bluuebunny/crossref_metadata_2025 huggingface dataset:
RNA Sequencing Demonstrates That Circular RNA Regulates Avian Influenza Virus Replication in Human Cells
Authors: Min Jie , Cao Ying , Liu Haizhou , Liu Di , Liu Wenjun , Li Jing
Published: September 2022

Circular RNAs (circRNAs) are involved in diverse biological processes. Avian influenza virus (AIV) can cross the species barrier to infect humans. Here, we employed RNA sequencing technology to profile circRNA, microRNA, and mRNA expression in human lung carcinoma cells in response to AIV or human influenza A virus (IAV) infection at viral replication. The analysis revealed that the expression of 475 common circRNAs were significantly regulated. The 381 and 1163 up-regulated circRNAs were induced by AIV at 8 and 16 h, respectively. Subsequently, gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses were also conducted for the AIV-specific up-regulated circRNAs. Moreover, the circRNAs were characterized, of which six were verified by quantitative real-time PCR. We further confirmed that expression of the selected circRNAs only increased following AIV infection. Knocking down the selected circRNAs promoted AIV proliferation, and overexpression of three of the candidate circRNAs restricted AIV replication and proliferation. We further analyzed that AIV-specific up-regulated circRNA mechanisms might function through the ceRNA network to affect the “Endocytosis” pathway and the “Cell cycle process”. These data provide the first expression profile of AIV-specific up-regulated circRNAs and shed new light on the pathogenesis of AIV infection. Our findings also suggest that these circRNAs serve an important role in AIV infection.
The Flagellar Transcriptional Regulator FtcR Controls Brucella melitensis 16M Biofilm Formation via a betI-Mediated Pathway in Response to Hyperosmotic Stress
Authors: Guo Jia , Deng Xingmei , Zhang Yu , Song Shengnan , Zhao Tianyi , Zhu Dexin , Cao Shuzhu , Baryshnikov Peter Ivanovic , Cao Gang , Blair Hugh T. , Chen Chuangfu , Gu Xinli , Liu Liangbo , Zhang Hui
Published: September 2022

The expression of flagellar proteins in Brucella species likely evolved through genetic transference from other microorganisms, and contributed to virulence, adaptability, and biofilm formation. Despite significant progress in defining the molecular mechanisms behind flagellar gene expression, the genetic program controlling biofilm formation remains unclear. The flagellar transcriptional factor (FtcR) is a master regulator of the flagellar system’s expression, and is critical for B. melitensis 16M’s flagellar biogenesis and virulence. Here, we demonstrate that FtcR mediates biofilm formation under hyperosmotic stress. Chromatin immunoprecipitation with next-generation sequencing for FtcR and RNA sequencing of ftcR-mutant and wild-type strains revealed a core set of FtcR target genes. We identified a novel FtcR-binding site in the promoter region of the osmotic-stress-response regulator gene betI, which is important for the survival of B. melitensis 16M under hyperosmotic stress. Strikingly, this site autoregulates its expression to benefit biofilm bacteria’s survival under hyperosmotic stress. Moreover, biofilm reduction in ftcR mutants is independent of the flagellar target gene fliF. Collectively, our study provides new insights into the extent and functionality of flagellar-related transcriptional networks in biofilm formation, and presents phenotypic and evolutionary adaptations that alter the regulation of B. melitensis 16M to confer increased tolerance to hyperosmotic stress.
Validation of the Pathogenic Effect of IGHMBP2 Gene Mutations Based on Yeast S. cerevisiae Model
Authors: Rzepnikowska Weronika , Kaminska Joanna , Kochański Andrzej
Published: September 2022

Spinal muscular atrophy with respiratory distress type 1 (SMARD1) is a heritable neurodegenerative disease characterized by rapid respiratory failure within the first months of life and progressive muscle weakness and wasting. Although the causative gene, IGHMBP2, is well defined, information on IGHMBP2 mutations is not always sufficient to diagnose particular patients, as the gene is highly polymorphic and the pathogenicity of many gene variants is unknown. In this study, we generated a simple yeast model to establish the significance of IGHMBP2 variants for disease development, especially those that are missense mutations. We have shown that cDNA of the human gene encodes protein which is functional in yeast cells and different pathogenic mutations affect this functionality. Furthermore, there is a correlation between the phenotype estimated in in vitro studies and our results, indicating that our model may be used to quickly and simply distinguish between pathogenic and non-pathogenic mutations identified in IGHMBP2 in patients.
Host mRNA Analysis of Periodontal Disease Patients Positive for Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans and Tannerella forsythia
Authors: Ursu Ramona Gabriela , Iancu Luminita Smaranda , Porumb-Andrese Elena , Damian Costin , Cobzaru Roxana Gabriela , Nichitean Giorgio , Ripa Carmen , Sandu Darius , Luchian Ionut
Published: September 2022

Periodontal disease is a frequent pathology worldwide, with a constantly increasing prevalence. For the optimal management of periodontal disease, there is a need to take advantage of actual technology to understand the bacterial etiology correlated with the pathogenic mechanisms, risk factors and treatment protocols. We analyzed the scientific literature published in the last 5 years regarding the recent applications of mRNA analysis in periodontal disease for the main known bacterial species considered to be the etiological agents: Porphyromonas gingivalis, Aggregatibacter actinomycetemcomitans and Tannerella forsythia. We identified new pathogenic mechanisms, therapeutic target genes and possible pathways to prevent periodontal disease. The mRNA analysis, as well as the important technological progress in recent years, supports its implementation in the routine management of periodontal disease patients.
In Silico Study of piRNA Interactions with the SARS-CoV-2 Genome
Authors: Akimniyazova Aigul , Yurikova Oxana , Pyrkova Anna , Rakhmetullina Aizhan , Niyazova Togzhan , Ryskulova Alma-Gul , Ivashchenko Anatoliy
Published: September 2022

