 1743 microRNA families. The inclusion of these new species allowed us to refine both the evolutionary node of appearance of a number of microRNA genes/families, as well as MirGeneDB’s phylogenetically informed nomenclature system. Updated covariance models of all microRNA families, along with all smallRNA read data are now downloadable. These enhanced annotations will allow researchers to analyze microRNA properties such as secondary structure and features of their biogenesis within a robust phylogenetic context and without the database plagued with numerous false positives and false negatives. In light of these improvements, MirGeneDB 3.0 will assume the responsibility for naming conserved novel metazoan microRNAs. MirGeneDB is part of RNAcentral and Elixir Norway, and is publicly and freely available atmaster.cloud.mirgenedb.org.Key PointsMajor update to the manually curated and uniformly named microRNA gene database MirGeneDB114 animal species, >1700 microRNA families and ∼20 000 genes searchable, browsable and downloadableNew features to download all smallRNA read data and updated covariance models for each family
novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection
Authors: Upadhyay Vikas , Anand Mohit , Maranas Costas D. 
Published: September 2024

AbstractComputational pathway design and retro-biosynthetic approaches can facilitate the development of innovative biochemical production routes, biodegradation strategies, and the funneling of multiple precursors into a single bioproduct. However, effective pathway design necessitates a comprehensive understanding of biochemistries, enzyme activities, and thermodynamic feasibility. Herein, we introduce novoStoic2.0, an integrated platform that combines tools for estimating overall stoichiometry, designing de novo synthesis pathways, assessing thermodynamic feasibility, and selecting enzymes. novoStoic2.0 offers a unified web-based interface as a part of the AlphaSynthesis platform (http://novostoic.platform.moleculemaker.org/) tailored for the synthesis of thermodynamically viable pathways as well as the selection of enzymes for re-engineering required for novel reaction steps. We exemplify the utility of the platform to identify novel pathways for hydroxytyrosol synthesis, which are shorter than the known pathways and require reduced cofactor usage. In summary, novoStoic2.0 aims to streamline the process of pathway design contributing to the development of sustainable biotechnological solutions.
Outer membrane changes enable evolutionary escape from bacterial predation
Authors: Mridha Subham , Loose Sarah-Luise , Mattmann Ove Ch. , Isele Saskia , Kümmerli Rolf , Huwiler Simona G. 
Published: September 2024

AbstractTo combat antimicrobial resistant pathogens, natural predatory bacteria, likeBdellovibrio bacteriovorus, represent potential alternatives.B. bacteriovoruscould be particularly potent as it kills a broad range of human bacterial pathogens, however, it remains unclear whether prey can evolve genetically-determined resistance against predation. Here, we show that the model bacteriumEscherichia coliK-12 consistently evolves resistance againstB. bacteriovorusduring experimental evolution. Selection for resistance scaled positively with predation pressure and was widespread after two cycles of predator exposure. Like antibiotics, predation resistance was costly, manifesting in a trade-off between predation resistance and fitness in the absence of predators. Genetic analysis identified changes in outer membrane porin OmpF as common resistance mechanism, while a mutation in cell envelope lipopolysaccharide-modifying enzyme WaaF was rarer but also conferred predation resistance. Our study uncovers evolutionary and mechanistic aspects of prey escape from predation, generating important knowledge on predator-prey interactions and to advance sustainable treatments.
Lymphatic dynamics visualized by native transient hypoxia imaging in areas of tissue damage, edema and in sentinel lymph nodes
Authors: Ochoa Marien I. , Reed Matthew S. , Zeng Weifeng , Poore Samuel O. , Hasan Tayyaba , Pogue Brian W. 
Published: October 2024

ABSTRACTImaging lymphatic compartments and their function has always been challenging, yet this capability is key to understanding the dynamics of immune response and lymph dysfunction in disease states. This study reports the first ever visualization of murine lymphatic pumping and function imaged from the inherent transient hypoxia that occurs within the lymph ducts and nodes. The lymphatic system appears as one of the few naturally hypoxic areas in vivo. Hypoxia in lymphatics is detected via delayed fluorescence (DF) of endogenous protoporphyrin IX (PpIX), enabling real-time imaging. Lymph nodes and their function were localized by hypoxia transcutaneous imaging and in surgically exposed nodes, followed by correlation of localization to indocyanine green (ICG) local injection. The lymphatic pumping frequency was altered through progressive damage from mild, moderate, and severe wound injuries, and hypoxia appeared readily in the sentinel lymph nodes near tumor regions. Cyclical pumping was observed at sites of edema and in nodes near tumors. Control data from uninjured anesthetized mice showed little lymphatic contrast, whereas awake mice exhibited hypoxia localized to lymph nodes. Unlike contrast injection-based regional lymph node imaging by ICG or MRI, DF hypoxia imaging appears to provide a natural whole-body contrast mechanism, highlighting its potential for visualizing lymphatic function and associated hypoxia dynamics. The value for localization of sentinel lymph nodes and for allowing for visualization of damaged lymph has very practical potential applications.
Improved robustness to gene tree incompleteness, estimation errors, and systematic homology errors with weighted TREE-QMC
Authors: Han Yunheng , Molloy Erin K. 
Published: October 2024

AbstractSummary methods are widely used to reconstruct species trees from gene trees while accounting for incomplete lineage sorting; however, it is increasingly recognized that their accuracy can be negatively impacted by incomplete and/or error-ridden gene trees. To address the latter, Zhang and Mirarab (2022) leverage gene tree branch lengths and support values to weight quartets within the popular summary method ASTRAL. Although these quartet weighting schemes improved the robustness of ASTRAL to gene tree estimation error, implementing the weighting schemes presented computational challenges, resulting in the authors abandoning ASTRAL’s original search algorithm (i.e., computing an exact solution within a constrained search space) in favor of search heuristics (i.e., hill climbing with nearest neighbor interchange moves from a starting tree constructed via randomized taxon addition). Here, we show that these quartet weighting schemes can be leveraged within the Quartet Max Cut framework of Snir and Rao (2010), with only a small increase in time complexity compared to the unweighted algorithm, which behaves more like a constant factor in our simulation study. Moreover, our new algorithm, implemented within the TREE-QMC software, was highly competitive with weighted ASTRAL, even outperforming it in terms of species tree accuracy on some challenging model conditions, such as large numbers of taxa. In comparing unweighted and weighted summary methods on two avian data sets, we found that weighting quartets by gene tree branch lengths improves their robustness tosystematichomology errors and is as effective as removing the impacted taxa from individual gene trees or removing the impacted gene trees entirely. Lastly, our study revealed that TREE-QMC is highly robust to high rates of missing data and is promising as a supertree method. TREE-QMC is written in C++ and is publicly available on Github:https://github.com/molloy-lab/TREE-QMC