Genomics Data最新文献

{"title":"Antitumor Effect of Zwitterions of Imidazolium Derived from <i>L</i>-methionine in BALB/c Mice with Lymphoma L5178Y.","authors":"Karen C Vargas-Castro, Ana M Puebla Pérez, Irma I Rangel-Salas, Jorge I Delgado-Saucedo, José B Pelayo-Vázquez, Elvia Becerra-Martínez, Alejandro A Peregrina-Lucano, Raul R Quiñonez-Lopez, Gabriela J Soltero-Reynoso, Sara A Cortes-Llamas","doi":"10.2174/1573406415666191206093754","DOIUrl":"10.2174/1573406415666191206093754","url":null,"abstract":"<p><strong>Background: </strong>In the therapy of cancer, several treatments have been designed using nanomaterials, among which gold nanoparticles (AuNPs) have been featured as a promising antitumoral agent. Our research group has developed the synthesis of gold nanoparticles L-AuNPs and D-AuNPs stabilized with zwitterions of imidazolium (L-1 and D-1) derived from L-methionine and D-methionine. Because the stabilizer agent is chiral, we observed through circular dichroism that AuNPs also present chirality; such chirality as well as the fact that the stabilizing agent contains fragments of methionine and imidazolium that are commonly involved in biological processes, opens up the possibility that this system may have biological compatibility. Additionally, the presence of methionine in the stabilizing agent opens the application of this system as a possible antitumor agent because methionine is involved in methylation processes of molecules such as DNA.</p><p><strong>Objective: </strong>The aim of this research is the evaluation of the antitumor activity of gold nanoparticles stabilized with zwitterions of imidazolium (L-AuNPs) derived from L-methionine in the model of BALB/c mice with lymphoma L5178Y.</p><p><strong>Methods: </strong>Taking as a parameter cell density, the evaluation of the inhibitory effect of L-AuNPs was carried out with a series of in vivo tests in BALB/c type mice; three groups of five mice each were formed (Groups 1, 2 and 3); all mice were i.p. inoculated with the lymphoblast murine L5178Y. Group 1 consisted of mice without treatment. In the Groups 2 and 3 the mice were treated with L-AuNPs at 0.3 mg/Kg on days 1, 7 and 14 by orally and intraperitonally respectively.</p><p><strong>Results: </strong>These results show low antitumor activity of these gold nanoparticles (L-NPsAu) but interestingly, the imidazolium stabilizing agent of gold nanoparticle (L-1) displayed promising antitumor activity. On the other hand, the enantiomer of L-1, (D-1) as well as asymmetric imidazole derivate from L-methionine (L-2), do not exhibit the same activity as L-1.</p><p><strong>Conclusion: </strong>The imidazolium stabilizing agent (L-1) displayed promising antitumor activity. Modifications in the structure of L-1 showed that, the stereochemistry (like D-1) and the presence of methionine fragments (like L-2) are determinants in the antitumor activity of this compound.</p>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"10 1","pages":"33-39"},"PeriodicalIF":2.3,"publicationDate":"2021-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76273558","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Instilling a culture of cleaning: Effectiveness of decontamination practices on non-disposable sphygmomanometer cuffs.","authors":"Peta-Anne Zimmerman, Michael Jacques, Dale Rowland","doi":"10.1177/1757177418780997","DOIUrl":"10.1177/1757177418780997","url":null,"abstract":"<p><strong>Background: </strong>Sphygmomanometers and their cuffs are non-critical items that can act as a fomite for transmission of pathogens which may cause healthcare-associated infection (HAI), leading to an argument that disposable equipment improves patient safety.</p><p><strong>Aim: </strong>The aim of this study was to demonstrate that decontamination decreased in microbial contamination of non-disposable sphygmomanometer cuffs, providing evidence to negate the need to purchase, and dispose of, single-patient-use cuffs, reducing cost and environmental impact.</p><p><strong>Methods: </strong>A pre-post intervention study of available sphygmomanometer cuffs and associated bedside patient monitors was conducted using a series of microbiological samples in a rural emergency department. A Wilcoxon signed-rank test analysed the effect of the decontamination intervention. To further examine the effect of the decontamination intervention, Mann-Whitney U-tests were conducted for each aspect.</p><p><strong>Findings: </strong>Contamination was significantly higher before decontamination than afterwards (Z = -5.14, U = 55.0, <i>P</i> < 0.001, η2 = 0.61 inner; Z = -5.05, U = 53.5, <i>P</i> < 0.001, η2 = 0.59 outer).