bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-micronized and micronized curcumin do not prevent the behavioral and neurochemical effects induced by acute stress in zebrafish
Authors: Sachett Adrieli , Gallas-Lopes Matheus , Benvenutti Radharani , Marcon Matheus , Linazzi Amanda M. , Aguiar Gean P. S. , Herrmann Ana P. , Oliveira J. Vladimir , Siebel Anna M. , Piato Angelo 
Published: October 2021

ABSTRACTCurcumin, a polyphenol extracted from the rhizome of Curcuma longa L. (Zingiberaceae), presents neuroprotective properties and can modulate neuronal pathways related to mental disorders. However, curcumin has low bioavailability, which can compromise its use. The micronization process can reduce the mean particle diameter and improve this compound’s bioavailability and therapeutic potential. In this study, we compared the behavioral (in the open tank test, OTT) and neurochemical (thiobarbituric acid reactive substances (TBARS) and non-protein thiols (NPSH) levels) effects of non-micronized curcumin (CUR, 10 mg/kg, i.p.) and micronized curcumin (MC, 10 mg/kg, i.p.) in adult zebrafish subjected to 90-minute acute restraint stress (ARS). ARS increased the time spent in the central area and the number of crossings and decreased the immobility time of the animals. These results suggest an increase in locomotor activity and a decrease in thigmotaxis behavior in the OTT. Furthermore, ARS also induced oxidative damage by increasing TBARS and decreasing NPSH levels. ARS-induced behavioral and biochemical effects were not blocked by any curcumin preparation. Therefore, we suppose that curcumin does not have anti-stress effects on the ARS in zebrafish.
Flagellin FLiC Enhances Resistance of Upland Cotton toVerticillium dahliae
Authors: Zhou Heng , Xie Yijing , Wang Yi , Zhu Heqin , Tang Canming 
Published: October 2021

AbstractThe mechanism by which flagellin induces an immune response in plants is still unclear. The purpose of this study is to reveal the effect and mechanism of flagellin in inducing plants to produce an immune response to increase the resistance toVerticillium dahliae(VD). The full-length flagellin gene C (FliC) was cloned from an endophytic bacteria (Pseudomonas) in the root of upland cotton cultivar Zhongmiansuo 41. The FliC protein purified in vitro has 47.50% and 32.42% biocontrol effects on resistant and susceptible cotton cultivars, respectively. FLiC can induce allergic reactions in tobacco leaf cells and immune responses in cotton plants. Smearing FLiC to cotton and performing RNA-seq analysis, it is significantly enriched in the activity of positive ion transporters such as potassium ions and calcium ions (Ca2+), diterpenoid biosynthesis, phenylpropane biosynthesis and other disease-resistant metabolic pathways. FLiC inhibits the expression of calcium antiporter activity gene (GhCAA) to accelerate intracellular Ca2+influx and stimulate the increase of intracellular hydrogen peroxide (H2O2) and nitric oxide (NO) content. The coordinated regulation of Ca2+, H2O2and NO enhances disease resistance. The resistance of transgenicFLiCgene Arabidopsis to VD was significantly improved. TheFLiCgene can be used as an anti-VD gene and as a regulator to improve resistance to VD.
Glycosuria alters uropathogenicEscherichia coliglobal gene expression and virulence
Authors: Islam Md. Jahirul , Bagale Kamal , John Preeti P , Kurtz Zachary , Kulkarni Ritwij 
Published: October 2021

ABSTRACTUropathogenicEscherichia coli(UPEC) is the principal etiology of more than half of urinary tract infections (UTI) in humans with diabetes mellitus. Epidemiological data and studies in mouse model of ascending UTI have elucidated various host factors responsible for increasing the susceptibility of diabetic hosts to UPEC-UTI. In contrast, the nature of alterations in UPEC physiology mediated by diabetic urinary microenvironment and the contributions of altered UPEC physiology in shaping UPEC-UTI pathogenesis in diabetes have not been examined. Our central hypothesis is that glycosuria directly induces urinary virulence of UPEC. We compared virulence characteristics and gene expression in human UPEC strains UTI89 (cystitis) and CFT073 (pyelonephritis) exposed for 2h,in vitroto human urine either in the presence or absence of glycosuria (600mg/dl glucose). Compared to control UPEC exposed to nutrient-rich culture medium LB, glycosuria-exposed UPEC exhibited significant increase in biofilm formation and reduction in the hemagglutination of Guinea pig erythrocytes (a surrogate measure of type 1 piliation). In addition, analysis of UTI89 transcriptome by RNA sequencing revealed that 2h-long,in vitroexposure to glycosuria also significantly alters expression of virulence and metabolic genes central to urinary virulence of UPEC. In summary, our results provide novel insights into how glycosuria-mediated early changes in UPEC fitness may facilitate UTI pathogenesis in the diabetic urinary microenvironment.IMPORTANCEUropathogenicEscherichia coli(UPEC) is an important causative agent of urinary tract infections in diabetic humans. We examined the effects ofin vitroexposure to glycosuria (presence of glucose in urine) on the virulence and gene expression by UPEC. Our results show that glycosuria rapidly (in 2h) alters UPEC gene expression, induces biofilm formation, and suppresses hemagglutination. These results offer a novel insight into the pathogenesis of UPEC in the urinary tract.
RNAi screen of RING/U-box domain ubiquitin ligases identifies critical regulators of tissue regeneration in planarians
Authors: Allen John M. , Balagtas Madison , Barajas Elizabeth , Macip Carolina Cano , Zepeda Sarai Alvarez , Iberkleid Ionit , Duncan Elizabeth M. , Zayas Ricardo M. 
Published: October 2021

