Evaluation of annotation strategies using an entire genome sequence

MOTIVATION: Genome-wide functional annotation either by manual or automatic means has raised considerable concerns regarding the accuracy of assignments and the reproducibility of methodologies. In addition, a performance evaluation of automated systems that attempt to tackle sequence analyses rapidly and reproducibly is generally missing. In order to quantify the accuracy and reproducibility of function assignments on a genome-wide scale, we have re-annotated the entire genome sequence of Chlamydia trachomatis (serovar D), in a collaborative manner. RESULTS: We have encoded all annotations in a structured format to allow further comparison and data exchange and have used a scale that records the different levels of potential annotation errors according to their propensity to propagate in the database due to transitive function assignments. We conclude that genome annotation may entail a considerable amount of errors, ranging from simple typographical errors to complex sequence analysis problems. The most surprising result of this comparative study is that automatic systems might perform as well as the teams of experts annotating genome sequences.     

Quantification of Superoxide Radical in the Brain of Rats with Experimentally Induced Obstructive Jaundice

The study aimed to directly measure in vivo superoxide radical (O₂⁻) a direct indicator of oxidative stress, in the brain of rats with experimentally induced obstructive jaundice by employing a new quantitative ultrasensitive fluorescent assay requiring minimum sample. O₂⁻ anion is specific for dihydroethidine (DHE) and upon reaction gives a characteristic product, namely 2-OH-ethidium. Ten male rats underwent laparotomy and were divided into two groups: I, sham operated and II bile duct ligation. Ten days later, following injection with DHE (a O₂⁻ trap), all animals were killed and samples from cerebral cortex, midbrain and cerebellum were removed for analysis. It was shown that compared to group I, in group II the O₂⁻ was increased by 67% in the cerebral cortex and by 37% in the midbrain as a consequence of experimental obstructive jaundice, while its levels were unaffected in the cerebellum. The data in this experimental obstructive jaundice model imply a region-specific increase of O₂⁻ formation rate, being higher in cerebral cortex, less so in the midbrain and not at all in cerebellum.     

The effects of laurel (Laurus nobilis L.) on development of two mycorrhizal fungi

Hundreds of aromatic plant species are growing naturally around Mediterranean. Plant essential oils are incorporated in aromatic plant material and follow the litter fall. During litter degradation, the presence of essential oils can affect soil microorganisms. Mycorrhizal fungi have never been investigated so far under the presence of volatile oils. The aim of this study was to explore the effect of aromatic Laurus nobilis L. on development of two mycorrhizal species Glomus deserticola and Glomus intraradices. The response of fungi colonization and host growth were monitored under different concentrations of L. nobilis leaves and essential oil. The major compounds of L. nobilis essential oil were 1,8-cineole (49.6%), sabinene (7.8%), ??-pinene (6.0%), eugenole (5.6%), ??-terpinyl acetate (5.2%) and ??-pinene (5.1%). Both mycorrhizal fungi colonized successfully the host plants whose growth was positively influenced by mycorrhizal fungi. G. deserticola presented higher infection level than G. intraradices. The addition of L. nobilis leaves in the soil resulted in mycorrhiza inhibition. The level of inhibition was positively correlated with the added amount of aromatic leaves in the soil. The essential oil presented a little higher inhibition than the leaves. The presence of this aromatic plant in many different ecosystems could contribute in mycorrhiza inhibition and it is suggested, when it’s possible, reduction of laurel litter before reforestation programs.     

How can ontologies help vector biology?

The reach of genomics has now extended to vector biology, with three mosquito genomes already sequenced and more arthropod vector genomes in the pipeline. The availability of these genomes has paved the way for high-throughput investigations on genome-wide gene expression and proteomics in vector biology. Such investigations would not have been possible without parallel progress in bioinformatics. It is now necessary to construct specific ontologies that will enable vector biologists to achieve computer-comprehensible annotation of genes and genomes, but also of various experimental, clinical and surveillance data. This will inevitably lead to the enhanced usage of such controlled vocabularies, and to an effort to develop novel ontologies, particularly in the context of disease control.     

