bluuebunny/crossref_metadata_2025 huggingface dataset:
Full-Length Transcriptome Sequencing and Identification of Genes Related to Terpenoid Biosynthesis in Cinnamomum migao H. W. Li
Authors: Ju Zhigang , Gong Qiuling , Liang Lin , Kong Dejing , Zhou Tao , Sun Wei , Pang Yuxin , Zhang Yongping
Published: October 2023

Cinnamomum migao H. W. Li is an evergreen woody plant that is only distributed in southwest China. The volatile oils from the fruits of C. migao have long been used as a special authentic medicinal herb by local ethnic minorities. Due to its low seed germination rate, destructive lumbering and low rates of artificial planting, C. migao is facing the danger of extinction. Therefore, it is urgent to exploit and protect this species using molecular biological technology, especially to target the genes involved in the biosynthesis of terpenoids in the volatile oil. However, the genomic data for this plant are not available. In this study, the transcriptome sequencing of C. migao was performed to obtain the key genes involved in terpenoid biosynthesis via a combination of full-length transcriptome and next-generation sequencing (NGS). More than 39.9 Gb of raw data was obtained and 515,929 circular consensus sequences (CCSs) were extracted. After clustering similar 472,858 full-length non-chimeric (FLNC) reads and correction with NGS data, 139,871 consensus isoforms were obtained. Meanwhile, 73,575 non-redundant transcripts were generated by removing redundant transcripts. Then, 70,427 isoforms were successfully annotated using public databases. Moreover, differentially expressed transcripts (DETs) in four different developmental stages of the C. migao fruit were analyzed and 5764 transcripts showed period-specific expression. Finally, 15 transcripts, 6 transcripts, and only 1 transcript were identified as being involved in the biosynthesis of sesquiterpenoids, diterpenoids, and monoterpenoids, respectively. This study provides a basis for future research in the gene mining, genetic breeding, and metabolic engineering of C. migao.
Fungi Inhabiting Stem Wounds of Quercus robur following Bark Stripping by Deer Animals
Authors: Marčiulynas Adas , Sirgedaitė-Šėžienė Vaida , Menkis Audrius
Published: October 2023

We investigated fungal communities in oak wounds to determine how fungal species richness and community composition changes depending on the age of wounds. The sampling of wood cores was carried out from 10-, 20-, 30-, 40-, and 50-year-old wounds. The fungal community was analyzed using high-throughput sequencing of ITS2 rDNA. Sequence analysis showed the presence of 534 fungal OTUs, which were 83.4% Ascomycota, 16.3% Basidiomycota, and 0.3% Mucoromycota. The fungal OTU richness changed over time: it increased as compared between 10- and 20-year-old wounds, remained similar in 20- to 40-year-old wounds, and decreased in 50-year-old wounds. The fungal community composition also changed over time with the largest differences detected between 10-year-old and older wounds (p < 0.001). The most common representatives of Basidiomycota were Laetiporus sulphureus (34.7%), Mycena galericulata (17.0%), and Cylindrobasidium evolvens (6.5%), and the most common of Ascomycota were Aposphaeria corallinolutea (13.6%), Sclerostagonospora cycadis (7.6%), and Cadophora malorum (5.8%). In conclusion, oak wounds of different ages were colonized by a high diversity of fungi including oak-associated species. Fungal communities in oak wounds underwent qualitative and quantitative changes over time, which led to the gradual shift from fungal generalists in young wounds to oak specialists in older wounds.
Effects of Truffle Inoculation on Root Physiology and Mycorrhizosphere Microbial Communities of Carya illinoinensis Seedlings
Authors: Chen Haoyu , Wu Jiawei , Liu Junping , Tan Pengpeng , Zhu Kaikai , Peng Fangren
Published: October 2023

Although they are a valuable edible ectomycorrhizal fungus, truffles (Tuber spp.) nevertheless face significant difficulties in the development of their scale. As a type of high economic value nut-like economic forest tree, the pecan (Carya illinoinensis) serves as a natural host for truffles. However, the technology for mycorrhizal synthesis in pecan has not yet been developed, and it is still unclear how certain microbes affect this process. In this study, we inoculated the pecan root system with a suspension of truffle spores and investigated the growth physiology of pecan seedlings with various infestation levels, as well as changes in the soil’s physicochemical properties and the makeup of the microbial community at the root level. The findings showed that tuber inoculation significantly increased the peroxidase activity of the pecan root system, significantly decreased the pH, and effective phosphorus content of mycorrhizosphere soil, while increasing the nitrate nitrogen content, and significantly increased the abundance and diversity of the mycorrhizosphere soil fungal community. Different groups of fungal and bacterial markers were formed in the mycorrhizosphere of pecan seedlings at different levels of infestation. In the highly infested group, Rozellomycota and lasiosphaeriaceae were the difference marker fungi, and Xanthobacteraceae, Rhizobiaceae as well as Streptococcaceae were the difference marker bacteria. In the low-infestation group, sphaerosporella was differential marker fungi, and Bacillus and Tumebacillus were differential marker bacteria. The fungal marker flora of the control group consisted of Chaetomium and Gilmaniella. Pseudomonas was the marker bacterial community. Additionally, these fungi included Collarina and Rozellomycota, and several bacteria from the genera Pseudomonas, Gemmatimonas, and others showed highly significant relationships with changes in soil pH, effective phosphorus, and nitrate nitrogen. In conclusion, pecan–truffle mycorrhizal seedlings have the potential to create the ideal microbial community structure needed for mycorrhizal growth, and these microorganisms have the potential to significantly alter the pH, effective phosphorus content, and nitrate nitrogen concentration of the mycorrhizosphere soil. Our results contribute to the understanding of how the mycorrhizosphere microbial community evolves when exogenous mycorrhizal fungi infest host plants and can offer some theoretical guidelines for growing pecan–truffle mycorrhizal seedlings.
The Analysis of Residents’ Intention to Consume Pre-Made Dishes in China: A Grounded Theory
Authors: Xiong Yanling , Lin Xiaoxi , Wen Xiaowei , Wang Yiqin , Liang Wenwen , Xing Tianyang
Published: October 2023

