The annotated budak

Evo-Devo in the Precambrian

Fossilized embryos predating the Cambrian Explosion by 10 million years provide evidence that early animals had already begun to adopt some of the structures and processes seen in today's embryos, say researchers from Indiana University Bloomington and nine other institutions in this week's Science. James Hagadorn of Amherst College led the multi-disciplinary international collaborative project.

The researchers from the US, UK, China, Sweden, Switzerland and Australia report the first direct evidence that primitive animals 550 million years ago were capable of asynchronous cell division during embryonic development. Asynchronous cell division allows the formation of unique shapes.

"We're learning something about how the very earliest multicellular animals formed embryos and how the embryos developed," said IU Bloomington biologist Rudolf Raff, a coauthor of the report. "This gives us an enormous and entirely surprising look at half-a-billion-year-old embryos in the act of cleaving. What a window on the past. We've had no prior idea what they might have done."

The researchers also believe they have identified specialized structures inside the cells, such as bubble-like vesicles that the cells might have used to transport, store or metabolize molecules. Slight aberrations during the fossilization of dead embryonic cells even reveal what appear to be dividing nuclei. It was assumed such structures existed in early animals, but until now, no known fossils of the structures existed.

The scientists procured 162 "relatively pristine" animal embryo fossils from the Doushantuo Formation of south central China. The embryos were still encased in a fertilization envelope, a protective husk that likely aided the preservation of the embryos long enough for fossilization to occur. To inspect the fossils' surfaces and even innards, the scientists used a bevy of imaging techniques, including X-ray computed tomography, scanning electron microscopy, transmission electron microscopy and thin-section petrography.

Even in larger embryo fossils estimated to contain 1,000 cells or more, the scientists did not observe a blastocoel, a fluid-filled gap in the middle of the embryo and a common feature among modern animal embryos. Raff said there are two likely explanations for the observation: "Either these embryos are primitive and don't have a clear blastocoel, or a blastocoel existed but didn't survive the preservation process."

In another study of embryos published by Raff, IUB Department of Biology Chair Elizabeth Raff and colleagues earlier this year, the scientists reported blastocoels were not always preserved under the kinds of preservation conditions that may have been involved in the formation of fossil embryos.

The Raffs and research associate F. Rudolf Turner provided electron micrographs of internal structures such as embryonic lipid vesicles in modern embryos that served as the key comparisons with structures observed in the fossil embryos, and were a source of expertise on the asynchronous cleavage of embryonic cells. Living embryos contain cell structures that form the basis for interpreting structures seen in fossils.

Biologists can provide critical information from living embryos to the studies of the fossils. Until only recently, many paleontologists doubted claims that fossilized embryos hundreds of millions of years old could exist. The Raffs and Philip Donoghue were lead co-authors of a paper in the April 11, 2006, Proceedings of the National Academy of Sciences demonstrating the feasibility of the fossilization of embryos. The present analysis of fossilized embryos in Science leaves even less room for doubt that such finds are real.

Fossilized embryos are very rare. Intact fossil embryos are even rarer. The Doushantuo Formation has proved a boon to paleontologists and evolutionary developmental biologists interested in the evolution of animal species during and prior to the Cambrian Explosion, a dramatic time period in which animals became bigger, more diverse, ecologically dominant and, in the late Stephen J. Gould's opinion, a lot more wonderful.

Other co-authors of the report are F. Rudolf Turner (IU Bloomington), Matthew McFeely (Amherst College), Kenneth Nealson (University of Southern California), Marco Stampanoni (Paul Scherrer Institut, Switzerland), Shuhai Xiao (Virginia Tech), Philip Donoghue, Neil Gostling and Maria Pawlowska (University of Bristol, England), and Stefan Bengtson (Swedish Museum of Natural History.

Does this mean I don't have to work out (notwithstanding my beer belly duck)?

The theory that animals die when they’ve expended their lifetime allotment of energy may be reaching the end of its own life, according to a study presented at The American Physiological Society conference, Comparative Physiology 2006. However, the longitudinal study leaves open a newer form of the theory -- that antioxidants help prolong life by limiting the damage that oxidative stress can cause to cells.

“These findings join a growing body of evidence suggesting that lifetime energy expenditure per se does not underlie senescence,” wrote Lobke Vaanholt, Serge Daan, Theodore Garland Jr. and G. Henk Visser in a summary of the study presented at Comparative Physiology 2006: Integrating Diversity. Vaanholt, Daan and Visser are from the University of Groningen, The Netherlands. Garland is from the University of California at Riverside. The conference takes place Oct. 8-11 in Virginia Beach, Virginia.

A bit of background: One early theory, the rate of living theory, held that every organism has a set amount of energy to expend. Once the animal expended that number of calories, the grim reaper was on the doorstep. Over the years, the theory has become much more sophisticated, but metabolic rate and aging have remained linked, Vaanholt explained.

