Yearly Archives: 2007

Adult Male Chimpanzees Don’t Stray Far From The Home:

When it comes to choosing a place to live, male chimpanzees in the wild don’t stray far from home, according to a new report. The researchers found that adult male chimps out on their own tend to follow in their mother’s footsteps, spending their days in the same familiar haunts where they grew up. Male chimpanzees are generally very social, but how they use space when they are alone might be critical to their survival, the researchers said.

Solving Another Mystery Of An Amazing Water Walker:

Walking on water may seem like a miracle to humans, but it is a ho-hum for the water strider and scientists who already solved the mystery of that amazing ability. Now researchers in Korea are reporting a long-sought explanation for the water strider’s baffling ability to leap onto a liquid surface without sinking.

Innovative Model Connects Circuit Theory To Wildlife Corridors:

Scientists at Northern Arizona University and the National Center for Ecological Analysis and Synthesis have developed a model that borrows from electronic circuit theory to predict gene flow across complex landscapes . Their approach could help biologists design better wildlife corridors, which are crucial to protecting threatened plant and animal populations.

Smelly Sounds: One Person Out Of Every 1,000 Has Synesthesia:

Surprising as it may seem, there are people who can smell sounds, see smells or hear colours. One person out of every thousand has synesthesia, a psychological phenomenon in which an individual can smell a sound or hear a color. Most of these people are not aware they are synesthetes: they think the way they experience the world is normal.

Sleep Chemical Central To Effectiveness Of Deep Brain Stimulation:

A brain chemical that makes us sleepy also appears to play a central role in the success of deep brain stimulation to ease symptoms in patients with Parkinson’s disease and other brain disorders. The surprising finding is outlined in a paper published online Dec. 23 in Nature Medicine. The work shows that adenosine, a brain chemical most widely known as the cause of drowsiness, is central to the effect of deep brain stimulation, or DBS. The technique is used to treat people affected by Parkinson’s disease and who have severe tremor, and it’s also being tested in people who have severe depression or obsessive-compulsive disorder.

On Fridays, I take a look at what’s new in PLoS Neglected Tropical Diseases, Pathogens, Computational Biology and Genetics. Here are some of my picks for this week:
Neglected Diseases and Poverty in “The Other America”: The Greatest Health Disparity in the United States?:

Large numbers of the poorest Americans living in the United States are suffering from some of the same parasitic infections that affect the poor in Africa, Asia, and Latin America.

The Long and Thorny Road to Publication in Quality Journals:

Within the “Ten Simple Rules” series in PLoS Computational Biology, Dr. Bourne suggests that for younger investigators it is better to publish one paper in a quality journal rather than having multiple papers in lesser journals [1]. While this is certainly advisable, it can be very difficult. Indeed, for young scientists or, more to the point, for researchers with a short record of publications, it may be almost impossible to make their work and themselves visible to a larger scientific community via higher impact journals. A not-too-small share of “seasoned” scientists will argue without malignity that “we experienced similar or the same” and “good researchers will eventually be recognized.” What they imply is that those who continue to provide good science shall be rewarded later, i.e., their papers will eventually find a home in quality journals, thus yielding better chances that the work will have impact. And yet, a much-cited case study ([2]; cited 264 times as of November 18, 2007, according to http://isiwebofknowledge.com/) may illustrate that the road to publication and recognition can be thorny and long for younger and less-recognized scientists.

Computational Biology in Argentina:

Sebastian Bassi and colleagues from the Universidad Nacional de Quilmes, Buenos Aires, reflect on the identity of the interdisciplinary field of computational biology both generally and specifically in their country, Argentina.

A Tribute to Marcy Carlson Speer, 1959-2007:

It is with great sadness that we say goodbye to Marcy Carlson Speer, who died on August 4, 2007, at the age of 47 after a two-year battle with breast cancer. Marcy was an extremely accomplished scientist who, at the time of her death, was the director of the Duke Center for Human Genetics and chief of the Division of Medical Genetics. During her career, she published 124 articles and 16 book chapters; the topics of her scholarly scientific work ranged from gene mapping and identification to method development in genetic epidemiology and authoritative book chapters on linkage analysis. Over her scientific career, Marcy was the recipient of 24 National Institutes of Health (NIH) grants; of these, she was principal investigator of 18.

