bluuebunny/crossref_metadata_2025_split huggingface dataset:
Interferons and tuft cell numbers are bottlenecks for persistent murine norovirus infection
Authors: Aggarwal Somya , Walker Forrest C. , Weagley James S. , McCune Broc T. , Wu Xiaofen , Schriefer Lawrence A. , Makimaa Heyde , Lawrence Dylan , Sridhar Pratyush , Baldridge Megan T. 
Published: February 2024

AbstractNoroviruses (NoVs) are a leading cause of viral gastroenteritis. Despite global clinical relevance, our understanding of how host factors, such as antiviral cytokines interferons (IFNs), modulate NoV population dynamics is limited. Murine NoV (MNoV) is a tractablein vivomodel for the study of host regulation of NoV. A persistent strain of MNoV, CR6, establishes a reservoir in intestinal tuft cells for chronic viral shedding in stool. However, the influence of host innate immunity and permissive cell numbers on viral population dynamics is an open question. We generated a pool of 20 different barcoded viruses (CR6BC) by inserting 6-nucleotide barcodes at the 3’ position of the NS4 gene and used this pool as our viral inoculum forin vivoinfections of different mouse lines. We found that over the course of persistent CR6 infection, shed virus was predominantly colon-derived, and viral barcode richness decreased over time irrespective of host immune status, suggesting that persistent infection involves a series of reinfection events. In mice lacking the IFN-λ receptor, intestinal barcode richness was enhanced, correlating with increased viral intestinal replication. IL-4 treatment, which increases tuft cell numbers, also increased barcode richness, indicating the abundance of permissive tuft cells to be a bottleneck during CR6 infection. In mice lacking type I IFN signaling (Ifnar1-/-) or all IFN signaling (Stat1-/-), barcode diversity at extraintestinal sites was dramatically increased, implicating different IFNs as critical bottlenecks at specific tissue sites. Of interest, extraintestinal barcodes were overlapping but distinct from intestinal barcodes, indicating that disseminated virus represents a distinct viral population than that replicating in the intestine. Barcoded viruses are a valuable tool to explore the influence of host factors on viral diversity in the context of establishment and maintenance of infection as well as dissemination and have provided important insights into how NoV infection proceeds in immunocompetent and immunocompromised hosts.
Plasmalogen oxidation induces the generation of excited molecules and electrophilic lipid species
Authors: Faria Rodrigo L. , Prado Fernanda M. , Junqueira Helena C. , Fabiano Karen C. , Diniz Larissa R. , Baptista Mauricio S. , Di Mascio Paolo , Miyamoto Sayuri 
Published: February 2024

AbstractPlasmalogens are glycerophospholipids with a vinyl-ether linkage at the sn-1 position of the glycerol backbone. Despite being suggested as antioxidants due to the high reactivity of their vinyl ether groups with reactive oxygen species (ROS), our study reveals the generation reactive oxygen and electrophilic lipid species from oxidized plasmalogen intermediates. By conducting a comprehensive analysis of the oxidation products by liquid chromatography coupled to high-resolution mass spectrometry (LC-MS) we demonstrate that singlet molecular oxygen [O2(1Δg)] reacts with the vinyl ether bond, producing hydroperoxyl acetal as major primary product (97%) together with minor quantities of dioxetane (3%). Furthermore, we show that these primary oxidized intermediates lead to the formation of excited triplet carbonyls, O2(1Δg), and electrophilic phospholipid and fatty aldehyde species, as secondary reactive products. The generation of excited triplet carbonyls from dioxetane thermal decomposition was confirmed by light emission measurements in the visible region using dibromoantracene as a triplet enhancer. Moreover, O2(1Δg) generation from dioxetane and hydroperoxyacetal was evidenced by detection of near-infrared light emission at 1270 nm and chemical trapping experiments. Additionally, we have thoroughly characterized alpha-beta unsaturated phopspholipid and fatty aldehydes by LC-MS analysis using two probes that specifically reacts with aldehydes and alpha-beta unsaturated carbonyls. Overall, our findings demonstrate the generation of excited molecules and electrophilic lipid species from oxidized plasmalogen species unveiling the potential prooxidant nature of plasmalogen oxidized products.Significance StatementPlasmalogens, the most abundant subclass of ether lipids in mammalian cells, have traditionally been regarded as antioxidants. However, our study reveals a new perspective, shedding light on the generation of chemiexcited and reactive lipid species during plasmalogen photooxidation. We provide direct evidence revealing the production of excited triplet carbonyls and singlet molecular oxygen as secondary reactive products originating from dioxetane and hydroperoxyacetal intermediates. Importantly, we also demonstrate the generation of electrophilic alpha-beta unsaturated phospholipids and fatty aldehydes through plasmalogen oxidation. These findings highlight the production of excited states and reactive lipid species resulting from plasmalogen oxidation, which can potentially induce oxidative modifications in biological systems.
5-Aza-Cytidine Enhances Terminal Polyadenylation Site Usage for Full-Length Transcripts in Cells
Authors: Ogunsola Samuel , Liu Ling , Das Urmi , Xie Jiuyong 
Published: February 2024

