Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function

The mammalian transcriptome contains many nonprotein-coding RNAs (ncRNAs), but most of these are of unclear significance and lack strong sequence conservation, prompting suggestions that they might be non-functional. However, certain long functional ncRNAs such as Air and Xist are also poorly conserved. In this article, we systematically analyzed the conservation of several groups of functional ncRNAs, including miRNAs, snoRNAs and longer ncRNAs whose function has been either documented or confidently predicted. As expected, miRNAs and snoRNAs were highly conserved. By contrast, the longer functional non-micro, non-sno ncRNAs were much less conserved with many displaying rapid sequence evolution. Our findings suggest that longer ncRNAs are under the influence of different evolutionary constraints and that the lack of conservation displayed by the thousands of candidate ncRNAs does not necessarily signify an absence of function.

An exceptionally rich complex of Sanguinicolidae von Graff, 1907 (Platyhelminthes : Trematoda) from Siganidae, Labridae and Mullidae (Teleostei : Perciformes) from the Indo-West Pacific Region

We describe an unprecedented radiation of sanguinicolid blood flukes ( Digenea: Sanguinicolidae) from two species of Labridae (Choerodon venustus and C. cauteroma), seven species of Mullidae (Mulloidichthys vanicolensis, Parupeneus barberinoides, P. barberinus, P. bifasciatus, P. cyclostomus, P. indicus and P. multifasciatus) and ten species of Siganidae (Siganus argenteus, S. corallinus, S. doliatus, S. fuscescens, S. lineatus, S. margaritiferus, S. puellus, S. punctatus, S. virgatus and S. vulpinus) from sites off Australia and Palau. The flukes were morphologically similar in having the combination of a long thread-like body, tegumental spines in lateral transverse rows, a vestigial oral sucker bearing concentric rows of fine spines, an H-shaped intestine, a cirrussac, a notch level with the male genital pore, a lateral or post-ovarian uterus, a uterine chamber and separate genital pores. These species are divided into two genera on the basis of testis number. Sanguinicolids from Siganus fuscescens have a single large testis between the intestinal bifurcation and the ovary and are placed in Ankistromeces Nolan & Cribb, 2004. Species from the remaining nine species of Siganidae, Labridae and Mullidae are placed in Phthinomita n. g.; these species have two testes, the anterior testis being large and between the intestinal bifurcation and the ovary whereas the small posterior testis is at the posterior end of the body and appears rudimentary or degenerate and probably non-functional. The second internal transcribed spacer (ITS2) of ribosomal DNA ( rDNA) from 29 host/parasite/location combinations (h/p/l) was sequenced together with that of Ankistromeces mariae Nolan & Cribb, 2004 for comparison. From 135 samples we found 19 distinct genotypes which were interpreted as representing at least that many species. Replicate sequences were obtained for 25 of 30 h/p/l combinations ( including A. mariae); there was no intraspecific variation between replicates sequences for any of these. Interspecific variation ranged from 1 - 41 base differences (0.3 - 12.7% sequence divergence). The 19 putative species were difficult to recognise by morphological examination. We describe 13 new species; we do not describe (= name) six species characterised solely by molecular sequences and three putative species for which morphological data is available but for which molecular data is not. We have neither morphological nor molecular data for sanguinicolids harboured in five hosts species ( Siganus margaritiferus, S. puellus, Choerodon cauteroma, Parupeneus indicus and P. multifasciatus) in which we have seen infections. Where host species were infected in different localities they almost always harboured distinct species. Some host species ( for example, S. argenteus and S. lineatus from Lizard Island) harboured two or three species in a single geographical location. This suggests that, for parts of this system, parasite speciation has outstripped host speciation. Distance analysis of ITS2 showed species from each host family ( Siganidae, Mullidae and Labridae) did not form monophyletic clades to the exclusion of species from other host families. However, a host defined clade was formed by the sequences from sanguinicolids from S. fuscescens.

Asymptomatic bacteriuria Escherichia coli strain 83972 carries mutations in the foc locus and is unable to express F1C fimbriae

Escherichia coli is the most common organism associated with asymptomatic bacteriuria (ABU). In contrast to uropathogenic E. coli (UPEC), which causes symptomatic urinary tract infection (UTI), very little is known about the mechanisms by which these strains colonize the urinary tract. Bacterial adhesion conferred by specific surface-associated adhesins is normally considered as a prerequisite for colonization of the urinary tract. The prototype ABU E coli strain 83972 was originally isolated from a girl who had carried it asymptomatically for 3 years. This study characterized the molecular status of one of the primary adhesion factors known to be associated with UTI, namely F1C fimbriae, encoded by the foc gene cluster. F1C fimbriae recognize receptors present in the human kidney and bladder. Expression of the foc genes was found to be up-regulated in human urine. It was also shown that although strain 83972 contains a seemingly intact foc gene cluster, F1C fimbriae are not expressed. Sequencing and genetic complementation revealed that the focD gene, encoding a component of the F1C transport and assembly system, was non-functional, explaining the inability of strain 83972 to express this adhesin. The data imply that E. coli 83972 has lost its ability to express this important colonization factor as a result of host-driven evolution. The ancestor of the strain seems to have been a pyelonephritis strain of phylogenetic group B2. Strain 83972 therefore represents an example of bacterial adaptation from pathogenicity to commensalism through virulence factor loss.

