bluuebunny/crossref_metadata_2025 huggingface dataset:
Pangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species
Authors: Tay Fernandez Cassandria Geraldine , Nestor Benjamin John , Danilevicz Monica Furaste , Gill Mitchell , Petereit Jakob , Bayer Philipp Emanuel , Finnegan Patrick Michael , Batley Jacqueline , Edwards David
Published: March 2022

Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (Zea mays), rice (Oryza sativa), Brassica (Brassica spp.), and soybean (Glycine max) have had pangenomes constructed and released, and this has led to the discovery of valuable genes associated with disease resistance and yield components. However, pangenome data are not available for many less prominent crop species that are currently under-utilised. Despite many under-utilised species being important food sources in regional populations, the scarcity of genomic data for these species hinders their improvement. Here, we assess several under-utilised crops and review the pangenome approaches that could be used to build resources for their improvement. Many of these under-utilised crops are cultivated in arid or semi-arid environments, suggesting that novel genes related to drought tolerance may be identified and used for introgression into related major crop species. In addition, we discuss how previously collected data could be used to enrich pangenome functional analysis in genome-wide association studies (GWAS) based on studies in major crops. Considering the technological advances in genome sequencing, pangenome references for under-utilised species are becoming more obtainable, offering the opportunity to identify novel genes related to agro-morphological traits in these species.
The Role of Autophagy and Apoptosis in Neuropathic Pain Formation
Authors: Liao Ming-Feng , Lu Kwok-Tung , Hsu Jung-Lung , Lee Chih-Hong , Cheng Mei-Yun , Ro Long-Sun
Published: March 2022

Neuropathic pain indicates pain caused by damage to the somatosensory system and is difficult to manage and treat. A new treatment strategy urgently needs to be developed. Both autophagy and apoptosis are critical adaptive mechanisms when neurons encounter stress or damage. Recent studies have shown that, after nerve damage, both autophagic and apoptotic activities in the injured nerve, dorsal root ganglia, and spinal dorsal horn change over time. Many studies have shown that upregulated autophagic activities may help myelin clearance, promote nerve regeneration, and attenuate pain behavior. On the other hand, there is no direct evidence that the inhibition of apoptotic activities in the injured neurons can attenuate pain behavior. Most studies have only shown that agents can simultaneously attenuate pain behavior and inhibit apoptotic activities in the injured dorsal root ganglia. Autophagy and apoptosis can crosstalk with each other through various proteins and proinflammatory cytokine expressions. Proinflammatory cytokines can promote both autophagic/apoptotic activities and neuropathic pain formation, whereas autophagy can inhibit proinflammatory cytokine activities and further attenuate pain behaviors. Thus, agents that can enhance autophagic activities but suppress apoptotic activities on the injured nerve and dorsal root ganglia can treat neuropathic pain. Here, we summarized the evolving changes in apoptotic and autophagic activities in the injured nerve, dorsal root ganglia, spinal cord, and brain after nerve damage. This review may help in further understanding the treatment strategy for neuropathic pain during nerve injury by modulating apoptotic/autophagic activities and proinflammatory cytokines in the nervous system.
Pediococcus acidilactici CECT9879 (pA1c) Counteracts the Effect of a High-Glucose Exposure in C. elegans by Affecting the Insulin Signaling Pathway (IIS)
Authors: Yavorov-Dayliev Deyan , Milagro Fermín I. , Ayo Josune , Oneca María , Aranaz Paula
Published: March 2022

The increasing prevalence of metabolic syndrome-related diseases, including type-2 diabetes and obesity, makes it urgent to develop new alternative therapies, such as probiotics. In this study, we have used Caenorhabditis elegans under a high-glucose condition as a model to examine the potential probiotic activities of Pediococcusacidilactici CECT9879 (pA1c). The supplementation with pA1c reduced C. elegans fat accumulation in a nematode growth medium (NGM) and in a high-glucose (10 mM) NGM medium. Moreover, treatment with pA1c counteracted the effect of the high glucose by reducing reactive oxygen species by 20%, retarding the aging process and extending the nematode median survival (>2 days in comparison with untreated control worms). Gene expression analyses demonstrated that the probiotic metabolic syndrome-alleviating activities were mediated by modulation of the insulin/IGF-1 signaling pathway (IIS) through the reversion of the glucose-nuclear-localization of daf-16 and the overexpression of ins-6 and daf-16 mediators, increased expression of fatty acid (FA) peroxisomal β-oxidation genes, and downregulation of FA biosynthesis key genes. Taken together, our data suggest that pA1c could be considered a potential probiotic strain for the prevention of the metabolic syndrome-related disturbances and highlight the use of C. elegans as an appropriate in vivo model for the study of the mechanisms underlying these diseases.
High Light Acclimation Mechanisms Deficient in a PsbS-Knockout Arabidopsis Mutant
Authors: Yang Young Nam , Le Thi Thuy Linh , Hwang Ji-Hye , Zulfugarov Ismayil S. , Kim Eun-Ha , Kim Hyun Uk , Jeon Jong-Seong , Lee Dong-Hee , Lee Choon-Hwan
Published: March 2022

