bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antiviral Activity of Rosemary Extract Against Zika Virus in Human Dermal Fibroblasts
Authors: Masi Jordan T. , Crozier Robert W.E. , Coish Jeremia M. , Hicks Natalie J. , Tsiani Evangelia , Patterson Edward I. , MacNeil Adam J. 
Published: February 2025

AbstractFlaviviruses have increasingly emerged and re-emerged in recent decades, infecting millions of people annually. Zika virus is particularly concerning due to its associated pathological complications, including microcephaly in newborns and Guillain-Barré syndrome in adults, posing a significant threat to public health. Despite efforts made by the scientific community, no licensed drugs against flaviviruses have been developed. Medicinal plants show promise as a novel source of antiviral agents, as they possess a diverse array of biologically active secondary metabolites, making them potential candidates for therapeutic use. We sought to investigate the antiviral potential of rosemary extract (RE) against ZIKV in human dermal fibroblasts (HFF-1 cells), one of the earliest targets of infection. ZIKV was treated with various concentrations of RE or its individual major polyphenols, including rosmarinic acid (RA), carnosic acid (CA), and carnosol (CO), and the remaining infectivity of each sample was measured by plaque reduction assay. To evaluate the impact of RE on different stages of the ZIKV replication cycle, HFF-1 cells were treated before, during, and after infection, or the virus was treated before infection. RE exerted potent antiviral activity against ZIKV in both Vero and HFF-1 cells by directly acting on virus particles before infection. Importantly, RE significantly inhibited the later stages of the virus replication cycle by interfering with post-entry mechanisms within the host cell. Moreover, major RE-derived polyphenols CA and CO, but not RA, were shown to significantly reduce ZIKV infectivity. Overall, RE significantly impairs ZIKV infectionin vitroby directly interacting with virus particles prior to adsorption and interfering with post-entry processes of the ZIKV replication cycle. This study provides rigorous evidence indicating the potential development of RE as an antiviral agent, warranting further investigation into the mechanisms underlying its inhibitory activity against ZIKV and its effects on other medically important flaviviruses.
Diversity of culturable endophytic fungi associated with avocado orchards under organic and conventional management
Authors: Sánchez-Hernández Daniel , Larsen John , Reverchon Frédérique 
Published: February 2025

AbstractEndophytic fungi constitute a great resource for the implementation of sustainable agricultural practices. However, their diversity may be altered by agrochemicals used in conventionally managed agrosystems. Here we explored the culturable diversity of endophytic fungi associated with avocado (Persea americanaMill.) in conventional and organic orchards from three counties of the world’s leading productive region. In total, 529 endophytic fungal isolates were obtained from branches and roots of avocado trees. Identification based on ITS sequencing showed that most isolates belonged to the Ascomycota phylum (98 %) and were grouped into 52 fungal genera, representing 102 tentative species. The endophytic fungal community was dominated by genera which were common to both management types, namelyFusarium, Colletotrichum, Dactylonectria, andDiaporthe/Phomopsis. Twenty fungal genera were exclusive to organic orchards (e.g.,HypoxylonandTalaromyces) and 10 were only found in conventional orchards (e.g.,Trichoderma). Fungal species richness and diversity were higher in organic than in conventional orchards. Ordination and clustering analyses revealed a stronger effect of site than of management type on endophytic fungal community structure, highlighting the influence of local factors in shaping the culturable endophytic fungal community. Overall, our findings confirm the negative impact of conventional management on the diversity of crop-associated endophytic fungi and the significant influence of local factors on endophytic fungal assemblages. Moreover, our results emphasize the need to assess the risk that possible latent fungal pathogens may represent for the crop or dominant forest species surrounding avocado orchards.
Genetic analysis of triplicated genes affecting sex-specific skeletal deficits in Down syndrome model mice
Authors: Sloan Kourtney , Piner Kristina M. , Arachchige Pathum Randunu Nawarathna Kandedura , Goodlett Charles R. , Herault Yann , Olbricht Gayla R. , Wallace Joseph M. , Roper Randall J. 
Published: February 2025

