bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transgenerational effect of drug-mediated inhibition of LSD1 on eye pigment expression in Drosophila
Authors: Hoyer-Fender Sigrid 
Published: May 2020

Abstract
Background: The Drosophila melanogaster mutant white-mottled is a well-established model for position-effect variegation (PEV). Transposition of the euchromatic white gene into the vicinity of the pericentric heterochromatin caused variegated expression of white due to heterochromatin spreading. The establishment of the euchromatin-heterochromatin boundary and spreading of silencing is regulated by mutually exclusive histone modifications, i.e. the methylations of histone H3 at lysine 9 and lysine 4. Demethylation of H3K4, catalysed by lysine-specific demethylase LSD1, is required for subsequent methylation of H3K9 to establish heterochromatin. LSD1 is therefore essential for heterochromatin formation and spreading. We asked, whether drug-mediated inhibition of LSD affects expression of white and if this induced change can be transmitted to those generations that have never been exposed to the triggering signal, i.e. transgenerational epigenetic inheritance.Results: We used the lysine-specific demethylase 1 (LSD1)-inhibitor Tranylcypromine to investigate its effect on eye colour expression in consecutive generations by feeding the parental and F1 generations of the Drosophila melanogaster mutant white-mottled . Quantitative Western blotting revealed that Tranylcypromine inhibits H3K4-demethylation both in vitro in S2 cells as well as in embryos when used as feeding additive. Eye colour expression in male flies was determined by optical measurement of pigment extracts and qRT-PCR of white gene expression. Flies raised in the presence of Tranylcypromine and its solvent DMSO showed increased eye pigment expression. Beyond that, eye pigment expression was also affected in consecutive generations including F3, which is the first generation without contact to the inhibitor.Conclusions: Our results show that feeding of Tranylcypromine and DMSO caused desilencing of white in treated flies of generation F1. Consecutive generations, raised on standard food without further supplements, are also affected by the drug-induced alteration of histone modifications. Although eye pigment expression eventually returned to the basal state, the observed long-lasting effect points to a memory capacity of previous epigenomes. Furthermore, our results indicate that food compounds potentially affect chromatin modification and hence gene expression, and that the alteration is putatively inherited not only parentally but transgenerationally.
Transcriptome changes induced by drought stress in Jerusalem artichoke (Helianthus tuberosus L.) and weighted gene co-expression network analysis (WGCNA)
Authors: Yang Shipeng , Wang Lihui , Zhong Qiwen , Zhang Guangnan , Zhang Dengshan , Sun Xuemei 
Published: May 2020

Abstract
Background: Jerusalem artichoke (Helianthus tuberosus L.) is strongly resistant to stress and an important plant used for ecological management in northern China in recent years. Currently, Jerusalem artichoke has been widely planted in the area around Qinghai Lake in Qinghai Province, China. Jerusalem artichoke can not only prevent land desertification but also has maintain most of its level of production. However, there is little research on the mechanism of drought resistance of Jerusalem artichoke.Results: We conducted transcriptome sequencing under drought stress and normal watering treatment for two varieties, QY1 and QY3, with differing degrees of drought tolerance. In the three stress periods of QY1 and QY3, 5,613, 12,985 and 24,923 differentially expressed genes (DEGs) were identified, respectively. GO analysis showed that there were more DEGs in QY1 than in QY3, but there were more up-regulated genes in QY3 than in QY1. Based on an additional analysis of the metabolic pathways under drought stress using MapMan, the most different types of metabolism included secondary metabolism, light reaction metabolism and cell wall. The up-regulated genes in QY3 were significantly more prevalent than those in QY1 and were primarily concentrated in flavor IDS, phenylpropanoids, and the shikimate and terpenoids pathway. As a whole, QY1 and QY3 both had a large number of up-regulated genes in the flavor pathway. In addition, the gene analysis of the ABA key metabolic pathway showed that QY3 had more genes in NAC and WRKY than QY1. A weighted gene co-expression network was constructed and divided into modules. By specifically analyzing the expressed modules, four modules were found to have the highest correlation with drought. Further research on the genes revealed that all 16 genes related to histone, ABA and protein kinase were the most significant in these pathways.Conclusions: In summary, these findings represent the first RNA-Seq analysis of drought stress in Jerusalem artichoke, which is of substantial significance to explore the function of drought resistance in Jerusalem artichoke and the unearthing of related genes.
Assessing the genetic diversity of cowpea [Vigna unguiculata (L.) Walp.] germplasm collections using phenotypic traits and SNP markers
Authors: Nkhoma Nelia , Shimelis Hussein , Laing Mark , Shayanowako Admire , Mathew Isack 
Published: May 2020

