bluuebunny/crossref_metadata_2025 huggingface dataset:
Pathophysiology of Inflammatory Bowel Disease: Innate Immune System
Authors: Saez Angela , Herrero-Fernandez Beatriz , Gomez-Bris Raquel , Sánchez-Martinez Hector , Gonzalez-Granado Jose M.
Published: January 2023

Inflammatory bowel disease (IBD), comprising Crohn’s disease (CD) and ulcerative colitis (UC), is a heterogeneous state of chronic intestinal inflammation with no exact known cause. Intestinal innate immunity is enacted by neutrophils, monocytes, macrophages, and dendritic cells (DCs), and innate lymphoid cells and NK cells, characterized by their capacity to produce a rapid and nonspecific reaction as a first-line response. Innate immune cells (IIC) defend against pathogens and excessive entry of intestinal microorganisms, while preserving immune tolerance to resident intestinal microbiota. Changes to this equilibrium are linked to intestinal inflammation in the gut and IBD. IICs mediate host defense responses, inflammation, and tissue healing by producing cytokines and chemokines, activating the complement cascade and phagocytosis, or presenting antigens to activate the adaptive immune response. IICs exert important functions that promote or ameliorate the cellular and molecular mechanisms that underlie and sustain IBD. A comprehensive understanding of the mechanisms underlying these clinical manifestations will be important for developing therapies targeting the innate immune system in IBD patients. This review examines the complex roles of and interactions among IICs, and their interactions with other immune and non-immune cells in homeostasis and pathological conditions.
Integrating Analysis to Identify Differential circRNAs Involved in Goat Endometrial Receptivity
Authors: Wang Wenjing , Zang Xupeng , Li Yaokun , Liu Dewu , Hong Linjun , Liu Guangbin
Published: January 2023

Endometrial receptivity is one of the main factors underlying a successful pregnancy, with reports substantiating the fact that suboptimal endometrial receptivity accounts for two-thirds of early implantation event failures. The association between circRNAs and endometrial receptivity in the goat remains unclear. This study aims to identify potential circRNAs and regulatory mechanisms related to goat endometrial receptivity. Therefore, the endometrial samples on day 16 of pregnancy and day 16 of the estrous cycle were analyzed using high-throughput RNA-seq and bioinformatics. The results show that 4666 circRNAs were identified, including 7 downregulated and 11 upregulated differentially expressed circRNAs (DE-circRNAs). Back-splicing and RNase R resistance verified the identified circRNAs. We predicted the competing endogenous RNA (ceRNA) regulatory mechanism and potential target genes of DE-circRNAs. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of these predicted target genes suggest that DE-circRNAs were significantly involved in establishing endometrial receptivity. Furthermore, Sanger sequencing, qPCR, correlation analysis and Fluorescence in Situ Hybridization (FISH) show that circ_MYRF derived from the host gene myelin regulatory factor (MYRF) might regulate the expression of interferon stimulating gene 15 (ISG15), thereby promoting the formation of endometrial receptivity. These novel findings may contribute to a better understanding of the molecular mechanisms regulating endometrial receptivity and promoting the maternal recognition of pregnancy (MRP).
Effect of Pore Defects on Uniaxial Mechanical Properties of Bulk Hexagonal Hydroxyapatite: A Molecular Dynamics Study
Authors: Snyder Alexander D. , Salehinia Iman
Published: January 2023

Hydroxyapatite (HAP) is a calcium apatite bioceramic used in various naturally-derived and synthetic forms for bone repair and regeneration. While useful for the regrowth of osseus tissue, the poor load-bearing capacity of this material relative to other biomaterials is worsened by the propensity for pore formation during the synthetic processing of scaffolds, blocks, and granules. Here we use molecular dynamics (MD) simulations to improve the current understanding of the defect-altered uniaxial mechanical response in hexagonal HAP single crystals relative to defect-free structures. The inclusion of a central spherical pore within a repeated lattice was found to reduce both the failure stress and failure strain in uniaxial tension and compression, with up to a 30% reduction in maximum stress at the point of failure compared to a perfect crystalline structure observed when a 30 Å diameter pore was included. The Z axis ([0 0 0 1] crystalline direction) was found to be the least susceptible to pore defects in tension but the most sensitive to pore inclusion in compression. The deformation mechanisms are discussed to explain the observed mechanical responses, for which charge imbalances and geometric stress concentration factor effects caused by pore inclusion play a significant role.
Effect of Antibiotic Exposure on Staphylococcus epidermidis Responsible for Catheter-Related Bacteremia
Authors: Pouget Cassandra , Chatre Clotilde , Lavigne Jean-Philippe , Pantel Alix , Reynes Jacques , Dunyach-Remy Catherine
Published: January 2023

Coagulase-negative staphylococci (CoNS) and especially Staphylococcus epidermidis are responsible for health care infections, notably in the presence of foreign material (e.g., venous or central-line catheters). Catheter-related bacteremia (CRB) increases health care costs and mortality. The aim of our study was to evaluate the impact of 15 days of antibiotic exposure (ceftobiprole, daptomycin, linezolid and vancomycin) at sub-inhibitory concentration on the resistance, fitness and genome evolution of 36 clinical strains of S. epidermidis responsible for CRB. Resistance was evaluated by antibiogram, the ability to adapt metabolism by the Biofilm Ring test® and the in vivo nematode virulence model. The impact of antibiotic exposure was determined by whole-genome sequencing (WGS) and biofilm formation experiments. We observed that S. epidermidis strains presented a wide variety of virulence potential and biofilm formation. After antibiotic exposure, S. epidermidis strains adapted their fitness with an increase in biofilm formation. Antibiotic exposure also affected genes involved in resistance and was responsible for cross-resistance between vancomycin, daptomycin and ceftobiprole. Our data confirmed that antibiotic exposure modified bacterial pathogenicity and the emergence of resistant bacteria.
Involvement of miR-135a-5p Downregulation in Acute and Chronic Stress Response in the Prefrontal Cortex of Rats
Authors: Mingardi Jessica , Paoli Caterina , La Via Luca , Carini Giulia , Misztak Paulina , Cifani Carlo , Popoli Maurizio , Barbon Alessandro , Musazzi Laura
Published: January 2023

