Yearly Archives: 2007

Some Tropical Birds Depend Completely On Army Ants To Flush Out Prey:

In the jungles of Central and South America, a group of birds has evolved a unique way of finding food — by following hordes of army ants and letting them do all the work.

Bone Structure ‘Vastly Different’ Than Previously Believed:

Researchers have discovered that the structure of human bones is vastly different than previously believed — findings which will have implications for how some debilitating bone disorders are treated.

Ear Infection Superbug Discovered To Be Resistant To All Pediatric Antibiotics:

Researchers have discovered a strain of bacteria resistant to all approved drugs used to fight ear infections in children, according to an article in the Journal of the American Medical Association. A pair of pediatricians discovered the strain because it is their standard practice to perform an uncommon procedure called tympanocentesis (ear tap) on children when several antibiotics fail to clear up their ear infections. The procedure involves puncturing the child’s eardrum and draining fluid to relieve pressure and pain. Analyzing the drained fluid is the only way to describe the bacterial strain causing the infection.

Upper Midwest Forests Are Losing Diversity, Complexity:

Forests in the nation’s Upper Midwest have changed greatly since the time of the early settlers. And more changes may be coming.

Tuna Fishing Fleets In The Pacific Pose Danger To Wildlife At Sea:

Thousands of seabirds and significant numbers of sharks and marine turtles are being caught and killed each year in long-line fishing nets targeting southern bluefin tuna, reveals a new WWF report.

After Drought, Diversity Dries Up And Ponds All Look The Same:

An ecologist at Washington University in St. Louis has discovered that after ponds dry up through drought in a region, when they revive, the community of species in each pond tends to be very similar to one another, like so many suburban houses made of ticky tacky.

Unique Spoon-billed Bird Facing Extinction:

Populations of one of the world’s strangest birds have crashed over the last decade, and surveys this summer of its breeding grounds in the remote Russian province of Chukotka suggest that the situation is now critical. The charismatic, and rather aptly named, Spoon-billed Sandpiper Eurynorhynchus pygmeus, is now worryingly close to becoming extinct. With only 200-300 pairs left, conservationists are calling for urgent help to tackle the decline.

Thirtieth Anniversary Of Discovery Of Third Domain Of Life:

Thirty years ago this month, researchers at the University of Illinois published a discovery that challenged basic assumptions about the broadest classifications of life. Their discovery – which was based on an analysis of ribosomal RNA, an ancient molecule essential to the replication of all cells – opened up a new field of study, and established a first draft of the evolutionary “tree of life.”

There are 21 new articles published tonight on PLoS ONE. As always, read, rate, comment, annotate, volunteer to do a Journal Club, and, if you blog about it, send trackbacks….Here are my picks:
A Televised, Web-Based Randomised Trial of an Herbal Remedy (Valerian) for Insomnia:

To combat the symptoms of insomnia, many people resort to non-prescribed herbal remedies such as valerian. In this randomised trial, the authors recruited 405 participants through a televised Norwegian health program and found only moderately beneficial effects of valerian on people with insomnia. However, the methods used to execute this trial suggest new ways of conducting research to evaluate the effects of health care interventions, and of improving public understanding and use of randomised trials.

Small-Scale Fisheries Bycatch Jeopardizes Endangered Pacific Loggerhead Turtles:

Industrial-scale fisheries are known to cause a decline in the number of large migratory animals through unintended catches. However the impact of smaller fisheries on these animals is poorly known. In this paper, Peckham and colleagues use satellite tracking data to monitor 30 North Pacific loggerhead turtles over a period of 10 years. Their results reveal that small-scale fisheries may be as detrimental to large migratory species as the larger industrial-scale fisheries.

