Controlling light-use by Rhodobacter capsulatus continuous cultures in a flat-panel photobioreactor

The main bottleneck in scale-up of phototrophic fermentation is the low efficiency of light energy conversion to the desired product, which is caused by an excessive dissipation of light energy to heat. The photoheterotrophic formation of hydrogen from acetate and light energy by the microorganism Rhodobacter capsulatus NCIMB 11773 was chosen as a case study in this work. A light energy balance was set up, in which the total bacterial light energy absorption is split up and attributed to its destinations. These are biomass growth and maintenance, generation of hydrogen and photosynthetic heat dissipation. The constants defined in the light energy balance were determined experimentally using a flat-panel photobioreactor with a 3-cm optical path. An experimental method called D-stat was applied. Continuous cultures were kept in a so-called pseudo steady state, while the dilution rate was reduced slowly and smoothly. The biomass yield and maintenance coefficients of Rhodobacter capsulatus biomass on light energy were determined at 12.4 W/m(2) (400-950 nm) and amounted to 2.58 x 10(-8) +/- 0.04 x 10(-8) kg/J and 102 +/- 3.5 W/kg, respectively. The fraction of the absorbed light energy that was dissipated to heat at 473 W/m(2) depended on the biomass concentration in the reactor and varied between 0.80 and 0.88, as the biomass concentration was increased from 2.0 to 8.0 kg/m(3). The process conditions were estimated at which a 3.7% conversion efficiency of absorbed light energy to produced hydrogen energy should be attainable at 473 W/m(2).     

Behaviour of Nif− mutants of Rhodobacter capsulatus in photosynthetic, ammonia-limited chemostat cultures

Abstract Nif⁻ mutants of Rhodobacter capsulatus carrying mutations either in the nifR4 regulatory gene or in the nifH structural gene both outgrew the wild-type strain B10 in mixed chemostat cultures under conditions favouring nitrogenase-mediated H₂ production by the wild-type (ammonia as limiting nutrient, inert argon atmosphere, light as energy source), whereas under aerobic conditions in the dark, or in batch culture, the growth of Nif⁻ mutants was not favoured. Nitrogenase-mediated H₂ production therefore appears to be detrimental to the growth of R. capsulatus in nitrogen-limited continuous culture, as may also be the case for other nitrogen fixers.     

The development of the photosynthetic apparatus and energy transduction in malate-limited phototrophic cultures of Rhodobacter capsulatus

The question was studied whether limited availability of the carbon source controls the development of the photosynthetic apparatus in Rhodobacter capsulatus. The organisms were grown phototrophically in a chemostat limited by malate as the sole source of reducing equivalents and carbon. The incident light-energy flux, representing the only energy source, was kept constant. Steady state levels of protein and dry weight of cells as well as molar growth yield coefficients (Y) decreased with increasing dilution rate (D, representing the growth rate, ) up to about D=0.14 h^-1. At higher D-values biomass levels as well as Y stayed largely constant. The specific rate of malate consumption leading to biomass production increased linearly while the rate representative of processes other than conversion of carbon into biomass increased almost exponentially with . Specific bacteriochlorophyll (Bchl) contents of cells as well as the specific rate of Bchl synthesis were rather low at low D-values. They increased as D was increased. Light energy fluxes required to half-maximally saturate proton extrusion by whole cells decreased when D was increased up to 0.1 h^-1; at higher D-values, however, they reached constancy. Maximal rates of proton extrusion as well as of photophosphorylation calculated on a Bchl basis decreased when D was increased up to 0.14 h^-1 and reached constancy at higher D-values. The results suggest that the availability of the growth limiting substrate controls the formation of the photosynthetic apparatus and, consequently, its functional properties including the efficiency of light-energy transduction. A relationship is assumed between malate conversion into biomass, i.e. Y-values, and the efficiency of light-energy transduction.Abbreviations ALA 5-aminoleyulinic acid - Bchl bacteriochlorophyll - D dilution rate [h^-1] - R Rhodobacter - Y molar growth yield coefficient - growth rate [h^-1]     

