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Orderly progression of the replication fork is essential for the timely and accurate duplication of our genetic material. Although the bacterial replisome is highly processive, capable of synthesizing megabase-long stretches of nascent duplex DNA without dissociating from the template, it is subject to many obstacles that can arrest replication forks. These obstacles can be chemical damage to the template bases (such as the formation of bulky adducts, abasic sites, or intra-strand thymidine dimers as a result of UV irradiation), nicks in one of the template strands, or frank double-strand breaks in the template. It is also the case that frozen protein-DNA complexes and trains of slow-moving RNA polymerases can block replication fork progression. In bacteria, the arrested replication forks must be restarted rapidly or asymmetric chromosome segregation will occur resulting in the production of chromosome-less, anucleate daughter cells. Repair of the DNA lesion may proceed replication restart or, as we have recently shown, the replisome may simply jump the damage and continue downstream. We have elaborated the biochemical pathways required for replication reactivation at several different DNA structures that can form when replication fork progression is arrested (Figure 1).
Stalled replication forks take two general forms, either the nascent leading strand is ahead of the nascent lagging strand or vice-versa (Figure 2). To study replication restart on stalled replication forks we devised a novel linear template that allows us to vary the structure of the forked end where the replisome will be loaded (Figure 3). Using this template, we have shown that there are two distinct biochemical pathways optimized for using these different substrates (Figure 4). These replication systems utilize the chromosomal replicase, the DNA polymerase III holoenzyme (Pol III HE), itself a 10-subunit enzyme, the single-stranded DNA-binding protein (SSB), and different combinations of the primosomal proteins that both recognize the stalled replication fork structures and re-load the replisome [PriA, PriB, PriC, DnaT, DnaC, DnaB (the replication fork DNA helicase), and DnaG (the primase)]. Our biochemical data demonstrated that the PriA system (composed of PriA, PriB, DnaT, DnaB, DnaC, and DnaG) prefers stalled replication fork structures where there is no gap in the nascent leading strand, whereas the PriC system (PriC, DnaB, DnaC, and DnaG) prefers stalled fork structures where there is a gap in the nascent leading strand. Because the PriA system also restarts replication at recombinant joint molecules that are generated after the formation of double-strand breaks in the template (Figure 2), these two replication restart systems are sufficient to restart any stalled replication fork in the cell. These biochemical observations agree with those of our colleague, Steve Sandler, who studies the genetics of replication restart.
Our studies on the biochemical pathways of replication restart suggested to us that DnaG could prime leading-strand synthesis de novo (see Figure 4 where, with the PriC system, even though a nascent leading strand is present at the fork, leading-strand synthesis appears to be dependent on the presence of the primase). This was a heretical concept. It had been accepted wisdom for over 40 years that leading-strand synthesis could only be primed at origins of replication. However, as shown in Fig. 5, both leading- and lagging-strand synthesis can be primed by DnaG de novo using the PriC system (and, for that matter, also the PriA system). This observation has led us to propose that replisomes that stall at a lesion in the leading-strand template can simply re-initiate replication downstream, leaving the template damage and a gap in the nascent leading strand behind (Figure 6). The damage can be repaired subsequently and the gap repaired by daughter-strand gap repair.
To be able to study these processes we have developed a new method for generating our linear template with a thymidine dimer in a specific location (Figure 7). Using these templates carrying DNA damage we can observe directly replication fork stalling and restart (Figure 8).
Among the questions that we are interested in answering are: What is the fate of the replication proteins when a replisome stalls? What is the structure of these stalled replication forks? What is the role of replication fork regression in restart? What are the requirements for replication restart? Do restart requirements differ depending on the type of DNA template damage? How do replication restart and lesion bypass cooperate? Is there a specific mechanism that displaces the Pol III HE from the DNA? And, can the same replisome jump template damage and restart downstream?