The photosystem II PsbS protein of thylakoid membranes is responsible for regulating the energy-dependent, non-photochemical quenching of excess chlorophyll excited states as a short-term mechanism for protection against high light (HL) stress. However, the role of PsbS protein in long-term HL acclimation processes remains poorly understood. Here we investigate the role of PsbS protein during long-term HL acclimation processes in wild-type (WT) and npq4-1 mutants of Arabidopsis which lack the PsbS protein. During long-term HL illumination, photosystem II photochemical efficiency initially dropped, followed by a recovery of electron transport and photochemical quenching (qL) in WT, but not in npq4-1 mutants. In addition, we observed a reduction in light-harvesting antenna size during HL treatment that ceased after HL treatment in WT, but not in npq4-1 mutants. When plants were adapted to HL, more reactive oxygen species (ROS) were accumulated in npq4-1 mutants compared to WT. Gene expression studies indicated that npq4-1 mutants failed to express genes involved in plastoquinone biosynthesis. These results suggest that the PsbS protein regulates recovery processes such as electron transport and qL during long-term HL acclimation by maintaining plastoquinone biosynthetic gene expression and enhancing ROS homeostasis.
Age Related Osteoporosis: Targeting Cellular Senescence
Authors: Föger-Samwald Ursula , Kerschan-Schindl Katharina , Butylina Maria , Pietschmann Peter
Published: March 2022

Age-related chronic diseases are an enormous burden to modern societies worldwide. Among these, osteoporosis, a condition that predisposes individuals to an increased risk of fractures, substantially contributes to increased mortality and health-care costs in elderly. It is now well accepted that advanced chronical age is one of the main risk factors for chronical diseases. Hence, targeting fundamental aging mechanisms such as senescence has become a promising option in the treatment of these diseases. Moreover, for osteoporosis, the main pathophysiological concepts arise from menopause causing estrogen deficiency, and from aging. Here, we focus on recent advances in the understanding of senescence-related mechanisms contributing to age-related bone loss. Furthermore, treatment options for senile osteoporosis targeting senescent cells are reviewed.
Genome-Wide Analyses of Heat Shock Protein Superfamily Provide New Insights on Adaptation to Sulfide-Rich Environments in Urechis unicinctus (Annelida, Echiura)
Authors: Liu Danwen , Qin Zhenkui , Wei Maokai , Kong Dexu , Zheng Qiaojun , Bai Shumiao , Lin Siyu , Zhang Zhifeng , Ma Yubin
Published: March 2022

The intertidal zone is a transitional area of the land-sea continuum, in which physical and chemical properties vary during the tidal cycle and highly toxic sulfides are rich in sediments due to the dynamic regimes. As a typical species thriving in this habitat, Urechis unicinctus presents strong sulfide tolerance and is expected to be a model species for sulfide stress research. Heat shock proteins (HSPs) consist of a large group of highly conserved molecular chaperones, which play important roles in stress responses. In this study, we systematically analyzed the composition and expression of HSPs in U. unicinctus. A total of eighty-six HSP genes from seven families were identified, in which two families, including sHSP and HSP70, showed moderate expansion, and this variation may be related to the benthic habitat of the intertidal zone. Furthermore, expression analysis revealed that almost all the HSP genes in U. unicinctus were significantly induced under sulfide stress, suggesting that they may be involved in sulfide stress response. Weighted gene co-expression network analysis (WGCNA) showed that 12 HSPs, including 5 sHSP and 4 HSP70 family genes, were highly correlated with the sulfide stress response which was distributed in steelblue and green modules. Our data indicate that HSPs, especially sHSP and HSP70 families, may play significant roles in response to sulfide stress in U. unicinctus. This systematic analysis provides valuable information for further understanding of the function of the HSP gene family for sulfide adaptation in U. unicinctus and contributes a better understanding of the species adaptation strategies of marine benthos in the intertidal zone.
The Role of l-Carnitine in Mitochondria, Prevention of Metabolic Inflexibility and Disease Initiation
Authors: Virmani Mohamed Ashraf , Cirulli Maria
Published: March 2022

Mitochondria control cellular fate by various mechanisms and are key drivers of cellular metabolism. Although the main function of mitochondria is energy production, they are also involved in cellular detoxification, cellular stabilization, as well as control of ketogenesis and glucogenesis. Conditions like neurodegenerative disease, insulin resistance, endocrine imbalances, liver and kidney disease are intimately linked to metabolic disorders or inflexibility and to mitochondrial dysfunction. Mitochondrial dysfunction due to a relative lack of micronutrients and substrates is implicated in the development of many chronic diseases. l-carnitine is one of the key nutrients for proper mitochondrial function and is notable for its role in fatty acid oxidation. l-carnitine also plays a major part in protecting cellular membranes, preventing fatty acid accumulation, modulating ketogenesis and glucogenesis and in the elimination of toxic metabolites. l-carnitine deficiency has been observed in many diseases including organic acidurias, inborn errors of metabolism, endocrine imbalances, liver and kidney disease. The protective effects of micronutrients targeting mitochondria hold considerable promise for the management of age and metabolic related diseases. Preventing nutrient deficiencies like l-carnitine can be beneficial in maintaining metabolic flexibility via the optimization of mitochondrial function. This paper reviews the critical role of l-carnitine in mitochondrial function, metabolic flexibility and in other pathophysiological cellular mechanisms.
Redox Properties of 3-Iodothyronamine (T1AM) and 3-Iodothyroacetic Acid (TA1)
Authors: Gencarelli Manuela , Lodovici Maura , Bellusci Lorenza , Raimondi Laura , Laurino Annunziatina
Published: March 2022

