Control of Hydrogen Photoproduction by the Proton Gradient Generated by Cyclic Electron Flow in Chlamydomonas reinhardtii

Hydrogen photoproduction by eukaryotic microalgae results from a connection between the photosynthetic electron transport chain and a plastidial hydrogenase. Algal H₂ production is a transitory phenomenon under most natural conditions, often viewed as a safety valve protecting the photosynthetic electron transport chain from overreduction. From the colony screening of an insertion mutant library of the unicellular green alga Chlamydomonas reinhardtii based on the analysis of dark-light chlorophyll fluorescence transients, we isolated a mutant impaired in cyclic electron flow around photosystem I (CEF) due to a defect in the Proton Gradient Regulation Like1 (PGRL1) protein. Under aerobiosis, nonphotochemical quenching of fluorescence (NPQ) is strongly decreased in pgrl1. Under anaerobiosis, H₂ photoproduction is strongly enhanced in the pgrl1 mutant, both during short-term and long-term measurements (in conditions of sulfur deprivation). Based on the light dependence of NPQ and hydrogen production, as well as on the enhanced hydrogen production observed in the wild-type strain in the presence of the uncoupling agent carbonyl cyanide p-trifluoromethoxyphenylhydrazone, we conclude that the proton gradient generated by CEF provokes a strong inhibition of electron supply to the hydrogenase in the wild-type strain, which is released in the pgrl1 mutant. Regulation of the trans-thylakoidal proton gradient by monitoring pgrl1 expression opens new perspectives toward reprogramming the cellular metabolism of microalgae for enhanced H₂ production.     

The Complexity of Sequences Generated by the Arc-Fractal System

We study properties of the symbolic sequences extracted from the fractals generated by the arc-fractal system introduced earlier by Huynh and Chew. The sequences consist of only a few symbols yet possess several nontrivial properties. First using an operator approach, we show that the sequences are not periodic, even though they are constructed from very simple rules. Second by employing the ϵ-machine approach developed by Crutchfield and Young, we measure the complexity and randomness of the sequences and show that they are indeed complex, i.e. neither periodic nor random, with the value of complexity measure being significant as compared to the known example of logistic map at the edge of chaos. The complexity and randomness of the sequences are then discussed in relation with the properties of associated fractal objects, such as their fractal dimension, symmetry and orientations of the arcs.     

Density Profile of a Plasma Layer Formed by an Electron Beam

Plasma Physics Reports - Results of particle-in-cell simulation of the formation of a near-wall plasma layer produced by an ionization source remote from the chamber walls are verified...     

Nucleosome Spacing Generated by ISWI and CHD1 Remodelers Is Constant Regardless of Nucleosome Density

Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density. We call this a clamping activity. Here, we show in a purified system that ISWI- and CHD1-type nucleosome remodelers have a clamping activity such that they not only generate regularly spaced nucleosome arrays but also generate constant spacing regardless of nucleosome density. This points to a functionally attractive nucleosome interaction that could be mediated either directly by nucleosome-nucleosome contacts or indirectly through the remodelers. Mutant Drosophila melanogaster ISWI without the HAND-SANT-SLIDE (HSS) domain had no detectable spacing activity even though it is known to remodel and slide nucleosomes. This suggests that the role of ISWI remodelers in generating constant spacing is not just to mediate nucleosome sliding; they actively contribute to the attractive interaction. Additional factors are necessary to set physiological spacing in absolute terms.     

Electron Density Sharpening as a General Technique in Crystallographic Studies

Sharpening is a powerful method to restore the details from blurred electron density in crystals with high overall temperature factors (B-factors). This valuable technique is currently not optimally used because of the uncertainty in the scope of its application and ambiguities in practice. We performed an analysis of ~ 2000 crystal data sets deposited in the Protein Data Bank and show that sharpening improves the electron density map in many cases across all resolution ranges, often with dramatic enhancement for mid- and low-resolution structures. It is effective when used with either experimental or model phases without introducing additional bias. Our tests also provide a practical guide for optimal sharpening. We further show that anisotropic diffraction correction improves electron density in many cases but should be used with caution. Our study demonstrates that a routine practice of electron density sharpening may have a broad impact on the outcomes of structural biology studies.     