Stress is a key risk factor in the onset of neuropsychiatric disorders. The study of the mechanisms underlying stress response is important to understand the etiopathogenetic mechanisms and identify new putative therapeutic targets. In this context, microRNAs (miRNAs) have emerged as key regulators of the complex patterns of gene/protein expression changes in the brain, where they have a crucial role in the regulation of neuroplasticity, neurogenesis, and neuronal differentiation. Among them, miR-135a-5p has been associated with stress response, synaptic plasticity, and the antidepressant effect in different brain areas. Here, we used acute unavoidable foot-shock stress (FS) and chronic mild stress (CMS) on male rats to study whether miR-135a-5p was involved in stress-induced changes in the prefrontal cortex (PFC). Both acute and chronic stress decreased miR-135a-5p levels in the PFC, although after CMS the reduction was induced only in animals vulnerable to CMS, according to a sucrose preference test. MiR-135a-5p downregulation in the primary neurons reduced dendritic spine density, while its overexpression exerted the opposite effect. Two bioinformatically predicted target genes, Kif5c and Cplx1/2, were increased in FS rats 24 h after stress. Altogether, we found that miR-135a-5p might play a role in stress response in PFC involving synaptic mechanisms.
Endoplasmic Reticulum Stress and Cancer: Could Unfolded Protein Response Be a Druggable Target for Cancer Therapy?
Authors: Bonsignore Gregorio , Martinotti Simona , Ranzato Elia
Published: January 2023

Unfolded protein response (UPR) is an adaptive response which is used for re-establishing protein homeostasis, and it is triggered by endoplasmic reticulum (ER) stress. Specific ER proteins mediate UPR activation, after dissociation from chaperone Glucose-Regulated Protein 78 (GRP78). UPR can decrease ER stress, producing an ER adaptive response, block UPR if ER homeostasis is restored, or regulate apoptosis. Some tumour types are linked to ER protein folding machinery disturbance, highlighting how UPR plays a pivotal role in cancer cells to keep malignancy and drug resistance. In this review, we focus on some molecules that have been revealed to target ER stress demonstrating as UPR could be a new target in cancer treatment.
Gender Differences and Cardiometabolic Risk: The Importance of the Risk Factors
Authors: Meloni Antonella , Cadeddu Christian , Cugusi Lucia , Donataccio Maria Pia , Deidda Martino , Sciomer Susanna , Gallina Sabina , Vassalle Cristina , Moscucci Federica , Mercuro Giuseppe , Maffei Silvia
Published: January 2023

Metabolic syndrome (Mets) is a clinical condition characterized by a cluster of major risk factors for cardiovascular disease (CVD) and type 2 diabetes: proatherogenic dyslipidemia, elevated blood pressure, dysglycemia, and abdominal obesity. Each risk factor has an independent effect, but, when aggregated, they become synergistic, doubling the risk of developing cardiovascular diseases and causing a 1.5-fold increase in all-cause mortality. We will highlight gender differences in the epidemiology, etiology, pathophysiology, and clinical expression of the aforementioned Mets components. Moreover, we will discuss gender differences in new biochemical markers of metabolic syndrome and cardiovascular risk.
Esculetin Alleviates Nonalcoholic Fatty Liver Disease on High-Cholesterol-Diet-Induced Larval Zebrafish and FFA-Induced BRL-3A Hepatocyte
Authors: Ma Ji , Deng Yang , Yang Tingting , Li Maoru , Shang Jing
Published: January 2023

Non-alcoholic fatty liver disease (NAFLD), defined in recent years as metabolic-associated fatty liver disease (MAFLD), is one of the most common liver diseases in the world, with no drugs on market. Esculetin (ESC) is an active compound discovered in a variety of natural products that modulates a wide range of metabolic diseases and is a potential drug for the treatment of NAFLD. In this study, we used an HCD-induced NAFLD larval zebrafish model in vivo and an FFA-induced BRL-3A hepatocyte model in vitro to evaluate the anti-NAFLD effect of ESC. Lipid lowering, anti-oxidation and anti-inflammation effects were revealed on ESC and related gene changes were observed. This study provides a reference for further study and development of ESC as a potential anti-NAFLD/MAFLD drug.
Cytoplasmic Expression of TP53INP2 Modulated by Demethylase FTO and Mutant NPM1 Promotes Autophagy in Leukemia Cells
Authors: Huang Junpeng , Sun Minghui , Tao Yonghong , Ren Jun , Peng Meixi , Jing Yipei , Xiao Qiaoling , Yang Jing , Lin Can , Lei Li , Yang Zailin , Zhang Ling
Published: January 2023

