Author Archives: Bora Zivkovic

Let’s see what is new in PLoS Pathogens, PLoS Genetics, PLoS Computational Biology and PLoS Neglected Tropical Diseases:
A new installment in the “Ten Simple Rules” series: Ten Simple Rules for Graduate Students

Choosing to go to graduate school is a major life decision. Whether you have already made that decision or are about to, now it is time to consider how best to be a successful graduate student. Here are some thoughts from someone who holds these memories fresh in her mind (JG) and from someone who has had a whole career to reflect back on the decisions made in graduate school, both good and bad (PEB). These thoughts taken together, from former student and mentor, represent experiences spanning some 25 or more years. For ease, these experiences are presented as ten simple rules, in approximate order of priority as defined by a number of graduate students we have consulted here in the US; but we hope the rules are more globally applicable, even though length, method of evaluation, and institutional structure of graduate education varies widely. These rules are intended as a companion to earlier editorials covering other areas of professional development.

Computational Biology in Cuba: An Opportunity to Promote Science in a Developing Country:

Computational biology can be considered a supradisciplinary field of knowledge that merges biology, chemistry, physics, and computer science into a broad-based science that is important to furthering our understanding of the life sciences. Although a relatively new area of research, it is recognized as a crucial field for scientific advancement in developing countries. This Perspective introduces our vision of the role of computational biology in biomedical research and teaching in Cuba. Except where individuals are directly quoted, any opinions expressed herein should be considered those of the authors.

Fortunately, nobody from PLoS will have to go prison for publishing research originating in Cuba.
Measuring the Burden of Neglected Tropical Diseases: The Global Burden of Disease Framework:

Governments and international agencies are faced with setting priorities for health research and investment in health systems and health interventions in a context of increasing health care costs, increasing availability of effective interventions, and numerous and diverse priorities and interest groups. Evidence on the magnitude and trends of diseases and their causes should be a critical input to decision making at the global, national, and local levels. Broad evaluation of the effectiveness of health systems and major health programs and policies also requires assessments of the causes of loss of health that are comparable not only across populations, but also over time.

Lessons from “Lower” Organisms: What Worms, Flies, and Zebrafish Can Teach Us about Human Energy Metabolism:

A pandemic of metabolic diseases (atherosclerosis, diabetes mellitus, and obesity), unleashed by multiple social and economic factors beyond the control of most individuals, threatens to diminish human life span for the first time in the modern era. Given the redundancy and inherent complexity of processes regulating the uptake, transport, catabolism, and synthesis of nutrients, magic bullets to target these diseases will be hard to find. Recent studies using the worm Caenorhabditis elegans, the fly Drosophila melanogaster, and the zebrafish Danio rerio indicate that these “lower” metazoans possess unique attributes that should help in identifying, investigating, and even validating new pharmaceutical targets for these diseases. We summarize findings in these organisms that shed light on highly conserved pathways of energy homeostasis.

Ocean Fertilization ‘Fix’ For Global Warming Discredited By New Research:

Scientists have revealed an important discovery that raises doubts concerning the viability of plans to fertilize the ocean to solve global warming, a projected $100 billion venture.

Separating The Therapeutic Benefits Of Cannabis From Its Mood-altering Side-effects:

Scientists from Queen Mary, University of London, have discovered a new way to separate the therapeutic benefits of cannabis from its mood-altering side-effects.

Human Genome Has Four Times More Imprinted Genes Than Previously Identified:

Scientists at Duke University have created the first map of imprinted genes throughout the human genome, and they say a modern-day Rosetta stone — a form of artificial intelligence called machine learning — was the key to their success. The study revealed four times as many imprinted genes as had been previously identified.

More Than One-quarter Of US Bird Species Imperiled, Report States:

One hundred seventy-eight species in the continental U.S. and 39 in Hawaii have the dubious distinction of landing on the newest and most scientifically sound list of America’s most imperiled birds. WatchList 2007, a joint effort of Audubon and American Bird Conservancy, reflects a comprehensive analysis of population size and trends, distribution, and threats for 700 bird species in the U.S. It reveals those in greatest need of immediate conservation help simply to survive amid a convergence of environmental challenges, including habitat loss, invasive species and global warming.

Endangered Brazilian Ocelot Kitten Born: Birth Significant For Species:

An endangered Brazilian ocelot kitten was born at the Louisville Zoo Sept. 23. This was the first offspring for mom Miguela and second for father Itirapua.

Gene Study Supports Single Main Migration Across Bering Strait:

Did a relatively small number of people from Siberia who trekked across a Bering Strait land bridge some 12,000 years ago give rise to the native peoples of North and South America?

