BioGPS Featured Article – Chemoproteomics reveals Toll-like receptor fatty acylation | The Su Lab

Here’s what you’ll need to know in order to appreciate and enjoy this week’s BioGPS Featured Article – Chemoproteomics reveals Toll-like receptor fatty acylation | The Su Lab.

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) Palmitic acid

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.

Palmitoylation can affect protein localization
Palmitoylation–depalmitoylation cycles mediate inter-compartment shuttling of proteins. By: Yuko Fukata & Masaki Fukata Nature Reviews Neuroscience 11, 161-175 (March 2010)

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.

The Immune response-TLR signaling pathways from Thomson-Reuters.

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

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BioGPS Featured Article – Anomalies in Network Bridges Involved in Bile Acid Metabolism Predict Outcomes of Colorectal Cancer Patients | The Su Lab

BioGPS Featured Article – Anomalies in Network Bridges Involved in Bile Acid Metabolism Predict Outcomes of Colorectal Cancer Patients | The Su Lab.

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.

Happy New Year from BioGPS

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.

Our excellent Gene of the Week writers, Melissa Lau and Kerin Higa have written about 40 different genes spanning a wide range of topics including, but not limited to: Blood-letting, Body Odors, Blood Brain Barrier, Beats, Breast milk, and Blood Type— all while incorporating all sorts of interesting references such as Pliny the Elder, Game of Thrones, King Oyster, the Iran Hostage Crisis, and so much more. As a fan of their works, I look forward to seeing what they come up with next in 2015!

The utility of BioGPS was augmented by the addition of 32 new plugins this year bringing the total BioGPS plugin count to 625 plugins, of which 366 are publicly shared amongst the BioGPS community.

As seen in our featured article series, BioGPS users study a huge variety of interesting and important subjects ranging from immunology and infectious disease (eg- pertussis and juunin virus) to evolution and model organism knowledge base development. BioGPS users conduct important research elucidating genes involved in circadian regulation in the heart or bone development or even the development of lung disease.

In addition to specific genes, BioGPS users study patterns of gene expression such as those which reveal how maternal obesity may affect fetal development, or those which one day could be used to detect patients at high risk of renal transplant rejection or even to determine if alcohol consumption played a role in an airplane accident.

Happy New Year!  Don't drink and drive!
BioGPS users are also investigating the role of alcohol in plane accidents. If you drink, please do it responsibly.

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.

BioGPS Featured Article – Microarray characterization of gene expression changes in blood during acute ethanol exposure | The Su Lab

BioGPS Featured Article – Microarray characterization of gene expression changes in blood during acute ethanol exposure | The Su Lab.

Just in time for the holiday travel rush, this week’s BioGPS featured article is like something out of CSI, but for the FAA.

Wait a second, did I read that right? The Federal Aviation Administration has a functional genomics team, and they use BioGPS? –AWESOME!

FAA Functional Genomics Team researcher prepping a qRT-PCR run image from: FAA’s site

Turns out, the FAA has more than just a functional genomics team conducting research on all aspects of making flying safer such as:
-Aerospace Medical
-Biochemistry
-Biodynamics
-Bioinformatics
-Cabin Safety
-Environmental Physiology
-Forensic Toxicology
-Radiobiology
-Vision Research

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.

Was there drinking or were the microbes just busy?
Was there drinking or were the microbes just busy?

Check out the BioGPS feature here: BioGPS Featured Article – Microarray characterization of gene expression changes in blood during acute ethanol exposure | The Su Lab.

Or, do some flight sleuthing of your own before you travel. The FAA has lots of interesting figures, stats, and other info on their site, here

BioGPS Featured Article – siRNA screen for genes that affect Junin virus entry uncovers voltage-gated calcium channels as a therapeutic target | The Su Lab

BioGPS Featured Article – siRNA screen for genes that affect Junin virus entry uncovers voltage-gated calcium channels as a therapeutic target | The Su Lab.

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.

Learn more about this paper and the researchers behind it here. Or go read it now ’cause it’s interesting and free!

BioGPS Featured Article – The kSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection: Results of the Multicenter AART Study | The Su Lab

BioGPS Featured Article – The kSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection: Results of the Multicenter AART Study | The Su Lab.

Here’s the skinny on this paper:

    WHO:

    • 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.

Learn more about this paper and the researchers behind it here. Or go read it now ’cause it’s interesting and free!