bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome-based analysis of the effects of salicylic acid and high light on lipid and astaxanthin accumulation in Haematococcus pluvialis
Authors: Hu Qunju , Huang Danqiong , Li Anguo , Hu Zhangli , Gao Zhengquan , Yang Yongli , Wang Chaogang 
Published: November 2020

Abstract
Background: The fresh water unicellular alga Haematococcus pluvialis has achieved considerable interests for its capacity to accumulate large amounts of triacylglycerol and astaxanthin under various environmental stresses. To our knowledge, works focusing on transcriptome research of H. pluvialis under exogenous hormones together with physical stresses is rare.Results: In the present study, the change patterns at transcriptome level were analyzed to distinguish the multiple defensive systems of astaxanthin and fatty acid metabolism against exogenous salicylic acid and high light (SAHL) stresses. Based on RNA-seq data, a total of 112,463 unigenes and 61,191 genes were annotated in six databases, including NR, KEGG, Swiss-Prot, PFAM, COG and GO. The top five categorized GO terms based on these genes were “catalytic activity”, “binding”, “cellular process”, “cell” and “cell part”. Furthermore, 705 unigenes predicted as putative transcription factors (TFs) were identified and assigned to 25 families. The top five most abundant TFs families were C3H, MYB, Nin-like, MTB_related and ERF, which were likely to be associated with the biosynthesis of astaxanthin and fatty acid in H. pluvialis upon exposure to the SAHL stresses. Analysis of differentially expressed genes (DEGs) in KEGG identified many transcripts that associated with the biosynthesis of primary and secondary metabolites, photosynthesis, and immune system responses. Additionally, fifteen key genes that involved in astaxanthin and fatty acid biosynthesis pathways presented the same transcriptional pattern in response to the SAHL stresses, and positive correlations were observed among them by Pearson Correlation (PC) analysis, indicating the coordination between astaxanthin and fatty acid biosynthesis. Furthermore, protein–protein interaction (PPI) network analysis also demonstrated that this coordination might be at transcriptional level.Conclusion: The results demonstrated in this study provide valuable information to illustrate the molecular mechanisms of coordinate relations between astaxanthin and fatty acid biosynthesis, which may play a role in both genetic and metabolic engineering efforts to improve astaxanthin and fatty acid production by H. pluvialis.
An in silico approach to target SARS-CoV-2 RNA dependent RNA polymerase of COVID-19 with naturally occurring phytochemicals
Authors: Mahrosh Hafiza Salaha , Mustafa Ghulam 
Published: November 2020

Abstract
The novel coronavirus disease 2019 (COVID-19) was firstly reported from Wuhan city of China found as highly contagious, transmittable and pathogenic viral infection. The World Health Organization declared COVID-19 as a pandemic since its emergence from China. The RNA dependent RNA polymerase (nsp-12) is a complex with nsp-7 and nsp-8 cofactors major constituent of viral replication and RNA synthesis machinery. In current study, the RdRp of virus was selected as a receptor protein for computational drug discovery. Computational homology modelling was done in order to find the hidden secondary structures and structural assessment of viral protein to target them via antiviral drugs. The study based on docking of different phytochemicals to check potential of different plant metabolites against viral replicative proteins. Out of 200 ligands used in this study from different plants the best ten were selected based on drug discovery parameters such as S-score, ligand interactions, hydrophobic interactions and drug likeness. The ten best selected ligands were Verbenalin, Epigallocatechin, Swertisin, Nobiletin, Pinoresinol, Caftaric acid, Hesperetin, Islandicin, Neochlorogenic acid and Sesamin that exploit the potency as antagonist of viral protein. Among binding interactions of all ligands Arg339 centred as the main interacting residue among almost all the ligands. Till now many antiviral agents have shown potency in only mild cases of SARS-CoV-2 but no effective drug has been found for critical pulmonary cases. In clinical trials many broad-spectrum antiviral agents have been still in trail periods of testing against SARS-CoV-2. Till date no effective drug or vaccine has been validated with significant efficacy and potency against the SARS-CoV-2 therefore there is an urgent need to design effective vaccine against nCoV-19 infections.
Transcriptome and metabolome analyses of cold and darkness-induced pellicle cysts of Scrippsiella trochoidea
Authors: Guo Xin , Wang Zhaohui , Liu Lei , Li Yang 
Published: November 2020