There are 30 new articles in PLoS ONE this week. Here are my picks:
Ultrasonic Communication in Rats: Can Playback of 50-kHz Calls Induce Approach Behavior?:

Rats emit distinct types of ultrasonic vocalizations, which differ depending on age, the subject’s current state and environmental factors. Since it was shown that 50-kHz calls can serve as indices of the animal’s positive subjective state, they have received increasing experimental attention, and have successfully been used to study neurobiological mechanisms of positive affect. However, it is likely that such calls do not only reflect a positive affective state, but that they also serve a communicative purpose. Actually, rats emit the highest rates of 50-kHz calls typically during social interactions, like reproductive behavior, juvenile play and tickling. Furthermore, it was recently shown that rats emit 50-kHz calls after separation from conspecifics. The aim of the present study was to test the communicative value of such 50-kHz calls. In a first experiment, conducted in juvenile rats situated singly on a radial maze apparatus, we showed that 50-kHz calls can induce behavioral activation and approach responses, which were selective to 50-kHz signals, since presentation of 22-kHz calls, considered to be aversive or threat signals, led to behavioral inhibition. In two other experiments, we used either natural 50-kHz calls, which had been previously recorded from other rats, or artificial sine wave stimuli, which were identical to these calls with respect to peak frequency, call length and temporal appearance. These signals were presented to either juvenile (Exp. 2) or adult (Exp. 3) male rats. Our data clearly show that 50-kHz signals can induce approach behavior, an effect, which was more pronounced in juvenile rats and which was not selective to natural calls, especially in adult rats. The recipient rats also emitted some 50-kHz calls in response to call presentation, but this effect was observed only in adult subjects. Together, our data show that 50-kHz calls can serve communicative purposes, namely as a social signal, which increases the likelihood of approach in the recipient conspecific.

An Animal Model of Emotional Blunting in Schizophrenia:

Schizophrenia is often associated with emotional blunting–the diminished ability to respond to emotionally salient stimuli–particularly those stimuli representative of negative emotional states, such as fear. This disturbance may stem from dysfunction of the amygdala, a brain region involved in fear processing. The present article describes a novel animal model of emotional blunting in schizophrenia. This model involves interfering with normal fear processing (classical conditioning) in rats by means of acute ketamine administration. We confirm, in a series of experiments comprised of cFos staining, behavioral analysis and neurochemical determinations, that ketamine interferes with the behavioral expression of fear and with normal fear processing in the amygdala and related brain regions. We further show that the atypical antipsychotic drug clozapine, but not the typical antipsychotic haloperidol nor an experimental glutamate receptor 2/3 agonist, inhibits ketamine’s effects and retains normal fear processing in the amygdala at a neurochemical level, despite the observation that fear-related behavior is still inhibited due to ketamine administration. Our results suggest that the relative resistance of emotional blunting to drug treatment may be partially due to an inability of conventional therapies to target the multiple anatomical and functional brain systems involved in emotional processing. A conceptual model reconciling our findings in terms of neurochemistry and behavior is postulated and discussed.

The Oral Cavity and Age: A Site of Chronic Inflammation?:

Aging may be accompanied by a low grade chronic up-regulation of inflammatory mediators. A variety of endogenous locally released mediators as well as inflammatory cells have been reported in the human oral cavity. The aim of this investigation was to determine the presence of different classes of inflammatory mediators in human saliva and correlate the levels with age. Unstimulated whole buccal salivary samples were obtained in the morning from 94 healthy volunteers within 30 minutes after waking. None of the participants had taken aspirin in the week prior to the saliva collection. Lysozyme activity, eicosanoid levels (prostaglandin E2 and leukotriene B4) and MMP-9 activity were measured. The antimicrobial activity (lysozyme activity) was not correlated with age whereas PGE2 levels were markedly correlated with age (r = 0.29; P40 years) demonstrated a significant increase in the mean values for PGE2 and MMP-9 activity with age. In addition, significant correlations were observed between LTB4 and PGE2 (r = 0.28; P<0.05; n = 56) and between LTB4 levels and MMP-9 activity in smokers (r = 0.78; P<0.001; n = 15). The presence of significant levels and activity of inflammatory mediators in saliva suggests that the oral cavity of healthy subjects may be in a constant low state of inflammation associated with age.

Songbirds Offer Clues To Highly Practiced Motor Skills In Humans:

The melodious sound of a songbird may appear effortless, but his elocutions are actually the result of rigorous training undergone in youth and maintained throughout adulthood. His tune has virtually “crystallized” by maturity. The same control is seen in the motor performance of top athletes and musicians. Yet, subtle variations in highly practiced skills persist in both songbirds and humans. Now, scientists think they know why.

