ResearchPad - in-brief https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[Probabilistic reversal learning under acute tryptophan depletion in healthy humans: a conventional analysis]]> https://www.researchpad.co/article/elastic_article_15533 The involvement of serotonin in responses to negative feedback is well established. Acute serotonin reuptake inhibition has enhanced sensitivity to negative feedback (SNF), modelled by behaviour in probabilistic reversal learning (PRL) paradigms. Whilst experiments employing acute tryptophan depletion (ATD) in humans, to reduce serotonin synthesis, have shown no clear effect on SNF, sample sizes have been small. We studied a large sample of healthy volunteers, male and female, and found ATD had no effect on core behavioural measures in PRL. These results indicate that ATD effects can differ from other manipulations of serotonin expected to have a parallel or opposing action.

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<![CDATA[Risk factors for death from COVID-19]]> https://www.researchpad.co/article/elastic_article_11218 <![CDATA[Kawasaki disease linked to COVID-19 in children]]> https://www.researchpad.co/article/elastic_article_11212 <![CDATA[Innate T cells in COVID-19: friend or foe?]]> https://www.researchpad.co/article/elastic_article_11210 <![CDATA[In This Issue/Research Watch/News-in-Brief]]> https://www.researchpad.co/article/elastic_article_10733 <![CDATA[Relationships Between Perspective-Taking, Empathic Concern, and Self-rating of Empathy as a Physician Among Medical Students]]> https://www.researchpad.co/article/elastic_article_9775 The aim of this study was to ascertain the relationships between perspective-taking, empathic concern, and self-rating of empathy as a physician among medical students.MethodsThis study analyzed the questionnaire responses of 152 medical students enrolled in Ajou University School of Medicine, Suwon, Republic of Korea, in 2018. As measurement instruments, the authors applied the Interpersonal Reactivity Index (IRI) and Korean Student Version of the Jefferson Scale of Physician Empathy (Korean JSPE-S), and then examined participant characteristic variables based on the obtained data and conducted subsequent correlation analyses of subscales, one-way ANOVA, and regression analyses.ResultsMedical students with clinical clerkship experience demonstrated higher levels of perspective-taking and empathy as physicians than did students without experience. Moreover, perspective-taking and empathic concern were significant predictors of medical students’ empathy as physicians in the regression model.ConclusionsMedical students with higher scores in perspective-taking and empathic concern demonstrated higher levels of perception regarding the necessity and importance of empathy as a physician in patient-physician relationships. Therefore, in actual medical situations with patient-centered therapy, to enhance the levels of physician empathy, medical education should focus on the understanding of other persons’ opinions and interpersonal interactions accompanied by empathic concern. ]]> <![CDATA[High-Frequency 4-Dimensional Ultrasound (4DUS): A Reliable Method for Assessing Murine Cardiac Function]]> https://www.researchpad.co/article/5c081820d5eed0c484f43d87

In vivo imaging has provided a unique framework for studying pathological progression in various mouse models of cardiac disease. Although conventional short-axis motion-mode (SAX MM) ultrasound and cine magnetic resonance imaging (MRI) are two of the most prevalent strategies used for quantifying cardiac function, there are few notable limitations including imprecision, inaccuracy, and geometric assumptions with ultrasound, or large and costly systems with substantial infrastructure requirements with MRI. Here we present an automated 4-dimensional ultrasound (4DUS) technique that provides comparable information to cine MRI through spatiotemporally synced imaging of cardiac motion. Cardiac function metrics derived from SAX MM, cine MRI, and 4DUS data show close agreement between cine MRI and 4DUS but overestimations by SAX MM. The inclusion of a mouse model of cardiac hypertrophy further highlights the precision of 4DUS compared with that of SAX MM, with narrower groupings of cardiac metrics based on health status. Our findings suggest that murine 4DUS can be used as a reliable, accurate, and cost-effective technique for longitudinal studies of cardiac function and disease progression.

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<![CDATA[DNA-seq analysis of Garcinia mangostana]]> https://www.researchpad.co/article/5af9f9f4463d7e20c44c5c29

Mangosteen (Garcinia mangostana Linn.) is a tropical tree mainly found in South East Asia and considered as “the queen of fruits”. The asexually produced fruit is dark purple or reddish in color, with white flesh which is slightly acidic with sweet flavor and a pleasant aroma. The purple pericarp tissue is rich in xanthones which are useful for medical purposes. We performed the first genome sequencing of this commercially important fruit tree to study its genome composition and attempted draft genome assembly. Raw reads of the DNA sequencing project have been deposited to SRA database with the accession number SRX1426419.

