bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Pacing Behaviors on Mass Start Speed Skating
Authors: Peng Qian , Li Feng , Liu Hui , Gomez Miguel-Angel
Published: August 2022

The mass start speed skating (MSSS) is a new event for the 2018 PyeongChang Winter Olympic Games. Considering that the event rankings were based on points gained on laps, it is worthwhile to investigate the pacing behaviors on each lap that directly influence the skater’s ranking at the end of the race. To the best of our knowledge, this is the first study investigating the pacing behavior on the MSSS. The aim of this study was to analyze the pacing behaviors and performance on MSSS regarding skaters’ level (SL), competition stage (semi-final/final) (CS), and gender (G). All the male and female races in the World Cup and World Championships were analyzed during the 2018–2019 and 2019–2020 seasons. As a result, a total of 601 skaters (male = 350 and female = 251) from 36 games (male = 21 and female = 15) were observed. The one-way ANOVA for repeated measures was used to compare skaters’ pacing behavior on each lap, and the three-way ANOVA for repeated measures was used to identify the influence of SL, CS, and G on skaters’ pacing behaviors and total time spent. In general, the results showed that the pacing behaviors from fast to slow were group one (laps 4, 8, 12, 15, 16), group two (laps 5, 9, 13, 14), group three (laps 3, 6, 7, 10, 11), and group four (laps 1 and 2) (p ≤ 0.001 for all groups). For CS, the total time spent in the final was less than the semi-final (p ≤ 0.001). For SL, top-level skaters spent less total time than the middle-level and low-level skaters (p ≤ 0.002), while there was no significant difference between the middle and low levels (p = 0.214). For G, the male skaters spent less total time than females on all laps (p ≤ 0.048). Current findings could help coaching staff to better understand the pacing behaviors regarding SL, CS, and G. In particular, the identified performance trends may allow controlling for pacing strategy and decision making before and during the race.
A Complete Reinforcement-Learning-Based Framework for Urban-Safety Perception
Authors: Wang Yaxuan , Zeng Zhixin , Li Qiushan , Deng Yingrui
Published: August 2022

Urban-safety perception is crucial for urban planning and pedestrian street preference studies. With the development of deep learning and the availability of high-resolution street images, the use of artificial intelligence methods to deal with urban-safety perception has been considered adequate by many researchers. However, most current methods are based on the feature-extraction capability of convolutional neural networks (CNNs) with large-scale annotated data for training, mainly aimed at providing a regression or classification model. There remains a lack of interpretable and complete evaluation systems for urban-safety perception. To improve the interpretability of evaluation models and achieve human-like safety perception, we proposed a complete decision-making framework based on reinforcement learning (RL). We developed a novel feature-extraction module, a scalable visual computational model based on visual semantic and functional features that could fully exploit the knowledge of domain experts. Furthermore, we designed the RL module—comprising a combination of a Markov decision process (MDP)-based street-view observation environment and an intelligent agent trained using a deep reinforcement-learning (DRL) algorithm—to achieve human-level perception abilities. Experimental results using our crowdsourced dataset showed that the framework achieved satisfactory prediction performance and excellent visual interpretability.
Aurisin A Complexed with 2,6-Di-O-methyl-β-cyclodextrin Enhances Aqueous Solubility, Thermal Stability, and Antiproliferative Activity against Lung Cancer Cells
Authors: Charoenwongpaiboon Thanapon , Oo Amy , Nasoontorn Sutita , Rungrotmongkol Thanyada , Kanokmedhakul Somdej , Mahalapbutr Panupong
Published: August 2022

Aurisin A (AA), an aristolane dimer sesquiterpene isolated from the luminescent mushroom Neonothopanus nambi, exhibits various biological and pharmacological effects. However, its poor solubility limits its use for further medicinal applications. This study aimed to improve the water solubility of AA via complexation with β-cyclodextrin (βCD) and its derivatives (2,6-di-O-methyl-βCD (DMβCD) and 2-hydroxypropyl-βCD (HPβCD). A phase solubility analysis demonstrated that the solubility of AA linearly enhanced with increasing concentrations of βCDs (ranked in the order of AA/DMβCD > AA/HPβCD > AA/βCD). Notably, βCDs, especially DMβCD, increased the thermal stability of the inclusion complexes. The thermodynamic study indicated that the complexation between AA and βCD(s) was a spontaneous endothermic reaction, and AA/DMβCD possesses the highest binding strength. The complex formation between AA and DMβCD was confirmed by means of FT-IR, DSC, and SEM. Molecular dynamics simulations revealed that the stability and compactness of the AA/DMβCD complex were higher than those of the DMβCD alone. The encapsulation of AA led to increased intramolecular H-bond formations on the wider rim of DMβCD, enhancing the complex stability. The antiproliferative activity of AA against A549 and H1975 lung cancer cells was significantly improved by complexation with DMβCD. Altogether, the satisfactory water solubility, high thermal stability, and enhanced antitumor potential of the AA/DMβCD inclusion complex would be useful for its application as healthcare products or herbal medicines.
TGF-β Signalling Mediates the Anti-Inflammatory Activity of Enamel Matrix Derivative In Vitro
Authors: Panahipour Layla , Sordi Mariane Beatriz , Kargarpour Zahra , Gruber Reinhard
Published: August 2022

