Variations in polymer fitness at elevated mutation rates

Two series expressions were obtained that give the first and second order rates of change in population fitness during competitive replication at elevated mutation rates. At their zeroerror limit, the respective power series reduces to the second (Fisher’s theorem) and third moments of the fitness distribution. The first series maximized the variation in mean polymer fitness, for a given amount of population covariance. From experimental results reported by Spiegelman’s group on evolutionin vitro among Qβ RNA variants, it was demonstrated: (i) terms in the (second) series fall-off at a rate broadly equal to the replicase error (ε≅10⁻⁴); (ii) the rate of change in mean RNA fitness (polymer formation rate constant) corresponds to the variance in fitness; and (iii) agreement exists between second order rate changes in fitness and the third moment (skewness) regression line, extending over 20 successive replication reactions. The impact of these findings on the standard model of evolution has been discussed.     

Characterization of aerobic granular sludge at various organic loading rates

Aerobic granular sludge was cultivated from activated sludge with two types of supports, namely bivalve shell carrier (BSC) and anaerobic granules (ANG). Granules were characterized at different organic loading rates (OLRs) ranging from 2.5 to 15 kg COD/m³ d and these granules were observed to withstand high OLRs. The physico-chemical characteristics of the aerobic granules were better than those of seed sludge. The granule formation with ANG support was found to be similar to that of non-support cultivation, i.e. formation from activated sludge only. By contrast, BSC support showed better performance in terms of faster settleability, compactness and especially resistance against organic shock loading. It also enabled self-cleaning effect by removing biofilm attached on the reactor wall during the start-up phase resulting rapid granulation process.     

Biotrickling air filtration of 2-chlorophenol at high loading rates

The degradation of 2-chlorophenol vapours in air was performed in a trickling biofilter packed with ceramic material seeded with the bacterium Pseudomonas pickettii, strain LD1. The system performance was evaluated under varying operating conditions (inlet 2-chlorophenol air concentrations from 0.10 to 3.50 g m^?3, and superficial air velocities of 30.0, 60.0, and 120.0 m h^?1). For all air velocity the maximum degradation rate was obtained for loading rates of 40 g m^?2 h^?1. Higher loading conditions resulted in strong inhibition of microbial activity, particularly severe at high air velocity. Process analysis, performed using data on pollutant concentration profiles along the filter packing obtained under different conditions of inlet concentration and air velocity, proves that best performance (i.e. maximum degradation efficiency and capacity) can be obtained for a narrow range of operating conditions, which can be ensured by proper design of biofilter size (i.e. diameter and height). Kinetic analysis of experimental data confirms that 2-CP inhibits microbial activity in the biofilter bed. Experimental data are satisfactorily fitted by the Haldane kinetic equation up to a critical value of loading rate, beyond which the experimental degradation rate is overestimated by the kinetic model. The inhibition appears to be affected by the loading rate, and the estimated inhibition constant linearly increases with increasing empty bed residence time.     

Inorganic nitrogen transformations at high loading rates in an oligohaline estuary

A well-defined nitrogen retention and turnover budget was estimated for a shallow oligohaline lake (Lake Pontchartrain, Louisiana, USA). In 1997 a month-long diversion of the Mississippi River filled the Lake with highly concentrated river water (80µM nitrate) and lowered the salinity to 0psu within 2 weeks. After the spillway was closed the Lake mixed with estuarine tidal waters and came to equilibrium over 4 months with the riverine, atmospheric and offshore water nitrogen sources. A flushing rate of 1.78% d^–1 was estimated by analyzing a plot of ln salinity versus time for the first 120 days after the diversion ceased. This flushing rate was similar to the loss rate for total nitrogen (1.75% d^–1), implying no significant net nitrogen losses or gains were occurring inside the Lake. The percent loss of dissolved inorganic nitrogen was higher than that for TN (4.11% d^–1), whereas the loss of organic nitrogen was lower (0.94% d^–1), which suggests a net transfer from inorganic to organic nitrogen. These changes occurred steadily as chlorophyll a concentration ranged from 5 to 200µg l^–1. The results demonstrate the potential significance of the organic nitrogen and interconversion of nitrogen forms when calculating estuarine nitrogen retention budgets and the necessity of measuring all nitrogen forms when performing mass balance estimates. The significance of denitrification in nitrogen removal is minimal at the high loading rates observed during this study. An implication to estuarine water quality management is that the relationships between nitrogen loading and retention are not linear and are controlled by factors other than water residence time.     

