Laboratory Web Site and Video Awards

You may remember, from several months ago, that Attila started a contest for the best designed lab web page.
Soon, the project became too big for a lone blogger to tackle. Especially after an article about this appeared on the online pages of Nature. So, as Attila announced today, the contest goes Big Time.
The Scientist is now hosting the official contest. Of course, Attila is one of the judges. Several web-pages have already been nominated and now it is your job to think of the best-designed, prettiest, most-functional and most up-to-date laboratory homepages and nominate them for the prize.
Also, spread the word about this.

Today’s Carnivals

Encephalon #33 is up on GNIF Brain Blogger
Grand Rounds Vol. 4, No. 3 are up on Nurse Ratched’s Place
Carnival of the Green #98 is up on Planet on a Plate

New and Exciting from PLoS Biology and Medicine

Genetic Dissection of Behavioural and Autonomic Effects of Δ9-Tetrahydrocannabinol in Mice and the accompanying editorial Understanding Cannabinoid Psychoactivity with Mouse Genetic Models:

The fact that cannabis is the most widely used illicit drug has motivated a great deal of research aimed at understanding how it produces its psychoactive effects. Here I use the term psychoactive to describe the mild euphoria, altered perceptions, sense of relaxation, and sociability that often, but not always, accompany recreational cannabis use. Despite the difficulties inherent in working with lipophilic cannabinoids such as Δ9-tetrahydrocannabinol (THC), which is the primary psychoactive component of cannabis, our understanding of the mechanism of action of these compounds at the cellular level has increased dramatically over the past 20 years. However, a complete understanding of how cannabis elicits its psychoactive effects would include an appreciation of its actions at the cellular and network level as well as an identification of the neural circuits perturbed. The cannabinoid field has now matured to the point where investigators can begin to relate the cellular mechanisms of THC action to the behavioral effects of cannabis.

HCV-HIV Coinfection: Simple Messages from a Complex Disease:

Hepatitis C virus (HCV) and HIV infection are both major global health problems, each with their own specific unsolved and difficult issues of prevention, pathogenesis, and therapy. For HIV, many of the clinical problems experienced are related to loss of immunological control over relatively commonly encountered pathogens. In most of these cases (e.g., cytomegalovirus [CMV], Pneumocystis jiroveci. human herpesvirus-8), normal immunological control is quite efficient, and these organisms behave as “opportunists.” HCV is slightly different, in that immunological control in normal HIV-uninfected individuals is often poor, and HCV infection alone can lead to the gradual evolution of end-stage liver disease in normal hosts. However, although a consensus is forming about the basic details of the immune responses associated with acute control of HCV monoinfection, the long-term relationships between immune responses, viral load, and most importantly, disease progression in those who are persistently infected are still poorly understood.

Genes vs./plus Environment

My former SciBling David Dobbs regularly posts on the SciAm Blog, usually bringing in guest contributors highlighting novel research in neuroscience. Today, he invited Charles Glatt to review an interesting study on the interaction between genes and environment in development of depression. David writes:

This week reviewer Charles Glatt reviews a study that takes this investigation a level deeper, examining how two different gene variants show their power — or not — depending on whether a child is abused, nurtured, or both. As Glatt describes, this study, despite its grim subject, suggests promising things about the power of nurture to magnify nature’s gifts or lift its burdens.

In the study, two candidate genes identified as potentially predisposing people to depression were checked in two different environments – a nurturing one and an abusive one. Charles concludes:

As with any behavioral genetic study, one must be careful not to overinterpret these findings, because virtually no study in behavioral genetics is consistently or completely replicated. Nonetheless, some additional points about this paper can help inform us on the nature-nurture debate. First, depression scores and categorical diagnoses of depression were significantly higher in children with a history of maltreatment versus controls even before any genetic analysis was factored in. In a similar vein, the highest average depression score of any genotype category in the unabused control children was lower than the average depression score for any genotype category in the maltreated children; genes alone weren’t likely to make the child depressed, but maltreatment alone could.
These findings suggest that, at least regarding these specific polymorphisms, nurture beats nature. This conclusion will come as a relief to believers in human free will. It also argues strongly for the identification of children at risk for maltreatment and strong actions to reverse the negative effects of this experience.

Read the whole thing for details.

Journal Clubs – think of the future!

The recent return of Journal Clubs on PLoS ONE has been quite a success so far. People are watching from outside and they like what they see.
The first Journal Club article, on microbial metagenomics, has already, in just one week, gathered 3 ratings, each accompanied with a short comment, one trackback (this will be the second) and 7 annotations and 4 discussions eliciting further 14 responses in the comment threads. The 12-comment-and-growing thread on the usefulness of the term ‘Prokaryote’ is quite exciting, showing that it is not so hard to comment on PLoS ONE after all, once you get over the initial reluctance. You should join in the conversation there right now!
If you encounter a technical problem, please contact the Webmaster so the glitch can be fixed promptly. For a brand-new software built in-house, TOPAZ is performing remarkably well, but glitches do sometimes happen. It is essential to report those to the Webmaster so the IT/Web team can fix them quickly and make the site better and better for all users as time goes on. Just like anything else in development, it needs feedback in order to improve over time. For the time being, I guess, compose in Notepad, WordPad or something similar before copying and pasting there. And thank you for your participation.
One thing to keep in mind is that a PLoS ONE article is not a blog post – the discussion is not over once the post goes off the front page. There is no such thing as going off the front page! The article is always there and the discussion can go on and on for years, reflecting the changes in understanding of the topic over longer periods of time.
Imagine if half a century ago there was Internet and there were Open Access journals with commenting capability like PLoS ONE. Now imagine if Watson and Crick published their paper on the DNA structure in such a journal. Now imagine logging in today and reading five decades of comments, ratings and annotations accumulated on the paper!!!! What a treasure-trove of information! You hire a new graduate student in molecular biology – or in history of science! – and the first assignment is to read all the commentary to that paper. There it is: all laid out – the complete history of molecular biology all in one spot, all the big names voicing their opinions, changing opinions over time, new papers getting published trackbacking back to the Watson-Crick paper and adding new information, debates flaring up and getting resolved, gossip now lost forever to history due to it being spoken at meetings, behind closed door or in hallways preserved forever for future students, historians and sociologists of science. What a fantastic resource to have!
Now imagine that every paper in history was like that (the first Darwin and Wallace letters to the Royal Society?!). Now realize that this is what you are doing by annotating PLoS ONE papers. It is not the matter so much of here-and-now as it is a contribution to a long-term assessment of the article, providing information to the future readers that you so wished someone left for you when you were reading other people’s papers in grad school and beyond. Which paper is good and which erroneous (and thus not to be, embarrassingly, cited approvingly) will not be a secret lab lore any more transmitted from advisor to student in the privacy of the office or lab, but out there for everyone to know. Every time you check out a paper that is new to you, you also get all the information on what others think about it. Isn’t that helpful, especially for students?
So, go forth and comment on papers in areas you are interested in. And if you are a member of a lab group, a graduate seminar, an honors class, or an AP Biology class, let me know if you would be interested in doing a Journal Club on one of the PLoS ONE papers in the future – a great exercise for you, nice exposure to your group, and a service to the scientific community of today and tomorrow.

