G2, G3, and complete basis set calculations of the thermodynamic properties of cis- and trans-triazene

Following our recent study on triazane, we present a follow-up study on the thermodynamic properties of triazane’s unsaturated analog, triazene. We predict optimized structural parameters, vibrational frequencies, enthalpies of formation, enthalpies of combustion, specific enthalpies of combustion, and proton affinities. Our results indicate that the cis form of triazene has a specific enthalpy of combustion of −15.2 kJ g⁻¹ and the trans form has a specific enthalpy of combustion of −14.7 kJ g⁻¹. Figure Structures of cis- and trans-triazane, N₃H₃     

Quantitative structure-activity relationships and the prediction of MHC supermotifs

The underlying assumption in quantitative structure-activity relationship (QSAR) methodology is that related chemical structures exhibit related biological activities. We review here two QSAR methods in terms of their applicability for human MHC supermotif definition. Supermotifs are motifs that characterise binding to more than one allele. Supermotif definition is the initial in silico step of epitope-based vaccine design. The first QSAR method we review here--the additive method--is based on the assumption that the binding affinity of a peptide depends on contributions from both amino acids and the interactions between them. The second method is a 3D-QSAR method: comparative molecular similarity indices analysis (CoMSIA). Both methods were applied to 771 peptides binding to 9 HLA alleles. Five of the alleles (A*0201, A*0202, A*0203, A*0206 and A*6802) belong to the HLA-A2 superfamily and the other four (A*0301, A*1101, A*3101 and A*6801) to the HLA-A3 superfamily. For each superfamily, supermotifs defined by the two QSAR methods agree closely and are supported by many experimental data.     

RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure

RNA–LIM is a procedure that can analyze various pseudo-potentials describing the affinity between single-stranded RNA (ssRNA) ribonucleotides and surface amino acids to produce a coarse-grained estimate of the structure of the ssRNA at the protein interface. The search algorithm works by evolving an ssRNA chain, of known sequence, as a series of walks between fixed sites on a protein surface. Optimal routes are found by application of a set of minimal “limiting” restraints derived jointly from (i) selective sampling of the ribonucleotide amino acid affinity pseudo-potential data, (ii) limited surface path exploration by prior determination of surface arc lengths, and (iii) RNA structural specification obtained from a statistical potential gathered from a library of experimentally determined ssRNA structures. We describe the general approach using a NAST (Nucleic Acid Simulation Tool)-like approximation of the ssRNA chain and a generalized pseudo-potential reflecting the location of nucleic acid binding residues. Minimum and maximum performance indicators of the methodology are established using both synthetic data, for which the pseudo-potential defining nucleic acid binding affinity is systematically degraded, and a representative real case, where the RNA binding sites are predicted by the amplified antisense RNA (aaRNA) method. Some potential uses and extensions of the routine are discussed. RNA–LIM analysis programs along with detailed instructions for their use are available on request from the authors.     

A phenetic study of the taxonomic delimitation of Quercus acutifolia and Q. conspersa (Fagaceae)

A phenetic study ofQuercus acutifolia andQ. conspersa (Fagaceae) is carried out. The study was based on morphological characters, and included cluster analysis and principal component analysis. The results revealed that the characters employed so far to separateQuercus acutifolia andQ. conspersa seem to be quite unreliable. Nevertheless, both species can still be recognized as taxonomically different entities, although mostly based on characters of leaf margins. We propose that the individuals that have leaves with dentate-aristate margins correspond toQ. acutifolia, whereas those that have leaves with entire and not dentate-aristate margins belong toQ. conspersa.     

Spatial distribution of fifty ornamental fish species on coral reefs in the Red Sea and Gulf of Aden

The spatial distribution of 50 ornamental fish species from shallow water habitats on coral reefs were investigated using visual census techniques, between latitudes 11−29°N in the Red Sea, in Jordan, Egypt, Saudi Arabia, and Yemen, and in the adjacent Gulf of Aden in Djibouti. One hundred eighteen transects (each 100×5 m) were examined in 29 sites (3−8 sites per country). A total of 522,523 fish individuals were counted during this survey, with mean abundance of 4428.2 ± 87.26 individual per 500 m² transect. In terms of relative abundance (RA), the most abundant species were Blue green damselfish, Chromis viridis (RA=54.4%),followed bySea goldie, Pseudanthias squamipinnis (RA= 34.7), Whitetail dascyllus, Dascyllus aruanus (RA= 2.6%), Marginate dascyllus, Dascyllus marginatus (RA= 2.0),Red Sea eightline flasher Paracheilinus octotaenia (RA=1.0),andKlunzinger’s wrasse, Thalassoma rueppellii (0.7%). The highest number of species (S) per 500 m² transect was found on reefs at the latitude 20° in Saudi Arabia (S=21.8), and the lowest number of species was found at the latitude 15° in Djibouti (S=11.11). The highest mean abundance (8565.8) was found on reefs at latitude 20° in Saudi Arabia and the lowest mean abundance (230) was found on reefs at latitude 22°, also in Saudi Arabia. Whereas, the highest Shannon-Wiener Diversity Index was found in reefs at the latitude 22° (H`=2.4) and the lowest was found in reefs at the latitude 20° (H`=0.6). This study revealed marked differences in the structure of ornamental fish assemblages with latitudinal distribution. The data support the presence of two major biogeographic groups of fishes in the Red Sea and Gulf of Aden: the southern Red Sea and Gulf of Aden group and the group in the northern and central Red Sea. Strong correlations were found between live coral cover and the number of fish species, abundance and Shannon-Wiener Diversity indices, and the strength of these correlations varied among the reefs. A conclusion was done that environmental differences among the reefs and the habitats investigated were important components of abundance variations and species diversity of ornamental fish along latitudinal gradients in the Red Sea and the Gulf of Aden.     