Abstract
Background: Dinoflagellates are a group of unicellular organisms that are a major component of aquatic eukaryotes and important contributors to marine primary production. Nevertheless, many dinoflagellates are considered harmful algal bloom (HAB) species due to their detrimental environmental and human health impacts. Cyst formation is widely perceived as an adaptive strategy of cyst-forming dinoflagellates in response to adverse environmental conditions. Dinoflagellate cysts play critical roles in bloom dynamics. However, our insight into the underlying molecular basis of encystment is still limited. To investigate the molecular processes regulating encystment in dinoflagellates, transcriptome and metabolome investigations were performed on cold and darkness-induced pellicle cysts of Scrippsiella trochoidea.Results: No significant transcriptional response was observed at 2 h; however, massive transcriptome and metabolome reprogramming occurred at 5 h and in pellicle cysts. The gene-to-metabolite network demonstrated that the initial transformation from vegetative cells into pellicle cysts was highly energy demanding through the activation of catabolism, including glycolysis, β-oxidation, TCA cycle and oxidative phosphorylation, to cope with cold-darkness-induced stress. However, after transformation into pellicle cysts, the metabolism was greatly reduced, and various sugars, polyunsaturated fatty acids and amino acids accumulated to prolong survival. The identification of 56 differentially expressed genes (DEGs) related to signal transduction indicated that S. trochoidea received a cold-darkness signal that activated multiple signal transduction pathways, leading to encystment. The elevated expression of genes encoding enzymes involved in ROS stress suggested that pellicle cysts respond to increased oxidative stress. Several cell cycle-related genes were repressed. Intriguingly, 11 DEGs associated with sexual reproduction suggested that pellicle cysts (or some portion thereof) may be a product of sexual reproduction. Conclusions: This study provides the first transcriptome and metabolome analyses conducted during the encystment of S. trochoidea, an event that requires complex regulatory mechanisms and impacts on population dynamics. The results reveal comprehensive molecular regulatory processes underlying life cycle regulation in dinoflagellates involving signal transduction, gene expression and metabolite profile, which will improve our ability to understand and monitor dinoflagellate blooms.
Genotyping and lipid profiling of 601 cultivated sunflower lines reveals novel genetic determinants of oil fatty acid content
Authors: Chernova Alina , Gubaev Rim , Singh Anupam , Sherbina Katrina , Goryunova Svetlana , Martynova Elena , Goryunov Denis , Boldyrev Stepan , Vanyushkina Anna , Anikanov Nikolay , Stekolshchikova Elena , Yushina Ekaterina , Demurin Yakov , Mukhina Zhanna , Gavrilova Vera , Anisimova Irina , Karabitsina Yulia , Alpatieva Natalia , Chang Peter L , Khaitovich Philipp , Mazin Pavel , Nuzhdin Sergey 
Published: November 2020

Abstract
Background: Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of the oil properties achieved by modulating its fatty acid composition is one of the main directions in modern oilseed crop breeding. Results: We searched for the genetic basis of fatty acid content variation by genotyping 601 inbred sunflower lines and assessing their lipid and fatty acid composition. Our genome-wide association analysis based on the genotypes of 15,483 SNPs and the concentrations of 23 fatty acids, including minor fatty acids, revealed significant genetic associations for eleven of them. Identified genomic regions included novel loci on chromosomes 3 and 14 cumulatively, explaining up to 34.5% of the total variation of docosanoic acid (22:0) in sunflower oil.Conclusions: This is the first large scale implementation of high-throughput lipidomic profiling on sunflower germplasm characterization. This study contributes to the genetic characterization of Russian collections, which made a substantial contribution to the development of a sunflower as the oilseed crop worldwide and provides new insights into the genetic control of oil composition that can be implemented in future studies.
Molecular dominance investigation for large-sized parents&nbsp;of Chinese Mitten Crab ( Eriocheir sinensis ) based on&nbsp;ovarian transcriptome
Authors: Xuan Fujun , Fu Longlong , Wang Kun , Hua Zonglin , Xiong Xinxin , Zhang Jianguang , Pan Jianlin , Tang Boping , Guan Weibing , Cheng Yongxu 
Published: November 2020