Acute myeloid leukemia (AML) with a nucleophosmin 1 (NPM1) mutation is a unique subtype of adult leukemia. Recent studies show that NPM1-mutated AML has high autophagy activity. However, the mechanism for upholding the high autophagic level is still not fully elucidated. In this study, we first identified that tumor protein p53 inducible nuclear protein 2 (TP53INP2) was highly expressed and cytoplasmically localized in NPM1-mutated AML cells. Subsequent data showed that the expression of TP53INP2 was upregulated by fat mass and obesity-associated protein (FTO)-mediated m6A modification. Meanwhile, TP53INP2 was delocalized to the cytoplasm by interacting with NPM1 mutants. Functionally, cytoplasmic TP53INP2 enhanced autophagy activity by promoting the interaction of microtubule-associated protein 1 light chain 3 (LC3) - autophagy-related 7 (ATG7) and further facilitated the survival of leukemia cells. Taken together, our study indicates that TP53INP2 plays an oncogenic role in maintaining the high autophagy activity of NPM1-mutated AML and provides further insight into autophagy-targeted therapy of this leukemia subtype.
Corydalis saxicola Bunting: A Review of Its Traditional Uses, Phytochemistry, Pharmacology, and Clinical Applications
Authors: Qin Feng , Chen Yao , Wang Fan-Fan , Tang Shao-Qing , Fang Yi-Lin
Published: January 2023

Corydalis saxicola Bunting (CSB), whose common name in Chinese is Yanhuanglian, is a herb in the family Papaveraceae. When applied in traditional Chinese medicine, it is used to treat various diseases including hepatitis, abdominal pain, and bleeding haemorrhoids. In addition, Corydalis saxicola Bunting injection (CSBI) is widely used against acute and chronic hepatitis. This review aims to provide up-to-date information on the botanical distribution, description, traditional uses, phytochemistry, pharmacology, and clinical applications of CSB. A comprehensive review was implemented on studies about CSB from several scientific databases, such as SciFinder, Elsevier, Springer, ACS Publications, Baidu Scholar, CNKI, and Wanfang Data. Phytochemical studies showed that 81 chemical constituents have been isolated and identified from CSB, most of which are alkaloids. This situation indicates that these alkaloids would be the main bioactive substances and that they have antitumour, liver protective, antiviral, and antibacterial pharmacological activities. CSBI can not only treat hepatitis and liver cancer but can also be used in combination with other drugs. However, the relationships between the traditional uses and modern pharmacological actions, the action mechanisms, quality standards, and the material basis need to be implemented in the future. Moreover, the pharmacokinetics of CSBI in vivo and the toxicology should be further investigated.
Advances and Highlights of miRNAs in Asthma: Biomarkers for Diagnosis and Treatment
Authors: Gil-Martínez Marta , Lorente-Sorolla Clara , Naharro Sara , Rodrigo-Muñoz José M. , del Pozo Victoria
Published: January 2023

Asthma is a heterogeneous inflammatory disease of the airways that causes breathing difficulties, episodes of cough and wheezing, and in more severe cases can greatly diminish quality of life. Epigenetic regulation, including post-transcriptional mediation of microRNAs (miRNAs), is one of the mechanisms behind the development of the range of asthma phenotypes and endotypes. As in every other immune-mediated disease, miRNAs regulate the behavior of cells that shape the airway structure as well as those in charge of the defense mechanisms in the bronchi and lungs, controlling cell survival, growth, proliferation, and the ability of cells to synthesize and secrete chemokines and immune mediators. More importantly, miRNAs are molecules with chemical and biological properties that make them appropriate biomarkers for disease, enabling stratification of patients for optimal drug selection and thereby simplifying clinical management and reducing both the economic burden and need for critical care associated with the disease. In this review, we summarize the roles of miRNAs in asthma and describe how they regulate the mechanisms of the disease. We further describe the current state of miRNAs as biomarkers for asthma phenotyping, endotyping, and treatment selection.
Synapse Dysfunctions in Multiple Sclerosis
Authors: Schwarz Karin , Schmitz Frank
Published: January 2023

Multiple sclerosis (MS) is a chronic neuroinflammatory disease of the central nervous system (CNS) affecting nearly three million humans worldwide. In MS, cells of an auto-reactive immune system invade the brain and cause neuroinflammation. Neuroinflammation triggers a complex, multi-faceted harmful process not only in the white matter but also in the grey matter of the brain. In the grey matter, neuroinflammation causes synapse dysfunctions. Synapse dysfunctions in MS occur early and independent from white matter demyelination and are likely correlates of cognitive and mental symptoms in MS. Disturbed synapse/glia interactions and elevated neuroinflammatory signals play a central role. Glutamatergic excitotoxic synapse damage emerges as a major mechanism. We review synapse/glia communication under normal conditions and summarize how this communication becomes malfunctional during neuroinflammation in MS. We discuss mechanisms of how disturbed glia/synapse communication can lead to synapse dysfunctions, signaling dysbalance, and neurodegeneration in MS.
siRNA-Mediated Timp1 Silencing Inhibited the Inflammatory Phenotype during Acute Lung Injury
Authors: Chernikov Ivan V. , Staroseletz Yaroslav Yu. , Tatarnikova Irina S. , Sen’kova Aleksandra V. , Savin Innokenty A. , Markov Andrey V. , Logashenko Evgeniya B. , Chernolovskaya Elena L. , Zenkova Marina A. , Vlassov Valentin V.
Published: January 2023

