Hanna Kokko will be giving the EEMB departmental seminar next week. Dr Kokko is a behavioral ecologist and theorist and will likely discuss her work on the evolution of sex roles, population dynamics, and sperm parasites (Amazon mollies).
Title:From individuals to populations ... and back
Date: Nov 2
Time: 4:00 pm
Location: MSR Auditorium
Jumat, 30 Oktober 2009
Kamis, 29 Oktober 2009
Fantastic opportunity
Part Time Research and Curatorial Assistant
Opportunity for Biology student with excellent computer and statistical skills to assist with curating of entomology collection, statistical analysis of collection data and creation of collection data-base. Hours are extremely flexible and can be adapted to your schedule, ideally averaging about 10 hours per week. Some work can be performed at your home, some where the collection is located about 15 minutes from campus. Potential exists for junior author status on future scientific papers.
Initial projects will include analysis of 20 years of flight period data for evidence of local impact of global warming, and comparison of post-wildfire collecting data with 10 years of base line records to evaluate habitat recovery.
This large (60,000 specimen) collection is in need of a good computerized data-base using File Maker Pro or other data base application on Mac OSX that will be compatible with data systems at two Natural History Museums. Other curatorial and collection organization tasks are also needed. This is could be a two year or even longer opportunity for the right student. There is additional potential for studies of the student's own design utilizing the collection.
Compensation: $10 per hour.
For further information or to apply contact Paul Russell, 805 682-6960, maliboo@verizon.net
Opportunity for Biology student with excellent computer and statistical skills to assist with curating of entomology collection, statistical analysis of collection data and creation of collection data-base. Hours are extremely flexible and can be adapted to your schedule, ideally averaging about 10 hours per week. Some work can be performed at your home, some where the collection is located about 15 minutes from campus. Potential exists for junior author status on future scientific papers.
Initial projects will include analysis of 20 years of flight period data for evidence of local impact of global warming, and comparison of post-wildfire collecting data with 10 years of base line records to evaluate habitat recovery.
This large (60,000 specimen) collection is in need of a good computerized data-base using File Maker Pro or other data base application on Mac OSX that will be compatible with data systems at two Natural History Museums. Other curatorial and collection organization tasks are also needed. This is could be a two year or even longer opportunity for the right student. There is additional potential for studies of the student's own design utilizing the collection.
Compensation: $10 per hour.
For further information or to apply contact Paul Russell, 805 682-6960, maliboo@verizon.net
Selasa, 27 Oktober 2009
We love you Cynthia Kenyon! A new video! (July 10th 2009)
Thank you, thank you, thank you for all your hard work Cynthia! So many diseases are caused by aging. Keeping people younger longer makes our society healthier, more experienced, and wiser. Oh this is so exciting!
Professor Cynthia Kenyon (University of California, San Francisco, USA)
Summary: Scientists have long thought that aging just happens. Yet because of their genes, different species have different lifespans. From the roundworm C. elegans, we now know that aging is regulated, by specific genes. These genes also influence life span in mammals, including humans. This system, and its evolution, will be discussed.
Professor Cynthia Kenyon (University of California, San Francisco, USA)
Summary: Scientists have long thought that aging just happens. Yet because of their genes, different species have different lifespans. From the roundworm C. elegans, we now know that aging is regulated, by specific genes. These genes also influence life span in mammals, including humans. This system, and its evolution, will be discussed.
iGEM 2009 K.U.Leuven: Essencia coli, the fragrance factory. Promo video
Video about how Essencia coli, the fragrance factory works. Visit their project's webpage at http://2009.igem.org/Team:KULeuven for more information.
IGEM 2009- Washington U Sunglasses for Sphaeroides
This is an overview of the project done in 2009 by undergraduate students at Washington University in St. Louis participating in the iGEM competition. For more information, please visit: http://2009.igem.org/Team:Wash_U
Minggu, 25 Oktober 2009
Scientists Discover Gene That 'Cancer-proofs' Naked Mole Rat's Cells
Quoted from: http://www.sciencedaily.com/releases/2009/10/091026152812.htm#at
ScienceDaily (Oct. 27, 2009) — Despite a 30-year lifespan that gives ample time for cells to grow cancerous, a small rodent species called a naked mole rat has never been found with tumors of any kind -- and now biologists at the University of Rochester think they know why. The findings, presented in The Proceedings of the National Academy of Sciences, show that the mole rat's cells express a gene called p16 that makes the cells "claustrophobic," stopping the cells' proliferation when too many of them crowd together, cutting off runaway growth before it can start. The effect of p16 is so pronounced that when researchers mutated the cells to induce a tumor, the cells' growth barely changed, whereas regular mouse cells became fully cancerous.
"We think we've found the reason these mole rats don't get cancer, and it's a bit of a surprise," says Vera Gorbunova, associate professor of biology at the University of Rochester and lead investigator on the discovery. "It's very early to speculate about the implications, but if the effect of p16 can be simulated in humans we might have a way to halt cancer before it starts."
Naked mole rats are strange, ugly, nearly hairless mouse-like creatures that live in underground communities. Unlike any other mammal, these communities consist of queens and workers more reminiscent of bees than rodents. Naked mole rats can live up to 30 years, which is exceptionally long for a small rodent. Despite large numbers of naked mole-rats under observation, there has never been a single recorded case of a mole rat contracting cancer, says Gorbunova. Adding to their mystery is the fact that mole rats appear to age very little until the very end of their lives.
Over the last three years, Gorbunova and Andrei Seluanov, research professor of biology at the University of Rochester, have worked an unusual angle on the quest to understand cancer: Investigating rodents from across the globe to get an idea of the similarities and differences of how varied but closely related species deal with cancer.