Abstract
Background
Productivity of cowpea [Vigna unguiculata (L.) Walp] in sub-Sahara Africa is curtailed by a lack of farmer-preferred and improved cultivars and modern production technologies. The objectives of the study were to determine the extent of genetic diversity present among a collection of cowpea accessions from Zambia and Malawi using phenotypic traits and single nucleotide polymorphism (SNP) markers and, to select distinct and complementary parental lines for cultivar development. One hundred cowpea genotypes were evaluated for agronomic traits in two selected sites in Zambia, using a 10 × 10 alpha lattice design with two replications. Ninety-four of the test genotypes were profiled with 14,116 SNP markers.
Results
Number of pods plant− 1 (NPP), pod length (PDL), and number of seeds pod− 1 (NSP), were significantly (p < 0.05) affected by genotype × environment interaction effects. Genotypes such as CP411, CP421, CP645, CP732, Chimponongo, and MS1-8-1-4 exhibited higher grain yield of > 1200 kg/ha with excellent performance in yield components such as NSP, PDL, HSW and GYD. Grain yield had significant (p < 0.05) associations with NPP (r = 0.50), NSP (r = 0.46) and PDL (r = 0.42) useful for simultaneous selection for yield improvement in cowpea. The SNP markers revealed gene diversity and polymorphic information content of 0.22 and 0.17, respectively, showing that the tested cowpea accessions were genetically diverse. Test genotypes were classified into four genetic groups irrespective of source of collection allowing selection and subsequent crosses to develop breeding populations for cultivar development.
Conclusions
Genotypes Bubebe, CP411, CP421, CP645, Chimponogo and MS1-8-1-4 were identified to be the most genetically divergent and high yielding making them ideal parental lines for breeding. This study provided a baseline information and identified promising cowpea genetic resources for effective breeding and systematic conservation.
Association between five types of Tumor Necrosis Factor-α Gene Polymorphism and Hepatocellular Carcinoma Risk: A Meta-Analysis
Authors: Wungu Citrawati Dyah Kencono , Ariyanto Fis Citra , Prabowo Gwenny Ichsan , Soetjipto Soetjipto , Handajani Retno 
Published: May 2020

Abstract
Background: Research focusing on the relationship between five types of tumor necrosis factor-alpha (TNF-α) SNPs and the risk of hepatocellular carcinoma (HCC) were still controversial. Hereby, we performed a meta-analysis to determine the association between TNF-α promoter SNPs: -1031 T/C, -863 C/A, -857 C/T, -308 G/A, and -238 G/A with HCC risk. Methods: We interrogated articles from journal database: PubMed, Pro-Quest, EBSCO, Science Direct, and Springer to determine the relationship between five types of SNPs in TNF-α gene with HCC risk. RevMan 5.3 software was used for analysis in fixed/random effect models. Results: This meta-analysis included 23 potential articles from 2004-2018 with 3,237 HCC cases and 4,843 controls. We found that SNP -863 C/A were associated with a significantly increased HCC risk (A vs C, OR=1.31, 95% CI=1.03-1.67; CA/AA vs CC, OR=1.19, 95% CI=1.03-1.36). Similar results were obtained in -857 C/T (TT/CT vs CC, OR=1.31, 95% CI=1.06-1.62), -308 G/A (G vs A, OR=1.98, 95% CI=1.62-2.42; AA/GA vs GG, OR=1.95, 95% CI=1.53-2.49; GG/GA vs AA, OR=2.52, 95% CI=1.69-3.76; AA vs GG, OR=3.14, 95% CI=2.06-4.79; and GA vs GG, OR=2.07, 95% CI=1.60-2.68), and -238 G/A (A vs G, OR=1.50, 95% CI=1.16-1.94; AA vs GG, OR=3.87, 95% CI=1.32-11.34; GA/GG vs AA, OR=2.67, 95% CI=1.17-6.10). While no associations were observed between SNP TNF-α -1031 T/C and HCC risk. Conclusions: The present meta-analysis showed that TNFα SNPs -863C/A, -857 C/T, -308 G/A, and -238 G/A were associated with the risk of HCC.
Effect of nutrition education on iodine deficiency disorder and iodized salt intake in south west Ethiopian women: a cluster randomized controlled trial
Authors: Asfaw Agize , Belachew Tefera , Gari Taye 
Published: May 2020