The demand for pre-made dishes has increased in China. However, a detailed understanding of residents’ intention to consume pre-made dishes is lacking in the existing studies. This research aims to investigate the consumer motives and intention to consume pre-made dishes. Through in-depth interviews and analysis, this research explores the factors influencing the residents’ intention along the research steps of grounded theory. Fifty-one residents participated in semi-structured interviews via face-to-face or online interviews. Three motives for purchasing pre-made dishes were attitude, subjective norm, and perceived control. These were influenced by external factors, including environmental features and product features. Subjective characteristics are pre-existing characteristics of individuals themselves, including cooking skills, food skills, housework allocation, and eating attitudes, which play a moderating role in the relationship between external factors and consumer motives. Based on the six major categories, this study built a model of the formation mechanism of the consumer intention to consume pre-made dishes. It revealed the psychological attribution of residents’ consumption of pre-made dishes. The finding of this study contributes to the understanding of the internal logic of PMDs’ consumer intention formation. It would be a guide for researchers to map out appropriate business development strategies, and provide evidence for the government in formulating management policies.
Inhibition of IEC-6 Cell Proliferation and the Mechanism of Ulcerative Colitis in C57BL/6 Mice by Dandelion Root Polysaccharides
Authors: Yan Shengkun , Yin Lijun , Dong Rong
Published: October 2023

An exploration was conducted on the potential therapeutic properties of dandelion polysaccharide (DP) in addressing 3% dextran sodium sulfate (DSS)-induced ulcerative colitis (UC) in murine models. Subsequent assessments focused on DP’s influence on inflammation, oxidative stress, and ferroptosis in IEC-6 cells damaged by H2O2. Results highlighted the efficacy of DP in mitigating weight loss, improving disease activity index scores, normalizing colon length, and alleviating histological abnormalities in the affected mice. DP repaired colonic mitochondrial damage by enhancing iron transport and inhibited iron death in colonic cells. Moreover, DP played a pivotal role in enhancing the antioxidant potential. This was evident from the increased expression levels of Nrf2, HO-1, NQO-1, and GSH, coupled with a decrease in MDA and 4-HNE markers in the UC-afflicted mice. Concurrently, DP manifested inhibitory effects on MPO activation and transcription levels of inflammatory mediators such as IL-1β, IL-6, TNF-α, and iNOS. An upsurge in the expression of occludin and ZO-1 was also observed. Restoration of intestinal tightness resulted in decreased serum LPS and LDH levels. Thereafter, administration of DP by gavage increased fecal flora diversity and relative abundance of probiotics in UC mice. Analysis of metabolites indicated that DP counteracted metabolic disturbances and augmented the levels of short-chain fatty acids in ulcerative colitis-affected mice. In vitro studies underscored the role of DP in triggering Nrf2 activation, which in turn exhibited anti-inflammatory, antioxidant, and anti-ferroptotic properties. Summarily, DP’s capacity to activate Nrf2 contributes to the suppression of ferroptotic processes in intestinal epithelial cells of UC-affected mice, enhancing the intestinal barrier’s integrity. Beyond that, DP possesses the ability to modulate the gut microbiome, rectify metabolic imbalances, rejuvenate short-chain fatty acid levels, and bolster the intestinal barrier as a therapeutic approach to UC.
Consumers’ Segmentation Influences Acceptance and Preferences of Cheeses with Sanitary Inspection and Artisanal Seals
Authors: Pereira Larissa Santos , de Moraes Bruna Klein Borges , Borba Elizandro Max , Roldan Bruna Bresolin , Padilha Rosiele Lappe , Sant’Anna Voltaire
Published: October 2023

Food labeling serves as a crucial medium for industries to communicate product qualities to consumers. Sanitary inspection and artisanal seals are significant markers for traditional cheeses, yet current information on this topic is limited. Therefore, this study aims to evaluate the impact of sanitary inspection and the ARTE seal on the acceptance of artisanal cheese. To achieve this objective, four hypothetical cheese labels featuring all combinations of sanitary inspection and ARTE seals were presented to 404 consumers. These consumers rated their acceptance of each label, a conjoint analysis was conducted, and the relative importance of each seal was calculated. Subsequently, consumers were segmented using hierarchical cluster analysis. Their socio-demographic profiles were statistically correlated to the clusters through a chi-squared method. The results revealed the existence of three distinct consumer groups: those who strongly prefer cheeses with a sanitary seal (assigning a relative importance of 80.2% to the seal), those who favor cheeses with an artisanal seal (assigning a relative importance of 52.5% to the seal), and those for whom the presence of either seal did not significantly affect acceptance. Consumers residing in metropolitan areas generally placed less value on both seals, whereas frequent purchasers of artisanal foods and residents of rural areas showed a preference for the artisanal seal. Other socio-demographic variables did not statistically correlate with cluster membership. In conclusion, consumer segmentation based on preferences for sanitary inspection and artisanal seals in food labeling is vital for developing effective marketing strategies and food safety education policies.
Effect of Ultrasound and High Hydrostatic Pressure Processing on Quality and Bioactive Compounds during the Shelf Life of a Broccoli and Carrot By-Products Beverage
Authors: Pérez Pablo , Hashemi Seyedehzeinab , Cano-Lamadrid Marina , Martínez-Zamora Lorena , Gómez Perla A. , Artés-Hernández Francisco
Published: October 2023

