bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distance between miRNA responsive elements selectively enhances target specificity with reduced cellular toxicity by miRNA-mediated synergism
Authors: Mazumder Sayani , Banerjee Urbee , Sinsinwar Simran , Mandal Saubhik , Prusty Debashis , Babele Prabhakar , Das Bhabatosh , Manna Soumen , Ray Jay Gopal , Chatterjee Raghunath 
Published: August 2024

ABSTRACTDespite the emergence of miRNAs as a promising therapeutic tool in cancer management, most of the clinical trials were not successful due to their cytotoxic effects. Here, we investigated the synergistic effect of miRNA-pairs on enhancing target specificity and reducing cellular toxicity by minimizing off-target effects. Synergistic reductions by the miRNA-pairs were observed only for the common target genes having 3’-UTRs with miRNA responsive elements (MREs) within a distance between 200-800bp. Deletions of either of the miRNA seed sequence resulted in a loss of synergism. Furthermore, to study the miRNA mediated synergism in cancer cells, we cotransfected oral cancer cells with reduced doses of miRNA-pairs and determined the expressions of their common and unique target genes at both gene and protein levels. Over expressions of miRNA-pairs significantly reduced cell proliferation, migration, and spheroid formation in cancer cells compared to those with the single miRNA. Proteomic data revealed that the let-7c-5p and miR-125b-5p miRNA-mimic pairs synergistically reduced the expressions of their common target genes, hexokinase 2 (HK2) and branched chain amino acid transaminase 1 (BCAT1). The unique target genes did not exhibit any significant synergistic down-regulation in their protein levels. Metabolomic analysis consistently reflected the effect of HK2 and BCAT1 downregulation by affecting the glycolysis and the BCAA degradation pathways, suggesting the importance of this strategy in enhancing the efficacy of miRNA-mimics in cancer therapy.
Acute stress causes sex-dependent changes to ventral subiculum synapses, circuitry, and anxiety-like behavior
Authors: Miller Carley N , Li Yuan , Beier Kevin T , Aoto Jason 
Published: August 2024

AbstractExperiencing a single severe stressor is sufficient to drive sexually dimorphic psychiatric disease development. The ventral subiculum (vSUB) emerges as a site where stress may induce sexually dimorphic adaptations due to its sex-specific organization and pivotal role in stress integration. Using a 1-hr acute restraint stress model, we uncover that stress causes a net decrease in vSUB activity in females that is potent, long-lasting, and driven by adrenergic receptor signaling. By contrast, males exhibit a net increase in vSUB activity that is transient and driven by corticosterone signaling. We further identified sex-dependent changes in vSUB output to the bed nucleus of the stria terminalis and in anxiety-like behavior in response to stress. These findings reveal striking changes in psychiatric disease-relevant brain regions and behavior following stress with sex-, cell-type, and synapse-specificity that contribute to our understanding of sex-dependent adaptations that may shape stress-related psychiatric disease risk.HighlightsvSUB BS cells are uniquely stress sensitiveStress causes sex-dependent changes to BS cell E/I balanceStress causes sex-dependent changes to vSUB activity to aBNSTin vivoStress causes anxiety-like behavior in females, but not males
Engineering ionizable lipids for rapid biodegradation balances mRNA vaccine efficacy and tolerability
Authors: Couture-Senécal Julien , Tilstra Grayson , Khan Omar F. 
Published: August 2024

AbstractThe optimization of lipid nanoparticles (LNPs) has played a key role in enhancing the efficacy of mRNA vaccines, yet challenges with LNP tolerability remain. The ionizable lipid component within LNPs is critical to the efficient delivery of mRNA. Ionizable lipids can also trigger innate immune activation, which is beneficial for vaccine efficacy but may contribute to adverse inflammatory reactions. Engineering ionizable lipids for rapid biodegradation is a promising, yet underexplored, strategy to dampen inflammation. Here, we report the rational design and optimization of biodegradable ionizable lipids for intramuscular mRNA vaccines in mice. We show that in vivo biodegradability is enhanced by controlling lipid hydrolysis kinetics and that protein output is maximized by tuning the LNP apparent pKa. In an influenza vaccine model, the lead lipid (δO3) generates equivalent neutralizing antibodies and stronger antigen-specific T cell responses compared to a benchmark lipid (SM-102) used in approved mRNA vaccines. Furthermore, by comparing ionizable lipid analogs with similar potency but opposing biodegradation kinetics, we find that faster lipid clearance from tissues coincides with a lower inflammatory response while preserving strong vaccine immunogenicity. These findings demonstrate that fast-degrading ionizable lipids can balance the efficacy and tolerability of mRNA vaccines, with implications for addressing side effects and patient acceptance of new vaccine applications.
Modeling glioblastoma tumor progression via CRISPR-engineered brain organoids
Authors: Ishahak Matthew , Han Rowland H. , Annamalai Devi , Woodiwiss Timothy , McCornack Colin , Cleary Ryan T. , DeSouza Patrick A. , Qu Xuan , Dahiya Sonika , Kim Albert H. , Millman Jeffrey R. 
Published: August 2024

