Direct Visualization of Exciton Reequilibration in the LH1 and LH2 Complexes of Rhodobacter sphaeroides by Multipulse Spectroscopy

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Cohen Stuart, T.A.; Vengris, M.; Novoderezhkin, V.I.; Cogdell, R.J.; Hunter, C.N.; van Grondelle, R.

2011-01-01

The dynamics of the excited states of the light-harvesting complexes LH1 and LH2 of Rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. In a pump-dump-probe experiment, the first pulse promotes LH1 or LH2 to its excited state and the second pulse dumps a

Engineering of a calcium-ion binding site into the RC-LH1-PufX complex of Rhodobacter sphaeroides to enable ion-dependent spectral red-shifting.

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Swainsbury, David J K; Martin, Elizabeth C; Vasilev, Cvetelin; Parkes-Loach, Pamela S; Loach, Paul A; Neil Hunter, C

2017-11-01

The reaction centre-light harvesting 1 (RC-LH1) complex of Thermochromatium (Tch.) tepidum has a unique calcium-ion binding site that enhances thermal stability and red-shifts the absorption of LH1 from 880nm to 915nm in the presence of calcium-ions. The LH1 antenna of mesophilic species of phototrophic bacteria such as Rhodobacter (Rba.) sphaeroides does not possess such properties. We have engineered calcium-ion binding into the LH1 antenna of Rba. sphaeroides by progressively modifying the native LH1 polypeptides with sequences from Tch. tepidum. We show that acquisition of the C-terminal domains from LH1 α and β of Tch. tepidum is sufficient to activate calcium-ion binding and the extent of red-shifting increases with the proportion of Tch. tepidum sequence incorporated. However, full exchange of the LH1 polypeptides with those of Tch. tepidum results in misassembled core complexes. Isolated α and β polypeptides from our most successful mutant were reconstituted in vitro with BChl a to form an LH1-type complex, which was stabilised 3-fold by calcium-ions. Additionally, carotenoid specificity was changed from spheroidene found in Rba. sphaeroides to spirilloxanthin found in Tch. tepidum, with the latter enhancing in vitro formation of LH1. These data show that the C-terminal LH1 α/β domains of Tch. tepidum behave autonomously, and are able to transmit calcium-ion induced conformational changes to BChls bound to the rest of a foreign antenna complex. Thus, elements of foreign antenna complexes, such as calcium-ion binding and blue/red switching of absorption, can be ported into Rhodobacter sphaeroides using careful design processes. Copyright © 2017 The Author(s). Published by Elsevier B.V. All rights reserved.

The prevalence of gene duplications and their ancient origin in Rhodobacter sphaeroides 2.4.1

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Cho Hyuk

2010-12-01

Full Text Available Abstract Background Rhodobacter sphaeroides 2.4.1 is a metabolically versatile organism that belongs to α-3 subdivision of Proteobacteria. The present study was to identify the extent, history, and role of gene duplications in R. sphaeroides 2.4.1, an organism that possesses two chromosomes. Results A protein similarity search (BLASTP identified 1247 orfs (~29.4% of the total protein coding orfs that are present in 2 or more copies, 37.5% (234 gene-pairs of which exist in duplicate copies. The distribution of the duplicate gene-pairs in all Clusters of Orthologous Groups (COGs differed significantly when compared to the COG distribution across the whole genome. Location plots revealed clusters of gene duplications that possessed the same COG classification. Phylogenetic analyses were performed to determine a tree topology predicting either a Type-A or Type-B phylogenetic relationship. A Type-A phylogenetic relationship shows that a copy of the protein-pair matches more with an ortholog from a species closely related to R. sphaeroides while a Type-B relationship predicts the highest match between both copies of the R. sphaeroides protein-pair. The results revealed that ~77% of the proteins exhibited a Type-A phylogenetic relationship demonstrating the ancient origin of these gene duplications. Additional analyses on three other strains of R. sphaeroides revealed varying levels of gene loss and retention in these strains. Also, analyses on common gene pairs among the four strains revealed that these genes experience similar functional constraints and undergo purifying selection. Conclusions Although the results suggest that the level of gene duplication in organisms with complex genome structuring (more than one chromosome seems to be not markedly different from that in organisms with only a single chromosome, these duplications may have aided in genome reorganization in this group of eubacteria prior to the formation of R. sphaeroides as gene

The role of Cercospora zeae-maydis homologs of Rhodobacter sphaeroides 1O2-resistance genes in resistance to the photoactivated toxin cercosporin.

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Beseli, Aydin; Goulart da Silva, Marilia; Daub, Margaret E

2015-01-01

The photosynthetic bacterium Rhodobacter sphaeroides and plant pathogenic fungus Cercospora nicotianae have been used as models for understanding resistance to singlet oxygen ((1)O(2)), a highly toxic reactive oxygen species. In Rhodobacter and Cercospora, (1)O(2) is derived, respectively, from photosynthesis and from the (1)O(2)-generating toxin cercosporin which the fungus produces to parasitize plants. We identified common genes recovered in transcriptome studies of putative (1)O(2)-resistance genes in these two systems, suggesting common (1)O(2)-resistance mechanisms. To determine if the Cercospora homologs of R. sphaeroides (1)O(2)-resistance genes are involved in resistance to cercosporin, we expressed the genes in the cercosporin-sensitive fungus Neurospora crassa and assayed for increases in cercosporin resistance. Neurospora crassa transformants expressing genes encoding aldo/keto reductase, succinyl-CoA ligase, O-acetylhomoserine (thiol) lyase, peptide methionine sulphoxide reductase and glutathione S-transferase did not have elevated levels of cercosporin resistance. Several transformants expressing aldehyde dehydrogenase were significantly more resistant to cercosporin. Expression of the transgene and enzyme activity did not correlate with resistance, however. We conclude that although the genes tested in this study are important in (1)O(2) resistance in R. sphaeroides, their Cercospora homologs are not involved in resistance to (1)O(2) generated from cercosporin. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Reusing pulp and paper mill effluent as a bioresource to produce biohydrogen through ultrasonicated Rhodobacter sphaeroides

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Hay, Jacqueline Xiao Wen; Wu, Ta Yeong; Ng, Boon Junn; Juan, Joon Ching; Md Jahim, Jamaliah

2016-01-01

Highlights: • Ultrasonication pretreatment on R. sphaeroides enhanced biohydrogen production. • Pretreatment using amplitude 30% for 10 min gave the highest biohydrogen yield. • Pretreatment using amplitude 45% for 15 min inhibited biohydrogen production. - Abstract: Pulp and paper industry is a water-intensive industry. This industry commonly produces considerable amount of effluent, especially from virgin raw materials processing. The effluent, namely pulp and paper mill effluent has the potential to adversely affect the receiving watercourses. However, the nutrients in the pulp and paper mill effluent could be reused as a substrate in biohydrogen production. In this study, photofermentative biohydrogen production was investigated using Rhodobacter sphaeroides and pulp and paper mill effluent as a substrate. An application of low power ultrasound on R. sphaeroides was predicted to increase photofermentative biohydrogen production but excessive ultrasound effects might inhibit the production due to possible cell disruption. Hence, various ultrasonication duration (5, 10 and 15 min) and amplitude (15%, 30% and 45%) were applied on the bacteria to determine the recommended ultrasonication conditions for improving biohydrogen production. The recommended conditions were operated at ultrasonication amplitude and duration of 30% and 10 min, respectively. A maximum biohydrogen yield of 9.62 mL bioH_2/mL medium was obtained under this condition, which was 66.7% higher than the result obtained using R. sphaeroides without undergoing ultrasonication (control). The light efficiency and cell concentration were increased by 67% and 150%, respectively, using ultrasonication amplitude and duration of 30% and 10 min, respectively as compared to the control. The present results demonstrated that moderate power of ultrasonication applied on R. sphaeroides was an effective method for enhancing photofermentative biohydrogen production using raw pulp and paper mill effluent as a

Characterization of D-tagatose-3-epimerase from Rhodobacter sphaeroides that converts D-fructose into D-psicose.

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Zhang, Longtao; Mu, Wanmeng; Jiang, Bo; Zhang, Tao

2009-06-01

A non-characterized gene, previously proposed as the D-tagatose-3-epimerase gene from Rhodobacter sphaeroides, was cloned and expressed in Escherichia coli. Its molecular mass was estimated to be 64 kDa with two identical subunits. The enzyme specificity was highest with D-fructose and decreased for other substrates in the order: D-tagatose, D-psicose, D-ribulose, D-xylulose and D-sorbose. Its activity was maximal at pH 9 and 40 degrees C while being enhanced by Mn(2+). At pH 9 and 40 degrees C, 118 g D-psicose l(-1) was produced from 700 g D-fructose l(-1) after 3 h.

Role of the Irr protein in the regulation of iron metabolism in Rhodobacter sphaeroides.

Directory of Open Access Journals (Sweden)

Verena Peuser

Full Text Available In Rhizobia the Irr protein is an important regulator for iron-dependent gene expression. We studied the role of the Irr homolog RSP_3179 in the photosynthetic alpha-proteobacterium Rhodobacter sphaeroides. While Irr had little effect on growth under iron-limiting or non-limiting conditions its deletion resulted in increased resistance to hydrogen peroxide and singlet oxygen. This correlates with an elevated expression of katE for catalase in the Irr mutant compared to the wild type under non-stress conditions. Transcriptome studies revealed that Irr affects the expression of genes for iron metabolism, but also has some influence on genes involved in stress response, citric acid cycle, oxidative phosphorylation, transport, and photosynthesis. Most genes showed higher expression levels in the wild type than in the mutant under normal growth conditions indicating an activator function of Irr. Irr was however not required to activate genes of the iron metabolism in response to iron limitation, which showed even stronger induction in the absence of Irr. This was also true for genes mbfA and ccpA, which were verified as direct targets for Irr. Our results suggest that in R. sphaeroides Irr diminishes the strong induction of genes for iron metabolism under iron starvation.

Ammonium and methylammonium transport in Rhodobacter sphaeroides

International Nuclear Information System (INIS)

Cordts, M.L.; Gibson, J.

1987-01-01

Rhodobacter spheroides maintained intracellular ammonium pools of 1.1 to 2.6 mM during growth in several fixed nitrogen sources as well as during diazotrophic growth. Addition of 0.15 mM NH 4 + to washed, nitrogen-free cell suspensions was followed by linear uptake of NH 4 + from the medium and transient formation of intracellular pools of 0.9 to 1.5 mM NH 4 + . Transport of NH 4 + was shown to be independent of assimilation by glutamine synthetase because intracellular pools of over 1 mM represented NH 4 + concentration gradients of at least 100-fold across the cytoplasmic membrane. Ammonium pools of over 1 mM were also found in non-growing cell suspensions in nitrogen-free medium after glutamine synthetase was inhibited with methionine sulfoximine. In NH 4 + -free cell suspensions, methylammonium ( 14 CH 3 NH 3 + ) was taken up rapidly, and intracellular concentrations of 0.4 to 0.5 mM were maintained. The 14 CN 3 NH 3 + pool was not affected by methionine sulfoximine. Unlike NH 4 + uptake, 14 CH 3 NH 3 + uptake in nitrogen-free cell suspensions was repressed by growth in NH 4 + . These results suggest that R. sphaeroides may produce an NH 4 + -specific transport system in addition to the NH 4 + / 14 CH 3 NH 3 + transporter. This second transporter is able to produce normal-size NH 4 + pools but has very little affinity for 14 CH 3 NH 3 + and is not repressed by growth in high concentrations of NH 4 +

Transient grating spectroscopy in photosynthetic purple bacteria Rhodobacter sphaeroides 2.4.1

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Sugisaki, Mitsuru, E-mail: mitsuru@sci.osaka-cu.ac.j [CREST-JST and Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585 (Japan); Fujiwara, Masazumi; Fujii, Ritsuko [CREST-JST and Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585 (Japan); Nakagawa, Katsunori; Nango, Mamoru [CREST-JST and Graduate School of Engineering, Nagoya Institute of Technology, Gokiso, Showa, Nagoya 466-8555 (Japan); Cogdell, Richard J. [Glasgow Biomedical Research Centre, IBLS, University of Glasgow, 126 University Place, Glasgow G12 8TA, Scotland (United Kingdom); Hashimoto, Hideki [CREST-JST and Graduate School of Science, Osaka City University, 3-3-138 Sugimoto, Sumiyoshi, Osaka 558-8585 (Japan)

2009-12-15

The vibronic coherence of photosynthetic pigment-protein complexes has been investigated by means of transient grating spectroscopy using sub 20 fs optical pulses. In the present work, we focus our attention on the LH2 antenna complexes from Rhodobacter sphaeroides 2.4.1 because the information about their structure investigated by the electron and atomic force microscopy is available and the electric levels of pigments are well resolved, resulting in clear absorption spectrum. The vibronic coherent oscillations with a period of a few tens of femtoseconds have been clearly observed. We found that the temporal change of the coherent oscillations reflects the vibrational relaxation in the ground state. Calculations based on the Brownian oscillator model were performed under the impulsive excitation limit. The spectral density has been determined from the Raman measurement of spheroidene. Good agreement between the calculation and the experimental results has been achieved in the linear absorption spectrum and transient grating signal, which strongly supports the validity of our model.

Connectivity of the intracytoplasmic membrane of Rhodobacter sphaeroides: a functional approach.

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Verméglio, André; Lavergne, Jérôme; Rappaport, Fabrice

2016-01-01

The photosynthetic apparatus in the bacterium Rhodobacter sphaeroides is mostly present in intracytoplasmic membrane invaginations. It has long been debated whether these invaginations remain in topological continuity with the cytoplasmic membrane, or form isolated chromatophore vesicles. This issue is revisited here by functional approaches. The ionophore gramicidin was used as a probe of the relative size of the electro-osmotic units in isolated chromatophores, spheroplasts, or intact cells. The decay of the membrane potential was monitored from the electrochromic shift of carotenoids. The half-time of the decay induced by a single channel in intact cells was about 6 ms, thus three orders of magnitude slower than in isolated chromatophores. In spheroplasts obtained by lysis of the cell wall, the single channel decay was still slower (~23 ms) and the sensitivity toward the gramicidin concentration was enhanced 1,000-fold with respect to isolated chromatophores. These results indicate that the area of the functional membrane in cells or spheroplasts is about three orders of magnitude larger than that of isolated chromatophores. Intracytoplasmic vesicles, if present, could contribute to at most 10% of the photosynthetic apparatus in intact cells of Rba. sphaeroides. Similar conclusions were obtained from the effect of a ∆pH-induced diffusion potential in intact cells. This caused a large electrochromic response of carotenoids, of similar amplitude as the light-induced change, indicating that most of the system is sensitive to a pH change of the external medium. A single internal membrane and periplasmic space may offer significant advantages concerning renewal of the photosynthetic apparatus and reallocation of the components shared with other bioenergetic pathways.

Timescales of Coherent Dynamics in the Light Harvesting Complex 2 (LH2) of Rhodobacter sphaeroides.

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Fidler, Andrew F; Singh, Ved P; Long, Phillip D; Dahlberg, Peter D; Engel, Gregory S

2013-05-02

The initial dynamics of energy transfer in the light harvesting complex 2 from Rhodobacter sphaeroides were investigated with polarization controlled two-dimensional spectroscopy. This method allows only the coherent electronic motions to be observed revealing the timescale of dephasing among the excited states. We observe persistent coherence among all states and assign ensemble dephasing rates for the various coherences. A simple model is utilized to connect the spectroscopic transitions to the molecular structure, allowing us to distinguish coherences between the two rings of chromophores and coherences within the rings. We also compare dephasing rates between excited states to dephasing rates between the ground and excited states, revealing that the coherences between excited states dephase on a slower timescale than coherences between the ground and excited states.

Assembly of functional photosystem complexes in Rhodobacter sphaeroides incorporating carotenoids from the spirilloxanthin pathway

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Chi, Shuang C.; Mothersole, David J.; Dilbeck, Preston; Niedzwiedzki, Dariusz M.; Zhang, Hao; Qian, Pu; Vasilev, Cvetelin; Grayson, Katie J.; Jackson, Philip J.; Martin, Elizabeth C.; Li, Ying; Holten, Dewey; Neil Hunter, C.

2015-01-01

Carotenoids protect the photosynthetic apparatus against harmful radicals arising from the presence of both light and oxygen. They also act as accessory pigments for harvesting solar energy, and are required for stable assembly of many light-harvesting complexes. In the phototrophic bacterium Rhodobacter (Rba.) sphaeroides phytoene desaturase (CrtI) catalyses three sequential desaturations of the colourless carotenoid phytoene, extending the number of conjugated carbon–carbon double bonds, N, from three to nine and producing the yellow carotenoid neurosporene; subsequent modifications produce the yellow/red carotenoids spheroidene/spheroidenone (N = 10/11). Genomic crtI replacements were used to swap the native three-step Rba. sphaeroides CrtI for the four-step Pantoea agglomerans enzyme, which re-routed carotenoid biosynthesis and culminated in the production of 2,2′-diketo-spirilloxanthin under semi-aerobic conditions. The new carotenoid pathway was elucidated using a combination of HPLC and mass spectrometry. Premature termination of this new pathway by inactivating crtC or crtD produced strains with lycopene or rhodopin as major carotenoids. All of the spirilloxanthin series carotenoids are accepted by the assembly pathways for LH2 and RC–LH1–PufX complexes. The efficiency of carotenoid-to-bacteriochlorophyll energy transfer for 2,2′-diketo-spirilloxanthin (15 conjugated C 000000000000 000000000000 000000000000 111111111111 000000000000 111111111111 000000000000 000000000000 000000000000 C bonds; N = 15) in LH2 complexes is low, at 35%. High energy transfer efficiencies were obtained for neurosporene (N = 9; 94%), spheroidene (N = 10; 96%) and spheroidenone (N = 11; 95%), whereas intermediate values were measured for lycopene (N = 11; 64%), rhodopin (N = 11; 62%) and spirilloxanthin (N = 13; 39%). The variety and stability of these novel Rba. sphaeroides antenna complexes make them useful experimental models for investigating the

Identification of the upper exciton component of the B850 bacteriochlorophylls of the LH2 antenna complex, using a B800-free mutant of Rhodobacter sphaeroides.

NARCIS (Netherlands)

Koolhaas, M.H.C.; Frese, R.N.; Fowler, G.J.S.; Bibby, T.S.; Georgakopoulou, S.; van der Zwan, G.; Hunter, C.N.; van Grondelle, R.

1998-01-01

In this paper, we report the circular dichroism (CD) spectra of two types of LH2 -only mutants of Rhodobacter sphaeroides. In the first, only the wild type LH2 is present, while in the second, the B800 binding site of LH2 has been either destabilized or removed. For the first time, we have

Ammonium and methylammonium transport in Rhodobacter sphaeroides

Energy Technology Data Exchange (ETDEWEB)

Cordts, M.L.; Gibson, J.

1987-04-01

Rhodobacter spheroides maintained intracellular ammonium pools of 1.1 to 2.6 mM during growth in several fixed nitrogen sources as well as during diazotrophic growth. Addition of 0.15 mM NH/sub 4//sup +/ to washed, nitrogen-free cell suspensions was followed by linear uptake of NH/sub 4//sup +/ from the medium and transient formation of intracellular pools of 0.9 to 1.5 mM NH/sub 4//sup +/. Transport of NH/sub 4//sup +/ was shown to be independent of assimilation by glutamine synthetase because intracellular pools of over 1 mM represented NH/sub 4//sup +/ concentration gradients of at least 100-fold across the cytoplasmic membrane. Ammonium pools of over 1 mM were also found in non-growing cell suspensions in nitrogen-free medium after glutamine synthetase was inhibited with methionine sulfoximine. In NH/sub 4//sup +/-free cell suspensions, methylammonium (/sup 14/CH/sub 3/NH/sub 3//sup +/) was taken up rapidly, and intracellular concentrations of 0.4 to 0.5 mM were maintained. The /sup 14/CN/sub 3/NH/sub 3//sup +/ pool was not affected by methionine sulfoximine. Unlike NH/sub 4//sup +/ uptake, /sup 14/CH/sub 3/NH/sub 3//sup +/ uptake in nitrogen-free cell suspensions was repressed by growth in NH/sub 4//sup +/. These results suggest that R. sphaeroides may produce an NH/sub 4//sup +/-specific transport system in addition to the NH/sub 4//sup +///sup 14/CH/sub 3/NH/sub 3//sup +/ transporter. This second transporter is able to produce normal-size NH/sub 4//sup +/ pools but has very little affinity for /sup 14/CH/sub 3/NH/sub 3//sup +/ and is not repressed by growth in high concentrations of NH/sub 4//sup +/.

Cloning, DNA sequence, and expression of the Rhodobacter sphaeroides cytochrome c/sub 2/ gene

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Donohue, T.J.; McEwan, A.G.; Kaplan, S.

1986-11-01

The Rhodobacter sphaeroides cytochrome c/sub 2/ functions as a mobile electron carrier in both aerobic and photosynthetic electron transport chains. Synthetic deoxyoligonucleotide probes, based on the known amino acid sequence of this protein (M/sub r/ 14,000), were used to identify and clone the cytochrome c/sub 2/ structural gene (cycA). DNA sequence analysis of the cycA gene indicated the presence of a typical procaryotic 21-residue signal sequence, suggesting that this periplasmic protein is synthesized in vivo as a precursor. Synthesis of an immunoreactive cytochrome c/sub 2/ precursor protein (M/sub r/ 15,500) was observed in vitro when plasmids containing the cycA gene were used as templates in an R. sphaeroides coupled transcription-translation system. Approximately 500 base pairs of DNA upstream of the cycA gene was sufficient to allow expression of this gene product in vitro. Northern blot analysis with an internal cycA-specific probe identified at least two possibly monocistronic transcripts present in both different cellular levels and relative stoichiometries in steady-state cells grown under different physiological conditions. The ratio of the small (740-mucleotide) and large (920-nucleotide) cycA-specific mRNA species was dependent on cultural conditions but was not affected by light intensity under photosynthetic conditions. These results suggest that the increase in the cellular level of the cytochrome c/sub 2/ protein found in photosynthetic cells was due, in part, to increased transcription of the single-copy cyc operon.

A cryptochrome-like protein is involved in the regulation of photosynthesis genes in Rhodobacter sphaeroides.

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Hendrischk, Anne-Kathrin; Frühwirth, Sebastian Walter; Moldt, Julia; Pokorny, Richard; Metz, Sebastian; Kaiser, Gebhard; Jäger, Andreas; Batschauer, Alfred; Klug, Gabriele

2009-11-01

Blue light receptors belonging to the cryptochrome/photolyase family are found in all kingdoms of life. The functions of photolyases in repair of UV-damaged DNA as well as of cryptochromes in the light-dependent regulation of photomorphogenetic processes and in the circadian clock in plants and animals are well analysed. In prokaryotes, the only role of members of this protein family that could be demonstrated is DNA repair. Recently, we identified a gene for a cryptochrome-like protein (CryB) in the alpha-proteobacterium Rhodobacter sphaeroides. The protein lacks the typical C-terminal extension of cryptochromes, and is not related to the Cry DASH family. Here we demonstrate that CryB binds flavin adenine dinucleotide that can be photoreduced by blue light. CryB binds single-stranded DNA with very high affinity (K(d) approximately 10(-8) M) but double-stranded DNA and single-stranded RNA with far lower affinity (K(d) approximately 10(-6) M). Despite of that, no in vitro repair activity for pyrimidine dimers in single-stranded DNA could be detected. However, we show that CryB clearly affects the expression of genes for pigment-binding proteins and consequently the amount of photosynthetic complexes in R. sphaeroides. Thus, for the first time a role of a bacterial cryptochrome in gene regulation together with a biological function is demonstrated.

Effect of pH on optimization of photofermentative hydrogen production by co-culture of Rhodobacter sphaeroides-NMBL-02 and Bacillus firmus-NMBL-03.

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Pandey, A; Dolly, S; Semwal, D; Pandey, A

2017-07-31

Rhodobacter sphaeroides NMBL-02, photosynthetic purple non sulfur (PNS) bacteria and associated Bacillus firmus NMBL-03 were isolated from water sample collected from 15-20 inches beneath the surface of ponds from Northern region of India in modified Sistrom's media (120 ml) containing 3 g/L malate and 1.2 g/L ammonium sulfate. The isolation was done in air tight serum bottles (120 ml) under tungsten bulb (1.8 kLux light intensity) at 30 oC ± 2 oC. The PNS and heterotrophic bacteria associated with the culture was purified by clonal selection method and characterized by 16S rDNA sequencing. The PNS isolate was identified as Rhodobacter sphaeroides NMBL-02 (ID: 1467407, Accession BANKIT: JN256030) and associated heterotroph as Bacillus firmus NMBL-03 (Gene Bank Accession no.: JN 256029). The effect of initial medium pH on optimization of hydrogen production was investigated in batch process. The maximum hydrogen potential and hydrogen production rate was 2310 ± 55 ml/L and 4.75 ml/L culture/h respectively using glutamate (1.7 mmol/L) as nitrogen source and malate (22.38 mmol/L) as carbon source with 76.39% malate conversion efficiency at initial medium pH 5.0. This co-culture has the ability to produce significant amount of hydrogen in the pH range of 5.0 to 10.0 with 76.39% to 35.71% malate conversion respectively.

Improved hydrogen production by uptake hydrogenase deficient mutant strain of Rhodobacter sphaeroides O.U.001

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Kars, Goekhan; Guenduez, Ufuk; Yuecel, Meral [Department of Biological Sciences, Middle East Technical University, 06531 Ankara (Turkey); Rakhely, Gabor; Kovacs, Kornel L. [Institute of Biophysics, Biological Research Centre, Hungarian Academy of Sciences, Szeged (Hungary); Eroglu, Inci [Department of Chemical Engineering, Middle East Technical University, 06531 Ankara (Turkey)

2008-06-15

Rhodobacter sphaeroides O.U.001 is a purple non-sulfur bacterium producing hydrogen under photoheterotrophic conditions. Hydrogen is produced by Mo-nitrogenase enzyme and substantial amount of H{sub 2} is reoxidized by a membrane-bound uptake hydrogenase in the wild type strain. To improve the hydrogen producing capacity of the cells, a suicide vector containing a gentamicin cassette in the hupSL genes was introduced into R. sphaeroiodes O.U.001 and the uptake hydrogenase genes were destroyed by site directed mutagenesis. The correct integration of the construct was confirmed by uptake hydrogenase activity measurement, PCR and subsequent sequence analysis. The wild type and the mutant cells showed similar growth patterns but the total volume of hydrogen gas evolved by the mutant was 20% higher than that of the wild type strain. This result demonstrated that the hydrogen produced by the nitrogenase was not consumed by uptake hydrogenase leading to higher hydrogen production. (author)

Photodynamics of the small BLUF protein BlrB from Rhodobacter sphaeroides.

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Zirak, P; Penzkofer, A; Schiereis, T; Hegemann, P; Jung, A; Schlichting, I

2006-06-01

The BLUF protein BlrB from the non-sulphur anoxyphototrophic purple bacterium Rhodobacter sphaeroides is characterized by absorption and emission spectroscopy. BlrB expressed from E. coli binding FAD, FMN, and riboflavin (called BrlB(I)) and recombinant BlrB containing only FAD (called BlrB(II)) are investigated. The dark-adapted proteins exist in two different receptor conformations (receptor states) with different sub-nanosecond fluorescence lifetimes (BLUF(r,f) and BLUF(r,sl)). Some of the flavin-cofactor (ca. 8%) is unbound in thermodynamic equilibrium with the bound cofactor. The two receptor conformations are transformed to putative signalling states (BLUF(s,f) and BLUF(s,sl)) of decreased fluorescence efficiency and shortened fluorescence lifetime by blue-light excitation. In the dark at room temperature both signalling states recover back to the initial receptor states with a time constant of about 2s. Quantum yields of signalling state formation of about 90% for BlrB(II) and about 40% for BlrB(I) were determined by intensity dependent transmission measurements. Extended blue-light excitation causes unbound flavin degradation (formation of lumichrome and lumiflavin-derivatives) and bound cofactor conversion to the semiquinone form. The flavin-semiquinone further reduces and the reduced flavin re-oxidizes back in the dark. A photo-dynamics scheme is presented and relevant quantum efficiencies and time constants are determined.

Quenching Capabilities of Long-Chain Carotenoids in Light-Harvesting-2 Complexes from Rhodobacter sphaeroides with an Engineered Carotenoid Synthesis Pathway.

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Dilbeck, Preston L; Tang, Qun; Mothersole, David J; Martin, Elizabeth C; Hunter, C Neil; Bocian, David F; Holten, Dewey; Niedzwiedzki, Dariusz M

2016-06-23

Six light-harvesting-2 complexes (LH2) from genetically modified strains of the purple photosynthetic bacterium Rhodobacter (Rb.) sphaeroides were studied using static and ultrafast optical methods and resonance Raman spectroscopy. These strains were engineered to incorporate carotenoids for which the number of conjugated groups (N = NC═C + NC═O) varies from 9 to 15. The Rb. sphaeroides strains incorporate their native carotenoids spheroidene (N = 10) and spheroidenone (N = 11), as well as longer-chain analogues including spirilloxanthin (N = 13) and diketospirilloxantion (N = 15) normally found in Rhodospirillum rubrum. Measurements of the properties of the carotenoid first singlet excited state (S1) in antennas from the Rb. sphaeroides set show that carotenoid-bacteriochlorophyll a (BChl a) interactions are similar to those in LH2 complexes from various other bacterial species and thus are not significantly impacted by differences in polypeptide composition. Instead, variations in carotenoid-to-BChl a energy transfer are primarily regulated by the N-determined energy of the carotenoid S1 excited state, which for long-chain (N ≥ 13) carotenoids is not involved in energy transfer. Furthermore, the role of the long-chain carotenoids switches from a light-harvesting supporter (via energy transfer to BChl a) to a quencher of the BChl a S1 excited state B850*. This quenching is manifested as a substantial (∼2-fold) reduction of the B850* lifetime and the B850* fluorescence quantum yield for LH2 housing the longest carotenoids.

Bioremediation of petroleum hydrocarbon contaminated soil by Rhodobacter sphaeroides biofertilizer and plants.

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Jiao, Haihua; Luo, Jinxue; Zhang, Yiming; Xu, Shengjun; Bai, Zhihui; Huang, Zhanbin

2015-09-01

Bio-augmentation is a promising technique for remediation of polluted soils. This study aimed to evaluate the bio-augmentation effect of Rhodobacter sphaeroides biofertilizer (RBF) on the bioremediation of total petroleum hydrocarbons (TPH) contaminated soil. A greenhouse pot experiment was conducted over a period of 120 days, three methods for enhancing bio-augmentation were tested on TPH contaminated soils, including single addition RBF, planting, and combining of RBF and three crop species, such as wheat (W), cabbage (C) and spinach (S), respectively. The results demonstrated that the best removal of TPH from contaminated soil in the RBF bio-augmentation rhizosphere soils was found to be 46.2%, 65.4%, 67.5% for W+RBF, C+RBF, S+RBF rhizosphere soils respectively. RBF supply impacted on the microbial community diversity (phospholipid fatty acids, PLFA) and the activity of soil enzymes, such as dehydrogenase (DH), alkaline phosphatase (AP) and urease (UR). There were significant difference among the soil only containing crude oil (CK), W, C and S rhizosphere soils and RBF bio-augmentation soils. Moreover, the changes were significantly distinct depended on crops species. It was concluded that the RBF is a valuable material for improving effect of remediation of TPH polluted soils.

Multi-PAS domain-mediated protein oligomerization of PpsR from Rhodobacter sphaeroides

International Nuclear Information System (INIS)

Heintz, Udo; Meinhart, Anton; Winkler, Andreas

2014-01-01

Crystal structures of two truncated variants of the transcription factor PpsR from R. sphaeroides are presented that enabled the phasing of a triple PAS domain construct. Together, these structures reveal the importance of α-helical PAS extensions for multi-PAS domain-mediated protein oligomerization and function. Per–ARNT–Sim (PAS) domains are essential modules of many multi-domain signalling proteins that mediate protein interaction and/or sense environmental stimuli. Frequently, multiple PAS domains are present within single polypeptide chains, where their interplay is required for protein function. Although many isolated PAS domain structures have been reported over the last decades, only a few structures of multi-PAS proteins are known. Therefore, the molecular mechanism of multi-PAS domain-mediated protein oligomerization and function is poorly understood. The transcription factor PpsR from Rhodobacter sphaeroides is such a multi-PAS domain protein that, in addition to its three PAS domains, contains a glutamine-rich linker and a C-terminal helix–turn–helix DNA-binding motif. Here, crystal structures of two N-terminally and C-terminally truncated PpsR variants that comprise a single (PpsR Q-PAS1 ) and two (PpsR N-Q-PAS1 ) PAS domains, respectively, are presented and the multi-step strategy required for the phasing of a triple PAS domain construct (PpsR ΔHTH ) is illustrated. While parts of the biologically relevant dimerization interface can already be observed in the two shorter constructs, the PpsR ΔHTH structure reveals how three PAS domains enable the formation of multiple oligomeric states (dimer, tetramer and octamer), highlighting that not only the PAS cores but also their α-helical extensions are essential for protein oligomerization. The results demonstrate that the long helical glutamine-rich linker of PpsR results from a direct fusion of the N-cap of the PAS1 domain with the C-terminal extension of the N-domain that plays an important

Study of the selenite reduction in Rhodobacter sphaeroides f. sp. denitrificans

International Nuclear Information System (INIS)

Bernier-Pierru, B.