Mechanistic modeling of sulfur‐deprived photosynthesis and hydrogen production in suspensions of Chlamydomonas reinhardtii

The ability of unicellular green algal species such as Chlamydomonas reinhardtii to produce hydrogen gas via iron‐hydrogenase is well known. However, the oxygen‐sensitive hydrogenase is closely linked to the photosynthetic chain in such a way that hydrogen and oxygen production need to be separated temporally for sustained photo‐production. Under illumination, sulfur‐deprivation has been shown to accommodate the production of hydrogen gas by partially‐deactivating O₂ evolution activity, leading to anaerobiosis in a sealed culture. As these facets are coupled, and the system complex, mathematical approaches potentially are of significant value since they may reveal improved or even optimal schemes for maximizing hydrogen production. Here, a mechanistic model of the system is constructed from consideration of the essential pathways and processes. The role of sulfur in photosynthesis (via PSII) and the storage and catabolism of endogenous substrate, and thus growth and decay of culture density, are explicitly modeled in order to describe and explore the complex interactions that lead to H₂ production during sulfur‐deprivation. As far as possible, functional forms and parameter values are determined or estimated from experimental data. The model is compared with published experimental studies and, encouragingly, qualitative agreement for trends in hydrogen yield and initiation time are found. It is then employed to probe optimal external sulfur and illumination conditions for hydrogen production, which are found to differ depending on whether a maximum yield of gas or initial production rate is required. The model constitutes a powerful theoretical tool for investigating novel sulfur cycling regimes that may ultimately be used to improve the commercial viability of hydrogen gas production from microorganisms. Biotechnol. Bioeng. 2014;111: 320–335. © 2013 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.     

The role of hydrogen mass transfer for the growth kinetics of Methanobacterium thermoautotrophicum in batch and chemostat cultures

Hydrogen concentration was determined in batch and chemostat cultures of Methanobacterium thermoautotrophicum, both in the headspace and in the medium using mass spectrometry. The calculated dissolved hydrogen concentration in the medium as derived from the headspace hydrogen concentration when equilibrium conditions between gas and liquid phase were assumed, was ten times higher than the experimentally determined hydrogen concentration. Variation of the partial pressure of hydrogen resulted in different values for substrate affinity for hydrogen (K_s) and yield (Y) of the cells. Upon hydrogen limitation, K_s decreased while the yield coefficient for hydrogen increased, indicating a change in the affinity of the cells towards hydrogen. Received 15 November 1996/ Accepted in revised form 21 July 1997     

Kinetic modeling of light limitation and sulfur deprivation effects in the induction of hydrogen production with Chlamydomonas reinhardtii: Part I. Model development and parameter identification

Chlamydomonas reinhardtii is a green microalga capable of turning its metabolism towards H2 production under specific conditions. However this H2 production, narrowly linked to the photosynthetic process, results from complex metabolic reactions highly dependent on the environmental conditions of the cells. A kinetic model has been developed to relate culture evolution from standard photosynthetic growth to H2 producing cells. It represents transition in sulfur-deprived conditions, known to lead to H2 production in Chlamydomonas reinhardtii, and the two main processes then induced which are an over-accumulation of intracellular starch and a progressive reduction of PSII activity for anoxia achievement. Because these phenomena are directly linked to the photosynthetic growth, two kinetic models were associated, the first (one) introducing light dependency (Haldane type model associated to a radiative light transfer model), the second (one) making growth a function of available sulfur amount under extracellular and intracellular forms (Droop formulation). The model parameters identification was realized from experimental data obtained with especially designed experiments and a sensitivity analysis of the model to its parameters was also conducted. Model behavior was finally studied showing interdependency between light transfer conditions, photosynthetic growth, sulfate uptake, photosynthetic activity and O2 release, during transition from oxygenic growth to anoxic H2 production conditions.     

