bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-Wide Comprehensive Analysis of the Nitrogen Metabolism Toolbox Reveals Its Evolution and Abiotic Stress Responsiveness in Rice (Oryza sativa L.)
Authors: Li Zhihui , Zhu Mingqiang , Huang Jinqiu , Jiang Shan , Xu Shuang , Zhang Zhihong , He Wenchuang , Huang Wenchao
Published: December 2022

Nitrogen metabolism (NM) plays an essential role in response to abiotic stresses for plants. Enzyme activities have been extensively studied for nitrogen metabolism-associated pathways, but the knowledge of nitrogen metabolism-associated genes involved in stress response is still limited, especially for rice. In this study, we performed the genome-wide characterization of the genes putatively involved in nitrogen metabolism. A total of 1110 potential genes were obtained to be involved in nitrogen metabolism from eight species (Arabidopsis thaliana (L.) Heynh., Glycine max (L.) Merr., Brassica napus L., Triticum aestivum L., Sorghum bicolor L., Zea mays L., Oryza sativa L. and Amborella trichopoda Baill.), especially 104 genes in rice. The comparative phylogenetic analysis of the superfamily revealed the complicated divergence of different NM genes. The expression analysis among different tissues in rice indicates the NM genes showed diverse functions in the pathway of nitrogen absorption and assimilation. Distinct expression patterns of NM genes were observed in rice under drought stress, heat stress, and salt stress, indicating that the NM genes play a curial role in response to abiotic stress. Most NM genes showed a down-regulated pattern under heat stress, while complicated expression patterns were observed for different genes under salt stress and drought stress. The function of four representative NM genes (OsGS2, OsGLU, OsGDH2, and OsAMT1;1) was further validated by using qRT-PCR analysis to confirm their responses to these abiotic stresses. Based on the predicted transcription factor binding sites (TFBSs), we built a co-expression regulatory network containing transcription factors (TFs) and NM genes, of which the constructed ERF and Dof genes may act as the core genes to respond to abiotic stresses. This study provides novel sights to the interaction between nitrogen metabolism and the response to abiotic stresses.
The Expression of miRNAs Involved in Long-Term Memory Formation in the CNS of the Mollusk Helix lucorum
Authors: Vasiliev Gennady V. , Ovchinnikov Vladimir Y. , Lisachev Pavel D. , Bondar Natalia P. , Grinkevich Larisa N.
Published: December 2022

Mollusks are unique animals with a relatively simple central nervous system (CNS) containing giant neurons with identified functions. With such simple CNS, mollusks yet display sufficiently complex behavior, thus ideal for various studies of behavioral processes, including long-term memory (LTM) formation. For our research, we use the formation of the fear avoidance reflex in the terrestrial mollusk Helix lucorum as a learning model. We have shown previously that LTM formation in Helix requires epigenetic modifications of histones leading to both activation and inactivation of the specific genes. It is known that microRNAs (miRNAs) negatively regulate the expression of genes; however, the role of miRNAs in behavioral regulation has been poorly investigated. Currently, there is no miRNAs sequencing data being published on Helix lucorum, which makes it impossible to investigate the role of miRNAs in the memory formation of this mollusk. In this study, we have performed sequencing and comparative bioinformatics analysis of the miRNAs from the CNS of Helix lucorum. We have identified 95 different microRNAs, including microRNAs belonging to the MIR-9, MIR-10, MIR-22, MIR-124, MIR-137, and MIR-153 families, known to be involved in various CNS processes of vertebrates and other species, particularly, in the fear behavior and LTM. We have shown that in the CNS of Helix lucorum MIR-10 family (26 miRNAs) is the most representative one, including Hlu-Mir-10-S5-5p and Hlu-Mir-10-S9-5p as top hits. Moreover, we have shown the involvement of the MIR-10 family in LTM formation in Helix. The expression of 17 representatives of MIR-10 differentially changes during different periods of LTM consolidation in the CNS of Helix. In addition, using comparative analysis of microRNA expression upon learning in normal snails and snails with deficient learning abilities with dysfunction of the serotonergic system, we identified a number of microRNAs from several families, including MIR-10, which expression changes only in normal animals. The obtained data can be used for further fundamental and applied behavioral research.
Expression and Regulation of a Novel Decidual Cells-Derived Estrogen Target during Decidualization
Authors: Lu Lin , Chen Yingni , Yang Zhenshan , Liang Shijin , Zhu Songqi , Liang Xiaohuan
Published: December 2022

During decidualization in rodents, uterine stromal cells undergo extensive reprogramming to differentiate into distinct cell types, forming primary decidual zones (PDZs), secondary decidual zones (SDZs), and layers of undifferentiated stromal cells. The formation of secondary decidual zones is accompanied by extensive angiogenesis. During early pregnancy, besides ovarian estrogen, de novo synthesis of estrogen in the uterus is essential for the progress of decidualization. However, the molecular mechanisms are not fully understood. Studies have shown that Cystatin B (Cstb) is highly expressed in the decidual tissue of the uterus, but the regulation and mechanism of Cstb in the process of decidualization have not been reported. Our results showed that Cstb was highly expressed in mouse decidua and artificially induced deciduoma via in situ hybridization and immunofluorescence. Estrogen stimulates the expression of Cstb through the Estrogen receptor (ER)α. Moreover, in situ synthesis of estrogen in the uterus during decidualization regulates the expression of Cstb. Silencing the expression of Cstb affects the migration ability of stromal cells. Knockdown Cstb by siRNA significantly inhibits the expression of Dtprp, a marker for mouse decidualization. Our study identifies a novel estrogen target, Cstb, during decidualization and reveals that Cstb may play a pivotal role in angiogenesis during mouse decidualization via the Angptl7.
PEO Coatings Modified with Halloysite Nanotubes: Composition, Properties, and Release Performance
Authors: Imshinetskiy Igor , Kashepa Victoria , Nadaraia Konstantine , Mashtalyar Dmitry , Suchkov Sergey , Zadorozhny Pavel , Ustinov Aleksander , Sinebryukhov Sergey , Gnedenkov Sergey
Published: December 2022

