bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomics Analyses Reveal Unique Classification, Population Structure and Novel Allele of Neo-Tetraploid Rice
Authors: Yu Hang , Li Qihang , Li Yudi , Yang Huijing , Lu Zijun , Wu Jinwen , Zhang Zemin , Shahid Muhammad Qasim , Liu Xiangdong 
Published: February 2021

Abstract
Background
Neo-tetraploid rice (NTR) is a useful new germplasm that developed from the descendants of the autotetraploid rice (ATR) hybrids. NTR showed improved fertility and yield potential, and produced high yield heterosis when crossed with indica ATR for commercial utilization. However, their classification, population structure and genomic feature remain elusive.

Results
Here, high-depth genome resequencing data of 15 NTRs and 18 ATRs, together with 38 publicly available data of diploid rice accessions, were analyzed to conduct classification, population structure and haplotype analyses. Five subpopulations were detected and NTRs were clustered into one independent group that was adjacent to japonica subspecies, which maybe the reason for high heterosis when NTRs crossed with indica ATRs. Haplotype patterns of 717 key genes that associated with yield and other agronomic traits were revealed in these NTRs. Moreover, a novel specific SNP variation was detected in the first exon of HSP101, a known heat-inducible gene, which was conserved in all NTRs but absent in ATRs, 3KRG and RiceVarMap2 databases. The novel allele was named as HSP101–1, which was confirmed to be a heat response factor by qRT-PCR, and knockout of HSP101–1 significantly decreased the thermotolerance capacity of NTR. Interestingly, HSP101–1 was also specifically expressed in the anthers of NTR at pre-meiotic and meiosis stages under optimal environment without heat stress, and its loss-of-function mutant showed significant decrease in fertility of NTR.

Conclusion
The construction of first genomic variation repository and the revelation of population structure provide invaluable information for optimizing the designs of tetraploid rice breeding. The detection of specific genomic variations offered useful genomic markers and new directions to resolve high fertility mechanism of NTR.
Quantum dots as targeted doxorubicin drug delivery nanosystems in human lung cancer cells
Authors: Ruzycka-Ayoush Monika , Kowalik Patrycja , Kowalczyk Agata , Bujak Piotr , Nowicka Anna M. , Wojewodzka Maria , Kruszewski Marcin , Grudzinski Ireneusz P. 
Published: February 2021

Abstract
Background
Lung cancer is one of the most frequently diagnosed cancers all over the world and is also one of the leading causes of cancer-related mortality. The main treatment option for small cell lung cancer, conventional chemotherapy, is characterized by a lack of specificity, resulting in severe adverse effects. Therefore, this study aimed at developing a new targeted drug delivery (TDD) system based on Ag–In–Zn–S quantum dots (QDs). For this purpose, the QD nanocrystals were modified with 11-mercaptoundecanoic acid (MUA), L-cysteine, and lipoic acid decorated with folic acid (FA) and used as a novel TDD system for targeting doxorubicin (DOX) to folate receptors (FARs) on adenocarcinomic human alveolar basal epithelial cells (A549). NIH/3T3 cells were used as FAR-negative controls. Comprehensive physicochemical, cytotoxicity, and genotoxicity studies were performed to characterize the developed novel TDDs.

Results
Fourier transformation infrared spectroscopy, dynamic light scattering, and fluorescence quenching confirmed the successful attachment of FA to the QD nanocrystals and of DOX to the QD–FA nanocarriers. UV–Vis analysis helped in determining the amount of FA and DOX covalently anchored to the surface of the QD nanocrystals. Biological screening revealed that the QD–FA–DOX nanoconjugates had higher cytotoxicity in comparison to the other forms of synthesized QD samples, suggesting the cytotoxic effect of DOX liberated from the QD constructs. Contrary to the QD–MUA–FA–DOX nanoconjugates which occurred to be the most cytotoxic against A549 cells among others, no such effect was observed for NIH/3T3 cells, confirming FARs as molecular targets. In vitro scratch assay also revealed significant inhibition of A549 cell migration after treatment with QD–MUA–FA–DOX. The performed studies evidenced that at IC50 all the nanoconjugates induced significantly more DNA breaks than that observed in nontreated cells. Overall, the QD–MUA–FA–DOX nanoconjugates showed the greatest cytotoxicity and genotoxicity, while significantly inhibiting the migratory potential of A549 cells.