2006-05-01

Selenium is an essential element for all living organisms at the low level; however it becomes toxic and mutagenic at higher concentrations. The predominant forms of selenium in natural environments are selenate and selenite which are toxic. Bacteria can use several mechanisms of detoxification such as methylation in volatile compounds or reduction in elemental selenium. In this way, our model, Rhodobacter sphaeroides f. sp. denitrificans, is able to reduce selenite into selenium. We have combined biochemical and molecular approaches to better characterize the mechanism and protagonists of this reduction. After studying the physiological response of the bacterium in the presence of selenite, we screened a transposon library in order to isolate mutants with a weakened reduction ability. Two of these selected mutants are affected in genes involved in the molybdenum cofactor synthesis, moaA and mogA. Several reductases, the molybdo enzymes, required this cofactor. Furthermore the addition of tungsten, a competitor for the molybdenum, in the culture medium, dramatically reduces the rate of selenite reduction. These results strongly suggest that a molybdo enzyme is involved in one of the selenite reduction pathways. The potential role of different proteins has been investigated, especially for the nitrate reductase, the DMSO reductase and the biotin sulfoxide reductase. We have also selected a mutant affected in the smoM gene which encodes a peri-plasmic component of a TRAP transporter. The phenotype of this mutant suggests the involvement of this transporter in the selenite import. (author)

Transient absorption study of two-photon excitation mechanism in the LH2 complex from purple bacterium Rhodobacter sphaeroides.

Science.gov (United States)

Stepanenko, Ilya; Kompanetz, Viktor; Makhneva, Zoya; Chekalin, Sergey; Moskalenko, Andrei; Razjivin, Andrei

2012-03-08

The mechanism of two-photon excitation of a peripheral light-harvesting complex LH2 (B800-850) from purple bacterium Rhodobacter sphaeroides was explained on the basis of femtosecond transient absorption data. Fast bleaching of the B850 absorption band was measured under two-photon excitation by 1350 nm femtosecond pulses, showing fast subpicosecond arrival of excitation energy to B850 circular aggregates. Any spectral changes connected with the B800 absorption band of B800-BChl molecules were absent. A similar picture was observed under one-photon excitation of the LH2 complex by 675 nm femtosecond pulses. We believe these effects may be attributed to direct excitation of high-energy excitonic states of a B850 circular aggregate or its vibrational manifold in accordance with the model of Abe [Chem. Phys. 2001, 264, 355-363].

A new nitrilase-producing strain named Rhodobacter sphaeroides LHS-305: biocatalytic characterization and substrate specificity.

Science.gov (United States)

Yang, Chunsheng; Wang, Xuedong; Wei, Dongzhi

2011-12-01

The characteristics of the new nitrilase-producing strain Rhodobacter sphaeroides LHS-305 were investigated. By investigating several parameters influencing nitrilase production, the specific cell activity was ultimately increased from 24.5 to 75.0 μmol g(-1) min(-1), and hereinto, the choice of inducer proved the most important factor. The aromatic nitriles (such as 3-cyanopyridine and benzonitrile) were found to be the most favorable substrates of the nitrilase by analyzing the substrate spectrum. It was speculated that the unsaturated carbon atom attached to the cyano group was crucial for this type of nitrilase. The value of apparent K (m), substrate inhibition constant, and product inhibition constant of the nitrilase against 3-cyanopyridine were 4.5 × 10(-2), 29.2, and 8.6 × 10(-3) mol L(-1), respectively. When applied in nicotinic acid preparation, the nitrilase is able to hydrolyze 200 mmol L(-1) 3-cyanopyridine with 93% conversion rate in 13 h by 6.1 g L(-1) cells (dry cell weight).

Absorption and fluorescence spectroscopic characterization of BLUF domain of AppA from Rhodobacter sphaeroides

Science.gov (United States)

Zirak, P.; Penzkofer, A.; Schiereis, T.; Hegemann, P.; Jung, A.; Schlichting, I.

2005-08-01

The BLUF domain of the transcriptional anti-repressor protein AppA from the non-sulfur anoxyphototrophic purple bacterium Rhodobacter sphaeroides was characterized by absorption and emission spectroscopy. The BLUF domain constructs AppA 148 (consisting of amino-acid residues 1-148) and AppA 126 (amino-acid residues 1-126) are investigated. The cofactor of the investigated domains is found to consist of a mixture of the flavins riboflavin, FMN, and FAD. The dark-adapted domains exist in two different active receptor conformations (receptor states) with different sub-nanosecond fluorescence lifetimes (BLUF r,f and BLUF r,sl) and a small non-interacting conformation (BLUF nc). The active receptor conformations are transformed to putative signalling states (BLUF s,f and BLUF s,sl) of low fluorescence efficiency and picosecond fluorescence lifetime by blue-light excitation (light-adapted domains). In the dark at room temperature both signalling states recover back to the initial receptor states with a time constant of about 17 min. A quantum yield of signalling state formation of about 25% was determined by intensity dependent transmission measurements. A photo-cycle scheme is presented including photo-induced charge transfer complex formation, charge recombination, and protein binding pocket reorganisation.

Absorption and fluorescence spectroscopic characterization of BLUF domain of AppA from Rhodobacter sphaeroides

International Nuclear Information System (INIS)

Zirak, P.; Penzkofer, A.; Schiereis, T.; Hegemann, P.; Jung, A.; Schlichting, I.

2005-01-01

The BLUF domain of the transcriptional anti-repressor protein AppA from the non-sulfur anoxyphototrophic purple bacterium Rhodobacter sphaeroides was characterized by absorption and emission spectroscopy. The BLUF domain constructs AppA 148 (consisting of amino-acid residues 1-148) and AppA 126 (amino-acid residues 1-126) are investigated. The cofactor of the investigated domains is found to consist of a mixture of the flavins riboflavin, FMN, and FAD. The dark-adapted domains exist in two different active receptor conformations (receptor states) with different sub-nanosecond fluorescence lifetimes (BLUF r,f and BLUF r,sl ) and a small non-interacting conformation (BLUF nc ). The active receptor conformations are transformed to putative signalling states (BLUF s,f and BLUF s,sl ) of low fluorescence efficiency and picosecond fluorescence lifetime by blue-light excitation (light-adapted domains). In the dark at room temperature both signalling states recover back to the initial receptor states with a time constant of about 17 min. A quantum yield of signalling state formation of about 25% was determined by intensity dependent transmission measurements. A photo-cycle scheme is presented including photo-induced charge transfer complex formation, charge recombination, and protein binding pocket reorganisation

A novel nitrilase from Rhodobacter sphaeroides LHS-305: cloning, heterologous expression and biochemical characterization.

Science.gov (United States)

Wang, Hualei; Li, Guinan; Li, Mingyang; Wei, Dongzhi; Wang, Xuedong

2014-01-01

In this study, a novel nitrilase gene from Rhodobacter sphaeroides was cloned and overexpressed in Escherichia coli. The open reading frame of the nitrilase gene includes 969 base pairs, which encodes a putative polypeptide of 322 amino acid residues. The molecular weight of the purified native nitrilase was about 560 kDa determined by size exclusion chromatography. This nitrilase showed one single band on SDS-PAGE with a molecular weight of 40 kDa. This suggested that the native nitrilase consisted of 14 subunits with identical size. The optimal pH and temperature of the purified enzyme were 7.0 and 40 °C, respectively. The kinetic parameters V max and K m toward 3-cyanopyridine were 77.5 μmol min(-1) mg(-1) and 73.1 mmol/l, respectively. The enzyme can easily convert aliphatic nitrile and aromatic nitriles to their corresponding acids. Furthermore, this enzyme demonstrated regioselectivity in hydrolysis of aliphatic dinitriles. This specific characteristic makes this nitrilase have a great potential for commercial production of various cyanocarboxylic acids by hydrolyzing readily available dinitriles.

Absorption and fluorescence spectroscopic characterization of BLUF domain of AppA from Rhodobacter sphaeroides

Energy Technology Data Exchange (ETDEWEB)

Zirak, P. [Institut II - Experimentelle und Angewandte Physik, Universitaet Regensburg, Universitaetstrasse 31, D-93053 Regensburg (Germany); Penzkofer, A. [Institut II - Experimentelle und Angewandte Physik, Universitaet Regensburg, Universitaetstrasse 31, D-93053 Regensburg (Germany)], E-mail: alfons.penzkofer@physik.uni-regensburg.de; Schiereis, T. [Institut fuer Biologie, Experimentelle Biophysik, Humboldt-Universitaet zu Berlin, Invalidenstrasse 42, D-10115 Berlin (Germany); Hegemann, P. [Institut fuer Biologie, Experimentelle Biophysik, Humboldt-Universitaet zu Berlin, Invalidenstrasse 42, D-10115 Berlin (Germany); Jung, A. [Max-Planck-Institut fuer medizinische Forschung, Abteilung Biomolekulare Mechanismen, Jahnstrasse 29, D-69120 Heidelberg (Germany); Schlichting, I. [Max-Planck-Institut fuer medizinische Forschung, Abteilung Biomolekulare Mechanismen, Jahnstrasse 29, D-69120 Heidelberg (Germany)

2005-08-08

The BLUF domain of the transcriptional anti-repressor protein AppA from the non-sulfur anoxyphototrophic purple bacterium Rhodobacter sphaeroides was characterized by absorption and emission spectroscopy. The BLUF domain constructs AppA{sub 148} (consisting of amino-acid residues 1-148) and AppA{sub 126} (amino-acid residues 1-126) are investigated. The cofactor of the investigated domains is found to consist of a mixture of the flavins riboflavin, FMN, and FAD. The dark-adapted domains exist in two different active receptor conformations (receptor states) with different sub-nanosecond fluorescence lifetimes (BLUF{sub r,f} and BLUF{sub r,sl}) and a small non-interacting conformation (BLUF{sub nc}). The active receptor conformations are transformed to putative signalling states (BLUF{sub s,f} and BLUF{sub s,sl}) of low fluorescence efficiency and picosecond fluorescence lifetime by blue-light excitation (light-adapted domains). In the dark at room temperature both signalling states recover back to the initial receptor states with a time constant of about 17 min. A quantum yield of signalling state formation of about 25% was determined by intensity dependent transmission measurements. A photo-cycle scheme is presented including photo-induced charge transfer complex formation, charge recombination, and protein binding pocket reorganisation.

Role of Rhodobacter sphaeroides photosynthetic reaction center residue M214 in the composition, absorbance properties, and conformations of H(A) and B(A) cofactors.

Science.gov (United States)

Saer, Rafael G; Hardjasa, Amelia; Rosell, Federico I; Mauk, A Grant; Murphy, Michael E P; Beatty, J Thomas

2013-04-02

In the native reaction center (RC) of Rhodobacter sphaeroides, the side chain of (M)L214 projects orthogonally toward the plane and into the center of the A branch bacteriopheophytin (BPhe) macrocycle. The possibility that this side chain is responsible for the dechelation of the central Mg(2+) of bacteriochlorophyll (BChl) was investigated by replacement of (M)214 with residues possessing small, nonpolar side chains that can neither coordinate nor block access to the central metal ion. The (M)L214 side chain was also replaced with Cys, Gln, and Asn to evaluate further the requirements for assembly of the RC with BChl in the HA pocket. Photoheterotrophic growth studies showed no difference in growth rates of the (M)214 nonpolar mutants at a low light intensity, but the growth of the amide-containing mutants was impaired. The absorbance spectra of purified RCs indicated that although absorbance changes are associated with the nonpolar mutations, the nonpolar mutant RC pigment compositions are the same as in the wild-type protein. Crystal structures of the (M)L214G, (M)L214A, and (M)L214N mutants were determined (determined to 2.2-2.85 Å resolution), confirming the presence of BPhe in the HA pocket and revealing alternative conformations of the phytyl tail of the accessory BChl in the BA site of these nonpolar mutants. Our results demonstrate that (i) BChl is converted to BPhe in a manner independent of the aliphatic side chain length of nonpolar residues replacing (M)214, (ii) BChl replaces BPhe if residue (M)214 has an amide-bearing side chain, (iii) (M)214 side chains containing sulfur are not sufficient to bind BChl in the HA pocket, and (iv) the (M)214 side chain influences the conformation of the phytyl tail of the BA BChl.

Conformational regulation of charge recombination reactions in a photosynthetic bacterial reaction center

DEFF Research Database (Denmark)

Katona, Gergely; Snijder, Arjan; Gourdon, Pontus Emanuel

2005-01-01

In bright light the photosynthetic reaction center (RC) of Rhodobacter sphaeroides stabilizes the P(+)(870).Q(-)(A) charge-separated state and thereby minimizes the potentially harmful effects of light saturation. Using X-ray diffraction we report a conformational change that occurs within the cy...... the cytoplasmic domain of this RC in response to prolonged illumination with bright light. Our observations suggest a novel structural mechanism for the regulation of electron transfer reactions in photosynthesis....

Direct visualization of exciton reequilibration in the LH1 and LH2 complexes of Rhodobacter sphaeroides by multipulse spectroscopy.

Science.gov (United States)

Cohen Stuart, Thomas A; Vengris, Mikas; Novoderezhkin, Vladimir I; Cogdell, Richard J; Hunter, C Neil; van Grondelle, Rienk

2011-05-04

The dynamics of the excited states of the light-harvesting complexes LH1 and LH2 of Rhodobacter sphaeroides are governed, mainly, by the excitonic nature of these ring-systems. In a pump-dump-probe experiment, the first pulse promotes LH1 or LH2 to its excited state and the second pulse dumps a portion of the excited state. By selective dumping, we can disentangle the dynamics normally hidden in the excited-state manifold. We find that by using this multiple-excitation technique we can visualize a 400-fs reequilibration reflecting relaxation between the two lowest exciton states that cannot be directly explored by conventional pump-probe. An oscillatory feature is observed within the exciton reequilibration, which is attributed to a coherent motion of a vibrational wavepacket with a period of ∼150 fs. Our disordered exciton model allows a quantitative interpretation of the observed reequilibration processes occurring in these antennas. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Enhancement of phototrophic hydrogen production by Rhodobacter sphaeroides ZX-5 using a novel strategy - shaking and extra-light supplementation approach

Energy Technology Data Exchange (ETDEWEB)

Li, Xu; Wang, Yong-Hong; Zhang, Si-Liang; Chu, Ju; Zhang, Ming; Huang, Ming-Zhi; Zhuang, Ying-Ping [State Key Laboratory of Bioreactor Engineering, P.O. Box 329, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237 (China)

2009-12-15

Biohydrogen has gained attention due to its potential as a sustainable alternative to conventional methods for hydrogen production. In this study, the effect of light intensity as well as cultivation method (standing- and shaking-culture) on the cell growth and hydrogen production of Rhodobacter sphaeroides ZX-5 were investigated in 38-ml anaerobic photobioreactor with RCVBN medium. Thus, a novel shaking and extra-light supplementation (SELS) approach was developed to enhance the phototrophic H{sub 2} production by R. sphaeroides ZX-5 using malate as the sole carbon source. The optimum illumination condition for shaking-culture by strain ZX-5 increased to 7000-8000 lux, markedly higher than that for standing-culture (4000-5000 lux). Under shaking and elevated illumination (7000-8000 lux), the culture was effective in promoting photo-H{sub 2} production, resulting in a 59% and 56% increase of the maximum and average hydrogen production rate, respectively, in comparison with the culture under standing and 4000-5000 lux conditions. The highest hydrogen-producing rate of 165.9 ml H{sub 2}/l h was observed under the application of SELS approach. To our knowledge, this record is currently the highest hydrogen production rate of non-immobilized purple non-sulphur (PNS) bacteria. This optimal performance of photo-H{sub 2} production using SELS approach is a favorable choice of sustainable and economically feasible strategy to improve phototrophic H{sub 2} production efficiency. (author)

Functional LH1 antenna complexes influence electron transfer in bacterial photosynthetic reaction centers

NARCIS (Netherlands)

Visschers, R.W.; Vulto, S.I.E.; Jones, M.R.; van Grondelle, R.; Kraayenhof, R.

1999-01-01

The effect of the light harvesting 1 (LH1) antenna complex on the driving force for light-driven electron transfer in the Rhodobacter sphaeroides reaction center has been examined. Equilibrium redox titrations show that the presence of the LH1 antenna complex influences the free energy change for

Functional LH1 antenna complexes influence electron transfer in bacterial photosynthetic reaction centers.

NARCIS (Netherlands)

Visschers, R.W.; Vulto, S.I.E.; Jones, M.R.; van Grondelle, R.; Kraayenhof, R.

1999-01-01

The effect of the light harvesting 1 (LH1) antenna complex on the driving force for light-driven electron transfer in the Rhodobacter sphaeroides reaction center has been examined. Equilibrium redox titrations show that the presence of the LH1 antenna complex influences the free energy change for

Effect of co-substrate on production of poly-β- hydroxybutyrate (PHB and copolymer PHBV from newly identified mutant Rhodobacter sphaeroides U7 cultivated under aerobic-dark condition

Directory of Open Access Journals (Sweden)

Kemarajt Kemavongse

2007-07-01

Full Text Available Photosynthetic bacterial mutant strain U7 was identified using both classical and molecular (16S rDNA techniques to be Rhodobacter sphaeroides. The glutamate-acetate (GA medium containing sodium acetate and sodium glutamate as carbon and nitrogen sources was used for production of poly-β-hydroxybutyrate (PHB from R. sphaeroides U7 cultivated under aerobic-dark condition (200 rpm at 37oC. Effect of auxiliary carbon sources (propionate and valerate and concentrations (molar ratio of 40/0, 40/20, 40/40 and 40/80 on copolymer production were studied. Both combinations of acetate with valerate and acetate with propionate were found to induce the accumulation of poly-β-hydroxybutyrate-co-β-hydroxyvalerate (PHBV within the cell. Acetate with propionate in the molar ratio of 40/40 gave the highest poly-β-hydroxyalkanoates (PHA content (77.68%, followed by acetate with valerate at the same molar ratio (77.42%. Although their polymer contents were similar, the presence of 40 mM valerate gave more than 4 times higher hydroxyvalerate (HV fraction (84.77% than in the presence of 40 mM propionate (19.12% HV fraction.

Biochemical analysis and the preliminary crystallographic characterization of D-tagatose 3-epimerase from Rhodobacter sphaeroides.

Science.gov (United States)

Qi, Zhengliang; Zhu, Zhangliang; Wang, Jian-Wen; Li, Songtao; Guo, Qianqian; Xu, Panpan; Lu, Fuping; Qin, Hui-Min

2017-11-09

D-Tagatose 3-epimerase epimerizes D-fructose to yield D-psicose, which is a rare sugar that exists in small quantities in nature and is difficult to synthesize chemically. We aim to explore potential industrial biocatalysts for commercial-scale manufacture of this rare sugar. A D-tagatose 3-epimerase from Rhodobacter sphaeroides (RsDTE) has recently been identified as a D-tagatose 3-epimerase that can epimerize D-fructose to yield D-psicose with a high conversion rate. The purified RsDTE by Ni-affinity chromatography, ionic exchange chromatography and gel filtration forms a tetramer in solution. The maximal activity was in Tris-HCl buffer pH 8.5, and the optimal temperature was at 35 °C. The product, D-psicose, was confirmed using HPLC and NMR. Crystals of RsDTE were obtained using crystal kits and further refined under crystallization conditions such as 10% PEG 8000,0.1 M HEPES pH 7.5, and 8% ethylene glycol at 20 °C using the sitting-drop vapor diffusion method. The RsDTE homology model showed that it possessed the characteristic TIM-barrel fold. Four residues, Glu156, Asp189, Gln215 and Glu250, forms a hydrogen bond network with the active Mn(II) for the hydride transfer reaction. These residues may constitute the catalytic tetrad of RsDTE. The residues around O1, O2 and O3 of the substrates were conserved. However, the binding-site residues are different at O4, O5 and O6. Arg118 formed the unique hydrogen bond with O4 of D-fructose which indicates RsDTE's preference of D-fructose more than any other family enzymes. RsDTE possesses a different metal-binding site. Arg118, forming unique hydrogen bond with O4 of D-fructose, regulates the substrate recognition. The research on D-tagatose 3-epimerase or D-psicose 3-epimerase enzymes attracts enormous commercial interest and would be widely used for rare sugar production in the future.

Elimination of polarity in the carotenoid terminus promotes the exposure of B850-binding sites (Tyr 44, 45) and ANS-mediated energy transfer in LH2 complexes of Rhodobacter sphaeroides.

Science.gov (United States)

Liu, Yuan; Wu, Yongqiang; Xu, Chunhe

2004-12-10

Carotenoids in the peripheral light-harvesting complexes (LH2) of the green mutant (GM309) of Rhodobacter sphaeroides were identified as containing neurosporenes, which lack the polar CH(3)O group, compared to spheroidenes in native-LH2 of R. sphaeroides 601. After LH2 complexes were treated with 1-anilino-8-naphthalene sulfonate (ANS), new energy transfer pathways from ANS or tryptophan to carotenoids were discovered in both native- and GM309-LH2. The carotenoid fluorescence intensity of GM309-LH2 was greater than that of native-LH2 when bound with ANS, suggesting that the elimination of polarity in the neurosporene increases the energy transfer from ANS to carotenoid. The fact that two alpha-tyrosines (alpha-Tyr 44, 45, B850-binding sites) in each alpha-apoprotein of GM309-LH2 were more easily modified than those of native-LH2 by N-acetylimidazole (NAI) indicates that the elimination of polarity in the neurosporene terminus increases the exposure of these sites to solution.

Electrostatic dominoes: long distance propagation of mutational effects in photosynthetic reaction centers of Rhodobacter capsulatus.

Science.gov (United States)

Sebban, P; Maróti, P; Schiffer, M; Hanson, D K

1995-07-04

Two point mutants from the purple bacterium Rhodobacter capsulatus, both modified in the M protein of the photosynthetic reaction center, have been studied by flash-induced absorbance spectroscopy. These strains carry either the M231Arg --> Leu or M43ASN --> Asp mutations, which are located 9 and 15 A, respectively, from the terminal electron acceptor QB. In the wild-type Rb. sphaeroides structure, M231Arg is involved in a conserved salt bridge with H125Glu and H232Glu and M43Asn is located among several polar residues that form or surround the QB binding site. These substitutions were originally uncovered in phenotypic revertants isolated from the photosynthetically incompetent L212Glu-L213Asp --> Ala-Ala site-specific double mutant. As second-site suppressor mutations, they have been shown to restore the proton transfer function that is interrupted in the L212Ala-L213Ala double mutant. The electrostatic effects that are induced in reaction centers by the M231Arg --> Leu and M43Asn --> Asp substitutions are roughly the same in either the double-mutant or wild-type backgrounds. In a reaction center that is otherwise wild type in sequence, they decrease the free energy gap between the QA- and QB- states by 24 +/- 5 and 45 +/- 5 meV, respectively. The pH dependences of K2, the QA-QB QAQB- equilibrium constant, are altered in reaction centers that carry either of these substitutions, revealing differences in the pKas of titratable groups compared to the wild type.(ABSTRACT TRUNCATED AT 250 WORDS)

The unusually strong hydrogen bond between the carbonyl of Q(A) and His M219 in the Rhodobacter sphaeroides reaction center is not essential for efficient electron transfer from Q(A)(-) to Q(B).

Science.gov (United States)

Breton, Jacques; Lavergne, Jérôme; Wakeham, Marion C; Nabedryk, Eliane; Jones, Michael R

2007-06-05

In native reaction centers (RCs) from photosynthetic purple bacteria the primary quinone (QA) and the secondary quinone (QB) are interconnected via a specific His-Fe-His bridge. In Rhodobacter sphaeroides RCs the C4=O carbonyl of QA forms a very strong hydrogen bond with the protonated Npi of His M219, and the Ntau of this residue is in turn coordinated to the non-heme iron atom. The second carbonyl of QA is engaged in a much weaker hydrogen bond with the backbone N-H of Ala M260. In previous work, a Trp side chain was introduced by site-directed mutagenesis at the M260 position in the RC of Rb. sphaeroides, resulting in a complex that is completely devoid of QA and therefore nonfunctional. A photochemically competent derivative of the AM260W mutant was isolated that contains a Cys side chain at the M260 position (denoted AM260(W-->C)). In the present work, the interactions between the carbonyl groups of QA and the protein in the AM260(W-->C) suppressor mutant have been characterized by light-induced FTIR difference spectroscopy of the photoreduction of QA. The QA-/QA difference spectrum demonstrates that the strong interaction between the C4=O carbonyl of QA and His M219 is lost in the mutant, and the coupled CO and CC modes of the QA- semiquinone are also strongly perturbed. In parallel, a band assigned to the perturbation of the C5-Ntau mode of His M219 upon QA- formation in the native RC is lacking in the spectrum of the mutant. Furthermore, a positive band between 2900 and 2400 cm-1 that is related to protons fluctuating within a network of highly polarizable hydrogen bonds in the native RC is reduced in amplitude in the mutant. On the other hand, the QB-/QB FTIR difference spectrum is essentially the same as for the native RC. The kinetics of electron transfer from QA- to QB were measured by the flash-induced absorption changes at 780 nm. Compared to native RCs the absorption transients are slowed by a factor of about 2 for both the slow phase (in the

The mutation of carotenoids affects the energy transfer in LH2 light harvesting complexes from Rhodobacter sphaeroides 601 at room temperature

International Nuclear Information System (INIS)

Liu Weimin; Liu Yuan; Guo Lijun; Xu Chunhe; Qian Shixiong

2006-01-01

Energy transfer in two kinds of peripheral antenna complexes LH2 from Rhodobacter sphaeroides 601 was studied by absorption, fluorescence emission, time-resolved fluorescence and femtosecond transient absorption spectroscopy at room temperature. These two complexes are LH2 (RS601) and green carotenoid mutated LH2 (GM309). The obtained results demonstrate that: (a) compared with spheroidenes, which have ten carbon-carbon double bonds in native RS601, carotenoids in GM309 were identified as containing neurosporenes with nine carbon-carbon double bonds, which show a significant blue shift of ∼20 nm in the three absorption peaks because of the higher energy levels of neurosporene than those of spheroidene, (b) the higher energy levels of neurosporene in GM309 induce a lower B800 → B850 energy transfer rate and efficiency as compared to that in RS601 resulting from the relatively higher band gap between the donor of B800 and the bridge of the carotenoids (c) the same lifetime of the B850 excited singlet state is observed in these two LH2 complexes

The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases.

Science.gov (United States)

Zarzycki, Jan; Kerfeld, Cheryl A

2013-11-09

Malyl-CoA lyase (MCL) is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related Coenzyme A (CoA) thioesters. This enzyme plays a crucial, multifunctional role in the 3-hydroxypropionate bi-cycle for autotrophic CO2 fixation in Chloroflexus aurantiacus. A second, phylogenetically distinct MCL from Rhodobacter sphaeroides is involved in the ethylmalonyl-CoA pathway for acetate assimilation. Both MCLs belong to the large superfamily of CitE-like enzymes, which includes the name-giving β-subunit of citrate lyase (CitE), malyl-CoA thioesterases and other enzymes of unknown physiological function. The CitE-like enzyme superfamily also bears sequence and structural resemblance to the malate synthases. All of these different enzymes share highly conserved catalytic residues, although they catalyze distinctly different reactions: C-C bond formation and cleavage, thioester hydrolysis, or both (the malate synthases). Here we report the first crystal structures of MCLs from two different phylogenetic subgroups in apo- and substrate-bound forms. Both the C. aurantiacus and the R. sphaeroides MCL contain elaborations on the canonical β8/α8 TIM barrel fold and form hexameric assemblies. Upon ligand binding, changes in the C-terminal domains of the MCLs result in closing of the active site, with the C-terminal domain of one monomer forming a lid over and contributing side chains to the active site of the adjacent monomer. The distinctive features of the two MCL subgroups were compared to known structures of other CitE-like superfamily enzymes and to malate synthases, providing insight into the structural subtleties that underlie the functional versatility of these enzymes. Although the C. aurantiacus and the R. sphaeroides MCLs have divergent primary structures (~37% identical), their tertiary and quaternary structures are very similar. It can be assumed that the C-C bond formation catalyzed by the MCLs occurs as proposed for

Structure of the dimeric PufX-containing core complex of Rhodobacter blasticus by in situ atomic force microscopy.

Science.gov (United States)

Scheuring, Simon; Busselez, Johan; Lévy, Daniel

2005-01-14

We have studied photosynthetic membranes of wild type Rhodobacter blasticus, a closely related strain to the well studied Rhodobacter sphaeroides, using atomic force microscopy. High-resolution atomic force microscopy topographs of both cytoplasmic and periplasmic surfaces of LH2 and RC-LH1-PufX (RC, reaction center) complexes were acquired in situ. The LH2 is a nonameric ring inserted into the membrane with the 9-fold axis perpendicular to the plane. The core complex is an S-shaped dimer composed of two RCs, each encircled by 13 LH1 alpha/beta-heterodimers, and two PufXs. The LH1 assembly is an open ellipse with a topography-free gap of approximately 25 A. The two PufXs, one of each core, are located at the dimer center. Based on our data, we propose a model of the core complex, which provides explanation for the PufX-induced dimerization of the Rhodobacter core complex. The QB site is located facing a approximately 25-A wide gap within LH1, explaining the PufX-favored quinone passage in and out of the core complex.

Photo dynamics of BLUF domain mutant H44R of AppA from Rhodobacter sphaeroides

International Nuclear Information System (INIS)

Zirak, P.; Penzkofer, A.; Hegemann, P.; Mathes, T.

2007-01-01

The photo-cycle dynamics of the H44R mutant of the BLUF domain of the transcriptional anti-repressor protein AppA (AppA-H44R) from the non-sulfur anoxyphototropic purple bacterium Rhodobacter sphaeroides is studied in order to gain information on the involvement of His44 in the photo-cyclic mechanism of the AppA BLUF domain and to add information to the involved processes. The amino acid residue histidine at position 44 is replaced by arginine. A 12 nm red-shifted signalling state is formed upon blue-light excitation, while in wild-type AppA (AppA-wt) the red-shift is 16 nm. The recovery to the receptor dark state is approximately a factor of 2.5 faster (τ rec ∼ 6.5 min) than the recovery of the wild-type counterpart. Extended light exposure of the mutant causes photo-degradation of flavin (mainly free flavin conversion to lumichrome and re-equilibration between free and non-covalently bound flavin) and protein aggregation (showing up as light scattering). No photo-degradation was observed for AppA-wt. The quantum efficiency of signalling-state formation determined by intensity dependent absorption measurements is found to be φ s ∼ 0.3 (for AppA-wt: φ s ∼ 0.24). A two-component single-exponential fluorescence relaxation was observed, which is interpreted as fast fluorescence quenching to an equilibrium value by photo-induced electron transfer followed by slower fluorescence decay due to charge recombination. Based on the experimental findings, an extended photo-cycle model for BLUF domains is proposed

Photo dynamics of BLUF domain mutant H44R of AppA from Rhodobacter sphaeroides

Science.gov (United States)

Zirak, P.; Penzkofer, A.; Hegemann, P.; Mathes, T.

2007-05-01

The photo-cycle dynamics of the H44R mutant of the BLUF domain of the transcriptional anti-repressor protein AppA (AppA-H44R) from the non-sulfur anoxyphototropic purple bacterium Rhodobacter sphaeroides is studied in order to gain information on the involvement of His44 in the photo-cyclic mechanism of the AppA BLUF domain and to add information to the involved processes. The amino acid residue histidine at position 44 is replaced by arginine. A 12 nm red-shifted signalling state is formed upon blue-light excitation, while in wild-type AppA (AppA-wt) the red-shift is 16 nm. The recovery to the receptor dark state is approximately a factor of 2.5 faster ( τrec ≈ 6.5 min) than the recovery of the wild-type counterpart. Extended light exposure of the mutant causes photo-degradation of flavin (mainly free flavin conversion to lumichrome and re-equilibration between free and non-covalently bound flavin) and protein aggregation (showing up as light scattering). No photo-degradation was observed for AppA-wt. The quantum efficiency of signalling-state formation determined by intensity dependent absorption measurements is found to be ϕs ≈ 0.3 (for AppA-wt: ϕs ≈ 0.24). A two-component single-exponential fluorescence relaxation was observed, which is interpreted as fast fluorescence quenching to an equilibrium value by photo-induced electron transfer followed by slower fluorescence decay due to charge recombination. Based on the experimental findings, an extended photo-cycle model for BLUF domains is proposed.

Profiling of ornithine lipids in bacterial extracts of Rhodobacter sphaeroides by reversed-phase liquid chromatography with electrospray ionization and multistage mass spectrometry (RPLC-ESI-MS(n)).

Science.gov (United States)

Granafei, Sara; Losito, Ilario; Trotta, Massimo; Italiano, Francesca; de Leo, Vincenzo; Agostiano, Angela; Palmisano, Francesco; Cataldi, Tommaso R I

2016-01-15

Ornithine lipids (OLs), a sub-group of the large (and of emerging interest) family of lipoamino acids of bacterial origin, contain a 3-hydroxy fatty acyl chain linked via an amide bond to the α-amino group of ornithine and via an ester bond to a second fatty acyl chain. OLs in extracts of Rhodobacter sphaeroides (R. sphaeroides) were investigated by high-performance reversed phase liquid chromatography (RPLC) with electrospray ionization mass spectrometry (ESI-MS) in negative ion mode using a linear ion trap (LIT). The presence of OLs bearing both saturated (i.e, 16:0, 17:0, 18:0, 19:0 and 20:0) and unsaturated chains (i.e., 18:1, 19:1, 19:2 and 20:1) was ascertained and their identification, even for isomeric, low abundance and partially co-eluting species, was achieved by low-energy collision induced dissociation (CID) multistage mass spectrometry (MS(n), n = 2-4). OLs signatures found in two R. sphaeroides strains, i.e., wild type 2.4.1 and mutant R26, were examined and up to 16 and 17 different OL species were successfully identified, respectively. OLs in both bacterial strains were characterized by several combinations of fatty chains on ester-linked and amide-linked 3-OH fatty acids. Multistage MS spectra of monoenoic amide-linked 3-OH acyl chains, allowed the identification of positional isomer of OL containing 18:1 (i.e. 9-octadecenoic) and 20:1 (i.e. 11-eicosenoic) fatty acids. The most abundant OL ([M-H](-) at m/z 717.5) in R. sphaeroides R26 was identified as OL 3-OH 20:1/19:1 (i.e., 3-OH-eicosenoic acid amide-linked to ornithine and esterified to a nonadecenoic chain containing a cyclopropane ring). An unusual OL (m/z 689.5 for the [M-H](-) ion), most likely containing a cyclopropene ester-linked acyl chain (i.e., OL 3-OH 18:0/19:2), was retrieved only in the carotenoidless mutant strain R26. Based on the biosynthetic pathways already known for cyclopropa(e)ne ring-including acyl chains, a plausible explanation was invoked for the enzymatic

Probing energy transfer events in the light harvesting complex 2 (LH2) of Rhodobacter sphaeroides with two-dimensional spectroscopy.