In this work, the properties of the coatings formed on the Mg-Mn-Ce alloy by plasma electrolytic oxidation (PEO) in electrolytes containing halloysite nanotubes (HNTs) were investigated. The incorporation of halloysite nanotubes into the PEO coatings improved their mechanical characteristics, increased thickness, and corrosion resistance. The studied layers reduced corrosion current density by more than two times in comparison with the base PEO layer without HNTs (from 1.1 × 10−7 A/cm2 to 4.9 × 10−8 A/cm2). The presence of halloysite nanotubes and products of their dihydroxylation that were formed under the PEO conditions had a positive impact on the microhardness of the obtained layers (this parameter increased from 4.5 ± 0.4 GPa to 7.3 ± 0.5 GPa). In comparison with the base PEO layer, coatings containing halloysite nanotubes exhibited sustained release and higher adsorption capacity regarding caffeine.
Aptamers for Addressed Boron Delivery in BNCT: Effect of Boron Cluster Attachment Site on Functional Activity
Authors: Novopashina Darya S. , Dymova Maya A. , Davydova Anna S. , Meschaninova Mariya I. , Malysheva Daria O. , Kuligina Elena V. , Richter Vladimir A. , Kolesnikov Iaroslav A. , Taskaev Sergey Yu. , Vorobyeva Mariya A.
Published: December 2022

Among the great variety of anti-cancer therapeutic strategies, boron neutron capture therapy (BNCT) represents a unique approach that doubles the targeting accuracy due to the precise positioning of a neutron beam and the addressed delivery of boron compounds. We have recently demonstrated the principal possibility of using a cell-specific 2′-F-RNA aptamer for the targeted delivery of boron clusters for BNCT. In the present study, we evaluated the amount of boron-loaded aptamer inside the cell via two independent methods: quantitative real-time polymerase chain reaction and inductive coupled plasma–atomic emission spectrometry. Both assays showed that the internalized boron level inside the cell exceeds 1 × 109 atoms/cell. We have synthesized closo-dodecaborate conjugates of 2′-F-RNA aptamers GL44 and Waz, with boron clusters attached either at the 3′- or at the 5′-end. The influence of cluster localization was evaluated in BNCT experiments on U-87 MG human glioblastoma cells and normal fibroblasts and subsequent analyses of cell viability via real-time cell monitoring and clonogenic assay. Both conjugates of GL44 aptamer provided a specific decrease in cell viability, while only the 3′-conjugate of the Waz aptamer showed the same effect. Thus, an individual adjustment of boron cluster localization is required for each aptamer. The efficacy of boron-loaded 2′-F-RNA conjugates was comparable to that of 10B-boronophenylalanine, so this type of boron delivery agent has good potential for BNCT due to such benefits as precise targeting, low toxicity and the possibility to use boron clusters made of natural, unenriched boron.
Solid–Water Interface Interaction of Selenium with Fe(II)-Bearing Minerals and Aqueous Fe(II) and S(-II) Ions in the Near-Field of the Radioactive Waste Disposal System
Authors: Matulová Michaela , Duborská Eva , Matúš Peter , Urík Martin
Published: December 2022

Selenium can be highly toxic in excess for both animals and humans. However, since its mobile forms can be easily adsorbed with ferric minerals, its mobility in the natural oxic environment is generally not an issue. Still, the removal and immobilization of the long-lived radioactive isotope 79Se from the contaminated anoxic waters is currently a significant concern. 79Se can be accessible in the case of radionuclidesˈ leaching from radioactive waste disposals, where anoxic conditions prevail and where ferrous ions and Fe(II)-bearing minerals predominate after corrosion processes (e.g., magnetite). Therefore, reductive and adsorptive immobilizations by Fe(II)-bearing minerals are the primary mechanisms for removing redox-sensitive selenium. Even though the information on the sorptive interactions of selenium and Fe(II)-bearing minerals seems to be well documented, this review focuses specifically on the state of the available information on the effects of the redox properties of Fe(II)-bearing solid phases (e.g., ferrous oxides, hydroxides, sulfides, and carbonates) on selenium speciation via redox transformation and co-occurring coprecipitation.
Air Pollution: Another Threat to HDL Function
Authors: Ossoli Alice , Cetti Federica , Gomaraschi Monica
Published: December 2022

Epidemiological studies have consistently demonstrated a positive association between exposure to air pollutants and the incidence of cardiovascular disease, with the strongest evidence for particles with a diameter < 2.5 μm (PM2.5). Therefore, air pollution has been included among the modifiable risk factor for cardiovascular outcomes as cardiovascular mortality, acute coronary syndrome, stroke, heart failure, and arrhythmias. Interestingly, the adverse effects of air pollution are more pronounced at higher levels of exposure but were also shown in countries with low levels of air pollution, indicating no apparent safe threshold. It is generally believed that exposure to air pollution in the long-term can accelerate atherosclerosis progression by promoting dyslipidemia, hypertension, and other metabolic disorders due to systemic inflammation and oxidative stress. Regarding high density lipoproteins (HDL), the impact of air pollution on plasma HDL-cholesterol levels is still debated, but there is accumulating evidence that HDL function can be impaired. In particular, the exposure to air pollution has been variably associated with a reduction in their cholesterol efflux capacity, antioxidant and anti-inflammatory potential, and ability to promote the release of nitric oxide. Further studies are needed to fully address the impact of various air pollutants on HDL functions and to elucidate the mechanisms responsible for HDL dysfunction.
In Contrast to Anti-CCP, MMP-Degraded and Citrullinated Vimentin (VICM) Is Both a Diagnostic and a Treatment Response Biomarker
Authors: Drobinski Patryk J. , Nissen Neel I. , Sinkeviciute Dovile , Willumsen Nicholas , Karsdal Morten A. , Bay-Jensen Anne C.
Published: December 2022