</p><p><strong>Discussion: </strong>Decontamination of non-disposable sphygmomanometer cuffs decreases microbial load and risk of HAI, providing evidence to negate arguments for disposable cuffs while being environmentally sensitive and supportive of a culture of patient safety and infection control.</p>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"7 1","pages":"294-299"},"PeriodicalIF":0.0,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11009562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76271721","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational deciphering of biotic stress associated genes in tomato (Solanum lycopersicum)","authors":"G. Tandon ,&nbsp;S. Singh ,&nbsp;S. Kaur ,&nbsp;Sarika ,&nbsp;M.A. Iquebal ,&nbsp;A. Rai ,&nbsp;D. Kumar","doi":"10.1016/j.gdata.2017.09.003","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.09.003","url":null,"abstract":"<div><p>Tomato (<em>Solanum lycopersicum</em>) is one of the major vegetable plant and a model system for fruit development. Its global importance is due to its lycopene pigment which has anti-oxidative and anti-cancerous properties. Though &gt;<!--> <!-->1.5<!--> <!-->M biotic stress associated ESTs of tomato are available but cumulative analysis to predict genes is warranted. Availability of whole genome de novo assembly can advantageously be used to map them over different chromosome. Further, available 0.14<!--> <!-->M catalogued markers can be used to introgress specific desirable genes in varietal improvement program. We report here 57 novel genes associated with biotic stress of tomato along with 50 genes having physical location over different chromosomes. We also report 52 cis-regulating elements and 69 putative miRNAs which are involved in regulation of these biotic stresses associated genes. These putative candidate genes associated with biotic stress can be used in molecular breeding in the endeavor of tomato productivity along with its sustainable germplasm management.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 82-90"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.09.003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification and tissue-specific expression analysis of nucleotide binding site-leucine rich repeat gene family in Cicer arietinum (kabuli chickpea)","authors":"Ranu Sharma ,&nbsp;Vimal Rawat ,&nbsp;C.G. Suresh","doi":"10.1016/j.gdata.2017.08.004","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.08.004","url":null,"abstract":"<div><p>The nucleotide binding site-leucine rich repeat (NBS-LRR) proteins play an important role in the defense mechanisms against pathogens. Using bioinformatics approach, we identified and annotated 104 NBS-LRR genes in chickpea. Phylogenetic analysis points to their diversification into two families namely TIR-NBS-LRR and non-TIR-NBS-LRR. Gene architecture revealed intron gain/loss events in this resistance gene family during their independent evolution into two families. Comparative genomics analysis elucidated its evolutionary relationship with other <em>fabaceae</em> species. Around 50% NBS-LRRs reside in macro-syntenic blocks underlining positional conservation along with sequence conservation of NBS-LRR genes in chickpea. Transcriptome sequencing data provided evidence for their transcription and tissue-specific expression. Four <em>cis</em>-regulatory elements namely WBOX, DRE, CBF, and GCC boxes, that commonly occur in resistance genes, were present in the promoter regions of these genes. Further, the findings will provide a strong background to use candidate disease resistance NBS-encoding genes and identify their specific roles in chickpea.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 24-31"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.08.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634700","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stroke-associated pattern of gene expression previously identified by machine-learning is diagnostically robust in an independent patient population","authors":"Grant C. O'Connell ,&nbsp;Paul D. Chantler ,&nbsp;Taura L. Barr","doi":"10.1016/j.gdata.2017.08.006","DOIUrl":"10.1016/j.gdata.2017.08.006","url":null,"abstract":"<div><p>Our group recently employed genome-wide transcriptional profiling in tandem with machine-learning based analysis to identify a ten-gene pattern of differential expression in peripheral blood which may have utility for detection of stroke. The objective of this study was to assess the diagnostic capacity and temporal stability of this stroke-associated transcriptional signature in an independent patient population. Publicly available whole blood microarray data generated from 23 ischemic stroke patients at 3, 5, and 24<!