Insights into Nonpilus Adhesin Functionality and the Molecular Determinants of Nontypeable Haemophilus influenzae Colonization

Bacterial colonization of the upper respiratory tract is the first step in the pathogenesis of nontypeable Haemophilus influenzae (NTHi) disease. Examination of the determinants of NTHi colonization process has been hampered by the lack of an appropriate animal model. To address this, we have developed a model of NTHi colonization in adult rhesus macaques that involves intranasal inoculation of 1x105 CFU and results in persistent colonization of the upper respiratory tract for at least three weeks with no signs of disease, mimicking asymptomatic colonization of humans. Using this model, we assessed the contributions to colonization of the HMW1 and HMW2 adhesive proteins. In competition experiments, the parent strain expressing both HMW1 and HMW2 was able to efficiently out-compete an isogenic mutant strain expressing neither HMW1 nor HMW2. In experiments involving inoculation of single isogenic derivatives of NTHi strain 12, the strains expressing HMW1 or HMW2 or both were able to colonize efficiently, while the strain expressing neither HMW1 nor HMW2 colonized inefficiently. Furthermore, colonization resulted in antibody production against HMW1 and HMW2 in one-third of the animals, demonstrating that colonization can be an immunizing event. In conclusion, we have established that NTHi is capable of colonizing the upper respiratory tract of rhesus macaques, in some cases associated with stimulation of an immune response. The HMW1 and HMW2 adhesive proteins play a major role in the process of colonization.

After establishing that the HMW1 and HMW2 proteins are colonization factors we further investigated the determinants of HMW1 function. HMW1 is encoded in the same genetic locus as two other proteins, HMW1B and HMW1C, with which HMW1 must interact in order to be functional. Interaction with HMW1C in the cytoplasm results in the glycosylation of HMW1. By employing homologues of HMW1C that glycosylate HMW1 in slightly different patterns we show that the pattern of modification is critical to HMW1 function. Structural analysis showed a change in protein structure when the pattern of HMW1 modification differed. We also identified two specific sites which must be glycosylated for HMW1 to function properly. These point mutations did not have a significant effect on protein structure, suggesting that glycosylation at those specific sites is instead necessary for interaction of HMW1 with its receptor. HMW1B is an outer membrane pore through which HMW1 is transported to reach the bacterial cell surface. We observed that HMW1 isolated from the cytoplasm has a different structure than HMW1 isolated from the bacterial cell surface. By forcing HMW1 to be secreted in a non-HMW1B dependent manner, we show that secretion alone is not sufficient for HMW1 to obtain a functional structure. This leads us to hypothesize that there is something specific in the interaction between HMW1 and HMW1B that aids in proper HMW1 folding.

The NTHi HMW1C glycosyltransferase mediates unconventional N-linked glycosylation of HMW1. In this system, HMW1 is modified in the cytoplasm by sequential transfer of hexose residues. To determine if this mechanism of N-linked glycosylation is employed by species other than NTHi, we examined Kingella kingae and Aggregatibacter aphrophilus homologues of HMW1C. We found both homologues to be functional glycosyltransferases and identified their substrates as the K. kingae Knh and the A. aphrophilus EmaA trimeric autotransporter proteins. LC-MS/MS analysis revealed multiple sites of N-linked glycosylation on Knh and EmaA. Without glycosylation, Knh and EmaA failed to facilitate wild type levels of bacterial autoaggregation or adherence to human epithelial cells, establishing that glycosylation is essential for proper protein function.

Genomic consequences of mating system evolution in the Pacific coastal dune endemic, Abronia umbellata (Nyctaginaceae)

