bluuebunny/crossref_metadata_2025 huggingface dataset:
The Role of MicroRNAs in Muscle Tissue Development in Beef Cattle
Authors: Raza Sayed Haidar Abbas , Kaster Nurgulsim , Khan Rajwali , Abdelnour Sameh A. , El-Hack Mohamed E. Abd , Khafaga Asmaa F. , Taha Ayman , Ohran Husein , Swelum Ayman A. , Schreurs Nicola M. , Zan Linsen
Published: March 2020

In this review, we highlight information on microRNA (miRNA) identification and functional characterization in the beef for muscle and carcass composition traits, with an emphasis on Qinchuan beef cattle, and discuss the current challenges and future directions for the use of miRNA as a biomarker in cattle for breeding programs to improve meat quality and carcass traits. MicroRNAs are endogenous and non-coding RNA that have the function of making post-transcriptional modifications during the process of preadipocyte differentiation in mammals. Many studies claim that diverse miRNAs have an impact on adipogenesis. Furthermore, their target genes are associated with every phase of adipocyte differentiation. It has been confirmed that, during adipogenesis, several miRNAs are differentially expressed, including miR-204, miR-224, and miR-33. The development of mammalian skeletal muscle is sequentially controlled by somite commitment into progenitor cells, followed by their fusion and migration, the proliferation of myoblasts, and final modification into fast- and slow-twitch muscle fibers. It has been reported that miRNA in the bovine MEG3-DIO3 locus has a regulatory function for myoblast differentiation. Likewise, miR-224 has been associated with controlling the differentiation of bovine adipocytes by targeting lipoprotein lipase. Through the posttranscriptional downregulation of KLF6, miR-148a-3p disrupts the proliferation of bovine myoblasts and stimulates apoptosis while the miR-23a~27a~24-2 cluster represses adipogenesis. Additional to influences on muscle and fat, bta-mir-182, bta-mir-183, and bta-mir-338 represent regulators of proteolysis in muscle, which influences meat tenderness.
Standards for Methods Utilizing Environmental DNA for Detection of Fish Species
Authors: Shu Lu , Ludwig Arne , Peng Zuogang
Published: March 2020

Environmental DNA (eDNA) techniques are gaining attention as cost-effective, non-invasive strategies for acquiring information on fish and other aquatic organisms from water samples. Currently, eDNA approaches are used to detect specific fish species and determine fish community diversity. Various protocols used with eDNA methods for aquatic organism detection have been reported in different eDNA studies, but there are no general recommendations for fish detection. Herein, we reviewed 168 papers to supplement and highlight the key criteria for each step of eDNA technology in fish detection and provide general suggestions for eliminating detection errors. Although there is no unified recommendation for the application of diverse eDNA in detecting fish species, in most cases, 1 or 2 L surface water collection and eDNA capture on 0.7-μm glass fiber filters followed by extraction with a DNeasy Blood and Tissue Kit or PowerWater DNA Isolation Kit are useful for obtaining high-quality eDNA. Subsequently, species-specific quantitative polymerase chain reaction (qPCR) assays based on mitochondrial cytochrome b gene markers or eDNA metabarcoding based on both 12S and 16S rRNA markers via high-throughput sequencing can effectively detect target DNA or estimate species richness. Furthermore, detection errors can be minimized by mitigating contamination, negative control, PCR replication, and using multiple genetic markers. Our aim is to provide a useful strategy for fish eDNA technology that can be applied by researchers, advisors, and managers.
CRISPR/Cas9-mediated Disruption of Fibroblast Growth Factor 5 in Rabbits Results in a Systemic Long Hair Phenotype by Prolonging Anagen
Authors: Xu Yuxin , Liu Hongmei , Pan Huilin , Wang Xinyue , Zhang Yuxin , Yao Bing , Li Nannan , Lai Liangxue , Li Zhanjun
Published: March 2020

Hair growth and morphology are generally regulated by the hair cycle in mammals. Fibroblast Growth Factor 5 (FGF5), which is a hair cycle regulator, has a role in regulating the hair cycle during the transition from the anagen phase to the catagen phase, and a hereditary long hair phenotype has been widely reported when FGF5 is mutated in humans and other species. However, there has been no such report in rabbits. Thus, the first exon of rabbit FGF5 was disrupted by the CRISPR/Cas9 system, and the phenotype of FGF5-/- rabbits was characterized while using hematoxylin and eosin (H&E) staining, immunohistochemistry, quantitative PCR, scanning electron microscopy, and western blotting. The results showed a significant and systemic long hair phenotype in the FGF5-/- rabbits, which indicated that FGF5 is a negative regulator of hair growth. In addition, a decreased diameter of the fiber and a higher area proportion of hair follicle clusters were determined in FGF5-/- rabbits as compared with the WT rabbits. Further investigation verified that prolonging the anagen phase in rabbits, with decreased BMP2/4 pathway signaling and increased VERSICAN pathway signaling, caused the systemic long hair phenotype. Taken together, these results indicate a systemic long hair phenotype by prolonging anagen in FGF5-/- rabbits, which could be widely used for Fur production and an ideal model for studying the mechanism of long hair in the future.
Expression Analysis of Cell Wall-Related Genes in the Plant Pathogenic Fungus Drechslera teres
Authors: Backes Aurélie , Hausman Jean-Francois , Renaut Jenny , Ait Barka Essaid , Jacquard Cédric , Guerriero Gea
Published: March 2020

