bluuebunny/crossref_metadata_2025 huggingface dataset:
Human populations with low survival at advanced ages and postponed fertility reduce long-term growth in high inflation environments
Authors: Mondal Rahul , Aburto José Manuel , Sear Rebecca , Tuljapurkar Shripad , Mishra Uday Shankar , Salguero-Gómez Roberto
Published: August 2024

Temporal variability in inflation can lead to important fluctuations in the long-term growth rate of human populations via their differential impacts on vital rates like survival and fertility. However, historically, demographic studies have overlooked this time-dependent relationship. Here, we test whether human populations have higher stochastic population growth rates when exposed to lower levels of inflation. We also examine if lower survival rates at older ages (>60 years) and fertility rates at the later reproductive years (>30 years) among populations exposed to higher inflation rates determine their expected lower long-term growth rate compared to those exposed to lower inflation rates. To explore the impact of variability in inflation on vital rates response, we develop a quantitative pipeline with four steps, and parameterise it with high-resolution economic and demographic data across 76 countries from 1971-2021. The four steps are (1) defining treatment groups based on levels of trend inflation (creeping inflation (0-3%), walking inflation (3-10%), galloping inflation (10-50%), and hyperinflation (>50%)) among which the stochastic population growth rates will be compared; (2) constructing matrix population models for each environmental state under every treatment. The environmental states for each treatment are defined on the basis of the duration of inflation (e.g., 0, 2, 4, six years or above); (3) estimating the stochastic population growth rate for each treatment by considering a Markovian environment dictated by the long-term frequency (f) and temporal autocorrelation (p) of the treatment; and (4) decomposing the differences in the population growth rate between treatments into contributions from environmental variability and vital rate differences between environments to test how vital rates impact on population growth under varying environmental scenarios. In agreement with our hypothesis, we find that the stochastic population growth rate at lower levels of inflation is systematically higher than that at a higher level of inflation at all stationary frequencies and temporal autocorrelation of the inflation environment. Moreover, the disadvantage in survival at older ages (>60 years) and fertility at ages >30 years led to the lower stochastic growth rate among populations exposed to higher level of inflation such as walking inflation compared to lower level of inflation, such as creeping inflation. Our framework explicitly links human population performance and inflation environment by describing nonlinear feedback between inflation, human survival, fertility, population growth, and its age structure. We discuss the potential of our approach to study the life-history strategies and population dynamics of a wide range of drivers of environmental variability.
Comprehensive transcription factor perturbations recapitulate fibroblast transcriptional states
Authors: Southard Kaden M. , Ardy Rico C. , Tang Anran , O’Sullivan Deirdre D. , Metzner Eli , Guruvayurappan Karthik , Norman Thomas M.
Published: August 2024

Cell atlas projects have nominated recurrent transcriptional states as drivers of biological processes and disease, but their origins, regulation, and properties remain unclear. To enable complementary functional studies, we developed a scalable approach for recapitulating cell statesin vitrousing CRISPR activation (CRISPRa) Perturb-seq. Aided by a novel multiplexing method, we activated 1,836 transcription factors in two cell types. Measuring 21,958 perturbations showed that CRISPRa activated targets within physiological ranges, that epigenetic features predicted activatable genes, and that the protospacer seed region drove an off-target effect. Perturbations recapitulatedin vivofibroblast states, including universal and inflammatory states, and identifiedKLF4andKLF5as key regulators of the universal state. Inducing the universal state suppressed disease-associated states, highlighting its therapeutic potential. Our findings cement CRISPRa as a tool for perturbing differentiated cells and indicate thatin vivostates can be elicited via perturbation, enabling studies of clinically relevant statesex vivo.
Investigating the links between trifluralin persistence in Western Australian soils and trifluralin resistance in resident annual ryegrass (Lolium rigidum) populations
Authors: Goggin Danica , Boyes Tim , Busi Roberto , Flower Ken
Published: August 2024

The pre-emergence herbicide trifluralin is widely used in the minimum-tillage cropping systems of Australia, with the result that resistance to trifluralin is increasing in the major weed of the region, annual ryegrass (Lolium rigidum). Repeated exposure to low herbicide rates is also known to result in the rapid evolution of resistance in weed populations. As trifluralin is highly volatile, readily photo-decomposed, metabolised by soil microbes and to bind strongly to soil organic matter, there are many factors that could result in weed populations receiving reduced (even sub-lethal) rates of the herbicide. To investigate whether trifluralin dissipation could play a role in the increasing levels of trifluralin resistance in annual ryegrass, resistance levels of populations from 18 Western Australian farms were compared with the dissipation rate of trifluralin applied to soil collected from these farms. Although there was no direct correlation between resistance level and trifluralin half-life, there were links between resistance and soil properties which suggest that higher rates of trifluralin dissipation could make a minor contribution to the development of resistance.
MOSTPLAS: A Self-correction Multi-label Learning Model for Plasmid Host Range Prediction
Authors: Zou Wei , Ji Yongxin , Guan Jiaojiao , Sun Yanni
Published: August 2024