Abstract
Background: Germplasm degradation is one of the important issues for the healthy development of Chinese Mitten Crab (Eriocheir sinensis) industry. Nowadays, nursery units and crab farmers have realized the seedling superiority of large-sized parents (≥200g male, ≥150g female), but the underlying molecular mechanisms remain unclear. Here we investigated the advantage of breeding with large-sized parents based on ovarian transcriptome.Results: RNA isolation and transcriptome sequencing were performed using ovarian tissue obtained from three large-sized female E. sinensis and three medium-sized female E. sinensis. The differentially expressed genes (DEGs) were investigated between two groups, followed by the exploration of common DEGs (co-DEGs) among the DEGs in the current study and published genes for growth, reproduction, and immune response pathways. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to validate all co-DEGs. Finally, a pathway enrichment analysis was performed to investigate the potential pathways associated with the validated co-DEGs. A total of 5,307 up-regulated genes and 3,465 down-regulated genes were investigated between the two groups, of which 43 co-DEGs were explored when all the DEGs in the current study were integrated with 338 genes in 15 reproductive, immune, and growth pathways. A total of nine co-DEGs, including TRINITY_DN13931_c0_g1, TRINITY_DN1908_c0_g2, and TRINITY_DN6686_c0_g1, were enrolled for further study after qRT-PCR validation. These validated co-DEGs were mainly enriched in pathways such as apoptosis, insulin signaling, and mTOR signaling. Conclusion: Our original work might lay an important molecular foundation for further exploring the advantages of using large-sized parents for E. sinensis breeding in the future. Based on the comparative analysis of gene expression, the advantages of breeding large-sized female E. sinensis parents at the molecular level, such as growth, reproduction, and immunity, were analyzed for the first time. The apoptosis pathways, insulin signaling pathways, and mTOR signaling pathway might be involved in the advantage of breeding large-sized female E. sinensis parents.
Genome-wide identification of sucrose nonfermenting-1-related protein kinase (SnRK) genes in barley and RNA-seq analyses of their expression in response to ABA treatment
Authors: Chen Zhiwei , Zhou Longhua , Jiang Panpan , Lu Ruiju , Halford Nigel G. , Liu Chenghong 
Published: November 2020

Abstract
Background: Sucrose nonfermenting-1 (SNF1)-related protein kinases (SnRKs) play important roles in regulating metabolism and stress responses in plants, providing a conduit for crosstalk between metabolic and stress signalling, in some cases involving the stress hormone, abscisic acid (ABA). The burgeoning and divergence of the plant gene family has led to the evolution of three subfamilies, SnRK1, SnRK2 and SnRK3, of which SnRK2 and SnRK3 are unique to plants. Therefore, the study of SnRKs in crops may lead to the development of strategies for breeding crop varieties that are more resilient under stress conditions. In the present study we describe the SnRK gene family of barley (Hordeum vulgare), the widespread cultivation of which can be attributed to its good adaptation to different environmentsResults: The barley HvSnRK gene family was elucidated in its entirety from publicly-available genome data and found to comprise 50 genes. Phylogenetic analyses assigned six of the genes to the HvSnRK1 subfamily, 10 to HvSnRK2 and 34 to HvSnRK3. The search was validated by applying it to Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome data, identifying 50 SnRK genes in rice (four OsSnRK1, 11 OsSnRK2 and 35 OsSnRK3) and 39 in Arabidopsis (three AtSnRK1, 10 AtSnRK2 and 26 AtSnRK3). Specific motifs were identified in the encoded barley proteins, and multiple putative regulatory elements were found in the gene promoters, with light-regulated elements (LRE), ABA response elements (ABRE) and methyl jasmonate response elements (MeJa) the most common. RNA-seq analysis of the roots of seedlings grown with and without ABA treatment showed that many of the genes responded to ABA, some positively, some negatively and some with complex time-dependent responses.Conclusions: The barley HvSnRK gene family is large, comprising 50 members, subdivided into HvSnRK1 (6 members), HvSnRK2 (10 members) and SnRK3 (34 members), showing differential positive and negative responses to ABA.
Carrageenan nasal spray may double the rate of recovery from coronavirus and influenza virus infections: re-analysis of randomized trial data
Authors: Hemilä Harri , Chalker Elizabeth 
Published: November 2020