Greg Laden and Jake Young comment.
Dogs Can Classify Complex Photos In Categories Like Humans Do:

Like us, our canine friends are able to form abstract concepts. Friederike Range and colleagues from the University of Vienna in Austria have shown for the first time that dogs can classify complex color photographs and place them into categories in the same way that humans do. And the dogs successfully demonstrate their learning through the use of computer automated touch-screens, eliminating potential human influence.

Using Beetle Biology To Protect Beehives:

A new way to lessen damage from small hive beetles in honey bee colonies has been developed by Agricultural Research Service (ARS) scientists in Gainesville, Fla. Small hive beetles (Aethina tumida) began appearing in U.S. hives during the past 15 to 20 years and now infest bee colonies throughout the East.

Stopping for Deer: Sensing, Movement And Behavior Illuminated:

Driving down a country road at night your car’s headlights illuminate a deer in your path, and the creature doesn’t move. Depending on your speed and other conditions, chances are good you will hit the deer. And if you do, it’s because you are in what is fittingly defined as the “collision mode,” according to a Northwestern University study.

There are 35 brand new papers on PLoS ONE tonight and it is difficult for me to pick the most exciting for the week. So, here is one on the effects of night-shift, one on melanopsin and light perception, one on time perception, one on limb regeneration in the Axolotl, a meta-analysis of the soil ecology literature and, a first for PLoS ONE, an article by a prominent philosopher of science that I expect to be discussed on blogs over the next few days:
Acute Sleep Deprivation and Circadian Misalignment Associated with Transition onto the First Night of Work Impairs Visual Selective Attention:

Overnight operations pose a challenge because our circadian biology promotes sleepiness and dissipates wakefulness at night. Since the circadian effect on cognitive functions magnifies with increasing sleep pressure, cognitive deficits associated with night work are likely to be most acute with extended wakefulness, such as during the transition from a day shift to night shift. To test this hypothesis we measured selective attention (with visual search), vigilance (with Psychomotor Vigilance Task [PVT]) and alertness (with a visual analog scale) in a shift work simulation protocol, which included four day shifts followed by three night shifts. There was a nocturnal decline in cognitive processes, some of which were most pronounced on the first night shift. The nighttime decrease in visual search sensitivity was most pronounced on the first night compared with subsequent nights (p = .04), and this was accompanied by a trend towards selective attention becoming ‘fast and sloppy’. The nighttime increase in attentional lapses on the PVT was significantly greater on the first night compared to subsequent nights (p<.05) indicating an impaired ability to sustain focus. The nighttime decrease in subjective alertness was also greatest on the first night compared with subsequent nights (p<.05). These nocturnal deficits in attention and alertness offer some insight into why occupational errors, accidents, and injuries are pronounced during night work compared to day work. Examination of the nighttime vulnerabilities underlying the deployment of attention can be informative for the design of optimal work schedules and the implementation of effective countermeasures for performance deficits during night work.

Brain Responses to Violet, Blue, and Green Monochromatic Light Exposures in Humans: Prominent Role of Blue Light and the Brainstem:

Melanopsin is a pigment that responds to light and is found in specialised light sensitive cells of the retina. In this paper, Maquet and colleagues investigated the spectral sensitivity of immediate brain responses to light by measuring brain activity in participants exposed to different wavelengths. Their results reveal that short exposures to light induce changes in brain activity and that the melanopsin system provides the most important contribution to these changes.

The Effect of Predictability on Subjective Duration:

Events can sometimes appear longer or shorter in duration than other events of equal length. For example, in a repeated presentation of auditory or visual stimuli, an unexpected object of equivalent duration appears to last longer. Illusions of duration distortion beg an important question of time representation: when durations dilate or contract, does time in general slow down or speed up during that moment? In other words, what entailments do duration distortions have with respect to other timing judgments? We here show that when a sound or visual flicker is presented in conjunction with an unexpected visual stimulus, neither the pitch of the sound nor the frequency of the flicker is affected by the apparent duration dilation. This demonstrates that subjective time in general is not slowed; instead, duration judgments can be manipulated with no concurrent impact on other temporal judgments. Like spatial vision, time perception appears to be underpinned by a collaboration of separate neural mechanisms that usually work in concert but are separable. We further show that the duration dilation of an unexpected stimulus is not enhanced by increasing its saliency, suggesting that the effect is more closely related to prediction violation than enhanced attention. Finally, duration distortions induced by violations of progressive number sequences implicate the involvement of high-level predictability, suggesting the involvement of areas higher than primary visual cortex. We suggest that duration distortions can be understood in terms of repetition suppression, in which neural responses to repeated stimuli are diminished.

