bluuebunny/crossref_metadata_2025 huggingface dataset:
CRISPR/Cas9 Gene Editing of NtAITRs, a Family of Transcription Repressor Genes, Leads to Enhanced Drought Tolerance in Tobacco
Authors: Li Guimin , Ma Yanxing , Wang Xiaoping , Cheng Nini , Meng Deyu , Chen Siyu , Wang Wei , Wang Xutong , Hu Xiaojun , Yan Li , Wang Shucai
Published: December 2022

Tobacco is a cash crop throughout the world, and its growth and development are affected by abiotic stresses including drought stress; therefore, drought-tolerant breeding may help to improve tobacco yield and quality under drought stress conditions. Considering that the plant hormone ABA (abscisic acid) is able to regulate plant responses to abiotic stresses via activating ABA response genes, the characterization of ABA response genes may enable the identification of genes that can be used for molecular breeding to improve drought tolerance in tobacco. We report here the identification of NtAITRs (Nicotiana tabacum ABA-induced transcription repressors) as a family of novel regulators of drought tolerance in tobacco. Bioinformatics analysis shows that there are a total of eight NtAITR genes in tobacco, and all the NtAITRs have a partially conserved LxLxL motif at their C-terminus. RT-PCR results show that the expression levels of at least some NtAITRs were increased in response to ABA and drought treatments, and NtAITRs, when recruited to the Gal4 promoter via a fused GD (Gal4 DNA-binding domain), were able to repress transcription activator LD-VP activated expression of the LexA-Gal4-GUS reporter gene. Roles of NtAITRs in regulating drought tolerance in tobacco were analyzed by generating CRISPR/Cas9 gene-edited mutants. A total of three Cas9-free ntaitr12356 quintuple mutants were obtained, and drought treatment assays show that drought tolerance was increased in the ntaitr12356 quintuple mutants. On the other hand, results of seed germination and seedling greening assays show that ABA sensitivity was increased in the ntaitr12356 quintuple mutants, and the expression levels of some ABA signaling key regulator genes were altered in the ntaitr12356-c3 mutant. Taken together, our results suggest that NtAITRs are ABA-responsive genes, and that NtAITRs function as transcription repressors and negatively regulate drought tolerance in tobacco, possibly by affecting plant ABA response via affecting the expression of ABA signaling key regulator genes.
Induced Pluripotent Stem Cells and Genome-Editing Tools in Determining Gene Function and Therapy for Inherited Retinal Disorders
Authors: Benati Daniela , Leung Amy , Perdigao Pedro , Toulis Vasileios , van der Spuy Jacqueline , Recchia Alessandra
Published: December 2022

Inherited retinal disorders (IRDs) affect millions of people worldwide and are a major cause of irreversible blindness. Therapies based on drugs, gene augmentation or transplantation approaches have been widely investigated and proposed. Among gene therapies for retinal degenerative diseases, the fast-evolving genome-editing CRISPR/Cas technology has emerged as a new potential treatment. The CRISPR/Cas system has been developed as a powerful genome-editing tool in ophthalmic studies and has been applied not only to gain proof of principle for gene therapies in vivo, but has also been extensively used in basic research to model diseases-in-a-dish. Indeed, the CRISPR/Cas technology has been exploited to genetically modify human induced pluripotent stem cells (iPSCs) to model retinal disorders in vitro, to test in vitro drugs and therapies and to provide a cell source for autologous transplantation. In this review, we will focus on the technological advances in iPSC-based cellular reprogramming and gene editing technologies to create human in vitro models that accurately recapitulate IRD mechanisms towards the development of treatments for retinal degenerative diseases.
Neomycin, but Not Neamine, Blocks Angiogenic Factor Induced Nitric Oxide Release through Inhibition of Akt Phosphorylation
Authors: Trouillon Raphaël , Kang Dong-Ku , Chang Soo-Ik , O’Hare Danny
Published: December 2022

Angiogenesis, the growth of new blood vessels, is a critical factor of carcinogenesis. Neomycin and neamine, two drugs blocking the nuclear translocation of angiogenin (ANG), have been proven to inhibit tumour growth in vivo. However, the high toxicity of neomycin prevents its therapeutic use, thus indicating that the less toxic neamine may be a better candidate. Endothelial cells were cultured on a biocompatible multiple microelectrode array (MMA). The release of NO evoked by ANG or vascular endothelial growth factor (VEGF) was detected electrochemically. The effects of neomycin and neamine on ANG- and VEGF-induced NO releases have been investigated. Neomycin totally blocks NO release for concentrations down to the pM range, probably through the inhibition of the Akt kinase phosphorylation, as revealed by confocal microscopy. On the other hand, both ANG- and VEGF-induced NO releases were not significantly hindered by the presence of high concentrations of neamine. The inhibition of the Akt pathway and NO release are expected to lead to a severe decrease in tissue growth and repair, thus indicating a possible cause for the toxicity of neomycin. Furthermore, the data presented here show that ANG- and VEGF-induced NO releases are not dependent on the nuclear translocation of angiogenin, as these events were not abolished by the presence of neamine.
The Phosphoserine Phosphatase Alters the Free Amino Acid Compositions and Fecundity in Cyrtorhinus lividipennis Reuter
Authors: Ahmad Sheraz , Zhang Jieyu , Wang Huaiqi , Zhu Haowen , Dong Qiaoqiao , Zong Suman , Wang Tingting , Chen Yu , Ge Linquan
Published: December 2022