Enamel matrix derivative (EMD) prepared from extracted porcine fetal tooth material can support the regrow of periodontal tissues. Previous findings suggest that EMD has anti-inflammatory properties and TGF-β activity in vitro. However, the anti-inflammatory activity of EMD is mediated via TGF-β has not been considered. To this aim, we first established a bioassay to confirm the anti-inflammatory activity of EMD. The bioassay was based on the RAW 264.7 macrophage cell line and proven with primary macrophages where EMD significantly reduced the forced expression of IL-6. We then confirmed the presence of TGF-β1 in EMD by immunoassay and by provoking the Smad2/3 nuclear translocation in RAW 264.7 macrophages. Next, we took advantage of the TGF-β receptor type I kinase-inhibitor SB431542 to block the respective signalling pathway. SB431542 reversed the anti-inflammatory activity of EMD and TGF-β in a bioassay when IL-6 and CXCL2 expression was driven by the LPS stimulation of RAW 264.7 macrophages. This central observation was supported by showing that SB431542 reversed the anti-inflammatory activity of EMD using IL-1β and TNF-α-stimulated ST2 bone marrow stromal cells. Together, these findings implicate that the TGF-β activity mediates at least part of the anti-inflammatory activity of EMD in vitro.
Study of Thermal Properties, Molecular Dynamics, and Physical Stability of Etoricoxib Mixtures with Octaacetylmaltose near the Glass Transition
Authors: Grzybowska Katarzyna , Rams-Baron Marzena , Łucak Kinga , Grzybowski Andrzej , Paluch Marian
Published: August 2022

In this paper, we thoroughly investigated the physical stability of the anti-inflammatory drug etoricoxib, which has been reported earlier to be resistant to recrystallization in its glassy and supercooled states at ambient pressure. Our unique application of the standard refractometry technique showed that the supercooled liquid of the drug was able to recrystallize during isothermal experiments in atmospheric conditions. This enabled us to determine the crystallization onset timescale and nucleation energy barrier of etoricoxib for the first time. As the physical instability of etoricoxib requires working out an efficient method for improving the drug’s resistance to recrystallization to maintain its amorphous form utility in potential pharmaceutical applications, we focused on finding a solution to this problem, and successfully achieved this purpose by preparing binary mixtures of etoricoxib with octaacetylmaltose. Our detailed thermal, refractometry, and molecular dynamics studies of the binary compositions near the glass transition revealed a peculiar behavior of the glass transition temperatures when changing the acetylated disaccharide concentration in the mixtures. Consequently, the anti-plasticization effect on the enhancement of physical stability could be excluded, and a key role for specific interactions in the improved resistance to recrystallization was expected. Invoking our previous results obtained for etoricoxib, the chemically similar drug celecoxib, and octaacetylmaltose, we formulated a hypothesis about the molecular mechanisms that may cause an impediment to crystal nuclei formation in the amorphous mixtures of etoricoxib with octaacetylmaltose. The most plausible scenario may rely on the formation of hydrogen-bonded heterodimers of the drug and excipient molecules, and the related drop in the population of the etoricoxib homodimers, which disables the nucleation. Nevertheless, this hypothesis requires further investigation. Additionally, we tested some widely discussed correlations between molecular mobility and crystallization properties, which turned out to be only partially satisfied for the examined mixtures. Our findings constitute not only a warning against manufacturing the amorphous form of pure etoricoxib, but also evidence for a promising outcome for the pharmaceutical application of the amorphous compositions with octaacetylmaltose.
How Can We Improve the Vaccination Response in Older People? Part II: Targeting Immunosenescence of Adaptive Immunity Cells
Authors: Garnica Maider , Aiello Anna , Ligotti Mattia Emanuela , Accardi Giulia , Arasanz Hugo , Bocanegra Ana , Blanco Ester , Calabrò Anna , Chocarro Luisa , Echaide Miriam , Kochan Grazyna , Fernandez-Rubio Leticia , Ramos Pablo , Pojero Fanny , Zareian Nahid , Piñeiro-Hermida Sergio , Farzaneh Farzin , Candore Giuseppina , Caruso Calogero , Escors David
Published: August 2022

The number of people that are 65 years old or older has been increasing due to the improvement in medicine and public health. However, this trend is not accompanied by an increase in quality of life, and this population is vulnerable to most illnesses, especially to infectious diseases. Vaccination is the best strategy to prevent this fact, but older people present a less efficient response, as their immune system is weaker due mainly to a phenomenon known as immunosenescence. The adaptive immune system is constituted by two types of lymphocytes, T and B cells, and the function and fitness of these cell populations are affected during ageing. Here, we review the impact of ageing on T and B cells and discuss the approaches that have been described or proposed to modulate and reverse the decline of the ageing adaptive immune system.
Rubella Virus Triggers Type I Interferon Antiviral Response in Cultured Human Neural Cells: Involvement in the Control of Viral Gene Expression and Infectious Progeny Production
Authors: Sakuragi Sayuri , Liao Huanan , Yajima Kodai , Fujiwara Shigeyoshi , Nakamura Hiroyuki
Published: August 2022