A prolonged pandemic with numerous human casualties requires a rapid search for means to control the various strains of SARS-CoV-2. Since only part of the human population is affected by coronaviruses, there are probably endogenous compounds preventing the spread of these viral pathogens. It has been shown that piRNA (PIWI-interacting RNAs) interact with the mRNA of human genes and can block protein synthesis at the stage of translation. Estimated the effects of piRNA on SARS-CoV-2 genomic RNA (gRNA) in silico. A cluster of 13 piRNA binding sites (BS) in the SARS-CoV-2 gRNA region encoding the oligopeptide was identified. The second cluster of BSs 39 piRNAs also encodes the oligopeptide. The third cluster of 24 piRNA BS encodes the oligopeptide. Twelve piRNAs were identified that strongly interact with the gRNA. Based on the identified functionally important endogenous piRNAs, synthetic piRNAs (spiRNAs) are proposed that will suppress the multiplication of the coronavirus even more strongly. These spiRNAs and selected endogenous piRNAs have little effect on human 17494 protein-coding genes, indicating a low probability of side effects. The piRNA and spiRNA selection methodology created for the control of SARS-CoV-2 (NC_045512.2) can be used to control all strains of SARS-CoV-2.
Zebrafish Models of Paediatric Brain Tumours
Authors: Basheer Faiza , Dhar Poshmaal , Samarasinghe Rasika M.
Published: September 2022

Paediatric brain cancer is the second most common childhood cancer and is the leading cause of cancer-related deaths in children. Despite significant advancements in the treatment modalities and improvements in the 5-year survival rate, it leaves long-term therapy-associated side effects in paediatric patients. Addressing these impairments demands further understanding of the molecularity and heterogeneity of these brain tumours, which can be demonstrated using different animal models of paediatric brain cancer. Here we review the use of zebrafish as potential in vivo models for paediatric brain tumour modelling, as well as catalogue the currently available zebrafish models used to study paediatric brain cancer pathophysiology, and discuss key findings, the unique attributes that these models add, current challenges and therapeutic significance.
Three-Dimensional Envelope and Subunit Interactions of the Plastid-Encoded RNA Polymerase from Sinapis alba
Authors: Ruedas Rémi , Muthukumar Soumiya Sankari , Kieffer-Jaquinod Sylvie , Gillet François-Xavier , Fenel Daphna , Effantin Grégory , Pfannschmidt Thomas , Couté Yohann , Blanvillain Robert , Cobessi David
Published: September 2022

RNA polymerases (RNAPs) are found in all living organisms. In the chloroplasts, the plastid-encoded RNA polymerase (PEP) is a prokaryotic-type multimeric RNAP involved in the selective transcription of the plastid genome. One of its active states requires the assembly of nuclear-encoded PEP-Associated Proteins (PAPs) on the catalytic core, producing a complex of more than 900 kDa, regarded as essential for chloroplast biogenesis. In this study, sequence alignments of the catalytic core subunits across various chloroplasts of the green lineage and prokaryotes combined with structural data show that variations are observed at the surface of the core, whereas internal amino acids associated with the catalytic activity are conserved. A purification procedure compatible with a structural analysis was used to enrich the native PEP from Sinapis alba chloroplasts. A mass spectrometry (MS)-based proteomic analysis revealed the core components, the PAPs and additional proteins, such as FLN2 and pTAC18. MS coupled with crosslinking (XL-MS) provided the initial structural information in the form of protein clusters, highlighting the relative position of some subunits with the surfaces of their interactions. Using negative stain electron microscopy, the PEP three-dimensional envelope was calculated. Particles classification shows that the protrusions are very well-conserved, offering a framework for the future positioning of all the PAPs. Overall, the results show that PEP-associated proteins are firmly and specifically associated with the catalytic core, giving to the plastid transcriptional complex a singular structure compared to other RNAPs.
Identification of Potential New Aedes aegypti Juvenile Hormone Inhibitors from N-Acyl Piperidine Derivatives: A Bioinformatics Approach
Authors: Lima Lúcio R. , Bastos Ruan S. , Ferreira Elenilze F. B. , Leão Rozires P. , Araújo Pedro H. F. , Pita Samuel S. da R. , De Freitas Humberto F. , Espejo-Román José M. , Dos Santos Edla L. V. S. , Ramos Ryan da S. , Macêdo Williams J. C. , Santos Cleydson B. R.
Published: September 2022

Aedes aegypti mosquitoes transmit several human pathogens that cause millions of deaths worldwide, mainly in Latin America. The indiscriminate use of insecticides has resulted in the development of species resistance to some such compounds. Piperidine, a natural alkaloid isolated from Piper nigrum, has been used as a hit compound due to its larvicidal activity against Aedes aegypti. In the present study, piperidine derivatives were studied through in silico methods: pharmacophoric evaluation (PharmaGist), pharmacophoric virtual screening (Pharmit), ADME/Tox prediction (Preadmet/Derek 10.0®), docking calculations (AutoDock 4.2) and molecular dynamics (MD) simulation on GROMACS-5.1.4. MP-416 and MP-073 molecules exhibiting ΔG binding (MMPBSA −265.95 ± 1.32 kJ/mol and −124.412 ± 1.08 kJ/mol, respectively) and comparable to holo (ΔG binding = −216.21 ± 0.97) and pyriproxyfen (a well-known larvicidal, ΔG binding= −435.95 ± 2.06 kJ/mol). Considering future in vivo assays, we elaborated the theoretical synthetic route and made predictions of the synthetic accessibility (SA) (SwissADME), lipophilicity and water solubility (SwissADME) of the promising compounds identified in the present study. Our in silico results show that MP-416 and MP-073 molecules could be potent insecticides against the Aedes aegypti mosquitoes.
Biomechanical, Microstructural and Material Properties of Tendon and Bone in the Young Oim Mice Model of Osteogenesis Imperfecta
Authors: Chretien Antoine , Couchot Malory , Mabilleau Guillaume , Behets Catherine
Published: September 2022

