Yearly Archives: 2007

Big Fossil ‘Raptor’ Tracks Show Group Behavior:

Everyone knows that “raptor” dinosaurs walked with their deadly sickle-shaped foot claws held off the ground and that they moved in packs … right? After all, it was in “Jurassic Park.” But until now, there was no direct evidence of either of these things. Now, an international team of Chinese, British, American and Japanese paleontologists reported fossilized footprints made by two different kinds of “raptors” from 120 million year old rocks in Shandong Province, China.

Resistance To Thoughts Of Chocolate Is Futile:

A research project carried out by a University of Hertfordshire academic has found that thought suppression can lead people to engage in the very behaviour they are trying to avoid. It also found that men who think about chocolate end up eating more of it than women who have the same thoughts.

Primates: Extinction Threat Growing For Mankind’s Closest Living Relatives:

Mankind’s closest living relatives — the world’s apes, monkeys, lemurs and other primates — are under unprecedented threat from destruction of tropical forests, illegal wildlife trade and commercial bushmeat hunting, with 29 percent of all species in danger of going extinct, according to a new report.

Why Do Autumn Leaves Turn Red? Soil May Dictate Fall Colors:

Soils may dictate the array of fall colors as much as the trees rooted in them, according to a forest survey out of North Carolina.

Social Standing Influences Elephant Movement:

When resources are scarce, who you know and where you’re positioned on the social totem pole affects how far you’ll go to search for food. At least that’s the case with African elephants, according to a study led by ecologists at the University of California, Berkeley, who collaborated with researchers at Save the Elephants, a non-profit research organization based in Kenya, and at the University of Oxford in England.

Longest Living Animal? Clam — 400 Years Old — Found In Icelandic Waters:

A clam dredged from Icelandic waters had lived for 400 years – is this the longest-lived animal known to science?

World’s Hottest Chile Pepper Discovered:

Researchers at New Mexico State University recently discovered the world’s hottest chile pepper. Bhut Jolokia, a variety of chile pepper originating in Assam, India, has earned Guiness World Records’ recognition as the world’s hottest chile pepper by blasting past the previous champion Red Savina.

Decoding Effects Of Toxins On Embryo Development Apparent:

Changes in gene expression patterns in zebrafish embryos resulting from exposure to environmental toxins can identify the individual toxins at work, according to research published in the online open access journal Genome Biology. The genetic response of zebrafish to each toxin can be read like a barcode, offering researchers a potential method for identifying the effects of the toxin on developing vertebrate embryos.

‘Nervous’ Birds Take More Risks:

Scientists have shown that birds with higher stress levels adopt bolder behaviour than their normally more relaxed peers in stressful situations. A University of Exeter research team studied zebra finches, which had been selectively bred to produce three distinct types — ‘laid-back’, ‘normal’ and ‘stressed’ — based on their levels of stress hormone. The group was surprised to find that the ‘stressed’ birds were bolder and took more risks in a new environment than the group that was usually more laid-back.

Same-sex Attraction Is Genetically Wired In Nematode’s Brain:

University of Utah biologists genetically manipulated nematode worms so the animals were attracted to worms of the same sex — part of a study that shows sexual orientation is wired in the creatures’ brains.

Secrets Behind Butterfly Wing Patterns Uncovered:

The genes that make a fruit fly’s eyes red also produce red wing patterns in the Heliconius butterfly found in South and Central America, finds a new study by a UC Irvine entomologist.

Ancient DNA Reveals That Some Neanderthals Were Redheads:

Ancient DNA retrieved from the bones of two Neanderthals suggests that at least some of them had red hair and pale skin, scientists report in the journal Science. The international team says that Neanderthals’ pigmentation may even have been as varied as that of modern humans, and that at least 1 percent of Neanderthals were likely redheads.

Colorful View For First Land Animals:

When prehistoric fish made their first forays onto land, what did they see? According to a study published in the online open access journal, BMC Evolutionary Biology, it’s likely that creatures venturing out of the depths viewed their new environment in full colour.

Endangered Wandering Albatross Catches Prey Differently Than Previously Thought:

An international team of scientists has overturned an ecological study on how some animals search for food. Previously it was believed that wandering albatrosses and other species forage using a Lévy flight strategy – a cluster of short moves connected by infrequent longer ones. Published this week in the journal Nature, the team discovered that further analyses and new data tell a different story for the albatrosses and possibly for other species too.

