|Example screenshot of open reading frame|
annotation within the Geneious program.
Tuesday, December 30, 2014
Thursday, November 27, 2014
|A CDC infographic highlighting the infectivity of|
IntroductionWe are all unfortunately familiar with the notorious stomach flu. Most of us have experienced that awful nausea, vomiting, diarrhea, and tiredness associated with catching some stomach bug. While there are many viral causes of the stomach flu (also called gastroenteritis), one of the most common is the Norovirus. The Norovirus is a common and contagious virus that is currently the leading cause of viral gastroenteritis. The infection can last a few days and, while most people recover, it can cause serious issues such as dehydration, and jeopardize the health of many at-risk populations. There is also no vaccine against the Norovirus right now (the flu vaccine does not protect you from the stomach flu), although researchers are working on it.
Sunday, November 9, 2014
|Clostridium difficile establishes infections following|
antibiotic treatment and causes diarrheal disease.
Sunday, October 12, 2014
|The big three artificial sweeteners. <Source>|
Thursday, September 18, 2014
Sometimes I want to easily calculate the average sequence length of our collection of sequences in either a fasta or fastq file. To address this, I wrote up a couple of small perl scripts to quickly calculate the median sequence length of a fasta or fastq file. You can find these perl scripts on GitHub in my "Microbiome_sequence_analysis_toolkit" repository. The nice thing about this script is that it returns the median and file name to the standard output, which makes it easier to loop across many files and collect the results into a single summary file.
Sunday, August 24, 2014
I write a lot of scripts in my day-to-day sequence analysis of microbiome data. While a lot of these are a bit project specific, some of these could be useful for others in their sequence analysis projects. A while back I posted about a script for formatting Qiime output files for input into the Lefse analysis toolkit, but now I am thinking it would be worth adding more. Therefore, I changed the "Lefse formatting" repository to be a more general "microbiome sequence analysis toolkit" repository. This seems like a nice place to periodically add scripts for easy use by others. To get this new repo started, I added a new script for removing "block fasta" formatting from fasta sequence files. It's relatively simple, but I think it's also pretty useful.
Sunday, August 3, 2014
| The Marine Microbiology Initiative is striving to build a|
community of virus ecology resources online.
Sunday, July 20, 2014
|The CRISPR-Cas system has been found to play roles|
in the antibiotic resistance of some bacteria. <Source>
In recent years, CRISPRs (Clustered, regularly interspaced, short palindromic repeats) have been gaining popularity in the microbiology field. Briefly, CRISPRs serve as an adaptive immune system for bacteria, meaning that they are able to remember what viruses (bacteriophages) or other entities have infected them and mount a targeted defensive response the next time they are infected with the same entity (think of it as an analog to our adaptive immune response which uses antibodies and other agents to target invading microbes). More specifically, the CRISPR-Cas (Cas are the CRISPR associated genes) system facilitates the integration of a small section of the foreign genomic DNA into the CRISPR array within the bacterial genome (see left side of the detailed diagram below). While in the array, this section of foreign DNA will serve as a template for recognizing the invading genome again if another infection occurs, and the template will be used for targeting that invading genome for rapid destruction. As can be seen in the figure below, this system is similar to the Eukaryotic RNA-interference system found in organisms including humans. I've already gotten pretty technical here, and anything more in-depth would be beyond the scope of this post, so please check out reference  for further reading.
Sunday, July 13, 2014
Gene Therapy for Hemophilia, Blindness, and Cancer, and the Tools That Make it Possible at the HMGS 2014 Symposium
Every blogger has those times when life gets busy and their blog takes a back seat. For me, this summer has been one of those times. Between meetings, research, our family trip back home, and the general effort involved in being a scientist, I have been behind in updating this blog. Despite my blog slacking, I'm sure it will be worth it when I have more cool stuff to write about in the next couple of months (especially when I have cool new research findings to talk about!). So let's get started with some awesome catchup!
A month ago, we here at Penn hosted the annual Howard Hughes Medical Institute (HHMI) Med Into Grad Scholars (HMGS) symposium for the participating northeast schools. This program was made to promote translational research in PhD training by integrating more medically relevant training into the PhD candidate curriculum (including coursework and clinical clerkships). For more information about the program, and to read about the symposium last year, check out my post here.
|Dr. Maus presenting her research to the students attending|
Sunday, June 15, 2014
A few weeks ago I attended the American Society for Microbiology (ASM) General Meeting in Boston. I wrote up a post about the virome workshop I attended (follow this link for the post), but I also want to write out a summary for the rest of the conference. The ASM meeting was huge (I'm talking thousands of microbiologists) with many full days of great science, so an in depth review of the meeting would be beyond the scope of this single blog post. Therefore my goal is to give you a brief summary of the meeting, along with some links and resources you can use if you want to get more information. Additionally, for another summary of the general meeting, check out this ASM summary episode of TWIM.