Abstract
Carrageenan is a sulfated polysaccharide that has been extensively used in food products. Since the 1980s, carrageenan has been shown to prevent infections due to several viruses in cell cultures, including rhinoviruses which cause the common cold. In animal studies it prevented mortality caused by influenza A. Carrageenan is generally regarded as safe by the FDA. This individual patient data meta-analysis examined the datasets of two randomized placebo-controlled trials which investigated the effect of carrageenan separately on children and adults. In both trials, iota-carrageenan was administered nasally 3 times per day for 7 days for patients with the common cold and follow-up lasted for 21 days. Nasal carrageenan increased the recovery rate from all colds by 54% (95% CI 15% to 105%; P = 0.003). The increase in recovery rate was 140% in coronavirus infections, 119% in influenza A infections, and 70% in rhinovirus infections. We used quantile regression to calculate the effect of carrageenan on colds of differing lengths, by dividing the distribution into 5 quintiles. The mean duration of colds in the placebo groups of the first four quintiles were 4.0, 6.8, 8.8 and 13.7 days, respectively. The fifth quintile contained patients with censored data. The 13.7-day colds were shortened by 3.8 days (28% reduction), and 8.8-day colds by 1.3 days (15% reduction). Carrageenan had no meaningful effect on shorter colds. In the placebo group, 21 patients had colds that lasted over 20 days, compared with 6 patients in the carrageenan group. This corresponds to a 71% (P = 0.003) reduction in the risk of longer colds. Finally, in the placebo group, 37 patients had recurring cold symptoms after first being cured, compared with 16 in the carrageenan group. This corresponds to a 56% (P = 0.002) reduction in the risk of recurring symptoms. Given that carrageenan has an effect on diverse virus groups, and its demonstrated effects on two old coronaviruses, it seems plausible that nasal carrageenan may also have an effect on the new coronavirus SARS-CoV-2. Further research on nasal iota-carrageenan is warranted.
Efficacy and Safety of Atropine to Control Myopia Progression: A Systematic Review and Meta-analysis
Authors: Zhao Congling , Cai Chunyan , Ding Qiang , Dai Hongbin 
Published: November 2020

Abstract
Background: The effect and safety of atropine on delaying the progression of myopia has been extensively studied, but its optimal effect dose is still unclear. Therefore, the purpose of this meta-analysis is to systematically evaluate the safety and effectiveness of atropine in controlling the progression of myopia, and to explore the relationship between the dose of atropine and the effect of controlling the progression of myopia. Methods: This work was done through the data search from PubMed, MEDLINE, EMBASE, and the Cochrane Central Register of Controlled Trials. The Cochrane Handbook was also used to evaluate the quality of these included studies. In addition, a meta-analysis was performed using Revman5.3 software. Results: A total of 10 randomized controlled trials (RCTs) were included. Myopia progression was mitigated greater in the atropine treatment group than the control group, with MD = -0.80, 95% CI (-0.94, -0.66) during the whole observation period. There was a statistical difference between 0.05%, 0.5%, and 1.0% atropine (P = 0.004). In addition, less axial elongation was showed, with MD = -0.26, 95% CI (-0.33, -0.18) during the whole observation period. Conclusion: The effect of atropine in controlling the progression of myopia was dose related. A 0.05% atropine was likely to be the optimal dose.
Prevalence of Metabolic Syndrome among Breast Cancer Survivors in East Coast of Peninsular Malaysia
Authors: Shahril Mohd Razif , Amirfaiz Syed , Lua Pei Lin , Nurnazahiah Ali , Zakarai Nor Syamimi , Kow Ving Lok , Ahmad Aryati , Sulaiman Suhaina 
Published: November 2020

