bluuebunny/crossref_metadata_2025 huggingface dataset:
What Is a Digital Twin? Experimental Design for a Data-Centric Machine Learning Perspective in Health
Authors: Emmert-Streib Frank , Yli-Harja Olli
Published: October 2022

The idea of a digital twin has recently gained widespread attention. While, so far, it has been used predominantly for problems in engineering and manufacturing, it is believed that a digital twin also holds great promise for applications in medicine and health. However, a problem that severely hampers progress in these fields is the lack of a solid definition of the concept behind a digital twin that would be directly amenable for such big data-driven fields requiring a statistical data analysis. In this paper, we address this problem. We will see that the term ’digital twin’, as used in the literature, is like a Matryoshka doll. For this reason, we unstack the concept via a data-centric machine learning perspective, allowing us to define its main components. As a consequence, we suggest to use the term Digital Twin System instead of digital twin because this highlights its complex interconnected substructure. In addition, we address ethical concerns that result from treatment suggestions for patients based on simulated data and a possible lack of explainability of the underling models.
Evolution of an Iron-Detoxifying Protein: Eukaryotic and Rickettsia Frataxins Contain a Conserved Site Which Is Not Present in Their Bacterial Homologues
Authors: Alves Rui , Pazos-Gil Maria , Medina-Carbonero Marta , Sanz-Alcázar Arabela , Delaspre Fabien , Tamarit Jordi
Published: October 2022

Friedreich’s ataxia is a neurodegenerative disease caused by mutations in the frataxin gene. Frataxin homologues, including bacterial CyaY proteins, can be found in most species and play a fundamental role in mitochondrial iron homeostasis, either promoting iron assembly into metaloproteins or contributing to iron detoxification. While several lines of evidence suggest that eukaryotic frataxins are more effective than bacterial ones in iron detoxification, the residues involved in this gain of function are unknown. In this work, we analyze conservation of amino acid sequence and protein structure among frataxins and CyaY proteins to identify four highly conserved residue clusters and group them into potential functional clusters. Clusters 1, 2, and 4 are present in eukaryotic frataxins and bacterial CyaY proteins. Cluster 3, containing two serines, a tyrosine, and a glutamate, is only present in eukaryotic frataxins and on CyaY proteins from the Rickettsia genus. Residues from cluster 3 are blocking a small cavity of about 40 Å present in E. coli’s CyaY. The function of this cluster is unknown, but we hypothesize that its tyrosine may contribute to prevent formation of reactive oxygen species during iron detoxification. This cluster provides an example of gain of function during evolution in a protein involved in iron homeostasis, as our results suggests that Cluster 3 was present in the endosymbiont ancestor of mitochondria and was conserved in eukaryotic frataxins.
Monitoring the Simultaneous Implantation of Ti and Tb Cations to a Sacrificial Template and the Sol-Gel Synthesis of Tb-Doped TiO2 (Anatase) Hollow Spheres and Their Transition to Rutile Phase
Authors: Colomer María Teresa , Vattier Florencia
Published: October 2022

Tb-doped TiO2 (anatase) micro-hollow spheres (HSs) with nano-shells, in the range 0.00–3.00 at.% Tb, were successfully synthesized by a simultaneous chemical implantation route of both Ti and Tb cations from chlorides to a poly-styrene (PST)-co-poly-divinyl benzene (PDVB) sacrificial template, followed by controlled hydrolysis and polycondensation reactions. After water addition to the mixture of the precursors with the template, a decrease in the intensity and a shift to lower wavenumbers of the C=O absorption band in the IR spectra can indicate not only the anchoring of Ti and Tb ions to the carbonyl group of the template but also the hydrolysis of the implanted precursors. This latter process can involve a proton attack on the Ti–Cl, Tb–Cl and C=O bonds, the occupation of a vacant site by a water molecule, and then the dissociation of the dangling Ti–Cl, Tb–Cl ligands and C=O bonds. It gives rise to Ti1−xTbx[(OH)4−uClv]@PST–PDVB and Ti1−xTbx[(OH)4−y]@PST–PDVB complexes (x = 0.00, 0.0012, 0.0170 and 0.030). Finally, polycondensation of these species leads to Ti1−xTbxO2−w′@PST–PDVB compounds. After subsequent thermal removal at 550 °C of the template, the IR bands of the core (template) totally vanished and new bands were observed in the 400–900 cm−1 region which can be attributed to the metalloxane bondings (M–O, M’–O, M–O–M, M–O–M’ and/or M’–O–M’, being M and M’ = Ti and Tb, respectively, i.e., mainly vibration modes of anatase). Then, micron-sized HSs of TiO2 and Tb-doped-TiO2 (anatase) were obtained with nano-shells according to field emission gun scanning electron microscopy (FEG-SEM) and transmission electron microscopy (TEM) observations. Furthermore, X-ray photoelectron spectroscopy (XPS) measurements confirmed the presence of Tb4+ (38.5 and 41.2% for 1.70 and 3.00 at.% Tb, respectively) in addition to Tb3+ in the resulting HSs, with increasing Tb4+ content with both Tb doping and higher calcination temperatures. Then, these HSs can be considered as rare earth (RE) co-doped systems, at least for 1.70 and 3.00 at.% Tb contents being the transition to rutile phase favored by Tb doping for those compositions. Finally, diffusion of Tb from the inner parts to the surface of the HSs with the calcination treatments was also observed by XPS.
Acetophenone-Based 3,4-Dihydropyrimidine-2(1H)-Thione as Potential Inhibitor of Tyrosinase and Ribonucleotide Reductase: Facile Synthesis, Crystal Structure, In-Vitro and In-Silico Investigations
Authors: Saeed Aamer , Ejaz Syeda Abida , Khalid Aqsa , Channar Pervaiz Ali , Aziz Mubashir , Abbas Qamar , Wani Tanveer A. , Alsaif Nawaf A. , Alanazi Mohammed M. , Al-Hossaini Abdullah M. , Altwaijry Nojood , Zargar Seema , Elhadi Muawya , Hökelek Tuncer
Published: October 2022