Acute lung injury is a complex cascade process that develops in response to various damaging factors, which can lead to acute respiratory distress syndrome. Within this study, based on bioinformatics reanalysis of available full-transcriptome data of acute lung injury induced in mice and humans by various factors, we selected a set of genes that could serve as good targets for suppressing inflammation in the lung tissue, evaluated their expression in the cells of different origins during LPS-induced inflammation, and chose the tissue inhibitor of metalloproteinase Timp1 as a promising target for suppressing inflammation. We designed an effective chemically modified anti-TIMP1 siRNA and showed that Timp1 silencing correlates with a decrease in the pro-inflammatory cytokine IL6 secretion in cultured macrophage cells and reduces the severity of LPS-induced acute lung injury in a mouse model.
COVID-19 Plasma Extracellular Vesicles Increase the Density of Lipid Rafts in Human Small Airway Epithelial Cells
Authors: Darwish Sara , Liu Lauren P. , Robinson Tanya O. , Tarugu Spurthi , Owings Anna H. , Glover Sarah C. , Alli Abdel A.
Published: January 2023

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus is the causative agent of the COVID-19 disease. COVID-19 viral infection can affect many cell types, including epithelial cells of the lungs and airways. Extracellular vesicles (EVs) are released by virtually all cell types, and their packaged cargo allows for intercellular communication, cell differentiation, and signal transduction. Cargo from virus-infected cells may include virally derived metabolites, miRNAs, nucleic acids, and proteins. We hypothesized that COVID-19 plasma EVs can induce the formation of signaling platforms known as lipid rafts after uptake by normal human small airway epithelial cells (SAECs). Circulating EVs from patients with or without COVID-19 were characterized by nanoparticle tracking analysis, Western blotting using specific antibodies, and transmission electron microscopy. Primary cultures of normal human small airway epithelial cells were challenged with EVs from the two patient groups, and lipid raft formation was measured by fluorescence microscopy and assessed by sucrose density gradient analysis. Collectively, our data suggest that circulating EVs from COVID-19-infected patients can induce the formation of lipid rafts in normal human small airway epithelial cells. These results suggest the need for future studies aimed at investigating whether the increased density of lipid rafts in these cells promotes viral entry and alteration of specific signaling pathways in the recipient cells.
The Use of Electrochemical Methods to Determine the Effect of Nitrides of Alloying Elements on the Electrochemical Properties of Titanium β-Alloys
Authors: Jírů Jitřenka , Hybášek Vojtěch , Vlčák Petr , Fojt Jaroslav
Published: January 2023

Titanium beta alloys represent the new generation of materials for the manufacturing of joint implants. Their Young’s modulus is lower and thus closer to the bone tissue compared to commonly used alloys. The surface tribological properties of these materials should be improved by ion implantation. The influence of this surface treatment on corrosion behaviour is unknown. The surface of Ti-36Nb-6Ta, Ti-36Nb-4Zr, and Ti-39Nb titanium β-alloys was modified using nitrogen ion implantation. X-ray photoelectron spectroscopy was used for surface analysis, which showed the presence of titanium, niobium, and tantalum nitrides in the treated samples and the elimination of less stable oxides. Electrochemical methods, electrochemical impedance spectra, polarisation resistance, and Mott–Schottky plot were measured in a physiological saline solution. The results of the measurements showed that ion implantation does not have a significant negative effect on the corrosion behaviour of the material. The best results of the alloys investigated were achieved by the Ti-36Nb-6Ta alloy. The combination of niobium and tantalum nitrides had a positive effect on the corrosion resistance of this alloy. After surface treatment, the polarization resistance of this alloy increased, 2.3 × 106 Ω·cm2, demonstrating higher corrosion resistance of the alloy. These results were also supported by the results of electrochemical impedance spectroscopy.
Prioritization of New Candidate Genes for Rare Genetic Diseases by a Disease-Aware Evaluation of Heterogeneous Molecular Networks
Authors: de la Fuente Lorena , Del Pozo-Valero Marta , Perea-Romero Irene , Blanco-Kelly Fiona , Fernández-Caballero Lidia , Cortón Marta , Ayuso Carmen , Mínguez Pablo
Published: January 2023

Screening for pathogenic variants in the diagnosis of rare genetic diseases can now be performed on all genes thanks to the application of whole exome and genome sequencing (WES, WGS). Yet the repertoire of gene–disease associations is not complete. Several computer-based algorithms and databases integrate distinct gene–gene functional networks to accelerate the discovery of gene–disease associations. We hypothesize that the ability of every type of information to extract relevant insights is disease-dependent. We compiled 33 functional networks classified into 13 knowledge categories (KCs) and observed large variability in their ability to recover genes associated with 91 genetic diseases, as measured using efficiency and exclusivity. We developed GLOWgenes, a network-based algorithm that applies random walk with restart to evaluate KCs’ ability to recover genes from a given list associated with a phenotype and modulates the prediction of new candidates accordingly. Comparison with other integration strategies and tools shows that our disease-aware approach can boost the discovery of new gene–disease associations, especially for the less obvious ones. KC contribution also varies if obtained using recently discovered genes. Applied to 15 unsolved WES, GLOWgenes proposed three new genes to be involved in the phenotypes of patients with syndromic inherited retinal dystrophies.
Cross-Talk between N6-Methyladenosine and Their Related RNAs Defined a Signature and Confirmed m6A Regulators for Diagnosis of Endometriosis
Authors: Wang Xiaotong , Zhao Xibo , Wang Jing , Wu Han , Cheng Yan , Guo Qiuyan , Liang Tian , Zhang Guangmei
Published: January 2023