Osteogenesis imperfecta (OI) is a genetic disorder of connective tissue characterized by low bone mass and spontaneous fractures, as well as extra-skeletal manifestations, such as dental abnormalities, blue sclera, hearing loss and joint hypermobility. Tendon ruptures have been reported in OI patients. Here, we characterized the biomechanical, structural and tissue material properties of bone and tendon in 5-week-old female osteogenesis imperfecta mice (oim), a validated model of severe type III OI, and compared these data with age- and sex-matched WT littermates. Oim tendons were less rigid and less resistant than those of WT mice. They also presented a significantly higher rate of pentosidine, without significant modification of enzymatic crosslinking. The oim bones were less resistant and avulsion fractures were evident at high tendinous stress areas. Alterations of trabecular and cortical bone microarchitectures were noticed in young female oim. Bone tissue material properties were also modified, with a less mature and more mineralized matrix in association with lower collagen maturity. Our data suggest that the tendon-to-bone unit is affected in young oim mice, which could explain tendon ruptures and bone fragility observed in OI patients.
Natural Weathering Effects on the Mechanical, Rheological, and Morphological Properties of Magnetorheological Elastomer (MRE) in Tropical Climate
Authors: Johari Mohd Aidy Faizal , Mazlan Saiful Amri , Ubaidillah Ubaidillah , Nordin Nur Azmah , Ahmad Khairi Muntaz Hana , Abdul Aziz Siti Aishah , Sedlacik Michal , Nikmat Leong Siti Asma’
Published: September 2022

Magnetorheological elastomer (MRE) materials have the potential to be used in a wide range of applications that require long-term service in hostile environments. These widespread applications will result in the emergence of MRE-specific durability issues, where durability refers to performance under in-service environmental conditions. In response, the outdoor tropical climatic environment, combined with the effects of weathering, will be the primary focus of this paper, specifically the photodegradation of the MRE. In this study, MRE made of silicone rubber (SR) and 70 wt% micron-sized carbonyl iron particles (CIP) were prepared and subjected to mechanical and rheological testing to evaluate the effects under natural weathering. Magnetorheological elastomer samples were exposed to the natural weathering conditions of a tropical climate in Kuala Lumpur, Malaysia, for 30 days. To obtain a comprehensive view of MRE degradation during natural weathering, mechanical testing, rheology, and morphological evaluation were all performed. The mechanical and rheological properties test results revealed that after 30 days of exposure and known meteorological parameters, Young’s modulus and storage modulus increased, while elongation at break decreased. The degradation processes of MRE during weathering, which are responsible for their undesirable change, were given special attention. With the help of morphological evidence, the relationship between these phenomena and the viscoelastic properties of MRE was comprehensively defined and discussed.
A Bioengineering Approach for the Development of Fibroblast Growth Factor-7-Functionalized Sericin Biomaterial Applicable for the Cultivation of Keratinocytes
Authors: Lian Ai Ai , Yamaji Yuka , Kajiwara Kazuki , Takaki Keiko , Mori Hajime , Liew Mervyn Wing On , Kotani Eiji , Maruta Rina
Published: September 2022

Growth factors, including fibroblast growth factor-7 (FGF-7), are a group of proteins that stimulate various cellular processes and are often used with carriers to prevent the rapid loss of their activities. Sericin with great biocompatibility has been investigated as a proteinaceous carrier to enhance the stability of incorporated proteins. The difficulties in obtaining intact sericin from silkworm cocoons and the handling of growth factors with poor stability necessitate an efficient technique to incorporate the protein into a sericin-based biomaterial. Here, we report the generation of a transgenic silkworm line simultaneously expressing and incorporating FGF-7 into cocoon shells containing almost exclusively sericin. Growth-factor-functionalized sericin cocoon shells requiring simple lyophilization and pulverization processes were successfully used to induce the proliferation and migration of keratinocytes. Moreover, FGF-7 incorporated into sericin-cocoon powder exhibited remarkable stability, with more than 70% of bioactivity being retained after being stored as a suspension at 25 °C for 3 months. Transgenic sericin-cocoon powder was used to continuously supply biologically active FGF-7 to generate a three-dimensionally cultured keratinocyte model in vitro. The outcomes of this study propound a feasible approach to producing cytokine-functionalized sericin materials that are ready to use for cell cultivation.
Caffeine Inhibits NLRP3 Inflammasome Activation by Downregulating TLR4/MAPK/NF-κB Signaling Pathway in an Experimental NASH Model
Authors: Vargas-Pozada Eduardo E. , Ramos-Tovar Erika , Rodriguez-Callejas Juan D. , Cardoso-Lezama Irina , Galindo-Gómez Silvia , Talamás-Lara Daniel , Vásquez-Garzón Verónica Rocío , Arellanes-Robledo Jaime , Tsutsumi Víctor , Villa-Treviño Saúl , Muriel Pablo
Published: September 2022

