Comparative analysis of hairpin ribozyme structures and interference data

Great strides in understanding the molecular underpinnings of RNA catalysis have been achieved with advances in RNA structure determination by NMR spectroscopy and X-ray crystallography. Despite these successes the functional relevance of a given structure can only be assessed upon comparison with biochemical studies performed on functioning RNA molecules. The hairpin ribozyme presents an excellent case study for such a comparison. The active site is comprised of two stems each with an internal loop that forms a series of non-canonical base pairs. These loops dock into each other to create an active site for catalysis. Recently, three independent structures have been determined for this catalytic RNA, including two NMR structures of the isolated loop A and loop B stems and a high-resolution crystal structure of both loops in a docked conformation. These structures differ significantly both in their tertiary fold and the nature of the non-canonical base pairs formed within each loop. Several of the chemical groups required to achieve a functioning hairpin ribozyme have been determined by nucleotide analog interference mapping (NAIM). Here we compare the three hairpin structures with previously published NAIM data to assess the convergence between the structural and functional data. While there is significant disparity between the interference data and the individual NMR loop structures, there is almost complete congruity with the X-ray structure. The only significant differences cluster around an occluded pocket adjacent to the scissile phosphate. These local differences may suggest a role for these atoms in the transition state, either directly in chemistry or via a local structural rearrangement.     

Lifetime reproductive output: individual stochasticity,variance, and sensitivity analysis

Lifetime reproductive output (LRO) determines per-generation growth rates, establishes criteria for population growth or decline, and is an important component of fitness. Empirical measurements of LRO reveal high variance among individuals. This variance may result from genuine heterogeneity in individual properties, or from individual stochasticity, the outcome of probabilistic demographic events during the life cycle. To evaluate the extent of individual stochasticity requires the calculation of the statistics of LRO from a demographic model. Mean LRO is routinely calculated (as the net reproductive rate), but the calculation of variances has only recently received attention. Here, we present a complete, exact, analytical, closed-form solution for all the moments of LRO, for age- and stage-classified populations. Previous studies have relied on simulation, iterative solutions, or closed-form analytical solutions that capture only part of the sources of variance. We also present the sensitivity and elasticity of all of the statistics of LRO to parameters defining survival, stage transitions, and (st)age-specific fertility. Selection can operate on variance in LRO only if the variance results from genetic heterogeneity. The potential opportunity for selection is quantified by Crow’s index \(\mathcal {I}\), the ratio of the variance to the square of the mean. But variance due to individual stochasticity is only an apparent opportunity for selection. In a comparison of a range of age-classified models for human populations, we find that proportional increases in mortality have very small effects on the mean and variance of LRO, but large positive effects on \(\mathcal {I}\). Proportional increases in fertility increase both the mean and variance of LRO, but reduce \(\mathcal {I}\). For a size-classified tree population, the elasticity of both mean and variance of LRO to stage-specific mortality are negative; the elasticities to stage-specific fertility are positive.     

Comparative analysis of the sensitivity of enterobacteria to bile

The analysis of the sensitivity of 195 enterobacterial cultures to bile revealed that their level of resistance decreased in the following row: Shigella > Salmonella > Klebsiella > Escherichia > Providencia. As shown on a sample of 136 E. coli isolates the level of resistance of these bacteria to bile depended on their isolation source: in E. coli isolated from bile in cholecystitis, from urine in pyelonephritis and from feces in intestinal dysbacteriosis resistance was 1.1-1.3 times higher than in E. coli isolated from the water of open reservoirs, from the feces of healthy persons and from extraintestinal foci of purulent inflammation. The level of sensitivity to bile is regarded as a property making it possible for enterobacteria to colonize biliary tracts and the proximal sections of the digestive tract.     

Comparative analysis of the human dystrophin and utrophin gene structures

We present analysis of intronic sequences in the human DMD and UTRN genes. In both genes accumulation of repeated elements could account for intron expansion. Out-of-frame rod-domain exons have stronger splice sites and are separated by significantly longer introns as compared to in-frame exons. These features are unique for the two homologs and not shared by other spectrin superfamily genes.     

