RNA2D3D: A program for Generating,Viewing, and Comparing 3-Dimensional Models of RNA

Abstract

Using primary and secondary structure information of an RNA molecule, the program RNA2D3D automatically and rapidly produces a first-order approximation of a 3-dimensional conformation consistent with this information. Applicable to structures of arbitrary branching complexity and pseudoknot content, it features efficient interactive graphical editing for the removal of any overlaps introduced by the initial generating procedure and for making conformational changes favorable to targeted features and subsequent refinement. With emphasis on fast exploration of alternative 3D conformations, one may interactively add or delete base-pairs, adjacent stems can be coaxially stacked or unstacked, single strands can be shaped to accommodate special constraints, and arbitrary subsets can be defined and manipulated as rigid bodies. Compaction, whereby base stacking within stems is optimally extended into connecting single strands, is also available as a means of strategically making the structures more compact and revealing folding motifs. Subsequent refinement of the first-order approximation, of modifications, and for the imposing of tertiary constraints is assisted with standard energy refinement techniques. Previously determined coordinates for any part of the molecule are readily incorporated, and any part of the modeled structure can be output as a PDB or XYZ file. Illustrative applications in the areas of ribozymes, viral kissing loops, viral internal ribosome entry sites, and nanobiology are presented.     

Circaseptan Rhythms of Semen Characteristics of a Brazilian Breed (“Mangalarga”) Stallion

We describe the semen characteristics of a 21-year old “mangalarga” stallion living under natural temperature and photoperiod conditions in São José do Rio Pardo, São Paulo, Brazil (latitude 21°36' S; longitude 46°53' W). The horse fed on natural pasture and a nutritionally balanced feed twice a day (11:00 and 17:00 h). Water and a mineral supplement were available “ad libitum”. Semen was collected for over 36 months (Oct 89-Dec 92) almost daily between 08:00 and 10:00 h by an artificial vagina and evaluated for volume of ejaculate, spermatozoa motility and concentration by standard procedures. Analysis of data from a total of 128-days was performed according to the Fast Fourier Transform Technique (FFT). Statistically significant periods of 7-day were demonstrated for volume, motility, and spermatozoa concentration. Circaseptan rhythms and, particularly, the circannual rhythm (already described in a previous publication) are probably related to ecological diversity and reproductive strategies.     

Generic delimitation of Gochnatia,Richterago and Ianthopappus (Compositae-Mutisieae) based on pollen morphology

Pollen grains of 20 taxa from Gochnatia , Ianthopappus , and Richterago (Compositae - Mutisieae) have been studied. Pollen morphological characters and intergeneric differences are described. Pollen of grains of Richterago and Ianthopappus are relatively larger with thickened exine in the mesocolpia and possess coarse, supratectal spinuliferous processes the height of which is less than their diameter at the base. In Gochnatia , the pollen is medium-sized, the exine is not thickened in the mesocolpia and has minute supratectal spinuliferous processes the height of which is equal or slightly more than 3 w m. Ianthopappus corymbosus is the only species in which the infratectum is thicker than the tectum. With reference to the pollen size and the exine thickness this species appears phylogenetically closer to Richterago than to Gochnatia .     

Transect for aerobiological studies from Antarctica to Poland

While returning from the 13th Polish Scientific Expedition to Antarctica, one of the authors (M.O.) collected airborne biological samples along the transect from the South Shetland Islands to Gdynia on the Baltic Seacoast of Poland. The journey aboard the Polish ship ORP “Heweliusz”, lasted from 4 March until 13 April 1990. During this period, two samples a day, exposed 12 h each, were collected in Petri dishes. The authors made preliminary identifications of plant and animal fragments in the samples. The most important finding was the presence of propagules of lichens (fragments of thallus, isidia soredia) in all samples. The relatively small number of pollen grains in samples could be accounted for by the season of collection when few pollen grains are airborne.     

Effects of dopaminergic system activation on feeding behavior and growth performance of the sea bass (Dicentrarchus labrax): A self-feeding approach

Dopamine is synthesized from l-dopa and subsequently processed into norepinephrine and epinephrine. Any excess neurotransmitter can be taken up again by the neurons to be broken down enzymatically into DOPAC. The effect of dopamine on mammalian food intake is controversial. Mice unable to synthesize central dopamine die of starvation. However, studies have also shown that central injection of dopamine inhibits food intake. The effect of dopaminergic system in the fish feeding behavior has been scarcely explored. We report that the inclusion of l-dopa in the diets results in the activation of sea bass central dopaminergic system but also in the significant increase of the hypothalamic serotonin levels. Dietary l-dopa induces a decrease of food intake and feed conversion efficiency that drives a decline of all growth parameters tested. No behavioral effects were observed after l-dopa treatment. l-dopa treatment stimulated central expression of NPY and CRF. It suggests that CRF might mediate l-dopa effects on food intake but also that CRF neurons lie downstream of NPY neurons in the hierarchical forebrain system, thus controlling energy balance. Unexpectedly, dietary administration of haloperidol, a D₂-receptor antagonist, cannot block dopamine effects but also induces a decline of the food intake. This decrease seems to be a side effect of haloperidol treatment since fish exhibited a decreased locomotor activity. We conclude that oral l-dopa inhibits sea bass food intake and growth. Mechanism could also involve an increase of hypothalamic serotoninergic tone.