Conclusion
QD–MUA–FA–DOX nanoconjugates can thus be considered as a potential drug delivery system for the effective treatment of adenocarcinomic human alveolar basal epithelial cells.
Targeting BMI-1 with PLGA–PEG nanoparticle-containing PTC209 modulates the behavior of human glioblastoma stem cells and cancer cells
Authors: Poonaki Elham , Ariakia Fatemeh , Jalili-Nik Mohammad , Shafiee Ardestani Mehdi , Tondro Gholamhossein , Samini Fariborz , Ghasemi Sepideh , Sahab-Negah Sajad , Gorji Ali 
Published: February 2021

AbstractDespite advances in glioblastoma (GBM) treatments, current approaches have failed to improve the overall survival of patients. The oncogene BMI-1, a core member of the polycomb group proteins, is a potential novel therapeutic target for GBM. To enhance the efficacy and reduce the toxicity, PTC209, a BMI-1 inhibitor, was loaded into a PLGA–PEG nanoparticle conjugated with CD133 antibody (Nano-PTC209) and its effect on the behavior of human GBM stem-like cells (GSCs) and the human glioblastoma cell line (U87MG) was assessed. Nano-PTC209 has a diameter of ~ 75 nm with efficient drug loading and controlled release. The IC50 values of Nano-PTC209 for GSCs and U87MG cells were considerably lower than PTC209. Nano-PTC209 significantly decreased the viability of both GSCs and U87MG cells in a dose-dependent manner and caused a significant enhancement of apoptosis and p53 levels as well as inhibition of AKT and JNK signaling pathways. Furthermore, Nano-PTC209 significantly inhibited the migration ability, decreased the activity of metalloproteinase-2 and -9, and increased the generation of reactive oxygen species in both GSCs and U87MG cells. Our data indicate that PLGA–PEG nanoparticle conjugated with CD133 antibody could be an ideal nanocarrier to deliver PTC209 and effectively target BMI-1 for potential approaches in the treatment of GBM.
Non-invasive transdermal delivery of chemotherapeutic molecules in vivo using superparamagnetic iron oxide nanoparticles
Authors: Raviraj Vanisri , Pham Binh T. T. , Kim Byung J. , Pham Nguyen T. H. , Kok Lai F. , Painter Nicole , Delic Naomi C. , Jones Stephen K. , Hawkett Brian S. , Lyons J. Guy 
Published: February 2021

Abstract
Background
The skin is both a target and a potential conduit for the delivery of drugs, but its cornified cell layer resists penetration by most molecules. This study investigated the potential of superparamagnetic iron oxide nanoparticles to facilitate the transdermal delivery of anticancer agents.

Results
Chemotherapeutic cancer drugs were applied with or without nanoparticles to the skin of hairless mice, and their ability to penetrate the skin was assessed using fluorescence microscopy and tumor growth. Nanoparticles enhanced the penetration of the skin by doxorubicin and 5-fluorouracil as determined by fluorescence microscopy and growth retardation of experimental melanoma in immunocompetent, syngeneic mice. This drug enhancement did not require conjugation or encapsulation of the drugs by the nanoparticles—simple co-administration sufficed. Nanoparticles applied topically to melanomas increased the cytotoxicity and immune cell infiltration induced by co-administered 5-fluorouracil, and also reduced vascularization of the tumors independently of 5-fluorouracil.

Conclusion
Correctly formulated superparamagnetic iron oxide nanoparticles can facilitate the chemotherapeutic effectiveness of cytotoxic drugs on skin tumors by both increasing their transdermal penetration and ameliorating host–tumor interactions. This enhancement of skin penetration occurs without the need for conjugation or encapsulation of the co-administered drugs, and so will likely be applicable to other drugs, also.
Investigation of ancestral alleles in the Bovinae subfamily
Authors: Naji Maulana M. , Utsunomiya Yuri T. , Sölkner Johann , Rosen Benjamin D. , Mészáros Gábor 
Published: February 2021

Abstract
Background
In evolutionary theory, divergence and speciation can arise from long periods of reproductive isolation, genetic mutation, selection and environmental adaptation. After divergence, alleles can either persist in their initial state (ancestral allele - AA), co-exist or be replaced by a mutated state (derived alleles -DA). In this study, we aligned whole genome sequences of individuals from the Bovinae subfamily to the cattle reference genome (ARS.UCD-1.2) for defining ancestral alleles necessary for selection signatures study.

