Author Archives: Bora Zivkovic

New articles in PLoS Pathogens, PLoS Computational Biology and PLoS Genetics were published on Friday. My picks for this week are:
Influenza Virus Transmission Is Dependent on Relative Humidity and Temperature:

In temperate regions influenza epidemics recur with marked seasonality: in the northern hemisphere the influenza season spans November to March, while in the southern hemisphere epidemics last from May until September. Although seasonality is one of the most familiar features of influenza, it is also one of the least understood. Indoor crowding during cold weather, seasonal fluctuations in host immune responses, and environmental factors, including relative humidity, temperature, and UV radiation have all been suggested to account for this phenomenon, but none of these hypotheses has been tested directly. Using the guinea pig model, we have evaluated the effects of temperature and relative humidity on influenza virus spread. By housing infected and naïve guinea pigs together in an environmental chamber, we carried out transmission experiments under conditions of controlled temperature and humidity. We found that low relative humidities of 20%-35% were most favorable, while transmission was completely blocked at a high relative humidity of 80%. Furthermore, when guinea pigs were kept at 5 °C, transmission occurred with greater frequency than at 20 °C, while at 30 °C, no transmission was detected. Our data implicate low relative humidities produced by indoor heating and cold temperatures as features of winter that favor influenza virus spread.

Brightness and Darkness as Perceptual Dimensions:

Vision scientists have long adhered to the classic opponent-coding theory of vision, which states that bright-dark, red-green, and blue-yellow form mutually exclusive color pairs. According to this theory, it is not possible to see both brightness and darkness at a single spatial location, or an extended set of locations, such as a uniform surface. One corollary of this statement is that all perceivable grey shades vary along a continuum from bright to dark. At first glance, the notion that brightness and darkness cannot coexist on a single surface accords with our common-sense notion that a given grey shade cannot be simultaneously both brighter and darker than any other grey shade. The results presented here suggest that this common-sense notion is not supported by experimental data. Our results imply that a given grey shade can indeed be simultaneously brighter and darker than another grey shade. This seemingly paradoxical conclusion arises naturally if one assumes that brightness and darkness constitute the dimensions of a two-dimensional perceptual space in which points represent grey shades. Our results may encourage scientists working in related fields to question the assumption that perceptual variables, rather than sensory variables, are encoded in opponent pairs.

Copy Number Variants and Common Disorders: Filling the Gaps and Exploring Complexity in Genome-Wide Association Studies:

Genome-wide association scans (GWASs) using single nucleotide polymorphisms (SNPs) have been completed successfully for several common disorders and have detected over 30 new associations. Considering the large sample sizes and genome-wide SNP coverage of the scans, one might have expected many of the common variants underpinning the genetic component of various disorders to have been identified by now. However, these studies have not evaluated the contribution of other forms of genetic variation, such as structural variation, mainly in the form of copy number variants (CNVs). Known CNVs account for over 15% of the assembled human genome sequence. Since CNVs are not easily tagged by SNPs, might have a wide range of copy number variability, and often fall in genomic regions not well covered by whole-genome arrays or not genotyped by the HapMap project, current GWASs have largely missed the contribution of CNVs to complex disorders. In fact, some CNVs have already been reported to show association with several complex disorders using candidate gene/region approaches, underpinning the importance of regions not investigated in current GWASs. This reveals the need for new generation arrays (some already in the market) and the use of tailored approaches to explore the full dimension of genome variability beyond the single nucleotide scale.

Power Of Altruism Confirmed In Wikipedia Contributions:

The beauty of open-source applications is that they are continually improved and updated by those who use them and care about them. Dartmouth researchers looked at the online encyclopedia Wikipedia to determine if the anonymous, infrequent contributors, the Good Samaritans, are as reliable as the people who update constantly and have a reputation to maintain.

X-effect: Female Chromosome Confirmed A Prime Driver Of Speciation:

Researchers at the University of Rochester believe they have just confirmed a controversial theory of evolution. The X chromosome is a strikingly powerful force in the origin of new species.

Accessory Protein Determines Whether Pheromones Are Detected:

Pheromones are like the molecules you taste as you chomp on a greasy french fry: big and fatty. In research to be published in Nature*, Rockefeller University researchers reveal an unanticipated role for a new CD36-like protein to help cells detect these invisible communication signals that drive a wide range of behaviors, from recognizing a sibling to courting a mate, a finding that may explain what pheromone communication, pathogen recognition and fat taste perception all have in common.