Science.gov (United States)

Fidler, Andrew F; Singh, Ved P; Long, Phillip D; Dahlberg, Peter D; Engel, Gregory S

2013-10-21

Excitation energy transfer events in the photosynthetic light harvesting complex 2 (LH2) of Rhodobacter sphaeroides are investigated with polarization controlled two-dimensional electronic spectroscopy. A spectrally broadened pulse allows simultaneous measurement of the energy transfer within and between the two absorption bands at 800 nm and 850 nm. The phased all-parallel polarization two-dimensional spectra resolve the initial events of energy transfer by separating the intra-band and inter-band relaxation processes across the two-dimensional map. The internal dynamics of the 800 nm region of the spectra are resolved as a cross peak that grows in on an ultrafast time scale, reflecting energy transfer between higher lying excitations of the B850 chromophores into the B800 states. We utilize a polarization sequence designed to highlight the initial excited state dynamics which uncovers an ultrafast transfer component between the two bands that was not observed in the all-parallel polarization data. We attribute the ultrafast transfer component to energy transfer from higher energy exciton states to lower energy states of the strongly coupled B850 chromophores. Connecting the spectroscopic signature to the molecular structure, we reveal multiple relaxation pathways including a cyclic transfer of energy between the two rings of the complex.

Probing energy transfer events in the light harvesting complex 2 (LH2) of Rhodobacter sphaeroides with two-dimensional spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Fidler, Andrew F.; Singh, Ved P.; Engel, Gregory S. [Department of Chemistry, The Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Long, Phillip D.; Dahlberg, Peter D. [Graduate Program in the Biophysical Sciences, The University of Chicago, Chicago, Illinois 60637 (United States)

2013-10-21

Excitation energy transfer events in the photosynthetic light harvesting complex 2 (LH2) of Rhodobacter sphaeroides are investigated with polarization controlled two-dimensional electronic spectroscopy. A spectrally broadened pulse allows simultaneous measurement of the energy transfer within and between the two absorption bands at 800 nm and 850 nm. The phased all-parallel polarization two-dimensional spectra resolve the initial events of energy transfer by separating the intra-band and inter-band relaxation processes across the two-dimensional map. The internal dynamics of the 800 nm region of the spectra are resolved as a cross peak that grows in on an ultrafast time scale, reflecting energy transfer between higher lying excitations of the B850 chromophores into the B800 states. We utilize a polarization sequence designed to highlight the initial excited state dynamics which uncovers an ultrafast transfer component between the two bands that was not observed in the all-parallel polarization data. We attribute the ultrafast transfer component to energy transfer from higher energy exciton states to lower energy states of the strongly coupled B850 chromophores. Connecting the spectroscopic signature to the molecular structure, we reveal multiple relaxation pathways including a cyclic transfer of energy between the two rings of the complex.

Probing energy transfer events in the light harvesting complex 2 (LH2) of Rhodobacter sphaeroides with two-dimensional spectroscopy

International Nuclear Information System (INIS)

Fidler, Andrew F.; Singh, Ved P.; Engel, Gregory S.; Long, Phillip D.; Dahlberg, Peter D.

2013-01-01

Excitation energy transfer events in the photosynthetic light harvesting complex 2 (LH2) of Rhodobacter sphaeroides are investigated with polarization controlled two-dimensional electronic spectroscopy. A spectrally broadened pulse allows simultaneous measurement of the energy transfer within and between the two absorption bands at 800 nm and 850 nm. The phased all-parallel polarization two-dimensional spectra resolve the initial events of energy transfer by separating the intra-band and inter-band relaxation processes across the two-dimensional map. The internal dynamics of the 800 nm region of the spectra are resolved as a cross peak that grows in on an ultrafast time scale, reflecting energy transfer between higher lying excitations of the B850 chromophores into the B800 states. We utilize a polarization sequence designed to highlight the initial excited state dynamics which uncovers an ultrafast transfer component between the two bands that was not observed in the all-parallel polarization data. We attribute the ultrafast transfer component to energy transfer from higher energy exciton states to lower energy states of the strongly coupled B850 chromophores. Connecting the spectroscopic signature to the molecular structure, we reveal multiple relaxation pathways including a cyclic transfer of energy between the two rings of the complex

Photo dynamics of BLUF domain mutant H44R of AppA from Rhodobacter sphaeroides

Energy Technology Data Exchange (ETDEWEB)

Zirak, P. [Institut II - Experimentelle und Angewandte Physik, Universitaet Regensburg, Universitaetstrasse 31, D-93053 Regensburg (Germany); Penzkofer, A. [Institut II - Experimentelle und Angewandte Physik, Universitaet Regensburg, Universitaetstrasse 31, D-93053 Regensburg (Germany)], E-mail: alfons.penzkofer@physik.uni-regensburg.de; Hegemann, P.; Mathes, T. [Institut fuer Biologie, Experimentelle Biophysik, Humboldt-Universitaet zu Berlin, Invalidenstr. 42, D-10115 Berlin (Germany)

2007-05-21

The photo-cycle dynamics of the H44R mutant of the BLUF domain of the transcriptional anti-repressor protein AppA (AppA-H44R) from the non-sulfur anoxyphototropic purple bacterium Rhodobacter sphaeroides is studied in order to gain information on the involvement of His44 in the photo-cyclic mechanism of the AppA BLUF domain and to add information to the involved processes. The amino acid residue histidine at position 44 is replaced by arginine. A 12 nm red-shifted signalling state is formed upon blue-light excitation, while in wild-type AppA (AppA-wt) the red-shift is 16 nm. The recovery to the receptor dark state is approximately a factor of 2.5 faster ({tau}{sub rec} {approx} 6.5 min) than the recovery of the wild-type counterpart. Extended light exposure of the mutant causes photo-degradation of flavin (mainly free flavin conversion to lumichrome and re-equilibration between free and non-covalently bound flavin) and protein aggregation (showing up as light scattering). No photo-degradation was observed for AppA-wt. The quantum efficiency of signalling-state formation determined by intensity dependent absorption measurements is found to be {phi}{sub s} {approx} 0.3 (for AppA-wt: {phi}{sub s} {approx} 0.24). A two-component single-exponential fluorescence relaxation was observed, which is interpreted as fast fluorescence quenching to an equilibrium value by photo-induced electron transfer followed by slower fluorescence decay due to charge recombination. Based on the experimental findings, an extended photo-cycle model for BLUF domains is proposed.

Monomeric RC-LH1 core complexes retard LH2 assembly and intracytoplasmic membrane formation in PufX-minus mutants of Rhodobacter sphaeroides.

Science.gov (United States)

Adams, Peter G; Mothersole, David J; Ng, Irene W; Olsen, John D; Hunter, C Neil

2011-09-01

In the model photosynthetic bacterium Rhodobacter sphaeroides domains of light-harvesting 2 (LH2) complexes surround and interconnect dimeric reaction centre-light-harvesting 1-PufX (RC-LH1-PufX) 'core' complexes, forming extensive networks for energy transfer and trapping. These complexes are housed in spherical intracytoplasmic membranes (ICMs), which are assembled in a stepwise process where biosynthesis of core complexes tends to dominate the early stages of membrane invagination. The kinetics of LH2 assembly were measured in PufX mutants that assemble monomeric core complexes, as a consequence of either a twelve-residue N-terminal truncation of PufX (PufXΔ12) or the complete removal of PufX (PufX(-)). Lower rates of LH2 assembly and retarded maturation of membrane invagination were observed for the larger and less curved ICM from the PufX(-) mutant, consistent with the proposition that local membrane curvature, initiated by arrays of bent RC-LH1-PufX dimers, creates a favourable environment for stable assembly of LH2 complexes. Transmission electron microscopy and high-resolution atomic force microscopy were used to examine ICM morphology and membrane protein organisation in these mutants. Some partitioning of core and LH2 complexes was observed in PufX(-) membranes, resulting in locally ordered clusters of monomeric RC-LH1 complexes. The distribution of core and LH2 complexes in the three types of membrane examined is consistent with previous models of membrane curvature and domain formation (Frese et al., 2008), which demonstrated that a combination of crowding and asymmetries in sizes and shapes of membrane protein complexes drives membrane organisation. 2011 Elsevier B.V. All rights reserved.

Functional characteristics of spirilloxanthin and keto-bearing Analogues in light-harvesting LH2 complexes from Rhodobacter sphaeroides with a genetically modified carotenoid synthesis pathway.

Science.gov (United States)

Niedzwiedzki, Dariusz M; Dilbeck, Preston L; Tang, Qun; Mothersole, David J; Martin, Elizabeth C; Bocian, David F; Holten, Dewey; Hunter, C Neil

2015-01-01

Light-harvesting 2 (LH2) complexes from a genetically modified strain of the purple photosynthetic bacterium Rhodobacter (Rba.) sphaeroides were studied using static and ultrafast optical methods and resonance Raman spectroscopy. Carotenoid synthesis in the Rba. sphaeroides strain was engineered to redirect carotenoid production away from spheroidene into the spirilloxanthin synthesis pathway. The strain assembles LH2 antennas with substantial amounts of spirilloxanthin (total double-bond conjugation length N=13) if grown anaerobically and of keto-bearing long-chain analogs [2-ketoanhydrorhodovibrin (N=13), 2-ketospirilloxanthin (N=14) and 2,2'-diketospirilloxanthin (N=15)] if grown semi-aerobically (with ratios that depend on growth conditions). We present the photophysical, electronic, and vibrational properties of these carotenoids, both isolated in organic media and assembled within LH2 complexes. Measurements of excited-state energy transfer to the array of excitonically coupled bacteriochlorophyll a molecules (B850) show that the mean lifetime of the first singlet excited state (S1) of the long-chain (N≥13) carotenoids does not change appreciably between organic media and the protein environment. In each case, the S1 state appears to lie lower in energy than that of B850. The energy-transfer yield is ~0.4 in LH2 (from the strain grown aerobically or semi-aerobically), which is less than half that achieved for LH2 that contains short-chain (N≤11) analogues. Collectively, the results suggest that the S1 excited state of the long-chain (N≥13) carotenoids participates little if at all in carotenoid-to-BChl a energy transfer, which occurs predominantly via the carotenoid S2 excited state in these antennas. Copyright © 2015 Elsevier B.V. All rights reserved.

Exploitation of dark fermented effluent of cheese whey by co-culture of Rhodobacter sphaeroides and Bacillus firmus for photo-hydrogen production.

Science.gov (United States)

Pandey, A; Pandey, A

2017-07-31

In this study photo-hydrogen production from cheese whey dark fermentation (DF) effluent by the co-culture of Rhodobacter sphaeroides -NMBL-01 and Bacillus firmus - NMBL-03 has been reported. The effect of pH, initial chemical oxygen demand (COD) and the concentration effect of FeSO4.7H2O on photo-hydrogen production have been investigated. The end products of dark fermentation effluent of cheese whey were mainly comprised of soluble organic acids, i.e. butyric acid and lactic acid. The batch process was carried out under light intensity of 2.5 kLux at 32 ± 2oC without any addition of extra carbon and nitrogen source. The single parameter optimization studies revealed optimum pH 6.5, initial COD 4.71 g/L and supplementation of Fe2+ concentration 100 mg/L. The maximum cumulative hydrogen production and yield were found to be 469 ± 45.8 ml H2/L and 146.56 ± 14.31 ml H2/g COD reduced (67.9% reduction in COD) respectively. The mutual interactions among the process parameters were also investigated by three factorial Box-Behnken design of response surface methodology. The optimized experimental values were found concurrent with the calculated values obtained from the theoretical model.

Grain dust-induced lung inflammation is reduced by Rhodobacter sphaeroides diphosphoryl lipid A.

Science.gov (United States)

Jagielo, P J; Quinn, T J; Qureshi, N; Schwartz, D A

1998-01-01

To further determine the importance of endotoxin in grain dust-induced inflammation of the lower respiratory tract, we evaluated the efficacy of pentaacylated diphosphoryl lipid A derived from the lipopolysaccharide of Rhodobacter sphaeroides (RsDPLA) as a partial agonist of grain dust-induced airway inflammation. RsDPLA is a relatively inactive compound compared with lipid A derived from Escherichia coli (LPS) and has been demonstrated to act as a partial agonist of LPS-induced inflammation. To assess the potential stimulatory effect of RsDPLA in relation to LPS, we incubated THP-1 cells with RsDPLA (0.001-100 micrograms/ml), LPS (0.02 microgram endotoxin activity/ml), or corn dust extract (CDE; 0.02 microgram endotoxin activity/ml). Incubation with RsDPLA revealed a tumor necrosis factor (TNF)-alpha stimulatory effect at 100 micrograms/ml. In contrast, incubation with LPS or CDE resulted in TNF-alpha release at 0.02 microgram/ml. Pretreatment of THP-1 cells with varying concentrations of RsDPLA before incubation with LPS or CDE (0.02 microgram endotoxin activity/ml) resulted in a dose-dependent reduction in the LPS- or CDE-induced release of TNF-alpha with concentrations of RsDPLA of up to 10 micrograms/ml but not at 100 micrograms/ml. To further understand the role of endotoxin in grain dust-induced airway inflammation, we utilized the unique LPS inhibitory property of RsDPLA to determine the inflammatory response to inhaled CDE in mice in the presence of RsDPLA. Ten micrograms of RsDPLA intratracheally did not cause a significant inflammatory response compared with intratracheal saline. However, pretreatment of mice with 10 micrograms of RsDPLA intratracheally before exposure to CDE (5.4 and 0.2 micrograms/m3) or LPS (7.2 and 0.28 micrograms/m3) resulted in significant reductions in the lung lavage concentrations of total cells, neutrophils, and specific proinflammatory cytokines compared with mice pretreated with sterile saline. These results confirm the LPS

Role of PufX protein in photosynthetic growth of Rhodobacter sphaeroides. 1. PufX is required for efficient light-driven electron transfer and photophosphorylation under anaerobic conditions.

Science.gov (United States)

Barz, W P; Francia, F; Venturoli, G; Melandri, B A; Verméglio, A; Oesterhelt, D

1995-11-21

The pufX gene is essential for photoheterotrophic growth of the purple bacterium Rhodobacter sphaeroides. In order to analyze the molecular function of the PufX membrane protein, we constructed a chromosomal pufX deletion mutant and phenotypically compared it to a pufX+ control strain and to two suppressor mutants which are able to grow photosynthetically in the absence of pufX. Using this genetic background, we confirmed that PufX is required for photoheterotrophic growth under anaerobic conditions, although all components of the photosynthetic apparatus were present in similar amounts in all strains investigated. We show that the deletion of PufX is not lethal for illuminated pufX- cells, suggesting that PufX is required for photosynthetic cell division. Since chromatophores isolated from the pufX- mutant were found to be unsealed vesicles, the role of PufX in photosynthetic energy transduction was studied in vivo. We show that PufX is essential for light-induced ATP synthesis (photophosphorylation) in anaerobically incubated cells. Measurements of absorption changes induced by a single turnover flash demonstrated that PufX is not required for electron flow through the reaction center and the cytochrome bc1 complex under anaerobic conditions. During prolonged illumination, however, PufX is essential for the generation of a sufficiently large membrane potential to allow photosynthetic growth. These in vivo results demonstrate that under anaerobic conditions PufX plays an essential role in facilitating effective interaction of the components of the photosynthetic apparatus.

Structure and function of cytochrome c2 in electron transfer complexes with the photosynthetic reaction center of Rhodobacter sphaeroides: optical linear dichroism and EPR.

Science.gov (United States)

Drepper, F; Mathis, P

1997-02-11

The photosynthetic reaction center (RC) and its secondary electron donor the water-soluble cytochrome (cyt) c2 from the purple bacterium Rhodobacter sphaeroides have been used in cross-linked and non-cross-linked complexes, oriented in compressed gels or partially dried multilayers, to study the respective orientation of the primary donor P (BChl dimer) and of cyt c2. Three methods were used: (i) Polarized optical absorption spectra at 295 and 10 K were measured and the linear dichroism of the two individual transitions (Qx, Qy), which are nearly degenerate within the alpha-band of reduced cyt c2, was determined. Attribution of the polarization directions to the molecular axes within the heme plane yielded the average cyt orientation in the complexes. (ii) Time-resolved flash absorption measurements using polarized light allowed determination of the orientation of cyt c2 in complexes which differ in their kinetics of electron transfer. (iii) EPR spectroscopy of ferricyt c2 in cross-linked RC-cyt c2 complexes was used to determine the angle between the heme and the membrane plane. The results suggest the following structural properties for the docking of cyt c2 to the RC: (i) In cross-linked complexes, the two cytochromes displaying half-lives of 0.7 and 60 micros for electron transfer to P+ are similarly oriented (difference plane is parallel to the symmetry axis of the RC (0 degrees +/- 10 degrees). Moreover, the Qy transition, which is assumed to be polarized within the ring III-ring I direction of the heme plane, makes an angle of 56 degrees +/- 1 degree with the symmetry axis. (iii) The dichroism spectrum for the fast phase (0.7 micros) for the non-cross-linked cyt c2-RC complex suggests an orientation similar to that of cross-linked cyt c2, but the heme plane is tilted about 20 degrees closer to the membrane. An alternative model is that two or more bound states of cyt c2 with heme plane tilt angles between 0 degrees and 30 degrees allow the fast electron

Chronic Exposure to Rhodobacter Sphaeroides Extract Lycogen™ Prevents UVA-Induced Malondialdehyde Accumulation and Procollagen I Down-Regulation in Human Dermal Fibroblasts

Science.gov (United States)

Yang, Tsai-Hsiu; Lai, Ying-Hsiu; Lin, Tsuey-Pin; Liu, Wen-Sheng; Kuan, Li-Chun; Liu, Chia-Chyuan

2014-01-01

UVA contributes to the pathogenesis of skin aging by downregulation of procollagen I content and induction of matrix metalloproteinase (MMP)-associated responses. Application of antioxidants such as lycopene has been demonstrated as a convenient way to achieve protection against skin aging. Lycogen™, derived from the extracts of Rhodobacter sphaeroides, exerts several biological effects similar to that of lycopene whereas most of its anti-aging efficacy remains uncertain. In this study, we attempted to examine whether Lycogen™ could suppress malondialdehyde (MDA) accumulation and restore downregulated procollagen I expression induced by UVA exposure. In human dermal fibroblasts Hs68 cells, UVA repressed cell viability and decreased procollagen I protein content accompanied with the induction of MMP-1 and MDA accumulation. Remarkably, incubation with 50 μM Lycogen™ for 24 h ameliorated UVA-induced cell death and restored UVA-induced downregulation of procollagen in a dose-related manner. Lycogen™ treatment also prevented the UVA-induced MMP-1 upregulation and intracellular MDA generation in Hs68 cells. Activation of NFκB levels, one of the downstream events induced by UVA irradiation and MMP-1 induction, were also prevented by Lycogen™ administration. Taken together, our findings demonstrate that Lycogen™ may be an alternative agent that prevents UVA-induced skin aging and could be used in cosmetic and pharmaceutical applications. PMID:24463291

NCBI nr-aa BLAST: CBRC-RMAC-01-0051 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-RMAC-01-0051 ref|YP_001033817.1| Ice nucleation protein [Rhodobacter sphaeroid...es 2.4.1] gb|ABA81712.1| Ice nucleation protein [Rhodobacter sphaeroides 2.4.1] YP_001033817.1 0.016 26% ...

NCBI nr-aa BLAST: CBRC-OLAT-26-0102 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OLAT-26-0102 ref|YP_001033817.1| Ice nucleation protein [Rhodobacter sphaeroid...es 2.4.1] gb|ABA81712.1| Ice nucleation protein [Rhodobacter sphaeroides 2.4.1] YP_001033817.1 0.45 25% ...

NCBI nr-aa BLAST: CBRC-XTRO-01-0470 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-XTRO-01-0470 ref|YP_001033817.1| Ice nucleation protein [Rhodobacter sphaeroid...es 2.4.1] gb|ABA81712.1| Ice nucleation protein [Rhodobacter sphaeroides 2.4.1] YP_001033817.1 1e-12 25% ...

NCBI nr-aa BLAST: CBRC-XTRO-01-0267 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-XTRO-01-0267 ref|YP_001033817.1| Ice nucleation protein [Rhodobacter sphaeroid...es 2.4.1] gb|ABA81712.1| Ice nucleation protein [Rhodobacter sphaeroides 2.4.1] YP_001033817.1 6e-27 25% ...

NCBI nr-aa BLAST: CBRC-TNIG-22-0265 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-TNIG-22-0265 ref|YP_001033817.1| Ice nucleation protein [Rhodobacter sphaeroid...es 2.4.1] gb|ABA81712.1| Ice nucleation protein [Rhodobacter sphaeroides 2.4.1] YP_001033817.1 4e-36 37% ...

NCBI nr-aa BLAST: CBRC-OGAR-01-0310 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-OGAR-01-0310 ref|YP_001033817.1| Ice nucleation protein [Rhodobacter sphaeroid...es 2.4.1] gb|ABA81712.1| Ice nucleation protein [Rhodobacter sphaeroides 2.4.1] YP_001033817.1 4e-07 24% ...

Effects of the cryptochrome CryB from Rhodobacter sphaeroides on global gene expression in the dark or blue light or in the presence of singlet oxygen.

Directory of Open Access Journals (Sweden)

Sebastian Frühwirth

Full Text Available Several regulators are controlling the formation of the photosynthetic apparatus in the facultatively photosynthetic bacterium Rhodobacter sphaeroides. Among the proteins affecting photosynthesis gene expression is the blue light photoreceptor cryptochrome CryB. This study addresses the effect of CryB on global gene expression. The data reveal that CryB does not only influence photosynthesis gene expression but also genes for the non-photosynthetic energy metabolism like citric acid cycle and oxidative phosphorylation. In addition several genes involved in RNA processing and in transcriptional regulation are affected by a cryB deletion. Although CryB was shown to undergo a photocycle it does not only affect gene expression in response to blue light illumination but also in response to singlet oxygen stress conditions. While there is a large overlap in these responses, some CryB-dependent effects are specific for blue-light or photooxidative stress. In addition to protein-coding genes some genes for sRNAs show CryB-dependent expression. These findings give new insight into the function of bacterial cryptochromes and demonstrate for the first time a function in the oxidative stress response.

Role of the PufX protein in photosynthetic growth of Rhodobacter sphaeroides. 2. PufX is required for efficient ubiquinone/ubiquinol exchange between the reaction center QB site and the cytochrome bc1 complex.

Science.gov (United States)

Barz, W P; Verméglio, A; Francia, F; Venturoli, G; Melandri, B A; Oesterhelt, D

1995-11-21

The PufX membrane protein is essential for photosynthetic growth of Rhodobacter sphaeroides because it is required for multiple-turnover electron transfer under anaerobic conditions [see accompanying article; Barz, W. P., Francia, F., Venturoli, G., Melandri, B. A., Verméglio, A., & Oesterhelt, D. (1995) Biochemistry 34, 15235-15247]. In order to understand the molecular role of PufX, light-induced absorption spectroscopy was performed using a pufX- mutant, a pufX+ strain, and two suppressor mutants. We show that the reaction center (RC) requires PufX for its functionality under different redox conditions than the cytochrome bc1 complex: When the kinetics of flash-induced reduction of cytochrome b561 were monitored in chromatophores, we observed a requirement of PufX for turnover of the cytochrome bc1 complex only at high redox potential (Eh > 140 mV), suggesting a function of PufX in lateral ubiquinol transfer from the RC. In contrast, PufX is required for multiple turnover of the RC only under reducing conditions: When the Q pool was partially oxidized in vivo using oxygen or electron acceptors like dimethyl sulfoxide or trimethylamine N-oxide, the deletion of PufX had no effect on light-driven electron flow through the RC. Flash train experiments under anaerobic in vivo conditions revealed that RC photochemistry does not depend on PufX for the first two flash excitations. Following the third and subsequent flashes, however, efficient charge separation requires PufX, indicating an important role of PufX for fast Q/QH2 exchange at the QB site of the RC. We show that the Q/QH2 exchange rate is reduced approximately 500-fold by the deletion of PufX when the Q pool is nearly completely reduced, demonstrating an essential role of PufX for the access of ubiquinone to the QB site. The fast ubiquinone/ubiquinol exchange is partially restored by suppressor mutations altering the macromolecular antenna structure. These results suggest an indirect role of PufX in

Resonance Raman and surface-enhanced resonance Raman spectra of LH2 antenna complex from Rhodobacter sphaeroides and Ectothiorhodospira sp. excited in the Qx and Qy transitions.

Science.gov (United States)

Chumanov, G; Picorel, R; Ortiz de Zarate, I; Cotton, T M; Seibert, M

2000-05-01

Well-resolved vibrational spectra of LH2 complex isolated from two photosynthetic bacteria, Rhodobacter sphaeroides and Ectothiorhodospira sp., were obtained using surface-enhanced resonance Raman scattering (SERRS) exciting into the Qx and the Qy transitions of bacteriochlorophyll a. High-quality SERRS spectra in the Qy region were accessible because the strong fluorescence background was quenched near the roughened Ag surface. A comparison of the spectra obtained with 590 nm and 752 nm excitation in the mid- and low-frequency regions revealed spectral differences between the two LH2 complexes as well as between the LH2 complexes and isolated bacteriochlorophyll a. Because peripheral modes of pigments contribute mainly to the low-frequency spectral region, frequencies and intensities of many vibrational bands in this region are affected by interactions with the protein. The results demonstrate that the microenvironment surrounding the pigments within the two LH2 complexes is somewhat different, despite the fact that the complexes exhibit similar electronic absorption spectra. These differences are most probably due to specific pigment-pigment and pigment-protein interactions within the LH2 complexes, and the approach might be useful for addressing subtle static and dynamic structural variances between pigment-protein complexes from different sources or in complexes altered chemically or genetically.

Role of charge-transfer states in bacterial photosynthesis

NARCIS (Netherlands)

Meech, S.R.; Hoff, A.J.

1986-01-01

Photon echo, photon-echo excitation, and "hole-burning" data recorded in the 800-990 nm region of Rhodobacter sphaeroides R26 and Rhodopseudomonas viridis reaction centers are reported. The primary process in these reaction centers, following excitation, was found to occur in ≈25 fsec; the

Dynamics of energy transfer from lycopene to bacteriochlorophyll in genetically-modified LH2 complexes of Rhodobacter sphaeroides.

Science.gov (United States)

Hörvin Billsten, H; Herek, J L; Garcia-Asua, G; Hashøj, L; Polívka, T; Hunter, C N; Sundström, V

2002-03-26

LH2 complexes from Rb. sphaeroides were modified genetically so that lycopene, with 11 saturated double bonds, replaced the native carotenoids which contain 10 saturated double bonds. Tuning the S1 level of the carotenoid in LH2 in this way affected the dynamics of energy transfer within LH2, which were investigated using both steady-state and time-resolved techniques. The S1 energy of lycopene in n-hexane was determined to be approximately 12 500 +/- 150 cm(-1), by direct measurement of the S1-S2 transient absorption spectrum using a femtosecond IR-probing technique, thus placing an upper limit on the S1 energy of lycopene in the LH2 complex. Fluorescence emission and excitation spectra demonstrated that energy can be transferred from lycopene to the bacteriochlorophyll molecules within this LH2 complex. The energy-transfer dynamics within the mutant complex were compared to wild-type LH2 from Rb. sphaeroides containing the carotenoid spheroidene and from Rs. molischianum, in which lycopene is the native carotenoid. The results show that the overall efficiency for Crt --> B850 energy transfer is approximately 80% in lyco-LH2 and approximately 95% in WT-LH2 of Rb. sphaeroides. The difference in overall Crt --> BChl transfer efficiency of lyco-LH2 and WT-LH2 mainly relates to the low efficiency of the Crt S(1) --> BChl pathway for complexes containing lycopene, which was 20% in lyco-LH2. These results show that in an LH2 complex where the Crt S1 energy is sufficiently high to provide efficient spectral overlap with both B800 and B850 Q(y) states, energy transfer via the Crt S1 state occurs to both pigments. However, the introduction of lycopene into the Rb. sphaeroides LH2 complex lowers the S1 level of the carotenoid sufficiently to prevent efficient transfer of energy to the B800 Q(y) state, leaving only the Crt S1 --> B850 channel, strongly suggesting that Crt S1 --> BChl energy transfer is controlled by the relative Crt S1 and BChl Q(y) energies.

Some experiments on the primary electron acceptor in reaction centres from Rhodopseudomanas sphaeroides

Energy Technology Data Exchange (ETDEWEB)

Wraight, C A; Cogdell, R J; Clayton, R K

1975-01-01

The bacterial reaction center absorbance change at 450 nm (A-450), assigned to an anionic semiquinone, has been suggested as a candidate for the reduced form of the primary electron acceptor in bacterial photosynthesis. In reaction centers of Rhodopseudomonas sphaeroides we have found kinetic discrepancies between the decay of A-450 and the recovery of photochemical competence. In addition, no proton uptake is measurable on the first turnover, although subsequent ones elicit one proton bound per electron. These results are taken to indicate that the acceptor reaction after a long dark period may be different for the first turnover than for subsequent ones. It is suggested that A-450 is still a likely candidate for the acceptor function but that in reaction centers, additional quinone may act as an adventitious primary acceptor when the ''true'' primary acceptor is reduced. Alternatively, the primary acceptor may act in a ''ping-pong'' fashion with respect to subsequent photoelectrons.

Spectral diffusion and electron-phonon coupling of the B800 BChl a molecules in LH2 complexes from three different species of purple bacteria.

Science.gov (United States)

Baier, J; Gabrielsen, M; Oellerich, S; Michel, H; van Heel, M; Cogdell, R J; Köhler, J

2009-11-04

We have investigated the spectral diffusion and the electron-phonon coupling of B800 bacteriochlorophyll a molecules in the peripheral light-harvesting complex LH2 for three different species of purple bacteria, Rhodobacter sphaeroides, Rhodospirillum molischianum, and Rhodopseudomonas acidophila. We come to the conclusion that B800 binding pockets for Rhodobacter sphaeroides and Rhodopseudomonas acidophila are rather similar with respect to the polarity of the protein environment but that the packaging of the alphabeta-polypeptides seems to be less tight in Rb. sphaeroides with respect to the other two species.

Photodynamics of BLUF domain proteins: a new class of the biological blue-light photoreceptors

OpenAIRE

Zirak Yousefabadi, Peyman

2008-01-01

BLUF domains are light sensors of many microorganisms. They are present in the multi-domain proteins e.g. AppA from the phototrophic proteobacterium Rhodobacter sphaeroides, YcgF from Escherichia coli, PAC (photoactive adenylyl cyclase) from the unicellular flagellate Euglena gracilis and single domain proteins e.g. BlrB from Rhodobacter sphaeroides, Slr1694 from cyanobacterium Synechocystis sp.PCC6803, and Tll0078 of the thermophilic unicellular cyanobacterium Thermosynechococcus elongates B...

Bioaugmentation of Lactobacillus delbrueckii ssp. bulgaricus TISTR 895 to enhance bio-hydrogen production of Rhodobacter sphaeroides KKU-PS5.

