小鼠胚胎干细胞在六种培养体系的培养观察

目的　观察小鼠胚胎干细胞在六种培养体系中的生长情况。方法　小鼠胚胎干细胞 (ESD3细胞株 )在以下六种培养体系中培养 :1 .原代小鼠胚胎成纤维细胞 (MEF)有血清培养 ,2 .MEF无血清培养 ,3.SNL细胞有血清培养 ,4.LIF(白血病抑制因子 )有血清无饲养层培养 ,5.LIF无血清无饲养层培养 ,6.大鼠肝细胞 (BRL)条件培养基培养。经体外培养 1 0代后 ,观察其克隆形态 ,同时进行碱性磷酸酶检测并将ES细胞接种于裸小鼠皮下 ,观察ESD3的未分化状态和多潜能性。结果　六种培养体系培养的ESD3具有典型的ES细胞克隆形态 :巢状 (集落状 )隆起生长 ,边缘清楚 ,表面平滑 ,结构致密 ;AKP强阳性 ;裸小鼠体内形成了由多种组织构成的畸胎瘤。结论　六种培养体系均能支持ESD3生长 ,并能保持其未分化性和多潜能性 ,为ES细胞的应用研究奠定了良好的基础。     

Smoldyn on graphics processing units: massively parallel Brownian dynamics simulations

Space is a very important aspect in the simulation of biochemical systems; recently, the need for simulation algorithms able to cope with space is becoming more and more compelling. Complex and detailed models of biochemical systems need to deal with the movement of single molecules and particles, taking into consideration localized fluctuations, transportation phenomena, and diffusion. A common drawback of spatial models lies in their complexity: models can become very large, and their simulation could be time consuming, especially if we want to capture the systems behavior in a reliable way using stochastic methods in conjunction with a high spatial resolution. In order to deliver the promise done by systems biology to be able to understand a system as whole, we need to scale up the size of models we are able to simulate, moving from sequential to parallel simulation algorithms. In this paper, we analyze Smoldyn, a widely diffused algorithm for stochastic simulation of chemical reactions with spatial resolution and single molecule detail, and we propose an alternative, innovative implementation that exploits the parallelism of Graphics Processing Units (GPUs). The implementation executes the most computational demanding steps (computation of diffusion, unimolecular, and bimolecular reaction, as well as the most common cases of molecule-surface interaction) on the GPU, computing them in parallel on each molecule of the system. The implementation offers good speed-ups and real time, high quality graphics output     

Characterization of compost biofiltration system degrading dichloromethane

The effects of acclimatization of microbial populations, compound concentration, and media pH on the biodegradation of low concentration dichloromethane emissions in biofiltration systems was evaluated. Greater than 98% removal efficiency was achieved for dichloromethane at superficial velocities from 1 to 1.5 m(3)/m(3). min (reactor residence times of 1 and 0.7 min, respectively) and inlet concentrations of 3 and 50 ppm Although acclimatization of microbial populations to toluene occurred within 2 weeks of operation start-up, initial dichloromethane acclimatization took place over a period of 10 weeks. This period was shortened to 10 days when a laboratory grown consortium of dichloromethane degrading organism, isolated from a previously acclimatized column, was introduced into fresh biofilter media. The mixed culture consisted to 12 members, which together were able to degrade dichloromethane at concentrations up to 500 mg/L. Only one member of the consortium was able to degrade dichloromethane were sustained for more than 4 months in a biofilter column receiving an inlet gas stream with 3 ppm(v) of dichloromethane acidification of the column and resulting decline in performance occurred when a 50-ppm(v) inlet concentration was used. A biofilm model incorporating first order biodegradation kinetics provided a good fit to observed concentration profiles, and may prove to be a useful tool for designing biofiltration systems for low concentration VOC emissions. (c) 1994 John Wiley & Sons, Inc.     

