Selasa, 30 Juni 2009

Is Being Overweight a Health Risk?

It depends on the question - a health risk for what? People who are overweight, defined by the U.S. government and the World Health Organization as a Body Mass Index (BMI) of between 25 and 30, apparently do have a slightly increased risk for certain diseases such as diabetes, coronary artery disease and hypertension. But for other parameters, such as risk of death, the evidence is not that clear-cut (See “Is ‘Overweight’ Overstated?”, pp. 346-347, Human Biology 5th ed.). In fact, a recent study of over 11,000 Canadian adults reveals that as a group, people who are defined as overweight have a slightly lower risk of death than the normal-weight group, though not by much.

Taking this new mortality data into account and reviewing the graph on p. 346 of Human Biology, one wonders whether the range of “normal” weight shouldn’t be shifted about 3 BMI to the right. A word of caution, however; the shape of the weight-vs.-risk curve is likely to be different for every disease, age group, etc. It’s probably going to be impossible to come up with a perfect functional definition of overweight, no matter how much we’d like to.

Sabtu, 27 Juni 2009

The Pandemic of 2009

The World Health Organization has officially declared a pandemic as a result of the rapid worldwide spread of Influenza A (H1N1), formerly known as swine flu. But that does NOT mean that a lot of people will die. By definition, a pandemic is simply a widespread outbreak of a new human flu virus that spreads rapidly from human to human, causing human illness.

Some flu pandemics cause only mild symptoms and few deaths – others can be quite deadly. The best-known pandemics of the last century were the deadly Spanish flu of 1918 (20-40 million deaths), and the milder Asian flu of 1957 (1-4 million deaths) and Hong Kong flu of 1968 (also 1-4 million deaths). In contrast, the milder seasonal flu that many of us get nearly every year kills “only” about a quarter of a million people each year.

Pandemics are of concern to public health officials (and the public!) because the virus spreads so quickly and because the consequences of the spread cannot always be predicted in advance. Fortunately, it now appears that this pandemic will be no more deadly than the typical seasonal flu that many of us get nearly every year. Most people who become infected with Influenza A (H1N1) are recovering without the need for medical care. But it could have been otherwise, and that’s why health officials were so concerned at first and why they are still watching it closely.

The other flu we worry about is avian flu (see Human Biology 5th ed., pp. 540-541). Avian flu is VERY deadly in the few cases in which it has been caught from birds, but human-to-human transmission is still exceedingly rare.

Kamis, 25 Juni 2009

Research Opportunity

The goal of the study is to compare the methane ground/atmosphere exchange between two sites, one using effluent organic fertilization and the other using solid manure fertilization. The site secured is a 500 acre dairy/orchard in the heart of the central valley. I have already secured instruments and lab space in cooperation with Prof. Schimel and will be in constant communication wtih him as well as Prof. Melack and Prof. King. I'm looking for someone that is interested in coming aboard to help me run samples within the lab.

Contact Matthew Christian if you are interested

Selasa, 23 Juni 2009

Freeze Your Eggs

Okay, so you’re a woman in her thirties who wants to have children some day but has not yet met “Mr. Right”. What to do? Well, some women have made the decision to freeze some of their eggs before their reproductive clock stops ticking, just in case. The basic techniques are readily available at any fertility clinic; stimulate egg maturation hormonally, harvest some eggs, and then (instead of fertilizing and implanting them) just freeze them.

Worldwide, only about a thousand children have been born from previously frozen eggs. In contrast, over 50,000 babies are born each year in the U.S as a consequence of in vitro fertilization and implantation (Human Biology 5th ed., p. 394). Obviously, the idea of older single women freezing their eggs has not yet caught on. But it just might!

See “Why I Froze My Eggs”, by Rachel Lehmann-Haupt. Newsweek May 11, 2009, pp. 50-52.

Steve Jobs' New Liver

It’s not official, but there are reports in the news media that Steve Jobs, CEO of Apple computers, received a liver transplant recently at an undisclosed location in Tennessee (The New York Times, June 23; “A Transplant That is Raising Many Questions”).