DonorsChoose Update

The news came from high above that the Seed Media Group Science Literacy Grants program will match your donations up to $15,000. So, at this point in the fundraiser, every dollar you donate is worth two!
So, check out my challenge and check out my SciBlings’ challenges as well.
And yes, don’t forget the prizes! I just got a mug and a t-shirt yesterday and they look good!
ABATC%20coffee%20mug.jpg

Science Blogging Conference – who is coming? (Science Museums)

2008NCSBClogo200.pngThere are 101 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. There are already many registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 230). Between now and the conference, I will be highlighting some of the people who will be there, for you to meet in person if you register in time.
mit_museum_logo.gifScience museums will be well represented at the Conference. So far, we know that John Durant, the Director of the MIT Museum, Troy Livingston, the Vice President for Innovation and Learning at the Museum of Life and Science in Durham, NC, and Roy Campbell, the Exhibit Director at North Carolina Museum of Natural Sciences in Raleigh, NC will be attending the proceedings.
Durham%20Museum%20Logo.jpg
NC%20museum%20logo.GIFIf you want to meet them in person, register today. Registration is free.

ClockQuotes

The curricula were unsophisticated, with a great deal of time wasted on penmanship and geography in the early grades and repetitions of the trivial history of New York City in higher grades.
– Martin Lewis Perl

Web

Some good, thought-provoking reads about the Web, social networking, publishing and blogging:
Aggregating scientific activity
Social Networks at Work Promise Bottom-Line Results
Would limiting career publication number revamp scientific publishing?
The Public Library of Science group
The Seven Principles of Community Building

My Picks from ScienceDaily

Genes From The Father Facilitate The Formation Of New Species:

The two closely related bird species, the collared flycatcher and the pied flycatcher, can reproduce with each other, but the females are more strongly attracted to a male of their own species. This has been shown by an international research team directed by Anna Qvarnström at Uppsala University and published in Science. They demonstrate that the gene for this sexual preference is found on the sex chromosome that is inherited from the father and that only females have a copy of. The discovery sheds new light on how new species are formed.

Primitive Plants Use Heat And Odor To Woo Pollinating Insects:

University of Utah scientists discovered a strange method of reproduction in primitive plants named cycads: The plants heat up and emit a toxic odor to drive pollen-covered insects out of male cycad cones, and then use a milder odor to draw the bugs into female cones so the plants are pollinated.

When Taking A Long Time Is Seen As A Good Thing:

Consumers often use the length of time a service takes as a measure of its quality. The longer a session lasts, the better the value. Indeed, a new study shows that this holds true even when judging something primarily by its duration can backfire — for example when a longer exercise program is actually less effective than a shorter regimen or for a lock-picking service.

Brain Images Make Cognitive Research More Believable:

People are more likely to believe findings from a neuroscience study when the report is paired with a colored image of a brain as opposed to other representational images of data such as bar graphs, according to a new Colorado State University study.

New Insights Into The Evolution Of The Human Genome:

Which came first, the chicken genome or the egg genome? Researchers have answered a similarly vexing (and far more relevant) genomic question: Which of the thousands of long stretches of repeated DNA in the human genome came first? And which are the duplicates?

Elephants’ Fear Of Angry Bees Could Help To Protect Them:

At a time when encroaching human development in former wildlife areas has compressed African elephants into ever smaller home ranges and increased levels of human-elephant conflict, a study in Current Biology, suggests that strategically placed beehives might offer a low-tech elephant deterrent and conservation measure.

Malaria Research Booming, But Scientific And Technical Gaps Apparent, Report Shows:

Malaria drug and vaccine research is booming. According to a new report launched in the UK by Australian researchers at The George Institute for International Health, 16 new malaria vaccine candidates are now in clinical trials; six new malaria drugs are about to reach the market; and by 2011 we will have up to 12 new anti-malarial drug product registered. However, this unprecedented level of malaria R&D activity is not necessarily all good news. The report’s authors found that the high number of malaria vaccine candidates was the result of scientific and technical gaps and lacking policy coordination rather than a reflection of cohesive global activity. Lack of coordination and planning mean that invested funding and efforts are not delivering as much as they should, and may be costing donors tens of millions of dollars.

How Do Cells Sense And Respond To Messages? Major Signal Transduction Discovery Made:

The chemical process known as acetylation plays a central role in cytokine receptor signal transduction – a fundamental biochemical cascade inside cells that controls the activity of antiviral and tumor-suppressing genes.

In Birds, Expecting To Mate Leads To Higher Fertilization Rates:

From an evolutionary perspective, the primary task of an organism is to pass along its genes to future generations. Such genetic transmission is usually assumed to be instinctive. However, a new study shows that species also learn to adapt to their surroundings in order to increase their “reproductive fitness”– the likelihood that they will successfully reproduce.

For Honey Bee Queens, Multiple Mating Makes Her Attractive To Workers:

The success of the “reign” of a honey bee queen appears to be determined to a large degree by the number of times she mates with drone bees.That is what research by scientists in the Department of Entomology and W.M. Keck Center for Behavioral Biology at North Carolina State University suggests. Dr. Freddie-Jeanne Richard, a post-doctoral research associate; Dr. David Tarpy, assistant professor and North Carolina Cooperative Extension apiculturist; and Dr. Christina Grozinger, assistant professor of insect genomics, found that the number of times a honey bee queen mates is a key factor in determining how attractive the queen is to the worker bees of a hive.

Say Hello to the newest Scibling!

This is really suspicious – magic perhaps! Every time I make a wish (and whisper it in prayer to the, hushhhhh, super-secret gods of atheists) for a favourite blog to get invited to join Scienceblogs.com, that actually happens in a matter of a few days. Poof! Just like that. Just look at today – Brian Switek just moved his lovely Laelaps blog from the old site to the new place right here.
Dinosaurs. Lots of dinosaurs! And much other good stuff – evolution, history of science, book reviews, cool animals… He’ll move his old legendary posts over to the new place gradually over time, so you should check the archives of his old site to get a glimpse, but for now, go to the new place and say Hello!

The Blogging Scholarship

You may remember last year’s contest, when my SciBling Shelley Batts was a Runner-up for the big prize.
The finalists for this year’s $10,000 scholarship have just been announced and Shelley is one of the finalists again. Hopefully, this year she’ll win.
And you can help her by voting for her.