ABSTRACTGlioblastoma (GBM) is an aggressive form of brain cancer that is highly resistant to therapy due to significant intra-tumoral heterogeneity. The lack of robust in vitro models to study early tumor progression has hindered the development of effective therapies. Here, we develop engineered GBM organoids (eGBOs) harboring GBM subtype-specific oncogenic mutations to investigate the underlying transcriptional regulation of tumor progression. Single-cell and spatial transcriptomic analyses revealed that these mutations disrupt normal neurodevelopment gene regulatory networks resulting in changes in cellular composition and spatial organization. Upon xenotransplantation into immunodeficient mice, eGBOs form tumors that recapitulate the transcriptional and spatial landscape of human GBM samples. Integrative single-cell trajectory analysis of both eGBO-derived tumor cells and patient GBM samples revealed the dynamic gene expression changes in developmental cell states underlying tumor progression. This analysis of eGBOs provides an important validation of engineered cancer organoid models and demonstrates their utility as a model of GBM tumorigenesis for future preclinical development of therapeutics.
Landscape of Differentiation Potentials as a “Hallmark” in Oral-derived MSCs
Authors: Chopra H , Cao C , Alice H , Kak S , Maska B , Tagett R , Sugai J , Garmire L , Kaigler D 
Published: August 2024

AbstractBackgroundMesenchymal stem cells (MSCs) offer clinical promise for use in cell therapy approaches for regenerative medicine. A therapeutic challenge is that MSCs from different tissues are phenotypically and functionally distinct. Therefore, this study aims to molecularly characterize oral-derived MSCs by defining one of the three hallmarks of MSCs, differentiation potential, to discern their true molecular identities.MethodsThree different populations of oral tissue MSCs (from alveolar bone-aBMSCs; from dental pulp-DPSCs; and from gingiva-GMSCs) from three different patients were isolated and cultured. These MSCs were characterized for their stemness by flow cytometry and multi-differentiation potential, and their RNA was also isolated and analyzed quantitatively with RNA sequencing. Total mRNA-seq was performed and differentially expressed genes (DEGs) were identified in pairwise (DPSCs vs. aBMSCs, GMSCs vs. aBMSCs, and GMSCs vs. DPSCs) and tissue-specific comparisons (aBMSCs vs. Others, DPSCs vs. Others, GMSCs vs. Others) (FDR,p<0.05). Further, these DEGs, either common between MSC populations or unique to a specific MSC population, were evaluated for pathways and biological processesResultsaBMSCs, DPSCs, and GMSCs were successfully isolated and characterized. The tissue-specific comparison revealed that DEGs were most numerous in DPSCs (693 genes) as compared to aBMSCs (103 genes) or DPSCs (232 genes). Statistically significant DEGs through pairwise comparisons present higher numbers in GMSCs vs. DPSCs (627) as compared to either DPSCs vs aBMSCs (286) or GMSCs vs. aBMSCs (82). Further analysis found that RUNX2, IBSP, SOX6, ACAN, and VCAM1 were significantly upregulated in aBMSCs. In DPSCs, BMP4 and IL6 were significantly downregulated, whereas AXL and NES were significantly upregulated. In GMSCs, AGPT1, SEMA4D, and PGDFA were significantly downregulated. Additionally, MAPK, PI3-AKT, and RAS signaling pathways were significantly regulated in GMSCs. Interestingly, aBMSCs and DPSCs revealed positive regulation of osteoblast differentiation, whereas GMSCs revealed negative regulation of osteoblast differentiation. DPSCs also revealed negative regulation of angiogenesis.ConclusionsOral-derived MSCs have an inherent “landscape” of differentiation defined by their tissue of origin; yet this differentiation potential can be modulated by their microenvironment.Graphical Abstract
Enhanced replication of contemporary human highly pathogenic avian influenza H5N1 virus isolate in human lung organoids compared to bovine isolate
Authors: Flagg Meaghan , Williamson Brandi N. , Ortiz-Morales Johan A. , Lutterman Tessa R. , de Wit Emmie 
Published: August 2024