Drechslera teres (D. teres) is an ascomycete, responsible for net blotch, the most serious barley disease causing an important economic impact. The cell wall is a crucial structure for the growth and development of fungi. Thus, understanding cell wall structure, composition and biosynthesis can help in designing new strategies for pest management. Despite the severity and economic impact of net blotch, this is the first study analyzing the cell wall-related genes in D. teres. We have identified key genes involved in the synthesis/remodeling of cell wall polysaccharides, namely chitin, β-(1,3)-glucan and mixed-linkage glucan synthases, as well as endo/exoglucanases and a mitogen-activated protein kinase. We have also analyzed the differential expression of these genes in D. teres spores and in the mycelium after cultivation on different media, as well as in the presence of Paraburkholderia phytofirmans strain PsJN, a plant growth-promoting bacterium (PGPB). The targeted gene expression analysis shows higher gene expression in the spores and in the mycelium with the application of PGPB. Besides analyzing key cell-wall-related genes, this study also identifies the most suitable reference genes to normalize qPCR results in D. teres, thus serving as a basis for future molecular studies on this ascomycete.
Hydraulic Conductivity and Pore Water Pressures in a Clayey Landslide: Experimental Data
Authors: Di Maio Caterina , De Rosa Jacopo , Vassallo Roberto , Coviello Roberto , Macchia Giuseppe
Published: March 2020

To analyze the response to hydrological conditions of an instable slope in a structurally complex clay formation, the hydraulic conductivity of the subsoil was estimated and pore water pressures were monitored. Two types of field tests were carried out: falling head tests in the Casagrande piezometers and localized seepage measurements in test boreholes. The experimental data show that in a narrow band around the slip surface, the hydraulic conductivity is higher—more than two orders of magnitude—than that of the landslide body and of the stable formation. Furthermore, the data of a long-term monitoring by Casagrande piezometers and vibrating wire cells show that the response of pore water pressures to the site hydrological conditions along the shear band is far faster than in the landslide body and in the stable formation. The slip band seems largely connected to the atmosphere, and the water pressures in the band are correlated with the deep displacement rates of all the inclinometers crossing the active slip surface.
Frailty Confers High Mortality Risk across Different Populations: Evidence from an Overview of Systematic Reviews and Meta-Analyses
Authors: Ofori-Asenso Richard , Chin Ken Lee , Sahle Berhe W. , Mazidi Mohsen , Zullo Andrew R. , Liew Danny
Published: March 2020

We performed an overview of systematic reviews and meta-analyses to summarize available data regarding the association between frailty and all-cause mortality. Medline, Embase, CINAHL, Web of Science, PsycINFO, and AMED (Allied and Complementary Medicine) databases were searched until February 2020 for meta-analyses examining the association between frailty and all-cause mortality. The AMSTAR2 checklist was used to evaluate methodological quality. Frailty exposure and the risk of all-cause mortality (hazard ratio [HR] or relative risk [RR]) were displayed in forest plots. We included 25 meta-analyses that pooled data from between 3 and 20 studies. The number of participants included in these meta-analyses ranged between <2000 and >500,000. Overall, 56%, 32%, and 12% of studies were rated as of moderate, low, and critically low quality, respectively. Frailty was associated with increased risk of all-cause mortality in 24/24 studies where the HR/RRs ranged from 1.35 [95% confidence interval (CI) 1.05–1.74] (patients with diabetes) to 7.95 [95% CI 4.88–12.96] (hospitalized patients). The median HR/RR across different meta-analyses was 1.98 (interquartile range 1.65–2.67). Pre-frailty was associated with a significantly increased risk of all-cause mortality in 7/7 studies with the HR/RR ranging from 1.09 to 3.65 (median 1.51, IQR 1.38–1.73). These data suggest that interventions to prevent frailty and pre-frailty are needed.
Suicide amongst the Inuit of Nunavut: An Exploration of Life Trajectories
Authors: Affleck William , Chachamovich Eduardo , Chawky Nadia , Beauchamp Guy , Turecki Gustavo , Séguin Monique
Published: March 2020

This article reports results of the life trajectories from 92 Inuit who died by suicide, matched for age and gender with 92 living-controls. A proxy-based procedure and semi-structured interviews with informants were conducted to obtain trajectories of developmental events occurring over the life course for suicide and community-matched controls. Results from this research indicate two different trajectories that differentiate the control-group from the suicide-group throughout the life course. Even though the number of suicide attempts are similar between both groups, the suicide-group had a more important burden of adversity, which seemed to create a cascading effect, leading to suicide.
Association of Economic Status and Mortality in Patients with Acute Respiratory Distress Syndrome
Authors: Oh Tak Kyu , Song In-Ae , Lee Jae Ho
Published: March 2020