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In brought to you by "Grand Belizean Estates", the next place to call home.
The toucan is a specialty of tropical America. In Belize, the keel-billed toucan has been designated the national bird in honor of its hilarious beauty.
When you see the capsized canoe beak (in rainbow hues) of the toucan, it is hard to imagine, that the bird could ever manage to roost high up into the air, much less pick up and cut fruit. This beak is an amazing when it comes to structural engineering. The horny outer shell is reinforced with a network of inner cellular fibers, providing strength without debilitating weight; it feels like laminated basla wood, but the serrated edges are more mindful of a stainless steel paring knife. The coloration is beyond belief: apple green, with an elongated orange triangle laid out along the lip of the upper beak and a streak of powder blue whisping across the lower beak. The beak is attached to the toucan's head by a black, patent leather strap. Science speculates that this gaudy display intimidates potential foe, but perhaps it simply bedazzles them, riveting them to the spot while the toucan decides on the best escape route.
Feather wise, this black bird wears a perfect bib of lemon yellow and, beneath its tail, a flash of cadmium red. Greenish skin rings its eyes. And, after all this and all that, its legs and feet are, unbelievably, an iridescent blue. All things considered, the keel-billed toucan is an amazing bird!
The toucan generally feeds on the fruits of larger forest trees. With its beak, it rips off a chunk from the fleshly portion; it juggles the morsel with the tip of its bill until it is positioned just so and then, with a toss of its head, it flips the food into the air and catches it somewhere en route to its throat. It drinks water in a similar fashion, dipping its bill below the surface, then lifting it high, making of it a gutter to conduct the liquid down. Toucans also eat insects, lizards and snakes, and have been known to help themselves to oropendola eggs.
This bird prefers large trees in open areas. It nests in holes such as those made by woodpeckers and which it will enlarge by removing dead wood - but only enough so that it can fit comfortably when folded up, its bill down its back and its tail hinged forward. Two to four white eggs are laid. The parents take turns with the incubating as well as with the task of filing the baby bills. The nesting stage is prolonged, lasting up to nine weeks.
These social birds may flock, in groups of six to eight, and often hold forth in a monotonous creaking croak. At the Belize Zoo, there is a Toucan named Rambo (originally Rainbow). If you catch him in the right mood, he will "purr" for you while you scratch his head.
So next time you're in Belize, stop by the Belize Zoo and say hello to Rambo for me.

subset: commoncrawl


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How 19-Year-Old Activist Zack Kopplin Is Making Life Hell for Louisiana's Creationists
High fives for Zack. He is facing down trolls, creationists, climate denialists and his own state legislature. I think we should keep an eye on this one.
For Zack Kopplin, it all started back in 2008 with the passing of the Louisiana Science Education Act. The bill made it considerably easier for teachers to introduce creationist textbooks into the classroom. Outraged, he wrote a research paper about it for a high school English class. Nearly five years later, the 19-year-old Kopplin has become one of the fiercest — and most feared — advocates for education reform in Louisiana. We recently spoke to him to learn more about how he's making a difference.
Kopplin, who is studying history at Rice University, had good reason to be upset after the passing of the LSEA — an insidious piece of legislation that allows teachers to bring in their own supplemental materials when discussing politically controversial topics like evolution or climate change. Soon after the act was passed, some of his teachers began to not just supplement existing texts, but to rid the classroom of established science books altogether. It was during the process to adopt a new life science textbook in 2010 that creationists barraged Louisiana's State Board of Education with complaints about the evidence-based science texts. Suddenly, it appeared that they were going to be successful in throwing out science textbooks.
A pivotal moment
How 19-year-old activist Zack Kopplin is making life hell for Louisiana's creationists "This was a pivotal moment for me," Kopplin told io9. "I had always been a shy kid and had never spoken out before — I found myself speaking at a meeting of an advisory committee to the State Board of Education and urging them to adopt good science textbooks — and we won." The LSEA still stood, but at least the science books could stay.
No one was more surprised of his becoming a science advocate than Kopplin himself. In fact, after writing his English paper in 2008 — when he was just 16-years-old — he assumed that someone else would publicly take on the law. But no one did.
More: How 19-Year-Old Activist Zack Kopplin Is Making Life Hell for Louisiana's Creationists


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"Since I don't eat meat, I almost didn't open a 'Thanksgiving' email from Allrecipes, but am I glad I did. This recipe is so good! Great cold-weather comfort food." – grandma
"Terrific. Made [this] with vegetable broth, baked in acorn squash. Great vegetarian meal!" – Doughgirl8
"This is a fantastic curl-up-by-the-fire-with-a-bowl-of-soup recipe! Tastes gourmet!" – CHERALEE
Top-rated recipes, party ideas, and cooking tips to inspire you year-round. Get a full year for just $7.99!


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In this video, you'll see how to make delicate white fish fried in brown butter. Watch Chef John ice fish from a top-secret location on the Finger Lakes in New York. With fish so fresh, you don't need (or want) to do too much to it. The fillets are simply dredged in seasoned flour and quickly fried in brown butter. It's so fast and easy! The fish is sweet and succulent, and the brown butter gives a toasty flavor and aroma. Fresh fish does not get any fresher than this! All it needs is a squirt of fresh lemon. Make this with any delicate white fish. Watch the video, then get the recipe for Chef John's Brown Butter Pan-Fried Perch.
Oh, man! Fresh fish is the best!