AbstractWe compared virus replication and host responses in human alveolar epithelium infected with highly pathogenic avian influenza (HPAI) H5N1 viruses. A/Vietnam/1203/2004 replicated most efficiently, followed by A/Texas/37/2024, then A/bovine/Ohio/B24OSU-342/2024. Induction of interferon-stimulated genes was lower with A/Texas/37/2024 and A/bovine/Ohio/B24OSU-342/2024, which may indicate a reduced disease severity of these viruses.
The estrous cycle modulates hippocampal spine dynamics, dendritic processing, and spatial coding
Authors: Wolcott Nora S. , Redman William T. , Karpinska Marie , Jacobs Emily G. , Goard Michael J. 
Published: August 2024

AbstractHistological evidence suggests that the estrous cycle exerts a powerful effect on CA1 neurons in mammalian hippocampus. Decades have passed since this landmark observation, yet how the estrous cycle shapes dendritic spine dynamics and hippocampal spatial codingin vivoremains a mystery. Here, we used a custom hippocampal microperiscope and two-photon calcium imaging to track CA1 pyramidal neurons in female mice over multiple cycles. Estrous cycle stage had a potent effect on spine dynamics, with heightened density during periods of greater estradiol (proestrus). These morphological changes were accompanied by greater somatodendritic coupling and increased infiltration of back-propagating action potentials into the apical dendrite. Finally, tracking CA1 response properties during navigation revealed enhanced place field stability during proestrus, evident at the single-cell and population level. These results establish the estrous cycle as a driver of large-scale structural and functional plasticity in hippocampal circuits essential for learning and memory.
Untrimmed ITS2 metabarcode sequences cause artificially reduced abundances of specific fungal taxa
Authors: Kyle Kathleen E. , Klassen Jonathan L. 
Published: August 2024

AbstractAdvances in DNA metabarcoding have greatly expanded our knowledge of microbial communities in recent years. Pipelines and parameters have been tested extensively for bacterial metabarcoding using the 16S rRNA gene and best practices are largely established. For fungal metabarcoding using the ITS gene, however, only a few studies have considered how such pipelines and parameters can affect community prediction. Here we report a novel bias uncovered during ITS2 sequencing ofTrichoderma-infected ant fungus gardens and confirmed using mock communities. Abnormally low forward read quality causedTrichodermaITS2 reads to be computationally filtered before and during read pair merging, thus almost entirely eliminatingTrichodermaASVs from the resulting fungal community profiles. Sliding window quality trimming before filtering allowed most of these reads to pass filtering and merge successfully, producing community profiles that now correlated with visual signs ofTrichodermainfection and matched the composition of the mock communities. Applying such sliding window trimming to a previously generated environmental ITS2 dataset increased the detected fungal diversity and again overcame read quality biases againstTrichodermato instead detect it in nearly every sample and often at high relative abundances. This analysis additionally identified a similar, but distinct, bias against a second fungal genusMeyerozyma. The prevalence of such quality biases against other fungal ITS sequences is unknown but may be widespread. We therefore advocate for routine use of sliding window quality trimming as a best practice in ITS2 metabarcoding analysis.ImportanceMetabarcode sequencing produces DNA abundance profiles that are presumed to reflect the actual microbial composition of the samples that they analyze. However, this assumption is not always tested, and taxon-specific biases are often not apparent, especially for low-abundance taxa in complex communities. Here we identified ITS2 read quality aberrations that caused dramatic reductions in the relative abundances of specific taxa in multiple datasets characterizing ant fungus gardens. Such taxon-specific biases in read quality may be widespread in other environments and for other fungal taxa, thereby causing incorrect descriptions of these mycobiomes.
The study on the impact of indoleacetic acid on enhancing the ability of the rumen’s original microecology to degrade aflatoxin B1
Authors: Sun Jiajin , Wang Zhonghao , Yan Xinyu , Zhao Yuqi , Tan Li , Miao Xuning , Zhao Rong , Huo Wenjie , Chen Lei , Li Qinghong , Liu Qiang , Wang Cong , Guo Gang 
Published: August 2024

