Current progress of the biological single-ion microbeam at FUDAN

A biological microbeam for precisely positioned single-ion/single cell irradiation is built in the Institute of Modern Physics in Fudan University, Shanghai, China, based on the tandem accelerator (2 × 3MV) in the laboratory. In this paper, the developing progress of the FUDAN microbeam is reported, including the newly constructed beam line, the microbeam collimator, the ion detection system, and the cell-imaging and targeting systems. Statistical models are proposed for evaluating the spatial resolution and dosage precision of the microbeam. By taking the collimated ions as a Gaussian beam, the spatial resolution can be evaluated by the full width at half maximum of the 2-D Gaussian distribution, which is determined by fitting the proportions of peripheral pits outside specific radii in the pit clusters etched on ion track detectors to a 2-D Gaussian distribution. In the preset hitting of defined ion number, by taking the real delivered number of ions as an independent identically distributed random variable (iidrv), according to the Law of Large Numbers and Central Limit Theorem, the expected value μ and standard deviation σ of the real delivered ion number in a preset N-ion hitting can be determined by approaching the normal distribution of N (μ, σ ²/n) with the proportions of the mean counts of pits in multiple pit clusters on ion track detectors. By the values of μ, σ and additional assumptions, statistical dosage precision evaluations can be made on the preset hitting. From the linear fit curve of μ(N) and the power function fit curve of σ(N) on different preset ion numbers, characteristic factors k, b, A, p can be extracted for a precision evaluation independent of the specific preset ion number.     

A model of photosystem II for the analysis of fast fluorescence rise in plant leaves

The polyphasic patterns of fluorescence induction rise in pea leaves in vivo and after the treatment with ionophores have been studied using a Plant Efficiency Analyzer. To analyze in detail photosystem II (PS II) electron transfer processes, an extended PS II model was applied, which included the sums of exponential functions to specify explicitly the light-driven formation of the transmembrane electric potential (ΔΨ(t)) as well as pH in the lumen (pH_L(t)) and stroma (pH_S(t)). PS II model parameters and numerical coefficients in ΔΨ(t), pH_L(t), and pH_S(t) were evaluated to fit fluorescence induction data for different experimental conditions: leaf in vivo or after ionophore treatment at low or high light intensity. The model imitated changes in the pattern of fluorescence induction rise due to the elimination of transmembrane potential in the presence of ionophores, when ΔΨ = 0 and pH_L(t), pH_S(t) changed to small extent relative to control values in vivo, with maximum ΔΨ(t) ∼ 90 mV and ΔΨ(t) ∼ 40 mV for the stationary state at ΔpH ≅ 1.8. As the light intensity was increased from 300 to 1200 μmol m⁻² s⁻¹, the heat dissipation rate constants increased threefold for nonradiative recombination of P680⁺Phe⁻ and by ∼30% for P680⁺Q_A⁻. The parameters ΔΨ, pH_S and pH_L were analyzed as factors of PS II redox state populations and fluorescence yield. The kinetic mechanism of fluorescence quenching is discussed, which is related with light-induced lumen acidification, when ⁺Q_A⁻ and P680⁺ recombination probability increases to regulate the Q_A reduction.     

Longevity and growth efficiency of two deep-dwelling Arctic zoarcids and comparison with eight other zoarcid species from different climatic regions