DonorsChoose Update

The first week of the DonorsChoose fund-drive is up and the donations are coming in rapidly to a variety of school projects via my SciBlings’ challenges.
You can check out all the projects picked by my SciBlings here and my own here.
You can get to my pledge also by clicking on the thermometer on my sidebar (scroll down a little bit) and watch how the mercury in all of our thermometers rise over time. As you can see, 37% of my challenge has already been funded!
<!– –>


Thank you so much! If you continue being so fast and generous and we reach our goal too soon, I will add more projects to the pledge. Remember, the drive lasts the entire month of October.
And now, let me introduce some special “bribes” for you. I have placed my beautiful banner (with the permission of the artist) on some merchandise on Cafe Press. There are coffee mugs, a wall clock (how appropriate!) and several styles of t-shirts. Send me your receipts from DonorsChoose to be eligible for prizes. One item of your choice will be sent to the following people (who, with their permission, will be announced here on November 1st):
– the reader who donates a single, one-time, largest donation to my challenge.
– the reader who donates the largest total amount over the month of October to my challenge.
– the reader who gives the largest number of times during October to my challenge.
– the reader who donates through the challenges of the largest number of my SciBlings (including mine).
So, if you want a mug, a clock or a t-shirt (or in your e-mail, if you are a winner, you can ask for something else that can be had at Cafe Press, e.g., baseball hat, baby bib, or, gasp, underwear!), pick your preferred strategy and get started. If you have already donated over the past week, you are still eligible. Thank you in advance!

A Challenger to Elizabeth Dole?

Kirk Ross in this week’s ‘Carrboro Citizen’:

Jim Neal, a key Democratic Party fundraiser, is on the verge of announcing a run for U.S. Senate, sources close to Neal say.
Neal, a native of Greensboro who now lives in Chapel Hill, will head to Asheville this weekend for the Vance-Aycock Dinner, a traditional gathering of Democratic Party movers and shakers and a place where potential candidates often test the waters. He is expected to file official paperwork as early as this week.
Neal was a top fundraiser for the John Kerry and John Edwards ticket in 2004 and a major supporter of Gen. Wesley Clark’s bid for the Democratic nomination that year.
He is a former investment banker and is currently a financial advisor.
Dole, a one-term incumbent who has already announced for re-election, has been raising money in preparation for the race. A recent Elon Poll found that 53 percent of respondents indicated they are satisfied or very satisfied with the senator’s representation of North Carolina and 24 percent disapproved or strongly disapproved.
But both Democratic and Republican election handicappers say Dole is vulnerable because of her support of President Bush’s Iraq policies. The same poll shows that only 32 percent of North Carolinians polled approved of her job performance on Iraq and 78 percent — the highest percentage — said the war will influence their vote in 2008.

Sounds like a party insider with money and connections. Not a very familiar name, though. We’ll wait and see.

Science Blogging Conference – who is coming? (Open Access)

2008NCSBClogo200.pngThere are 102 days until the Science Blogging Conference. The wiki is looking good, the Program (now completely reshuffled) is shaping up nicely, and there is more and more blog and media coverage already. There are already 82 registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 230). Between now and the conference, I will be highlighting some of the people who will be there, for you to meet in person if you register in time.
Hemai%202.jpgHemai Parthasarathy is a dear friend of mine, and one of the Biggest Stars we managed to attract to our conference. After getting degrees in biophysics and systems neuroscience and some postdoc time in neuroscience, she decided to change her career trajectory and accepted the invitation from Nature to serve as an editor, where she remained for five years, and then joined the team that founded PLoS Biology where she worked as the Managing Editor for another 4.5 years. She has talked and written quite a lot about Open Access and the business of science publishing and you can hear her talking about it in this podcast recorded at the last SXSW conference.
At the Conference, she will lead the session on Open Science and you are invited to add questions, comments and ideas for the session by editing this wiki page. To meet Hemai in person, you’ll have to register for the conference – registration is free!

UNC researcher wins a Nobel for the Knock-Out Mouse

Dr. Oliver Smithies, the Excellence Professor of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC, USA, together with Mario R. Capecchi and Martin J. Evans, won this year’s Nobel Prize in Physiology and Medicine:

This year’s Nobel Laureates have made a series of ground-breaking discoveries concerning embryonic stem cells and DNA recombination in mammals. Their discoveries led to the creation of an immensely powerful technology referred to as gene targeting in mice. It is now being applied to virtually all areas of biomedicine – from basic research to the development of new therapies.
Gene targeting is often used to inactivate single genes. Such gene “knockout” experiments have elucidated the roles of numerous genes in embryonic development, adult physiology, aging and disease. To date, more than ten thousand mouse genes (approximately half of the genes in the mammalian genome) have been knocked out. Ongoing international efforts will make “knockout mice” for all genes available within the near future.

Update: Here is the UNC press release.
[Hat-tip to Abel]

ClockQuotes

Regret for the things we did can be tempered by time; it is regret for the things we did not do that is inconsolable.
– Sydney J. Harris

New on….

Chris Clarke explains eloquently what is, essentially, my blog commenting policy (though I transgress on other people’s blogs…sorry).
The Senate vote on the mandatory free access to NIH-funded research has been postponed, which gives you all a few more days to do your part!
John Dupuis interviews Richard Akerman. I met Richard at Scifoo, and John is coming to SBC. Both are science bloggers interested in new technologies and how they impact science libraries, so the interview is quite enlightening.
Dicyemida: Leading a double life – an invertebrate you probably never heard of, but if you love Cephalopods you should get worried….
Friday Ark #159 is up on The Modulator and Steve has picthed the Animeme to just the right audience for it. More and more posts are sprouting around the Web responding to the meme.
How to use Facebook as part of your business strategy – an excellent article by Steve Outing.
Waaay coool: Eigenfactor: Ranking and mapping scientific knowledge
Medical Student Bloggers, Best Medical Blogs and another list of Best Medical Blogs.
Evo-devo of mammalian molars – PZ Myers in his finest science blogging style (but read the preamble first).
Council of Europe accepts resolution opposing the teaching of creationism as a scientific discipline – read PvM and Archy.
Development of assymetry in the nervous system.
Spandrels: here, here and here.
RPM of evolgen is posting original, previously unpublished data on his blog. See the entire series (so far) here, here, here, here, here and here.

My Picks from ScienceDaily

Chimpanzees, Unlike Humans, Apply Economic Principles To Ultimatum Game:

New research from the Max Planck Institute of Evolutionary Anthropology in Leipzig, Germany shows that unlike humans, chimpanzees conform to traditional economic models. The research used a modification of one of the most widely used and accepted economic tools, the ultimatum game.

New Telomere Discovery Could Help Explain Why Cancer Cells Never Stop Dividing:

A group working at the Swiss Institute for Experimental Cancer Research (ISREC) in collaboration with the University of Pavia has discovered that telomeres, the repeated DNA-protein complexes at the end of chromosomes that progressively shorten every time a cell divides, also contain RNA.

Key Step Bird Flu Virus Takes To Spread Readily In Humans Identified:

Since it first appeared in Hong Kong in 1997, the H5N1 avian flu virus has been slowly evolving into a pathogen better equipped to infect humans. The final form of the virus, biomedical researchers fear, will be a highly pathogenic strain of influenza that spreads easily among humans.

Why Emotionally Charged Events Are So Memorable:

Both extensive psychological research and personal experiences confirm that events that happen during heightened states of emotion such as fear, anger and joy are far more memorable than less dramatic occurrences.

Negativity Is Contagious, Study Finds:

Though we may not care to admit it, what other people think about something can affect what we think about it. This is how critics become influential and why our parents’ opinions about our life choices continue to matter, long after we’ve moved out. But what kind of opinions have the most effect” An important new study in the Journal of Consumer Research reveals that negative opinions cause the greatest attitude shifts, not just from good to bad, but also from bad to worse.