The acetophenone-based 3,4-dihydropyrimidine-2(1H)-thione was synthesized by the reaction of 4-methylpent-3-en-2-one (1), 4-acetyl aniline (2) and potassium thiocyanate. The spectroscopic analysis including: FTIR, 1H-NMR, and single crystal analysis proved the structure of synthesized compound (4), with the six-membered nonplanar ring in envelope conformation. In crystal structure, the intermolecular N–H ⋯ S and C–H ⋯ O hydrogen bonds link the molecule in a two-dimensional manner which is parallel to (010) the plane enclosing R22 (8) and R22 (10) ring motifs. After that, the Hirshfeld surfaces and their related two-dimensional fingerprint plots were used for thorough investigation of intermolecular interactions. According to Hirshfeld surface analysis, the most substantial contributions to the crystal packing are from H ⋯ H (59.5%), H ⋯ S/S ⋯ H (16.1%), and H ⋯ C/C ⋯ H (13.1%) interactions. The electronic properties and stability of the compound were investigated through density functional theory (DFT) studies using B3LYP functional and 6-31G* as a basis set. The compound 4 displayed the high chemical reactivity with chemical softness of 2.48. In comparison to the already reported known tyrosinase inhibitor, the newly synthesized derivatives exhibited almost seven-fold better inhibition of tyrosinase (IC50 = 1.97 μM), which was further supported by molecular docking studies. The compound 4 inside the active pocket of ribonucleotide reductase (RNR) exhibited a binding energy of −19.68 kJ/mol, and with mammalian deoxy ribonucleic acid (DNA) it acts as an effective DNA groove binder with a binding energy of −21.32 kJ/mol. The results suggested further exploration of this compound at molecular level to synthesize more potential leads for the treatment of cancer.
Microglial Extracellular Vesicles as Modulators of Brain Microenvironment in Glioma
Authors: Catalano Myriam , Serpe Carmela , Limatola Cristina
Published: October 2022

Microglial cells represent the resident immune elements of the central nervous system, where they exert constant monitoring and contribute to preserving neuronal activity and function. In the context of glioblastoma (GBM), a common type of tumor originating in the brain, microglial cells deeply modify their phenotype, lose their homeostatic functions, invade the tumoral mass and support the growth and further invasion of the tumoral cells into the surrounding brain parenchyma. These modifications are, at least in part, induced by bidirectional communication among microglial and tumoral cells through the release of soluble molecules and extracellular vesicles (EVs). EVs produced by GBM and microglial cells transfer different kinds of biological information to receiving cells, deeply modifying their phenotype and activity and could represent important diagnostic markers and therapeutic targets. Recent evidence demonstrates that in GBM, microglial-derived EVs contribute to the immune suppression of the tumor microenvironment (TME), thus favoring GBM immune escape. In this review, we report the current knowledge on EV formation, biogenesis, cargo and functions, with a focus on the effects of microglia-derived EVs in GBM. What clearly emerges from this analysis is that we are at the beginning of a full understanding of the complete picture of the biological effects of microglial-derived EVs and that further investigations using multidisciplinary approaches are necessary to validate their use in GBM diagnosis and therapy.
Genome-Wide Identification, Expression and Interaction Analysis of GmSnRK2 and Type A PP2C Genes in Response to Abscisic Acid Treatment and Drought Stress in Soybean Plant
Authors: Shen Xinjie , Nan Hong , Jiang Yuzhuang , Zhou Yujia , Pan Xuejun
Published: October 2022

As a typical ancient tetraploid, soybean (Glycine max) is an important oil crop species and plays a crucial role in supplying edible oil, plant protein and animal fodder worldwide. As global warming intensifies, the yield of soybean in the field is often strongly restricted by drought stress. SNF1-related protein kinase 2 (SnRK2) and type A protein phosphatase 2C (PP2C-A) family members are core components of the abscisic acid (ABA) signal transduction pathway in plants and have been suggested to play important roles in increasing plant tolerance to drought stress, but genetic information supporting this idea is still lacking in soybean. Here, we cloned the GmSnRK2s and GmPP2C-A family genes from the reference genome of Williams 82 soybean. The results showed that the expression patterns of GmSnRK2s and GmPP2C-As are spatiotemporally distinct. The expression of GmSnRK2s in response to ABA and drought signals is not strictly the same as that of Arabidopsis SnRK2 homologous genes. Moreover, our results indicated that the duplicate pairs of GmSnRK2s and GmPP2C-As have similar expression patterns, cis-elements and relationships. GmSnRK2.2 may have a distinct function in the drought-mediated ABA signaling pathway. Furthermore, the results of yeast two-hybrid (Y2H) assays between GmSnRK2s and GmPP2C-As revealed that GmSnRK2.17, GmSnRK2.18, GmSnRK2.22, GmPP2C5, GmPP2C7, GmPP2C10 and GmPP2C17 may play central roles in the crosstalk among ABA signals in response to drought stress. Furthermore, GmPP2C-As and GmSnRKs were targeted by miRNA and validated by degradome sequencing, which may play multiple roles in the crosstalk between ABA and drought signals and other stress signals. Taken together, these results indicate that GmSnRK2s and GmPP2C-As may play a variety of roles in the drought-mediated ABA signaling pathway.
Chiral Discrimination Mechanisms by Silylated-Acetylated Cyclodextrins: Superficial Interactions vs. Inclusion
Authors: Balzano Federica , Uccello-Barretta Gloria , Sicoli Giuseppe , Vanni Letizia , Recchimurzo Alessandra , Aiello Federica
Published: October 2022