An RNA modification known as N6-methyladenosine (m6A) interacts with a range of coding and non-coding RNAs. The majority of the research has focused on identifying m6A regulators that are differentially expressed in endometriosis, but it has ignored their mechanisms that are derived from the alterations of modifications among RNAs, affecting the disease progression primarily. Here, we aimed to investigate the potential roles of m6A regulators in the diagnostic potency, immune microenvironment, and clinicopathological features of endometriosis through interacting genes. A GEO cohort was incorporated into this study. Variance expression profiling was executed via the “limma” R package. Pearson analysis was performed to investigate the correlations among 767 interacting lncRNAs, 374 interacting mRNAs, and 23 m6A regulators. K-means clustering analysis, based on patterns of mRNA modifications, was applied to perform clinical feature analysis. Infiltrating immune cells and stromal cells were calculated using the Cibersort method. An m6A-related risk model was created and supported by an independent risk assay. LASSO regression analysis and Cox analyses were implemented to determine the diagnostic genes. The diagnostic targets of endometriosis were verified using PCR and the WB method. Results: A thorough investigation of the m6A modification patterns in the GEO database was carried out, based on mRNAs and lncRNAs related to these m6A regulators. Two molecular subtypes were identified using unsupervised clustering analysis, resulting in further complex infiltration levels of immune microenvironment cells in diversified endometriosis pathology types. We identified two m6A regulators, namely METTL3 and YTHDF2, as diagnostic targets of endometriosis following the usage of overlapping genes to construct a diagnostic m6A signature of endometriosis through multivariate logistic regression, and we validated it using independent GSE86534 and GSE105764 cohorts. Finally, we found that m6A alterations might be one of the important reasons for the progression of endometriosis, especially with significant downregulation of the expressions of METTL3 and YTHDF2. Finally, m6A modification patterns have significant effects on the diversity and complexity of the progression and immune microenvironment, and might be key diagnostic markers for endometriosis.
Different Geographic Strains of Dinoflagellate Karlodinium veneficum Host Highly Diverse Fungal Community and Potentially Serve as Possible Niche for Colonization of Fungal Endophytes
Authors: Deng Yunyan , Wang Kui , Hu Zhangxi , Hu Qiang , Tang Yingzhong
Published: January 2023

In numerous studies, researchers have explored the interactions between fungi and their hosting biota in terrestrial systems, while much less attention has been paid to the counterpart interactions in aquatic, and particularly marine, ecosystems. Despite the growing recognition of the potential functions of fungi in structuring phytoplankton communities, the current insights were mostly derived from phytoplankton hosts, such as diatoms, green microalgae, and cyanobacteria. Dinoflagellates are the second most abundant group of phytoplankton in coastal marine ecosystems, and they are notorious for causing harmful algal blooms (HABs). In this study, we used high-throughput amplicon sequencing to capture global snapshots of specific fungal assemblages associated with laboratory-cultured marine dinoflagellate. We investigated a total of 13 clonal cultures of the dinoflagellate Karlodinium veneficum that were previously isolated from 5 geographic origins and have been maintained in our laboratory from several months to more than 14 years. The total recovered fungal microbiome, which consisted of 349 ASVs (amplicon sequencing variants, sequences clustered at a 100% sequence identity), could be assigned to 4 phyla, 18 classes, 37 orders, 65 families, 97 genera, and 131 species. The fungal consortium displayed high diversity and was dominated by filamentous fungi and ascomycetous and basidiomycetous yeasts. A core set of three genera among all the detected fungi was constitutively present in the K. veneficum strains isolated from geographically distant regions, with the top two most abundant genera, Thyridium and Pseudeurotium, capable of using hydrocarbons as the sole or major source of carbon and energy. In addition, fungal taxa previously documented as endophytes in other hosts were also found in all tested strains of K. veneficum. Because host–endophyte interactions are highly variable and strongly case-dependent, these fungal taxa were not necessarily genuine endosymbionts of K. veneficum; instead, it raised the possibility that dinoflagellates could potentially serve as an alternative ecological niche for the colonization of fungal endophytes. Our findings lay the foundation for further investigations into the potential roles or functions of fungi in the regulation of the growth dynamics and HABs of marine dinoflagellates in the field.
Hydroxylated Coumarin-Based Thiosemicarbazones as Dual Antityrosinase and Antioxidant Agents
Authors: Masuri Sebastiano , Era Benedetta , Pintus Francesca , Cadoni Enzo , Cabiddu Maria Grazia , Fais Antonella , Pivetta Tiziana
Published: January 2023

The design of novel antityrosinase agents appears extremely important in medical and industrial sectors because an irregular production of melanin is related to the insurgence of several skin-related disorders (e.g., melanoma) and the browning process of fruits and vegetables. Because melanogenesis also involves a nonenzymatic oxidative process, developing dual antioxidant and antityrosinase agents is advantageous. In this work, we evaluated the antioxidant and tyrosinase inhibition ability of two new bishydroxylated and two new monohydroxylated derivatives of (1E)-2-(1-(2-oxo-2H-chromen-3-yl)ethylidene)hydrazine-1-carbothioamide (T1) using different experimental and computational approaches. The study was also carried out on another monohydroxylated derivative of T1 for comparison. Interestingly, these molecules have more potent tyrosinase-inhibitory properties than the reference compound, kojic acid. Moreover, the antioxidant activity appears to be influenced according to the number and substitution pattern of the hydroxyl groups. The safety of the compounds without (T1), with one (T3), and with two (T6) hydroxyl groups, has also been assessed by studying their cytotoxicity on melanocytes. These results indicate that (1E)-2-(1-(2-oxo-2H-chromen-3-yl)ethylidene)hydrazine-1-carbothioamide and its hydroxylated derivatives are promising molecules for further drug development studies.
Properties of Gaseous Deprotonated L-Cysteine S-Sulfate Anion [cysS-SO3]−: Intramolecular H-Bond Network, Electron Affinity, Chemically Active Site, and Vibrational Fingerprints
Authors: Wang Qiaolin , Qin Zhengbo , Hou Gao-Lei , Yang Zheng , Valiev Marat , Wang Xue-Bin , Zheng Xianfeng , Cui Zhifeng
Published: January 2023

