Palmitoylation is a kind of fatty acylation where a palmitoyl group (derived from palmitic acid see below) is added to specific amino acid residues on a protein (usually cysteine, but some times serine or threonine)
This post-transcriptional modification of proteins can play an important regulatory role by affecting where the proteins localize, how they interact with other proteins, etc.
In spite of playing an important regulatory role, the palmitoyl proteome has yet to be fully elucidated. The researchers behind this week’s BioGPS featured article used bioinformatics to identified over 200 potential palmitoylation targets, including Toll-Like Receptor 2 which plays an important role in the immune response.
Learn more about the researchers, their work, and how they used BioGPS in the feature post and check out their cool findings in their open access article
Happy New Year! May you enjoy new relationships and build new bridges in your personal network. Speaking of networks, this week’s BioGPS featured article looks at protein interactions and metabolic networks to uncover bridge proteins in bile acid metabolism which may have prognostic potential for colorectal cancer.
The researchers defined a new metric, “Bridgeness” (which represent the degrees of connection between sensors and enzymes) in their network-based approach for finding prognostic markers in colorectal cancer. Although it’s too early to say whether or not this research will lead to improved prognostic tools, it’s still very exciting, considering the current methods for colorectal cancer screening. Sorry, but endoscopies or colonoscopies for screening purposes are such a pain in the butt!
Think their research is cool? See the BioGPS featured article for the researcher’s perspective/insight on their work here, or read the original research article. You can also comment on their open access paper here.
This year, BioGPS has received 40K more queries than last year, and that’s not even counting this month’s queries!* According to google scholar, the BioGPS paper has been cited 586 of which 143 were publications in 2014. Publications about the default data sets used in BioGPS were cited 4957 times of which 414 citations were from publications this year. The most recent BioGPS application paper about BioGPS and MyGene.info was cited 36 times this year for a total of 51 citations.
Thank you for using BioGPS and letting us know about your awesome research. We hope you will continue to add new plugins and tell us (and your colleagues) how BioGPS has been incorporated into your research. Happy New Year!
*2014.01.02 edit – December’s usage stats were a record-breaking 101252 queries! This means the total usage in 2014, was 140k queries higher than in 2013.
Turns out, the FAA has more than just a functional genomics team conducting research on all aspects of making flying safer such as:
All of which is exciting and intriguing, but before we digress any further, why is the FAA even interested in this topic?
One reason is microbes! Post-mortem microbial fermentation can produce ethanol in a cadaver, making it difficult to determine if the deceased had been drinking or not based solely on blood alcohol levels. In order to help accident investigators distinguish the source of the blood alcohol content, the FAA Functional genomics team profiled gene expression changes in the blood during acute ethanol exposure. This enabled researchers to identify several patterns of gene expression changes related to alcohol consumption as well as potential biomarkers for future investigation. Not only does this have important implications in investigating the cause of plane crashes, it also has enormous potential for verifying whether or not alcohol played a role in other accidents.
One might think that all the hype and panic surrounding Ebola in the US would help to raise awareness for infectious diseases closer to home, but many New World hemorrhagic fever viruses remain largely unknown to the public at large. Junin virus is one such arenavirus that has caused hemorrhagic fever outbreaks in Argentina. Fortunately a vaccine has helped to curb the incidence of disease; however, there are few treatment options available once someone is infected with this virus. Hence, it is important to better understand the behavior of the virus in the host from infection to pathogenesis. Better understanding could lead to better treatment options for not just Junin virus, but also related hemorrhagic fever arenaviruses. The researchers behind this paper used and siRNA screen to find genes that affect Junin virus entry into cells and discovered a potential therapeutic target.
Investigated By: Researchers for 8 renal transplant centers
Has implications for: Renal transplant patients and their medical providers (pending further validation studies, regulatory trials and approvals)
WHY: 15-20% of renal transplant patients experience acute rejection, but the current method to detect acute rejection involves taking a biopsy following suspicious blood test results (in other words, more surgery!). Worse yet, the suspicious blood test results are non-specific for acute rejection, and usually a bit too late when it is indicative of acute rejection.
WHAT: A blood test to detect risk of acute kidney transplant rejection called the Kidney Solid Organ Response Test (kSORT)
HOW: Analyzing gene expression of >500 blood samples from 436 renal transplant patients divided into 1 training set and 3 validation sets.