Cyclodextrin derivatives constitute a powerful class of auxiliary agents for the discrimination of apolar chiral substrates. Both host–guest inclusion phenomena and interactions with the derivatizing groups located on the surface of the macrocycle could drive the enantiodiscrimination; thus, it is important to understand the role that these processes play in the rational design of new chiral selectors. The purpose of this study is to compare via nuclear magnetic resonance (NMR) spectroscopy the efficiency of silylated-acetylated α-, β-, and γ-cyclodextrins in the chiral discrimination of 1,1,1,3,3-pentafluoro-2-(fluoromethoxy)-3-methoxypropane (compound B) and methyl 2-chloropropionate (MCP). NMR DOSY (Diffusion Ordered SpectroscopY) experiments were conducted for the determination of the bound molar fractions and the association constants, whereas ROESY (Rotating-frame Overhauser Enhancement SpectroscopY) measurements provided information on the hosts’ conformation and on the interaction phenomena with the guests. Compound B, endowed with fluorinated moieties, is not deeply included due to attractive Si-F interactions occurring at the external surface of the cyclodextrins. Therefore, a low selectivity toward the size of cyclodextrin cavity is found. By contrast, enantiodiscrimination of MCP relies on the optimal fitting between the size of the guest and that of the cyclodextrin cavity.
Identification of SLC15A4/PHT1 Gene Products Upregulation Marking the Intestinal Epithelial Monolayer of Ulcerative Colitis Patients
Authors: Mazzei Aurora , Serino Grazia , Romano Alessandro , Piccinno Emanuele , Scalavino Viviana , Valentini Anna , Armentano Raffaele , Schiavone Roberta , Giannelli Gianluigi , Verri Tiziano , Barca Amilcare
Published: October 2022

SLC15A4/PHT1 is an endolysosome-resident carrier of oligopeptides and histidine recently come into view as a key path marker of immune/autoimmune/inflammatory pathways in immune cells. Yet, its emerging role in inflammatory processes directly targeting the gastrointestinal epithelial layer, as in the multifactorial pathophysiology of inflammatory bowel disease (IBD), is poorly investigated. Here, the first identification of SLC15A4/PHT1 gene products in human colonic epithelium of ulcerative colitis (UC) patients is reported, showing protein primarily localized in intracellular vesicle-like compartments. Qualitative and quantitative immunohistochemical analyses of colon biopsies revealed overexpression of SLC15A4/PHT1 protein product in the epithelial layer of UC patients. Results were successfully mirrored in vitro, in spontaneously differentiated enterocyte-like monolayers of Caco-2 cells specifically exposed to DSS (dextran sodium sulphate) to mimic IBD inflammatory onsets. SLC15A4/PHT1 expression and cellular localization were characterized confirming its (dys)regulation traits in inflamed vs. healthy epithelia, strongly hinting the hypothesis of SLC15A4/PHT1 increased function associated with epithelial inflammation in IBD patients.
Long Non-Coding RNAs, Extracellular Vesicles and Inflammation in Alzheimer’s Disease
Authors: Canseco-Rodriguez Ania , Masola Valeria , Aliperti Vincenza , Meseguer-Beltran Maria , Donizetti Aldo , Sanchez-Perez Ana María
Published: October 2022

Alzheimer’s Disease (AD) has currently no effective treatment; however, preventive measures have the potential to reduce AD risk. Thus, accurate and early prediction of risk is an important strategy to alleviate the AD burden. Neuroinflammation is a major factor prompting the onset of the disease. Inflammation exerts its toxic effect via multiple mechanisms. Amongst others, it is affecting gene expression via modulation of non-coding RNAs (ncRNAs), such as miRNAs. Recent evidence supports that inflammation can also affect long non-coding RNA (lncRNA) expression. While the association between miRNAs and inflammation in AD has been studied, the role of lncRNAs in neurodegenerative diseases has been less explored. In this review, we focus on lncRNAs and inflammation in the context of AD. Furthermore, since plasma-isolated extracellular vesicles (EVs) are increasingly recognized as an effective monitoring strategy for brain pathologies, we have focused on the studies reporting dysregulated lncRNAs in EVs isolated from AD patients and controls. The revised literature shows a positive association between pro-inflammatory lncRNAs and AD. However, the reports evaluating lncRNA alterations in EVs isolated from the plasma of patients and controls, although still limited, confirm the value of specific lncRNAs associated with AD as reliable biomarkers. This is an emerging field that will open new avenues to improve risk prediction and patient stratification, and may lead to the discovery of potential novel therapeutic targets for AD.
Structure-Guided Approach to Discover Tuberosin as a Potent Activator of Pyruvate Kinase M2, Targeting Cancer Therapy
Authors: Adnan Mohd , Shamsi Anas , Elasbali Abdelbaset , Siddiqui Arif , Patel Mitesh , Alshammari Nawaf , Alharethi Salem , Alhassan Hassan , Bardakci Fevzi , Hassan Md.
Published: October 2022