Biodiversity in aerobic granule membrane bioreactor at high organic loading rates

Antibacterial peptide CM4 (ABP-CM4) is a small cationic peptide with broad-spectrum activities against bacteria, fungi, and tumor cells, which may possibly be used as an antimicrobial agent. We report here the application of small ubiquitin-related modifier (SUMO) fusion technology to the expression and purification of cationic antibacterial peptide ABP-CM4. The fusion protein expressed in a soluble form was purified to a purity of 90% by Ni-IDA chromatography and 112 mg protein of interest was obtained per liter of fermentation culture. After the SUMO–CM4 fusion protein was cleaved by the SUMO protease at 30 °C for 1 h, the cleaved sample was re-applied to a Ni-IDA. Finally, about 24 mg recombinant CM4 was obtained from 1 l fermentation culture with no less than 96% purity and the recombinant CM4 had similar antimicrobial properties to the synthetic CM4. Thus, the SUMO-mediated peptide expression and purification system potentially could be employed for the production of recombinant cytotoxic peptides.     

Strain-rate sensitivity of the rabbit MCL diminishes at traumatic loading rates

This study was performed to determine whether the viscoelastic behavior of ligaments persists at high rates of loading, such as those associated with sports-related trauma or motor vehicle accidents. Medial collateral ligaments (MCLs) from 22 skeletally mature New Zealand White rabbits were tensile tested quasi-statically and via two impact conditions at displacement rates of 0.17 mm/s (n=22), 640+/-160 mm/s (n=10) and 2500+/-270 mm/s (n=12) (corresponding to strain rates of approximately 1.0%/s, 3660%/s and 14,000%/s, respectively). Despite dramatic increases in displacement rate, only a modest strain-rate effect was observed when the specimens tested quasi-statically were compared to those tested via impact (24% and 37% increases in stiffness and failure load, respectively). There were no differences in the structural (e.g. 145+/-30 and 136+/-29 N/mm stiffness values, respectively) or failure properties (e.g. 434+/-91 and 443+/-154 N failure load values, respectively) of the two impact-tested groups. Our findings suggest that the rabbit MCL is not viscoelastic at loading rates approximating those associated with high-energy trauma.     

Pseudomonas aeruginosa: characteristics of biofilm process

Definition of the biofilm process as one of the types of intercellular bacterial communications is presented. The modern data concerning the structure of the Pseudomonas aeruginosa biofilm matrix and genetic mechanisms necessary for its production are described. Active and passive rejections of biofilm bacteria, which are the basis of bacterial spreading to new surfaces, are discussed. The complexity and chain type of the reactions associated with biofilm formation are emphasized.     

Microarray scanner calibration curves: characteristics and implications

Background

Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration curve can be nonlinear.

Results

By scanning a microarray scanner calibration slide containing known concentrations of fluorescent dyes under 18 PMT gains, we were able to evaluate the differences in calibration characteristics of Cy5 and Cy3. First, the calibration curve for the same dye under the same PMT gain is nonlinear at both the high and low intensity ends. Second, the degree of nonlinearity of the calibration curve depends on the PMT gain. Third, the two PMTs (for Cy5 and Cy3) behave differently even under the same gain. Fourth, the background intensity for the Cy3 channel is higher than that for the Cy5 channel. The impact of such characteristics on the accuracy and reproducibility of measured mRNA abundance and the calculated ratios was demonstrated. Combined with simulation results, we provided explanations to the existence of ratio underestimation, intensity-dependence of ratio bias, and anti-correlation of ratios in dye-swap replicates. We further demonstrated that although Lowess normalization effectively eliminates the intensity-dependence of ratio bias, the systematic deviation from true ratios largely remained. A method of calculating ratios based on concentrations estimated from the calibration curves was proposed for correcting ratio bias.

Conclusion

It is preferable to scan microarray slides at fixed, optimal gain settings under which the linearity between concentration and intensity is maximized. Although normalization methods improve reproducibility of microarray measurements, they appear less effective in improving accuracy.

     

Partial nitritation and anammox of a livestock manure digester liquor and analysis of its microbial community

A swim-bed reactor for partial nitritation with polymeric coagulant treatment and an UASB reactor for anammox were applied to the treatment of livestock manure digester liquor. The partial nitritation was maintained for 32 days under a 1.6 kg N/m³/d nitrogen loading rate (NLR) with an average conversion efficiency of 51%, and achieved 1.65 kg N/m³/d of the maximum nitrite production rate under 2.58 kg N/m³/d of NLR. Although 200 mg/L of TOC remained in the effluent of the partial nitritation reactor, the anammox nitrogen removal rate was not significantly decreased and a relatively high rate of 2.0 kg N/m³/d was obtained under a NLR of 2.2 kg N/m³/d. 16S rRNA gene analysis showed that Nitrosomonas and KSU-1 were dominant in the partial nitritation and anammox reactor, respectively. The results of this study demonstrated that the partial nitritation-anammox process has possibility of applying to the nitrogen removal of livestock manure digester liquor.     