In 2006, Gorbunova discovered that telomerase -- an enzyme that can lengthen the lives of cells, but can also increase the rate of cancer -- is highly active in small rodents, but not in large ones.
Until Gorbunova and Seluanov's research, the prevailing wisdom had assumed that an animal that lived as long as we humans do needed to suppress telomerase activity to guard against cancer. Telomerase helps cells reproduce, and cancer is essentially runaway cellular reproduction, so an animal living for 70 years has a lot of chances for its cells to mutate into cancer, says Gorbunova. A mouse's life expectancy is shortened by other factors in nature, such as predation, so it was thought the mouse could afford the slim cancer risk to benefit from telomerase's ability to speed healing.
While the findings were a surprise, they revealed another question: What about small animals like the common grey squirrel that live for 24 years or more? With telomerase fully active over such a long period, why isn't cancer rampant in these creatures?
Gorbunova sought to answer that question, and in 2008 confirmed that small-bodied rodents with long lifespans had evolved a previously unknown anti-cancer mechanism that appears to be different from any anticancer mechanisms employed by humans or other large mammals. At the time she was not able to identify just what the mechanism might be, saying: "We haven't come across this anticancer mechanism before because it doesn't exist in the two species most often used for cancer research: mice and humans. Mice are short-lived and humans are large-bodied. But this mechanism appears to exist only in small, long-lived animals."
Now, Gorbunova believes she has found the primary reason these small animals are staying cancer-free, and it appears to be a kind of overcrowding early-warning gene that the naked mole rat expresses in its cells.
When Gorbunova and her team began specifically investigating mole rat cells, they were surprised at how difficult it was to grow the cells in the lab for study. The cells simply refused to replicate once a certain number of them occupied a space. Other cells, such as human cells, also cease replication when their populations become too dense, but the mole rat cells were reaching their limit much earlier than other animals' cells.
"Since cancer is basically runaway cell replication, we realized that whatever was doing this was probably the same thing that prevented cancer from ever getting started in the mole rats," says Gorbunova.
Like many animals, including humans, the mole rats have a gene called p27 that prevents cellular overcrowding, but the mole rats use another, earlier defense in gene p16. Cancer cells tend to find ways around p27, but mole rats have a double barrier that a cell must overcome before it can grow uncontrollably.
"We believe the additional layer of protection conferred by this two-tiered contact inhibition contributes to the remarkable tumor resistance of the naked mole rat," says Gorbunova in the PNAS paper.
Gorbunova and Seluanov are now planning to delve deeper into the mole rat's genetics to see if their cancer resistance might be applicable to humans.
This research was funded by the National Institutes of Health and the Ellison Medical Foundation.
Adapted from materials provided by University of Rochester.
ScienceDaily (Oct. 27, 2009) — Despite a 30-year lifespan that gives ample time for cells to grow cancerous, a small rodent species called a naked mole rat has never been found with tumors of any kind -- and now biologists at the University of Rochester think they know why. The findings, presented in The Proceedings of the National Academy of Sciences, show that the mole rat's cells express a gene called p16 that makes the cells "claustrophobic," stopping the cells' proliferation when too many of them crowd together, cutting off runaway growth before it can start. The effect of p16 is so pronounced that when researchers mutated the cells to induce a tumor, the cells' growth barely changed, whereas regular mouse cells became fully cancerous.
"We think we've found the reason these mole rats don't get cancer, and it's a bit of a surprise," says Vera Gorbunova, associate professor of biology at the University of Rochester and lead investigator on the discovery. "It's very early to speculate about the implications, but if the effect of p16 can be simulated in humans we might have a way to halt cancer before it starts."
Naked mole rats are strange, ugly, nearly hairless mouse-like creatures that live in underground communities. Unlike any other mammal, these communities consist of queens and workers more reminiscent of bees than rodents. Naked mole rats can live up to 30 years, which is exceptionally long for a small rodent. Despite large numbers of naked mole-rats under observation, there has never been a single recorded case of a mole rat contracting cancer, says Gorbunova. Adding to their mystery is the fact that mole rats appear to age very little until the very end of their lives.
Over the last three years, Gorbunova and Andrei Seluanov, research professor of biology at the University of Rochester, have worked an unusual angle on the quest to understand cancer: Investigating rodents from across the globe to get an idea of the similarities and differences of how varied but closely related species deal with cancer.
In 2006, Gorbunova discovered that telomerase -- an enzyme that can lengthen the lives of cells, but can also increase the rate of cancer -- is highly active in small rodents, but not in large ones.
Until Gorbunova and Seluanov's research, the prevailing wisdom had assumed that an animal that lived as long as we humans do needed to suppress telomerase activity to guard against cancer. Telomerase helps cells reproduce, and cancer is essentially runaway cellular reproduction, so an animal living for 70 years has a lot of chances for its cells to mutate into cancer, says Gorbunova. A mouse's life expectancy is shortened by other factors in nature, such as predation, so it was thought the mouse could afford the slim cancer risk to benefit from telomerase's ability to speed healing.
While the findings were a surprise, they revealed another question: What about small animals like the common grey squirrel that live for 24 years or more? With telomerase fully active over such a long period, why isn't cancer rampant in these creatures?
Gorbunova sought to answer that question, and in 2008 confirmed that small-bodied rodents with long lifespans had evolved a previously unknown anti-cancer mechanism that appears to be different from any anticancer mechanisms employed by humans or other large mammals. At the time she was not able to identify just what the mechanism might be, saying: "We haven't come across this anticancer mechanism before because it doesn't exist in the two species most often used for cancer research: mice and humans. Mice are short-lived and humans are large-bodied. But this mechanism appears to exist only in small, long-lived animals."