3-iodothyronamine (T1AM) and 3-iodothyroacetic acid (TA1) are thyroid-hormone-related compounds endowed with pharmacological activity through mechanisms that remain elusive. Some evidence suggests that they may have redox features. We assessed the chemical activity of T1AM and TA1 at pro-oxidant conditions. Further, in the cell model consisting of brown adipocytes (BAs) differentiated for 6 days in the absence (M cells) or in the presence of 20 nM T1AM (M + T1AM cells), characterized by pro-oxidant metabolism, or TA1 (M + TA1 cells), we investigated the expression/activity levels of pro- and anti-oxidant proteins, including UCP-1, sirtuin-1 (SIRT1), mitochondrial monoamine (MAO-A and MAO-B), semicarbazide-sensitive amine oxidase (SSAO), and reactive oxygen species (ROS)-dependent lipoperoxidation. T1AM and TA1 showed in-vitro antioxidant and superoxide scavenging properties, while only TA1 acted as a hydroxyl radical scavenger. M + T1AM cells showed higher lipoperoxidation levels and reduced SIRT1 expression and activity, similar MAO-A, but higher MAO-B activity in terms of M cells. Instead, the M + TA1 cells exhibited increased levels of SIRT1 protein and activity and significantly lower UCP-1, MAO-A, MAO-B, and SSAO in comparison with the M cells, and did not show signs of lipoperoxidation. Our results suggest that SIRT1 is the mediator of T1AM and TA1 pro-or anti-oxidant effects as a result of ROS intracellular levels, including the hydroxyl radical. Here, we provide evidence indicating that T1AM and TA1 administration impacts on the redox status of a biological system, a feature that indicates the novel mechanism of action of these two thyroid-hormone-related compounds.
Parallel Particle Swarm Optimization Using Apache Beam
Authors: Liu Jie , Zhu Tao , Zhang Yang , Liu Zhenyu
Published: March 2022

The majority of complex research problems can be formulated as optimization problems. Particle Swarm Optimization (PSO) algorithm is very effective in solving optimization problems because of its robustness, simplicity, and global search capabilities. Since the computational cost of these problems is usually high, it has been necessary to develop optimization algorithms with parallelization. With the advent of big-data technology, such problems can be solved by distributed parallel computing. In previous related work, MapReduce (a programming model that implements a distributed parallel approach to processing and producing large datasets on a cluster) has been used to parallelize the PSO algorithm, but frequent file reads and writes make the execution time of MRPSO very long. We propose Apache Beam particle swarm optimization (BPSO), which uses Apache Beam parallel programming model. In the experiment, we compared BPSO and PSO based on MapReduce (MRPSO) on four benchmark functions by changing the number of particles and optimizing the dimensions of the problem. The experimental results show that, as the number of particles increases, MRPSO remains largely constant when the number of particles is small (<1000), while the time required for algorithm execution increases rapidly when the number of particles exceeds a certain amount (>1000), while BPSO grows slowly and tends to yield better results than MRPSO. As the dimensionality of the optimization problem increases, BPSO can take half the time of MRPSO and obtain better results than it does. MRPSO requires more execution time than BPSO, as the problem complexity varies, but both MRPSO and BPSO are not very sensitive to problem complexity. All program code and input data are uploaded to GitHub.
Land Use Influences the Composition and Antimicrobial Effects of Propolis
Authors: Orth Amara J. , Curran Emma H. , Haas Eric J. , Kraemer Andrew C. , Anderson Audrey M. , Mason Nicholas J. , Fassbinder-Orth Carol A.
Published: March 2022

Honey bee propolis is a complex, resinous mixture created by bees using plant sources such as leaves, flowers, and bud exudates. This study characterized how cropland surrounding apiaries affects the chemical composition and antimicrobial effects of propolis. The chemical composition and compound abundance of the propolis samples were analyzed using Gas Chromatography-Mass Spectrometry (GC-MS) and the antimicrobial effects were analyzed using the 50% minimum inhibitory concentration (MIC50) assay against four relevant bee pathogens, Serratia marcescens, Paenibacillus larvae, Lysinibacillus sphaericus, and Klebsiella pneumoniae. Propolis composition varied significantly with apiary, and cropland coverage predicted mean sum abundance of compounds. The apiary with the highest cropland coverage exhibited significantly higher MIC50 values for S. marcescens and K. pneumoniae compared to other apiaries. These results demonstrate that agricultural land use surrounding honey bee apiaries decreases the chemical quality and antimicrobial effects of propolis, which may have implications for the impacts of land use on hive immunity to potential pathogens.
Visible beyond Violet: How Butterflies Manage Ultraviolet
Authors: Stella David , Kleisner Karel
Published: March 2022

Ultraviolet (UV) means ‘beyond violet’ (from Latin ‘ultra’, meaning ‘beyond’), whereby violet is the colour with the highest frequencies in the ‘visible’ light spectrum. By ‘visible’ we mean human vision, but, in comparison to many other organisms, human visual perception is rather limited in terms of the wavelengths it can perceive. Still, this is why communication in the UV spectrum is often called hidden, although it most likely plays an important role in communicating various kinds of information among a wide variety of organisms. Since Silberglied’s revolutionary Communication in the Ultraviolet, comprehensive studies on UV signals in a wide list of genera are lacking. This review investigates the significance of UV reflectance (and UV absorption)—a feature often neglected in intra- and interspecific communication studies—mainly in Lepidoptera. Although the text focuses on various butterfly families, links and connections to other animal groups, such as birds, are also discussed in the context of ecology and the evolution of species. The basic mechanisms of UV colouration and factors shaping the characteristics of UV patterns are also discussed in a broad context of lepidopteran communication.
Interactions between Rice Resistance to Planthoppers and Honeydew-Related Egg Parasitism under Varying Levels of Nitrogenous Fertilizer
Authors: Peñalver-Cruz Ainara , Horgan Finbarr G.
Published: March 2022