Comparative study on ovarian structures in scorpaenids: possible evolutional process of reproductive mode

The reproductive modes of the Scorpaenidae are extremely varied: oviparity, viviparity, and even spawning of internally fertilized eggs or embryos (zygoparity or embryoparity), as in Helicolenus, are known. The ovarian structure of this family is divided into two types by the arrangement of the stroma and the ovarian cavity. One type is the ovary in which the lamella-like stroma develops from the ovarian hilus located on the dorsal side and where the ovarian cavity is located on the ventral side of ovary, classified as “cystovarian type II-1” by Takano (1989). In the other type, the stroma in the ovary develops radially around the blood circulatory system that traverses the center of the ovary, and then the ovarian cavity surrounds all the ovary, classified as “cystovarian type II-3” by Takano (1989). In the present analysis, previous reports about ovarian structure and the relationship to the reproductive mode of scorpaenids were described, and the ovarian structure of eight genera of Scorpaenidae was examined. The ovary of cystovarian type II-1 is seen only in viviparous genera and is not seen in oviparous genera. However, the cystovarian type II-1 is a general structure in other families of Scorpaeniformes, and this structure could be considered a primitive type of ovary rather than that acquired by the process of evolution from oviparity to viviparity. The ovary of cystovarian type II-3 is seen in all six oviparous genera and the one zygoparous genus examined. The ovary of this type is not found in any other family of teleosts, so it could be a structure originally divided in Scorpaenidae. In the genera having the cystovarian type II-3 ovary, there is a common feature of spawning: a floating egg mass encompassed by the gelatinous material. We postulate that the evolution of reproductive mode in the scorpaenid fishes is as follows: Sebastes and Sebastiscus have a primitive ovary in which viviparity has developed, whereas the genera that spawn a floating egg mass evolved the ovarian structure from primitive type to cystovarian type II-3, and further zygoparity, such as in Helicolenus, evolved from them.     

Comparative sequence analysis and patterns of covariation in RNA secondary structures

A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3' untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3' UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3' UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations.     

Comparative analysis of functions of cow and reindeer female reproductive organs: Progesterone content in vessels of reproductive organs

Progesterone content in blood from paired ovarian and uterine veins as well as from jugular veins of cows and reindeers was studied in the estrous cycle lutein phase and at the earlier stages of pregancy. In the both species, maximal progesterone concentration was detected in blood from vein of the ovary carrying corpus luteum (p < 0.001). In cows, a higher hormone concentration, as compared with jugular vein, has also been determined in vein of the uterus horn closest to ovary with corpus luteum (p < 0.01). In reindeers, blood from all studied vessels of reproductive organs had the progesterone concentration that was statistically significantly higher (p < 0.001) than that from jugular vein. In cows, progesterone concentration in blood from the ovarian vein was found to be higher when corpus luteum was located on the right ovary (p < 0.05) as compared with left-side corpus luteum location. No functional asymmetry of ovaries was revealed in reindeers. A possible role of mechanisms of the hormone local transport between ovary and uterus in adaptation of ruminants to reproduction under Nordic conditions is discussed.     

Comparative analysis of human reproductive proteomes identifies candidate proteins of sperm maturation

Male reproductive proteomes provide basis for studying gene products and its involvement or regulation in sperm physiology. Here, a comparative study between these proteomes was performed to find potential proteins and functions associated with human sperm maturation. Seven reproductive proteomes associated with human sperm physiology were integrated. Gene ontology analysis were performed using DAVID and Panther tools to determine enriched functions. Total of 270 proteins overlapped between epididymal, prostatic milieu and sperm proteome were thought to be candidate proteins involved in sperm maturation, and they showed enriched functions of proteasomal protein catabolic process and protein folding. 34 epididymal milieu proteins and 274 prostatic milieu proteins were contributed to the composition of seminal fluids proteome. Literatures have confirmed the involvements in sperm maturation of many of these proteins The spatial expressions of 24 epididymal milieu proteins involved in chaperone and antioxidant activity were authenticated by real-time RT-PCR. These proteins may serve as candidate molecules for future studies of sperm maturation and male infertility.     