Characterization of aerobic granules by microbial density at different COD loading rates

Aerobic granules were cultivated under temporal alternating aerobic and anoxic conditions without the presence of a carrier material in a sequencing batch reactor (SBR) with a high column height/column diameter ratio. The reactor was operated for 6h per cycle (aerobic: 4.75 h, anoxic: 1.25 h). To determine a new parameter for the definition of aerobic granules, a protocol of 4,6-diamidino-2-phenylindole hydrochloride staining and fluorescence image processing was developed. The d(tm) analysis showed that the increase in the chemical oxygen demand (COD) loading rate promoted no more growth of the aerobic granules. It was inconsistent with the results of the analysis of the sludge volume index (SVI) value but matched well with the results of the COD and nitrogen removal of the SBR and the particle size distribution by LS-PSA. The optimum COD loading rate for aerobic granulation in the SBR was 2.52 kg/m(3)d. When d(tm) was correlated with the biomass concentration and the SVI value during the period of granule formation, d(tm) could be used as a more sensitive and accurate parameter for classifying aerobic granules and optimizing the operational conditions for aerobic granulation processes.     

Potential cause of aerobic granular sludge breakdown at high organic loading rates

Aerobic sludge granules are compact, strong microbial aggregates that have excellent settling ability and capability to efficiently treat high-strength and toxic wastewaters. Aerobic granules disintegrate under high organic loading rates (OLR). This study cultivated aerobic granules using acetate as the sole carbon and energy source in three identical sequencing batch reactors operated under OLR of 9–21.3 kg chemical oxygen demand (COD) m⁻³ day⁻¹. The cultivated granules removed 94–96% of fed COD at OLR up to 9–19.5 kg COD m⁻³ day⁻¹, and disintegrated at OLR of 21.3 kg COD m⁻³ day⁻¹. Most tested isolates did not grow in the medium at >3,000 mg COD l⁻¹; additionally, these strains lost capability for auto-aggregation and protein or polysaccharide productivity. This critical COD regime correlates strongly with the OLR range in which granules started disintegrating. Reduced protein quantity secreted by isolates was associated with the noted poor granule integrity under high OLR. This work identified a potential cause of biological nature for aerobic granules breakdown.     

Inoculum effects on community composition and nitritation performance of autotrophic nitrifying biofilm reactors with counter‐diffusion geometry

The link between nitritation success in a membrane‐aerated biofilm reactor (MABR) and the composition of the initial ammonia‐ and nitrite‐oxidizing bacterial (AOB and NOB) population was investigated. Four identically operated flat‐sheet type MABRs were initiated with two different inocula: from an autotrophic nitrifying bioreactor (Inoculum A) or from a municipal wastewater treatment plant (Inoculum B). Higher nitritation efficiencies (NO₂^‐‐N/NH₄⁺‐N) were obtained in the Inoculum B‐ (55.2–56.4%) versus the Inoculum A‐ (20.2–22.1%) initiated reactors. The biofilms had similar oxygen penetration depths (100–150 µm), but the AOB profiles [based on 16S rRNA gene targeted real‐time quantitative PCR (qPCR)] revealed different peak densities at or distant from the membrane surface in the Inoculum B‐ versus A‐initiated reactors, respectively. Quantitative fluorescence in situ hybridization (FISH) revealed that the predominant AOB in the Inoculum A‐ and B‐initiated reactors were Nitrosospira spp. (48.9–61.2%) versus halophilic and halotolerant Nitrosomonas spp. (54.8–63.7%), respectively. The latter biofilm displayed a higher specific AOB activity than the former biofilm (1.65 fmol cell^?1 h^?1 versus 0.79 fmol cell^?1 h^?1). These observations suggest that the AOB and NOB population compositions of the inoculum may determine dominant AOB in the MABR biofilm, which in turn affects the degree of attainable nitritation in an MABR.     