Transforming Growth Factor: β Signaling Is Essential for Limb Regeneration in Axolotls:

The axolotl limb has been widely studied in developmental biology because of its unusual ability to regenerate following injury. In this study, the authors investigated the role of the transforming growth factor-beta (TGF-β) family members in axolotl limb regeneration. Their results show that the inhibition of TGF-β stopped the redevelopment process, thus suggesting that TGF-β is essential in limb regeneration.

A Tale of Four Stories: Soil Ecology, Theory, Evolution and the Publication System:

Soil ecology has produced a huge corpus of results on relations between soil organisms, ecosystem processes controlled by these organisms and links between belowground and aboveground processes. However, some soil scientists think that soil ecology is short of modelling and evolutionary approaches and has developed too independently from general ecology. We have tested quantitatively these hypotheses through a bibliographic study (about 23000 articles) comparing soil ecology journals, generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. We have shown that soil ecology is not well represented in generalist ecology journals and that soil ecologists poorly use modelling and evolutionary approaches. Moreover, the articles published by a typical soil ecology journal (Soil Biology and Biochemistry) are cited by and cite low percentages of articles published in generalist ecology journals, evolutionary ecology journals and theoretical ecology journals. This confirms our hypotheses and suggests that soil ecology would benefit from an effort towards modelling and evolutionary approaches. This effort should promote the building of a general conceptual framework for soil ecology and bridges between soil ecology and general ecology. We give some historical reasons for the parsimonious use of modelling and evolutionary approaches by soil ecologists. We finally suggest that a publication system that classifies journals according to their Impact Factors and their level of generality is probably inadequate to integrate “particularity” (empirical observations) and “generality” (general theories), which is the goal of all natural sciences. Such a system might also be particularly detrimental to the development of a science such as ecology that is intrinsically multidisciplinary.

Beyond the Gene by Evelyn Fox Keller and David Harel:

This paper is a response to the increasing difficulty biologists find in agreeing upon a definition of the gene, and indeed, the increasing disarray in which that concept finds itself. After briefly reviewing these problems, we propose an alternative to both the concept and the word gene–an alternative that, like the gene, is intended to capture the essence of inheritance, but which is both richer and more expressive. It is also clearer in its separation of what the organism statically is (what it tangibly inherits) and what it dynamically does (its functionality and behavior). Our proposal of a genetic functor, or genitor, is a sweeping extension of the classical genotype/phenotype paradigm, yet it appears to be faithful to the findings of contemporary biology, encompassing many of the recently emerging–and surprisingly complex–links between structure and functionality.

Bear Hunting Altered Genetics More Than Ice Age Isolation:

It was not the isolation of the Ice Age that determined the genetic distribution of bears, as has long been thought. This is shown by an international research team led from Uppsala University in Sweden in the latest issue of Molecular Ecology. One possible interpretation is that the hunting of bears by humans and human land use have been crucial factors.

Mediterranean Sea: Most Dangerous Place On Earth For Sharks And Rays:

The first complete IUCN Red List assessment of the status of all Mediterranean sharks and rays has revealed that 42% of the species are threatened with extinction. Overfishing, including bycatch (non-target species caught incidentally), is the main cause of decline, according to the research.

Nicotine May Enhance Attention And Working Memory In Recovering Alcoholics:

Detoxified alcoholics in the early stages of recovery tend to have impaired cognitive functioning. Many alcoholics also smoke, and nicotine is known to have enhancing effects on attentional processes. New findings indicate that nicotine patches can enhance cognitive function among newly recovering alcoholics with a history of smoking.

Facial Expressions Have Greater Impact On Kids With Bipolar Disorder:

Children with bipolar disorder respond differently to facial expressions than children without psychiatric disorders, according to a new study led by a Bradley Hospital researcher. These findings provide additional insight into the neurobiology of pediatric bipolar disorder.

Why Age Doesn’t Matter For Motherhood:

The assumption that those born to mothers outside the optimum age for reproduction are disadvantaged has been challenged by scientists at the University of Exeter. Their research found that mothers adjust their pre and post-natal care to compensate for any health problems their babies might face as a result of them being below or above the best age to give birth.

Ripening Secrets Of The Vine Revealed:

Whether you prefer a Cabernet Sauvignon or a Pinot Noir grape variety, two new research articles offer a host of new genetic information on fruit ripening for this economically important fruit crop.

Environmental Researchers Propose Radical ‘Human-centric’ Map Of The World:

Ecologists pay too much attention to increasingly rare “pristine” ecosystems while ignoring the overwhelming influence of humans on the environment, say researchers from McGill University and the University of Maryland, Baltimore County (UMBC).