L-cysteine S-sulfate, Cys-SSO3H, and their derivatives play essential roles in biological chemistry and pharmaceutical synthesis, yet their intrinsic molecular properties have not been studied to date. In this contribution, the deprotonated anion [cysS-SO3]− was introduced in the gas phase by electrospray and characterized by size-selected, cryogenic, negative ion photoelectron spectroscopy. The electron affinity of the [cysS-SO3]• radical was determined to be 4.95 ± 0.10 eV. In combination with theoretical calculations, it was found that the most stable structure of [cysS-SO3]− (S1) is stabilized via three intramolecular hydrogen bonds (HBs); i.e., one O−H⋯⋯N between the –COOH and –NH2 groups, and two N−H⋯⋯O HBs between –NH2 and –SO3, in which the amino group serves as both HB acceptor and donor. In addition, a nearly iso-energetic conformer (S2) with the formation of an O−H⋯⋯N−H⋯⋯O−S chain-type binding motif competes with S1 in the source. The most reactive site of the molecule susceptible for electrophilic attacks is the linkage S atom. Theoretically predicted infrared spectra indicate that O−H and N−H stretching modes are the fingerprint region (2800 to 3600 cm−1) to distinguish different isomers. The obtained information lays out a foundation to better understand the transformation and structure–reactivity correlation of Cys-SSO3H in biologic settings.
Ionophore Toxicity in Animals: A Review of Clinical and Molecular Aspects
Authors: Ekinci İlksen Berfin , Chłodowska Agnieszka , Olejnik Małgorzata
Published: January 2023

For many years, ionophores have been used to control coccidiosis in poultry. However, misuse of ionophores can cause toxicity with significant clinical symptoms. The most critical factors influencing ionophores’ toxicity are administration dose, species, and animal age. Although clinical signs of ionophore intoxication are well studied, the toxicity mechanisms of the ionophores at the molecular level still are not fully elucidated. This review summarizes the studies focused on polyether ionophores toxicity mechanisms in animals at the clinical and molecular levels. Studies show that ionophore toxicity mainly affects myocardial and skeletal muscle cells. The molecular mechanism of the toxication could be explained by the inhibition of oxidative phosphorylation via dysregulation of ion concentration. Tiamulin-ionophore interaction and the synergetic effect of tiamulin in ionophore biotransformation are discussed. Furthermore, in recent years ionophores were candidates for reprofiling as antibacterial and anti-cancer drugs. Identifying ionophores’ toxicity mechanisms at the cellular level will likely help develop novel therapies in veterinary and human medicine.
GLP-1 Receptor Agonists in Non-Alcoholic Fatty Liver Disease: Current Evidence and Future Perspectives
Authors: Nevola Riccardo , Epifani Raffaella , Imbriani Simona , Tortorella Giovanni , Aprea Concetta , Galiero Raffaele , Rinaldi Luca , Marfella Raffaele , Sasso Ferdinando Carlo
Published: January 2023

To date, non-alcoholic fatty liver disease (NAFLD) is the most frequent liver disease, affecting up to 70% of patients with diabetes. Currently, there are no specific drugs available for its treatment. Beyond their anti-hyperglycemic effect and the surprising role of cardio- and nephroprotection, GLP-1 receptor agonists (GLP-1 RAs) have shown a significant impact on body weight and clinical, biochemical and histological markers of fatty liver and fibrosis in patients with NAFLD. Therefore, GLP-1 RAs could be a weapon for the treatment of both diabetes mellitus and NAFLD. The aim of this review is to summarize the evidence currently available on the role of GLP-1 RAs in the treatment of NAFLD and to hypothesize potential future scenarios.
Jasmonic Acid-Induced β-Cyclocitral Confers Resistance to Bacterial Blight and Negatively Affects Abscisic Acid Biosynthesis in Rice
Authors: Taniguchi Shiduku , Takeda Aya , Kiryu Masaki , Gomi Kenji
Published: January 2023

Jasmonic acid (JA) regulates the production of several plant volatiles that are involved in plant defense mechanisms. In this study, we report that the JA-responsive volatile apocarotenoid, β-cyclocitral (β-cyc), negatively affects abscisic acid (ABA) biosynthesis and induces a defense response against Xanthomonas oryzae pv. oryzae (Xoo), which causes bacterial blight in rice (Oryza sativa L.). JA-induced accumulation of β-cyc was regulated by OsJAZ8, a repressor of JA signaling in rice. Treatment with β-cyc induced resistance against Xoo and upregulated the expression of defense-related genes in rice. Conversely, the expression of ABA-responsive genes, including ABA-biosynthesis genes, was downregulated by JA and β-cyc treatment, resulting in a decrease in ABA levels in rice. β-cyc did not inhibit the ABA-dependent interactions between OsPYL/RCAR5 and OsPP2C49 in yeast cells. Furthermore, we revealed that JA-responsive rice carotenoid cleavage dioxygenase 4b (OsCCD4b) was localized in the chloroplast and produced β-cyc both in vitro and in planta. These results suggest that β-cyc plays an important role in the JA-mediated resistance against Xoo in rice.
Antibacterial Thin Films Deposited from Propane–Butane Mixture in Atmospheric Pressure Discharge
Authors: Sťahel Pavel , Mazánková Věra , Podzemná Daniela , Podzemná Erika , Pizúrová Veronika , Jurmanová Jana , Prokeš Lubomír , Lehocký Marián , Ozaltin Kadir , Pištěková Hana , Trunec David
Published: January 2023