Comparative analysis of the sequences and structures of HIV-1 and HIV-2 proteases

The different isolates available for HIV-1 and HIV-2 were compared for the region of the protease (PR) sequence, and the variations in amino acids were analyzed with respect to the crystal structure of HIV-1 PR with inhibitor. Based on the extensive homology (39 identical out of 99 residues), models were built of the HIV-2 PR complexed with two different aspartic protease inhibitors, acetylpepstatin and a renin inhibitor, H-261. Comparison of the HIV-1 PR crystal structure and the HIV-2 PR model structure and the analysis of the changes found in different isolates showed that correlated substitutions occur in the hydrophobic interior of the molecule and at surface residues involved in ionic or hydrogen bond interactions. The substrate binding residues of HIV-1 and HIV-2 PRs show conservative substitutions of four residues. The difference in affinity of HIV-1 and HIV-2 PRs for the two inhibitors appears to be due in part to the change of Val 32 in HIV-1 PR to Ile in HIV-2 PR.     

Coevolution of male and female reproductive structures in Drosophila

The morphology of male genitalia whilst stable within species, exhibits huge interspecific variation. This variation is likely to be as a result of sexual selection due to the direct involvement of these reproductive structures in mating and sperm transfer. In contrast, internal soft tissue components of the genitalia are generally poorly investigated as they are not directly involved in physical and mechanical adequacy during sperm transfer. However, these soft tissue structures may also drive differential male–female interactions, particularly in internally fertilising organisms where females have the ability to store sperm and bias male reproductive success. In this paper we use the drosophila model to investigate the role of male and female reproductive elements in sexual selection. Our meta-analysis supplemented with additional new data clearly shows that within species, sperm length versus testis length, and sperm length versus seminal receptacle length, are highly correlated. Thus, independent of the phylogenetic relationship among species, gamete evolution is likely to result in sexual selection interactions that drive the evolution of internal reproductive components in both sexes. Our results and discussion of the literature highlight the importance of considering internal soft structures that may influence fertilisation, when investigating selective forces acting on the evolution of reproductive traits.     

Comparative analysis of function of reproductive organs of cow and female reindeer. Cellular composition of blood in vessels of reproductive organs

Cellular composition of blood was studied in vessels of reproductive organs and jugular vein in females of reindeer and cow depending on their physiological state. Physiological leukocytosis was revealed in reproductive organs of the animals, the most expressed in reindeer. In both species, during the estrous cycle, in blood of vessels of reproductive organs the content of lymphocytes and monocytes is higher than that of granulocytes. With onset of pregnancy, in vessels of ovary and uterus in reindeer and cow the number of lymphocytes and monocytes decreases, while the number of granulocytes increases due to a rise of eosinophils and basophils. The more successful reproduction of reindeer females under conditions of North seems to be owing to an increased immune reactivity of reproductive organs.     

Comparative analysis of antibiotic sensitivity of Streptococcus pneumoniae strains isolated from patients and carriers

The data on antibiotic sensitivity of 38 strains of S. pneumoniae isolated from children and 46 strains isolated from carriers are presented. The isolates from the carriers had significantly higher sensitivity to benzylpenicillin, ampicillin, methicillin, oxacillin, cefazolin, erythromycin, oleandomycin and lincomycin. Resistance to gentamicin was more frequent in the strains isolated from the carriers. Among the strains of S. pneumoniae isolated from the patients and carriers representatives of serovar K19 were more frequent. There were no statistically reliable difference in them by sensitivity to benzylpenicillin, ampicillin, cefazolin, lincomycin and rifampicin. Still, the isolates from the carriers were much more sensitive to methicillin, oxacillin, oleandomycin and erythromycin.     

Comparative statics of joint reproductive allocation

We perform a perturbation analysis (comparative statics) of how optimal reproductive effort and per offspring investment are jointly affected by different selective factors. The factors considered are: (1) mortality sources, classified according to affected stage (juvenile or adult) and to its nature (avoidable or unavoidable), and (2) resource (energy) availability for the adult individual. The joint approach reveals both direct and indirect effects of each selective pressure. These interactive effects spring from the nonlinearity of reproductive expenditure, separated into a part devoted to endowing offspring (provisioning cost) and another part invested to make reproduction possible (requisite cost). The latter is envisioned as a reverse sigmoid function of fecundity (most models, so far, have considered only the first kind of cost). The indirect effects have the consequence of enlarging the class of selective pressures that can induce changes of offspring size and clutch size, as compared with current explanations. So, they illuminate new causes for some effects, and show new effects for some well-known selective causes. Several joint patterns in the two variables, shown by animals and plants in the field, can thus be given more appropriate interpretations than traditional, piecewise, ones.     