Now, Gorbunova believes she has found the primary reason these small animals are staying cancer-free, and it appears to be a kind of overcrowding early-warning gene that the naked mole rat expresses in its cells.
When Gorbunova and her team began specifically investigating mole rat cells, they were surprised at how difficult it was to grow the cells in the lab for study. The cells simply refused to replicate once a certain number of them occupied a space. Other cells, such as human cells, also cease replication when their populations become too dense, but the mole rat cells were reaching their limit much earlier than other animals' cells.
"Since cancer is basically runaway cell replication, we realized that whatever was doing this was probably the same thing that prevented cancer from ever getting started in the mole rats," says Gorbunova.
Like many animals, including humans, the mole rats have a gene called p27 that prevents cellular overcrowding, but the mole rats use another, earlier defense in gene p16. Cancer cells tend to find ways around p27, but mole rats have a double barrier that a cell must overcome before it can grow uncontrollably.
"We believe the additional layer of protection conferred by this two-tiered contact inhibition contributes to the remarkable tumor resistance of the naked mole rat," says Gorbunova in the PNAS paper.
Gorbunova and Seluanov are now planning to delve deeper into the mole rat's genetics to see if their cancer resistance might be applicable to humans.
This research was funded by the National Institutes of Health and the Ellison Medical Foundation.
Adapted from materials provided by University of Rochester.
Sabtu, 24 Oktober 2009
Infertility Patients Favor Stem Cell Research
Most couples that have had to resort to in vitro fertilization (IVF) techniques in order to have a child are in favor of stem cell research. When asked in a national survey what they might choose to do with their frozen embryos left over after they have successfully had a child, 60% reported that they were “somewhat likely” or “very likely” to donate them for stem cell research. In contrast, less than a quarter of the respondents planned to discard their frozen embryos, or expressed a desire to donate them to another couple.
Infertility patients are especially aware of the advances in science that have made it possible for them to have children. Perhaps they are just more grateful than most, but apparently most of them have resolved any internal moral dilemma over what to do with their leftover embryos. It is interesting, however, that most of them would rather donate their embryos to research than to know that their biological child was being raised by another couple.
Infertility patients are especially aware of the advances in science that have made it possible for them to have children. Perhaps they are just more grateful than most, but apparently most of them have resolved any internal moral dilemma over what to do with their leftover embryos. It is interesting, however, that most of them would rather donate their embryos to research than to know that their biological child was being raised by another couple.
Kamis, 22 Oktober 2009
Phosphate Recovery From Sewage
In this blog (June 1, 2009) I talked about the world’s dwindling phosphate supplies, and how the key to sustainability of phosphate supplies would be recycling. But who among us has even thought about how we might recycle the gram and a half of precious phosphate we excrete in urine every day?
Well, a researcher at the University of British Columbia did, and then he set out to do something about it. Today, a phosphate recovery system based on his design is producing about a ton of slow-release phosphate fertilizer every day from a sewage treatment facility serving Portland, Oregon. The fertilizer is in such high demand that the recovery system will pay for itself in less than five years. Other recovery plants are planned, including larger ones to recover the waste from dairy and pig farms.
So if you live in Portland, Oregon, count yourself lucky; you already ARE recycling your phosphate! (Or at least somebody is.)
Reference: Tweed, Katherine. Sewage’s Cash Crop. Scientific American Nov. 2009, p. 28.
Well, a researcher at the University of British Columbia did, and then he set out to do something about it. Today, a phosphate recovery system based on his design is producing about a ton of slow-release phosphate fertilizer every day from a sewage treatment facility serving Portland, Oregon. The fertilizer is in such high demand that the recovery system will pay for itself in less than five years. Other recovery plants are planned, including larger ones to recover the waste from dairy and pig farms.
So if you live in Portland, Oregon, count yourself lucky; you already ARE recycling your phosphate! (Or at least somebody is.)
Reference: Tweed, Katherine. Sewage’s Cash Crop. Scientific American Nov. 2009, p. 28.
Senin, 19 Oktober 2009
Tasting the Bubbles
It used to be assumed that the tingling sensation of carbonated beverages was due to stimulation of mechanoreceptors by bursting bubbles of CO2. In fact, researchers now know that we also have chemoreceptors for CO2, and that they are located on the same taste cells that detect sour taste. The receptor molecule is the enzyme carbonic anhydrase, which converts CO2 (plus a water molecule) into bicarbonate and a proton. Protons activate the taste cell, which in turn activates the sensory neuron that synapses with it.
Why don’t carbonated beverages taste sour, given that the carbonic anhydrase is located on the sour-detecting taste cells? No one knows for sure, but researchers speculate that the brain interprets CO2 receptor activation plus mechanoreceptor stimulation as primarily a tingling sensation.
Why don’t carbonated beverages taste sour, given that the carbonic anhydrase is located on the sour-detecting taste cells? No one knows for sure, but researchers speculate that the brain interprets CO2 receptor activation plus mechanoreceptor stimulation as primarily a tingling sensation.
