bluuebunny/crossref_metadata_2025 huggingface dataset:
Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet
Authors: Gong Yongyong , Liu Xin , Chen Sixue , Li Hongli , Duanmu Huizi
Published: October 2022

As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.
Cell-Free Filtrates (CFF) as Vectors of a Transmissible Pathologic Tissue Memory Code: A Hypothetical and Narrative Review
Authors: Berlanga-Acosta Jorge , Fernandez-Mayola Maday , Mendoza-Mari Yssel , Garcia-Ojalvo Ariana , Martinez-Jimenez Indira , Rodriguez-Rodriguez Nadia , Garcia del Barco Herrera Diana , Guillén-Nieto Gerardo
Published: October 2022

Cellular memory is a controversial concept representing the ability of cells to “write and memorize” stressful experiences via epigenetic operators. The progressive course of chronic, non-communicable diseases such as type 2 diabetes mellitus, cancer, and arteriosclerosis, is likely driven through an abnormal epigenetic reprogramming, fostering the hypothesis of a cellular pathologic memory. Accordingly, cultured diabetic and cancer patient-derived cells recall behavioral traits as when in the donor’s organism irrespective to culture time and conditions. Here, we analyze the data of studies conducted by our group and led by a cascade of hypothesis, in which we aimed to validate the hypothetical existence and transmissibility of a cellular pathologic memory in diabetes, arteriosclerotic peripheral arterial disease, and cancer. These experiments were based on the administration to otherwise healthy animals of cell-free filtrates prepared from human pathologic tissue samples representative of each disease condition. The administration of each pathologic tissue homogenate consistently induced the faithful recapitulation of: (1) Diabetic archetypical changes in cutaneous arterioles and nerves. (2) Non-thrombotic arteriosclerotic thickening, collagenous arterial encroachment, aberrant angiogenesis, and vascular remodeling. (3) Pre-malignant and malignant epithelial and mesenchymal tumors in different organs; all evocative of the donor’s tissue histopathology and with no barriers for interspecies transmission. We hypothesize that homogenates contain pathologic tissue memory codes represented in soluble drivers that “infiltrate” host’s animal cells, and ultimately impose their phenotypic signatures. The identification and validation of the actors in behind may pave the way for future therapies.
Exscalate4CoV: Innovative High Performing Computing (HPC) Strategies to Tackle Pandemic Crisis
Authors: Beccari Andrea R. , Vistoli Giulio
Published: October 2022

This Special Issue was intended as a dissemination forum where the major results pursued by the EXSCALATE4CoV project (E4C, https://www [...]
Activation of the ROS/CncC Signaling Pathway Regulates Cytochrome P450 CYP4BQ1 Responsible for (+)-α-Pinene Tolerance in Dendroctonus armandi
Authors: Liu Bin , Tang Ming , Chen Hui
Published: October 2022

Bark beetles mainly rely on detoxification enzymes to resist the host tree’s defense against oleoresin terpenes. Cytochrome P450 enzymes (CYPs) play an important role in the detoxification of plant allelochemicals and pesticides in insect. One P450 gene (DaCYP4BQ1) is associated with the response of (+)-α-pinene in Dendroctonus armandi. However, the regulatory mechanism of this P450 gene response to (+)-α-pinene is still unknown. In this study, spatiotemporal expression profiling indicated that CYP4BQ1 was highly expressed in adult and larval stages of D. armandi, and it was predominantly expressed in fat body, midgut, and Malpighian tubules of adults. Moreover, the expression of CYP4BQ1 significantly increased after exposure to (+)-α-pinene, and depletion of it decreased the tolerance of adults to (+)-α-pinene. In addition, (+)-α-pinene treatment induced the expression of the transcription factors cap ‘n’ collar isoform C (CncC) and its binding factor muscle aponeurosis fibromatosis (Maf), elevated the level of hydrogen peroxide (H2O2), and increased the activities of antioxidant enzymes. Silencing CncC suppressed CYP4BQ1 expression and enhanced the susceptibility of beetles to (+)-α-pinene. Similarly, application of the reactive oxygen species (ROS) scavenger N-acetylcysteine reduced the production and accumulation of H2O2, suppressed the expression of CncC, Maf, and CYP4BQ1 and led to decreased tolerance of adults to (+)-α-pinene. In contrast, ingestion of the CncC agonist curcumin elevated CYP4BQ1 expression and enhanced (+)-α-pinene tolerance. The results demonstrate that, in D. armandi, (+)-α-pinene induces CYP4BQ1 via activation of the ROS/CncC signaling pathway.
Discovery and In Vivo Efficacy of Trace Amine-Associated Receptor 1 (TAAR1) Agonist 4-(2-Aminoethyl)-N-(3,5-dimethylphenyl)piperidine-1-carboxamide Hydrochloride (AP163) for the Treatment of Psychotic Disorders
Authors: Krasavin Mikhail , Peshkov Anatoly A. , Lukin Alexey , Komarova Kristina , Vinogradova Lyubov , Smirnova Daria , Kanov Evgeny V. , Kuvarzin Savelii R. , Murtazina Ramilya Z. , Efimova Evgeniya V. , Gureev Maxim , Onokhin Kirill , Zakharov Konstantin , Gainetdinov Raul R.
Published: October 2022