The mirid bug Cyrtorhinus lividipennis (Reuter) is an important predator that consumes eggs and young nymphs of the brown planthopper Nilaparvata lugens as a primary food source and thus becomes an important member of the rice ecosystem. We identified and characterized the ClPSP gene in C. lividipennis encoding the phosphoserine phosphatase enzyme. The ClPSP has an open reading frame (ORF) of 957 bp encoding a protein with a length of 294bp and it possesses a haloacid dehalogenase-like (HAD) hydrolase, phosphoserine phosphatase, eukaryotic-like (HAD_PSP_eu) conserved domain. Furthermore, the in silico analysis of the ClPSP gene unveiled its distinct characteristics and it serves as a key player in the modulation of amino acids. The ClPSP showed expression in all developmental stages, with higher expression observed in the ovary and fat body. Silencing the ClPSP by RNA interference (RNAi) significantly decreased PSP enzyme activity and expression compared to dsGFP at two days after emergence (2DAE). The dsPSP treatment altered free hemolymph amino acid compositions, resulting in a significant reduction of serine (Ser) and Arginine (Arg) proportions and a significant increase of Threonine (Thr), Cystine (Cys), and Tyrosine (Tyr) in the C. lividipennis female at 2 DAE. Additionally, a hindered total protein concentration in the ovary and fat body, and reduced vitellogenin (Vg) expression, body weight, and number of laid eggs, were also observed. The same treatment also prolonged the preoviposition period and hindered ovarian development. Our data, for the first time, demonstrated the influential role of the PSP gene in modulating the fecundity of C. lividipennis and provide a platform for future insect pest control programs using the PSP gene in modulating fecundity.
Identification of Novel Hub Genes Associated with Psoriasis Using Integrated Bioinformatics Analysis
Authors: Yue Qi , Li Zhaoxiang , Zhang Qi , Jin Quanxin , Zhang Xinyuan , Jin Guihua
Published: December 2022

Psoriasis is a chronic, prolonged, and recurrent inflammatory skin disease and the current therapeutics can only alleviate the symptoms rather than cure it completely. Therefore, we aimed to identify the molecular signatures and specific biomarkers of psoriasis to provide novel clues for psoriasis and targeted therapy. In the present study, the Gene Expression Omnibus (GEO) database was used to retrieve three microarray datasets (GSE166388, GSE50790 and GSE42632) and to explore the differentially expressed genes (DEGs) in psoriasis using the Affy package in R software. The gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway enrichment were utilized to determine the common DEGs and their capabilities. The STRING database was used to develop DEG-encoded proteins and a protein–protein interaction network (PPI) and the Cytohubba plugin to classify hub genes. Using the NetworkAnalyst platform, we detected transcription factors (TFs), microRNAs and drug candidates interacting with hub genes. In addition, the expression levels of hub genes in HaCaT cells were detected by western blot. We screened the up- and downregulated DEGs from the transcriptome microarrays of corresponding psoriasis patients. Functional enrichment of DEGs in psoriasis was mainly associated with positive regulation of leukocyte cell–cell adhesion and T cell activation, cytokine binding, cytokine activity and the Wnt signaling pathway. Through further data processing, we obtained 57 intersecting genes in the three datasets and probed them in STRING to determine the interaction of their expressed proteins and we obtained the critical 10 hub genes in the Cytohubba plugin, including TOP2A, CDKN3, MCM10, PBK, HMMR, CEP55, ASPM, KIAA0101, ESC02, and IL-1β. Using these hub genes as targets, we obtained 35 TFs and 213 miRNAs that may regulate these genes and 33 potential therapeutic agents for psoriasis. Furthermore, the expression levels of TOP2A, MCM10, PBK, ASPM, KIAA0101 and IL-1β were observably increased in HaCaT cells. In conclusion, we identified potential biomarkers, risk factors and drugs for psoriasis.
Proteomic-Based Approach Reveals the Involvement of Apolipoprotein A-I in Related Phenotypes of Autism Spectrum Disorder in the BTBR Mouse Model
Authors: Li Qi , Shi Yaxin , Li Xiang , Yang Yuan , Zhang Xirui , Xu Lisha , Ma Zhe , Wang Jia , Fan Lili , Wu Lijie
Published: December 2022

Autism spectrum disorder (ASD) is a neurodevelopmental disorder. Abnormal lipid metabolism has been suggested to contribute to its pathogenesis. Further exploration of its underlying biochemical mechanisms is needed. In a search for reliable biomarkers for the pathophysiology of ASD, hippocampal tissues from the ASD model BTBR T+ Itpr3tf/J (BTBR) mice and C57BL/6J mice were analyzed, using four-dimensional (4D) label-free proteomic analysis and bioinformatics analysis. Differentially expressed proteins were significantly enriched in lipid metabolic pathways. Among them, apolipoprotein A-I (ApoA-I) is a hub protein and its expression was significantly higher in the BTBR mice. The investigation of protein levels (using Western blotting) also confirmed this observation. Furthermore, expressions of SphK2 and S1P in the ApoA-I pathway both increased. Using the SphK inhibitor (SKI-II), ASD core phenotype and phenotype-related protein levels of P-CREB, P-CaMKII, and GAD1 were improved, as shown via behavioral and molecular biology experiments. Moreover, by using SKI-II, we found proteins related to the development and function of neuron synapses, including ERK, caspase-3, Bax, Bcl-2, CDK5 and KCNQ2 in BTBR mice, whose levels were restored to protein levels comparable to those in the controls. Elucidating the possible mechanism of ApoA-I in ASD-associated phenotypes will provide new ideas for studies on the etiology of ASD.
Aggregated Alpha-Synuclein Inclusions within the Nucleus Predict Impending Neuronal Cell Death in a Mouse Model of Parkinsonism
Authors: Weston Leah J. , Bowman Anna M. , Osterberg Valerie R. , Meshul Charles K. , Woltjer Randall L. , Unni Vivek K.
Published: December 2022