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<![CDATA[Toxicogenomic analysis of pharmacological active coumarins isolated from Calophyllum brasiliense]]> https://www.researchpad.co/article/5af66b12463d7e44c8bd73a8

Calophyllum brasiliense (Calophyllaceae) is a tropical rain forest tree, mainly distributed in South and Central America. It is an important source of bioactive natural products like, for instance soulatrolide, and mammea type coumarins. Soulatrolide is a tetracyclic dipyranocoumarins and a potent inhibitor of HIV-1 reverse transcriptase and Mycobacterium tuberculosis. Mammea A/BA and A/BB coumarins, pure or as a mixture, are highly active against several leukemia cell lines, Trypanosoma cruzi and Leishmania amazonensis. In the present work, a toxicogenomic analysis of Soulatrolide and Mammea A/BA + A/BB (3:1) mixture was performed in order to validate the toxicological potential of this type of compounds. Soulatrolide or mixture of mammea A/BA + A/BB (3:1) was administered orally to male mice (CD-1) at dose of 100 mg/kg/daily, for 1 week. After this time, mice were sacrificed, and RNA extracted from the liver of treated animals. Transcriptomic analysis was performed using Affymetrix Mouse Gene 1.0 ST Array. Robust microarray analysis (RMA) and two way ANOVA test revealed for mammea mixture treatment 46 genes upregulated and 72 downregulated genes; meanwhile, for soulatrolide 665 were upregulated and 1077 downregulated genes. Enrichment analysis for such genes revealed that in both type of treatments genetic expression were mainly involved in drug metabolism. Overall results indicate a safety profile. The microarray data complies with MIAME guidelines and are deposited in GEO under accession number GSE72755.

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<![CDATA[Genome assembly of Chryseobacterium sp. strain IHBB 10212 from glacier top-surface soil in the Indian trans-Himalayas with potential for hydrolytic enzymes]]> https://www.researchpad.co/article/5b40dcd3463d7e5eb8c0fe28

The cold-active esterases are gaining importance due to their catalytic activities finding applications in chemical industry, food processes and detergent industry as additives, and organic synthesis of unstable compounds as catalysts. In the present study, the complete genome sequence of 4,843,645 bp with an average 34.08% G + C content and 4260 protein-coding genes are reported for the low temperature-active esterase-producing novel strain of Chrysobacterium isolated from the top-surface soil of a glacier in the cold deserts of the Indian trans-Himalayas. The genome contained two plasmids of 16,553 and 11,450 bp with 40.54 and 40.37% G + C contents, respectively. Several genes encoding the hydrolysis of ester linkages of triglycerides into fatty acids and glycerol were predicted in the genome. The annotation also predicted the genes encoding proteases, lipases, amylases, β-glucosidases, endoglucanases and xylanases involved in biotechnological processes. The complete genome sequence of Chryseobacterium sp. strain IHBB 10212 and two plasmids have been deposited vide accession numbers CP015199, CP015200 and CP015201 at DDBJ/EMBL/GenBank.

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<![CDATA[Identification of biomarkers in breast cancer by gene expression profiling using human tissues]]> https://www.researchpad.co/article/5bc2ec8e40307c76b6df390e

Breast cancer is the second leading cause of death by cancer in women. To identify biomarkers with potential diagnostic and therapeutic utilities in breast cancer, gene expression profiling from real patient tissues was used to discover significantly deregulated genes out of 50,739 genes of human transcriptome. Total RNAs were extracted, and the gene expression profiles of 32 cancerous and normal tissues were established using Agilent gene expression microarray technology. The results were analyzed with Agilent GeneSpring 12.6 software. Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE57297.

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<![CDATA[Transcriptional profiling of SNAI2 regulated genes in primary human keratinocytes]]> https://www.researchpad.co/article/5bc2ecc640307c76b6df3922

Epithelial to mesenchymal transition transcription factors (EMT-TFs) such as SNAI2 have been found to be expressed endogenously in epidermal stem and progenitor cells and downregulated upon differentiation. The presence of SNAI2 in progenitor cells is necessary to repress the expression of differentiation genes by binding directly to their promoters. SNAI2 is downregulated upon differentiation which allows expression of differentiation genes. Furthermore overexpression of SNAI2 can block the differentiation process suggesting that the levels of SNAI2 are crucial to epidermal cell fate decisions. To address on a genome wide level the genes that are impacted by changing the levels of SNAI2, we performed microarray analysis on SNAI2 knockdown and overexpressing epidermal progenitor cells. Here we provide detailed methods and analysis on these microarray data which has been deposited in Gene Expression Omnibus (GEO): GSE55269.