Starting from a screening hit, a set of analogs was synthesized based on a 4-(2-aminoethyl)piperidine core not associated previously with trace amine-associated receptor 1 (TAAR1) modulation in the literature. Several structure–activity relationship generalizations have been drawn from the observed data, some of which were corroborated by molecular modeling against the crystal structure of TAAR1. The four most active compounds (EC50 for TAAR1 agonistic activity ranging from 0.033 to 0.112 μM) were nominated for evaluation in vivo. The dopamine transporter knockout (DAT-KO) rat model of dopamine-dependent hyperlocomotion was used to evaluate compounds’ efficacy in vivo. Out of four compounds, only one compound (AP163) displayed a statistically significant and dose-dependent reduction in hyperlocomotion in DAT-KO rats. As such, compound AP163 represents a viable lead for further preclinical characterization as a potential novel treatment option for disorders associated with increased dopaminergic function, such as schizophrenia.
Physiological and Comparative Transcriptome Analyses of the High-Tillering Mutant mtn1 Reveal Regulatory Mechanisms in the Tillering of Centipedegrass (Eremochloa ophiuroides (Munro) Hack.)
Authors: Li Ling , Xie Chenming , Zong Junqin , Guo Hailin , Li Dandan , Liu Jianxiu
Published: October 2022

Tillering is a key factor that determines the reproductive yields of centipedegrass, which is an important perennial warm-season turfgrass. However, the regulatory mechanism of tillering in perennial plants is poorly understood, especially in perennial turfgrasses. In this study, we created and characterised a cold plasma-mutagenised centipedegrass mutant, mtn1 (more tillering number 1). Phenotypic analysis showed that the mtn1 mutant exhibited high tillering, short internodes, long seeds and a heavy 1000-seed weight. Then, a comparative transcriptomic analysis of the mtn1 mutant and wild-type was performed to explore the molecular mechanisms of centipedegrass tillering. The results revealed that plant hormone signalling pathways, as well as starch and sucrose metabolism, might play important roles in centipedegrass tillering. Hormone and soluble sugar content measurements and exogenous treatment results validated that plant hormones and sugars play important roles in centipedegrass tiller development. In particular, the overexpression of the auxin transporter ATP-binding cassette B 11 (EoABCB11) in Arabidopsis resulted in more branches. Single nucleotide polymorphisms (SNPs) were also identified, which will provide a useful resource for molecular marker-assisted breeding in centipedegrass. According to the physiological characteristics and transcriptional expression levels of the related genes, the regulatory mechanism of centipedegrass tillering was systematically revealed. This research provides a new breeding resource for further studies into the molecular mechanism that regulates tillering in perennial plants and for breeding high-tillering centipedegrass varieties.
Analysis of Long Non-Coding RNA (lncRNA) UCA1, MALAT1, TC0101441, and H19 Expression in Endometriosis
Authors: Szaflik Tomasz , Romanowicz Hanna , Szyłło Krzysztof , Kołaciński Radosław , Michalska Magdalena M. , Samulak Dariusz , Smolarz Beata
Published: October 2022

Endometriosis is a disease of complex etiology. Hormonal, immunological, and environmental factors are involved in its formation. In recent years, special attention has been paid to genetic mechanisms that can have a significant impact on the increased incidence of endometriosis. The study aimed to analyze the expression of four long non-coding RNA (lncRNA) genes, UCA1, MALAT1, TC0101441, and H19, in the context of the risk of developing endometriosis. The material for genetic testing for the expression of lncRNA genes were tissue slices embedded in paraffin blocks from patients with endometriosis (n = 100) and the control group (n = 100). Gene expression was determined by the RT-PCR technique. The expression of the H19 gene in endometriosis patients was statistically significantly lower than in the control group. A statistically significant association was found between H19 gene expression in relation to The Revised American Society for Reproductive Medicine classification of endometriosis (rASRM) in the group of patients with endometriosis. Research suggests that H19 expression plays an important role in the pathogenesis of endometriosis.
Inhibition of Complex I of the Respiratory Chain, but Not Complex III, Attenuates Degranulation and Cytokine Secretion in Human Skin Mast Cells
Authors: Buttgereit Thomas , Pfeiffenberger Moritz , Frischbutter Stefan , Krauß Pierre-Louis , Chen Yuling , Maurer Marcus , Buttgereit Frank , Gaber Timo
Published: October 2022

The mechanisms of mast cell (MC) degranulation and MC-driven skin symptoms are well-described. In contrast, data about the role of mitochondrial respiration for immune functions of human skin MCs are lacking. Oxygen consumption rate (OCR) in primary human skin MCs during IgE-mediated activation in the absence of glucose was examined using a metabolic flux analyzer. Effects of the inhibition of mitochondrial complex I (by rotenone A) and III (by myxothiazol) on degranulation and cytokine secretion (IL-4, IL-5, IL-6, IL-13, TNF-α, and GM-CSF) were explored by the β-hexosaminidase release assay and multiplex ELISA. IgE-mediated activation rapidly increased the mitochondrial OCR and extracellular acidification; the contribution of non-mitochondrial oxygen consumption remained unchanged at lower levels. Both myxothiazol and rotenone A reduced OCR, the mitochondrial parameters, and extracellular acidification; however, myxothiazol did not affect degranulation and cytokine secretion. In contrast, degranulation and the secretion of IL-6, IL-13, TNF-α, and GM-CSF were reduced by rotenone A, whereas the secretion of IL-4 and IL-5 was not significantly affected. The inhibitors did not affect cell viability. Our results highlight the important role played by mitochondrial respiration in primary human skin MCs and allow for a conclusion on a hierarchy of their effector functions. Drugs targeting specific pathways in mitochondria may provide future options to control MC-driven skin symptoms.
Nonthermal Plasma Effects on Fungi: Applications, Fungal Responses, and Future Perspectives
Authors: Hoppanová Lucia , Kryštofová Svetlana
Published: October 2022