Our basic knowledge of the ecology, especially the age and growth of polar deep-sea biota is still scarce. This study provides first data about the age and growth of the two abundant Arctic fish species Lycodes frigidus and Lycodes squamiventer (Zoarcidae). Lycodes frigidus was caught at the deeper parts (1,546–3,576 m depth) of the HAUSGARTEN observatory (HG), west of Svalbard. The congener Lycodes squamiventer was caught at two HG stations (1,273–1,546 m) and at the H?kon Mosby Mud Volcano (HMMV, ~1,250 m), a cold seep in the southwestern Barents Sea. Age was determined by sagittal otolith increment analysis. Growth performance was assessed by fitting age–length data to a von Bertalanffy growth equation. Our data suggest that L. frigidus and L. squamiventer attain maximum ages of 33 and 21 years, respectively. Lycodes squamiventer from the HMMV had significantly higher growth rates and their maximum age and length was slightly lower compared to conspecifics from the shallow HG stations. Von Bertalanffy growth equations were L _t  = 58.9 ∗ (1 − e^(−0.042*t)) for L. frigidus, and L _t  = 25.3 ∗ (1 − e^(−0.074*t)) and L _t  = 24.2 ∗ (1 − e^{(−0.099 * t)}) for L. squamiventer from HG and the HMMV, respectively. A comparison of these data with those of eight other zoarcids indicates that growth performances are correlated with temperature: the higher the annual mean temperatures experienced, the higher the growth rates. However, maximum ages decrease with increasing temperatures.     

Drift-ice and under-ice water communities in the Gulf of Bothnia (Baltic Sea)

The algal, protozoan and metazoan communities within different drift-ice types (newly formed, pancake and rafted ice) and in under-ice water were studied in the Gulf of Bothnia in March 2006. In ice, diatoms together with unidentified flagellates dominated the algal biomass (226 ± 154 μg ww l⁻¹) and rotifers the metazoan and protozoan biomass (32 ± 25 μg ww l⁻¹). The under-ice water communities were dominated by flagellates and ciliates, which resulted in lower biomasses (97 ± 25 and 21 ± 14 μg ww l⁻¹, respectively). The under-ice water and newly formed ice separated from all other samples to their own cluster in hierarchical cluster analysis. The most important discriminating factors, according to discriminant analysis, were chlorophyll-a, phosphate and silicate. The under-ice water/newly formed ice cluster was characterized by high nutrient and low chlorophyll-a values, while the opposite held true for the ice cluster. Increasing trends in chlorophyll-a concentration and biomass were observed with increasing ice thickness. Within the thick ice columns (>40 cm), the highest chlorophyll-a concentrations (6.6–22.2 μg l⁻¹) were in the bottom layers indicating photoacclimation of the sympagic community. The ice algal biomass showed additional peaks in the centric diatom-dominated surface layers coinciding with the highest photosynthetic efficiencies [0.019–0.032 μg C (μg Chl-a ⁻¹ h⁻¹) (μE m⁻² s⁻¹)⁻¹] and maximum photosynthetic capacities [0.43-1.29 μg C (μg Chl-a ⁻¹ h⁻¹)]. Rafting and snow-ice formation, determined from thin sections and stable oxygen isotopic composition, strongly influenced the physical, chemical and biological properties of the ice. Snow-ice formation provided the surface layers with nutrients and possibly habitable space, which seemed to have favored centric diatoms in our study.     

Theory of transport in linear biological systems: I. Fundamental integral equation

The conditions under which the output,γ _b (t), of a biological system is related to the input,γ _a (t), by an integral equation of the typeγ _b (t) = ∫ ₀ ^t γ _a (ω)w(t−ω)dω, where ω(t) is a transport functioncharacteristic of the system, are analyzed in detail. Methods of solving this type of integral equation are briefly discussed. The theory is then applied to problems in tracer kinetics in which input and output are sums of exponentials, and explicit formulae, which are applicable whether or not the pool is uniformly mixed, are derived for “turnover time” and “pool” size.     

Species abundance distributions in neutral models with immigration or mutation and general lifetimes