Science.gov (United States)

Laocharoen, Sucheera; Reungsang, Alissara; Plangklang, Pensri

2015-01-01

Bioaugmentation or an addition of the desired microorganisms or specialized microbial strains into the anaerobic digesters can enhance the performance of microbial community in the hydrogen production process. Most of the studies focused on a bioaugmentation of native microorganisms capable of producing hydrogen with the dark-fermentative hydrogen producers while information on bioaugmentation of purple non-sulfur photosynthetic bacteria (PNSB) with lactic acid-producing bacteria (LAB) is still limited. In our study, bioaugmentation of Rhodobacter sphaeroides KKU-PS5 with Lactobacillus delbrueckii ssp. bulgaricus TISTR 895 was conducted as a method to produce hydrogen. Unfortunately, even though well-characterized microorganisms were used in the fermentation system, a cultivation of two different organisms in the same bioreactor was still difficult because of the differences in their metabolic types, optimal conditions, and nutritional requirements. Therefore, evaluation of the physical and chemical factors affecting hydrogen production of PNSB augmented with LAB was conducted using a full factorial design followed by response surface methodology (RSM) with central composite design (CCD). A suitable LAB/PNSB ratio and initial cell concentration were found to be 1/12 (w/w) and 0.15 g/L, respectively. The optimal initial pH, light intensity, and Mo concentration obtained from RSM with CCD were 7.92, 8.37 klux and 0.44 mg/L, respectively. Under these optimal conditions, a cumulative hydrogen production of 3396 ± 66 mL H2/L, a hydrogen production rate (HPR) of 9.1 ± 0.2 mL H2/L h, and a hydrogen yield (HY) of 9.65 ± 0.23 mol H2/mol glucose were obtained. KKU-PS5 augmented with TISTR 895 produced hydrogen from glucose at a relatively high HY, 9.65 ± 0.23 mol H2/mol glucose, i.e., 80 % of the theoretical yield. The ratio of the strains TISTR 895/KKU-PS5 and their initial cell concentrations affected the rate of lactic acid production and its

Imaging of solid tumor using near-infrared emitting purple bacteria

International Nuclear Information System (INIS)

Moon, Sung Min; Min, Jung Joon; Kim, Sun A; Choy, Hyon E.; Bom, Hee Seung

2005-01-01

Rhodobacter sphaeroides 2.4.1 is α-3 purple nonsulfur eubacterium with an extensive metabolism. Under anaerobic conditions, it is able to grow by photosynthesis, respiration and fermentation. When grown photosynthetically, it uses wavelengths of light in the near-infrared and contains a reaction center that is the peripheral light-harvesting (LH2) complex. These molecules absorb and emit near-infrared light. Using this near-infrared fluorescent bacterial we investigated its targeting capacity of solid tumor in small animals. R. sphaeroides 2.4.1 strains were cultured in sistrons minimal medium A (SIS) at 32 C. Xenograft tumor model has been established by subcutaneous injection of CT26 mouse colon cancer cell line. 1X10 8 Rhodobacter sphaeroides cells suspended in 100 ul of PBS were injected via tail vein with 1-cc insulin syringe into tumor bearing mouse. In vivo fluorescence imaging has been done after 20 min to 30 days of purple bacteria using indocyanine (ICG) emission filter (Em=810∼835 nm). Near-infrared imaging signal from Rhodobacter sphaeroides was initially detected at liver for 3 days but at the necrotic region of tumor mass thereafter. Total photon flux measured 5.5X10 8 (p/s/cm 2 /sr) at Day 1. Also it was increased to 7.8X10 8 (p/s/cm 2 /sr) at 12 day. One of important characteristic is that the signal appeared only at central necrosis area. It has been monitored for 36 day. We successfully imaged cancer with near-infrared fluorescence bacteria. Our result indicate that near-infrared fluorescence purple bacteria are able to be used to monitor bacterial trafficking in living tumor models

Tuning cofactor redox potentials: the 2-methoxy dihedral angle generates a redox potential difference of >160 mV between the primary (Q(A)) and secondary (Q(B)) quinones of the bacterial photosynthetic reaction center.

Science.gov (United States)

Taguchi, Alexander T; Mattis, Aidas J; O'Malley, Patrick J; Dikanov, Sergei A; Wraight, Colin A

2013-10-15

Only quinones with a 2-methoxy group can act simultaneously as the primary (QA) and secondary (QB) electron acceptors in photosynthetic reaction centers from Rhodobacter sphaeroides. (13)C hyperfine sublevel correlation measurements of the 2-methoxy in the semiquinone states, SQA and SQB, were compared with quantum mechanics calculations of the (13)C couplings as a function of the dihedral angle. X-ray structures support dihedral angle assignments corresponding to a redox potential gap (ΔEm) between QA and QB of ~180 mV. This is consistent with the failure of a ubiquinone analogue lacking the 2-methoxy to function as QB in mutant reaction centers with a ΔEm of ≈160-195 mV.

Chemical proprieties of the iron-quinone complex in mutated reaction centers of Rb. sphaeroides

International Nuclear Information System (INIS)

Hałas, Agnieszka; Derrien, Valerie; Sebban, Pierre; Matlak, Krzysztof; Korecki, Józef; Kruk, Jerzy; Burda, Kvĕtoslava

2012-01-01

We investigated type II bacterial photosynthetic reaction centers, which contain a quinone - iron complex (Q A -Fe-Q B ) on their acceptor side. Under physiological conditions it was observed mainly in a reduced high spin state but its low spin ferrous states were also observed. Therefore, it was suggested that it might regulate the dynamical properties of the iron–quinone complex and the protonation and deprotonation events in its neighbourhood. In order to get insight into the molecular mechanism of the NHFe low spin state formation, we preformed Mössbauer studies of a wild type of Rb. sphaeroides and its two mutated forms. Our Mössbauer measurements show that the hydrophobicity of the Q A binding site can be crucial for stabilization of the high spin ferrous state of NHFe.

The three-dimensional structures of bacterial reaction centers.

Science.gov (United States)

Olson, T L; Williams, J C; Allen, J P

2014-05-01

This review presents a broad overview of the research that enabled the structure determination of the bacterial reaction centers from Blastochloris viridis and Rhodobacter sphaeroides, with a focus on the contributions from Duysens, Clayton, and Feher. Early experiments performed in the laboratory of Duysens and others demonstrated the utility of spectroscopic techniques and the presence of photosynthetic complexes in both oxygenic and anoxygenic photosynthesis. The laboratories of Clayton and Feher led efforts to isolate and characterize the bacterial reaction centers. The availability of well-characterized preparations of pure and stable reaction centers allowed the crystallization and subsequent determination of the structures using X-ray diffraction. The three-dimensional structures of reaction centers revealed an overall arrangement of two symmetrical branches of cofactors surrounded by transmembrane helices from the L and M subunits, which also are related by the same twofold symmetry axis. The structure has served as a framework to address several issues concerning bacterial photosynthesis, including the directionality of electron transfer, the properties of the reaction center-cytochrome c 2 complex, and the coupling of proton and electron transfer. Together, these research efforts laid the foundation for ongoing efforts to address an outstanding question in oxygenic photosynthesis, namely the molecular mechanism of water oxidation.

Hydrogen bonds in the vicinity of the special pair of the bacterial reaction center probed by hydrostatic high-pressure absorption spectroscopy.

Science.gov (United States)

Kangur, Liina; Jones, Michael R; Freiberg, Arvi

2017-12-01

Using the native bacteriochlorophyll a pigment cofactors as local probes, we investigated the response to external hydrostatic high pressure of reaction center membrane protein complexes from the photosynthetic bacterium Rhodobacter sphaeroides. Wild-type and engineered complexes were used with a varied number (0, 1 or 2) of hydrogen bonds that bind the reaction center primary donor bacteriochlorophyll cofactors to the surrounding protein scaffold. A pressure-induced breakage of hydrogen bonds was established for both detergent-purified and membrane-embedded reaction centers, but at rather different pressures: between 0.2 and 0.3GPa and at about 0.55GPa, respectively. The free energy change associated with the rupture of the single hydrogen bond present in wild-type reaction centers was estimated to be equal to 13-14kJ/mol. In the mutant with two symmetrical hydrogen bonds (FM197H) a single cooperative rupture of the two bonds was observed corresponding to an about twice stronger bond, rather than a sequential rupture of two individual bonds. Copyright © 2017 Elsevier B.V. All rights reserved.

Continuous Cultivation of Photosynthetic Bacteria for Fatty Acids Production

DEFF Research Database (Denmark)

Kim, Dong-Hoon; Lee, Ji-Hye; Hwang, Yuhoon

2013-01-01

In the present work, we introduced a novel approach for microbial fatty acids (FA) production. Photosynthetic bacteria, Rhodobacter sphaeroides KD131, were cultivated in a continuous-flow, stirred-tank reactor (CFSTR) at various substrate (lactate) concentrations.At hydraulic retention time (HRT)....... sphaeroides was around 35% of dry cell weight, mainly composed of vaccenic acid (C18:1, omega-7)....

Reverse micelles as suitable microreactor for increased biohydrogen production

Energy Technology Data Exchange (ETDEWEB)

Pandey, Anjana [Nanotechnology and Molecular Biology Laboratory, Centre of Biotechnology, University of Allahabad, Allahabad 211002 (India); Pandey, Ashutosh [Centre of Energy Studies, MNNIT, Allahabad 211004 (India)

2008-01-15

Reverse micelles have been shown to act as efficient microreactors for enzymic reactions and whole cell entrapment in organic (non-aqueous) media wherein the reactants are protected from denaturation by the surrounding organic solvent. These micelles are thermodynamically stable, micrometer sized water droplets dispersed in an organic phase by a surfactant. It has been observed that when whole cells of photosynthetic bacteria (Rhodopseudomonas sphaeroides or Rhodobacter sphaeroides 2.4.1) are entrapped inside these reverse micelles, the H{sub 2} production enhanced from 25 to 35 folds. That is, 1.71mmol(mgprotein){sup -1}h{sup -1} in case of R. sphaeroides which is 25 fold higher in benzene-sodium lauryl sulfate reverse micelles. Whereas, in case of R. sphaeroides 2.4.1 the H{sub 2} production was increased by 35 fold within AOT-isooctane reverse micelles i.e. 11.5mmol(mgprotein){sup -1}h{sup -1}. The observations indicate that the entrapment of whole cells of microbes within reverse micelles provides a novel and efficient technique to produce hydrogen by the inexhaustible biological route. The two microorganisms R. sphaeroides 2.4.1 (a photosynthetic bacteria) and Citrobacter Y19 (a facultative anaerobic bacteria) together are also entrapped within AOT-isooctane and H{sub 2} production was measured i.e. 69mmol(mgprotein){sup -1}h{sup -1}. The nitrogenase enzyme responsible for hydrogen production by R. sphaeroides/R. sphaeroides 2.4.1 cells is oxygen sensitive, and very well protected within reverse micelles by the use of combined approach of two cells (R. sphaeroides 2.4.1 and Citrobacter Y19). In this case glucose present in the medium of Citrobacter Y19 serves double roles in enhancing the sustained production rate of hydrogen. Firstly, it quenches the free O{sub 2}liberated as a side product of reaction catalyzed by nitrogenase, which is O{sub 2} labile. Secondly, organic acid produced by this reaction is utilized by the Citrobacter Y19 as organic substrate in

Modeling the bacterial photosynthetic reaction center. VII. Full simulation of the intervalence hole-transfer absorption spectrum of the special-pair radical cation

International Nuclear Information System (INIS)

Reimers, Jeffrey R.; Hush, Noel S.

2003-01-01

ENDOR data suggests that the special-pair radical cation P + from Rhodobacter sphaeroides is 68% localized on P L while simple interpretations of FTIR difference spectra based primarily on intensity information, but to some extent also bandwidths, suggest near-complete charge localization. We provide a complete a priori spectral simulation of the spectrum of P + in the range 0-5000 cm-1, including explicit treatment of the high-resolution vibrational transitions, the low-resolution hole-transfer absorption centered at 2700 cm-1, and the resonance with the SHOMO to HOMO transition at 2200 cm-1 that resolve the issues concerning the nature of P + . The description of the vibrational aspects of the problem were taken from results of previous density-functional calculations, and a qualitatively realistic large number of vibrational modes (50 antisymmetric and 18-20 symmetric) were included. To facilitate the calculations, a new representation of the vibronic-coupling Hamiltonian for intervalence hole-transfer or electron-transfer problems is introduced, allowing the spectrum to be simulated efficiently using only up to 4x10 9 vibronic basis functions and leading also to new general analytical relationships. Observed spectra are fitted using seven adjustable chemical parameters describing the interactions between the four electronic states involved. The resulting fits provide unique descriptions of the parameters that are insensitive to the source of the observed spectrum or the nature of the symmetric modes used in the model, and all fitted parameters are found to be close in value to those from independent estimates. We determine the electronic coupling, antisymmetric-mode reorganization energy, and redox asymmetry to be J=0.126±0.002 eV, λ=0.139±0.003 eV, and E 0 =0.069±0.002 eV, respectively. Our description forms the basis of understanding for a wide range of other properties observed for Rhodobacter sphaeroides mutants, as well as the properties of the

Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s

OpenAIRE

Chandler, Danielle E.; Gumbart, James; Stack, John D.; Chipot, Christophe; Schulten, Klaus

2009-01-01

The photosynthetic apparatus of purple bacteria is contained within organelles called chromatophores, which form as extensions of the cytoplasmic membrane. The shape of these chromatophores can be spherical (as in Rhodobacter sphaeroides), lamellar (as in Rhodopseudomonas acidophila and Phaeospirillum molischianum), or tubular (as in certain Rb. sphaeroides mutants). Chromatophore shape is thought to be influenced by the integral membrane proteins Light Harvesting Complexes I and II (LH1 and ...

Paepalanthus sphaeroides, a new species of Eriocaulaceae from the Atlantic Forest, Brazil

NARCIS (Netherlands)

Trovó, M.; Echternacht, L.; Sano, P.T.

2012-01-01

We describe and illustrate Paepalanthus sphaeroides (Eriocaulaceae, Paepalanthoideae) from the Mantiqueira Range in South-eastern Brazil and compare it with the morphologically most similar species: Paepalanthus aequalis and Paepalanthus eriophaeus. Paepalanthus sphaeroides has unique membranaceous

NCBI nr-aa BLAST: CBRC-ATHA-01-0056 [SEVENS

Lifescience Database Archive (English)

Full Text Available CBRC-ATHA-01-0056 ref|YP_354669.1| ABC nitrate/sulfonate/bicarbonate transporter fa...mily, periplasmic substrate-binding protein [Rhodobacter sphaeroides 2.4.1] gb|ABA80768.1| ABC nitrate/sulfonate/bicarbonate

The binding of quinone to the photosynthetic reaction centers: kinetics and thermodynamics of reactions occurring at the QB-site in zwitterionic and anionic liposomes.

Science.gov (United States)

Mavelli, Fabio; Trotta, Massimo; Ciriaco, Fulvio; Agostiano, Angela; Giotta, Livia; Italiano, Francesca; Milano, Francesco

2014-07-01

Liposomes represent a versatile biomimetic environment for studying the interaction between integral membrane proteins and hydrophobic ligands. In this paper, the quinone binding to the QB-site of the photosynthetic reaction centers (RC) from Rhodobacter sphaeroides has been investigated in liposomes prepared with either the zwitterionic phosphatidylcholine (PC) or the negatively charged phosphatidylglycerol (PG) to highlight the role of the different phospholipid polar heads. Quinone binding (K Q) and interquinone electron transfer (L AB) equilibrium constants in the two type of liposomes were obtained by charge recombination reaction of QB-depleted RC in the presence of increasing amounts of ubiquinone-10 over the temperature interval 6-35 °C. The kinetic of the charge recombination reactions has been fitted by numerically solving the ordinary differential equations set associated with a detailed kinetic scheme involving electron transfer reactions coupled with quinone release and uptake. The entire set of traces at each temperature was accurately fitted using the sole quinone release constants (both in a neutral and a charge separated state) as adjustable parameters. The temperature dependence of the quinone exchange rate at the QB-site was, hence, obtained. It was found that the quinone exchange regime was always fast for PC while it switched from slow to fast in PG as the temperature rose above 20 °C. A new method was introduced in this paper for the evaluation of constant K Q using the area underneath the charge recombination traces as the indicator of the amount of quinone bound to the QB-site.

Biosynthesis of Chlorophyll a in a Purple Bacterial Phototroph and Assembly into a Plant Chlorophyll-Protein Complex.

Science.gov (United States)

Hitchcock, Andrew; Jackson, Philip J; Chidgey, Jack W; Dickman, Mark J; Hunter, C Neil; Canniffe, Daniel P

2016-09-16

Improvements to photosynthetic efficiency could be achieved by manipulating pigment biosynthetic pathways of photosynthetic organisms in order to increase the spectral coverage for light absorption. The development of organisms that can produce both bacteriochlorophylls and chlorophylls is one way to achieve this aim, and accordingly we have engineered the bacteriochlorophyll-utilizing anoxygenic phototroph Rhodobacter sphaeroides to make chlorophyll a. Bacteriochlorophyll and chlorophyll share a common biosynthetic pathway up to the precursor chlorophyllide. Deletion of genes responsible for the bacteriochlorophyll-specific modifications of chlorophyllide and replacement of the native bacteriochlorophyll synthase with a cyanobacterial chlorophyll synthase resulted in the production of chlorophyll a. This pigment could be assembled in vivo into the plant water-soluble chlorophyll protein, heterologously produced in Rhodobacter sphaeroides, which represents a proof-of-principle for the engineering of novel antenna complexes that enhance the spectral range of photosynthesis.

Early Bacteriopheophytin Reduction in Charge Separation in Reaction Centers of Rhodobacter sphaeroides

NARCIS (Netherlands)

Zhu, J.; van Stokkum, I.H.M.; Paparelli, L.; Jones, M.R.; Groot, M.L.

2013-01-01

A question at the forefront of biophysical sciences is, to what extent do quantum effects and protein conformational changes play a role in processes such as biological sensing and energy conversion? At the heart of photosynthetic energy transduction lie processes involving ultrafast energy and

Investigation of the effects of different carotenoids on the absorption and CD signals of light harvesting 1 complexes

NARCIS (Netherlands)

Georgakopoulou, S.; van der Zwan, G.; Olsen, J.D.; Hunter, C.N.; Niederman, R.A.; van Grondelle, R.

2006-01-01

Absorption and circular dichroism (CD) spectra of light-harvesting (LH)1 complexes from the purple bacteria Rhodobacter (Rba.) sphaeroides and Rhodospirillum (Rsp.) rubrum are presented. The complexes exhibit very low intensity, highly nonconservative, near-infrared (NIR) CD spectra. Absorption and

Engineered photoproteins that give rise to photosynthetically-incompetent bacteria are effective as photovoltaic materials for biohybrid photoelectrochemical cells.

Science.gov (United States)

Liu, Juntai; Friebe, Vincent M; Swainsbury, David J K; Crouch, Lucy I; Szabo, David A; Frese, Raoul N; Jones, Michael R

2018-04-17

Reaction centre/light harvesting proteins such as the RCLH1X complex from Rhodobacter sphaeroides carry out highly quantum-efficient conversion of solar energy through ultrafast energy transfer and charge separation, and these pigment-proteins have been incorporated into biohybrid photoelectrochemical cells for a variety of applications. In this work we demonstrate that, despite not being able to support normal photosynthetic growth of Rhodobacter sphaeroides, an engineered variant of this RCLH1X complex lacking the PufX protein and with an enlarged light harvesting antenna is unimpaired in its capacity for photocurrent generation in two types of bio-photoelectrochemical cells. Removal of PufX also did not impair the ability of the RCLH1 complex to act as an acceptor of energy from synthetic light harvesting quantum dots. Unexpectedly, the removal of PufX led to a marked improvement in the overall stability of the RCLH1 complex under heat stress. We conclude that PufX-deficient RCLH1 complexes are fully functional in solar energy conversion in a device setting and that their enhanced structural stability could make them a preferred choice over their native PufX-containing counterpart. Our findings on the competence of RCLH1 complexes for light energy conversion in vitro are discussed with reference to the reason why these PufX-deficient proteins are not capable of light energy conversion in vivo.

Respiratory Syncytial Virus Fusion Protein-Induced Toll-Like Receptor 4 (TLR4) Signaling Is Inhibited by the TLR4 Antagonists Rhodobacter sphaeroides Lipopolysaccharide and Eritoran (E5564) and Requires Direct Interaction with MD-2

Science.gov (United States)

Rallabhandi, Prasad; Phillips, Rachel L.; Boukhvalova, Marina S.; Pletneva, Lioubov M.; Shirey, Kari Ann; Gioannini, Theresa L.; Weiss, Jerrold P.; Chow, Jesse C.; Hawkins, Lynn D.; Vogel, Stefanie N.; Blanco, Jorge C. G.

2012-01-01

ABSTRACT Respiratory syncytial virus (RSV) is a leading cause of infant mortality worldwide. Toll-like receptor 4 (TLR4), a signaling receptor for structurally diverse microbe-associated molecular patterns, is activated by the RSV fusion (F) protein and by bacterial lipopolysaccharide (LPS) in a CD14-dependent manner. TLR4 signaling by LPS also requires the presence of an additional protein, MD-2. Thus, it is possible that F protein-mediated TLR4 activation relies on MD-2 as well, although this hypothesis has not been formally tested. LPS-free RSV F protein was found to activate NF-κB in HEK293T transfectants that express wild-type (WT) TLR4 and CD14, but only when MD-2 was coexpressed. These findings were confirmed by measuring F-protein-induced interleukin 1β (IL-1β) mRNA in WT versus MD-2−/− macrophages, where MD-2−/− macrophages failed to show IL-1β expression upon F-protein treatment, in contrast to the WT. Both Rhodobacter sphaeroides LPS and synthetic E5564 (eritoran), LPS antagonists that inhibit TLR4 signaling by binding a hydrophobic pocket in MD-2, significantly reduced RSV F-protein-mediated TLR4 activity in HEK293T-TLR4–CD14–MD-2 transfectants in a dose-dependent manner, while TLR4-independent NF-κB activation by tumor necrosis factor alpha (TNF-α) was unaffected. In vitro coimmunoprecipitation studies confirmed a physical interaction between native RSV F protein and MD-2. Further, we demonstrated that the N-terminal domain of the F1 segment of RSV F protein interacts with MD-2. These data provide new insights into the importance of MD-2 in RSV F-protein-mediated TLR4 activation. Thus, targeting the interaction between MD-2 and RSV F protein may potentially lead to novel therapeutic approaches to help control RSV-induced inflammation and pathology. PMID:22872782

Long-Range Energy Propagation in Nanometer Arrays of Light Harvesting Antenna Complexes

NARCIS (Netherlands)

Escalantet, Maryana; Escalante Marun, M.; Lenferink, Aufrid T.M.; Zhao, Yiping; Tas, Niels Roelof; Huskens, Jurriaan; Hunter, C. Neil; Subramaniam, Vinod; Otto, Cornelis

2010-01-01

Here we report the first observation of long-range transport of excitation energy within a biomimetic molecular nanoarray constructed from LH2 antenna complexes from Rhodobacter sphaeroides. Fluorescence microscopy of the emission of light after local excitation with a diffraction-limited light beam

Bacterial PerO Permeases Transport Sulfate and Related Oxyanions.

Science.gov (United States)

Hoffmann, Marie-Christine; Pfänder, Yvonne; Tintel, Marc; Masepohl, Bernd

2017-07-15

Rhodobacter capsulatus synthesizes the high-affinity ABC transporters CysTWA and ModABC to specifically import the chemically related oxyanions sulfate and molybdate, respectively. In addition, R. capsulatus has the low-affinity permease PerO acting as a general oxyanion transporter, whose elimination increases tolerance to molybdate and tungstate. Although PerO-like permeases are widespread in bacteria, their function has not been examined in any other species to date. Here, we present evidence that PerO permeases from the alphaproteobacteria Agrobacterium tumefaciens , Dinoroseobacter shibae , Rhodobacter sphaeroides , and Sinorhizobium meliloti and the gammaproteobacterium Pseudomonas stutzeri functionally substitute for R. capsulatus PerO in sulfate uptake and sulfate-dependent growth, as shown by assimilation of radioactively labeled sulfate and heterologous complementation. Disruption of perO genes in A. tumefaciens , R. sphaeroides , and S. meliloti increased tolerance to tungstate and, in the case of R. sphaeroides , to molybdate, suggesting that heterometal oxyanions are common substrates of PerO permeases. This study supports the view that bacterial PerO permeases typically transport sulfate and related oxyanions and, hence, form a functionally conserved permease family. IMPORTANCE Despite the widespread distribution of PerO-like permeases in bacteria, our knowledge about PerO function until now was limited to one species, Rhodobacter capsulatus In this study, we showed that PerO proteins from diverse bacteria are functionally similar to the R. capsulatus prototype, suggesting that PerO permeases form a conserved family whose members transport sulfate and related oxyanions. Copyright © 2017 American Society for Microbiology.

The lateral distance between a proton pump and ATP synthase determines the ATP-synthesis rate

Czech Academy of Sciences Publication Activity Database

Sjöholm, C.; Bergstrand, J.; Nilsson, T.; Šachl, Radek; von Ballmoos, Ch.; Widengren, J.; Brzezinski, P.

2017-01-01

Roč. 7, č. 1 (2017), č. článku 2926. ISSN 2045-2322 Institutional support: RVO:61388955 Keywords : biological energy -conversion * cytochrome-c-oxidase * membrane-surface * rhodobacter-sphaeroides Subject RIV: CF - Physical ; Theoretical Chemistry OBOR OECD: Physical chemistry Impact factor: 4.259, year: 2016

Molecular Regulation of Photosynthetic Carbon Dioxide Fixation in Nonsulfur Purple Bacteria

Energy Technology Data Exchange (ETDEWEB)

Tabita, Fred Robert [The Ohio State Univ., Columbus, OH (United States)

2015-12-01

The overall objective of this project is to determine the mechanism by which a transcriptional activator protein affects CO₂ fixation (cbb) gene expression in nonsulfur purple photosynthetic bacteria, with special emphasis to Rhodobacter sphaeroides and with comparison to Rhodopseudomonas palustris. These studies culminated in several publications which indicated that additional regulators interact with the master regulator CbbR in both R. sphaeroides and R. palustris. In addition, the interactive control of the carbon and nitrogen assimilatory pathways was studied and unique regulatory signals were discovered.

Antagonistic Activities of Purple Non-sulfur Bacterial Extracts Against Antibiotic Resistant Vibrio sp.

Directory of Open Access Journals (Sweden)

Chandrasekaran, R.

2011-01-01

Full Text Available Solvent extracts of native purple non-sulfur bacterial (PNSB isolates from the effluents of brackish shrimp culture ponds, near Nagapattinam coast (South India were evaluated for antibacterial activity by the disc diffusion method. Best results were shown by the chloroform extracts against oxytetracycline resistant Vibrio harveyi and Vibrio fischerii. Among the purple non-sulfur bacterial isolates, Rhodobacter sphaeroides, showed maximum antagonistic activity. The findings suggest that the antagonistic extracts from Rba. sphaeroides could be used as an effective antibiotic in controlling Vibrio spp., in aquaculture systems.

Photocycle of the flavin-binding photoreceptor AppA, a bacterial transcriptional antirepressor of photosynthesis genes

NARCIS (Netherlands)

Gauden, M.L.; Yeremenko, S.; Laan, W.; van Stokkum, I.H.M.; Ihalainen, J.A.; van Grondelle, R.; Hellingwerf, K.J.; Kennis, J.T.M.

2005-01-01

The flavoprotein AppA from Rhodobacter sphaeroides contains an N-terminal domain belonging to a new class of photoreceptors designated BLUF domains. AppA was shown to control photosynthesis gene expression in response to blue light and oxygen tension. We have investigated the photocycle of the AppA

GenBank blastx search result: AK061856 [KOME

Lifescience Database Archive (English)

Full Text Available AK061856 001-040-G03 AF018073.1 Rhodobacter sphaeroides operon regulator (smoC), periplasmic sorbitol...-binding protein (smoE), sorbitol/mannitol transport inner membrane protein (smoF), sorbitol.../mannitol transport inner membrane protein (smoG), sorbitol/mannitol transport ATP-binding transport protein (smoK), sorbitol

Conserved Chloroplast Open-reading Frame ycf54 Is Required for Activity of the Magnesium Protoporphyrin Monomethylester Oxidative Cyclase in Synechocystis PCC 6803

Czech Academy of Sciences Publication Activity Database

Hollingshead, S.; Kopečná, Jana; Jackson, P. J.; Canniffe, D. P.; Davidson, P. A.; Dickman, M. J.; Sobotka, Roman; Hunter, C. N.

2012-01-01

Roč. 287, č. 33 (2012), s. 27823-27833 ISSN 0021-9258 R&D Projects: GA ČR GAP501/10/1000; GA MŠk(CZ) ED2.1.00/03.0110 Institutional support: RVO:61388971 Keywords : CHLOROPHYLL ISOCYCLIC RING * RHODOBACTER-SPHAEROIDES * SP PCC-6803 Subject RIV: CE - Biochemistry Impact factor: 4.651, year: 2012

Ferrochelatase from Rhodopseudomonas sphaeroides: substrate specificity and role of sulfhydryl and arginyl residues

International Nuclear Information System (INIS)

Dailey, H.A.; Fleming, J.E.; Harbin, B.M.

1986-01-01

Purified ferrochelatase from the bacterium Rhodopseudomonas sphaeroides was examined to determine the roles of cationic and sulfhydryl residues in substrate binding. Reaction of the enzyme sulfhydryl residues with N-ethylmaleimide or monobromobimane resulted in a rapid loss of enzyme activity. Ferrous iron, but not porphyrin substrate, had a protective effect against inactivation by these two reagents. Quantitation with 3 H-labeled N-ethylmaleimide revealed that inactivation required one to two sulfhydryl groups to be modified. Modification of arginyl residues with either 2,3-butanedione or camphorquinone 10-sulfonate resulted in a loss of ferrochelatase activity. A kinetic analysis of the modified enzyme showed that the K/sub m/ for ferrous iron was not altered but that the K/sub m/ for the prophyrin substrate was increased. These data suggested that arginyl residues may be involved in porphyrin binding, possibly via charge pair interactions between the arginyl residue and the anionic porphyrin propionate side chain. Modification of lysyl residues had no effect on enzyme activity. The authors also examined the ability of bacterial ferrochelatase to use various 2,4-disubstituted porphyrins as substrates. The authors found that 2,4-bis-acetal- and 2,4-disulfonate deuteroporphyrins were effective substrates for the purified bacterial enzyme and that N-methylprotoporphyrin was an effective inhibitor of the enzyme. Data for the ferrochelatase of R. sphaeroides are compared with previously published data for the eucaryotic enzyme

Effects of light intensity and quality on phycobiliprotein accumulation in the cyanobacterium Nostoc sphaeroides Kützing.

Science.gov (United States)

Ma, Rui; Lu, Fan; Bi, Yonghong; Hu, Zhengyu

2015-08-01

To assess the effects of light intensity and quality on the growth and phycobiliproteins (PBP) accumulation in Nostoc sphaeroides Kützing (N. sphaeroides). Dry weights, dry matter, protein, chlorophyll and PBP contents were higher under 90 μmol m(-2) s(-1) than under other intensities (both higher and lower). Phycocyanin and allophycocyanin increased with light intensity while phycoerythrin decreased. Fresh weights, protein and PBP contents increased at the highest rates under blue light. Red light resulted in higher values of dry matter, phycocyanin and chlorophyll a. White light at 90 μmol m(-2) s(-1) or blue light 30 μmol m(-2) s(-1) were optimal for the growth and phycobiliprotein accumulation in N. sphaeroides.

Magnitude and direction of the change in dipole moment associated with excitation of the primary electron donor in Rhodopseudomonas sphaeroides reaction centers

Energy Technology Data Exchange (ETDEWEB)

Lockhart, D.J.; Boxer, S.G.

1987-02-10

The magnitude and direction of the change in dipole moment, ..delta mu.., associated with the Q/sub y/ transition of the dimeric primary electron donor (special pair or P870) in Rhodopseudomonas sphaeroides reaction centers have been measured by Stark spectroscopy at 20 /sup 0/C. The magnitude of ..delta mu.. is found to be f/sup -1/ (10.3 +/- 0.7) D, where f is a correction factor for the local dielectric properties of the protein matrix. With the spherical cavity approximation and an effective local dielectric constant of 2, f = 1.2, and absolute value of ..delta mu.. is 8.6 +/- 0.6 D. Absolute value of ..delta mu.. for the Q/sub y/ transition of the special pair is approximately a factor of 3.4 and 2 greater than for the monomeric bacteriochlorophylls and bacteriopheophytins, respectively, in the reaction center. The angle between ..delta mu.. and the transition dipole moment for excitation of the first singlet electron state of the special pair was found to be 24 +/- 2/sup 0/. The measured values are combined to suggest a physical model in which the lowest excited singlet state of the special pair has substantial charge-transfer character and where charge is separated between the two monomers comprising the dimeric special pair. This leads to the hypothesis that the first charge-separated state in bacterial photosynthesis is formed directly upon photoexcitation. These data provide stringent values for comparison with theoretical calculations of the electronic structure of the chromophores in the reaction center.

The effects of protein crowding in bacterial photosynthetic membranes on the flow of quinone redox species between the photochemical reaction center and the ubiquinol-cytochrome c2 oxidoreductase.

Science.gov (United States)

Woronowicz, Kamil; Sha, Daniel; Frese, Raoul N; Sturgis, James N; Nanda, Vikas; Niederman, Robert A

2011-08-01

Atomic force microscopy (AFM) of the native architecture of the intracytoplasmic membrane (ICM) of a variety of species of purple photosynthetic bacteria, obtained at submolecular resolution, shows a tightly packed arrangement of light harvesting (LH) and reaction center (RC) complexes. Since there are no unattributed structures or gaps with space sufficient for the cytochrome bc(1) or ATPase complexes, they are localized in membrane domains distinct from the flat regions imaged by AFM. This has generated a renewed interest in possible long-range pathways for lateral diffusion of UQ redox species that functionally link the RC and the bc(1) complexes. Recent proposals to account for UQ flow in the membrane bilayer are reviewed, along with new experimental evidence provided from an analysis of intrinsic near-IR fluorescence emission that has served to test these hypotheses. The results suggest that different mechanism of UQ flow exist between species such as Rhodobacter sphaeroides, with a highly organized arrangement of LH and RC complexes and fast RC electron transfer turnover, and Phaeospirillum molischianum with a more random organization and slower RC turnover. It is concluded that packing density of the peripheral LH2 antenna in the Rba. sphaeroides ICM imposes constraints that significantly slow the diffusion of UQ redox species between the RC and cytochrome bc(1) complex, while in Phs. molischianum, the crowding of the ICM with LH3 has little effect upon UQ diffusion. This supports the proposal that in this type of ICM, a network of RC-LH1 core complexes observed in AFM provides a pathway for long-range quinone diffusion that is unaffected by differences in LH complex composition or organization.

