Non-enzymatic recombination of RNA: Ligation in loops

Background

While the RNA world hypothesis is widely accepted, it is still far from complete: the existence of self-replicating ribozyme, consisting of potentially hundreds of nucleotides, is a core assumption for the majority of RNA world models. The appearance of such long RNA molecules under prebiotic conditions is not self-evident. Recombination seems to be a plausible way of creating RNA diversity, resulting in the appearance of functional RNAs, capable of self-replicating.

Prediction of Severe Disease in Children with Diarrhea in a Resource-Limited Setting

Objective

To investigate the accuracy of three clinical scales for predicting severe disease (severe dehydration or death) in children with diarrhea in a resource-limited setting.

Methods

Participants included 178 children admitted to three Rwandan hospitals with diarrhea. A local physician or nurse assessed each child on arrival using the World Health Organization (WHO) severe dehydration scale and the Centers for Disease Control (CDC) scale. Children were weighed on arrival and daily until they achieved a stable weight, with a 10% increase between admission weight and stable weight considered severe dehydration. The Clinical Dehydration Scale was then constructed post-hoc using the data collected for the other two scales. Receiver Operator Characteristic (ROC) curves were constructed for each scale compared to the composite outcome of severe dehydration or death.

Results

The WHO severe dehydration scale, CDC scale, and Clinical Dehydration Scale had areas under the ROC curves (AUCs) of 0.72 (95% CI 0.60, 0.85), 0.73 (95% CI 0.62, 0.84), and 0.80 (95% CI 0.71, 0.89), respectively, in the full cohort. Only the Clinical Dehydration Scale was a significant predictor of severe disease when used in infants, with an AUC of 0.77 (95% CI 0.61, 0.93), and when used by nurses, with an AUC of 0.78 (95% CI 0.63, 0.93).

Conclusions

While all three scales were moderate predictors of severe disease in children with diarrhea, scale accuracy varied based on provider training and age of the child. Future research should focus on developing or validating clinical tools that can be used accurately by nurses and other less-skilled providers to assess all children with diarrhea in resource-limited settings.     

Photoperiodic Control of Developmental Diapause in Nymphs of Prostriate Ixodid Ticks (Acari: Ixodidae)

Extrinsic control of developmental diapause in nymphs of prostriate ticks of the subgenus Ixodes sensu stricto (Ixodes ricinus and Ixodes persulcatus from Eurasia and Ixodes scapularis from North America) appears to be based on a complex two-step photoperiodic reaction of a short-day/long-day type. Diapause control in the subgenus Afrixodes (the South African tick Ixodes rubicundus) appears to be based on a simple long-day reaction. The option between non-diapause development and diapausing arrest in engorged nymphs is determined by both pre- and post-feeding photoperiodic regimes. Consequently diapausing arrest in engorged nymphs of Ixodes sensu stricto can be induced either by a short-day (after their engorgement) or by a long-day regime (in unfed nymphs), while active, non-diapause development is possible only when the short-day pre-feeding regime is followed by a long-day post-feeding regime. The photoperiodic response in I. (Afrixodes) rubicundus nymphs seems to be of the long-day type both before and after feeding. Consequently this non-diapause development is enabled by a long-day regime, while diapause is induced by a short-day regime of exposure. Nevertheless, there are some indications that the control of nymphal diapause in the latter species is also of a complex nature. This revised version was published online in July 2006 with corrections to the Cover Date.     

Atomistic simulation approach to a continuum description of self-assembled beta-sheet filaments

We investigated the supramolecular structure and continuum mechanical properties of a beta-sheet nanofiber comprised of a self-assembling peptide ac-[RARADADA]2-am using computer simulations. The supramolecular structure was determined by constructing candidate filaments with dimensions compatible with those observed in atomic force microscopy and selecting the most stable ones after running molecular dynamics simulations on each of them. Four structures with different backbone hydrogen-bonding patterns were identified to be similarly stable. We then quantified the continuum mechanical properties of these identified structures by running three independent simulations: thermal motion analysis, normal mode analysis, and steered molecular dynamics. Within the range of deformations investigated, the filament showed linear elasticity in transverse directions with an estimated persistence length of 1.2-4.8 microm. Although side-chain interactions govern the propensity and energetics of filament self-assembly, we found that backbone hydrogen-bonding interactions are the primary determinant of filament elasticity, as demonstrated by its effective thickness, which is smaller than that estimated by atomic force microscopy or from the molecular geometry, as well as by the similar bending stiffness of a model filament without charged side chains. The generality of our approach suggests that it should be applicable to developing continuum elastic ribbon models of other beta-sheet filaments and amyloid fibrils.     