The special optical properties and application of the heterocyclic compound diethyl 6‐anilino‐5H‐2,3‐dithia‐5,7‐diazacyclopenta(cd)indene‐1,4‐dicarboxylate

The heterocyclic compound diethyl 6‐anilino‐5H‐2,3‐dithia‐5,7‐diazacyclopenta(cd)indene‐1,4‐dicarboxylate (D1) was found to form highly emissive aggregates in polar solvents, and the aggregate emission can be tuned by the simple addition of water to a dimethylsulfoxide solution. A theoretical study based on Density functional theory (DFT) calculations, shows that intermolecular interactions of D1 with solvent may be potential factors in the fluorescence change. In addition, the phenyl ring in D1 plays an important role because of its response to solvent. In the non‐aggregated state, deprotonation of the N–H of D1 can proceed easily on the addition of base, and the deprotonated compound might interact with Ag⁺, resulting in a significant change in color and fluorescence quenching, which make it a potential chemosensor for the selective detection of trace amounts of Ag⁺. Copyright © 2013 John Wiley & Sons, Ltd.     

Mechanisms of age‐related changes in forest production: the influence of physiological and successional changes

Net primary production (NPP) declines as forests age, but the causal role of decreased gross primary production (GPP), or increased autotrophic respiration (R_a) is still a matter of debate. This uncertainty complicates predicted responses to future climate, as higher atmospheric carbon dioxide (CO₂) concentrations may amplify the carbon (C)‐sink in temperate forests if GPP controls the decline in NPP, but increased temperatures may decrease this C‐sink if R_a controls the NPP decline. We quantified NPP in forests dominated by loblolly pine (Pinus taeda) in North Carolina, USA that varied from 14 to 115 years old. We used a sap‐flow approach to quantify summer canopy photosynthesis by pines and later‐successional hardwood trees, and measured wood CO₂ efflux to investigate age‐related changes in pine R_a. Despite increasing production by later‐successional hardwoods, an 80% decline in pine NPP caused ecosystem NPP to decline with age by ～40%. The decline in pine NPP was explained by reduced stomatal conductance and photosynthesis, supporting the hypothesis that increasing hydraulic limitation and declining GPP drove the age‐related decline of NPP in this species. The difference between GPP and NPP indicated that pine R_a also declined with age; this was corroborated by measurements of reduced stem CO₂ efflux with increasing age. These results indicate that C cycling in these successional temperate forests is controlled by C input from GPP, and elements of global change that increase GPP may increase the C‐sink in aging warm‐temperate pine forests.     

The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the NrdH‐redoxin family

NrdH‐redoxins shuffle electrons from the NADPH pool in the cell to Class Ib ribonucleotide reductases, which in turn provide the precursors for DNA replication and repair. NrdH‐redoxins have a CVQC active site motif and belong to the thioredoxin‐fold protein family. As for other thioredoxin‐fold proteins, the pK_a of the nucleophilic cysteine of NrdH‐redoxins is of particular interest since it affects the catalytic reaction rate of the enzymes. Recently, the pK_a value of this cysteine in Corynebacterium glutamicum and Mycobacterium tuberculosis NrdH‐redoxins were determined, but structural insights explaining the relatively low pK_a remained elusive. We subjected C. glutamicum NrdH‐redoxin to an extensive molecular dynamics simulation to expose the factors regulating the pK_a of the nucleophilic cysteine. We found that the nucleophilic cysteine receives three hydrogen bonds from residues within the CVQC active site motif. Additionally, a fourth hydrogen bond with a lysine located N‐terminal of the active site further lowers the cysteine pK_a. However, site‐directed mutagenesis data show that the major contribution to the lowering of the cysteine pK_a comes from the positive charge of the lysine and not from the additional Lys‐Cys hydrogen bond. In 12% of the NrdH‐redoxin family, this lysine is replaced by an arginine that also lowers the cysteine pK_a. All together, the four hydrogen bonds and the electrostatic effect of a lysine or an arginine located N‐terminally of the active site dynamically regulate the pK_a of the nucleophilic cysteine in NrdH‐redoxins.     