Simplest Circadian Clocks Operate Via Orderly Phosphate Transfers:

Researchers at Harvard University and the Howard Hughes Medical Institute have found that a simple circadian clock found in some bacteria operates by the rhythmic addition and subtraction of phosphate groups at two key locations on a single protein. This phosphate pattern is influenced by two other proteins, driving phosphorylation to oscillate according to a remarkably accurate 24-hour cycle.

Related: A Circadian Clock that works in a test-tube explained and Bacteria do it differently

Science Blogging Conference – who is coming? (SciBlings)

2008NCSBClogo200.pngThere are 103 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. There are already many registered participants and if you do not register soon, it may be too late once you decide to do so (we’ll cap at about 230). Here are some of the people who will be there, for you to meet in person if you register in time.
Zuska%27s%20headshot.jpgMy Scibling and dear friend, Suzanne Franks, aka Zuska describes herself as…well, go and read how she describes herself. If you write something sexist, Super-Zuska will put her cape on, fly to wherever in the world you are, and puke on your shoes. And if you donate to schools through Zuska’s Challenge on DonorsChoose, you will be eligible to win the Grand Prize: a t-shirt emblazoned with the unforgettable words: “Zuska says: Don’t make me puke on your shoes.”

Karen%27s%20headshot.JPGKaren Ventii, besides being a SciBling, is a Ph.D. student of biochemistry at Emory University in Atlanta GA and is looking for a career in science journalism or writing. Karen and Zuska will co-moderate a session on Gender and Race in science: online and offline. You can already start asking questions (by editing that wiki page).

ClockQuotes

For historians ought to be precise, truthful, and quite unprejudiced, and neither interest nor fear, hatred nor affection, should cause them to swerve from the path of truth, whose mother is history, the rival of time, the depository of great actions, the witness of what is past, the example and instruction of the present, the monitor of the future.
– Miguel de Cervantes

Dinosaurs are coming to Raleigh!

OK, I live here, yet I had to learn from Brian that the AMNH dinosaur exhibit is coming to the North Carolina Museum of Natural Sciences in downtown Raleigh. The exhibit will be open from October 26, 2007 till March 2, 2008 and I will make sure to go and see it while it is in town (and take pictures if they’ll let me and then blog about it). If you come from out of town to see the exhibit, don’t forget to also see the dinos that are on permanent display at the Museum: the Acrocanthosaurus (the only skeleton of its kind displayed anywhere – and it is not a cast either but the real thing) and Thescelosaurus ‘Willo’, the dinosaur with a heart.

Science 2.0 at SILS

Jeffrey Pomerantz invited me to give a brownbag lunch presentation on Science 2.0 yesterday at noon at the School of Information and Library Science at University of North Carolina at Chapel Hill. It was fun for me and I hope it was fun for the others in the room, about 20 or so of faculty and students in the School.
This was my first attempt at putting together such a presentation, something I will be called on to do several times over the next couple of months and more. I was happy I made it within one hour, excellent questions included, though I probably talked too long about blogs and too little on science video (and barely mentioned Second Life). I’ll be working on it in the future. Here are the links I used during the presentation (they will probably give you a pretty good idea what I was talking about):
My old posts about science blogging and Science 2.0:
Science Blogging – what it can be?
PLoS 500
Science 2.0
Nature Precedings
Where and how to find science blogs:
some science blogs and carnivals
An example of a carnival homepage
Last year’s Conference blog/media coverage
Blog collectives;
Scienceblogs.com
Nature Blog Network
Example of a successful/popular science blog:
Pharyngula
Examples of classroom science blogs:
Developmental Biology at UMM
BIO101 at NCWC
An example of Open Notebook Science:
Useful Chemistry Blog
Useful Chemistry Wiki
A Masters Thesis on a wiki
‘Nature’ experiments in Science 2.0:
Postgenomic
Connotea
Scintilla
Pre-peer-review pre-publishing:
Nature Precedings
Science on Facebook:
a post with a good collection of examples
PLoS group
Science on Second Life:
Drexel Island
Scifoo Lives On
Second Life Molecules
Science Social Networks:
Knowble
JeffsBench
Erudix
MyExperiment
Science video sites:
SciVee
JoVE
SciTalks
LabAction
Bioscreencast
DNATube
ScienceHack
FreeScienceLectures
Open Access Publishing:
Directory of Open Access Journals
Definition of Open Access
Open Access Resources
Public Library of Science

Could TRIPS save lives in Third World Countries by opening research articles?

That is one very interesting idea! This provision is usually used for getting medicines to 3rd world countries in times of emergency. So, why not research papers if the emergency warrants it? Gavin writes:

Imagine a scenario in which a developing country is facing a national health emergency, and there’s a research article that contains information that is highly relevant to addressing that emergency. Let’s say the emergency is an alarmingly high rate of mother-to-child transmission of HIV, and a new study shows a major breakthrough in preventing such transmission. And let’s say that unfortunately the article copyright is owned by the publisher (not the author), and the article is locked away behind a typical subscription barrier (usually around $30 per person to view it).
Could the government, asked Shahram, invoke TRIPs [The Agreement on Trade Related Aspects of Intellectual Property Rights] to simply bypass the copyright holder and disseminate the article across the nation?

Tell Gavin what you think.

Science Blogging Conference – who is coming? (Organizers)

2008NCSBClogo200.pngThere are 104 days until the Science Blogging Conference. The wiki is looking good, the Program is shaping up nicely, and there is more and more blog and media coverage already. There are already 81 registered participants and if you do not register soon, it may be too late once you decide to do so(we’ll cap at about 230). Starting today, I’ll start introducing the participants here, pretty much daily. I’ll start by getting the organizers out of the way first 😉

Anton.jpgAnton Zuiker is a blogger and a journalist, and currently works as manager of internal communications at Duke Medicine. He is the founder of BlogTogether and the driving force behind the local blogging community – no meetups, bloggercons or other events would have happened without him. Not to mention such initiatives as Storyblogging and Foodblogging. Read a nice recent story about Anton in the Raleigh News & Observer.

Blogger%20BBQ%20005.jpgBrian Russell is an independent Social Software and Multimedia Consultant and the local podcast and multimedia guru. A couple of years ago, he organized a Podcastercon about which I wrote this post. With his wife Ruby and a few other local political activists, he also writes Orange Politics, the popular hub of the local political scene (if you don’t show up there, you cannot win a local election, pretty much). Also, as far as I know, Brian and Ruby were the fist couple ever to use a blog to get their friends, in the comments, to suggest details about their wedding, from location and decorations, to the menu and her dress.

Blogger%20BBQ%20010.jpgPaul Jones is a blogger, a poet, a Blooker Prize judge, the director (and founder?) of Ibiblio.org and a professor at UNC schools of Journalism, where he teaches classes on topics like Blogging, We the Media and Virtual Communities. And again, being online is ‘in the family’ – as his wife Sally Greene (Go Greene!) is a member of the City Council who blogs beautifully.