The kingdom of Fungi is rich in species that live in various environments and exhibit different lifestyles. Many are beneficial and indispensable for the environment and industries, but some can threaten plants, animals, and humans as pathogens. Various strategies have been applied to eliminate fungal pathogens by relying on chemical and nonchemical antifungal agents and tools. Nonthermal plasma (NTP) is a potential tool to inactivate pathogenic and food-contaminating fungi and genetically improve fungal strains used in industry as enzyme and metabolite producers. The NTP mode of action is due to many highly reactive species and their interactions with biological molecules. The interaction of the NTP with living cells is believed to be synergistic yet not well understood. This review aims to summarize the current NTP designs, applications, and challenges that involve fungi, as well as provide brief descriptions of underlying mechanisms employed by fungi in interactions with the NTP components
Can TPO as Photoinitiator Replace “Golden Mean” Camphorquinone and Tertiary Amines in Dental Composites? Testing Experimental Composites Containing Different Concentration of Diphenyl(2,4,6-trimethylbenzoyl)phosphine Oxide
Authors: Kowalska Andrea , Sokołowski Jerzy , Szynkowska-Jóźwik Małgorzata Iwona , Gozdek Tomasz , Kopacz Karolina , Bociong Kinga
Published: October 2022

The aim of this research was to compare the biomechanical properties of experimental composites containing a classic photoinitiating system (camphorquinone and 2-(dimethylami-no)ethyl methacrylate) or diphenyl(2,4,6-trimethylbenzoyl)phosphine oxide (TPO) as a photoinitiator. The produced light-cured composites consisted of an organic matrix-Bis-GMA (60 wt.%), TEGDMA (40 wt.%) and silanized silica filler (45 wt.%). Composites contained 0.27; 0.5; 0.75 or 1 wt.% TPO. Vickers hardness, microhardness (in the nanoindentation test), diametral tensile strength, resistance to three-point bending and the CIE L* a* b* colorimetric analysis was performed with each composite produced. The highest average Vickers hardness values were obtained for the composite containing 1 wt.% TPO (43.18 ± 1.7HV). The diametral tensile strength remains on regardless of the type and amount of photoinitiator statistically the same level, except for the composite containing 0.5 wt.% TPO for which DTS = 22.70 ± 4.7 MPa and is the lowest recorded value. The highest average diametral tensile strength was obtained for the composite containing 0.75 wt.% TPO (29.73 ± 4.8 MPa). The highest modulus of elasticity characterized the composite containing 0.75 wt.% TPO (5383.33 ± 1067.1 MPa). Composite containing 0.75 wt.% TPO has optimal results in terms of Vickers hardness, diametral tensile strength, flexural strength and modulus of elasticity. Moreover, these results are better than the parameters characterizing the composite containing the CQ/DMAEMA system. In terms of an aesthetic composite containing 0.75 wt.%. TPO is less yellow in color than the composite containing CQ/DMAEMA. This conclusion was objectively confirmed by test CIE L* a* b*.
Reactivation of Vertebral Growth Plate Function in Vertebral Body Tethering in an Animal Model
Authors: Latalski Michał , Szponder Tomasz , Starobrat Grzegorz , Warda Edward , Wójciak Magdalena , Dresler Sławomir , Danielewicz Anna , Sawicki Jan , Sowa Ireneusz
Published: October 2022

Flexible spine tethering is a relatively novel fusionless surgical technique that aims to correct scoliosis based on growth modulation due to the pressure exerted on the vertebral body epiphyseal growth plate. The correction occurs in two phases: immediate intraoperative and postoperative with growth. The aim of this study was to evaluate the reactivation of vertebral growth plate function after applying corrective forces. The rat tail model was used. Asymmetric compression and distraction of caudal growth plates were performed using a modified external fixation apparatus. Radiological and histopathological data were analysed. After three weeks of correction, the activity of the structures increased across the entire growth plate width, and the plate was thickened. The height of the hypertrophic layer and chondrocytes on the concave side doubled in height. The height of chondrocytes and the cartilage thickness on the concave and central sides after the correction did not differ statistically significantly from the control group. Initiation of the correction of scoliosis in the growing spine, with relief of the pressure on the growth plate, allows the return of the physiological activity of the growth cartilage and restoration of the deformed vertebral body.
Genome-Wide Survey and Functional Verification of the NAC Transcription Factor Family in Wild Emmer Wheat
Authors: Gong Fangyi , Zhang Tian , Wang Zhe , Qi Tiangang , Lu Yusen , Liu Yuhang , Zhao Shuhong , Liu Ruiqing , Yi Rui , He Jingshu , Tu Bin , Zhang Tao , Zhang Lianquan , Hao Ming , Zheng Youliang , Liu Dengcai , Huang Lin , Wu Bihua
Published: October 2022