AbstractAs an inhibitor of DNA methyltransferases (DNMT) and anti-cancer drug, the many effects of 5-aza-cytidine (5-azaC) on gene expression remains unknown. Here we show that 5-azaC treatment of cultured pituitary tumour cells increases the relative usage of the genomic terminal exons (GTE) across the transcriptome. This effect is largely achieved by switching mRNA polyadenylation (poly(A)) from proximal sites to the GTE, which have a more optimal poly(A) signal consensus motif. Consistently, 5-azaC upregulates mRNA anti-terminators Scaf4 and Scaf8 while downregulating the early termination enhancer E2f2. In MOLM-13 leukaemia cells, 5-azaC similarly promotes full-length transcript production, regulating alternative polyadenylation factors in both common and cell-specific ways. Unexpectedly, PCF11, known to promote proximal poly(A) site usage, is upregulated in both cell lines, reminiscent of a homeostatic effort by the tumour/cancer cells to maintain their shortened transcripts during the 5-azaC treatment. This study highlights a previously unknown aspect of 5-azaC’s effect on gene expression as a DNMT inhibitor and anti-cancer drug: to directionally promote the terminal polyadenylation site usage to switch from the shortened to full-length transcripts of cancer cells and consequently the alternative usage of strings of 3’ exons.
Placental cytotrophoblast microvillar stabilization is required for cell-cell fusion
Authors: Duan Wendy K. , Shaha Sumaiyah Z. , Patel Khushali J. , Domingo Ivan K. , Riddell Meghan R. 
Published: February 2024

AbstractThe placenta is an essential organ of pregnancy required for maternal-fetal transport and communication. The surface of the placenta facing the maternal blood is formed by a single giant multinucleate cell: the syncytiotrophoblast. The syncytiotrophoblast is formed and maintained via fusion of progenitor cytotrophoblasts. Cell-cell fusion is a tightly regulated process, and in non-trophoblastic cells is accompanied by stereotypical alterations in cell shape by cells that have attained fusion-competence. The most prominent feature is the formation of actin-based membrane protrusions, but whether stereotypic morphological changes occur in fusion-competent cytotrophoblasts has not been characterized. Using a human placental explant model, we characterized cell shape factors associated with the attainment of cytotrophoblast fusion competence. We found that fusion-competent cytotrophoblasts are hypertrophic, elongated cells, that form microvilli at the apical membrane. The actin-membrane cross linker protein ezrin was found to have highly polarized expression within cytotrophoblast microvilli. Inhibition of ezrin activation destabilized cytotrophoblast microvilli and prevented cytotrophoblast fusion. Thus, we propose that the polarized activation of ezrin within apical microvilli and actin-mediated changes in membrane dynamics are necessary for cytotrophoblast fusion.Summary statementFusion-competent cytotrophoblasts undergo dynamic changes in cell morphology including the acquisition of apically localized microvilli. Microvillar stabilization facilitates effective fusion and differentiation.
Deep phenotypic profiling of neuroactive drugs in larval zebrafish
Authors: Gendelev Leo , Taylor Jack , Myers-Turnbull Douglas , Chen Steven , McCarroll Matthew N. , Arkin Michelle R. , Kokel David , Keiser Michael J. 
Published: February 2024