The role of cometary particle Coalescence in chemical evolution

Important prebiotic organic compounds might have been transported to Earth in dust or produced in vapor clouds resulting from atmospheric explosions or impacts of comets. These compounds coalesced in the upper atmosphere with particles ejected from craters formed by impacts of large objects. Coalescence during exposure to UV radiation concentrated organic monomers and enhanced formation of oligomers. Continuing coalescence added material to the growing particles and shielded prebiotic compounds from prolonged UV radiation. These particles settled into the lower atmosphere where they were scavenged by rain. Aqueous chemistry and evaporation of raindrops containing nomomers in high temperature regions near the Earth's surface also promoted continued formation of oligomers. Finally, these oligomers were deposited in the oceans where continued prebiotic evolution led to the most primitive cell. Results of our studies suggest that prebiotic chemical evolution may be an inevitable consequence of impacting comets during the late accretion of planets anywhere in the universe if oceans remained on those planetary surfaces.     

Developmental morphology of branching flowers in Nymphaea prolifera

Nymphaea and Nuphar (Nymphaeaceae) share an extra-axillary mode of floral inception in the shoot apical meristem (SAM). Some leaf sites along the ontogenetic spiral are occupied by floral primordia lacking a subtending bract. This pattern of flower initiation in leaf sites is repeated inside branching flowers of Nymphaea prolifera (Central and South America). Instead of fertile flowers this species usually produces sterile tuberiferous flowers that act as vegetative propagules. N. prolifera changes the meristem identity from reproductive to vegetative or vice versa repeatedly. Each branching flower first produces some perianth-like leaves, then it switches back to the vegetative meristem identity of the SAM with the formation of foliage leaves and another set of branching flowers. This process is repeated up to three times giving rise to more than 100 vegetative propagules. The developmental morphology of the branching flowers of N. prolifera is described using both microtome sections and scanning electron microscopy.     

The South Hesse Oak Project (SHOP): Species- and site-specific efficiency of the photosynthetic apparatus of Mediterranean and Central European Oaks

In three experimental sites in Southern Hesse, differing in management procedures, one- to three-year-old saplings of Quercus robur, Q.pubescens, and Q.ilex were planted to study their performance under Central European climate conditions. Toward the end of the growth period (mid–late September 2011), during a very dry period, we measured JIP transients of photosystem II chlorophyll fluorescence induction curves to evaluate the effects of abiotic site factors on the photosynthetic apparatus by comparing them to data from well-watered saplings measured before the onset of senescence processes. In all three sites, Q. robur saplings in September showed the strongest deviation from the measurements in August, followed by Q. pubescens. Q. ilex, in general, was nearly unaffected by September climate conditions or performed better than plants measured in August. Differences in the behavior between species and sites could be explained by the species’ different drought susceptibility and by differential induction of early leaf senescence (in Q. robur and Q. pubescens). We conclude that measurement of the JIP transient is a feasible method in forestry to compare adverse microclimatic site effects and genetically fixed reactions of the photosynthetic apparatus in the field.     

Improved de novo peptide sequencing using LC retention time information

Background

Liquid chromatography combined with tandem mass spectrometry is an important tool in proteomics for peptide identification. Liquid chromatography temporally separates the peptides in a sample. The peptides that elute one after another are analyzed via tandem mass spectrometry by measuring the mass-to-charge ratio of a peptide and its fragments. De novo peptide sequencing is the problem of reconstructing the amino acid sequences of a peptide from this measurement data. Past de novo sequencing algorithms solely consider the mass spectrum of the fragments for reconstructing a sequence.

Results

We propose to additionally exploit the information obtained from liquid chromatography. We study the problem of computing a sequence that is not only in accordance with the experimental mass spectrum, but also with the chromatographic retention time. We consider three models for predicting the retention time and develop algorithms for de novo sequencing for each model.

Conclusions

Based on an evaluation for two prediction models on experimental data from synthesized peptides we conclude that the identification rates are improved by exploiting the chromatographic information. In our evaluation, we compare our algorithms using the retention time information with algorithms using the same scoring model, but not the retention time.

     

Non-territorial nightingales prospect territories during the dawn chorus

Male songbirds usually sing when they have occupied a territory, but the territory prospecting of non-territorial males is more elusive and has been rarely studied. Here, we simulated newly arriving, non-territorial males by translocating unmated male nightingales (Luscinia megarhynchos) to our study site. We show that territory prospecting of translocated males was largely confined to the hour before sunrise. The radio-tagged males made extensive excursions visiting several singing males at dawn, but after dawn they remained stationary outside occupied territories. As in many other songbird species, dawn was also the time when resident males sang the most. These results suggest that nonterritorial male nightingales use the dawn chorus to assess singing residents or territory occupancy. For resident males, dawn singing may be important to announce territory occupancy to prospecting males and may thus play a role in territory maintenance.