Oh, and I’ll be there, too:
bora.JPG

So, if you want to meet us in person, you need to register – it’s free!

IgNobels announced!

The folks at the Journal of Improbable Research have announced this years winners!
This is the first time I have ever blogged about a study before it won an IgNobel!
So cool!

ClockQuotes

Life is a waste of time, time is a waste of life, so get wasted all of the time and have the time of your life.
– Michelle Mastrolacasa

New and Exciting in PLoS Community Journals

As always on Friday, there are new article published in the community journals – PLoS Pathogens, PLoS Computational Biology and PLoS Genetics. Here are few of my picks:
Growth of H5N1 Influenza A Viruses in the Upper Respiratory Tracts of Mice
A Single Mutation in the PB1-F2 of H5N1 (HK/97) and 1918 Influenza A Viruses Contributes to Increased Virulence
Universally Sloppy Parameter Sensitivities in Systems Biology Models
Ancient Exaptation of a CORE-SINE Retroposon into a Highly Conserved Mammalian Neuronal Enhancer of the Proopiomelanocortin Gene

My Picks from ScienceDaily

Fossil Data Plugs Gaps In Current Knowledge, Study Shows:

Researchers have shown for the first time that fossils can be used as effectively as living species in understanding the complex branching in the evolutionary tree of life.

Cilia: Small Organelles, Big Decisions:

Johns Hopkins researchers say they have figured out how human and all animal cells tune in to a key signal, one that literally transmits the instructions that shape their final bodies. It turns out the cells assemble their own little radio antenna on their surfaces to help them relay the proper signal to the developmental proteins “listening” on the inside of the cell.

Avoiding Sweets May Spell A Longer Life, Study In Worms Suggests:

A new study in Cell Metabolism reveals that worms live to an older age when they are unable to process the simple sugar glucose. Glucose is a primary source of energy for the body and can be found in all major dietary carbohydrates as a component of starches and other forms of sugar, including sucrose (table sugar) and lactose.

My Picks from ScienceDaily

Engineers Study Brain Folding In Higher Mammals:

Engineers at Washington University in St. Louis are finding common ground between the shaping of the brain and the heart during embryonic development.

Fungus Genome Yielding Answers To Protect Grains, People And Animals:

Why a pathogen is a pathogen may be answered as scientists study the recently mapped genetic makeup of a fungus that spawns the worst cereal grains disease known and also can produce toxins potentially fatal to people and livestock.

Large-scale Head Lice Finding Kits Effective:

Working with parents and schools to provide a bug busting approach to head lice is helping to reduce infestation levels, tackle health inequalities and reduce healthcare costs, according to a review in the Journal of Clinical Nursing.

Hydrothermal Vents: Hot Spots Of Microbial Diversity:

Thousands of new kinds of marine microbes have been discovered at two deep-sea hydrothermal vents off the Oregon coast by scientists at the MBL (Marine Biological Laboratory) and University of Washington’s Joint Institute for the Study of Atmosphere and Ocean.

Census Of Protein Architectures Offers New View Of History Of Life:

The present can tell you a lot about the past, but you need to know where to look. A new study appearing this month in Genome Research reveals that protein architectures – the three-dimensional structures of specific regions within proteins – provide an extraordinary window on the history of life.

ClockQuotes

Nobody can be exactly like me. Sometimes even I have trouble doing it.
– Tallulah Bankhead

My Picks from ScienceDaily

Genes Determine Mate Choice, At Least For Fat Tailed Dwarf Lemurs:

How do we choose our mates? For quite some time now, scientists suspect that it is not for looks or fashion, neither for love or sympathy. It may be the genes that determine our preference for certain males or females. A new study provides support for this idea by looking at lemurs in Madagascar.

Beyond A ‘Speed Limit’ On Mutations, Species Risk Extinction:

Harvard University scientists have identified a virtual “speed limit” on the rate of molecular evolution in organisms, and the magic number appears to be 6 mutations per genome per generation — a level beyond which species run the strong risk of extinction as their genomes lose stability.

Genetic Differences In Clover Make One Type Toxic:

That clover necklace you make for your child could well be a ring of poison. That’s because some clovers have evolved genes that help the plant produce cyanide — to protect itself against little herbivores, such as snails, slugs and voles, that eat clover. Other clover plants that do not make cyanide are found in climates with colder temperatures. So, in picking your poison, er, clover, ecology and geography play important roles.

Spouses Often Mirror Each Other’s Health Habits:

If one spouse exercises, quits smoking, stops drinking alcohol, receives a flu shot, or undergoes a cholesterol screening, the other spouse is more likely to do the same, according to a new study in Health Services Research.

Galapagos Hawk’s Evolutionary History Illuminated:

Scientists at the University of Missouri-St. Louis used DNA sequences from feather lice to study how island populations of their host, the Galápagos Hawk might have colonized the Galápagos islands, home to the endangered and declining raptor.

Today’s Carnivals

I and the Bird #59 is up on Naturalist Notebook
Carnival of Space #23 is up on Advanced nanotechnology
Philosophia Naturalis #14 is up on Dynamics of Cats
The latest Change of Shift is up at Madness: tales of an emergency room nurse

Blogrolling for Today

All but one species


DNApes


Stephen Fry


Correlations


Sauropod Vertebra Picture of the Week


SWOP East Sex Workers Outreach Project

ClockQuotes

Time is a file that wears and makes no noise.
– English proverb

SBC-NC’08

2008NCSBClogo200.pngThere are already 80 registered participants for the Science Blogging Conference with almost four months still to go! Reserve a place for yourself by registering today!

New in Science Publishing, etc.

From Pierre, we hear about a new system for calculating individuals’ research impact – Publish Or Perish, based on Google Scholar.
Deepak, Pedro, Mark and Deepak again take a first look at Clinical Trials Hub and like what they see.
Jeff published a paper, but his Mom was more worried (in the comments) about the way he looks, with Congrats relegated to the afterthought.
SXSW Podcast on Open Knowledge vs. Controlled Knowledge has now been posted online. Worth a listen.
There is an article in Wired on science video sites, including JoVE, LabAction and SciVee and Attila provides deeper commentary.
Is “prokaryotic” an outdated term? Join the discussion (on this paper).
I love this quote: One Plos One Equals Three… in the sense that Open Access publishing is synergetically better.
Yes, I’ll be there.
A new Open Access physics journal.

Nerdy Licence Plates

Karl of Inoculated Mind blog just got a new set of plates for his truck and, of course, the plates read: INOCUL8.
Karl now wants to collect examples of nerdy, sciency licence plates and perhaps make a set on Flickr (similar to Carl Zimmer‘s Science Tatoo Gallery), so send him the picture of yours (of course you have one!) or your lab mates’ plates.
Some time ago, when I used to park at the Genetics/Entomology parking lot at NCSU, there were several regulars there with plates that read RNA, FRUITFLY, ILUVBUGS, PHEROMON, etc. I actually do not have a vanity plate, although the NC limit of 8 letters would accomodate COTURNIX.
Jonathan Eisen has a licence plate that says PLOS ORG. Now that is dedication to Open Access! Perhaps next time I need new plates I can get a PLOS one as well (his is California, mine would be North Carolina).
So, what do you have?