Novel camptothecin analogue (gimatecan)-containing liposomes prepared by the ethanol injection method

Small-sized liposomes have several advantages as drug delivery systems, and the ethanol injection method is a suitable technique to obtain the spontaneous formation of liposomes having a small average radius. In this paper, we show that liposomal drug formulations can be prepared in situ, by simply injecting a drug-containing lipid(s) organic solution into an aqueous solution. Several parameters should be optimized in order to obtain a final suitable formulation, and this paper is devoted to such an investigation. Firstly, we study the liposome size distributions determined by dynamic light scattering (DLS), as function of the lipid concentration and composition, as well as the organic and aqueous phases content. This was carried out, firstly, by focusing on POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) then on the novel L-carnitine derivative PUCE (palmitoyl-(R)-carnitine undecyl ester chloride), showing that it is possible to obtain monomodal size distributions of rather small vesicles. In particular, depending on the conditions, it was possible to achieve a population of liposomes with a mean size of 100 nm, when a 50 mM POPC ethanol solution was injected in pure water; in the case of 50 mM PUCE the mean size was around 30 nm, when injected in saline (0.9% NaCl). The novel anticancer drug Gimatecan, a camptothecin derivative, was used as an example of lipophilic drug loading by the injection method. Conditions could be found, under which the resultant liposome size distributions were not affected by the presence of Gimatecan, in the case of POPC as well as in the case of PUCE. To increase the overall camptothecin concentration in the final liposomal dispersion, the novel technique of "multiple injection method" was used, and up to a final 5 times larger amount of liposomal drug could be reached by maintaining approximately the same size distribution. Once prepared, the physical and chemical stability of the liposome formulations was satisfactory within 24, as judged by DLS analysis and HPLC quantitation of lipids and drug. The Gimatecan-containing liposomes formulations were also tested for in vitro and in vivo activity, against the human nonsmall cell lung carcinoma NCI-H460 and a murine Lewis lung carcinoma 3 LL cell lines. In the in vitro tests, we did not observe any improvement or reduction of the Gimatecan pharmacological effect by the liposomal delivery system. More interestingly, in the in vivo Lewis lung carcinoma model, the intravenously administration of liposomal Gimatecan formulation showed a mild but significant increase of Tumor Volume Inhibition with respect to the oral no-liposomal formulation (92% vs. 86 %, respectively; p < 0.05). Finally, our study showed that the liposomal formulation was able to realize a delivery system of a water-insoluble drug, providing a Gimatecan formulation for intravenous administration with a preserved antitumoral activity.     

Structure of an otter (Lutra lutra) population in Germany – results of DNA and hormone analyses from faecal samples

Population size, one of the basic biological parameters is particularly difficult to estimate for nocturnal animals with cryptic life style and little individual distinctiveness like Eurasian otters (Lutra lutra). Because telemetric methods often fail and also expose the animals to a high risk of injuries and even mortality, we analysed DNA and hormones of spraints to obtain data on population density and structure of free-living otters in a Nature Park in north-eastern Germany. We were able to assign 53 different individual profiles from faecal samples and obtained six more profiles from animals found dead inside the park. The total population estimate (n=59) consisted of at least 32 males and 27 females; 33 animals were adult, 23 younger than 2 years (three of unknown age). Marking points were frequented by up to 12 individuals. Estimated density was one animal per 4.7 km of shoreline. The genotypically estimated total population size was more than 2.5 times as high as estimated in the past census. The method was also suited to compare otter population densities in different areas or at different times in the same area.     

Spin-spin relaxation of the phosphodiester resonance in the 31P NMR spectrum of human brain. The determination of the concentrations of phosphodiester components

The phosphodiester peak in 31P nuclear magnetic resonance spectra of human brain in vivo is often the most prominent feature of the spectrum. We have demonstrated that this resonance exhibits bi-exponential spin-spin relaxation, giving relaxation times of 2 and 10 ms. We interpret this in terms of the two components which make up the peak, bilayer lipids and the small cytosolic phosphates glycerophosphoethanolamine and glycerophosphocholine. Using the relaxation times and the relative peak heights of the two components we have also been able to quantitate the concentration of the bilayer lipids as 20-40 times that of ATP.     