Expression of water-soluble, ligand-binding concatameric extracellular domains of the human neuronal nicotinic receptor alpha4 and beta2 subunits in the yeast Pichia pastoris: glycosylation is not required for ligand binding

Nicotinic acetylcholine receptors (nAChRs) are ligand-gated cation channels that are responsible for cell communication via the neurotransmitter acetylcholine. The predominant nAChR subtype in the mammalian brain with a high affinity for nicotine is composed of α4 and β2 subunits. This nAChR subtype is responsible for addiction to nicotine and is thought to be implicated in Alzheimer and Parkinson diseases and therefore presents an important target for drug design. In an effort to obtain water-soluble, ligand-binding domains of the human α4β2 nAChR for structural studies, we expressed the extracellular domains (ECDs) of these subunits in the eukaryotic expression system Pichia pastoris. The wild-type ECDs and their mutants containing the more hydrophilic Cys-loop from the snail acetylcholine-binding protein (individually expressed or coexpressed) did not demonstrate any specific interaction with ligands. We then linked the mutated ECDs with the 24-amino acid peptide (AGS)(8) and observed that the β2-24-α4 ECD concatamer, but not the α4-24-β2 one, exhibited very satisfactory water solubility and ligand binding properties. The (125)I-epibatidine and [(3)H]nicotine bound to β2-24-α4 with dissociation constants (K(d)) of 0.38 and 19 nm, respectively, close to the published values for the intact α4β2 AChR. In addition, (125)I-epibatidine binding was blocked by nicotine, cytisine, acetylcholine, and carbamylcholine with inhibition constants (K(i)) of 20.64, 3.24, 242, and 2,254 nm, respectively. Interestingly, deglycosylation of the concatamer did not affect its ligand binding properties. Furthermore, the deglycosylated β2-24-α4 ECD existed mainly in monomeric form, thus forming an appropriate material for structural studies and possibly for pharmacological evaluation of novel α4β2 nAChR-specific agonists.     

Coumarin derivatives protection against ROS production in cellular models of Abeta toxicities

The role of oxidative stress and free radicals in the development of Alzheimer's disease (AD) has been the focus of many recent studies. The role of hydrogen peroxide (H(2)O(2)) in AD is thought to be associated with Abeta (amyloid - beta) damage in cells. A number of coumarin derivatives were previously found to be potent anti-inflammatory and antioxidant agents. Herein, these coumarin derivatives were tested as H(2)O(2) scavengers with the DCF assay using two types of neuronal cells: (a) wild type (N2a) neuroblastoma cells and (b) APP/PS1 transgenic cell line expressing Abeta. Their scavenging activity was varied between the types of cell cultures and it was found to be concentration and time dependent in the mutant cells. Their protective role against cell death further supports this notion. These results suggest that these compounds could be used as a template in the design of new molecules with a possible role in AD.     

Does Observation of Postural Imbalance Induce a Postural Reaction?

Background

Several studies bring evidence that action observation elicits contagious responses during social interactions. However automatic imitative tendencies are generally inhibited and it remains unclear in which conditions mere action observation triggers motor behaviours. In this study, we addressed the question of contagious postural responses when observing human imbalance.

Methodology/Principal Findings

We recorded participants'' body sway while they observed a fixation cross (control condition), an upright point-light display of a gymnast balancing on a rope, and the same point-light display presented upside down. Our results showed that, when the upright stimulus was displayed prior to the inverted one, centre of pressure area and antero-posterior path length were significantly greater in the upright condition compared to the control and upside down conditions.

Conclusions/Significance

These results demonstrate a contagious postural reaction suggesting a partial inefficiency of inhibitory processes. Further, kinematic information was sufficient to trigger this reaction. The difference recorded between the upright and upside down conditions indicates that the contagion effect was dependent on the integration of gravity constraints by body kinematics. Interestingly, the postural response was sensitive to habituation, and seemed to disappear when the observer was previously shown an inverted display. The motor contagion recorded here is consistent with previous work showing vegetative output during observation of an effortful movement and could indicate that lower level control facilitates contagion effects.