The NAC transcription factor (TF) family is one of the largest TF families in plants, which has been widely reported in rice, maize and common wheat. However, the significance of the NAC TF family in wild emmer wheat (Triticum turgidum ssp. dicoccoides) is not yet well understood. In this study, a genome-wide investigation of NAC genes was conducted in the wild emmer genome and 249 NAC family members (TdNACs) were identified. The results showed that all of these genes contained NAM/NAC-conserved domains and most of them were predicted to be located on the nucleus. Phylogenetic analysis showed that these 249 TdNACs can be classified into seven clades, which are likely to be involved in the regulation of grain protein content, starch synthesis and response to biotic and abiotic stresses. Expression pattern analysis revealed that TdNACs were highly expressed in different wheat tissues such as grain, root, leaves and shoots. We found that TdNAC8470 was phylogenetically close to NAC genes that regulate either grain protein or starch accumulation. Overexpression of TdNAC8470 in rice showed increased grain starch concentration but decreased grain Fe, Zn and Mn contents compared with wild-type plants. Protein interaction analysis indicated that TdNAC8470 might interact with granule-bound starch synthase 1 (TdGBSS1) to regulate grain starch accumulation. Our work provides a comprehensive understanding of the NAC TFs family in wild emmer wheat and establishes the way for future functional analysis and genetic improvement of increasing grain starch content in wheat.
Genome-Wide Investigation and Expression Analysis of the Nitraria sibirica Pall. CIPK Gene Family
Authors: Zhu Liming , Fang Hao , Lian Ziming , Zhang Jingbo , Li Xinle , Shi Jisen , Lu Lu , Lu Ye , Chen Jinhui , Cheng Tielong
Published: October 2022

The calcineurin B-like-interacting protein kinase (CIPK) protein family plays a key role in the plant calcium ion-mediated signal transduction pathway, which regulates a plant’s response to abiotic stress. Nitraria sibirica pall. (N. sibirica) is a halophyte with a strong tolerance for high salt environments, yet how it is able to deal with salt stress on a molecular level is still unknown. Due to their function as described in other plant species, CIPK genes are prime candidates for a role in salt stress signaling in N. sibirica. In this study, we identified and analyzed the phylogenetic makeup and gene expression of the N. sibirica CIPK gene family. A total of 14 CIPKs were identified from the N. sibirica genome and were clustered into seven groups based on their phylogeny. The promoters of NsCIPK genes contained multiple elements involved in hormonal and stress response. Synteny analysis identified a total of three pairs of synteny relationships between NsCIPK genes. Each gene showed its own specific expression pattern across different tissues, with the overall expression of CIPK6 being the lowest, and that of CIPK20 being the highest. Almost all CIPK genes tended to respond to salt, drought, and cold stress, but with different sensitivity levels. In this study, we have provided a general description of the NsCIPK gene family and its expression, which will be of great significance for further understanding of the NsCIPK gene family function.
Proteomics Profiling of Stool Samples from Preterm Neonates with SWATH/DIA Mass Spectrometry for Predicting Necrotizing Enterocolitis
Authors: Gagné David , Shajari Elmira , Thibault Marie-Pier , Noël Jean-François , Boisvert François-Michel , Babakissa Corentin , Levy Emile , Gagnon Hugo , Brunet Marie A. , Grynspan David , Ferretti Emanuela , Bertelle Valérie , Beaulieu Jean-François
Published: October 2022

Necrotizing enterocolitis (NEC) is a life-threatening condition for premature infants in neonatal intensive care units. Finding indicators that can predict NEC development before symptoms appear would provide more time to apply targeted interventions. In this study, stools from 132 very-low-birth-weight (VLBW) infants were collected daily in the context of a multi-center prospective study aimed at investigating the potential of fecal biomarkers for NEC prediction using proteomics technology. Eight of the VLBW infants received a stage-3 NEC diagnosis. Stools collected from the NEC infants up to 10 days before their diagnosis were available for seven of them. Their samples were matched with those from seven pairs of non-NEC controls. The samples were processed for liquid chromatography-tandem mass spectrometry analysis using SWATH/DIA acquisition and cross-compatible proteomic software to perform label-free quantification. ROC curve and principal component analyses were used to explore discriminating information and to evaluate candidate protein markers. A series of 36 proteins showed the most efficient capacity with a signature that predicted all seven NEC infants at least a week in advance. Overall, our study demonstrates that multiplexed proteomic signature detection constitutes a promising approach for the early detection of NEC development in premature infants.
Acute Endotoxemia-Induced Respiratory and Intestinal Dysbiosis
Authors: Goossens Evy , Li Jianhui , Callens Chana , Van Rysselberghe Nathalie Van , Kettunen Hannele , Vuorenmaa Juhani , Garcia Gonzalez Natalia Garcia , Libert Claude , Ducatelle Richard , Van Immerseel Filip Van
Published: October 2022