The type I interferon (IFN) response is one of the primary defense systems against various pathogens. Although rubella virus (RuV) infection is known to cause dysfunction of various organs and systems, including the central nervous system, little is known about how human neural cells evoke protective immunity against RuV infection, leading to controlling RuV replication. Using cultured human neural cells experimentally infected with RuV RA27/3 strain, we characterized the type I IFN immune response against the virus. RuV infected cultured human neural cell lines and induced IFN-β production, leading to the activation of signal transducer and activator of transcription 1 (STAT1) and the increased expression of IFN-stimulated genes (ISGs). Melanoma-differentiation-associated gene 5 (MDA5), one of the cytoplasmic retinoic acid-inducible gene I (RIG-I)-like receptors, is required for the RuV-triggered IFN-β mRNA induction in U373MG cells. We also showed that upregulation of RuV-triggered ISGs was attenuated by blocking IFN-α/β receptor subunit 2 (IFNAR2) using an IFNAR2-specific neutralizing antibody or by repressing mitochondrial antiviral signaling protein (MAVS) expression using MAVS-targeting short hairpin RNA (shRNA). Furthermore, treating RuV-infected cells with BX-795, a TANK-binding kinase 1 (TBK1)/I kappa B kinase ε (IKKε) inhibitor, robustly reduced STAT1 phosphorylation and expression of ISGs, enhancing viral gene expression and infectious virion production. Overall, our findings suggest that the RuV-triggered type I IFN-mediated antiviral response is essential in controlling RuV gene expression and viral replication in human neural cells.
Bioenergetic and Metabolic Impairments in Induced Pluripotent Stem Cell-Derived Cardiomyocytes Generated from Duchenne Muscular Dystrophy Patients
Authors: Willi Lubna , Abramovich Ifat , Fernandez-Garcia Jonatan , Agranovich Bella , Shulman Margarita , Milman Helena , Baskin Polina , Eisen Binyamin , Michele Daniel E. , Arad Michael , Binah Ofer , Gottlieb Eyal
Published: August 2022

Duchenne muscular dystrophy (DMD) is caused by mutations in the dystrophin gene and dilated cardiomyopathy (DCM) is a major cause of morbidity and mortality in DMD patients. We tested the hypothesis that DCM is caused by metabolic impairments by employing induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) generated from four DMD patients; an adult male, an adult female, a 7-year-old (7y) male and a 13-year-old (13y) male, all compared to two healthy volunteers. To test the hypothesis, we measured the bioenergetics, metabolomics, electrophysiology, mitochondrial morphology and mitochondrial activity of CMs, using respirometry, LC–MS, patch clamp, electron microscopy (EM) and confocal microscopy methods. We found that: (1) adult DMD CMs exhibited impaired energy metabolism and abnormal mitochondrial structure and function. (2) The 7y CMs demonstrated arrhythmia-free spontaneous firing along with “healthy-like” metabolic status, normal mitochondrial morphology and activity. In contrast, the 13y CMs were mildly arrhythmogenic and showed adult DMD-like bioenergetics deficiencies. (3) In DMD adult CMs, mitochondrial activities were attenuated by 45–48%, whereas the 7y CM activity was similar to that of healthy CMs. (4) In DMD CMs, but not in 7y CMs, there was a 75% decrease in the mitochondrial ATP production rate compared to healthy iPSC-CMs. In summary, DMD iPSC-CMs exhibit bioenergetic and metabolic impairments that are associated with rhythm disturbances corresponding to the patient’s phenotype, thereby constituting novel targets for alleviating cardiomyopathy in DMD patients.
Macrophage Activation Markers Predict Liver-Related Complications in Primary Biliary Cholangitis
Authors: Fujinaga Yukihisa , Namisaki Tadashi , Tsuji Yuki , Suzuki Junya , Murata Koji , Takeda Soichi , Takaya Hiroaki , Inoue Takashi , Noguchi Ryuichi , Fujimoto Yuki , Enomoto Masahide , Nishimura Norihisa , Kitagawa Koh , Kaji Kosuke , Kawaratani Hideto , Akahane Takemi , Mitoro Akira , Yoshiji Hitoshi
Published: August 2022

Primary biliary cholangitis (PBC) has a wide variation in clinical presentation and course. There is no significant correlation between these symptoms and the disease stage, although patients with more advanced stages generally have more symptoms. It is important to develop biomarkers in order to identify patients with an increased risk of complications and end-stage liver disease. This study investigated surrogate markers for risk estimation of PBC-related complications, including a study population of 77 patients with PBC who underwent liver biopsy and were measured for serum levels of macrophage activation markers, soluble CD163 (sCD163), soluble mannose receptor (sMR), and zonulin. Patients with PBC were divided into symptomatic (Group S, n = 20) and asymptomatic (Group A, n = 57) groups. The correlations of histological stages based on both Scheuer and Nakanuma classifications with the three serum markers were investigated. The Nakanuma classification involves grading for liver fibrosis and bile duct loss. The three biomarkers were assessed for their diagnostic ability to identify patients with PBC having high risk of developing complications. The predictive factors of these complications were examined as well. Group S had significantly higher serum sMR (p = 0.011) and sCD163 (p = 0.048) levels versus Group A. A composite index of sMR and sCD163 measurements had significantly better prediction performance than sCD163 alone (p = 0.012), although not when compared to sMR alone (p = 0.129). Serum sMR was an independent factor for developing complications on both univariate (Odds ratio (OR) = 30.20, 95% confidence interval (95% CI): 3.410–267.0, p = 0.00220), and multivariate (OR = 33.70, 95% CI: 3.6600–311.0, p = 0.0019) analyses. Patients with PBC having sMR of ≥56.6 had a higher incidence of clinical complications versus those with a sMR of <56.6. Serum sMR predicts the development of complications in patients with PBC. sMR plus sCD163 showed better predictive power than either marker alone, although the addition of sCD163 did not improve the predictive power of sMR. Future prospective studies are required in order to validate the findings of the present study.
Antisense Morpholino-Based In Vitro Correction of a Pseudoexon-Generating Variant in the SGCB Gene
Authors: Magri Francesca , Zanotti Simona , Salani Sabrina , Fortunato Francesco , Ciscato Patrizia , Gerevini Simonetta , Maggi Lorenzo , Sciacco Monica , Moggio Maurizio , Corti Stefania , Bresolin Nereo , Comi Giacomo Pietro , Ronchi Dario
Published: August 2022