Protein citrullination and degradation by matrix metalloproteinases (MMP) plays a central role in the pathology of rheumatoid arthritis (RA). Autoantibodies are known to target citrullinated vimentin. The aim of this study was to investigate the relationship between the blood levels of MMP-degraded and citrullinated vimentin (VICM), as compared with the levels of MMP-degraded and non-citrullinated vimentin (VIM), and the standard anti-CCP biomarker in RA patients undergoing treatment. Thus, VIM, VICM and anti-CCP were quantified by ELISA in serum samples from baseline and week 8 of patients (n = 257) with RA, treated with either tocilizumab (8 mg/kg), methotrexate (7.5–15 mg/kg) or a placebo and compared with a reference cohort (n = 64). The three biomarkers were elevated in RA serum compared with the reference cohort: medians were 1.7 vs. 0.8 ng/mL (p < 0.05) for VIM; 7.5 vs. 0.7 ng/mL (p < 0.0001) for VICM; 57 vs. 4 RU/mL (p < 0.001) for anti-CCP. VICM was decreased in response to tocilizumab (2.9-fold, p < 0.0001) and to methotrexate (1.5-fold, p < 0.05) compared with the placebo, while anti-CCP was not. Serum VIM was also modulated by both drugs, although to a lesser degree. A high baseline level of VICM was predictive of a low disease activity response at week 8. In conclusion, VICM can differentiate between RA and healthy donors in a similar manner to anti-CCP; furthermore, VICM is also a pharmacodynamic marker.
Establishment of an Absolute Quantitative Method to Detect a Plasma tRNA-Derived Fragment and Its Application in the Non-Invasive Diagnosis of Gastric Cancer
Authors: Yu Xiuchong , Song Xuemei , Xie Yaoyao , Zhang Shuangshuang , Guo Junming
Published: December 2022

(1) Transfer RNA (tRNA)-derived fragments (tRFs) are a new category of regulatory non-coding RNAs with distinct biological functions in cancer. They are produced from pre-tRNAs or mature tRNAs and their sequences are relatively short; thus, the amplification of tRFs, especially those in body fluids, is faced with certain technical difficulties. In this study, we established a quantitative method to detect plasma tRF-27-87R8WP9N1E5 (tRF-27) and used it to screen gastric cancer patients. (2) A specific stem-loop-structure reverse transcription primer, a TaqMan probe, and amplification primers for tRF-27 were prepared, and the absolute quantitative method was used to measure plasma tRF-27 levels. To determine the noninvasive diagnostic value of tRF-27 in gastric cancer, plasma tRF-27 levels in patients with benign and malignant lesions (120 healthy individuals, 48 patients with benign lesions, 48 patients with precancerous lesions, and 72 patients with early gastric cancer) were analyzed. Plasma tRF-27 levels were also analyzed in 106 preoperative gastric cancer patients, 106 postoperative gastric cancer patients, and 120 healthy individuals. Survival curves and Cox regression models were established and analyzed. (3) A new absolute quantitative method to determine the plasma tRF-27 copy number was established. Plasma tRF-27 levels were significantly increased in gastric cancer patients compared to healthy individuals, and the area under the receiver operating characteristic curve was 0.7767, when the cutoff value was 724,807 copies/mL, with sensitivity and specificity values of 0.6226 and 0.8917, respectively. The positive predictive and negative predictive values were 83.50% and 72.80%, respectively. Plasma tRF-27 levels in postoperative gastric cancer patients were significantly decreased compared to preoperative gastric cancer patients and tended to the levels of healthy individuals. Moreover, tRF-27 levels were closely related to tumor size and Ki67 expression in gastric cancer patients. Prognostic analysis showed that tRF-27 may be an independent predictor of overall survival. (4) This novel and non-invasive method of measuring plasma tRF-27 levels was valuable in the early diagnosis of gastric cancer.
Characterization of Diabetic Retinopathy in Two Mouse Models and Response to a Single Injection of Anti-Vascular Endothelial Growth Factor
Authors: Azrad-Leibovich Tamar , Zahavi Alon , Gohas Moran Friedman , Brookman Myles , Barinfeld Orit , Muhsinoglu Orkun , Michowiz Shalom , Fixler Dror , Goldenberg-Cohen Nitza
Published: December 2022

In this study, we characterized diabetic retinopathy in two mouse models and the response to anti-vascular endothelial growth factor (VEGF) injection. The study was conducted in 58 transgenic, non-obese diabetic (NOD) mice with spontaneous type 1 diabetes (n = 30, DMT1-NOD) or chemically induced (n = 28, streptozotocin, STZ-NOD) type 1 diabetes and 20 transgenic db/db mice with type 2 diabetes (DMT2-db/db); 30 NOD and 8 wild-type mice served as controls. Mice were examined at 21 days for vasculopathy, retinal thickness, and expression of genes involved in oxidative stress, angiogenesis, gliosis, and diabetes. The right eye was histologically examined one week after injection of bevacizumab, ranibizumab, saline, or no treatment. Flat mounts revealed microaneurysms and one apparent area of tufts of neovascularization in the diabetic retina. Immunostaining revealed activation of Müller glia and prominent Müller cells. Mean retinal thickness was greater in diabetic mice. RAGE increased and GFAP decreased in DMT1-NOD mice; GFAP and SOX-9 mildly increased in db/db mice. Anti-VEGF treatment led to reduced retinal thickness. Retinas showed vasculopathy and edema in DMT1-NOD and DMT2-db/db mice and activation of Müller glia in DMT1-NOD mice, with some response to anti-VEGF treatment. Given the similarity of diabetic retinopathy in mice and humans, comparisons of type 1 and type 2 diabetic mouse models may assist in the development of new treatment modalities.
The Bio-Aging of Biofilms on Behalf of Various Oral Status on Different Titanium Implant Materials
Authors: Liao Min , Shi Yangyang , Chen Enni , Shou Yuke , Dai Dongyue , Xian Wenpan , Ren Biao , Xiao Shimeng , Cheng Lei
Published: December 2022