Caffeine elicits protective effects against liver diseases, such as NASH; however, its mechanism of action involving the pyrin domain-containing-3 (NLRP3) inflammasome signaling pathway remains to be elucidated. This study aimed to evaluate the effect of caffeine on the NLRP3 inflammasome signaling pathway in a rat model of NASH. NASH was induced by feeding rats a high-fat, -sucrose, and -cholesterol diet (HFSCD) for 15 weeks along with a weekly low dose (400 mg/kg, i.p.) of CCl4. Caffeine was administered at 50 mg/kg p.o. The effects of HFSCD+CCl4 and caffeine on the liver were evaluated using biochemical, ultrastructural, histological, and molecular biological approaches. The HFSCD+CCl4-treated rats showed fat accumulation in the liver, elevated levels of inflammatory mediators, NLRP3 inflammasome activation, antioxidant dysregulation, and liver fibrosis. Caffeine reduced necrosis, cholestasis, oxidative stress, and fibrosis. Caffeine exhibited anti-inflammatory effects by attenuating NLRP3 inflammasome activation. Moreover, caffeine prevented increases in toll-like receptor 4 (TLR4) and nuclear factor-κB (NF-κB) protein levels and mitigated the phosphorylation of mitogen-activated protein kinase (MAPK). Importantly, caffeine prevented the activation of hepatic stellate cells. This study is the first to report that caffeine ameliorates NASH by inhibiting NLRP3 inflammasome activation through the suppression of the TLR4/MAPK/NF-κB signaling pathway.
Deciphering the Regulatory Circuits of RA3 Replication Module - Mechanisms of the Copy Number Control
Authors: Markowska-Barkic Aleksandra , Lewicka Ewa , Czeredys Magdalena , Mitura Monika , Jagura-Burdzy Grazyna
Published: September 2022

The RA3 plasmid, the archetype of IncU incompatibility group, represents a mosaic-modular genome of 45.9 kb. The replication module encompasses repA and repB (initiator) surrounded by two long repetitive sequences DR1 and DR2 of unknown function. Here, we mapped the origin of replication oriV to the 3′ end of repB and showed that oriV was activated by the transcription coming from orf02revp in the adjacent stability module. Using various in vivo and in vitro methods we demonstrated that the repB expression proceeded either from repBp located in the intergenic repA-repB region or from the upstream strong repAp that was autoregulated by RepA. Additionally, the repBp activity was modulated by the transcription from the overlapping, divergently oriented repXp. Both repXmRNA (antisense for repAmRNA) and its small polypeptide product, RepX, were strong incompatibility determinants. Hence, we showed that the sophisticated RA3 copy number control combined the multivalent regulation of repB expression, RepB titration by DR1, and transcriptional activation of oriV, dependent on the RA3 global regulatory network. Similarly organized replicons have been found in diverse bacterial species confirming the significance of these mechanisms in establishing the IncU plasmids in a broad spectrum of hosts.
CCL5 Levels Predict Stroke Volume Growth in Acute Ischemic Stroke and Significantly Diminish in Hemorrhagic Stroke Patients
Authors: Julián-Villaverde Francisco José , Serrano-Ponz Marta , Ramalle-Gómara Enrique , Martínez Alfredo , Ochoa-Callejero Laura
Published: September 2022

Stroke remains an important health challenge. Here, we study whether circulating chemokine (C-C motif) ligand 5 (CCL5) levels may predict clinical outcomes for stroke patients. A total of 100 consecutive stroke patients (36 acute ischemic and 64 hemorrhagic) were admitted to the stroke unit. Clinical history data and monitoring parameters were recorded. Blood serum was collected at days 0, 1, and hospital discharge to measure CCL5 levels by ELISA. Infarct or hemorrhagic volume, neurological severity (NIHSS), and functional prognosis (mRankin scale) were measured as clinical outcomes. CCL5 levels were lower in patients with hemorrhagic stroke than in patients with acute ischemic stroke. No differences were found between females and males in both types of stroke. Ischemic stroke patients whose infarct volume grew had lower CCL5 levels at day 0. Levels of CCL5 in ischemic and hemorrhagic patients were not associated with more severe symptoms/worse prognosis (NIHSS > 3; mRankin > 2) at admission or at 3 months. CCL5 could be used as a diagnostic marker to distinguish between ischemic and hemorrhagic strokes. Furthermore, CCL5 levels could predict the infarct volume outcomes in ischemic patients.
Ectopic Expression of CsSUN in Tomato Results in Elongated Fruit Shape via Regulation of Longitudinal Cell Division
Authors: Li Hao , Han Jing , Chen Linjie , Han Ni , Hu Yajing , Ge Qian , Ren Zhonghai , Wang Lina
Published: September 2022