AbstractAflatoxin B1 (AFB1) poses a serious threat to the health of cattle and is strictly monitored in their diets. Rumen microorganisms in cattle have the ability to degrade AFB1, but this capability is limited. Enhancing the degradation capacity of the original rumen microecology for AFB1 is a novel approach. From a molecular perspective,indoleacetic-3-acid (IAA) promotes the expression of cytochromes, which can improve the degradation of AFB1. Therefore, this study aims to investigate the impact of different concentrations of IAA on the degradation of AFB1 by the rumen microecology. Experiments used rumen fluid from three adult cows as donors, and the cows were all fed the same total mixed ration. Rumen fluid was collected from these three cannulated cows before morning feeding to prepare in vitro fermentation fluid. The experiments used a completely randomized design, with each treatment repeated four times. The results showed that as the fermentation time increased, the content of AFB1 gradually decreased, with a degradation rate of up to 75.73% after 24 h. AFB1 altered the rumen fermentation pattern, with a significant reduction in the content of acetic acid (P<0.05) and a significant decrease in the acetic acid to propionic acid ratio (P<0.05). It also affected the rumen microecology, causing a significant reduction in the abundance ofRuminococcus amylophilus, Prevotella ruminicola, andFusobacterium succinogenes(P<0.05). In addition, this study found that with the increase in the amount of IAA added, the content of AFB1 in the rumen gradually decreased. IAA enhances the degradation capacity of the original rumen microecology for AFB1, and the addition of IAA alleviates the impact of AFB1 onRuminococcus amylophilus, Prevotella ruminicola, andFusobacterium succinogenesin the rumen (P<0.05). Moreover, the addition of IAA can promote the stability of the rumen microecology, with significantly higher acetic acid and acetic acid to propionic acid ratios in the fermentation fluid compared to the non-added group (P<0.05). In summary, the addition of IAA can improve the degradation capacity of the rumen microecology for AFB1, providing a new solution for alleviating the impact of AFB1 on animal health.
Spatial variability of agricultural soil carbon dioxide and nitrous oxide fluxes: characterization and recommendations from spatially high-resolution, multi-year dataset
Authors: Kim Nakian , Jang Chunhwa , Yang Wendy H. , Guan Kaiyu , DeLucia Evan H. , Lee DoKyoung 
Published: August 2024

AbstractMitigating agricultural soil greenhouse gas (GHG) emissions can contribute to meeting the global climate goals. High spatial and temporal resolution, large-scale, and multi-year data are necessary to characterize and predict spatial patterns of soil GHG fluxes to establish well-informed mitigation strategies, but not many of such datasets are currently available. To address this gap in data we collected two years of high spatial resolution (7.4 sampling points ha−1over 2.0 to 5.4 ha area) in-season soil carbon dioxide (CO2) and nitrous oxide (N2O) fluxes from three commercial sites in central Illinois, one conventionally managed continuous corn and two under conservation practices in corn-soybean rotations typical of the region. At the field-scale, the spatial variability of CO2was comparable across sites, years, and management practices, but N2O was on average 77% more spatially variable in the conventionally managed site. Analysis of N2O hotspots revealed that although they represent a similar proportion of the sampling areas across sites (conventional: 12%; conservation: 13%), hotspot contribution to field-wide emission was greater in the conventional site than in the conservation sites (conventional: 51%; conservation: 34%). Also, the spatial patterns, especially hotspot locations, of both gases were inter-annually inconsistent, with hotspots rarely occurring in the same location. Overall, our result indicated that traditional field-scale monitoring with gas chambers may not be the optimal approach to detect GHG hotspots in row crop systems, due to the unpredictable spatial heterogeneity of management practices. Still, our sensitivity analysis on the dataset demonstrated that sampling at a spatial resolution of 1.6 and 5.6 points ha−1can provide reliable (< 25% error) estimates of field-scale soil CO2and N2O fluxes, respectively.
Generation of antagonistic biparatopic anti-CD30 antibody from an agonistic antibody by precise epitope determination and utilization of structural characteristics of CD30 molecule
Authors: Akiba Hiroki , Ise Tomoko , Satoh Reiko , Abe Yasuhiro , Tsumoto Kouhei , Ohno Hiroaki , Kamada Haruhiko , Nagata Satoshi 
Published: August 2024