Host plant resistance is the most researched method for the management of planthoppers and leafhoppers in tropical rice. For optimal effects, resistance should be resilient to fertilizer inputs and work in synergy with natural enemies. In field plot experiments, we examined how rice resistance and fertilizer inputs affect mortality of planthopper and leafhopper eggs by hymenopteran parasitoids. We used IR62 as a variety with resistance to Nilaparvata lugens (Stål) [BPH], Sogatella furcifera (Horváth) [WBPH] and Nephotettix virescens (Distant) [GLH], and IR64 as a susceptible control. The herbivores were more abundant during wet season sampling in low-nitrogen plots. During this study, parasitoids killed between 31 and 38% of BPH eggs and 24 and 52% of WBPH eggs during four days of field exposure. Parasitism, mainly due to Oligosita spp., was generally higher in high-nitrogen and IR64 plots. Similar densities of eggs in exposed plants suggest that these trends were mediated by semiochemicals and therefore support the Optimal Defense Hypothesis. Honeydew from BPH on IR62 had more xylem-derived wastes than honeydew on IR64. We applied honeydew from both varieties to sentinel plants. Parasitism by Anagrus spp. was higher on plants of either variety treated with honeydew derived from IR62; however, the effect was only apparent in high-nitrogen plots. Results suggest that Anagrus spp., by responding to honeydew, will counter the nitrogen-induced enhancement of planthopper fitness on resistant rice.
A Survey on Botnets, Issues, Threats, Methods, Detection and Prevention
Authors: Owen Harry , Zarrin Javad , Pour Shahrzad M.
Published: March 2022

Botnets have become increasingly common and progressively dangerous to both business and domestic networks alike. Due to the Covid-19 pandemic, a large quantity of the population has been performing corporate activities from their homes. This leads to speculation that most computer users and employees working remotely do not have proper defences against botnets, resulting in botnet infection propagating to other devices connected to the target network. Consequently, not only did botnet infection occur within the target user’s machine but also neighbouring devices. The focus of this paper is to review and investigate current state of the art and research works for both methods of infection, such as how a botnet could penetrate a system or network directly or indirectly, and standard detection strategies that had been used in the past. Furthermore, we investigate the capabilities of Artificial Intelligence (AI) to create innovative approaches for botnet detection to enable making predictions as to whether there are botnets present within a network. The paper also discusses methods that threat-actors may be used to infect target devices with botnet code. Machine learning algorithms are examined to determine how they may be used to assist AI-based detection and what advantages and disadvantages they would have to compare the most suitable algorithm businesses could use. Finally, current botnet prevention and countermeasures are discussed to determine how botnets can be prevented from corporate and domestic networks and ensure that future attacks can be prevented.
Multi-Stimulus Responsive Multilayer Coating for Treatment of Device-Associated Infections
Authors: Li Wenlong , Hua Guanping , Cai Jingfeng , Zhou Yaming , Zhou Xi , Wang Miao , Wang Xiumin , Fu Baoqing , Ren Lei
Published: March 2022

Antibacterial coating with antibiotics is highly effective in avoiding device-associated infections (DAIs) which is an unsolved healthcare problem that causes significant morbidity and mortality rates. However, bacterial drug resistance caused by uncontrolled release of antibiotics seriously restricts clinical efficacy of antibacterial coating. Hence, a local and controlled-release system which can release antibiotics in response to bacterial infected signals is necessary in antibacterial coating. Herein, a multi-stimulus responsive multilayer antibacterial coating was prepared through layer-by-layer (LbL) self-assembly of montmorillonite (MMT), chlorhexidine acetate (CHA) and Poly(protocatechuic acid-polyethylene glycol 1000-bis(phenylboronic acid carbamoyl) cystamine) (PPPB). The coating can be covered on various substrates such as cellulose acetate membrane, polyacrylonitrile membrane, polyvinyl chloride membrane, and polyurethane membrane, proving it is a versatile coating. Under the stimulation of acids, glucose or dithiothreitol, this coating was able to achieve controlled release of CHA and kill more than 99% of Staphylococcus aureus and Escherichia coli (4 × 108 CFU/mL) within 4 h. In the mouse infection model, CHA releasing of the coating was triggered by infected microenvironment to completely kill bacteria, achieving wounds healing within 14 days.
Extracting New Temporal Features to Improve the Interpretability of Undiagnosed Type 2 Diabetes Mellitus Prediction Models
Authors: Kocbek Simon , Kocbek Primož , Gosak Lucija , Fijačko Nino , Štiglic Gregor
Published: March 2022

Type 2 diabetes mellitus (T2DM) often results in high morbidity and mortality. In addition, T2DM presents a substantial financial burden for individuals and their families, health systems, and societies. According to studies and reports, globally, the incidence and prevalence of T2DM are increasing rapidly. Several models have been built to predict T2DM onset in the future or detect undiagnosed T2DM in patients. Additional to the performance of such models, their interpretability is crucial for health experts, especially in personalized clinical prediction models. Data collected over 42 months from health check-up examinations and prescribed drugs data repositories of four primary healthcare providers were used in this study. We propose a framework consisting of LogicRegression based feature extraction and Least Absolute Shrinkage and Selection operator based prediction modeling for undiagnosed T2DM prediction. Performance of the models was measured using Area under the ROC curve (AUC) with corresponding confidence intervals. Results show that using LogicRegression based feature extraction resulted in simpler models, which are easier for healthcare experts to interpret, especially in cases with many binary features. Models developed using the proposed framework resulted in an AUC of 0.818 (95% Confidence Interval (CI): 0.812−0.823) that was comparable to more complex models (i.e., models with a larger number of features), where all features were included in prediction model development with the AUC of 0.816 (95% CI: 0.810−0.822). However, the difference in the number of used features was significant. This study proposes a framework for building interpretable models in healthcare that can contribute to higher trust in prediction models from healthcare experts.
Association of Metabolic Parameter Variability with Esophageal Cancer Risk: A Nationwide Population-Based Study
Authors: Lee Ji Eun , Han Kyungdo , Yoo Juhwan , Yeo Yohwan , Cho In Young , Cho Belong , Kwon Hyuktae , Shin Dong Wook , Cho Jong Ho , Park Yong-Moon
Published: March 2022