Alpha-synuclein (aSyn) is a 14 kD protein encoded by the SNCA gene that is expressed in vertebrates and normally localizes to presynaptic terminals and the nucleus. aSyn forms pathological intracellular aggregates that typify a group of important neurodegenerative diseases called synucleinopathies. Previous work in human tissue and model systems indicates that some of these aggregates can be intranuclear, but the significance of aSyn aggregation within the nucleus is not clear. We used a mouse model that develops aggregated aSyn nuclear inclusions. Using aSyn preformed fibril injections in GFP-tagged aSyn transgenic mice, we were able to induce the formation of nuclear aSyn inclusions and study their properties in fixed tissue and in vivo using multiphoton microscopy. In addition, we analyzed human synucleinopathy patient tissue to better understand this pathology. Our data demonstrate that nuclear aSyn inclusions may form through the transmission of aSyn between neurons, and these intranuclear aggregates bear the hallmarks of cytoplasmic Lewy pathology. Neuronal nuclear aSyn inclusions can form rod-like structures that do not contain actin, excluding them from being previously described nuclear actin rods. Longitudinal, in vivo multiphoton imaging indicates that certain morphologies of neuronal nuclear aSyn inclusions predict cell death within 14 days. Human multiple system atrophy cases contain neurons and glia with similar nuclear inclusions, but we were unable to detect such inclusions in Lewy body dementia cases. This study suggests that the dysregulation of a nuclear aSyn function associated with nuclear inclusion formation could play a role in the forms of neurodegeneration associated with synucleinopathy.
Transcriptomic and Metabolomic Analyses Reveal That Fullerol Improves Drought Tolerance in Brassica napus L
Authors: Xiong Jun-Lan , Ma Ni
Published: December 2022

Carbon nanoparticles have potential threats to plant growth and stress tolerance. The polyhydroxy fullerene—fullerol (one of the carbon nanoparticles) could increase biomass accumulation in several plants subjected to drought; however, the underlying molecular and metabolic mechanisms governed by fullerol in improving drought tolerance in Brassica napus remain unclear. In the present study, exogenous fullerol was applied to the leaves of B. napus seedlings under drought conditions. The results of transcriptomic and metabolomic analyses revealed changes in the molecular and metabolic profiles of B. napus. The differentially expressed genes and the differentially accumulated metabolites, induced by drought or fullerol treatment, were mainly enriched in the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to carbohydrate metabolism (e.g., “carbon metabolism” and “galactose metabolism”), amino acid metabolism (e.g., “biosynthesis of amino acids” and “arginine and proline metabolism”), and secondary metabolite metabolism (e.g., “biosynthesis of secondary metabolites”). For carbohydrate metabolism, the accumulation of oligosaccharides (e.g., sucrose) was decreased, whereas that of monosaccharides (e.g., mannose and myo-inositol) was increased by drought. With regard to amino acid metabolism, under drought stress, the accumulation of amino acids such as phenylalanine and tryptophan decreased, whereas that of glutamate and proline increased. Further, for secondary metabolite metabolism, B. napus subjected to soil drying showed a reduction in phenolics and flavonoids, such as hyperoside and trans-3-coumaric acid. However, the accumulation of carbohydrates was almost unchanged in fullerol-treated B. napus subjected to drought. When exposed to water shortage, the accumulation of amino acids, such as proline, was decreased upon fullerol treatment. However, that of phenolics and flavonoids, such as luteolin and trans-3-coumaric acid, was enhanced. Our findings suggest that fullerol can alleviate the inhibitory effects of drought on phenolics and flavonoids to enhance drought tolerance in B. napus.
Occurrence and Variability of the Efflux Pump Gene norA across the Staphylococcus Genus
Authors: Ferreira Carolina , Abrantes Patrícia , Costa Sofia Santos , Viveiros Miguel , Couto Isabel
Published: December 2022

NorA is one of the main native MDR efflux pumps of Staphylococcus aureus, contributing to reduced susceptibility towards fluoroquinolones and biocides, but little is known about its variability within S. aureus or its distribution and conservation among other staphylococci. We screened for sequences homologous to S. aureus norA and found it in 61 out of the 63 Staphylococcus species described. To the best of our knowledge, this is the first study to report the occurrence of norA across the Staphylococcus genus. The norA phylogenetic tree follows the evolutionary relations of staphylococci and the closely related Mammalliicoccus genus. Comparative analyses suggest a conservation of the NorA function in staphylococci. We also analyzed the variability of norA within S. aureus, for which there are several circulating norA alleles, differing up to 10% at the nucleotide level, which may hamper proper norA detection. We demonstrate the applicability of a PCR-based algorithm to detect and differentiate norA alleles in 52 S. aureus representing a wider collection of 89 isolates from different hosts. Our results highlight the prevalence of norAI and norAII in different settings and the association of norA alleles with specific S. aureus clonal lineages. Ultimately, it confirms the applicability of our PCR-based algorithm to rapidly detect and assign the different norA alleles, a trait that may impact antimicrobial efflux capacity and the search for potential NorA inhibitors.
Enhancing the Expression of the OsF3H Gene in Oryza sativa Leads to the Regulation of Multiple Biosynthetic Pathways and Transcriptomic Changes That Influence Insect Resistance
Authors: Jan Rahmatullah , Asaf Sajjad , Lubna  , Asif Saleem , Kim Eun-Gyeong , Jang Yoon-Hee , Kim Nari , Al-Harrasi Ahmed , Lee Gang-Seob , Kim Kyung-Min
Published: December 2022

