Mapping of origin of replication in Themococcales

Genome replication is a crucial and essential process for the continuity of life.In all organisms it starts at a specific region of the genome known as origin of replication (Ori) site. The number of Ori sites varies in prokaryotes and eukaryotes. Replication starts at a single Ori site in bacteria, but in eukaryotes multiple Ori sites are used for fast copying across all chromosomes. The situation becomes complex in archaea, where some groups have single and others have multiple origins of replication. Themococcales, are a hyperthermophilic order of archaea. They are anaerobes and heterotrophs-peptide fermenters, sulphate reducers, methanogens being some of the examples of metabolic types. In this paper we have applied a combination of multiple in silico approaches - Z curve, the cell division cycle (cdc6) gene location and location of consensus origin recognition box (ORB) sequences for location of origin of replication in Thermococcus onnurineus, Thermococcus gammatolerans and other Themococcales and compared the results to that of the well-documented case of Pyrococcus abyssi. The motivation behind this study is to find the number of Ori sites based on the data available for members of this order. Results from this in silico analysis show that the Themococcales have a single origin of replication.     

Evaluation of antifungal pharmacodynamic characteristics of AmBisome against Candida albicans

A liposomal formulation of Amphotericin B (AmBisome), with small unilamellar vesicles containing amphotericin B, shows characteristic pharmacokinetics as liposomes, and in consequence, has different pharmacological activity and toxicity from amphotericin B deoxycholate (Fungizone). In this study, we evaluated the antifungal pharmacodynamic characteristics of AmBisome against Candida albicans using the in vitro time-kill method and murine systemic infection model. A time-kill study indicated that the in vitro fungicidal activities of AmBisome and Fungizone against C. albicans ATCC 90029 increased with increasing drug concentration. For in vivo experiments, leucopenic mice were infected intravenously with the isolate 4 hr prior to the start of therapy. The infected mice were treated for 24 hr with twelve dosing regimens of AmBisome administered at 8-, 12-, 24-hr dosing intervals. Correlation analysis between the fungal burden in the kidney after 24 hr of therapy and each pharmacokinetic/pharmacodynamic parameter showed that the peak level/MIC ratio was the best predictive parameter of the in vivo outcome of AmBisome. These results suggest that AmBisome, as well as Fungizone, has concentration-dependent antifungal activity. Furthermore, since AmBisome can safely achieve higher concentrations in serum than Fungizone, AmBisome is thought to have superior potency to Fungizone against fungal infections.     

Factors affecting phase synchronization in integrate-and-fire oscillators

Step changes in input current are known to induce partial phase synchrony in ensembles of leaky integrate-and-fire neurons operating in the oscillatory or “regular firing” regime. An analysis of this phenomenon in the absence of noise is presented based on the probability flux within an ensemble of generalized integrate-and-fire neurons. It is shown that the induction of phase synchrony by a step input can be determined by calculating the ratio of the voltage densities obtained from fully desynchronized ensembles firing at the pre and post-step firing rates. In the limit of low noise and in the absence of phase synchrony, the probability density as a function of voltage is inversely proportional to the time derivative along the voltage trajectory. It follows that the magnitude of phase synchronization depends on the degree to which a change in input leads to a uniform multiplication of the voltage derivative over the range from reset to spike threshold. This analysis is used to investigate several factors affecting phase synchronization including high firing rates, inputs modeled as conductances rather than currents, peri-threshold sodium currents, and spike-triggered potassium currents. Finally, we show that without noise, the equilibrium ensemble density is proportional to the phase response curve commonly used to analyze oscillatory systems. Action Editor: John Rinzel     

Importance of assemblage‐level thinning: A field experiment in an alpine meadow on the Tibet plateau

Question: Which fraction of the decrease in species richness under fertilization can be explained by assemblage‐level thinning? Location: An alpine meadow on the eastern Tibet plateau. Methods: 60‐m² plots were randomly assigned to a control or one of four levels of ammonium phosphate fertilizer. Treatments were repeated for three years. The effect of as semblage‐level thinning was decided based on similarity in quadrats within and between fertilizing levels, bootstrap simulation based on random thinning of the high density (low production, low fertility) quadrats and correlation of species’ biomass in low fertility and high fertility. Results: Fertilization increased production, reduced species richness and reduced density of individuals. Heavily fertilized quadrats are more similar in species composition in 2000 but less similar in 2001 and 2002. Rarefaction showed that a decrease in density can account for 32.3‐42.9% decrease of species richness, but the simulated species richness is always significantly higher than the observed one. When production and species richness are similar at two levels of fertilization, species biomass in the higher fertility treatment is positively correlated with biomass at lower fertility. When the two fertilizer levels differed in production and species richness, there was no evidence of correlation in species biomass, suggesting that assemblage level thinning cannot explain all the loss of species. Conclusion: Although a decrease in density could explain much of the decrease (up to 42.9%) in species richness when this alpine meadow was fertilized, other important mechanisms such as interspecific competition cannot be ignored. Future studies should investigate the effect of assemblage level thinning on species diversity, and search for mechanisms responsible for a decrease in diversity.     