The complex effects of the slow‐releasing hydrogen sulfide donor GYY4137 in a model of acute joint inflammation and in human cartilage cells

The role of hydrogen sulfide (H₂S) in inflammation remains unclear with both pro- and anti-inflammatory actions of this gas described. We have now assessed the effect of GYY4137 (a slow-releasing H₂S donor) on lipopolysaccharide (LPS)-evoked release of inflammatory mediators from human synoviocytes (HFLS) and articular chondrocytes (HAC) in vitro. We have also examined the effect of GYY4137 in a complete Freund''s adjuvant (CFA) model of acute joint inflammation in the mouse. GYY4137 (0.1–0.5 mM) decreased LPS-induced production of nitrite (NO₂⁻), PGE₂, TNF-α and IL-6 from HFLS and HAC, reduced the levels and catalytic activity of inducible nitric oxide synthase (iNOS) and cyclooxygenase-2 (COX-2) and reduced LPS-induced NF-κB activation in vitro. Using recombinant human enzymes, GYY4137 inhibited the activity of COX-2, iNOS and TNF-α converting enzyme (TACE). In the CFA-treated mouse, GYY4137 (50 mg/kg, i.p.) injected 1 hr prior to CFA increased knee joint swelling while an anti-inflammatory effect, as demonstrated by reduced synovial fluid myeloperoxidase (MPO) and N-acetyl-β-D-glucosaminidase (NAG) activity and decreased TNF-α, IL-1β, IL-6 and IL-8 concentration, was apparent when GYY4137 was injected 6 hrs after CFA. GYY4137 was also anti-inflammatory when given 18 hrs after CFA. Thus, although GYY4137 consistently reduced the generation of pro-inflammatory mediators from human joint cells in vitro, its effect on acute joint inflammation in vivo depended on the timing of administration.     

The impact of age on oncogenic potential: tumor‐initiating cells and the brain microenvironment

Paradoxically, aging leads to both decreased regenerative capacity in the brain and an increased risk of tumorigenesis, particularly the most common adult‐onset brain tumor, glioma. A shared factor contributing to both phenomena is thought to be age‐related alterations in neural progenitor cells (NPCs), which function normally to produce new neurons and glia, but are also considered likely cells of origin for malignant glioma. Upon oncogenic transformation, cells acquire characteristics known as the hallmarks of cancer, including unlimited replication, altered responses to growth and anti‐growth factors, increased capacity for angiogenesis, potential for invasion, genetic instability, apoptotic evasion, escape from immune surveillance, and an adaptive metabolic phenotype. The precise molecular pathogenesis and temporal acquisition of these malignant characteristics is largely a mystery. Recent studies characterizing NPCs during normal aging, however, have begun to elucidate mechanisms underlying the age‐associated increase in their malignant potential. Aging cells are dependent upon multiple compensatory pathways to maintain cell cycle control, normal niche interactions, genetic stability, programmed cell death, and oxidative metabolism. A few multi‐functional proteins act as ‘critical nodes’ in the coordination of these various cellular activities, although both intracellular signaling and elements within the brain environment are critical to maintaining a balance between senescence and tumorigenesis. Here, we provide an overview of recent progress in our understanding of how mechanisms underlying cellular aging inform on glioma pathogenesis and malignancy.     