Limb-girdle muscular dystrophies (LGMD) are clinically and genetically heterogenous presentations displaying predominantly proximal muscle weakness due to the loss of skeletal muscle fibers. Beta-sarcoglycanopathy (LGMDR4) results from biallelic molecular defects in SGCB and features pediatric onset with limb-girdle involvement, often complicated by respiratory and heart dysfunction. Here we describe a patient who presented at the age of 12 years reporting high creatine kinase levels and onset of cramps after strenuous exercise. Instrumental investigations, including a muscle biopsy, pointed towards a diagnosis of beta-sarcoglycanopathy. NGS panel sequencing identified two variants in the SGCB gene, one of which (c.243+1548T>C) was found to promote the inclusion of a pseudoexon between exons 2 and 3 in the SGCB transcript. Interestingly, we detected the same genotype in a previously reported LGMDR4 patient, deceased more than twenty years ago, who had escaped molecular diagnosis so far. After the delivery of morpholino oligomers targeting the pseudoexon in patient-specific induced pluripotent stem cells, we observed the correction of the physiological splicing and partial restoration of protein levels. Our findings prompt the analysis of the c.243+1548T>C variant in suspected LGMDR4 patients, especially those harbouring monoallelic SGCB variants, and provide a further example of the efficacy of antisense technology for the correction of molecular defects resulting in splicing abnormalities.
Using the Maize Nested Association Mapping (NAM) Population to Partition Arbuscular Mycorrhizal Effects on Drought Stress Tolerance into Hormonal and Hydraulic Components
Authors: Ruiz-Lozano Juan Manuel , Quiroga Gabriela , Erice Gorka , Pérez-Tienda Jacob , Zamarreño Ángel María , García-Mina José María , Aroca Ricardo
Published: August 2022

In this study, a first experiment was conducted with the objective of determining how drought stress alters the radial water flow and physiology in the whole maize nested association mapping (NAM) population and to find out which contrasting maize lines should be tested in a second experiment for their responses to drought in combination with an arbuscular mycorrhizal (AM) fungus. Emphasis was placed on determining the role of plant aquaporins and phytohormones in the responses of these contrasting maize lines to cope with drought stress. Results showed that both plant aquaporins and hormones are altered by the AM symbiosis and are highly involved in the physiological responses of maize plants to drought stress. The regulation by the AM symbiosis of aquaporins involved in water transport across cell membranes alters radial water transport in host plants. Hormones such as IAA, SA, ABA and jasmonates must be involved in this process either by regulating the own plant-AM fungus interaction and the activity of aquaporins, or by inducing posttranscriptional changes in these aquaporins, which in turns alter their water transport capacity. An intricate relationship between root hydraulic conductivity, aquaporins and phytohormones has been observed, revealing a complex network controlling water transport in maize roots.
Theoretical and Experimental Assay of Shock Experienced by Yeast Cells during Laser Bioprinting
Authors: Grosfeld Erika V. , Zhigarkov Vyacheslav S. , Alexandrov Alexander I. , Minaev Nikita V. , Yusupov Vladimir I.
Published: August 2022

Laser-induced forward transfer (LIFT) is a useful technique for bioprinting using gel-embedded cells. However, little is known about the stresses experienced by cells during LIFT. This paper theoretically and experimentally explores the levels of laser pulse irradiation and pulsed heating experienced by yeast cells during LIFT. It has been found that only 5% of the cells in the gel layer adjacent to the absorbing Ti film should be significantly heated for fractions of microseconds, which was confirmed by the fact that a corresponding population of cells died during LIFT. This was accompanied by the near-complete dimming of intracellular green fluorescent protein, also observed in response to heat shock. It is shown that microorganisms in the gel layer experience laser irradiation with an energy density of ~0.1–6 J/cm2. This level of irradiation had no effect on yeast on its own. We conclude that in a wide range of laser fluences, bioprinting kills only a minority of the cell population. Importantly, we detected a previously unobserved change in membrane permeability in viable cells. Our data provide a wider perspective on the effects of LIFT-based bioprinting on living organisms and might provide new uses for the procedure based on its effects on cell permeability.
Recurrent Translocations in Topoisomerase Inhibitor-Related Leukemia Are Determined by the Features of DNA Breaks Rather Than by the Proximity of the Translocating Genes
Authors: Lomov Nikolai A. , Viushkov Vladimir S. , Ulianov Sergey V. , Gavrilov Alexey A. , Alexeyevsky Daniil A. , Artemov Artem V. , Razin Sergey V. , Rubtsov Mikhail A.
Published: August 2022