AbstractDown syndrome (DS) is caused by triplication of human chromosome 21 (Hsa21), resulting in skeletal insufficiency and altered postnatal bone development in individuals with DS. DS mouse models have shown similar deficits to humans with DS, mimicking differences between ages, sexes, and bone compartments. The historic mouse model, Ts65Dn, has provided much of the mechanistic insight behind these DS-related skeletal deficits, but there are concerns over its genetic construct validity. Ts65Dn mice have an additional 60 trisomic genes that are homologous to Hsa6. These genes, acting either directly or through interactions with trisomic, Hsa21-homologous or disomic genes, may produce phenotypes not related to DS; so, Ts66Yah mice were derived to remove these genes. After assessing individual densitometric and morphometric parameters in femurs, skeletal phenotypes were directly compared between male and female Ts65Dn and Ts66Yah mice at postnatal day (P) 36 and 6-weeks and between male mice at 16-weeks using multivariate principal components analyses on these parameters. These comparisons confirmed male Ts66Yah mice have trabecular and cortical deficits similar to male Ts65Dn mice at all ages. In contrast, female Ts66Yah mice lacked trabecular deficits evident in female Ts65Dn mice at P36, but both ages had similar cortical deficits. Copy number normalization ofDyrk1a,a trisomic, Hsa21-orthologous gene, failed to rescue deficits in male or improve trabecular bone in female Ts66Yah mice at P36 as observed in Ts65Dn mice. Thus, mechanisms behind trabecular phenotypes in both sexes of Ts66Yah mice likely differ from those of Ts65Dn mice. Overall, the trisomic, Hsa6-homologous genes in Ts65Dn mice may result in differences in trabecular phenotypes or mechanisms prior to 6 weeks but do not impact later trabecular or cortical phenotypes.
HIV-1 Vpr drives epigenetic remodeling to enhance virus transcription and latency reactivation
Authors: Saladino Nicholas , Leavitt Emily , Wong Hoi Tong , Ji Jae-Hoon , Ebrahimi Diako , Salamango Daniel J 
Published: February 2025

AbstractDespite decades of research, the primary proviral function of the HIV-1 Vpr accessory protein remains enigmatic. Vpr is essential for pathogenesisin vivoand for virus replication in myeloid cells, but the underlying cause-and-effect mechanism(s) driving these phenomena are poorly understood. Canonically, Vpr hijacks a cellular ubiquitin ligase complex to target several dozen host proteins for proteasomal degradation. Many of these substrates were recently revealed to be involved in DNA damage repair (DDR), which rationalizes the longstanding observation that Vpr induces constitutive activation of DDR signaling. Here, we use a combination of functional, biochemical, and genetic approaches establish a clear mechanistic link between Vpr-induced DDR signaling and remodeling of the epigenetic landscape to enhance HIV-1 promoter activity during acute infection and virus reactivation from latency. Functional, genetic, and bimolecular fluorescence complementation experiments reveal that Vpr utilizes degradation-dependent and -independent mechanisms to induce epigenetic remodeling and that Vpr segregates into two discrete pools with dedicated activities—A multimeric pool in the nucleus that is associated with chromatin and a monomeric pool associated with DCAF1 in the cytoplasm. Vpr function in remodeling the nuclear environment is present in common HIV-1 subtypes worldwide and provides a mechanistic rationale for its essentiality in virus replication.Author summaryWhile HIV-1 Vpr plays an essential role in virus replication, the molecular mechanisms underlying its essentiality remain enigmatic. Vpr’s best characterized function is the ability to induce the depletion of several dozen host proteins by hijacking a cellular E3-ubiquitin ligase complex. Here, we establish that Vpr promotes global epigenetic remodeling to enhance HIV-1 promoter activity during acute infection and virus reactivation from latency.We demonstrate that epigenetic remodeling activity is linked to Vpr’s ability to induce constitutive DNA damage repair signaling, and that it occurs through both degradation-dependent and -independent mechanisms. Moreover, this Vpr function is present in common HIV-1 subtypes circulating globally. This study provides novel mechanistic insights into how HIV-1 exploits host DNA repair pathways and sheds light on Vpr’s proviral function.
Subcellular determinants of orthoflavivirus protease activity
Authors: Corliss Lochlain , Petit Chad M. , Lennemann Nicholas J. 
Published: February 2025