AbstractBehavioral larval zebrafish screens leverage a high-throughput small molecule discovery format to find neuroactive molecules relevant to mammalian physiology. We screened a library of 650 central nervous system active compounds in high replicate to train a deep metric learning model on zebrafish behavioral profiles. The machine learning initially exploited subtle artifacts in the phenotypic screen, necessitating a complete experimental re-run with rigorous well-wise randomization. These large matched phenotypic screening datasets (initial and well-randomized) provided a unique opportunity to quantify and understand shortcut learning in a full-scale, real-world drug discovery dataset. The final deep metric learning model substantially outperforms correlation distance–the canonical way of computing distances between profiles–and generalizes to an orthogonal dataset of novel druglike compounds. We validated predictions by prospectivein vitroradio-ligand binding assays against human protein targets, achieving a hit rate of 58% despite crossing species and chemical scaffold boundaries. These newly discovered neuroactive compounds exhibited diverse chemical scaffolds, demonstrating that zebrafish phenotypic screens combined with metric learning achieve robust scaffold hopping capabilities.
How Fungi Biosynthesize 3-Nitropropanoic Acid: the Simplest yet Lethal Mycotoxin
Authors: Johnson Colin W. , Ohashi Masao , Tang Yi 
Published: February 2024

AbstractWe uncovered the biosynthetic pathway of the lethal mycotoxin 3-nitropropanoic acid (3-NPA) from koji moldAspergillus oryzaethrough genome mining, genetic inactivation and biochemical characterization. The biosynthetic gene cluster (BGC) of 3-NPA, which encodes an amine oxidase and a decarboxylase, is conserved in many fungi used in food processing, although most of the strains have not been reported to produce 3-NPA. Our discovery will lead to efforts that improve the safety profiles of these indispensable microorganisms in making food, alcoholic beverages, and seasoning.
A synergistic culture dependent and independent approach reveals a conserved wheat seed mycobiome
Authors: Becker Lindsey E. , Marshall David , Cubeta Marc A. 
Published: February 2024

ABSTRACTThe occurrence of pathogenic fungal taxa associated with wheat (Triticum aestivumL.) seeds is well studied, but less is known about non-pathogenic taxa of the wheat seed mycobiome. The goal of our research is to characterize wheat seed fungal endophyte diversity with a synergistic culture dependent and independent experimental approach. Four publicly available winter wheat cultivars developed in the southeastern United States with varying phenotypic and disease resistance traits were examined over a period of two years: Catawba, Hilliard, Shirley, and USG 3640. Our culture dependent methods involving two nutrient media generated 645 fungal isolates representing twelve genera sampled from multiple cultivars. Metabarcoding analysis identified a broader range of fungal taxa and a greater number of unique sequences than culture dependent methods. When examining fungal diversity across cultivars and years, richness decreased in 2021 for both culture dependent and independent approaches. However, wheat seed fungal community structure was stable across cultivars and years. Our results highlight the importance of combining culture independent and dependent methods to capture and establish a diverse endophytic fungal catalog associated with the wheat seed and highlight areas where future culture dependent efforts can focus their efforts.
The physiology of bud dormancy and cell cycle status in grapevine
Authors: Hermawaty Dina , Clode Peta L. , Considine John A. , Signorelli Santiago , Considine Michael J. 
Published: February 2024

ABSTRACTEvaluating the cell cycle status during dormancy of multicellular organisms is problematic. This is particularly so for woody perennial buds, where dormant and quiescent states are diffuse, and the organ may remain visibly unchanged for six to nine months of the year. In this study, we investigate cell cycle status of dormant grapevine buds by measuring mitotic index using an optimised method developed for grapevine bud tissue. The experimental material showed a dynamic range in the depth of dormancy, declining from 200 days in March to less than 60 days in May and 30 days in August, measured as the time to reach 50% bud burst in forcing conditions. Despite these differences, flow cytometry analysis showed that most nuclei isolated from these buds were arrested at the G1 phase. Ultrastructure analysis of the cells in the region of the shoot apical meristem confirmed that the mitotic activities of buds remained low at all time points, together with the development of starch grains and the relative absence of organelle development.HIGHLIGHTThe cell cycle and ultrastructure data suggest interesting evidence correspond to the growth resumption capacity of grapevine cv. Cabernet Sauvignon buds, i.e., absence of mitosis activities regardless of dormancy depth and starch accumulation irrespective of chilling accumulation.
Spatial kinetics and immune control of murine cytomegalovirus infection in the salivary glands
Authors: Byrne Catherine , Márquez Ana Citlali , Cai Bing , Coombs Daniel , Gantt Soren 
Published: February 2024