Growth characteristics of Nostoc flagelliforme at intermittent elevated CO2 concentrations

Algal cultivation is a potential candidate for CO₂ mitigation. CO₂ plays important roles in mass cultivation of algae, including supplying carbon source and adjusting medium pH. To assess the possibility of using edible cyanobacterium Nostoc flagelliforme as carbon storage device, the growth characteristics of N. flagelliforme batch cultured under elevated CO₂ concentrations (0, 2.5, 5, 20, and 40%) were investigated in this study. Results showed that the net photosynthetic rate, efficiency and carbon sequestration rate at 20% CO₂ were increased at a maximum of 121 μmol O₂ (mg chla)^?1 h^?1 8.40% and 0.17 g CO₂ L^?1 day^?1, and increased by 0.42, 1.03 and 1.13 folds compared with that of the control, respectively. Higher CO₂ concentration resulted in the declines in photosynthetic rate, efficiency and carbon sequestration rate because of medium pH reduction. Accordingly, the dry cell weight, amount of exopolysaccharides and protein content of N. flagelliforme cells at 20% CO₂ were obtained at a maximum of 1.45 g L^?1, 54.98 mg L^?1 and 57.75%, increased by 0.93, 0.29 and 0.8 folds compared with that of the control, respectively. These results provided important information for CO₂ mitigation by N. flagelliforme and would shed more light on elucidating the mechanisms of CO₂ tolerance in cyanobacterium.     

Methanotrophic attached-film reactor development and biofilm characteristics

The feasibility of using methanotrophs in an attached-film, fluidized-bed (MAFFB) reactor system has been under investigation since 1987. Mixed culture, methane-utilizing attached biofilms were developed on diatomaceous earth particles and on granular activated carbon. The required feed gases, methane and oxygen, were supplied to the attached biofilm in disolved form using separate gas-liquid aeration columns. Biofilm growth was steady despite low influent dissolved methane concentrations (1 to 3 mg/L). A breeder MAFFB operated consistently for 4.1 years with attached biofilm concentrations as high as 51.7 g VS/L static-bed with minimal biomass wasting and with minimal buffer and nutrient inputs. The maximum biomass concentration observed was 75.6 g VS/L static-bed in a MAFFB reactor treating trichloroethene. Biofilm thickness reached 160 mum with typical values of 70 mum under methane and oxygen growht-rate-limited conditions. Biofilm densities of 120 to 190 g VS/L film were observed. Growth rates varied from <0.01/d to 0.17/d. Greater than 90% of the biomass concentration in the bed was attached, and effluent total suspended solids ranged from 5 to 74 mg/L, with an average of 24 mg/L over 27 runs in four MAFFB systems at upflow velocities of 11.4 to 25 m/h. Heterotrophic attached-film methanotrophs appear to be stable and useful for applications in toxics treatment, and other product manipulations. (c) 1992 John Wiley & Sons, Inc.     

曲霉生物膜的形成过程与结构特征

目的 研究曲霉生物膜的形成过程和结构特征.方法 我们利用一个曲霉生物膜体外模型研究其形成过程和结构特征.将200 μL浓度为1×10<'5>孢子/mL的受试曲霉(烟曲霉AF293,黄曲霉BMU03940,土曲霉BMU00802,黑曲霉BMU04689)的孢子悬液加到24孔组织培养板中的无菌塑料细胞培养盖玻片上,37℃孵育不同时间(0、2、4、8、10、12、16、18、24、48、72 h),加入25 μmol/L的FUN-1室温避光染色后,用波长488 nm激光激发,通过共聚焦激光扫描显微镜观察曲霉生物膜的形成过程;再用波长为488 am和633 am激光同时激发,将两个波长下的图像叠加后观察曲霉生物膜的活力;利用:XYZ轴成像观察其结构特征.在上述不同的时间点用钙荧光白染色后,用波长为405 nm的紫外光激发,观察曲霉生物膜细胞外基质的产生.结果 烟曲霉AF293在第4 h即开始有散在的孢子黏附于盖玻片上;8 h时孢子开始萌芽,10～12 h菌丝延长形成单细胞层;16～20 h菌丝缠绕形成多层立体结构;24 h形成一个具有复杂的三维立体结构特征的多细胞菌落,菌丝有序排列,细胞外基质弥散的分布在菌丝的周围;48～72 h生物膜逐渐成熟.成熟的烟曲霉生物膜是由细胞外基质包裹的有序排列的菌丝形成的复杂立体结构.黄曲霉BMU03940、土曲霉BMU00802、黑曲霉BMU04689与烟曲霉AF293有类似的生物膜发育阶段,包括黏附、孢子萌芽、菌丝延长、菌丝有序排列形成三维立体结构.结论 烟曲霉、黄曲霉、土曲霉和黑曲霉在体外都能形成典型的生物膜,它的形成过程和结构特征与其他真菌生物膜类似.     