Vegetable beverages are a convenient strategy to enhance the consumption of horticultural commodities, with the possibility of being fortified with plant by-products to increase functional quality. The main objective was to develop a new veggie beverage from broccoli stalks and carrot by-products seasoned with natural antioxidants and antimicrobial ingredients. Pasteurization, Ultrasound (US), and High Hydrostatic Pressure (HHP) and their combinations were used as processing treatments, while no treatment was used as a control (CTRL). A shelf-life study of 28 days at 4 °C was assayed. Microbial load, antioxidant capacity, and bioactive compounds were periodically measured. Non-thermal treatments have successfully preserved antioxidants (~6 mg/L ΣCarotenoids) and sulfur compounds (~1.25 g/L ΣGlucosinolates and ~5.5 mg/L sulforaphane) throughout the refrigerated storage, with a longer shelf life compared to a pasteurized beverage. Total vial count was reduced by 1.5–2 log CFU/mL at day 0 and by 6 log CFU/mL at the end of the storage in HHP treatments. Thus, the product developed in this study could help increase the daily intake of glucosinolates and carotenoids. These beverages can be a good strategy to revitalize broccoli and carrot by-products with high nutritional potential while maintaining a pleasant sensory perception for the final consumer.
The Iterative Properties for Positive Solutions of a Tempered Fractional Equation
Authors: Zhang Xinguang , Chen Peng , Tian Hui , Wu Yonghong
Published: October 2023

In this article, we investigate the iterative properties of positive solutions for a tempered fractional equation under the case where the boundary conditions and nonlinearity all involve tempered fractional derivatives of unknown functions. By weakening a basic growth condition, some new and complete results on the iterative properties of the positive solutions to the equation are established, which include the uniqueness and existence of positive solutions, the iterative sequence converging to the unique solution, the error estimate of the solution and convergence rate as well as the asymptotic behavior of the solution. In particular, the iterative process is easy to implement as it can start from a known initial value function.
Numerical Solution of Advection–Diffusion Equation of Fractional Order Using Chebyshev Collocation Method
Authors: Ali Shah Farman , Kamran  , Boulila Wadii , Koubaa Anis , Mlaiki Nabil
Published: October 2023

This work presents a highly accurate method for the numerical solution of the advection–diffusion equation of fractional order. In our proposed method, we apply the Laplace transform to handle the time-fractional derivative and utilize the Chebyshev spectral collocation method for spatial discretization. The primary motivation for using the Laplace transform is its ability to avoid the classical time-stepping scheme and overcome the adverse effects of time steps on numerical accuracy and stability. Our method comprises three primary steps: (i) reducing the time-dependent equation to a time-independent equation via the Laplace transform, (ii) employing the Chebyshev spectral collocation method to approximate the solution of the transformed equation, and (iii) numerically inverting the Laplace transform. We discuss the convergence and stability of the method and assess its accuracy and efficiency by solving various problems in two dimensions.
The Müntz–Legendre Wavelet Collocation Method for Solving Weakly Singular Integro-Differential Equations with Fractional Derivatives
Authors: Bin Jebreen Haifa
Published: October 2023

We offer a wavelet collocation method for solving the weakly singular integro-differential equations with fractional derivatives (WSIDE). Our approach is based on the reduction of the desired equation to the corresponding Volterra integral equation. The Müntz–Legendre (ML) wavelet is introduced, and a fractional integration operational matrix is constructed for it. The obtained integral equation is reduced to a system of nonlinear algebraic equations using the collocation method and the operational matrix of fractional integration. The presented method’s error bound is investigated, and some numerical simulations demonstrate the efficiency and accuracy of the method. According to the obtained results, the presented method solves this type of equation well and gives significant results.
Analysis of the Corneal Geometry of the Human Eye with an Artificial Neural Network
Authors: Waseem  , Ullah Asad , Awwad Fuad A. , Ismail Emad A. A.
Published: October 2023

In this paper, a hybrid cuckoo search technique is combined with a single-layer neural network (BHCS-ANN) to approximate the solution to a differential equation describing the curvature shape of the cornea of the human eye. The proposed problem is transformed into an optimization problem such that the L2–error remains minimal. A single hidden layer is chosen to reduce the sink of the local minimum values. The weights in the neural network are trained with a hybrid cuckoo search algorithm to refine them so that we obtain a better approximate solution for the given problem. To show the efficacy of our method, we considered six different corneal models. For validation, the solution with Adam’s method is taken as a reference solution. The results are presented in the form of figures and tables. The obtained results are compared with the fractional order Darwinian particle swarm optimization (FO-DPSO). We determined that results obtained with BHCS-ANN outperformed the ones acquired with other numerical routines. Our findings suggest that BHCS-ANN is a better methodology for solving real-world problems.
Identification of the RPGR Gene Pathogenic Variants in a Cohort of Polish Male Patients with Retinitis Pigmentosa Phenotype
Authors: Nowomiejska Katarzyna , Baltaziak Katarzyna , Całka Paulina , Ciesielka Marzanna , Teresiński Grzegorz , Rejdak Robert
Published: October 2023

