Justin's Microbiology Journal
Thursday, August 26, 2004
It's been a hiatus of about 2 months for me from doing any bio research. Since my daughter got out of school, we've been travelling (Taiwan, Japan) and hiking (White Mountains, Kings Canyon) and playing some video games (AC, Doom 3). So lots of relaxing, but I'm getting back into work mode this week since coming back from Japan.
I've been refreshing my knowledge of computational biology and string algorithms from when I worked on Dan Gusfeld's team at UC Davis as a student. I'll be applying to some biotech companies as a computer programmer rather than a biologist, since I've got no credentials in biology but have tons in CS. I briefly flirted with being a doctor, but there's no getting around the 7 year pipeline for a full MD. Eventually I hope to leverage my skills from CS into Bio within the same company, and get hands on experience in both realms in biotech.
Thursday, June 10, 2004
Currently finishing up food-borne pathogens such as salmonella, campylobacter, and clostridium. After that I have one chapter on microorganisms and industry, and it's off to organic chemistry.
I'm starting to have reservations about working in labs with stories like these. Luckily anthrax is very manageable when you have a known exposure, unlike some other viruses and exotoxins.
Friday, June 04, 2004
Apparently it's not particularly safe to run a lab from your home. Not necessarily from a health perspective but from a legal perspective. Here's a professor who was charged with bioterrorism. I have to take issue with the professor's stated goals, his agenda was not purely benign. Anyone who professes to believe in releasing mutated strains of plants or bacteria into the wild is basically irresponsible.
It's depressing to me, but it really does take just a limited amount of knowledge and readily available supplies for terrorists to culture harmful bioagents. It's not a question of if, but a question of when some terrorist will kill more people than Aum Shinrikyo.
But the more people we have working in microbiology and related fields, the more we'll learn about vaccination, detection, and clinical treatment for various ailments. I'm glad I'm in the field now.
Thursday, June 03, 2004
Spent today observing clinical practice at a local ER. I tip my hats to the doctors, nurses and administrators who work the ER, it's exhausting. Just 4 or so hours there and I was tired (but incredibly interested).
I was especially interested in the lab reports for various patients and the frequencies and correlations for various bacteriological problems. Lots of E Coli UTIs, lesser amounts of other UTIs, and a few wound or blood based staphylococcus aureus.
It was good to see the lab results showed some drug resistances, but given testing against a complement of 6-10 antibiotics, each culture was susceptible to at least one or two common antibiotics, including the Staph Aureus.
One of the more interesting ones was a majorly resistant e coli strain. It was resistant to many of the beta lactam derivative antibiotics, but did now show signs of a plasmid mediated beta-lactamase, one route of resistance for cephalosporins, penicillins, and aztreonam. Apparently several different routes for antibiotic resistance exist, including modifying their DNA gyrase, creating cellular membrane pumps to remove antibiotics, and methylating their ribosomes to deactivate antibiotic binding.
Monday, May 24, 2004
Ebola seems to be in the news a lot lately. A Russian scientist just died from a needle prick in a lab, and a new strain of Ebola seems to be responsible for the illnesses seen in Sudan. I also noticed that an America post-doc grazed her finger and survived an attenuated strain, although she had to spend time in the Slammer.
I found the analog to the CDC worldwide, PROMED, the program for monitoring emerging infectious diseases and toxins.
Right now I'm studying clinical microbiology and immunology. It includes growth dependent clinical identification methods, immunology and diagnostics, and molecular and visual methods. I finally learned how the blood type classification of A,B, AB, and O and Rh factor work molecularly as antigens expressed on red blood cells.
Friday, May 21, 2004
To follow up on the viral hemmorrhagic fever post, a new ebola like outbreak has been reported in southern Sudan. Here's a post with more information, no word yet on whether it's different from Ebola or a variant of it. Here's the WHO page.
Hard at work studying the immune system. I've got to say this is some of the harder biology for me to understand so far.
Last few days I've covered immune response, antigens, T Cells, cellular immunity, antibodies, immunization, and immune response diseases.
Right now I'm working more specifically on molecular immunology. Looking at the details of the immunoglobin gene superfamily, major histocompatibility complex cellular membrane proteins, antibody proteins and antigen binding, TCR proteins and genes, and molecular signals in immunity.
I've also started a rough draft of my resume. Since I haven't written one for 9+ years, I'm not sure what I need to say. I think I can leave off anything more than 15 or so years old.
I'm also a bit sick right now, probably a rhinovirus from Elena, who's had a runny nose, sore throat recently. Going through the first stages where the virus is causing minor rhinitis, general malaise, and sore throat.
Rhinoviruses are single stranded RNA viruses in the picornavirus group, although other viruses cause colds as well. Coronaviruses (like the SARS family) cause about 15% of colds, adenoviruses, coxsackie viruses, respiratory synctial viruses and orthomyxoviruses cause a total of around 10%.
We really don't have any effective antiviral drugs, although work is ongoing. One such drug is called WIN 52084 binds to the virus surface and disrupts the cellular binding site.
Sunday, May 16, 2004
Finished reading The Hot Zone, about Ebola and other filoviridae hemorrhagic virii. A good read, and a good reason why I want to get into biology research. There's lots of knowledge out there, and lots of conflicting memes in the world, so work is needed on getting all bioterror weapons effective vaccines, supportive treatment options, and quicker detection techniques. Seems as of 2003, I've read one report that a virus has been shown effective in monkeys. Pravda also reported 4 days ago a new vaccine developed by Russian scientists. Not sure how accurate that is even though I got the link off Google news.
The last outbreak of Ebola was in January 2004 in Mbomo in the Republic of the Congo, with 35 cases, and 29 deaths.
Right now there are 3 major disease outbreaks going on in the world: Dengue Fever in Indonesia, Yellow Fever in Burkina Faso, and SARS in China. Here's a page from the WHO that lists all disease outbreaks going on in the world. Disease Outbreaks.
Out here in California, the biggest occurring viral concern is probably hantavirus, which has a mortality rate of 40-50%, but is still quite rare.
