Distraction from Blogging

Hey Kids,
Sorry i haven't been active the last couple of weeks. I've been at the bench pushing back the boundaries of science in my own small way. Hopefuly next week i'll finish all the posts i've started writing and pop them on here for the masses to read (cough, hmm).
James

Google Search Meme

Christie over at observations of a nerd meme tagged me with this little bit of Google silliness, far more fun than Google whacking, you have to try and find your blog with the funniest search terms you can think of. Here is what I came up with.

Fuzzy pubic lice
Biologist fever
James Hale is too friendly with fruit bats
James Hale is a diseased atheist

And my personal favorite, but I dispute its claim

James got pubic lice from gorillas and gave them to Darwin

I’m going to try and be a bit ambitious and tag Ben Goldacre over at Bad Science, My friend Ricardo and John Logsdon at sex, genes and evolution.

The use of twitter as a research tool/aid

Ever since I’ve started using twitter, I've become increasing reliant and amazed at its use as a research tool. There seems to be a number of fellow scientists and research institutes/websites/publishers all using twitter. This not only makes keeping up with the latest stories, research and job information possible, but it’s become pleasurable and far from the monumental task of repeatedly checking numerous websites each day to keep up with the latest news.

Obviously it can be used to keep your friends updated with what you’ve just eaten for lunch but the research community has made something a bit more pure out of twitter.It seems we’ve built up quite a community on twitter and I’m looking forward to seeing how this type of media develops over the next few months

Here are some Twitters I recommend following

rdmpage / Roderic Page
Irradiatus / Daniel Brown
NerdyChristie / Christie
sciam / Scientific American
bengoldacre / ben goldacre
carlzimmer /carl zimmer
kejames / Karen James
evoldir / EvolDir
PLoS / PLoS
ResearchBlogs / ResearchBlogging.org

Yersinia pestis

Yersinia pestis (formerly Pasteurella pestis) is a Gram-negative rod-shaped bacterium belonging to the family Enterobacteriaceae. It is a facultative anaerobe that can infect humans and other animals.

Also known as the plague, Y. pestis ravaged the European population through the dark ages (Justinian’s plague 541-767 AD) arriving from East and central Africa, spreading to most of the Mediterranean (1), and most of the Middle Ages radiating out from the Caspian Sea. Between the years 1347-1353 plague caused the death of one third of the European population, making it one of the most deadly of all human diseases. First characterized by Yersin in 1894 during the final plague pandemic, which spread out from the Yunnan region of China (ref 2 3).

Primarily a disease of rodents or other wild mammals that usually transmitted by fleas and often is fatal. Human disease is now rare but is usually contracted through contact with rodents and their fleas.
Y. pestis is split into three biovars; Antiqua, Medievalis, and Orentalis, based on small phenotypic differences. Each biovar has been attributed to a particular pandemic event; Antiqua to Justinian’s plague, Medievalis to, resident in central Asia to the pandemics of the middle ages and finally Orentalis to the final Yunnan pandemic of 1894 (4).

Recent DNA-DNA hybridization studies have revealed that Y. pestis is highly related to Y. pseudotuberculosis with the 16s rRNAs being an exact match.
Y. pestis and Y. pseudotuberculosis differ in the diseases that they cause, Y. pestis causes fatal bubonic plague and is transmitted by flea bites or person to person (pneumonic plague), whilst Y. pseudotuberculosis is transmitted person to person through fecal-oral route and rarely results in death.

Symptoms differ depending on the type of Y. pestis infection bubonic, septicemic and pneumonic (5).

Bubonic plague
There is an incubation period of 2-6 days, whilst the bacteria replicate in the lymph nodes. This s followed by lethargy, fever, headache and chills occur suddenly at the end of the incubation period. From this point the infection is resolved or lethal. There will also be the characteristic swelling of lymph nodes resulting in buboes; this is the classic sign of bubonic plague

Septicemic plague
Following the initial incubation period symptoms that may arise include, hypotension, hepatosplenomegaly, delirium, seizures in children, shock, fever. The other symptoms of Bubonic or Pneumonic Plague, not always present

Pneumonic plague
Characterised by Fever, Chills, Cough, Chest pain, dyspnea, hemoptysis, lethargy, hypotension and shock.