Age Increases Chance Of Success As Two-timer For Coal Tit Males:

Older coal tit males conceive significantly more offspring with a ‘bit’ on the side than younger ones. The coal tit appears to live a strictly monogamous life. Couples often stay together for their whole lives. But researchers found out that’s only a façade. This indigenous songbird is among the top ten two-timers worldwide.

Not ‘Junk DNA’ After All: Tiny RNAs Play Big Role Controlling Genes:

A study by researchers at the Yale Stem Cell Center for the first time demonstrates that piRNAs, a recently discovered class of tiny RNAs, play an important role in controlling gene function.

As always on Fridays, there are new papers published in PLoS Genetics, PLoS Pathogens and PLoS Computational Biology. A few picks – but you go and check them all out:
Surveillance of Arthropod Vector-Borne Infectious Diseases Using Remote Sensing Techniques: A Review:

Kalluri et al. review the status of remote sensing studies of arthropod vectorborne diseases, including simple image classification techniques associating land use and land cover types with vector habitats, and more complex statistical models linking satellite-derived multi-temporal meteorological observations with vector biology and abundance.

Contrasting Infection Strategies in Generalist and Specialist Wasp Parasitoids of Drosophila melanogaster:

The authors use two kinds of wasp venom to compare the benefits and drawbacks of relatively immune suppressive versus relatively immune evasive parasite infection strategies in a natural system.

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

Xavier Estivill and Lluís Armengol explore the contribution of copy number variants to common human disorders and evaluate the caveats of SNP-based genome-wide association scans in covering regions of the genome that could play an important role in disease susceptibility.

Ten Simple Rules for Doing Your Best Research, According to Hamming:

The thoughts of mathematician Richard Hamming on ‘How to do great science’, presented at the Bell Communications Research Colloquium Seminar in 1986, serve as a preface to the Ten Simple Rules series.

Getting Started in Tiling Microarray Analysis:

In the first article of the new “Getting Started In…” series from the ISCB and PLoS Computational Biology, Dr. Xiaole Shirley Liu introduces tiling microarray analysis. The series provides an essential introductory aid for students and researchers aiming to start out in different areas of bioinformatics, computational biology, and genomics.

Via Russlings (here, here and here so far), information about the effects of San Diego wildfires on the San Diego Zoo:
San Diego zoo ordered closed, Wild Animal park in immediate danger
Fire Update from the Panda Station from a blog by a zoo researcher, and Fire Update from the Wild Animal Park from the Zoo public relations person.
Finally, the oft-updated fire page of the San Diego Zoo blog: October 2007 Fire Updates
Apparently, the zoo was quite threatened, but survived OK and will re-open soon after a big clean-up. Some of the employees were affected by the wildfire, though, and some animals are sheltered indoors during the fire.

Travelling delayed me a little bit, but as you already learned to expect by now, new articles get published on PLoS ONE on Tuesday afternoons. Before I showcase the papers I personally find interesting, first let me remind you to join in the discussion on our ongoing Journal Club on the article Parts, Wholes, and Context in Reading: A Triple Dissociation: read, rate, annotate, comment, blog about and send trackbacks if your software supports them. Now, to this week’s wealth of papers – 24 appeared this week and here are those I like the best:
Analysis of the Trajectory of Drosophila melanogaster in a Circular Open Field Arena:

Studying the neural mechanisms of behavior often requires researchers to accurately follow the movement of a free-living organism over extended periods of time. In this study, Valente and colleagues use a video tracking system to record and describe the behavior and interaction of a single fly walking in an open arena. The methods used in this study may prove valuable for other similar behavioral studies.

Mast Fruiting Is a Frequent Strategy in Woody Species of Eastern South America:

The synchronized production of large seed crops in the tropics is thought to be extremely rare. These authors developed a model for the variability of seed production of 20 climbing vine species and 28 tree species in a Central French Guianan tropical rainforest over a five-year period. Their results reveal that almost a quarter of the species studied showed patterns of synchronized mass seed production, suggesting that the process may encourage species coexistence.

Growth Environment and Sex Differences in Lipids, Body Shape and Diabetes Risk:

This paper reports a cross-sectional study that aims to investigate whether the place of birth and early life environment is associated with ischaemic heart disease (IHD), diabetes and obesity risks in men and women. The results show that differences in early life environment affect IHD risk in men and women differently. Such dichotomies may explain the trends and sex differences in IHD that are seen with economic development.