AbstractOrthoflaviviruses are small, enveloped, positive-sense RNA viruses that cause over 500 million infections globally each year for which there are no antiviral treatments. The viral protease is an attractive target for therapeutics due to its critical functions throughout infection. Many studies have reported on the structure, function, and importance of orthoflavivirus proteases; However, the molecular determinants for cleavage of intracellular substrates by orthoflavivirus proteases and how these factors affect viral fitness are unknown. In this study, we used our fluorescent, protease-activity reporter system to investigate the subcellular determinants involved in orthoflavivirus protease cleavage. By modifying our reporter platform, we identified endoplasmic reticulum (ER) subdomain localization and membrane proximity of the substrate cut site as two previously uncharacterized molecular determinants for cleavage. We also altered the amino acid composition of the reporter cut site to introduce sequences present at the cytoplasmic junctions within orthoflavivirus polyproteins and found that each protease processed the sequence located at the junction between NS4A and the 2K peptide least efficiently. Live-cell imaging revealed that cleavage of the NS4A|2K sequence is significantly delayed compared to the capsid cleavage sequence. We further determined that introducing a more efficient cleavage sequence into the NS4A|2K junctions of orthoflavivirus infectious clones abolished virus recovery. Overall, this study identifies ER subdomain localization and membrane proximity of the cut site as molecular determinants for cleavage by orthoflavivirus proteases and provides insight into the role that sequence specificity plays in the coordinated processing of the viral polyprotein and establishing productive infections.ImportanceOrthoflaviviruses are the most prevalent and dangerous arthropod-borne viruses (arboviruses) leading to over 500 million global infections annually. Orthoflavivirus infection can cause severe pathologies, including hemorrhagic conditions and neurological disease, that lead to hundreds of thousands of deaths each year. The viral protease complex, responsible for processing the viral polyprotein into its functional subunits, is an attractive target for antiviral therapeutic development. Despite extensive research efforts on these viral protein complexes, all protease inhibitor candidates have fallen short of clinical efficacy, highlighting a considerable gap in knowledge of the viral protease’s complex intracellular activity. The significance of our research is in characterizing the subcellular determinants associated with orthoflavivirus protease cleavage efficiency and how these factors can influence viral fitness. These findings contribute to closing this gap in knowledge of the mechanisms of orthoflavivirus proteases which can ultimately lead to the successful development of targeted antivirals.
R-Spondin1 regulates fate of enteric neural progenitors via differential LGR4/5/6-expression in mice and humans
Authors: Scharr Melanie , Scherer Simon , Fuchs Jörg , Hirt Bernhard , Neckel Peter H. 
Published: February 2025

SummaryRegeneration and cytodifferentiation of various adult epithelial stem cell compartments are controlled by the Wnt-agonist R-Spondin1 (RSPO1) and the Leucin-rich-repeat-containing G-protein-coupled-receptors (LGR4/5/6). We hypothesized that RSPO1-LGR-signaling also is involved in regulating neuro-regeneration and homeostasis of the postnatal enteric nervous system (ENS). If applied to murine and human ENS-progenitors, RSPO1 led to an increased proliferation, followed by enhanced enteric neurogenesis. This coincided with an upregulation of LGR4 expression during ENS-progenitor proliferationin vitro. In contrast, we observed a reduced proliferation in ENS-progenitors expressing LGR5, while LGR6 was not expressed by proliferative ENS-progenitors. Instead, LGR5 and LGR6 expression increased over the course of induced neuronal differentiation, consistent with thein vivoexpression. LGR-receptor expression therefore might represent a previously unknown mechanism influencing the fate decision of ENS-progenitor cells between proliferation and neuronal differentiation. Thus, our study is essential for our understanding of regenerative aspects of the postnatal ENS in health and disease.
What is a Differentially Expressed Gene?
Authors: Hoerbst Franziska , Sidhu Gurpinder Singh , Tomkins Melissa , Morris Richard J. 
Published: February 2025