Scientist On Quest For Disappearing Eel:

A Queen’s environmental scientist will head a new international study to determine whether American eels – the slimy, snake-like fish considered worldwide to be a food delicacy – are dying from chemical pollution in Lake Ontario.

Photo-monitoring Whale Sharks: Largest Fish In The Sea Appear To Thrive Under Regulated Ecotourism:

Up to 20 meters long and weighing as much as 20 tons, its enormous size gives the whale shark (Rhincodon typus) its name. Known as the ‘gentle giant’ for its non-predatory behavior, this fish, with its broad, flattened head and minute teeth, eats tiny zooplankton, sieving them through a fine mesh of gill-rakers. Listed as a rare species, relatively little is known about whale sharks, which live in tropical and warm seas, including the western Atlantic and southern Pacific.

Two ‘Noses’ Are Necessary For Flies To Navigate Well:

Animals and insects communicate through an invisible world of scents. By exploiting infrared technology, researchers at Rockefeller University just made that world visible. With the ability to see smells, these scientists now show that when fly larvae detect smells with both olfactory organs they find their way toward a scented target more accurately than when they detect them with one.

Lots of good stuff in PLoS Biology this week:
Cognitive Dimensions of Predator Responses to Imperfect Mimicry:

Many palatable animals, for example hoverflies, deter predators by mimicking well-defended insects such as wasps. However, for human observers, these flies often seem to be little better than caricatures of wasps–their visual appearance and behaviour are easily distinguishable from those which they are attempting to mimic. This imperfect mimicry baffles evolutionary biologists, because one might expect natural selection to do a more thorough job. Here we discuss two types of cognitive processes that might explain why distinguishable mimics could enjoy increased protection from predation. Speed-accuracy tradeoffs in predator decision making might give imperfect mimics sufficient time to escape, and predators under time constraint might avoid time-consuming discriminations between well-defended models and inaccurate edible mimics and instead adopt a “safety first” policy of avoiding insects with similar appearance. Categorisation of prey types by predators could mean that wholly dissimilar mimics may be protected, provided they share some common property with noxious prey. If predators use experience with multiple prey types to learn rules rather than just memorising the appearance of individual prey types, it follows that different individual predators should form different categories, each including separate types of novel prey. Experimental studies to test these hypotheses should be straightforward, because we can use the relatively simple signals (e.g., striped patterns) with which prey manipulate predator behaviour as tools for investigating cognitive processes that underlie decision making and object recognition in animals’ daily lives.

Going against the Grain:

The data that would change the course of Jonathan Tilly’s career and cause an uproar in the field of ovarian biology almost never saw the light of day. In Tilly’s cell death lab, postdoctoral fellow Tomoko Kaneko had twice repeated her experiments to kill off mouse egg cells, but something was wrong because the egg cell numbers were still high after treatment with a chemotherapy drug. Kaneko consulted another postdoc in the lab, Josh Johnson, and together they tried to determine if she had made a technical mistake or perhaps switched her control and experimental groups.
“All of us ‘knew’ that egg regeneration couldn’t be occurring,” says Johnson, referring to the long-held view that adult female mammals are born with a fixed pool of oocytes, or egg cells, which gradually declines in number with age. The work appeared to be an anomaly, but Johnson prodded Kaneko to take it to their advisor’s office. That 2002 meeting was the birth of an ongoing controversy that has shaken up the field of reproductive biology, with Tilly’s laboratory publishing data they interpret as evidence of egg regeneration occurring in adult mice.

Sex, Dose, and Equality:

As a rule, genes and chromosomes come in pairs. Sex chromosomes are an exception to this rule. Males of many species have only one X chromosome, a male-specific Y chromosome, and a set of autosomes (AA). Individuals with two X chromosomes and a set of autosomes (XX;AA) are female. Sex chromosomes were first noticed for this distinct unpaired morphology and are now known to have substantially different gene content [1]. These unusual cases have attracted a great deal of attention over the years, not only because of the role they often play in sex determination, but also as windows into more basic features of genes and gene networks. One such feature is the relationship between gene function and dose. Sex chromosomes allow us to question the importance of having a pair of each gene. With current knowledge of gene regulation, one can make an argument that gene dose should not matter. In textbooks and manuscripts, one often finds figures showing the relationship between genes in a pathway or network, replete with elegant feed-back and feed-forward regulatory interactions, parallel pathways, etc. At the transcript level, it seems logical that any inherent 2-fold quantitative difference due to gene dose should be dwarfed, or even nullified, by the high-magnitude changes resulting from transcriptional regulation by proteins that are arrayed at enhancers or silencers. Basic textbook knowledge of genetics also suggests that dose is not very important. Having a single copy of most genes is not deleterious–there are few dominant alleles due to haploinsufficiency. These observations suggest that genes come in pairs to facilitate reproduction, and perhaps to provide a backup in case of spontaneous mutations occurring during the course of somatic development. It seems likely that the dose of most genes is unimportant because of robustness in gene networks, which buffers against noise and mutation [2].