Cytochrome P450 monooxygenase from Clostridium acetobutylicum: a new alpha-fatty acid hydroxylase

Cytochrome P450 monooxygenase from the anaerobic microorganism Clostridium acetobutylicum (CYP152A2) has been produced in Escherichia coli. CYP152A2 was shown to bind a broad range of saturated and unsaturated fatty acids and corresponding methyl esters and demonstrated a high peroxygenase activity of up to 200min(-1) with myristic acid. Although a high concentration of hydrogen peroxide of 200microM was necessary for high activities of the enzyme, it led to a fast enzyme inactivation within 2-4min. This might reflect the natural function of CYP152A2 as a rapid hydrogen peroxide scavenging enzyme. In two different reconstituted systems with NADPH, CYP152A2 was able to convert 10 times more substrate, if provided with flavodoxin and flavodoxin reductase from E. coli and even 30-40 times more substrate with the CYP102A1-reductase from Bacillus megaterium. According to the clear preference for hydroxylation at alpha-position, CYP152A2 can be referred to as fatty acid alpha-hydroxylase.     

Capturing the essence of a metabolic network: A flux balance analysis approach

As genome-scale metabolic reconstructions emerge, tools to manage their size and complexity will be increasingly important. Flux balance analysis (FBA) is a constraint-based approach widely used to study the metabolic capabilities of cellular or subcellular systems. FBA problems are highly underdetermined and many different phenotypes can satisfy any set of constraints through which the metabolic system is represented.Two of the main concerns in FBA are exploring the space of solutions for a given metabolic network and finding a specific phenotype which is representative for a given task such as maximal growth rate. Here, we introduce a recursive algorithm suitable for overcoming both of these concerns. The method proposed is able to find the alternate optimal patterns of active reactions of an FBA problem and identify the minimal subnetwork able to perform a specific task as optimally as the whole.Our method represents an alternative to and an extension of other approaches conceived for exploring the space of solutions of an FBA problem. It may also be particularly helpful in defining a scaffold of reactions upon which to build up a dynamic model, when the important pathways of the system have not yet been well-defined.     

Evaluation of DEPMPO as a spin trapping agent in biological systems

Cellular toxicity, pharmacokinetics, and the in vitro and in vivo stability of the SO3*- spin adduct of the spin trap, 5-diethoxyphosphoryl-5-methyl-1-pyrroline-n-oxide (DEPMPO), was investigated, and the results were compared with those of the widely used spin trap 5,5-dimethyl-1-pyrroline-N-oxide (DMPO). Similar to DMPO, DEPMPO was quickly taken up (<15 min) after intraperitoneal injection, and distributed evenly in the liver, heart, and blood of the mice. In the presence of ascorbate the in vitro stability of the adduct DEPMPO/SO3*- was 7 times better than DMPO/SO3*-. Under in vivo conditions, the spin adduct DEPMPO/SO3*- was 2-4 times more stable than DMPO/ SO3*-, depending on the route of administration of the adducts. Using a low frequency EPR spectrometer, we were able to observe the spin trapped SO3*- radical both with DMPO and DEPMPO directly in the intact mouse. DEPMPO had a detectable spin adduct signal at a concentration as low as 1 mM, as compared to 5 mM for DMPO. We conclude that DEPMPO is potentially a good candidate for trapping radicals in functioning biological systems, and represents an improvement over the commonly used trap DMPO.     