The properties of titanium implants are affected by bio-aging due to long-term exposure to the oral microenvironment. This study aimed to investigate probable changes in titanium plates after different biofilm bio-aging processes, representing various oral status. Titanium plates with different surface treatments were used, including polish, sandblasted with large grit and acid etched (SLA), microarc oxidation (MAO), and hydroxyapatite coating (HA). We established dual-species biofilms of Staphylococcus aureus (S. aureus)–Candida albicans (C. albicans) and saliva biofilms from the healthy and patients with stage III–IV periodontitis, respectively. After bio-aging with these biofilms for 30 days, the surface morphology, chemical composition, and water contact angles were measured. The adhesion of human gingival epithelial cells, human gingival fibroblasts, and three-species biofilms (Streptococcus sanguis, Porphyromonas gingivalis, and Fusobacterium nucleatum) were evaluated. The polished specimens showed no significant changes after bio-aging with these biofilms. The MAO- and SLA-treated samples showed mild corrosion after bio-aging with the salivary biofilms. The HA-coated specimens were the most vulnerable. Salivary biofilms, especially saliva from patients with periodontitis, exhibited a more distinct erosion on the HA-coating than the S. aureus–C. albicans dual-biofilms. The coating became thinner and even fell from the substrate. The surface became more hydrophilic and more prone to the adhesion of bacteria. The S. aureus–C. albicans dual-biofilms had a comparatively mild corrosion effect on these samples. The HA-coated samples showed more severe erosion after bio-aging with the salivary biofilms from patients with periodontitis compared to those of the healthy, which emphasized the importance of oral hygiene and periodontal health to implants in the long run.
Effect of B-NIPOx in Experimental Trypanosoma cruzi Infection in Mice
Authors: Reséndiz-Mora Albany , Barrera-Aveleida Giovanna , Sotelo-Rodríguez Anahi , Galarce-Sosa Iván , Nevárez-Lechuga Irene , Santiago-Hernández Juan Carlos , Nogueda-Torres Benjamín , Meza-Toledo Sergio , Gómez-Manzo Saúl , Wong-Baeza Isabel , Baeza Isabel , Wong-Baeza Carlos
Published: December 2022

Chagas disease is caused by Trypanosoma cruzi and represents a major public health problem, which is endemic in Latin America and emerging in the rest of the world. The two drugs that are currently available for its treatment, Benznidazole and Nifurtimox, are partially effective in the chronic phase of the disease. In this study, we designed and synthesized the benzyl ester of N-isopropyl oxamic acid (B-NIPOx), which is a non-polar molecule that crosses cell membranes. B-NIPOx is cleaved inside the parasite by carboxylesterases, releasing benzyl alcohol (a molecule with antimicrobial activity), and NIPOx, which is an inhibitor of α-hydroxy acid dehydrogenase isozyme II (HADH-II), a key enzyme in T. cruzi metabolism. We evaluated B-NIPOx cytotoxicity, its toxicity in mice, and its inhibitory activity on purified HADH-II and on T. cruzi homogenates. We then evaluated the trypanocidal activity of B-NIPOx in vitro and in vivo and its effect in the intestine of T. cruzi-infected mice. We found that B-NIPOx had higher trypanocidal activity on epimastigotes and trypomastigotes than Benznidazole and Nifurtimox, that it was more effective to reduce blood parasitemia and amastigote nests in infected mice, and that, in contrast to the reference drugs, it prevented the development of Chagasic enteropathy.
Structural Characterization, Antioxidant and Antitumor Activities of the Two Novel Exopolysaccharides Produced by Debaryomyces hansenii DH-1
Authors: Yang Yajing , Chen Guoqiang , Zhao Xiaoqi , Cao Xiaohe , Wang Lei , Mu Jingjiu , Qi Fenghui , Liu Lijuan , Zhang Haibo
Published: December 2022

Exopolysaccharides produced by edible microorganisms exhibit excellent constructive physicochemical and significant biological activity, which provide advantages for the food or pharmaceutical industries. Two novel exopolysaccharides produced by Debaryomyces hansenii DH-1 were characterized, named S1 and S2, respectively. S1, with a molecular weight of 34.594 kDa, primarily consisted of mannose and glucose in a molar ratio of 12.19:1.00, which contained a backbone fragment of α-D-Manp-(1→4)-α-D-Manp-(1→2)-α-D-Glcp-(1→3)-α-D-Manp-(1→3)-β-D-Glcp-(1→4)-β-D-Manp-(1→. S2, with a molecular weight of 24.657 kDa, was mainly composed of mannose and galactose in a molar ratio of 4.00:1.00, which had a backbone fragment of α-D-Manp-(1→6)-β-D-Manp-(1→2)-α-D-Manp-(1→4)-α-D-Galp-(1→3)-β-D-Manp-(1→6)-α-D-Manp-(1→. Both S1 and S2 exhibited good thermal stability and potent hydroxyl radical scavenging activity, with ~98%. Moreover, S1 possessed an additional strong iron-reducing capacity. In vitro antitumor assays showed that S1 and S2 significantly inhibited the proliferation of Hela, HepG2, and PC-9 cancer cells. Moreover, PC-9 was more sensitive to S1 compared with S2. The above results indicate that S1 and S2 have great potential to be utilized as natural antioxidants and candidates for cancer treatment in the food and pharmaceutical industries.
Role Played by Paraoxonase-2 Enzyme in Cell Viability, Proliferation and Sensitivity to Chemotherapy of Oral Squamous Cell Carcinoma Cell Lines
Authors: Campagna Roberto , Belloni Alessia , Pozzi Valentina , Salvucci Alessia , Notarstefano Valentina , Togni Lucrezia , Mascitti Marco , Sartini Davide , Giorgini Elisabetta , Salvolini Eleonora , Santarelli Andrea , Lo Muzio Lorenzo , Emanuelli Monica
Published: December 2022