Preventing Establishment: An Inventory of Introduced Plants in Puerto Villamil, Isabela Island, Galapagos:

As part of an island-wide project to identify and eradicate potentially invasive plant species before they become established, a program of inventories is being carried out in the urban and agricultural zones of the four inhabited islands in Galapagos. This study reports the results of the inventory from Puerto Villamil, a coastal village representing the urban zone of Isabela Island. We visited all 1193 village properties to record the presence of the introduced plants. In addition, information was collected from half of the properties to determine evidence for potential invasiveness of the plant species. We recorded 261 vascular taxa, 13 of which were new records for Galapagos. Most of the species were intentionally grown (cultivated) (73.3%) and used principally as ornamentals. The most frequent taxa we encountered were Cocos nucifera (coconut tree) (22.1%) as a cultivated plant and Paspalum vaginatum (salt water couch) (13.2%) as a non cultivated plant. In addition 39 taxa were naturalized. On the basis of the invasiveness study, we recommend five species for eradication (Abutilon dianthum, Datura inoxia, Datura metel, Senna alata and Solanum capsicoides), one species for hybridization studies (Opuntia ficus-indica) and three species for control (Furcraea hexapetala, Leucaena leucocephala and Paspalum vaginatum).

Identification and Classification of Hubs in Brain Networks:

Brain regions in the mammalian cerebral cortex are linked by a complex network of fiber bundles. These inter-regional networks have previously been analyzed in terms of their node degree, structural motif, path length and clustering coefficient distributions. In this paper we focus on the identification and classification of hub regions, which are thought to play pivotal roles in the coordination of information flow. We identify hubs and characterize their network contributions by examining motif fingerprints and centrality indices for all regions within the cerebral cortices of both the cat and the macaque. Motif fingerprints capture the statistics of local connection patterns, while measures of centrality identify regions that lie on many of the shortest paths between parts of the network. Within both cat and macaque networks, we find that a combination of degree, motif participation, betweenness centrality and closeness centrality allows for reliable identification of hub regions, many of which have previously been functionally classified as polysensory or multimodal. We then classify hubs as either provincial (intra-cluster) hubs or connector (inter-cluster) hubs, and proceed to show that lesioning hubs of each type from the network produces opposite effects on the small-world index. Our study presents an approach to the identification and classification of putative hub regions in brain networks on the basis of multiple network attributes and charts potential links between the structural embedding of such regions and their functional roles.

The Origins of Novel Protein Interactions during Animal Opsin Evolution:

Biologists are gaining an increased understanding of the genetic bases of phenotypic change during evolution. Nevertheless, the origins of phenotypes mediated by novel protein-protein interactions remain largely undocumented.
Here we analyze the evolution of opsin visual pigment proteins from the genomes of early branching animals, including a new class of opsins from Cnidaria. We combine these data with existing knowledge of the molecular basis of opsin function in a rigorous phylogenetic framework. We identify adaptive amino acid substitutions in duplicated opsin genes that correlate with a diversification of physiological pathways mediated by different protein-protein interactions.
This study documents how gene duplication events early in the history of animals followed by adaptive structural mutations increased organismal complexity by adding novel protein-protein interactions that underlie different physiological pathways. These pathways are central to vision and other photo-reactive phenotypes in most extant animals. Similar evolutionary processes may have been at work in generating other metazoan sensory systems and other physiological processes mediated by signal transduction.

Kate reviews the latest paper by Ellen Ketterson et al. and since she did it so well, I decided not to do it myself, as it comes too close to my own stuff…
Mountain Top Removal? See why this is not a good idea.
Two conservatives, two views on environmentalism (and no, I will not go into details why I disagree with both of them):
The Embrace of Environmentalism Will Be the Doom of Traditional Religion
Interview with Seymour Garte, Author of Where We Stand
The Mystery of the Sleepy Teenager – pay attention!
Raleigh News & Observer covers the local angle on the story about queen honeybee pheromones.
In the same issue in which it showcased feminist bloggers (including Feministe, Feministing, Pandagon and Echidne of the Snakes), Newsweek also had an article on the 10 hottest nerds, who are supposedly the “10 of the most esteemed biologists” in the world. But, as Jonathan noted, all of them are old, white, rich, politically powerful bosses of big genomics labs. Those are not the revolutionaries for the 21st century as Newsweek says. I can, in a matter of a few seconds, come up with 10 names of brilliant biologists who are young, female or non-white and truly poised to change biology in the 21st century, none of whom work in genomics, and that is just those I have met in person! You add your own names….
The first World Toilet Summit, organized by World Toilet Organization (via Thomas Goetz).