We consider a general, neutral, dynamical model of biodiversity. Individuals have i.i.d. lifetime durations, which are not necessarily exponentially distributed, and each individual gives birth independently at constant rate λ. Thus, the population size is a homogeneous, binary Crump–Mode–Jagers process (which is not necessarily a Markov process). We assume that types are clonally inherited. We consider two classes of speciation models in this setting. In the immigration model, new individuals of an entirely new species singly enter the population at constant rate μ (e.g., from the mainland into the island). In the mutation model, each individual independently experiences point mutations in its germ line, at constant rate θ. We are interested in the species abundance distribution, i.e., in the numbers, denoted I _n (k) in the immigration model and A _n (k) in the mutation model, of species represented by k individuals, k = 1, 2, . . . , n, when there are n individuals in the total population. In the immigration model, we prove that the numbers (I _t (k); k ≥ 1) of species represented by k individuals at time t, are independent Poisson variables with parameters as in Fisher’s log-series. When conditioning on the total size of the population to equal n, this results in species abundance distributions given by Ewens’ sampling formula. In particular, I _n (k) converges as n → ∞ to a Poisson r.v. with mean γ/k, where γ : = μ/λ. In the mutation model, as n → ∞, we obtain the almost sure convergence of n ⁻¹ A _n (k) to a nonrandom explicit constant. In the case of a critical, linear birth–death process, this constant is given by Fisher’s log-series, namely n ⁻¹ A _n (k) converges to α ^k /k, where α : = λ/(λ + θ). In both models, the abundances of the most abundant species are briefly discussed.     

Fast Kalman filtering on quasilinear dendritic trees

Optimal filtering of noisy voltage signals on dendritic trees is a key problem in computational cellular neuroscience. However, the state variable in this problem—the vector of voltages at every compartment—is very high-dimensional: realistic multicompartmental models often have on the order of N = 10⁴ compartments. Standard implementations of the Kalman filter require O(N ³) time and O(N ²) space, and are therefore impractical. Here we take advantage of three special features of the dendritic filtering problem to construct an efficient filter: (1) dendritic dynamics are governed by a cable equation on a tree, which may be solved using sparse matrix methods in O(N) time; and current methods for observing dendritic voltage (2) provide low SNR observations and (3) only image a relatively small number of compartments at a time. The idea is to approximate the Kalman equations in terms of a low-rank perturbation of the steady-state (zero-SNR) solution, which may be obtained in O(N) time using methods that exploit the sparse tree structure of dendritic dynamics. The resulting methods give a very good approximation to the exact Kalman solution, but only require O(N) time and space. We illustrate the method with applications to real and simulated dendritic branching structures, and describe how to extend the techniques to incorporate spatially subsampled, temporally filtered, and nonlinearly transformed observations.     

Mutagenic and Genotoxic Effects of <Emphasis Type="Italic">cis</Emphasis>-(Dichloro)tetraammineruthenium(III) Chloride on Human Peripheral Blood Lymphocytes

Chemotherapeutic agents play an important role in cancer treatment mostly due their systemic action on human organism allowing access to liquid tumors and even metastases. Among these drugs, ruthenium compounds have been showing promising results to treat tumors and represent an important development of new antitumor therapy. This study presents the evaluation of cis-(dichloro)tetraammineruthenium(III) chloride, cis-[RuCl₂(NH₃)₄]Cl, genotoxic effects using human peripheral blood lymphocytes cultured in vitro. Mitotic index (MI), chromosome aberrations (CA), and DNA damage using the comet assay were analyzed. MI in human peripheral blood lymphocyte cultures treated with 1, 10, 100, and 1,000 μg mL⁻¹ cis-[RuCl₂(NH₃)₄]Cl were 5.9%, 4.6%, 3.9%, and 0%, respectively. Doxorubicin chloridate was used as the positive control. CA derived from 1, 10, and 100 μg mL⁻¹ concentrations were defined as spontaneous when compared with the negative control, and at the concentration of 1,000 μg mL⁻¹, the cell cycle was inhibited (IM = 0%). Results obtained for the comet assay using cis-[RuCl₂(NH₃)₄]Cl suggest that this compound has no genotoxic activity against cultured human peripheral blood lymphocytes.     