--> <!-->h post-symptom onset, as well from 23 cardiovascular disease controls, were obtained via the National Center for Biotechnology Information Gene Expression Omnibus. Expression levels of the ten candidate genes (<em>ANTXR2</em>, <em>STK3</em>, <em>PDK4</em>, <em>CD163</em>, <em>MAL</em>, <em>GRAP</em>, <em>ID3</em>, <em>CTSZ</em>, <em>KIF1B</em>, and <em>PLXDC2</em>) were extracted, compared between groups, and evaluated for their discriminatory ability at each time point. We observed a largely identical pattern of differential expression between stroke patients and controls across the ten candidate genes as reported in our prior work. Furthermore, the coordinate expression levels of the ten candidate genes were able to discriminate between stroke patients and controls with levels of sensitivity and specificity upwards of 90% across all three time points. These findings confirm the diagnostic robustness of the previously identified pattern of differential expression in an independent patient population, and further suggest that it is temporally stable over the first 24<!--> <!-->h of stroke pathology.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 47-52"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.08.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35424733","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Complete mitochondrial genome sequence of fruit-piercing moth Eudocima phalonia (Linnaeus, 1763) (Lepidoptera: Noctuoidea)","authors":"Kuppusamy Sivasankaran ,&nbsp;Pratheesh Mathew ,&nbsp;Sekar Anand ,&nbsp;Stanislaus Antony Ceasar ,&nbsp;Soosaimanikam Mariapackiam ,&nbsp;Savarimuthu Ignacimuthu","doi":"10.1016/j.gdata.2017.09.004","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.09.004","url":null,"abstract":"<div><p>The complete mitochondrial genome of the fruit piercing moth <em>Eudocima phalonia</em> (Linnaeus, 1763) (Lepidoptera: Noctuoidea) was sequenced and characterized (Genbank Accession No: KY196412). The complete mitogenome is a circular molecule of 15,575<!--> <!-->bp length, consisting of 13 protein-coding genes (PCGs), two ribosomal RNA genes (<em>rrnS</em> and <em>rrnL</em>), 22 transfer RNA (tRNA) genes and an A<!--> <!-->+<!--> <!-->T-rich region (D-loop). The nucleotide composition of the genome is highly A<!--> <!-->+<!--> <!-->T biased, accounting for 80.67% of nucleotides. All tRNAs have putative secondary structures that are characteristic of mitochondrial tRNA. Most of the PCGs were initiated by typical ATN codons. Five genes were initiated by unusual codons. <em>Cox1</em> gene was initiated by an unusual CGA codon and terminated by the typical stop codon GAA. Six genes ended with a single T. The A<!--> <!-->+<!--> <!-->T-rich region of 336<!--> <!-->bp consisted of repetitive sequences, including two ATAGA motifs, a 19<!--> <!-->bp poly-T stretch and three microsatellite-like regions ((TA)₄, (TA)₆ and two (TA)₇)_. Moreover, three large tandem (one 40<!--> <!-->bp and two 25<!--> <!-->bp) repeated elements were identified in A<!--> <!-->+<!--> <!-->T-rich region. Phylogenetic analysis using PCGs revealed that Superfamily Noctuoidea is a monophyletic group.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 66-81"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.09.004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Whole genome shotgun sequencing of Indian strains of Streptococcus agalactiae","authors":"Balaji Veeraraghavan ,&nbsp;Naveen Kumar Devanga Ragupathi ,&nbsp;Sridhar Santhanam ,&nbsp;Valsan Philip Verghese ,&nbsp;Francis Yesurajan Inbanathan ,&nbsp;Charles Livingston","doi":"10.1016/j.gdata.2017.10.001","DOIUrl":"10.1016/j.gdata.2017.10.001","url":null,"abstract":"<div><p>Group B streptococcus is known as a leading cause of neonatal infections in developing countries. The present study describes the whole genome shotgun sequences of four Group B Streptococcus (GBS) isolates. Molecular data on clonality is lacking for GBS in India. The present genome report will add important information on the scarce genome data of GBS and will help in deriving comparative genome studies of GBS isolates at global level. This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession numbers NHPL00000000 – NHPO00000000.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 63-65"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.10.