Abstract
Background: Although iodine nutrition status is improving globally, the progress is not uniform throughout the world due to several factors. Among these, poor knowledge, negative attitude and improper practice of iodized salt are the main risk factors for poor iodine nutrition in Ethiopia.Objectives: This study was aimed to assess the effect of nutrition education intervention in improving the knowledge, attitude and practice (KAP) towards iodine deficiency disorder and iodized salt intake in southwest Ethiopia.Methods: A cluster randomized controlled trial was carried out among 652 women of reproductive age group in southwest Ethiopia. A total of 24 clusters were selected and randomized in to an intervention and control villages. Women in the intervention village received iodine nutrition related education for six months; while those in the control village did not receive any education. Baseline and endline data were collected from both groups. Generalized Estimating Equations (GEE) was used to determine the effect of intervention.Results: A total of 647 (99.2%) participants were successfully involved in the study. In the intervention group the median attendance was 10 out of 12 education sessions. There was significant change in mean KAP scores for intervention group (p < .001). In multivariable GEE model, after adjusting for other background characteristics, the knowledge score from the baseline increased by approximately nine points (β= 8.674, P<0.0001) and three points for both attitude ((β=3.193, P<0.0001) and practice (β=2.926, P<0.0001) after six months of intervention.Conclusions: Well designed and community-based iodine nutrition education is an effective strategy to improve the KAP of iodine deficiency disorder and iodized salt utilization.Trial registration: PACTR201809544276357 (Retrospectively registered on 14, Sept. 2018), http://www.pactr.org
Analysis across diverse fish species highlights no conserved transcriptome signature for proactive behaviour
Authors: Planellas Sonia Rey , Jin Xingkun , Damsgard Borge , Begout Marie-Laure , Mackenzie Simon 
Published: May 2020

Abstract
Background: Consistent individual differences in behaviour, known as animal personalities, have been demonstrated within and across species. In fish, studies applying an animal personality approach have been used to resolve variation in physiological and molecular data suggesting a linkage, genotype-phenotype, between behaviour and transcriptome regulation. In this study, using three fish species (zebrafish; Danio rerio, Atlantic salmon; Salmo salar and European sea bass; Dicentrarchus labrax), we firstly address whether personality-specific mRNA transcript abundances are transferrable across distantly-related fish species and secondly whether a proactive transcriptome signature is conserved across all three species.Results: Previous zebrafish transcriptome data was used as a foundation to produce a curated list of mRNA transcripts related to animal personality across all three species. mRNA transcript copy numbers for selected gene targets show that differential mRNA transcript abundance in the brain appears to be partially conserved across species relative to personality type. Secondly, we performed RNA-Seq using whole brains from S. salar and D. labrax scoring positively for both behavioural and molecular assays for proactive behaviour. We further enriched this dataset by incorporating a zebrafish brain transcriptome dataset specific to the proactive phenotype. Our results indicate that cross-species molecular signatures related to proactive behaviour are functionally conserved where shared functional pathways suggest that evolutionary convergence may be more important than individual mRNAs.Conclusions: Our data supports the proposition that highly polygenic clusters of genes, with small additive effects, likely support the underpinning molecular variation related to the animal personalities in the fish used in this study. The polygenic nature of the proactive brain transcriptome across all three species questions the existence of specific molecular signatures for proactive behaviour, at least at the granularity of specific regulatory gene modules, level of genes, gene networks and molecular functions.
BK polyomavirus infection promotes growth and aggressiveness in bladder cancer
Authors: Sun Jiajia , Zeng Yigang , Bao Juan , Zhu Tongyu 
Published: May 2020