Showcasing the application of synchrotron‐based X‐ray computed tomography in host–pathogen interactions: The role of wheat rachilla and rachis nodes in Type‐II resistance to Fusarium graminearum

Fusarium head blight, caused primarily by Fusarium graminearum (Fg), is one of the most devastating diseases of wheat. Host resistance in wheat is classified into five types (Type‐I to Type‐V), and a majority of moderately resistant genotypes carry Type‐II resistance (resistance to pathogen spread in the rachis) alleles, mainly from the Chinese cultivar Sumai 3. Histopathological studies in the past failed to identify the key tissue in the spike conferring resistance to pathogen spread, and most of the studies used destructive techniques, potentially damaging the tissue(s) under study. In the present study, nondestructive synchrotron‐based phase contrast X‐ray imaging and computed tomography techniques were used to confirm the part of the wheat spike conferring Type‐II resistance to Fg spread, thus showcasing the application of synchrotron‐based techniques to image host–pathogen interactions. Seven wheat genotypes of moderate resistance to Fusarium head blight were studied for changes in the void space volume fraction and grayscale/voxel intensity following Fg inoculation. Cell‐wall biopolymeric compounds were quantified using Fourier‐transform midinfrared spectroscopy for all genotype‐treatment combinations. The study revealed that the rachilla and rachis nodes together are structurally important in conferring Type‐II resistance. The structural reinforcement was not necessarily observed from lignin deposition but rather from an unknown mechanism.     

The easy road to genome‐wide medium density SNP screening in a non‐model species: development and application of a 10 K SNP‐chip for the house sparrow (Passer domesticus)

With the advent of next generation sequencing, new avenues have opened to study genomics in wild populations of non‐model species. Here, we describe a successful approach to a genome‐wide medium density Single Nucleotide Polymorphism (SNP) panel in a non‐model species, the house sparrow (Passer domesticus), through the development of a 10 K Illumina iSelect HD BeadChip. Genomic DNA and cDNA derived from six individuals were sequenced on a 454 GS FLX system and generated a total of 1.2 million sequences, in which SNPs were detected. As no reference genome exists for the house sparrow, we used the zebra finch (Taeniopygia guttata) reference genome to determine the most likely position of each SNP. The 10 000 SNPs on the SNP‐chip were selected to be distributed evenly across 31 chromosomes, giving on average one SNP per 100 000 bp. The SNP‐chip was screened across 1968 individual house sparrows from four island populations. Of the original 10 000 SNPs, 7413 were found to be variable, and 99% of these SNPs were successfully called in at least 93% of all individuals. We used the SNP‐chip to demonstrate the ability of such genome‐wide marker data to detect population sub‐division, and compared these results to similar analyses using microsatellites. The SNP‐chip will be used to map Quantitative Trait Loci (QTL) for fitness‐related phenotypic traits in natural populations.     

NDRG1 is down‐regulated in the early apoptotic event induced by camptothecin analogs: The potential role in proteolytic activation of PKCδ and apoptosis

We previously reported that NSC606985, a new camptothecin analog, induces apoptosis of acute myeloid leukemic cells, which is triggered by proteolytic activation of protein kinase C delta (PKCδ). Here, we performed quantitative proteomic analysis of NSC606985‐treated and untreated leukemic U937 cells with two‐dimensional fluorescence difference gel electrophoresis (2‐D DIGE) in combination with matrix‐assisted laser desorption/ionization time‐of‐flight/time‐of‐flight tandem mass spectrometry. Thirty‐three proteins were found to be deregulated. Then, we focused on N‐myc downstream regulated gene 1 (NDRG1) down‐regulated during apoptosis induction. The results demonstrated that the down‐regulation of NDRG1 protein but not its mRNA was an early event prior to proteolytic activation of PKCδ in U937 cells under treatments of NSC606985 as well as other camptothecin analogs. With the ectopic expression of NDRG1, the proteolytic activation of PKCδ in NSC606985‐treated leukemic cells was delayed and the cells were less sensitive to apoptosis. On the contrary, the suppression of NDRG1 expression by specific small interfering RNA significantly enhanced NSC606985‐induced activation of PKCδ and apoptosis of U937 cells. In summary, our study suggests that the down‐regulation of NDRG1 is involved in proteolytic activation of PKCδ during apoptosis induction, which would shed new light on the understanding the apoptotic process initiated by camptothecin.