My Picks from ScienceDaily

Huge New Dinosaur Had A Serious Bite:

The newest dinosaur species to emerge from Grand Staircase-Escalante National Monument had some serious bite, according to researchers from the Utah Museum of Natural History at the University of Utah.

New Species Of Frog Discovered: Smallest Indian Land Vertebrate:

The India’s smallest land vertebrate, a 10-millimeter frog, has been discovered from the Western Ghats of Kerala by Delhi University Systematics Biologist, S D Biju and his colleagues.

No Faking It, Crocodile Tears Are Real:

When someone feigns sadness they “cry crocodile tears,” a phrase that comes from an old myth that the animals cry while eating. Now, a University of Florida researcher has concluded that crocodiles really do bawl while banqueting – but for physiological reasons rather than rascally reptilian remorse.

Sea Otter, Peregrine Falcon Back From The Brink Of Extinction But Other Species At Risk In Canada:

There’s good news and bad news in the report the Committee on the Status of Endangered Wildlife in Canada (COSEWIC) just dropped on the Minister of the Environment’s desk.

New Suspect Identified In West Nile Deaths Of Pelicans:

Stable flies are the latest suspect that may be involved in the West Nile virus deaths of hundreds of pelican chicks at the Medicine Lake National Wildlife Refuge in northeast Montana. West Nile virus killed 800 to 1,000 pelican chicks in 2003, averaged 400 in each of the next three summers and more than 600 this year.

Individual Differences Caused By Shuffled Chunks Of DNA In The Human Genome:

A study by Yale researchers offers a new view of what causes the greatest genetic variability among individuals — suggesting that it is due less to single point mutations than to the presence of structural changes that cause extended segments of the human genome to be missing, rearranged, or present in extra copies.

Today’s Carnivals

Circus of the Spineless #25 is up on The annotated budak
The latest issue of the Carnival of Education is up on Evolution… not just a theory anymore

World Health Organization breaks embargo and messes up.

Before two papers passed the peer-review and got published, WHO (which was given the data) made its own interpretation of the findings and included it in its press kit, including the errors they made in that interpretation. A complex story – what’s your take on it?

How to blog a conference

I regularly check Anton Zuiker’s Sugarcubes, displayed in his sidebar. There, I recently discovered that Ethan Zuckerman and Bruno Giussani put together a booklet that explains how to liveblog a conference – Tips for conference bloggers (choose between a large PDF and a small PDF). Pretty good information overall.
When I went to the first BloggerCon in Chapel Hill, I was still a newbie: I sat next to and chatted with Dave Winer without knowing who he was. I do not remember now, but I believe I wrote a brief post about the BloggerCon afterwards.
The following year, at Podcastercon, I sat back and enjoyed myself, and only felt compelled to, afterwards at home, write a post that was mostly about Dave Warlick’s amazing session on podcasting in the classroom. That was the first time many of us have seen The Wizard in action (he usually travels around the country doing this), but that experience was instrumental in our seeking out early and getting Dave to lead a session on the use of the Web and the concept of the Flat Classroom in science education for the Science Blogging Conference.
At last year’s ConvergeSouth, which was only one day long, I wrote only a one-post summary, but the year before, I wrote a whole lot of posts, session-by-session (the last post in the series has links to all the others on the bottom). But that was not liveblogging – I wrote all those posts over about ten days after I got home from the conference. From memory! I did not even take any notes!
Blogging from Scifoo was closer to real-time than is my usual practice (well, that was the first time I actually had a laptop, and I had it with me!), but even that was not real liveblogging. In the sessions, I want to pay attention and to interact with others. If I am crafting a sentence to write about what I just heard, I will miss the next ten sentences and loose the thread. I’d rather digest the entire session in my mind and write about it afterwards.
As an organizer, I do not have time to liveblog the Science Blogging Conference as I have to be at so many different places at the same time, making sure everything is going smoothly. But last year, a number of people did a great job liveblogging and post-blogging the conference. So I hope that there will be good blogging from the next one as well. Perhaps the Zuckerman-Giussani handbook will be helpful for the livebloggers here in January.

My Picks from ScienceDaily

How ‘Mother Of Thousands’ Makes Baby Plants:

New research shows how the houseplant “mother of thousands” (Kalanchoe diagremontiana) makes the tiny plantlets that drop from the edges of its leaves. Having lost the ability to make viable seeds, the plant has shifted some of the processes that make seeds to the leaves, said Neelima Sinha, professor of plant biology at UC Davis.

Red Wine Ingredient — Resveratrol — Fights Diabetes In Mice:

Even relatively low doses of resveratrol–a chemical found in the skins of red grapes and in red wine–can improve the sensitivity of mice to the hormone insulin, according to a new report. As insulin resistance is often characterized as the most critical factor contributing to the development of type 2 diabetes, the findings “provide a potential new therapeutic approach for preventing or treating” both conditions, the researchers said.

In Dogs, A Shortcut To Mapping Disease Genes:

Nearly two years ago, Broad Institute researchers and their colleagues announced they had successfully decoded the genome of the domestic dog, a species coaxed into hundreds of distinct types through selective breeding by humans over the past two centuries.

Dogs That Bite Children Have Often Not Bitten Kids Before:

Dogs that bite children have often not bitten kids before, but they tend to have underlying behavioural or medical problems, indicates research in the journal Injury Prevention.

Biologists Close In On Mystery Of Sea Turtles’ ‘Lost Years’:

Biologists have found a major clue in a 50-year-old mystery about what happens to green sea turtles after they crawl out of their sandy nests and vanish into the surf, only to reappear several years later relatively close to shore.

Of Mice And Men: New Male Contraceptives Successful In Rodents And Humans:

Pills, sponges, IUDs, diaphragms — women have many options for planning their fertility, none of them quite perfect. But what if men want to help out? They have only two options — vasectomy, which is usually permanent, and condoms, which are crucial for dating but get old in long-term relationships. Will men ever have a way to reliably make sure that nobody is every calling them “Daddy” before they are ready?

ClockQuotes

I find that we all get more legendary as time goes by. Legend means, basically, bullshit.
– Joel Rosenberg

There is no Soul. Deal with it.

Galilei kicked us out of the Center of the Universe.
Darwin kicked us off the Pinnacle of Creation
Freud kicked the Soul out of our Brains.
Few remain adherents of Geocentrism.
The opponents of evolution are legion and very vocal (in this country, and a couple of Middle Eastern ones), but they have been defeated so soundly so many times, they had to concede more and more ground, and though they are getting sneakier with time, their efforts are becoming more and more laughable and pitiful.
So, the last Big Fight will be about the Soul. The next area of science to experience a big frontal attack will be Neuroscience.
There is no Soul. Your mind is the subjective experience of what the molecules in your brain cells are doing. Period. But for many, that is the last straw. And the attack will, unlike Creationism, be coming from all sides of the political spectrum, as there are as many adherents of Spirituality crap on the Left as there are believers in the Soul on the Right. They just cannot bear the idea that there isn’t “something more to it” than “just materialism”!
Witness the new book “Spritiual Brain” which is so bad that it cannot even be fisked argument by argument as no arguments are actually presented (at least Creationists have their usual list of idiotic statements that can be effectively demonstrated to be wrong). Shelley Batts and PZ Myers tried hard, but there is just no ‘there’ there.
And even serious neurofolks, like Alvaro and colleagues who are organizing a meeting in Aspen on some of the coolest aspects of neuroplasticity – a hot area of neuroscience that studies how events in the internal and external environment modify the functioning of the brain, which affects the subjective experience, something that is potentially useful in treating people with mental or emotional problems, get slammed for being too materialistic.
If it is non-materialistic, then, by definition, it does not exist. Not just that it is not amenable to scientific study. It.Does.Not.Exist.

