Friday, December 4, 2009

Please Take This Survey


One of my colleagues is working on a Ph.D. dissertation and she is interested in knowing how people perceive encyclopedia articles. She has sent me a survey that she would like to use as part of her research. She said that is should take about ten minutes to complete.

Thanks for participating in this survey. Please email me after finishing the survey to let me know you have done it.

http://www.uvm.edu/~ikubisze/experiment/

Tuesday, December 1, 2009

Slime Molds



Readings

Introduction to the Slime Molds- UC Berkeley Museum
http://www.ucmp.berkeley.edu/protista/slimemolds.html

Slime Mold Factsheet- Cornell University
http://plantclinic.cornell.edu/FactSheets/slimemold/slimemold.htm

http://www.discoverlife.org/20/q?search=Eumycetozoa

Powerpoint Presentation

http://www.slideshare.net/secret/g0zJfjt4xfG5ca

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- distinguish between plasmodial and cellular slime molds

- discuss the life cycle of plasmodial and cellular slime molds

- discuss altruism, cheating, and kin recognition in the life cycle of cellular slime molds

Plant-mycorrhizal fungi interactions


Readings

Symbiosis Mycorrhiza and Lichens
http://www.botany.hawaii.edu/faculty/wong/BOT135/Lect26.htm

Powerpoint Presentation

http://www.slideshare.net/secret/1jjuM1QpoCit0i


Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- list important plant macronutrients

- disucss nutrient uptake in plants

- discuss the basic characteristics of fungi

- discuss why fungi are unusual and important

- distinguish between sexes and mating types

- distinguish between ectomycorhhiza and endomycorrhiza

Thursday, November 19, 2009

Rhizobia-Legume Interactions


Readings

General

Rhizobia-http://en.wikipedia.org/wiki/Rhizobia

Scientific Literature

Here are some papers from the scientific literature examining this system. We don't expect you to understand everything in these papers, but we would like you to see the diversity of approaches that moderm scientists are using to study this system.

Lifestyle alternatives for rhizobia: mutualism, parasitism,
and forgoing- symbiosis
http://people.umass.edu/lsadler/adlersite/kiers/Alternativelifestyles1.pdf

Host sanctions and the legume–rhizobium mutualism-
http://www.nature.com/nature/journal/v425/n6953/abs/nature01931.html (then click on "full text"

A mechanistic molecular test of the plant-sanction hypothesis in legume–rhizobia mutualism
http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VR3-4WPS9PP-1&_user=2605799&_rdoc=1&_fmt=&_orig=search&_sort=d&_docanchor=&view=c&_searchStrId=1100808123&_rerunOrigin=google&_acct=C000055350&_version=1&_urlVersion=0&_userid=2605799&md5=491bf0585068046d9ae2f49e3bb7a905

Powerpoint Presentation

Plant-Microbe Interactions: Rhizobia/Legumes
http://www.slideshare.net/secret/AZNj5BIH5bqGC8

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss how and why participants in an apparently mutualistic relationship should be "selfish"

- describe the pattern of nodule formation

- discuss the importance of nitrogenase and leghaemogolbin for nitrogen fixation

- discuss circumstances under which plants would like to limit nodulation or nitrogen fixation by rhizobia

- discuss "partner choice" and "santioning" in this system

- intepret data and draw conclusions in experiments examining rhizobia-legume interactions

Writing Assignment # 4



Reading

A Mutual Affair- http://judson.blogs.nytimes.com/2008/04/08/a-mutual-affair/

Assignment

This article by Olivia Judson from the New York Times discusses a number of interesting issues in mutualisms. In this class we have discussed the roles that microbes play as parasites, predators, competitors, and mutualists.

Using the knowledge you have gained during this course, and from reading the assignmed article, discuss the variety of ecological roles through which microbes affect humans. For each of the ecological roles that you discuss in your paper, we would like you to mention at least one interesting or "cool" thing that you have learned about the behavior of microbes in those interactions.

Your essay should be a minimum of two pages and a maximum of three pages in length.