AbstractThe concept of ‘Differentially Expressed Genes’ (DEGs) is central to RNA-Seq studies, yet their identification suffers from reproducibility issues. This is largely a consequence of the inherent biological and technical variation that cannot be captured with small numbers of replicates. When thresholds for p-values and log2fold changes are introduced, this variability can propagate an incomplete description of the data, leading to differing interpretations. Here, we compare traditional binary DEG classification with a rank-based method, grounded in Bayesian statistics, using a published yeast dataset comprising over 40 replicates. This analysis reveals how the choice of thresholds and number of replicates results in discrepancies between studies and potentially interesting genes being overlooked. Furthermore, by comparing wild-type with wild-type samples, we show how variability in gene expression can be mistaken for differential expression. Evaluating current practices for navigating the accuracy-error trade-off in the search for differentially expressed genes leads us to advocate rank-based methods and Bayesian statistics to mitigate the limitations of binary classifications and communicate uncertainty.
AMPK signaling is dysregulated in human tendinopathy and loss of AMPKα1 leads to cell, matrix and mechanical dysfunction in mouse Achilles tendon
Authors: Hold LeeAnn A. , Migotsky Nicole , Lamia Syeda N. , Steltzer Steph S. , Grossman Sydney , Chen Jessica , Bae Seung-Ho , Cordts Paige , Phillips Tessa , O’Meara Matthew J. , Davis Carol , Brooks Susan V. , Akbar Moeed , Millar Neal , Killian Megan L. , Abraham Adam C. 
Published: February 2025

SUMMARYTendinopathy is a tendon disorder that is caused by the failure to self-repair and has many pathological characteristics such as disorganized ECM and decreased cell viability. We have identified a possible target to combat these changes, AMPK, an energy stress sensor that was shown to maintain intracellular homeostasis. Through bulk RNA-sequencing of healthy and tendinopathic tendons from humans we have identified a novel finding of downregulation of AMPK signaling in the tendinopathic samples which suggests AMPK plays a role in tendon homeostasis. Our studies utilizing a conditional knock-out of Prkaa1 in tendon in mice showed that loss of AMPK results in degenerative ECM, impaired biomechanical properties and increased cellular senescence in Achilles tendon through the lifespan. Additionally, we found that exercise can delay senescence onset independent of AMPK. These findings highlight the importance of energy metabolism in tendon health which will assist in understanding the onset and progression of tendinopathy.
Genome sequence of the blue floweringCentaurea cyanus
Authors: Dassow Chiara Marie , Friedhoff Ronja , Pucker Boas 
Published: February 2025

AbstractThe genome of the cornflower (Centaureacyanus) was sequenced with long reads (ONT) to reveal the full sequences of genes in the flavonoid biosynthesis. Of particular interest are genes responsible for the striking blue pigmentation of the flower. Through basecalling, read correction and assembling the sequenced DNA strands, we were able to generate a genome sequence with 98.8% BUSCO completeness, N50 of 16 Mbp, and an accuracy of 72 reported by Merqury. HERRO-based correction of the R10 nanopore sequencing reads resulted in a substantially improved assembly compared to uncorrected reads. The gene prediction revealed structural genes of the flavonoid biosynthesis and associated MYB and bHLH transcription factors. A tandem duplication of F3’H was discovered. Additionally, a putative tandem duplication resulting in three copies of the anthocyanin biosynthesis activating MYB was observed.
Enterococcus faecalis-derived lactic acid facilitates persistent and polymicrobial wound infections by suppressing macrophage activation
Authors: da Silva Ronni A. G. , Tien Brenda Yin Qi , Kao Patrick Hsien Neng , Celik Cenk , Tan Ai Zhu Casandra , Ismail Muhammad Hafiz , Hu Guangan , Chong Kelvin Kian Long , Thibault Guillaume , Chen Jianzhu , Kline Kimberly A. 
Published: February 2025

