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1.  What Does the Cochrane Collaboration Say about Rehabilitation Interventions for Shoulder Dysfunction? 
Physiotherapy Canada  2016;68(2):208.
doi:10.3138/ptc.68.2.cochrane
PMCID: PMC5125492  PMID: 27909368
2.  Society news 
Neuro-Oncology  2015;17(8):1177.
doi:10.1093/neuonc/nov130
PMCID: PMC4490882
4.  Towards Reconciliation of Several Dualities in Physician Leadership 
Healthcare Policy  2015;10(3):23-31.
Leadership has a renewed focus in healthcare, and physicians are being increasingly involved in a range of leadership roles. The aim of this paper is to discuss several dualities that exert tensions at the systems and individual levels. Although oppositional, the common dualities of physician leadership are not mutually exclusive but represent a complex, dynamic and interdependent relationship, often coexisting with each other and exerting tensions in multiple dimensions. The authors contend that a dialectic understanding – instead of either/or or finding a middle ground – of the opposite poles of these dualities allows for generating meaningful leadership perspectives and choices.
PMCID: PMC4748340  PMID: 25947031
5.  Editorial Board 
doi:10.1128/JCM.masthead.53-6
PMCID: PMC4432073
6.  Genome-wide expression analysis comparing hypertrophic changes in normal and dysferlinopathy mice 
Genomics Data  2015;6:253-257.
Because myostatin normally limits skeletal muscle growth, there are extensive efforts to develop myostatin inhibitors for clinical use. One potential concern is that in muscle degenerative diseases, inducing hypertrophy may increase stress on dystrophic fibers. Our study shows that blocking this pathway in dysferlin deficient mice results in early improvement in histopathology but ultimately accelerates muscle degeneration. Hence, benefits of this approach should be weighed against these potential detrimental effects. Here, we present detailed experimental methods and analysis for the gene expression profiling described in our recently published study in Human Molecular Genetics (Lee et al., 2015). Our data sets have been deposited in the Gene Expression Omnibus (GEO) database (GSE62945) and are available at http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62945. Our data provide a resource for exploring molecular mechanisms that are related to hypertrophy-induced, accelerated muscular degeneration in dysferlinopathy.
doi:10.1016/j.gdata.2015.10.010
PMCID: PMC4664771  PMID: 26697388
Myostatin; Follistatin; ACVR2B/Fc; Dysferlinopathy; Skeletal muscle
7.  Transcriptional changes in sensory ganglia associated with primary afferent axon collateral sprouting in spared dermatome model 
Genomics Data  2015;6:249-252.
Primary afferent collateral sprouting is a process whereby non-injured primary afferent neurons respond to some stimulus and extend new branches from existing axons. Neurons of both the central and peripheral nervous systems undergo this process, which contributes to both adaptive and maladaptive plasticity (e.g., [1], [2], [3], [4], [5], [6], [7], [8], [9]). In the model used here (the “spared dermatome” model), the intact sensory neurons respond to the denervation of adjacent areas of skin by sprouting new axon branches into that adjacent denervated territory. Investigations of gene expression changes associated with collateral sprouting can provide a better understanding of the molecular mechanisms controlling this process. Consequently, it can be used to develop treatments to promote functional recovery for spinal cord injury and other similar conditions. This report includes raw gene expression data files from microarray experiments in order to study the gene regulation in spared sensory ganglia in the initiation (7 days) and maintenance (14 days) phases of the spared dermatome model relative to intact (“naïve”) sensory ganglia. Data has been deposited into GEO (GSE72551).
doi:10.1016/j.gdata.2015.10.005
PMCID: PMC4664766  PMID: 26697387
Axonal plasticity; Axon growth; Pain; Nerve injury; Transcriptomics
8.  Genome wide transcription profiling of the effects of overexpression of Spc1 and its kinase dead mutant in Schizosaccharomyces pombe 
Genomics Data  2015;6:241-244.
The Mitogen Activated Protein Kinase Spc1 (p38 homolog) is a major player in stress responses of the unicellular fission yeast Schizosaccharomyces pombe. This pathway is therefore also known as the SAPK or Stress Activated Protein Kinase pathway. Spc1 is a known activator of transcription factors that control gene expression in response to extracellular stimuli and is also known to interact with the translation machinery [1], [2], [3], [4], [5], [6], [7], [8]. Spc1 has also been implicated in cell cycle regulation and meiosis in S. pombe[1], [2], [9], [10]. Given its documented role in modulating gene expression, we performed a microarray based identification of genes whose expression in unperturbed cells (absence of stress stimuli) is dependent on Spc1. For this we overexpressed Spc1 in S. pombe. Additionally we also overexpressed Spc1K49R (a kinase dead mutant of Spc1) to understand the contribution of Spc1's kinase activity towards the observed gene expression changes. The microarray data are available at NCBI's Gene Expression Omnibus (GEO) Series (accession number GSE73618). Here we report the annotation of the genes whose expression get altered by Spc1/Spc1K49R overexpression and also provide details related to sample processing and statistical analysis of our microarray data.
doi:10.1016/j.gdata.2015.10.007
PMCID: PMC4664770  PMID: 26697385
Spc1; S. pombe; Spc1K49R; Microarray
9.  Toxicogenomic analysis of pharmacological active coumarins isolated from Calophyllum brasiliense 
Genomics Data  2015;6:258-259.