The advent of next-generation sequencing has significantly reduced the cost of obtaining large-scale genetic resources, opening the door for genomic studies of non-model but ecologically interesting species. The shift in mating system, from outcrossing to selfing, has occurred thousands of times in angiosperms and is accompanied by profound changes in the population genetics and ecology of a species. A large body of work has been devoted to understanding why the shift occurs and the impact of the shift on the genetics of the resulting selfing populations, however, the causes and consequences of the transition to selfing involve a complicated interaction of genetic and demographic factors which are difficult to untangle. Abronia umbellata is a Pacific coastal dune endemic which displays a striking shift in mating system across its geographic range, with large-flowered outcrossing populations south of San Francisco and small-flowered selfing populations to the north. Abronia umbellata is an attractive model system for the study of mating system transitions because the shift appears to be recent and therefore less obscured by post-shift processes, it has a near one-dimensional geographic range which simplifies analysis and interpretation, and demographic data has been collected for many of the populations. In this study, we generated transcriptome-level data for 12 plants including individuals from both subspecies, along with a resequencing study of 48 individuals from populations across the range. The genetic analysis revealed a recent transition to selfing involving a drastic reduction in genetic diversity in the selfing lineage, potentially indicative of a recent population bottleneck and a transition to selfing due to reproductive assurance. Interestingly, the genetic structure of the populations was not coincident with the current subspecies demarcation, and two large-flowered populations were classified with the selfing subspecies, suggesting a potential need for re-evaluation of the current subspecies classification. Our finding of low diversity in selfing populations may also have implications for the conservation value of the threatened selfing subspecies.

Effects of a harmful algal bloom on the community ecology, movements and spatial distributions of fishes in a microtidal estuary

Harmful algal blooms can adversely affect fish communities, though their impacts are highly context-dependent and typically differ between fish species. Various approaches, comprising univariate and multivariate analyses and multimetric Fish Community Indices (FCI), were employed to characterise the perceived impacts of a Karlodinium veneficum bloom on the fish communities and ecological condition of the Swan Canning Estuary, Western Australia. The combined evidence suggests that a large proportion of the more mobile fish species in the offshore waters of the bloom-affected area relocated to other regions during the bloom. This was indicated by marked declines in mean species richness, catch rates and FCI scores in the bloom region but concomitant increases in these characteristics in more distal regions, and by pronounced and atypical shifts in the pattern of inter-regional similarities in fish community composition during the bloom. The lack of any significant changes among the nearshore fish communities revealed that bloom impacts were less severe there than in deeper, offshore waters. Nearshore habitats, which generally are in better ecological condition than adjacent offshore waters in this system, may provide refuges for fish during algal blooms and other perturbations, mirroring similar observations of fish avoidance responses to such stressors in estuaries worldwide.

Effects of a harmful algal bloom on the community ecology, movements and spatial distributions of fishes in a microtidal estuary

Harmful algal blooms can adversely affect fish communities, though their impacts are highly context-dependent and typically differ between fish species. Various approaches, comprising univariate and multivariate analyses and multimetric Fish Community Indices (FCI), were employed to characterise the perceived impacts of a Karlodinium veneficum bloom on the fish communities and ecological condition of the Swan Canning Estuary, Western Australia. The combined evidence suggests that a large proportion of the more mobile fish species in the offshore waters of the bloom-affected area relocated to other regions during the bloom. This was indicated by marked declines in mean species richness, catch rates and FCI scores in the bloom region but concomitant increases in these characteristics in more distal regions, and by pronounced and atypical shifts in the pattern of inter-regional similarities in fish community composition during the bloom. The lack of any significant changes among the nearshore fish communities revealed that bloom impacts were less severe there than in deeper, offshore waters. Nearshore habitats, which generally are in better ecological condition than adjacent offshore waters in this system, may provide refuges for fish during algal blooms and other perturbations, mirroring similar observations of fish avoidance responses to such stressors in estuaries worldwide.

The HARPS-N Rocky Planet Search. I. HD 219134 b: A transiting rocky planet in a multi-planet system at 6.5 pc from the Sun