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www.98six.com - Articles on many health topics.
www.goaskalice.columbia.edu - questions and answers to many health questions.
www.medicinenet.com - good database for lots of health info.
http://familydoctor.org/ - patient handouts from the American Academy of Family Physicians
www.aafp.org/ - American Academy of Family Practice - has wonderful self help sites.
There are several good information sources on the internet. By listing them, we are saying only that they provide information. They do not substitute for counseling or therapy. Our listing does not imply endorsement of all the information which is included. Be your own judge of what is reasonable and what is not. Once you have done some exploring, you may want to bring the results and talk them over with a counselor.
First of all, you can go to your favorite search engine and type in the term you want to explore, such as anxiety, depression, or eating disorders. Be prepared to get a flood of information this way.
You may also want to explore the following sites. Each provides a listing of topics from which you can choose the one(s) which interest you. If you find a particularly useful one, you may want to print it out and save it for further reference.


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Here's a marketing challenge: What do you do when you're trying to put a fresh look on a 20-year-old e-mail system? Well, if you're
Last week, IBM's
I've fallen for this so many times in the past 20 years that I feel like Charlie Brown going once more for the football. Nevertheless, I bit, and I even stayed late on a Friday, with a nasty head cold to boot, to learn of the big news.
The release was promising, opening with talk of the "open computer revolution" and promising a new solution that would let customers avoid "the vendor lock-in associated with Microsoft's
So what, exactly, is it? Scroll down through the press release and you find out it's basically a combo of Lotus Notes (e-mail and collaboration), Lotus Sametime (instant messaging) and a couple of other pieces that can all run on Windows, Linux or the Mac.
The Linux part of the equation comes from
The idea is that even if you're a Windows shop, you can now bring in loads of Linux desktops, plop the Open Client on top of everything and have a single desktop suite for everyone–which makes it easier to manage.
Maybe you're wondering, as I was, whether the name "Open Client" means that the software IBM is shipping is open-source, meaning its underlying instructions are available for users to study, share and copy. Er, no. The Lotus stuff remains closed-source. But the Open Client runs on top of a program called Eclipse, which is open-source.
While it might be great to run the same client software on every desktop regardless of operating system, the one time this rule does not apply is when the client software is Lotus Notes.
Lotus Notes is far and away the most horrible software on the planet. Sure, people grumble about Microsoft products. But that's nothing compared to how people feel about Notes. People hate Notes. As in, they want to change jobs just so they can stop using it. I'm pretty sure there are shrinks who have built practices around it. I get desperate e-mails from people whose companies have been acquired by IBM, saying that of all the bad things about having to work for IBM, by far the worst is having to use Notes.
On top of that, once customers start using Notes, it's really hard for them to switch. So they're stuck with it unless they want to endure a really painful migration to a different e-mail system. The only virtue of Notes is that often, IBM will throw it in at no cost if you buy a bunch of its other stuff.
Ah, but see, now it's not Notes. It's the "Open Client." And it's all about Linux, and revolution, and breaking free of the tyranny of Microsoft and its one-vendor lock-in, man.
And saving money, too. IBM claims that because the Open Client is the same across all three operating systems, you won't have to hire specialists to take care of each OS. So even if you're on Windows now, you can put new users on Linux and you won't have to hire all sorts of new Linux experts.
But come on. Is there anyone left in the world who really believes Linux is cheaper than Windows? (Red Hat on the server actually costs more.) Does anyone think the way to make life easier is to go from dealing with Microsoft to dealing with Microsoft, IBM, Red Hat and Novell?
For that matter, is there anyone who seriously believes that IBM's big goal in life is to help customers save money? The best line in the entire press release is the last one, where IBM says the Open Client is currently available and "priced according to customer requirements." Not sure, but I think that means they'll start by sending in some consultants to do a needs analysis.
Remember one thing: As much as you may hate Windows, the reason Windows became popular in the first place was because it saved the world from IBM's attempt to monopolize the desktop with OS/2 and Presentation Manager.
But maybe you really believe that IBM has changed, and that it really wants to save you money and make you free and empower you with loads of choice and help you simplify your life. In which case, this no-list-price, non-open "Open Client" installed by consultants and delivered by three vendors working at cross-purposes may be just the thing for you.