Plasmids play an essential role in horizontal gene transfer among diverse microorganisms, aiding their host bacteria in acquiring beneficial traits like antibiotic and metal resistance. Identifying the host bacteria where a plasmid can transfer, replicate or persist provides insights into how plasmids promote bacterial evolution. Plasmid host range prediction tools can be categorized as alignment-based and learning-based. Alignment-based tools have high precision but fail to align many newly sequenced plasmids with characterized ones in reference databases. In contrast, learning-based tools help predict the host range of these newly discovered plasmids. Although previous researches have demonstrated the existence of broad-host-range (BHR) plasmids, there is no database providing their detailed and complete host labels. Without adequate well-annotated training samples, learning-based tools fail to extract discriminative feature representations and obtain limited performance. To address this problem, we propose a self-correction multi-label learning model called MOSTPLAS. We design a pseudo label learning algorithm and a self-correction asymmetric loss to facilitate the training of multi-label learning model with samples containing some unknown missing positive labels. Experimental results on multi-host plasmids generated from the NCBI RefSeq database, metagenomic data, and real-world plasmid sequences with experimentally determined host range demonstrate the superiority of MOSTPLAS.
Lack of pathogenic involvement of CCL4 and its receptor CCR5 in arthritogenic alphavirus disease
Authors: Hameed Muddassar , Solomon Norman A. , Weger-Lucarelli James
Published: August 2024

Arthritogenic alphaviruses, including chikungunya virus (CHIKV), Mayaro virus (MAYV), Ross River virus (RRV), and O’nyong nyong virus (ONNV) are emerging and reemerging viruses that cause disease characterized by fever, rash, and incapacitating joint swelling. Alphavirus infection induces robust immune responses in infected hosts, leading to the upregulation of several cytokines and chemokines, including chemokine C ligand 4 (CCL4). CCL4 is a chemoattractant for immune cells such as T cells, natural killer cells, monocytes/macrophages, and dendritic cells, recruiting these cells to the site of infection, stimulating the release of proinflammatory mediators, and inducing T cell differentiation. CCL4 has been found at high levels in both the acute and chronic phases of chikungunya disease; however, the role of CCL4 in arthritogenic alphavirus disease development remains unexplored. Here, we tested the effect of CCL4 on MAYV infection in mice through antibody depletion and treatment with recombinant mouse CCL4. We observed no differences in mice depleted of CCL4 or treated with recombinant CCL4 in terms of disease progression such as weight loss and footpad swelling or the development of viremia. CCL4 uses the G protein-coupled receptor C-C chemokine receptor type 5 (CCR5). To determine whether CCR5 deficiency would alter disease outcomes or virus replication in mice, we inoculated CCR5 knockout (CCR5-/-) mice with MAYV and observed no effect on disease development and immune cell profile of blood and footpads between CCR5-/-and wild type mice. These studies failed to identify a clear role for CCL4 or its receptor CCR5 in MAYV infection.
Target enrichment phylogenomics and biogeographic analyses unravel rapid radiation and reticulate evolution between Hainan-South China mainland -Vietnam in SectionNintooa(Lonicera, Caprifoliaceae)
Authors: Zuo Shi-You , Sun Qing-Hui , Morales-Briones Diego F. , Wang Hong-Xin , Landis Jacob B. , Li Hong-Yang , Dong Hong-Jin , Wen Jun , Wang Hua-Feng
Published: August 2024