Decades ago, physiologists discovered that during metabolism, oxygen (O2) can split into single oxygen atoms, known as free radicals. These rogue oxygen atoms can remain on their own or combine with hydrogen atoms to form reactive oxygen species (ROS), which wreak havoc with enzymes and proteins and adversely affect cell function. The faster the metabolism, the more ROS produced, the modern theory goes.

Energy expenditure not the key
In this study the researchers divided the mice into three groups of 100 mice each. Two groups were “runner” mice, that is, mice that loved to run on the running wheels placed in their cages. One group of runner mice had access to running wheels, but the second group of runner mice did not. The third group consisted of regular laboratory mice that had a running wheel.

Vaanholt’s team followed 60 mice from each of the three groups throughout their natural lives, nearly three years. They measured wheel running activity and took periodic measurements of body mass.

They found:
•Runner mice that had access to a wheel expended 25% more energy over the course of their lives compared to both the runner group that did not have a wheel and the regular mice
•Both groups of mice bred for running, one group with the wheel and one without, lived about 90 days less than the regular mice
•The regular (non-runner) mice lived longest, 826 days, compared to the runners with a wheel, 735 days and runners without a wheel, 725 days

The rate of living theory would have predicted that the running group that expended more energy would die earlier than the two groups that did not, Vaanholt said. This was not the case. There was no difference in life span between the two runner groups, even though one expended more energy.

In addition, the rate of living theory would have predicted that the runner mice without the wheel and the normal mice would live approximately the same life span because there was no difference in energy expenditure between the two. This was not the case. The runner mice without the wheel died sooner.

“The shorter life span cannot, therefore, be explained by a difference in metabolism,” Vaanholt concluded. “There must be something else going on that causes these animals to age and die.”

More activity = higher metabolism = more antioxidants?

A second portion of the experiment involved the remaining 40 mice in each of the three groups. The researchers periodically used mice from these three groups to determine energy expenditure, body composition and the antioxidant enzyme levels and protein synthesis in the heart and liver tissues. The researchers selected mice, at two months, 10 months, 18 months and 26 months for this analysis.

Since the group of runner mice that expended more energy lived as long as the runner group that was less active, the researchers tested whether there was a difference in antioxidant production between the two groups. Since metabolic rate rises with activity level and oxidative stress rises with metabolic rate, perhaps the runner mice that expended more energy also produced more antioxidants, the body’s defense against oxidative stress, Vaanholt said.

However, the study found no difference in antioxidant levels among the groups, at least in the heart and the liver, regardless of energy expenditure. “We would have expected additional antioxidants among the group of mice that expended 25% more energy, but that was not the case,” Vaanholt said.

“We can conclude that the presence of a running wheel resulted in increased daily energy expenditure without a change in lifespan or in antioxidant enzyme activity in the heart and liver,” Vaanholt explained.

Further research must examine whether tissues in other areas of the body generated additional antioxidants to help cope with the increased oxidative stress brought on with increased activity and metabolic rate, she said. In addition, future studies may examine whether other mechanisms are at work, including whether activity level is connected to DNA repair rates.

A bird as clever as my duck!

Keeping track of one set of keys is difficult enough, but imagine having to remember the locations of thousands of sets of keys. Do you use landmarks to remember where you put them? Do you have a mental map of their locations?

Scientists at the University of New Hampshire hope to learn more about memory and its evolution by studying the Clark’s nutcracker, a bird with a particularly challenging task: remembering where it buried its supply of food for winter in a 15-mile area. Like many animals preparing for the winter, every fall the Clark’s nutcracker spends several weeks gathering food stores. What makes it unique is that it harvests more than 30,000 pine nuts, buries them in up to 5,000 caches, and then relies almost solely on its memory of where those caches are located to survive through winter.

Brett Gibson, a scientist studying animal behavior, began studying Clark’s nutcrackers in graduate school and is continuing his research into memory and the behavior of nutcrackers as an assistant professor in UNH’s psychology department.

“Nutcrackers are almost exclusively dependent upon cache recovery for their survival so if they don’t remember where they’ve made those caches, then they are in trouble,” Gibson says. “During winter, their cache locations are covered with snow so many of the small local features in the landscape during fall are no longer available to them. What’s clear is that they are using spatial memory to recover these caches. They are remembering these caches based on landmarks and other features of the terrain.”

The study of memory is important for several reasons. It helps us understand how memory develops and evolves. It teaches us about how we and other species successfully navigate using memory. It provides insights across species about brain function and the hippocampus, a part of the brain important for memory and one of the first regions of the brain to suffer damage in Alzheimer’s patients.

“For us it would probably be very difficult to remember where we put 33,000 items, but these guys do it really well because of the environment they live in,” Gibson says. “It’s a problem evolution has solved by developing this very good memory for spatial information.”