Minggu, 18 Oktober 2009
Mesa Community College Biology 181 Fall 2009 Course Videos
Dr. Dennis Wilson
COURSE - Biology 181 - August 26, 2009
COURSE - Biology 181 - August 28th, 2009
COURSE - Biology 181 - September 2nd, 2009
COURSE - Biology 181 - September 4th, 2009
COURSE - Biology 181 - September 9th, 2009
COURSE - Biology 181 - September 11th, 2009
COURSE - Biology 181 - September 16th, 2009
COURSE - Biology 181 - September 18th, 2009
COURSE - Biology 181 - September 23rd, 2009
COURSE - Biology 181 - October 7th, 2009
COURSE - Biology 181 - October 9th, 2009
COURSE - Biology 181 - October 14, 2009
More Lectures will be posted in the future: To see them go to http://www.youtube.com/user/mesacc#grid/user/DC901D5F2BFF60A9
COURSE - Biology 181 - August 26, 2009
COURSE - Biology 181 - August 28th, 2009
COURSE - Biology 181 - September 2nd, 2009
COURSE - Biology 181 - September 4th, 2009
COURSE - Biology 181 - September 9th, 2009
COURSE - Biology 181 - September 11th, 2009
COURSE - Biology 181 - September 16th, 2009
COURSE - Biology 181 - September 18th, 2009
COURSE - Biology 181 - September 23rd, 2009
COURSE - Biology 181 - October 7th, 2009
COURSE - Biology 181 - October 9th, 2009
COURSE - Biology 181 - October 14, 2009
More Lectures will be posted in the future: To see them go to http://www.youtube.com/user/mesacc#grid/user/DC901D5F2BFF60A9
Sabtu, 17 Oktober 2009
Voyage of the Beagle finger puppets
Brilliant. Check out the three finches with three different beaks.....You know you want to make them....
There's a template available here along with patterns for various other crocheted items (octopus, squid, jellyfish, prawn and mustaches (?))
Stem Cell Therapy for Parkinson's?
Researchers in Europe are about to begin a long and expensive series of experiments to determine if transplantation of fetal brain cells into the brains of patients with Parkinson’s disease will improve the patients’ condition. The study is raising some eyebrows in scientific quarters. Two similar experiments carried out in the U.S. in the 1990s, admittedly when the techniques were less well developed, failed miserably.
If they get final approval to go ahead, the researchers will harvest fetal brain cells from 6-9-week-old human fetuses and then inject the cells into the brains of patients with Parkinson’s disease. Up to six fetuses will be needed to obtain the 8 million cells to be transplanted into each Parkinson’s patient, according to a news article in Science. The first patients will receive the injections in 2012 as part of a safety study. If all goes well, a double-blind trial complete with sham surgeries will be carried out to see if the procedure actually benefits patients.
Controversial? Yes. Worthwhile? You decide.
If they get final approval to go ahead, the researchers will harvest fetal brain cells from 6-9-week-old human fetuses and then inject the cells into the brains of patients with Parkinson’s disease. Up to six fetuses will be needed to obtain the 8 million cells to be transplanted into each Parkinson’s patient, according to a news article in Science. The first patients will receive the injections in 2012 as part of a safety study. If all goes well, a double-blind trial complete with sham surgeries will be carried out to see if the procedure actually benefits patients.
Controversial? Yes. Worthwhile? You decide.
Jumat, 16 Oktober 2009
Charles Darwin - The True story
THIS EVENT HAS BEEN CANCELED.
CHARLES DARWIN - THE TRUE STORY
Dr. John van Wyhe
Christ's College, Cambridge
Director, The Complete Work of Charles Darwin Online
WEDNESDAY OCTOBER 21st
2:00 PM, Webb Hall 1100
This year is the 200th anniversary of the birth of Charles Darwin and the 150th of the publication of Origin of Species. Yet much of what is commonly known about Darwin is wrong. He did not discover evolution on the Galapagos, Darwin's finches were not the turning point, he did not keep his theory secret for 20 years, he was not trying undermine religion and he was not an atheist. This talk reveals the real Darwin and outlines what he really did and said in a clear and entertaining way.
CHARLES DARWIN - THE TRUE STORY
Dr. John van Wyhe
Christ's College, Cambridge
Director, The Complete Work of Charles Darwin Online
WEDNESDAY OCTOBER 21st
2:00 PM, Webb Hall 1100
This year is the 200th anniversary of the birth of Charles Darwin and the 150th of the publication of Origin of Species. Yet much of what is commonly known about Darwin is wrong. He did not discover evolution on the Galapagos, Darwin's finches were not the turning point, he did not keep his theory secret for 20 years, he was not trying undermine religion and he was not an atheist. This talk reveals the real Darwin and outlines what he really did and said in a clear and entertaining way.
Selasa, 13 Oktober 2009
RISE - Research Internships in Science and Engineering
This looks like a great opportunity to pursue summer research activities in Germany in the fields of biology, chemistry, physics, earth sciences & Engineering.http://www.daad.de/rise/en/index.html
Undergraduate students work with research groups at universities and top research institutions across Germany for a period of 1.5 to 3 months during the summer. RISE interns are matched with doctoral students whom they assist and who serve as their mentors. The working language will be English. All scholarship holders receive stipends from the DAAD to help cover living expenses, while partner universities and research institutes provide housing assistance. In 2010 we hope to have 300 interns.
The application period for undergraduate students from the US, Canada, and the UK, who wish to take part in an internship during summer 2010, is:
December 7, 2009 to January 31, 2010.
Sabtu, 10 Oktober 2009
The DIYbio Community - Presented at Ignite Boston 5 (2009)
The DIYbio Community - Presented at Ignite Boston 5 (2009) from mac cowell on Vimeo.
"We founded diybio.org, a community for amateur scientists, last year in May, just in time to present at ignite boston 2008. Since then, the community has grown. In this talk, I spend 5 minutes giving a lighting overview of the community and the current hot projects members are working on: new, cheap, diy-hardware, distributed science experiments (think flashmobs for science), a biohacking coworking space, and some molecular biology experiments (including making genetically engineered fluorescent yogurt, a melamine biosensor, and a biological counter)." - Mac Cowell
Safety First!!! If you are a student working in a lab here are some additional safety videos to go along with your formal training
This video series provides guidance and instruction on how to control risks associated with protocols and practices used in the modern biology laboratory. The series will make laboratory personnel aware of the intrinsic hazards associated with biomedical research and provide instruction in safe techniques that will enable workers to protect themselves from these hazards. The information will introduce new staff to good laboratory practices and provide meaningful technical review in safety for the more experienced laboratory worker.