The binding of HIV-1 protease inhibitors to human serum proteins

The non-specific binding of a drug to plasma proteins is an important determinant of its biological efficacy since it modulates the availability of the drug to its intended target. In the case of HIV-1 protease inhibitors, binding to human serum albumin (HSA) and alpha(1)-acid glycoprotein (AAG) appears to be an important modulator of drug bioavailability. From a thermodynamic point of view, the issue of drug availability to the desired target can be formulated as a multiple equilibrium problem in which a ligand is able to bind to different proteins or other macromolecules with different binding affinities. Previously, we have measured the binding thermodynamics of HIV-1 protease inhibitors to their target. In this article, the binding energetics of four inhibitors currently in clinical use (saquinavir, indinavir, ritonavir and nelfinavir) and a second-generation inhibitor (KNI-764) to human HSA and AAG has been studied by isothermal titration calorimetry. All inhibitors exhibited a significant affinity for AAG (K(a) approximately 0.5-10 x 10(5) M(-1)) and a relatively low affinity for HSA (K(a) approximately 5-15 x 10(3) M(-1)). It is shown that under conditions that simulate in vivo concentrations of serum proteins, the inhibitor concentrations required to achieve 95% protease inhibition can be up to 10 times higher than those required in the absence of serum proteins. The effect is compounded in patients infected with drug resistant HIV-1 strains that exhibit a lower affinity for protease inhibitors. In these cases the required inhibitor concentrations can be up to 2000 times higher and beyond the solubility limits of the inhibitors.     

In situ radiation explains the frequency of dioecious palms on islands

Background and AimsDioecy has evolved up to 5000 times in angiosperms, despite the potentially high intrinsic costs to unisexuality. Dioecy prevents inbreeding, which is especially relevant on isolated islands when gene pools are small. Dioecy is also associated with certain dispersal traits, such as fruit size and type. However, the influence of dioecy on other life history traits and island distribution remains poorly understood. Here, we test the effect of dioecy on palm (Arecaceae) speciation rates, fruit size and frequency on islands.MethodsWe used phylogenetic comparative methods to estimate the ancestral state of the sexual system and its impact on speciation rates and fruit size. Frequency of sexual systems, effect of insularity on the probability of being dioecious, and phylogenetic clustering of island dioecious vs. mainland species were inferred. Lastly, we determined the interplay of insularity and sexual system on speciation rates.Key ResultsPalms repeatedly evolved different sexual systems (dioecy, monoecy and polygamy) from a hermaphrodite origin. Differences in speciation rates and fruit size among the different sexual systems were not identified. An effect of islands on the probability of the palms being dioecious was also not found. However, we found a high frequency and phylogenetic clustering of dioecious palms on islands, which were not correlated with higher speciation rates.ConclusionsThe high frequency and phylogenetic clustering may be the result of in situ radiation and suggest an ‘island effect’ for dioecious palms, which was not explained by differential speciation rates. This island effect also cannot be attributed to long-distance dispersal due to the lack of fruit size difference among sexual systems, and particularly because palm dispersal to islands is highly constrained by the interaction between the sizes of fruit and frugivores. Taken together, we suggest that trait flexibility in sexual system evolution and the in situ radiation of dioecious lineages are the underlying causes of the outstanding distribution of palms on islands.     

Seed dispersal anachronisms: rethinking the fruits extinct megafauna ate

Background

Some neotropical, fleshy-fruited plants have fruits structurally similar to paleotropical fruits dispersed by megafauna (mammals >10³ kg), yet these dispersers were extinct in South America 10–15 Kyr BP. Anachronic dispersal systems are best explained by interactions with extinct animals and show impaired dispersal resulting in altered seed dispersal dynamics.

Methodology/Principal Findings

We introduce an operational definition of megafaunal fruits and perform a comparative analysis of 103 Neotropical fruit species fitting this dispersal mode. We define two megafaunal fruit types based on previous analyses of elephant fruits: fruits 4–10 cm in diameter with up to five large seeds, and fruits >10 cm diameter with numerous small seeds. Megafaunal fruits are well represented in unrelated families such as Sapotaceae, Fabaceae, Solanaceae, Apocynaceae, Malvaceae, Caryocaraceae, and Arecaceae and combine an overbuilt design (large fruit mass and size) with either a single or few (<3 seeds) extremely large seeds or many small seeds (usually >100 seeds). Within-family and within-genus contrasts between megafaunal and non-megafaunal groups of species indicate a marked difference in fruit diameter and fruit mass but less so for individual seed mass, with a significant trend for megafaunal fruits to have larger seeds and seediness.