Influence of synchronization between adult emergence and host plant phenology on the population density of Pseudasphondylia neolitseae (Diptera: Cecidomyiidae) inducing leaf galls on Neolitsea sericea (Lauraceae)

Synchronization between the appearance of herbivorous insects and their host-plant phenology is a critical event, especially for short-lived insects such as gall midges. We studied a natural population of Pseudasphondylia neolitseae (Diptera: Cecidomyiidae) that induces leaf galls on Neolitsea sericea (Lauraceae) to evaluate the effect of synchronization on gall density in the subsequent generation. To do so, we combined quantitative data on host resources with time lag between emergence and host-available seasons. The gamma distribution model was applied to the emergence curve of P. neolitseae and the normal distribution model to the daily changes in the number of host buds suitable for oviposition; the latter model was transformed into an available-resource curve based on the mean number of host buds required for a single female to realize her eggs. By superimposing the emergence curve on the available-resource curve and calculating overlapped area, the degree of synchronization was evaluated more accurately than previous studies, which had treated only the time lag. The number of females that synchronized with host buds affected gall density in the next generation.     

Exposure to ultraviolet radiation delays photosynthetic recovery in Arctic kelp zoospores

Seasonal reproduction in some Arctic Laminariales coincides with increased UV-B radiation due to stratospheric ozone depletion and relatively high water temperatures during polar spring. To find out the capacity to cope with different spectral irradiance, the kinetics of photosynthetic recovery was investigated in zoospores of four Arctic species of the order Laminariales, the kelps Saccorhiza dermatodea, Alaria esculenta, Laminaria digitata, and Laminaria saccharina. The physiology of light harvesting, changes in photosynthetic efficiency and kinetics of photosynthetic recovery were measured by in vivo fluorescence changes of Photosystem II (PSII). Saturation irradiance of freshly released spores showed minimal I _k values (photon fluence rate where initial slope intersects horizontal asymptote of the curve) values ranging from 13 to 18 μmol photons m⁻² s⁻¹ among species collected at different depths, confirming that spores are low-light adapted. Exposure to different radiation spectra consisting of photosynthetically active radiation (PAR; 400–700 nm), PAR+UV-A radiation (UV-A; 320–400 nm), and PAR+ UV-A+UV-B radiation (UV-B; 280–320 nm) showed that the cumulative effects of increasing PAR fluence and the additional effect of UV-A and UV-B radiations on photoinhibition of photosynthesis are species specific. After long exposures, Laminaria saccharina was more sensitive to the different light treatments than the other three species investigated. Kinetics of recovery in zoospores showed a fast phase in S. dermatodea, which indicates a reduction of the photoprotective process while a slow phase in L. saccharina indicates recovery from severe photodamage. This first attempt to study photoinhibition and kinetics of recovery in zoospores showed that zoospores are the stage in the life history of seaweeds most susceptible to light stress and that ultraviolet radiation (UVR) effectively delays photosynthetic recovery. The viability of spores is important on the recruitment of the gametophytic and sporophytic life stages. The impact of UVR on the zoospores is related to the vertical depth distribution of the large sporophytes in the field.     

Landscape-scale variation in the seed banks of floodplain wetlands with contrasting hydrology in China

1. At a local scale, the species composition, diversity and spatial variation of wetland plant communities are determined primarily by spatial and temporal heterogeneity in their environments. Less is known about variation at a landscape‐level. The floodplain of the Changjiang (Yangtze) River in China includes hydrologically connected, subtropical wetlands with different hydrological characteristics. 2. We examined seed‐bank species composition and richness in marshes of two contrasting hydrological types: permanent marshes, fed by local runoff, and lakeshore marshes more closely connected to the regulated river. Lakeshore marshes are flooded annually to depth of approximately 1 m and during flooding they support an alternate, aquatic vegetation type. The soil seed bank in March was a comparative estimator of species diversity. At the beginning of the growing season it included seeds from both phases of alternating vegetation types associated with the annual hydrological cycle. 3. A regional pool of 101 species was detected in the seed banks of six wetlands associated with the river and its tributaries: 56 occurred in permanent marshes and 59 in lakeshore marshes, with only 15 common to both. Species rarefaction curves indicated that more species occurred in permanent than lakeshore marshes at equal numbers of individuals sampled. However, the more heterogeneous lakeshore seed banks were estimated (Chao 2) to have greater total species richness (81) than permanent marsh (60). 4. Analysis using Sørensen's coefficient of similarity and DCA ordination revealed complex variation, with much greater differences between hydrological types than within them, irrespective of geographical distance. The types also differed significantly in the composition of four functional groups of species. 5. Despite the potential for dispersal of propagules via the annually pulsing river system (hydrochory), at a regional and landscape scale, diversity is maintained largely by large‐scale temporal hydrological heterogeneity and smaller scale spatial and topographic heterogeneity.     