Important Dates

Tuesday November 24th- Rough draft due

Thursday November 26th- Eat excessive amounts of turkey (or tofurkey)

Thusday December 3rd- Workshop papers (and remind Dr. McG that it is his Mom's birthday)

Tuesday December 9th- Final draft due

Wednesday, November 18, 2009

Microbial Diseases


Readings

Understanding Microbes in Sickness or Health- National Institute of Allergy and Infectious Disease

http://www3.niaid.nih.gov/topics/microbes/PDF/microbesbook.pdf

Websites

Nanobugs- http://www.nanobugs.com/
This website, designed for kids, is cool/cute/creepy but it might give you some basic background on important microbial diseases.

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss reservoirs for diseases
- discuss how microbes can enter their hosts
- discuss strategies microbes use to adhere, colonize, and invade their hosts
- discuss ways that microbes evade host defenses
- discuss the production of virulence factors
- discuss the endysymbiotic origin in mitochondria
- define pathogenicity islands
- define PROMISCUOUS and use it in a sentence

Thursday, November 5, 2009

Global Climate Change Webinar


Here is the link to the Climate change webinar that Dr. San Francisco talked about.

http://learningcenter.nsta.org/products/symposia_seminars/fall09/NOAA/webseminar1.aspx

Microbes and Coral Reefs


Readings

Coral reefs- http://www.eoearth.org/article/Coral_reef

Threats to Coral Reefs-
http://www.eoearth.org/article/Threats_to_coral_reefs

Cnidaria- http://www.eoearth.org/article/Cnidaria

Zooxanthellae- http://www.eoearth.org/article/Zooxanthellae

Global warming takes a toll on coral reefs
http://www.eoearth.org/article/Global_warming_takes_a_toll_on_coral_reefs

Patterns of CAribbean coral loss
http://www.eoearth.org/article/Patterns_of_Caribbean_coral_loss

Coral disease-
http://www.reef.crc.org.au/discover/coralreefs/Coraldisease.htm

Coral stress and disease
http://www.reefrelief.org/Image_archive/diseases/index.shtml

Powerpoint Presentation

http://www.slideshare.net/secret/MXAjnaF502X8PL

Expected Learning Outcomes

By the end of this course a fully engaged student will be able to

- discuss the characteristics or the cnidarian polyps and zooxanthellae that make up a corals

- discuss the "dilema of the inverteed trophic pyramid" and the role that the discovery of zooxanthellae played in solving that mystery

- discuss the mutualism between cnidarian polyps and zooxanthellae

- discuss some of the threats facing coral reefs

- discuss coral bleaching and some of the proposed mechanisms of bleaching

- discuss the characteristics of some of the important coral diseases

Tuesday, October 20, 2009

Atmosphere, Solar Radiation, Microbes, and You




Reading

Electromagnetic Radiation- http://www.eoearth.org/article/Electromagnetic_radiation

Atmospheric Composition- http://www.eoearth.org/article/Atmospheric_composition

Photosynthesis- http://www.eoearth.org/article/Photosynthesis

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- Discuss electromagnetic energy and identify the portion of the electromagnetic spectrum that is used for photosynthesis

- discuss the composition of the atmosphere

- identify organisms capapble of photosynthesis

- define carbon fixation

- briefly discuss what happens in the light dependent reactions of photosynthesis

- briefly discuss what happens in the light independent reactions of photosynthesis

- discuss the processes involved in cycling organic carbon to carbon dioxide and back in aerobic and anaerobic environments.

- define the photo zone

- discuss conditions at the bottom of the ocean

-

Friday, October 16, 2009

Writing Assignment #2


Here are some recent news articles that address some of the issues that we have covered in class.

Nobel prize for chemistry: antibiotics scientists share 2009 award
http://www.telegraph.co.uk/science/science-news/6268585/Nobel-prize-for-chemistry-antibiotics-scientists-share-2009-award.html

Dangerous liaisons: Bacterial 'sex' causes antibiotic resistance
http://esciencenews.com/articles/2009/06/11/dangerous.liaisons.bacterial.sex.causes.antibiotic.resistance
TIMELY ASSIGNMENT NOTE- The play "Dangerous Liaisons" is being performed on campus this weekend.