The white-backed planthopper (WBPH) is a major pest of rice crops and causes severe loss of yield. We previously developed the WBPH-resistant rice cultivar “OxF3H” by overexpressing the OsF3H gene. Although there was a higher accumulation of the flavonoids kaempferol (Kr) and quercetin (Qu) as well as salicylic acid (SA) in OxF3H transgenic (OsF3H or Trans) plants compared to the wild type (WT), it is still unclear how OsF3H overexpression affects these WBPH resistant-related changes in gene expression in OxF3H plants. In this study, we analyze RNA-seq data from OxF3H and WT at several points (0 h, 3 h, 12 h, and 24 h) after WBPH infection to explain how overall changes in gene expression happen in these two cultivars. RT-qPCR further validated a number of the genes. Results revealed that the highest number of DEGs (4735) between the two genotypes was detected after 24 h of infection. Interestingly, it was found that several of the DEGs between the WT and OsF3H under control conditions were also differentially expressed in OsF3H in response to WBPH infestation. These results indicate that significant differences in gene expression between the “OxF3H” and “WT” exist as the infection time increases. Many of these DEGs were related to oxidoreductase activity, response to stress, salicylic acid biosynthesis, metabolic process, defense response to pathogen, cellular response to toxic substance, and regulation of hormone levels. Moreover, genes involved in salicylic acid (SA) and ethylene (Et) biosynthesis were upregulated in OxF3H plants, while jasmonic acid (JA), brassinosteroid (Br), and abscisic acid (ABA) signaling pathways were found downregulated in OxF3H plants during WBPH infestation. Interestingly, many DEGs related to pathogenesis, such as OsPR1, OsPR1b, OsNPR1, OsNPR3, and OsNPR5, were found to be significantly upregulated in OxF3H plants. Additionally, genes related to the MAPKs pathway and about 30 WRKY genes involved in different pathways were upregulated in OxF3H plants after WBPH infestation. This suggests that overexpression of the OxF3H gene leads to multiple transcriptomic changes and impacts plant hormones and pathogenic-related and secondary-metabolites-related genes, enhancing the plant’s resistance to WBPH infestation.
Increased Expression of Galectin-3 in Skin Fibrosis: Evidence from In Vitro and In Vivo Studies
Authors: Peiró Teresa , Alonso-Carpio Miriam , Ribera Pilar , Almudéver Patricia , Roger Inés , Montero Paula , Marín Severiano , Milara Javier , Cortijo Julio
Published: December 2022

Skin fibrosis is a hallmark of a wide array of dermatological diseases which can greatly impact the patients’ quality of life. Galectin-3 (GAL-3) has emerged as a central regulator of tissue fibrosis, playing an important pro-fibrotic role in numerous organs. Various studies are highlighting its importance as a skin fibrotic diseases biomarker; however, there is a need for further studies that clarify its role. This paper aims to ascertain whether the expression of GAL-3 is increased in relevant in vitro and in vivo models of skin fibrosis. We studied the role of GAL-3 in vitro using normal human dermal fibroblasts (NHDF) and fibrocytes. In addition, we used a skin fibrosis murine model (BALB/c mice) and human biopsies of healthy or keloid tissue. GAL-3 expression was analyzed using real time PCR, Western blot and immunostaining techniques. We report a significantly increased expression of GAL-3 in NHDF and fibrocytes cell cultures following stimulation with transforming growth factor β1 (TGFβ1). In vivo, GAL-3 expression was increased in a murine model of systemic sclerosis and in human keloid biopsies. In sum, this study underlines the involvement of GAL-3 in skin fibrosis using several models of the disease and highlights its role as a relevant target.
Comprehensive Analysis of Copy Number Variations on Glycoside Hydrolase 45 Genes among Different Bursaphelenchus xylophilus Strains
Authors: Ding Xiaolei , Zhao Ruiwen , Dai Yonglin , Zhang Yue , Lin Sixi , Ye Jianren
Published: December 2022

Bursaphelenchus xylophilus is considered the most dangerous quarantine pest in China. It causes enormous economic and ecological losses in many countries from Asia and Europe. The glycoside hydrolase 45 gene family has been demonstrated in early studies to contribute to the cell wall degradation ability of B. xylophilus during its infection. However, the copy number variation (CNV) of the GH45 gene and its association with B. xylophilus pathogenicity were not fully elucidated. In this study, we found that the GH45 gene with two copies is the most predominant type among 259 B. xylophilus strains collected from China and Japan. Additionally, 18 strains are identified as GH45 genes with a single copy, and only two strains are verified to have three copies. Subsequent expression analysis and inoculation test suggest that the copy numbers of the GH45 gene are correlated with gene expression as well as the B. xylophilus pathogenicity. B. xylophilus strains with more copies of the GH45 gene usually exhibit more abundant expression and cause more severe wilt symptoms on pine trees. The aforementioned results indicated the potential regulatory effects of CNV in B. xylophilus and provided novel information to better understand the molecular pathogenesis of this devastating pest.
Locus Coeruleus Neurons’ Firing Pattern Is Regulated by ERG Voltage-Gated K+ Channels
Authors: Hasan Sonia , Delicata Francis , Guasti Leonardo , Duranti Claudia , Haidar Fatemah Mousalem , Arcangeli Annarosa , Imbrici Paola , Pessia Mauro , Valentino Mario , D’Adamo Maria Cristina
Published: December 2022