Periodic habitat loss alters the competitive coexistence between brown trout and bullheads in a small stream over 34 years

1. Changes in the population density of juvenile sea trout Salmo trutta L. and bullheads Cottus gobio L. were compared in a small stream over 34 years. Both species have a similar diet and obviously live in the same general habitat. Habitat loss was most marked in seven summer droughts: severest in 1976, 1983, 1984, 1995, and less severe but followed by autumn droughts in 1969, 1989 and 1993. The contrasting effects of habitat loss on the two species were examined. 2. For both species, the Ricker curvilinear model significantly fit (P < 0.001) the relationship between initial egg density and survivor density for successive life stages, even though egg densities were much lower for bullheads than trout. These analyses provided evidence for density-dependent population regulation and also identified extreme outliers, most being for year-classes affected by summer droughts. 3. The variable effects of changes in habitable area (= % wettable area in sampling section) were quantified by using the residuals, each residual being the absolute value expressed as a percentage of the expected value from the Ricker curve. Significant relationships between the residuals and habitable area showed that habitat loss had a marked effect on survivor density, this being negative for 0+ and 1+ trout, and positive for 0+, 1+ and 2+/3+ bullheads. 4. Therefore, during periods of habitat loss in the summer months, bullhead density increased at the expense of trout density. Low flows and a decrease in wettable area were associated with a marked reduction in habitat quality for drift-feeding trout and an increase in habitat quality, and perhaps also quantity, for benthic-feeding bullheads. This case study shows that, during a major perturbation, the relationship between the densities of two species can change markedly in favour of the less numerous species. The competitive coexistence between the two species is therefore a dynamic process that changes through time with periodic changes in the environment.     

Quantitative measurement of damage caused by 1064-nm wavelength optical trapping of Escherichia coli cells using on-chip single cell cultivation system

We quantitatively examined the possible damage to the growth and cell division ability of Escherichia coli caused by 1064-nm optical trapping. Using the synchronous behavior of two sister E. coli cells, the growth and interdivision times between those two cells, one of which was trapped by optical tweezers, the other was not irradiated, were compared using an on-chip single cell cultivation system. Cell growth stopped during the optical trapping period, even with the smallest irradiated power on the trapped cells. Moreover, the damage to the cell's growth and interdivision period was proportional to the total irradiated energy (work) on the cell, i.e., irradiation time multiplied by irradiation power. The division ability was more easily affected by a smaller energy, 0.36 J, which was 30% smaller than the energy that adversely affected growth, 0.54 J. The results indicate that the damage caused by optical trapping can be estimated from the total energy applied to cells, and furthermore, that the use of optical trapping for manipulating cells might cause damage to cell division and growth mechanisms, even at wavelengths under 1064 nm, if the total irradiation energy is excessive.     

Determination of synergistic effects of antibiotics and Zno NPs against isolated E. Coli and A. Baumannii bacterial strains from clinical samples

The mortality rates has been increased globally due to multidrug resistant (MDR) E.coli and A.baumanii bacterial strains and also there is an emerging resistance of the Enterobacteriaceae family of bacteria to Carbapenem antibiotics (CRE) in Saudi Arabia. The main aim of our research study is to isolate E.coli and A. baumannii bacterial species from various collected clinical samples and to evaluate the MIC and FICI of Colistin, Ciprofloxacin, Meropenem and ZnO NPs and in combination of Colistin, Ciprofloxacin, Meropenem with ZnO NPs.The clinical isolated strains of A. baumannii (MRO-17-13) and A. baumannii (MRO-17–25) was found to be sensitive towards colistin with 0.5 μg/mL concentration, whereas, all the isolated A. baumannii strains showed similar MIC value 2 mg/mL when tested with ZnO NPs, the MIC value for the ZnO NPs was found to be similar for all the E.coli strains 0.25 mg/mL. The effects of all Ciprofloxacin concentrations used in the study were bacteriostatic against E. coli (01UR19006568-01) strain but 1 mg/mL concentration of ZnO NPs alone is showed bactericidal activity, ZnO NPs effect was found to be concentration dependent, as highest concentration of ZnO NPs showed strongest antibacterial effect. In conclusion, more investigation is required to evaluate the acceptable concentration of Zno NPs and antibiotics selected to avoid toxicity and must be tested against more clinically isolated gram-negative bacterial strains.