Produced by Schumann Productions Inc. for the Howard Hughes Medical Institute Office of Laboratory Safety
© Howard Hughes Medical Institute
Produced by Schumann Productions Inc. for the Howard Hughes Medical Institute Office of Laboratory Safety
© Howard Hughes Medical Institute
Chemical Storage Hazards from benny on Vimeo.
Glassware Washing Hazards from benny on Vimeo.
Centrifugation Hazards from benny on Vimeo.
Chemical Hazards from benny on Vimeo.
A list of iPhone apps every biologist needs
Peruse a PhD student's top 10 smart phone applications that boost his efficiency and speed his research
Although the desktop computer has long been the workhorse for modern scientists, it is high time for academics to embrace the next technological wave that is mobile computing. We have all been comforted by the efficiency with which today's computers allow us to process data and information. Now, emerging mobile computing platforms will allow researchers to access and manipulate information no matter where we are. The iPhone is a good example of a mobile device that can yield a substantial productivity boost for scientists. If you are an academic and use the iPhone or iPod Touch, here are the 10 apps that will benefit you most. Feel free to add apps that you like and use for your work in the comments.
1) Molecules
Molecules is an application for viewing 3D protein structures. Need to quickly look up a protein structure? Just pull up the Molecules app and browse through the Research Collaboratory for Structural Bioinformatics database, download the structure, and you're good to go.
Price: Free
2) Solutions
Solutions is an app from the programmers atMekentosj, who make nifty software tools for the "mac-a-demic." It's a must have calculator for making quick calculations required to prepare stock solutions and buffers. The app is very well designed, keeps lists of recently entered chemicals and their molecular weights, and has the ability to search for chemicals and their molecular weights in online databases.
Price: $2.99
3) Promega
Promega is a bundle of useful stuff from the Promega website thrown together as a handy iPhone app. This is mostly a web app, which means the application itself just provides an interface to the content on the Promega site. The BioMath calculators are the best part of the app. They help you handle conversions like μg to pmol, molar ratios of insert:vector concentrations, melting temperature calculations and more.
Price: Free
4) iCut DNA
Molecular biologists can typically remember the restriction sites of a couple of enzymes, but it's tough to memorize the sites for more than 10 or so. That's where iCut DNA comes in. This app brings New England Biolab's Restriction Enzyme Database (REBASE) of around 2000 enzymes onto your mobile device, allowing you to look up the recognition sequence of any type II restriction enzyme available on REBASE. The interface is seamless, and tracking down any enzyme is a snap. The app also lets you to select molecules based on enzyme name (with a handy auto-suggest drop down menu that narrows down enzymes based on your text input) or recognition sequence (again with auto-suggest drop down entries).
Price: $4.99
5) PubSearch Plus
PubSearch Plus gives you the ability to search PubMed from the comfort of your iPhone or iPod Touch, and lets you read and email selected publications. Though the iPhone screen isn't ideal for viewing high resolution images in research papers, it definitely helps when you're looking up a specific piece of information from a particular paper. The app also supports EZProxy so you can connect to journals that are available only through institutional access.
Price: $1.99
6) Papers
Papers is iTunes for research literature. Just as iTunes lets you sync your music with your iPod - the Papers app now has a companion app for the iPhone/iPod Touch that allows you to sync your collected journal papers. You can keep copies of all or some of your research papers on your mobile device for quick reading and reference. The built in pdf reader on the Papers app does the job comfortably and can be handled with versatile touch gestures. Papers also features "beaming" where users can send a pdf to another user or sync their library with a desktop wirelessly.
Price: $9.99
7) The Chemical Touch
The Chemical Touch is an app that brings a souped-up periodic table to the iPhone and iPod Touch. An additional table of amino acids is one of the most useful parts of the app. The 20 amino acids appear with their single letter and three letter codes, isoelectric point, RNA codons, etc.
Price: $0.99
8) Labtimer
Labtimer can be as useful in the lab as in the kitchen. As the name implies, it's a timer app that provides the feel of a conventional lab timer. There are four individual timers that can be set with corresponding text labels. The alarms on the app also play over any music that you may be listening to, making it useful even when you have your headphones in at the bench.
Price: Free
9) Evernote
Evernote, which started out as a simple note taking tool, is now a solid information manager that can handle everything from voice notes to clippings pulled from the web. The beauty of Evernote is its versatility. I frequently use Evernote to collect notes from meetings and whiteboards directly to my mobile device, adding voice memos for better clarity. It has helped make me more efficient, especially with its ability to sync with all the different devices on which I'm running Evernote. I take a note on my iPhone, and it gets automatically synced to my desktop at home, my notebook, my netbook, and my work PC.
Price: Free
10)RSS Reader
RSS feeds are essential tools for anybody who deals with information overload. As researchers we are always looking for information online, be it research publications, news articles, Journal TOCs or blog posts. A mobile RSS reader helps cut down on information clutter, and several are available for the iPhone and iPod Touch. I would recommend an app that can sync with an online service where your feeds are handled so that they can be accessed via the computer as well as your mobile device. Newsstand and Byline are two wonderful RSS reader apps that you should try.