Impact of Nonuniform Electron Density on Plasmonic Properties of Metal Nanoparticles

The interfacial nonuniformity of the electron density that occurs in metals as a result of atomic imperfections can strongly affect the plasmonic properties of metallic nanostructures. Under certain conditions, it induces the bulk plasmon resonance in the transition area and can significantly change scattering and absorption of light by metallic nanostructures in a broad frequency range. This effect is numerically demonstrated for radially nonuniform spherical silver nanoparticles and analytically investigated with respect to the resonant coupling with the dipolar surface plasmons of the metal core.     

Dna Damage by Chemically Generated Singlet Oxygen

A naphthalenic endoperoxide was used as a non-photochemical source of singlet oxygen (¹O₂) to examine some interactions between this reactive oxygen species and DNA. High molecular weight DNA (ca. 10⁸ daltons) was exposed to 120 mol m^?31O₂ (cumulative concentration) and analyzed for interstrand crosslinkage by hydroxyl apatite chromatography following formamide denaturation. No evidence for ¹O₂-induced interstrand crosslinking was obtained. The capacity of ¹O₂ to generate strand breaks in single-stranded (ss) and double-stranded (ds) DNA was investigated by sucrose gradient centrifugation analysis of bacteriophage øX174 DNA. No direct strand breaks could be detected at neutral pH, whereas extensive strand breakage was observed after treatment with alkali. Possible biological consequences of ¹O₂ -exposure were assessed by examining the plaque-forming capacity of ss and ds øX 174 DNA molecules using wildtype Escherichia coli spheroplasts as recipients. Without any further treatment with heat or alkali, exposure to the endoperoxide resulted in a time- and dose-dependent inactivation, ss DNA being considerably more sensitive than ds DNA. From the present results and those reported earlier (Nieuwint et al.,²⁰) we infer that ¹O₂-induced inactivation of øX174 DNA is not due to DNA backbone breakage nor to interstrand crosslinking, but rather to some form of damage to the base or sugar moiety of the DNA, the exact nature of which remains to be elucidated.     

Experiment with Split-Plot Generated by PBIB Designs

The paper refers to the construction of two-factor experiments carried out in incomplete split-plot design in which levels of both factors occur as treatments in PBIB designs. It presents also the analysis of variance of these experiments based on partial analyses in the so called strata. These strata are connected with the variability between subplots inside wholeplots, between the wholeplots inside blocks and between blocks inside the total experiment.     

AC Electrokinetic Phenomena Generated by Microelectrode Structures

The field of AC electrokinetics is rapidly growing due to its ability to perform dynamic fluid and particle manipulation on the micro- and nano-scale, which is essential for Lab-on-a-Chip applications. AC electrokinetic phenomena use electric fields to generate forces that act on fluids or suspended particles (including those made of dielectric or biological material) and cause them to move in astonishing ways^{1, 2}. Within a single channel, AC electrokinetics can accomplish many essential on-chip operations such as active micro-mixing, particle separation, particle positioning and micro-pattering. A single device may accomplish several of those operations by simply adjusting operating parameters such as frequency or amplitude of the applied voltage. Suitable electric fields can be readily created by micro-electrodes integrated into microchannels. It is clear from the tremendous growth in this field that AC electrokinetics will likely have a profound effect on healthcare diagnostics^3-5, environmental monitoring⁶ and homeland security⁷.In general, there are three AC Electrokinetic phenomena (AC electroosmosis, dielectrophoresis and AC electrothermal effect) each with unique dependencies on the operating parameters. A change in these operating parameters can cause one phenomena to become dominant over another, thus changing the particle or fluid behavior. It is difficult to predict the behavior of particles and fluids due to the complicated physics that underlie AC electrokinetics. It is the goal of this publication to explain the physics and elucidate particle and fluid behavior. Our analysis also covers how to fabricate the electrode structures that generate them, and how to interpret a wide number of experimental observations using several popular device designs. This video article will help scientists and engineers understand these phenomena and may encourage them to start using AC Electrokinetics in their research.Download video file.^{(251M, mp4)}     

