bluuebunny/crossref_metadata_2025 huggingface dataset:
Testing Serum Albumins and Cyclodextrins as Potential Binders of the Mycotoxin Metabolites Alternariol-3-Sulfate, Alternariol-9-Monomethylether and Alternariol-9-Monomethylether-3-Sulfate
Authors: Lemli Beáta , Vilmányi Péter , Fliszár-Nyúl Eszter , Zsidó Balázs Zoltán , Hetényi Csaba , Szente Lajos , Poór Miklós
Published: November 2022

Alternaria mycotoxins, including alternariol (AOH), alternariol-9-monomethylether (AME), and their masked/modified derivatives (e.g., sulfates or glycosides), are common food contaminants. Their acute toxicity is relatively low, while chronic exposure can lead to the development of adverse health effects. Masked/modified metabolites can probably release the more toxic parent mycotoxin due to their enzymatic hydrolysis in the intestines. Previously, we demonstrated the complex formation of AOH with serum albumins and cyclodextrins; these interactions were successfully applied for the extraction of AOH from aqueous matrices (including beverages). Therefore, in this study, the interactions of AME, alternariol-3-sulfate (AS), and alternariol-9-monomethylether-3-sulfate (AMS) were investigated with albumins (human, bovine, porcine, and rat) and with cyclodextrins (sulfobutylether-β-cyclodextrin, sugammadex, and cyclodextrin bead polymers). Our major results/conclusions are the following: (1) The stability of mycotoxin–albumin complexes showed only minor species dependent variations. (2) AS and AMS formed highly stable complexes with albumins in a wide pH range, while AME–albumin interactions preferred alkaline conditions. (3) AME formed more stable complexes with the cyclodextrins examined than AS and AMS. (4) Beta-cyclodextrin bead polymer proved to be highly suitable for the extraction of AME, AS, and AMS from aqueous solution. (5) Albumins and cyclodextrins are promising binders of the mycotoxins tested.
Comparative Transcriptome Analysis Reveals Key Insights into Fertility Conversion in the Thermo-Sensitive Cytoplasmic Male Sterile Wheat
Authors: Liu Zihan , Niu Fuqiang , Yuan Shaohua , Feng Shuying , Li Yanmei , Lu Fengkun , Zhang Tianbao , Bai Jianfang , Zhao Changping , Zhang Liping
Published: November 2022

Thermo-sensitive cytoplasmic male sterility (TCMS) plays a crucial role in hybrid production and hybrid breeding; however, there are few studies on molecular mechanisms related to anther abortion in the wheat TCMS line. In this study, FA99, a new wheat thermo-sensitive cytoplasmic male sterility line, was investigated. Fertility conversion analysis showed that FA99 was mainly controlled by temperature, and the temperature-sensitive stage was pollen mother cell formation to a uninucleate stage. Further phenotypic identification and paraffin section showed that FA99 was characterized by indehiscent anthers and aborted pollen in a sterile environment and tapetum was degraded prematurely during the tetrad period, which was the critical abortion period of FA99. The contents of O2−, H2O2, MDA and POD were significantly changed in FA99 under a sterile environment by the determination of physiological indexes. Furthermore, through transcriptome analysis, 252 differentially expressed genes were identified, including 218 downregulated and 34 upregulated genes. Based on KOG function classification, GO enrichment and KEGG pathways analysis, it was evident that significant transcriptomic changes in FA99 under different fertility environments, and the major differences were “phenylalanine metabolism”, “phenylpropanoid biosynthesis”, “cutin, suberine and wax biosynthesis”, “phenylalanine, tyrosine and tryptophan biosynthesis” and “citrate cycle (TCA cycle)”. Finally, we proposed an intriguing transcriptome-mediated pollen abortion and male sterility network for FA99. These findings provided data on the molecular mechanism of fertility conversion in thermo-sensitive cytoplasmic male sterility wheat.
Dietary Polyphenols and In Vitro Intestinal Fructose Uptake and Transport: A Systematic Literature Review
Authors: Iametti Stefania , Bonomi Francesco , Di Nunzio Mattia
Published: November 2022

Recent evidence links chronic consumption of large amounts of fructose (FRU) with several non-communicable disease. After ingestion, dietary FRU is absorbed into the intestinal tract by glucose transporter (GLUT) 5 and transported to the portal vein via GLUT2. GLUT2 is primarily localized on the basolateral membrane, but GLUT2 may be dislocated post-prandially from the basolateral membrane of intestinal cells to the apical one. Polyphenols (PP) are plant secondary metabolites that exert hypoglycemic properties by modulating intracellular insulin signaling pathways and by inhibiting intestinal enzymes and transporters. Post-prandially, PP may reach high concentrations in the gut lumen, making the inhibition of FRU absorption a prime target for exploring the effects of PP on FRU metabolism. Herein, we have systematically reviewed studies on the effect of PP and PP-rich products on FRU uptake and transport in intestinal cells. In spite of expectations, the very different experimental conditions in the various individual studies do not allow definitive conclusions to be drawn. Future investigations should rely on standardized conditions in order to obtain comparable results that allow a credible rating of polyphenols and polyphenol-rich products as inhibitors of fructose uptake.
The Mucus Binding Factor Is Not Necessary for Lacticaseibacillus rhamnosus CRL1505 to Exert Its Immunomodulatory Activities in Local and Distal Mucosal Sites
Authors: Tomotsune Kae , Raya Tonetti Fernanda , Mizuno Hiroya , Elean Mariano , Fukuyama Kohtaro , Zhou Binghui , Ikeda-Ohtsubo Wakako , Nishiyama Keita , Yamamura Akihiro , Karasawa Hideaki , Ohnuma Shinobu , Horii Akira , Saito Tadao , Kitazawa Haruki , Villena Julio
Published: November 2022