Analysis of ancient human genomes

High‐capacity sequencing technologies have dramatically reduced both the cost and time required to generate complete human genome sequences. Besides expanding our knowledge about existing diversity, the nature of these technologies makes it possible to extend knowledge in yet another dimension: time. Recently, the complete genome sequence of a 4,000‐year‐old human from the Saqqaq culture of Greenland was determined to 20‐fold coverage. These data make it possible to investigate the population affinities of this enigmatic culture and, by identifying several phenotypic traits of this individual, provide a limited glimpse into how these people may have looked. While undoubtedly a milestone in ancient DNA research, the cost to generate an ancient genome, even from such an exceptionally preserved specimen, remains out of reach for most. Nonetheless, recently developed DNA capture methods, already applied to Neanderthal and fossil human mitochondrial DNA, may soon make large‐scale genome‐wide analysis of ancient human diversity a reality, providing a fresh look at human population history.     

Autoradiographic Visualization of Kappa Opioid Receptors with Labelled Dynorphins in Guinea Pig Brain

Abstract

The distribution of kappa opioid receptors in guinea pig brain was measured by in vitro receptor autoradiography using [³H]dynorphin A_1–9, [³H]dynorphin A_1–8 and [³H]bremazocine as ligands. The sites labelled by the two dynorphins had identical, heterogeneous distributions in brain sections. High levels of kappa receptors were seen in striatum, claustrum, nucleus accumbens and laminae V and VI of the cerebral cortex. The substantia nigra and superior colliculus also had high dynorphin binding levels. The [³H]dynorphin autoradiographs were closely similar to those obtained using [³H]bremazocine in the presence of mu and delta receptor displacers. It is concluded that tritiated dynorphin A fragments can be used for autoradiographic studies of kappa opioid receptors in brain.     

BREEDING OF THE INDIAN WHITEBACKED VULTURE AT JODHPUR

Vulture populations have declined globally as well as regionally within Africa. Little is known about the status of the African White-backed Vulture Gyps africanus in Kenya, but ongoing studies indicate that its population has declined over the last two decades. A total of 32 African White-backed Vulture nests were monitored in the Masai Mara National Reserve over a five-year period between 2003 and 2007. Mean nesting success was 59%, which is comparable to that of populations from southern Africa. Nearest neighbour distances were significantly closer in wooded habitats (‘trees and shrubs savanna’) than in more open grassland habitats (‘open low shrubs’). Based on nearest neighbour distances, the estimated total breeding population within the Masai Mara National Reserve is 1 106 pairs, a figure that may be an overestimate and requires ground-truthing. Collecting baseline data on numbers of breeding pairs and regular nest monitoring are essential in order to assess the impact of various threats to vultures in Kenya, which include growing threats (elephant-mediated habitat disturbance and fire) as well as emerging threats (such as poisoning with the carbamate-based pesticide Furadan?).     

Composition Patterns of Caribbean Limestone Forests: Are Parsimony,Classification, and Ordination Analyses Congruent?1

This study presents an analysis of floristic composition patterns for limestone vegetation from three Caribbean islands: Hispaniola, Mona, and Puerto Rico. The physical setting of these communities varies from very dry to wet climates, and from ridgetops, slopes, to plateaus. Consequently, vegetation communities have variable species composition. The questions addressed were: (1) What are the patterns of species composition among limestone vegetation types based on a parsimony analysis of species assemblages (PASA) and how congruent are they widi geography, climate, topography, and vegetation physiognomy? and (2) How do PASA patterns compare to floristic patterns obtained with a classification (UPGMA) and an ordination (NMS)? The main distinction of floristic categories was between communities of humid and dry climates, followed by a finer separation of communities congruent with topography; vegetation physiognomy corresponded with both. PASA, UPGMA, and NMS produced highly coincident floristic groups; however, affinities among groups were different. Advantages of PASA over UPGMA and NMS are that PASA produces groupings strictly based on the shared species and provides different measures of support for floristic groups. The three techniques indicated that the humid and dry limestone areas of Puerto Rico had floristically divergent dry‐type vegetation, even when they were structurally and physiognomically convergent. Also, floristic affinities of dry communities in Puerto Rico were stronger with dry communities on other islands than to more humid communities on the same island; thus, humidity regime is stronger than geography in promoting floristic links among limestone vegetation communities of die Caribbean. Almost every conclusion obtained from UPGMA and NMS was also taken from PASA, and so all diree techniques are compatible. The methodological, theoretical, and interpretive simplicity of PASA is what makes it an attractive procedure for studies that examine composition patterns.