Results
Accommodating independent divergent of each lineage from the initial ancestral state, AA were defined based on fixed alleles on at least two groups of yak, bison and gayal-gaur-banteng resulting in ~ 32.4 million variants. Using non-overlapping scanning windows of 10 Kb, we counted the AA observed within taurine and zebu cattle. We focused on the extreme points, regions with top 0. 1% (high count) and regions without any occurrence of AA (null count). High count regions preserved gene functions from ancestral states that are still beneficial in the current condition, while null counts regions were linked to mutated ones. For both cattle, high count regions were associated with basal lipid metabolism, essential for survival of various environmental pressures. Mutated regions were associated to productive traits in taurine, i.e. higher metabolism, cell development and behaviors and in immune response domain for zebu.

Conclusions
Our findings suggest that retaining and losing AA in some regions are varied and made it species-specific with possibility of overlapping as it depends on the selective pressure they had to experience.
Geranylgeranylacetone attenuates cerebral ischemia–reperfusion injury in rats through the augmentation of HSP 27 phosphorylation: a preliminary study
Authors: Matsuo Kazuya , Hosoda Kohkichi , Tanaka Jun , Yamamoto Yusuke , Imahori Taichiro , Nakai Tomoaki , Irino Yasuhiro , Shinohara Masakazu , Sasayama Takashi , Kohmura Eiji 
Published: February 2021

Abstract
Background
We previously reported that heat shock protein 27 (HSP27) phosphorylation plays an important role in the activation of glucose-6-phosphate dehydrogenase (G6PD), resulting in the upregulation of the pentose phosphate pathway and antioxidant effects against cerebral ischemia–reperfusion injury. The present study investigated the effect of geranylgeranylacetone, an inducer of HSP27, on ischemia–reperfusion injury in male rats as a preliminary study to see if further research of the effects of geranylgeranylacetone on the ischemic stroke was warranted.

Methods
In all experiments, male Wistar rats were used. First, we conducted pathway activity profiling based on a gas chromatography–mass spectrometry to identify ischemia–reperfusion-related metabolic pathways. Next, we investigated the effects of geranylgeranylacetone on the pentose phosphate pathway and ischemia–reperfusion injury by real-time polymerase chain reaction (RT-PCR), immunoblotting, and G6PD activity, protein carbonylation and infarct volume analysis. Geranylgeranylacetone or vehicle was injected intracerebroventricularly 3 h prior to middle cerebral artery occlusion or sham operation.

Results
Pathway activity profiling demonstrated that changes in the metabolic state depended on reperfusion time and that the pentose phosphate pathway and taurine-hypotaurine metabolism pathway were the most strongly related to reperfusion among 137 metabolic pathways. RT-PCR demonstrated that geranylgeranylacetone did not significantly affect the increase in HSP27 transcript levels after ischemia–reperfusion. Immunoblotting showed that geranylgeranylacetone did not significantly affect the elevation of HSP27 protein levels. However, geranylgeranylacetone significantly increase the elevation of phosphorylation of HSP27 after ischemia–reperfusion. In addition, geranylgeranylacetone significantly affected the increase in G6PD activity, and reduced the increase in protein carbonylation after ischemia–reperfusion. Accordingly, geranylgeranylacetone significantly reduced the infarct size (median 31.3% vs 19.9%, p = 0.0013).

Conclusions
As a preliminary study, these findings suggest that geranylgeranylacetone may be a promising agent for the treatment of ischemic stroke and would be worthy of further study. Further studies are required to clearly delineate the mechanism of geranylgeranylacetone-induced HSP27 phosphorylation in antioxidant effects, which may guide the development of new approaches for minimizing the impact of cerebral ischemia–reperfusion injury.
Cloning and overexpression of PeWRKY31 from Populus × euramericana enhances salt and biological tolerance in transgenic Nicotiana
Authors: Yu Xiaoyue , Pan Yu , Dong Yan , Lu Bin , Zhang Chao , Yang Minsheng , Zuo Lihui 
Published: February 2021

Abstract
Background
As important forest tree species, biological stress and soil salinization are important factors that restrict the growth of Populus × euramericana. WRKYs are important transcription factors in plants that can regulate plant responses to biotic and abiotic stresses. In this study, PeWRKY31 was isolated from Populus × euramericana, and its bioinformation, salt resistance and insect resistance were analyzed. This study aims to provide guidance for producing salt-resistant and insect-resistant poplars.