Both viable and non-viable orally administered Lacticaseibacillus rhamnosus CRL1505 modulate immunity in local (intestine) and distal (respiratory) mucosal sites. So, intestinal adhesion and colonization are not necessary for this probiotic strain to exert its immunomodulatory effects. In this work, a mucus-binding factor knockout CRL1505 strain (ΔmbfCRL1505) was obtained and the lack of binding ability to both intestinal epithelial cells and mucin was demonstrated in vitro. In addition, two sets of in vivo experiments in 6-week-old Balb/c mice were performed to evaluate ΔmbfCRL1505 immunomodulatory activities. (A) Orally administered ΔmbfCRL1505 prior to intraperitoneal injection of the Toll-like receptor 3 (TLR3) agonist poly(I:C) significantly reduced intraepithelial lymphocytes (CD3+NK1.1+CD8αα+) and pro-inflammatory mediators (TNF-α, IL-6 and IL-15) in the intestinal mucosa. (B) Orally administered ΔmbfCRL1505 prior to nasal stimulation with poly(I:C) significantly decreased the levels of the biochemical markers of lung tissue damage. In addition, reduced recruitment of neutrophils and levels of pro-inflammatory mediators (TNF-α, IL-6 and IL-8) as well as increased IFN-β and IFN-γ in the respiratory mucosa were observed in ΔmbfCRL1505-treated mice when compared to untreated control mice. The immunological changes induced by the ΔmbfCRL1505 strain were not different from those observed for the wild-type CRL1505 strain. Although it is generally accepted that the expression of adhesion factors is necessary for immunobiotics to induce their beneficial effects, it was demonstrated here that the mbf protein is not required for L. rhamnosus CRL1505 to exert its immunomodulatory activities in local and distal mucosal sites. These results are a step forward towards understanding the mechanisms involved in the immunomodulatory capabilities of L. rhamnosus CRL1505.
A Hybrid Docking and Machine Learning Approach to Enhance the Performance of Virtual Screening Carried out on Protein–Protein Interfaces
Authors: Singh Natesh , Villoutreix Bruno O.
Published: November 2022

The modulation of protein–protein interactions (PPIs) by small chemical compounds is challenging. PPIs play a critical role in most cellular processes and are involved in numerous disease pathways. As such, novel strategies that assist the design of PPI inhibitors are of major importance. We previously reported that the knowledge-based DLIGAND2 scoring tool was the best-rescoring function for improving receptor-based virtual screening (VS) performed with the Surflex docking engine applied to several PPI targets with experimentally known active and inactive compounds. Here, we extend our investigation by assessing the vs. potential of other types of scoring functions with an emphasis on docking-pose derived solvent accessible surface area (SASA) descriptors, with or without the use of machine learning (ML) classifiers. First, we explored rescoring strategies of Surflex-generated docking poses with five GOLD scoring functions (GoldScore, ChemScore, ASP, ChemPLP, ChemScore with Receptor Depth Scaling) and with consensus scoring. The top-ranked poses were post-processed to derive a set of protein and ligand SASA descriptors in the bound and unbound states, which were combined to derive descriptors of the docked protein-ligand complexes. Further, eight ML models (tree, bagged forest, random forest, Bayesian, support vector machine, logistic regression, neural network, and neural network with bagging) were trained using the derivatized SASA descriptors and validated on test sets. The results show that many SASA descriptors are better than Surflex and GOLD scoring functions in terms of overall performance and early recovery success on the used dataset. The ML models were superior to all scoring functions and rescoring approaches for most targets yielding up to a seven-fold increase in enrichment factors at 1% of the screened collections. In particular, the neural networks and random forest-based ML emerged as the best techniques for this PPI dataset, making them robust and attractive vs. tools for hit-finding efforts. The presented results suggest that exploring further docking-pose derived SASA descriptors could be valuable for structure-based virtual screening projects, and in the present case, to assist the rational design of small-molecule PPI inhibitors.
Durable CD8 T Cell Memory against SARS-CoV-2 by Prime/Boost and Multi-Dose Vaccination: Considerations on Inter-Dose Time Intervals
Authors: Natalini Ambra , Simonetti Sonia , Sher Carmel , D’Oro Ugo , Hayday Adrian C. , Di Rosa Francesca
Published: November 2022

Facing the COVID-19 pandemic, anti-SARS-CoV-2 vaccines were developed at unprecedented pace, productively exploiting contemporary fundamental research and prior art. Large-scale use of anti-SARS-CoV-2 vaccines has greatly limited severe morbidity and mortality. Protection has been correlated with high serum titres of neutralizing antibodies capable of blocking the interaction between the viral surface protein spike and the host SARS-CoV-2 receptor, ACE-2. Yet, vaccine-induced protection subsides over time, and breakthrough infections are commonly observed, mostly reflecting the decay of neutralizing antibodies and the emergence of variant viruses with mutant spike proteins. Memory CD8 T cells are a potent weapon against viruses, as they are against tumour cells. Anti-SARS-CoV-2 memory CD8 T cells are induced by either natural infection or vaccination and can be potentially exploited against spike-mutated viruses. We offer here an overview of current research about the induction of anti-SARS-CoV-2 memory CD8 T cells by vaccination, in the context of prior knowledge on vaccines and on fundamental mechanisms of immunological memory. We focus particularly on how vaccination by two doses (prime/boost) or more (boosters) promotes differentiation of memory CD8 T cells, and on how the time-length of inter-dose intervals may influence the magnitude and persistence of CD8 T cell memory.
Transgenic Improvement for Biotic Resistance of Crops
Authors: Yu Haoqiang , Wang Yingge , Fu Fengling , Li Wanchen
Published: November 2022