Price: Byline $4.99, Newsstand $4.99
Balachandar Radhakrishnan is a PhD student at the University of Kassel, Germany, working on RNAi in the slime mold Dictyostelium. Bala has always been fascinated by technology, especially mobile technology and how it can help researchers in their endeavors. You can find more of his tips and advice here"
Quoted from The Scientist Magazine: http://www.the-scientist.com/templates/trackable/display/news.jsp?type=news&o_url=news/display/56049&id=5604
By Balachandar Radhakrishnan
Although the desktop computer has long been the workhorse for modern scientists, it is high time for academics to embrace the next technological wave that is mobile computing. We have all been comforted by the efficiency with which today's computers allow us to process data and information. Now, emerging mobile computing platforms will allow researchers to access and manipulate information no matter where we are. The iPhone is a good example of a mobile device that can yield a substantial productivity boost for scientists. If you are an academic and use the iPhone or iPod Touch, here are the 10 apps that will benefit you most. Feel free to add apps that you like and use for your work in the comments.
Molecules is an application for viewing 3D protein structures. Need to quickly look up a protein structure? Just pull up the Molecules app and browse through the Research Collaboratory for Structural Bioinformatics database, download the structure, and you're good to go.
Price: Free
Solutions is an app from the programmers atMekentosj, who make nifty software tools for the "mac-a-demic." It's a must have calculator for making quick calculations required to prepare stock solutions and buffers. The app is very well designed, keeps lists of recently entered chemicals and their molecular weights, and has the ability to search for chemicals and their molecular weights in online databases.
Price: $2.99
Promega is a bundle of useful stuff from the Promega website thrown together as a handy iPhone app. This is mostly a web app, which means the application itself just provides an interface to the content on the Promega site. The BioMath calculators are the best part of the app. They help you handle conversions like μg to pmol, molar ratios of insert:vector concentrations, melting temperature calculations and more.
Price: Free
Molecular biologists can typically remember the restriction sites of a couple of enzymes, but it's tough to memorize the sites for more than 10 or so. That's where iCut DNA comes in. This app brings New England Biolab's Restriction Enzyme Database (REBASE) of around 2000 enzymes onto your mobile device, allowing you to look up the recognition sequence of any type II restriction enzyme available on REBASE. The interface is seamless, and tracking down any enzyme is a snap. The app also lets you to select molecules based on enzyme name (with a handy auto-suggest drop down menu that narrows down enzymes based on your text input) or recognition sequence (again with auto-suggest drop down entries).
Price: $4.99
PubSearch Plus gives you the ability to search PubMed from the comfort of your iPhone or iPod Touch, and lets you read and email selected publications. Though the iPhone screen isn't ideal for viewing high resolution images in research papers, it definitely helps when you're looking up a specific piece of information from a particular paper. The app also supports EZProxy so you can connect to journals that are available only through institutional access.
Price: $1.99
Papers is iTunes for research literature. Just as iTunes lets you sync your music with your iPod - the Papers app now has a companion app for the iPhone/iPod Touch that allows you to sync your collected journal papers. You can keep copies of all or some of your research papers on your mobile device for quick reading and reference. The built in pdf reader on the Papers app does the job comfortably and can be handled with versatile touch gestures. Papers also features "beaming" where users can send a pdf to another user or sync their library with a desktop wirelessly.
Price: $9.99
The Chemical Touch is an app that brings a souped-up periodic table to the iPhone and iPod Touch. An additional table of amino acids is one of the most useful parts of the app. The 20 amino acids appear with their single letter and three letter codes, isoelectric point, RNA codons, etc.
Price: $0.99
Labtimer can be as useful in the lab as in the kitchen. As the name implies, it's a timer app that provides the feel of a conventional lab timer. There are four individual timers that can be set with corresponding text labels. The alarms on the app also play over any music that you may be listening to, making it useful even when you have your headphones in at the bench.
Price: Free
Evernote, which started out as a simple note taking tool, is now a solid information manager that can handle everything from voice notes to clippings pulled from the web. The beauty of Evernote is its versatility. I frequently use Evernote to collect notes from meetings and whiteboards directly to my mobile device, adding voice memos for better clarity. It has helped make me more efficient, especially with its ability to sync with all the different devices on which I'm running Evernote. I take a note on my iPhone, and it gets automatically synced to my desktop at home, my notebook, my netbook, and my work PC.
Price: Free
RSS feeds are essential tools for anybody who deals with information overload. As researchers we are always looking for information online, be it research publications, news articles, Journal TOCs or blog posts. A mobile RSS reader helps cut down on information clutter, and several are available for the iPhone and iPod Touch. I would recommend an app that can sync with an online service where your feeds are handled so that they can be accessed via the computer as well as your mobile device. Newsstand and Byline are two wonderful RSS reader apps that you should try.
Price: Byline $4.99, Newsstand $4.99
Balachandar Radhakrishnan is a PhD student at the University of Kassel, Germany, working on RNAi in the slime mold Dictyostelium. Bala has always been fascinated by technology, especially mobile technology and how it can help researchers in their endeavors. You can find more of his tips and advice here"
Jumat, 09 Oktober 2009
Thomas A. Steitz, 2009 Nobel Prize in chemistry winner, discusses his work.
2009 Nobel Prize in chemistry winner Thomas A. Steitz, Sterling professor of Molecular Biophysics and Biochemistry and Professor of Chemistry at Yale.
Steitz is one of three winners for his work describing the structure and function of the ribosome, the protein making factory key to the function of all life.
Steitz, a Howard Hughes Medical Institute investigator, shares the $1.4 million award with Venkatraman Ramakrishnan of the MRC Laboratory of Molecular Biology, Cambridge, United Kingdom and Ada E. Yonath, Weizmann Institute of Science, Rehovot, Israel.
All three used a technology called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome. While the work began as a quest to answer basic questions about the makeup of ribosomes, knowledge of its structure has created targets for a new generation of antibiotics.