Obama, Farm Industry Clash Over Antibiotics
http://www.wired.com/wiredscience/2009/07/farmantibiotic/

Assignment

Write a 1-2 page organized paper dealing with 1 or more of these topics. Include in your paper:

An Introduction-Set up the problem at hand and its general importance

Body-discuss why this topic is important to medicine, human health and society at large; what are pros and cons of different perspectives on these issues

Coda-Your own thoughts about the future related to the topic

Important Dates

Rough Draft Due- Tuesday October 20

Workshop- Thursday October 22

Final Draft Due- Tuesday October 27

Literature cited-References

Targets of Antibiotics and Mechanisms of Antibiotic Resistance




Readings

Targets of Antibiotics (figure)
http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=mboc4.figgrp.4624

How antibiotics work: the mechanisms of action
http://www.tufts.edu/med/apua/Miscellaneous/mechanisms.html

Antibiotics that affect the cell envelope
http://pathmicro.med.sc.edu/fox/antibiotics1.htm

Mechanisms of Antibiotic Resistance in the Microbial World
http://www.moleculartb.org/gb/pdf/transcriptions/11_YZhang.pdf

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss the targets of antibiotics
- discuss the mechanisms of antibiotic resistance
- pronounce "efflux" correctly

Tuesday, October 6, 2009

Antibiotic Resistance



Further Reading

Evolution of Antibiotic Resistance-
http://www.pbs.org/wgbh/evolution/library/10/4/l_104_03.html

Antibiotic resistance: Questions and Answers- CDC
http://www.cdc.gov/getsmart/antibiotic-use/anitbiotic-resistance-faqs.html

Antibiotic resistance- delaying the inevitable (parts 1 and 2) UC Berkeley
http://evolution.berkeley.edu/evosite/relevance/IA1antibiotics2.shtml

HIV the ultimate evolver (parts 1-3) UC Berkeley
http://evolution.berkeley.edu/evosite/relevance/IA2HIV.shtml

Resisting our drugs-
http://understandingevolution.com/evolibrary/article/0_0_0/bergstrom_03

Turbochared evolution-
http://understandingevolution.com/evolibrary/article/side_0_0/turboevolution_01

Relevance of evolution:medicine-
http://understandingevolution.com/evolibrary/article/0_0_0/medicine_01

Powerpoint Presentation

Here is a link the the powerpoint presentation I used in class.

http://www.slideshare.net/secret/rPekyBdLalUvFY

Expected Learning Outcomes

By the end of the course a fully engaged students should be able to

- discuss the causes of the development of antibiotic resistance

- discuss where antibiotics come from

- discuss what we have learned from ecology and evolutionary biology about potentila problems associated with antibiotic use

- discuss what we have learned from evolutionary biology that should help us fight microbial diseases more effectively

Friday, October 2, 2009

Sex Lives of Bacteria


Reading

Genetic recombination in bacteria
http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Avery.html

Recombination in bacteria
http://www.emunix.emich.edu/~rwinning/genetics/bactrec.htm

Expected Learning Outcomes

By the end of the course a fully engaged students should be able to

- discuss how mutation, transformation, conjugation, and transduction adds to the genetic variation of bacteria.

Microbes and the Evolution of Sex



Based on our understanding of natural selection, at first glance sexual reproduction doesn't appear to be advantageous from the female perspective (due to the two-fold cost of sex). However, the fact that sexual reproduction is so common in all groups of organisms suggests that there must be some major benefits of sex that outweight the costs.

Reading

The Advantages of Sex- Matt Ridley
http://www.pbs.org/wgbh/evolution/sex/advantage/index.html

Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- explain "the two-fold costs of sex"
- discuss possible benefits of sexual reproduction including adaptation to environmental uncertainty and fighting disease
- be able to discuss the problem of the evolution of antiobiotic resistant microbes
- be able to discuss what the medical field may be able to learn from observing how nature fights disease.

Monday, September 28, 2009

Natural Selection


An understanding of the process of natural selection helps us to understand the amazing diversity of life on the earth.

Expected Learning Outcomes

By the end of the course a fully engaged students should be able to

1) define the process of natural selection

2) distinguish between the patterns of stabilizing, disruptive, and directional selection and provide examples of each pattern

3) describe how the process of natural selection has produced a trait that is an adaptation to a particular environmental condition.