The high cost of treatment for acute respiratory distress syndrome (ARDS) is a concern for healthcare systems, while the impact of patients’ socio-economic status on the risk of ARDS-associated mortality remains controversial. This study investigated associations between patients’ income at the time of ARDS diagnosis and ARDS-specific mortality rate after treatment initiation. Data from records provided by the National Health Insurance Service of South Korea were used. Adult patients admitted for ARDS treatment from 2013 to 2017 were included in the study. Patients’ income in the year of diagnosis was evaluated. A total of 14,600 ARDS cases were included in the analysis. The 30-day and 1-year mortality rates were 48.6% and 70.3%, respectively. In multivariable Cox regression model, we compared income quartiles, showing that compared to income strata Q1, the Q2 (p = 0.719), Q3 (p = 0.946), and Q4 (p = 0.542) groups of income level did not affect the risk of 30-day mortality, respectively. Additionally, compared to income strata Q1, the Q2 (p = 0.762), Q3 (p = 0.420), and Q4 (p = 0.189) strata did not affect the risk of 1-year mortality. Patient income at the time of ARDS diagnosis did not affect the risk of 30-day or 1-year mortality in the present study based on South Korea’s health insurance data.
Mexican Validation of the Engagement and Disaffection in Physical Education Scale
Authors: Rodríguez-Medellín René , Zamarripa Jorge , Marentes-Castillo María , Otero-Saborido Fernando , Baños Raúl , Morquecho-Sánchez Raquel
Published: March 2020

To date, no instrument adapted and validated that measures engagement and disaffection in the physical education class has been found, which limits the generation of knowledge of this area in Mexico. The aims of this study were to translate and adapt the engagement and disaffection scale to the context of physical education in Mexico and to examine its reliability, structure (two and four factors), and factorial invariance by gender in Mexican fifth- and sixth-grade elementary school students. A total of 1470 students participated (50.6% boys) with ages between 10 and 14 years (mean (M) = 10.56; standard deviation (SD) = 0.77) from federal (89.3%) and state (10.7%) elementary schools. Two factorial structures were tested (with four factors and two factors). The fit indexes of both models were satisfactory, and the factorial saturations were significant. The differences between the fit indexes of both models were irrelevant; therefore, the two-factor model was considered more suitable. The total strict invariance by gender was confirmed, and the reliabilities of the engagement and disaffection scale were acceptable. The Mexican version of the course engagement and disaffection scale in physical education is valid and useful to measure these constructs in the context of physical education in Mexico.
Effects of Sulfamethoxazole and 2-Ethylhexyl-4-Methoxycinnamate on the Dissimilatory Nitrate Reduction Processes and N2O Release in Sediments in the Yarlung Zangbo River
Authors: Xu Huiping , Lu Guanghua , Xue Chenwang
Published: March 2020

The nitrogen pollution of rivers as a global environmental problem has received great attentions in recent years. The occurrence of emerging pollutants in high-altitude rivers will inevitably affect the dissimilatory nitrate reduction processes. In this study, sediment slurry experiments combined with 15N tracer techniques were conducted to investigate the influence of pharmaceutical and personal care products (alone and in combination) on denitrification and the anaerobic ammonium oxidation (anammox) process and the resulting N2O release in the sediments of the Yarlung Zangbo River. The results showed that the denitrification rates were inhibited by sulfamethoxazole (SMX) treatments (1–100 μg L−1) and the anammox rates decreased as the SMX concentrations increased, which may be due to the inhibitory effect of this antibiotic on nitrate reducing microbes. 2-Ethylhexyl-4-methoxycinnamate (EHMC) impacted nitrogen transformation mainly though the inhibition of the anammox processes. SMX and EHMC showed a superposition effect on the denitrification processes. The expression levels of the denitrifying functional genes nirS and nosZ were decreased and N2O release was stimulated due to the presence of SMX and/or EHMC in the sediments. To the best of our knowledge, this study is the first to report the effects of EHMC and its mixtures on the dissimilatory nitrate reduction processes and N2O releases in river sediments. Our results indicated that the widespread occurrence of emerging pollutants in high-altitude rivers may disturb the nitrogen transformation processes and increase the pressure of global warming.
Factors Associated with High Mercury Levels in Women and Girls from The Mojana Region, Colombia, 2013–2015
Authors: Diaz Sonia Mireya , Palma Ruth Marien , Muñoz Maria Nathalia , Becerra-Arias Carolina , Fernández Niño Julián Alfredo
Published: March 2020

Women are primarily exposed to mercury through the consumption of fish contaminated by gold mining activities. The main systems affected are the central nervous and renal systems, although effects on the reproductive system have also been found. Objective: To explore the relationship between mercury levels in women and their possible sources of contamination. A cross-sectional study was conducted from 2013 to 2015 with women residing in 11 municipalities in La Mojana, Colombia, using non-random sampling. Standardized instruments were used to identify sociodemographic characteristics, mercury use, mining-related activities, water and fish consumption, and other factors. Blood, urine, and hair samples were taken to quantify mercury levels. A logistic regression model was used to identify factors associated with elevated mercury values in the participants’ samples. A total of 428 women were included, with an average age of 36.7 ± 16.7 years, 3.3% of whom were pregnant at the time of the survey and 8.4% of whom were exposed occupationally. High levels of mercury were present in 62.8% of the women, in any one of the three samples processed. Those exposed occupationally and environmentally had similar values (p = 0.821). Frequency of fish consumption and source of drinking water were associated with higher levels of mercury (p < 0.05).
Malaria Case Fatality Rate among Children under Five in Burkina Faso: An Assessment of the Spatiotemporal Trends Following the Implementation of Control Programs
Authors: Ouédraogo Mady , Kangoye David Tiga , Samadoulougou Sékou , Rouamba Toussaint , Donnen Philippe , Kirakoya-Samadoulougou Fati
Published: March 2020