Antibacterial coatings on biomedical instruments are of great interest because they can suppress bacterial colonization on these instruments. In this study, antibacterial polymeric thin coatings were deposited on teflon substrates using atmospheric pressure plasma polymerization from a propane–butane mixture. The plasma polymerization was performed by means of surface dielectric barrier discharge burning in nitrogen at atmospheric pressure. The chemical composition of plasma polymerized propane–butane films was studied by energy-dispersive X-ray spectroscopy (EDX) and FTIR. The film surface properties were studied by SEM and by surface energy measurement. The EDX analysis showed that the films consisted of carbon, nitrogen and oxygen from ambient air. The FTIR analysis confirmed, in particular, the presence of alkyl, nitrile, acetylene, imide and amine groups. The deposited films were hydrophilic with a water contact angle in the range of 13–23°. The thin film deposited samples were highly active against both S. aureus and E. coli strains in general. On the other hand, the films were cytocompatible, reaching more than 80% of the cell viability threshold compared to reference polystyrene tissue.
Lipidomics—Paving the Road towards Better Insight and Precision Medicine in Rare Metabolic Diseases
Authors: Zandl-Lang Martina , Plecko Barbara , Köfeler Harald
Published: January 2023

Even though the application of Next-Generation Sequencing (NGS) has significantly facilitated the identification of disease-associated mutations, the diagnostic rate of rare diseases is still below 50%. This causes a diagnostic odyssey and prevents specific treatment, as well as genetic counseling for further family planning. Increasing the diagnostic rate and reducing the time to diagnosis in children with unclear disease are crucial for a better patient outcome and improvement of quality of life. In many cases, NGS reveals variants of unknown significance (VUS) that need further investigations. The delineation of novel (lipid) biomarkers is not only crucial to prove the pathogenicity of VUS, but provides surrogate parameters for the monitoring of disease progression and therapeutic interventions. Lipids are essential organic compounds in living organisms, serving as building blocks for cellular membranes, energy storage and signaling molecules. Among other disorders, an imbalance in lipid homeostasis can lead to chronic inflammation, vascular dysfunction and neurodegenerative diseases. Therefore, analyzing lipids in biological samples provides great insight into the underlying functional role of lipids in healthy and disease statuses. The method of choice for lipid analysis and/or huge assemblies of lipids (=lipidome) is mass spectrometry due to its high sensitivity and specificity. Due to the inherent chemical complexity of the lipidome and the consequent challenges associated with analyzing it, progress in the field of lipidomics has lagged behind other omics disciplines. However, compared to the previous decade, the output of publications on lipidomics has increased more than 17-fold within the last decade and has, therefore, become one of the fastest-growing research fields. Combining multiple omics approaches will provide a unique and efficient tool for determining pathogenicity of VUS at the functional level, and thereby identifying rare, as well as novel, genetic disorders by molecular techniques and biochemical analyses.
Establishment of Mucoepidermoid Carcinoma Cell Lines from Surgical and Recurrence Biopsy Specimens
Authors: Yamanaka Shunpei , Suzuki Susumu , Ito Hideaki , Sivasundaram Karnan , Hanamura Ichiro , Okubo Ikuko , Yoshikawa Kazuhiro , Ono Shoya , Takahara Taishi , Satou Akira , Tsuzuki Toyonori , Ueda Ryuzo , Ogawa Tetsuya , Fujimoto Yasushi
Published: January 2023

Patients with advanced/recurrent mucoepidermoid carcinoma (MEC) have a poor prognosis. This study aimed to establish and characterize human mucoepidermoid carcinoma cell lines from the initial surgical specimen and biopsy specimen upon recurrence from the same patient to provide a resource for MEC research. MEC specimens from the initial surgical procedure and biopsy upon recurrence were used to establish cell lines. The established cell lines were cytogenetically characterized using multi-color fluorescence in situ hybridization and detection, and the sequence of the CRTC1-MAML2 chimeric gene was determined. Furthermore, the susceptibility of head and neck mucoepidermoid carcinoma to standard treatment drugs such as cisplatin, 5-fluorouracil, and cetuximab was investigated. We successfully established unique MEC cell lines, AMU-MEC1, from an initial surgical specimen and AMU-MEC1-R1 and AMU-MEC1-R2 from the recurrent biopsy specimen in the same patient. These cell lines exhibited epithelial morphology and developed in vitro-like cobblestones. They shared eight chromosomal abnormalities, including der(19)ins(19;11)(p13;?), which resulted in a chimeric CRTC1-MAML2 gene, indicating the same origin of the cell lines. The susceptibility of all cell lines to cisplatin and 5-fluorouracil was low. Interestingly, EGFR dependency for cell growth decreased in AMU-MEC-R1 and AMU-MEC-R2 but was retained in AMU-MEC1. These cytogenetic and biochemical findings suggest that the established cell lines can be used to investigate the disease progression mechanisms and develop novel therapeutics for MEC.
Cervical Secretion Methylation Is Associated with the Pregnancy Outcome of Frozen-Thawed Embryo Transfer
Authors: Lee Yi-Xuan , Su Po-Hsuan , Do Anh Q. , Tzeng Chii-Ruei , Hu Yu-Ming , Chen Chi-Huang , Chen Chien-Wen , Liao Chi-Chun , Chen Lin-Yu , Weng Yu-Chun , Wang Hui-Chen , Lai Hung-Cheng
Published: January 2023