Degenerate dentition of the dugong (Dugong dugon), or why a grazer does not need teeth: morphology, occlusion and wear of mouthparts

The morphology and functional occlusion of the cheekteeth of 57 dugongs Dugong dugon of both sexes were examined using reflected light and scanning electron microscopy, radiography, hardness testing and skull manipulation. The functional morphology of the horny oral pads was also described. Mouthparts and body size allometry was examined for ontogenetic and gender-related trends. We found that the worn erupted cheekteeth of the dugong are simple flat pegs composed of soft degenerative dentine. During occlusion, the mandible moves in a mainly antero-lingual direction, with the possibility of mandibular retraction in some individuals. Anterior parts of the cheektooth row may become non-functional as a dugong ages. As a function of body size, dugong cheekteeth are extremely small compared with those of other mammalian herbivores, and with other hindgut fermenters in particular. The morphology, small size and occlusal variability of the cheekteeth suggest that there has not been strong selective pressure acting to maintain an effective dentition. In contrast, great development of the horny pads and associated skull parameters and their lower size variability suggest that the horny pads may have assumed the major role in food comminution.

Mechanical disruption of seagrass in the digestive tract of the dugong

The cheek teeth in dugongs are considered to be largely non-functional whereas the oral horny pads are important both in mechanical disruption of the diet and in conveying seagrass through the mouth. Particle size distributions of digesta from 41 dead stranded dugongs were examined to investigate the relationship between degree of food breakdown, gut region and functional surface area of the mouthparts. The in vitro ease of fracture of major dietary seagrass species were compared. The rate of food breakdown through the gut appears to be more closely linked to fibre level of the diet than to size or age of the dugong and its mouthparts. Low fibre seagrass, for example Halophila ovalis, breaks down at a faster rate than high fibre seagrass, for example Zostera capricorni both in dugong guts and in vitro. Several structural characteristics of seagrass, including level and arrangement of fibre, and water content, make it particularly amenable to mechanical breakdown. The soft mouthparts of the dugong are highly modified so that the entire oral cavity functions to crush low fibre seagrasses. Thus, the dugong has developed an efficient method of food ingestion and mastication that is suited to processing large quantities of soft seagrass during short dive times. The potential cost to the dugong in having lost its hard dental surfaces is that it has become restricted to a low fibre diet.

Relevance of the deletion polymorphisms of the glutathione S-transferases GSTT1 and GSTM1 in pharmacology and toxicology

Although cytosolic glutathione S-transterase (GST) enzymes occupy a key position in biological detoxification processes, two of the most relevant human isoenzymes. GST1-1 and GSTM1-1, are genetically deleted (non-functional alleles GSTT1*0 and GsTM1*0) in a high percentage of the human population, with major ethnic differences. The structures of the GSTT and GSTM gene areas explain the underlying genetic processes. GSTT1-1 is highly conserved during evolution and plays a major role in phase-II biotransformation of a number of drugs and industrial chemicals. e.g. cytostatic drugs, hydrocarbons and halogenated hydrocarbons. GSTM1-1 is particularly relevant in the deactivation of carcinogenic intermediates of polycyclic aromatic hydrocarbons. Several lines of evidence Suggest that hGSTT1-1 and/or hGSTM1-1 play a role in the deactivation of reactive oxygen species that are likely to be involved in cellular processes of inflammation, ageing and degenerative diseases. There is cumulating evidence that combinations of the GSTM1*0 state with other genetic traits affecting the metabolism of carcinogens (CYP1A1, GSTP1) may predispose the aero-digestivc tract and lung, especially in smokers, to a higher risk of cancer. The GSTM1*0 status appears also associated with a modest increase in the risk of bladder cancer, consistent with a GSTM1 interaction with carcinogenic tobacco smoke constituents. Both human GST deletions, although largely counterbalanced by overlapping substrate affinities within the GST superfamily, have consequences when the organism comes into contact with distinct man-made chemicals. This appears relevant in industrial toxicology and in drug metabolism.