Comparative Permeabilities of the Paracellular and Transcellular Pathways of Corneal Endothelial Layers

Layers of rabbit corneal endothelial cells were cultured on permeable inserts. We characterized the diffusional permeability of the cell layer to nonelectrolyte and charged molecules and compared the diffusional and filtration permeabilities of the paracellular and transcellular pathways. We determined the rates of diffusion of ³H- and ¹⁴C-labeled nonelectrolyte test molecules and estimated the equivalent pore radius of the tight junction. Negatively charged molecules permeate slower than neutral molecules, while positively charged molecules permeate faster. Palmitoyl-dl-carnitine, which opens tight junctions, caused an increase of permeability and equivalent pore radius. Diffusional water permeability was determined with ³H-labeled water; the permeabilities of the tight junction and lateral intercellular space were calculated using tissue geometry and the Renkin equation. The diffusional permeability (P _d ) of the paracellular pathway to water is 0.57 μm s⁻¹ and that of the transcellular path is 2.52 μm s⁻¹. From the P _d data we calculated the filtration permeabilities (P _f ) for the paracellular and transcellular pathways as 41.3 and 30.2 μm s⁻¹, respectively. In conclusion, the movement of hydrophilic molecules through tight junctions corresponds to diffusion through negatively charged pores (r = 2.1 ± 0.35 nm). The paracellular water permeability represents 58% of the filtration permeability of the layer, which points to that route as the site of sizable water transport. In addition, we calculated for NaCl a reflection coefficient of 0.16 ≤ σ_NaCl ≤ 0.33, which militates against osmosis through the junctions and, hence, indirectly supports the electro-osmosis hypothesis.     

Response of cyanobacteria to arsenic toxicity

Arsenic content of cyanobacterial biomass, soil and water samples from arsenic-contaminated area of eastern India were estimated. It was found that arsenic content in cyanobacterial biomass (276.9 μg g⁻¹) was more than soil (19.01 μg g⁻¹) or water sample (244.13 μg L⁻¹). Shallow tube well water showed more arsenic (244.13 μg L⁻¹) than deep tube well water (146.13 μg L⁻¹). Arsenic resistant genera recorded from the contaminated area were Oscillatoria princeps, Oscillatoria limosa, Anabaena sp. and Phormidium laminosum. Among these, P. laminosum was isolated and exposed to different concentration of Arsenic in vitro (0.1–100 ppm) to study the toxicity level of arsenic. Modulation in stress enzymes and stress-related compounds were studied in relation to lipid peroxidase, catalase, super oxide dismutase (SOD), ascorbate peroxidase (APX), reduced glutathione and carotenoids in arsenic exposed biomass to understand the resistance mechanism of the genus both in laboratory condition as well as in natural condition. Arsenic content of cyanobacterial biomass from contaminated area was more (276.9 μg g⁻¹) than laboratory exposed sample (37.17 μg g⁻¹), indicating bioconcentration of arsenic in long-term-exposed natural biomass. Overall, more activity of catalase was recorded in cyanobacterial biomass of natural condition whereas SOD and APX were at higher level in laboratory culture.     

Seed germination and seedling physiology of Larix kaempferi and Pinus densiflora in seedbeds with charcoal and elevated CO2

We investigated the effect of ectomycorrhizal colonization, charcoal and CO₂ levels on the germination of seeds of Larix kaempferi and Pinus densiflora, and also their subsequent physiological activity and growth. The seeds were sown in brown forest soil or brown forest soil mixed with charcoal, at ambient CO₂ (360 μmol mol⁻¹) or elevated CO₂ (720 μmol mol⁻¹), with or without ectomycorrhiza. The proportions of both conifer seeds that germinated in forest soil mixed with charcoal were significantly greater than for seeds sown in forest soil grown at each CO₂ level (P < 0.05; t-test). However, the ectomycorrhizal colonization rate of each species grown in brown forest soil mixed with charcoal was significantly lower than in forest soil at each CO₂ treatment [CO₂] (P < 0.01; t-test). The phosphorus concentrations in needles of each seedling colonized with ectomycorrhiza and grown in forest soil were greater than in nonectomycorrhizal seedlings at each CO₂ level, especially for L. kaempferi seedlings (P < 0.05; t-test), but the concentrations in seedlings grown in brown forest soil mixed with charcoal were not increased at any CO₂ level. Moreover, the maximum net photosynthetic rate of each seedling for light and CO₂ saturation (P _max) increased when the seedlings were grown with ectomycorrhiza at 720 μmol mol⁻¹ [CO₂]. Ectomycorrhizal colonization led to an increase in the stem diameter of each species grown in each soil treatment at each CO₂ level. However, charcoal slowed the initial growth of both species of seedling, constraining ectomycorrhizal development. These results indicate that charcoal strongly assists seed germination and physiological activity.     