Systemic inflammatory response syndrome (SIRS) is a severe condition characterized by systemic inflammation, which may lead to multiple organ failure, shock and death. SIRS is common in burn patients, pancreatitis and sepsis. SIRS is often accompanied by intestinal dysbiosis. However, the mechanism, role and details of microbiome alterations during the early phase of acute SIRS are not completely understood. The current study aimed to characterize the dynamic alterations of both the intestinal and respiratory microbiome at two timepoints during the early phase of acute SIRS (4 and 8 h after LPS) and link these to the host response in a mouse model of a LPS-induced lethal SIRS. Acute SIRS had no effect on the microbiome in the large intestine but induced a rapid dysbiosis in the small intestine, which resembled the microbiome alterations commonly observed in SIRS patients. Later in the disease progression, a dysbiosis of the respiratory microbiome was observed, which was associated with the MMP9 expression in the lungs. Although similar bacteria were increased in both the lung and the small intestine, no evidence for a gut-lung translocation was observed. Gut dysbiosis is commonly observed in diseases involving inflammation in the gut. However, whether the inflammatory response associated with SIRS and sepsis can directly cause gut dysbiosis was still unclear. In the current study we provide evidence that a LPS-induced SIRS can directly cause dysbiosis of the small intestinal and respiratory microbiome.
Antisense Transcription in Plants: A Systematic Review and an Update on cis-NATs of Sugarcane
Authors: Santini Luciane , Yoshida Leonardo , de Oliveira Kaique Dias , Lembke Carolina Gimiliani , Diniz Augusto Lima , Cantelli Geraldo Cesar , Nishiyama-Junior Milton Yutaka , Souza Glaucia Mendes
Published: October 2022

Initially, natural antisense transcripts (NATs, natRNAs, or asRNAs) were considered repressors; however, their functions in gene regulation are diverse. Positive, negative, or neutral correlations to the cognate gene expression have been noted. Although the first studies were published about 50 years ago, there is still much to be investigated regarding antisense transcripts in plants. A systematic review of scientific publications available in the Web of Science databases was conducted to contextualize how the studying of antisense transcripts has been addressed. Studies were classified considering three categories: “Natural antisense” (208), artificial antisense used in “Genetic Engineering” (797), or “Natural antisense and Genetic Engineering”-related publications (96). A similar string was used for a systematic search in the NCBI Gene database. Of the 1132 antisense sequences found for plants, only 0.8% were cited in PubMed and had antisense information confirmed. This value was the lowest when compared to fungi (2.9%), bacteria (2.3%), and mice (54.1%). Finally, we present an update for the cis-NATs identified in Saccharum spp. Of the 1413 antisense transcripts found in different experiments, 25 showed concordant expressions, 22 were discordant, 1264 did not correlate with the cognate genes, and 102 presented variable results depending on the experiment.
Engineered Mesoporous Silica-Based Core-Shell Nanoarchitectures for Synergistic Chemo-Photodynamic Therapies
Authors: Gao Yue-Mei , Chiu Shih-Han , Busa Prabhakar , Liu Chen-Lun , Kankala Ranjith Kumar , Lee Chia-Hung
Published: October 2022

Combinatorial therapies have garnered enormous interest from researchers in efficiently devastating malignant tumors through synergistic effects. To explore the combinatorial approach, multiple therapeutic agents are typically loaded in the delivery vehicles, controlling their release profiles and executing subsequent therapeutic purposes. Herein, we report the fabrication of core (silica)-shell (mesoporous silica nanoparticles, MSNs) architectures to deliver methylene blue (MB) and cupric doxorubicin (Dox) as model drugs for synergistic photodynamic therapy (PDT), chemotherapy, and chemodynamic therapy (CDT). MB, as the photosensitizer, is initially loaded and stabilized in the silica core for efficient singlet oxygen generation under light irradiation towards PDT. The most outside shell with imidazole silane-modified MSNs is immobilized with a chemotherapeutic agent of Dox molecules through the metal (Copper, Cu)-ligand coordination interactions, achieving the pH-sensitive release and triggering the production of intracellular hydrogen peroxide and subsequent Fenton-like reaction-assisted Cu-catalyzed free radicals for CDT. Further, the designed architectures are systematically characterized using various physicochemical characterization techniques and demonstrate the potent anti-cancer efficacy against skin melanoma. Together our results demonstrated that the MSNs-based core-shell nanoarchitectures have great potential as an effective strategy in synergistically ablating cancer through chemo-, chemodynamic, and photodynamic therapies.
Clinical Value of the PD-1/PD-L1/PD-L2 Pathway in Patients Suffering from Endometriosis
Authors: Suszczyk Dorota , Skiba Wiktoria , Zardzewiały Witold , Pawłowska Anna , Włodarczyk Karolina , Polak Grzegorz , Tarkowski Rafał , Wertel Iwona
Published: October 2022

The interaction between dendritic cells (DCs) and T cells mediated by the programmed cell death 1 (PD-1)/programmed cell death ligand 1 (PD-L1)/programmed cell death ligand 2 (PD-L2) pathway is the most important point in regulating immunological tolerance and autoimmunity. Disturbances in the quantity, maturity, and activity of DCs may be involved in the implantation and growth of endometrial tissue outside the uterus in endometriosis (EMS). However, little is known about the role of the immune checkpoint pathways in EMS. In our study, we examined the expression of PD-L1/PD-L2 on myeloid DCs (mDCs) and plasmacytoid DCs (pDCs) in the peripheral blood (PB) and peritoneal fluid (PF) of both EMS patients (n = 72) and healthy subjects (n = 20) via flow cytometry. The concentration of soluble PD-L1 and PD-L2 in the plasma and PF of EMS patients and the control group were determined using ELISA. We demonstrated an elevated percentage of mDCs, mDCs and pDCs with the PD-L1or PD-L2 expression, and a higher concentration of the soluble forms of PD-L1 and PD-L2 in the PF than in the plasma of EMS patients. We conclude that the peritoneal cavity environment and the PD-1/PD-L1/PD-L2 axis may play an important role in the modulation of immune response and the development and/or progression of EMS.
A Tripartite Efflux System Affects Flagellum Stability in Helicobacter pylori
Authors: Gibson Katherine , Chu Joshua K. , Zhu Shiwei , Nguyen Doreen , Mrázek Jan , Liu Jun , Hoover Timothy R.
Published: October 2022

