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Saturday, February 10, 2018

Publication roundup: IPA in literature

Scientific literature frequently provides inspiration and insight when we see how our customers are advancing their knowledge of the world. QIAGEN’s Ingenuity® Pathway Analysis (IPA®) is a powerful analysis and interpretation tool for uncovering network interactions and identifying new targets or candidate biomarkers within the context of biological systems. Here, we take a brief look at some recent papers that cite IPA used during the research process.

 

Liver proteomic analysis of postpartum Holstein cows exposed to heat stress or cooling conditions during the dry period

First author: Amy L. Skibiel

A group of US and Israeli scientists studied the impact of heat-related stress on cow performance and disease outcomes, and published their results in The Journal of Dairy Science. The team focused the metabolic rates and pathways within the liver proteome of postpartum cows as they transitioned from gestation to lactation, providing either hot or cool conditions for the animals. They used QIAGEN’s IPA to analyze proteins to determine the most relevant pathways, physiological functions and networks, and identified 75 out of more than 3000 proteins that were differentially expressed between hot and cool cows. The results suggest that keeping cows cool might improve production, reduce oxidative stress, increase milk yield and decrease susceptibility to disease.

 

Inflammatory gene expression signatures in idiopathic intracranial hypertension: Possible implications in microgravity-induced ICP elevation

First author: Susana B. Zanello

The Microgravity journal recently ran a report submitted by a group of scientists based in Texas and Massachusetts. The team investigated idiopathic intracranial hypertension (IIH), a neuro-ophthalmologic condition suffered by many astronauts returning from extensive missions in outer space, symptoms of which include visual impairment and intracranial pressure. They applied QIAGEN IPA’s Target Filter Analysis to the differentially expressed gene data set to study molecular pathways associated with the elevation of IIH-related intracranial pressure. The report confirms that neurophysiological alterations and neuro-immunomodulation are present in IIH and suggests further research on the topic.

 

Impaired IFN-α-mediated signal in dendritic cells differentiates active from latent tuberculosis

First author: Stefania Parlato

PLoS One recently reported a study by Italian researchers who wanted to understand how active tuberculosis (TB) might develop in individuals exposed to Mycobacterium tuberculosis (Mtb), which can also remain latent. The team used IPA to identify biological functions, gene networks and canonical pathways. They found that active TB patients have an impaired IFN-α signal in their dendritic cells, which are significant in dictating antibacterial immunity, and which might account for an inability to generate a T-cell response against Mtb.

 

Uncovering a predictive molecular signature for the onset of NASH-related fibrosis in a translational NASH mouse model

First author: Arianne van Koppen

A team of researchers from The Netherlands, the US and Japan collaborated to gain insight on the increasing prevalence of nonalcoholic steatohepatitis (NASH), which is the progressive form of nonalcoholic fatty liver disease – the most common chronic liver disease found in developed countries. The researchers looked at the key molecular processes typically involved, ranking early markers for hepatic fibrosis. The team used QIAGEN IPA’s Path Explorer tool to calculate the most efficient path between signature genes and four defined key processes. The resulting report, which was published in Cellular and Molecular Gastroenterology and Hepatology, identified an early predictive model signature that marked the early onset of histopathologic fibrosis. This can aid in early detection of the onset of NASH – in addition to new blood-based biomarkers which may aid in the development of new therapeutics and help cut down on (pre)clinical experimental timeframes.

 

Genome re-sequencing to identify single nucleotide polymorphism markers for muscle color traits in broiler chickens

First author: H. R. Kong

Using genetic selection, efficient production systems, improved nutrition and regular veterinary attention, the poultry industry has successfully improved growth and yield of chickens used for broiler meat. This very success may also have had a negative impact on meat qualities – including muscle color – so researchers from the University of Arkansas investigated the specific genetic elements that regulate muscle color in chicken meat. Their study, published in the Asian-Australasian Journal of Sciences, used IPA to analyze functional interpretation of chicken genes retaining SNPs. The results helped identify a link between meat color in chickens with chromosomal DNA stability, the functions of ubiquitylation and the quality and quantity of collagen subtypes.

 

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