Locus coeruleus (LC) neurons, with their extensive innervations throughout the brain, control a broad range of physiological processes. Several ion channels have been characterized in LC neurons that control intrinsic membrane properties and excitability. However, ERG (ether-à-go-go–related gene) K+ channels that are particularly important in setting neuronal firing rhythms and automaticity have not as yet been discovered in the LC. Moreover, the neurophysiological and pathophysiological roles of ERG channels in the brain remain unclear despite their expression in several structures. By performing immunohistochemical investigations, we found that ERG-1A, ERG-1B, ERG-2 and ERG-3 are highly expressed in the LC neurons of mice. To examine the functional role of ERG channels, current-clamp recordings were performed on mouse LC neurons in brain slices under visual control. ERG channel blockade by WAY-123,398, a class III anti-arrhythmic agent, increased the spontaneous firing activity and discharge irregularity of LC neurons. Here, we have shown the presence of distinct ERG channel subunits in the LC which play an imperative role in modulating neuronal discharge patterns. Thus, we propose that ERG channels are important players behind the changes in, and/or maintenance of, LC firing patterns that are implicated in the generation of different behaviors and in several disorders.
Shifting the pH Optima of (R)-Selective Transaminases by Protein Engineering
Authors: Xiang Chao , Ao Yu-Fei , Höhne Matthias , Bornscheuer Uwe T.
Published: December 2022

Amine transaminases (ATAs) are powerful biocatalysts for the stereoselective synthesis of chiral amines. However, wild-type ATAs usually show pH optima at slightly alkaline values and exhibit low catalytic activity under physiological conditions. For efficient asymmetric synthesis ATAs are commonly used in combination with lactate dehydrogenase (LDH, optimal pH: 7.5) and glucose dehydrogenase (GDH, optimal pH: 7.75) to shift the equilibrium towards the synthesis of the target chiral amine and hence their pH optima should fit to each other. Based on a protein structure alignment, variants of (R)-selective transaminases were rationally designed, produced in E. coli, purified and subjected to biochemical characterization. This resulted in the discovery of the variant E49Q of the ATA from Aspergillus fumigatus, for which the pH optimum was successfully shifted from pH 8.5 to 7.5 and this variant furthermore had a two times higher specific activity than the wild-type protein at pH 7.5. A possible mechanism for this shift of the optimal pH is proposed. Asymmetric synthesis of (R)-1-phenylethylamine from acetophenone in combination with LDH and GDH confirmed that the variant E49Q shows superior performance at pH 7.5 compared to the wild-type enzyme.
Expression Patterns and Gonadotropin Regulation of the TGF-β II Receptor (Bmpr2) during Ovarian Development in the Ricefield Eel Monopterus albus
Authors: He Zhi , Zheng Li , Chen Qiqi , Xiong Sen , He Zhide , Hu Jiaxiang , Ma Zhijun , Zhang Qian , He Jiayang , Ye Lijuan , He Liang , Luo Jie , Gu Xiaobin , Zhang Mingwang , Tang Ziting , Jiao Yuanyuan , Pu Yong , Xiong Jinxin , Gao Kuo , Lai Bolin , Yang Shiyong , Yang Deying , Yan Taiming
Published: December 2022

Bmpr2 plays a central role in the regulation of reproductive development in mammals, but its role during ovarian development in fish is still unclear. To ascertain the function of bmpr2 in ovarian development in the ricefield eel, we isolated and characterized the bmpr2 cDNA sequence; the localization of Bmpr2 protein was determined by immunohistochemical staining; and the expression patterns of bmpr2 in ovarian tissue incubated with FSH and hCG in vitro were analyzed. The full-length bmpr2 cDNA was 3311 bp, with 1061 amino acids encoded. Compared to other tissues, bmpr2 was abundantly expressed in the ovary and highly expressed in the early yolk accumulation (EV) stages of the ovary. In addition, a positive signal for Bmpr2 was detected in the cytoplasm of oocytes in primary growth (PG) and EV stages. In vitro, the expression level of gdf9, the ligand of bmpr2, in the 10 ng/mL FSH treatment group was significantly higher after incubation for 4 h than after incubation for different durations. However, bmpr2 expression in the 10 ng/mL FSH treatment group at 2 h, 4 h and 10 h was significantly lower. Importantly, the expression level of bmpr2 and gdf9 in the 100 IU/mL hCG group had similar changes that were significantly decreased at 4 h and 10 h. In summary, Bmpr2 might play a pivotal role in ovarian growth in the ricefield eel, and these results provide a better understanding of the function of bmpr2 in ovarian development and the basic data for further exploration of the regulatory mechanism of gdf9 in oocyte development.
Genetic Variation of SAMM50 Is Not an Independent Risk Factor for Alcoholic Hepatocellular Carcinoma in Caucasian Patients
Authors: Nischalke Hans Dieter , Schmalz Franziska , Buch Stephan , Fischer Janett , Möller Christine , Matz-Soja Madlen , Krämer Benjamin , Langhans Bettina , Klüners Alexandra , Soyka Michael , Stickel Felix , Nattermann Jacob , Berg Thomas , Strassburg Christian P. , Lutz Philipp
Published: December 2022