Biotic constraints, including pathogenic fungi, viruses and bacteria, herbivory insects, as well as parasitic nematodes, cause significant yield loss and quality deterioration of crops. The effect of conventional management of these biotic constraints is limited. The advances in transgenic technologies provide a direct and directional approach to improve crops for biotic resistance. More than a hundred transgenic events and hundreds of cultivars resistant to herbivory insects, pathogenic viruses, and fungi have been developed by the heterologous expression of exogenous genes and RNAi, authorized for cultivation and market, and resulted in a significant reduction in yield loss and quality deterioration. However, the exploration of transgenic improvement for resistance to bacteria and nematodes by overexpression of endogenous genes and RNAi remains at the testing stage. Recent advances in RNAi and CRISPR/Cas technologies open up possibilities to improve the resistance of crops to pathogenic bacteria and plant parasitic nematodes, as well as other biotic constraints.
Antiproliferative Activity Predictor: A New Reliable In Silico Tool for Drug Response Prediction against NCI60 Panel
Authors: Martorana Annamaria , La Monica Gabriele , Bono Alessia , Mannino Salvatore , Buscemi Silvestre , Palumbo Piccionello Antonio , Gentile Carla , Lauria Antonino , Peri Daniele
Published: November 2022

In vitro antiproliferative assays still represent one of the most important tools in the anticancer drug discovery field, especially to gain insights into the mechanisms of action of anticancer small molecules. The NCI-DTP (National Cancer Institute Developmental Therapeutics Program) undoubtedly represents the most famous project aimed at rapidly testing thousands of compounds against multiple tumor cell lines (NCI60). The large amount of biological data stored in the National Cancer Institute (NCI) database and many other databases has led researchers in the fields of computational biology and medicinal chemistry to develop tools to predict the anticancer properties of new agents in advance. In this work, based on the available antiproliferative data collected by the NCI and the manipulation of molecular descriptors, we propose the new in silico Antiproliferative Activity Predictor (AAP) tool to calculate the GI50 values of input structures against the NCI60 panel. This ligand-based protocol, validated by both internal and external sets of structures, has proven to be highly reliable and robust. The obtained GI50 values of a test set of 99 structures present an error of less than ±1 unit. The AAP is more powerful for GI50 calculation in the range of 4–6, showing that the results strictly correlate with the experimental data. The encouraging results were further supported by the examination of an in-house database of curcumin analogues that have already been studied as antiproliferative agents. The AAP tool identified several potentially active compounds, and a subsequent evaluation of a set of molecules selected by the NCI for the one-dose/five-dose antiproliferative assays confirmed the great potential of our protocol for the development of new anticancer small molecules. The integration of the AAP tool in the free web service DRUDIT provides an interesting device for the discovery and/or optimization of anticancer drugs to the medicinal chemistry community. The training set will be updated with new NCI-tested compounds to cover more chemical spaces, activities, and cell lines. Currently, the same protocol is being developed for predicting the TGI (total growth inhibition) and LC50 (median lethal concentration) parameters to estimate toxicity profiles of small molecules.
DNA Damage Stress Response and Follicle Activation: Signaling Routes of Mammalian Ovarian Reserve
Authors: Gonfloni Stefania , Jodice Carla , Gustavino Bianca , Valentini Elvia
Published: November 2022

Chemotherapy regimens and radiotherapy are common strategies to fight cancer. In women, these therapies may cause side effects such as premature ovarian insufficiency (POI) and infertility. Clinical strategies to protect the ovarian reserve from the lethal effect of cancer therapies needs better understanding of the mechanisms underlying iatrogenic loss of follicle reserve. Recent reports demonstrate a critical role for p53 and CHK2 in the oocyte response to different DNA stressors, which are commonly used to treat cancer. Here we review the molecular mechanisms underlying the DNA damage stress response (DDR) and discuss crosstalk between DDR and signaling pathways implicated in primordial follicle activation.
Mendelian Randomization Indicates a Causal Role for Omega-3 Fatty Acids in Inflammatory Bowel Disease
Authors: Astore Courtney , Nagpal Sini , Gibson Greg
Published: November 2022

Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal system. Omega-3 (ω3) fatty acids are polyunsaturated fatty acids (PUFAs) that are largely obtained from diet and have been speculated to decrease the inflammatory response that is involved in IBD; however, the causality of this association has not been established. A two-sample Mendelian randomization (MR) was used to assess genetic associations between 249 circulating metabolites measured in the UK Biobank as exposures and IBD as the outcome. The genome-wide association study summary level data for metabolite measurements and IBD were derived from large European ancestry cohorts. We observed ω3 fatty acids as a significant protective association with IBD, with multiple modes of MR evidence replicated in three IBD summary genetic datasets. The instrumental variables that were involved in the causal association of ω3 fatty acids with IBD highlighted an intronic SNP, rs174564, in FADS2, a protein engaged in the first step of alpha-linolenic acid desaturation leading to anti-inflammatory EPA and thence DHA production. A low ratio of ω3 to ω6 fatty acids was observed to be a causal risk factor, particularly for Crohn’s disease. ω3 fatty acid supplementation may provide anti-inflammatory responses that are required to attenuate inflammation that is involved in IBD.
Dual Inhibition of BRAF-MAPK and STAT3 Signaling Pathways in Resveratrol-Suppressed Anaplastic Thyroid Cancer Cells with BRAF Mutations
Authors: Lu Meng-Di , Li Hong , Nie Jun-Hua , Li Sheng , Ye Hai-Shan , Li Ting-Ting , Wu Mo-Li , Liu Jia
Published: November 2022