Introduction: Certain metabolic parameters increase the risk of esophageal cancer. This study investigated the association between the variability in metabolic parameters and esophageal cancer incidence using large nationally representative data. Methods: Using the health checkup and claims data provided by the Korean National Health Insurance Service (NHIS), we included 8,376,233 subjects who underwent NHIS-provided health checkups between 2009 and 2010 (index year) and two or more health checkups within five years before the index year. Hazard ratios (HRs) and 95% confidence intervals (CIs) for esophageal cancer were obtained using Cox proportional hazards models according to the quartiles of variability of each metabolic parameter: fasting blood glucose (FBG), weight, systolic blood pressure (SBP), and total cholesterol (TC) as well as a cumulative number of high-variability parameters. Results: A total of 6,455 cases of esophageal cancer occurred during a mean (±SD) follow-up of 8.8 (±1.1) years. The following metabolic parameters were used, with an adjusted HR and 95% CI: FBG (1.11, 1.03–1.18), weight (1.15, 1.07–1.23), SBP (1.08, 1.01–1.16), and TC (1.23, 1.15–1.32). The risk of esophageal cancer was higher in the highest quartile of variability than the lower quartiles. The risk of esophageal cancer gradually increased with a greater number of high-variability parameters: 1.08 (1.02–1.15), 1.22 (1.14–1.31), and 1.33 (1.21–1.46) for 1, 2, and 3–4 high-variability parameters (vs. none). Conclusions: A high variability of metabolic parameters was associated with an increased esophageal cancer risk. Further studies are needed to replicate our findings in other populations.
A Formal Approach to Coercion Resistance and Its Application to E-Voting
Authors: Riou Stanislas , Kulyk Oksana , Marcos del Blanco David Yeregui
Published: March 2022

The outbreak of the COVID-19 pandemic brought renewed attention to electronic voting—this time as a potential option to contain the spread during elections. One of the long unresolved topics with remote voting is the risk of voter’s coercion due to the uncontrolled environment in which it takes place, indicating the importance of the coercion resistance property. In the present article, the authors conduct a database analysis of over 350 articles to present different formal definitions of coercion resistance based on three frameworks (game-based definitions, applied pi-calculus, and logic). Finally, the different security properties of each one are studied and compared in order to facilitate the development of electronic voting schemes.
Sesquiterpene and Sorbicillinoid Glycosides from the Endophytic Fungus Trichoderma longibrachiatum EN-586 Derived from the Marine Red Alga Laurencia obtusa
Authors: Wang Ying , Li Xiao-Ming , Yang Sui-Qun , Zhang Fan-Zhong , Wang Bin-Gui , Li Hong-Lei , Meng Ling-Hong
Published: March 2022

An unusual sesquiterpene glycoside trichoacorside A (1) and two novel sorbicillinoid glycosides sorbicillisides A (2) and B (3), together with a known compound sorbicillin (4), were isolated and identified from the culture extract of an endophytic fungus Trichoderma longibrachiatum EN-586, obtained from the marine red alga Laurencia obtusa. Trichoacorside A (1) is the first representative of a glucosamine-coupled acorane-type sesquiterpenoid. Their structures were elucidated based on detailed interpretation of NMR and mass spectroscopic data. The absolute configurations were determined by X-ray crystallographic analysis, chemical derivatization, and DP4+ probability analysis. The antimicrobial activities of compounds 1–4 against several human, aquatic, and plant pathogens were evaluated.
Aurasperone A Inhibits SARS CoV-2 In Vitro: An Integrated In Vitro and In Silico Study
Authors: ElNaggar Mai H. , Abdelwahab Ghada M. , Kutkat Omnia , GabAllah Mohamed , Ali Mohamed A. , El-Metwally Mohamed E. A. , Sayed Ahmed M. , Abdelmohsen Usama Ramadan , Khalil Ashraf T.
Published: March 2022

Several natural products recovered from a marine-derived Aspergillus niger were tested for their inhibitory activity against SARS CoV-2 in vitro. Aurasperone A (3) was found to inhibit SARS CoV-2 efficiently (IC50 = 12.25 µM) with comparable activity with the positive control remdesivir (IC50 = 10.11 µM). Aurasperone A exerted minimal cytotoxicity on Vero E6 cells (CC50 = 32.36 mM, SI = 2641.5) and it was found to be much safer than remdesivir (CC50 = 415.22 µM, SI = 41.07). To putatively highlight its molecular target, aurasperone A was subjected to molecular docking against several key-viral protein targets followed by a series of molecular dynamics-based in silico experiments that suggested Mpro to be its primary viral protein target. More potent anti-SARS CoV-2 Mpro inhibitors can be developed according to our findings presented in the present investigation.
Versatile Photo/Electricity Responsive Properties of a Coordination Polymer Based on Extended Viologen Ligands
Authors: Peng Xiaohan , Shi Yuchen , Zeng Zhiqiang , Zheng Jianming , Xu Chunye
Published: March 2022