Metabolic reprogramming is a key attribute of cancer progression. An altered expression of pyruvate kinase M2 (PKM2), a phosphotyrosine-binding protein is observed in many human cancers. PKM2 plays a vital role in metabolic reprogramming, transcription and cell cycle progression and thus is deliberated as an attractive target in anticancer drug development. The expression of PKM2 is essential for aerobic glycolysis and cell proliferation, especially in cancer cells, facilitating selective targeting of PKM2 in cell metabolism for cancer therapeutics. We have screened a virtual library of phytochemicals from the IMPPAT (Indian Medicinal Plants, Phytochemistry and Therapeutics) database of Indian medicinal plants to identify potential activators of PKM2. The initial screening was carried out for the physicochemical properties of the compounds, and then structure-based molecular docking was performed to select compounds based on their binding affinity towards PKM2. Subsequently, the ADMET (absorption, distribution, metabolism, excretion and toxicity) properties, PAINS (Pan-assay interference compounds) patterns, and PASS evaluation were carried out to find more potent hits against PKM2. Here, Tuberosin was identified from the screening process bearing appreciable binding affinity toward the PKM2-binding pocket and showed a worthy set of drug-like properties. Finally, molecular dynamics simulation for 100 ns was performed, which showed decent stability of the protein-ligand complex and relatival conformational dynamics throughout the trajectory. The study suggests that modulating PKM2 with natural compounds is an attractive approach in treating human malignancy after required validation.
Optical and Flame-Retardant Properties of a Series of Polyimides Containing Side Chained Bulky Phosphaphenanthrene Units
Authors: Homocianu Mihaela , Serbezeanu Diana , Lisa Gabriela , Brebu Mihai , Vlad-Bubulac Tăchiță
Published: October 2022

Among the multitude of polymers with carbon-based macromolecular architectures that easily ignite in certain applications where short circuits may occur, polyimide has evolved as a class of polymers with high thermal stability while exhibiting intrinsic flame retardancy at elevated temperatures via a char-forming mechanism. However, high amounts of aromatic rings in the macromolecular backbone are required for these results, which may affect other properties such as film-forming capacity or mechanical properties; thus, much work has been done to structurally derivatize or make hybrid polyimide systems. In this respect, flexible polyimide films (PI(1–4)) containing bulky 9,10-dihydro-9-oxa-10-phosphaphenanthrene-10-oxide (DOPO) units have been developed starting from commercial dianhydrides and an aromatic diamine containing two side chain bulky DOPO groups. The chemical structure of PI(1–4)) was characterized by 1H NMR, 13C NMR and 31P NMR spectroscopy. The optical properties, including absorption and luminescence spectra of these polymers, were analyzed. All polyimides containing DOPO derivatives emitted blue light with an emission maxima in the range of 340–445 nm, in solvents such as N,N-dimethylformamide, N-methyl-2-pyrrolidone, chloroform, and N,N-dimethylacetamide, while green light emission (λem = 487 nm for PI-4) was evidenced in a thin-film state. The thermal decomposition mechanism and flame-retardant behavior of the resulting materials were investigated by pyrolysis-gas-chromatography spectrometry (Py-GC), scanning electron microscopy (SEM), EDX maps and FTIR spectroscopy. The residues resulting from the TGA experiments were examined by SEM microscopy images and FTIR spectra to understand the pyrolysis mechanism.
Polysaccharides of Salsola passerina: Extraction, Structural Characterization and Antioxidant Activity
Authors: Golovchenko Victoria , Popov Sergey , Smirnov Vasily , Khlopin Victor , Vityazev Fedor , Naranmandakh Shinen , Dmitrenok Andrey S. , Shashkov Alexander S.
Published: October 2022

The above-ground part of the Salsola passerine was found to contain ~13% (w/w) of polysaccharides extractable with water and aqueous solutions of ammonium oxalate and sodium carbonate. The fractions extracted with aqueous sodium carbonate solutions had the highest yield. The polysaccharides of majority fractions are characterized by similar monosaccharide composition; namely, galacturonic acid and arabinose residues are the principal components of their carbohydrate chains. The present study focused on the determination of antioxidant activity of the extracted polysaccharide fractions and elucidation of the structure of polysaccharides using nuclear magnetic resonance (NMR) spectroscopy. Homogalacturonan (HG), consisting of 1,4-linked residues of α-D-galactopyranosyluronic acid (GalpA), rhamnogalacturonan-I (RG-I), which contains a diglycosyl repeating unit with a strictly alternating sequence of 1,4-linked D-GalpA and 1,2-linked L-rhamnopyranose (Rhap) residues in the backbone, and arabinan, were identified as the structural units of the obtained polysaccharides. HMBC spectra showed that arabinan consisted of alternating regions formed by 3,5-substituted and 1,5-linked arabinofuranose residues, but there was no alternation of these residues in the arabinan structure. Polysaccharide fractions scavenged the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical at 0.2–1.8 mg/mL. The correlation analysis showed that the DPPH scavenging activity of polysaccharide fractions was associated with the content of phenolic compounds (PCs).
Immunothrombosis and the Role of Platelets in Venous Thromboembolic Diseases
Authors: Heestermans Marco , Poenou Géraldine , Duchez Anne-Claire , Hamzeh-Cognasse Hind , Bertoletti Laurent , Cognasse Fabrice
Published: October 2022

Venous thromboembolism (VTE) is the third leading cardiovascular cause of death and is conventionally treated with anticoagulants that directly antagonize coagulation. However, recent data have demonstrated that also platelets play a crucial role in VTE pathophysiology. In the current review, we outline how platelets are involved during all stages of experimental venous thrombosis. Platelets mediate initiation of the disease by attaching to the vessel wall upon which they mediate leukocyte recruitment. This process is referred to as immunothrombosis, and within this novel concept inflammatory cells such as leukocytes and platelets directly drive the progression of VTE. In addition to their involvement in immunothrombosis, activated platelets can directly drive venous thrombosis by supporting coagulation and secreting procoagulant factors. Furthermore, fibrinolysis and vessel resolution are (partly) mediated by platelets. Finally, we summarize how conventional antiplatelet therapy can prevent experimental venous thrombosis and impacts (recurrent) VTE in humans.
Four-Component Relativistic Calculations of NMR Shielding Constants of the Transition Metal Complexes—Part 2: Nitrogen-Coordinated Complexes of Cobalt
Authors: Samultsev Dmitry O. , Semenov Valentin A. , Rusakova Irina L. , Krivdin Leonid B.
Published: October 2022