Oral squamous cell carcinoma represents the most aggressive and frequent form of head and neck cancer. Due to drug resistance, the 5-year survival rate of patients with advanced disease is less than 50%. In order to identify molecular targets for effective oral cancer treatment, we focused on paraoxonase-2 enzyme. Indeed, based on data previously obtained from preliminary immunohistochemistry and Western blot analyses performed on tissue specimens, the enzyme was found to be upregulated in tumor compared with normal oral mucosa. Therefore, paraoxonase-2 gene silencing was achieved in HSC-3 and HOC621 oral cancer cell lines, and the effect on cell proliferation, viability, apoptosis induction and sensitivity to cisplatin and 5-fluorouracil treatment was evaluated. Fourier Transform InfraRed Microspectroscopy analyzed alterations of cellular macromolecules upon treatment. Enzyme level and cell proliferation were also determined in cisplatin-resistant clones obtained from HOC621 cell line, as well as in parental cells. Reported data showed that paraoxonase-2 knockdown led to a reduction of cell proliferation and viability, as well as to an enhancement of sensitivity to cisplatin, together with the activation of apoptosis pathway. Spectroscopical data demonstrated that, under treatment with cisplatin, oxidative damage exerted on lipids and proteins was markedly more evident in cells down-regulating paraoxonase-2 compared to controls. Interestingly, enzyme expression, as well as cell proliferation were significantly higher in cisplatin-resistant compared with control HOC621 cells. Taken together these results seem to candidate the enzyme as a promising target for molecular treatment of this neoplasm.
Ligand-Based Drug Design of Novel Antimicrobials against Staphylococcus aureus by Targeting Bacterial Transcription
Authors: Ye Jiqing , Yang Xiao , Ma Cong
Published: December 2022

Staphylococcus aureus is a common human commensal pathogen that causes a wide range of infectious diseases. Due to the generation of antimicrobial resistance, the pathogen becomes resistant to more and more antibiotics, resulting in methicillin-resistant S. aureus (MRSA) and even multidrug-resistant S. aureus (MDRSA), namely ‘superbugs’. This situation highlights the urgent need for novel antimicrobials. Bacterial transcription, which is responsible for bacterial RNA synthesis, is a valid but underutilized target for developing antimicrobials. Previously, we reported a novel class of antimicrobials, coined nusbiarylins, that inhibited bacterial transcription by interrupting the protein–protein interaction (PPI) between two transcription factors NusB and NusE. In this work, we developed a ligand-based workflow based on the chemical structures of nusbiarylins and their activity against S. aureus. The ligand-based models—including the pharmacophore model, 3D QSAR, AutoQSAR, and ADME/T calculation—were integrated and used in the following virtual screening of the ChemDiv PPI database. As a result, four compounds, including J098-0498, 1067-0401, M013-0558, and F186-026, were identified as potential antimicrobials against S. aureus, with predicted pMIC values ranging from 3.8 to 4.2. The docking study showed that these molecules bound to NusB tightly with the binding free energy ranging from −58 to −66 kcal/mol.
Subcellular Localization of Homomeric TASK3 Channels and Its Presumed Functional Significances in Trigeminal Motoneurons
Authors: Saito Mitsuru , Tanaka Chie , Toyoda Hiroki , Kang Youngnam
Published: December 2022

Somatic expressions of either heteromeric TASK1/3 or homomeric TASK1/1 channels have been reported in various neurons, while expression of homomeric TASK3/3 channels has been re-ported only in dendrites. However, it is not known why homomeric TASK3/3 channels are hardly seen in somata of CNS neurons. Given the absence of somatic TASK3/3 channels, it should be clarified why dendritic expression of TASK3/3 channels is inevitable and necessary and how differentially distributed TASK1/1 and TASK3/3 channels play roles in soma-to-dendritic integration. Here, we addressed these questions. We found that TASK3-transfected HEK293 cells showed decreases in cell volume after being transferred from the cultured medium to HEPES Ringer, suggesting that expressions of TASK3 channels in cell bodies cause an osmolarity problem. Using TASK1- and TASK3-transfected oocytes, we also found that cGMP application slightly suppressed TASK3 currents while it largely enhanced TASK1 currents, alleviating the difference between TASK1 and TASK3 currents at physiological pH. As larger motoneurons have extensive dendritic trees while smaller motoneurons have poor ones, cGMP could integrate Ia-EPSPs to recruit small and large motoneurons synchronously by differentially modulating TASKI and TASK3 channels which were complementary distributed in soma and dendrites of motoneurons in the dorsolateral part of the trigeminal motor nucleus.
Depression Pathophysiology: Astrocyte Mitochondrial Melatonergic Pathway as Crucial Hub
Authors: Anderson George
Published: December 2022