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<![CDATA[Transcriptional profiling of MEF2-regulated genes in human neural progenitor cells derived from embryonic stem cells]]> https://www.researchpad.co/article/5bc2ec9d40307c76b6df3913

The myocyte enhancer factor 2 (MEF2) family of transcription factors is highly expressed in the brain and constitutes a key determinant of neuronal survival, differentiation, and synaptic plasticity. However, genome-wide transcriptional profiling of MEF2-regulated genes has not yet been fully elucidated, particularly at the neural stem cell stage. Here we report the results of microarray analysis comparing mRNAs isolated from human neural progenitor/stem cells (hNPCs) derived from embryonic stem cells expressing a control vector versus progenitors expressing a constitutively-active form of MEF2 (MEF2CA), which increases MEF2 activity. Microarray experiments were performed using the Illumina Human HT-12 V4.0 expression beadchip (GEO#: GSE57184). By comparing vector-control cells to MEF2CA cells, microarray analysis identified 1880 unique genes that were differentially expressed. Among these genes, 1121 genes were up-regulated and 759 genes were down-regulated. Our results provide a valuable resource for identifying transcriptional targets of MEF2 in hNPCs.

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<![CDATA[Transcriptomic profiling of splenic B lymphomas spontaneously developed in B cell-specific TRAF3-deficient mice]]> https://www.researchpad.co/article/5bc2ec9140307c76b6df390f

TRAF3, a critical regulator of B cell survival, was recently recognized as a tumor suppressor gene in B lymphocytes. Specific deletion of TRAF3 from B lymphocytes leads to spontaneous development of marginal zone lymphomas (MZL) or B1 lymphomas in mice. To identify novel oncogenes and tumor suppressive genes involved in malignant transformation of TRAF3-deficient B cells, we performed a microarray analysis to identify genes differentially expressed in TRAF3−/− mouse splenic B lymphomas. We have identified 160 up-regulated genes and 244 down-regulated genes in TRAF3−/−B lymphomas as compared to littermate control splenocytes. Here we describe the samples, quality control assessment, as well as the data analysis methods in detail for the transcriptomic profiling study. Data are archived at NIH GEO with accession number GSE48818.

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<![CDATA[Discovery of gene regulation pattern in lung cancer by gene expression profiling using human tissues]]> https://www.researchpad.co/article/5bc2ecb240307c76b6df391b

Lung cancer continues to be one the most prevalent and life threatening cancers worldwide. In order to study the gene regulation pattern in lung cancer for new therapeutics discovery, gene expression profiling using human lung cancer tissues was conducted. The gene expression profiles were established using Affymetrix Human Exon 1.0 ST Array with RNA extracts from six clinical patients (five lung cancer samples and one normal control). The raw data were analyzed with Affymetrix Expression Console and Affymetrix Transcriptome Analysis Console 2.0. The regulation of several genes was further validated using real-time reverse transcription quantitative polymerase chain reaction (RT-qPCR). Here we provide detailed experimental methods and analysis for the microarray data, which have been deposited into Gene Expression Omnibus (GEO) under GSE63571.

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<![CDATA[Genome wide mapping of Foxo1 binding-sites in murine T lymphocytes]]> https://www.researchpad.co/article/5bc2ec8940307c76b6df390c

The Forkhead box O (Foxo) family of transcription factors has a critical role in controlling the development, differentiation, and function of T cells. However, the direct target genes of Foxo transcription factors in T cells have not been well characterized. In this study, we focused on mapping the genome wide Foxo1-binding sites in naïve CD4+ T cells, CD8+ T cells, and Foxp3+ regulatory T (Treg) cells. By using chromatin immunoprecipitation coupled with deep sequencing (ChIP-Seq), we identified Foxo1 binding sites that were shared among or specific to the three T cell populations. Here we describe the experiments, quality controls, as well as the deep sequencing data. Part of the data analysis has been published by Ouyang W et al. in Nature 2012 [1] and Kim MV et al. in Immunity 2013 [2], and the associated data set were uploaded to NCBI Gene Expression Omnibus.

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<![CDATA[Genome-wide redistribution of BRD4 binding sites in transformation resistant cells]]> https://www.researchpad.co/article/5bc2ec9a40307c76b6df3912

Hutchinson–Gilford progeria syndrome (HGPS) patients do not develop cancer despite a significant accumulation of DNA damage in their cells. We have recently reported that HGPS cells are refractory to experimental oncogenic transformation and we identified the bromodomain-containing 4 protein (BRD4) as a mediator of the transformation resistance. ChIP-sequencing experiments revealed distinct genome-wide binding patterns for BRD4 in HGPS cells when compared to control wild type cells. Here we provide a detailed description of the ChIP-seq dataset (NCBI GEO accession number GSE61325), the specific and common BRD4 binding sites between HGPS and control cells, and the data analysis procedure associated with the publication by Fernandez et al., 2014 in Cell Reports 9, 248-260 [1].