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.
doi:10.1016/j.gdata.2015.10.006
PMCID: PMC4664773  PMID: 26697389
10.  Draft genome sequence of Acidithiobacillus ferrooxidans YQH-1 
Genomics Data  2015;6:269-270.
Acidithiobacillus ferrooxidans YQH-1 is a moderate acidophilic bacterium isolated from a river in a volcano of Northeast China. Here, we describe the draft genome of strain YQH-1, which was assembled into 123 contigs containing 3,111,222 bp with a G + C content of 58.63%. A large number of genes related to carbon dioxide fixation, dinitrogen fixation, pH tolerance, heavy metal detoxification, and oxidative stress defense were detected. The genome sequence can be accessed at DDBJ/EMBL/GenBank under the accession no. LJBT00000000.
doi:10.1016/j.gdata.2015.10.009
PMCID: PMC4664765  PMID: 26697394
Acidithiobacillus ferrooxidans; Genome; Iron-oxidizing bacteria; Bioleaching; Volcano
11.  De novo transcriptome assembly of two different apricot cultivars 
Genomics Data  2015;6:275-276.
Apricot (Prunus armeniaca) belonging to the Prunus species is a popular kind of stone fruit tree. Apricot is native to Armenia and is currently cultivated in many countries with climates adaptable for apricot growth. In general, fresh fruits as well as dried apricot are produced. However, the information associated with genes and genetic markers for apricot is very limited. In this study, we carried out de novo transcriptome assembly for two selected apricot cultivars referred to as Harcot and Ungarische Beste, which are commercially important apricot cultivars in the world, using next generation sequencing. We obtained a total of 9.31 GB and 8.88 GB raw data from Harcot and Ungarische Beste (NCBI accession numbers: SRX1186946 and SRX1186893), respectively. De novo transcriptome assembly using Trinity identified 147,501 and 152,235 transcripts for Harcot and Ungarische Beste, respectively. Next, we identified 113,565 and 126,444 proteins from Harcot and Ungarische Beste using the TransDecoder program. We performed BLASTP against an NCBI non-redundant (nr) dataset to annotate identified proteins. Taken together, we provide transcriptomes of two different apricot cultivars by RNA-Seq.
doi:10.1016/j.gdata.2015.10.012
PMCID: PMC4664767  PMID: 26697397
Apricot; Cultivar; RNA-Seq; Transcriptome
12.  De novo transcriptome assembly of a sour cherry cultivar, Schattenmorelle 
Genomics Data  2015;6:271-272.
Sour cherry (Prunus cerasus) in the genus Prunus in the family Rosaceae is one of the most popular stone fruit trees worldwide. Of known sour cherry cultivars, the Schattenmorelle is a famous old sour cherry with a high amount of fruit production. The Schattenmorelle was selected before 1650 and described in the 1800s. This cultivar was named after gardens of the Chateau de Moreille in which the cultivar was initially found. In order to identify new genes and to develop genetic markers for sour cherry, we performed a transcriptome analysis of a sour cherry. We selected the cultivar Schattenmorelle, which is among commercially important cultivars in Europe and North America. We obtained 2.05 GB raw data from the Schattenmorelle (NCBI accession number: SRX1187170). De novo transcriptome assembly using Trinity identified 61,053 transcripts in which N50 was 611 bp. Next, we identified 25,585 protein coding sequences using TransDecoder. The identified proteins were blasted against NCBI's non-redundant database for annotation. Based on blast search, we taxonomically classified the obtained sequences. As a result, we provide the transcriptome of sour cherry cultivar Schattenmorelle using next generation sequencing.
doi:10.1016/j.gdata.2015.10.013
PMCID: PMC4664768  PMID: 26697395
Cherry; Cultivar; RNA-Seq; Transcriptome
13.  De novo transcriptome assembly of two different Prunus salicina cultivars 
Genomics Data  2015;6:262-263.