AbstractCD30 is a type I membrane protein that has been successfully targeted for lymphoma therapy using Brentuximab vedotin, an antibody-drug conjugate. Recently, the potential of blocking CD30-dependent NF-κB intracellular signaling has gained attention for treating inflammatory disorders. Development of antibody-based CD30 antagonists would broaden therapeutic strategies. A challenge in developing antagonistic antibodies is that the bivalent form of natural antibody format inevitably cross-links trace amounts of CD30 molecules, leading to signal transduction. In this study, we developed a series of biparatopic antibodies with each pair of antibody variable domains (Fvs) binding to distinct epitopes on CD30, and evaluated their biological activities and binding modes. Initially, we precisely identified epitope sites of the nine antibodies precisely by assessing binding to multiple orthologous CD30 proteins and mutants. We then produced 36 biparatopic antibodies covering all possible combinations of the nine Fvs, and analyzed their biological activities. Among these, we identified both potent agonists and antagonists. Notably, a significant proportion of the biparatopic antibodies displayed reduced agonistic activities, including 1:1-binding antagonists derived from a Fv of a strong agonist previously developed for lymphoma therapy, AC10. The mechanism of signaling activity induction is discussed using epitope information, which leads to the strategies of the development of biparatopic antibodies.
Gut Microbiome Perturbation Affected Conjugative Transfer of Antimicrobial Resistance Genes
Authors: Yilmaz Gokhan , Chan Maria , Lau Calvin Ho-Fung , Capitani Sabrina , Kang Mingsong , Charron Philippe , Hoover Emily , Topp Edward , Guan Jiewen 
Published: August 2024

AbstractThe global spread of antimicrobial resistance genes (ARGs) poses a significant threat to public health. While antibiotics effectively treat bacterial infections, they can also induce gut dysbiosis, the severity of which varies depending on the specific antibiotic treatment used. However, it remains unclear how gut dysbiosis affects the mobility and dynamics of ARGs. To address this, mice were pre-treated with streptomycin, ampicillin, or sulfamethazine, and then orally inoculated withSalmonella entericaserovar Typhimurium andS. Heidelberg carrying a multi-drug resistance IncA/C plasmid. The streptomycin pre- treatment caused severe microbiome perturbation, promoting high-density colonization ofS. Heidelberg andS. Typhimurium, and enabling IncA/C transfer fromS. Heidelberg toS. Typhimurium and a commensalEscherichia coli. The ampicillin pre-treatment induced moderate microbiome perturbation, supporting onlyS. Heidelberg colonization and IncA/C transfer to commensalE. coli. The sulfamethazine pre-treatment led to mild microbiome perturbation, favoring neitherSalmonella spp. colonization nor conjugative plasmid transfer. The degree of gut dysbiosis also influenced the enrichment or depletion of ARGs associated with mobile plasmids or core commensal bacteria, respectively. These findings underscore the significance of pre-existing gut dysbiosis induced by various antibiotic treatments on ARG dissemination and may inform prudent antibiotic use practices.
Phylogeny, morphology, and behavior of the new ciliate speciesStentor stipatus
Authors: Rajan D. , Lee B. , Albright A. , Tang E. , Maravillas A. , Vargas C. , Marshall W. F. , Cortes D. 
Published: August 2024

ABSTRACTThe study of evolution at the cellular level traditionally has focused on the evolution of metabolic pathways, endomembrane systems, and genomes, but there has been increasing interest in evolution of more complex cellular structures and behaviors, particularly in the eukaryotes. Ciliates have major advantages for such studies due to their easily visible surface patterning and their dramatic and complex behaviors that can be easily analyzed. Among the ciliates, the genusStentorepitomizes the features that are useful for studying evolution: they are widespread in freshwater environments, easy to visualize because of their large size, and capable of complex behaviors such as learning, decision-making, and phototaxis.Here, we introduce the discovery of a new species within this genus:Stentor stipatus, so named for their distinctive dark brown aggregates. We present morphological, phylogenetic, ecological, and behavioral characterizations of these cells. TheS. stipatusclade has a bootstrap value of 93 and is phylogenetically distinct fromS. amethystinus, the closest related species which shares a sequence similarity of 98.9%.S. stipatusis capable of phototaxis and can also habituate more quickly thanS. coeruleus, theStentorspecies in which most habituation studies have previously been conducted. These findings expand our understanding ofStentorspecies diversity, natural history, and demonstrate common principles of complex behavior that are present in single-celled organisms.