The South China mainland and nearby islands are biodiversity hotspots. SectionNintooa, widely distributed across mainland China, Vietnam, and Hainan Island, exhibits a typical disjunct distribution pattern. However, the origins of the flora of Hainan Island and the phylogenetic relationships within SectionNintooaremain contentious. In this study, we collected 81 samples encompassing all recognized species of SectionNintooa, along with samples from other sections ofLonicera. We reconstructed the phylogenetic relationships using 491 orthologous nuclear genes and complete plastomes generated by target enrichment and genome skimming sequencing. Our nuclear gene-based species and concatenated trees support the monophyly of SectionNintooa. The species tree indicates that the Vietnamese and Hainan populations form sister clades. However, the plastome results indicate that SectionNintooais polyphyletic, with subsectionVolubilisforming a monophyletic group and subsectionCalcarataeforming a sister clade with other members of subgenusChamaecerasus. Our hybridization network analysis reveals extensive gene flow within SectionNintooa, whereas subsectionCalcarataeshows no gene flow with subsectionVolubilis, leaving the origin ofCalcarataeunclear.Loniceraspecies from Hainan Island exhibit unstable phylogenetic positions and underwent a rapid radiation during the Miocene. Biogeographical results indicate that populations from Vietnam and Hainan both originated from mainland China. Overall, our findings enhance the understanding of the evolutionary diversification history ofLonicera.
Targeting mechanistic target of rapamycin complex 2 attenuates immunopathology in Systemic Lupus Erythematosus
Authors: Ai Minji , Zhou Xian , Carrer Michele , Jafar-nejad Paymaan , Li Yanfeng , Gades D.V.M. Naomi , Alexander Mariam , Bautista Mario A. , Duarte Garcia Ali A. , Zeng Hu
Published: August 2024

Objective

We aim to explore the role of mechanistic target of rapamycin complex (mTORC) 2 in systemic lupus erythematosus (SLE) development, the invivoregulation of mTORC2 by type I interferon (IFN) signaling in autoimmunity, and to use mTORC2 targeting therapy to ameliorate lupus-like symptoms in anin vivolupus mouse model and anin vitrococulture model using human PBMCs.

Method

We first induced lupus-like disease in T cell specificRictor, a key component of mTORC2, deficient mice by topical application of imiquimod (IMQ) and monitored disease development. Next, we investigated the changes of mTORC2 signaling and immunological phenotypes in type I IFNAR deficient Lpr mice. We then tested the beneficial effects of anti-Rictorantisense oligonucleotide (Rictor-ASO) in a mouse model of lupus: MRL/lprmice. Finally, we examined the beneficial effects ofRICTOR-ASO on SLE patients’ PBMCs using anin vitroT-B cell coculture assay.

Results

T cell specificRictordeficient mice have reduced age-associated B cells, plasma cells and germinal center B cells, and less autoantibody production than WT mice following IMQ treatment. IFNAR1 deficient Lpr mice have reduced mTORC2 activity in CD4+T cells accompanied by restored CD4+T cell glucose metabolism, partially recovered T cell trafficking, and reduced systemic inflammation.In vivo Rictor-ASO treatment improves renal function and pathology in MRL/lprmice, along with improved immunopathology. In human SLE (N = 5) PBMCs derived T-B coculture assay,RICTOR-ASO significantly reduce immunoglobulin and autoantibodies production (P < 0.05).

Conclusion

Targeting mTORC2 could be a promising therapeutic for SLE.
Exploration of the Metabolomic Mechanisms of Postmenopausal Hypertension Induced by Low Estrogen State
Authors: Li Yao , Xin Hui , Lian Zhexun , Zhang Wei
Published: August 2024

Background

Estrogen significantly impacts women’s health, and postmenopausal hypertension is a common issue characterized by blood pressure fluctuations. Current control strategies for this condition are limited in efficacy, necessitating further research into the underlying mechanisms. Although metabolomics has been applied to study various diseases, its use in understanding postmenopausal hypertension is scarce.

Methods

An ovariectomized rat model was used to simulate postmenopausal conditions. Estrogen levels, blood pressure, and aortic tissue metabolomics were analyzed. Animal models were divided into Sham, OVX, and OVX+E groups. Serum estrogen levels, blood pressure measurements, and aortic tissue metabolomics analyses were performed using radioimmunoassay, UHPLC-Q-TOF, and bioinformatics techniques.

Results

The study successfully established a correlation between low estrogen levels and postmenopausal hypertension in rats. Notable differences in blood pressure parameters and aortic tissue metabolites were observed across the experimental groups. Specifically, metabolites that were differentially expressed, particularly L-alpha-aminobutyric acid (L-AABA), showed potential as a biomarker for postmenopausal hypertension, potentially exerting a protective function through macrophage activation and vascular remodeling. Enrichment analysis revealed alterations in sugar metabolism pathways, such as the Warburg effect and glycolysis, indicating their involvement in postmenopausal hypertension.