Male or Female? The Answer Depends on When You Ask:

Akey decision in the life of an organism is whether to be male or female. In Drosophila, each cell makes this choice independently of its neighbors such that diploid cells with one X chromosome (XY) are male and those with two chromosomes (XX) are female. In classic experiments carried out more than 80 years ago, Calvin Bridges made two important conclusions about how sex is determined in flies [1-3]. He showed that the Y chromosome is not a factor and suggested that sex is determined not simply by counting X chromosomes, but by calculating the ratio of X chromosomes to the number of sets of autosomes (known as the X:A ratio). The concept that sex is determined by a mechanism that evaluates the number of X chromosomes relative to autosomes was invoked to explain the observation that animals with two X chromosomes and three sets of autosomes (XX; AAA) develop as sexual mosaics rather than females. According to this model, animals with the same number of X chromosomes as autosome sets (ratio of 1) are female, animals with half as many X chromosomes as sets of autosomes are male (ratio of 0.5), and those with an intermediate ratio (XX; AAA; ratio of 0.67) are sexual mosaics. With the finding that haploid cells (X; A; ratio of 1) are female [4,5], the idea that sex is determined by the X:A ratio became enshrined in the literature.

A Neural Computation for Visual Acuity in the Presence of Eye Movements:

Like a camera, the eye projects an image of the world onto our retina. But unlike a camera, the eye continues to execute small, random movements, even when we fix our gaze. Consequently, the projected image jitters over the retina. In a camera, such jitter leads to a blurred image on the film. Interestingly, our visual acuity is many times sharper than expected from the motion blur. Apparently, the brain uses an active process to track the image through its jittering motion across the retina. Here, we propose an algorithm for how this can be accomplished. The algorithm uses realistic spike responses of optic nerve fibers to reconstruct the visual image, and requires no knowledge of the eye movement trajectory. Its performance can account for human visual acuity. Furthermore, we show that this algorithm could be implemented biologically by the neural circuits of primary visual cortex.

Study Of Bear Hair Will Reveal Genetic Diversity Of Yellowstone’s Grizzlies:

Locks of hair from more than 400 grizzly bears are stored at Montana State University, waiting to tell the tale of genetic diversity in the Yellowstone Ecosystem.

My friend Tim Langer has done a very similar study here in North Carolina.
Squirrels Use Old Snake Skins To Mask Their Scent From Predators:

California ground squirrels and rock squirrels chew up rattlesnake skin and smear it on their fur to mask their scent from predators, according to a new study by researchers at UC Davis.

Anne-Marie has more.
Pinot Noir Grape Sequenced:

Viticulture, the growing of grapes (Vitis vinifera) chiefly to make wine, is an ancient form of agriculture, evidence of which has been found from the Neolithic and Early Bronze Ages. We have a detailed understanding of how nurture affects the qualities of a grape harvest leading to the concept of terroir (the range of local influences that carry over into a wine). The nature of the grapes themselves has been less well understood but our knowledge of this is substantially increased by the publication of a high quality draft genome sequence of a Pinot Noir grape by an Italian-based multinational consortium.

Success Of Invasive Argentine Ants Linked To Diet Shifts:

The Argentine ant, Linepithema humile, is one of the most successful invasive species in the world, having colonized parts of five continents in addition to its native range in South America. A new study sheds light on the secrets of its success.

Snake Venoms Share Similar Ingredients:

Venoms from different snake families may have many deadly ingredients in common, more than was previously thought. A study published in the online open access journal BMC Molecular Biology has unexpectedly discovered three-finger toxins in a subspecies of the Massasauga Rattlesnake, as well as evidence for a novel toxin genes resulting from gene fusion.

Dolphin ‘Therapy’ A Dangerous Fad, Researchers Warn:

People suffering from chronic mental or physical disabilities should not resort to a dolphin “healing” experience, warn two researchers from Emory University. Lori Marino, senior lecturer in the Neuroscience and Behavioral Biology Program, has teamed with Scott Lilienfeld, professor in the Department of Psychology, to launch an educational campaign countering claims made by purveyors of what is known as dolphin-assisted therapy (DAT).