Reducing the 2015 level of malaria mortality by 90% by 2030 is a goal set by the World Health Organization (WHO). In Burkina Faso, several malaria control programs proven to be effective were implemented over the last decade. In parallel, the progressive strengthening of the health surveillance system is generating valuable data, which represents a great opportunity for analyzing the trends in malaria burden and assessing the effect of these control programs. Complementary programs were rolled out at different time points and paces, and the present work aims at investigating both the spatial and temporal pattern of malaria case fatality rate (mCFR) by considering the effect of combining specific and unspecific malaria control programs. To this end, data on severe malaria cases and malaria deaths, aggregated at health district level between January 2013 and December 2018, were extracted from the national health data repository (ENDOS-BF). A Bayesian spatiotemporal zero-inflated Poisson model was fitted to quantify the strength of the association of malaria control programs with monthly mCFR trends at health district level. The model was adjusted for contextual variables. We found that monthly mCFR decreased from 2.0 (95% IC 1.9–2.1%) to 0.9 (95% IC 0.8–1.0%) deaths for 100 severe malaria cases in 2013 and 2018, respectively. Health districts with high mCFR were identified in the northern, northwestern and southwestern parts of the country. The availability of malaria rapid diagnosis tests (IRR: 0.54; CrI: 0.47, 0.62) and treatment (IRR: 0.50; CrI: 0.41, 0.61) were significantly associated with a reduction in the mCFR. The risk of dying from malaria was lower in the period after the free healthcare policy compared with the period before (IRR: 0.47; CrI: 0.38, 0.58). Our findings highlighted locations that are most in need of targeted interventions and the necessity to sustain and strengthen the launched health programs to further reduce the malaria deaths in Burkina Faso.
Assessment of Microbiological Quality and Mycotoxin in Dried Chili by Morphological Identification, Molecular Detection, and Chromatography Analysis
Authors: Wikandari Rachma , Mayningsih Inggrid Chrisanti , Sari Maura Dania Permata , Purwandari Fiametta Ayu , Setyaningsih Widiastuti , Rahayu Endang Sutriswati , Taherzadeh Mohammad J.
Published: March 2020

The growing interest in spicy foods leads to the global demand for spices, particularly dried chili. This study aimed to assay both aflatoxin (AFs) and ochratoxin A (OTA) contamination using an integrative method of morphological identification, molecular detection, and chromatography analysis on dried chili provided from traditional and modern markets in Indonesia. The results showed that total fungal infection ranged from 1-408 × 103 CFU/g. Eighty percent of the chili obtained from both the traditional and the modern markets were infected by Aspergillus spp., in which 50% of the infections were identified as A. parasiticus and A. flavus. A complete set of targeted genes involved in AF production and OTA were detected in two isolates of A. flavus and one isolate of A. carbonarius, respectively. The levels of AFs B1, B2, and OTA in the contaminated dried chilies were in the range of 39.3–139.5 µg/kg, 2.6–33.3 µg/kg, and 23.7–84.6 µg/kg, respectively. In contrast, no AFs G1 and G2 were detected. This study showed that the fungal infection of Indonesian dried chili occurs both in the field and during storage; thus, it is suggested to implement good agricultural and handling processes.
Job Burnout and Occupational Stressors among Chinese Healthcare Professionals at County-Level Health Alliances
Authors: Liu Yan , Lu Li , Wang Wen-Xin , Liu Shou , Chen Hong-Ru , Gao Xiang , Huang Ming-Yu , Liu Yong-Nian , Ren Yan-Ming , Wang Chao-Cai
Published: March 2020

Background: This study aimed to examine the degrees of job burnout and occupational stressors and their associations among healthcare professionals from county-level health alliances in Qinghai–Tibet Plateau, China. Methods: A cross-sectional study was conducted in county-level health alliances in Qinghai Province, China, in November 2018. The Maslach Burnout Inventory—General Survey and the 38-item Chinese version of the “Scale for occupational stressors on clinicians” were used. Medical staff in four health alliances from two counties were invited to complete the questionnaire. Results: A total of 1052 (age: 34.06 ± 9.22 years, 79.1% females) healthcare professionals were included, 68.2% (95% CI: 65.2–71.0%) of the participants had job burnout symptoms. Occupational stressors had positive associations with moderate (OR = 1.06, 95% CI: 1.05–1.07) and serious (OR = 1.15, 95% CI: 1.13–1.19) level of job burnout. Stressors from vocational interest produced the greatest magnitude of odds ratio (OR = 1.76, 95% CI: 1.62–1.92) for serious degree of burnout, followed by doctor–patient relationship, interpersonal relationship as well as other domains of occupational stressors. Conclusions: Job burnout was very common among healthcare professionals working in Chinese county-level health alliances, different occupational stressors had associations with job burnout. Appropriate and effective policies and measures should be developed and implemented.
Identifying Users’ Requirements for Emergency Mapping Team Operations in the Dominican Republic
Authors: Rosario Michel Gregorio , Muñoz Tapia Santiago , Manzano Aybar Fernando , Guzmán Javier Vladimir , Crompvoets Joep
Published: March 2020