Fruit shape, an important agronomic trait of cucumber (Cucumis sativus L.), is tightly controlled by a series of genes such as CsSUN, a homologue of SlSUN that is responsible for the tomato (Solanum lycopersicum) fruit shape via the modulation of cell division. However, the direct genetic evidence about the CsSUN-mediated regulation of fruit shape is still scarce, limiting our mechanistic understanding of the biological functions of CsSUN. Here, we introduced CsSUN into the round-fruited tomato inbred line ‘SN1′ (wild type, WT) via the Agrobacterium tumefaciens-mediated method. The high and constitutive expression of CsSUN was revealed by real-time PCR in all the tested tissues of the transgenic plants, especially in the fruits and ovaries. Phenotypic analyses showed that the ectopic expression of CsSUN increased fruit length while it decreased fruit diameter, thus leading to the enhanced fruit shape index in the transgenic tomato lines relative to the WT. Additionally, the reduction in the seed size and seed-setting rate and the stimulation of seed germination were observed in the CsSUN-expressed tomato. A histological survey demonstrated that the elongated fruits were mainly derived from the significant increasing of the longitudinal cell number, which compensated for the negative effects of decreased cell area in the central columellae. These observations are different from action mode of SlSUN, thus shedding new insights into the SUN-mediated regulation of fruit shape.
In Vivo Two-Photon Imaging Analysis of Dynamic Degradation of Hepatic Lipid Droplets in MS-275-Treated Mouse Liver
Authors: Lee Chang-Gun , Lee Soo-Jin , Park Seokho , Choi Sung-E , Song Min-Woo , Lee Hyo Won , Kim Hae Jin , Kang Yup , Lee Kwan Woo , Kim Hwan Myung , Kwak Jong-Young , Lee In-Jeong , Jeon Ja Young
Published: September 2022

The accumulation of hepatic lipid droplets (LDs) is a hallmark of non-alcoholic fatty liver disease (NAFLD). Appropriate degradation of hepatic LDs and oxidation of complete free fatty acids (FFAs) are important for preventing the development of NAFLD. Histone deacetylase (HDAC) is involved in the impaired lipid metabolism seen in high-fat diet (HFD)-induced obese mice. Here, we evaluated the effect of MS-275, an inhibitor of HDAC1/3, on the degradation of hepatic LDs and FFA oxidation in HFD-induced NAFLD mice. To assess the dynamic degradation of hepatic LDs and FFA oxidation in fatty livers of MS-275-treated HFD C57BL/6J mice, an intravital two-photon imaging system was used and biochemical analysis was performed. The MS-275 improved hepatic metabolic alterations in HFD-induced fatty liver by increasing the dynamic degradation of hepatic LDs and the interaction between LDs and lysozyme in the fatty liver. Numerous peri-droplet mitochondria, lipolysis, and lipophagy were observed in the MS-275-treated mouse fatty liver. Biochemical analysis revealed that the lipolysis and autophagy pathways were activated in MS-275 treated mouse liver. In addition, MS-275 reduced the de novo lipogenesis, but increased the mitochondrial oxidation and the expression levels of oxidation-related genes, such as PPARa, MCAD, CPT1b, and FGF21. Taken together, these results suggest that MS-275 stimulates the degradation of hepatic LDs and mitochondrial free fatty acid oxidation, thus protecting against HFD-induced NAFLD.
Multiomics Molecular Research into the Recalcitrant and Orphan Quercus ilex Tree Species: Why, What for, and How
Authors: Maldonado-Alconada Ana María , Castillejo María Ángeles , Rey María-Dolores , Labella-Ortega Mónica , Tienda-Parrilla Marta , Hernández-Lao Tamara , Honrubia-Gómez Irene , Ramírez-García Javier , Guerrero-Sanchez Víctor M. , López-Hidalgo Cristina , Valledor Luis , Navarro-Cerrillo Rafael M. , Jorrin-Novo Jesús V.
Published: September 2022

The holm oak (Quercus ilex L.) is the dominant tree species of the Mediterranean forest and the Spanish agrosilvopastoral ecosystem, “dehesa.” It has been, since the prehistoric period, an important part of the Iberian population from a social, cultural, and religious point of view, providing an ample variety of goods and services, and forming the basis of the economy in rural areas. Currently, there is renewed interest in its use for dietary diversification and sustainable food production. It is part of cultural richness, both economically (tangible) and environmentally (intangible), and must be preserved for future generations. However, a worrisome degradation of the species and associated ecosystems is occurring, observed in an increase in tree decline and mortality, which requires urgent action. Breeding programs based on the selection of elite genotypes by molecular markers is the only plausible biotechnological approach. To this end, the authors’ group started, in 2004, a research line aimed at characterizing the molecular biology of Q. ilex. It has been a challenging task due to its biological characteristics (long life cycle, allogamous, high phenotypic variability) and recalcitrant nature. The biology of this species has been characterized following the central dogma of molecular biology using the omics cascade. Molecular responses to biotic and abiotic stresses, as well as seed maturation and germination, are the two main objectives of our research. The contributions of the group to the knowledge of the species at the level of DNA-based markers, genomics, epigenomics, transcriptomics, proteomics, and metabolomics are discussed here. Moreover, data are compared with those reported for Quercus spp. All omics data generated, and the genome of Q. ilex available, will be integrated with morphological and physiological data in the systems biology direction. Thus, we will propose possible molecular markers related to resilient and productive genotypes to be used in reforestation programs. In addition, possible markers related to the nutritional value of acorn and derivate products, as well as bioactive compounds (peptides and phenolics) and allergens, will be suggested. Subsequently, the selected molecular markers will be validated by both genome-wide association and functional genomic analyses.
NAD/NAMPT and mTOR Pathways in Melanoma: Drivers of Drug Resistance and Prospective Therapeutic Targets
Authors: Indini Alice , Fiorilla Irene , Ponzone Luca , Calautti Enzo , Audrito Valentina
Published: September 2022