AbstractRegenerative processes depend on the interpretation of signals to coordinate cell behaviors. The role of ubiquitin-mediated signaling is known to be important in many cellular and biological contexts, but its role in regeneration is not well understood. To investigate how ubiquitylation impacts tissue regeneration in vivo, we are studying planarians that are capable of regenerating after nearly any injury using a population of stem cells. Here we used RNAi to screen RING/U-box E3 ubiquitin ligases that are highly expressed in planarian stem cells and stem cell progeny. RNAi screening identified nine genes with functions in regeneration, including the spliceosomal factor prpf19 and histone modifier rnf2; based on their known roles in developmental processes, we further investigated these two genes. We found that prpf19 was required for animal survival but not for stem cell maintenance, suggesting a role in promoting cell differentiation. Because RNF2 is the catalytic subunit of the Polycomb Repressive Complex 1 (PRC1), we also examined other putative members of this complex (CBX and PHC). We observed a striking phenotype of regional tissue misspecification in cbx and phc RNAi planarians. To identify genes regulated by PRC1, we performed RNA-seq after knocking down rnf2 or phc. Although these proteins are predicted to function in the same complex, we found that the set of genes differentially expressed in rnf2 versus phc RNAi were largely non-overlapping. Using in situ hybridization, we showed that rnf2 regulates gene expression levels within a tissue type, whereas phc is necessary for the spatial restriction of gene expression, findings consistent with their respective in vivo phenotypes. This work not only uncovered roles for RING/U-box E3 ligases in stem cell regulation and regeneration, but also identified differential gene targets for two putative PRC1 factors required for maintaining cell-type-specific gene expression in planarians.
Macrophage Innate Training Induced by IL-4 and IL-13 Activation Enhances OXPHOS Driven Anti-Mycobacterial Responses
Authors: Lundahl Mimmi L. E. , Mitermite Morgane , Ryan Dylan G. , Case Sarah , Williams Niamh C. , Yang Ming , Lynch Roisin I. , Lagan Eimear , Lebre Filipa , Gorman Aoife L. , Stojkovic Bojan , Bracken Adrian P. , Frezza Christian , Sheedy Fred J. , Scanlan Eoin M. , O’Neill Luke A. J. , Gordon Stephen V. , Lavelle Ed C. 
Published: October 2021

AbstractMacrophages are a highly adaptive population of innate immune cells. Polarization with IFNγ and LPS into the “classically activated” M1 macrophage enhances pro-inflammatory and microbicidal responses, important for eradicating bacteria such as Mycobacterium tuberculosis. By contrast, “alternatively activated” M2 macrophages, polarized with IL-4, oppose bactericidal mechanisms and allow mycobacterial growth. These activation states are accompanied by distinct metabolic profiles, where M1 macrophages favor near exclusive use of glycolysis, whereas M2 macrophages up-regulate oxidative phosphorylation (OXPHOS). Here we demonstrate that activation with IL-4 and IL-13 counterintuitively induces protective innate memory against mycobacterial challenge. In human and murine models, prior activation with IL-4/13 enhances pro-inflammatory cytokine secretion in response to a secondary stimulation with mycobacterial ligands. In our murine model, enhanced killing capacity is also demonstrated. Despite this switch in phenotype, IL-4/13 trained murine macrophages do not demonstrate M1-typical metabolism, instead retaining heightened use of OXPHOS. Moreover, inhibition of OXPHOS with oligomycin, 2-deoxy glucose or BPTES all impeded heightened pro-inflammatory cytokine responses from IL-4/13 trained macrophages. Lastly, this work identifies that IL-10 attenuates protective IL-4/13 training, impeding pro-inflammatory and bactericidal mechanisms. In summary, this work provides new and unexpected insight into alternative macrophage activation states in the context of mycobacterial infection.
Aged human iPSC-RPE organoid cultures display hallmarks of drusen formation
Authors: Mesch Lena , Pashkovskaia Natalia , Cora Virginia , Pars Selin , Corti Serena , Cipriano Madalena , Loskill Peter , Koertvely Elod , Kustermann Stefan , Mesquida Marina , Kleger Alexander , Liebau Stefan , Achberger Kevin 
Published: October 2021