AbstractHuman cytomegalovirus (HCMV) is the most common congenital infection. Several HCMV vaccines are in development, but none have yet been approved. An understanding of the kinetics of CMV replication and transmission may inform the rational design of vaccines to prevent this infection. The salivary glands (SG) are an important site of sustained CMV replication following primary infection and during viral reactivation from latency. As such, the strength of the immune response in the SG likely influences viral dissemination within and between hosts. To study the relationship between the immune response and viral replication in the SG, and viral dissemination from the SG to other tissues, mice were infected with low doses of murine CMV (MCMV). Following intra-SG inoculation, we characterized the viral and immunological dynamics in the SG, blood, and spleen, and identified organ-specific immune correlates of protection. Using these data, we constructed compartmental mathematical models of MCMV infection. Model fitting to data and analysis indicate the importance of cellular immune responses in different organs and point to a threshold of infection within the SG necessary for the establishment and spread of infection.Author SummaryCytomegalovirus (CMV) is the most common congenital infection and causes an enormous burden of childhood disease. To gain insight into the immune requirements for controlling infection, we used a mouse model to reproduce characteristics of natural CMV infection, employing a low viral inoculum, and delivering the virus to the salivary glands (SG), a key site of CMV replication. Our results provide detailed data on the spatial and temporal spread of infection throughout the body and identify key immune correlates of the control of viral replication. By translating these findings into mechanistic mathematical models, we revealed the importance of organ-specific immune responses, particularly the requirement of TNF-αand IFN-γto control infection within the salivary glands. Furthermore, our mathematical modeling allowed us to compare known characteristics of human CMV infection related to infection establishment and spread to those predicted in mice, underscoring the suitability of the MCMV model to study its human homologue. These insights provide guidance for developing targeted vaccines to prevent CMV infection and disease.
Acceptability of fixed-dose combination treatments for hypertension in Kenya: a qualitative study using the Theoretical Framework of Acceptability
Authors: Mbuthia Daniel , Willis Ruth , Gichagua Mary , Nzinga Jacinta , Mugo Peter , Murphy Adrianna 
Published: February 2024

AbstractBackgroundFixed-dose combinations (FDCs) – 2-3 anti-hypertensive medications in a single pill - have the potential to improve hypertension treatment and outcomes. Yet, they are not widely implemented. Factors undermining implementation remain unknown, particularly in sub– Saharan Africa, where hypertension is a major cause of disease burden and is poorly treated.MethodsWe used in-depth semi-structured interviews to explore the acceptability of FDCs among patients, caregivers, and healthcare workers. We interviewed a total of 58 participants across four purposively selected health facilities in one county in Kenya. Data were analyzed using abductive thematic analysis approach, and emergent themes categorized according to the Theoretical Framework of Acceptability.ResultsOverall, FDCs are potentially acceptable to all participant groups. Acceptability is supported by a perception of FDCs as a means of reducing treatment burden (for patients and healthcare workers) and improving treatment adherence, and patients’ deferral to and trust in health workers. Acceptability among health workers may be undermined by variable levels of FDC coherence, concerns among health workers about FDCs as an “inflexible” treatment that does not allow dose titration or identifying causes of side effects, and concerns about consistent availability and affordability of FDCs in Kenya.ConclusionFDCs are a potentially acceptable treatment approach for hypertension in Kenya. Efforts to improve acceptability and thus implementation of FDCs in Kenya should consider improving understanding of treatment and strengthening the capacity of all health worker cadres to appropriately prescribe, inform about, and support adherence to FDCs. These efforts must align with work to address upstream health system factors such as poor availability and affordability.
Cardiovascular risk management in the elderly with type 2 diabetes prior to death: A Danish nationwide register study of discontinuation patterns
Authors: Kosjerina Vanja , Scheuer Stine H. , Carstensen Bendix , Jørgensen Marit E. , Brock Birgitte , Christensen Hanne R , Andersen Gregers S , Rungby Jørgen 
Published: February 2024