Different Transcript Patterns in Response to Specialist and Generalist Herbivores in the Wild Arabidopsis Relative Boechera divaricarpa:

Plants defend themselves against herbivorous insects, utilizing both constitutive and inducible defenses. Induced defenses are controlled by several phytohormone-mediated signaling pathways. Here, we analyze transcriptional changes in the North American Arabidopsis relative Boechera divaricarpa in response to larval herbivory by the crucifer specialist lepidopteran Plutella xylostella (diamondback moth) and by the generalist lepidopteran Trichoplusia ni (cabbage semilooper), and compare them to wounding and exogenous phytohormone application.
We use a custom macroarray constructed from B. divaricarpa herbivory-regulated cDNAs identified by suppression subtractive hybridization and from known stress-responsive A. thaliana genes for transcript profiling after insect herbivory, wounding and in response to jasmonate, salicylate and ethylene. In addition, we introduce path analysis as a novel approach to analyze transcript profiles. Path analyses reveal that transcriptional responses to the crucifer specialist P. xylostella are primarily determined by direct effects of the ethylene and salicylate pathways, whereas responses to the generalist T. ni are influenced by the ethylene and jasmonate pathways. Wound-induced transcriptional changes are influenced by all three pathways, with jasmonate having the strongest effect.
Our results show that insect herbivory is distinct from simple mechanical plant damage, and that different lepidopteran herbivores elicit different transcriptional responses.

Horizontal Gene Transfer Regulation in Bacteria as a “Spandrel” of DNA Repair Mechanisms:

Horizontal gene transfer (HGT) is recognized as the major force for bacterial genome evolution. Yet, numerous questions remain about the transferred genes, their function, quantity and frequency. The extent to which genetic transformation by exogenous DNA has occurred over evolutionary time was initially addressed by an in silico approach using the complete genome sequence of the Ralstonia solanacearum GMI1000 strain. Methods based on phylogenetic reconstruction of prokaryote homologous genes families detected 151 genes (13.3%) of foreign origin in the R. solanacearum genome and tentatively identified their bacterial origin. These putative transfers were analyzed in comparison to experimental transformation tests involving 18 different genomic DNA positions in the genome as sites for homologous or homeologous recombination. Significant transformation frequency differences were observed among these positions tested regardless of the overall genomic divergence of the R. solanacearum strains tested as recipients. The genomic positions containing the putative exogenous DNA were not systematically transformed at the highest frequencies. The two genomic “hot spots”, which contain recA and mutS genes, exhibited transformation frequencies from 2 to more than 4 orders of magnitude higher than positions associated with other genes depending on the recipient strain. These results support the notion that the bacterial cell is equipped with active mechanisms to modulate acquisition of new DNA in different genomic positions. Bio-informatics study correlated recombination “hot-spots” to the presence of Chi-like signature sequences with which recombination might be preferentially initiated. The fundamental role of HGT is certainly not limited to the critical impact that the very rare foreign genes acquired mainly by chance can have on the bacterial adaptation potential. The frequency to which HGT with homologous and homeologous DNA happens in the environment might have led the bacteria to hijack DNA repair mechanisms in order to generate genetic diversity without losing too much genomic stability.

Illusory Stimuli Can Be Used to Identify Retinal Blind Spots:

Identification of visual field loss in people with retinal disease is not straightforward as people with eye disease are frequently unaware of substantial deficits in their visual field, as a consequence of perceptual completion (“filling-in”) of affected areas. We attempted to induce a compelling visual illusion known as the induced twinkle after-effect (TwAE) in eight patients with retinal scotomas. Half of these patients experience filling-in of their scotomas such that they are unaware of the presence of their scotoma, and conventional campimetric techniques can not be used to identify their vision loss. The region of the TwAE was compared to microperimetry maps of the retinal lesion. Six of our eight participants experienced the TwAE. This effect occurred in three of the four people who filled-in their scotoma. The boundary of the TwAE showed good agreement with the boundary of lesion, as determined by microperimetry. For the first time, we have determined vision loss by asking patients to report the presence of an illusory percept in blind areas, rather than the absence of a real stimulus. This illusory technique is quick, accurate and not subject to the effects of filling-in.