AbstractAge-related macular degeneration (AMD) is among the most common causes of irreversible vision loss. Disease progression is strongly associated with age-related pathological changes of retinal pigment epithelial (RPE) cells, such as accumulation of intracellular lipid-containing cell debris, extracellular lipid-rich deposits (drusen) and collagen-rich basal laminar deposits. Current AMD models provide a limited understanding of the complex pathomechanisms, revealing the lack of adequate physiological human AMD models. In this study, we developed anin vitromodel applicable for the exploration of AMD pathomechanisms and risk factors for AMD progression and drusen formation. Advanced 3D culturing technologies allow long-term cultivation of hiPSC-derived RPE organoids (RPEorg) for up to 360 days, which is the time frame necessary for the development of an AMD-like phenotype. Aged RPEorg exhibit hallmarks of AMD and age-related alterations such as increased autofluorescence, accumulation of lipid droplets, calcification, and the formation of extracellular clusters of the drusen-associated proteins such as apolipoprotein E (APOE) and tissue inhibitor of metalloproteinases 3 (TIMP3). Electron microscopy further reveals drusen-like extracellular deposits mimicking the signs of late drusen formation and AMD progression. In summary, our results demonstrate that hiPSC-derived 3D RPEorg provide a promising model to study age-associated RPE pathology and drusen formation. We show here that RPEorg are applicable for disease modelling studies and early stages of drug development and provide the opportunity to uncover inter-individual genetic and epigenetic factors that alter the course of the disease.
Chemical inhibition of auxin inactivation pathway uncovers the metabolic turnover of auxin homeostasis
Authors: Fukui Kosuke , Arai Kazushi , Tanaka Yuka , Aoi Yuki , Kukshal Vandna , Jez Joseph M , Kubes Martin F , Napier Richard , Zhao Yunde , Kasahara Hiroyuki , Hayashi Ken-ichiro 
Published: October 2021

AbstractThe phytohormone auxin, specifically indole-3-acetic acid (IAA) plays a prominent role in plant development. Cellular auxin concentration is coordinately regulated by auxin synthesis, transport, and inactivation to maintain auxin homeostasis; however, the physiological contribution of auxin inactivation to auxin homeostasis has remained elusive. The GH3 genes encode auxin amino acid conjugating enzymes that perform a central role in auxin inactivation. The chemical inhibition of GH3s in planta is challenging because the inhibition of GH3 enzymes leads to IAA overaccumulation that rapidly induces GH3 expression. Here, we developed a potent GH3 inhibitor, designated as kakeimide (KKI), that selectively targets auxin-conjugating GH3s. Chemical knockdown of the auxin inactivation pathway demonstrates that auxin turnover is very rapid (about 10 min), indicating auxin biosynthesis and inactivation dynamically regulate auxin homeostasis.
High levels of origin licensing during Xenopus cleavage divisions ensures complete and timely genome duplication
Authors: Gillespie Peter J. , Kisielewska Jolanta , Mamun Mohammed Al , Khoudoli Guennadi , Creavin Kevin , Score Alan J. , Blow J. Julian 
Published: October 2021

AbstractCells face several challenges to completing genome duplication. One challenge is the irreversible stalling of converging replication forks (‘double fork stalls’). Cell types that cannot delay mitotic entry must also ensure that no replication origins are too far apart (the ‘random gap problem’). We show how these challenges can be met in early Xenopus embryos by the very abundant licensing of replication origins: one MCM2-7 double hexamer every ∼250 bp. Licensing does not change nucleosome spacing, consistent with MCM2-7 being assembled onto inter-nucleosomal linker DNA. We show that later embryonic development can occur successfully with a per-cell cycle failure rate of <0.2% in early embryos. The high density of licensed origins in the early embryo reduces cell cycle failures from random gaps and from double fork stalls to levels compatible with subsequent development, suggesting that Xenopus early embryonic cells can ensure complete genome duplication without requiring unconventional replication mechanisms.
CD20+T cells are associated with inflammatory responses in experimental arthritis
Authors: Pineda Miguel , Pan Piaopiao , Wang Yilin , Khan Aneesah , Nyirenda Mukanthu H. 
Published: October 2021