Nostoc sphaeroides Kützing, an excellent candidate producer for CELSS

Science.gov (United States)

Hao, Zongjie; Li, Dunhai; Li, Yanhui; Wang, Zhicong; Xiao, Yuan; Wang, Gaohong; Liu, Yongding; Hu, Chunxiang; Liu, Qifang

2011-11-01

Some phytoplankton can be regarded as possible candidates in the establishment of Controlled Ecological Life Support System (CELSS) for some intrinsic characteristics, the first characteristic is that they should grow rapidly, secondly, they should be able to endure some stress factors and develop some corresponding adaptive strategies; also it is very important that they could provide food rich in nutritious protein and vitamins for the crew; the last but not the least is they can also fulfill the other main functions of CELSS, including supplying oxygen, removing carbon dioxide and recycling the metabolic waste. According to these characteristics, Nostoc sphaeroides, a potential healthy food in China, was selected as the potential producer in CELSS. It was found that the oxygen average evolution rate of this algae is about 150 μmol O 2 mg -1 h -1, and the size of them are ranged from 2 to 20 mm. Also it can be cultured with high population density, which indicated that the potential productivity of Nostoc sphaeroides is higher than other algae in limited volume. We measured the nutrient contents of the cyanobacterium and concluded it was a good food for the crew. Based on above advantages, Nostoc sphaeroides was assumed to a suitable phytoplankton for the establishment of Controlled Ecological Life Support System. We plan to develop suitable bioreactor with the cyanobacterium for supplying oxygen and food in future space missions.

GenBank blastx search result: AK241729 [KOME

Lifescience Database Archive (English)

Full Text Available AK241729 J065199L10 AF018073.1 AF018073 Rhodobacter sphaeroides operon regulator (smoC), periplasmic sorbito...l-binding protein (smoE), sorbitol/mannitol transport inner membrane protein (smoF), sorbitol.../mannitol transport inner membrane protein (smoG), sorbitol/mannitol transport ATP-binding transport protein (smoK), sorbit...ol dehydrogenase (smoS), mannitol dehydrogenase (mtlK),

GenBank blastx search result: AK240874 [KOME

Lifescience Database Archive (English)

Full Text Available AK240874 J065025K09 AF018073.1 AF018073 Rhodobacter sphaeroides operon regulator (smoC), periplasmic sorbito...l-binding protein (smoE), sorbitol/mannitol transport inner membrane protein (smoF), sorbitol.../mannitol transport inner membrane protein (smoG), sorbitol/mannitol transport ATP-binding transport protein (smoK), sorbit...ol dehydrogenase (smoS), mannitol dehydrogenase (mtlK),

GenBank blastx search result: AK243680 [KOME

Lifescience Database Archive (English)

Full Text Available AK243680 J100090I20 AF018073.1 AF018073 Rhodobacter sphaeroides operon regulator (smoC), periplasmic sorbito...l-binding protein (smoE), sorbitol/mannitol transport inner membrane protein (smoF), sorbitol.../mannitol transport inner membrane protein (smoG), sorbitol/mannitol transport ATP-binding transport protein (smoK), sorbit...ol dehydrogenase (smoS), mannitol dehydrogenase (mtlK),

Interface for Light-Driven Electron Transfer by Photosynthetic Complexes Across Block Copolymer Membranes.

Science.gov (United States)

Kuang, Liangju; Olson, Tien L; Lin, Su; Flores, Marco; Jiang, Yunjiang; Zheng, Wan; Williams, JoAnn C; Allen, James P; Liang, Hongjun

2014-03-06

Incorporation of membrane proteins into nanodevices to mediate recognition and transport in a collective and scalable fashion remains a challenging problem. We demonstrate how nanoscale photovoltaics could be designed using robust synthetic nanomembranes with incorporated photosynthetic reaction centers (RCs). Specifically, RCs from Rhodobacter sphaeroides are reconstituted spontaneously into rationally designed polybutadiene membranes to form hierarchically organized proteopolymer membrane arrays via a charge-interaction-directed reconstitution mechanism. Once incorporated, the RCs are fully active for prolonged periods based upon a variety of spectroscopic measurements, underscoring preservation of their 3D pigment configuration critical for light-driven charge transfer. This result provides a strategy to construct solar conversion devices using structurally versatile proteopolymer membranes with integrated RC functions to harvest broad regions of the solar spectrum.

Laue image analysis. Pt. 2

International Nuclear Information System (INIS)

Greenhough, T.J.; Shrive, A.K.

1994-01-01

Many Laue diffraction patterns from crystals of particular biological or chemical interest are of insufficient quality for their analysis to be feasible. In many cases, this is because of pronounced streaking of the spots owing to either large mosaic spread or disorder introduced during reactions in the crystal. Methods for the analysis of exposures exhibiting radial or near-radial streaking are described, along with their application in Laue diffraction studies of form-II crystals of Met-tRNA synthetase and a photosynthetic reaction centre from Rhodobacter sphaeroides. In both cases, variable elliptical radial masking has led to significant improvements in data quality and quantity and exposures that previously were too streaked to process may now be analysed. These masks can also provide circular profiles as a special case for processing high-quality Laue exposures and spatial-overlap deconvolution may be performed using the elliptical or circular masks. (orig.)

Effects of radio frequency and high pressure steam sterilisation on the colour and flavour of prepared Nostoc sphaeroides.

Science.gov (United States)

Xu, Jicheng; Zhang, Min; An, Yanjun; Roknul, Azam Sm; Adhikari, Benu

2018-03-01

Nostoc sphaeroides has been used as a highly effective herbal medicine and dietary supplement for thousands of years. The desired dark green colour of fresh N. sphaeroides is converted into an undesirable dark brown during conventional high pressure (HP) steam sterilisation. Radio frequency (RF) sterilisation technology was used in this study to determine its effectiveness in sterilising N. sphaeroides and to achieve better preservation of natural colour and desirable flavour. Sterilisation was carried out using a 6 kW, 27 MHz RF instrument for 10, 20 and 30 min. The degree of microbial kill and the effects of RF sterilisation on colour and flavour were determined and compared with those obtained from HP steam (121 °C, 30 min) sterilisation. The effects of RF sterilisation on colour and flavour (measured using electronic nose) parameters were significantly lower than that in HP steam sterilisation. The RF sterilisation carried out for 20 min achieved logarithmic reduction of bacterial population and met China's national standard while preserving the colour and flavour better. Results of the present study indicated that application of RF sterilisation would improve the quality of sterilised N. sphaeroides and broaden its application in the food and health food industries. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

Manipulating the Energetics and Rates of Electron Transfer in Rhodobacter capsulatus Reaction Centers with Asymmetric Pigment Content

Energy Technology Data Exchange (ETDEWEB)

Faries, Kaitlyn M. [Department; Dylla, Nicholas P. [Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States; Hanson, Deborah K. [Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States; Holten, Dewey [Department; Laible, Philip D. [Biosciences Division, Argonne National Laboratory, Lemont, Illinois 60439, United States; Kirmaier, Christine [Department

2017-07-17

Seemingly redundant parallel pathways for electron transfer (ET), composed of identical sets of cofactors, are a cornerstone feature of photosynthetic reaction centers (RCs) involved in light-energy conversion. In native bacterial RCs, both A and B branches house one bacteriochlorophyll (BChl) and one bacteriopheophytin (BPh), but the A branch is used exclusively. Described herein are the results-obtained for two Rhodobacter capsulatus RCs with an unnaturally high degree of cofactor asymmetry, two BPh on the RC's B side and two BChl on the A side. These pigment changes derive, respectively, from the His(M180)Leu mutation [a BPh ((Phi(B)) replaces the B-side BChl (BB)], and the Leu(M212)His mutation [a BChl (beta(A))) replaces the A-side BPh (H-A)]. Additionally, Tyr(M208)Phe was employed to disfavor ET to the A branch; in one mutant, Val(M131)Glu creates a hydrogen bond to H-B to enhance ET to H-B. In both Phi(B) mutants, the decay kinetics of the excited primary ET donor (P*) resolve three populations with lifetimes of similar to 9 ps (50-60%), similar to 40 ps (10-20%), and similar to 200 ps (20-30%), with P+Phi(-)(B) formed predominantly from the 9 ps fraction. The 50-60% yield of P+Phi(B)- is the highest yet observed for a Phi(B)-containing RC. The results provide insight into factors needed for efficient multistep ET.

High-pressure modulation of the structure of the bacterial photochemical reaction center at physiological and cryogenic temperatures

Science.gov (United States)

Timpmann, Kõu; Kangur, Liina; Lõhmus, Ants; Freiberg, Arvi

2017-07-01

The optical absorption and fluorescence response to external high pressure of the reaction center membrane chromoprotein complex from the wild-type non-sulfur photosynthetic bacterium Rhodobacter sphaeroides was investigated using the native pigment cofactors as local molecular probes of the reaction center structure at physiological (ambient) and cryogenic (79 K) temperatures. In detergent-purified complexes at ambient temperature, abrupt blue shift and accompanied broadening of the special pair band was observed at about 265 MPa. These reversible in pressure features were assigned to a pressure-induced rupture of a lone hydrogen bond that binds the photo-chemically active L-branch primary electron donor bacteriochlorophyll cofactor to the surrounding protein scaffold. In native membrane-protected complexes the hydrogen bond rupture appeared significantly restricted and occurred close to about 500 MPa. The free energy change associated with the rupture of the special pair hydrogen bond in isolate complexes was estimated to be equal to about 12 kJ mol-1. In frozen samples at cryogenic temperatures the hydrogen bond remained apparently intact up to the maximum utilized pressure of 600 MPa. In this case, however, heterogeneous spectral response of the cofactors from the L-and M-branches was observed due to anisotropic build-up of the protein structure. While in solid phase, the special pair fluorescence as a function of pressure exactly followed the respective absorption spectrum at a constant Stokes shift, at ambient temperature, the two paths began to deviate strongly from one other at the hydrogen bond rupture pressure. This effect was tentatively interpreted by different emission properties of hydrogen-bound and hydrogen-unbound special pair exciton states.

A structural basis for electron transfer in bacterial photosynthesis

International Nuclear Information System (INIS)

Norris, J.R.; DiMagno, T.J.; Angerhofer, A.; Chang, C.H.; El-Kabbani, O.; Schiffer, M.

1989-01-01

Triplet data for the primary donor in single crystals of bacterial reaction centers of Rhodobacter sphaeroides and Rhodopseudomonas viridis are interpreted in terms of the corresponding x-ray structures. The analysis of electron paramagnetic resonance data from single crystals (triplet zero field splitting and cation and triplet linewidth of the primary special pair donor of bacterial reaction centers) is extended to systems of a non-crystalline nature. A unified interpretation based on frontier molecular orbitals concludes that the special pair behaves like a supermolecule in all wild-type bacteria investigated here. However, in heterodimers of Rb. capsulatus (His M200 changed to Leu or Phe with the result that the M-half of the special pair is converted to bacteriopheophytin) the special pair possesses the EPR properties more appropriately described in terms of a monomer. In all cases the triplet state and cation EPR properties appear to be dominated by the highest occupied molecular orbitals. These conclusions derived from EPR experiments are supplemented by data from Stark spectroscopy of reaction centers from Rb. capsulatus. 41 refs., 3 tabs

Interaction of two photoreceptors in the regulation of bacterial photosynthesis genes

OpenAIRE

Metz, Sebastian; Haberzettl, Kerstin; Frühwirth, Sebastian; Teich, Kristin; Hasewinkel, Christian; Klug, Gabriele

2012-01-01

The expression of photosynthesis genes in the facultatively photosynthetic bacterium Rhodobacter sphaeroides is controlled by the oxygen tension and by light quantity. Two photoreceptor proteins, AppA and CryB, have been identified in the past, which are involved in this regulation. AppA senses light by its N-terminal BLUF domain, its C-terminal part binds heme and is redox-responsive. Through its interaction to the transcriptional repressor PpsR the AppA photoreceptor controls expression of ...

Comparison of calculated and experimental isotope edited FTIR difference spectra for purple bacterial photosynthetic reaction centers with different quinones incorporated into the QA binding site.

Directory of Open Access Journals (Sweden)

Nan eZhao

2013-08-01

Full Text Available Previously we have shown that ONIOM type (QM/MM calculations can be used to simulate isotope edited FTIR difference spectra for neutral ubiquinone in the QA binding site in Rhodobacter sphaeroides photosynthetic reaction centers. Here we considerably extend upon this previous work by calculating isotope edited FTIR difference spectra for reaction centers with a variety of unlabeled and 18O labeled foreign quinones incorporated into the QA binding site. Isotope edited spectra were calculated for reaction centers with 2,3-dimethoxy-5,6-dimethyl-1,4-benzoquinone (MQ0, 2,3,5,6-tetramethyl-1,4-benzoquinone (duroquinone, DQ, and 2,3-dimethyl-l,4-naphthoquinone (DMNQ incorporated, and compared to corresponding experimental spectra. The calculated and experimental spectra agree well, further demonstrating the utility and applicability of our ONIOM approach for calculating the vibrational properties of pigments in protein binding sites.The normal modes that contribute to the bands in the calculated spectra, their composition, frequency and intensity, and how these quantities are modified upon 18O labeling, are presented. This computed information leads to a new and more detailed understanding/interpretation of the experimental FTIR difference spectra. Hydrogen bonding to the carbonyl groups of the incorporated quinones is shown to be relatively weak. It is also shown that there is some asymmetry in hydrogen bonding, accounting for 10-13 cm-1 separation in the frequencies of the carbonyl vibrational modes of the incorporated quinones. The extent of asymmetry H-bonding could only be established by considering the spectra for various types of quinones incorporated into the QA binding site. The quinones listed above are tail-less. Spectra were also calculated for reaction centers with corresponding tail containing quinones incorporated, and it is found that replacement of the quinone methyl group by a phytyl or prenyl chain does not alter ONIOM calculated s

Identification of protein W, the elusive sixth subunit of the Rhodopseudomonas palustris reaction center-light harvesting 1 core complex.

Science.gov (United States)

Jackson, Philip J; Hitchcock, Andrew; Swainsbury, David J K; Qian, Pu; Martin, Elizabeth C; Farmer, David A; Dickman, Mark J; Canniffe, Daniel P; Hunter, C Neil

2018-02-01

The X-ray crystal structure of the Rhodopseudomonas (Rps.) palustris reaction center-light harvesting 1 (RC-LH1) core complex revealed the presence of a sixth protein component, variably referred to in the literature as helix W, subunit W or protein W. The position of this protein prevents closure of the LH1 ring, possibly to allow diffusion of ubiquinone/ubiquinol between the RC and the cytochrome bc 1 complex in analogous fashion to the well-studied PufX protein from Rhodobacter sphaeroides. The identity and function of helix W have remained unknown for over 13years; here we use a combination of biochemistry, mass spectrometry, molecular genetics and electron microscopy to identify this protein as RPA4402 in Rps. palustris CGA009. Protein W shares key conserved sequence features with PufX homologs, and although a deletion mutant was able to grow under photosynthetic conditions with no discernible phenotype, we show that a tagged version of protein W pulls down the RC-LH1 complex. Protein W is not encoded in the photosynthesis gene cluster and our data indicate that only approximately 10% of wild-type Rps. palustris core complexes contain this non-essential subunit; functional and evolutionary consequences of this observation are discussed. The ability to purify uniform RC-LH1 and RC-LH1-protein W preparations will also be beneficial for future structural studies of these bacterial core complexes. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Supplementing in the diet of lactating Holstein cows may naturally produce coenzyme Q10-enriched milk

Directory of Open Access Journals (Sweden)

Gui-Seck Bae

2018-01-01

Full Text Available Objective To examine the effects of Rhodobacter sphaeroides (R. sphaeroides supplementation as a direct-fed microbial (DFM on rumen fermentation in dairy cows and on coenzyme Q10 (CoQ10 transition into milk, an in vitro rumen simulation batch culture and an in vivo dairy cow experiment were conducted. Methods The characteristics of in vitro ruminal fermentation were investigated using rumen fluids from six cannulated Holstein dairy cows at 2 h post-afternoon feeding. A control treatment was included in the experiments based on a typified total mixed ration (TMR for lactating dairy cows, which was identical to the one used in the in vivo study, plus R. sphaeroides at 0.1%, 0.3%, and 0.5% TMR dry matter. The in vivo study employed six ruminally cannulated lactating Holstein cows randomly allotted to either the control TMR (C-TMR treatment or to a diet supplemented with a 0.5% R. sphaeroides culture (S-TMR, dry matter basis ad libitum. The presence of R. sphaeroides was verified using denaturing gradient gel electrophoresis (DGGE applied to the bacterial samples obtained from the in vivo study. The concentration of CoQ10 in milk and in the supernatant from the in vitro study was determined using high performance liquid chromatography. Results The results of the in vitro batch culture and DGGE showed that the concentration of CoQ10 significantly increased after 2 h of R. sphaeroides supplementation above 0.1%. When supplemented to the diet of lactating cows at the level of 0.5%, R. sphaeroides did not present any adverse effect on dry matter intake and milk yield. However, the concentration of CoQ10 in milk dramatically increased, with treated cows producing 70.9% more CoQ10 than control cows. Conclusion The CoQ10 concentration in milk increased via the use of a novel DFM, and R. sphaeroides might be used for producing value-added milk and dairy products in the future.

Detection of Singlet Oxygen Formation inside Photoactive Biohybrid Composite Material

Directory of Open Access Journals (Sweden)

Kata Hajdu

2017-12-01

Full Text Available Photosynthetic reaction center proteins (RCs are the most efficient light energy converter systems in nature. The first steps of the primary charge separation in photosynthesis take place in these proteins. Due to their unique properties, combining RCs with nano-structures promising applications can be predicted in optoelectronic systems. In the present work RCs purified from Rhodobacter sphaeroides purple bacteria were immobilized on multiwalled carbon nanotubes (CNTs. Carboxyl—and amine-functionalised CNTs were used, so different binding procedures, physical sorption and chemical sorption as well, could be applied as immobilization techniques. Light-induced singlet oxygen production was measured in the prepared photoactive biocomposites in water-based suspension by histidine mediated chemical trapping. Carbon nanotubes were applied under different conditions in order to understand their role in the equilibration of singlet oxygen concentration in the suspension. CNTs acted as effective quenchers of 1O2 either by physical (resonance energy transfer or by chemical (oxidation reaction and their efficiency showed dependence on the diffusion distance of 1O2.

Electron spin relaxation enhancement measurements of interspin distances in human, porcine, and Rhodobacter electron transfer flavoprotein ubiquinone oxidoreductase (ETF QO)

Science.gov (United States)

Fielding, Alistair J.; Usselman, Robert J.; Watmough, Nicholas; Simkovic, Martin; Frerman, Frank E.; Eaton, Gareth R.; Eaton, Sandra S.

2008-02-01

Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a membrane-bound electron transfer protein that links primary flavoprotein dehydrogenases with the main respiratory chain. Human, porcine, and Rhodobacter sphaeroides ETF-QO each contain a single [4Fe-4S] 2+,1+ cluster and one equivalent of FAD, which are diamagnetic in the isolated enzyme and become paramagnetic on reduction with the enzymatic electron donor or with dithionite. The anionic flavin semiquinone can be reduced further to diamagnetic hydroquinone. The redox potentials for the three redox couples are so similar that it is not possible to poise the proteins in a state where both the [4Fe-4S] + cluster and the flavoquinone are fully in the paramagnetic form. Inversion recovery was used to measure the electron spin-lattice relaxation rates for the [4Fe-4S] + between 8 and 18 K and for semiquinone between 25 and 65 K. At higher temperatures the spin-lattice relaxation rates for the [4Fe-4S] + were calculated from the temperature-dependent contributions to the continuous wave linewidths. Although mixtures of the redox states are present, it was possible to analyze the enhancement of the electron spin relaxation of the FAD semiquinone signal due to dipolar interaction with the more rapidly relaxing [4Fe-4S] + and obtain point-dipole interspin distances of 18.6 ± 1 Å for the three proteins. The point-dipole distances are within experimental uncertainty of the value calculated based on the crystal structure of porcine ETF-QO when spin delocalization is taken into account. The results demonstrate that electron spin relaxation enhancement can be used to measure distances in redox poised proteins even when several redox states are present.

Electron spin relaxation enhancement measurements of interspin distances in human, porcine, and Rhodobacter electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO).

Science.gov (United States)

Fielding, Alistair J; Usselman, Robert J; Watmough, Nicholas; Simkovic, Martin; Frerman, Frank E; Eaton, Gareth R; Eaton, Sandra S

2008-02-01

Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a membrane-bound electron transfer protein that links primary flavoprotein dehydrogenases with the main respiratory chain. Human, porcine, and Rhodobacter sphaeroides ETF-QO each contain a single [4Fe-4S](2+,1+) cluster and one equivalent of FAD, which are diamagnetic in the isolated enzyme and become paramagnetic on reduction with the enzymatic electron donor or with dithionite. The anionic flavin semiquinone can be reduced further to diamagnetic hydroquinone. The redox potentials for the three redox couples are so similar that it is not possible to poise the proteins in a state where both the [4Fe-4S](+) cluster and the flavoquinone are fully in the paramagnetic form. Inversion recovery was used to measure the electron spin-lattice relaxation rates for the [4Fe-4S](+) between 8 and 18K and for semiquinone between 25 and 65K. At higher temperatures the spin-lattice relaxation rates for the [4Fe-4S](+) were calculated from the temperature-dependent contributions to the continuous wave linewidths. Although mixtures of the redox states are present, it was possible to analyze the enhancement of the electron spin relaxation of the FAD semiquinone signal due to dipolar interaction with the more rapidly relaxing [4Fe-4S](+) and obtain point-dipole interspin distances of 18.6+/-1A for the three proteins. The point-dipole distances are within experimental uncertainty of the value calculated based on the crystal structure of porcine ETF-QO when spin delocalization is taken into account. The results demonstrate that electron spin relaxation enhancement can be used to measure distances in redox poised proteins even when several redox states are present.

Nostoc sphaeroides Kütz, a candidate producer par excellence for CELSS

Science.gov (United States)

Wang, Gaohong; Hao, Zongjie; Liu, Yongding

A lot of aquatic organisms could be regarded as suitable candidates par excellence in the establishment of CELSS, since they are relatively easy and fast to grow and resistant to changes in environmental condition as well as providing nutritious, protein-and vitamin-rich foods for the crew, which can fulfill the main functions of CELSS, including supplying oxygen, water and food, removing carbon dioxide and making daily life waste reusable. Our labotory has developed mass culture of Nostoc sphaeroides Kütz, which is one of traditional healthy food in China and. The oxygen evolution rate of the cyanobacterium is about 150 molO2.mg-1.h-1, and it usually grows into colony with size between 2-20mm, which is easy to be harvested. It also can be cultured with high density, which show that the productivity of the cyanobacterium in limited volume is higher than other microalgae. We had measured the nutrient content of the cyanobacterium and developed some Chinese Dishes and Soups with Nostoc sphaeroides Kütz, which showed that it was a good food for crew. Using remote sensing technique, we also investigated its growth in Closed System under microgravity by SHENZHOU-2 spacecraft in January 2001. We plan to develop suitable bioreactor with the cyanobacterium for supplying oxygen and food to crew in future.

Hydrogen production by using Rhodobacter capsulatus mutants with genetically modified electron transfer chains

Energy Technology Data Exchange (ETDEWEB)

OEztuerk, Yavuz; Yuecel, Meral; Guenduez, Ufuk [Department of Biology, Middle East Technical University, Ankara (Turkey); Daldal, Fevzi [Department of Biology, Plant Science Institute, University of Pennsylvania, Philadelphia, PA 19104-6018 (United States); Mandaci, Sevnur [TUEBITAK Research Institute for Genetic Engineering and Biotechnology, Gebze Kocaeli 41470 (Turkey); Tuerker, Lemi [Department of Chemistry, Middle East Technical University, Ankara (Turkey); Eroglu, Inci [Department of Chemical Engineering, Middle East Technical University, Ankara (Turkey)

2006-09-15

In Rhodobacter capsulatus excess reducing equivalents generated by organic acid oxidation is consumed to reduce protons into hydrogen by the activity of nitrogenase. Nitrogenase serves as a redox-balancing tool and is activated by the RegB/RegA global regulatory system during photosynthetic growth. The terminal cytochrome cbb{sub 3} oxidase and the redox state of the cyclic photosynthetic electron transfer chain serve redox signaling to the RegB/RegA regulatory systems in Rhodobacter. In this study, hydrogen production of various R. capsulatus strains harboring the genetically modified electron carrier cytochromes or lacking the cyt cbb{sub 3} oxidase or the quinol oxidase were compared with the wild type. The results indicated that hydrogen production of mutant strains with modified electron carrier cytochromes decreased 3- to 4-fold, but the rate of hydrogen production increased significantly in a cbb{sub 3}{sup -} mutant. Moreover, hydrogen production efficiency of various R. capsulatus strains further increased by inactivation of uptake hydrogenase genes. (author)

Electrostatics of the photosynthetic bacterial reaction center. Protonation of Glu L 212 and Asp L 213 - A new method of calculation.

Science.gov (United States)

Ptushenko, Vasily V; Cherepanov, Dmitry A; Krishtalik, Lev I

2015-12-01

Continuum electrostatic calculation of the transfer energies of anions from water into aprotic solvents gives the figures erroneous by order of magnitude. This is due to the hydrogen bond disruption that suggests the necessity to reconsider the traditional approach of the purely electrostatic calculation of the transfer energy from water into protein. In this paper, the method combining the experimental estimates of the transfer energies from water into aprotic solvent and the electrostatic calculation of the transfer energies from aprotic solvent into protein is proposed. Hydrogen bonds between aprotic solvent and solute are taken into account by introducing an imaginary aprotic medium incapable to form hydrogen bonds with the solute. Besides, a new treatment of the heterogeneous intraprotein dielectric permittivity based on the microscopic protein structure and electrometric measurements is elaborated. The method accounts semi-quantitatively for the electrostatic effect of diverse charged amino acid substitutions in the donor and acceptor parts of the photosynthetic bacterial reaction center from Rhodobacter sphaeroides. Analysis of the volatile secondary acceptor site QB revealed that in the conformation with a minimal distance between quinone QB and Glu L 212 the proton uptake upon the reduction of QB is prompted by Glu L 212 in alkaline and by Asp L 213 in slightly acidic regions. This agrees with the pH dependences of protonation degrees and the proton uptake. The method of pK calculation was applied successfully also for dissociation of Asp 26 in bacterial thioredoxin. Copyright © 2015 Elsevier B.V. All rights reserved.

Embryonic, Larval, and Early Juvenile Development of the Tropical Sea Urchin, Salmacis sphaeroides (Echinodermata: Echinoidea

Directory of Open Access Journals (Sweden)

M. Aminur Rahman

2012-01-01

Full Text Available Salmacis sphaeroides (Linnaeus, 1758 is one of the regular echinoids, occuring in the warm Indo-West Pacific, including Johor Straits, between Malaysia and Singapore. In order to investigate the developmental basis of morphological changes in embryos and larvae, we documented the ontogeny of S. sphaeroides in laboratory condition. Gametes were obtained from adult individuals by 0.5 M KCl injection into the coelomic cavity. Fertilization rate at limited sperm concentration (10−5 dilution was 96.6±1.4% and the resulting embryos were reared at 24°C. First cleavage (2-cell, 4-cell, 8-cell, 16-cell, 32-cell, and multicell (Morulla stages were achieved 01.12, 02.03, 02.28, 02.51, 03.12, and 03.32 h postfertilization. Ciliated blastulae with a mean length of 174.72±4.43 μm hatched 08.45 h after sperm entry. The gastrulae formed 16.15 h postfertilization and the archenteron elongated constantly while ectodermal red-pigmented cells migrated synchronously to the apical plate. Pluteus larva started to feed unicellular algae in 2 d, grew continuously, and finally attained metamorphic competence in 35 d after fertilization. Metamorphosis took approximately 1 h 30 min from attachment to the complete resorption of larval tissues and the development of complete juvenile structure with adult spines, extended tubefeet and well-developed pedicellaria, the whole event of which usually took place within 1 d postsettlement. This study represents the first successful investigation on embryonic, larval, and early juvenile development of S. sphaeroides. The findings would greatly be helpful towards the understanding of ontogeny and life-history strategies, which will facilitate us to develop the breeding, seed production, and culture techniques of sea urchins in captive condition.

Structural and phylogenetic analysis of Rhodobacter capsulatus NifF: uncovering general features of nitrogen-fixation (nif)-flavodoxins.

Science.gov (United States)

Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A

2013-01-09

Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50's loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as "short-chain" with the firmicutes flavodoxins and the "long-chain" with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

Structural and Phylogenetic Analysis of Rhodobacter capsulatus NifF: Uncovering General Features of Nitrogen-fixation (nif-Flavodoxins

Directory of Open Access Journals (Sweden)

Inmaculada Pérez-Dorado

2013-01-01

Full Text Available Analysis of the crystal structure of NifF from Rhodobacter capsulatus and its homologues reported so far reflects the existence of unique structural features in nif flavodoxins: a leucine at the re face of the isoalloxazine, an eight-residue insertion at the C-terminus of the 50’s loop and a remarkable difference in the electrostatic potential surface with respect to non-nif flavodoxins. A phylogenetic study on 64 sequences from 52 bacterial species revealed four clusters, including different functional prototypes, correlating the previously defined as “short-chain” with the firmicutes flavodoxins and the “long-chain” with gram-negative species. The comparison of Rhodobacter NifF structure with other bacterial flavodoxin prototypes discloses the concurrence of specific features of these functional electron donors to nitrogenase.

Directed assembly of functional light harvesting antenna complexes onto chemically patterned surfaces

International Nuclear Information System (INIS)

Escalante, Maryana; Maury, Pascale; Bruinink, Christiaan M; Werf, Kees van der; Olsen, John D; Timney, John A; Huskens, Jurriaan; Hunter, C Neil; Subramaniam, Vinod; Otto, Cees

2008-01-01

We report the directed assembly of the photosynthetic membrane proteins LH1 and LH2 isolated from the purple bacterium Rhodobacter sphaeroides onto chemically patterned substrates. Nanoimprint lithography was used to pattern discrete regions of amino- and fluoro-terminated or poly(ethylene glycol) self-assembled monolayers onto a glass substrate. Densely packed layers of assembled protein complexes were observed with atomic force microscopy. The protein complexes attached selectively to the amino-terminated regions by electrostatic interactions. Spectral images generated with a hybrid scanning probe and fluorescence microscope confirmed that the patterned proteins retained their native optical signatures

Directed assembly of functional light harvesting antenna complexes onto chemically patterned surfaces

Energy Technology Data Exchange (ETDEWEB)

Escalante, Maryana [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Maury, Pascale [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Bruinink, Christiaan M [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Werf, Kees van der [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Olsen, John D [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Timney, John A [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Huskens, Jurriaan [Molecular Nanofabrication Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Hunter, C Neil [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom); Subramaniam, Vinod [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands); Otto, Cees [Biophysical Engineering Group, MESA and Institute for Nanotechnology, University of Twente, PO Box 217, 7500 AE Enschede (Netherlands)

2008-01-16

We report the directed assembly of the photosynthetic membrane proteins LH1 and LH2 isolated from the purple bacterium Rhodobacter sphaeroides onto chemically patterned substrates. Nanoimprint lithography was used to pattern discrete regions of amino- and fluoro-terminated or poly(ethylene glycol) self-assembled monolayers onto a glass substrate. Densely packed layers of assembled protein complexes were observed with atomic force microscopy. The protein complexes attached selectively to the amino-terminated regions by electrostatic interactions. Spectral images generated with a hybrid scanning probe and fluorescence microscope confirmed that the patterned proteins retained their native optical signatures.

Electrochemical determination of hydrogen peroxide using Rhodobacter capsulatus cytochrome c peroxidase at a gold electrode

NARCIS (Netherlands)

De Wael, K.; Buschop, H.; Heering, H.A.; De Smet, L.; Van Beeumen, J.; Devreese, B.; Adriaens, A.

2007-01-01

We describe the redox behaviour of horse heart cytochrome c (HHC) and Rhodobacter capsulatus cytochrome c peroxidase (RcCCP) at a gold electrode modified with 4,4?-bipyridyl. RcCCP shows no additional oxidation or reduction peaks compared to the electrochemistry of only HHC, which indicates that it

Hypocholesterolemic Response to Karaya Saponin and Rhodobacter capsulatus in Broiler Chickens

OpenAIRE

Afrose, Sadia; Hossain, Md. Sharoare; Maki, Takaaki; Tsujii, Hirotada

2010-01-01

Dietary karaya saponin and Rhodobacter capsulatus (R. capsulatus) are known to have hypocholesterolemic actions, as reported in our previous studies. This study examined possible synergistic hypocholesterolemic effects of karaya saponin and R. capsulatus in broilers. A total of 150 broilers were allocated into 10 treatments: control, saponin 25 mg, saponin 50 mg, saponin 75 mg, saponin 25 mg+R. capsulatus 0.2 g, saponin 25 mg+R. capsulatus 0.4 g, saponin 50 mg+R. capsulatus 0.2 g, saponin 50 ...

Purple-bacterial photosynthetic reaction centers and quantum-dot hybrid-assemblies in lecithin liposomes and thin films.

Science.gov (United States)

Lukashev, Eugeny P; Knox, Petr P; Gorokhov, Vladimir V; Grishanova, Nadezda P; Seifullina, Nuranija Kh; Krikunova, Maria; Lokstein, Heiko; Paschenko, Vladimir Z

2016-11-01

Quantum dots (QDs) absorb ultraviolet and long-wavelength visible light energy much more efficiently than natural bacterial light-harvesting proteins and can transfer the excitation energy to photosynthetic reaction centers (RCs). Inclusion of RCs combined with QDs as antennae into liposomes opens new opportunities for using such hybrid systems as a basis for artificial energy-transforming devices that potentially can operate with greater efficiency and stability than devices based only on biological components or inorganic components alone. RCs from Rhodobacter sphaeroides and QDs (CdSe/ZnS with hydrophilic covering) were embedded in lecithin liposomes by extrusion of a solution of multilayer lipid vesicles through a polycarbonate membrane or by dialysis of lipids and proteins dispersed with excess detergent. The efficiency of RC and QD interaction within the liposomes was estimated using fluorescence excitation spectra of the photoactive bacteriochlorophyll of the RCs and by measuring the fluorescence decay kinetics of the QDs. The functional activity of the RCs in hybrid complexes was fully maintained, and their stability was even increased. The efficiency of energy transfer between QDs and RCs and conditions of long-term stability of function of such hybrid complexes in film preparations were investigated as well. It was found that dry films containing RCs and QDs, maintained at atmospheric humidity, are capable of maintaining their functional activity for at least some months as judged by measurements of their spectral characteristics, efficiency of energy transfer from QDs to RCs and RC electron transport activity. Addition of trehalose to the films increases the stability further, especially for films maintained at low humidity. These stable hybrid film structures are promising for further studies towards developing new phototransformation devices for biotechnological applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Phosphoenolpyruvate-Dependent Fructose Phosphotransferase System of Rhodopseudomonas sphaeroides : Purification and Physicochemical and Immunochemical Characterization of a Membrane-Associated Enzyme I

NARCIS (Netherlands)

Brouwer, Marius; Elferink, Marieke G.L.; Robillard, George T.