Normally, patients who need an organ transplant place themselves on the transplant list of one of eleven regional Organ Procurement Organizations (OPOs) in the U.S. Waiting times can vary. When an organ becomes available the regional OPO offers it to a patient already on its list, with the highest priority given to the sickest patients and those who have been on the list the longest time.

Most patients sign up for the transplant list at only one OPO, because insurance companies will only pay for an organ transplant performed in a person’s “home” OPO. Nevertheless, patients who are willing to pay for the transplant themselves (and with access to a plane so they can get to the hospital within six hours) can increase their odds for a transplant by placing themselves on the transplant lists of several different OPOs simultaneously. No one has said whether or not Mr. Jobs was on more than one list at the time of his transplant, or how long he waited for his new liver.

For a discussion of whether the current organ allocation system is fair, see “How Should We Allocate Scarce Organs?” in Human Biology 5th ed., pp. 368-369.

Minggu, 21 Juni 2009

Jen from Standford University shows us how to do DNA extraction from Strawberries

An excellent first time project, that is completely safe, requires only a kitchen, and will give you visible DNA in a glass. And Jennifer is delightful! The video's are so easy to follow, they work for any level and any age group. Thanks Jen, This is great.

This article is from the Home Activities section of Stanford University's understanding genetics website:
For your convenience it has been pasted below:

Do-It-Yourself Strawberry DNA (Kiwi's and Banana's work too)

Strawberries, bacteria, humans—all living things have genes, and all of these genes are made of DNA. That's why scientists can take a gene from one living thing and put it into another. For example, they can put human genes into bacteria to make new medicines.

How do scientists take DNA out of a living thing? It's not that hard—there are lots of ways to do it! You can follow the directions in the video above to get DNA out of a strawberry. Or you can follow the steps below. Either way you'll have strawberry DNA at the end!

What you need:

* measuring cup
* measuring spoons
* rubbing alcohol
* 1/2 teaspoon salt
* 1/3 cup water
* 1 tablespoon Dawn dishwashing detergent
* glass or small bowl
* cheesecloth
* funnel
* tall drinking glass
* 3 strawberries (green tops removed)
* reclosable plastic sandwich bags
* test tube or small glass jar (like the kind spices come in)
* bamboo skewer (find them at the grocery store)

What to do:

1. Chill the rubbing alcohol in the freezer. (You'll need it later.)
2. Mix the salt, water, and Dawn detergent in a glass or small bowl. Set the mixture aside. This is your extraction liquid.
3. Line the funnel with the cheesecloth, and put the funnel's tube into the glass.
4. Put the strawberries in the plastic bag and push out all the extra air. Seal it tightly.
5. With your fingers, squeeze and smash the strawberry mixture for 2 minutes.
6. Add 3 tablespoons of the extraction liquid you made in Step 2 to the strawberries in the bag. Push out all the extra air and reseal the bag.
7. Squeeze the strawberry mixture with your fingers for 1 minute.
8. Pour the strawberry mixture from the bag into the funnel. Let it drip into the glass until there is no liquid left in the funnel.
9. Throw away the cheesecloth and the strawberry pulp inside. Pour the contents of the glass into the test tube or small glass jar so it is 1/4 full.
10. Tilt the test tube or jar and very slowly pour the cold rubbing alcohol down the side. The alcohol should form a layer on top of the strawberry liquid. (Don't let the alcohol and strawberry liquid mix. The DNA collects between the two layers!)
11. Dip the bamboo skewer into the test tube where the alcohol and strawberry layers meet. Pull up the skewer. The whitish, stringy stuff is DNA containing strawberry genes!

You can try these steps to purify DNA from lots of other living things. Grab some oatmeal or kiwis from the kitchen and try it again! Which foods give you the most DNA?

And here's the DIY BIO NYC Group doing Strawberry DNA extraction in shot and wine glasses, and trying out a homemade gel electrophoresis box.

NYC's DIY BIO GROUP Insert Green Flourescent Protein Genes into DNA

Using a kit developed for high school students, NYC DIY BIO transform E. coli with a plasmid carrying the gene for Green Fluorescent Protein (GFP). It's a little hard to understand at times, but the on screen titles help out. Great work NYC DIY BIO!

The work area met all criteria for Biosafety Level 1 as defined by the Centers for Disease Control.