The goal of the study was to explore the spectrum of pathogenic variants in the RPGR gene in a group of male Polish patients with a retinitis pigmentosa (RP) phenotype. A total of 45 male index patients, including twins, being members of 44 families, were screened for pathogenic variants in the RPGR gene via the direct sequencing of PCR-amplified genomic DNA and underwent a comprehensive ophthalmological examination in one center located in Poland. A total of two pathogenic and five likely pathogenic variants in eight patients (18%) were detected in the studied cohort. Of these, five variants were novel, and five disease-causing variants (71%) were identified within the ORF15 mutational hotspot of the RPGR gene. The median age of onset of the disease was 10 years (range 6–14 years), the median age during the examination was 30 years (range 20–47 years), and the median visual acuity was 0.4 (range 0.01–0.7). The majority of patients had middle constriction of the visual field and thinning of the central foveal thickness. Dizygotic twins bearing the same hemizygous mutation showed a different retinal phenotype in regard to the severity of the symptoms. This is the first RPGR mutation screening in Poland showing a prevalence of 18% of RPGR pathogenic mutations and likely pathogenic variants in the studied cohort of male patients with an RP phenotype.
The Role of miRNA Expression Profile in Sudden Cardiac Death Cases
Authors: Bernini Di Michele Alessia , Onofri Valerio , Pesaresi Mauro , Turchi Chiara
Published: October 2023

Sudden cardiac death (SCD) is one of the leading causes of death in the world and for this reason it has attracted the attention of numerous researchers in the field of legal medicine. It is not easy to determine the cause in a SCD case and the available methods used for diagnosis cannot always give an exhaustive answer. In addition, the molecular analysis of genes does not lead to a clear conclusion, but it could be interesting to focus attention on the expression level of miRNAs, a class of non-coding RNA of about 22 nucleotides. The role of miRNAs is to regulate the gene expression through complementary binding to 3′-untraslated regions of miRNAs, leading to the inhibition of translation or to mRNA degradation. In recent years, several studies were performed with the aim of exploring the use of these molecules as biomarkers for SCD cases, and to also distinguish the causes that lead to cardiac death. In this review, we summarize experiments, evidence, and results of different studies on the implication of miRNAs in SCD cases. We discuss the different biological starting materials with their respective advantages and disadvantages, studying miRNA expression on tissue (fresh-frozen tissue and FFPE tissue), circulating cell-free miRNAs in blood of patients affected by cardiac disease at high risk of SCD, and exosomal miRNAs analyzed from serum of people who died from SCD.
Public Awareness Regarding Corticosteroid Use and Side Effects: A Cross-Sectional Study in Riyadh, Saudi Arabia
Authors: Qutob Rayan Abubakker , Alhusaini Bassam Abdulaziz , Aljarba Najd Khalid , Alzaid Omar Nasser , Aljahili Nawaf Abdulaziz , Alzahrani Khalid Saad , Sharaf Mohammed Mahmoud , Alghamdi Abdullah Hussien , Alaryni Abdullah Abdulaziz , Alammari Yousef Mohammed , Alanazi Abdulrahman Mohammed , Faqihi Fahad Ali , Al Harbi Khalid Mohammed , Alsolamy Eysa Nahar , Hakami Osamah Ahmad
Published: October 2023

The administration of corticosteroids may have possible hazards, ranging from minor adverse medication reactions to more serious considerations. We aimed to assess levels of public awareness concerning corticosteroid use, side effects, and predictors of its use. A cross-sectional study was conducted online throughout the period of May to July 2023. The present investigation utilized a previously developed questionnaire tool. The study encompassed a cohort of 732 individuals. Upon inquiry regarding the adverse effects of corticosteroid treatment, the participants predominantly reported weight gain, skin alterations, and fluid retention leading to breathing difficulties, constituting 44.4%, 30.3%, and 27.7% of the responses, respectively. The prevailing adverse effects observed in individuals using corticosteroids were weight gain, alterations in mood, and changes in skin characteristics, which accounted for 38.1%, 25.7%, and 21.8% of reported cases, respectively. Individuals within the age range of 41–50 years and those who are currently not working show a higher propensity for utilizing corticosteroids in comparison to other demographic groups (p < 0.05). The level of general public knowledge about corticosteroids and the side effects connected with them in Saudi Arabia was adequate. Demographic factors, such as age, gender, and education, have an impact on the use of corticosteroids.
Control of Brown Rot Produced by Monilinia fructicola in Peaches Using a Full-Spectrum Extract of Zuccagnia punctata Cav.
Authors: Di Liberto Melina G. , Stegmayer María Inés , Fernández Laura N. , Quiroga Ariel D. , Svetaz Laura A. , Derita Marcos G.
Published: October 2023