In recent years, a growing number of stakeholders have been taking part in the generation and delivery of geospatial information and services to reduce the impact of severe natural disasters on the communities. This is mainly due to a huge demand for accurate, current and relevant knowledge about the impacted areas for a wide range of applications in risk-informed decision makings. The aim of this paper is to identify users’ requirements for emergency mapping team (EMT) operations in the Dominican Republic (DR). An online survey was applied to collect data from key users involved in the Inter-Institutional Geospatial Information Team in DR. Our findings suggest a set of users’ requirements for EMT operations: (1) standardization; (2) establishing and maintaining a spatial data infrastructure; (3) partnership; (4) effective communication among stakeholders; and (5) capacity building. A better understanding of the users’ requirements and the associated information workflows will lead to a superior level of readiness for EMT operations in DR. This knowledge will support future studies/practices at the local and national levels in the Caribbean region, which share similar challenges in terms of natural hazards and development issues.
Dynamic Online 3D Visualization Framework for Real-Time Energy Simulation Based on 3D Tiles
Authors: Mao Bo , Ban Yifang , Laumert Björn
Published: March 2020

Energy co-simulation can be used to analyze the dynamic energy consumption of a building or a region, which is essential for decision making in the planning and management of smart cities. To increase the accessibility of energy simulation results, a dynamic online 3D city model visualization framework based on 3D Tiles is proposed in this paper. Two types of styling methods are studied, attribute-based and ID map-based. We first perform the energy co-simulation and save the results in CityGML format with EnergyADE. Then the 3D geometry data of these city objects are combined with its simulation results as attributes or just with object ID information to generate Batched 3D Models (B3DM) in 3D Tiles. Next, styling strategies are pre-defined and can be selected by end-users to show different scenarios. Finally, during the visualization process, dynamic interactions and data sources are integrated into the styling generation to support real-time visualization. This framework is implemented with Cesium. Compared with existing dynamic online 3D visualization framework such as directly styling or Cesium Language (CZML), a JSON format for describing a time-dynamic graphical scene, primarily for display in a web browser running Cesium, the proposed framework is more flexible and has higher performance in both data transmission and rendering which is essential for real-time GIS applications.
NR2F2 Orphan Nuclear Receptor is Involved in Estrogen Receptor Alpha-Mediated Transcriptional Regulation in Luminal A Breast Cancer Cells
Authors: Erdős Edina , Bálint Bálint László
Published: March 2020

Nuclear Receptor Subfamily 2 Group F Member 2 (NR2F2) is a member of the steroid/thyroid hormone receptor superfamily with a crucial role in organogenesis, angiogenesis, cardiovascular development and tumorigenesis. However, there is limited knowledge about the cistrome and transcriptome of NR2F2 in breast cancer. In this study, we mapped the regulatory mechanism by NR2F2 using functional genomic methods. To investigate the clinical significance of NR2F2 in breast cancer, The Cancer Genome Atlas (TCGA) data were used. These results show that a high NR2F2 is associated with better survival of a specific subset of patients, namely those with luminal A breast cancer. Therefore, genome-wide NR2F2 and estrogen receptor alpha (ERα) binding sites were mapped in luminal A breast cancer cells using chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-Seq), revealing that most NR2F2 overlap with ERα that are co-occupied by forkhead box A1 (FOXA1) and GATA binding protein 3 (GATA3) in active enhancer regions. NR2F2 overlaps with highly frequent ERα chromatin interactions, which are essential for the formation of ERα-bound super-enhancers. In the process of the transcriptome profiling of NR2F2-depleted breast cancer cells such differentially expressed genes have been identified that are involved in endocrine therapy resistance and are also ERα target genes. Overall, these findings demonstrate that the NR2F2 nuclear receptor has a key role in ERα-mediated transcription and it can offer a potential therapeutic target in patients with luminal A breast cancer.
The p38 Pathway: From Biology to Cancer Therapy
Authors: Martínez-Limón Adrián , Joaquin Manel , Caballero María , Posas Francesc , de Nadal Eulàlia
Published: March 2020

The p38 MAPK pathway is well known for its role in transducing stress signals from the environment. Many key players and regulatory mechanisms of this signaling cascade have been described to some extent. Nevertheless, p38 participates in a broad range of cellular activities, for many of which detailed molecular pictures are still lacking. Originally described as a tumor-suppressor kinase for its inhibitory role in RAS-dependent transformation, p38 can also function as a tumor promoter, as demonstrated by extensive experimental data. This finding has prompted the development of specific inhibitors that have been used in clinical trials to treat several human malignancies, although without much success to date. However, elucidating critical aspects of p38 biology, such as isoform-specific functions or its apparent dual nature during tumorigenesis, might open up new possibilities for therapy with unexpected potential. In this review, we provide an extensive description of the main biological functions of p38 and focus on recent studies that have addressed its role in cancer. Furthermore, we provide an updated overview of therapeutic strategies targeting p38 in cancer and promising alternatives currently being explored.
Antimicrobial Resistance in Veterinary Medicine: An Overview
Authors: Palma Ernesto , Tilocca Bruno , Roncada Paola
Published: March 2020