Conclusions/Significance

Megafaunal fruits allow plants to circumvent the trade-off between seed size and dispersal by relying on frugivores able to disperse enormous seed loads over long-distances. Present-day seed dispersal by scatter-hoarding rodents, introduced livestock, runoff, flooding, gravity, and human-mediated dispersal allowed survival of megafauna-dependent fruit species after extinction of the major seed dispersers. Megafauna extinction had several potential consequences, such as a scale shift reducing the seed dispersal distances, increasingly clumped spatial patterns, reduced geographic ranges and limited genetic variation and increased among-population structuring. These effects could be extended to other plant species dispersed by large vertebrates in present-day, defaunated communities.     

Novel Camptothecin Analogue (Gimatecan)‐Containing Liposomes Prepared by the Ethanol Injection Method

Small‐sized liposomes have several advantages as drug delivery systems, and the ethanol injection method is a suitable technique to obtain the spontaneous formation of liposomes having a small average radius. In this paper, we show that liposomal drug formulations can be prepared in situ, by simply injecting a drug‐containing lipid(s) organic solution into an aqueous solution. Several parameters should be optimized in order to obtain a final suitable formulation, and this paper is devoted to such an investigation. Firstly, we study the liposome size distributions determined by dynamic light scattering (DLS), as function of the lipid concentration and composition, as well as the organic and aqueous phases content. This was carried out, firstly, by focusing on POPC (1‐palmitoyl‐2‐oleoyl‐sn‐glycero‐3‐phosphocholine) then on the novel L‐carnitine derivative PUCE (palmitoyl‐(R)‐carnitine undecyl ester chloride), showing that it is possible to obtain monomodal size distributions of rather small vesicles. In particular, depending on the conditions, it was possible to achieve a population of liposomes with a mean size of 100 nm, when a 50 mM POPC ethanol solution was injected in pure water; in the case of 50 mM PUCE the mean size was around 30 nm, when injected in saline (0.9% NaCl). The novel anticancer drug Gimatecan, a camptothecin derivative, was used as an example of lipophilic drug loading by the injection method. Conditions could be found, under which the resultant liposome size distributions were not affected by the presence of Gimatecan, in the case of POPC as well as in the case of PUCE. To increase the overall camptothecin concentration in the final liposomal dispersion, the novel technique of “multiple injection method” was used, and up to a final 5 times larger amount of liposomal drug could be reached by maintaining approximately the same size distribution. Once prepared, the physical and chemical stability of the liposome formulations was satisfactory within 24, as judged by DLS analysis and HPLC quantitation of lipids and drug. The Gimatecan‐containing liposomes formulations were also tested for in vitro and in vivo activity, against the human nonsmall cell lung carcinoma NCI‐H460 and a murine Lewis lung carcinoma 3 LL cell lines. In the in vitro tests, we did not observe any improvement or reduction of the Gimatecan pharmacological effect by the liposomal delivery system. More interestingly, in the in vivo Lewis lung carcinoma model, the intravenously administration of liposomal Gimatecan formulation showed a mild but significant increase of Tumor Volume Inhibition with respect to the oral no‐liposomal formulation (92% vs. 86 %, respectively; p < 0.05). Finally, our study showed that the liposomal formulation was able to realize a delivery system of a water‐insoluble drug, providing a Gimatecan formulation for intravenous administration with a preserved antitumoral activity.     

Accurate retention time determination of co‐eluting proteins in analytical chromatography by means of spectral data

Chromatography is the method of choice for the separation of proteins, at both analytical and preparative scale. Orthogonal purification strategies for industrial use can easily be implemented by combining different modes of adsorption. Nevertheless, with flexibility comes the freedom of choice and optimal conditions for consecutive steps need to be identified in a robust and reproducible fashion. One way to address this issue is the use of mathematical models that allow for an in silico process optimization. Although this has been shown to work, model parameter estimation for complex feedstocks becomes the bottleneck in process development. An integral part of parameter assessment is the accurate measurement of retention times in a series of isocratic or gradient elution experiments. As high‐resolution analytics that can differentiate between proteins are often not readily available, pure protein is mandatory for parameter determination. In this work, we present an approach that has the potential to solve this problem. Based on the uniqueness of UV absorption spectra of proteins, we were able to accurately measure retention times in systems of up to four co‐eluting compounds. The presented approach is calibration‐free, meaning that prior knowledge of pure component absorption spectra is not required. Actually, pure protein spectra can be determined from co‐eluting proteins as part of the methodology. The approach was tested for size‐exclusion chromatograms of 38 mixtures of co‐eluting proteins. Retention times were determined with an average error of 0.6 s (1.6% of average peak width), approximated and measured pure component spectra showed an average coefficient of correlation of 0.992. Biotechnol. Bioeng. 2013; 110: 683–693. © 2012 Wiley Periodicals, Inc.     