1982-01-01

The phosphotransferase system (PTS) of the phototrophic bacterium Rhodopseudomonas sphaeroides consists of a component located in the cytoplasmic membrane and a membrane-associated enzyme called “soluble factor” (SF). SF has been partially purified by a combination of hydrophobic interaction and

Communication: Coherences observed in vivo in photosynthetic bacteria using two-dimensional electronic spectroscopy

International Nuclear Information System (INIS)

Dahlberg, Peter D.; Norris, Graham J.; Wang, Cheng; Viswanathan, Subha; Singh, Ved P.; Engel, Gregory S.

2015-01-01

Energy transfer through large disordered antenna networks in photosynthetic organisms can occur with a quantum efficiency of nearly 100%. This energy transfer is facilitated by the electronic structure of the photosynthetic antennae as well as interactions between electronic states and the surrounding environment. Coherences in time-domain spectroscopy provide a fine probe of how a system interacts with its surroundings. In two-dimensional electronic spectroscopy, coherences can appear on both the ground and excited state surfaces revealing detailed information regarding electronic structure, system-bath coupling, energy transfer, and energetic coupling in complex chemical systems. Numerous studies have revealed coherences in isolated photosynthetic pigment-protein complexes, but these coherences have not been observed in vivo due to the small amplitude of these signals and the intense scatter from whole cells. Here, we present data acquired using ultrafast video-acquisition gradient-assisted photon echo spectroscopy to observe quantum beating signals from coherences in vivo. Experiments were conducted on isolated light harvesting complex II (LH2) from Rhodobacter sphaeroides, whole cells of R. sphaeroides, and whole cells of R. sphaeroides grown in 30% deuterated media. A vibronic coherence was observed following laser excitation at ambient temperature between the B850 and the B850 ∗ states of LH2 in each of the 3 samples with a lifetime of ∼40-60 fs

Communication: Coherences observed in vivo in photosynthetic bacteria using two-dimensional electronic spectroscopy

Energy Technology Data Exchange (ETDEWEB)

Dahlberg, Peter D. [Graduate Program in the Biophysical Sciences, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States); Norris, Graham J.; Wang, Cheng; Viswanathan, Subha; Singh, Ved P.; Engel, Gregory S., E-mail: gsengel@uchicago.edu [Department of Chemistry, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

2015-09-14

Energy transfer through large disordered antenna networks in photosynthetic organisms can occur with a quantum efficiency of nearly 100%. This energy transfer is facilitated by the electronic structure of the photosynthetic antennae as well as interactions between electronic states and the surrounding environment. Coherences in time-domain spectroscopy provide a fine probe of how a system interacts with its surroundings. In two-dimensional electronic spectroscopy, coherences can appear on both the ground and excited state surfaces revealing detailed information regarding electronic structure, system-bath coupling, energy transfer, and energetic coupling in complex chemical systems. Numerous studies have revealed coherences in isolated photosynthetic pigment-protein complexes, but these coherences have not been observed in vivo due to the small amplitude of these signals and the intense scatter from whole cells. Here, we present data acquired using ultrafast video-acquisition gradient-assisted photon echo spectroscopy to observe quantum beating signals from coherences in vivo. Experiments were conducted on isolated light harvesting complex II (LH2) from Rhodobacter sphaeroides, whole cells of R. sphaeroides, and whole cells of R. sphaeroides grown in 30% deuterated media. A vibronic coherence was observed following laser excitation at ambient temperature between the B850 and the B850{sup ∗} states of LH2 in each of the 3 samples with a lifetime of ∼40-60 fs.

Removal of the effect of ammonium on the regulation of nitrogenase enzyme in Rhodobacter capsulatus DSM1710 for improved hydrogen production

Energy Technology Data Exchange (ETDEWEB)

Pekgoez, Guelsah; Guenduez, Ufuk [Middle East Technical Univ. (Turkey). Dept. of Biology; Eroglu, Inci [Middle East Technical Univ. (Turkey). Dept. of Chemical Engineering; Rakhely, Gabor [Szeged Univ. (Hungary). Dept. of Biotechnology

2010-07-01

Photofermentative biohydrogen production by purple non-sulfur (PNS) bacteria is a renewable and clean way of producing hydrogen. Hydrogen production by PNS bacteria, Rhodobacter capsulatus, is mediated mainly by nitrogenases, which primarily fix molecular nitrogen to ammonium and produce hydrogen as byproduct. The reaction catalyzed by nitrogenases requires a lot of energy. Hence, there is a complex regulation on nitrogenase enzyme complex, consequently, on hydrogen production. Whenever ammonium, which is the end product of nitrogen fixation reaction, is found in the environment, hydrogen production stops. GlnB and GlnK proteins are the critical regulatory proteins in ammonium dependent regulation of the nitrogenase gene expression. In this study, the aim is to release the ammonium regulation on nitrogenase enzyme by inactivating glnB and glnK genes. For this purpose, relevant recombinant vectors were constructed; R.capsulatus glnB- strain was obtained. The double R.capsulatus glnB{sup -}glnK{sup -} strain, able to produce hydrogen independent of ammonium concentration of the environment is to be obtained. (orig.)

[Regulation of alternative CO{sub 2} fixation pathways in procaryotic and eucaryotic photosynthetic organisms]. Progress report

Energy Technology Data Exchange (ETDEWEB)

1992-12-31

The major goal of this project is to determine how microorganisms regulate the assimilation of CO{sup 2} via pathways alternative to the usual Calvin reductive pentose phosphate scheme. In particular, we are interest in the molecular basis for switches in CO{sub 2} metabolic paths. Several earlier studies had indicated that purple nonsulfur photosynthetic bacteria assimilate significant amounts of CO{sub 2} via alternative non-Calvin routes. We have deleted the gene that encodes. RubisCo (ribulose bisphosphate carboxylase/oxygenase) in both the Rhodobacter sphaeroids and Rhodospirillum rubrum. The R. sphaeroides RubisCO deletion strain (strain 16) could not grow under photoheterotrophic conditions with malate as electron donor and CO{sub 2} as the electron acceptor; however the R. rub RubisCO deletion strain (strain I-19) could. Over the past year we have sought to physiologically characterize strain 16PHC. We found that, 16PHC exhibited rates of whole-cell CO{sub 2} fixation which were significantly higher than strain 16. Strain 16PHC could not grow photolithoautotrophically in a CO{sub 2} atmosphere; however, CO{sub 2} fixation catalyzed by photoheterotrophically grown 16PHC was repressed by the addition of DMSO. Likewise, we found that cells initially grown in the presence of DMSO could induce the CO{sub 2} fixation system when DMSO was removed. Thus, these results suggested that both PHC and I-19 could be used to study alternative CO{sub 2} fixation reactions and their significance in R. sphaexoides and R. rubrum.

[Regulation of alternative CO[sub 2] fixation pathways in procaryotic and eucaryotic photosynthetic organisms

Energy Technology Data Exchange (ETDEWEB)

1992-01-01

The major goal of this project is to determine how microorganisms regulate the assimilation of CO[sup 2] via pathways alternative to the usual Calvin reductive pentose phosphate scheme. In particular, we are interest in the molecular basis for switches in CO[sub 2] metabolic paths. Several earlier studies had indicated that purple nonsulfur photosynthetic bacteria assimilate significant amounts of CO[sub 2] via alternative non-Calvin routes. We have deleted the gene that encodes. RubisCo (ribulose bisphosphate carboxylase/oxygenase) in both the Rhodobacter sphaeroids and Rhodospirillum rubrum. The R. sphaeroides RubisCO deletion strain (strain 16) could not grow under photoheterotrophic conditions with malate as electron donor and CO[sub 2] as the electron acceptor; however the R. rub RubisCO deletion strain (strain I-19) could. Over the past year we have sought to physiologically characterize strain 16PHC. We found that, 16PHC exhibited rates of whole-cell CO[sub 2] fixation which were significantly higher than strain 16. Strain 16PHC could not grow photolithoautotrophically in a CO[sub 2] atmosphere; however, CO[sub 2] fixation catalyzed by photoheterotrophically grown 16PHC was repressed by the addition of DMSO. Likewise, we found that cells initially grown in the presence of DMSO could induce the CO[sub 2] fixation system when DMSO was removed. Thus, these results suggested that both PHC and I-19 could be used to study alternative CO[sub 2] fixation reactions and their significance in R. sphaexoides and R. rubrum.

Assembly and structural organization of pigment-protein complexes in membranes of Rhodopseudomonas sphaeroides

International Nuclear Information System (INIS)

Hunter, C.N.; Pennoyer, J.D.; Niederman, R.A.

1982-01-01

The B875 and B800-850 light-harvesting pigment-protein complexes of Rhodopseudomonas sphaeroides are characterized further by lithium dodecyl sulfate/polyacrylamide gel electrophoresis at 4 degrees C. Bacteriochlorophyll a was shown in reconstruction studies to remain complexed with its respective binding proteins during this procedure. From distributions in these gels, a quantitative description for the arrangement of the complexes is proposed. Assembly of the complexes was examined in delta-aminolevulinate-requiring mutant H-5 after a shift from high- to low-light intensity. After 10 h of delta-[ 3 H]aminolevulinate labeling, the specific radioactivity of bacteriochlorophyll in a fraction containing putative membrane invaginations reached the maximal level, while that of the mature photosynthetic membrane was at only one-third this level. This suggests that membrane invaginations are sites of preferential bacteriochlorophyll synthesis in which completed pigment-proteins exist transiently. Analysis of the 3 H distribution after electrophoretic separation further suggests that photosynthetic membranes grow mainly by addition of B800-850 to preformed membrane consisting largely of B875 and photochemical reaction centers. These results corroborate the above model for the structural organization of the light-harvesting system and indicate that the structurally and functionally discrete B800-850 pool is not completely assembled until all B875 sites for B800-850 interactions are occupied

PucC and LhaA direct efficient assembly of the light-harvesting complexes in Rhodobacter sphaeroides

DEFF Research Database (Denmark)

Mothersole, David; Jackson, Philip J.; Vasilev, Cvetelin

2016-01-01

. Here we investigate the assembly of light-harvesting LH2 and reaction centre-light-harvesting1-PufX (RC-LH1-PufX) photosystem complexes using spectroscopy, pull-downs, native gel electrophoresis, quantitative mass spectrometry and fluorescence lifetime microscopy to characterise a series of lha......A and pucC mutants. LhaA and PucC are important for specific assembly of LH1 or LH2 complexes, respectively, but they are not essential; the few LH1 subunits found in ΔlhaA mutants assemble to form normal RC-LH1-PufX core complexes showing that, once initiated, LH1 assembly round the RC is cooperative...

Self-trapped excitons in LH2 bacteriochlorophyll-protein complexes under high pressure

International Nuclear Information System (INIS)

Timpmann, K.; Ellervee, Aleksandr; Kuznetsov, Anatoli; Laisaar, Arlentin; Trinkunas, Gediminas; Freiberg, Arvi

2003-01-01

The absorption and emission spectra of excitons in LH2 antenna complexes from the photosynthetic purple bacterium Rhodobacter sphaeroides have been studied under hydrostatic pressure. The measurements made between ambient pressure and 6 kbar over a broad temperature range reveal largely different rates of the pressure-induced shifts for the absorption and emission bands. Numerical calculations based on exciton polaron model provide evidence for the exciton self-trapping at ambient pressure as well as for the pressure stabilization of the self-trapped exciton states responsible for the emission, whereas the light absorbing states belong to nearly free excitons over the whole pressure and temperature ranges studied

A mixed incoherent feed-forward loop contributes to the regulation of bacterial photosynthesis genes.

Science.gov (United States)

Mank, Nils N; Berghoff, Bork A; Klug, Gabriele

2013-03-01

Living cells use a variety of regulatory network motifs for accurate gene expression in response to changes in their environment or during differentiation processes. In Rhodobacter sphaeroides, a complex regulatory network controls expression of photosynthesis genes to guarantee optimal energy supply on one hand and to avoid photooxidative stress on the other hand. Recently, we identified a mixed incoherent feed-forward loop comprising the transcription factor PrrA, the sRNA PcrZ and photosynthesis target genes as part of this regulatory network. This point-of-view provides a comparison to other described feed-forward loops and discusses the physiological relevance of PcrZ in more detail.

The mechanisms of protection of antioxidants on Nostoc sphaeroides against UV-B radiation

Science.gov (United States)

Wang, G. H.

UV radiation is one of space harmful factor for earth organisms in space exploration In the present work we studied on the role of antioxidant system in Nostoc sphaeroides K u tz Cyanobacteria and the effects of exogenous antioxidant molecules on its photosynthetic rate under UV-B radiation It was found that UV-B radiation decreased the photosynthetic activity of cyanobacterium but promoted the activity of antioxidant system to protect photosystem II PSII and exogenous antioxidant sodium nitroprusside SNP N-acetylcysteine NAC had an obvious protection on PSII activity under UV-B radiation The activity of SOD Superoxide Dismutase EC 1 15 1 1 CAT Catalase EC 1 11 1 6 POD Peroxidase EC 1 11 1 7 and content of MDA and ASC were improved by 0 5mM and 1mM SNP but 0 1mM SNP decreased the activity of antioxide system Exogenous NAC addition decreased the activity of SOD POD CAT and the content MDA and ASC but exogenous NAC addition increased the content of GSH The results suggested that exogenous SNP and NAC may protect algae by different mechanisms in which SNP maybe play double roles as sources of reactive free radicals or ROS scavengers in formation of algae s protection of PSII under UV-B radiation while NAC does function as antioxidant reagent or precursor of glutathione which could protect PSII directly from UV-B radiation Keyword antioxidant system exogenous or endogenous antioxidant Nostoc sphaeroides photosynthesis UV-B radiation

The rate of second electron transfer to QB(-) in bacterial reaction center of impaired proton delivery shows hydrogen-isotope effect.

Science.gov (United States)

Maróti, Ágnes; Wraight, Colin A; Maróti, Péter

2015-02-01

The 2nd electron transfer in reaction center of photosynthetic bacterium Rhodobacter sphaeroides is a two step process in which protonation of QB(-) precedes interquinone electron transfer. The thermal activation and pH dependence of the overall rate constants of different RC variants were measured and compared in solvents of water (H2O) and heavy water (D2O). The electron transfer variants where the electron transfer is rate limiting (wild type and M17DN, L210DN and H173EQ mutants) do not show solvent isotope effect and the significant decrease of the rate constant of the second electron transfer in these mutants is due to lowering the operational pKa of QB(-)/QBH: 4.5 (native), 3.9 (L210DN), 3.7 (M17DN) and 3.1 (H173EQ) at pH7. On the other hand, the proton transfer variants where the proton transfer is rate limiting demonstrate solvent isotope effect of pH-independent moderate magnitude (2.11±0.26 (WT+Ni(2+)), 2.16±0.35 (WT+Cd(2+)) and 2.34±0.44 (L210DN/M17DN)) or pH-dependent large magnitude (5.7 at pH4 (L213DN)). Upon deuteration, the free energy and the enthalpy of activation increase in all proton transfer variants by about 1 kcal/mol and the entropy of activation becomes negligible in L210DN/M17DN mutant. The results are interpreted as manifestation of equilibrium and kinetic solvent isotope effects and the structural, energetic and kinetic possibility of alternate proton delivery pathways are discussed. Copyright © 2014 Elsevier B.V. All rights reserved.

Two dimensional crystals of LH2 light-harvesting complexes from Ectothiorhodospira sp. and Rhodobacter capsulatus investigated by electron microscopy

NARCIS (Netherlands)

Oling, Frank; Boekema, EJ; deZarate, IO; Visschers, R; vanGrondelle, R; Keegstra, W; Brisson, A; Picorel, R

1996-01-01

Two-dimensional crystals of LH2 (B800-850) light-harvesting complexes from Ectothiorhodospira sp, and Rhodobacter capsulatus were obtained by reconstitution of purified protein into phospholipid vesicles and characterized by electron microscopy. The size of the crystals was up to several

Two-dimensional crystals of LH2 light-harvesting complexes from Ectothiorhodospira sp. and Rhodobacter capsulatus investigated by electron microscopy.

NARCIS (Netherlands)

Oling, F.; Boekema, E.J.; Ortiz de Zarate, I.; Visschers, R.W.; van Grondelle, R.; Keegstra, W.; Brisson, A.; Picorel, R.

1996-01-01

Two-dimensional crystals of LH2 (B800-850) light-harvesting complexes from Ectothiorhodospira sp. and Rhodobacter capsulatus were obtained by reconstitution of purified protein into phospholipid vesicles and characterized by electron microscopy. The size of the crystals was up to several

Mechanisms for hydrogen production by different bacteria during mixed-acid and photo-fermentation and perspectives of hydrogen production biotechnology.

Science.gov (United States)

Trchounian, Armen

2015-03-01

H2 has a great potential as an ecologically-clean, renewable and capable fuel. It can be mainly produced via hydrogenases (Hyd) by different bacteria, especially Escherichia coli and Rhodobacter sphaeroides. The operation direction and activity of multiple Hyd enzymes in E. coli during mixed-acid fermentation might determine H2 production; some metabolic cross-talk between Hyd enzymes is proposed. Manipulating the activity of different Hyd enzymes is an effective way to enhance H2 production by E. coli in biotechnology. Moreover, a novel approach would be the use of glycerol as feedstock in fermentation processes leading to H2 production. Mixed carbon (sugar and glycerol) utilization studies enlarge the kind of organic wastes used in biotechnology. During photo-fermentation under limited nitrogen conditions, H2 production by Rh. sphaeroides is observed when carbon and nitrogen sources are supplemented. The relationship of H2 production with H(+) transport across the membrane and membrane-associated ATPase activity is shown. On the other hand, combination of carbon sources (succinate, malate) with different nitrogen sources (yeast extract, glutamate, glycine) as well as different metal (Fe, Ni, Mg) ions might regulate H2 production. All these can enhance H2 production yield by Rh. sphaeroides in biotechnology Finally, two of these bacteria might be combined to develop and consequently to optimize two stages of H2 production biotechnology with high efficiency transformation of different organic sources.

A disordered polaron model for polarized fluorescence excitation spectra of LH1 and LH2 bacteriochlorophyll antenna aggregates

International Nuclear Information System (INIS)

Trinkunas, Gediminas; Freiberg, Arvi

2006-01-01

Excitonic polarons in antenna complexes are subject to static lattice disorder. A model has been developed to analyze polarized fluorescence excitation spectra of circular light-harvesting complexes from purple photosynthetic bacteria containing bacteriochlorophyll as the main photoactive pigment that includes both diagonal (energetic) and off-diagonal (structural) disorders. Essential differences of disorder realizations seem to exist between the core LH1 and peripheral LH2 complexes from the bacterium Rhodobacter sphaeroides. The disorder in LH1 appears to be dominated by the structural disorder, while that in LH2, by energetic one. These differences may be due to relatively bigger size of the LH1 complex and, consequently, with its enhanced structural flexibility

Energetics of bacterial photosynthesis.

Science.gov (United States)

Lebard, David N; Matyushov, Dmitry V

2009-09-10

We report the results of extensive numerical simulations and theoretical calculations of electronic transitions in the reaction center of Rhodobacter sphaeroides photosynthetic bacterium. The energetics and kinetics of five electronic transitions related to the kinetic scheme of primary charge separation have been analyzed and compared to experimental observations. Nonergodic formulation of the reaction kinetics is required for the calculation of the rates due to a severe breakdown of the system ergodicity on the time scale of primary charge separation, with the consequent inapplicability of the standard canonical prescription to calculate the activation barrier. Common to all reactions studied is a significant excess of the charge-transfer reorganization energy from the width of the energy gap fluctuations over that from the Stokes shift of the transition. This property of the hydrated proteins, breaking the linear response of the thermal bath, allows the reaction center to significantly reduce the reaction free energy of near-activationless electron hops and thus raise the overall energetic efficiency of the biological charge-transfer chain. The increase of the rate of primary charge separation with cooling is explained in terms of the temperature variation of induction solvation, which dominates the average donor-acceptor energy gap for all electronic transitions in the reaction center. It is also suggested that the experimentally observed break in the Arrhenius slope of the primary recombination rate, occurring near the temperature of the dynamical transition in proteins, can be traced back to a significant drop of the solvent reorganization energy close to that temperature.

Exploration of the hydrogen producing potential of Rhodobacter capsulatus chemostat cultures: The application of deceleration-stat and gradient-stat methodology

NARCIS (Netherlands)

Hoekema, S.; Breukelen, van F.R.; Janssen, M.G.J.; Tramper, J.; Wijffels, R.H.

2009-01-01

In this work, the dependency of the volumetric hydrogen production rate of ammonium-limited Rhodobacter capsulatus chemostat cultures on their imposed biomass concentration and dilution rate was investigated. A deceleration-stat experiment was performed by lowering the dilution rate from 1.0 d-1 to

Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane

International Nuclear Information System (INIS)

Hsin, J; Sener, M; Schulten, K; Struempfer, J; Qian, P; Hunter, C N

2010-01-01

Light absorption and the subsequent transfer of excitation energy are the first two steps in the photosynthetic process, carried out by protein-bound pigments, mainly bacteriochlorophylls (BChls), in photosynthetic bacteria. BChls are anchored in light-harvesting (LH) complexes, such as light-harvesting complex I (LH1), which directly associates with the reaction center (RC), forming the RC-LH1 core complex. In Rhodobacter sphaeroides, RC-LH1 core complexes contain an additional protein, PufX, and assemble into dimeric RC-LH1-PufX core complexes. In the absence of LH complex II (LH2), the former complexes can aggregate into a helically ordered tubular photosynthetic membrane. We have examined the excitation transfer dynamics in a single RC-LH1-PufX core complex dimer using the hierarchical equations of motion for dissipative quantum dynamics that accurately, yet in a computationally costly manner, treat the coupling between BChls and their protein environment. A widely employed description, the generalized Foerster (GF) theory, was also used to calculate the transfer rates of the same excitonic system in order to verify the accuracy of this computationally cheap method. Additionally, in light of the structural uncertainties in the Rba. sphaeroides RC-LH1-PufX core complex, geometrical alterations were introduced into the BChl organization. It is shown that the energy transfer dynamics are not affected by the considered changes in the BChl organization and that the GF theory provides accurate transfer rates. An all-atom model for a tubular photosynthetic membrane is then constructed on the basis of electron microscopy data, and the overall energy transfer properties of this membrane are computed.

Energy transfer dynamics in an RC-LH1-PufX tubular photosynthetic membrane

Energy Technology Data Exchange (ETDEWEB)

Hsin, J; Sener, M; Schulten, K [Department of Physics and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana (United States); Struempfer, J [Center for Biophysics and Computational Biology and Beckman Institute, University of Illinois at Urbana-Champaign, Urbana (United States); Qian, P; Hunter, C N, E-mail: kschulte@ks.uiuc.ed [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN (United Kingdom)

2010-08-15

Light absorption and the subsequent transfer of excitation energy are the first two steps in the photosynthetic process, carried out by protein-bound pigments, mainly bacteriochlorophylls (BChls), in photosynthetic bacteria. BChls are anchored in light-harvesting (LH) complexes, such as light-harvesting complex I (LH1), which directly associates with the reaction center (RC), forming the RC-LH1 core complex. In Rhodobacter sphaeroides, RC-LH1 core complexes contain an additional protein, PufX, and assemble into dimeric RC-LH1-PufX core complexes. In the absence of LH complex II (LH2), the former complexes can aggregate into a helically ordered tubular photosynthetic membrane. We have examined the excitation transfer dynamics in a single RC-LH1-PufX core complex dimer using the hierarchical equations of motion for dissipative quantum dynamics that accurately, yet in a computationally costly manner, treat the coupling between BChls and their protein environment. A widely employed description, the generalized Foerster (GF) theory, was also used to calculate the transfer rates of the same excitonic system in order to verify the accuracy of this computationally cheap method. Additionally, in light of the structural uncertainties in the Rba. sphaeroides RC-LH1-PufX core complex, geometrical alterations were introduced into the BChl organization. It is shown that the energy transfer dynamics are not affected by the considered changes in the BChl organization and that the GF theory provides accurate transfer rates. An all-atom model for a tubular photosynthetic membrane is then constructed on the basis of electron microscopy data, and the overall energy transfer properties of this membrane are computed.

Evidence for a Very Early Intermediate in Bacterial Photosynthesis. A Photon-Echo and Hole-Burning Study of the Primary Donor Band in Rhodopseudomonas Sphaeroides

NARCIS (Netherlands)

Meech, S.R.; Hoff, A.J.

1985-01-01

Two coherent spectroscopic methods, accumulated photon echo and population bottleneck hole-burning, have been employed in a study of the decay rate of the primary donor (P) of Rhodopseudomonas sphaeroides at 1.5 K. The decay rate is instrument-limited in the photon-echo experiment, implying a

Regulation of bacterial photosynthesis genes by the small noncoding RNA PcrZ.

Science.gov (United States)

Mank, Nils N; Berghoff, Bork A; Hermanns, Yannick N; Klug, Gabriele

2012-10-02

The small RNA PcrZ (photosynthesis control RNA Z) of the facultative phototrophic bacterium Rhodobacter sphaeroides is induced upon a drop of oxygen tension with similar kinetics to those of genes for components of photosynthetic complexes. High expression of PcrZ depends on PrrA, the response regulator of the PrrB/PrrA two-component system with a central role in redox regulation in R. sphaeroides. In addition the FnrL protein, an activator of some photosynthesis genes at low oxygen tension, is involved in redox-dependent expression of this small (s)RNA. Overexpression of full-length PcrZ in R. sphaeroides affects expression of a small subset of genes, most of them with a function in photosynthesis. Some mRNAs from the photosynthetic gene cluster were predicted to be putative PcrZ targets and results from an in vivo reporter system support these predictions. Our data reveal a negative effect of PcrZ on expression of its target mRNAs. Thus, PcrZ counteracts the redox-dependent induction of photosynthesis genes, which is mediated by protein regulators. Because PrrA directly activates photosynthesis genes and at the same time PcrZ, which negatively affects photosynthesis gene expression, this is one of the rare cases of an incoherent feed-forward loop including an sRNA. Our data identified PcrZ as a trans acting sRNA with a direct regulatory function in formation of photosynthetic complexes and provide a model for the control of photosynthesis gene expression by a regulatory network consisting of proteins and a small noncoding RNA.

Two-photon excitation spectroscopy of carotenoid-containing and carotenoid-depleted LH2 complexes from purple bacteria.

Science.gov (United States)

Stepanenko, Ilya; Kompanetz, Viktor; Makhneva, Zoya; Chekalin, Sergey; Moskalenko, Andrei; Razjivin, Andrei

2009-08-27

We applied two-photon fluorescence excitation spectroscopy to LH2 complex from purple bacteria Allochromatium minutissimum and Rhodobacter sphaeroides . Bacteriochlorophyll fluorescence was measured under two-photon excitation of the samples within the 1200-1500 nm region. Spectra were obtained for both carotenoid-containing and -depleted complexes of each bacterium to allow their direct comparison. The depletion of carotenoids did not alter the two-photon excitation spectra of either bacteria. The spectra featured a wide excitation band around 1350 nm (2x675 nm, 14,800 cm(-1)) which strongly resembled two-photon fluorescence excitation spectra of similar complexes published by other authors. We consider obtained experimental data to be evidence of direct two-photon excitation of bacteriochlorophyll excitonic states in this spectral region.

Energetics and kinetics of primary charge separation in bacterial photosynthesis.

Science.gov (United States)

LeBard, David N; Kapko, Vitaliy; Matyushov, Dmitry V

2008-08-21

We report the results of molecular dynamics (MD) simulations and formal modeling of the free-energy surfaces and reaction rates of primary charge separation in the reaction center of Rhodobacter sphaeroides. Two simulation protocols were used to produce MD trajectories. Standard force-field potentials were employed in the first protocol. In the second protocol, the special pair was made polarizable to reproduce a high polarizability of its photoexcited state observed by Stark spectroscopy. The charge distribution between covalent and charge-transfer states of the special pair was dynamically adjusted during the simulation run. We found from both protocols that the breadth of electrostatic fluctuations of the protein/water environment far exceeds previous estimates, resulting in about 1.6 eV reorganization energy of electron transfer in the first protocol and 2.5 eV in the second protocol. Most of these electrostatic fluctuations become dynamically frozen on the time scale of primary charge separation, resulting in much smaller solvation contributions to the activation barrier. While water dominates solvation thermodynamics on long observation times, protein emerges as the major thermal bath coupled to electron transfer on the picosecond time of the reaction. Marcus parabolas were obtained for the free-energy surfaces of electron transfer by using the first protocol, while a highly asymmetric surface was obtained in the second protocol. A nonergodic formulation of the diffusion-reaction electron-transfer kinetics has allowed us to reproduce the experimental results for both the temperature dependence of the rate and the nonexponential decay of the population of the photoexcited special pair.

A simple method for encapsulating single cells in alginate microspheres allows for direct PCR and whole genome amplification.

Directory of Open Access Journals (Sweden)

Saharnaz Bigdeli

Full Text Available Microdroplets are an effective platform for segregating individual cells and amplifying DNA. However, a key challenge is to recover the contents of individual droplets for downstream analysis. This paper offers a method for embedding cells in alginate microspheres and performing multiple serial operations on the isolated cells. Rhodobacter sphaeroides cells were diluted in alginate polymer and sprayed into microdroplets using a fingertip aerosol sprayer. The encapsulated cells were lysed and subjected either to conventional PCR, or whole genome amplification using either multiple displacement amplification (MDA or a two-step PCR protocol. Microscopic examination after PCR showed that the lumen of the occupied microspheres contained fluorescently stained DNA product, but multiple displacement amplification with phi29 produced only a small number of polymerase colonies. The 2-step WGA protocol was successful in generating fluorescent material, and quantitative PCR from DNA extracted from aliquots of microspheres suggested that the copy number inside the microspheres was amplified up to 3 orders of magnitude. Microspheres containing fluorescent material were sorted by a dilution series and screened with a fluorescent plate reader to identify single microspheres. The DNA was extracted from individual isolates, re-amplified with full-length sequencing adapters, and then a single isolate was sequenced using the Illumina MiSeq platform. After filtering the reads, the only sequences that collectively matched a genome in the NCBI nucleotide database belonged to R. sphaeroides. This demonstrated that sequencing-ready DNA could be generated from the contents of a single microsphere without culturing. However, the 2-step WGA strategy showed limitations in terms of low genome coverage and an uneven frequency distribution of reads across the genome. This paper offers a simple method for embedding cells in alginate microspheres and performing PCR on isolated

Langmuir-Blodgett and X-ray diffraction studies of isolated photosystem II reaction centers in monolayers and multilayers: physical dimensions of the complex.

Science.gov (United States)

Uphaus, R A; Fang, J Y; Picorel, R; Chumanov, G; Wang, J Y; Cotton, T M; Seibert, M

1997-04-01

The photosystem II (PSII) reaction center (RC) is a hydrophobic intrinsic protein complex that drives the water-oxidation process of photosynthesis. Unlike the bacterial RC complex, an X-ray crystal structure of the PSII RC is not available. In order to determine the physical dimensions of the isolated PSII RC complex, we applied Langmuir techniques to determine the cross-sectional area of an isolated RC in a condensed monolayer film. Low-angle X-ray diffraction results obtained by examining Langmuir-Blodgett multilayer films of alternating PSII RC/Cd stearate monolayers were used to determine the length (or height; z-direction, perpendicular to the plane of the original membrane) of the complex. The values obtained for a PSII RC monomer were 26 nm2 and 4.8 nm, respectively, and the structural integrity of the RC in the multilayer film was confirmed by several approaches. Assuming a cylindrical-type RC structure, the above dimensions lead to a predicted volume of about 125 nm3. This value is very close to the expected volume of 118 nm3, calculated from the known molecular weight and partial specific volume of the PSII RC proteins. This same type of comparison was also made with the Rhodobacter sphaeroides RC based on published data, and we conclude that the PSII RC is much shorter in length and has a more regular solid geometric structure than the bacterial RC. Furthermore, the above dimensions of the PSII RC and those of PSII core (RC plus proximal antenna) proteins protruding outside the plane of the PSII membrane into the lumenal space as imaged by scanning tunneling microscopy (Seibert, Aust. J. Pl. Physiol. 22, 161-166, 1995) fit easily into the known dimensions of the PSII core complex visualized by others as electron-density projection maps. From this we conclude that the in situ PSII core complex is a dimeric structure containing two copies of the PSII RC.

Absorbance changes accompanying the fast fluorescence induction in the purple bacterium Rhodobacter sphaeroides

Czech Academy of Sciences Publication Activity Database

Bína, David; Litvín, Radek; Vácha, František

2010-01-01

Roč. 105, č. 2 (2010), s. 115-121 ISSN 0166-8595 R&D Projects: GA AV ČR IAA608170603 Institutional research plan: CEZ:AV0Z50510513 Keywords : Photosynthesis * Charge separation * Membrane potential Subject RIV: CE - Biochemistry Impact factor: 2.410, year: 2010

Potential of Rhodobacter capsulatus Grown in Anaerobic-Light or Aerobic-Dark Conditions as Bioremediation Agent for Biological Wastewater Treatments

OpenAIRE

Stefania Costa; Saverio Ganzerli; Irene Rugiero; Simone Pellizzari; Paola Pedrini; Elena Tamburini

2017-01-01

The use of microorganisms to clean up wastewater provides a cheaper alternative to the conventional treatment plant. The efficiency of this method can be improved by the choice of microorganism with the potential of removing contaminants. One such group is photosynthetic bacteria. Rhodobacter capsulatus is a purple non-sulfur bacterium (PNSB) found to be capable of different metabolic activities depending on the environmental conditions. Cell growth in different media and conditions was teste...