Writing, Reading, and Reviewing Scientific Articles
This coming week in the bio colloquium we're reading an article from the primary literature. To provide general background on the elements of a scientific paper we also handed out "guidelines for writing a scientific paper". To help you think about it from the other end (reviewer vs. writer) you may want to see what guidelines the scientific journals provide their reviewers, that is, what helps us decide whether a paper is "publishable" by a given journal. This is useful in writing (and reading) a paper to see what the "critics" are looking for.Here is the link for reviewers for the journal, Ecology:
http://esapubs.org/esapubs/reviewers.htm
Also informative is the "Reviewers Information Pack" (http://www.nxtbook.com/nxteu/elsevier/reviewersinfopack/) for everything you might want to know about the review process for journal articles. This is provided by Elsevier, which publishes Developmental Biology, and hundreds of other journals (http://www.elsevier.com/wps/find/journal_browse.cws_home)
Here's their reviewers' home page:
http://www.elsevier.com/wps/find/reviewershome.reviewers
Eric Allen's Biochemistry Lectures
Eric Allen's slides are simple and beautifully designed, and his commentary is direct and insightful. This is a great series for studying Biochemistry. Enjoy!
Overview of Biochemistry 28 Aug 2009
Water Part 1, 2 Sept 2009
Water Part 2, 4 Sept 2009
Thermodynamics Part 2, 2 Sept 2009
Carbohydrates Part 2, 11 Sept 2009
Carbohydrates Part 3, 14 Sept 2009
Proteins Primary Structure Part 1, 25 Sept 2009
Proteins Primary Structure Part 2, 28 Sept 2009
Proteins Primary Structure Part 3, 30 Sept 2009
Nucleotides and Nucleic Acids Part 1, 14 Spet 2009
Nucleotides and Nucleic Acids Part 2, 16 Sept 2009
Lipids and Biological Membranes, 16 Sept 2009
Amino Acids Part 1, 21 Sept 2009
Amino Acids Part 2, 23 Sept 2009
Protein Three Dimensional Structure Part 1, 2 Oct 2009
Proteins Three Dimensional Structure Part 2, 5 Oct 2009
Proteins Three Dimensional Structure Part 3, 7 Oct 2009
Protein Function Myoglobin and Hemoglobin Part 1, 7 Oct 2009
Introduction to Metabolism
Glycogen Metabolism Part 1
Glucose Catabolism Part 2
Glucose Catabolism Part 3
Eric continues to post regularly, see his new videos by going to is Vimeo channel here... http://www.vimeo.com/eallain/videos/sort:newest
Overview of Biochemistry 28 Aug 2009
Overview of Biochemistry 28 Aug 2009 from Eric Allain on Vimeo.
Water Part 1, 2 Sept 2009
Water Part 1, 2 Sept 2009 from Eric Allain on Vimeo.
Water Part 2, 4 Sept 2009
Water Part 2, 4 Sept 2009 from Eric Allain on Vimeo.
Thermodynamics Part 2, 2 Sept 2009
Thermodynamics Part 2, 2 Sept 2009 from Eric Allain on Vimeo.
Carbohydrates Part 2, 11 Sept 2009
Carbohydrates Part 2, 11 Sept 2009 from Eric Allain on Vimeo.
Carbohydrates Part 3, 14 Sept 2009
Carbohydrates Part 3, 14 Sept 2009
from Eric Allain on Vimeo.
Proteins Primary Structure Part 1, 25 Sept 2009
Proteins Primary Structure Part 1, 25 Sept 2009 from Eric Allain on Vimeo.
Proteins Primary Structure Part 2, 28 Sept 2009
Proteins Primary Structure Part 2, 28 Sept 2009 from Eric Allain on Vimeo.
Proteins Primary Structure Part 3, 30 Sept 2009
Proteins Primary Structure Part 3, 30 Sept 2009 from Eric Allain on Vimeo.
Nucleotides and Nucleic Acids Part 1, 14 Spet 2009
Nucleotides and Nucleic Acids Part 1, 14 Spet 2009 from Eric Allain on Vimeo.
Nucleotides and Nucleic Acids Part 2, 16 Sept 2009
Nucleotides and Nucleic Acids Part 2, 16 Sept 2009 from Eric Allain on Vimeo.
Lipids and Biological Membranes, 16 Sept 2009
Lipids and Biological Membranes, 16 Sept 2009 from Eric Allain on Vimeo.
Amino Acids Part 1, 21 Sept 2009
Amino Acids Part 1, 21 Sept 2009 from Eric Allain on Vimeo.
Amino Acids Part 2, 23 Sept 2009
Amino Acids Part 2, 23 Sept 2009 from Eric Allain on Vimeo.
Protein Three Dimensional Structure Part 1, 2 Oct 2009
Protein Three Dimensional Structure Part 1, 2 Oct 2009 from Eric Allain on Vimeo.
Proteins Three Dimensional Structure Part 2, 5 Oct 2009
Proteins Three Dimensional Structure Part 2, 5 Oct 2009 from Eric Allain on Vimeo.
Proteins Three Dimensional Structure Part 3, 7 Oct 2009
Proteins Three Dimensional Structure Part 3, 7 Oct 2009 from Eric Allain on Vimeo.
Protein Function Myoglobin and Hemoglobin Part 1, 7 Oct 2009
Protein Function Myoglobin and Hemoglobin Part 1, 7 Oct 2009 from Eric Allain on Vimeo.
Introduction to Metabolism
Introduction to Metabolism from Eric Allain on Vimeo.
Glycogen Metabolism Part 1
Glycogen Metabolism Part 1 from Eric Allain on Vimeo.
Glucose Catabolism Part 2
Glucose Catabolism Part 2 from Eric Allain on Vimeo.