Fish Get Insomnia, Eyes Wide Open, Say Sleep Researchers:

Scientists at the Stanford University School of Medicine have hooked a fish that suffers from insomnia in their quest to understand the genetics behind sleep disorders.

Ugly Duckling Mole Rats Might Hold Key To Longevity:

Who would have thought that the secrets to long life might exist in the naked, wrinkled body of one of the world’s ugliest animals? Probably not many, but current research may be leading seekers of the Fountain of Youth to a strange little beast — the naked mole rat.

Note: I think blind mole rats are beautiful. Stop callin them ‘ugly’!
Deep Sea Discoveries Off Canada’s East Coast:

Researchers from Fisheries and Oceans Canada and Memorial University of Newfoundland took part in an exciting survey of unexplored depths of the Atlantic Ocean during a three-week mission in July 2007. Deep water corals were a primary focus of the research.

Why Do Leaves Change Color In The Fall?:

Many of the colors we see in fall are always present, but normally they’re hidden from view, says UW-Madison Arboretum native plant gardener Susan Carpenter.

Brain Imaging Shows Similarities & Differences In Thoughts Of Chimps And Humans:

In the first study of its kind, researchers at the Yerkes National Primate Research Center, Emory University, used functional brain imaging to assess resting-state brain activity in chimpanzees as a potential window into their mental world and to compare chimpanzee brain activity to that of humans.

Testosterone Turns Male Junco Birds Into Blustery Hunks — And Bad Dads:

The ability to ramp up testosterone production appears to drive male dark-eyed juncos to find and win mates, but it comes with an evolutionary cost. Big fluctuations in testosterone may also cause males to lose interest in parenting their own young, scientists have learned.

Blind To Beauty: How And Where Do We Process Attractiveness?:

Beauty may be in the eye of the beholder, but according to research conducted by a UBC medical student, eye candy fails to find a sweet tooth in patients with a rare disorder.

After Drought, Diversity Dries Up And Ponds All Look The Same:

An ecologist at Washington University in St. Louis has discovered that after ponds dry up through drought in a region, when they revive, the community of species in each pond tends to be very similar to one another, like so many suburban houses made of ticky tacky.

A Gene Divided Reveals The Details Of Natural Selection:

In a molecular tour de force, researchers at the University of Wisconsin-Madison have provided an exquisitely detailed picture of natural selection as it occurs at the genetic level.

Monday – the day for checking in PLoS Biology and PLoS Medicine for the newest published articles. And there is some good stuff:
Characterization of Sleep in Zebrafish and Insomnia in Hypocretin Receptor Mutants

Sleep disorders are common and poorly understood. Further, how and why the brain generates sleep is the object of intense speculations. In this study, we demonstrate that a bony fish used for genetic studies sleeps and that a molecule, hypocretin, involved in causing narcolepsy, is conserved. In humans, narcolepsy is a sleep disorder associated with sleepiness, abnormal dreaming, and paralysis and insomnia. We generated a mutant fish in which the hypocretin system was disrupted. Intriguingly, this fish sleep mutant does not display sleepiness or paralysis but has a 30% reduction of its sleep time at night and a 60% decrease in sleep bout length compared with non-mutant fish. We also studied the relationships between the hypocretin system and other sleep regulatory brain systems in zebrafish and found differences in expression patterns in the brain that may explain the differences in behavior. Our study illustrates how a sleep regulatory system may have evolved across vertebrate phylogeny. Zebrafish, a powerful genetic model that has the advantage of transparency to study neuronal networks in vivo, can be used to study sleep.