Abstract
Background Recent studies have confirmed the integration of the BK polyomavirus (BKPyV) gene into the cellular genome of urothelial carcinomas in transplant recipients, further confirming the correlation between BKPyV and urothelial carcinomas after transplantation. However, the role BKPyV infections play in the biological function of bladder cancer remains unclear.Methods We developed a BKPyV-infected bladder cancer cell model and a mice tumor model to discuss the role of BKPyV infections.Results Our research proves that BKPyV infections promote the proliferation, invasion and migration of bladder cancer, while the activation of β-catenin signaling pathway is one of its mediation mechanisms.Conclusions We first described BKPyV infection promotes the proliferation, invasion and migration of bladder cancer. We verified the role of β-catenin signaling pathway and Epithelial-Mesenchymal Transition effect in BKPyV-infected bladder cancer. These results provide meaningful information towards the diagnosis and treatment of clinical bladder cancer.
Increase of Oxidative Stress is Positively Associated with High-Sensitivity C-Reactive Protein in Women Using Combined Oral Contraceptives: An Observational Study
Authors: Cauci Sabina , Francescato Maria Pia , Colannino Chiara , Barbina Mattia , Barbina Giuseppe , Xodo Serena 
Published: May 2020

Abstract
Background

Information concerning oxidative stress and low-grade inflammation in oral contraception users is scarce. We investigated relationships of oxidative stress and high-sensitivity C-reactive protein (hsCRP) in women by oral combined contraceptive (OC) use.
Methods

Caucasian Italian healthy non-obese women (n = 290; 100 OC-users; 190 non-OC-users; mean age 23.2 ± 4.7 years) were analyzed. Blood hydroperoxides, as oxidative stress biomarkers, were assessed by Free Oxygen Radical Test (FORT), and serum hsCRP was determined by routine methods.
Results

Oxidative stress levels were elevated (≥ 400 FORT Units) in 77.0% and 15.8% of OC-users and non-OC-users, respectively (odds ratio (OR) = 209, 95%CI = 60.9-715.4, p < 0.001); hsCRP levels ≥ 2.0 mg/L were found in 41.0% and 9.5% of OC-users and non-users, respectively (OR = 6.6, 95%CI 3.5–12.4, p < 0.001). Continuous hydroperoxides values in OC-users were 1.7-fold higher compared to non-users (median 472 versus 270 FORT Units, p < 0.001); OC-users had 3.7-fold higher hsCRP values compared to non-OC-users (median 1.31 versus 0.35 mg/L, p < 0.001). Hydroperoxides were strongly positively correlated to hsCRP in all women (rs=0.622, p < 0.001), in OC-users (rs=0.442, p < 0.001), and in non-OC-users (rs=0.426, p < 0.001). Women with hydroperoxides ≥ 400 FORT Units were 8 times as likely to have hsCRP ≥ 2 mg/L. In non-OC-users only, hydroperoxides values were positively correlated with weight and body mass index, but negatively correlated with red meat, fish and chocolate consumption.
Conclusions

Our cross-sectional observational study is the first finding a strong positive correlation of serum hydroperoxides with hsCRP, a marker of inflammation. Further research is needed to elucidate the potential role of these two biomarkers in OC-use side-effects, like thromboembolism.
Concurrent ipsilateral Tillaux fracture and medial malleolar fracture in adolescence: management and outcome
Authors: yuan quanwen , Guo Zhixiong , Wang Xiaodong , Dai Jin , Zhang Fuyong , Fang Jianfeng , Yin Chunhua , Yu Wentao , Zhen Yunfang 
Published: May 2020

Abstract
Background
The concurrent ipsilateral Tillaux fracture with medial malleolar fracture in adolescence commonly suffer from high-energy injury, making treatment more difficult. The aim of this study was to discuss the mechanism on injury, diagnosis and treatment of this complex fracture pattern.
Methods
The charts and radiographs of six patients were reviewed. The functional was assessed by the American Orthopedic Foot and Ankle Society ankle-hindfoot scores.
Results
The mean age at operation was 12.8 years. The mean interval from injury to operation was 7.7 days. Five Tillaux fractures and all medial malleolar fractures were shown on AP plain radiographs. One Tillaux fracture and two cases with avulsion of posterolateral tibial aspect were confirmed in axial computerized tomography. Talar subluxation laterally with medial space widening in three, and syndesmotic disruption in one. There were five patients sustaining ipsilateral distal fibular fractures. All fractures, except nonunion in two medial malleolar fractures and in one Tillaux fracture, healed within 6–8 weeks. There was one case of osteoarthritis of ankle joint. The average AOFAS score was 88.7.
Conclusions
Computerized tomography is helpful in identifying the fracture pattern. Anatomic reduction and internal fixation of Tillaux and medial malleolar fracture was recommended to restore the articular surface congruity and ankle stability.
Role of SNPs in the biogenesis of mature miRNAs
Authors: Wang Ying , Ru Jidong , Xianglian Meng 
Published: May 2020