Abstract
To date, limited data are available on metabolic syndrome prevalence among breast cancer survivors in Malaysia. Therefore, this study was conducted to determine the prevalence of metabolic syndrome and abnormal metabolic syndrome components among breast cancer survivors in East Coast of Peninsular Malaysia. This cross-sectional study included 95 breast cancer survivors (age 53.7±7.6 years) who have completed main cancer treatments for ≥6 months. Cancer survivors were recruited from two main government hospitals in Kelantan and Terengganu using a purposive sampling method. According to the Harmonized criteria, the metabolic syndrome prevalence was 50.5%. Among those with metabolic syndrome, the most prevalent abnormal metabolic components were triglycerides (91.2%), fasting blood glucose (79.6%) and HDL-c level (78.4%). Except for total cholesterol and LDL-c, all other metabolic syndrome components were significantly different (p<0.05) between those with and without metabolic syndrome. Significant differences between metabolic syndrome and non-metabolic syndrome groups were found for weight, BMI, waist circumference, body fat percentage and cancer stages (p<0.05). However, no significant relationship was reported between sociodemographic, clinical parameters and metabolic syndrome among breast cancer survivors in this study. In conclusion, metabolic syndrome was highly prevalent among breast cancer survivors. It is recommended for health care professionals to closely monitor and improve the triglycerides, blood glucose and HDL-c level of the breast cancer survivors under their care to control the detrimental effect of metabolic syndrome.
The prevalence of depression, stress and anxiety symptoms in patients with chronic heart failure&nbsp;
Authors: Tsabedze Nqoba , Kinsey Jamie-Leigh , Mpanya Dineo , Mogashoa Vanessa , Klug Eric , Manga Pravin 
Published: November 2020

Abstract
Background: Mental health illnesses are associated with frequent rehospitalisation and an increased risk of all-cause mortality. Despite the high prevalence of depression in patients with chronic heart failure (CHF), there is a paucity of data on this subject from low and middle-income countries (LMIC). This study aimed to determine the prevalence of depression, anxiety and stress symptoms in patients attending a dedicated chronic heart failure clinic. Methods: A prospective study was conducted at an outpatient heart failure clinic in a tertiary academic centre. The study participants completed a Depression, Anxiety and Stress (DASS-21) questionnaire to screen for the presence and severity of depression, anxiety and stress symptoms. Furthermore, the Minnesota Living with Heart Failure Questionnaire (MLHFQ) was completed and used to evaluate the impact of CHF on health-related quality of life. Descriptive statistics were used to describe patients' characteristics and logistic regression analysis to identify predictors of symptoms of depression.Results: The study population comprised of 103 patients, predominantly female (62.1%) with a median age of 53 (interquartile range 38 – 61) years. Symptoms of depression were reported by 52.4%, with 11.7% reporting symptoms suggestive of extremely severe depression. Anxiety was diagnosed in 53.4% of patients and extremely severe anxiety reported by 18.4% of patients. Fifty patients were classified as stressed, and only 7.7% had extremely severe stress. More than half of the patients (54.4%) were in New York Heart Association (NYHA) functional class I with a mean (SD) left ventricular ejection fraction (LVEF) of 30.5% (11.1). In the multivariable logistic regression model, permanent employment [odds ratio (OR) -1.22, 95% CI:-0.01– -0.00, p=0.012], the six-minute walk test [OR -0.07, 95% CI: 0.02 – 0.06, p=0.001] and orthopnoea [OR 1.89, 95% CI: -0.01 – -0.00, p=0.012] were identified as independent predictors of depression.Conclusion: Depression and anxiety symptoms were found in over half of patients attending the chronic heart failure clinic. We recommend that mental health screening should be routinely performed in patients with chronic heart failure. Prospective, adequately powered, multicentre studies from LMIC investigating the impact of depression, anxiety and stress on CHF hospitalisation and mortality are required.