Also check the accompanying synopsis: Let Sleeping Zebrafish Lie: A New Model for Sleep Studies:

Although the function of sleep is hotly debated, one thing is clear–we, and most other animals, cannot do without it. In a new study, Yokogawa et al. describe how zebrafish sleep, finding both striking similarities to mammalian sleep and its regulation and intriguing differences.

Also, on the 4th birthday of PLoS Biology, a good editorial: When Is Open Access Not Open Access?

Since 2003, when PLoS Biology was launched, there has been a spectacular growth in “open-access” journals. The Directory of Open Access Journals (http://www.doaj.org/), hosted by Lund University Libraries, lists 2,816 open-access journals as this article goes to press (and probably more by the time you read this). Authors also have various “open-access” options within existing subscription journals offered by traditional publishers (e.g., Blackwell, Springer, Oxford University Press, and many others). In return for a fee to the publisher, an author’s individual article is made freely available and (sometimes) deposited in PubMed Central (PMC). But, as open access grows in prominence, so too has confusion about what open access means, particularly with regard to unrestricted use of content–which true open access allows. This confusion is being promulgated by journal publishers at the expense of authors and funding agencies wanting to support open access.

And check these two important articles on observatinal studies in epidemiology:
The Strengthening the Reporting of Observational Studies in Epidemiology (STROBE) Statement: Guidelines for Reporting Observational Studies
Strengthening the Reporting of Observational Studies in Epidemiology (STROBE): Explanation and Elaboration

Humans Perceive Others’ Fear Faster Than Other Emotions:

You may not be fully dressed without a smile, but a look of horror will make a faster first impression. Vanderbilt University researchers have discovered that the brain becomes aware of fearful faces more quickly than those showing other emotions.

Pasturing Cows Convert Soil To A Source Of Methane, Potent Greenhouse Gas:

The cow as a killer of the climate: This inglorious role of our four-legged friends, peaceful in itself, is well-enough recognised, because, with their digestion, the animals produce methane, which is expelled continuously. Now, however, a team of German scientists from the Institute of Soil Ecology of the GSF – National Research Center for Environment and Health (Helmholtz Association of German Research Centres) and Czech colleagues at the Budweis Academy of Science have been able to show that bovine animals can also boost the production of this climate gas in soil.

Portable Diagnostic System For Foot-and-mouth Disease And Avian Flu Designed:

Smiths Detection is to launch a portable detection system that will enable veterinarians to carry out on-site diagnosis of animal diseases such as foot-and-mouth and avian flu. This new technology means vets will be able to diagnose diseases in livestock and birds in the field in less than 90 minutes rather than having to send samples for laboratory analysis.

Red Wine And Grape Juice Help Defend Against Food-borne Diseases, Study Suggests:

Red wine is known to have multiple health benefits. Researchers at the University of Missouri-Columbia have found that red wine may also protect humans from common food-borne diseases.

Want Antioxidants? Have You Eaten Micro-algae Lately?:

Some consumers want more than just their traditional nourishment requirements met. Micro-algae (eaten by humans in pre-Columbian America) are more than just nutritive. Spirulina microalgae could be a good source of antioxidants due to the presence of carotenoids deriving from chlorophyll, and provide bacterial growth inhibiting action because of certain fatty acids. Microalgae have turned out to be a potential alternative to the use of synthetic sources for these ingredients.

Buying And Selling Habitats To Help Wildlife:

Tradable permits are all the rage in environmental policy. They are already used internationally to reduce carbon emissions and improve air quality. A group of economists and ecologists from the UK, the Netherlands and Germany, are working together to find out whether such schemes could work for wildlife too. So far, it looks promising, but probably only for cultural landscapes like farmland.