Major depressive disorder (MDD) is widely accepted as having a heterogenous pathophysiology involving a complex mixture of systemic and CNS processes. A developmental etiology coupled to genetic and epigenetic risk factors as well as lifestyle and social process influences add further to the complexity. Consequently, antidepressant treatment is generally regarded as open to improvement, undoubtedly as a consequence of inappropriately targeted pathophysiological processes. This article reviews the diverse array of pathophysiological processes linked to MDD, and integrates these within a perspective that emphasizes alterations in mitochondrial function, both centrally and systemically. It is proposed that the long-standing association of MDD with suppressed serotonin availability is reflective of the role of serotonin as a precursor for the mitochondrial melatonergic pathway. Astrocytes, and the astrocyte mitochondrial melatonergic pathway, are highlighted as crucial hubs in the integration of the wide array of biological underpinnings of MDD, including gut dysbiosis and permeability, as well as developmental and social stressors, which can act to suppress the capacity of mitochondria to upregulate the melatonergic pathway, with consequences for oxidant-induced changes in patterned microRNAs and subsequent patterned gene responses. This is placed within a development context, including how social processes, such as discrimination, can physiologically regulate a susceptibility to MDD. Future research directions and treatment implications are derived from this.
Gene Expression Analysis in gla-Mutant Zebrafish Reveals Enhanced Ca2+ Signaling Similar to Fabry Disease
Authors: Elsaid Hassan Osman Alhassan , Tjeldnes Håkon , Rivedal Mariell , Serre Camille , Eikrem Øystein , Svarstad Einar , Tøndel Camilla , Marti Hans-Peter , Furriol Jessica , Babickova Janka
Published: December 2022

Fabry disease (FD) is an X-linked inborn metabolic disorder due to partial or complete lysosomal α-galactosidase A deficiency. FD is characterized by progressive renal insufficiency and cardio- and cerebrovascular involvement. Restricted access on Gb3-independent tissue injury experimental models has limited the understanding of FD pathophysiology and delayed the development of new therapies. Accumulating glycosphingolipids, mainly Gb3 and lysoGb3, are Fabry specific markers used in clinical follow up. However, recent studies suggest there is a need for additional markers to monitor FD clinical course or response to treatment. We used a gla-knockout zebrafish (ZF) to investigate alternative biomarkers in Gb3-free-conditions. RNA sequencing was used to identify transcriptomic signatures in kidney tissues discriminating gla-mutant (M) from wild type (WT) ZF. Gene Ontology (GO) and KEGG pathways analysis showed upregulation of immune system activation and downregulation of oxidative phosphorylation pathways in kidneys from M ZF. In addition, upregulation of the Ca2+ signaling pathway was also detectable in M ZF kidneys. Importantly, disruption of mitochondrial and lysosome-related pathways observed in M ZF was validated by immunohistochemistry. Thus, this ZF model expands the pathophysiological understanding of FD, the Gb3-independent effects of gla mutations could be used to explore new therapeutic targets for FD.
Induction of Oxidative Stress in SH-SY5Y Cells by Overexpression of hTau40 and Its Mitigation by Redox-Active Nanoparticles
Authors: Pieńkowska Natalia , Fahnestock Margaret , Mahadeo Crystal , Zaborniak Izabela , Chmielarz Paweł , Bartosz Grzegorz , Sadowska-Bartosz Izabela
Published: December 2022

Abnormally phosphorylated tau protein is the principal component of neurofibrillary tangles, accumulating in the brain in many neurodegenerative diseases, including Alzheimer’s disease. The aim of this study was to examine whether overexpression of tau protein leads to changes in the redox status of human neuroblastoma SH-SY5Y cells. The level of reactive oxygen species (ROS) was elevated in tau-overexpressing cells (TAU cells) as compared with cells transfected with the empty vector (EP cells). The level of glutathione was increased in TAU cells, apparently due to overproduction as an adaptation to oxidative stress. The TAU cells had elevated mitochondrial mass. They were more sensitive to 6-hydroxydopamine, delphinidin, 4-amino-TEMPO, and nitroxide-containing nanoparticles (NPs) compared to EP controls. These results indicate that overexpression of the tau protein imposes oxidative stress on the cells. The nitroxide 4-amino-TEMPO and nitroxide-containing nanoparticles (NPs) mitigated oxidative stress in TAU cells, decreasing the level of ROS. Nitroxide-containing nanoparticles lowered the level of lipid peroxidation in both TAU and EP cells, suggesting that nitroxides and NPs may mitigate tau-protein-induced oxidative stress.
Biomimetic Catalysts Based on Au@TiO2-MoS2-CeO2 Composites for the Production of Hydrogen by Water Splitting
Authors: Fontánez Kenneth , García Diego , Ortiz Dayna , Sampayo Paola , Hernández Luis , Cotto María , Ducongé José , Díaz Francisco , Morant Carmen , Petrescu Florian , Machín Abniel , Márquez Francisco
Published: December 2022

The photocatalytic hydrogen evolution reaction (HER) by water splitting has been studied, using catalysts based on crystalline TiO2 nanowires (TiO2NWs), which were synthesized by a hydrothermal procedure. This nanomaterial was subsequently modified by incorporating different loadings (1%, 3% and 5%) of gold nanoparticles (AuNPs) on the surface, previously exfoliated MoS2 nanosheets, and CeO2 nanoparticles (CeO2NPs). These nanomaterials, as well as the different synthesized catalysts, were characterized by electron microscopy (HR-SEM and HR-TEM), XPS, XRD, Raman, Reflectance and BET surface area. HER studies were performed in aqueous solution, under irradiation at different wavelengths (UV-visible), which were selected through the appropriate use of optical filters. The results obtained show that there is a synergistic effect between the different nanomaterials of the catalysts. The specific area of the catalyst, and especially the increased loading of MoS2 and CeO2NPs in the catalyst substantially improved the H2 production, with values of ca. 1114 μm/hg for the catalyst that had the best efficiency. Recyclability studies showed only a decrease in activity of approx. 7% after 15 cycles of use, possibly due to partial leaching of gold nanoparticles during catalyst use cycles. The results obtained in this research are certainly relevant and open many possibilities regarding the potential use and scaling of these heterostructures in the photocatalytic production of H2 from water.
Inhibitory Effects of Ursolic Acid on the Stemness and Progression of Human Breast Cancer Cells by Modulating Argonaute-2
Authors: Liao Wen-Ling , Liu Yu-Fan , Ying Tsung-Ho , Shieh Jia-Ching , Hung Yueh-Tzu , Lee Huei-Jane , Shen Chen-Yang , Cheng Chun-Wen
Published: December 2022