Representation of Ecological Systems within the Protected Areas Network of the Continental United States

If conservation of biodiversity is the goal, then the protected areas network of the continental US may be one of our best conservation tools for safeguarding ecological systems (i.e., vegetation communities). We evaluated representation of ecological systems in the current protected areas network and found insufficient representation at three vegetation community levels within lower elevations and moderate to high productivity soils. We used national-level data for ecological systems and a protected areas database to explore alternative ways we might be able to increase representation of ecological systems within the continental US. By following one or more of these alternatives it may be possible to increase the representation of ecological systems in the protected areas network both quantitatively (from 10% up to 39%) and geographically and come closer to meeting the suggested Convention on Biological Diversity target of 17% for terrestrial areas. We used the Landscape Conservation Cooperative framework for regional analysis and found that increased conservation on some private and public lands may be important to the conservation of ecological systems in Western US, while increased public-private partnerships may be important in the conservation of ecological systems in Eastern US. We have not assessed the pros and cons of following the national or regional alternatives, but rather present them as possibilities that may be considered and evaluated as decisions are made to increase the representation of ecological systems in the protected areas network across their range of ecological, geographical, and geophysical occurrence in the continental US into the future.     

Effect of albumin and polyanion on the structure of DNA complexes with polycation containing hydrophilic nonionic block.

Self-assembling systems based on ionic complexes of DNA with block copolymer of N-(2-hydroxypropyl)methacrylamide with 2-(trimethylammonio)ethyl methacrylate were studied as systems suitable for gene delivery. In this study, the influence of albumin and polyanion on parameters of the DNA polyelectrolyte complexes in aqueous solutions was investigated. Static and dynamic light-scattering methods were used as a main tool for characterizing these interactions. It was found that albumin is not able to release free DNA, but it can rather bind to the complexes forming ternary DNA-polycation-albumin complexes with increased hydrodynamic radii of about 10 nm. Polyanion tested, sodium poly(styrenesulfonate), was able to release free DNA in the presence of a low-molecular-weight electrolyte. In the absence of a low-molecular-weight electrolyte, only formation of ternary complexes and no DNA release was observed. The in vivo biodistribution analysis of DNA complexes showed no effect of the presence of hydrophilic nonionic poly(HPMA) on the circulatory time or organ distribution. The interaction of DNA complexes with albumin and other plasma proteins was suggested to be a major reason for the short circulatory times.     

Physical foundations of the probability of biogenesis.

For bigenesis-a particular kind of systmogenesis-to occur, certain physical and informative requirements were indispensable, especially: (1) the selforganization of new kind of negative feed-backs supported by the trans-substantial channels of information. These were certainly at first organized only on the submolecular level, each of them consisting of many charge-transfer connections. The accomplishment of requirement (1) depends on (2) and (3): (2) the organization of a sufficiently complex structure inside the agglomerated system. We should mention here the desagglomerated inorganic systems according to the archaic models: 'A' (Atoms) and P (astro-Planetary systems). In these prebiotic models the selfregulation background consists of the kind of negative opposing forces). (3) the availability of molecules in which the structure complexity is sufficiently high to be able to contribute to the organization of the trans-substantial channels. Biogenesis of spontaneous trans-substantialization of information channels in feed-backs. The trans-substantial channels are spontaneously organized in the biotic model, but they are also present in many technical electronic models of systems constructed by man. Therefore, it is no wonder that biogenesis probably occurred at the 10--6 m size level (compare the diameter of the microspheres of Fox and the concept of Ponnamperuma who mentions the size of the contemporary Micrococcus). Such a system position - inside the biotic unicellular sub-band (extended actually from 10--6 to 10--1 m) is faviourable for the organization of the high complexity of the structurogenic processes trajectories. It is at the nearest possible level to this region on the dimensional scale where a maximal plurality of the different joining forces exists...     