We know now from radial velocity surveys and transit space missions thatplanets only a few times more massive than our Earth are frequent aroundsolar-type stars. Fundamental questions about their formation history,physical properties, internal structure, and atmosphere composition are,however, still to be solved. We present here the detection of a systemof four low-mass planets around the bright (V = 5.5) and close-by (6.5pc) star HD 219134. This is the first result of the Rocky Planet Searchprogramme with HARPS-N on the Telescopio Nazionale Galileo in La Palma.The inner planet orbits the star in 3.0935 ± 0.0003 days, on aquasi-circular orbit with a semi-major axis of 0.0382 ± 0.0003AU. Spitzer observations allowed us to detect the transit of the planetin front of the star making HD 219134 b the nearest known transitingplanet to date. From the amplitude of the radial velocity variation(2.25 ± 0.22 ms-1) and observed depth of the transit(359 ± 38 ppm), the planet mass and radius are estimated to be4.36 ± 0.44 M⊕ and 1.606 ± 0.086R⊕, leading to a mean density of 5.76 ± 1.09 gcm-3, suggesting a rocky composition. One additional planetwith minimum-mass of 2.78 ± 0.65 M⊕ moves on aclose-in, quasi-circular orbit with a period of 6.767 ± 0.004days. The third planet in the system has a period of 46.66 ± 0.08days and a minimum-mass of 8.94 ± 1.13 M⊕, at0.233 ± 0.002 AU from the star. Its eccentricity is 0.46 ±0.11. The period of this planet is close to the rotational period of thestar estimated from variations of activity indicators (42.3 ± 0.1days). The planetary origin of the signal is, however, thepreferredsolution as no indication of variation at the corresponding frequency isobserved for activity-sensitive parameters. Finally, a fourth additionallonger-period planet of mass of 71 M⊕ orbits the starin 1842 days, on an eccentric orbit (e = 0.34 ± 0.17) at adistance of 2.56 AU.The photometric time series and radial velocities used in this work areavailable in electronic form at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr(ftp://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/584/A72

Increased water charges improve efficiency and equity in an irrigation system

Conventional wisdom in many agricultural systems across the world is that farmers cannot, will not, or should not pay the full costs associated with surface water delivery. Across Organisation for Economic Co-operation and Development (OECD) countries, only a handful can claim complete recovery of operation, maintenance, and capital costs; across Central and South Asia, fees are lower still, with farmers in Nepal, India, and Kazakhstan paying fractions of a U.S. penny for a cubic meter of water. In Pakistan, fees amount to roughly USD 1-2 per acre per season. However, farmers in Pakistan spend orders of magnitude more for diesel fuel to pump groundwater each season, suggesting a latent willingness to spend for water that, under the right conditions, could potentially be directed toward water-use fees for surface water supply. Although overall performance could be expected to improve with greater cost recovery, asymmetric access to water in canal irrigation systems leaves the question open as to whether those benefits would be equitably shared among all farmers in the system. We develop an agent-based model (ABM) of a small irrigation command to examine efficiency and equity outcomes across a range of different cost structures for the maintenance of the system, levels of market development, and assessed water charges. We find that, robust to a range of different cost and structural conditions, increased water charges lead to gains in both efficiency and concomitant improvements in equity as investments in canal infrastructure and system maintenance improve the conveyance of water resources further down watercourses. This suggests that, under conditions in which (1) farmers are currently spending money to pump groundwater to compensate for a failing surface water system, and (2) there is the possibility that through initial investment to provide perceptibly better water supply, genuine win-win solutions can be attained through higher water-use fees to beneficiary farmers.

Effect of diatom supplementation during the nursery rearing of Litopenaeus vannamei (Boone, 1931) in a heterotrophic culture system

Bio-floc shrimp culture systems have been investigated in an attempt to optimize water use and prevent the discharge of effluent into the environment. The importance of microalgae in maintaining water quality and nutrition of the shrimp is well known in conventional systems; however, its maintenance amid bio-flocs and its role in the shrimp performance in this system are still poorly understood. The aim of this study was to evaluate the contribution of diatoms in the performance of Litopenaeus vannamei reared during the nursery phase in intensive system with minimal water exchange. Shrimp (0.31 ± 0.10 g) were reared among diatoms, bio-flocs and the combination of the two forming the mixture medium. The survival of shrimp was high in all treatments (90–97%). However, the shrimp reared among diatoms showed higher weight gain (P\0.05) and feed conversion ratio significantly more efficient, reaching a value of 0.47. The results indicate the importance of diatoms in bio-floc culture systems and points out to future research in an attempt to maintain a constant presence of these microalgae in culture medium without requiring successive inoculations.