In the last video they finish the transformation of E. coli with a plasmid containing the GFP (Green Fluorescent Protein) gene and succeed in generating green bacterial colonies. Next meeting we will purify the GFP and visualize it under black light and with gel electrophoresis.

For more info on GFP check out these archived posts:

BIO LAB EXPERIMENT WALK THROUGH VIDEOS - Mike White's Entire Collection - Inserting GFP into bacteria, Mixing Agar, and More!

2. Futures in Biotech 37: Just A Touch Of Green - Published on Dec 29, 2008 GREEN FLUORESCENT PROTEIN DISCOVERY and HOW ORGANISMS SENSE TOUCH
In these podcast's Marty Chalfie, the discoverer of GFP! Describes how he developed one of the most important tools of modern molecular biology, one that allows us to see inside a living cells, down to the protein level. With green fluorescent protein, or GFP, we can now track the life of a protein, from when the gene that makes the protein is turned on, to where it goes, to where it dies.

3. 11 Excellent Videos introducing GFP:

4. Green fluorescent protein Virtual Lab! Narrated in a flash classroom and Student Protocols are Included!

PSYORG Article: New tool isolates RNA within specific cells (w/Video)


A team of University of Oregon biologists, using fruit flies, has created a way to isolate RNA from specific cells, opening a new window on how gene expression drives normal development and disease-causing breakdowns.

While DNA (deoxyribonucleic acid) provides an identical in every cell,
(ribonucleic acid) decodes genetic instructions that turn protein molecules on and off in different cell types.

The new tagging method, tested in a variety of subsets of Drosophila , is described in a paper put on line ahead of regular publication by the journal . Instead of scientists needing to physically separate cell types, they now can inject a chemically modified gene from the one-celled organism Toxoplasma gondii and activate it in only one cell type within a tissue. Only newly generated RNA in this cell type is then tagged and isolated. "By analyzing RNA from different cell types, we can begin to understand how cellular differences are generated," said lead author Michael R. Miller, a National Science Foundation-funded doctoral student in the lab of Chris Doe, a UO biologist and Howard Hughes Medical Institute (HHMI) investigator. "Our new TU-tagging method should be useful for isolating cell-type specific RNA from other organisms, including mammals, and should be useful in broad areas of research including studies of development, neurobiology and disease." The new non-toxic, non-invasive method makes it possible to "listen in" to the messages -- in fact, messenger RNA -- that the nucleus is sending each cell, without perturbing the cell, Doe said. "It is much like eavesdropping on a phone conversation, rather than pulling the person out of the house for questioning. The cell has no idea that its RNAs are being 'tagged' for isolation and study. That's good, because we get a more accurate idea of what the cell is saying."

That, Doe added, could be helpful for 'listening' to host cells before and after the initiation of a disease to determine how cells respond, or, for example study healthy immune cells versus bacterially-challenged immune cells or neurons before they learn a task and after they learn a task to determine what changes in the cell are caused by the experience. The new UO-developed tool builds on work led by co-author Michael D. Cleary, who as a doctoral student at Stanford University unveiled the T. gondii-based approach for use in analyzing RNA synthesis and decay in 2005 in Nature Biotechnology. Cleary, now a faculty member at the University of California, Merced, worked on the UO project as a postdoctoral fellowship funded by the National Institutes of Health and HHMI.

Cleary's group built its tool with the enzyme uracil phosphoribosyltransferase (UPRT), a nucleotide salvage enzyme that prepares nucleotides for incorporation into newly synthesized RNA. By altering the nucleotide analog 4-thiouracil, the UPRT enzyme caused RNA to become tagged with thiouracil (TU), allowing the "TU-tagged" RNA to be purified from untagged RNA. In Doe's lab, Miller, Cleary and research technician Kristin J. Robinson of the UO's institutes of Neuroscience and Molecular Biology manipulated Drosophila so that they would only express UPRT in specific target cells. The group tested the new approach in embryos, larvae and adults using microarray technology to detect cell type-specific gene expression. The researchers say the method should work in other systems, including vertebrates, by using gene transfer, retroviral delivery, electrical pulses of molecules through cell membranes, or messenger RNA injection. Source: University of Oregon

Drool Worthy! If money was no object. Amazing Lab Equipment

This video released last month from QIAGEN, shows how many lab activities are becoming increasingly automated. Amazing...