Y. pestis can now be treated with standard antibiotic therapies but there is evidence of resistant strains emerging

1. Brossollet J, & Mollaret H (1994) Pourquoi la peste? Le rat, la puce et le bubon (Gallimard, Paris, France).
2. Yersin A (1894) Ann Inst Pasteur 2:428–430.
3. Perry R D &Fetherston J D (
   Perry, R.D.,, Fetherston, J.D. (1997). Yersinia pestis--etiologic agent of plague Clinical Microbiology Reviews DOI: 8993858
4. Devignat, R. (1951). Varieties of Pasteurella pestis; new hypothesis. Bulletin of the World Health Organization 4:247–263, pmid:14859080.
5. http://en.wikipedia.org/wiki/Yersinia_pestis
   

Marburg Hemorrhagic Fever

Given that there have been a recent reports of a case of Marburg hemorrhagic fever arriving in the USA, I thought I would make it the next pathogen top trump.

Marburg hemorrhagic fever is rare hemorraghic fever that affects both humans and non-human primates. Caused by a genetically unique zoonotic (that is, animal-borne) RNA virus of the filovirus family, after its identification in 1967 it led to the creation of this virus family. The More recent additions to the filovirus family include the four species of Ebola virus, which are the only other known members of the filovirus family.

Marburg was identified when outbreaks of hemorrhagic fever occurred simultaneously in laboratories in Marburg and Frankfurt, Germany and in Belgrade, Yugoslavia (now Serbia). A total of 37 people became ill; they included laboratory workers as well as several medical personnel and family members who had cared for them. The first people infected had been exposed to African green monkeys or their tissues. In Marburg, the monkeys had been imported for research and to prepare polio vaccine. The more recent outbreak Within the USA was due to the infected individual being infected from contaminated fruit bat droppings after visiting python cave in Maramagambo Forest, Queen Elizabeth Park, Uganda. Fruit bats are also believed to a vector for Ebola virus but a true animal reservoir has still to be identified. Marburg virus is indigenous to Africa. While the geographic area to which it is native is unknown, this area appears to include at least parts of Uganda and Western Kenya, and perhaps Zimbabwe.

There is a prolonged incubation period of 5-10 days, yet after incubation the onset of the disease is sudden and is marked by fever, chills, headache, and myalgia. After 5 days of being sypmtomatic, a maculopapular rash, most prominent on the trunk (chest, back, stomach), may occur. There may be one or all of the following symptoms; Nausea, vomiting, chest pain, a sore throat, abdominal pain, and diarrhea. Symptoms will then become increasingly severe and may include jaundice, inflammation of the pancreas, severe weight loss, delirium, shock, liver failure, massive hemorrhaging, and multi-organ dysfunction. Marburg hemorrhagic fever is fatal in 23-25% of cases and there is no known cure or treatment other than the usual supportive hospital therapies.
After the infection has passed recovery is slow and prolonged and may be accompanied by the onset of orchititis, recurrent hepatitis, transverse myelitis or uvetis. Other possible complications include inflammation of the testis, spinal cord, eye, parotid gland, or by prolonged hepatitis.

Bausch DG, Borchert M, Grein T, Roth C, Swanepoel R, Libande ML, Talarmin A, Bertherat E, Muyembe-Tamfum JJ, Tugume B, Colebunders R, Kondé KM, Pirad P, Olinda LL, Rodier GR, Campbell P, Tomori O, Ksiazek TG, Rollin PE. (2003). Risk factors for Marburg hemorrhagic fever, Democratic Republic of the Congo. Emerging infectious diseases DOI: 14720391

Problems with Python Programming, second edition by Michael Dawson.

I would like to say that learning python has gotten easier, but the book i'm learning from is so full of errors its taking me hours to get through each section. I find myself constantly trying to work out if its mine or the authors typos causing the programs not to work. Bad times. Does anyone know of any good books?

Darwins Birthday

It's 200 years since the founder of our science was born, what better way to celebrate than to read some of the many blogs about his life and works at http://citizenship.typepad.com/blogfordarwin . Happy Darwin day one and all!