Primer3Plus, an enhanced web interface to Primer3

Untergasser, Andreas; Nijveen, Harm; Rao, Xiangyu; Bisseling, Ton; Geurts, René; Leunissen, Jack A. M.

doi:10.1093/nar/gkm306

Cited by 2,389 publications

(1,787 citation statements)

References 7 publications

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“…Cycling conditions were 5 min at 95°C, then 45 cycles with denaturation (10 sec at 95°C), annealing (10 sec at 60°C), and elongation (10 sec at 72°C). Primers were designed using Primer3Plus (Untergasser et al, 2007) or Quantprime (Wolffe and Matzke, 1999) and tested for quality and specificity by melt-curve analysis, gel electrophoresis and appropriate negative controls. Forward primer (FP) and reverse primer (RP) sequences were as follows: …”

Section: Reverse Transcription Quantitative Real-time Pcr (Rt-qpcr)mentioning

confidence: 99%

Hippocampal gene expression induced by cold swim stress depends on sex and handling

Bohacek

Manuella

Roszkowski

et al. 2015

Psychoneuroendocrinology

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Summary: Stress-related disorders such as PTSD and depression are more prevalent in women than men. One reason for such discordance may be that brain regions involved in stress responses are more sensitive to stress in females. Here, we compared the effects of acute stress on gene transcription in the hippocampus of female and male mice, and also examined the involvement of two key stress-related hormones, corticosterone and corticotropin releasing hormone (Crh). Using quantitative reverse transcription polymerase chain reaction (RT-qPCR), we measured gene expression of Fos, Per1 and Sgk1 45 min after exposure to brief cold swim stress. Stress induced a stronger increase in Fos and Per1 expression in females than males. The handling control procedure increased Fos in both sexes, but occluded the effects of stress in males. Further, handling increased Per1 only in males. Sgk1 was insensitive to handling, and increased in response to stress similarly in males and females. The transcriptional changes observed after swim stress were not mimicked by corticosterone injections, and the stress-induced increase in Fos, Per1 and Sgk1 could neither be prevented by pharmacologically blocking glucocorticoid receptor (GR) nor by blocking Crh receptor 1 (Crhr1) before stress exposure. Finally, we demonstrate that the effects are stressor-specific, as the expression of target genes could not be increased by brief restraint stress in either sex. In summary, we find strong effects of acute swim stress on hippocampal gene expression, complex interactions between handling and sex, and a remarkably unique response pattern for each gene. Overall, females respond to a cold swim challenge with stronger hippocampal gene transcription than males, independent of two classic mediators of the stress response, corticosterone and Crh. These findings may have important implications for understanding the higher vulnerability of women to certain stress-related neuropsychiatric diseases. In summary, we find strong effects of acute swim stress on hippocampal gene expression, complex interactions between handling and sex, and a remarkably unique response pattern for each gene. Overall, females respond to a cold swim challenge with stronger hippocampal gene transcription than males, independent of two classic mediators of the stress response, corticosterone and Crh. These findings may have important implications for understanding the higher vulnerability of women to certain stress-related neuropsychiatric diseases.

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Section: Reverse Transcription Quantitative Real-time Pcr (Rt-qpcr)mentioning

confidence: 99%

Hippocampal gene expression induced by cold swim stress depends on sex and handling

Bohacek

Manuella

Roszkowski

et al. 2015

Psychoneuroendocrinology

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“…Gene-specific primers for reference genes and target genes were designed as previously described (Ellefsen et al 2008), using Primer3 Plus (Untergasser et al 2007). For each gene, a three or four primer pairs were designed, with exception of the MyHC genes, for which a minimum of five primer pairs were designed.…”

Section: Gene Expressionmentioning

confidence: 99%

Irisin and FNDC5: effects of 12-week strength training, and relations to muscle phenotype and body mass composition in untrained women

Ellefsen¹,

Vikmoen²,

Slettaløkken³

et al. 2014

Eur J Appl Physiol

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This file was dowloaded from the institutional repository Brage NIH -brage.bibsys.no/nih Ellefsen, S., Vikmoen, O., Slettaløkken, G., Whist, J. E., Nygård, H., Hollan, I.... Rønnestad, B. (2014). Irisin and FNDC5: effects of 12-week strength training, and relations to muscle phenotype and body mass composition in untrained women. MethodsEighteen untrained women performed 12 weeks of progressive whole body heavy strength training, with measurement of strength, body composition, expression of irisin-related genes (FNDC5 and PGC1α) in two different skeletal muscles, and levels of serum-irisin and -thyroid hormones, before and after the training intervention. ResultsThe strength training intervention did not result in changes in serum-irisin or muscle FNDC5 expression, despite considerable effects on strength, lean body mass (LBM) and skeletal muscle phenotype. However, our data indicate that training affects irisin biology in a LBM-dependent

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“…Specific primers were designed using Primer 3 plus online software (http://www.bioinformatics.nl/primer3plus.) [13]. Screening analysis was performed for two prevalent mutations of CETP gene, Int14+1A and D442G, using RFLP method as previously described [9].…”

Section: Genetic Analysesmentioning

confidence: 99%

Novel mutations of cholesteryl ester transfer protein (CETP) gene in Japanese hyperalphalipoproteinemic subjects

Ohtani

Inazu

Noji

et al. 2012

Clinica Chimica Acta

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Background: The half of hyperalphalipoproteinemia (HALP) in Japan is caused by CETP gene mutations. Other than two prevalent mutations (D442G and Intron 14 splicing donor site +1 G>A), some rare CETP mutations are found in Japanese HALP subjects.Methods: CETP gene analysis of genomic DNA from subjects was performed by restriction fragment length polymorphism (RFLP) and sequencing analysis. Mutations which were suspected to cause a splicing defect or a protein secretion defect were investigated in COS-1 cells transfected with a CETP minigene construct or a cDNA expression vector.Results: Each of three subjects was identified as a carrier of CETP gene mutation of a compound heterozygote of c.653_654delGGinsAAAC and Intron 14 splicing donor site +1 G>A, a heterozygote of c.658G>A or a homozygote of L261R. The c.658G>A mutation was located at the last nucleotide of exon 7, and it was confirmed to cause splicing abnormality revealed by the CETP minigene analysis. The L261R CETP was not secreted to conditioned media of the cells.Conclusions: Three novel CETP gene mutations are responsible for HALP by CETP deficiency. It is predicted that there are more rare CETP gene mutations in Japanese, and these multiple rare mutations alone or a combination with each of prevalent mutations responsible for mild-to-moderate or marked HALP, respectively.3

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Primer3Plus, an enhanced web interface to Primer3

Cited by 2,389 publications

References 7 publications

Hippocampal gene expression induced by cold swim stress depends on sex and handling

Hippocampal gene expression induced by cold swim stress depends on sex and handling

Irisin and FNDC5: effects of 12-week strength training, and relations to muscle phenotype and body mass composition in untrained women

Novel mutations of cholesteryl ester transfer protein (CETP) gene in Japanese hyperalphalipoproteinemic subjects

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