Hepatocellular carcinoma (HCC) is a severe complication of advanced alcoholic liver disease, which is modulated by genetic predisposition. Identifying new genetic loci might improve screening. Genetic variation of SAMM50 was linked to HCC. We aimed to validate this finding in a large cohort of patients with advanced alcoholic liver disease (ALD). A large, well-characterised cohort of patients with alcoholic cirrhosis without (n = 674) and with (n = 386) HCC, as well as controls with HCC due to viral hepatitis (n = 134), controls with heavy alcohol abuse without liver disease (n = 266) and healthy subjects (n = 237), were genotyped for SAMM50 rs3827385 and rs3761472 and for PNPLA3 rs738409. Genotype frequencies were compared between patients with alcohol-associated cirrhosis with and without HCC by uni- and multivariate analysis. Minor variants in both SAMM50 rs3827385 and rs3761472 were significantly more frequent in patients with alcoholic HCC versus alcoholic cirrhosis and versus the control cohorts. An even stronger association was noted for PNPLA3 rs738409. The univariate analysis resulted in an odds ratio (OR) of 1.8 for carriers of at least one minor variant of SAMM50 rs3827385 and rs3761472 (each p < 0.001), but this association was lost in multivariate analysis with age (OR 1.1/year), male sex (OR 3.2), diabetes (OR 1.9) and carriage of PNPLA3 148M (OR 2.1) remaining in the final model. Although minor variants of both SAMM50 loci are strongly associated with alcoholic HCC, this association is not independent of carriage of the well-known risk variant PNPLA3 148M.
Shoot Phenology in Bambusoideae: A Review
Authors: Chan Khin Nyein , Liang Zhiwei , Kisvarga Szilvia , Veres Anikó , Hamar-Farkas Dóra , Orlóci László , Neményi András
Published: December 2022

The study of plant phenology is important nowadays since global climate-changing phenomena are impacting the growing patterns and growing periods of plants. Bamboo is of great importance to the agriculture and forestry of temperate, subtropical to tropical regions, especially of Asia. Although some temperate genera can thrive under different climatic conditions, from the Korean Peninsula to South China, it is not known how bamboo will be affected by climate change, so the collection of data related to bamboo phenology could be of interest to research related to climate change. In this review, we describe available data on the phenology of 8 temperate genera, including 79 species, varieties and forms and 4 subtropical–tropical bamboo genera, including 19 species. Primarily, culm shoot physiology is discussed with some reference to leaf phenology data, where available, as well as their interaction. Since the data available in Western literature is often limited to the definition of season rather than exact dates and periods of given months, there is still a great need to explore more about the exact phenology of individual bamboo species to be able to determine the impact of periodic changes in weather patterns or climate change on bamboo phenology in the future.
The Impact of Story Structure, Meaningfulness, and Concentration in Serious Games
Authors: Pescarin Sofia , Martinez Pandiani Delfina S.
Published: December 2022

This contribution analyzes the impact of factors related to story structure, meaningfulness, and concentration in the design of Serious Games. To explore them, the authors carried out an experimental evaluation aiming to identify relevant aspects affecting the cognitive-emotional impact of immersive Virtual Reality (VR), specifically Educational Environmental Narrative (EEN) Games. The experiment was designed around three main research questions: if passive or active interaction is preferable for factual and spatial knowledge acquisition; whether meaningfulness is a relevant experience in a serious game (SG) context; and if concentration impacts knowledge acquisition and engagement also in VR educational games. The findings highlight that passive interaction should only be encouraged for factual knowledge acquisition, that meaningfulness is a relevant experience and should be included in serious game design, and, finally, that concentration is a factor that impacts the experience in immersive games. The authors discuss potential design paths to improve both factual and spatial knowledge acquisition, such as abstract concept-oriented design, concluding that SGs should contain game mechanics explicitly supporting players’ moments of reflection, and story structures explicitly aligned to educational facts.
How Is Endodontics Taught in Italy? A Survey of Italian Dental Schools
Authors: Mergoni Giovanni , Citterio Irene , Toffoli Andrea , Macaluso Guido Maria , Manfredi Maddalena
Published: December 2022

The aim of our study was to investigate how endodontics is taught in Italian universities. An online survey was conducted from August to December 2021. A comparison between courses led by full or associate professors (Group 1) versus courses led by other figures, such as researchers or temporary lecturers (Group 2), was made. A total of 28 out of 36 schools participated (78%). In most schools, endodontics is taught in the fifth year to 15–29 students. All schools planned pre-clinical endodontic training, and in 25/28 schools (89.3%), clinical endodontic training was also provided. The course programs varied among schools, and significantly more hours were allocated to teaching nonsurgical root canal treatment in Group 1 schools than in Group 2 schools. The average numbers of hours of preclinical and clinical training were 34.3 ± 23.6 and 84.1 ± 76.7, respectively. All schools used rotary NiTi files in their clinical training, and the vertical condensation of hot gutta-percha was the most frequently taught obturation technique. As expected, the scenario of endodontic education in Italian universities was variable and needs harmonization. Courses led by full or associate professors seem to be better structured.
Low Intra-Abdominal Pressure with Complete Neuromuscular Blockage Reduces Post-Operative Complications in Major Laparoscopic Urologic Surgery: A before–after Study
Authors: Brusasco Claudia , Germinale Federico , Dotta Federico , Benelli Andrea , Guano Giovanni , Campodonico Fabio , Ennas Marco , Di Domenico Antonia , Santori Gregorio , Introini Carlo , Corradi Francesco
Published: December 2022