Malignant melanoma represents the most fatal skin cancer due to its aggressive behavior and high metastatic potential. The introduction of BRAF/MEK inhibitors and immune-checkpoint inhibitors (ICIs) in the clinic has dramatically improved patient survival over the last decade. However, many patients either display primary (i.e., innate) or develop secondary (i.e., acquired) resistance to systemic treatments. Therapeutic resistance relies on the rewiring of multiple processes, including cancer metabolism, epigenetics, gene expression, and interactions with the tumor microenvironment that are only partially understood. Therefore, reliable biomarkers of resistance or response, capable of facilitating the choice of the best treatment option for each patient, are currently missing. Recently, activation of nicotinamide adenine dinucleotide (NAD) metabolism and, in particular, of its rate-limiting enzyme nicotinamide phosphoribosyltransferase (NAMPT) have been identified as key drivers of targeted therapy resistance and melanoma progression. Another major player in this context is the mammalian target of rapamycin (mTOR) pathway, which plays key roles in the regulation of melanoma cell anabolic functions and energy metabolism at the switch between sensitivity and resistance to targeted therapy. In this review, we summarize known resistance mechanisms to ICIs and targeted therapy, focusing on metabolic adaptation as one main mechanism of drug resistance. In particular, we highlight the roles of NAD/NAMPT and mTOR signaling axes in this context and overview data in support of their inhibition as a promising strategy to overcome treatment resistance.
Engineering Bio-Adhesives Based on Protein–Polysaccharide Phase Separation
Authors: Bashir Zoobia , Yu Wenting , Xu Zhengyu , Li Yiran , Lai Jiancheng , Li Ying , Cao Yi , Xue Bin
Published: September 2022

Glue-type bio-adhesives are in high demand for many applications, including hemostasis, wound closure, and integration of bioelectronic devices, due to their injectable ability and in situ adhesion. However, most glue-type bio-adhesives cannot be used for short-term tissue adhesion due to their weak instant cohesion. Here, we show a novel glue-type bio-adhesive based on the phase separation of proteins and polysaccharides by functionalizing polysaccharides with dopa. The bio-adhesive exhibits increased adhesion performance and enhanced phase separation behaviors. Because of the cohesion from phase separation and adhesion from dopa, the bio-adhesive shows excellent instant and long-term adhesion performance for both organic and inorganic substrates. The long-term adhesion strength of the bio-glue on wet tissues reached 1.48 MPa (shear strength), while the interfacial toughness reached ~880 J m−2. Due to the unique phase separation behaviors, the bio-glue can even work normally in aqueous environments. At last, the feasibility of this glue-type bio-adhesive in the adhesion of various visceral tissues in vitro was demonstrated to have excellent biocompatibility. Given the convenience of application, biocompatibility, and robust bio-adhesion, we anticipate the bio-glue may find broad biomedical and clinical applications.
HOX-Gene Cluster Organization and Genome Duplications in Fishes and Mammals: Transcript Variant Distribution along the Anterior–Posterior Axis
Authors: Ozernyuk Nikolay , Schepetov Dimitry
Published: September 2022

Hox genes play a crucial role in morphogenesis, especially in anterior–posterior body axis patterning. The organization of Hox clusters in vertebrates is a result of several genome duplications: two rounds of duplication in the ancestors of all vertebrates and a third round that was specific for teleost fishes. Teleostei cluster structure has been significantly modified in the evolutionary processes by Hox gene losses and co-options, while mammals show no such tendency. In mammals, the Hox gene number in a single cluster is stable and generally large, and the numbers are similar to those in the Chondrichthyes. Hox gene alternative splicing activity slightly differs between fishes and mammals. Fishes and mammals have differences in their known alternative splicing activity for Hox gene distribution along the anterior–posterior body axis. The analyzed fish groups—the Coelacanthiformes, Chondrichthyes, and Teleostei—all have higher known alternative mRNA numbers from the anterior and posterior regions, whereas mammals have a more uniform Hox transcript distribution along this axis. In fishes, most Hox transcripts produce functioning proteins, whereas mammals have significantly more known transcripts that do not produce functioning proteins.
Pathomorphogenesis of Glycogen-Ground Glass Hepatocytic Inclusions (Polyglucosan Bodies) in Children after Liver Transplantation
Authors: Callea Francesco , Francalanci Paola , Grimaldi Chiara , Camassei Francesca Diomedi , Devito Rita , Facchetti Fabio , Alaggio Rita , Bellacchio Emanuele
Published: September 2022

Seventeen out of 764 liver biopsies from transplanted (Tx) livers in children showed glycogen-ground glass (GGG) hepatocytic inclusions. The inclusions were not present in pre-Tx or in the explanted or donor’s liver. Under the electron microscope (EM), the stored material within the cytosol appeared as non-membrane-bound aggregates of electron-lucent globoid or fibrillar granules, previously described as abnormally structured glycogen and identified as Polyglucosan bodies (PB). The appearance of GGG in our children was analogous to that of PB-GGG occurring in a number of congenital diseases due to gene mutations such as Lafora’s d., Andersen’s d., Adult Polyglucosan Body Disease and glycogenin deficiency. The same type of GGG was previously reported in the liver of patients undergoing transplants, immunosuppressive or antiblastic treatment. To explore the potential mechanism of GGG formation, we examined whether the drugs after whose treatment this phenomenon was observed could have a role. By carrying out molecular docking, we found that such drugs somehow present a high binding affinity for the active region of glycogenin, implicating that they can inactivate the protein, thus preventing its interaction with glycogen synthase (GS), as well as the maturation of the nascent glycogen towards gamma, beta or alfa glycogen granules. We could also demonstrate that PG inclusions consist of a complex of PAS positive material (glycogen) and glycogen-associated proteins, i.e., glicogenin-1 and -2 and ubiquitin. These features appear to be analogous to congenital GGG, suggesting that, in both cases, they result from the simultaneous dysregulation of glycogen synthesis and degradation. Drug-induced GGG appear to be toxic to the cell, despite their reversibility.
Information Adoption Patterns and Online Knowledge Payment Behavior: The Moderating Role of Product Type
Authors: Daradkeh Mohammad , Gawanmeh Amjad , Mansoor Wathiq
Published: September 2022