SummaryMacrophage activation is critical for the innate immune response, and its suppression by pathogens represents a significant barrier to immune clearance. Here we identifyE. faecalis-derived lactic acid as a key factor in suppressing macrophage activation via extracellular acidification. We demonstrate thatE. faecalismutants lacking lactate dehydrogenase (ldh), essential for lactic acid production and extracellular pH reduction, fail to suppress NF-κB. Mechanistically,E. faecalis-derived lactic acid acts via MCT-1 and GPR81, to impair ERK and STAT3 phosphorylation, leading to reduced STAT3 binding to theMyd88promoter and reduced MyD88 protein levels, and ultimately to reduced NF-κB activity in macrophages. Consequently, in a wound infection model, the immunosuppressive microenvironment created byE. faecalispromotes long-term virulence and the virulence of co-infecting bacteria such asEscherichia coli.These findings highlight that bacterial-derived lactic acid contributes to the subversion of host immunity to promote persistent and polymicrobial infections.
The distribution of highly deleterious variants across human ancestry groups
Authors: Stolyarova Anastasia , Coop Graham , Przeworski Molly 
Published: February 2025

AbstractA major focus of human genetics is to map severe disease mutations. Increasingly that goal is understood as requiring huge numbers of people to be sequenced from every broadly-defined genetic ancestry group, so as not to miss “ancestry-specific variants.” Here, we argue that this focus is unwarranted. We start with first principles considerations, based on models of mutation-drift-selection balance, which suggest highly pathogenic mutations should be at similarly low frequencies across ancestry groups. Severe disease mutations tend to be strongly deleterious, and thus evolutionarily young, and are kept at relatively constant frequency through recurrent mutation. Therefore, highly pathogenic alleles are shared identical by descent within extended families, not broad ancestry groups, and sequencing more people should yield similar numbers regardless of ancestry. We illustrate these points using gnomAD genetic ancestry groupings, and show that the classes of variants most likely to be highly pathogenic, notably sets of loss of function alleles at strongly constrained genes, conform well to these predictions. While there are many important reasons to diversify genomic research, strongly deleterious alleles will be found at comparable rates in people of all ancestries, and the information they provide about human biology is shared across ancestries.
Fractional differential equations of Riemann–Liouville of variable order with anti-periodic boundary conditions
Authors: Zoubida Bouazza , Souid Mohammed Said , Günerhan Hatira , Rezazadeh Hadi 
Published: February 2025

PurposeThe purpose of this paper is to investigate the existence, uniqueness and stability of solutions to a class of Riemann–Liouville fractional differential equations with anti-periodic boundary conditions of variable order (R-LFDEAPBCVO). The study utilizes standard fixed point theorems (FiPoTh) to establish the existence and uniqueness of solutions. Additionally, the Ulam-Hyers-Rassias (Ul-HyRa) stability of the considered problem is examined. The obtained results are supported by an illustrative example. This research contributes to the understanding of fractional differential equations with variable order and anti-periodic boundary conditions, providing valuable insights for further studies in this field.Design/methodology/approach This paper (1) defines the Riemann–Liouville fractional differential equations with anti-periodic boundary conditions of variable order (R-LFDEAPBCVO); (2) discusses the existence and uniqueness of solutions to these equations using standard FiPoTh; (3) investigates the stability of the considered problem using the Ul-HyRa stability concept (Ul-HyRa); (4) provides a detailed explanation of the design and methodology used to obtain the results and (5) supports the obtained results with a relevant example.FindingsThe authors confirm that no funds, grants or any other form of financial support were received during the preparation of this manuscript.Originality/valueThe originality/value of our paper lies in its contribution to the field of fractional differential equations. Specifically, we address the existence, uniqueness and stability of solutions to a class of Riemann–Liouville fractional differential equations with anti-periodic boundary conditions of variable order. By utilizing standard FiPoTh and investigating Ul-HyRa stability, we provide novel insights into this problem. The results obtained are supported by an example, further enhancing the credibility and applicability of your findings. Overall, our paper adds to the existing knowledge and understanding of Riemann–Liouville fractional differential equations with anti-periodic boundary conditions, making it valuable to the scientific community.