Topoisomerase inhibitors are widely used in cancer chemotherapy. However, one of the potential long-term adverse effects of such therapy is acute leukemia. A key feature of such therapy-induced acute myeloid leukemia (t-AML) is recurrent chromosomal translocations involving AML1 (RUNX1) or MLL (KMT2A) genes. The formation of chromosomal translocation depends on the spatial proximity of translocation partners and the mobility of the DNA ends. It is unclear which of these two factors might be decisive for recurrent t-AML translocations. Here, we used fluorescence in situ hybridization (FISH) and chromosome conformation capture followed by sequencing (4C-seq) to investigate double-strand DNA break formation and the mobility of broken ends upon etoposide treatment, as well as contacts between translocation partner genes. We detected the separation of the parts of the broken AML1 gene, as well as the increased mobility of these separated parts. 4C-seq analysis showed no evident contacts of AML1 and MLL with loci, implicated in recurrent t-AML translocations, either before or after etoposide treatment. We suggest that separation of the break ends and their increased non-targeted mobility—but not spatial predisposition of the rearrangement partners—plays a major role in the formation of these translocations.
A Double-Edged Sword: The Two Faces of PARylation
Authors: Kang Mincheol , Park Seojin , Park Seong-Hoon , Lee Hee Gu , Park Jun Hong
Published: August 2022

Poly ADP-ribosylation (PARylation) is a post-translational modification process. Following the discovery of PARP-1, numerous studies have demonstrated the role of PARylation in the DNA damage and repair responses for cellular stress and DNA damage. Originally, studies on PARylation were confined to PARP-1 activation in the DNA repair pathway. However, the interplay between PARylation and DNA repair suggests that PARylation is important for the efficiency and accuracy of DNA repair. PARylation has contradicting roles; however, recent evidence implicates its importance in inflammation, metabolism, and cell death. These differences might be dependent on specific cellular conditions or experimental models used, and suggest that PARylation may play two opposing roles in cellular homeostasis. Understanding the role of PARylation in cellular function is not only important for identifying novel therapeutic approaches; it is also essential for gaining insight into the mechanisms of unexplored diseases. In this review, we discuss recent reports on the role of PARylation in mediating diverse cellular functions and homeostasis, such as DNA repair, inflammation, metabolism, and cell death.
Isolation and Functional Analysis of MbCBF2, a Malus baccata (L.) Borkh CBF Transcription Factor Gene, with Functions in Tolerance to Cold and Salt Stress in Transgenic Arabidopsis thaliana
Authors: Li Xingguo , Liang Xiaoqi , Li Wenhui , Yao Anqi , Liu Wanda , Wang Yu , Yang Guohui , Han Deguo
Published: August 2022

CBF transcription factors (TFs) are key regulators of plant stress tolerance and play an integral role in plant tolerance to adverse growth environments. However, in the current research situation, there are few reports on the response of the CBF gene to Begonia stress. Therefore, this experiment investigated a novel CBF TF gene, named MbCBF2, which was isolated from M. baccata seedlings. According to the subcellular localization results, the MbCBF2 protein was located in the nucleus. In addition, the expression level of MbCBF2 was higher in new leaves and roots under low-temperature and high-salt induction. After the introduction of MbCBF2 into Arabidopsis thaliana, the adaptability of transgenic A. thaliana to cold and high-salt environments was significantly enhanced. In addition, the high expression of MbCBF2 can also change many physiological indicators in transgenic A. thaliana, such as increased chlorophyll and proline content, superoxide dismutase (SOD), peroxidase (POD) and catalase (CAT) activity, and reduced malondialdehyde (MDA) content. Therefore, it can be seen from the above results that MbCBF2 can positively regulate the response of A. thaliana to low-temperature and osmotic stress. In addition, MbCBF2 can also regulate the expression of its downstream genes in transgenic lines. It can not only positively regulate the expression of the downstream key genes AtCOR15a, AtERD10, AtRD29a/b and AtCOR6.6/47, related to cold stress at low temperatures, but can also positively regulate the expression of the downstream key genes AtNCED3, AtCAT1, AtP5CS, AtPIF1/4 and AtSnRK2.4, related to salt stress. That is, the overexpression of the MbCBF2 gene further improved the adaptability and tolerance of transgenic plants to low-temperature and high-salt environments.
Interdomain Linker Effect on the Mechanical Stability of Ig Domains in Titin
Authors: Tong Bei , Tian Fang , Zheng Peng
Published: August 2022

Titin is the largest protein in humans, composed of more than one hundred immunoglobulin (Ig) domains, and plays a critical role in muscle’s passive elasticity. Thus, the molecular design of this giant polyprotein is responsible for its mechanical function. Interestingly, most of these Ig domains are connected directly with very few interdomain residues/linker, which suggests such a design is necessary for its mechanical stability. To understand this design, we chose six representative Ig domains in titin and added nine glycine residues (9G) as an artificial interdomain linker between these Ig domains. We measured their mechanical stabilities using atomic force microscopy-based single-molecule force spectroscopy (AFM-SMFS) and compared them to the natural sequence. The AFM results showed that the linker affected the mechanical stability of Ig domains. The linker mostly reduces its mechanical stability to a moderate extent, but the opposite situation can happen. Thus, this effect is very complex and may depend on each particular domain’s property.
NEXGB: A Network Embedding Framework for Anticancer Drug Combination Prediction
Authors: Meng Fanjie , Li Feng , Liu Jin-Xing , Shang Junliang , Liu Xikui , Li Yan
Published: August 2022