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35598339","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Rhizospheric metagenome of the terrestrial mangrove fern Acrostichum from Indian Sunderbans","authors":"Sayak Ganguli ,&nbsp;Sabdar Rahaman ,&nbsp;Abhishek R. Bera ,&nbsp;Vineet Vishal ,&nbsp;Shelvia Malik ,&nbsp;Roopalakshmi K. ,&nbsp;Pankaj K. Singh","doi":"10.1016/j.gdata.2017.09.001","DOIUrl":"https://doi.org/10.1016/j.gdata.2017.09.001","url":null,"abstract":"<div><p>This study reports the analyses of the rhizospheric microbiome of the terrestrial mangrove fern <em>Acrostichum aureum</em> Linn. from the Indian Sunderbans. Samples were collected using standard protocols and 16S rRNA gene V3–V4 region amplicon sequencing was performed to identify the microbial communities prevalent in the rhizosphere. A total of 1,931,252 quality checked <strong>reads</strong> were assembled into 204,818 contigs and were analysed using QIIME to reveal the abundance of Proteobacteria, Acidobacteria and Planctomycetes. The data is available at the NCBI - Sequence Read Archive with accession number: SRX2660456. This is the first report of the rhizospheric microbiome belonging to a fern species.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 53-55"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.09.001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91634703","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene expression profiling of ramie roots during hydroponic induction and adaption to aquatic environment","authors":"Gang Gao,&nbsp;Heping Xiong,&nbsp;Kunmei Chen,&nbsp;Jikang Chen,&nbsp;Ping Chen,&nbsp;Chunming Yu,&nbsp;Aiguo Zhu","doi":"10.1016/j.gdata.2017.08.002","DOIUrl":"10.1016/j.gdata.2017.08.002","url":null,"abstract":"<div><p>Ramie (<em>Boehmeria nivea</em> (L.) Gaud.) is a traditionally terrestrial fiber crop. However, hydroponic technology can enhance the quantity and quality of disease free Ramie plant seedlings for field cultivation. To date, few studies have attempted to examine the hydroponic induction of ramie roots and the molecular responses of ramie roots to aquatic environment. In this study, ramie tender stems was grown in the soil or in a hydroponic water solution, and cultured in the same environmental conditions. Root samples of terrestrial ramie, and different developmental stages of hydroponic ramie (5<!--> <!-->days, 30<!--> <!-->days), were firstly pooled for reference transcriptome sequencing by Illumina Hiseq 2000. Gene expression levels of each samples were quantified using the BGISEQ500 platform to help understand the distribution of aquatic root development related genes at the macro level (GSE98903). Our data resources provided an opportunity to elucidate the adaptation mechanisms of ramie seedlings roots in aquatic environment.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 32-35"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.08.002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35458619","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Co-expression network analysis identified six hub genes in association with progression and prognosis in human clear cell renal cell carcinoma (ccRCC)","authors":"Lushun Yuan ,&nbsp;Liang Chen ,&nbsp;Kaiyu Qian ,&nbsp;Guofeng Qian ,&nbsp;Chin-Lee Wu ,&nbsp;Xinghuan Wang ,&nbsp;Yu Xiao","doi":"10.1016/j.gdata.2017.10.006","DOIUrl":"10.1016/j.gdata.2017.10.006","url":null,"abstract":"<div><p>Human clear cell renal cell carcinoma (ccRCC) is one of the most common types of malignant adult kidney tumors. We constructed a weighted gene co-expression network to identify gene modules associated with clinical features of ccRCC (<em>n</em> <!-->=<!--> <!-->97). Six hub genes (<em>CCNB2</em>, <em>CDC20</em>, <em>CEP55</em>, <em>KIF20A</em>, <em>TOP2A</em> and <em>UBE2C</em>) were identified in both co-expression and protein-protein interaction (PPI) networks, which were highly correlated with pathologic stage. The significance of expression of the hub genes in ccRCC was ranked top 4 among all cancers and correlated with poor prognosis. Functional analysis revealed that the hub genes were significantly enriched in cell cycle regulation and cell division. Gene set enrichment analysis suggested that the samples with highly expressed hub gene were correlated with cell cycle and p53 signaling pathway. Taken together, six hub genes were identified to be associated with progression and prognosis of ccRCC, and they might lead to poor prognosis by regulating p53 signaling pathway.</p></div>","PeriodicalId":56340,"journal":{"name":"Genomics Data","volume":"14 ","pages":"Pages 132-140"},"PeriodicalIF":0.0,"publicationDate":"2017-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1016/j.gdata.2017.10.006","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35629897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}