He survived, so he is not eligible for a Darwin Award

But he definitely deserves an Honorable Mention (hat-tip: Tanja):

New and Exciting in PLoS ONE

There are 37 new articles on PLoS ONE today, breaking the 1000 barrier! Yes, there are now more than a thousand papers on ONE. And this week is again an embarassment of riches – so many bloggable papers! And here are some of my quick picks for this week – read them, rate them, annotate them, blog about them:
Composition and Hierarchical Organisation of a Spider Silk:

Albeit silks are fairly well understood on a molecular level, their hierarchical organisation and the full complexity of constituents in the spun fibre remain poorly defined. Here we link morphological defined structural elements in dragline silk of Nephila clavipes to their biochemical composition and physicochemical properties. Five layers of different make-ups could be distinguished. Of these only the two core layers contained the known silk proteins, but all can vitally contribute to the mechanical performance or properties of the silk fibre. Understanding the composite nature of silk and its supra-molecular organisation will open avenues in the production of high performance fibres based on artificially spun silk material.

Sexual Risk Factors for HIV Infection in Early and Advanced HIV Epidemics in Sub-Saharan Africa: Systematic Overview of 68 Epidemiological Studies:

It is commonly assumed that sexual risk factors for heterosexual HIV transmission in sub-Saharan Africa, such as multi-partner sex, paid sex and co-infections, become less important as HIV epidemics mature and prevalence increases.
We conducted a systematic review of 68 African epidemiological studies from 1986 to 2006 involving 17,000 HIV positive adults and 73,000 controls. We used random-effects methods and stratified results by gender, time, background HIV prevalence rates and other variables. The number of sex partners, history of paid sex, and infection with herpes simplex virus (HSV-2) or other sexually-transmitted infections (STIs) each showed significant associations with HIV infection. Among the general population, the odds ratio (OR) of HIV infection for women reporting 3+ sex partners versus 0-2 was 3.64 (95%CI [2.87-4.62]), with similar risks for men. About 9% of infected women reported ever having been paid for sex, versus 4% of control women (OR = 2.29, [1.45-3.62]). About 31% of infected men reported ever paying for sex versus 18% of uninfected men (OR = 1.75, [1.30-2.36]). HSV-2 infection carried the largest risk of HIV infection: OR = 4.62, [2.85-7.47] in women, and OR = 6.97, [4.68-10.38] in men. These risks changed little over time and stratification by lower and higher HIV background prevalence showed that risk ratios for most variables were larger in high prevalence settings. Among uninfected controls, the male-female differences in the number of sex partners and in paid sex were more extreme in the higher HIV prevalence settings than in the lower prevalence settings.
Multi-partner sex, paid sex, STIs and HSV-2 infection are as important to HIV transmission in advanced as in early HIV epidemics. Even in high prevalence settings, prevention among people with high rates of partner change, such as female sex workers and their male clients, is likely to reduce transmission overall.

Inflated Impact Factors? The True Impact of Evolutionary Papers in Non-Evolutionary Journals:

Amongst the numerous problems associated with the use of impact factors as a measure of quality are the systematic differences in impact factors that exist among scientific fields. While in theory this can be circumvented by limiting comparisons to journals within the same field, for a diverse and multidisciplinary field like evolutionary biology, in which the majority of papers are published in journals that publish both evolutionary and non-evolutionary papers, this is impossible. However, a journal’s overall impact factor may well be a poor predictor for the impact of its evolutionary papers. The extremely high impact factors of some multidisciplinary journals, for example, are by many believed to be driven mostly by publications from other fields. Despite plenty of speculation, however, we know as yet very little about the true impact of evolutionary papers in journals not specifically classified as evolutionary. Here I present, for a wide range of journals, an analysis of the number of evolutionary papers they publish and their average impact. I show that there are large differences in impact among evolutionary and non-evolutionary papers within journals; while the impact of evolutionary papers published in multidisciplinary journals is substantially overestimated by their overall impact factor, the impact of evolutionary papers in many of the more specialized, non-evolutionary journals is significantly underestimated. This suggests that, for evolutionary biologists, publishing in high-impact multidisciplinary journals should not receive as much weight as it does now, while evolutionary papers in more narrowly defined journals are currently undervalued. Importantly, however, their ranking remains largely unaffected. While journal impact factors may thus indeed provide a meaningful qualitative measure of impact, a fair quantitative comparison requires a more sophisticated journal classification system, together with multiple field-specific impact statistics per journal.

Ant Species Differences Determined by Epistasis between Brood and Worker Genomes:

Epistasis arising from physiological interactions between gene products often contributes to species differences, particularly those involved in reproductive isolation. In social organisms, phenotypes are influenced by the genotypes of multiple interacting individuals. In theory, social interactions can give rise to an additional type of epistasis between the genomes of social partners that can contribute to species differences. Using a full-factorial cross-fostering design with three species of closely related Temnothorax ants, I found that adult worker size was determined by an interaction between the genotypes of developing brood and care-giving workers, i.e. intergenomic epistasis. Such intergenomic social epistasis provides a strong signature of coevolution between social partners. These results demonstrate that just as physiologically interacting genes coevolve, diverge, and contribute to species differences, so do socially interacting genes. Coevolution and conflict between social partners, especially relatives such as parents and offspring, has long been recognized as having widespread evolutionary effects. This coevolutionary process may often result in coevolved socially-interacting gene complexes that contribute to species differences.

Phylogeny, Diet, and Cranial Integration in Australodelphian Marsupials:

Studies of morphological integration provide valuable information on the correlated evolution of traits and its relationship to long-term patterns of morphological evolution. Thus far, studies of morphological integration in mammals have focused on placentals and have demonstrated that similarity in integration is broadly correlated with phylogenetic distance and dietary similarity. Detailed studies have also demonstrated a significant correlation between developmental relationships among structures and adult morphological integration. However, these studies have not yet been applied to marsupial taxa, which differ greatly from placentals in reproductive strategy and cranial development and could provide the diversity necessary to assess the relationships among phylogeny, ecology, development, and cranial integration. This study presents analyses of morphological integration in 20 species of australodelphian marsupials, and shows that phylogeny is significantly correlated with similarity of morphological integration in most clades. Size-related correlations have a significant affect on results, particularly in Peramelia, which shows a striking decrease in similarity of integration among species when size is removed. Diet is not significantly correlated with similarity of integration in any marsupial clade. These results show that marsupials differ markedly from placental mammals in the relationships of cranial integration, phylogeny, and diet, which may be related to the accelerated development of the masticatory apparatus in marsupials.