Brown rot of stone fruit, caused by Monilinia spp., is one of the most important diseases worldwide, causing significant production losses. Currently, the standard practices for controlling this infection consist of repetitive use of synthetic fungicides. The global tendency encourages the demand for high-quality food products harmless to health and the environment, leading to a reduction in the use of these types of substances. Zuccagnia punctata (Fabaceae) is a perennial shrub extensively used for the treatment of fungal and bacterial infections in Argentinean traditional medicine. In this study, we isolated and characterized (morphologically and molecularly) a pathogenic and virulent strain of Monilinia fructicola, which is the most hostile species of the genus. Consequently, we explored the in vitro antifungal activity of the ethanolic extract of Z. punctata against this phytopathogen. The chalcones 2′,4′-dihydroxy-3′-methoxychalcone and 2′,4′-dihydroxychalcone were isolated from the extract and evaluated against M. fructicola demonstrating that they were responsible for this activity. To promote full-spectrum extract rather than pure compounds, we performed ex-vivo assays using fresh peaches inoculated with the pathogen, and then treated by immersion in an extract solution of 250 µg/mL concentration. Treatment with Z. punctata extract did not show a statistically significant difference from commercial fungicides in the control of fruit rot. In addition, Huh7 cell cytotoxicity evaluation showed that Z. punctata extract was less cytotoxic than commercial fungicides at the assayed concentrations. Based on our research, this plant extract could potentially offer a safer alternative to commercial fungicides for treating peach brown rot.
Active School Commuting in School Children: A Narrative Review of Current Evidence and Future Research Implications
Authors: Lam Ho Yeung , Jayasinghe Sisitha , Ahuja Kiran D. K. , Hills Andrew P.
Published: October 2023

Active school commuting (ASC) has been proposed as a practical way to inculcate positive physical activity habits in children. This paper reviews the current evidence regarding ASC among children, highlights advances in research techniques and existing limitations in the field, and outlines future implications for research and promotion. A comprehensive literature search was conducted to identify English language studies on ASC among children aged 6–12 years, followed by a narrative review. ASC has witnessed a global decline, despite evidence of its contribution to physical activity levels. Context-dependent factors such as commuting distance and parental safety concerns are consistently identified as key determinants of ASC. Several promising interventions have been identified. Despite the limitations in intervention scope and quality, notable advancements in research techniques, such as multilevel regression and agent-based modelling, have been identified. Effective promotion of ASC to tackle childhood physical inactivity requires collaborative efforts among schools, parents, and the government, and should be tailored to address multilevel determinants within the local context. Future research should leverage recent advancements in research techniques to develop effective promotion strategies, while considering the context-dependent nature of ASC behaviours and addressing existing limitations, including the lack of standardised definitions and limited geographical and age coverage.
Occurrence of Vibrio spp. in Selected Recreational Water Bodies in Belgium during 2021 Bathing Season
Authors: Sacheli Rosalie , Philippe Camille , Meex Cécile , Mzougui Samy , Melin Pierrette , Hayette Marie-Pierre
Published: October 2023

In recent years, a global increase in the number of reports of human vibriosis involving V. cholerae non-O1/O139 (NOVC) and other Vibrio spp. has been observed. In this context, the Belgian National Reference Center for Vibrio conducted an assessment of the presence of Vibrio spp. in recreational waters. Water sampling was performed monthly in different lakes in Wallonia and Flanders, including the North Sea. The collected water was then filtrated and cultured, and Vibrio spp. was quantified according to the Most Probable Number (MPN). Presumptive colonies were confirmed via MALDI-TOF, and PCR for virulence genes was applied if justified. No Vibrio spp. was found in the analyzed water bodies in Wallonia. However, NOVC was isolated from three different lakes in Flanders and from coastal water. In addition, V. alginolyticus and V. parahaemolyticus were also detected in coastal water. No clear impact of the pH and temperature was observed on Vibrio spp. occurrence. Our study demonstrates the presence of Vibrio spp. in different bathing water bodies, mostly in the north of Belgium, and supports the recommendation to include Vibrio spp. as a water quality indicator for bathing water quality assessment to ensure the safety of water recreational users in Belgium.
Chemical Insights into Oxidative and Nitrative Modifications of DNA
Authors: Andrés Celia María Curieses , Lastra José Manuel Pérez de la , Juan Celia Andrés , Plou Francisco J. , Pérez-Lebeña Eduardo
Published: October 2023

This review focuses on DNA damage caused by a variety of oxidizing, alkylating, and nitrating species, and it may play an important role in the pathophysiology of inflammation, cancer, and degenerative diseases. Infection and chronic inflammation have been recognized as important factors in carcinogenesis. Under inflammatory conditions, reactive oxygen species (ROS) and reactive nitrogen species (RNS) are generated from inflammatory and epithelial cells, and result in the formation of oxidative and nitrative DNA lesions, such as 8-oxo-7,8-dihydro-2′-deoxyguanosine (8-oxodG) and 8-nitroguanine. Cellular DNA is continuously exposed to a very high level of genotoxic stress caused by physical, chemical, and biological agents, with an estimated 10,000 modifications occurring every hour in the genetic material of each of our cells. This review highlights recent developments in the chemical biology and toxicology of 2′-deoxyribose oxidation products in DNA.
BMP-9 Improves the Osteogenic Differentiation Ability over BMP-2 through p53 Signaling In Vitro in Human Periosteum-Derived Cells
Authors: Park Jin-Ho , Koh Eun-Byeol , Seo Young-Jin , Oh Hye-Seong , Byun June-Ho
Published: October 2023