Both four-component relativistic and nonrelativistic computations within the GIAO-DFT(PBE0) formalism have been carried out for 15N and 59Co NMR shielding constants and chemical shifts of a number of the nitrogen-coordinated complexes of cobalt. It was found that the total values of the calculated nitrogen chemical shifts of considered cobalt complexes span over a range of more than 580 ppm, varying from −452 to +136 ppm. At that, the relativistic corrections to nitrogen shielding constants and chemical shifts were demonstrated to be substantial, changing accordingly from ca. −19 to +74 ppm and from −68 to +25 ppm. Solvent effects on 15N shielding constants and chemical shifts were shown to have contributions no less important than the relativistic effects, namely from −35 to +63 ppm and from −74 to +23 ppm, respectively. Cobalt shielding constants and chemical shifts were found to vary in the ranges of, accordingly, −20,157 to −11,373 ppm and from +3781 to +13,811. The relativistic effects are of major importance in the cobalt shielding constants, resulting in about 4% for the shielding-type contributions, while solvent corrections to cobalt shielding constants appeared to be of less significance, providing corrections of about 1.4% to the gas phase values.
Apigenin Modulates AnxA6- and TNAP-Mediated Osteoblast Mineralization
Authors: Mroczek Joanna , Pikula Slawomir , Suski Szymon , Weremiejczyk Lilianna , Biesaga Magdalena , Strzelecka-Kiliszek Agnieszka
Published: October 2022

Mineralization-competent cells like osteoblasts and chondrocytes release matrix vesicles (MVs) which accumulate Ca2+ and Pi, creating an optimal environment for apatite formation. The mineralization process requires the involvement of proteins, such as annexins (Anx) and tissue-nonspecific alkaline phosphatase (TNAP), as well as low molecular-weight compounds. Apigenin, a flavonoid compound, has been reported to affect bone metabolism, but there are doubts about its mechanism of action under physiological and pathological conditions. In this report, apigenin potency to modulate annexin A6 (AnxA6)- and TNAP-mediated osteoblast mineralization was explored using three cell lines: human fetal osteoblastic hFOB 1.19, human osteosarcoma Saos-2, and human coronary artery smooth muscle cells HCASMC. We compared the mineralization competence, the morphology and composition of minerals, and the protein distribution in control and apigenin-treated cells and vesicles. The mineralization ability was monitored by AR-S/CPC analysis, and TNAP activity was determined by ELISA assay. Apigenin affected the mineral structure and modulated TNAP activity depending on the concentration. We also observed increased mineralization in Saos-2 cells. Based on TEM-EDX, we found that apigenin influenced the mineral composition. This flavonoid also disturbed the intracellular distribution of AnxA6 and TNAP, especially blocking AnxA6 aggregation and TNAP attachment to the membrane, as examined by FM analysis of cells and TEM-gold analysis of vesicles. In summary, apigenin modulates the mineralization process by regulating AnxA6 and TNAP, as well as through various effects on normal and cancer bone tissues or atherosclerotic soft tissue.
The Cytokine Growth Differentiation Factor-15 and Skeletal Muscle Health: Portrait of an Emerging Widely Applicable Disease Biomarker
Authors: De Paepe Boel
Published: October 2022

Growth differentiation factor 15 (GDF-15) is a stress-induced transforming growth factor-β superfamily cytokine with versatile functions in human health. Elevated GDF-15 blood levels associate with multiple pathological conditions, and are currently extensively explored for diagnosis, and as a means to monitor disease progression and evaluate therapeutic responses. This review analyzes GDF-15 in human conditions specifically focusing on its association with muscle manifestations of sarcopenia, mitochondrial myopathy, and autoimmune and viral myositis. The use of GDF-15 as a widely applicable health biomarker to monitor muscle disease is discussed, and its potential as a therapeutic target is explored.
Molecular Mechanisms of Neural Plasticity: From Basic Research to Implications for Visual Functional Rescue
Authors: Sale Alessandro
Published: October 2022

Visual system plasticity, the capability of visual connections to modify their structure and function in response to experience, is an essential property underlying the maturation of visual functions during development, behavioral flexibility in response to subtle environmental changes, and adaptive repair in conditions of disease or trauma [...]
Effects of Substance P and Neurokinin A on the Contractile Activity of Inflamed Porcine Uterus
Authors: Brzozowska Marta , Romaniewicz Marta , Całka Jarosław , Jana Barbara
Published: October 2022

Disturbances in uterine contractile activity contribute to the development of inflammation, and recent evidence indicates that tachykinins, including substance P (SP) and neurokinin A (NKA), are involved in controlling uterine function. Here, we determined the effect of Escherichia coli (E. coli)-induced inflammation on expression of protein receptor subtypes for substance P (NK1R) and neurokinin A (NK2R) in the pig myometrium as well as their role in contractility of inflamed uterus. The severe acute endometritis developed in the E. coli group and the expression of NK1R and NK2R proteins increased in the myometrium. Compared to the pre-administration period, SP (10−6 M) reduced the amplitude and frequency in the myometrium of the E. coli group and the amplitude was higher and the frequency was lower versus other groups. NKA reduced the amplitude and increased the frequency in endometrium/myometrium of the E. coli group. In this group, the amplitude was lower and the frequency was higher than in the CON and SAL groups. Our research showed that NK2R (10−6 M) antagonist application abolished the NKA inhibitory effect on uterine amplitude. The application of the NK1R (10−5 M) antagonist together with SP revealed that the inhibitory effect of SP on uterine contractility is achieved independently of the NKR1. Additionally, taking into account the fact that NKA shows an inhibitory effect with the use of NK2R on uterine amplitude suggests the possibility of therapeutic use of the antagonist as a drug increasing uterine contractility in inflammation.
Phosphonate Inhibitors of Pyruvate Dehydrogenase Perturb Homeostasis of Amino Acids and Protein Succinylation in the Brain
Authors: Artiukhov Artem V. , Aleshin Vasily A. , Karlina Irina S. , Kazantsev Alexey V. , Sibiryakina Daria A. , Ksenofontov Alexander L. , Lukashev Nikolay V. , Graf Anastasia V. , Bunik Victoria I.
Published: October 2022