Effects of preservation method on stable carbon and nitrogen isotope values

Some methods of tissue preservation have significant effects on values of stable isotopes of carbon (delta(13)C) and nitrogen (delta(15)N), but studies on this topic are scattered in the literature. The goals of this study were to (1) summarize the results from studies of preservation effects in the literature and (2) test the effects of four common preservatives on delta(13)C and delta(15)N in epidermis tissue of three turtle species. Turtle tissue samples were subjected to up to five time intervals in five methods of preservation: drying at 60 degrees C for 24 h (the control), immersion in a 70% ethanol solution, immersion in a saturated NaCl aqueous solution, freezing at -10 degrees C in a frost-free freezer, and immersion in a dimethyl sulfoxide (DMSO)-ethylenediaminetetraacetic acid buffer. The delta(13)C and delta(15)N values for tissues preserved in 70% ethanol and NaCl aqueous solution were not significantly different from those of tissues dried at 60 degrees C, but samples preserved in DMSO were significantly different from dried samples. Freezing preservation had a significant effect on delta(13)C and delta(15)N at 60 d, which may have resulted from the use of a frost-free freezer. The effects of 20 different preservative methods on delta(13)C and delta(15)N in different tissues are summarized.     

Hyperthermic sensitivity and growth stage in Escherichia coli

Hyperthermic sensitivities of Escherichia coli B/r and Bs-1 were determined for lag-, midlog-, and stationary-phase cells at 47, 48, and 49 degrees C. In both strains midlog-phase cells were strikingly more heat sensitive (100-fold greater killing after 4 h at 48 degrees C) than stationary-phase cells, with intermediate sensitivity for lag-phase cells. In contrast to the reported difference in the radiation sensitivity between these two strains, very little difference in heat sensitivity was seen. Patterns of fatty acid composition of both strains were very similar at each phase of growth. From midlog to stationary phase, 16:1 and 18:1 unsaturated fatty acids decrease from 16 and 30% to 0.5 and 3%, respectively, while the C17 and C19 cyclopropane fatty acids increase from 7 and 3% to 22 and 25%, respectively. Concomitant with these changes in fatty acid composition, substantially higher membrane microviscosity values were recorded for stationary-phase cells. Total membrane microviscosity was positively associated with the C17 and C19 cyclopropane fatty acid composition and with cell survival following hyperthermia. In contrast to hyperthermic sensitivity, radiation survival differences between B/r and Bs-1 are little affected by growth stage. We propose that these results are consistent with a critical influence of membrane lipids on cellular hyperthermic sensitivity and further that the target sites for radiation and hyperthermia are different in these cells.     

Enhanced sensitivity of DNA- and rRNA-based stable isotope probing by fractionation and quantitative analysis of isopycnic centrifugation gradients

Stable isotope probing (SIP) of nucleic acids allows the detection and identification of active members of natural microbial populations that are involved in the assimilation of an isotopically labelled compound into nucleic acids. SIP is based on the separation of isotopically labelled DNA or rRNA by isopycnic density gradient centrifugation. We have developed a highly sensitive protocol for the detection of 'light' and 'heavy' nucleic acids in fractions of centrifugation gradients. It involves the fluorometric quantification of total DNA or rRNA, and the quantification of either 16S rRNA genes or 16S rRNA in gradient fractions by real-time PCR with domain-specific primers. Using this approach, we found that fully 13C-labelled DNA or rRNA of Methylobacterium extorquens was quantitatively resolved from unlabelled DNA or rRNA of Methanosarcina barkeri by cesium chloride or cesium trifluoroacetate density gradient centrifugation respectively. However, a constant low background of unspecific nucleic acids was detected in all DNA or rRNA gradient fractions, which is important for the interpretation of environmental SIP results. Consequently, quantitative analysis of gradient fractions provides a higher precision and finer resolution for retrieval of isotopically enriched nucleic acids than possible using ethidium bromide or gradient fractionation combined with fingerprinting analyses. This is a prerequisite for the fine-scale tracing of microbial populations metabolizing 13C-labelled compounds in natural ecosystems.