Bone morphogenetic proteins (BMPs) have tremendous therapeutic potential regarding the treatment of bone and musculoskeletal disorders due to their osteo-inductive ability. More than twenty BMPs have been identified in the human body with various functions, such as embryonic development, skeleton genesis, hematopoiesis, and neurogenesis. BMPs can induce the differentiation of MSCs into the osteoblast lineage and promote the proliferation of osteoblasts and chondrocytes. BMP signaling is also involved in tissue remodeling and regeneration processes to maintain homeostasis in adults. In particular, growth factors, such as BMP-2 and BMP-7, have already been approved and are being used as treatments, but it is unclear as to whether they are the most potent BMPs that induce bone formation. According to recent studies, BMP-9 is known to be the most potent inducer of the osteogenic differentiation of mesenchymal stem cells, both in vitro and in vivo. However, its exact role in the skeletal system is still unclear. In addition, research results suggest that the molecular mechanism of BMP-9-mediated bone formation is also different from the previously known BMP family, suggesting that research on signaling pathways related to BMP-9-mediated bone formation is actively being conducted. In this study, we performed a phosphorylation array to investigate the signaling mechanism of BMP-9 compared with BMP-2, another influential bone-forming growth factor, and we compared the downstream signaling system. We present a mechanism for the signal transduction of BMP-9, focusing on the previously known pathway and the p53 factor, which is relatively upregulated compared with BMP-2.
Challenges in Imaging Analyses of Biomolecular Condensates in Cells Infected with Influenza A Virus
Authors: Etibor Temitope Akhigbe , O’Riain Aidan , Alenquer Marta , Diwo Christian , Vale-Costa Sílvia , Amorim Maria João
Published: October 2023

Biomolecular condensates are crucial compartments within cells, relying on their material properties for function. They form and persist through weak, transient interactions, often undetectable by classical biochemical approaches. Hence, microscopy-based techniques have been the most reliable methods to detail the molecular mechanisms controlling their formation, material properties, and alterations, including dissolution or phase transitions due to cellular manipulation and disease, and to search for novel therapeutic strategies targeting biomolecular condensates. However, technical challenges in microscopy-based analysis persist. This paper discusses imaging, data acquisition, and analytical methodologies’ advantages, challenges, and limitations in determining biophysical parameters explaining biomolecular condensate formation, dissolution, and phase transitions. In addition, we mention how machine learning is increasingly important for efficient image analysis, teaching programs what a condensate should resemble, aiding in the correlation and interpretation of information from diverse data sources. Influenza A virus forms liquid viral inclusions in the infected cell cytosol that serve as model biomolecular condensates for this study. Our previous work showcased the possibility of hardening these liquid inclusions, potentially leading to novel antiviral strategies. This was established using a framework involving live cell imaging to measure dynamics, internal rearrangement capacity, coalescence, and relaxation time. Additionally, we integrated thermodynamic characteristics by analysing fixed images through Z-projections. The aforementioned paper laid the foundation for this subsequent technical paper, which explores how different modalities in data acquisition and processing impact the robustness of results to detect bona fide phase transitions by measuring thermodynamic traits in fixed cells. Using solely this approach would greatly simplify screening pipelines. For this, we tested how single focal plane images, Z-projections, or volumetric analyses of images stained with antibodies or live tagged proteins altered the quantification of thermodynamic measurements. Customizing methodologies for different biomolecular condensates through advanced bioimaging significantly contributes to biological research and potential therapeutic advancements.
Adipocytes in the Uterine Wall during Experimental Healing and in Cesarean Scars during Pregnancy
Authors: Tikhonova Natalia , Milovanov Andrey P. , Aleksankina Valentina V. , Kulikov Ilyas A. , Fokina Tatiana V. , Aleksankin Andrey P. , Belousova Tamara N. , Mikhaleva Ludmila M. , Niziaeva Natalya V.
Published: October 2023

We have suggested that adipocytes in uterine scars may affect the development of the placenta accrete spectrum (PAS). In the experimental part, we explored adipocytes in the uterine wall by the twelfth sexual cycle after surgery. In the clinical part, we investigated adipocyte clusters in the cesarean scar of pregnant women with and without PAS. The uterine wall was evaluated in gross and histological sections using morphometry, histochemistry (hematoxylin and eosin stain, Mallory stain), and immunohistochemistry for FABP4 (adipocyte markers), CD68, CD163, CD206 (macrophages), CD 34 (endothelium), cytokeratin 8 (epithelium), aSMA (smooth muscle cells). The design included an experimental study on Sprague–Dawley rats (n = 18) after a full-thickness surgical incision on the seventh (n = 6), 30th (n = 6), and 60th day (n = 6). The clinical groups include pregnant women without uterine scars (n = 10), pregnant women with a uterine scar after previous cesarean sections (n = 10), and women with PAS (n = 11). Statistical processing was carried out using nonparametric methods. Comparisons were conducted using the Mann–Whitney U-test and Kruskal–Wallis test. Statistical significance was considered at p < 0.05. On the seventh day, the rat uterine horn was enveloped by adipose tissue, which contained crown-like structures with FABP4+, CD68+, CD206+, and CD163+ cells. FABP4+ cells in the uterine wall were absent by the 30th day. The number of CD206+ and CD163+ cells in the adipose tissue decreased by the 30th day. On the 60th day, the attachment of fat tissue was revealed in the form of single strands. The serous layer around the damaged area totally recovered on the 60th day. FABP4+ cells were not detected in the uterine wall samples from pregnant women without a previous cesarean section. Adipocytes were found in the scar during non-complicated pregnancy and with PAS. Reducing the number of CD68+ cells in adipocyte clusters, there were in myometrium with PAS. Increased CD206+ and CD163+ cells were revealed in uterine adipocyte clusters of the group. According to the experimental finding, adipocytes should be absent in the uterine wall by the 12th sexual cycle after a full-thickness surgical incision. The presence of adipocyte clusters in cesarean scar indicated the disturbance of cell interaction. Differences in the numbers of CD206 and CD163 cells in adipocyte clusters between groups with and without PAS may be indirect evidence that uterine adipocytes affect the development of PAS.
Deubiquitinase USP17 Regulates Osteoblast Differentiation by Increasing Osterix Protein Stability
Authors: Kim Myeong Ji , Piao Meiyu , Li Yuankuan , Lee Sung Ho , Lee Kwang Youl
Published: October 2023