Kamis, 18 Juni 2009

Stretching and Sports Injuries

Does stretching before exercise reduce the risk of sports injuries? Many coaches, trainers, and athletes swear that it does, but no one knows for sure because the critical experiment has never been done.

Now researchers are attempting to do the experiment. Sponsored by USA Track & Field (USATF), the researchers are currently enrolling people who run at least 10 miles per week. Participants must agree to be assigned randomly to either the "stretch" or the "no-stretch" group and to adhere to the study protocol for three months. Runners in both groups are expected to report their injuries during the study period.

Runners can apply to be participants at So far several thousand runners have signed up, though not all of them have completed the study protocol and submitted their reports. The results will be made public as soon as enough runners have completed the protocol for there to be a statistically significant difference between the groups, or when enough data has accumulated to show that there is no difference. Ultimately, up to 10,000 runners may be needed.

Runners, this is your golden opportunity to contribute to the advancement of science.

Selasa, 16 Juni 2009

$59 400x Zoom USB Microscope

This is interesting. A 400x zoom USB from Celestron for 59$.

Here's the lens in action on youtube:

but it might be more trouble than its worth. It has be discontinued from the manufacturer - could be because of this...

Stormin Norman from Arizona on 4/3/2008 writes.
Pros:Quality Lenses, Strong Construction
Cons:Difficult to Use, Go from 20x to 400x hard, Sticky Zoom, Vibrates when focusing
"Is great to use but difficult to change from 20x to 400x. The manufacturer has a problem. Had to use pliers on the first one and broke a fingernail and the replacement was better but 400 x was still difficult to use and focus. Not like the one demonstrated at the CES in Las Vegas in January. "

Here's the demo Norman's talking about:

Anyone else have this?

NPR TODAY RADIO: Kay Aull discussing her home DNA Lab for genotyping her HFE gene


Thanks to Jason Bobe on the DIYBIO mailing list letting us know about this...
23-year-old Kay Aull set up a do it yourself DNA lab in her closet! The MIT graduate says with just $300 and a little bit of knowledge, almost anyone can start combing through their DNA. She brings her lab equipment to our studio to show us how it all works.


Windows Media Player:

Real Player:

Selasa, 09 Juni 2009

Habitat Restoration Assistant

UCSB’s Coal Oil Point Reserve currently has an opening for a Habitat Restoration Assistant beginning July1st , and continuing through the end of the year. The Assistant will help with implementing restoration projects and gain valuable experience with hands-on restoration techniques and principles. The assistant will work with the Reserve Steward, a Restoration Ecologist and student interns and participate in all aspects of restoration: removal of non-native plants, seed collection, plant propagation, preparation for intern and volunteer workdays, and
enhancement and preservation of existing restoration sites.

This is a great opportunity to gain field experience in restoration techniques, native plant propagation, and volunteer supervision. The assistant will be employed for approximately 6-10hours/ week at a pay rate of $10/hour. Applicant must be a UCSB student, and available for the entire summer. Preferred availability is Friday mornings (~8:30-12:30) plus one other weekday morning (9-12noon), and able to commit to occasional weekend time (~one Saturday/per month). Students eligible for work study in the Fall are strongly encouraged to apply!

To apply, send resume and class schedule/time availability for summer and fall quarter to: Tara Longwell at and Darlene Chirman

Kamis, 04 Juni 2009

Neurobiology research opportunity

CCS Bio major Veronica Pessino tells me that a that a grad- student friend of hers in the Feinstein lab is looking for an undergrad to help him out. He would love a CCS student and asked Veronica to see if anyone is interested. His name is Jack Reifert.

If any of you are interested in neurobiology writ large, this could be a real opportunity to get a great start at lab research in a very nice lab!