Helicobacter pylori uses a cluster of polar, sheathed flagella for swimming motility. A search for homologs of H. pylori proteins that were conserved in Helicobacter species that possess flagellar sheaths but were underrepresented in Helicobacter species with unsheathed flagella identified several candidate proteins. Four of the identified proteins are predicted to form part of a tripartite efflux system that includes two transmembrane domains of an ABC transporter (HP1487 and HP1486), a periplasmic membrane fusion protein (HP1488), and a TolC-like outer membrane efflux protein (HP1489). Deleting hp1486/hp1487 and hp1489 homologs in H. pylori B128 resulted in reductions in motility and the number of flagella per cell. Cryo-electron tomography studies of intact motors of the Δhp1489 and Δhp1486/hp1487 mutants revealed many of the cells contained a potential flagellum disassembly product consisting of decorated L and P rings, which has been reported in other bacteria. Aberrant motors lacking specific components, including a cage-like structure that surrounds the motor, were also observed in the Δhp1489 mutant. These findings suggest a role for the H. pylori HP1486-HP1489 tripartite efflux system in flagellum stability. Three independent variants of the Δhp1486/hp1487 mutant with enhanced motility were isolated. All three motile variants had the same frameshift mutation in fliL, suggesting a role for FliL in flagellum disassembly.
The Interplay between GSK3β and Tau Ser262 Phosphorylation during the Progression of Tau Pathology
Authors: Song Liqing , Oseid Daniel E. , Wells Evan A. , Robinson Anne Skaja
Published: October 2022

Tau hyperphosphorylation has been linked directly to the formation of toxic neurofibrillary tangles (NFTs) in tauopathies, however, prior to NFT formation, the sequence of pathological events involving tau phosphorylation remains unclear. Here, the effect of glycogen synthase kinase 3β (GSK3β) on tau pathology was examined independently for each step of transcellular propagation; namely, tau intracellular aggregation, release, cellular uptake and seeding activity. We find that overexpression of GSK3β-induced phosphorylated 0N4R tau led to a higher level of tau oligomerization in SH-SY5Y neuroblastoma cells than wild type 0N4R, as determined by several orthogonal assays. Interestingly, the presence of GSK3β also enhanced tau release. Further, we demonstrated that cells endocytosed more monomeric tau protein when pre-phosphorylated by GSK3β. Using an extracellular vesicle (EVs)-assisted tau neuronal delivery system, we show that exosomal GSK3β-phosphorylated tau, when added to differentiated SH-SY5Y cells, induced more efficient tau transfer, showing much higher total tau levels and increased tau aggregate formation as compared to wild type exosomal tau. The role of a primary tau phosphorylation site targeted by microtubule-affinity regulating kinases (MARKs), Ser262, was tested by pseudo-phosphorylation using site-directed mutagenesis to aspartate (S262D). S262D tau overexpression significantly enhanced tau release and intracellular tau accumulation, which were concurrent with the increase of pathological states of tau, as determined by immunodetection. Importantly, phosphorylation-induced tau accumulation was augmented by co-transfecting S262D tau with GSK3β, suggesting a possible interplay between Ser262 phosphorylation and GSK3β activity in tau pathology. Lastly, we found that pre-treatment of cells with amyloid-β (Aβ) further tau phosphorylation and accumulation when Ser262 pre-phosphorylation was present, suggesting that S262 may be a primary mediator of Aβ-induced tau toxicity. These findings provide a potential therapeutic target for treating tau-related disorders by targeting specific phospho-tau isoforms and further elucidate the GSK3β-mediated pathological seeding mechanisms.
Studying Synaptic Connectivity and Strength with Optogenetics and Patch-Clamp Electrophysiology
Authors: Linders Louisa E. , Supiot Laura. F. , Du Wenjie , D’Angelo Roberto , Adan Roger A. H. , Riga Danai , Meye Frank J.
Published: October 2022

Over the last two decades the combination of brain slice patch clamp electrophysiology with optogenetic stimulation has proven to be a powerful approach to analyze the architecture of neural circuits and (experience-dependent) synaptic plasticity in such networks. Using this combination of methods, originally termed channelrhodopsin-assisted circuit mapping (CRACM), a multitude of measures of synaptic functioning can be taken. The current review discusses their rationale, current applications in the field, and their associated caveats. Specifically, the review addresses: (1) How to assess the presence of synaptic connections, both in terms of ionotropic versus metabotropic receptor signaling, and in terms of mono- versus polysynaptic connectivity. (2) How to acquire and interpret measures for synaptic strength and function, like AMPAR/NMDAR, AMPAR rectification, paired-pulse ratio (PPR), coefficient of variance and input-specific quantal sizes. We also address how synaptic modulation by G protein-coupled receptors can be studied with pharmacological approaches and advanced technology. (3) Finally, we elaborate on advances on the use of dual color optogenetics in concurrent investigation of multiple synaptic pathways. Overall, with this review we seek to provide practical insights into the methods used to study neural circuits and synapses, by combining optogenetics and patch-clamp electrophysiology.
Inhibitory Effect of Bacterial Lysates Extracted from Pediococcus acidilactici on the Differentiation of 3T3-L1 Pre-Adipocytes
Authors: Lee Han Bin , Kang Seok-Seong
Published: October 2022