Women More Likely Than Men To Be Affected By Acne As Adults:

While acne is oftentimes as much a part of being a teenager as dating and Friday night football games, a new study examining the prevalence of acne in adults age 20 and older confirms that a significant proportion of adults continue to be plagued by acne well beyond the teenage years. In particular, women experience acne at higher rates than their male counterparts across all age groups 20 years and older.

Sex Hormone Signature Indicates Gender Rather Than Just Chromosomes:

Help with assigning gender could one day be at hand for intersex individuals whose genital phenotypes and sex chromosomes don’t match, thanks to the discovery of a stable sex hormone signature in our cells.

How Singing Bats Communicate:

Bats are the most vocal mammals other than humans, and understanding how they communicate during their nocturnal outings could lead to better treatments for human speech disorders, say researchers at Texas A&M University.

Anne-Marie has more on this story.

Feeling Sleepy Is All In Your Genes:

Genes responsible for our 24 hour body clock influence not only the timing of sleep, but also appear to be central to the actual restorative process of sleep, according to research published in BMC Neuroscience. The study identified changes in the brain that lead to the increased desire and need for sleep during time spent awake.

Cringe at the title. Someone please send me the paper itself…
Level Of Oxytocin In Pregnant Women Predicts Mother-child Bond:

Humans are hard-wired to form enduring bonds with others. One of the primary bonds across the mammalian species is the mother-infant bond. Evolutionarily speaking, it is in a mother’s best interest to foster the well-being of her child; however, some mothers just seem a bit more maternal than others do. Now, new research points to a hormone that predicts the level of bonding between mother and child.

Kate already covered this study expertly.
Modafinil Is Effective In Treating Excessive Sleepiness, Study Suggests:

A study published in the October 15 issue of the Journal of Clinical Sleep Medicine finds that modafinil is well-tolerated in the treatment of excessive sleepiness associated with disorders of sleep and wakefulness such as shift work sleep disorder, obstructive sleep apnea (OSA) and narcolepsy, and does not affect cardiovascular or sleep parameters.

Feminism And Romance Go Hand In Hand:

Contrary to popular opinion, feminism and romance are not incompatible and feminism may actually improve the quality of heterosexual relationships, according to Laurie Rudman and Julie Phelan, from Rutgers University in the US. Their study* also shows that unflattering feminist stereotypes, that tend to stigmatize feminists as unattractive and sexually unappealing, are unsupported.

Pathway Required For Normal Reproductive Development Identified:

Massachusetts General Hospital (MGH) clinical researchers, in collaboration with basic scientists from the University of California, Irvine (UC Irvine) have identified a new molecular pathway required for normal development of the reproductive, olfactory and circadian systems in both humans and mice. In their report to appear in the Proceedings of the National Academy of Sciences, the team describes defects in a gene called PROK2 (prokineticin 2) in human siblings with two different forms of infertility. The UC Irvine team had previously reported that mice lacking PROK2 had abnormal olfactory structures and disrupted circadian rhythm.

I’d like to read this paper as well, please….

Dawn Of Animal Vision Discovered:

By peering deep into evolutionary history, scientists at the University of California, Santa Barbara have discovered the origins of photosensitivity in animals. The scientists studied the aquatic animal Hydra, a member of Cnidaria, which are animals that have existed for hundreds of millions of years. The authors are the first scientists to look at light-receptive genes in cnidarians, an ancient class of animals that includes corals, jellyfish, and sea anemones.

Ecologists Discover City Is ‘Uber-forest’ For Big Owls:

Charlotte has a spooky secret: the North Carolina city is home to a robust population of very large barred owls — a species long-believed by ornithologists to require old growth forest for survival. According to ecologists doing the most extensive field study ever done on the species, the owls see urban life as an upgrade on the old woods, and Charlotteans are not at all creeped out by the big birds that share their yards.

Endangered Wild Ox Given Lifeline:

Twenty years after its discovery in the forested mountains of Vietnam, local authorities here have agreed to establish new nature reserves to protect a critically endangered wild ox.

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