4) explain why organisms are not expected to be perfectly adapted to their environments

5) discuss the conditions that would cause natural selection to stop

6) explain why natural selection is expected to produce selfish traits

Readings

Natural selection http://www.eoearth.org/article/Natural_selection


Here is a link to a website from UC Berkeley-

http://evolution.berkeley.edu/evolibrary/article/evo_25

Friday, September 25, 2009

Africa's Big Three


Tuberculosis

Readings

Tuberculosis Fact Sheet- Centers for Disease Control and Prevention
http://www.cdc.gov/tb/publications/factsheets/general/tb.htm

Pulmonary Tuberculosis- https://www.google.com/health/ref/Pulmonary+tuberculosis

Tackling Tuberculosis in Africa http://web.worldbank.org/WBSITE/EXTERNAL/COUNTRIES/AFRICAEXT/0,,contentMDK:21696343~pagePK:146736~piPK:226340~theSitePK:258644,00.html


Malaria

Readings

Malaria- http://www.eoearth.org/article/Malaria

Malaria in Africa
http://www.rollbackmalaria.org/cmc_upload/0/000/015/370/RBMInfosheet_3.htm

Diseases and development challenges in Africa
http://www.eoearth.org/article/Diseases_and_development_challenges_in_Africa


HIV

Readings

HIV Basic Information - Centers for Disease Control and Prevention
http://www.cdc.gov/hiv/topics/basic/index.htm

HIV and AIDS in Africa
http://www.avert.org/aafrica.htm


Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- briefly discuss the biological characteristics of the causal agents for the Big Three diseases

- discuss the means of transmission of these diseases

- discuss the means of preventing the spread of these diseases

- discuss the impact that these diseases have had on people in Aftica

Articles about AIDS Vaccine



AIDS vaccine promising; experts urge caution- San Francisco Chronicle
http://www.sfgate.com/cgi-bin/article.cgi?f=/c/a/2009/09/24/BANM19S3NR.DTL

For the first time AIDS vaccine shows some success- New York Times
http://www.nytimes.com/2009/09/25/health/research/25aids.html?_r=2

Thanks to Mathew Sexton for forwarding this link to us.

Thursday, September 24, 2009

H1N1 Flu



Readings

H1N1 Swine Flu- from Centes for Disease Control and Prevention/
http://www.cdc.gov/H1N1FLU/

H1N1- www.flu.gov

2009 Flu Pandemic- http://en.wikipedia.org/wiki/2009_flu_pandemic

Swine Flu 2009/2010
Honors College recommendations for students, faculty and staff


If you must miss work or class because you have symptoms of the flu described below, and must see a doctor, please do not forget to bring a note indicating that you have done so. Students, please be aware that while reasonable extensions will be permitted to make up work due to the flu will be granted, you are ultimately responsible for your work. Please also be sure to contact your professor as soon as possible if you are ill. Faculty, please make your students aware of how you will permit make-up work for short- and long-term absences because of the flu. Also provide the dean’s office with information of how you wish your class to be covered in case of an extended absence by you because of the flu. Staff, please notify your supervisor as soon as possible if you have to miss work.

Our recommendations are taken directly from the Centers for Disease Control.
http://www.cdc.gov/h1n1flu/qa.htm

What are the signs and symptoms of this virus in people?

The symptoms of 2009 H1N1 flu virus in people include fever, cough, sore throat, runny or stuffy nose, body aches, headache, chills and fatigue. A significant number of people who have been infected with this virus also have reported diarrhea and vomiting. Severe illnesses and death has occurred as a result of illness associated with this virus.

What can I do to protect myself from getting sick?

There is no vaccine available right now to protect against 2009 H1N1 virus. However, a 2009 H1N1 vaccine is currently in production and may be ready for the public in the fall. As always, a vaccine will be available to protect against seasonal influenza

Actions that can help prevent the spread of germs that cause respiratory illnesses like influenza are presented below.
Take these everyday steps to protect your health:
Cover your nose and mouth with a tissue when you cough or sneeze. Throw the tissue in the trash after you use it.
Wash your hands often with soap and water. If soap and water are not available, use an alcohol-based hand rub.*
Avoid touching your eyes, nose or mouth. Germs spread this way.
Try to avoid close contact with sick people.
If you are sick with flu-like illness, CDC recommends that you stay home for at least 24 hours after your fever is gone except to get medical care or for other necessities. (Your fever should be gone without the use of a fever-reducing medicine.) Keep away from others as much as possible to keep from making others sick.