AbstractCD20+T cells comprise a small but highly inflammatory subset that has been implicated in autoimmunity, including rheumatoid arthritis (RA). We sought to characterise the CD20+T cell subset at the site of inflammation in murine collagen-induced arthritis (CIA) model of RA and investigate the phenotype and functional relevance of CD3+CD20+T cells in the lymph nodes and arthritic joints using flow cytometry and immunohistochemistry. We demonstrate that CD3+CD4+CD20+and CD3+CD8+CD20+T cells are expanded in the draining lymph nodes of CIA mice. In addition, compared to naïve mice and those that did not develop clinical symptoms, CD20 expressing T cells of arthritic mice produced increased levels of pro-inflammatory cytokines (GM-CSF, TNF-a, IL-17, and INF-g). Notably, CD3+CD4+CD20+and CD3+CD8+CD20+T cells of disease mice were enriched with CXCR5+PD-1+T follicular helper cells and CXCR5-PD-1+peripheral T helper cells, subsets of T cells that have been implicated in promoting B-cell responses and antibody production within pathologically inflamed non-lymphoid tissues in RA. Importantly, CD3+CD20+T cells were detected in the inflamed regions in the lymph nodes and paws of arthritic mice. Our findings suggest that CD20+T cells are associated with inflammatory responses in the arthritic joint and may exacerbate pathology by promoting inflammatory B cell responses.
Long-range migration of centrioles to the apical surface of the olfactory epithelium
Authors: Ching Kaitlin , Wang Jennifer T. , Stearns Tim 
Published: October 2021

AbstractOlfactory sensory neurons (OSNs) in vertebrates detect odorants using multiple cilia, which protrude from the end of the dendrite and require centrioles for their formation. In mouse olfactory epithelium, the centrioles originate in progenitor cells near the basal lamina, often 50 to 100 μm from the apical surface. It is unknown how centrioles traverse this distance or mature to form cilia. Using high-resolution expansion microscopy, we found that centrioles migrate together, with multiple centrioles per group and multiple groups per OSN, during dendrite outgrowth. Centrioles were found by live imaging to migrate slowly, with a maximum rate of 0.18 μm/min. Centrioles in migrating groups were associated with microtubule nucleation factors, but acquired rootletin and appendages only in mature OSNs. The parental centriole had preexisting appendages, formed a single cilium prior to other centrioles, and retained its unique appendage configuration in the mature OSN. We developed an air-liquid interface explant culture system for OSNs and used it to show that centriole migration can be perturbed ex vivo by stabilizing microtubules. We consider these results in the context of a comprehensive model for centriole formation, migration, and maturation in this important sensory cell type.
STOICHIOMETRY OF THE SODIUM PUMP-PHOSPHOLEMMAN REGULATORY COMPLEX
Authors: Seflova Jaroslava , Habibi Nima R. , Yap John Q. , Cleary Sean R. , Fang Xuan , Kekenes-Huskey Peter M. , Espinoza-Fonseca L. Michel , Bossuyt Julie B. , Robia Seth L. 
Published: October 2021

AbstractThe sodium-potassium ATPase (NKA) establishes ion gradients that facilitate many physiological processes. In the heart, NKA activity is regulated by its interaction with phospholemman (PLM, FXYD1). Here we used a novel fluorescence lifetime-based assay to investigate the structure, stoichiometry, and affinity of the NKA-PLM regulatory complex. We observed concentration dependent association of the subunits of NKA-PLM regulatory complex, with avid association of the alpha subunit with the essential beta subunit followed by lower affinity alpha-alpha and alpha-PLM interactions. The data provide the first evidence that the regulatory complex is composed of two alpha subunits associated with two beta subunits, decorated with two PLM regulatory subunits in intact cells. Docking and molecular dynamics simulations generated a structural model of the complex that is consistent with our experimental observations. We propose that alpha-alpha subunit interactions support conformational coupling of the catalytic subunits, which may enhance NKA turnover rate. These observations provide insight into the pathophysiology of heart failure, wherein low NKA expression may be insufficient to support formation of the complete regulatory complex with stoichiometry (alpha-beta-PLM)2.
Topoisomerase II poisons inhibit vertebrate DNA replication through distinct mechanisms
Authors: Van Ravenstein Sabrina X. , Mehta Kavi P. , Kavlashvili Tamar , Byl Jo Ann , Zhao Runxiang , Osheroff Neil , Cortez David , Dewar James M. 
Published: October 2021