The effectiveness of styrene-maleic acid (SMA) copolymers for solubilisation of integral membrane proteins from SMA-accessible and SMA-resistant membranes.

Science.gov (United States)

Swainsbury, David J K; Scheidelaar, Stefan; Foster, Nicholas; van Grondelle, Rienk; Killian, J Antoinette; Jones, Michael R

2017-10-01

Solubilisation of biological lipid bilayer membranes for analysis of their protein complement has traditionally been carried out using detergents, but there is increasing interest in the use of amphiphilic copolymers such as styrene maleic acid (SMA) for the solubilisation, purification and characterisation of integral membrane proteins in the form of protein/lipid nanodiscs. Here we survey the effectiveness of various commercially-available formulations of the SMA copolymer in solubilising Rhodobacter sphaeroides reaction centres (RCs) from photosynthetic membranes. We find that formulations of SMA with a 2:1 or 3:1 ratio of styrene to maleic acid are almost as effective as detergent in solubilising RCs, with the best solubilisation by short chain variants (membranes was uniformly low, but could be increased through a variety of treatments to increase the lipid:protein ratio. However, proteins isolated from such membranes comprised clusters of complexes in small membrane patches rather than individual proteins. We conclude that short-chain 2:1 and 3:1 formulations of SMA are the most effective in solubilising integral membrane proteins, but that solubilisation efficiencies are strongly influenced by the size of the target protein and the density of packing of proteins in the membrane. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Monitoring sequential electron transfer with EPR

International Nuclear Information System (INIS)

Thurnauer, M.C.; Feezel, L.L.; Snyder, S.W.; Tang, J.; Norris, J.R.; Morris, A.L.; Rustandi, R.R.

1989-01-01

A completely general model which treats electron spin polarization (ESP) found in a system in which radical pairs with different magnetic interactions are formed sequentially has been described. This treatment has been applied specifically to the ESP found in the bacterial reaction center. Test cases show clearly how parameters such as structure, lifetime, and magnetic interactions within the successive radical pairs affect the ESP, and demonstrate that previous treatments of this problem have been incomplete. The photosynthetic bacterial reaction center protein is an ideal system for testing the general model of ESP. The radical pair which exhibits ESP, P 870 + Q - (P 870 + is the oxidized, primary electron donor, a bacteriochlorophyll special pair and Q - is the reduced, primary quinone acceptor) is formed via sequential electron transport through the intermediary radical pair P 870 + I - (I - is the reduced, intermediary electron acceptor, a bacteriopheophytin). In addition, it is possible to experimentally vary most of the important parameters, such as the lifetime of the intermediary radical pair and the magnetic interactions in each pair. It has been shown how selective isotopic substitution ( 1 H or 2 H) on P 870 , I and Q affects the ESP of the EPR spectrum of P 870 + Q - , observed at two different microwave frequencies, in Fe 2+ -depleted bacterial reaction centers of Rhodobacter sphaeroides R26. Thus, the relative magnitudes of the magnetic properties (nuclear hyperfine and g-factor differences) which influence ESP development were varied. The results support the general model of ESP in that they suggest that the P 870 + Q - radical pair interactions are the dominant source of ESP production in 2 H bacterial reaction centers

Open reading frame 176 in the photosynthesis gene cluster of Rhodobacter capsulatus encodes idi, a gene for isopentenyl diphosphate isomerase.

OpenAIRE

Hahn, F M; Baker, J A; Poulter, C D

1996-01-01

Isopentenyl diphosphate (IPP) isomerase catalyzes an essential activation step in the isoprenoid biosynthetic pathway. A database search based on probes from the highly conserved regions in three eukaryotic IPP isomerases revealed substantial similarity with ORF176 in the photosynthesis gene cluster in Rhodobacter capsulatus. The open reading frame was cloned into an Escherichia coli expression vector. The encoded 20-kDa protein, which was purified in two steps by ion exchange and hydrophobic...

Hydrogen bonding between the QB site ubisemiquinone and Ser-L223 in the bacterial reaction centre – a combined spectroscopic and computational perspective^

OpenAIRE

Martin, Erik; Baldansuren, Amgalanbaatar; Lin, Tzu-Jen; Samoilova, Rimma I.; Wraight, Colin A.; Dikanov, Sergei A.; O’Malley, Patrick J.

2012-01-01

In the QB site of the Rba. sphaeroides photosynthetic reaction centre the donation of a hydrogen bond from the hydroxyl group of Ser-L223 to the ubisemiquinone formed after the first flash is debatable. In this study we use a combination of spectroscopy and quantum mechanics/molecular mechanics (QM/MM) calculations to comprehensively explore this topic. We show that ENDOR, ESEEM and HYSCORE spectroscopic differences between the mutant L223SA and the wild type sample (WT) are negligible, indic...

Directed formation of micro- and nanoscale patterns of functional light-harvesting LH2 complexes.

Science.gov (United States)

Reynolds, Nicholas P; Janusz, Stefan; Escalante-Marun, Maryana; Timney, John; Ducker, Robert E; Olsen, John D; Otto, Cees; Subramaniam, Vinod; Leggett, Graham J; Hunter, C Neil

2007-11-28

The precision placement of the desired protein components on a suitable substrate is an essential prelude to any hybrid "biochip" device, but a second and equally important condition must also be met: the retention of full biological activity. Here we demonstrate the selective binding of an optically active membrane protein, the light-harvesting LH2 complex from Rhodobacter sphaeroides, to patterned self-assembled monolayers at the micron scale and the fabrication of nanometer-scale patterns of these molecules using near-field photolithographic methods. In contrast to plasma proteins, which are reversibly adsorbed on many surfaces, the LH2 complex is readily patterned simply by spatial control of surface polarity. Near-field photolithography has yielded rows of light-harvesting complexes only 98 nm wide. Retention of the native optical properties of patterned LH2 molecules was demonstrated using in situ fluorescence emission spectroscopy.

Cellulose synthases: new insights from crystallography and modeling.

Science.gov (United States)

Slabaugh, Erin; Davis, Jonathan K; Haigler, Candace H; Yingling, Yaroslava G; Zimmer, Jochen

2014-02-01

Detailed information about the structure and biochemical mechanisms of cellulose synthase (CelS) proteins remained elusive until a complex containing the catalytic subunit (BcsA) of CelS from Rhodobacter sphaeroides was crystalized. Additionally, a 3D structure of most of the cytosolic domain of a plant CelS (GhCESA1 from cotton, Gossypium hirsutum) was produced by computational modeling. This predicted structure contributes to our understanding of how plant CelS proteins may be similar and different as compared with BcsA. In this review, we highlight how these structures impact our understanding of the synthesis of cellulose and other extracellular polysaccharides. We show how the structures can be used to generate hypotheses for experiments testing mechanisms of glucan synthesis and translocation in plant CelS. Copyright © 2013 Elsevier Ltd. All rights reserved.

Crystallization of a flavodoxin involved in nitrogen fixation in Rhodobacter capsulatus

Energy Technology Data Exchange (ETDEWEB)

Pérez-Dorado, Inmaculada [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain); Bortolotti, Ana; Cortez, Néstor [Instituto de Biología Molecular y Celular de Rosario (Universidad Nacional de Rosario y CONICET), Suipacha 531, S2002LRK Rosario (Argentina); Hermoso, Juan A., E-mail: xjuan@iqfr.csic.es [Grupo de Cristalografía Macromolecular y Biología Estructural, Instituto de Química-Física Rocasolano, CSIC, Serrano 119, 28006 Madrid (Spain)

2008-05-01

The flavodoxin NifF from R. capsulatus, a candidate for nitrogenase reduction during nitrogen fixation, has been crystallized using the hanging-drop vapour-diffusion method. Preliminary X-ray data processing at 2.17 Å resolution allowed determination of the crystal system and unit-cell parameters. Flavodoxins are small electron-transfer proteins that contain one molecule of noncovalently bound flavin mononucleotide (FMN). The flavodoxin NifF from the photosynthetic bacterium Rhodobacter capsulatus is reduced by one electron from ferredoxin/flavodoxin:NADP(H) reductase and was postulated to be an electron donor to nitrogenase in vivo. NifF was cloned and overexpressed in Escherichia coli, purified and concentrated for crystallization using the hanging-drop vapour-diffusion method at 291 K. Crystals grew from a mixture of PEG 3350 and PEG 400 at pH 5.5 and belong to the tetragonal space group P4{sub 1}2{sub 1}2, with unit-cell parameters a = b = 66.49, c = 121.32 Å. X-ray data sets have been collected to 2.17 Å resolution.

Crystallization of a flavodoxin involved in nitrogen fixation in Rhodobacter capsulatus

International Nuclear Information System (INIS)

Pérez-Dorado, Inmaculada; Bortolotti, Ana; Cortez, Néstor; Hermoso, Juan A.

2008-01-01

The flavodoxin NifF from R. capsulatus, a candidate for nitrogenase reduction during nitrogen fixation, has been crystallized using the hanging-drop vapour-diffusion method. Preliminary X-ray data processing at 2.17 Å resolution allowed determination of the crystal system and unit-cell parameters. Flavodoxins are small electron-transfer proteins that contain one molecule of noncovalently bound flavin mononucleotide (FMN). The flavodoxin NifF from the photosynthetic bacterium Rhodobacter capsulatus is reduced by one electron from ferredoxin/flavodoxin:NADP(H) reductase and was postulated to be an electron donor to nitrogenase in vivo. NifF was cloned and overexpressed in Escherichia coli, purified and concentrated for crystallization using the hanging-drop vapour-diffusion method at 291 K. Crystals grew from a mixture of PEG 3350 and PEG 400 at pH 5.5 and belong to the tetragonal space group P4 1 2 1 2, with unit-cell parameters a = b = 66.49, c = 121.32 Å. X-ray data sets have been collected to 2.17 Å resolution

ADP-ribosylation of dinitrogenase reductase in Rhodobacter capsulatus

International Nuclear Information System (INIS)

Jouanneau, Y.; Roby, C.; Meyer, C.M.; Vignais, P.M.

1989-01-01

In the photosynthetic bacterium Rhodobacter capsulatus, nitrogenase is regulated by a reversible covalent modification of Fe protein or dinitrogenase reductase (Rc2). The linkage of the modifying group to inactive Rc2 was found to be sensitive to alkali and to neutral hydroxylamine. Complete release of the modifying group was achieved by incubation of inactive Rc2 in 0.4 or 1 M hydroxylamine. After hydroxylamine treatment of the Rc2 preparation, the modifying group could be isolated and purified by affinity chromatography and ion-exchange HPLC. The modifying group comigrated with ADP-ribose on both ion-exchange HPLC and thin-layer chromatography. Analyses by 31 P NMR spectroscopy and mass spectrometry provided further evidence that the modifying group was ADP-ribose. The NMR spectrum of inactive Rc2 exhibited signals characteristic of ADP-ribose; integration of these signals allowed calculation of a molar ration ADP-ribose/Rc2 of 0.63. A hexapeptide carrying the ADP-ribose moiety was purified from a subtilisin digest of inactive Rc2. The structure of this peptide, determined by amino acid analysis and sequencing, is Gly-Arg(ADP-ribose)-Gly-Val-Ile-Thr. This structure allows identification of the binding site for ADP-ribose as Arg 101 of the polypeptide chain of Rc2. It is concluded that nitrogenase activity in R. capsulatus is regulated by reversible ADP-ribosylation of a specific arginyl residue of dinitrogenase reductase

Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

Energy Technology Data Exchange (ETDEWEB)

Burke-Agueero, D.H.

1992-08-01

Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight bch'' genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

Molecular genetic and molecular evolutionary studies on the bacteriochlorophyll synthesis genes of Rhodobacter capsulatus

Energy Technology Data Exchange (ETDEWEB)

Burke-Agueero, Donald H. [Univ. of California, Berkeley, CA (United States)

1992-08-01

Rhodobacter capsulatus, purple bacterium capable of either aerobic or photosynthetic growth, has proven to be very useful in genetic studies of photosynthesis. Forty-four genes clustered together within a 46 kilobase region are required to establish photosynthetic ability in R. capsulatus. Approximately twenty of these genes are involved in bacteriochlorophyll synthesis of which eight ``bch`` genes are the subject of this thesis. Six of these genes were found to code for the two ring reductases. The first converts protochlorophyllide (PChlide) into a chlorin, the immediate precursor to chlorophyll a, and then into a bacteriochlorin. Each reductase is shown to be made up of three subunits. PChlide reductase is coded by the genes bchN, bchB, and bchL. Proteins with amino acid sequences markedly similar to those of bchN and bchL have been shown in other organisms to be required for chlorophyll synthesis; hence, their designation as chlN and chlB. A third chloroplast-encoded gene of heretofore unknown function shares amino acid identities with bchB and is probably the third subunit of the plant PChlide reductase. The bchA locus, which encodes the chlorin reductase, is found to be made up of three separate, translationally coupled genes, referred to as bchX, bchY, and bchZ. Amino acid similarities between bchX, bchL, and the nitrogenase reductase protein nifH suggest that all three classes of proteins share certain three-dimensional structural features, including elements that are central to the enzymatic mechanism of nifH. PChlide reductase and chlorin reductase are clearly derived from a common ancestor. Several lines of analysis suggests the ancestor of both enzyme systems reduced PChlide twice to produce bacteriochlorophyll supporting the concept bacteriochlorophyll as the ancestral reaction center pigment.

Hydrogen gas production by fermentation from various organic wastewater using Clostridium butyricum NCIB 9576 and Rhodopseudomonas sphaeroides E15-1

Energy Technology Data Exchange (ETDEWEB)

Yoon, Young Sue; Kim, Hyun Kyung; Rye, Hye Yeon; Lee, In Gu; Kim, Mi Sun [Biomass Research Team, Korea Institute of Energy Research, Taejeon (Korea)

2000-03-01

Anaerobic fermentation using Clostidium butyricum NCIB 9576, and phto-fermentation using Rhodopseudomonas sphaeroides E15-1 were studied for the production of hydrogen from Makkoli, fruits (orange and apple, watermelon and melon) and Tofu wastewaters. From the Makkoli wastewater, which contained 0.94 g/liter sugars and 2.74 g/liter solubel starch, approximately 49 mM H{sub 2}/liter wastewater was produced during the initial 18h of the anaerobic fermentation with pH control between 6.5-7.0. Several organic acids such as butyric acid, acetic acid, propionic acid, lactic acid and ethanol were also produced. From watermelon and melon wastewater, which contained 43 g/liter sugars, generated about approximately 71 mM H{sub 2}/liter wastewater was produced during the initial 24h of the anaerobic fermentation. Tofu wastewater, pH 6.5, containing 12.6 g/liter soluble starch and 0.74 g/liter sugars, generated about 30mM H{sub 2}/liter wastewater, along with some organic acids, during the initial 24 h of anaerobic fermentation. Makkoli and Tofu wastewaters as substrates for the photo-fermentation by Rhodopseudomonas sphaeroides E15-1 produced approximately 37.9 and 22.2 {mu}M H{sub 2}/ml wastewaters, respectively for 9 days of incubation under the average of 9,000010,000 lux illumination at the surface of reactor using tungsten halogen lamps. Orange and apple wastewater, which contained 93.4 g/l produced approximately 13.1 {mu}M H{sub 2}/ml wastewater only for 2 days of photo-fermentation and the growth of Rhodopseudomonas spnaeroides E15-1 and hydrogen production were stopped. 22 refs, 4 figs., 2 tabs.

Bacterial Survival under Extreme UV Radiation: A Comparative Proteomics Study of Rhodobacter sp., Isolated from High Altitude Wetlands in Chile

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Vilma Pérez

2017-06-01

Full Text Available Salar de Huasco, defined as a polyextreme environment, is a high altitude saline wetland in the Chilean Altiplano (3800 m.a.s.l., permanently exposed to the highest solar radiation doses registered in the world. We present here the first comparative proteomics study of a photoheterotrophic bacterium, Rhodobacter sp., isolated from this remote and hostile habitat. We developed an innovative experimental approach using different sources of radiation (in situ sunlight and UVB lamps, cut-off filters (Mylar, Lee filters and a high-throughput, label-free quantitative proteomics method to comprehensively analyze the effect of seven spectral bands on protein regulation. A hierarchical cluster analysis of 40 common proteins revealed that all conditions containing the most damaging UVB radiation induced similar pattern of protein regulation compared with UVA and visible light spectral bands. Moreover, it appeared that the cellular adaptation of Rhodobacter sp. to osmotic stress encountered in the hypersaline environment from which it was originally isolated, might further a higher resistance to damaging UV radiation. Indeed, proteins involved in the synthesis and transport of key osmoprotectants, such as glycine betaine and inositol, were found in very high abundance under UV radiation compared to the dark control, suggesting the function of osmolytes as efficient reactive oxygen scavengers. Our study also revealed a RecA-independent response and a tightly regulated network of protein quality control involving proteases and chaperones to selectively degrade misfolded and/or damaged proteins.

Nicotinamide nucleotide transhydrogenase from Rhodobacter capsulatus; the H+/H- ratio and the activation state of the enzyme during reduction of acetyl pyridine adenine dinucleotide.

Science.gov (United States)

Palmer, T; Jackson, J B

1992-02-21

Chromatophores from Rhodobacter capsulatus were incubated in the dark with NADPH and acetylpyridineadenine dinucleotide (AcPdAD+) in the presence of different concentrations of myxothiazol. The transhydrogenase activity was monitored until an appropriate mass action ratio, [AcPdAD+][NADPH]/[AcPdADH][NADP+], was reached. The sample was then illuminated and the initial rate of either AcPdAD+ reduction by NADPH or AcPdADH oxidation by NADP+ was recorded. The ratio of H+ translocated per H- equivalent transferred by transhydrogenase was calculated from the value of the membrane potential (delta pH = 0) at which illumination caused no net reaction in either direction. The mean value for the H+/H- ratio was 0.55. At greater values of [AcPdAD+][NADPH]/[AcPdADH][NADP+] than were employed in the above experiments and over a wider range of concentrations of myxothiazol, it was found that incremental increases in the membrane potential always gave rise to a decrease, never an increase in the rate of AcPdAD+ reduction. In contrast to the H(+)-ATP synthase, there is no evidence of any activation/deactivation of H(+)-transhydrogenase by the protonmotive force.

Crystallographic snapshot of cellulose synthesis and membrane translocation.

Science.gov (United States)

Morgan, Jacob L W; Strumillo, Joanna; Zimmer, Jochen

2013-01-10

Cellulose, the most abundant biological macromolecule, is an extracellular, linear polymer of glucose molecules. It represents an essential component of plant cell walls but is also found in algae and bacteria. In bacteria, cellulose production frequently correlates with the formation of biofilms, a sessile, multicellular growth form. Cellulose synthesis and transport across the inner bacterial membrane is mediated by a complex of the membrane-integrated catalytic BcsA subunit and the membrane-anchored, periplasmic BcsB protein. Here we present the crystal structure of a complex of BcsA and BcsB from Rhodobacter sphaeroides containing a translocating polysaccharide. The structure of the BcsA-BcsB translocation intermediate reveals the architecture of the cellulose synthase, demonstrates how BcsA forms a cellulose-conducting channel, and suggests a model for the coupling of cellulose synthesis and translocation in which the nascent polysaccharide is extended by one glucose molecule at a time.

Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers

Energy Technology Data Exchange (ETDEWEB)

Reppert, Mike; Kell, Adam; Pruitt, Thomas [Department of Chemistry, Kansas State University, Manhattan, Kansas 66506 (United States); Jankowiak, Ryszard, E-mail: ryszard@ksu.edu [Department of Chemistry, Kansas State University, Manhattan, Kansas 66506 (United States); Department of Physics, Kansas State University, Manhattan, Kansas 66506 (United States)

2015-03-07

The vibrational spectral density is an important physical parameter needed to describe both linear and non-linear spectra of multi-chromophore systems such as photosynthetic complexes. Low-temperature techniques such as hole burning (HB) and fluorescence line narrowing are commonly used to extract the spectral density for a given electronic transition from experimental data. We report here that the lineshape function formula reported by Hayes et al. [J. Phys. Chem. 98, 7337 (1994)] in the mean-phonon approximation and frequently applied to analyzing HB data contains inconsistencies in notation, leading to essentially incorrect expressions in cases of moderate and strong electron-phonon (el-ph) coupling strengths. A corrected lineshape function L(ω) is given that retains the computational and intuitive advantages of the expression of Hayes et al. [J. Phys. Chem. 98, 7337 (1994)]. Although the corrected lineshape function could be used in modeling studies of various optical spectra, we suggest that it is better to calculate the lineshape function numerically, without introducing the mean-phonon approximation. New theoretical fits of the P870 and P960 absorption bands and frequency-dependent resonant HB spectra of Rb. sphaeroides and Rps. viridis reaction centers are provided as examples to demonstrate the importance of correct lineshape expressions. Comparison with the previously determined el-ph coupling parameters [Johnson et al., J. Phys. Chem. 94, 5849 (1990); Lyle et al., ibid. 97, 6924 (1993); Reddy et al., ibid. 97, 6934 (1993)] is also provided. The new fits lead to modified el-ph coupling strengths and different frequencies of the special pair marker mode, ω{sub sp}, for Rb. sphaeroides that could be used in the future for more advanced calculations of absorption and HB spectra obtained for various bacterial reaction centers.

Comments on the optical lineshape function: Application to transient hole-burned spectra of bacterial reaction centers

International Nuclear Information System (INIS)

Reppert, Mike; Kell, Adam; Pruitt, Thomas; Jankowiak, Ryszard

2015-01-01

The vibrational spectral density is an important physical parameter needed to describe both linear and non-linear spectra of multi-chromophore systems such as photosynthetic complexes. Low-temperature techniques such as hole burning (HB) and fluorescence line narrowing are commonly used to extract the spectral density for a given electronic transition from experimental data. We report here that the lineshape function formula reported by Hayes et al. [J. Phys. Chem. 98, 7337 (1994)] in the mean-phonon approximation and frequently applied to analyzing HB data contains inconsistencies in notation, leading to essentially incorrect expressions in cases of moderate and strong electron-phonon (el-ph) coupling strengths. A corrected lineshape function L(ω) is given that retains the computational and intuitive advantages of the expression of Hayes et al. [J. Phys. Chem. 98, 7337 (1994)]. Although the corrected lineshape function could be used in modeling studies of various optical spectra, we suggest that it is better to calculate the lineshape function numerically, without introducing the mean-phonon approximation. New theoretical fits of the P870 and P960 absorption bands and frequency-dependent resonant HB spectra of Rb. sphaeroides and Rps. viridis reaction centers are provided as examples to demonstrate the importance of correct lineshape expressions. Comparison with the previously determined el-ph coupling parameters [Johnson et al., J. Phys. Chem. 94, 5849 (1990); Lyle et al., ibid. 97, 6924 (1993); Reddy et al., ibid. 97, 6934 (1993)] is also provided. The new fits lead to modified el-ph coupling strengths and different frequencies of the special pair marker mode, ω sp , for Rb. sphaeroides that could be used in the future for more advanced calculations of absorption and HB spectra obtained for various bacterial reaction centers

Investigation on characteristics of 3D printing using Nostoc sphaeroides biomass.

Science.gov (United States)

An, Yan-Jun; Guo, Chao-Fan; Zhang, Min; Zhong, Ze-Ping

2018-06-27

Gel-like constructs can be produced using an extrusion-based 3D food printing (3D-FP) technique. Nostoc sphaeroides biomass is a natural gel material. Considering its good nutrition and rheological properties, these algae were chosen in this study as supply material (ink) for 3D-FP. With this gel material, the extrusion-based 3D printing system was set as a model, and the printing behavior was investigated. Furthermore, the 3D-FP mechanisms were explained through low-field nuclear magnetic resonance and rheological measurements. Results indicated that although fresh biomass gel was printable, nonuniformity and instability occurred during printing. Blanched inks showed nonsmooth printing behavior, which was associated with a decrease in elasticity and viscosity. The printability was improved by increasing the rehydration time to 24 h when rehydrated powder was used. Increasing the rehydration time increased the water-binding degree. Pre-gelatinized potato starch was added to the mixture at ratios ranging from 1 to 100 g kg -1 . The best printing outcome was observed at 40 g kg -1 potato starch. We emphasize that elasticity and viscosity balance is an essential parameter to achieve printability. The strategies adopted in this work provide new insights into the development of personalized food regarding texture and nutritional additive content. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Evidence for high-pressure-induced rupture of hydrogen bonds in LH2 photosynthetic antenna pigment-protein complexes

International Nuclear Information System (INIS)

Kangur, L; Leiger, K; Freiberg, A

2008-01-01

The bacteriochlorophyll a-containing LH2 light harvesting complex is an integral membrane protein that catalyzes the photosynthetic process in purple photosynthetic bacteria. The LH2 complexes from Rhodobacter sphaeroides show characteristic strong absorbance at 800 and 850 nm due to the bacteriochlorophyll a molecules confined in two separate areas of the protein. Using these cofactors as intrinsic probes to monitor changes in membrane protein structure, we investigate the response to high hydrostatic pressure up to 2.1 GPa of LH2 complexes embedded into natural membrane environment or extracted with detergent. We demonstrate that high pressure does induce significant alterations to the tertiary structure of the protein in proximity of the protein-bound bacteriochlorophyll a molecules, including breakage of the hydrogen bond they are involved in. The membrane-embedded complexes appear more resilient to damaging effects of the compression than the complexes extracted into detergent environment. This difference has tentatively been explained by more compact structure of the membrane-embedded complexes

Evidence for high-pressure-induced rupture of hydrogen bonds in LH2 photosynthetic antenna pigment-protein complexes

Energy Technology Data Exchange (ETDEWEB)

Kangur, L; Leiger, K; Freiberg, A [Institute of Physics, University of Tartu, Riia 142, Tartu 51014 (Estonia)

2008-07-15

The bacteriochlorophyll a-containing LH2 light harvesting complex is an integral membrane protein that catalyzes the photosynthetic process in purple photosynthetic bacteria. The LH2 complexes from Rhodobacter sphaeroides show characteristic strong absorbance at 800 and 850 nm due to the bacteriochlorophyll a molecules confined in two separate areas of the protein. Using these cofactors as intrinsic probes to monitor changes in membrane protein structure, we investigate the response to high hydrostatic pressure up to 2.1 GPa of LH2 complexes embedded into natural membrane environment or extracted with detergent. We demonstrate that high pressure does induce significant alterations to the tertiary structure of the protein in proximity of the protein-bound bacteriochlorophyll a molecules, including breakage of the hydrogen bond they are involved in. The membrane-embedded complexes appear more resilient to damaging effects of the compression than the complexes extracted into detergent environment. This difference has tentatively been explained by more compact structure of the membrane-embedded complexes.

In vitro assembly of a prohead-like structure of the Rhodobacter capsulatus gene transfer agent

International Nuclear Information System (INIS)

Spano, Anthony J.; Chen, Frank S.; Goodman, Benjamin E.; Sabat, Agnes E.; Simon, Martha N.; Wall, Joseph S.; Correia, John J.; McIvor, Wilson; Newcomb, William W.; Brown, Jay C.; Schnur, Joel M.; Lebedev, Nikolai

2007-01-01

The gene transfer agent (GTA) is a phage-like particle capable of exchanging double-stranded DNA fragments between cells of the photosynthetic bacterium Rhodobacter capsulatus. Here we show that the major capsid protein of GTA, expressed in E. coli, can be assembled into prohead-like structures in the presence of calcium ions in vitro. Transmission electron microscopy (TEM) of uranyl acetate staining material and thin sections of glutaraldehyde-fixed material demonstrates that these associates have spherical structures with diameters in the range of 27-35 nm. The analysis of scanning TEM images revealed particles of mass ∼ 4.3 MDa, representing 101 ± 11 copies of the monomeric subunit. The establishment of this simple and rapid method to form prohead-like particles permits the GTA system to be used for genome manipulation within the photosynthetic bacterium, for specific targeted drug delivery, and for the construction of biologically based distributed autonomous sensors for environmental monitoring

Potential use of thermophilic dark fermentation effluents in photofermentative hydrogen production by Rhodobacter capsulatus

Energy Technology Data Exchange (ETDEWEB)

Ozgura, E.; Afsar, N.; Eroglu, I. [Middle East Technical University, Department of Chemical Engineering, 06531 Ankara (Turkey); De Vrije, T.; Claassen, P.A.M. [Wageningen UR, Agrotechnology and Food Sciences Group, Wageningen UR, P.O. Box 17, 6700 AA Wageningen (Netherlands); Yucel, M.; Gunduz, U. [Middle East Technical University, Department of Biology, 06531 Ankara (Turkey)

2010-12-15

Biological hydrogen production by a sequential operation of dark and photofermentation is a promising route to produce hydrogen. The possibility of using renewable resources, like biomass and agro-industrial wastes, provides a dual effect of sustainability in biohydrogen production and simultaneous waste removal. In this study, photofermentative hydrogen production on effluents of thermophilic dark fermentations on glucose, potato steam peels (PSP) hydrolysate and molasses was investigated in indoor, batch operated bioreactors. An extreme thermophile Caldicellulosiruptor saccharolyticus was used in the dark fermentation step, and Rhodobacter capsulatus (DSM1710) was used in the photofermentation step. Addition of buffer, Fe and Mo to dark fermentor effluents (DFEs) improved the overall efficiency of hydrogen production. The initial acetate concentration in the DFE needed to be adjusted to 30-40 mM by dilution to increase the yield of hydrogen in batch light-supported fermentations. The thermophilic DFEs are suitable for photofermentative hydrogen production, provided that they are supplemented with buffer and nutrients. The overall hydrogen yield of the two-step fermentations was higher than the yield of single step dark fermentations.

Field evidence for the potential of Rhodobacter capsulatus as Biofertilizer for flooded rice.

Science.gov (United States)

Gamal-Eldin, Hosny; Elbanna, Khaled

2011-02-01

In a previous study, we evaluated the effects of inoculating rice plants with the phototrophic purple nonsulfur bacterium Rhodobacter capsulatus (Rc) on growth and yield of rice in pots and lysimeter experiments and the results obtained have been highly encouraging. In this study, we carried out two field experiments: one in the experimental farm of the Faculty of Agriculture, Fayoum University, and the second in a farmer's field in Kafr El-sheikh, to assess the effects of Rc on growth and yield of rice in comparison and in combination with chemical nitrogen fertilizer (CNF) and farmyard manure. The results indicated that both biological and grain yields in all the Rc inoculated treatments were significantly higher than those in the uninoculated corresponding treatments in both fields. With regard to grain yield, the major factor for determining the effectiveness of any agricultural treatment, inoculation with Rc in combination with 50% of the recommended CNF rate gave a grain yield that was statistically equivalent to that obtained with 100% of the recommended CNF rate. These results provide a clear evidence for the potential of Rc as biofertilizer for flooded rice under field conditions.

Physicochemical Characterization and Functional Analysis of the Polysaccharide from the Edible Microalga Nostoc sphaeroides

Directory of Open Access Journals (Sweden)

Haifeng Li

2018-02-01

Full Text Available Nostoc colonies have been used as food and medicine for centuries, and their main supporting matrix is polysaccharides, which help Nostoc cells resist various environmental stresses including oxidative stress. Here we isolated a polysaccharide, nostoglycan, from cultured Nostoc sphaeroides colonies and determined its physicochemical properties, which revealed a characteristic infrared absorption spectrum typical of polysaccharides and an amorphous morphology with rough surfaces. We also show that nostoglycan has strong moisture absorption and retention capacities and a high relative viscosity. Using Caenorhabditis elegans models, we then demonstrate that nostoglycan is capable of improving overall survival rate of the animals under increased oxidative stress caused by paraquat. Nostoglycan also reduces reactive oxygen species level, inhibits protein carbonyl formation and lipid peroxidation, and increases activities of superoxide dismutase and catalase in paraquat-exposed nematodes. As oxidative stress may drive tumor progression, we further demonstrate that nostoglycan can suppress the proliferation of several types of tumor cells and induce apoptosis of human lung adenocarcinoma A549 cells via caspase-3 activation. Together, our results yield important information on the physicochemical characteristics and demonstrate the antioxidant and anti-proliferative functions of nostoglycan, and thus provide an insight into its potential in food and health industries.

Bio-Photoelectrochemical Solar Cells Incorporating Reaction Center and Reaction Center Plus Light Harvesting Complexes

Science.gov (United States)

Yaghoubi, Houman

onto Au electrodes via surface exposed cysteine residues. This resulted in photocurrent densities as large as ~600 nA cm-2 while still the incident photon to generated electron quantum efficiency was as low as %3 x 10-4. 2- The second approach is to immobilize wild type RCs of Rhodobacter sphaeroides on the surface of a Au underlying electrode using self-assembled monolayers of carboxylic acid terminated oligomers and cytochrome c charge mediating layers, with a preferential orientation from the primary electron donor site. This approach resulted in EQE of up to 0.06%, which showed 200 times efficiency improvement comparing to the first approach. In the third approach, instead of isolated protein complexes, RCs plus light harvesting (LH) complexes were employed for a better photon absorption. Direct attachment of RC-LH1 complexes on Au working electrodes, resulted in 0.21% EQE which showed 3.5 times efficiency improvement over the second approach (700 times higher than the first approach). The main impact of this work is the harnessing of biological RCs for efficient energy harvesting in man-made structures. Specifically, the results in this work will advance the application of RCs in devices for energy harvesting and will enable a better understanding of bio and nanomaterial interfaces, thereby advancing the application of biological materials in electronic devices. At the end, this work offers general guidelines that can serve to improve the performance of bio-hybrid solar cells.