Antimicrobial resistance (AMR) represents one of the most important human- and animal health-threatening issues worldwide. Bacterial capability to face antimicrobial compounds is an ancient feature, enabling bacterial survival over time and the dynamic surrounding. Moreover, bacteria make use of their evolutionary machinery to adapt to the selective pressure exerted by antibiotic treatments, resulting in reduced efficacy of the therapeutic intervention against human and animal infections. The mechanisms responsible for both innate and acquired AMR are thoroughly investigated. Commonly, AMR traits are included in mobilizable genetic elements enabling the homogeneous diffusion of the AMR traits pool between the ecosystems of diverse sectors, such as human medicine, veterinary medicine, and the environment. Thus, a coordinated multisectoral approach, such as One-Health, provides a detailed comprehensive picture of the AMR onset and diffusion. Following a general revision of the molecular mechanisms responsible for both innate and acquired AMR, the present manuscript focuses on reviewing the contribution of veterinary medicine to the overall issue of AMR. The main sources of AMR amenable to veterinary medicine are described, driving the attention towards the indissoluble cross-talk existing between the diverse ecosystems and sectors and their cumulative cooperation to this warning phenomenon.
Injection Molded Capsules for Colon Delivery Combining Time-Controlled and Enzyme-Triggered Approaches
Authors: Casati Federica , Melocchi Alice , Moutaharrik Saliha , Uboldi Marco , Foppoli Anastasia , Maroni Alessandra , Zema Lucia , Neut Christel , Siepmann Florence , Siepmann Juergen , Gazzaniga Andrea
Published: March 2020

A new type of colon targeting system is presented, combining time-controlled and enzyme-triggered approaches. Empty capsule shells were prepared by injection molding of blends of a high-amylose starch and hydroxypropyl methylcellulose (HPMC) of different chain lengths. The dissolution/erosion of the HPMC network assures a time-controlled drug release, i.e., drug release starts upon sufficient shell swelling/dissolution/erosion. In addition, the presence of high-amylose starch ensures enzyme-triggered drug release. Once the colon is reached, the local highly concentrated bacterial enzymes effectively degrade this polysaccharide, resulting in accelerated drug release. Importantly, the concentration of bacterial enzymes is much lower in the upper gastrointestinal tract, thus enabling site-specific drug delivery. The proposed capsules were filled with acetaminophen and exposed to several aqueous media, simulating the contents of the gastrointestinal tract using different experimental setups. Importantly, drug release was pulsatile and occurred much faster in the presence of fecal samples from patients. The respective lag times were reduced and the release rates increased once the drug started to be released. It can be expected that variations in the device design (e.g., polymer blend ratio, capsule shell geometry and thickness) allow for a large variety of possible colon targeting release profiles.
Molecular Dynamics Study of the Interaction of Carbon Nanotubes with Telomeric DNA Fragment Containing Noncanonical G-Quadruplex and i-Motif Forms
Authors: Panczyk Tomasz , Wojton Patrycja , Wolski Pawel
Published: March 2020

This work deals with molecular dynamics simulations of systems composed of telomeric dsDNA fragments, iG, and functionalized carbon nanotubes, fCNT. The iG contains 90 nucleotides in total and in its middle part the noncanonical i-motif and G-quadruplex are formed. Two chiralities of the fCNT were used, i.e., (10,0) and (20,0) and these nanotubes were either on-tip functionalized by guanine containing functional groups or left without functionalization. We proposed a dedicated computational procedure, based on the replica exchange concept, for finding a thermodynamically optimal conformation of iG and fCNT without destroying the very fragile noncanonical parts of the iG. We found that iG forms a V-shape spatial structure with the noncanonical fragments located at the edge and the remaining dsDNA strands forming the arms of V letter. The optimal configuration of iG in reference to fCNT strongly depends on the on-tip functionalization of the fCNT. The carbon nanotube without functionalization moves freely between the dsDNA arms, while the presence of guanine residues leads to immobilization of the fCNT and preferential location of the nanotube tip near the junction between the dsDNA duplex and i-motif and G-quadruplex. We also studied how the presence of fCNT affects the stability of the i-motif at the neutral pH when the cytosine pairs are nonprotonated. We concluded that carbon nanotubes do not improve the stability of the spatial structure of i-motif also when it is a part of a bigger structure like the iG. Such an effect was described in literature in reference to carboxylated nanotubes. Our current results suggest that the stabilization of i-motif is most probably related to easy formation of semiprotonated cytosine pairs at neutral pH due to interaction with carboxylated carbon nanotubes.
Ligand Binding Mechanism and Its Relationship with Conformational Changes in Adenine Riboswitch
Authors: Hu Guodong , Li Haiyan , Xu Shicai , Wang Jihua
Published: March 2020