Deubiquitinases (DUBs) are essential for bone remodeling by regulating the differentiation of osteoblast and osteoclast. USP17 encodes for a deubiquitinating enzyme, specifically known as ubiquitin-specific protease 17, which plays a critical role in regulating protein stability and cellular signaling pathways. However, the role of USP17 during osteoblast differentiation has not been elusive. In this study, we initially investigated whether USP17 could regulate the differentiation of osteoblasts. Moreover, USP17 overexpression experiments were conducted to assess the impact on osteoblast differentiation induced by bone morphogenetic protein 4 (BMP4). The positive effect was confirmed through alkaline phosphatase (ALP) expression and activity studies since ALP is a representative marker of osteoblast differentiation. To confirm this effect, Usp17 knockdown was performed, and its impact on BMP4-induced osteoblast differentiation was examined. As expected, knockdown of Usp17 led to the suppression of both ALP expression and activity. Mechanistically, it was observed that USP17 interacted with Osterix (Osx), which is a key transcription factor involved in osteoblast differentiation. Furthermore, overexpression of USP17 led to an increase in Osx protein levels. Thus, to investigate whether this effect was due to the intrinsic function of USP17 in deubiquitination, protein stabilization experiments and ubiquitination analysis were conducted. An increase in Osx protein levels was attributed to an enhancement in protein stabilization via USP17-mediated deubiquitination. In conclusion, USP17 participates in the deubiquitination of Osx, contributing to its protein stabilization, and ultimately promoting the differentiation of osteoblasts.
Exploring the Prognosis-Related Genetic Variation in Gastric Cancer Based on mGWAS
Authors: Zhang Yuling , Lyu Yanping , Chen Liangping , Cao Kang , Chen Jingwen , He Chenzhou , Lyu Xuejie , Jiang Yu , Xiang Jianjun , Liu Baoying , Wu Chuancheng
Published: October 2023

The use of metabolome genome-wide association studies (mGWAS) has been shown to be effective in identifying functional genes in complex diseases. While mGWAS has been applied to biomedical and pharmaceutical studies, its potential in predicting gastric cancer prognosis has yet to be explored. This study aims to address this gap and provide insights into the genetic basis of GC survival, as well as identify vital regulatory pathways in GC cell progression. Genome-wide association analysis of plasma metabolites related to gastric cancer prognosis was performed based on the Generalized Linear Model (GLM). We used a log-rank test, LASSO regression, multivariate Cox regression, GO enrichment analysis, and the Cytoscape software to visualize the complex regulatory network of genes and metabolites and explored in-depth genetic variation in gastric cancer prognosis based on mGWAS. We found 32 genetic variation loci significantly associated with GC survival-related metabolites, corresponding to seven genes, VENTX, PCDH 7, JAKMIP1, MIR202HG, MIR378D1, LINC02472, and LINC02310. Furthermore, this study identified 722 Single nucleotide polymorphism (SNP) sites, suggesting an association with GC prognosis-related metabolites, corresponding to 206 genes. These 206 possible functional genes for gastric cancer prognosis were mainly involved in cellular signaling molecules related to cellular components, which are mainly involved in the growth and development of the body and neurological regulatory functions related to the body. The expression of 23 of these genes was shown to be associated with survival outcome in gastric cancer patients in The Cancer Genome Atlas (TCGA) database. Based on the genome-wide association analysis of prognosis-related metabolites in gastric cancer, we suggest that gastric cancer survival-related genes may influence the proliferation and infiltration of gastric cancer cells, which provides a new idea to resolve the complex regulatory network of gastric cancer prognosis.
Single-Nucleotide Polymorphism in Genes Encoding G Protein Subunits GNB3 and GNAQ Increase the Risk of Cardiovascular Morbidity among Patients Undergoing Renal Replacement Therapy
Authors: Birkner Simon , Möhlendick Birte , Wilde Benjamin , Schoenfelder Kristina , Boss Kristina , Siffert Winfried , Kribben Andreas , Friebus-Kardash Justa
Published: October 2023