Postbiotics, including bacterial lysates, are considered alternatives to probiotics. The aim of the current study was to investigate the effect of bacterial lysates (BLs) extracted from Pediococcus acidilactici K10 (K10 BL) and P. acidilactici HW01 (HW01 BL) on the differentiation of 3T3-L1 pre-adipocytes. Both K10 and HW01 BLs significantly reduced the accumulation of lipid droplets and the amounts of cellular glycerides in 3T3-L1 cells (p < 0.05). However, another postbiotic molecule, peptidoglycan of P. acidilactici K10 and P. acidilactici HW01, moderately inhibited the accumulation of lipid droplets, whereas heat-killed P. acidilactici did not effectively inhibit the lipid accumulation. The mRNA and protein levels of the transcription factors, peroxisome proliferator-activated receptor γ and CCAAT/enhancer-binding protein α, responsible for the differentiation of 3T3-L1 cells, were significantly inhibited by K10 BL and HW01 BL (p < 0.05). Both K10 and HW01 BLs decreased adipocyte-related molecules, adipocyte fatty acid-binding protein and lipoprotein lipase, at the mRNA and protein levels. Furthermore, both K10 and HW01 BLs also downregulated the mRNA expression of leptin, but not resistin. Taken together, these results suggest that P. acidilactici BLs mediate anti-adipogenic effects by inhibiting adipogenic-related transcription factors and their target molecules.
Molecular Pathogenesis of Colorectal Cancer: Impact of Oncogenic Targets Regulated by Tumor Suppressive miR-139-3p
Authors: Yasudome Ryutaro , Seki Naohiko , Asai Shunichi , Goto Yusuke , Kita Yoshiaki , Hozaka Yuto , Wada Masumi , Tanabe Kan , Idichi Tetsuya , Mori Shinichiro , Ohtsuka Takao
Published: October 2022

We recently determined the RNA sequencing-based microRNA (miRNA) expression signature of colorectal cancer (CRC). Analysis of the signature showed that the expression of both strands of pre-miR-139 (miR-139-5p, the guide strand, and miR-139-3p, the passenger strand) was significantly reduced in CRC tissues. Transient transfection assays revealed that expression of miR-139-3p blocked cancer cell malignant transformation (e.g., cell proliferation, migration, and invasion). Notably, expression of miR-139-3p markedly blocked RAC-alpha serine/threonine-protein kinase (AKT) phosphorylation in CRC cells. A combination of in silico database and gene expression analyses of miR-139-3p-transfected cells revealed 29 putative targets regulated by miR-139-3p in CRC cells. RNA immunoprecipitation analysis using an Argonaute2 (AGO2) antibody revealed that KRT80 was efficiently incorporated into the RNA-induced silencing complex. Aberrant expression of Keratin 80 (KRT80) was detected in CRC clinical specimens by immunostaining. A knockdown assay using small interfering RNA (siRNA) targeting KRT80 showed that reducing KRT80 expression suppressed the malignant transformation (cancer cell migration and invasion) of CRC cells. Importantly, inhibiting KRT80 expression reduced AKT phosphorylation in CRC cells. Moreover, hexokinase-2 (HK2) expression was reduced in cells transfected with the KRT80 siRNAs or miR-139-3p. The involvement of miRNA passenger strands (e.g., miR-139-3p) in CRC cells is a new concept in miRNA studies. Our tumor-suppressive miRNA-based approach helps elucidate the molecular pathogenesis of CRC.
Analysis of the Influence of Both the Average Molecular Weight and the Content of Crosslinking Agent on Physicochemical Properties of PVP-Based Hydrogels Developed as Innovative Dressings
Authors: Kędzierska Magdalena , Jamroży Mateusz , Drabczyk Anna , Kudłacik-Kramarczyk Sonia , Bańkosz Magdalena , Gruca Mateusz , Potemski Piotr , Tyliszczak Bożena
Published: October 2022

Hydrogels belong to the group of polymers with a three-dimensional crosslinked structure, and their crosslinking density strongly affects their physicochemical properties. Here, we verified the impact of both the average molecular weight of crosslinking agents used during the photopolymerization of hydrogels and that of their content on selected properties of these materials. First, PVP-based hydrogels modified with Aloe vera juice and L-ascorbic acid were prepared using UV radiation. Next, their surface morphology was characterized via optical scanning electron microscopy, whereas their chemical structure was investigated by FT-IR spectroscopy. Moreover, we verified the tendency of the hydrogels to degrade in selected physiological liquids, as well as their tensile strength, percentage of elongation, and swelling capability. We found that the more crosslinking agent in the hydrogel matrix, the higher its tensile strength and the less elongation. The hydrogels showed the highest stability during incubation in SBF and 2% hemoglobin solution. A sharp decrease in the pH of distilled water observed during the incubation of the hydrogels was probably due to the release of Aloe vera juice from the hydrogel matrices. This was additionally confirmed by the decrease in the intensity of the absorption band derived from the polysaccharides included in this additive and by the decrease in the swelling ratio after 48 h. Importantly, all hydrogels demonstrated swelling properties, and it was proven that the higher content of the crosslinking agent in hydrogels, the lower their swelling ability.
Effects of Age and Lifelong Moderate-Intensity Exercise Training on Rats’ Testicular Function
Authors: Silva Joana V. , Santiago Joana , Matos Bárbara , Henriques Magda C. , Patrício Daniela , Martins Ana D. , Duarte José A. , Ferreira Rita , Alves Marco G. , Oliveira Paula , Oliveira Pedro F. , Fardilha Margarida
Published: October 2022