Results
PeWRKY31 has a predicted open reading frame (ORF) of 1842 bp that encodes 613 amino acids. The predicted protein is the unstable, acidic, and hydrophilic protein with a molecular weight of 66.34 kDa, and it has numerous potential phosphorylation sites, chiefly on serines and threonines. PeWRKY31 is a zinc-finger C2H2 type-II WRKY TF that is closely related to WRKY TFs of Populus tomentosa, and localizes to the nucleus. A PeWRKY31 overexpression vector was constructed and transformed into Nicotiana tabacum L. Overexpression of PeWRKY31 improved the salt tolerance and insect resistance of the transgenic tobacco. Transcriptome sequencing and KEGG enrichment analysis showed the elevated expression of genes related to glutathione metabolism, plant hormone signal transduction, and MAPK signaling pathways, the functions of which were important in plant salt tolerance and insect resistance in the overexpressing tobacco line.

Conclusions
PeWRKY31 was isolated from Populus × euramericana. Overexpression of PeWRKY31 improved the resistance of transgenic plant to salt stress and pest stress. The study provides references for the generation of stress-resistant lines with potentially great economic benefit.
New insights into the role of MADS-box transcription factor gene CmANR1 on root and shoot development in chrysanthemum (Chrysanthemum morifolium)
Authors: Sun Cui-Hui , Wang Jia-Hui , Gu Kai-Di , Zhang Peng , Zhang Xin-Yi , Zheng Cheng-Shu , Hu Da-Gang , Ma Fangfang 
Published: February 2021

Abstract
Background
MADS-box transcription factors (TFs) are the key regulators of multiple developmental processes in plants; among them, a chrysanthemum MADS-box TF CmANR1 has been isolated and described as functioning in root development in response to high nitrate concentration signals. However, how CmANR1 affects root and shoot development remains unclear.

Results
We report that CmANR1 plays a positive role in root system development in chrysanthemum throughout the developmental stages of in vitro tissue cultures. Metabolomics combined with transcriptomics assays show that CmANR1 promotes robust root system development by facilitating nitrate assimilation, and influencing the metabolic pathways of amino acid, glycolysis, and the tricarboxylic acid cycle (TCA) cycle. Also, we found that the expression levels of TFs associated with the nitrate signaling pathways, such as AGL8, AGL21, and LBD29, are significantly up-regulated in CmANR1-transgenic plants relative to the wild-type (WT) control; by contrast, the expression levels of RHD3-LIKE, LBD37, and GATA23 were significantly down-regulated. These results suggest that these nitrate signaling associated TFs are involved in CmANR1-modulated control of root development. In addition, CmANR1 also acts as a positive regulator to control shoot growth and development.

Conclusions
These findings provide potential mechanisms of MADS-box TF CmANR1 modulation of root and shoot development, which occurs by regulating a series of nitrate signaling associated TFs, and influencing the metabolic pathways of amino acid and glycolysis, as well as TCA cycle and nitrate assimilation.
Drought-induced ABA, H2O2 and JA positively regulate CmCAD genes and lignin synthesis in melon stems
Authors: Liu Wei , Jiang Yun , Jin Yazhong , Wang Chenghui , Yang Juan , Qi Hongyan 
Published: February 2021

Abstract
Background
Cinnamyl alcohol dehydrogenase (CAD) is an important enzyme functions at the last step in lignin monomer synthesis pathway. Our previous work found that drought induced the expressions of CmCAD genes and promoted lignin biosynthesis in melon stems.

Results
Here we studied the effects of abscisic acid (ABA), hydrogen peroxide (H2O2) and jasmonic acid (JA) to CmCADs under drought stress. Results discovered that drought-induced ABA, H2O2 and MeJA were prevented efficiently from increasing in melon stems pretreated with fluridone (Flu, ABA inhibitor), imidazole (Imi, H2O2 scavenger) and ibuprofen (Ibu, JA inhibitor). ABA and H2O2 are involved in the positive regulations to CmCAD1, 2, 3, and 5, and JA is involved in the positive regulations to CmCAD2, 3, and 5. According to the expression profiles of lignin biosynthesis genes, ABA, H2O2 and MeJA all showed positive regulations to CmPAL2-like, CmPOD1-like, CmPOD2-like and CmLAC4-like. In addition, positive regulations were also observed with ABA to CmPAL1-like, CmC4H and CmCOMT, with H2O2 to CmPAL1-like, CmC4H, CmCCR and CmLAC17-like, and with JA to CmCCR, CmCOMT, CmLAC11-like and CmLAC17-like. As expected, the signal molecules positively regulated CAD activity and lignin biosynthesis under drought stress. Promoter::GUS assays not only further confirmed the regulations of the signal molecules to CmCAD1~3, but also revealed the important role of CmCAD3 in lignin synthesis due to the strongest staining of CmCAD3 promoter::GUS.