Responsive chromogenic materials have attracted increasing interest among researchers; however, up until now, few materials have exhibited multifunctional chromogenic properties. The coordination polymers (CPs) provide intriguing platforms to design and construct multifunctional materials. Here, a multifunctional photo/electricity responsive CP named Zn−Oxv, which is based on the “extended viologen” (ExV) ligand, was synthesized. The Zn−Oxv exhibited reversible photochromism, photomodulated fluorescence, electrochromism and electrofluorochromism. Furthermore, we prepared Zn−Oxv thin films and investigated electrochromic (EC) properties of viologen−based CPs for the first time. Zn−Oxv thin films showed excellent EC performance with a rapid switching speed (both coloring and bleaching time within 1 s), high coloration efficiency (102.9 cm2/C) and transmittance change (exceeding 40%). Notably, the Zn−Oxv is by far the fastest CP EC material based on redox−active ligands ever reported, indicating that the viologen−based CPs could open up a new field of materials for EC applications. Therefore, viologen−based CPs are attractive candidates for the design of novel multi−responsive chromogenic materials and EC materials that could promise creative applications in intelligent technology, dynamic displays and smart sensors.
Light Field Intensification in Optical Films Induced by Intercoupling of Defects and Organic Contamination
Authors: Chen Xin , Ling Xiu-Lan , Liu Ji , Liu Xiao-Feng
Published: March 2022

Based on the finite-difference time-domain method, light field intensification in optical films due to the intercoupling of defects and organic contamination was analyzed. The results show that the intercoupling between the defect and the organic contamination droplet leads to an increase in the local electric field and the coupling effect enhances with the decreasing distance between the defect and the organic contamination droplet and the increasing diameter of the organic contamination droplet. The coupling effect of the defect and the organic contamination layer depends on not only the thickness of the organic contamination layer but also the refractive index of the organic contamination layer. With the thickness and the refractive index of the organic contamination layer increasing, the peak value of the electric field decreases. This work deepens the physical understanding of the degradation mechanism of laser-induced damage in optical thin films used in vacuum.
Potential of the Compounds from Bixa orellana Purified Annatto Oil and Its Granules (Chronic®) against Dyslipidemia and Inflammatory Diseases: In Silico Studies with Geranylgeraniol and Tocotrienols
Authors: Batista Mateus Alves , de Lima Teixeira dos Santos Abrahão Victor Tavares , do Nascimento Aline Lopes , Moreira Luiz Fernando , Souza Indira Ramos Senna , da Silva Heitor Ribeiro , Pereira Arlindo César Matias , da Silva Hage-Melim Lorane Izabel , Carvalho José Carlos Tavares
Published: March 2022

Some significant compounds present in annatto are geranylgeraniol and tocotrienols. These compounds have beneficial effects against hyperlipidemia and chronic diseases, where oxidative stress and inflammation are present, but the exact mechanism of action of such activities is still a subject of research. This study aimed to evaluate possible mechanisms of action that could be underlying the activities of these molecules. For this, in silico approaches such as ligand topology (PASS and SEA servers) and molecular docking with the software GOLD were used. Additionally, we screened some pharmacokinetic and toxicological parameters using the servers PreADMET, SwissADME, and ProTox-II. The results corroborate the antidyslipidemia and anti-inflammatory activities of geranylgeraniol and tocotrienols. Notably, some new mechanisms of action were predicted to be potentially underlying the activities of these compounds, including inhibition of squalene monooxygenase, lanosterol synthase, and phospholipase A2. These results give new insight into new mechanisms of action involved in these molecules from annatto and Chronic®.
Combination of GC-MS Molecular Networking and Larvicidal Effect against Aedes aegypti for the Discovery of Bioactive Substances in Commercial Essential Oils
Authors: Pilon Alan Cesar , Del Grande Marcelo , Silvério Maíra R. S. , Silva Ricardo R. , Albernaz Lorena C. , Vieira Paulo Cézar , Lopes João Luis Callegari , Espindola Laila S. , Lopes Norberto Peporine
Published: March 2022

Dengue is a neglected disease, present mainly in tropical countries, with more than 5.2 million cases reported in 2019. Vector control remains the most effective protective measure against dengue and other arboviruses. Synthetic insecticides based on organophosphates, pyrethroids, carbamates, neonicotinoids and oxadiazines are unattractive due to their high degree of toxicity to humans, animals and the environment. Conversely, natural-product-based larvicides/insecticides, such as essential oils, present high efficiency, low environmental toxicity and can be easily scaled up for industrial processes. However, essential oils are highly complex and require modern analytical and computational approaches to streamline the identification of bioactive substances. This study combined the GC-MS spectral similarity network approach with larvicidal assays as a new strategy for the discovery of potential bioactive substances in complex biological samples, enabling the systematic and simultaneous annotation of substances in 20 essential oils through LC50 larvicidal assays. This strategy allowed rapid intuitive discovery of distribution patterns between families and metabolic classes in clusters, and the prediction of larvicidal properties of acyclic monoterpene derivatives, including citral, neral, citronellal and citronellol, and their acetate forms (LC50 < 50 µg/mL).
Recovery of Bioactive Ellagitannins by Ultrasound/Microwave-Assisted Extraction from Mexican Rambutan Peel (Nephelium lappaceum L.)
Authors: Estrada-Gil Luis , Contreras-Esquivel Juan C. , Flores-Gallegos Carolina , Zugasti-Cruz Alejandro , Govea-Salas Mayela , Mata-Gómez Marco A. , Rodríguez-Herrera Raúl , Ascacio-Valdés Juan A.
Published: March 2022