Conclusion

This research provides insights into the metabolic changes associated with postmenopausal hypertension, highlighting the role of AABA and sugar metabolism reprogramming in aortic tissue. The findings suggest a potential link between low estrogen levels, macrophage function, and vascular remodeling in the pathogenesis of postmenopausal hypertension. Further investigations are needed to validate these findings and explore their clinical implications for postmenopausal women.
A map of integrated cis-regulatory elements enhances gene regulatory analysis in maize
Authors: Manosalva Pérez Nicolás , Staut Jasper , Ferrando Andrés Matres , Dissanayake Indeewari , Vandepoele Klaas
Published: August 2024

Cis-regulatory elements (CREs) are non-coding DNA sequences that modulate gene expression. Their identification is critical to study the transcriptional regulation of genes controlling key traits that govern plant growth and development. They are also crucial components for the delineation of gene regulatory networks, which represent regulatory interactions between transcription factors (TFs) and target genes. In maize, CREs have been profiled using different computational and experimental methods, but the extent to which these methods complement each other in identifying functional CREs is unclear. Here, we report the data-driven integration of different maize CRE profiling methods to optimize the capture of experimentally-confirmed TF binding sites, resulting in maps of integrated CREs (iCREs) showing increased levels of completeness and precision. We combined the iCREs with a wide diversity of gene expression data under drought conditions to perform motif enrichment and infer drought-specific GRNs. Mining these organ-specific GRNs revealed previously characterized and novel candidate regulators of maize drought response. Furthermore, by studying the transposable elements (TEs) overlapping with iCREs, we identified few TE superfamilies displaying typical epigenetic features of regulatory DNA that are potentially involved in wiring specific TF-target gene regulatory interactions. Overall, our study showcases the integration of different omics data sources to generate a high-quality collection of CREs, together with their applicability to better characterize gene regulation in the complex maize genome.
A causative SNP in the promoter of myogenin is essential for myogenic differentiation
Authors: Lin Zhuhu , Wang Xiaoyu , Liang Ziyun , Xu Rong , Chen Meilin , Tong Xian , Li Chenggan , Xiong Yanyun , Yuan Renqiang , Chen Yaosheng , Zhao Yunxiang , Liu Xiaohong , Mo Delin
Published: August 2024

Single nucleotide polymorphisms (SNPs) widely existing in different breeds genome represent population-specific. Under the influence of long-term evolution and artificial selection, there are a large number of SNPs between western lean-type pig breeds and Chinese indigenous pig breeds, but until now, little is known about their roles in inter-breed differences. Our study revealed SNP rs3471653254 C>T generated from the two types of pigs mentioned above, located in the promoter shared by MyoG and Myoparr, played an important role in the differentiation of myoblast by influencing the enrichment of HOXA5 to regulate the transcription of MyoG and Myoparr. Meanwhile, Myoparr could be used as the sponge of mir-30b-3p which repressed myogenic differentiation and muscle regeneration through targeting MyoD. Our results indicated that SNP rs3471653254 C>T is essential for myogenic differentiation and regeneration and could be used as an ideal site for increasing lean meat production in pigs.
Loss function of tumor suppressor FRMD8 confers resistance to tamoxifen therapy via a dual mechanism
Authors: Wu Weijie , Yu Miao , Li Qianchen , Zhao Yiqian , Zhang Lei , Sun Yi , Wang Zhenbin , Gong Yuqing , Wang Wenjing , Liu Chenying , Zhang Jing , Tang Yan , Xu Xiaojie , Guo Xiaojing , Zhan Jun , Zhang Hongquan
Published: August 2024

Approximately 40% ERα-positive breast cancer patients suffer from therapeutic resistance to tamoxifen. Although reduced ERα level is the major cause of tamoxifen resistance, the underlying mechanisms remain elusive. Here, we report that FRMD8 raises the level of ERα at both transcriptional and post-translational layers. FRMD8 deficiency inMMTV-Cre+;Frmd8fl/fl;PyMTmice accelerates mammary tumor growth and loss of luminal phenotype, and confers tamoxifen resistance. Single-cell RNA profiling reveals that Frmd8 loss decreases the proportion of hormone-sensing differentiated epithelial cells and downregulates the levels of ERα. Mechanically, on one hand, loss of FRMD8 inhibitsESR1transcription via suppressing the expression of FOXO3A, a transcription factor ofESR1. On the other hand, FRMD8 interacts both with ERα and UBE3A, and disrupts the interaction of UBE3A with ERα, thereby blocking UBE3A-mediated ERα degradation. In breast cancer patients,FRMD8gene promoter is found hypermethylated and low level of FRMD8 predicts poor prognosis. Therefore, FRMD8 is an important regulator of ERα and may control therapeutic sensitivity to tamoxifen in ERα-positive breast cancer patients.