Effects of Insemination Quantity on Honey Bee Queen Physiology:

Mating has profound effects on the physiology and behavior of female insects, and in honey bee (Apis mellifera) queens, these changes are permanent. Queens mate with multiple males during a brief period in their early adult lives, and shortly thereafter they initiate egg-laying. Furthermore, the pheromone profiles of mated queens differ from those of virgins, and these pheromones regulate many different aspects of worker behavior and colony organization. While it is clear that mating causes dramatic changes in queens, it is unclear if mating number has more subtle effects on queen physiology or queen-worker interactions; indeed, the effect of multiple matings on female insect physiology has not been broadly addressed. Because it is not possible to control the natural mating behavior of queens, we used instrumental insemination and compared queens inseminated with semen from either a single drone (single-drone inseminated, or SDI) or 10 drones (multi-drone inseminated, or MDI). We used observation hives to monitor attraction of workers to SDI or MDI queens in colonies, and cage studies to monitor the attraction of workers to virgin, SDI, and MDI queen mandibular gland extracts (the main source of queen pheromone). The chemical profiles of the mandibular glands of virgin, SDI, and MDI queens were characterized using GC-MS. Finally, we measured brain expression levels in SDI and MDI queens of a gene associated with phototaxis in worker honey bees (Amfor). Here, we demonstrate for the first time that insemination quantity significantly affects mandibular gland chemical profiles, queen-worker interactions, and brain gene expression. Further research will be necessary to elucidate the mechanistic bases for these effects: insemination volume, sperm and seminal protein quantity, and genetic diversity of the sperm may all be important factors contributing to this profound change in honey bee queen physiology, queen behavior, and social interactions in the colony.

The Genetic Signature of Sex-Biased Migration in Patrilocal Chimpanzees and Humans:

A large body of theoretical work suggests that analyses of variation at the maternally inherited mitochondrial (mt)DNA and the paternally inherited non-recombining portion of the Y chromosome (NRY) are a potentially powerful way to reveal the differing migratory histories of men and women across human societies. However, the few empirical studies comparing mtDNA and NRY variation and known patterns of sex-biased migration have produced conflicting results. Here we review some methodological reasons for these inconsistencies, and take them into account to provide an unbiased characterization of mtDNA and NRY variation in chimpanzees, one of the few mammalian taxa where males routinely remain in and females typically disperse from their natal groups. We show that patterns of mtDNA and NRY variation are more strongly contrasting in patrilocal chimpanzees compared with patrilocal human societies. The chimpanzee data we present here thus provide a valuable comparative benchmark of the patterns of mtDNA and NRY variation to be expected in a society with extremely female-biased dispersal.

Non-Invasive In Vivo Imaging of Calcium Signaling in Mice:

Rapid and transient elevations of Ca2+ within cellular microdomains play a critical role in the regulation of many signal transduction pathways. Described here is a genetic approach for non-invasive detection of localized Ca2+ concentration ([Ca2+]) rises in live animals using bioluminescence imaging (BLI). Transgenic mice conditionally expressing the Ca2+-sensitive bioluminescent reporter GFP-aequorin targeted to the mitochondrial matrix were studied in several experimental paradigms. Rapid [Ca2+] rises inside the mitochondrial matrix could be readily detected during single-twitch muscle contractions. Whole body patterns of [Ca2+] were monitored in freely moving mice and during epileptic seizures. Furthermore, variations in mitochondrial [Ca2+] correlated to behavioral components of the sleep/wake cycle were observed during prolonged whole body recordings of newborn mice. This non-invasive imaging technique opens new avenues for the analysis of Ca2+ signaling whenever whole body information in freely moving animals is desired, in particular during behavioral and developmental studies.

Design and Pre-Clinical Evaluation of a Universal HIV-1 Vaccine:

One of the big roadblocks in development of HIV-1/AIDS vaccines is the enormous diversity of HIV-1, which could limit the value of any HIV-1 vaccine candidate currently under test.
To address the HIV-1 variation, we designed a novel T cell immunogen, designated HIVCONSV, by assembling the 14 most conserved regions of the HIV-1 proteome into one chimaeric protein. Each segment is a consensus sequence from one of the four major HIV-1 clades A, B, C and D, which alternate to ensure equal clade coverage. The gene coding for the HIVCONSV protein was inserted into the three most studied vaccine vectors, plasmid DNA, human adenovirus serotype 5 and modified vaccine virus Ankara (MVA), and induced HIV-1-specific T cell responses in mice. We also demonstrated that these conserved regions prime CD8+ and CD4+ T cell to highly conserved epitopes in humans and that these epitopes, although usually subdominant, generate memory T cells in patients during natural HIV-1 infection.
Therefore, this vaccine approach provides an attractive and testable alternative for overcoming the HIV-1 variability, while focusing T cell responses on regions of the virus that are less likely to mutate and escape. Furthermore, this approach has merit in the simplicity of design and delivery, requiring only a single immunogen to provide extensive coverage of global HIV-1 population diversity.

Participate in Journal Clubs on PLoS ONE!

Journal Clubs are a popular feature on PLoS ONE papers. There were several of them in the spring. Now, after a brief summer break, the Journal Clubs are going live again and they will happen on a regular basis, perhaps as frequently as one per week.
What does it mean – a Journal Club? In short, a lab group volunteers to discuss one of the more recent (or even upcoming, not yet published) PLoS ONE papers and to post their discussion as a series of comments, annotations and ratings on the paper itself, triggering a discussion within a broader scientific community.
The first group that will start our Fall series is the Bacterial Metagenomics group led by Dr.Jonathan Eisen at UC-Davis. They chose to discuss last week’s ONE article Metagenomics of the Deep Mediterranean, a Warm Bathypelagic Habitat. It is a good and interesting paper and they have posted their discussion on it already.
If the name Jonathan Eisen rings a bell, it is probably because you are reading his blog. Perhaps you will recognize that one of his students participating in the Journal Club is also familiar to you through her blog as well.
So, what would l really like you to do is to go and read the paper and what the Eisen group wrote about it, then join in the conversation – add your own commentary, including annotations and ratings to the article. If you decide to blog about it at your own site, try to trigger a trackback.
And if you and your group would like to do a Journal Club in the future, let us know – e-mail me at: Bora@plos.org
[cross-posted]

Today’s Carnivals

Scientiae #12 is up on Wayfarer Scientista
Festival of the Trees #16 is up on Trees if you please
Bio::Blogs #15 is up on Public Rambling
Carnival of the Green # 97 is up on World is Green
Oh, The Grand Rounds you will have! A very creative Dr.Seuss-styled Grand Rounds 4.02 are up on Distractible
The 92nd Edition of the Carnival of Homeschooling is up on Tami’s Blog

Bribes for DonorsChoose?!

So, I see that several of my sciblings are offering special incentives to their readers who donate through DonorsChoose. So, what could I offer? Should I place my beautiful banner on some Cafe Press merchandise? Give me some ideas.