The stemness and metastasis of cancer cells are crucial features in determining cancer progression. Argonaute-2 (AGO2) overexpression was reported to be associated with microRNA (miRNA) biogenesis, supporting the self-renewal and differentiation characteristics of cancer stem cells (CSCs). Ursolic acid (UA), a triterpene compound, has multiple biological functions, including anticancer activity. In this study, we find that UA inhibits the proliferation of MDA-MB-231 and MCF-7 breast cancer cell lines using the CCK-8 assay. UA induced a significant decrease in the fraction of CSC in which it was examined by changes in the expression of stemness biomarkers, including the Nanog and Oct4 genes. UA altered invasion and migration capacities by significant decreases in the levels of epithelial-to-mesenchymal transition (EMT) proteins of slug and vimentin. Furthermore, the co-reduction in oncogenic miRNA levels (miR-9 and miR-221) was a result of the down-modulation in AGO2 in breast cancer cells in vitro. Mechanically, UA increases PTEN expression to inactivate the FAK/PI3K/Akt/mTOR signaling pathway and the decreased level of c-Myc in quantitative RT-PCR and Western blot imaging analyses. Our current understanding of the anticancer potential of UA in interrupting between EMT programming and the state of CSC suggests that UA can contribute to improvements in the clinical practice of breast cancer.
The Landscape of Gene Expression during Hyperfilamentous Biofilm Development in Oral Candida albicans Isolated from a Lung Cancer Patient
Authors: Chudzik-Rząd Beata , Zalewski Daniel , Kasela Martyna , Sawicki Rafał , Szymańska Jolanta , Bogucka-Kocka Anna , Malm Anna
Published: December 2022

The filamentation ability of Candida albicans represents one of the main virulence factors allowing for host tissue penetration and biofilm formation. The aim of this paper was to study the genetic background of the hyperfilamentous biofilm development in vitro in C. albicans isolated from the oral cavity of a lung cancer patient. Analyzed C. albicans isolates (CA1, CA2, CA3) were chosen based on their different structures of mature biofilm. The CA3 isolate possessing hyperfilamentation properties and forming high biofilm was compared with CA1 and CA2 isolates exhibiting low or average biofilm-forming ability, respectively. The detailed biofilm organization was studied with the use of confocal scanning laser microscopy. The whole transcriptome analysis was conducted during three stages of biofilm development (24 h, 48 h, 72 h). In contrast to CA1 and/or CA2 isolate, the CA3 isolate was characterized by a significant upregulation of genes encoding for cell wall proteins (HWP1, PGA13, PGA44, ALS3) and candidalysin (ECE1), as well as being involved in iron metabolism (FRE1, ALS3), sulfur metabolism (HAL21), the degradation of aromatic compounds (HQD2), and membrane transport (DIP5, PHO89, TNA1). In contrast, some genes (SCW11, FGR41, RBE1) in the CA3 were downregulated. We also observed the overexpression of a few genes over time—mainly FRE1, ATX1, CSA2 involved in iron metabolism. This is the first insight into the potential function of multiple genes in the hyperfilamentous biofilm formation in C. albicans, primarily isolated from host tissue, which may have an important clinical impact on cancer patients. Moreover, the presented data can lay the foundation for further research on novel pathogen-specific targets for antifungal drugs.
Circadian Rhythm Disorders Aggravate Periodontitis by Modulating BMAL1
Authors: Liu Xiaomeng , Cao Niuben , Liu Xinchan , Deng Yu , Xin Yu , Fu Ruobing , Xin Xirui , Hou Yubo , Yu Weixian
Published: December 2022

Circadian rhythms regulate the body’s homeostasis through the temporal control of tissue-specific circadian rhythm control genes. Circadian rhythm disorders (CRD) affect the expression levels of circadian rhythms-associated genes in brain and muscle aryl hydrocarbon receptor nuclear translocator-like-1(BMAL1), which is thought to contribute to metabolic disorders and an altered immune system. However, the relationship between CRD and the development of periodontitis was poorly reported. Therefore, this study aimed to investigate the role played by BMAL1 in periodontitis. We used a modified multi-platform approach (MMPM) to induce circadian rhythm disturbances in rats to investigate the role of BMAL1 in periodontitis. Our results showed significant downregulation of BMAL1 in the CRD with periodontitis group, significant resorption of alveolar bone, increased osteoclast differentiation, and upregulation of the inflammatory signaling molecule NF-κB. In addition, apoptosis and oxidative stress levels were increased in periodontal tissues. Collectively, our study suggests that BMAL1 is a key regulator in periodontitis exacerbated by CRD and that CRD may lead to the downregulation of BMAL1, thereby exacerbating oxidative stress and apoptosis in periodontal tissues. Our study found that BMAL1 may be associated with the progression of periodontitis and provides a new perspective on the treatment of periodontitis.
Prognostic and Immunological Implications of FAM72A in Pan-Cancer and Functional Validations
Authors: Bai Yuwen , Cao Kui , Zhang Ping , Ma Jianqun , Zhu Jinhong
Published: December 2022