Rambutan (Nephelium lappaceum L.) is a tropical fruit from Asia which has become the main target of many studies involving polyphenolic analysis. Mexico produces over 8 million tons per year of rambutan, generating a huge amount of agro-industrial waste since only the pulp is used and the peel, which comprises around 45% of the fruit’s weight, is left behind. This waste can later be used in the recovery of polyphenolic fractions. In this work, emerging technologies such as microwave, ultrasound, and the hybridization of both were tested in the extraction of phenolic compounds from Mexican rambutan peel. The results show that the hybrid technology extraction yielded the highest polyphenolic content (176.38 mg GAE/g of dry rambutan peel). The HPLC/MS/ESI analysis revealed three majoritarian compounds: geraniin, corilagin, and ellagic acid. These compounds explain the excellent results for the biological assays, namely antioxidant activity evaluated by the DPPH, ABTS, and LOI (Lipid oxidation inhibition) assays that exhibited great antioxidant capacity with IC50 values of 0.098, 0.335, and 0.034 mg/mL respectively, as well as prebiotic activity demonstrated by a µMax (maximum growth) of 0.203 for Lactobacillus paracasei. Lastly, these compounds have shown no hemolytic activity, opening the door for the elaboration of different products in the food, cosmetic, and pharmaceutical industries.
Synthesis and Fluorescent Properties of Aminopyridines and the Application in “Click and Probing”
Authors: Li Zongyang , Li Yaxuan , Chang Wenxu , Pang Sen , Li Xuefeng , Duan Liusheng , Zhang Zhenhua
Published: March 2022

Unsubstituted pyridin-2-amine has a high quantum yield and is a potential scaffold for a fluorescent probe. However, the facile access to conjugated highly substituted aminopyridines and the study of their fluorescent properties is scarce. In this paper, synthesis and fluorescent properties of multisubstituted aminopyridines were studied based on a recently developed Rh-catalyzed coupling of vinyl azide with isonitrile to form a vinyl carbodiimide intermediate, following tandem cyclization with an alkyne. An aminopyridine substituted with an azide group as a potential probe was further designed, synthesized, and evaluated. The “clicking-and-probing” experiment of it on BSA protein showed the potential of aminopyridine as a scaffold of a biological probe.
The Antiviral Effects of Jasminin via Endogenous TNF-α and the Underlying TNF-α-Inducing Action
Authors: Zhu Xiaohong , Hu Ziwei , Yu Tian , Hu Hao , Zhao Yunshi , Li Chenyang , Zhu Qinchang , Wang Mingzhong , Zhai Peng , He Longxia , Riaz Rajoka Muhammad Shahid , Song Xun , He Zhendan
Published: March 2022

Previous studies have reported that recombinant tumor necrosis factor (TNF)-α has powerful antiviral activity but severe systematic side effects. Jasminin is a common bioactive component found in Chinese herbal medicine beverage “Jasmine Tea”. Here, we report that jasminin-induced endogenous TNF-α showed antiviral activity in vitro. The underlying TNF-α-inducing action of jasminin was also investigated in RAW264.7 cells. The level of endogenous TNF-α stimulated by jasminin was first analyzed by an enzyme-linked immunosorbent assay (ELISA) from the cell culture supernatant of RAW264.7 cells. The supernatants were then collected to investigate the potential antiviral effect against herpes simplex virus 1 (HSV-1). The antiviral effects of jasminin alone or its supernatants were evaluated by a plaque reduction assay. The potential activation of the PI3K–Akt pathway, three main mitogen-activated protein kinases (MAPKs), and nuclear factor (NF)–κB signaling pathways that induce TNF-α production were also investigated. Jasminin induces TNF-α protein expression in RAW264.7 cells without additional stimuli 10-fold more than the control. No significant up-expression of type I, II, and III interferons; interleukins 2 and 10; nor TNF-β were observed by the jasminin stimuli. The supernatants, containing jasminin-induced-TNF-α, showed antiviral activity against HSV-1. The jasminin-stimulated cells caused the simultaneous activation of the Akt, MAPKs, and NF–κB signal pathways. Furthermore, the pretreatment of the cells with the Akt, MAPKs, and NF–κB inhibitors effectively suppressed jasminin-induced TNF-α production. Our research provides evidence that endogenous TNF-α can be used as a strategy to encounter viral infections. Additionally, the Akt, MAPKs, and NF–κB signaling pathways are involved in the TNF-α synthesis that induced by jasminin.
Catch, Modify and Analyze: Methods of Chemoselective Modification of Cysteine-Containing Peptides
Authors: Kowalska Marta , Bąchor Remigiusz
Published: March 2022

One effective solution in the analysis of complex mixtures, including protein or cell hydrolysates, is based on chemoselective derivatization of a selected group of compounds by using selective tags to facilitate detection. Another method is based on the capture of the desired compounds by properly designed solid supports, resulting in sample enrichment. Cysteine is one of the rarest amino acids, but at least one cysteine residue is present in more than 91% of human proteins, which clearly confirms its important role in biological systems. Some cysteine-containing peptides may serve as significant molecular biomarkers, which may emerge as key indices in the management of patients with particular diseases. In the current review, we describe recent advances in the development of cysteine-containing peptide modification techniques based on solution and solid phase derivatization and enrichment strategies.
Assessment of Antioxidant and Anticancer Activities of Microgreen Alga Chlorella vulgaris and Its Blend with Different Vitamins
Authors: Hamouda Ragaa A. , Abd El Latif Amera , Elkaw Ebtihal M. , Alotaibi Amenah S. , Alenzi Asma Massad , Hamza Hanafy A.
Published: March 2022