Aging is associated with testicular morphological and functional alterations, but the underlying molecular mechanisms and the impact of physical exercise are poorly understood. In this study, we examined the effects of age and lifelong moderate-intensity exercise on rat testis. Mature adults (35 weeks) and middle-aged (61 weeks) Wistar Unilever male rats were maintained as sedentary or subjected to a lifelong moderate-intensity treadmill training protocol. Testis weight and histology, mitochondrial biogenesis and function, and proteins involved in protein synthesis and stress response were evaluated. Our results illustrate an age-induced testicular atrophy that was associated with alterations in stress response, and mitochondrial biogenesis and function. Aging was associated with increased testicular levels of heat shock protein beta-1 (HSP27) and antioxidant enzymes. Aging was also associated with decreased mRNA abundance of the nuclear respiratory factor 1 (Nrf1), a key transcription factor for mitochondrial biogenesis, which was accompanied by decreased protein levels of the oxidative phosphorylation system (OXPHOS) complexes subunits in the testes of older animals. On the other hand, exercise did not protect against age-induced testicular atrophy and led to deleterious effects on sperm morphology. Exercise led to an even more pronounced decrease in the Nrf1 mRNA levels in testes of both age groups and was associated with decreased mRNA abundance of other mitochondrial biogenesis markers and decreased protein levels of OXPHOS complexes subunits. Lifelong moderate-intensity exercise training was also associated with an increase in testicular oxidative stress markers and possibly with reduced translation. Together, our results indicate that exercise did not protect against age-induced testicular atrophy and was not associated with beneficial changes in mitochondria and stress response, further activating mechanisms of protein synthesis inhibition.
Transcriptomic Analysis to Unravel Potential Pathways and Genes Involved in Pecan (Carya illinoinensis) Resistance to Pestalotiopsis microspora
Authors: Chen Yu , Zhang Shijie , Zhao Yuqiang , Mo Zhenghai , Wang Wu , Zhu Cancan
Published: October 2022

Fruit black spot (FBS), a fungal disease of pecan (Carya illinoinensis (Wangenh) K. Koch) caused by the pathogen Pestalotiopsis microspora, is a serious disease and poses a critical threat to pecan yield and quality. However, the details of pecan responses to FBS infection at the transcriptional level remain to be elucidated. In present study, we used RNA-Seq to analyze differential gene expression in three pecan cultivars with varied resistance to FBS infection: Xinxuan-4 (X4), Mahan (M), and Wichita (W), which were categorized as having low, mild, and high susceptibility to FBS, respectively. Nine RNA-Seq libraries were constructed, comprising a total of 58.56 Gb of high-quality bases, and 2420, 4380, and 8754 differentially expressed genes (DEGs) with |log2Fold change| ≥ 1 and p-value < 0.05 were identified between M vs. X4, W vs. M, and W vs. X4, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway analyses were performed to further annotate DEGs that were part of specific pathways, which revealed that out of 134 total pathways, MAPK signaling pathway, plant–pathogen interaction, and plant hormone signal transduction were highly enriched. Transcriptomic profiling analysis revealed that 1681 pathogen-related genes (PRGs), including 24 genes encoding WRKY transcription factors, potentially participate in the process of defense against Pestalotiopsis microspora infection in pecan. The correlation of WRKY TFs and PRGs was also performed to reveal the potential interaction networks among disease-resistance/pathogenesis-related genes and WRKY TFs. Expression profiling of nine genes annotated as TIFY, WRKY TF, and disease-resistance protein-related genes was performed using qRT-PCR, and the results were correlated with RNA-Seq data. This study provides valuable information on the molecular basis of pecan–Pestalotiopsis microspora interaction mechanisms and offers a repertoire of candidate genes related to pecan fruit response to FBS infection.
Switching of Photocatalytic Tyrosine/Histidine Labeling and Application to Photocatalytic Proximity Labeling
Authors: Nakane Keita , Nagasawa Haruto , Fujimura Chizu , Koyanagi Eri , Tomoshige Shusuke , Ishikawa Minoru , Sato Shinichi
Published: October 2022

Weak and transient protein interactions are involved in dynamic biological responses and are an important research subject; however, methods to elucidate such interactions are lacking. Proximity labeling is a promising technique for labeling transient ligand–binding proteins and protein–protein interaction partners of analytes via an irreversible covalent bond. Expanding chemical tools for proximity labeling is required to analyze the interactome. We developed several photocatalytic proximity-labeling reactions mediated by two different mechanisms. We found that numerous dye molecules can function as catalysts for protein labeling. We also identified catalysts that selectively modify tyrosine and histidine residues and evaluated their mechanisms. Model experiments using HaloTag were performed to demonstrate photocatalytic proximity labeling. We found that both ATTO465, which catalyzes labeling by a single electron transfer, and BODIPY, which catalyzes labeling by singlet oxygen, catalyze proximity labeling in cells.