The dependence of root system properties on root system biomass of 10 North American grassland species

Dependence of the properties of root systems on the size of the root system may alter conclusions about differences in plant growth in different environments and among species. To determine whether important root system properties changed as root systems aged and accumulated biomass, we measured three important properties of fine roots (tissue density, diameter, and C:N) and three biomass ratios (root:shoot, fine:coarse, and shallow:deep) of monocultures of 10 North American grassland species five times during their second and third years of growth. With increasing belowground biomass, root tissue density increased and diameter decreased. This may reflect cortical loss associated with the aging of roots. For non-legumes, fine root C:N decreased with increasing root biomass, associated with decreases in soil solution NO^{3 –} concentrations. No changes in fine root C:N were detected with increasing belowground biomass for the two legumes we studied. Among all 10 species, there were generally no changes in the relative amounts of biomass in coarse and fine roots, root:shoot, or the depth placement of fine roots in the soil profile as belowground biomass increased. Though further research is needed to separate the influence of root system size, age of the roots, and changes in nutrient availability, these factors will need to be considered when comparing root functional traits among species and treatments.     

Construction and utility of 10-kb libraries for efficient clone-gap closure for rice genome sequencing

Rice is an important crop and a model system for monocot genomics, and is a target for whole genome sequencing by the International Rice Genome Sequencing Project (IRGSP). The IRGSP is using a clone by clone approach to sequence rice based on minimum tiles of BAC or PAC clones. For chromosomes 10 and 3 we are using an integrated physical map based on two fingerprinted and end-sequenced BAC libraries to identifying a minimum tiling path of clones. In this study we constructed and tested two rice genomic libraries with an average insert size of 10 kb (10-kb library) to support the gap closure and finishing phases of the rice genome sequencing project. The HaeIII library contains 166,752 clones covering approximately 4.6x rice genome equivalents with an average insert size of 10.5 kb. The Sau3AI library contains 138,960 clones covering 4.2x genome equivalents with an average insert size of 11.6 kb. Both libraries were gridded in duplicate onto 11 high-density filters in a 5 x 5 pattern to facilitate screening by hybridization. The libraries contain an unbiased coverage of the rice genome with less than 5% contamination by clones containing organelle DNA or no insert. An efficient method was developed, consisting of pooled overgo hybridization, the selection of 10-kb gap spanning clones using end sequences, transposon sequencing and utilization of in silico draft sequence, to close relatively small gaps between sequenced BAC clones. Using this method we were able to close a majority of the gaps (up to approximately 50 kb) identified during the finishing phase of chromosome-10 sequencing. This method represents a useful way to close clone gaps and thus to complete the entire rice genome.     

Cytochalasin D abolishes the schistosomicidal activity of praziquantel

To test the hypothesis that calcium channels of schistosomes are the targets for the action of praziquantel, we subjected schistosomes in vitro to pharmacological agents capable of interfering with the functioning of calcium channels. After 1-h exposure to these agents, praziquantel was added and incubation continued overnight. Worms were then washed, resuspended in drug-free medium and observed during the following 7-10 days. About 50% of schistosomes pre-exposed to the calcium channel blockers nicardipine and nifedipine were able to survive a praziquantel concentration (3 microM) that normally killed the majority of adult male worms. Since the organization of the actin cytoskeleton controls the activity of calcium channels in a number of different systems, we also pre-exposed schistosomes to the actin depolymerizing agent cytochalasin D. This treatment rendered the parasites completely refractory to the effects of very high praziquantel levels (up to 36 microM). These results are consistent with the hypothesis that schistosome calcium channels are involved in the mechanism of action of praziquantel.