Clark’s nutcrackers are native to the upper elevations of western North America, such as the Colorado Rocky Mountains. They are a member of the corvid family, which also includes blue jays and crows that are native to New England.

Gibson was part of an initial program of research focused on studying the Clark’s nutcracker’s spatial memory and how it compared to other members of the corvid family. That research has found that nutcrackers have a better spatial memory compared to related birds that are not as dependent upon the recovery of food caches during the winter for their survival.

His most recent research with the Clark’s nutcracker looks at the nature of the spatial cues specified by memory – how the bird uses these cues to find its food caches. “How do they use landmarks? What information do they remember about these landmarks? Are they using just one landmark as a beacon? Do they remember multiple landmarks and the geometrical relationship between those landmarks and the goal location?” Gibson says.

“These pine seeds are very small and these caches are very small so they have to be very accurate about how they use these landmarks to remember those cache locations,” he says.

One way that nutcrackers might solve the problem of returning to their caches is by developing a mental map of landmarks in their environment and recalling the location of the caches relative to the landmarks in the map. If they do have a map then they might be able to plan efficient routes to get from one cache site to the next – a problem called the Traveling Salesman Problem.

“Some mathematicians love this problem. We were interested in seeing how efficiently a non-human animal could solve it so we looked at pigeons. They were actually pretty very good at it so we’re going to start looking at the same problem with nutcrackers,” Gibson says. “We think they may be even better because nutcrackers have all of these places they have to travel in their environment; you might expect them to be very efficient in terms of where they travel.”

Gibson, in collaboration with his graduate student Tyler Wilks, also is looking at whether the birds use another navigational strategy in finding their food -- dead reckoning, part of an internal sense of direction. Dead reckoning integrates awareness of direction and distance traveled in order to return to a previous location; no landmarks are used.

“As humans we rely on landmarks a lot so we don’t think a lot about dead reckoning. But when you get lost in a forest and there aren’t a lot of familiar landmarks, your dead reckoning system kicks in and you try to determine the direction from which you came,” he says.

Investigations of dead reckoning in Clark’s nutcrackers have been limited, although it has been explored in other animals, from ants to primates. “We suspect it might play an important role because they have this great demand for remembering locations in the environment,” Gibson says.

Gibson also is interested in how animals create tools such as hooks and barbs out of items like twigs and branches, and use them to find food. “The Clark’s nutcracker being a member of the corvid family might be quite good at understanding some of the physical relationships involved in solving problems that require using tools,” he says.

Hot sightings

A new McGill University study that used thermal imaging technology for the first time ever to measure sexual arousal rates has turned the conventional wisdom that women become aroused more slowly than men on its head.

“Comparing sexual arousal between men and women, we see that there is no difference in the amount of time it takes healthy young men and women to reach peak arousal,” said Dr. Irv Binik, psychology professor and founder and director of the Sex and Couple Therapy Service of Royal Victoria Hospital, which is part of the McGill University Health Centre (MUHC).

Thermal imaging, or thermography, is infrared imaging using thermographic cameras that detect radiation emitted by objects based on their temperature. Because of its usefulness in detecting warm objects in the dark, most people know it as the technology used in night vision goggles for military operations.

Previously, sex researchers have measured arousal with instruments that require genital contact and manipulation. Binik focused thermographic cameras on his subjects’ genitals while they watched a montage of material from pornography to horror movies to The Best of Mr. Bean to Canadian tourism travelogues to provide a base of control data. During the arousal experiment, the male and female subjects watched separate sexually explicit films procured from the Kinsey Institute and determined to be sexually arousing to specific genders. They watched the images through special video goggles to minimize distractions.

As the subjects responded, the Binik team monitored body-temperature changes to within a 100th of a degree from a computer in another room. Both the men and the women began showing arousal within 30 seconds. The men reached maximal arousal in 664.6 seconds (roughly ten minutes), the women in 743 seconds – a statistically negligible difference.

“In any experiment on sexual arousal done in a laboratory, there is some distraction,” said Binik. “But compared to previous techniques involving invasive measures or electrodes, this is minimally invasive and the same measurements are used for men and women, which makes it very interesting that the data ended up being the same.”

Dr. Binik’s PhD student, Tuuli Kukkonen, said, “This will help diagnose and treat sexual dysfunction in women, such as female sexual arousal disorder, which is poorly understood.” Kukkonen will present a paper on the findings Saturday at the Canadian Sex Research Forum conference in Ottawa. The Journal of Sexual Medicine will publish the paper in its next issue, in January.

Why I never liked watercress

I hate the taste of watercress and now I know why.

Scientists at the Monell Chemical Senses Center have found that a person's bitter taste perception of vegetables is influenced by an interaction between variants of taste genes and the presence of naturally-occurring toxins in the vegetable. Their study appears in the September 19 issue of Current Biology.