Sunday, May 25, 2014
Sunday, April 27, 2014
The lab is a place where we see some really cool and beautiful things (especially when doing microscopy). For this post I want to quickly share a cool picture I took in the lab this week, as well as give you a little background about the method I used to get it.
Saturday, April 5, 2014
This week the kind folks from the NDSEG (National Defense Science and Engineering Graduate) Fellowship program highlighted me as their weekly featured fellow. This is an announcement the group puts out weekly on their Facebook and Twitter pages to highlight the cool work their fellows are doing. I am honored to be their featured fellow, and am thankful for their support. The announcement from their Facebook page is as follows:
Monday, March 17, 2014
In my last post I talked about PLOS's efforts to improve data sharing, and how important it is to make your data and analyses tools available when you publish, especially in microbiome research. This importance of sharing published data and analysis scripts was also highlighted in a recent article in the journal Microbiome (see reference below). Now the code versioning and sharing software site GitHub is even getting on board by officially supporting students and classrooms with free micro and organization accounts to improve coding education and data sharing practices. I'll also note that, as they point out in their blog, this is something they had done for a while but now they made it official.
Sunday, March 2, 2014
PLOS (the Public Library Of Science) is a popular scientific journal publisher whose journals include PLOS Genetics, PLOS Pathogens, and of course, PLOS ONE. What makes PLOS stand out is not that they publish great science (which they do, of course), but rather their leadership in open access publishing (open access means that anybody can read their publications for free). Recently PLOS announced that they will be taking their open access policies to the next level by requiring all published data to be openly and clearly accessible to the public. Specifically their blog stated that "authors must make all data publicly available, without restriction, immediately upon publication of the article". This has already sparked some important conversations about the feasibility of such a requirement.
Saturday, February 22, 2014
The first data from Oxford Nanopore's promising MinION sequencing platform was released a couple of days ago. The sequencing data was released at the Advances in Genome Biology and Technology Meeting in Florida, and was presented by Dr David Jaffe of the Broad Institute in Cambridge, MA. The reported data is a bit underwhelming because it failed to live up to the goals set by the company a couple of years ago, and because it does not seem to offer anything new to the field of DNA sequencing. Here I am briefly going to go over the way the MinION system works, how it is performing, and what we can possibly expect in the future. I also have my sources below, so check those out for further reading.
Thursday, February 13, 2014
Biomarker discovery is a big part of medical research. A biomarker is a clinical signal, like the presence of a gene in your genome or colonization of your lungs with a certain bacterial species, whose presence or absence indicates a disease state or predicts an increased risk for developing a disease state. These play important roles in medicine because they can allow for disease diagnosis (ie. the physician can test for the disease biomarker) or provide a prediction of whether the patient is at a higher risk for developing a condition (ie. a gene that puts a patient at higher risk for developing diabetes). There are some good programs out there for biomarker discovery, but one I particularly like is Lefse.
Tuesday, February 4, 2014
Saturday, January 18, 2014
Details and Perspectives as Illumina Announces their Newest DNA Sequencing Machines and the $1,000 Human Genome
Illumina (one of the major DNA sequencing technology companies) announced their newest line sequencing machines. The two new DNA sequencers are the NextSeq 500 and the HiSeq X10, with the NextSeq 500 being marketed for everyday laboratory use, and the HiSeq X10 being marketed as a factory level, population sequencer (this is the higher power model). These are going to be powerful, state-of-the-art machines that are going to have a significant impact on both research and clinical applications. Here I am going to briefly cover what these new machines are and what their release means for contemporary research and clinical applications. As always, I will also point you in the right direction for further reading, in case you are interested in more.
Sunday, January 12, 2014
A few days ago our lab, in collaboration with some folks here at the Hospital of the University of Pennsylvania Orthopaedics Department, published a manuscript in the Journal of Orthopedic Research. The title of our manuscript was "Culture-independent pilot study of microbiota colonizing open fractures and association with severity, mechanism, location, and complication from presentation to early outpatient follow-up". This is a report of our ongoing prospective study in which we are characterizing the microbial communities associated with open fracture wounds and their adjacent healthy skin, as well as describing correlations between the microbiome and clinical factors (such as healing complications and wound severity). Unfortunately this paper is not open access, so you are going to have to access it through a university or local library subscription to the journal.