Anaplastic thyroid cancer is an extremely lethal malignancy without reliable treatment. BRAFV600E point mutation is common in ATCs, which leads to MAPK signaling activation and is regarded as a therapeutic target. Resveratrol inhibits ATC cell growth, while its impact on BRAF-MAPK signaling remains unknown. This study aims to address this issue by elucidating the statuses of BRAF-MAPK and STAT3 signaling activities in resveratrol-treated THJ-11T, THJ-16T, and THJ-21T ATC cells and Nthyori 3-1 thyroid epithelial cells. RT-PCR and Sanger sequencing revealed MKRN1-BRAF fusion mutation in THJ-16T, BRAF V600E point mutation in THJ-21T, and wild-type BRAF genes in THJ-11T and Nthyori 3-1 cells. Western blotting and immunocytochemical staining showed elevated pBRAF, pMEK, and pERK levels in THJ-16T and THJ-21T, but not in THJ-11T or Nthyori 3-1 cells. Calcein/PI, EdU, and TUNEL assays showed that compared with docetaxel and doxorubicin and MAPK-targeting dabrafenib and trametinib, resveratrol exerted more powerful inhibitory effects on mutant BRAF-harboring THJ-16T and THJ-21T cells, accompanied by reduced levels of MAPK pathway-associated proteins and pSTAT3. Trametinib- and dabrafenib-enhanced STAT3 activation was efficiently suppressed by resveratrol. In conclusion, resveratrol acts as dual BRAF-MAPK and STAT3 signaling inhibitor and a promising agent against ATCs with BRAF mutation.
Epstein–Barr Virus (EBV) Epithelial Associated Malignancies: Exploring Pathologies and Current Treatments
Authors: Shechter Oren , Sausen Daniel G. , Gallo Elisa S. , Dahari Harel , Borenstein Ronen
Published: November 2022

Epstein–Barr virus (EBV) is one of eight known herpesviruses with the potential to infect humans. Globally, it is estimated that between 90–95% of the population has been infected with EBV. EBV is an oncogenic virus that has been strongly linked to various epithelial malignancies such as nasopharyngeal and gastric cancer. Recent evidence suggests a link between EBV and breast cancer. Additionally, there are other, rarer cancers with weaker evidence linking them to EBV. In this review, we discuss the currently known epithelial malignancies associated with EBV. Additionally, we discuss and establish which treatments and therapies are most recommended for each cancer associated with EBV.
Intermittent ELF-MF Induce an Amplitude-Window Effect on Umbilical Cord Blood Lymphocytes
Authors: Zastko Lucián , Makinistian Leonardo , Tvarožná Andrea , Belyaev Igor
Published: November 2022

In a previous study of the effects of intermittent extremely low frequency (ELF) magnetic fields (MF) on umbilical cord blood lymphocytes (UCBL), we evaluated MF amplitudes between 6 µT and 24 µT and found an effect only for those below 13 µT. This suggested the existence of an amplitude window. In this brief communication, we further tested this hypothesis. UCBLs from healthy newborns were isolated and exposed for 72 h to an intermittent ELF-MF (triangular, 7.8 Hz, 250 s ON/250 s OFF) with 6 different amplitudes between 3 µT and 12 µT, utilizing an oblong coil. Percentage of viable, early apoptotic (EA), and late apoptotic/necrotic (LAN) cells were determined by flow cytometry. Moreover, reactive oxygen species (ROS) were determined at 1 h and 3 h of the exposure. Like in our previous work, neither EA, nor LAN, nor ROS were statistically significantly affected by the intermittent ELF-MF. However, the percentage of viable cells was decreased by exposure to the fields with intensities of 6.5 µT and 12 µT (p < 0.05; and p = 0.057 for 8.5 µT). ELF-MF decreased the percentage of viable cells for fields down to 6.5 µT, but not for 5 µT, 4 µT, or 3 µT. Combined with our previous findings, the results reported here indicate an amplitude window effect between 6 µT and 13 µT. The obtained data are in line with a notion of amplitude and frequency windows, which request scanning of both amplitude and frequency while studying the ELF-MF effects.
Developing 3D Organoid Raft Cultures from Patient-Derived Xenografts as Rapid Models to Screen Efficacy of Experimental Therapeutics
Authors: Bajpai Prachi , Banerjee Nilam Sanjib , Moore Dianne W. , Kim Hyung-Gyoon , Afaq Farrukh , Contreras Carlo M. , Heslin Martin J. , Reddy Vishnu B. , Peter Shajan , Varambally Sooryanarayana , Al Diffalha Sameer , Manne Upender
Published: November 2022

Reliable preclinical models are needed for screening new cancer drugs. Thus, we developed an improved 3D tumor organoid model termed “organoid raft cultures” (ORCs). Development of ORCs involved culturing tumors ex vivo on collagen beds (boats) with grid supports to maintain their morphological structure. The ORCs were developed from patient-derived xenografts (PDXs) of colon cancers excised from immune-deficient mice (NOD/SCID/IL2Rgammanull). We utilized these new models to evaluate the efficacy of an investigational drug, Navitoclax (ABT-263). We tested the efficacy of ABT-263, an inhibitor of BCL-2 family proteins, in these ORCs derived from a PDX that showed high expression of antiapoptotic BCL2 family proteins (BCL-2, BCL-XL, and BCL-W). Hematoxylin and eosin staining evaluation of PDXs and corresponding ORCs indicated the retention of morphological and other histological integrity of ORCs. ORCs treated with ABT-263 showed decreased expression of antiapoptotic proteins (BCL2, BCL-XL and BCL-W) and increased proapoptotic proteins (BAX and PUMA), with concomitant activation of caspase 3. These studies support the usefulness of the ORCs, developed from PDXs, as an alternative to PDXs and as faster screening models.
Human Osteoblast-Conditioned Media Can Influence Staphylococcus aureus Biofilm Formation
Authors: Lamret Fabien , Varin-Simon Jennifer , Six Mélodie , Thoraval Léa , Chevrier Julie , Adam Cloé , Guillaume Christine , Velard Frédéric , Gangloff Sophie C. , Reffuveille Fany
Published: November 2022