Impact Statement

Tumor suppressive protein FRMD8 inhibits breast cancer progression by regulating the level of ERα and has the possibility to be a potential target for overcoming tamoxifen treatment resistance.
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

Despite 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.
Biophysical Simulation Enables Multi-Scale Segmentation and Atlas Mapping for Top-Down Spatial Omics of the Nervous System
Authors: Mohammed Ali Lina K , Yim Aldrin Kay Yuen , Gerbi Emanuel B , Nguyen Thien , Tu Nicholas K , Ikede Faith P , Sampaleanu Remi , Grigore Diana , Waligorski Jason E , Kremitzki Colin L , Yuan Liya , Dong Wendy , Mitra Robi David , Milbrandt Jeffrey D , Buchser William J
Published: August 2024

Spatial omics (SO) has produced high-definition mapping of subcellular molecules (like transcripts or proteins) within tissue samples. Mapping transcripts to anatomical regions requires segmentation, but even segmenting nuclei remains challenging for tissues like nerve cross sections, let alone for larger regions such as within the spinal cord. Neural networks could address this but need extensive human annotations-a bottleneck. We present SiDoLa-NS (Simulate, Don't Label - Nervous System), an image-driven (top-down) approach to SO analysis in the nervous system. We utilize biophysical properties of tissue architectures to design synthetic images mimicking tissue samples. With these in silico samples, we train supervised instance segmentation convolutional neural networks (CNNs) for nucleus segmentation, achieving precision and F1-scores > 0.95. We take this a step further with generalizable CNNs that can identify macroscopic tissue structures in the mouse brain (mAP50 = 0.869), spinal cord (mAP50 = 0.96), and pig sciatic nerve (mAP50 = 0.995).
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

Experiencing 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.

Highlights

vSUB BS cells are uniquely stress sensitive

Stress causes sex-dependent changes to BS cell E/I balance

Stress causes sex-dependent changes to vSUB activity to aBNSTin vivo

Stress 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

The 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

Glioblastoma (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

Background

Mesenchymal 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.

Methods

Three 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 processes

Results

aBMSCs, 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.

Conclusions

Oral-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
Computational design of highly active de novo enzymes
Authors: Braun Markus , Tripp Adrian , Chakatok Morakot , Kaltenbrunner Sigrid , Totaro Massimo G. , Stoll David , Bijelic Aleksandar , Elaily Wael , Hoch Shlomo Yakir Yakir , Aleotti Matteo , Hall Melanie , Oberdorfer Gustav
Published: August 2024

Custom designed enzymes can further enhance the use of biocatalysts in industrial biotransformations, thereby helping to tackle biotechnological challenges of the 21st century. We present rotamer inverted fragment finder - diffusion (Riff-Diff) a hybrid machine learning and atomistic modeling strategy for scaffolding catalytic arrays in de novo protein backbones with custom substrate pockets. We used Riff-Diff to scaffold a catalytic tetrad capable of efficiently catalyzing the retro-aldol reaction. Functional designs exhibit a high fold diversity, with substrate pockets similar to natural enzymes. Some of the thus generated de novo enzymes show activities rivaling those optimized by in-vitro evolution. The design strategy can, in principle, be applied to any catalytically competent amino acid constellation. These findings are paving the way to address factors for the practical applicability of de novo protein catalysts in industrial processes and shed light on fundamental principles of enzyme catalysis.
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

We 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

Abstract

Histological 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

Advances 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.

Importance

Metabarcode 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

Aflatoxin 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

Mitigating 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

CD30 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

The 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

The 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.
A comprehensive genetic catalog of human double-strand break repair
Authors: López de Alba Ernesto , Salguero Israel , Giménez-Llorente Daniel , Fernández-Sanromán Ángel , Casajús-Pelegay Ester , Terrón-Bautista José , Barroso-González Jonathan , Bernal Juan A. , Macintyre Geoff , Fernández-Leiro Rafael , Losada Ana , Cortés-Ledesma Felipe
Published: August 2024

The analysis of DNA sequence outcomes provides molecular insights into double-strand break (DSB) repair mechanisms. By employing parallel in-pool profiling of Cas9-induced indels within a genome-wide knockout library, we present a comprehensive catalog detailing how virtually every human gene influences the DSB repair process. This REPAIRome resource is validated through the identification of novel mechanisms, pathways and factors involved in DSB repair, including unexpected opposing roles for XLF and PAXX in DNA end processing, a molecular explanation for Cas9-induced multi-nucleotide insertions, the identification of HLTF as a DSB-repair factor, the involvement of the SAGA complex in microhomology-mediated end joining, and importantly, an indel mutational signature linked to VHL loss, renal carcinoma and hypoxia. Collectively, these results exemplify the potential of REPAIRome to drive future discoveries in DSB repair, CRISPR-Cas gene editing and the etiology of cancer mutational signatures.