Anti-Digoxin Fab Variants Generated by Phage Display

Digoxin is a pharmaceutical used in the control of cardiac dysfunction. Its therapeutic window is narrow, with effect dosage very close to the toxic dosage. To counteract the toxic effect, polyclonal Fab fragments are commercially available. Our study is based on a monoclonal anti-digoxin antibody, which would provide a product with a specific potency and more precise dosage for the detoxification of patients under digoxin treatment. Phage display technology was used to select variants with high affinity. From an anti-digoxin hybridoma, RNA was extracted for subsequent cDNA synthesis. Specific primers were used for the LC and Fd amplifications, then cloned sequentially in a phagemid vector (pComb3X) for the combinatorial Fab library construction. Clones were selected for their ability to bind to digoxin-BSA. The presence of light and heavy chains was checked, randomly selected clones then sequenced and induced to produce soluble Fabs, and subsequently analyzed for anti-digoxin expression. Out of ten clones randomly chosen, six resulted positive expression of the product. The sequencing of these revealed two identical clones and one presenting a pseudogene in the LC. Four clones presenting variations in the framework1 showed binding to digoxin-BSA by ELISA and western blotting. The specific binding was further confirmed by Biacore^®, which allowed ranking of the clones. The development of these clones allowed the selection of variants with higher affinity than the original version.     

慢病毒载体法制备红色荧光蛋白转基因小鼠

目的利用慢病毒介导的转基因方法制备红色荧光蛋白（mRFP）转基因小鼠,并建立转基因小鼠的技术平台。方法将携带mRFP基因的慢病毒注入ICR鼠单细胞受精卵卵周隙以感染受精卵,胚胎移植进假孕母鼠以获得仔代鼠,然后应用小动物活体成像仪、体视荧光显微镜和PCR等鉴定并获得mRFP转基因鼠。结果移植卵周隙注射有慢病毒的胚胎40枚给2只假孕母鼠,共获得仔鼠6只;利用体视荧光显微镜检测mRFP表达,在蛋白水平证实6只F0代中,2只（R3和R4）鼠耳高表达mRFP,其余的弱表达mRFP（R1、R2和R5）或荧光强度（R6）与野生型ICR鼠无明显差别,而DNA水平检测证实,6只F0代中,5只（R1、R2、R3、R4和R5）基因组中整合有外源转基因hUb-mRFP,预示基因型鉴定结果很好验证了体视荧光显微镜鉴定结果。此外,mRFP转基因首建鼠基因组中整合的mRFP基因可稳定遗传和表达。结论建立了慢病毒法快速制备转基因小鼠的技术平台,这为针对不同基因建立相应转基因小鼠以实现恒定或条件性的转基因过表达或RNA干涉（RNAi）,并进而在体内解析相应基因功能和建立人类疾病模型等奠定了坚实基础。     

Computing Projections into Cones Generated by a Matrix

A method is described for computing orthogonal projections into finitely generated cones. This method can be used to solve nonnegative least squares approximation problems, to find the multivariate onesided Maximum Likelihood estimator and also determines the most stringent somewhere most powerful test of Schaafsma. The gist of the procedure is the unconstrained maximization of a numerically simple function. This function has a global maximum and allows an uncomplicated maximum search since local maxima do not exist. The maximum can be obtained after a finite number of iterations.     