Glucose Catabolism Part 3
Glucose Catabolism Part 3 from Eric Allain on Vimeo.
Eric continues to post regularly, see his new videos by going to is Vimeo channel here... http://www.vimeo.com/eallain/videos/sort:newest
Kamis, 08 Oktober 2009
Scholarships
I wish to bring the following scholarship competitions to the attention of students and faculty in your program.
Scholarships with Campus Application Deadline of January 7, 2010
Students interested in applying should begin the application process NOW.
Please contact the Campus Scholarship Director, as soon as possible to confirm your interest and to have your questions answered regarding the campus application and nomination processes.
Scholarships with Campus Application Deadline of January 7, 2010
- Barry M. Goldwater Scholarship
- Harry S. Truman Scholarship
- David Boren Scholarships for Study Abroad
- Beinecke Scholarship
- Donald A. Strauss Scholarship
- Morris K. Udall Scholarship
Students interested in applying should begin the application process NOW.
Please contact the Campus Scholarship Director, as soon as possible to confirm your interest and to have your questions answered regarding the campus application and nomination processes.
Minggu, 04 Oktober 2009
Oldest Known Human Ancestor
In the October 2, 2009 issue of Science, scientists report on the discovery and reconstruction of the oldest known nearly complete skeleton of a female pre-human ancestor. Named Ardipithecus ramidus, “Ardi” stood only four feet tall and weighed about 110 pounds. Apparently she was a “facultative” biped, meaning that she could walk upright on the ground but was still able to climb and walk in trees.
The first bones of Ardipithecus ramidus were discovered in 1992, but it has taken this long to find and reconstruct enough of a skeleton to be confident enough to publish the results. And the results are stunning. At 4.4 million years old, Ardi pushes back the dawn of bipedalism by more than a million years. (“Lucy”, the celebrated Australopithecus afarensis shown on p. 518 of Human Biology, 5th ed., is 3.2 million years old).
It’s the biggest find in decades. You can find 11 scientific articles on Ardipithecus ramidus in Science online. For a summary, read the Perspectives article by Ann Gibbons entitled “A new kind of ancestor: Ardipithecus unveiled”.
Sabtu, 03 Oktober 2009
Encouraging Organ Donations
Fewer than 40% of all adults have signed a donor card or other legal document indicating their willingness to donate their organs after death. Perhaps it’s a form of avoidance, but for whatever reason we just don’t seem to get around to it. "Presumed consent" laws are one solution, but some people find presumed consent laws objectionable on the grounds that they are a form of religious discrimination. Under presumed consent, it's people who do not wish to donate (perhaps for religious reasons) who must make their wishes known in advance, not the other way around.
One innovative and eminently fair solution is to require everyone to make their wishes known. Its called “mandated choice”. In the State of Illinois, every person over the age of 18 who renews a driver’s license must answer the question, “Do you wish to be an organ donor?” The state now has a donor signup rate of 60%. Several other states (Pennsylvania, for one) ask the question as well, but it's for informational purposes only. In Illinois, the answer is considered legally binding, meaning that relatives cannot later overturn it.
Jumat, 02 Oktober 2009
you are being shagged by a rare parrot.
http://www.youtube.com/watch?v=9T1vfsHYiKY&feature=popular
I thought you guys would find this funny. :)
I thought you guys would find this funny. :)
Kamis, 01 Oktober 2009
Regional Evolution Meeting and Lab opportunity
The Oakley lab is looking for some volunteers... it wouldn't be very high level stuff, but it would be a nice introduction to lab work - possibly ideal for freshmen who just want to wet their toes a little without fear of a commitment! It would be a couple hours a week helping with a behavioral experiment to determine mate choice in ostracods. If you are interested in this then contact me (John) and I will pass on the contact information. Also, courtesy of Todd Oakley, comes the following announcement:
This year the WEB (Western Evolutionary Biologists) meeting will be held at UC-Berkeley. The UC organization NERE funds travel expenses to the meeting. Each campus has funds for this, for which Todd Oakley has responsibility at UCSB. UCSB-NERE will fund the travel expenses on a first come-first serve basis. First people to register get priority for free travel. In the past, there has been enough funds to fund everyone interested, but this year is the first year in more distant Berkeley.
If you'd like to give a talk or poster, note the deadline for abstract submission is not too long from now (Oct 16).
The WEB web site and registration is here:
http://www.lifesci.ucsb.edu/nere-web/
This year the WEB (Western Evolutionary Biologists) meeting will be held at UC-Berkeley. The UC organization NERE funds travel expenses to the meeting. Each campus has funds for this, for which Todd Oakley has responsibility at UCSB. UCSB-NERE will fund the travel expenses on a first come-first serve basis. First people to register get priority for free travel. In the past, there has been enough funds to fund everyone interested, but this year is the first year in more distant Berkeley.
If you'd like to give a talk or poster, note the deadline for abstract submission is not too long from now (Oct 16).
The WEB web site and registration is here:
http://www.lifesci.ucsb.edu/nere-web/
Movie about life in a molecular biology lab
MCDB Movie
Thursday, October 1, 2009
3:30pm
LSB Auditorium (1001)
Movie screening: "Naturally Obsessed: the making of a scientist" (links to movie website)
Mixing humor with heartbreak, the film takes a profoundly real yet intensely dramatic story about life in a molecular biology lab.
Film review from the Washington Post
Thursday, October 1, 2009
3:30pm
LSB Auditorium (1001)
Movie screening: "Naturally Obsessed: the making of a scientist" (links to movie website)
Mixing humor with heartbreak, the film takes a profoundly real yet intensely dramatic story about life in a molecular biology lab.
Film review from the Washington Post
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