Bitter taste has long been assumed to have evolved as a defense mechanism to detect potentially harmful toxins in plants. The Current Biology paper provides the first direct evidence in support of this hypothesis by establishing that variants of the bitter taste receptor TAS2R38 can detect glucosinolates, a class of compounds with potentially harmful physiological actions, in natural foods.

“The findings show that our taste receptors are capable of detecting toxins in the natural setting of the fruit and vegetable plant matrix,” said senior author Paul Breslin, a Monell sensory scientist.

Glucosinolates act as anti-thyroid compounds. The thyroid converts iodine into thyroid hormones, which are essential for protein synthesis and regulation of the body’s metabolism. Glucosinolates inhibit iodine uptake by the thyroid, increasing risk for goiter and altering levels of thyroid hormones. The ability to detect and avoid naturally-occurring glucosinolates would confer a selective advantage to the over 1 billion people who presently have low iodine status and are at risk for thyroid insufficiency.

In the study, 35 healthy adults were genotyped for the hTAS2R38 bitter taste receptor gene; the three genotypes were PAV/PAV (sensitive to the bitter-tasting chemical PTC, AVI/AVI (insensitive), and PAV/AVI (intermediate).

Subjects then rated bitterness of various vegetables; some contained glucosinolates while others did not. Examples of the 17 glucosinolate-containing vegetables include watercress, broccoli, bok choy, kale, kohlrabi, and turnip; the 11 non-glucosinolate foods included radicchio, endive, eggplant and spinach. Subjects with the sensitive PAV/PAV form of the receptor rated the glucosinolate-containing vegetables as 60% more bitter than did subjects with the insensitive (AVI/AVI) form. The other vegetables were rated equally bitter by the two groups, demonstrating that variations in the hTAS2R38 gene affect bitter perception specifically of foods containing glucosinolate toxins.

Together, the findings provide a complete picture describing individual differences in responses to actual foods at multiple levels: evolutionary, genetic, receptor, and perceptual. “The sense of taste enables us to detect bitter toxins within foods, and genetically-based differences in our bitter taste receptors affect how we each perceive foods containing a particular set of toxins,” summarizes Breslin.

Breslin notes, “The contents of the veggies are a double-edged sword, depending upon the physiological context of the individual eating them. Most people in industrialized cultures can and should enjoy these foods. In addition to providing essential nutrients and vitamins, many are reported to have anti-cancer properties.”

Lead author Mari Sandell comments on additional nutritional and practical implications of the study, “Taste has a great impact on food acceptability and choice. A comprehensive understanding how food components contribute to taste is necessary to develop modern tools for both nutritional counseling and food development.”

The Monell Chemical Senses Center is a nonprofit basic research institute based in Philadelphia, Pennsylvania, focusing on understanding the senses of smell, taste and chemical irritation: how they function and affect lives from before birth through old age.

CITATION: Mari A. Sandell and Paul A.S. Breslin. Variability in a taste-receptor gene determines whether we taste toxins in food. Current Biology, 2006, 16, R792-R794.

FUNDING: National Institute on Deafness and Other Communication Disorders, National Institutes of Health

My foot...

These footprints look more like those made by a giant duck, I'd say. But then again, rude noises are the trademark of hungry primates...

Somebody was also Googling around for "mrs budak mop". I should like to assure her that no duck would dare to attempt such an association atrocity. Instead, I should like to offer this mopsy researcher a truer taste of mrs budak.

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From the New Straits Times:

Fresh 'Bigfoot' footprints located near a stream in Panti Forest
R. Sittamparam

JOHOR BARU, Sat 18 Feb 2006: PHYSICAL evidence of what could have been Bigfoot's was today found at the foothills of Panti Forest by bio-diversity researchers and media who investigated claims by villagers that they heard the creature's spine-chilling calls on Tuesday.

Following a three-hour trek into the jungle near Kampung Lukut in Panti, the team saw giant footprints and broken foliage two metres above ground which could only have been reached by a tall creature. It was reported yesterday that residents of Kampung Lukut had been rudely awakened by the howling over the past four days.

Local biodiversity researcher Vincent Chow who led the group, including the NST and British Broadcasting Corporation (BBC) media crew, said although wild buffaloes in the area had trampled over the tracks found at a stream, the group managed to find some untouched footprints believed to have been made by Bigfoot.

Plantation worker Yazid Jaafar, 29, said he first saw the footprints on Tuesday while investigating the source of the early morning howling.

"We could clearly see the large human like footprints with four toes and big toe bent about 90 degrees away from the other toes like a monkey's foot. The footprint tracks stretched along the banks of the stream.

"The creature appeared to have walked along the bank, probably feeding on leaves growing there before returning into the jungle," he said.