Ancestral Inference and the Study of Codon Bias Evolution: Implications for Molecular Evolutionary Analyses of the Drosophila melanogaster Subgroup:

Reliable inference of ancestral sequences can be critical to identifying both patterns and causes of molecular evolution. Robustness of ancestral inference is often assumed among closely related species, but tests of this assumption have been limited. Here, we examine the performance of inference methods for data simulated under scenarios of codon bias evolution within the Drosophila melanogaster subgroup. Genome sequence data for multiple, closely related species within this subgroup make it an important system for studying molecular evolutionary genetics. The effects of asymmetric and lineage-specific substitution rates (i.e., varying levels of codon usage bias and departures from equilibrium) on the reliability of ancestral codon usage was investigated. Maximum parsimony inference, which has been widely employed in analyses of Drosophila codon bias evolution, was compared to an approach that attempts to account for uncertainty in ancestral inference by weighting ancestral reconstructions by their posterior probabilities. The latter approach employs maximum likelihood estimation of rate and base composition parameters. For equilibrium and most non-equilibrium scenarios that were investigated, the probabilistic method appears to generate reliable ancestral codon bias inferences for molecular evolutionary studies within the D. melanogaster subgroup. These reconstructions are more reliable than parsimony inference, especially when codon usage is strongly skewed. However, inference biases are considerable for both methods under particular departures from stationarity (i.e., when adaptive evolution is prevalent). Reliability of inference can be sensitive to branch lengths, asymmetry in substitution rates, and the locations and nature of lineage-specific processes within a gene tree. Inference reliability, even among closely related species, can be strongly affected by (potentially unknown) patterns of molecular evolution in lineages ancestral to those of interest.

A New Method to Extract Dental Pulp DNA: Application to Universal Detection of Bacteria:

Dental pulp is used for PCR-based detection of DNA derived from host and bacteremic microorganims. Current protocols require odontology expertise for proper recovery of the dental pulp. Dental pulp specimen exposed to laboratory environment yields contaminants detected using universal 16S rDNA-based detection of bacteria.
We developed a new protocol by encasing decontaminated tooth into sterile resin, extracting DNA into the dental pulp chamber itself and decontaminating PCR reagents by filtration and double restriction enzyme digestion. Application to 16S rDNA-based detection of bacteria in 144 teeth collected in 86 healthy people yielded a unique sequence in only 14 teeth (9.7%) from 12 individuals (14%). Each individual yielded a unique 16S rDNA sequence in 1-2 teeth per individual. Negative controls remained negative. Bacterial identifications were all confirmed by amplification and sequencing of specific rpoB sequence.
The new protocol prevented laboratory contamination of the dental pulp. It allowed the detection of bacteria responsible for dental pulp colonization from blood and periodontal tissue. Only 10% such samples contained 16S rDNA. It provides a new tool for the retrospective diagnostic of bacteremia by allowing the universal detection of bacterial DNA in animal and human, contemporary or ancient tooth. It could be further applied to identification of host DNA in forensic medicine and anthropology.

St. Bernard Study Shows Human-directed Evolution At Work:

The St Bernard dog – named after the 11th century priest Bernard of Menthon – is living proof that evolution does occur, say scientists. Biologists at The University of Manchester say that changes to the shape of the breed’s head over the years can only be explained through human-directed evolution through selective breeding, an artificial version of natural selection.

Humans And Monkeys Share Machiavellian Intelligence:

When it comes to their social behavior, people sometimes act like monkeys, or more specifically, like rhesus macaques, a type of monkey that shares with humans strong tendencies for nepotism and political maneuvering, according to research by Dario Maestripieri, an expert on primate behavior and an Associate Professor in Comparative Human Development and Evolutionary Biology at the University of Chicago.

Critically Endangered Amur Leopard Captured:

A rare Amur leopard (Panthera pardus orientalis), one of only an estimated 30 left in the wild has been captured and health-checked by experts from a consortium of conservation organizations, before being released.

New Light Trap Captures Larval Stage Of New Species; DNA Barcode Technology Used:

When David Jones, a fisheries oceanographer at the Cooperative Institute for Marine and Atmospheric Studies (CIMAS) located at the University of Miami’s Rosenstiel School, set out to design a better light trap to collect young reef fishes, he never imagined his invention would contribute to the discovery of a new species. But, after finding a goby that didn’t quite fit any known description, his catch turned out to be the answer to another scientist’s twenty-five-year-old research conundrum. The larval stage captured in Jones’s new trap was matched to the adult form of a previously unknown species of reef fish by new DNA barcoding technology — which confirmed both were members of a new species.