Abstract
BackgroundSNPs within pre-miRNA regions play a significant role in miRNA generation, processing and function by different molecular mechanisms and are thought to be major contributors to the variations in phenotypes and diseases. Therefore, whole-genome analysis of how SNPs affect mature miRNA biogenesis is important for precision medicine. ResultsIn this study, aiming to analyze the role of SNPs in mature miRNA biogenesis genome-wide, we constructed a SNP-pre-miRNA database, named miRSNPBase, consisting of 886 pre-miRNAs and 2640 SNPs based on the latest data. Then, we identified 10574 SNP-pre-miRNAs based on 886 pre-miRNAs and their associated 2640 SNPs, and we performed genome-wide association analyses to identify isoform miRNAs (isomiRs) based on miRFind that are associated with the mechanism of SNPs affecting miRNA maturation. A total of 4235 nor-SNP-pre-miRNAs based on 480 nor-pre-miRNAs and 1250 nor-SNPs were identified. We analyzed the effects of SNP type, SNP location and SNP-mediated free energy change during mature miRNA biogenesis and found that they are closely related to mature miRNA biogenesis. In addition, the MAF distribution of the iso-pre-miRNAs and nor-SNPs was analyzed based on the 1000 Genomes Project. The results demonstrated that individuals who contained the iso-SNPs were in the minority, and those who contained the nor-SNPs were in the majority. Notably, to verify our method and identify important biomarkers, we identified isomiRs and iso-SNPs in 18 GBR individuals of European origin. In the results, 209 iso-pre-miRNA candidates and 71 verified iso-pre-miRNAs of the 18 GBR samples were identified, and 2667 isomiRs of 209 pre-miRNAs were verified by miRNA sequencing data.ConclusionsOur results clearly indicated that SNPs that altered the mature miRNA splicing mechanism and led to the production of isomiRs, were closely related to and affected normal life processes, and led to epigenetic changes and diseases.
Potential value of combining CTX-II with C2C in evaluating and diagnosing early rat osteoarthritis
Authors: Shen Meilun , Zhang Zhiheng , Ma Xiangying , Li Rouqian , Jin Xiaodi , Ma Tianwen , Gao Li , Wang Zhi 
Published: May 2020

Abstract
Background

This article aims to study the changes of CTX-II and C2C biomarker concentrations during the pathogenesis of osteoarthritis with SD rats as the research object. Through the longitudinal and joint detection of the content of CTX-II and C2C markers in the serum of anterior cruciate ligament resection (ACLT) rats, the evaluation and early diagnosis of OA disease can be realized, and the theoretical basis for the rapid diagnosis technology of OA can be provided.
Methods

SD rats were randomly divided into two groups: Sham operation group and OA model group. The OA model was established by anterior cruciate ligament excision (ACLT) for 2, 4, 6, 8, and 10 weeks, respectively. The cartilage gross score and Mankin score were used to evaluate the model. The tibia of the right hind limb was sampled for pathological histology and HE staining. The collected blood samples are used to detect changes in the concentration of CTX-II and C2C in serum. The receiver operating characteristic curve (ROC) was used to compare the area under the curve (AUC) of CTX-II, C2C and combined biomarkers.
Results

In the model group, the content of CTX-II and C2C in SD rat serum increased significantly, and the content of CTX-II and C2C increased with the prolonged modeling time, which was time dependent; The levels of CTX-II and C2C in the serum of rats in the sham operation group did not change significantly; both macroscopic observations and Mankin scores increased significantly. The AUC of the combined biomarker is higher than that of CTX-II and C2C. Finally, CTX-II and C2C levels were positively correlated with Mankin score.
Conclusion

Early combined detection of serum CTX-II and C2C concentrations has potential value for the evaluation and diagnosis of osteoarthritis.