The causes of implantation failure remain a black box in reproductive medicine. The exact mechanism behind the regulation of endometrial receptivity is still unknown. Epigenetic modifications influence gene expression patterns and may alter the receptivity of human endometrium. Cervical secretions contain endometrial genetic material, which can be used as an indicator of the endometrial condition. This study evaluates the association between the cervical secretion gene methylation profile and pregnancy outcome in a frozen-thawed embryonic transfer (FET) cycle. Cervical secretions were collected from women who entered the FET cycle with a blastocyst transfer (36 pregnant and 36 non-pregnant women). The DNA methylation profiles of six candidate genes selected from the literature review were measured by quantitative methylation-specific PCR (qMSP). Bioinformatic analysis of six selected candidate genes showed significant differences in DNA methylation between receptive and pre-receptive endometrium. All candidate genes showed different degrees of correlation with the pregnancy outcomes in the logistic regression model. A machine learning approach showed that the combination of candidate genes’ DNA methylation profiles could differentiate pregnant from non-pregnant samples with an accuracy as high as 86.67% and an AUC of 0.81. This study demonstrated the association between cervical secretion methylation profiles and pregnancy outcomes in an FET cycle and provides a basis for potential clinical application as a non-invasive method for implantation prediction.
Epigenetic Modification of Cytosines in Hematopoietic Differentiation and Malignant Transformation
Authors: An Jungeun , Ko Myunggon
Published: January 2023

The mammalian DNA methylation landscape is established and maintained by the combined activities of the two key epigenetic modifiers, DNA methyltransferases (DNMT) and Ten-eleven-translocation (TET) enzymes. Once DNMTs produce 5-methylcytosine (5mC), TET proteins fine-tune the DNA methylation status by consecutively oxidizing 5mC to 5-hydroxymethylcytosine (5hmC) and further oxidized derivatives. The 5mC and oxidized methylcytosines are essential for the maintenance of cellular identity and function during differentiation. Cytosine modifications with DNMT and TET enzymes exert pleiotropic effects on various aspects of hematopoiesis, including self-renewal of hematopoietic stem/progenitor cells (HSPCs), lineage determination, differentiation, and function. Under pathological conditions, these enzymes are frequently dysregulated, leading to loss of function. In particular, the loss of DNMT3A and TET2 function is conspicuous in diverse hematological disorders, including myeloid and lymphoid malignancies, and causally related to clonal hematopoiesis and malignant transformation. Here, we update recent advances in understanding how the maintenance of DNA methylation homeostasis by DNMT and TET proteins influences normal hematopoiesis and malignant transformation, highlighting the potential impact of DNMT3A and TET2 dysregulation on clonal dominance and evolution of pre-leukemic stem cells to full-blown malignancies. Clarification of the normal and pathological functions of DNA-modifying epigenetic regulators will be crucial to future innovations in epigenetic therapies for treating hematological disorders.
Yth m6A RNA-Binding Protein 1 Regulates Osteogenesis of MC3T3-E1 Cells under Hypoxia via Translational Control of Thrombospondin-1
Authors: Shi Diwen , Liu Xiaohan , Li Xinyun , Li Tian , Liu Jie , Wu Lin
Published: January 2023

Peri-implantitis is a major factor affecting implant prognosis, and the specific anatomy of the peri-implant area makes it more vulnerable to the local hypoxic environment caused by inflammation. N6-methyladenosine (m6A) plays a vital role in a multitude of biological processes, and its main “reader” Yth m6A RNA-binding protein 1 (YTHDF1) is suggested to affect osteogenic differentiation. However, the mechanism underlying the effect of YTHDF1 on osteogenic differentiation under hypoxic conditions remains unclear. To address this question, we examined the expression of YTHDF1 under hypoxia and observed that hypoxia suppressed osteogenic differentiation but promoted the expression of YTHDF1. Then we knocked down YTHDF1 and found decreased levels of osteogenic-related markers, alkaline phosphatase (ALP) activity, and alizarin red staining (ARS) under normoxia or hypoxia treatment. Bioinformatics analysis identified Thrombospondin-1 (THBS1) might be a downstream factor of YTHDF1. The results revealed that YTHDF1 enhanced the stability of THBS1 mRNA, and immunofluorescence assays found co-localization with YTHDF1 and THBS1 under hypoxia. Loss of function studies showed knocking down YTHDF1 or THBS1 exacerbated the osteogenic inhibition caused by hypoxia. All data imply that hypoxia suppresses osteogenic differentiation and promotes the expression of YTHDF1, which translationally regulates THBS1 in an m6A-dependent manner, potentially counteracting hypoxia-induced osteogenic inhibition through the YTHDF1/THBS1 pathway. The results of this study reveal for the first time the molecular mechanism of the regulation of osteogenic differentiation by YTHDF1 under hypoxia and suggest that YTHDF1, together with its downstream factor THBS1, may be critical targets to counteract osteogenic inhibition under hypoxic conditions, providing promising therapeutic strategy for the hypoxia-induced bone loss in peri-implantitis.
Genomics: Infectious Disease and Host–Pathogen Interaction
Authors: Chow Franklin Wang-Ngai
Published: January 2023

Infectious diseases, which are caused by pathogens such as bacteria, viruses, fungi, and parasites, pose a serious threat to humans, animals, and plants [...]