Other important actions that you can take are:
Follow public health advice regarding school closures, avoiding crowds and other social distancing measures.
Be prepared in case you get sick and need to stay home for a week or so; a supply of over-the-counter medicines, alcohol-based hand rubs,* tissues and other related items might could be useful and help avoid the need to make trips out in public while you are sick and contagious

What is the best way to keep from spreading the virus through coughing or sneezing?

If you are sick with flu-like illness, CDC recommends that you stay home for at least 24 hours after your fever is gone except to get medical care or for other necessities. (Your fever should be gone without the use of a fever-reducing medicine.) Keep away from others as much as possible. Cover your mouth and nose with a tissue when coughing or sneezing. Put your used tissue in the waste basket. Then, clean your hands, and do so every time you cough or sneeze.

If I have a family member at home who is sick with 2009 H1N1 flu, should I go to work?
Employee
s who are well but who have an ill family member at home with 2009 H1N1 flu can go to work as usual. These employees should monitor their health every day, and take everyday precautions including washing their hands often with soap and water, especially after they cough or sneeze. Alcohol-based hand cleaners are also effective. If they become ill, they should notify their supervisor and stay home. Employees who have an underlying medical condition or who are pregnant should call their health care provider for advice, because they might need to receive influenza antiviral drugs to prevent illness. For more information please see General Business and Workplace Guidance for the Prevention of Novel Influenza A (H1N1) Flu in Workers.

What is the best technique for washing my hands to avoid getting the flu?

Washing your hands often will help protect you from germs. Wash with soap and water or clean with alcohol-based hand cleaner*. CDC recommends that when you wash your hands -- with soap and warm water -- that you wash for 15 to 20 seconds. When soap and water are not available, alcohol-based disposable hand wipes or gel sanitizers may be used. You can find them in most supermarkets and drugstores. If using gel, rub your hands until the gel is dry. The gel doesn't need water to work; the alcohol in it kills the germs on your hands.

What should I do if I get sick?

If you live in areas where people have been identified with 2009 H1N1 flu and become ill with influenza-like symptoms, including fever, body aches, runny or stuffy nose, sore throat, nausea, or vomiting or diarrhea, you should stay home and avoid contact with other people. CDC recommends that you stay home for at least 24 hours after your fever is gone except to get medical care or for other necessities. (Your fever should be gone without the use of a fever-reducing medicine.) Stay away from others as much as possible to keep from making others sick. Staying at home means that you should not leave your home except to seek medical care. This means avoiding normal activities, including work, school, travel, shopping, social events, and public gatherings.

If you have severe illness or you are at high risk for flu complications, contact your health care provider or seek medical care. Your health care provider will determine whether flu testing or treatment is needed.
If you become ill and experience any of the following warning signs, seek emergency medical care.

In adults, emergency warning signs that need urgent medical attention include:
Difficulty breathing or shortness of breath
Pain or pressure in the chest or abdomen
Sudden dizziness
Confusion
Severe or persistent vomiting
Flu-like symptoms improve but then return with fever and worse cough

What is the positive, definitive test for the swine flu?

The ONLY way a test can be confirmed positive is through PCR or culture methods!! Some doctors’ offices are reporting positive results for H1N1-swine-like from the “rapid flu tests”. These tests can indicate that you have the flu but not the SWINE FLU. If you want to read some more go to www.flu.gov for info. H1N1 can be seasonal or swine-like as well, a rapid can't determine the difference.

Tuesday, September 22, 2009

Gene Therapy


Readings

Gene Therapy- Human Genome Project Information

http://www.ornl.gov/sci/techresources/Human_Genome/medicine/genetherapy.shtml

Viruses


Readings

Introduction to the Viruses- http://www.ucmp.berkeley.edu/alllife/virus.html

Viruses, viruses, viruses by David Baltimore
http://eands.caltech.edu/articles/LXVII1/viruses.html


Expected Learning Outcomes

By the end of this course a fully engaged student should be able to

- discuss the characteristics of a virus
- discuss the basic shapes of viruses
- define "bacteriophage"
- compare and contrast the mechanism gene injection of viruses that infect bacteria and those that attack animal cells
- distinguish between the infection pathways of DNA viruses, simple RNA viruses, and retroviruses