Mitochondrial pyruvate dehydrogenase complex (PDHC) is essential for brain glucose and neurotransmitter metabolism, which is dysregulated in many pathologies. Using specific inhibitors of PDHC in vivo, we determine biochemical and physiological responses to PDHC dysfunction. Dose dependence of the responses to membrane-permeable dimethyl acetylphosphonate (AcPMe2) is non-monotonous. Primary decreases in glutathione and its redox potential, methionine, and ethanolamine are alleviated with increasing PDHC inhibition, the alleviation accompanied by physiological changes. A comparison of 39 brain biochemical parameters after administration of four phosphinate and phosphonate analogs of pyruvate at a fixed dose of 0.1 mmol/kg reveals no primary, but secondary changes, such as activation of 2-oxoglutarate dehydrogenase complex (OGDHC) and decreased levels of glutamate, isoleucine and leucine. The accompanying decreases in freezing time are most pronounced after administration of methyl acetylphosphinate and dimethyl acetylphosphonate. The PDHC inhibitors do not significantly change the levels of PDHA1 expression and phosphorylation, sirtuin 3 and total protein acetylation, but increase total protein succinylation and glutarylation, affecting sirtuin 5 expression. Thus, decreased production of the tricarboxylic acid cycle substrate acetyl-CoA by inhibited PDHC is compensated by increased degradation of amino acids through the activated OGDHC, increasing total protein succinylation/glutarylation. Simultaneously, parasympathetic activity and anxiety indicators decrease.
Identification of Low-Nitrogen-Related miRNAs and Their Target Genes in Sugarcane and the Role of miR156 in Nitrogen Assimilation
Authors: Gao Shiwu , Yang Yingying , Yang Yuting , Zhang Xu , Su Yachun , Guo Jinlong , Que Youxiong , Xu Liping
Published: October 2022

Chemical nitrogen (N) fertilizer is widely used in sugarcane production, especially in China and India. Understanding the molecular mechanisms and mining miRNAs and their target genes associated with nitrogen use efficiency (NUE) in sugarcane can aid in developing the N-efficient varieties, and thus is beneficial to reduce N fertilizer application. In this study, the root miRNA database of N-efficient sugarcane variety ROC22 under low N stress (0.3 mM NH4NO3) for 3 h was constructed, along with their transcriptome-rearranged data. KEGG analysis indicated that those candidate target genes, corresponding to differentially expressed miRNAs, were mainly enriched in N metabolism, amino acid metabolism, carbohydrate metabolism, photosynthesis, and hormone signal transduction pathways. It was found that under low N stress for 0–24 h, there was a negative correlation between miR168 and SPX, along with miR396 and acnA. Furthermore, the expression of miR156 in the roots of ROC22 was significantly up-regulated under low N treatment. Compared with the wild-type, the Arabidopsis plants overexpressing sugarcane miR156 exhibited significantly improved length and surface area of roots, while the expression of one NO3− transporter gene NRT1.1, three N assimilation key genes (NR1, NIR1, and GS), and the activity of two N assimilation key enzymes (NR and GS) were up-regulated under low N treatment. It can be reasonably deduced that sugarcane miR156 can enhance the nitrogen assimilation ability of the overexpressed Arabidopsis plants under low N application, and thus has a potential ability for improving sugarcane NUE. The present study should be helpful for understanding the molecular regulatory network in the N-efficient sugarcane genotype responding to low N stress and could provide the candidate miRNAs with a potential function in improving sugarcane NUE.
GDNF Increases Inhibitory Synaptic Drive on Principal Neurons in the Hippocampus via Activation of the Ret Pathway
Authors: Mikroulis Apostolos , Waloschková Eliška , Bengzon Johan , Woldbye David , Pinborg Lars H. , Jespersen Bo , Avila Anna Sanchez , Laszlo Zsofia I. , Henstridge Christopher , Ledri Marco , Kokaia Merab
Published: October 2022

Glial cell line-derived neurotrophic factor (GDNF) has been shown to counteract seizures when overexpressed or delivered into the brain in various animal models of epileptogenesis or chronic epilepsy. The mechanisms underlying this effect have not been investigated. We here demonstrate for the first time that GDNF enhances GABAergic inhibitory drive onto mouse pyramidal neurons by modulating postsynaptic GABAA receptors, particularly in perisomatic inhibitory synapses, by GFRα1 mediated activation of the Ret receptor pathway. Other GDNF receptors, such as NCAM or Syndecan3, are not contributing to this effect. We observed similar alterations by GDNF in human hippocampal slices resected from epilepsy patients. These data indicate that GDNF may exert its seizure-suppressant action by enhancing GABAergic inhibitory transmission in the hippocampal network, thus counteracting the increased excitability of the epileptic brain. This new knowledge can contribute to the development of novel, more precise treatment strategies based on a GDNF gene therapy approach.
Molecularly Imprinted Polymers Based on Chitosan for 2,4-Dichlorophenoxyacetic Acid Removal
Authors: Silvestro Ilaria , Fernández-García Marta , Ciarlantini Clarissa , Francolini Iolanda , Girelli Annamaria , Piozzi Antonella
Published: October 2022