Most urological interventions are now performed with minimally invasive surgery techniques such as laparoscopic surgery. Combining ERAS protocols with minimally invasive surgery techniques may be the best option to reduce hospital length-of-stay and post-operative complications. We designed this study to test the hypothesis that using low intra-abdominal pressures (IAP) during laparoscopy may reduce post-operative complications, especially those related to reduced intra-operative splanchnic perfusion or increased splanchnic congestion. We applied a complete neuromuscular blockade (NMB) to maintain an optimal space and surgical view. We compared 115 patients treated with standard IAP and moderate NMB with 148 patients treated with low IAP and complete NMB undergoing major urologic surgery. Low IAP in combination with complete NMB was associated with fewer total post-operative complications than standard IAP with moderate NMB (22.3% vs. 41.2%, p < 0.001), with a reduction in all medical post-operative complications (17 vs. 34, p < 0.001). The post-operative complications mostly reduced were acute kidney injury (15.5% vs. 30.4%, p = 0.004), anemia (6.8% vs. 16.5%, p = 0.049) and reoperation (2% vs. 7.8%, p = 0.035). The intra-operative management of laparoscopic interventions for major urologic surgeries with low IAP and complete NMB is feasible without hindering surgical conditions and might reduce most medical post-operative complications.
ANN-Based Estimation of the Defect Severity in the Drilling of GFRP/Ti Multilayered Composite Structure
Authors: Zhilyaev Igor , Chigrinets Evgeny , Shevtsov Sergey , Chotchaeva Samira , Snezhina Natalia
Published: December 2022

The main purpose of this study was to develop a model for predicting the quality of holes drilled in the root part of the spar of helicopter main rotor blades made of glass fiber-reinforced plastic (GFRP)-Ti multilayer polymer composite. As the main quality criterion, delaminations at the entry and exit of the drill from the hole were taken. In the experimental study, a conventional drill and two modified geometry drills, a double-point angle drill and a dagger drill, were used. Preliminary experiments showed the best hole quality when using modified drills, which allowed further detailed study only with both modified drills at different drilling speeds and feed rates. Its results in the form of training sets were used to build artificial neural networks (ANNs) to predict delamination at the entry and exit of the drilled holes. An analysis of the fitted response functions presented as 3D surface plots and contour plots led to the selection of the best tool, a double-point angle drill, which demonstrated the lowest achievable delamination both at the entry and at the exit of the holes approximately 1.5 times less (0.45/0.48 mm) compared to dagger drills (0.68/0.7 mm) and determined the ~5 times larger optimal area for the drilling speed and feed rate. The results obtained confirm the possibility of effective prediction of the quality and productivity of mechanically processed composites of complex reinforcement using ANN to quantify the quality criteria and search for the optimal modes of such technologies.
DNA Mismatch Repair Proteins and BRAF V600E Detection by Immunohistochemistry in Colorectal Cancer Demonstrates Concordance with Next Generation Sequencing
Authors: Yambert Joel , Henricksen Leigh A. , Clements June , Hannon Andrew , Jordan Alyssa , Singh Shalini , Dvorak Katerina , Pritchard Colin C. , Konnick Eric Q.
Published: December 2022

Background and Aims: Multiple laboratory methods are used to screen patients with colorectal cancer (CRC) for mismatch repair (MMR) protein deficiency to identify possible Lynch syndrome patients. The goal of this study was to compare the agreement between ready-to-use immunohistochemistry (IHC) assays for MLH-1, PMS-2, MSH-2, MSH-6, and mutated BRAF at V600E and molecular methods in CRC cases. The inclusion of the BRAF V600E mutation testing is important for the identification of patients with sporadic CRC, as the BRAF V600E mutation is very rarely observed in patients with Lynch syndrome tumors. Methods: CRC cases were analyzed by ColoSeqTM tumor sequencing assay and VENTANA MMR IHC Panel that included anti-MLH1, anti-PMS2, anti-MSH2, anti-MSH6, and anti-BRAF V600E antibodies. Additionally, CRC cases with MLH1 IHC loss were evaluated for MLH1 promoter hypermethylation. Results: One hundred and eighteen cases were analyzed. The overall percent agreement (OPA) for each evaluated marker status compared to next-generation sequencing (NGS) exceeded 96%. Twenty-three cases were positive for the BRAF V600E mutation by IHC and NGS, and twenty cases showed loss of MLH1 protein and were positive for MLH1 hypermethylation. Samples with loss of MMR protein expression by IHC demonstrated genetic and/or epigenetic alterations that were consistent with the observed protein expression patterns. Conclusions: The results of this study indicate that ready-to-use IHC assays can correctly identify the loss of MMR proteins and the presence of mutated BRAF V600E protein, supporting the utility of the VENTANA MMR IHC Panel as an aid to stratify patients with sporadic CRC vs. potential Lynch syndrome.
Thermomechanical Analysis of a PFC Integrating W Lattice Armour in Response to Different Plasma Scenarios Predicted in the EU-DEMO Tokamak
Authors: Paoletti Damiano , Fanelli Pierluigi , De Luca Riccardo , Stefanini Chiara , Vivio Francesco , Belardi Valerio Gioachino , Trupiano Simone , Calabrò Giuseppe , You Jeong-Ha , Neu Rudolf
Published: December 2022