ABSTRACTBackgroundCardioprotective medication usage among elderly individuals with type 2 diabetes (T2D) is prevalent, however, the degree and timing of discontinuation is unknown. This study aims to describe the extent, timing, and secular changes of discontinuation of cardioprotective medication in elderly with T2D.MethodsIn this register-based cohort study all individuals with T2D, deceased between 2006-2018 at an age of 80 years or older, were identified through Danish nation-wide registers. We followed the population backward in time, from death to last intake of antihypertensive, lipid-lowering, and antithrombotic medication. Poisson regression models were used to model rates of discontinuation prior to death while binomial models were used to estimate the proportion on medication at time of death.ResultsWe identified 52,523 individuals (55% women) with a mean (SD) age at T2D diagnosis of 77.3 (7.8) years and median (Q1-Q3) age at death of 86.5 [83.3-90.3] years. The proportion on any antihypertensive and antithrombotic medication was high (approximately 78% [95% CI 77-78] and 48% [95% CI 47-49%] at time of death, respectively) and increased slightly with increasing calendar year of death. Discontinuations occurred predominantly in the last year of life but were initiated earlier for individuals who died in recent calendar years. However, for angiotensin-converting enzyme, thiazides, and acetylsalicylic acid we found a more continuous discontinuation in the decade prior to death in the recent calendar years of death. The proportion on statins increased markedly with calendar year of death, peaking at 34% [95% CI 33-35%] in 2016 with a subsequent decrease to 29% [95% CI 28-30%] in 2018. Discontinuation patterns shifted from predominantly occurring in the last years of life to continues discontinuation in the decade before death.ConclusionOur results suggest an intensification with cardioprotective medication among elderly with type 2 diabetes and a more pronounced discontinuation during the last years of life. This may be a result of increased focus on individualized-treatment-regimens.
Speech therapy combined with Cerebrolysin in enhancing aphasia recovery after acute ischemic stroke: ESCAS pilot study
Authors: Homberg Volker , Jianu Dragoș Cătălin , Stan Adina , Strilciuc Ștefan , Chelaru Vlad-Florin , Karliński Michał , Brainin Michael , Heiss Wolf Dieter , Mureșanu Dafin , Enderby Pamela M 
Published: February 2024

AbstractBackgroundStroke-induced aphasia significantly impacts communication and quality of life. Despite the standard treatment being speech and language therapy (SLT), outcomes vary, highlighting the need for additional therapies. Cerebrolysin, a neuroprotective and neurotrophic agent, has shown potential in stroke management. This study examines the effectiveness of combining Cerebrolysin with SLT in treating post-stroke aphasia.MethodsThe ESCAS trial, a prospective, randomized-controlled, double-blinded phase 4 study, was conducted in two Romanian stroke centers. Participants included those with left middle cerebral artery territory ischemic stroke and Broca or mixed non-fluent aphasia, enrolled 3-5 days post-stroke. Inclusion criteria were right-handedness and Romanian as mother tongue; exclusion criteria were prior strokes, severe comprehension deficits, contraindications to MRI, and pre-existing neurodegenerative or psychiatric diseases. Participants received Cerebrolysin or a placebo combined with SLT in ten-day cycles over three intervals.ResultsOut of 132 enrolled patients, 123 were included in the Intention To Treat analysis, and 120 in the Per Protocol analysis. The Cerebrolysin group showed significant improvement in Western Aphasia Battery scores (p < 0.001) and National Institutes of Health Stroke Scale scores (p < 0.001). Modified Rankin Scale and Barthel index scores also improved, with notable differences at the final study visit (Day 90). Safety analysis raised no concerns.ConclusionsCerebrolysin combined with SLT offers promising potential for enhancing recovery in post-stroke aphasia. Significant improvements were observed in language and neurological deficits, underscoring the importance of adjunctive therapies in aphasia rehabilitation. Further research with larger cohorts is needed to fully establish the efficacy of this combination therapy.Clinical Trial Registrationhttps://www.isrctn.com/ISRCTN54581790