Riboswitches are naturally occurring RNA aptamers that control the expression of essential bacterial genes by binding to specific small molecules. The binding with both high affinity and specificity induces conformational changes. Thus, riboswitches were proposed as a possible molecular target for developing antibiotics and chemical tools. The adenine riboswitch can bind not only to purine analogues but also to pyrimidine analogues. Here, long molecular dynamics (MD) simulations and molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) computational methodologies were carried out to show the differences in the binding model and the conformational changes upon five ligands binding. The binding free energies of the guanine riboswitch aptamer with C74U mutation complexes were compared to the binding free energies of the adenine riboswitch (AR) aptamer complexes. The calculated results are in agreement with the experimental data. The differences for the same ligand binding to two different aptamers are related to the electrostatic contribution. Binding dynamical analysis suggests a flexible binding pocket for the pyrimidine ligand in comparison with the purine ligand. The 18 μs of MD simulations in total indicate that both ligand-unbound and ligand-bound aptamers transfer their conformation between open and closed states. The ligand binding obviously affects the conformational change. The conformational states of the aptamer are associated with the distance between the mass center of two key nucleotides (U51 and A52) and the mass center of the other two key nucleotides (C74 and C75). The results suggest that the dynamical character of the binding pocket would affect its biofunction. To design new ligands of the adenine riboswitch, it is recommended to consider the binding affinities of the ligand and the conformational change of the ligand binding pocket.
NEAT1 is Required for the Expression of the Liver Cancer Stem Cell Marker CD44
Authors: Koyama Shigemi , Tsuchiya Hiroyuki , Amisaki Masataka , Sakaguchi Hiromi , Honjo Soichiro , Fujiwara Yoshiyuki , Shiota Goshi
Published: March 2020

CD44, a cancer stem cell (CSC) marker, is required for maintaining CSC properties in hepatocellular carcinoma (HCC). Nuclear enriched abundant transcript 1 (NEAT1), a long noncoding RNA (lncRNA), is an oncogenic driver in HCC. In the present study, we investigated the significance of the NEAT1 gene in association with CD44 expression in liver CSCs of human HCC cell lines. The CSC properties were evaluated by spheroid culture, CSC marker expression, and sensitivity to anti-cancer drugs. The expression of both NEAT1 variant 1 (NEAT1v1) and variant 2 (NEAT1v2) as well as CD44 was significantly increased in the spheroid culture, compared with that in monolayer culture. Overexpression of Neat1v1, but not Neat1v2, enhanced the CSC properties, while knockout of the NEAT1 gene suppressed them. CD44 expression was increased by the overexpression of Neat1v1 and abrogated by NEAT1 knockout. The overexpression of NEAT1v1 restored the CSC properties and CD44 expression in NEAT1-knockout cells. NEAT1v1 expression in HCC tissues was correlated with poor prognosis and CD44 expression. These results suggest that NEAT1v1 is required for CD44 expression. To our surprise, NEAT1v1 also restored the CSC properties even in CD44-deficient cells, suggesting that NEAT1v1 maintains the properties of CSCs in a CD44-independent manner.
Tumor Cell Invasion in Glioblastoma
Authors: Vollmann-Zwerenz Arabel , Leidgens Verena , Feliciello Giancarlo , Klein Christoph A. , Hau Peter
Published: March 2020

Glioblastoma (GBM) is a particularly devastating tumor with a median survival of about 16 months. Recent research has revealed novel insights into the outstanding heterogeneity of this type of brain cancer. However, all GBM subtypes share the hallmark feature of aggressive invasion into the surrounding tissue. Invasive glioblastoma cells escape surgery and focal therapies and thus represent a major obstacle for curative therapy. This review aims to provide a comprehensive understanding of glioma invasion mechanisms with respect to tumor-cell-intrinsic properties as well as cues provided by the microenvironment. We discuss genetic programs that may influence the dissemination and plasticity of GBM cells as well as their different invasion patterns. We also review how tumor cells shape their microenvironment and how, vice versa, components of the extracellular matrix and factors from non-neoplastic cells influence tumor cell motility. We further discuss different research platforms for modeling invasion. Finally, we highlight the importance of accounting for the complex interplay between tumor cell invasion and treatment resistance in glioblastoma when considering new therapeutic approaches.
Effects of High-Dose Ionizing Radiation in Human Gene Expression: A Meta-Analysis
Authors: Kanakoglou Dimitrios S. , Michalettou Theodora-Dafni , Vasileiou Christina , Gioukakis Evangelos , Maneta Dorothea , Kyriakidis Konstantinos V. , Georgakilas Alexandros G. , Michalopoulos Ioannis
Published: March 2020

The use of high-dose Ionizing Radiation (IR) is currently one of the most common modalities in treatment of many types of cancer. The objective of this work was to investigate the effects of high-dose ionizing radiation on healthy human tissue, utilizing quantitative analysis of gene expression. To this end, publicly available transcriptomics datasets from human samples irradiated with a high dose of radiation and non-irradiated (control) ones were selected, and gene expression was determined using RNA-Seq data analysis. Raw data from these studies were subjected to quality control and trimming. Mapping of RNA-Seq reads was performed by the partial selective alignment method, and differential gene expression analysis was conducted. Subsequently, a meta-analysis was performed to select differentially expressed genes across datasets. Based on the differentially expressed genes discovered by meta-analysis, we constructed a protein-to-protein interaction network, and we identified biological pathways and processes related to high-dose IR effects. Our findings suggest that cell cycle arrest is activated, supported by our top down-regulated genes associated with cell cycle activation. DNA repair genes are down-regulated in their majority. However, several genes implicated in the nucleotide excision repair pathway are upregulated. Nevertheless, apoptotic mechanisms seem to be activated probably due to severe high-dose-induced complex DNA damage. The significant upregulation of CDKN1A, as a downstream gene of TP53, further validates programmed cell death. Finally, down-regulation of TIMELESS, signifies a correlation between IR response and circadian rhythm. Nonetheless, high-dose IR exposure effects regarding normal tissue (radiation toxicity) and its possible long-term outcomes should be studied to a greater extend.
Cold Atmospheric Plasma and Silymarin Nanoemulsion Activate Autophagy in Human Melanoma Cells
Authors: Adhikari Manish , Adhikari Bhawana , Ghimire Bhagirath , Baboota Sanjula , Choi Eun Ha
Published: March 2020