Non-additivity of attractive potentials in modeling of N-2 and Ar adsorption isotherms on graphitized carbon black and porous carbon by means of density functional theory

We present a new approach accounting for the nonadditivity of attractive parts of solid-fluid and fluidfluid potentials to improve the quality of the description of nitrogen and argon adsorption isotherms on graphitized carbon black in the framework of non-local density functional theory. We show that the strong solid-fluid interaction in the first monolayer decreases the fluid-fluid interaction, which prevents the twodimensional phase transition to occur. This results in smoother isotherm, which agrees much better with experimental data. In the region of multi-layer coverage the conventional non-local density functional theory and grand canonical Monte Carlo simulations are known to over-predict the amount adsorbed against experimental isotherms. Accounting for the non-additivity factor decreases the solid-fluid interaction with the increase of intermolecular interactions in the dense adsorbed fluid, preventing the over-prediction of loading in the region of multi-layer adsorption. Such an improvement of the non-local density functional theory allows us to describe experimental nitrogen and argon isotherms on carbon black quite accurately with mean error of 2.5 to 5.8% instead of 17 to 26% in the conventional technique. With this approach, the local isotherms of model pores can be derived, and consequently a more reliab * le pore size distribution can be obtained. We illustrate this by applying our theory against nitrogen and argon isotherms on a number of activated carbons. The fitting between our model and the data is much better than the conventional NLDFT, suggesting the more reliable PSD obtained with our approach.

The functional roles of passive electroreception in non-electric fishes

Passive electroreception is a complex and specialised sense found in a large range of aquatic vertebrates primarily designed for the detection of weak bioelectric fields. Particular attention has traditionally focused on cartilaginous fishes, but a range of teleost and non-teleost fishes from a diversity of habitats have also been examined. As more species are investigated, it has become apparent that the role of electroreception in fishes is not restricted to locating prey, but is utilised in other complex behaviours. This paper presents the various functional roles of passive electroreception in non-electric fishes, by reviewing much of the recent research on the detection of prey in the context of differences in species' habitat (shallow water, deep-sea, freshwater and saltwater). A special case study on the distribution and neural groupings of ampullary organs in the omnihaline bull shark, Carcharhinus leucas, is also presented and reveals that prey-capture, rather than navigation, may be an important determinant of pore distribution. The discrimination between potential predators and conspecifics and the role of bioelectric stimuli in social behaviour is discussed, as is the ability to migrate over short or long distances in order to locate environmentally favourable conditions. The various theories proposed regarding the importance and mediation of geomagnetic orientation by either an electroreceptive and/or a magnetite-based sensory system receives particular attention. The importance of electroreception to many species is emphasised by highlighting what still remains to be investigated, especially with respect to the physical, biochemical and neural properties of the ampullary organs and the signals that give rise to the large range of observed behaviours.

Comparison of nitrogen adsorption at 77 K on non-porous silica and pore wall of MCM-41 materials by means of density functional theory

Nitrogen adsorption on a surface of a non-porous reference material is widely used in the characterization. Traditionally, the enhancement of solid-fluid potential in a porous solid is accounted for by incorporating the surface curvature into the solid-fluid Potential of the flat reference surface. However, this calculation procedure has not been justified experimentally. In this paper, we derive the solid-fluid potential of mesoporous MCM-41 solid by using solely the adsorption isotherm of that solid. This solid-fluid potential is then compared with that of the non-porous reference surface. In derivation of the solid-fluid potential for both reference surface and mesoporous MCM-41 silica (diameter ranging front 3 to 6.5 nm) we employ the nonlocal density functional theory developed for amorphous solids. It is found that, to out, surprise, the solid-fluid potential of a porous solid is practically the same as that for the reference surface, indicating that there is no enhancement due to Surface curvature. This requires further investigations to explain this unusual departure from our conventional wisdom of curvature-induced enhancement. Accepting the curvature-independent solid-fluid potential derived from the non-porous reference surface, we analyze the hysteresis features of a series of MCM-41 samples. (c) 2005 Elsevier Inc. All rights reserved.

Highly organized structure in the non-coding region of the psbA minicircle from clade C Symbiodinium