The development of online knowledge payment platforms in recent years has increased their respective market value by nurturing content resources and improving content ecology. Yet, the underlying factors of knowledge seekers’ payment behaviors and their information adoption mechanisms are poorly understood. Based on the information adoption model, this study develops a research model to examine the relationship between information adoption patterns and knowledge seekers’ payment behavior, and explore the moderating effect of product type on this relationship. To test the research model and hypotheses, we used a multi-analytic approach combining text and regression analysis on a sample of 4366 social Q&A data collected from Quora+ between August 2021 and August 2022. We further classified the product types into utilitarian and hedonic, and compared the differences in influence paths between product types. The results show that the completeness, vividness, and relevance of the product description have a significant positive impact on knowledge payment behavior. The reputation, experience, and integrity of the knowledge provider have a positive impact on knowledge payment behavior. Compared to utilitarian knowledge products, the payment behavior for hedonic products is more related to the reputation and experience of the knowledge provider. This study provides insights into the factors that influence online knowledge payment behavior and practical guidance for the development of online knowledge payment services and platforms.
First Level Pre- and Post-Earthquake Building Seismic Assessment Protocol Based on Dynamic Characteristics Extracted In Situ
Authors: Damikoukas Spyros , Chatzieleftheriou Stavros , Lagaros Nikos D.
Published: September 2022

The present work is concerned with the introduction of a new first level pre- and post-earthquake seismic assessment protocol for buildings that relies on the use of recorded structural response. As earthquakes represent a constant and unpredictable threat for the building stock around the globe, the protocols already in use for assessing the risk should be revised and should also take into account the information hidden in data recorded in the field. Nowadays, data collection does not require expensive equipment and over-qualified personnel. In this direction, the proposed seismic assessment protocol aims to illustrate the ease of widely adopting Structural Health Monitoring (SHM) equipment (e.g., accelerographs), based on the work that has been carried out over the past years on subjects related to earthquake risk estimation. Building taxonomy and damage estimation, like those found in Hazus®–MH and other hazard assessment tools, can be enriched and modified properly to distinguish and classify the very earthquake-prone buildings from the others, and tag them for further assessment and rehabilitation as seismic codes suggest.
Facile Construction of Bi2Sn2O7/g-C3N4 Heterojunction with Enhanced Photocatalytic Degradation of Norfloxacin
Authors: Zhu Zhengru , Xia Haiwen , Li Hong , Han Songlin
Published: September 2022

To mitigate antibiotic residues in the water environment, Bi2Sn2O7/g-C3N4 (BSCN) heterojunction was fabricated by a facile ultrasound-assisted hydrothermal method. The microstructure, morphology, and optical properties of Bi2Sn2O7/g-C3N4 heterojunction was studied by XRD, FTIR, XPS, SEM, TEM, UV–Vis DRS, and PL. The degradation rate of 20 mg/L norfloxacin (NOR) under visible light for 3 h was adopted as one of the indexes to evaluate the photocatalytic performance of Bi2Sn2O7/g-C3N4 heterojunction. Embellished with 20% Bi2Sn2O7 (BSO), the Bi2Sn2O7/g-C3N4 heterojunction decomposed 94% NOR in the experimental solution, which was 2.35 and 3.03 times as much as pristine g-C3N4 and bare Bi2Sn2O7, respectively. In addition, the Bi2Sn2O7/g-C3N4 heterojunction still eliminated 89% of NOR after five cycles, portending outstanding stability and cyclability of photocatalytic activity. A possible photocatalytic mechanism of Bi2Sn2O7/g-C3N4 heterojunction for NOR degradation is proposed.
Genetic Structure and Colonization of North America by Depressaria depressana (Fabricius 1775) (Lepidoptera: Depressariidae) over 15 Years; Contrasts with Westward Expansion of Depressaria radiella (Goeze, 1783) over 160 Years
Authors: Dean Charles A. E. , Easley Jack , Katz Aron D. , Berlocher Stewart H. , Berenbaum May R.
Published: September 2022

Depressaria depressana, the purple carrot seed moth, is a Eurasian species first reported in North America in 2008 and currently undergoing range expansion. This invasion follows that of its Eurasion congener Depressaria radiella (parsnip webworm), first documented in North America 160 years ago. Unlike D. depressana, which utilizes hostplants across multiple tribes of Apiaceae, Depressaria radiella is a “superspecialist” effectively restricted in its native and non-indigenous ranges to two closely related apiaceous genera. We investigated the genetic structure of D. depressana populations across latitudinal and longitudinal gradients in the eastern United States by constructing COI haplotype networks and then comparing these with haplotype networks constructed from available COI sequence data from contemporary European D. depressana populations and from European and North American D. radiella populations. Haplotype data revealed higher genetic diversity in D. depressana, indicating high dispersal capacity, multiple introductions, and/or a genetically diverse founding population. Museum and literature records of D. radiella date back to 1862 and indicate that range expansion to the West Coast required more than 50 years. Higher levels of genetic diversity observed in D. depressana compared to its congener may indicate a greater propensity for dispersal, colonization and establishment in its non-indigenous range.
Competitive Plant-Mediated and Intraguild Predation Interactions of the Invasive Spodoptera frugiperda and Resident Stemborers Busseola fusca and Chilo partellus in Maize Cropping Systems in Kenya
Authors: Mutua Johnstone Mutiso , Mutyambai Daniel Munyao , Asudi George Ochieng’ , Khamis Fathiya , Niassy Saliou , Jalloh Abdul A. , Salifu Daisy , Magara Henlay J. O. , Calatayud Paul-André , Subramanian Sevgan
Published: September 2022