Compared to single-drug therapy, drug combinations have shown great potential in cancer treatment. Most of the current methods employ genomic data and chemical information to construct drug–cancer cell line features, but there is still a need to explore methods to combine topological information in the protein interaction network (PPI). Therefore, we propose a network-embedding-based prediction model, NEXGB, which integrates the corresponding protein modules of drug–cancer cell lines with PPI network information. NEXGB extracts the topological features of each protein node in a PPI network by struc2vec. Then, we combine the topological features with the target protein information of drug–cancer cell lines, to generate drug features and cancer cell line features, and utilize extreme gradient boosting (XGBoost) to predict the synergistic relationship between drug combinations and cancer cell lines. We apply our model on two recently developed datasets, the Oncology-Screen dataset (Oncology-Screen) and the large drug combination dataset (DrugCombDB). The experimental results show that NEXGB outperforms five current methods, and it effectively improves the predictive power in discovering relationships between drug combinations and cancer cell lines. This further demonstrates that the network information is valid for detecting combination therapies for cancer and other complex diseases.
Melatonin Improves Ischemia-Induced Circulation Recovery Impairment in Mice with Streptozotocin-Induced Diabetes by Improving the Endothelial Progenitor Cells Functioning
Authors: Kuo Chin-Sung , Chen Chi-Yu , Huang Hsin-Lei , Tsai Hsiao-Ya , Chou Ruey-Hsing , Wei Jih-Hua , Huang Po-Hsun , Lin Shing-Jong
Published: August 2022

Patients with diabetes mellitus tend to develop ischemia-related complications and have compromised endothelial progenitor cell (EPC) function. Melatonin protects against ischemic injury, possibly via EPC modulation. We investigated whether melatonin pretreatment could restore EPC function impairment and improve circulation recovery in a diabetic critical limb ischemia mouse model. Under 25 mM high-glucose medium in vitro, EPC proliferation, nitric oxide production, tube formation, and endothelial nitric oxide synthase (eNOS) phosphorylation were significantly suppressed. Hyperglycemia promoted EPC senescence and apoptosis as well as increased reactive oxygen species (ROS) production. Melatonin treatment reversed the harmful effects of hyperglycemia on EPC through adenosine monophosphate–activated protein kinase-related mechanisms to increase eNOS phosphorylation and heme oxygenase-1 expression. In an in-vivo study, after a 4-week surgical induction of hindlimb ischemia, mice with streptozotocin (STZ)-induced diabetes showed significant reductions in new vessel formation, tissue reperfusion, and EPC mobilization in ischemic hindlimbs compared to non-diabetic mice. Mice with STZ-induced diabetes that received melatonin treatment (10 mg/kg/day, intraperitoneal) had significantly improved blood perfusion ratios of ischemic to non-ischemic limb, EPC mobilization, and densities of capillaries. In addition, a murine bone marrow transplantation model to support these findings demonstrated that melatonin stimulated bone marrow-originated EPCs to differentiate into vascular endothelial cells in femoral ligation-induced ischemic muscles. In summary, this study suggests that melatonin treatment augments EPC function along with neovascularization in response to ischemia in diabetic mice. We illustrated the protective effects of melatonin on EPC H2O2 production, senescence, and migration through melatonin receptors and modulating eNOS, AMPK, and HO-1 activities at the cellular level. Thus, melatonin might be used to treat the impairment of EPC mobilization and circulation recuperation in response to ischemic injury caused by chronic hyperglycemia. Additional studies are needed to elucidate the applicability of the results in humans.
Insights into the Structures, Inhibitors, and Improvement Strategies of Glucose Oxidase
Authors: Wang Fan , Chen Xiaona , Wang Yonggang , Li Xing , Wan Minglai , Zhang Ge , Leng Feifan , Zhang Haibo
Published: August 2022

Glucose oxidase, which uses molecular oxygen as an electron acceptor to specifically catalyze the conversion of β-d-glucose to gluconic acid and hydrogen peroxide (H2O2), has been considered an important enzyme in increasing environmental sustainability and food security. However, achieving the high yield, low price and high activity required for commercial viability remains challenging. In this review, we first present a brief introduction, looking at the sources, characteristics, catalytic process, and applications of glucose oxidase. Then, the predictive structures of glucose oxidase from two different sources are comparatively discussed. We summarize the inhibitors of glucose oxidase. Finally, we highlight how the production of glucose oxidase can be improved by optimizing the culture conditions and microbial metabolic engineering.
Heparan Sulfate and Sialic Acid in Viral Attachment: Two Sides of the Same Coin?
Authors: Ramos-Martínez Ivan Emmanuel , Ramos-Martínez Edgar , Segura-Velázquez René Álvaro , Saavedra-Montañez Manuel , Cervantes-Torres Jacquelynne Brenda , Cerbón Marco , Papy-Garcia Dulce , Zenteno Edgar , Sánchez-Betancourt José Ivan
Published: August 2022

Sialic acids and heparan sulfates make up the outermost part of the cell membrane and the extracellular matrix. Both structures are characterized by being negatively charged, serving as receptors for various pathogens, and are highly expressed in the respiratory and digestive tracts. Numerous viruses use heparan sulfates as receptors to infect cells; in this group are HSV, HPV, and SARS-CoV-2. Other viruses require the cell to express sialic acids, as is the case in influenza A viruses and adenoviruses. This review aims to present, in a general way, the participation of glycoconjugates in viral entry, and therapeutic strategies focused on inhibiting the interaction between the virus and the glycoconjugates. Interestingly, there are few studies that suggest the participation of both glycoconjugates in the viruses addressed here. Considering the biological redundancy that exists between heparan sulfates and sialic acids, we propose that it is important to jointly evaluate and design strategies that contemplate inhibiting the interactions of both glycoconjugates. This approach will allow identifying new receptors and lead to a deeper understanding of interspecies transmission.
An Update on Photodynamic Therapy of Psoriasis—Current Strategies and Nanotechnology as a Future Perspective
Authors: Makuch Sebastian , Dróżdż Mateusz , Makarec Alicja , Ziółkowski Piotr , Woźniak Marta
Published: August 2022