Osteoblasts are bone-forming and highly active cells participating in bone homeostasis. In the case of osteomyelitis and more specifically prosthetic joint infections (PJI) for which Staphylococcus aureus (S. aureus) is mainly involved, the interaction between osteoblasts and S. aureus results in impaired bone homeostasis. If, so far, most of the studies of osteoblasts and S. aureus interactions were focused on osteoblast response following direct interactions with co-culture and/or internalization models, less is known about the effect of osteoblast factors on S. aureus biofilm formation. In the present study, we investigated the effect of human osteoblast culture supernatant on methicillin sensitive S. aureus (MSSA) SH1000 and methicillin resistant S. aureus (MRSA) USA300. Firstly, Saos-2 cell line was incubated with either medium containing TNF-α to mimic the inflammatory periprosthetic environment or with regular medium. Biofilm biomass was slightly increased for both strains in the presence of culture supernatant collected from Saos-2 cells, stimulated or not with TNF-α. In such conditions, SH1000 was able to develop microcolonies, suggesting a rearrangement in biofilm organization. However, the biofilm matrix and regulation of genes dedicated to biofilm formation were not substantially changed. Secondly, culture supernatant obtained from primary osteoblast culture induced varied response from SH1000 strain depending on the different donors tested, whereas USA300 was only slightly affected. This suggested that the sensitivity to bone cell secretions is strain dependent. Our results have shown the impact of osteoblast secretions on bacteria and further identification of involved factors will help to manage PJI.
Emerging Role of NLRP3 Inflammasome and Pyroptosis in Liver Transplantation
Authors: Lucas-Ruiz Fernando , Peñín-Franch Alejandro , Pons José Antonio , Ramírez Pablo , Pelegrín Pablo , Cuevas Santiago , Baroja-Mazo Alberto
Published: November 2022

The nucleotide-binding domain leucine-rich repeat-receptor, pyrin domain-containing-3 (NLRP3) inflammasome contributes to the inflammatory response by activating caspase-1, which in turn participates in the maturation of interleukin (IL)-1β and IL-18, which are mainly secreted via pyroptosis. Pyroptosis is a lytic type of cell death that is controlled by caspase-1 processing gasdermin D. The amino-terminal fragment of gasdermin D inserts into the plasma membrane, creating stable pores and enabling the release of several proinflammatory factors. The activation of NLRP3 inflammasome and pyroptosis has been involved in the progression of liver fibrosis and its end-stage cirrhosis, which is among the main etiologies for liver transplantation (LT). Moreover, the NLRP3 inflammasome is involved in ischemia–reperfusion injury and early inflammation and rejection after LT. In this review, we summarize the recent literature addressing the role of the NLRP3 inflammasome and pyroptosis in all stages involved in LT and argue the potential targeting of this pathway as a future therapeutic strategy to improve LT outcomes. Likewise, we also discuss the impact of graft quality influenced by donation after circulatory death and the expected role of machine perfusion technology to modify the injury response related to inflammasome activation.
NEAT1 Confers Radioresistance to Hepatocellular Carcinoma Cells by Inducing PINK1/Parkin-Mediated Mitophagy
Authors: Tsuchiya Hiroyuki , Shinonaga Ririko , Sakaguchi Hiromi , Kitagawa Yutaka , Yoshida Kenji , Shiota Goshi
Published: November 2022

A long noncoding RNA, nuclear paraspeckle assembly transcript 1 (NEAT1) variant 1 (NEAT1v1), confers radioresistance to hepatocellular carcinoma (HCC) cells by inducing autophagy via γ-aminobutyric acid A receptor-associated protein (GABARAP). Radiation induces oxidative stress to damage cellular components and organelles, but it remains unclear how NEAT1v1 protects HCC cells from radiation-induced oxidative stress via autophagy. To address this, we precisely investigated NEAT1v1-induced autophagy in irradiated HCC cell lines. X-ray irradiation significantly increased cellular and mitochondrial oxidative stress and mitochondrial DNA content in HCC cells while NEAT1v1 suppressed them. NEAT1v1 concomitantly induced the phosphatase and tensin homolog-induced kinase 1 (PINK1)/parkin-mediated mitophagy. Interestingly, parkin expression was constitutively upregulated in NEAT1v1-overexpressing HCC cells, leading to increased mitochondrial parkin levels. Superoxide dismutase 2 (SOD2) was also upregulated by NEAT1v1, and GABARAP or SOD2 knockdown in NEAT1v1-overexpressing cells increased mitochondrial oxidative stress and mitochondrial DNA content after irradiation. Moreover, it was suggested that SOD2 was involved in NEAT1v1-induced parkin expression, and that GABARAP promoted parkin degradation via mitophagy. This study highlights the unprecedented roles of NEAT1v1 in connecting radioresistance and mitophagy in HCC.
Conjunctival Fluid Secretion Impairment via CaCC-CFTR Dysfunction Is the Key Mechanism in Environmental Dry Eye
Authors: Zhang Jinyu , Lin Limian , Chen Xiaomin , Wang Shuyi , Wei Yuan , Zhou Wenliang , Yang Shuangjian , Zhou Shiyou
Published: November 2022