There is a very vital antioxidant extracted from microgreen alga. Chlorella vulgaris has major advantages and requires high yield worldwide. Some microalgae require vitamins for their growth promotion. This study was held to determine the impact of different vitamins including Thiamine (B1), Riboflavin (B2), Pyridoxine (B6), and Ascorbic acid (c) at concentrations of 0.02, 0.04, 0.06, and 0.08 mg/L of each. Each vitamin was added to the BG11 growth medium to determine the effect on growth, total carbohydrate, total protein, pigments content, antioxidant activities of Chlorella vulgaris. Moreover, antitumor effects of methanol extract of C. vulgaris without and with the supplement of thiamine against Human prostate cancer (PC-3), Hepatocellular carcinoma (HEPG-2), Colorectal carcinoma (HCT-116) and Epitheliod Carcinoma (Hela) was estimated in vitro. C. vulgaris supplemented with various vitamins showed a significant increase in biomass, pigment content, total protein, and total carbohydrates in comparison to the control. Thiamine was the best vitamin influencing as an antioxidant. C. vulgaris supplemented with thiamine had high antitumor effects in vitro. So, it’s necessary to add vitamins to BG11 media for enhancement of the growth and metabolites.
Novel Pomegranate-Nanoparticles Ameliorate Cisplatin-Induced Nephrotoxicity and Improves Cisplatin Anti-Cancer Efficacy in Ehrlich Carcinoma Mice Model
Authors: Harakeh Steve , Almuhayawi Mohammed S. , Akefe Isaac O. , Saber Saber H. , Al Jaouni Soad K. , Alzughaibi Torki , Almehmadi Yousef , Ali Soad Shaker , Bharali Dhruba J. , Mousa Shaker
Published: March 2022

Cisplatin (CISP) is one of the most widely used anti-cancer chemotherapeutic agents with remarkable efficacy against various types of cancers. However, it has been associated with nephrotoxicity amongst other undesirable side effects. Pomegranate (PE) is a potent antioxidant and anti-inflammatory agent effective against cancer, with a superior benefit of not being associated with the common toxicities related to the use of conventional chemotherapeutic agents. However, the application of PE is limited by its reduced solubility and decreased bioavailability. We investigated the potential of a novel nanoparticle (NP) enclosing PE to enhance its solubility and improve its bioavailability, and efficacy to prevent CISP-associated nephrotoxicity in a mice model of Ehrlich solid carcinoma (ESC). All mice were grouped into four cohorts: (I) control, (II) tumor, (III) CISP, and (IV) CISP + PE-NPs. The data obtained demonstrated that PE-NPs was beneficial in potently ameliorating CISP-induced nephrotoxicity in ESC mice. PE-NPs significantly attenuated CISP-induced oxidative stress and lipid peroxidation in the kidney via improving activities of antioxidants (SOD, GSH, and CAT). Additionally, PE-NPs considerably decreased CISP-induced inflammation in the kidney by decreasing the levels of NF-kB, IL-1β, and TNF-α. Notably, PE-NPs did not assuage the antitumor efficacy of CISP as revealed by histological assessment and tumor weight data. In summary, PE-NPs may be a potent alternative anticancer therapy devoid of nephrotoxicity.
The Effect of Sodium Total Substitution on the Quality Characteristics of Green Pickled Tomatoes (Solanum lycopersicum L.)
Authors: Mocanu Gabriel-Dănuț , Nistor Oana-Viorela , Constantin Oana Emilia , Andronoiu Doina Georgeta , Barbu Viorica Vasilica , Botez Elisabeta
Published: March 2022

Green pickled tomatoes are a traditional fermented product in Romania. This study was focused on the effect of total substitution of NaCl with KCl and MgCl2 on physicochemical and microbiological quality; bioactive compounds; and microstructural, textural, and sensorial properties of fresh and pickled green tomatoes during 28 days of fermentation. By the means of physicochemical composition, the NaCl addition induced the most stable characteristics for the pickles compared to the other two types of salts. The content of total flavonoids in green pickled tomatoes with NaCl (34.72 ± 0.43 mg CE/g DW) was significantly lower compared with the control sample (63.80 ± 0.55 mg CE/g DW). The total number of lactic acid bacteria (LAB) at the final stage of fermentation varied between 4.11 and 4.63 log CFU for all variants. The textural analysis revealed that the NaCl has the lowest influence on the textural parameters. Finally, the overall acceptance of green pickled tomatoes containing KCl and MgCl2 was found to be proper to be consumed as a substitute for pickles with NaCl.
Dynamic Entropy of Two-Dimensional Active Brownian Systems in Colloidal Plasmas
Authors: Koss Xeniya , Kononov Evgenii , Lisina Irina , Vasiliev Mikhail , Petrov Oleg
Published: March 2022

We analyze the experimental data on the motion of active Brownian micrograins in RF discharge plasmas. In the experiments, two types of microparticles were used: first—plastic grains fully covered with metal, and second—Janus particles with a thin metal cap. We have tracked the trajectories of the separate grains and plotted the pair correlation functions of the observed structures. To examine the motion of the grains, we studied the dependencies of the MFPT dynamic entropy on the coarsening parameter, the fractal dimension of the system on its mean kinetic temperature, and the mean localization area of the grain on its mean kinetic temperature. Based on the obtained results, we conclude that the character of motion of our active Brownian systems changes as the power of an illuminating laser (and, therefore, the mean kinetic temperature of the grains) increases. Janus particles change their trajectories from more chaotic to spiral-like ones; in the case of fully covered particles, we observe the dynamical phase transition from the more ordered structure to the less ordered one.