Relative contribution of natural productivity and compound feed to tissue growth in blue shrimp (Litopenaeus stylirostris) reared in biofloc: Assessment by C and N stable isotope ratios and effect on key digestive enzymes

The aim of this study was to assess the relative contribution of natural productivity and compound food to the growth of the juvenile blue shrimp Litopenaeus stylirostris reared in a biofloc system. Two experiments were carried out based on the same protocol with three treatments: clear water with experimental diet (CW), biofloc with experimental diet (BF) and biofloc unfed (BU). Shrimp survival was significantly higher in biofloc rearing than in CW rearing. The contribution of the biofloc to shrimp diet was estimated through measurement of carbon and nitrogen stable isotope ratios in shrimp and food sources. Different isotopic compositions between feeds were obtained by feeding natural productivity with a mixture rich in fish meal and the shrimps with a pellet containing a high level of soy protein concentrate. Using a two source one-isotope mixing model, we found that the natural productivity of the biofloc system contributed to shrimp growth at a level of 39.8% and 36.9%, for C and N, respectively. The natural food consumed by the shrimps reared in the biofloc system resulted in higher gene expression (mRNA transcript abundance) and activities of two digestive enzymes in their digestive gland: α-amylase and trypsin. The growth of shrimp biomass reared in biofloc was, on average, 4.4 times that of those grown in clear water. Our results confirmed the best survival and promoted growth of shrimps using biofloc technology and highlighted the key role of the biofloc in the nutrition of rearing shrimps. Statement of relevance In this study, we have applied an original protocol to determine the respective contribution of natural productivity and artificial feeds on the alimentation of the juvenile blue shrimp L. stylirostris reared in biofloc system by using C and N natural stable isotope analysis. Moreover, we have compared, in shrimp digestive gland, the α-amylase and trypsin enzyme activities at biochemical and molecular levels for two different shrimp rearing systems, biofloc and clear water. In our knowledge, the use of molecular tool to study the influence of biofloc consumption on digest process of shrimp was never carried out. We think that our research is new and important to increase knowledge on biofloc topic.

The OPIT system part I.

The OPIT program is briefly described. OPIT is a basis-set-optimising, self-consistent field, molecular orbital program for calculating properties of closed-shell ground states of atoms and molecules. A file handling technique is then put forward which enables core storage to be used efficiently in large FORTRAN scientific applications programs. Hashing and list processing techniques, of the type frequently used in writing system software and computer operating systems, are here applied to the creation of data files (integral label and value lists etc.). Files consist of a chained series of blocks which may exist in core or on backing store or both. Efficient use of core store is achieved and the processes of file deletion, file re-writing and garbage collection of unused blocks can be easily arranged. The scheme is exemplified with reference to the OPIT program. A subsequent paper will describe a job scheduling scheme for large programs of this sort.

The sources of inequity in the education system of Serbia and how to combat them

The concept of equal opportunity for all students is deeply embedded in the Serbian constitution and in education laws. On that level, there is no doubt that everyone is ensured an opportunity to receive quality education. Many measures in education policy have been created specifically to achieve this objective and make the system fair and inclusive. The Coleman Report was linked to a wave of optimism that certain educational measures would help in achieving these noble goals. This aim is a high priority in education in a democratic country, and due to its importance needs to be re-examined. Thus, the present research examines the equity of students in the Serbian education system, detecting areas on all educational levels that could be (or already are) systemic sources of inequity (e.g., criteria for preschool institution enrolment, the system of student awards, rationalisation of the school network, the concept of entrance exams to secondary school or university, etc.). A number of measures have already been taken in the system specifically to deal with inequity (e.g., the Preschool Preparatory Programme, dropout measures, inclusion, scholarships, etc.). The effects of these measures in particular are analysed in the present work. In addition to an analysis of the systemic sources of inequity in the Serbian education system, the article also makes recommendations for their overcoming. (DIPF/Orig.)