Evaluation of the cytogenetic damage induced by the organophosphorous insecticide acephate

The organophosphorous insecticide acephate was tested for its ability to induce in vitro cytogenetic effect in human peripheral lymphocytes by using the chromosomal aberrations (CAs), sister chromatid exchange (SCE) and micronuclei (MN) assay. The level of nuclear DNA damage of acephate was evaluated by using the comet assay. Concentrations of 12.5, 25, 50, 100 and 200 μg mL⁻¹ of acephate were used. All concentrations of acephate induced significant increase in the frequency of CAs and in the formation of MN dose dependently (r = 0.92 at 24 h, r = 0.95 at 48 h for CAs, r = 0.87 for MN). A significant increase was observed in induction of SCE at 50, 100 and 200 μg mL⁻¹ concentrations during 24 h treatment and at all concentrations (except 12.5 μg mL⁻¹) during 48 h treatment period in a dose-dependent manner (r = 0.84 at 24 h, r = 0.88 at 48 h). Acephate did not affect the replicative index and cytokinesis-block proliferation index (CBPI). However, it significantly decreased the mitotic index at all three highest concentrations (50, 100, 200 μg mL⁻¹) for 24 h treatment and at all concentrations (except 12.5 μg mL⁻¹) for 48 h treatment, dose-dependently (r = 0.94 at 24 h, r = 0.92 at 48 h). A significant increase in mean comet tail length was observed at 100 and 200 μg mL⁻¹ concentrations compared with negative control in a concentration-dependent manner (r = 0.94). The mean comet tail intensity was significantly increased at only 200 μg mL⁻¹ concentration. The present results indicate that acephate is a clastogenic, cytotoxic agent and it causes DNA damage at high concentrations in human lymphocytes in culture.     

Establishment and characterization of <Emphasis Type="Italic">Prosopis laevigata</Emphasis> (Humb. &; Bonpl. ex Willd) M.C. Johnst. cell suspension culture: a biotechnology approach for mesquite gum production

This study presents a protocol for the establishment of Prosopis laevigata cell suspension culture as a strategy to obtain an in vitro mesquite gum productive cell line. The callus used for this purpose was obtained with hypocotyls from 15-day-old plantlets, placed on Murashige–Skoog medium with two different plant growth regulators (PGRs), 2,4,5-trichlorophenoxy acetic acid (2,4,5-T; 5.0 μM) and kinetin (KIN; 5.0 μM). With this PGRs treatment, after four subcultures (30 days each) an exuded gum-like substance was observed on the callus surface. The growth kinetics of the cell suspension culture showed a specific cell growth rate (μ) of 0.14 d⁻¹ and doubling time (t _d) of 6.6 days, respectively. The gum-like substance from callus culture and the broth from cell suspension culture were subjected to chemical analysis and compared with the mesquite gum exuded from wild trees. Both, gum-like substance from callus culture and the broth from cell suspension culture showed the presence of Arabinogalactan-proteins, and their polysaccharide fraction presented the same monosaccharides as those isolated from mesquite gum. In addition, the emulsifying properties of gum-like substance from callus culture and the broth from cell suspension culture were compared to those of mesquite gum and all three samples exhibited similar emulsifying capacity and emulsification stability.     