The Application of Platform-Based Design to Embedded Electronics and Synthetic Biological Systems (Video 2/26/2009)

Watch Video
From the Series: CSE Colloquia - 2009 Produced by: University of Washington

This talk will outline Platform Based Design techniques as they relate to both embedded electronics and synthetic biology. Platform-Based Design is a design methodology within Computer Aided Design which at its core promotes the separation of functionality from implementation. Rigorous and formal applications of PBD have been shown to be very useful in the design of embedded electronic systems. This work has manifested itself in the development of the Polis, Metropolis, and Metro II design environments at UC Berkeley. PBD's true power lies in its ability to cross into new application areas. Download Video as MP4

Rabu, 03 Juni 2009

The Royal Academy of Engineering's MAY 2009 Report on Synthetic Biology

Click here to download the PDF
"This report aims to define the term ‘synthetic biology’, review the state of the field and consider potential future developments and their likely technological, economic and societal impact. It will also attempt to assess the requirements for the development of the field and to identify key policy issues."

The following is a summary of the central themes and issues that the report
has investigated, and the resulting recommendations.

Defining synthetic biology
We define synthetic biology thus:
“Synthetic biology aims to design and engineer biologically based parts, novel
devices and systems as well as redesigning existing, natural biological systems.”
This definition, while maintaining a certain level of simplicity, expresses the key
aspects of synthetic biology. It is consistent with the views of most researchers
in the field (both in the UK and abroad) and those of The Royal Academy of
Engineering. Synthetic biology strives to make the engineering of biology easier and more predictable.

Current activity and applications
There is considerable activity in a number of areas including health, energy, the
environment, agriculture and applications in other industrial sectors.
A synthetic version of the anti-malarial drug artemisinin is being developed
using synthetic biology methods. This makes it amenable to large scale
industrial production - if successful, it will have a major impact on the
treatment of malaria in the developing world. The cost of treatment should be
low as the development of the drug is being funded by the Gates Foundation.

Journal Article (Free Full Text): Opportunities for microfluidic technologies in synthetic biology

Opportunities for microfluidic
technologies in synthetic biology

"We introduce microfluidics technologies as a key foundational technology for synthetic biology experimentation. Recent advances in the field of microfluidics are reviewed and the potential of such a technological platform to support the rapid development of synthetic biology solutions is discussed."
  1. Full TextFree
  2. Full Text (PDF)Free

Selasa, 02 Juni 2009

This is the end

Okay I'm all blogged out. If anyone is still reading this then here are a couple of end of quarter wrap up announcements.
  • The last lectures are now up as pdf files on the right hand side. I think the only one missing is the first part of today.
  • The answers to the ecology quiz I handed out are here with a few comments.
  • For Thursday remember YOU are presenting. Don't make it a lecture, make it INTERESTING (oops, that didn't sound right). Remember you are supposed to be passionate about this so tell us something cool you investigated.

Senin, 01 Juni 2009


Dwindling Phosphorus Supplies

The world’s supply of phosphorus for agricultural fertilizers is dwindling, according to a recent article in Scientific American. Global reserves are expected to run out in about 100 years unless new reserves are found or better techniques are developed for extracting phosphate from phosphate-rich rock.

As phosphorus supplies decline and as the world demand for agricultural fertilizers grows, we can expect fertilizer price spikes, phosphate shortages, and perhaps even disruption of food production. Countries with large phosphorus reserves such as Morocco will benefit economically. Morocco could be among the wealthiest nations in the world in 50-100 years.


On Friday I thought I'd post something about the bioswales at Manzanita village that I briefly mentioned in class. However I couldn't actually find any particularly good links online.

Today I open 93106, the weekly faculty and staff newspaper to find an article about the restoration project and the bioswales - Restoration Project Provides Model for Future Environmental Efforts.

The principal challenge of the restoration was creating an ecologically functional habitat in such close proximity to an urban environment. If untreated, fertilizers from the courtyard lawns and seagull guano from the residence hall roofs are washed into the ocean and nearby lagoon during rainstorms. This can cause algal blooms that are unsightly and can smother the fish.
CCBER used the excess nutrients in the water to its advantage by creating bioswales — vegetated channels that use plants to purify water runoff before it flows into the nearby lagoon. More than 1,300 feet of bioswales treat some 75 percent of Manzanita’s storm water runoff.
Copyright 2010 Biology Blog Education. All rights reserved.
Themes by Ex Templates Blogger Templates l Home Recordings l Studio Rekaman