Dinosaur soft tissue–just bacterial biofilm?

ResearchBlogging.org An interesting new paper is just out today in PLoS ONE. You recall the announcement a few years back that soft tissue that resembled organic tissue had been isolated from a Tyrannosaurus femur. This started off a huge controversy in the field (and beyond)–researchers disagreeing with each other whether the structures seen were indeed blood cells and vessels; creationists crowing about how this finding represented “proof” that the earth was indeed young and dinosaurs had existed just a few thousand years ago; and of course, talk of cloning and DNA analysis. On the side of “soft tissue = dino blood” were findings that reported identification of the iron-containing protein heme (potentially from the red blood cells) and morphology of cells and vessels similar to that seen in modern-day ostriches and emu. However, the new paper by Kaye et al. provides an alternative explanation: that the structures aren’t actual vessels and cells, but are instead iron-rich bacterial biofilms. More on that below.
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Helicobacter pylori: an introduction

Helicobacter pylori is, by bacteriological standards, a relative newcomer to medicine. Although its pathogenesis has been studied for only about the past 20 years, there are reports from as far back as the late 19th century of small, helical bacteria in the stomachs of some patients. Largely these anecdotal reports were relegated to the “hmm, interesting” file and not followed up for many years. It wasn’t necessarily that others didn’t follow (or care about) the research; the lack of studies on them, despite occasional reports in the literature, is probably due more to the fact that we hadn’t figured out yet how to culture them outside of the body. Prior to the era of molecular biology, this made studies of bacteria such as Helicobacter difficult, if not impossible.

However, studies began in the late 1970s by Robin Warren and Barry Marshall led initially to the culture of Helicobacter pylori (previously designated Vibrio rugula and Campylobacter pylori) from human stomachs–and a quarter-century later, a Nobel prize for their discovery and subsequent work showing the relationship between Helicobacter pylori and gastritis and gastric ulcer disease. The bacterium has also been shown to play a role in the development of several types of gastric cancers.

Additionally, Helicobacter research has extended far beyond the stomach, providing clues about the development of other diseases and even human migration. I’ll write more about these topics later this week, highlighting two new papers featuring this fascinating gastric bacterium.

Image from http://upload.wikimedia.org/wikipedia/commons/d/d6/EMpylori.jpg

For the jump haters…

Thomas asks in the comments:

“More after the jump…” WTF? Why must people insist on using this trite, meaningless phrase? Don’t they know it immediately makes people hate them for using it? I’m pretty sure people know how to scroll down to see if the article continues. And when all that “jump” is is a double-spaced line… WFT!?

I’m not a big fan of this phrase either, but I started using it after talking with readers who 1) came in from the home page and it wasn’t always clear from the portion of the post appearing there if there was additional text at the link; and 2) read via RSS feed and would only click through if it was also obvious there was more to read that way. I realize, though, that it makes it a bit awkward for readers coming in via a link from the Sb home page or elsewhere, though–so I’m certainly open to any suggestions.

Field work 101…a crash course for my summer students

As I’ve mentioned, this has been a busy year. In the span of 3 months, 3 small grants were funded; enough to keep me busy for the next year. Though my training prior to arriving here was almost exclusively in bench microbiology (mostly molecular microbiology/molecular epidemiology), I knew when I took my current job that I wanted to expand that and go beyond just examining whatever samples someone else had on hand, and set up my own studies. Being Iowa, a big focus of our work is rural health and agriculture, so this has taken me out to cattle and pig farms–previously with a technician who worked for me, and a large animal veterinarian who we work with. This summer so far it’s been just me, my grad student, and our summer interns (including some who’d never been on a farm before)–pictures included after the jump.
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Janet blogs her mammogram

So it’s not quite a colonoscopy on live TV, but Janet’s done the public health world a favor and blogged her mammogram.

However, one commenter notes:

How about a discussion of the ethics of this particular screening method since it’s fairly equivocal whether it’s actually worth the hassle and all the false positives in women aged 40?

I don’t follow cancer diagnostics enough to be able to comment with any authority on that, so I’d be interested in hearing more from people out there with expertise in that area. However, a 2007 review and meta-analysis says this:

Meta-analyses of randomized, controlled trials demonstrate a 7% to 23% reduction in breast cancer mortality rates with screening mammography in women 40 to 49 years of age. Screening mammography is associated with an increased risk for mastectomy but a decreased risk for adjuvant chemotherapy and hormone therapy. The risk for death due to breast cancer from the radiation exposure involved in mammography screening is small and is outweighed by a reduction in breast cancer mortality rates from early detection. Rates of false-positive results are high (20% to 56% after 10 mammograms), but false-positive results have little effect on psychological health or subsequent mammography adherence. Although many women report pain at the time of the mammography, few see pain as a deterrent to future screening. Evidence about the effect of negative screening mammography on psychological well-being or the subsequent clinical presentation of breast cancer is insufficient.

Personally, I’d rather have to deal with a false positive than wait for a mammogram, but ideally the patient would be presented with the pros and cons of the screening procedure so they know what they’re getting into. For me, the decrease in death rate justifies the potential false alarm, but others may be more freaked out than I am about a potentially positive result.

[Edited to add] And just as I publish this, Janet steps in with a follow-up post on the pros and cons of mammography for breast cancer screening in her age group (under 50). Go check hers out for more of the nuances…

In the field…

Back out swabbing today (noses this time, not asses). Heading out with 3 grad students who’ve never done field work before, so should be a fun day. Meanwhile, just got another manuscript submitted last night; that makes four currently under review with still a few other in draft. In the meantime, don’t feel [or feed–TS] the troll(s)–I’ll be back to clean up when I can.

How much does a flood cost a city?

How about over a billion dollars in Cedar Rapids (where flooding affected 9.2 square miles–roughly 1/7th of the city) alone?

City officials last night estimated the cost to clean up and repair or replace flood-damaged city buildings and other infrastructure at $504 million.

In addition, the officials estimated that it would cost another $810 million to protect the city against future floods through an assortment of mitigation efforts like levees, floodwalls, a possible reservoir and property buyouts.

City Manager Jim Prosser called the numbers “staggering.”

He spoke in billions: half a billion dollars for cleanup, repair and replacement; $1.3 billion in total including future flood protection.

Here in Iowa City, damage to the University was recently estimated at almost a quarter of a billion dollars, and it will likely reach close to that figure by the time the final tallies are finished. Damage to the city properties isn’t included in that total. Damage to agriculture in the midwest has been estimated at 8 billion dollars–half of that in Iowa. And in some areas, clean-up haven’t even begun; the river just officially dropped below flood stage only a few days ago. Many roads remain closed due to either flood waters or the damage said waters inflicted, and in areas where cleanup has begun, the landscape is awash with dumpsters and buildings stripped down to the studs. And some of the flooded houses likely won’t ever be repaired:

Increasingly clear, though, Bell said, is that the city is apt to see many houses sitting empty because they have sustained too much damage and are too costly to repair.

She reported that 51 percent of those who have registered here for flood relief from the Federal Emergency Management Agency are over the age of 60. Some of those people owned their houses outright, didn’t have flood insurance and live on fixed incomes.

And as I mentioned previously, infections and injuries associated with flooding have been reported, and unfortunately few people seem to be heeding (or remembering) flood safety instructions.

The specter of the Great Flood of ’08 will cast a pall over this area for a long time to come…