Fractional exponential decay in the capture of ligands by randomly distributed traps in one dimension

In many biophysical and biochemical experiments one observes the decay of some ligand population by an appropriate system of traps. We analyse this decay for a one-dimensional system of randomly distributed traps, and show that one can distinguish three different regimes. The decay starts with a fractional exponential of the form exp[−(t/t ₀)^1/2], which changes into a fractional exponential of the form exp[−(t/t ₁)^1/3] for long times, which in its turn changes into a pure exponential time dependence, i.e. exp[−t/t ₂] for very long times. With these three regimes, we associate three time scales, related to the average trap density and the diffusion constant characterizing the motion of the ligands.     

Winter-time ecology in the Bothnian Bay, Baltic Sea: nutrients and algae in fast ice

Landfast ice algal communities were studied in the strongly riverine-influenced northernmost part of the Baltic Sea, the Bothnian Bay, during the winter-spring transition of 2004. The under-ice river plume, detected by its low salinity and elevated nutrient concentrations, was observed only at the station closest to the river mouth. The bottommost ice layer at this station was formed from the plume water (brine volume 0.71%). This was reflected by the low flagellate-dominated (93%) algal biomass in the bottom layer, which was one-fifth of the diatom-dominated (74%) surface-layer biomass of 88 μg C l⁻¹. Our results indicate that habitable space plays a controlling role for ice algae in the Bothnian Bay fast ice. Similarly to the water column in the Bothnian Bay, average dissolved inorganic N:P-ratios in the ice were high, varying between 12 and 265. The integrated chlorophyll a (0.1–2.2 mg m⁻²) and algal biomass in the ice (1–31 mg C m⁻²) correlated significantly (Spearman ρ = 0.79), with the highest values being measured close to the river mouth in March and during the melt season in April. Flagellates <20 μm generally dominated in both the ice and water columns in February–March. In April the main ice-algal biomass was composed of Melosira arctica and unidentified pennate diatoms, while in the water column Achnanthes taeniata, Scrippsiella hangoei and flagellates dominated. The photosynthetic efficiency (0.003–0.013 (μg C [μg chl a ⁻¹] h⁻¹)(μE m⁻²s⁻¹)⁻¹) and maximum capacity (0.18–1.11 μg C [μg chl a ⁻¹] h⁻¹) could not always be linked to the algal composition, but in the case of a clear diatom dominance, pennate species showed to be more dark-adapted than centric diatoms.     

Quasi steady state growth of <Emphasis Type="Italic">Lactococcus lactis</Emphasis> in glucose-limited acceleration stat (A-stat) cultures

Quasi steady state growth of Lactococcus lactis IL 1403 was studied in glucose-limited A-stat cultivation experiments with acceleration rates (a) from 0.003 to 0.06 h⁻² after initial stabilization of the cultures in chemostat at D = 0.2–0.3 h⁻¹. It was shown that the high limit of quasi steady state growth rate depended on the acceleration rate used—at an acceleration rate 0.003 h⁻² the quasi steady state growth was observed until μ _crit = 0.59 h⁻¹, which is also the μ _max value for the culture. Lower values of μ _crit were observed at higher acceleration rates. The steady state growth of bacteria stabilized at dilution rate 0.2 h⁻¹ was immediately disrupted after initiating acceleration at the highest acceleration rate studied—0.06 h⁻². Observation was made that differences [Δ(μ − D)] of the specific growth rates from pre-programmed dilution rates were the lowest using an acceleration rate of 0.003 h⁻² (< 4% of preset changing growth rate). The adaptability of cells to follow preprogrammed growth rate was found to decrease with increasing dilution rate—it was shown that lower acceleration rates should be applied at higher growth rates to maintain the culture in the quasi steady state. The critical specific growth rate and the biomass yields based on glucose consumption were higher if the medium contained S ₀ = 5 g L⁻¹ glucose instead of S ₀ = 10 g L⁻¹. It was assumed that this was due to the inhibitory effect of lactate accumulating at higher concentrations in the latter cultures. Parallel A-stat experiments at the same acceleration and dilution rates showed good reproducibility—Δ(μ − D) was less than 5%, standard deviations of biomass yields per ATP produced (Y _ATP), and biomass yields per glucose consumed (Y _XS) were less than 15%.