Despite the high performance exhibited by tungsten (W), no material would be able to withstand the huge loads expected with extreme plasma transients in EU-DEMO and future reactors, where the installation of sacrificial first wall limiters is essential to prevent excessive wall degradation. The integration of W lattices in the architecture of such components can allow for meeting their conflictual requirements: indeed, they must ensure the effective exhaust of the nominal thermal load during stationary operation; when transients occur, they must thermally insulate and decouple the surface from the heat sink, promoting prompt vapour shielding formation. Starting from the optimised layouts highlighted in a previous study, in this work, a detailed 3D finite element model was developed to analyse in depth the influence of the actual features of the latticed metamaterial on the overall performance of the EU-DEMO limiter PFC on the basis of a flat tile configuration. Its main goal is to help in identifying the most promising layout as a preconceptual design for the fabrication of a small-scale mock-up. For this purpose, the complex geometry of a W-based lattice armour was faithfully reproduced in the model and analysed. This allowed for a detailed assessment of the thermally induced stresses that develop in the component because of the temperature field in response to a number of plasma scenarios—above all, normal operation and ramp down. Structural integrity was verified through the acceptance criteria established for ITER. The two optimised layouts proposed for the PFC were able to effectively meet the requirements under normal reactor operating conditions, while they missed some requirements in the ramp-down case. However, the first HHF tests will be performed in order to benchmark the analyses.
The Impact of Land Use on Time-Varying Passenger Flow Based on Site Classification
Authors: Lei Kexin , Hou Quanhua , Li Weijia , Zhao Meng , Zhou Jizhe , Zhang Lingda , Chen Shihan , Duan Yaqiong
Published: December 2022

During the different periods of a day, the imbalanced distribution of inbound ridership, that is related to land use, results in extreme flow, which makes metro management challenging. The causes of imbalanced passenger flow from the perspective of land use in metro station areas are studied in this paper. More specifically, based on site classification, the impact of land use, including the floor area ratio and gross floor area on passenger flow, was explored by using a multiple linear regression model. The results first indicate that the impact intensities of the floor area ratio on peak hourly flow were 0.41, 0.21, and 0.20 around business, residential, and mixed sites, respectively. Second, for the abovementioned sites, the types with the greatest impact intensities of gross floor area on peak hourly flow were commercial and business facilities (B), residential (R), as well as administration and public services (A), which were 0.73, 0.32, and 0.87, respectively. Finally, for the land-development-control schemes for business, residential, and mixed sites, the maximum values of the floor area ratio were roughly 7.2, 5.3, and 8.2, respectively. The results presented in this study provide guidance for land development in metro station areas and contribute to avoiding the emergence of extreme passenger flow.
Just Energy Transition: Learning from the Past for a More Just and Sustainable Hydrogen Transition in West Africa
Authors: Löhr Katharina , Matavel Custódio Efraim , Tadesse Sophia , Yazdanpanah Masoud , Sieber Stefan , Komendantova Nadejda
Published: December 2022

The rising demand for energy and the aim of moving away from fossil fuels and to low-carbon power have led many countries to move to alternative sources including solar energy, wind, geothermal energy, biomass, and hydrogen. Hydrogen is often considered a “missing link” in guaranteeing the energy transition, providing storage, and covering the volatility and intermittency of renewable energy generation. However, due to potential injustice with regard to the distribution of risks, benefits, and costs (i.e., in regard to competing for land use), the large-scale deployment of hydrogen is a contested policy issue. This paper draws from a historical analysis of past energy projects to contribute to a more informed policy-making process toward a more just transition to the hydrogen economy. We perform a systematic literature review to identify relevant conflict factors that can influence the outcome of hydrogen energy transition projects in selected Economic Community of West African States countries, namely Nigeria and Mali. To better address potential challenges, policymakers must not only facilitate technology development, access, and market structures for hydrogen energy policies but also focus on energy access to affected communities. Further research should monitor hydrogen implementation with a special focus on societal impacts in producing countries.
The Rise and Fall of Land Use Mix: Review and Prospects
Authors: Zhuo Yuefei , Jing Xin , Wang Xiaoying , Li Guan , Xu Zhongguo , Chen Yang , Wang Xueqi
Published: December 2022

Faced with problems such as unordered expansion, inefficient utilization, and the decay of old cities in the current urban development process, many scholars have considered introducing land use mix as a coping strategy. However, due to a lack of understanding of the evolution process and the theoretical connotation of land use mix, it fails to guide its role in practice. Therefore, this study summarizes the theoretical evolution of land use mix from four levels: ideological evolution, conceptual model, quantitative measurements, and influential factors and effects. It is found that after decades of evolution, although the land use mix theory initially formed a certain theoretical and methodological system, there are still some gaps or deficiencies that need to be filled or improved: (1) the theoretical framework lags behind the needs of practice; (2) in the process of evolution, the idea of modern land use mix has been given a deeper meaning; (3) the conceptual model still needs to be further improved; (4) the influencing mechanism is still unclear.
Vegetation Growth Trends of Grasslands and Impact Factors in the Three Rivers Headwater Region
Authors: Sun Xiaoping , Xiao Yang
Published: December 2022

Areas of grassland improvement and degradation were mapped and assessed to identify the driving forces of change in vegetation cover in the Three Rivers headwater region of Qinghai, China. Based on linear regression at the pixel level, we analyzed the vegetation dynamics of the grasslands of this region using MODIS NDVI data sets from 2000 to 2010. Correlation coefficients were computed to quantitatively characterize the long-term interrelationship between vegetation NDVI and precipitation/temperature variability during this period. The use of time series residuals of the NDVI/precipitation linear regression to normalize the effect of precipitation on vegetation productivity and to identify long-term degradation was extended to the local scale. Results showed that significant improvements occurred in 26.4% of the grassland area in the Three Rivers Headwater region between 2000 and 2010. The study area, which represents about 86.4% of the total grassland area of this headwater region, showed a general trend of improvement with no obvious trend of degradation.