The chloroplast genes of dinoflagellates are distributed among small, circular dsDNA molecules termed minicircles. In this paper, we describe the structure of the non-coding region of the psbA minicircle from Symbiodinium. DNA sequence was obtained from five Symbiodinium strains obtained from four different coral host species (Goniopora tenuidens, Heliofungia actiniformis, Leptastrea purpurea and Pocillopora damicornis), which had previously been determined to be closely related using LSU rDNA region D1/D2 sequence analysis. Eight distinct sequence blocks, consisting of four conserved cores interspersed with two metastable regions and flanked by two variable regions, occurred at similar positions in all strains. Inverted repeats (IRs) occurred in tandem or 'twin' formation within two of the four cores. The metastable regions also consisted of twin IRs and had modular behaviour, being either fully present or completely absent in the different strains. These twin IRs are similar in sequence to double-hairpin elements (DHEs) found in the mitochondrial genomes of some fungi, and may be mobile elements or may serve a functional role in recombination or replication. Within the central unit (consisting of the cores plus the metastable regions), all IRs contained perfect sequence inverses, implying they are highly evolved. IRs were also present outside the central unit but these were imperfect and possessed by individual strains only. A central adenine-rich sequence most closely resembled one in the centre of the non-coding part of Amphidinium operculatum minicircles, and is a potential origin of replication. Sequence polymorphism was extremely high in the variable regions, suggesting that these regions may be useful for distinguishing strains that cannot be differentiated using molecular markers currently available for Symbiodinium.

Health characteristics of older Australian dietary supplement users compared to non-supplement users

The aim of this study was to measure the prevalence of dietary and health supplement use among Australians aged 65 years and over, and to contrast the health differences between supplement users and non-supplement users. Data was obtained from 1,263 randomly selected older Australians, who provided general demographic data, in addition to information related to their health, symptoms experienced and uses of medication, including dietary supplements. Supplement use was reported by 43% of the sample (52% of females and 35% of males). This investigation has revealed distinct differences in the health profile of older supplement users compared to non-users. Although there was no difference in the number of visits to medical doctors or self-rated health status between supplement users and non-supplement users, supplement users were more likely to report arthritis and osteoporosis, and experience more symptoms and consume more medication than non-supplement users. In contrast, there was a reduced likelihood of taking a supplement for those with hypertension and by those using blood pressure medication and heart tablets. These results suggest that older dietary supplement users may benefit from education and professional advice to assist them make appropriate and informed choices, particularly if they expect these preparations to attenuate their health concerns.

Assessment of diastolic function: What the general cardiologist needs to know

Diastolic dysfunction has a major impact on symptom status, functional capacity, medical treatment, and prognosis in both systolic and diastolic heart failure (HF), irrespective of the cause.w1 w2 When systolic dysfunction is clearly present, the central clinical question concerns the presence or absence of elevated filling pressure; a restrictive filling pattern is highly specific for elevated pulmonary wedge pressure in this setting.1w3 The transmitral flow pattern is also predictive of outcome; non-reversibility of restrictive filling with treatment portends a very poor prognosis.2 Thus, diastolic evaluation is an important component of the evaluation of the patient with systolic left ventricular (LV) impairment.

Application of density functional theory to equilibrium adsorption of argon and nitrogen on amorphous silica surface

We present a new version of non-local density functional theory (NL-DFT) adapted to description of vapor adsorption isotherms on amorphous materials like non-porous silica. The novel feature of this approach is that it accounts for the roughness of adsorbent surface. The solid–fluid interaction is described in the same framework as in the case of fluid–fluid interactions, using the Weeks–Chandler–Andersen (WCA) scheme and the Carnahan–Starling (CS) equation for attractive and repulsive parts of the Helmholtz free energy, respectively. Application to nitrogen and argon adsorption isotherms on non-porous silica LiChrospher Si-1000 at their boiling points, recently published by Jaroniec and co-workers, has shown an excellent correlative ability of our approach over the complete range of pressures, which suggests that the surface roughness is mostly the reason for the observed behavior of adsorption isotherms. From the analysis of these data, we found that in the case of nitrogen adsorption short-range interactions between oxygen atoms on the silica surface and quadrupole of nitrogen molecules play an important role. The approach presented in this paper may be further used in quantitative analysis of adsorption and desorption isotherms in cylindrical pores such as MCM-41 and carbon nanotubes.

Adsorption of argon and nitrogen in cylindrical pores of MCM-41 materials: application of density functional theory

Adsorption of argon and nitrogen at their respective boiling points in cylindrical pores of MCM-41 type silica-like adsorbents is studied by means of a non-local density functional theory (NLDFT), which is modified to deal with amorphous solids. By matching the theoretical results of the pore filling pressure versus pore diameter against the experimental data, we arrive at a conclusion that the adsorption branch (rather than desorption) corresponds to the true thermodynamic equilibrium. If this is accepted, we derive the optimal values for the solid–fluid molecular parameters for the system amorphous silica–Ar and amorphous silica–N2, and at the same time we could derive reliably the specific surface area of non-porous and mesoporous silica-like adsorbents, without a recourse to the BET method. This method is then logically extended to describe the local adsorption isotherms of argon and nitrogen in silica-like pores, which are then used as the bases (kernel) to determine the pore size distribution. We test this with a number of adsorption isotherms on the MCM-41 samples, and the results are quite realistic and in excellent agreement with the XRD results, justifying the approach adopted in this paper.