Dry eye disease (DED) is a multifactorial disease with an incidence of approximately 50% worldwide. DED seriously affects quality of life and work. The prevalence of environmental DED (eDED) ranges from 35 to 48%. Conjunctival fluid secretion dysfunction may be one of the major causes of DED. Notably, the Cl– flux corresponds to the conjunctival fluid secretion and could be affected by ATP. Both the cystic fibrosis transmembrane conductance regulator (CFTR) and the Ca2+-activated Cl– channel (CaCC) are Cl– channels involved in epithelial fluid secretion. Conjunctival fluid secretion could be increased by activating P2Y2R (an ATP receptor) in DED. However, the role of the CaCC and CFTR channels regulated by P2Y2R in eDED remains unclear. In this study, we established a rabbit eDED model using a controlled drying system. A Ussing chamber was used to perform a conjunctival short-circuit current induced by ATP to evaluate the reactivity of the ion channels to the ATP. Our results revealed that eDED accompanied by conjunctival fluid secretion impairment was caused by a P2Y2R dysfunction, which is related to CaCC-CFTR signaling in the conjunctiva epithelium. Notably, the coupling effect of the ATP-induced CaCC-CFTR activation and intracellular Ca2+ may represent a promising therapeutic target for treating eDED.
Analysis of ADORA2A rs5760423 and CYP1A2 rs762551 Genetic Variants in Patients with Alzheimer’s Disease
Authors: Siokas Vasileios , Mouliou Dimitra S. , Liampas Ioannis , Aloizou Athina-Maria , Folia Vasiliki , Zoupa Elli , Papadimitriou Anastasios , Lavdas Eleftherios , Bogdanos Dimitrios P. , Dardiotis Efthimios
Published: November 2022

Various studies have been conducted, exploring the genetic susceptibility of Alzheimer’s disease (AD). Adenosine receptor subtype A2a (ADORA2A) and cytochrome P450 1A2 (CYP1A2) are implicated in pathways such as oxidative stress and caffeine metabolism, which are associated with AD. The aim of this study was to explore for any potential association between the ADORA2A rs5760423 and the CYP1A2 rs762551 genetic variants and AD. A case–control study was performed with a total of 654 subjects (327 healthy controls and 327 patients with AD). Five genetic models were assumed. We also examined the allele–allele combination of both variants. The value of 0.05 was considered as the statistical significance threshold. A statistically significant association was found between ADORA2A rs5760423 and AD, as the “T” allele was associated with increased AD risk in recessive (OR = 1.51 (1.03–2.21)) and log-additive (OR = 1.30 (1.04–1.62)) genetic modes. In the codominant model, the TT genotype was more prevalent compared to the GG genotype (OR = 1.71 (1.09–2.66)). The statistical significance was maintained after adjustment for sex. No association between CYP1A2 rs762551 or allele–allele combination and AD was detected. We provide preliminary indication for a possible association between the ADORA2A rs5760423 genetic polymorphism and AD.
Design, Synthesis and Pharmacological Evaluation of Novel C2,C3-Quinoxaline Derivatives as Promising Anxiolytic Agents
Authors: Maltsev Dmitriy V. , Skripka Maria O. , Spasov Alexander A. , Vassiliev Pavel M. , Perfiliev Maxim A. , Divaeva Lyudmila N. , Zubenko Alexander A. , Morkovnik Anatolii S. , Klimenko Alexander I. , Miroshnikov Mikhail V. , Klochkov Vladlen G. , Ianalieva Laura R.
Published: November 2022

A new series of quinoxaline derivatives, 2a–4b, were synthesized and their anxiolytic potential was evaluated in vivo using elevated plus maze (EPM), open field (OF) and light-dark box (LDB) techniques. According to the results of the EPM, four active compounds were found in 2a, 2b, 2c, 4b. Their anxiolytic properties were confirmed in terms of LDB and the most active was compound 2b. In the OF, only 2c had an influence on the locomotor activity of the rodents. Thus, the most promising substance was determined; this was 2b, which has the structure of 2-(2-{[3-(4-tert-butylphenyl)quinoxaline-2-yl]methyl}-4,5-dimethoxyphenyl)-N-methylethan-1-amine hydrochloride. The obtained data were analyzed with the pharmacophore feature prediction approach, which made it possible to compare the structures of the studied compounds with the reference drug diazepam, and to determine the contribution of pharmacophores to the manifestation of the activity under study. ADMET analysis was carried out for compound 2b and the acute oral toxicity of this substance was also tested in vivo. As a result of the study, a promising compound with a high anxiolytic effect and low level of toxicity 2b was found, which is of interest for further preclinical study of its properties.
FaesAP3_1 Regulates the FaesELF3 Gene Involved in Filament-Length Determination of Long-Homostyle Fagopyrum esculentum
Authors: Ma Zhiyuan , Yang Qingyu , Zeng Lingtian , Li Jiayi , Jiao Xinyu , Liu Zhixiong
Published: November 2022

The identification downstream genes of floral organ identity regulators are critical to revealing the molecular mechanisms underlying floral morphogenesis. However, a general regulatory pathway between floral organ identity genes and their downstream targets is still unclear because of the lack of studies in nonmodel species. Here, we screened a direct downstream target gene, FaesELF3, of a stamen identity transcription factor, FaesAP3_1, in long-homostyle (LH) Fagopyrum esculentum moench by using yeast one-hybrid (Y1H) and dual-luciferase reporter (DR) assays. Furthermore, FaesAP3_1-silenced LH plants that produced flowers with part stamens or anthers homeotically converted into a tepaloid structure, and FaesELF3-silenced plants that had flowers with part stamens consisting of a short filament and empty anther (male sterile anther). All these suggested that transcription factor (TF) FaesAP3_1 directly activates FaesELF3 in order to regulate filament elongation and pollen grain development in LH buckwheat. Our data also suggested that other stamen development pathways independent of FaesAP3_1 remain in F. esculentum.
Kinetic Features of 3′–5′–Exonuclease Activity of Apurinic/Apyrimidinic Endonuclease Apn2 from Saccharomyces cerevisiae
Authors: Kuznetsova Aleksandra A. , Gavrilova Anastasia A. , Ishchenko Alexander A. , Saparbaev Murat , Fedorova Olga S. , Kuznetsov Nikita A.
Published: November 2022