Positional Information Generated by Spatially Distributed Signaling Cascades

The temporal and stationary behavior of protein modification cascades has been extensively studied, yet little is known about the spatial aspects of signal propagation. We have previously shown that the spatial separation of opposing enzymes, such as a kinase and a phosphatase, creates signaling activity gradients. Here we show under what conditions signals stall in the space or robustly propagate through spatially distributed signaling cascades. Robust signal propagation results in activity gradients with long plateaus, which abruptly decay at successive spatial locations. We derive an approximate analytical solution that relates the maximal amplitude and propagation length of each activation profile with the cascade level, protein diffusivity, and the ratio of the opposing enzyme activities. The control of the spatial signal propagation appears to be very different from the control of transient temporal responses for spatially homogenous cascades. For spatially distributed cascades where activating and deactivating enzymes operate far from saturation, the ratio of the opposing enzyme activities is shown to be a key parameter controlling signal propagation. The signaling gradients characteristic for robust signal propagation exemplify a pattern formation mechanism that generates precise spatial guidance for multiple cellular processes and conveys information about the cell size to the nucleus.     

Precipitating Antigen-Antibody System of High Density Lipoproteins

PEOPLE who have received blood transfusions on numerous occasions (multiply-transfused) often develop antibodies against antigenic structures of the same animal species. These antibodies are easily detected by immunoprecipitation reactions and are called isoprecipitins. The reactor specificities are often present in the beta lipoproteins and have been shown to be inherited as autosomal dominant traits. Several polymorphisms are known¹. Beaumont² reported the Pg antigen to be a specificity common to the alpha (high density) and beta (low density) lipoproteins, detected by an autoantibody of an IgA myeloma protein. Polymorphism of this antigen has not been demonstrated since the Pg was observed in all human and animal sera studied.     

Casein-Derived Antimicrobial Peptides Generated by Lactobacillus acidophilus DPC6026

Three peptides produced by a Lactobacillus acidophilus DPC6026 fermentation of sodium caseinate and showing antibacterial activity against pathogenic strains Enterobacter sakazakii ATCC 12868 and Escherichia coli DPC5063 were characterized. These peptides were all generated from bovine α_s1-casein and identified as IKHQGLPQE, VLNENLLR, and SDIPNPIGSENSEK. These peptides may have bioprotective applicability and potential use in milk-based formula, which has been linked to E. sakazakii infection in neonates.     

Sequentially Generated Designs

Procedures for sequential generation of nearly D-optimal designs are described. Two kinds of designs can be obtained: symmetrical block designs and nonsymmetrical ones. It is shown that in a special case when the number of the support points of a continuous D-optimal design equals to the number of regression coefficients the sequential designs can be constructed very easy without use of a computer. A Catalogue containing 135 designs has been developed by use of these procedures. 34 of them can be used for experiments in cuboidal factor space and the remaining for experiments with mixture and process variables. Comparison with other designs is done.     

Variables Affecting Two Electron Transport System Assays

Several methodological variables were critical in two commonly used electron transport activity assays. The dehydrogenase assay based on triphenyl formazan production exhibited a nonlinear relationship between formazan production (dehydrogenase activity) and sediment dilution, and linear formazan production occurred for 1 h in sediment slurries. Activity decreased with increased time of sediment storage at 4°C. Extraction efficiencies of formazan from sediment varied with alcohol type; methanol was unsatisfactory. Phosphate buffer (0.06 M) produced higher activity than did either U.S. Environmental Protection Agency reconstituted hard water or Tris buffer sediment diluents. Intracellular formazan crystals were dissolved within minutes when in contact with immersion oil. Greater crystal production (respiration) detected by a tetrazolium salt assay occurred at increased substrate concentrations. Test diluents containing macrophyte exudates produced greater activity than did phosphate buffer, U.S. Environmental Protection Agency water, or ultrapure water diluents. Both assays showed decreases in sediment or bacterial activity through time.