As always on Fridays, there are new articles published in PLoS Computational Biology, PLoS Genetics and PLoS Pathogens. Look around to see what’s new. My pick for this week:
Inconsistencies in Neanderthal Genomic DNA Sequences:

One of the enduring questions in human evolution is the relationship of fossil groups, such as Neanderthals, with people alive today. Were Neanderthals direct ancestors of contemporary humans or an evolutionary side branch that eventually died out? Two recent papers describing the sequencing of Neanderthal nuclear DNA from fossil bone held promise for finally answering this question. However, the two studies came to very different conclusions regarding the ancestral role of Neanderthals. In this paper, we reanalyzed the data from the two original studies. We found that the two studies are inconsistent with each other, which implies that the data from at least one of the studies is probably incorrect. The likely culprit is contamination with modern human DNA, which we believe compromised the findings of one of the original Neanderthal DNA studies.

New Hearing Mechanism Discovered:

MIT researchers have discovered a hearing mechanism that fundamentally changes the current understanding of inner ear function. This new mechanism could help explain the ear’s remarkable ability to sense and discriminate sounds. Its discovery could eventually lead to improved systems for restoring hearing.

People Are Programmed To Love Chocolate, Study Finds:

For the first time, scientists have linked the all-too-human preference for a food — chocolate — to a specific, chemical signature that may be programmed into the metabolic system and is detectable by laboratory tests. The signature reads ‘chocolate lover’ in some people and indifference to the popular sweet in others, the researchers say.

Green Algae: The Nexus Of Plant-Animal Ancestry:

Genes of a tiny, single-celled green alga called Chlamydomonas reinhardtii may contain scores more data about the common ancestry of plants and animals than the richest paleontological dig. This work is described in an article in Science.

Frozen Sperm Worked For White Rhino:

Scientists from the Leibniz Institute for Zoo and Wildlife Research in Berlin successfully inseminated a rhino with formerly frozen sperm. This world-first artificial insemination of a white rhino with frozen rhino sperm took place in Budapest Zoo.

Spread Of Endogenous Retrovirus K Is Similar In The DNA Of Humans And Rhesus Monkeys:

According to paleontologic and molecular studies, the chimpanzee (Pan troglodytes) is the closer relative to the humans (Homo sapiens) and that both lineages had a common ancestor at 5 to 7 million years ago.

Benefits Of 80 Million Years Without Sex:

Scientists have discovered how a microscopic organism has benefited from nearly 80 million years without sex. Bdelloid rotifers are asexual organisms, meaning that they reproduce without males. Without sex, these animals lack many of the ways in which sexual animals adapt over generations to survive in their natural environment.

Herding Aphids: How ‘Farmer’ Ants Keep Control Of Their Food:

Chemicals on ants’ feet tranquilise and subdue colonies of aphids, keeping them close-by as a ready source of food, says new research. The study throws new light on the complex relationship between ants and the colonies of aphids whose sugary secretions the ants eat.

Discovery Of Retinal Cell Type Ends 40-year Search:

A research team combining high-energy physicists from the University of California, Santa Cruz, and neuroscientists from the Salk Institute in La Jolla, Calif., has discovered a type of retinal cell that may help monkeys, apes, and humans see motion.

Ticks Don’t Come Out In The Wash:

Before venturing into tick-infested territory, you used a topical repellent on exposed skin and outer clothing. When you returned, you did a body check and threw your clothes in the wash. But clean clothes may not be tick-free clothes. When he found a live lone star tick (Amblyomma americanum) on the agitator of his washing machine, Agricultural Research Service (ARS) entomologist John Carroll decided to find out how tough ticks are. So he bagged up nymphs from two species–the lone star tick and the deer tick, (Ixodes scapularis), the creature that transmits Lyme disease–and put them in the washing machine.

In Biology, Polarization Is A Good Thing:

Using a molecular cellular compass, individual cells in complex organisms know which way is up or down, in epithelial cells known as apical-basal polarity. Determining the orientation is essential for an individual cell to perform it’s designated tasks. Now it appears that the same compass also defines the direction of cells when migrating by establishing a morphological back and a front.