Following its recent invasion of African countries, fall armyworm (FAW), Spodoptera frugiperda (Lepidoptera: Noctuidae), now co-exists with resident stemborers such as Busseola fusca (Lepidoptera: Noctuidae) and Chilo partellus (Lepidoptera: Crambidae) causing severe damage to maize crops. Due to niche overlap, interspecific interactions occur among the three species, but the mechanisms and degree remain unclear. In this study, we assessed plant-mediated intraspecific and interspecific interactions, predation in laboratory and semi-field settings, and larval field occurrence of S. frugiperda and the two stemborer species. Larval feeding assays to evaluate competitive plant-mediated interactions demonstrated that initial S. frugiperda feeding negatively affected subsequent stemborer larval feeding and survival, suggesting induction of herbivore-induced mechanisms by S. frugiperda, which deters establishment and survival of competing species. Predation assays showed that, at different developmental larval stages, second–sixth instars of S. frugiperda preyed on larvae of both B. fusca and C. partellus. Predation rates of S. frugiperda on stemborers was significantly higher than cannibalism of S. frugiperda and its conspecifics (p < 0.001). Cannibalism of S. frugiperda in the presence of stemborers was significantly lower than in the presence of conspecifics (p = 0.04). Field surveys showed a significantly higher number of S. frugiperda larvae than stemborers across three altitudinally different agroecological zones (p < 0.001). In conclusion, this study showed that the invasive S. frugiperda exhibited a clear competitive advantage over resident stemborers within maize cropping systems in Kenya. Our findings reveal some of the possible mechanisms employed by S. frugiperda to outcompete resident stemborers and provide crucial information for developing pest management strategies for these lepidopteran pests.
Turnip Mosaic Virus Infection Differentially Modifies Cabbage Aphid Probing Behavior in Spring and Winter Oilseed Rape (Brassica napus)
Authors: Hao Zhong-Ping , Sheng Lei , Feng Zeng-Bei , Fei Wei-Xin , Hou Shu-Min
Published: September 2022

Direct and indirect effects of plant virus infection on vector behavior have been discovered to improve virus transmission efficiency, but the impact of plant cultivars in virus–vector–plant interactions has received little attention. Electropenetrography (EPG) allows real-time tracking and quantification of stylet penetration behaviors, pathogen transmission, and plant resistance mechanisms. Quantitative probing behaviors on a spring oilseed rape cultivar, ‘Xinyou17’, and a winter oilseed rape cultivar, ‘Zheping4’, were investigated using EPG to compare turnip mosaic virus (TuMV) regulation of cabbage aphid probing behavior. Results for indirect effects showed that compared to mock-inoculated plants, cabbage aphids on infected plants increased brief probing frequency, cell penetration frequency, intracellular probing time, and decreased time to first probe and pathway time, potentially promoting viral acquisition. TuMV also directly influences aphid probing behavior. Viruliferous aphids had reduced pathway time, increased cell penetration frequency, increased intracellular probing time, increased salivation frequency, and ingested less sap than non-viruliferous aphids, primed for viral infection. Although oilseed rape cultivars can also influence aphid behavior, the main effect of cultivars was not significant on TuMV-infected plants.
Aedes Mosquito Surveillance Using Ovitraps, Sweep Nets, and Biogent Traps in the City of Yaoundé, Cameroon
Authors: Djiappi-Tchamen Borel , Nana-Ndjangwo Mariette Stella , Nchoutpouen Elysée , Makoudjou Idene , Ngangue-Siewe Idriss Nasser , Talipouo Abdou , Mayi Marie Paul Audrey , Awono-Ambene Parfait , Wondji Charles , Tchuinkam Timoléon , Antonio-Nkondjio Christophe
Published: September 2022

Arbovirus diseases represent a significant public health problem in Cameroon and vector surveillance is a key component of prevention strategies. However, there is still not enough evidence of the efficacy of different sampling methods used to monitor Aedes mosquito population dynamic in different epidemiological settings. The present study provides data on the evaluation of ovitraps and different adult sampling methods in the city of Yaoundé and its close vicinity. Entomological surveys were carried out from February 2020 to March 2021 in two urban (Obili, Mvan), two peri-urban (Simbock, Ahala), and two rural (Lendom, Elig-essomballa) sites in the city of Yaoundé. The efficacy of three sampling methods, namely ovitraps, Biogent Sentinel trap, and sweep nets, was evaluated. Different ovitrap indices were used to assess the infestation levels across study sites; a general linear model was used to determine if there are statistical differences between positive ovitraps across ecological zones. A total of 16,264 Aedes mosquitoes were collected during entomological surveys. Ovitraps provided the highest mosquito abundance (15,323; 91.14%) and the highest species diversity. Of the five Aedes species collected, Aedes albopictus (59.74%) was the most commonly recorded in both urban and rural settings. Different Aedes species were collected in the same ovitrap. The ovitrap positivity index was high in all sites and varied from 58.3% in Obili in the urban area to 86.08% in Lendom in the rural area. The egg density index varied from 6.42 in Mvan (urban site) to 13.70 in Lendom (rural area). Adult sampling methods recorded mostly Aedes albopictus. The present study supports high infestation of Aedes species in the city of Yaoundé. Ovitraps were highly efficient in detecting Aedes distribution across study sites. The situation calls for regular surveillance and control of Aedes population to prevent sudden occurrence of outbreaks.