Multiple sequence alignment with the Clustal series of programs

Ramu, Chenna; Sugawara, Hideaki; Koike, Tadashi; López, Rodrigo; Gibson, Toby J.; Higgins, Desmond G.; Thompson, Julie

doi:10.1093/nar/gkg500

Cited by 4,387 publications

(3,093 citation statements)

References 17 publications

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“…They are highly homologous at the mRNA and protein levels. Using the ClustalW webtool (http://www.ebi.ac.uk/clustalw/) [6], we determined that human and mouse proteins are approximately 80% identical and 93% similar overall.…”

Section: Resultsmentioning

confidence: 99%

PI3K is negatively regulated by PIK3IP1, a novel p110 interacting protein

Zhu¹,

He²,

Johnson³

et al. 2007

Biochemical and Biophysical Research Communications

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Signaling initiated by Class Ia phosphatidylinositol-3-kinases (PI3Ks) is essential for cell proliferation and survival. We discovered a novel protein we call PI3K Interacting Protein 1 (PIK3IP1) that shares homology with the p85 regulatory PI3K subunit. Using a variety of in vitro and cell based assays, we demonstrate that PIK3IP1 directly binds to the p110 catalytic subunit and modulates PI3K activity. Our studies suggest that PIK3IP1 is a new type of PI3K regulator.

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Section: Resultsmentioning

confidence: 99%

PI3K is negatively regulated by PIK3IP1, a novel p110 interacting protein

Zhu¹,

He²,

Johnson³

et al. 2007

Biochemical and Biophysical Research Communications

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“…Additional HA and NA sequences from swine in Latin America (in this case, Brazil and Colombia) were added, for which whole‐genome sequences were not available. Separate alignments for each of the eight genome segments were made using ClustalW (v1.83) 35. As there was no evidence of reassortment between the HA and NA for our data, the HA and NA segments were concatenated36 for greater phylogenetic resolution and visual clarity in Figure 3.…”

Section: Methodsmentioning

confidence: 99%

Transmission dynamics of pandemic influenza A(H1N1)pdm09 virus in humans and swine in backyard farms in Tumbes, Peru

Tinoco

Kasper

Nelson

et al. 2015

Influenza Resp Viruses

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ObjectivesWe aimed to determine the frequency of pH1N1 transmission between humans and swine on backyard farms in Tumbes, Peru.DesignTwo‐year serial cross‐sectional study comprising four sampling periods: March 2009 (pre‐pandemic), October 2009 (peak of the pandemic in Peru), April 2010 (1st post‐pandemic period), and October 2011 (2nd post‐pandemic period).SampleBackyard swine serum, tracheal swabs, and lung sample were collected during each sampling period.Main outcome measuresWe assessed current and past pH1N1 infection in swine through serological testing, virus culture, and RT‐PCR and compared the results with human incidence data from a population‐based active surveillance cohort study in Peru.ResultsAmong 1303 swine sampled, the antibody prevalence to pH1N1 was 0% pre‐pandemic, 8% at the peak of the human pandemic (October 2009), and 24% in April 2010 and 1% in October 2011 (post‐pandemic sampling periods). Trends in swine seropositivity paralleled those seen in humans in Tumbes. The pH1N1 virus was isolated from three pigs during the peak of the pandemic. Phylogenetic analysis revealed that these viruses likely represent two separate human‐to‐swine transmission events in backyard farm settings.ConclusionsOur findings suggest that human‐to‐swine pH1N1 transmission occurred during the pandemic among backyard farms in Peru, emphasizing the importance of interspecies transmission in backyard pig populations. Continued surveillance for influenza viruses in backyard farms is warranted.

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“…PCR products were directly sequenced using the BigDye Terminator Sequencing kit v3.1 (Applied Biosystems) in an ABI-3100 capillary electrophoresis system (Applied Biosystems). Sequences obtained were edited Expression analyses on pig HMGCR gene using the Sequencing software (Applied Biosystems) and aligned with the ClustalW program (Chenna et al, 2003).…”

Section: Methodsmentioning

confidence: 99%

Functional and association studies on the pig HMGCR gene, a cholesterol-synthesis limiting enzyme

Cánovas

Quintanilla

Gallardo

et al. 2010

Animal

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The 3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) is the rate-limiting enzyme in the biosynthesis of cholesterol. We have studied the role of theHMGCRgene in pig lipid metabolism by means of expression and structural analysis. We describe here the complete coding region of this gene in pigs and report two synonymous single nucleotide polymorphisms in the coding region. We have, additionally, studied the association of one of these polymorphisms (HMGCR:c.807A>C) with several lipid deposition- and cholesterol-related traits in a half-sib population generated from a commercial Duroc line, showing in some families a positive relationship ofHMGCR:c.807Aallele with serum low-density lipoprotein (LDL)-bound cholesterol and triglyceride levels, and also with intramuscular fat (IMF) content ofgluteus mediusmuscle. We have also assessed the expression levels in muscle and in liver from 68 Duroc individuals corresponding to the most extreme animals for the analysed traits. LiverHMGCRexpression correlated negatively with the serum high-density lipoprotein (HDL) levels, carcass lean percentage and stearic acid content, while muscle expression correlated also negatively with the carcass lean percentage, stearic and linoleic acids content, but showed a positive correlation with the serum lipid cholesterol (HDL, LDL and total cholesterol), IMF and muscle oleic and palmitic fatty acid content. With this information, we have performed an association analysis of expression data with lipid metabolism phenotypic levels and theHMGCRgenotype. The results indicate thatHMGCRexpression levels in muscle are different in the two groups of pigs with extreme values for fat deposition and total cholesterol levels, and also between animals with the differentHMGCRgenotypes.

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Multiple sequence alignment with the Clustal series of programs

Cited by 4,387 publications

References 17 publications

PI3K is negatively regulated by PIK3IP1, a novel p110 interacting protein

PI3K is negatively regulated by PIK3IP1, a novel p110 interacting protein

Transmission dynamics of pandemic influenza A(H1N1)pdm09 virus in humans and swine in backyard farms in Tumbes, Peru

Functional and association studies on the pig HMGCR gene, a cholesterol-synthesis limiting enzyme

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