Conclusions
CmCADs but CmCAD4 are positively regulated by ABA, H2O2 and JA under drought stress and participate in lignin synthesis.
Effect of ABCA1 promoter methylation on premature coronary artery disease and its relationship with inflammation
Authors: An Fang , Liu Chao , Wang Xiujuan , Li Tan , Fu Hao , Bao Buhe , Cong Hongliang , Zhao Jihong 
Published: February 2021

Abstract
Background
ATP-binding cassette transporter A1 (ABCA1) plays a major role in high-density lipoprotein (HDL) metabolism and reverse cholesterol transport (RCT) and exerts anti-inflammatory effects. Increased ABCA1 promoter methylation level may result in the progression of coronary artery disease. Thus, the present study investigated the association between promoter methylation status of ABCA1 and inflammation in the development of premature coronary artery disease (pCAD).

Methods
PCAD patients and healthy individuals (n = 90 each) were recruited from the Characteristic Medical Center of the Chinese People's Armed Police Force from June to December 2019. Using pyrosequencing, the levels of ABCA1 promoter methylation in their blood samples were evaluated. Serum concentrations of lipids, interleukin 1β (IL-1β), C-reactive protein (CRP), and circulating free DNA/Neutrophil extracellular traps (cfDNA/NETs) were also routinely measured and compared between the two groups. P values < 0.05 were considered statistically significant.

Results
The mean ABCA1 promoter methylation levels were significantly higher in the pCAD group than in the control group (44.24% ± 3.66 vs. 36.05% ± 2.99, P < 0.001). Based on binary logistic regression analysis, ABCA1 promoter methylation level was identified as an independent risk factor for pCAD development (odds ratio = 2.878, 95% confidence interval: 1.802–4.594, P < 0.001). Furthermore, ABCA1 promoter methylation levels were negatively correlated with HDL levels (r =  − 0.488, P < 0.001) and positively correlated with the levels of CRP, cfDNA/NETs, and IL-1β (r = 0.389, 0.404, 0.385, respectively; P < 0.001). Multiple regression analysis showed that the serum levels of CRP, IL-1β, and cfDNA/NETs independently affect ABCA1 promoter methylation.

Conclusions
Our findings indicate that high methylation levels at the ABCA1 promoter are associated with low HDL cholesterol levels and an increased risk of pCAD. Inflammatory factors and NETs may be involved in the progression of pCAD by affecting ABCA1 promoter methylation levels.
Value of quantitative analysis of left ventricular systolic function in patients on maintenance hemodialysis based on myocardial work technique
Authors: Liu Chang , Feng Yi-Ping , Yan Zi-Ning , Fan Li , Rui Yi-Fei , Cui Ling 
Published: February 2021

Abstract
Background
This study aimed to determine the left ventricular (LV) systolic function in patients on maintenance hemodialysis (MHD) using the myocardial work (MW) technique and investigate the clinical value of the MW technique for the quantitative analysis of left ventricular (LV) systolic function in MHD patients with left ventricular hypertrophy (LVH).

Methods

A total of 68 MHD patients and 35 controls were registered in this study. The MHD patients were divided into the non-left ventricular hypertrophy (NLVH) group (n = 35) and the LVH group (n = 33) according to the LV mass index (LVMI). MW was used to generate the LV global longitudinal strain (GLS), global work index (GWI), global constructive work (GCW), and global wasted work (GWW), global work efficiency (GWE). GLS and the MW parameters (GWI, GCW, GWW, GWE) were compared between groups and the correlations between these parameters and the LV ejection fraction (LVEF) in the LVH group were examined. The receiver operating characteristic (ROC) curve was used to evaluate the efficacy of MW parameters and GLS for the assessment of LV systolic dysfunction in MHD with LVH patients.

Results
The LVH group had significantly lower GWE, GWI, GCW, and GLS but higher GWW than the control and NLVH groups. Compared with the control group, the NLVH group had significantly lower GWE and GLS and higher GWW, but no significant differences in GWI, GCW were observed between these two groups. The LVEF was negatively correlated with GWW in MHD patients, but positively correlated with GWI, GWE, and GCW in the LVH group. Receiver operating characteristic curve (ROC) analysis revealed that GWE, GWW, GWI, and GCW had appreciable area under the curve (AUC), sensitivity, and specificity for evaluating LV function in LVH patients on MHD.

Conclusions
The MW parameters can quantitatively represent the LV myocardial work in MHD patients. Thus, the technique provides a new method for the quantitative evaluation of LV systolic function in MHD with LVH patients.