In yeast Saccharomyces cerevisiae cells, apurinic/apyrimidinic (AP) sites are primarily repaired by base excision repair. Base excision repair is initiated by one of two AP endonucleases: Apn1 or Apn2. AP endonucleases catalyze hydrolytic cleavage of the phosphodiester backbone on the 5′ side of an AP site, thereby forming a single–strand break containing 3′–OH and 5′–dRP ends. In addition, Apn2 has 3′–phosphodiesterase activity (removing 3′–blocking groups) and 3′ → 5′ exonuclease activity (both much stronger than its AP endonuclease activity). Nonetheless, the role of the 3′–5′–exonuclease activity of Apn2 remains unclear and presumably is involved in the repair of damage containing single–strand breaks. In this work, by separating reaction products in a polyacrylamide gel and by a stopped–flow assay, we performed a kinetic analysis of the interaction of Apn2 with various model DNA substrates containing a 5′ overhang. The results allowed us to propose a mechanism for the cleaving off of nucleotides and to determine the rate of the catalytic stage of the process. It was found that dissociation of a reaction product from the enzyme active site is not a rate–limiting step in the enzymatic reaction. We determined an influence of the nature of the 3′–terminal nucleotide that can be cleaved off on the course of the enzymatic reaction. Finally, it was found that the efficiency of the enzymatic reaction is context–specific.
The Genotoxicity of Acrylfentanyl, Ocfentanyl and Furanylfentanyl Raises the Concern of Long-Term Consequences
Authors: Gasperini Sofia , Bilel Sabrine , Cocchi Veronica , Marti Matteo , Lenzi Monia , Hrelia Patrizia
Published: November 2022

Three fentanyl analogues Acrylfentanyl, Ocfentanyl and Furanylfentanyl are potent, rapid-acting synthetic analgesics that recently appeared on the illicit market of new psychoactive substances (NPS) under the class of new synthetic opioids (NSO). Pharmacotoxicological data on these three non-pharmaceutical fentanyl analogues are limited and studies on their genotoxicity are not yet available. Therefore, the aim of the present study was to investigate this property. The ability to induce structural and numerical chromosomal aberrations in human lymphoblastoid TK6 cells was evaluated by employing the flow cytometric protocol of the in vitro mammalian cell micronucleus test. Our study demonstrated the non-genotoxicity of Fentanyl, i.e., the pharmaceutical progenitor of the class, while its illicit non-pharmaceutical analogues were found to be genotoxic. In particular, Acrylfentanyl led to a statistically significant increase in the MNi frequency at the highest concentration tested (75 μM), while Ocfentanyl and Furanylfentnyl each did so at both concentrations tested (150, 200 μM and 25, 50 μM, respectively). The study ended by investigating reactive oxygen species (ROS) induction as a possible mechanism linked to the proved genotoxic effect. The results showed a non-statistically significant increase in ROS levels in the cultures treated with all molecules under study. Overall, the proved genotoxicity raises concern about the possibility of serious long-term consequences.
Evaluation of the Properties of PHB Composite Filled with Kaolin Particles for 3D Printing Applications Using the Design of Experiment
Authors: Menčík Přemysl , Přikryl Radek , Krobot Štěpán , Melčová Veronika , Kontárová Soňa , Plavec Roderik , Bočkaj Jan , Horváth Vojtech , Alexy Pavol
Published: November 2022

In the presented work, poly(3-hydroxybutyrate)-PHB-based composites for 3D printing as bio-sourced and biodegradable alternatives to synthetic plastics are characterized. The PHB matrix was modified by polylactide (PLA) and plasticized by tributyl citrate. Kaolin particles were used as a filler. The mathematical method “Design of Experiment” (DoE) was used to create a matrix of samples for further evaluation. Firstly, the optimal printing temperature of the first and upper layers was determined. Secondly, the 3D printed samples were tested with regards to the warping during the 3D printing. Testing specimens were prepared using the determined optimal printing conditions to measure the tensile properties, impact strength, and heat deflection temperature (HDT) of the samples. The results describe the effect of adding individual components (PHB, PLA, plasticizer, and filler) in the prepared composite sample on the resulting material properties. Two composite samples were prepared based on the theoretical results of DoE (one with the maximum printability and one with the maximum HDT) to compare them with the real data measured. The tests of these two composite samples showed 25% lower warping and 8.9% higher HDT than was expected by the theory.
Successes and Failures of Static Aptamer-Target 3D Docking Models
Authors: Bruno John G.
Published: November 2022

While Molecular Dynamics simulation programs are probably superior for predicting the binding and affinity of aptamers and their cognate ligands, such molecular dynamics programs require more computing power and analysis time than static docking programs that are more widely accessible to the scientific community on the internet. Static docking programs can be used to investigate the geometric fit of rigid DNA or RNA aptamer 3D structures and their ligands to aid in predicting the relative affinities and cross-reactivity of various potential ligands. Herein, the author describes when such static 3D docking analysis has worked well to produce useful predictions or confirmation of high-affinity aptamer interactions or successful aptamer beacon behavior and when it has not worked well. The analysis of why failures may occur with static 3D computer models is also discussed.
Microplastics Exacerbate Cadmium-Induced Kidney Injury by Enhancing Oxidative Stress, Autophagy, Apoptosis, and Fibrosis
Authors: Zou Hui , Chen Yan , Qu Huayi , Sun Jian , Wang Tao , Ma Yonggang , Yuan Yan , Bian Jianchun , Liu Zongping
Published: November 2022