Psoriasis (PS) is an immune-mediated skin disease with substantial negative effects on patient quality of life. Despite significant progress in the development of novel treatment options over the past few decades, a high percentage of patients with psoriasis remain undertreated and require new medications with superior long-term efficacy and safety. One of the most promising treatment options against psoriatic lesions is a form of phototherapy known as photodynamic therapy (PDT), which involves either the systemic or local application of a cell-targeting photosensitizing compound, followed by selective illumination of the lesion with visible light. However, the effectiveness of clinically incorporated photosensitizers in psoriasis treatment is limited, and adverse effects such as pain or burning sensations are frequently reported. In this study, we performed a literature review and attempted to provide a pooled estimate of the efficacy and short-term safety of targeted PDT in the treatment of psoriasis. Despite some encouraging results, PDT remains clinically underutilized. This highlights the need for further studies that will aim to evaluate the efficacy of a wider spectrum of photosensitizers and the potential of nanotechnology in psoriasis treatment.
Gastrointestinal Tract Stabilized Protein Delivery Using Disulfide Thermostable Exoshell System
Authors: Sadeghi Samira , Vallerinteavide Mavelli Girish , Vaidya Siddhesh Sujit , Drum Chester Lee
Published: August 2022

Thermostable exoshells (tES) are engineered proteinaceous nanoparticles used for the rapid encapsulation of therapeutic proteins/enzymes, whereby the nanoplatform protects the payload from proteases and other denaturants. Given the significance of oral delivery as the preferred model for drug administration, we structurally improved the stability of tES through multiple inter-subunit disulfide linkages that were initially absent in the parent molecule. The disulfide-linked tES, as compared to tES, significantly stabilized the activity of encapsulated horseradish peroxidase (HRP) at acidic pH and against the primary human digestive enzymes, pepsin, and trypsin. Furthermore, the disulfide-linked tES (DS-tES) exhibited significant intestinal permeability as evaluated using Caco2 cells. In vivo bioluminescence assay showed that encapsulated Renilla luciferase (rluc) was ~3 times more stable in mice compared to the free enzyme. DS-tES collected mice feces had ~100 times more active enzyme in comparison to the control (free enzyme) after 24 h of oral administration, demonstrating strong intestinal stability. Taken together, the in vitro and in vivo results demonstrate the potential of DS-tES for intraluminal and systemic oral drug delivery applications.
Staphylococcus aureus Exfoliative Toxin E, Oligomeric State and Flip of P186: Implications for Its Action Mechanism
Authors: Gismene Carolina , Hernández González Jorge Enrique , Santisteban Angela Rocio Niño , Ziem Nascimento Andrey Fabricio , dos Santos Cunha Lucas , de Moraes Fábio Rogério , de Oliveira Cristiano Luis Pinto , Oliveira Caio C. , Jocelan Scarin Provazzi Paola , Pascutti Pedro Geraldo , Arni Raghuvir Krishnaswamy , Barros Mariutti Ricardo
Published: August 2022

Staphylococcal exfoliative toxins (ETs) are glutamyl endopeptidases that specifically cleave the Glu381-Gly382 bond in the ectodomains of desmoglein 1 (Dsg1) via complex action mechanisms. To date, four ETs have been identified in different Staphylococcus aureus strains and ETE is the most recently characterized. The unusual properties of ETs have been attributed to a unique structural feature, i.e., the 180° flip of the carbonyl oxygen (O) of the nonconserved residue 192/186 (ETA/ETE numbering), not conducive to the oxyanion hole formation. We report the crystal structure of ETE determined at 1.61 Å resolution, in which P186(O) adopts two conformations displaying a 180° rotation. This finding, together with free energy calculations, supports the existence of a dynamic transition between the conformations under the tested conditions. Moreover, enzymatic assays showed no significant differences in the esterolytic efficiency of ETE and ETE/P186G, a mutant predicted to possess a functional oxyanion hole, thus downplaying the influence of the flip on the activity. Finally, we observed the formation of ETE homodimers in solution and the predicted homodimeric structure revealed the participation of a characteristic nonconserved loop in the interface and the partial occlusion of the protein active site, suggesting that monomerization is required for enzymatic activity.
Improving the Laboratory Diagnosis of M-like Variants Related to Alpha1-Antitrypsin Deficiency
Authors: Barzon Valentina , Ottaviani Stefania , Balderacchi Alice Maria , Corino Alessandra , Piloni Davide , Accordino Giulia , Coretti Manuela , Mariani Francesca , Corsico Angelo Guido , Ferrarotti Ilaria
Published: August 2022