The development of low-cost and eco-friendly materials for the removal of pollutants from water is one of the main modern challenges. For this purpose, molecularly imprinted polymers were prepared under optimized conditions starting from chitosan (CS), chemically or ionically modified with glycidyl methacrylate (GMA) or itaconic acid (ITA), respectively. 2,4-Dichlorophenoxyacetic acid (2,4-D) was used as a template, obtaining the CS_GMA and CS_ITA series. The influence of the template concentration on the MIPs’ (molecularly imprinted polymers) morphology, thermal behaviour and swelling ability, as well as on the 2,4-D removal capacity, were analyzed. The amount of the template used for the imprinting, together with the different permeability of the matrices, were the key factors driving the analyte uptake process. Despite the good performance shown by the non-imprinted CS_GMA sample, the best results were obtained when CS_GMA was imprinted with the highest amount (5%) of template (CS_GMA_5). This system was also more efficient when consecutive adsorption experiments were carried out. In addition, CS_GMA_5 had a desorption efficiency of 90–100% when a low pesticide concentration was used. These findings suggest that the presence of imprinted cavities could be useful in improving the performance of sorbent materials making CS_GMA_5 a possible candidate for 2,4-D removal.
miR-31-5p-Modified RAW 264.7 Macrophages Affect Profibrotic Phenotype of Lymphatic Endothelial Cells In Vitro
Authors: Moskalik Aneta , Ratajska Anna , Majchrzak Barbara , Jankowska-Steifer Ewa , Bartkowiak Krzysztof , Bartkowiak Mateusz , Niderla-Bielińska Justyna
Published: October 2022

Cardiac lymphatic vessel (LyV) remodeling as a contributor to heart failure has not been extensively evaluated in metabolic syndrome (MetS). Our studies have shown structural changes in cardiac LyV in MetS that contribute to the development of edema and lead to myocardial fibrosis. Tissue macrophages may affect LyV via secretion of various substances, including noncoding RNAs. The aim of the study was to evaluate the influence of macrophages modified by miR-31-5p, a molecule that regulates fibrosis and lymphangiogenesis, on lymphatic endothelial cells (LECs) in vitro. The experiments were carried out on the RAW 264.7 macrophage cell line and primary dermal lymphatic endothelial cells. RAW 264.7 macrophages were transfected with miR-31-5p and supernatant from this culture was used for LEC stimulation. mRNA expression levels for genes associated with lymphangiogenesis and fibrosis were measured with qRT-PCR. Selected results were confirmed with ELISA or Western blotting. miR-31-5p-modified RAW 264.7 macrophages secreted increased amounts of VEGF-C and TGF-β and a decreased amount of IGF-1. The supernatant from miR-31-5p-modified RAW 264.7 downregulated the mRNA expression for genes regulating endothelial-to-mesenchymal transition (EndoMT) and fibrosis in LECs. Our results suggest that macrophages under the influence of miR-31-5p show the potential to inhibit LEC-dependent fibrosis. However, more studies are needed to confirm this effect in vivo.
One Step before Synthesis: Structure–Property–Condition Relationship Models to Sustainable Design of Efficient TiO2-Based Multicomponent Nanomaterials
Authors: Mikolajczyk Alicja , Falkowski Dawid
Published: October 2022

To control the photocatalytic activity, it is essential to consider several parameters affecting the structure of ordered multicomponent TiO2-based photocatalytic nanotubes. The lack of systematic knowledge about the relationship between structure, property, and preparation parameters may be provided by applying a machine learning (ML) methodology and predictive models based on the quantitative structure-property-condition relationship (QSPCR). In the present study, for the first time, the quantitative mapping of preparation parameters, morphology, and photocatalytic activity of 136 TiO2 NTs doped with metal and non-metal nanoparticles synthesized with the one-step anodization method has been investigated via linear and nonlinear ML methods. Moreover, the developed QSPCR model, for the first time, provides systematic knowledge supporting the design of effective TiO2-based nanotubes by proper structure manipulation. The proposed computer-aided methodology reduces cost and speeds up the process (optimize) of efficient photocatalysts’ design at the earliest possible stage (before synthesis) in line with the sustainability-by-design strategy.
High-Resolution Crystal Structure of Muscle Phosphoglycerate Mutase Provides Insight into Its Nuclear Import and Role
Authors: Wiśniewski Janusz , Barciszewski Jakub , Turlik Jakub , Baran Karolina , Duda Przemysław , Jaskolski Mariusz , Rakus Dariusz
Published: October 2022

Phosphoglycerate mutase (PGAM) is a glycolytic enzyme converting 3-phosphoglycerate to 2-phosphoglycerate, which in mammalian cells is expressed in two isoforms: brain (PGAM1) and muscle (PGAM2). Recently, it was shown that besides its enzymatic function, PGAM2 can be imported to the cell nucleus where it co-localizes with the nucleoli. It was suggested that it functions there to stabilize the nucleolar structure, maintain mRNA expression, and assist in the assembly of new pre-ribosomal subunits. However, the precise mechanism by which the protein translocates to the nucleus is unknown. In this study, we present the first crystal structure of PGAM2, identify the residues involved in the nuclear localization of the protein and propose that PGAM contains a “quaternary nuclear localization sequence (NLS)”, i.e., one that consists of residues from different protein chains. Additionally, we identify potential interaction partners for PGAM2 in the nucleoli and demonstrate that 14-3-3ζ/δ is indeed an interaction partner of PGAM2 in the nucleus. We also present evidence that the insulin/IGF1–PI3K–Akt–mTOR signaling pathway is responsible for the nuclear localization of PGAM2.
Morphological and Mechanical Characterization of Extracellular Vesicles and Parent Human Synoviocytes under Physiological and Inflammatory Conditions
Authors: Filali Samira , Darragi-Raies Nesrine , Ben-Trad Layth , Piednoir Agnès , Hong Saw-See , Pirot Fabrice , Landoulsi Ahmed , Girard-Egrot Agnès , Granjon Thierry , Maniti Ofelia , Miossec Pierre , Trunfio-Sfarghiu Ana-Maria
Published: October 2022