AbstractTopoisomerase II (Top2) unlinks chromosomes during vertebrate DNA replication. Top2 ‘poisons’ are widely-used chemotherapeutics that stabilize Top2 complexes on DNA, leading to cytotoxic DNA breaks. However, it is unclear how these drugs affect DNA replication, which is a major target of Top2 poisons. Using Xenopus egg extracts, we show that the Top2 poisons etoposide and doxorubicin both inhibit DNA replication through different mechanisms. Etoposide induces Top2-dependent DNA breaks and induces Top2-dependent fork stalling by trapping Top2 behind replication forks. In contrast, doxorubicin does not lead to appreciable break formation and instead intercalates into parental DNA to inhibit replication fork progression. In human cells, etoposide stalls replication forks in a Top2-dependent manner, while doxorubicin stalls forks independently of Top2. However, both drugs exhibit Top2-dependent cytotoxicity. Thus, despite shared genetic requirements for cytotoxicity etoposide and doxorubicin inhibit DNA replication through distinct mechanisms.
Rapid carbon accumulation at a saltmarsh restored by managed realignment far exceeds carbon emitted in site construction
Authors: Mossman Hannah L. , Pontee Nigel , Born Katie , Lawrence Peter J. , Rae Stuart , Scott James , Serato Beatriz , Sparkes Robert B. , Sullivan Martin J.P. , Dunk Rachel M. 
Published: October 2021

AbstractIncreasing attention is being paid to the carbon sequestration and storage services provided by coastal blue carbon ecosystems such as saltmarshes. Sites restored by managed realignment, where existing sea walls are breached to reinstate tidal inundation to the land behind, have considerable potential to accumulate carbon through deposition of sediment brought in by the tide and burial of vegetation in the site. While this potential has been recognised, it is not yet a common motivating factor for saltmarsh restoration, partly due to uncertainties about the rate of carbon accumulation and how this balances against the greenhouse gases emitted during site construction. We use a combination of field measurements over four years and remote sensing to quantify carbon accumulation at a large managed realignment site, Steart Marshes, UK. Sediment accumulated rapidly at Steart Marshes (mean of 75 mm yr-1) and had a high carbon content (4.4% total carbon, 2.2% total organic carbon), resulting in carbon accumulation of 36.6 t ha-1yr-1total carbon (19.4 t ha- 1yr-1total organic carbon). This rate of carbon accumulation is an order of magnitude higher than reported in many other restored saltmarshes, and is higher although more similar to values previously reported from another hypertidal system (Bay of Fundy, Canada). The estimated carbon emissions associated with the construction of the site were ∼2-4% of the observed carbon accumulation during the study period, supporting the view that managed realignment projects in such settings are likely to have significant carbon accumulation benefits. We outline further considerations that are needed to move towards a full carbon budget for saltmarsh restoration.
The extrachromosomal circular DNAs of the rice blast pathogenMagnaporthe oryzaecontain a wide variety of LTR retrotransposons, genes, and effectors
Authors: Joubert Pierre M. , Krasileva Ksenia V. 
Published: October 2021

AbstractBackgroundOne of the ways genomes respond to stress is by producing extrachromosomal circular DNAs (eccDNAs). EccDNAs can contain genes and dramatically increase their copy number. They can also reinsert into the genome, generating structural variation. They have been shown to provide a source of phenotypic and genotypic plasticity in several species. However, whole circularome studies have so far been limited to a few model organisms. Fungal plant pathogens are a serious threat to global food security in part because of their rapid adaptation to disease prevention strategies. Understanding the mechanisms fungal pathogens use to escape disease control is paramount to curbing their threat.ResultsWe present a whole circularome sequencing study of the rice blast pathogenMagnaporthe oryzae. We find thatM. oryzaehas a highly diverse circularome containing many genes and showing evidence of large LTR retrotransposon activity. We find that genes enriched on eccDNAs inM. oryzaeoccur in genomic regions prone to presence-absence variation and that disease associated genes are frequently on eccDNAs. Finally, we find that a subset of genes is never present on eccDNAs in our data, which indicates that the presence of these genes on eccDNAs is selected against.ConclusionsOur study paves the way to understanding how eccDNAs contribute to adaptation inM. oryzae. Our analysis also reveals howM. oryzaeeccDNAs differ from those of other species and highlights the need for further comparative characterization of eccDNAs across species to gain a better understanding of these molecules.