The interplay between tectonics, sediment dynamics and gateways evolution in the Danube system from the Pannonian Basin to the western Black Sea

Understanding the natural evolution of a river–delta–sea system is important to develop a strong scientific basis for efficient integrated management plans. The distribution of sediment fluxes is linked with the natural connection between sediment source areas situated in uplifting mountain chains and deposition in plains, deltas and, ultimately, in the capturing oceans and seas. The Danube River–western Black Sea is one of the most active European systems in terms of sediment re-distribution that poses significant societal challenges. We aim to derive the tectonic and sedimentological background of human-induced changes in this system and discuss their interplay. This is obtained by analysing the tectonic and associated vertical movements, the evolution of relevant basins and the key events affecting sediment routing and deposition. The analysis of the main source and sink areas is focused in particular on the Miocene evolution of the Carpatho-Balkanides, Dinarides and their sedimentary basins including the western Black Sea. The vertical movements of mountains chains created the main moments of basin connectivity observed in the Danube system. Their timing and effects are observed in sediments deposited in the vicinity of gateways, such as the transition between the Pannonian/Transylvanian and Dacian basins and between the Dacian Basin and western Black Sea. The results demonstrate the importance of understanding threshold conditions driving rapid basins connectivity changes superposed over the longer time scale of tectonic-induced vertical movements associated with background erosion and sedimentation. The spatial and temporal scale of such processes is contrastingly different and challenging. The long-term patterns interact with recent or anthropogenic induced modifications in the natural system and may result in rapid changes at threshold conditions that can be quantified and predicted. Their understanding is critical because of frequent occurrence during orogenic evolution, as commonly observed in the Mediterranean area and discussed elsewhere.

Detecting Motifs in System Call Sequences

The search for patterns or motifs in data represents an area of key interest to many researchers. In this paper we present the Motif Tracking Algorithm, a novel immune inspired pattern identification tool that is able to identify unknown motifs which repeat within time series data. The power of the algorithm is derived from its use of a small number of parameters with minimal assumptions. The algorithm searches from a completely neutral perspective that is independent of the data being analysed and the underlying motifs. In this paper the motif tracking algorithm is applied to the search for patterns within sequences of low level system calls between the Linux kernel and the operating system’s user space. The MTA is able to compress data found in large system call data sets to a limited number of motifs which summarise that data. The motifs provide a resource from which a profile of executed processes can be built. The potential for these profiles and new implications for security research are highlighted. A higher level system call language for measuring similarity between patterns of such calls is also suggested.

Bidirectional cargo transport by microtubule-based molecular motors

We have reconstituted a simple in vitro system using only mammalian dynein and mammalian kinesin attached to a single cargo. These cargoes undergo saltatory motion typically seen in vivo, indicating that the motors engage in a tug-of-war. When the complex hits a barrier, the cargo often reverses direction. In some cases, it tries several up-and-back motions, during which time the dynein likely pulls the cargo onto a different protofilament, and is sometimes able to bypass the blockage. This explains why eliminating kinesin or dynein stops motion in both directions in vivo. We also find that mammalian dynein, but not kinesin, often takes backwards steps when under backward force. However, yeast dynein coupled with mammalian kinesin does not display these attributes, as expected.

Stochastic simulation of time-series models combined with geostatistics to predict water-table scenarios in a Guarani Aquifer System outcrop area, Brazil

Stochastic methods based on time-series modeling combined with geostatistics can be useful tools to describe the variability of water-table levels in time and space and to account for uncertainty. Monitoring water-level networks can give information about the dynamic of the aquifer domain in both dimensions. Time-series modeling is an elegant way to treat monitoring data without the complexity of physical mechanistic models. Time-series model predictions can be interpolated spatially, with the spatial differences in water-table dynamics determined by the spatial variation in the system properties and the temporal variation driven by the dynamics of the inputs into the system. An integration of stochastic methods is presented, based on time-series modeling and geostatistics as a framework to predict water levels for decision making in groundwater management and land-use planning. The methodology is applied in a case study in a Guarani Aquifer System (GAS) outcrop area located in the southeastern part of Brazil. Communication of results in a clear and understandable form, via simulated scenarios, is discussed as an alternative, when translating scientific knowledge into applications of stochastic hydrogeology in large aquifers with limited monitoring network coverage like the GAS.

Early Warning System Potential for Single Sourcing Risk Mitigation

Part 17: Risk Analysis