Alpha1-antitrypsin (AAT) is a serine protease inhibitor that is encoded by the highly polymorphic SERPINA1 gene. Mutations in this gene can lead to AAT deficiency (AATD), which is associated with an increased risk of lung and/or liver disease. On the basis of electrophoretic migration, AAT variants are named with capital letters; M (medium) signifies the normal protein. Among pathological variants, the M-like ones represent a heterogeneous group of rare allelic variants that exhibit the same electrophoretic pattern as the M wild-type protein, which makes them difficult to detect with routine methods. In order to avoid their misdiagnosis, the present study defines and validates effective methods for the detection of two pathogenic M-like variants, Mwurzburg and Mwhitstable. Comparison of protein phenotypes using isoelectric focusing of samples that presented the Mwurzburg variant, as revealed by exons 5 sequencing, identified a particular electrophoretic pattern amenable to the Mwurzburg protein. The specific phenotyping pattern was retrospectively validated, thus enabling the detection of 16 patients with Mwurzburg variant among the subjects already tested but not sequenced according to our diagnostic algorithm. The Mwhitstable allele was detected by intron 4 sequencing of SERPINA1 gene. Mwurzburg and Mwhitstable are often misdiagnosed and the introduction of diagnostic improvements can help the clinical management, especially in patients with established lung disease without any other reported risk factors.
Sensitivity of the Transport of Plastic Nanoparticles to Typical Phosphates Associated with Ionic Strength and Solution pH
Authors: Liu Xingyu , Liang Yan , Peng Yongtao , Meng Tingting , Xu Liling , Dong Pengcheng
Published: August 2022

The influence of phosphates on the transport of plastic particles in porous media is environmentally relevant due to their ubiquitous coexistence in the subsurface environment. This study investigated the transport of plastic nanoparticles (PNPs) via column experiments, paired with Derjaguin–Landau–Verwey–Overbeek calculations and numerical simulations. The trends of PNP transport vary with increasing concentrations of NaH2PO4 and Na2HPO4 due to the coupled effects of increased electrostatic repulsion, the competition for retention sites, and the compression of the double layer. Higher pH tends to increase PNP transport due to the enhanced deprotonation of surfaces. The release of retained PNPs under reduced IS and increased pH is limited because most of the PNPs were irreversibly captured in deep primary minima. The presence of physicochemical heterogeneities on solid surfaces can reduce PNP transport and increase the sensitivity of the transport to IS. Furthermore, variations in the hydrogen bonding when the two phosphates act as proton donors will result in different influences on PNP transport at the same IS. This study highlights the sensitivity of PNP transport to phosphates associated with the solution chemistries (e.g., IS and pH) and is helpful for better understanding the fate of PNPs and other colloidal contaminants in the subsurface environment.
Alpha-Synuclein: The Spark That Flames Dopaminergic Neurons, In Vitro and In Vivo Evidence
Authors: Henriques Alexandre , Rouvière Laura , Giorla Elodie , Farrugia Clémence , El Waly Bilal , Poindron Philippe , Callizot Noëlle
Published: August 2022

Mitochondria, α-syn fibrils and the endo-lysosomal system are key players in the pathophysiology of Parkinson’s disease. The toxicity of α-syn is amplified by cell-to-cell transmission and aggregation of endogenous species in newly invaded neurons. Toxicity of α-syn PFF was investigated using primary cultures of dopaminergic neurons or on aged mice after infusion in the SNpc and combined with mild inhibition of GBA. In primary dopaminergic neurons, application of α-syn PFF induced a progressive cytotoxicity associated with mitochondrial dysfunction, oxidative stress, and accumulation of lysosomes suggesting that exogenous α-syn reached the lysosome (from the endosome). Counteracting the α-syn endocytosis with a clathrin inhibitor, dopaminergic neuron degeneration was prevented. In vivo, α-syn PFF induced progressive neurodegeneration of dopaminergic neurons associated with motor deficits. Histology revealed progressive aggregation of α-syn and microglial activation and accounted for the seeding role of α-syn, injection of which acted as a spark suggesting a triggering of cell-to-cell toxicity. We showed for the first time that a localized SNpc α-syn administration combined with a slight lysosomal deficiency and aging triggered a progressive lesion. The cellular and animal models described could help in the understanding of the human disease and might contribute to the development of new therapies.
Selenoprotein P Concentrations in the Cerebrospinal Fluid and Serum of Individuals Affected by Amyotrophic Lateral Sclerosis, Mild Cognitive Impairment and Alzheimer’s Dementia
Authors: Urbano Teresa , Vinceti Marco , Mandrioli Jessica , Chiari Annalisa , Filippini Tommaso , Bedin Roberta , Tondelli Manuela , Simonini Cecilia , Zamboni Giovanna , Shimizu Misaki , Saito Yoshiro
Published: August 2022

Selenoprotein P, a selenium-transporter protein, has been hypothesized to play a role in the etiology of neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and Alzheimer’s dementia (AD). However, data in humans are scarce and largely confined to autoptic samples. In this case–control study, we determined selenoprotein P concentrations in both the cerebrospinal fluid (CSF) and the serum of 50 individuals diagnosed with ALS, 30 with AD, 54 with mild cognitive impairment (MCI) and of 30 controls, using sandwich enzyme-linked immunosorbent assay (ELISA) methods. We found a positive and generally linear association between CSF and serum selenoprotein P concentrations in all groups. CSF selenoprotein P and biomarkers of neurodegeneration were positively associated in AD, while for MCI, we found an inverted-U-shaped relation. CSF selenoprotein P concentrations were higher in AD and MCI than in ALS and controls, while in serum, the highest concentrations were found in MCI and ALS. Logistic and cubic spline regression analyses showed an inverse association between CSF selenoprotein P levels and ALS risk, and a positive association for AD risk, while an inverted-U-shaped relation with MCI risk emerged. Conversely, serum selenoprotein P concentrations were positively associated with risk of all conditions but only in their lower range. Overall, these findings indicate some abnormalities of selenoprotein P concentrations in both the central nervous system and blood associated with ALS and neurocognitive disorders, though in different directions. These alterations may reflect either phenomena of etiologic relevance or disease-induced alterations of nutritional and metabolic status.