The family with sequence similarity 72 Member A (FAM72A) is overexpressed in several types of cancer. However, its contributions to tumorigenesis remain largely unknown. Based on The Cancer Genome Atlas (TCGA) database, FAM72A was upregulated across 33 types of cancer. Accordingly, high levels of FAM72A predicted inferior outcomes in half of the cancer types using survival analysis (the Kaplan-Meier curve and univariate Cox regression model). Receiver operating characteristic (ROC) analysis demonstrated that FAM72A showed high accuracy in distinguishing cancerous tissues from normal ones. FAM72A was correlated with immune and stromal scores and immune cell infiltrations in various tumors. Moreover, FAM72A was also associated with tumor mutation burden (TMB), microsatellite instability (MSI), and immune checkpoint genes. Immunophenoscore (IPS) further validated that the FAM72Alow tumor showed high immunogenicity and tended to respond to anti-PD1/PDL1/PDL2, anti-CTLA4 treatment, and combined immunotherapies. We also investigated the functional role of FAM72A in lung adenocarcinoma (LUAD). In vitro studies demonstrated that the ectopic expression of FAM72A accelerated the proliferation and migration of NSCLC cells, whereas silencing FAM72A showed the opposite effects on them. In short, FAM72A had prognostic potential and correlated with tumor immunogenicity in various tumors. Functional analysis indicated that FAM72A is an oncogene in LUAD.
Targeting MYC Regulation with Polypurine Reverse Hoogsteen Oligonucleotides
Authors: Valiuska Simonas , Psaras Alexandra Maria , Noé Véronique , Brooks Tracy A. , Ciudad Carlos J.
Published: December 2022

The oncogene MYC has key roles in transcription, proliferation, deregulating cellular energetics, and more. Modulating the expression or function of the MYC protein is a viable therapeutic goal in an array of cancer types, and potential inhibitors of MYC with high specificity and selectivity are of great interest. In cancer cells addicted to their aberrant MYC function, suppression can lead to apoptosis, with minimal effects on non-addicted, non-oncogenic cells, providing a wide therapeutic window for specific and efficacious anti-tumor treatment. Within the promoter of MYC lies a GC-rich, G-quadruplex (G4)-forming region, wherein G4 formation is capable of mediating transcriptional downregulation of MYC. Such GC-rich regions of DNA are prime targets for regulation with Polypurine Reverse Hoogsteen hairpins (PPRHs). The current study designed and examined PPRHs targeting the G4-forming and four other GC-rich regions of DNA within the promoter or intronic regions. Six total PPRHs were designed, examined in cell-free conditions for target engagement and in cells for transcriptional modulation, and correlating cytotoxic activity in pancreatic, prostate, neuroblastoma, colorectal, ovarian, and breast cancer cells. Two lead PPRHs, one targeting the promoter G4 and one targeting Intron 1, were identified with high potential for further development as an innovative approach to both G4 stabilization and MYC modulation.
Plastid Phylogenomics Provide Evidence to Accept Two New Members of Ligusticopsis (Apiaceae, Angiosperms)
Authors: Liu Changkun , Deng Jiaojiao , Zhou Renxiu , Song Boni , Zhou Songdong , He Xingjin
Published: December 2022

Peucedanum nanum and P. violaceum are recognized as members of the genus Peucedanum because of their dorsally compressed mericarps with slightly prominent dorsal ribs and narrowly winged lateral ribs. However, these species are not similar to other Peucedanum taxa but resemble Ligusticopsis in overall morphology. To check the taxonomic positions of P. nanum and P. violaceum, we sequenced their complete plastid genome (plastome) sequences and, together with eleven previously published Ligusticopsis plastomes, performed comprehensively comparative analyses. The thirteen plastomes were highly conserved and similar in structure, size, GC content, gene content and order, IR borders, and the patterns of codon bias, RNA editing, and simple sequence repeats (SSRs). Nevertheless, twelve mutation hotspots (matK, ndhC, rps15, rps8, ycf2, ccsA-ndhD, petN-psbM, psbA-trnK, rps2-rpoC2, rps4-trnT, trnH-psbA, and ycf2-trnL) were selected. Moreover, both the phylogenetic analyses based on plastomes and on nuclear ribosomal DNA internal transcribed spacer (ITS) sequences robustly supported that P. nanum and P. violaceum nested in Ligusticopsis, and this was further confirmed by the morphological evidence. Hence, transferring P. nanum and P. violaceum into Ligusticopsis genus is reasonable and convincing, and two new combinations are presented.
The Functional Characterization of Carboxylesterases Involved in the Degradation of Volatile Esters Produced in Strawberry Fruits
Authors: Zhang Lingjie , Zhou Kang , Wang Maohao , Li Rui , Dai Xinlong , Liu Yajun , Jiang Xiaolan , Xia Tao , Gao Liping
Published: December 2022

Volatile ester compounds are important contributors to the flavor of strawberry, which affect consumer preference. Here, the GC-MS results showed that volatile esters are the basic aroma components of strawberry, banana, apple, pear, and peach, and the volatile esters were significantly accumulated with the maturation of strawberry fruits. The main purpose of this study is to discuss the relationship between carboxylesterases (CXEs) and the accumulation of volatile ester components in strawberries. FaCXE2 and FaCXE3 were found to have the activity of hydrolyzing hexyl acetate, Z-3-hexenyl acetate, and E-2-hexenyl acetate to the corresponding alcohols. The enzyme kinetics results showed that FaCXE3 had the higher affinity for hexyl acetate, E-2-hexenyl acetate, and Z-3-hexenyl acetate compared with FaCXE2. The volatile esters were mainly accumulated at the maturity stages in strawberry fruits, less at the early stages, and the least during the following maturation stages. The expression of FaCXE2 gradually increased with fruit ripening and the expression level of FaCXE3 showed a decreasing trend, which suggested the complexity of the true function of CXEs. The transient expression of FaCXE2 and FaCXE3 genes in strawberry fruits resulted in a significantly decreased content of volatile esters, such as Z-3-hexenyl acetate, methyl hexanoate, methyl butyrate, and other volatile esters. Taken together, FaCXE2 and FaCXE3 are indeed involved in the regulation of the synthesis and degradation of strawberry volatile esters.