The mechanical behaviour of intracondylar cancellous bone of the femur at different loading rates

The compressive properties of human cancellous bone of the distal intracondylar femur in its wet condition were determined. Specimens were obtained from six cadaveric femora and were tested at a strain rate of 0.002, 0.10 and 9.16 sec⁻¹. It was found that the compressive strength decreases with an increasing vertical distance from the joint. The highest compressive strength level was recorded in the posterior medial condyle. Correlations among the mechanical properties, the bulk specimen density and the bone mineral content yield (i) highly significant correlations between the compressive strength and the elastic modulus (ii) highly significant correlations between the compressive strength or the modulus of elasticity and the bulk specimen density (iii) a doubtful correlation between the compressive strength and the bone mineral content. All recorded graphs of the impact loaded specimens displayed several well defined stress peaks, unlike the graphs recorded at low loading rates. It can be concluded that upon impact loading the localized trabecular failure which is associated with each peak, does not affect the spongy bone's stress capacity in a detrimental way.     

Treatment of urban wastewater in a membrane bioreactor at high organic loading rates.

Membrane bioreactors can replace the activated sludge process and the final clarification step in municipal wastewater treatment. The combination of bioreactor and crossflow microfiltration allows for a high chemical oxygen demand (COD) reduction of synthetic wastewater. From biomass, grown at high production rates in the aerobic bioreactor, energy rich biogas can be obtained in a subsequent anaerobic bioreactor. In this paper, experimental data from a laboratory scale membrane bioreactor are presented. The degradation of synthetic wastewater at short hydraulic retention times down to 1.5 h has been studied. The organic loading rate (OLR) has been varied in the range of 6-13 kg m(-3) per day. At steady state a high quality filtrate could be obtained at different operating conditions. At biomass concentrations of 10-22 g l(-1), COD reduction was above 95%.     

Thermophiles: A life at elevated temperatures

Interest in the ecology, physiology and evolution of microorganisms adapted to growth at relatively high temperatures (up to 110°C) has increased enormously during the past two decades. This interest was stimulated by the discovery of marine hydrothermal vent ecosystems, and also by awareness of the potential of thermophilic microbes in biotechnological processes. Subsequent attempts to isolate new thermophilic organisms have been very successful. Moreover, these results, in combination with much-improved techniques for studying the phylogeny of microorganisms, have renewed interest in the evolution of microbes and the early development of life.     

Cheek pouch capacities and loading rates of heteromyid rodents

Rodents of the family Heteromyidae are proficient gatherers and hoarders of seeds. A major component of their adaptive specialization for harvesting and transporting seeds is their spacious, fur-lined cheek pouches. Precise measurements of cheek pouch capacities are essential if ecologists are to understand the foraging ecology, possible constraints on locomotion patterns, and competitive relationships of heteromyid rodents. To measure the size of these cheek pouches and the rate at which animals load seeds into their pouches during seed harvest, we attracted 56 individuals representing ten species of heteromyid rodents to bait stations in the field and allowed them to fill their cheek pouches with seeds several times while we observed and timed the events with the aid of night-vision equipment. The largest load taken by each individual was used as an estimate of its cheek pouch capacity. At the end of observations, each subject was captured and its mass and other data gathered. The allometric relationship between cheek pouch capacity and body mass for ten species of heteromyids was significant [pouch capacity (ml) = 0.148 body mass (g)^0.992, r ²=0.91, P<0.0001]. The regression coefficient is ≈1.0, which indicates that the volume of the cheek pouches scales in direct proportion to body size. When the data were subdivided into quadrupeds (Perognathus and Chaetodipus) and bipeds (Dipodomys) (n=5 for each), the relationships between pouch capacity and body mass were significant, but the two regressions were not significantly different from each other. When all loads (full and partial) were considered, subjects filled their cheek pouches an average of 93 ± 10% of pouch capacity (n=185). Cheek pouch capacities from published studies of artificially filled pouches of heteromyids in the laboratory averaged about 40% below the field measurements obtained here. The allometric relationship between mean loading rate and body mass was also significant [seeds/s=1.067 bodymass (g)^0.830, r ²=0.85,P=0.0011), but when quadrupeds and bipeds were considered separately, the relationships were not significant. Seed densities and bulk densities were used to calculate packing coefficients for seed species, which, when used in conjunction with the allometric relationship between cheek pouch capacity and body size, can be used to estimate the maximum load carried by a heteromyid. Except for the very largest kangaroo rat species, a full pouch load of Indian ricegrass seeds represents less than the daily energy requirements of an active heteromyid. Received: 3 March 1997 / Accepted: 15 July 1997