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<![CDATA[Development of novel filtering criteria to analyze RNA-sequencing data obtained from the murine ocular lens during embryogenesis]]> https://www.researchpad.co/article/5bc2ec9740307c76b6df3911

Next-generation sequencing of the transcriptome (RNA-Seq) is a powerful method that allows for the quantitative determination of absolute gene expression, and can be used to investigate how these levels change in response to an experimental manipulation or disease condition. The sensitivity of this method allows one to analyze transcript levels of all expressed genes, including low abundance transcripts that encode important regulatory molecules, providing valuable insights into the global effects of experimental manipulations. However, this increased sensitivity can also make it challenging to ascertain which expression changes are biologically significant. Here, we describe a novel set of filtering criteria – based on biological insights and computational approaches – that were applied to prioritize genes for further study from an extensive number of differentially expressed transcripts in lenses lacking Smad interacting protein 1 (Sip1) obtained via RNA-Seq by Manthey and colleagues in Mechanisms of Development (Manthey et al., 2014). Notably, this workflow allowed an original list of over 7100 statistically significant differentially expressed genes (DEGs) to be winnowed down to 190 DEGs that likely play a biologically significant role in Sip1 function during lens development. Focusing on genes whose expression was upregulated or downregulated in a manner opposite to what normally occurs during lens development, we identified 78 genes that appear to be strongly dependent on Sip1 function. From these data (GEO accession number GSE49949), it appears that Sip1 regulates multiple genes in the lens that are generally distinct from those regulated by Sip1 in other cellular contexts, including genes whose expression is prominent in the early head ectoderm, from which the lens differentiates. Further, the analysis criteria outlined here represent a filtering scheme that can be used to prioritize genes in future RNA-Seq investigations performed at this stage of ocular lens development.

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<![CDATA[Transcriptome response to copper heavy metal stress in hard-shelled mussel (Mytilus coruscus)]]> https://www.researchpad.co/article/5af9fa3c463d7e20c44c5c2a

The hard-shelled mussel (Mytilus coruscus) has considerably one of the most economically important marine shellfish worldwide and considered as a good invertebrate model for ecotoxicity study for a long time. In the present study, we used Illumina sequencing technology (HiSeq2000) to sequence, assemble and annotate the transcriptome of the hard-shelled mussel which challenged with copper pollution. A total of 21,723,913 paired-end clean reads (NCBI SRA database SRX1411195) were generated from HiSeq2000 sequencer and 96,403 contigs (with N50 = 1118 bp) were obtained after de novo assembling with Trinity software. Digital gene expression analysis reveals 1156 unigenes are upregulated and 1681 unigenes are downregulated when challenged with copper. By KEGG pathway enrichment analysis, we found that unigenes in four KEGG pathways (aminoacyl-tRNA biosynthesis, apoptosis, DNA replication and mismatch repair) show significant differential expressed between control and copper treated groups. We hope that the gill transcriptome in copper treated hard-shelled mussel can give useful information to understand how mussel handles with heavy metal stress at molecular level.

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<![CDATA[Transcriptional profiling of CRP-regulated genes in deep-sea bacterium Shewanella piezotolerans WP3]]> https://www.researchpad.co/article/5af24472463d7e3c8faa582e

The cAMP receptor protein (CRP) is a conserved regulator in bacteria and involved in regulation of energy metabolism, such as glucose, galactose, and citrate (Green et al., 2014 [1]). As an important catabolite activator protein, it has been well characterized in model microorganism such as Escherichia coli. However, our understanding of the roles of CRP in deep-sea bacteria is rather limited. To indentify the function of CRP, we performed whole genome transcriptional profiling using a custom designed microarray which contains 95% open reading frames of Shewanella piezotolerans WP3, which was isolated from West Pacific sediment at a depth of 1914 m (Xiao et al., 2007 [2]; Wang et al., 2008 [3]). Here we describe the experimental procedures and methods in detail to reproduce the results (available at Gene Expression Omnibus database under GSE67731 and GSE67732) and provide resource to be employed for comparative analyses of CRP regulon and the regulatory network of anaerobic respiration in microorganisms which inhabited in different environments, and thus broaden our understanding of mechanism of bacteria against various environment stresses.

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