The morphology of fibroblast-like synoviocytes (FLS) issued from the synovial fluid (SF) of patients suffering from osteoarthritis (OA), rheumatoid arthritis (RA), or from healthy subjects (H), as well as the ultrastructure and mechanical properties of the FLS-secreted extracellular vesicles (EV), were analyzed by confocal microscopy, transmission electron microscopy, atomic force microscopy, and tribological tests. EV released under healthy conditions were constituted of several lipid bilayers surrounding a viscous inner core. This “gel-in” vesicular structure ensured high mechanical resistance of single vesicles and good tribological properties of the lubricant. RA, and to a lesser extent OA, synovial vesicles had altered morphology, corresponding to a “gel-out” situation with vesicles surrounded by a viscous gel, poor mechanical resistance, and poor lubricating qualities. When subjected to inflammatory conditions, healthy cells developed phenotypes similar to that of RA samples, which reinforces the importance of inflammatory processes in the loss of lubricating properties of SF.
The BRCT Domain from the Homologue of the Oncogene PES1 in Leishmania major (LmjPES) Promotes Malignancy and Drug Resistance in Mammalian Cells
Authors: Larrea Esther , Fernández-Rubio Celia , Peña-Guerrero José , Guruceaga Elizabeth , Nguewa Paul A.
Published: October 2022

Around 15% of cancer cases are attributable to infectious agents. Epidemiological studies suggest that an association between leishmaniasis and cancer does exist. Recently, the homologue of PES1 in Leishmania major (LmjPES) was described to be involved in parasite infectivity. Mammalian PES1 protein has been implicated in cellular processes like cell cycle regulation. Its BRCT domain has been identified as a key factor in DNA damage-responsive checkpoints. This work aimed to elucidate the hypothetical oncogenic implication of BRCT domain from LmjPES in host cells. We generated a lentivirus carrying this BRCT domain sequence (lentiBRCT) and a lentivirus expressing the luciferase protein (lentiLuc), as control. Then, HEK293T and NIH/3T3 mammalian cells were infected with these lentiviruses. We observed that the expression of BRCT domain from LmjPES conferred to mammal cells in vitro a greater replication rate and higher survival. In in vivo experiments, we observed faster tumor growth in mice inoculated with lentiBRCT respect to lentiLuc HEK293T infected cells. Moreover, the lentiBRCT infected cells were less sensitive to the genotoxic drugs. Accordingly, gene expression profiling analysis revealed that BRCT domain from LmjPES protein altered the expression of proliferation- (DTX3L, CPA4, BHLHE41, BMP2, DHRS2, S100A1 and PARP9), survival- (BMP2 and CARD9) and chemoresistance-related genes (DPYD, Dok3, DTX3L, PARP9 and DHRS2). Altogether, our results reinforced the idea that in eukaryotes, horizontal gene transfer might be also achieved by parasitism like Leishmania infection driving therefore to some crucial biological changes such as proliferation and drug resistance.
Overexpression of β-Ketoacyl CoA Synthase 2B.1 from Chenopodium quinoa Promotes Suberin Monomers’ Production and Salt Tolerance in Arabidopsis thaliana
Authors: Tariq Faheem , Zhao Shuangshuang , Ahmad Naveed , Wang Pingping , Shao Qun , Ma Changle , Yang Xianpeng
Published: October 2022

Very-long-chain fatty acids (VLCFAs) are precursors for the synthesis of various lipids, such as triacylglycerols, sphingolipids, cuticular waxes, and suberin monomers, which play important roles in plant growth and stress responses. However, the underlying molecular mechanism regulating VLCFAs’ biosynthesis in quinoa (Chenopodium quinoa Willd.) remains unclear. In this study, we identified and functionally characterized putative 3-ketoacyl-CoA synthases (KCSs) from quinoa. Among these KCS genes, CqKCS2B.1 showed high transcript levels in the root tissues and these were rapidly induced by salt stress. CqKCS2B.1 was localized to the endoplasmic reticulum. Overexpression of CqKCS2B.1 in Arabidopsis resulted in significantly longer primary roots and more lateral roots. Ectopic expression of CqKCS2B.1 in Arabidopsis promoted the accumulation of suberin monomers. The occurrence of VLCFAs with C22–C24 chain lengths in the overexpression lines suggested that CqKCS2B.1 plays an important role in the elongation of VLCFAs from C20 to C24. The transgenic lines of overexpressed CqKCS2B.1 showed increased salt tolerance, as indicated by an increased germination rate and improved plant growth and survival under salt stress. These findings highlight the significant role of CqKCS2B.1 in VLCFAs’ production, thereby regulating suberin biosynthesis and responses to salt stress. CqKCS2B.1 could be utilized as a candidate gene locus to breed superior, stress-tolerant quinoa cultivars.
Solutions to a Radical Problem: Overview of Current and Future Treatment Strategies in Leber’s Hereditary Opic Neuropathy
Authors: Spiegel Samuel J. , Sadun Alfredo A.
Published: October 2022

Leber’s Hereditary Optic Neuropathy (LHON) is the most common primary mitochondrial DNA disorder. It is characterized by bilateral severe central subacute vision loss due to specific loss of Retinal Ganglion Cells and their axons. Historically, treatment options have been quite limited, but ongoing clinical trials show promise, with significant advances being made in the testing of free radical scavengers and gene therapy. In this review, we summarize management strategies and rational of treatment based on current insights from molecular research. This includes preventative recommendations for unaffected genetic carriers, current medical and supportive treatments for those affected, and emerging evidence for future potential therapeutics.