Are Current Projections Of Climate Change Impacts On Biodiversity Misleading?:

Are patterns of current climate sufficient to explain and predict the diversity of life? This is the urgent question arising from the study “Quaternary climate changes explain diversity among reptiles and amphibians,” published in the journal Ecography. The new theory proposes that historical climate patterns are of strong importance to diversity prediction.

Yup, it’s Monday evening:
Light Activates Output from Evening Neurons and Inhibits Output from Morning Neurons in the Drosophila Circadian Clock:

Living organisms have evolved circadian clocks that anticipate daily changes in their environment. Their clockwork is fully endogenous, but can be reset by external cues. (Light is the most efficient cue.) The circadian neuronal network of the fruit fly (Drosophila) brain perceives light through the visual system and a dedicated photoreceptor molecule, cryptochrome. Flies exhibit a bimodal locomotor activity pattern that peaks at dawn and dusk in light-dark conditions. These morning and evening activity bouts are controlled by two distinct neuronal clocks in the fly brain. By using flies with a deficient cryptochrome pathway, we have uncovered an unexpected role for light in the circadian system. In addition to synchronizing the two oscillators to solar time, light also controls their behavioral output. The morning oscillator can periodically rouse the fly when in constant darkness, but not in constant light, whereas the evening oscillator can do the same in constant light, but not in constant darkness. This suggests the existence of a light-dependent switch between oscillators that appears to require the visual system. Such a mechanism likely contributes to better separate the active periods of the fly at dawn and dusk, and may help the animal to adapt to seasonal changes in day length.

How Can We Draw the Line between Clinical Care and Medical Research:

A Policy Forum published in this month’s PLoS Medicine highlights an issue that the PLoS Medicine editors have often debated: when research takes place within the context of clinical care, how can we distinguish which activities constitute care, and which research? The World Medical Association Code of Medical Ethics declares that a physician must always “act in the patient’s best interest when providing medical care” [1]. Yet increasingly physicians also undertake research, which involves possibly unknown risks and benefits. These risks, and the uncertainty of benefit, might therefore conflict with a patient’s best interests.

Bioclocks Work By Controlling Chromosome Coiling:

There is a new twist on the question of how biological clocks work. In recent years, scientists have discovered that biological clocks help organize a dizzying array of biochemical processes in the body. Despite a number of hypotheses, exactly how the microscopic pacemakers in every cell in the body exert such a widespread influence has remained a mystery.
Now, a new study provides direct evidence that biological clocks can influence the activity of a large number of different genes in an ingenious fashion, simply by causing chromosomes to coil more tightly during the day and to relax at night.

Is The Beauty Of A Sculpture In The Brain Of The Beholder?:

Is there an objective biological basis for the experience of beauty in art? Or is aesthetic experience entirely subjective? This question has been addressed in a new article by Cinzia Di Dio, Emiliano Macaluso and Giacomo Rizzolatti. The researchers used fMRI scans to study the neural activity in subjects with no knowledge of art criticism, who were shown images of Classical and Renaissance sculptures.

Carnivorous Plants Use Pitchers Of ‘Slimy Saliva’ To Catch Their Prey:

Carnivorous plants supplement the meager diet available from the nutrient-poor soils in which they grow by trapping and digesting insects and other small arthropods. Pitcher plants of the genus Nepenthes were thought to capture their prey with a simple passive trap but in a paper in PLoS One, Laurence Gaume and Yoel Forterre, a biologist and a physicist from the CNRS, working respectively in the University of Montpellier and the University of Marseille, France show that they employ slimy secretions to doom their victims.

Horses Disperse Alien Plants Along Recreational Trails:

Plant invasions are rapidly becoming a threat to wildlands. One of the ways these aliens are dispersed is through large mammals that forage and excrete seeds in new locations. A new study has found horses to be a source of dispersal along recreational trails in Colorado.

Polar Bears Threatened By Hunting Policy Favoring The Killing Of Male Bears:

Policies that encourage hunters to go after male polar bears in order to conserve females, could make it harder for the animals to find mates. University of Alberta researchers determined there is a critical threshold in the male-to-female ratio. Below it, their model predicts a sudden and rapid collapse in fertilization rates.

Giant Fossil Sea Scorpion Bigger Than Man:

The discovery of a giant fossilised claw from an ancient sea scorpion indicates that when alive it would have been about two and a half meters long, much taller than the average man.

Unraveling the Silky Spider Web:

Web-making spiders employ a host of silk glands to synthesize a variety of silk filaments with different mechanical properties. Although it is widely believed that the aciniform glands are one such silk factory, there has been no hard evidence linking aciniform-derived proteins and silk –until now.