Background: Autophagy is reported as a survival or death-promoting pathway that is highly debatable in different kinds of cancer. Here, we examined the co-effect of cold atmospheric plasma (CAP) and silymarin nanoemulsion (SN) treatment on G-361 human melanoma cells via autophagy induction. Methods: The temperature and pH of the media, along with the cell number, were evaluated. The intracellular glucose level and PI3K/mTOR and EGFR downstream pathways were assessed. Autophagy-related genes, related transcriptional factors, and autophagy induction were estimated using confocal microscopy, flow cytometry, and ELISA. Results: CAP treatment increased the temperature and pH of the media, while its combination with SN resulted in a decrease in intracellular ATP with the downregulation of PI3K/AKT/mTOR survival and RAS/MEK transcriptional pathways. Co-treatment blocked downstream paths of survival pathways and reduced PI3K (2 times), mTOR (10 times), EGFR (5 times), HRAS (5 times), and MEK (10 times). CAP and SN co-treated treatment modulates transcriptional factor expressions (ZKSCAN3, TFEB, FOXO1, CRTC2, and CREBBP) and specific genes (BECN-1, AMBRA-1, MAP1LC3A, and SQSTM) related to autophagy induction. Conclusion: CAP and SN together activate autophagy in G-361 cells by activating PI3K/mTOR and EGFR pathways, expressing autophagy-related transcription factors and genes.
Fighting Against Promoter DNA Hyper-Methylation: Protective Histone Modification Profiles of Stress-Resistant Intestinal Stem Cells
Authors: Thalheim Torsten , Hopp Lydia , Herberg Maria , Siebert Susann , Kerner Christiane , Quaas Marianne , Schweiger Michal R. , Aust Gabriela , Galle Joerg
Published: March 2020

Aberrant DNA methylation in stem cells is a hallmark of aging and tumor development. Recently, we have suggested that promoter DNA hyper-methylation originates in DNA repair and that even successful DNA repair might confer this kind of epigenetic long-term change. Here, we ask for interrelations between promoter DNA methylation and histone modification changes observed in the intestine weeks after irradiation and/or following Msh2 loss. We focus on H3K4me3 recruitment to the promoter of H3K27me3 target genes. By RNA- and histone ChIP-sequencing, we demonstrate that this recruitment occurs without changes of the average gene transcription and does not involve H3K9me3. Applying a mathematical model of epigenetic regulation of transcription, we show that the recruitment can be explained by stronger DNA binding of H3K4me3 and H3K27me3 histone methyl-transferases as a consequence of lower DNA methylation. This scenario implicates stable transcription despite of H3K4me3 recruitment, in agreement with our RNA-seq data. Following several kinds of stress, including moderate irradiation, stress-sensitive intestinal stem cell (ISCs) are known to become replaced by more resistant populations. Our simulation results suggest that the stress-resistant ISCs are largely protected against promoter hyper-methylation of H3K27me3 target genes.
Integrated miRNA/mRNA Counter-Expression Analysis Highlights Oxidative Stress-Related Genes CCR7 and FOXO1 as Blood Markers of Coronary Arterial Disease
Authors: Hueso Miguel , Mallén Adrián , Casas Ángela , Guiteras Jordi , Sbraga Fabrizio , Blasco-Lucas Arnau , Lloberas Núria , Torras Joan , Cruzado Josep M , Navarro Estanislao
Published: March 2020

Our interest in the mechanisms of atherosclerosis progression (ATHp) has led to the recent identification of 13 miRNAs and 1285 mRNAs whose expression was altered during ATHp. Here, we deepen the functional relationship among these 13 miRNAs and genes associated to oxidative stress, a crucial step in the onset and progression of vascular disease. We first compiled a list of genes associated to the response to oxidative stress (Oxstress genes) by performing a reverse Gene Ontology analysis (rGO, from the GO terms to the genes) with the GO terms GO0006979, GO1902882, GO1902883 and GO1902884, which included a total of 417 unique Oxstress genes. Next, we identified 108 putative targets of the 13 miRNAs among these unique Oxstress genes, which were validated by an integrated miRNA/mRNA counter-expression analysis with the 1285 mRNAs that yielded 14 genes, Map2k1, Mapk1, Mapk9, Dapk1, Atp2a2, Gata4, Fos, Egfr, Foxo1, Ccr7, Vkorc1l1, Rnf7, Kcnh3, and Mgat3. GO enrichment analysis and a protein–protein-interaction network analysis (PPI) identified most of the validated Oxstress transcripts as components of signaling pathways, highlighting a role for MAP signaling in ATHp. Lastly, expression of these Oxstress transcripts was measured in PBMCs from patients suffering severe coronary artery disease, a serious consequence of ATHp. This allowed the identification of FOXO1 and CCR7 as blood markers downregulated in CAD. These results are discussed in the context of the interaction of the Oxstress transcripts with the ATHp-associated miRNAs.