Cadmium (Cd) is a potential pathogenic factor in the urinary system that is associated with various kidney diseases. Microplastics (MPs), comprising of plastic particles less than 5 mm in diameter, are a major carrier of contaminants. We applied 10 mg/L particle 5 μm MPs and 50 mg/L CdCl2 in water for three months in vivo assay to assess the damaging effects of MPs and Cd exposure on the kidney. In vivo tests showed that MPs exacerbated Cd-induced kidney injury. In addition, the involvement of oxidative stress, autophagy, apoptosis, and fibrosis in the damaging effects of MPs and Cd on mouse kidneys were investigated. The results showed that MPs aggravated Cd-induced kidney injury by enhancing oxidative stress, autophagy, apoptosis, and fibrosis. These findings provide new insights into the toxic effects of MPs on the mouse kidney.
MR1- and HLA-E-Dependent Antigen Presentation of Mycobacterium tuberculosis
Authors: Kim Se-Jin , Karamooz Elham
Published: November 2022

MR1 and HLA-E are highly conserved nonclassical antigen-presenting molecules. They can present antigens derived from Mycobacterium tuberculosis to a distinct subset of MR1-restricted or HLA-restricted CD8+ T cells. MR1 presents small microbial metabolites, and HLA-E presents peptides and glycopeptides. In this review, we will discuss the current understanding of MR1 and HLA-E antigen presentation in the context of Mycobacterium tuberculosis infection.
Role of Cardiac Natriuretic Peptides in Heart Structure and Function
Authors: Sarzani Riccardo , Allevi Massimiliano , Di Pentima Chiara , Schiavi Paola , Spannella Francesco , Giulietti Federico
Published: November 2022

Cardiac natriuretic peptides (NPs), atrial NP (ANP) and B-type NP (BNP) are true hormones produced and released by cardiomyocytes, exerting several systemic effects. Together with C-type NP (CNP), mainly expressed by endothelial cells, they also exert several paracrine and autocrine activities on the heart itself, contributing to cardiovascular (CV) health. In addition to their natriuretic, vasorelaxant, metabolic and antiproliferative systemic properties, NPs prevent cardiac hypertrophy, fibrosis, arrhythmias and cardiomyopathies, counteracting the development and progression of heart failure (HF). Moreover, recent studies revealed that a protein structurally similar to NPs mainly produced by skeletal muscles and osteoblasts called musclin/osteocrin is able to interact with the NPs clearance receptor, attenuating cardiac dysfunction and myocardial fibrosis and promoting heart protection during pathological overload. This narrative review is focused on the direct activities of this molecule family on the heart, reporting both experimental and human studies that are clinically relevant for physicians.
Analysis of QTLs and Candidate Genes for Tassel Symptoms in Maize Infected with Sporisorium reilianum
Authors: Zhou Yu , Yao Minhao , Wang Qian , Zhang Xiaoming , Di Hong , Zhang Lin , Dong Ling , Xu Qingyu , Liu Xianjun , Zeng Xing , Wang Zhenhua
Published: November 2022

Heat smut is a fungal soil-borne disease caused by Sporisorium reilianum, and affects the development of male and female tassels. Our previous research found that the tassel symptoms in maize infected with Sporisorium reilianum significantly differed in inbred lines with Sipingtou blood, and exhibited stable heredity over time at multiple locations. In this study, cytological analysis demonstrated that the cellular organization structures of three typical inbred lines (Huangzao4, Jing7, and Chang7-2) showed significant discrepancies at the VT stage. QTLs that control the different symptoms of maize tassels infected with Sporisorium reilianum were located in two F2 populations, which were constructed using three typical inbred lines. The BSA (bulked segregation analysis) method was used to construct mixed gene pools based on typical tassel symptoms. The QTLs of different symptoms of maize tassels infected with Sporisorium reilianum were detected with 869 SSR markers covering the whole maize genome. The mixed gene pools were screened with polymorphic markers between the parents. Additional SSR markers were added near the above marker to detect genotypes in partially single plants in F2 populations. The QTL controlling tassel symptoms in the Huangzao4 and Jing7 lines was located on the bin 1.06 region, between the markers of umc1590 and bnlg1598, and explained 21.12% of the phenotypic variation with an additive effect of 0.6524. The QTL controlling the tassel symptoms of the Jing7 and Chang7-2 lines was located on the bin 2.07 region, between the markers of umc1042 and bnlg1335, and explained 11.26% phenotypic variation with an additive effect of 0.4355. Two candidate genes (ZmABP2 and Zm00001D006403) were identified by a conjoint analysis of label-free quantification proteome sequencings.
KARAJ: An Efficient Adaptive Multi-Processor Tool to Streamline Genomic and Transcriptomic Sequence Data Acquisition
Authors: Labani Mahdieh , Beheshti Amin , Lovell Nigel H. , Alinejad-Rokny Hamid , Afrasiabi Ali
Published: November 2022

Here we developed KARAJ, a fast and flexible Linux command-line tool to automate the end-to-end process of querying and downloading a wide range of genomic and transcriptomic sequence data types. The input to KARAJ is a list of PMCIDs or publication URLs or various types of accession numbers to automate four tasks as follows; firstly, it provides a summary list of accessible datasets generated by or used in these scientific articles, enabling users to select appropriate datasets; secondly, KARAJ calculates the size of files that users want to download and confirms the availability of adequate space on the local disk; thirdly, it generates a metadata table containing sample information and the experimental design of the corresponding study; and lastly, it enables users to download supplementary data tables attached to publications. Further, KARAJ provides a parallel downloading framework powered by Aspera connect which reduces the downloading time significantly.