Single-nucleotide polymorphisms in G protein subunits are linked to an increased risk of cardiovascular events among the general population. We assessed the effects of GNB3 c.825C > T, GNAQ −695/−694GC > TT, and GNAS c.393C > T polymorphisms on the risk of cardiovascular events among 454 patients undergoing renal replacement therapy. The patients were followed up for a median of 4.5 years after the initiation of dialysis. Carriers of the TT/TT genotype of GNAQ required stenting because of coronary artery stenosis (p = 0.0009) and developed cardiovascular events involving more than one organ system (p = 0.03) significantly earlier and more frequently than did the GC/TT or GC/GC genotypes. Multivariate analysis found that the TT/TT genotype of GNAQ was an independent risk factor for coronary artery stenosis requiring stent (hazard ratio, 4.5; p = 0.001), cardiovascular events (hazard ratio, 1.93; p = 0.04) and cardiovascular events affecting multiple organs (hazard ratio, 4.9; p = 0.03). In the subgroup of male patients left ventricular dilatation with abnormally increased LVEDD values occurred significantly more frequently in TT genotypes of GNB3 than in CT/CC genotypes (p = 0.007). Our findings suggest that male dialysis patients carrying the TT genotype of GNB3 are at higher risk of left ventricular dilatation and that dialysis patients carrying the TT/TT genotype of GNAQ are prone to coronary artery stenosis and severe cardiovascular events.
CWH43 Is a Novel Tumor Suppressor Gene with Negative Regulation of TTK in Colorectal Cancer
Authors: Lee Cheng-Chin , Tsai Kuei-Yen , Lee Ai-Wei , Wei Po-Li , Huang Chien-Yu , Batzorig Uyanga , Chang Yu-Jia
Published: October 2023

Colorectal cancer (CRC) ranks among the most prevalent forms of cancer globally, and its late-stage survival outcomes are less than optimal. A more nuanced understanding of the underlying mechanisms behind CRC’s development is crucial for enhancing patient survival rates. Existing research suggests that the expression of Cell Wall Biogenesis 43 C-Terminal Homolog (CWH43) is reduced in CRC. However, the specific role that CWH43 plays in cancer progression remains ambiguous. Our research seeks to elucidate the influence of CWH43 on CRC’s biological behavior and to shed light on its potential as a therapeutic target in CRC management. Utilizing publicly available databases, we examined the expression levels of CWH43 in CRC tissue samples and their adjacent non-cancerous tissues. Our findings indicated lower levels of both mRNA and protein expressions of CWH43 in cancerous tissues. Moreover, we found that a decrease in CWH43 expression correlates with poorer prognoses for CRC patients. In vitro experiments demonstrated that the suppression of CWH43 led to increased cell proliferation, migration, and invasiveness, while its overexpression had inhibitory effects. Further evidence from xenograft models showed enhanced tumor growth upon CWH43 silencing. Leveraging data from The Cancer Genome Atlas (TCGA), our Gene Set Enrichment Analysis (GSEA) indicated a positive relationship between low CWH43 expression and the activation of the epithelial–mesenchymal Transition (EMT) pathway. We conducted RNA sequencing to analyze gene expression changes under both silenced and overexpressed CWH43 conditions. By identifying core genes and executing KEGG pathway analysis, we discovered that CWH43 appears to have regulatory influence over the TTK-mediated cell cycle. Importantly, inhibition of TTK counteracted the tumor-promoting effects caused by CWH43 downregulation. Our findings propose that the decreased expression of CWH43 amplifies TTK-mediated cell cycle activities, thus encouraging tumor growth. This newly identified mechanism offers promising avenues for targeted CRC treatment strategies.
The Usefulness of Elastin Staining to Detect Vascular Invasion in Cancer
Authors: Gonzalez Jeffrey , Bahmad Hisham F. , Ocejo Stephanie , Abreu Alvaro , Popp Meagan , Gogola Samantha , Fernandez Vielka , Recine Monica , Poppiti Robert
Published: October 2023

Tumor prognosis hinges on accurate cancer staging, a pivotal process influenced by the identification of lymphovascular invasion (LVI), i.e., blood vessel and lymphatic vessel invasion. Protocols by the College of American Pathologists (CAP) and the World Health Organization (WHO) have been established to assess LVI in various tumor types, including, but not limited to, breast cancer, colorectal cancer (CRC), pancreatic exocrine tumors, and thyroid carcinomas. The CAP refers to blood vessel invasion as “angioinvasion” (vascular invasion) to differentiate it from lymphatic vessel invasion (lymphatic invasion). For clarity, the latter terms will be used throughout this review. The presence of lymphatic and/or vascular invasion has emerged as a pivotal prognostic factor; therefore, its accurate identification is crucial not only for staging but also for providing the patient with an honest understanding of his/her prognosis. Given the prognostic importance of the correct identification of LVI, specific staining techniques are employed to distinguish lymphatic vessel invasion from angioinvasion and to differentiate true LVI from artifact. These encompass hematoxylin and eosin (H&E) staining, elastic staining, Factor VIII staining, Ulex europaeus I agglutinin staining, CD31, CD34, D2-40, ERG, and D2-40 (podoplanin) immunohistochemical (IHC) stains among others. Based on a review of numerous publications regarding the efficacy of various methods for LVI detection, elastin staining demonstrated superior accuracy and prognostic value, allowing for more targeted treatment strategies. The clinical significance of accurately detecting LVI cannot be overstated, as it is strongly linked to higher cancer-related mortality and an increased risk of tumor recurrence. This review aims to examine the existing literature on the use of elastin stains in the detection of vascular invasion among different types of tumors and its prognostic value.