Plum is a globally grown stone fruit and can be divided into several species. In particular, the Prunus salicina, which is native to China, is widely grown in many fruit orchards in Korea and Japan, as well as the United States and Australia. The transcriptome data for Prunus salicina has not been reported to our knowledge. In this study, we performed de novo transcriptome assembly for two selected P. salicina cultivars referred to as Akihime and Formosa (commercially important plum cultivars in Korea) using next generation sequencing. We obtained a total of 9.04 GB and 8.68 GB raw data from Akihime and Formosa, respectively. De novo transcriptome assembly using Trinity revealed 155,169 and 160,186 transcripts for Akihime and Formosa. Next, we identified 121,278 and 116,544 proteins from Akihime and Formosa using TransDecoder. We performed BLASTP against the NCBI non-redundant (nr) dataset to annotate proteins. Taken together, this is the first transcriptome data for P. salicina to our knowledge.
doi:10.1016/j.gdata.2015.10.015
PMCID: PMC4664772  PMID: 26697391
Cultivar; Plum; Prunus salicina; RNA-Seq; Transcriptome
14.  Transcriptomic profile of aguR deletion mutant of Lactococcus lactis subsp. cremoris CECT 8666 
Genomics Data  2015;6:228-230.
Lactococcus lactis subsp. cremoris CECT 8666 (formerly GE2-14) is a dairy strain that catabolizes agmatine (a decarboxylated derivative of arginine) into the biogenic amine putrescine by the agmatine deiminase (AGDI) pathway [1]. The AGDI cluster of L. lactis is composed by five genes aguR, aguB, aguD, aguA and aguC. The last four genes are responsible for the deamination of agmatine to putrescine and are co-transcribed as a single policistronic mRNA forming the catabolic operon aguBDAC[1]. aguR encodes a transmembrane protein that functions as a one-component signal transduction system that senses the agmatine concentration of the medium and accordingly regulates the transcription of aguBDAC[2], which is also transcriptionally regulated by carbon catabolic repression (CCR) via glucose, but not by other sugars such as lactose and galactose [1], [3]. Here we report the transcriptional profiling of the aguR gene deletion mutant (L. lactis subsp. cremoris CECT 8666 ∆aguR) [2] compared to the wild type strain, both grown in M17 medium with galactose as carbon source and supplemented with agmatine. The transcriptional profiling data of AguR-regulated genes were deposited in the Gene Expression Omnibus (GEO) database under accession no. GSE59514.
doi:10.1016/j.gdata.2015.10.002
PMCID: PMC4664769  PMID: 26697381
Lactococcus lactis; Putrescine; Agmatine deiminase cluster; AguR; Microarray
15.  Draft genome sequence of Citrobacter freundii strain ST2, a γ-proteobacterium that produces N-acylhomoserine lactones 
Genomics Data  2015;6:234-236.
Citrobacter freundii strain ST2, isolated from the algae bloom sample, possesses an N-acylhomoserine lactone (AHL) production activity that secretes short-chain AHL molecules. In this study, we sequenced the complete genome of C. freundii strain ST2 to understand the molecular regulation of the AHL system and to search for the AHL gene in this bacterium. The results show that the genome size is 4.89 Mb with a G + C content of 51.96%. 4626 function proteins were predicted and 3647 proteins were assigned to COG functional categories. A predicted AHL-coding gene LuxR was found at contig 4 and the length was 1541 bp. The strain temporary deposited at Shenzhen Public Platform of Screening & Application of Marine Microbial Resources (Shenzhen, China), and the genome sequence can be accessed at GenBank under the accession no. LJSQ00000000.
doi:10.1016/j.gdata.2015.10.003
PMCID: PMC4664774  PMID: 26697383
Citrobacter freundii; Genome sequence; N-acylhomoserine lactone; LuxR
17.  Author Index 
Bioinformatics  2014;30(17):i646-i647.
doi:10.1093/bioinformatics/btu543
PMCID: PMC4147933
18.  AUTHOR INDEX 
Bioinformatics  2014;30(12):i338-i339.
doi:10.1093/bioinformatics/btu371
PMCID: PMC4058915
19.  ISMB 2014 Proceedings Papers Committee 
Bioinformatics  2014;30(12):i3-i8.
doi:10.1093/bioinformatics/btu322
PMCID: PMC4058949
20.  Author Index 
Bioinformatics  2013;29(13):i371.
doi:10.1093/bioinformatics/btt346
PMCID: PMC3694637
21.  ISMB/ECCB 2013 Proceedings Papers Committee 
Bioinformatics  2013;29(13):i3-i8.
doi:10.1093/bioinformatics/btt281
PMCID: PMC3694660
22.  Author Index 
Bioinformatics  2011;27(13):i410-i411.
doi:10.1093/bioinformatics/btr352
PMCID: PMC3117335
23.  Authors' Index 
Cartilage  2009;1(1 Suppl):165-172.
doi:10.1177/194760350900101S04
PMCID: PMC4513499  PMID: 27076869
24.  Author Index 
Bioinformatics  2009;25(12):i383-i384.
doi:10.1093/bioinformatics/btp315
PMCID: PMC2687995
25.  Author Index 
Bioinformatics  2008;24(13):i414-i415.
doi:10.1093/bioinformatics/btn303
PMCID: PMC2718675

Results 1-25 (25)