Energetic change of the primary quinone in photosynthetic reaction center. Mutation, delayed fluorescence and model calculations (Theses of the Ph.D. dissertation)

International Nuclear Information System (INIS)

Rinyu, L.

2007-01-01

Complete text of publication follows. Photosynthesis is one of the basic metabolic processes of living organisms. Photosynthesizing species (bacteria, algae and higher class plants) convert the energy of light into other forms of free energy (redox potential, electro- chemical potential of ions and protons and phosphate-potential) which are directly suit- able either to cover the energy need of the vital processes of the cell or to storage. In reaction center (RC) protein of photo- synthetic bacteria, electron transfer is initiated upon light excitation from the excited bacteriochlorophyll dimer (P) to the secondary quinone (Q B ) via bacteriopheophytine (Bph) and the primary quinone (Q A ). In Rhodobacter sphaeroides purple bacteria, both quinones are ubiquinone-10, but due to the different protein environment, their electrochemical properties is highly different. Whereas Q A makes one-electron chemistry, Q B can be doubly reduced to form hydroquinone, Q B H 2 by uptake of two protons. Q B H 2 subsequently leaves the RC and is replaced by an oxidized quinone from to membrane pool. The semiquinones are important intermediates in the quinone reduction cycle of the RC. The redox midpoint potentials of the Q/Q - redox pairs (E m ) are also different: the Q A /Q A - has 60 mV more negative potential than the Q B /Q B - couple (pH 8) to make the (interquinone) electron transfer favorable. For fine tuning of the midpoint redox potentials of the quinones, the protein assures appropriate steric and electrostatic environment. The most important aim of this study was the design and production of reaction center mutants in the binding pocket of the primary quinone to investigate the effect of the amino acids of the protein and lipids of the membrane on the thermodynamics of the primary quinone. The first priority was the determination of the absolute free energy gap between the P* and the P + Q A - states in wild type and mutant reaction centers by comparison of the

Proton conduction within the reaction centers of Rhodobacter capsulatus: the electrostatic role of the protein.

OpenAIRE

Maróti, P; Hanson, D K; Baciou, L; Schiffer, M; Sebban, P

1994-01-01

Light-induced charge separation in the photosynthetic reaction center results in delivery of two electrons and two protons to the terminal quinone acceptor QB. In this paper, we have used flash-induced absorbance spectroscopy to study three strains that share identical amino acid sequences in the QB binding site, all of which lack the protonatable amino acids Glu-L212 and Asp-L213. These strains are the photosynthetically incompetent site-specific mutant Glu-L212/Asp-L213-->Ala-L212/Ala-L213 ...

The photosynthetic bacteria Rhodobacter capsulatus and Synechocystis sp. PCC 6803 as new hosts for cyclic plant triterpene biosynthesis.

Directory of Open Access Journals (Sweden)

Anita Loeschcke

Full Text Available Cyclic triterpenes constitute one of the most diverse groups of plant natural products. Besides the intriguing biochemistry of their biosynthetic pathways, plant triterpenes exhibit versatile bioactivities, including antimicrobial effects against plant and human pathogens. While prokaryotes have been extensively used for the heterologous production of other classes of terpenes, the synthesis of cyclic triterpenes, which inherently includes the two-step catalytic formation of the universal linear precursor 2,3-oxidosqualene, is still a major challenge. We thus explored the suitability of the metabolically versatile photosynthetic α-proteobacterium Rhodobacter capsulatus SB1003 and cyanobacterium Synechocystis sp. PCC 6803 as alternative hosts for biosynthesis of cyclic plant triterpenes. Therefore, 2,3-oxidosqualene production was implemented and subsequently combined with different cyclization reactions catalyzed by the representative oxidosqualene cyclases CAS1 (cycloartenol synthase, LUP1 (lupeol synthase, THAS1 (thalianol synthase and MRN1 (marneral synthase derived from model plant Arabidopsis thaliana. While successful accumulation of 2,3-oxidosqualene could be detected by LC-MS analysis in both hosts, cyclase expression resulted in differential production profiles. CAS1 catalyzed conversion to only cycloartenol, but expression of LUP1 yielded lupeol and a triterpenoid matching an oxidation product of lupeol, in both hosts. In contrast, THAS1 expression did not lead to cyclic product formation in either host, whereas MRN1-dependent production of marnerol and hydroxymarnerol was observed in Synechocystis but not in R. capsulatus. Our findings thus indicate that 2,3-oxidosqualene cyclization in heterologous phototrophic bacteria is basically feasible but efficient conversion depends on both the respective cyclase enzyme and individual host properties. Therefore, photosynthetic α-proteo- and cyanobacteria are promising alternative candidates

Monoolein lipid phases as incorporation and enrichment materials for membrane protein crystallization.

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Ellen Wallace

Full Text Available The crystallization of membrane proteins in amphiphile-rich materials such as lipidic cubic phases is an established methodology in many structural biology laboratories. The standard procedure employed with this methodology requires the generation of a highly viscous lipidic material by mixing lipid, for instance monoolein, with a solution of the detergent solubilized membrane protein. This preparation is often carried out with specialized mixing tools that allow handling of the highly viscous materials while minimizing dead volume to save precious membrane protein sample. The processes that occur during the initial mixing of the lipid with the membrane protein are not well understood. Here we show that the formation of the lipidic phases and the incorporation of the membrane protein into such materials can be separated experimentally. Specifically, we have investigated the effect of different initial monoolein-based lipid phase states on the crystallization behavior of the colored photosynthetic reaction center from Rhodobacter sphaeroides. We find that the detergent solubilized photosynthetic reaction center spontaneously inserts into and concentrates in the lipid matrix without any mixing, and that the initial lipid material phase state is irrelevant for productive crystallization. A substantial in-situ enrichment of the membrane protein to concentration levels that are otherwise unobtainable occurs in a thin layer on the surface of the lipidic material. These results have important practical applications and hence we suggest a simplified protocol for membrane protein crystallization within amphiphile rich materials, eliminating any specialized mixing tools to prepare crystallization experiments within lipidic cubic phases. Furthermore, by virtue of sampling a membrane protein concentration gradient within a single crystallization experiment, this crystallization technique is more robust and increases the efficiency of identifying productive

The swimming of a perfect deforming helix

Science.gov (United States)

Koens, Lyndon; Zhang, Hang; Mourran, Ahmed; Lauga, Eric

2017-11-01

Many bacteria rotate helical flagellar filaments in order to swim. When at rest or rotated counter-clockwise these flagella are left handed helices but they undergo polymorphic transformations to right-handed helices when the motor is reversed. These helical deformations themselves can generate motion, with for example Rhodobacter sphaeroides using the polymorphic transformation of the flagellum to generate rotation, or Spiroplasma propagating a change of helix handedness across its body's length to generate forward motion. Recent experiments reported on an artificial helical microswimmer generating motion without a propagating change in handedness. Made of a temperature sensitive gel, these swimmers moved by changing the dimensions of the helix in a non-reciprocal way. Inspired by these results and helix's ubiquitous presence in the bacterial world, we investigate how a deforming helix moves within a viscous fluid. Maintaining a single handedness along its entire length, we discuss how a perfect deforming helix can create a non-reciprocal swimming stroke, identify its principle directions of motion, and calculate the swimming kinematics asymptotically.

Redox thermodynamics of the native and alkaline forms of eukaryotic and bacterial class I cytochromes c.

Science.gov (United States)

Battistuzzi, G; Borsari, M; Sola, M; Francia, F

1997-12-23

The reduction potentials of beef heart cytochrome c and cytochromes c2 from Rhodopseudomonas palustris, Rhodobacter sphaeroides, and Rhodobacter capsulatus were measured through direct electrochemistry at a surface-modified gold electrode as a function of temperature in nonisothermal experiments carried out at neutral and alkaline pH values. The thermodynamic parameters for protein reduction (DeltaS degrees rc and DeltaH degrees rc) were determined for the native and alkaline conformers. Enthalpy and entropy terms underlying species-dependent differences in E degrees and pH- and temperature-induced E degrees changes for a given cytochrome were analyzed. The difference of about +0.1 V in E degrees between cytochromes c2 and the eukaryotic species can be separated into an enthalpic term (-DeltaDeltaH degrees rc/F) of +0.130 V and an entropic term (TDeltaDeltaS degrees rc/F) of -0.040 V. Hence, the higher potential of the bacterial species appears to be determined entirely by a greater enthalpic stabilization of the reduced state. Analogously, the much lower potential of the alkaline conformer(s) as compared to the native species is by far enthalpic in origin for both protein families, and is largely determined by the substitution of Met for Lys in axial heme ligation. Instead, the biphasic E degrees /temperature profile for the native cytochromes is due to a difference in reduction entropy between the conformers at low and high temperatures. Temperature-dependent 1H NMR experiments suggest that the temperature-induced transition also involves a change in orientation of the axial methionine ligand with respect to the heme plane.

Improving the hydrogen production capacity of Rhodobacter capsulatus by genetically modifying redox balancing pathways

Energy Technology Data Exchange (ETDEWEB)

Oeztuerk, Yavuz [TUEBITAK Research Institute for Genetic Engineering and Biotechnology, Gebze Kocaeli (Turkey); Goekce, Abdulmecit [Istanbul Technical Univ. (Turkey). Dept. of Molecular Biology and Genetics; Guergan, Muazzez; Yuecel, Meral [Middle East Technical Univ., Ankara (Turkey). Dept. of Biology

2010-07-01

In Rhodobacter capsulatus, balancing the oxidation-reduction potential (redox-balance) is maintained via a number of inter-dependent regulatory mechanisms that enable these organisms to accommodate divergent growth modes. In order to maintain redox homeostasis, this bacterium possesses regulatory mechanisms functioning as electron sinks affecting the oxidation-reduction state of the ubiquinone pool. Under the photoheterotrophic growth conditions with reduced carbon sources, the excess reducing equivalents are primarily consumed via the reduction of CO{sub 2} through the Calvin-Benson-Bassham (CBB) pathway or by the reduction of protons into hydrogen with the use of dinitrogenase enzyme system. In this study, our aim was to develop strategies to funnel the excess reducing equivalents to nitrogenase-dependent hydrogen production by blocking the carbon-fixation pathway. To realize this purpose, CO{sub 2} fixation was blocked by inactivating the Phosphoribulokinase (PRK) of CBB pathway in wild type (MT1131), uptake-hydrogenase (YO3) and cyt cbb{sub 3} oxidase deficient (YO4) strains. The hydrogen production capacity of newly generated strains deficient in the Calvin-Benson-Bassham pathway were analyzed and compared with wild type strains. The results indicated that, the hydrogen production efficiency and capacity of R. capsulatus was further improved by directing the excess reducing equivalents to dinitrogenase-dependent hydrogen production. (orig.)

Crystallization and preliminary crystallographic studies of FoxE from Rhodobacter ferrooxidans SW2, an FeII oxidoreductase involved in photoferrotrophy

International Nuclear Information System (INIS)

Pereira, L.; Saraiva, I. H.; Coelho, R.; Newman, D. K.; Louro, R. O.; Frazão, C.

2012-01-01

Crystals of the R. ferrooxidans SW2 iron oxidoreductase FoxE were obtained and the phase problem was solved by Fe SAD at 2.44 Å resolution. FoxE is a protein encoded by the foxEYZ operon of Rhodobacter ferrooxidans SW2 that is involved in Fe II -based anoxygenic photosynthesis (‘photoferrotrophy’). It is thought to reside in the periplasm, where it stimulates light-dependent Fe II oxidation. It contains 259 residues, including two haem c-binding motifs. As no three-dimensional model is available and there is no structure with a similar sequence, crystals of FoxE were produced. They diffracted to 2.44 Å resolution using synchrotron radiation at the Fe edge. The phase problem was solved by SAD using SHELXC/D/E and the experimental maps confirmed the presence of two haems per molecule

Proton conduction within the reaction centers of Rhodobacter capsulatus: the electrostatic role of the protein.

Science.gov (United States)

Maróti, P; Hanson, D K; Baciou, L; Schiffer, M; Sebban, P

1994-06-07

Light-induced charge separation in the photosynthetic reaction center results in delivery of two electrons and two protons to the terminal quinone acceptor QB. In this paper, we have used flash-induced absorbance spectroscopy to study three strains that share identical amino acid sequences in the QB binding site, all of which lack the protonatable amino acids Glu-L212 and Asp-L213. These strains are the photosynthetically incompetent site-specific mutant Glu-L212/Asp-L213-->Ala-L212/Ala-L213 and two different photocompetent derivatives that carry both alanine substitutions and an intergenic suppressor mutation located far from QB (class 3 strain, Ala-Ala + Arg-M231-->Leu; class 4 strain, Ala-Ala + Asn-M43-->Asp). At pH 8 in the double mutant, we observe a concomitant decrease of nearly 4 orders of magnitude in the rate constants of second electron and proton transfer to QB compared to the wild type. Surprisingly, these rates are increased to about the same extent in both types of suppressor strains but remain > 2 orders of magnitude smaller than those of the wild type. In the double mutant, at pH 8, the loss of Asp-L213 and Glu-L212 leads to a substantial stabilization (> or = 60 meV) of the semiquinone energy level. Both types of compensatory mutations partially restore, to nearly the same level, the original free energy difference for electron transfer from primary quinone QA to QB. The pH dependence of the electron and proton transfer processes in the double-mutant and the suppressor strains suggests that when reaction centers of the double mutant are shifted to lower pH (1.5-2 units), they function like those of the suppressor strains at physiological pH. Our data suggest that the main effect of the compensatory mutations is to partially restore the negative electrostatic environment of QB and to increase an apparent "functional" pK of the system for efficient proton transfer to the active site. This emphasizes the role of the protein in tuning the

Kinetics of two-stage fermentation process for the production of hydrogen

Energy Technology Data Exchange (ETDEWEB)

Nath, Kaushik [Department of Chemical Engineering, G.H. Patel College of Engineering and Technology, Vallabh Vidyanagar 388 120, Gujarat (India); Muthukumar, Manoj; Kumar, Anish; Das, Debabrata [Fermentation Technology Laboratory, Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302 (India)

2008-02-15

Two-stage process described in the present work is a combination of dark and photofermentation in a sequential batch mode. In the first stage glucose is fermented to acetate, CO{sub 2} and H{sub 2} in an anaerobic dark fermentation by Enterobacter cloacae DM11. This is followed by a successive second stage where acetate is converted to H{sub 2} and CO{sub 2} in a photobioreactor by photosynthetic bacteria, Rhodobacter sphaeroides O.U. 001. The yield of hydrogen in the first stage was about 3.31molH{sub 2}(molglucose){sup -1} (approximately 82% of theoretical) and that in the second stage was about 1.5-1.72molH{sub 2}(molaceticacid){sup -1} (approximately 37-43% of theoretical). The overall yield of hydrogen in two-stage process considering glucose as preliminary substrate was found to be higher compared to a single stage process. Monod model, with incorporation of substrate inhibition term, has been used to determine the growth kinetic parameters for the first stage. The values of maximum specific growth rate ({mu} {sub max}) and K{sub s} (saturation constant) were 0.398h{sup -1} and 5.509gl{sup -1}, respectively, using glucose as substrate. The experimental substrate and biomass concentration profiles have good resemblance with those obtained by kinetic model predictions. A model based on logistic equation has been developed to describe the growth of R. sphaeroides O.U 001 in the second stage. Modified Gompertz equation was applied to estimate the hydrogen production potential, rate and lag phase time in a batch process for various initial concentration of glucose, based on the cumulative hydrogen production curves. Both the curve fitting and statistical analysis showed that the equation was suitable to describe the progress of cumulative hydrogen production. (author)

Automated ensemble assembly and validation of microbial genomes

Science.gov (United States)

2014-01-01

Background The continued democratization of DNA sequencing has sparked a new wave of development of genome assembly and assembly validation methods. As individual research labs, rather than centralized centers, begin to sequence the majority of new genomes, it is important to establish best practices for genome assembly. However, recent evaluations such as GAGE and the Assemblathon have concluded that there is no single best approach to genome assembly. Instead, it is preferable to generate multiple assemblies and validate them to determine which is most useful for the desired analysis; this is a labor-intensive process that is often impossible or unfeasible. Results To encourage best practices supported by the community, we present iMetAMOS, an automated ensemble assembly pipeline; iMetAMOS encapsulates the process of running, validating, and selecting a single assembly from multiple assemblies. iMetAMOS packages several leading open-source tools into a single binary that automates parameter selection and execution of multiple assemblers, scores the resulting assemblies based on multiple validation metrics, and annotates the assemblies for genes and contaminants. We demonstrate the utility of the ensemble process on 225 previously unassembled Mycobacterium tuberculosis genomes as well as a Rhodobacter sphaeroides benchmark dataset. On these real data, iMetAMOS reliably produces validated assemblies and identifies potential contamination without user intervention. In addition, intelligent parameter selection produces assemblies of R. sphaeroides comparable to or exceeding the quality of those from the GAGE-B evaluation, affecting the relative ranking of some assemblers. Conclusions Ensemble assembly with iMetAMOS provides users with multiple, validated assemblies for each genome. Although computationally limited to small or mid-sized genomes, this approach is the most effective and reproducible means for generating high-quality assemblies and enables users to

Production of bioplastics and hydrogen gas by photosynthetic microorganisms

Science.gov (United States)

Yasuo, Asada; Masato, Miyake; Jun, Miyake

1998-03-01

Our efforts have been aimed at the technological basis of photosynthetic-microbial production of materials and an energy carrier. We report here accumulation of poly-(3-hydroxybutyrate) (PHB), a raw material of biodegradable plastics and for production of hydrogen gas, and a renewable energy carrier by photosynthetic microorganisms (tentatively defined as cyanobacteria plus photosynthetic bateria, in this report). A thermophilic cyanobacterium, Synechococcus sp. MA19 that accumulates PHB at more than 20% of cell dry wt under nitrogen-starved conditions was isolated and microbiologically identified. The mechanism of PHB accumulation was studied. A mesophilic Synechococcus PCC7942 was transformed with the genes encoding PHB-synthesizing enzymes from Alcaligenes eutrophus. The transformant accumulated PHB under nitrogen-starved conditions. The optimal conditions for PHB accumulation by a photosynthetic bacterium grown on acetate were studied. Hydrogen production by photosynthetic microorganisms was studied. Cyanobacteria can produce hydrogen gas by nitrogenase or hydrogenase. Hydrogen production mediated by native hydrogenase in cyanobacteria was revealed to be in the dark anaerobic degradation of intracellular glycogen. A new system for light-dependent hydrogen production was targeted. In vitro and in vivo coupling of cyanobacterial ferredoxin with a heterologous hydrogenase was shown to produce hydrogen under light conditions. A trial for genetic trasformation of Synechococcus PCC7942 with the hydrogenase gene from Clostridium pasteurianum is going on. The strong hydrogen producers among photosynthetic bacteria were isolated and characterized. Co-culture of Rhodobacter and Clostriumdium was applied to produce hydrogen from glucose. Conversely in the case of cyanobacteria, genetic regulation of photosynthetic proteins was intended to improve conversion efficiency in hydrogen production by the photosynthetic bacterium, Rhodobacter sphaeroides RV. A mutant acquired by

Atomic force microscopy studies of native photosynthetic membranes.

Science.gov (United States)

Sturgis, James N; Tucker, Jaimey D; Olsen, John D; Hunter, C Neil; Niederman, Robert A

2009-05-05

In addition to providing the earliest surface images of a native photosynthetic membrane at submolecular resolution, examination of the intracytoplasmic membrane (ICM) of purple bacteria by atomic force microscopy (AFM) has revealed a wide diversity of species-dependent arrangements of closely packed light-harvesting (LH) antennae, capable of fulfilling the basic requirements for efficient collection, transmission, and trapping of radiant energy. A highly organized architecture was observed with fused preparations of the pseudocrystalline ICM of Blastochloris viridis, consiting of hexagonally packed monomeric reaction center light-harvesting 1 (RC-LH1) core complexes. Among strains which also form a peripheral LH2 antenna, images of ICM patches from Rhodobacter sphaeroides exhibited well-ordered, interconnected networks of dimeric RC-LH1 core complexes intercalated by rows of LH2, coexisting with LH2-only domains. Other peripheral antenna-containing species, notably Rhodospirillum photometricum and Rhodopseudomonas palustris, showed a less regular organization, with mixed regions of LH2 and RC-LH1 cores, intermingled with large, paracrystalline domains. The ATP synthase and cytochrome bc(1) complex were not observed in any of these topographs and are thought to be localized in the adjacent cytoplasmic membrane or in inaccessible ICM regions separated from the flat regions imaged by AFM. The AFM images have served as a basis for atomic-resolution modeling of the ICM vesicle surface, as well as forces driving segregation of photosynthetic complexes into distinct domains. Docking of atomic-resolution molecular structures into AFM topographs of Rsp. photometricum membranes generated precise in situ structural models of the core complex surrounded by LH2 rings and a region of tightly packed LH2 complexes. A similar approach has generated a model of the highly curved LH2-only membranes of Rba. sphaeroides which predicts that sufficient space exists between LH2 complexes

Electron paramagnetic resonance detection of carotenoid triplet states

International Nuclear Information System (INIS)

Frank, H.A.; Bolt, J.D.; deCosta, S.M.; Sauer, K.

1980-01-01

Triplet states of carotenoids have been detected by X-band electron paramagnetic resonance (EPR) and are reported here for the first time. The systems in which carotenoid triplets are observed include cells of photosynthetic bacteria, isolated bacteriochlorophyll-protein complexes, and detergent micelles which contain β-carotene. It is well known that if electron transfer is blocked following the initial acceptor in the bacterial photochemical reaction center, back reaction of the primary radical pair produces a bacteriochlorophyll dimer triplet. Previous optical studies have shown that in reaction centers containing carotenoids the bacteriochlorophyll dimer triplet sensitizes the carotenoid triplet. We have observed this carotenoid triplet state by EPR in reaction centers of Rhodopseudomonas sphaeroides, strain 2.4.1 (wild type), which contain the carotenoid spheroidene. The zero-field splitting parameters of the triplet spectrum are /D/ = 0.0290 +- 0.0005 cm -1 and /E/ = 0.0044 +-0.0006 cm -1 , in contrast with the parameters of the bacteriochlorophyll dimer triplet, which are /D/ = 0.0189 +- 0.0004 cm -1 and /E/ = 0.0032 +- 0.004 cm -1 . Bacteriochlorophyll in a light harvesting protein complex from Rps. sphaeroides, wild type, also sensitizes carotenoid triplet formation. In whole cells the EPR spectra vary with temperature between 100 and 10 K. Carotenoid triplets also have been observed by EPR in whole cells of Rps. sphaeroides and cells of Rhodospirillum rubrum which contain the carotenoid spirilloxanthin. Attempts to observe the triplet state EPR spectrum of β-carotene in numerous organic solvents failed. However, in nonionic detergent micelles and in phospholipid bilayer vesicles β-carotene gives a triplet state spectrum with /D/ = 0.0333 +- 0.0010 cm -1 and /E/ = 0.0037 +- 0.0010 cm -1 . 6 figures, 1 table

Overall energy conversion efficiency of a photosynthetic vesicle

Energy Technology Data Exchange (ETDEWEB)

Sener, Melih [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States; Strumpfer, Johan [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States; Singharoy, Abhishek [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States; Hunter, C. Neil [Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, United Kingdom; Schulten, Klaus [Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, United States; Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States; Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, United States

2016-08-26

The chromatophore of purple bacteria is an intracellular spherical vesicle that exists in numerous copies in the cell and that efficiently converts sunlight into ATP synthesis, operating typically under low light conditions. Building on an atomic-level structural model of a low-light-adapted chromatophore vesicle from Rhodobacter sphaeroides, we investigate the cooperation between more than a hundred protein complexes in the vesicle. The steady-state ATP production rate as a function of incident light intensity is determined after identifying quinol turnover at the cytochrome bc1 complex (cytbc1) as rate limiting and assuming that the quinone/quinol pool of about 900 molecules acts in a quasi-stationary state. For an illumination condition equivalent to 1% of full sunlight, the vesicle exhibits an ATP production rate of 82 ATP molecules/s. The energy conversion efficiency of ATP synthesis at illuminations corresponding to 1%–5% of full sunlight is calculated to be 0.12-0.04, respectively. The vesicle stoichiometry, evolutionarily adapted to the low light intensities in the habitat of purple bacteria, is suboptimal for steady-state ATP turnover for the benefit of protection against over-illumination.

Effect of light intensity and initial pH during hydrogen production by an integrated dark and photofermentation process

Energy Technology Data Exchange (ETDEWEB)

Nath, Kaushik [Department of Chemical Engineering, GH Patel College of Engineering and Technology, Vallabh Vidyanagar 388 120, Gujarat (India); Das, Debabrata [Fermentation Technology Laboratory, Department of Biotechnology, Indian Institute of Technology, Kharagpur 721302 (India)

2009-09-15

Photofermentation was carried out with the spent fermentation broth obtained from the anaerobic dark fermentation in a two-stage process. For the first stage, i.e. dark fermentation Enterobacter cloacae DM 11 was used as hydrogen producing microorganism. For photofermentation Rhodobacter sphaeroides O.U. 001, a photo-heterotrophic purple non-sulfur bacterium, was used. pH study revealed that cumulative hydrogen production was maximum at initial medium pH of 7.0 {+-} 0.2. Biomass yield was also high at the vicinity of pH 7.0 and it decreased as the pH increased from 7.0 to 8.0. Increased light intensity resulted in an increase in the total volume of hydrogen evolved and also hydrogen production rate. However, light conversion efficiency decreased by increasing light intensity. A four-fold increase in light intensity resulted in a three-fold decrease in light conversion efficiency although the cumulative volume of hydrogen gas production increased. It was observed that only a maximum of 0.51% light conversion efficiency could be achieved but at the expense of very low light intensity of 2500 lux (3.75 W m{sup -2}). (author)

Interaction of two photoreceptors in the regulation of bacterial photosynthesis genes.

Science.gov (United States)

Metz, Sebastian; Haberzettl, Kerstin; Frühwirth, Sebastian; Teich, Kristin; Hasewinkel, Christian; Klug, Gabriele

2012-07-01

The expression of photosynthesis genes in the facultatively photosynthetic bacterium Rhodobacter sphaeroides is controlled by the oxygen tension and by light quantity. Two photoreceptor proteins, AppA and CryB, have been identified in the past, which are involved in this regulation. AppA senses light by its N-terminal BLUF domain, its C-terminal part binds heme and is redox-responsive. Through its interaction to the transcriptional repressor PpsR the AppA photoreceptor controls expression of photosynthesis genes. The cryptochrome-like protein CryB was shown to affect regulation of photosynthesis genes, but the underlying signal chain remained unknown. Here we show that CryB interacts with the C-terminal domain of AppA and modulates the binding of AppA to the transcriptional repressor PpsR in a light-dependent manner. Consequently, binding of the transcription factor PpsR to its DNA target is affected by CryB. In agreement with this, all genes of the PpsR regulon showed altered expression levels in a CryB deletion strain after blue-light illumination. These results elucidate for the first time how a bacterial cryptochrome affects gene expression.

Atomic force microscopy reveals multiple patterns of antenna organization in purple bacteria: implications for energy transduction mechanisms and membrane modeling.

Science.gov (United States)

Sturgis, James N; Niederman, Robert A

2008-01-01

Recent topographs of the intracytoplasmic membrane (ICM) of purple bacteria obtained by atomic force microscopy (AFM) have provided the first surface views of the native architecture of a multicomponent biological membrane at submolecular resolution, representing an important landmark in structural biology. A variety of species-dependent, closely packed arrangements of light-harvesting (LH) complexes was revealed: the most highly organized was found in Rhodobacter sphaeroides in which the peripheral LH2 antenna was seen either in large clusters or in fixed rows interspersed among ordered arrays of dimeric LH1-reaction center (RC) core complexes. A more random organization was observed in other species containing both the LH1 and LH2 complexes, as typified by Rhododspirillum photometricum with randomly packed monomeric LH1-RC core complexes intermingled with large, paracrystalline domains of LH2 antenna. Surprisingly, no structures that could be identified as the ATP synthase or cytochrome bc (1) complexes were observed, which may reflect their localization at ICM vesicle poles or in curved membrane areas, out of view from the flat regions imaged by AFM. This possible arrangement of energy transducing complexes has required a reassessment of energy tranduction mechanisms which place the cytochrome bc (1) complex in close association with the RC. Instead, more plausible proposals must account for the movement of quinone redox species over considerable membrane distances on appropriate time scales. AFM, together with atomic resolution structures are also providing the basis for molecular modeling of the ICM that is leading to an improved picture of the supramolecular organization of photosynthetic complexes, as well as the forces that drive their segregation into distinct domains.

The SOS Response Master Regulator LexA Regulates the Gene Transfer Agent of Rhodobacter capsulatus and Represses Transcription of the Signal Transduction Protein CckA.

Science.gov (United States)

Kuchinski, Kevin S; Brimacombe, Cedric A; Westbye, Alexander B; Ding, Hao; Beatty, J Thomas

2016-02-01

The gene transfer agent of Rhodobacter capsulatus (RcGTA) is a genetic exchange element that combines central aspects of bacteriophage-mediated transduction and natural transformation. RcGTA particles resemble a small double-stranded DNA bacteriophage, package random ∼4-kb fragments of the producing cell genome, and are released from a subpopulation (SOS response in many bacteria, as a regulator of RcGTA activity. Deletion of the lexA gene resulted in the abolition of detectable RcGTA production and an ∼10-fold reduction in recipient capability. A search for SOS box sequences in the R. capsulatus genome sequence identified a number of putative binding sites located 5' of typical SOS response coding sequences and also 5' of the RcGTA regulatory gene cckA, which encodes a hybrid histidine kinase homolog. Expression of cckA was increased >5-fold in the lexA mutant, and a lexA cckA double mutant was found to have the same phenotype as a ΔcckA single mutant in terms of RcGTA production. The data indicate that LexA is required for RcGTA production and maximal recipient capability and that the RcGTA-deficient phenotype of the lexA mutant is largely due to the overexpression of cckA. This work describes an unusual phenotype of a lexA mutant of the alphaproteobacterium Rhodobacter capsulatus in respect to the phage transduction-like genetic exchange carried out by the R. capsulatus gene transfer agent (RcGTA). Instead of the expected SOS response characteristic of prophage induction, this lexA mutation not only abolishes the production of RcGTA particles but also impairs the ability of cells to receive RcGTA-borne genes. The data show that, despite an apparent evolutionary relationship to lambdoid phages, the regulation of RcGTA gene expression differs radically. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Rhodobacter capsulatus gains a competitive advantage from respiratory nitrate reduction during light-dark transitions.

Science.gov (United States)

Ellington, M J K; Richardson, D J; Ferguson, S J

2003-04-01

Rhodobacter capsulatus N22DNAR(+) possesses a periplasmic nitrate reductase and is capable of reducing nitrate to nitrite under anaerobic conditions. In the absence of light this ability cannot support chemoheterotrophic growth in batch cultures. This study investigated the effect of nitrate reduction on the growth of R. capsulatus N22DNAR(+) during multiple light-dark cycles of anaerobic photoheterotrophic/dark chemoheterotrophic growth conditions in carbon-limited continuous cultures. The reduction of nitrate did not affect the photoheterotrophic growth yield of R. capsulatus N22DNAR(+). After a transition from photoheterotrophic to dark chemoheterotrophic growth conditions, the reduction of nitrate slowed the initial washout of a R. capsulatus N22DNAR(+) culture. Towards the end of a period of darkness nitrate-reducing cultures maintained higher viable cell counts than non-nitrate-reducing cultures. During light-dark cycling of a mixed culture, the strain able to reduce nitrate (N22DNAR(+)) outcompeted the strain which was unable to reduce nitrate (N22). The evidence indicates that the periplasmic nitrate reductase activity supports slow growth that retards the washout of a culture during anaerobic chemoheterotrophic conditions, and provides a protonmotive force for cell maintenance during the dark period before reillumination. This translates into a selective advantage during repeated light-dark cycles, such that in mixed culture N22DNAR(+) outcompetes N22. Exposure to light-dark cycles will be a common feature for R. capsulatus in its natural habitats, and this study shows that nitrate respiration may provide a selective advantage under such conditions.

Diverse Arrangement of Photosynthetic Gene Clusters in Aerobic Anoxygenic Phototrophic Bacteria

Czech Academy of Sciences Publication Activity Database

Zheng, Q.; Zhang, R.; Koblížek, Michal; Boldareva, Ekaterina; Yurkov, V.; Shi, Y.

2011-01-01

Roč. 6, č. 9 (2011), s. 1-7 E-ISSN 1932-6203 R&D Projects: GA ČR GAP501/10/0221 Institutional research plan: CEZ:AV0Z50200510 Keywords : RHODOBACTER-CAPSULATUS * CITROMICROBIUM-BATHYOMARINUM * REACTION CENTERS Subject RIV: EE - Microbiology, Virology Impact factor: 4.092, year: 2011

Dimers of light-harvesting complex 2 from Rhodobacter sphaeroides characterized in reconstituted 2D crystals with atomic force microscopy

NARCIS (Netherlands)

Liu, Lu-Ning; Aartsma, Thijs J.; Frese, Raoul N.

Microscopic and light spectroscopic investigations on the supramolecular architecture of bacterial photosynthetic membranes have revealed the photosynthetic protein complexes to be arranged in a densely packed energy-transducing network. Protein packing may play a determining role in the formation

Potential of Rhodobacter capsulatus Grown in Anaerobic-Light or Aerobic-Dark Conditions as Bioremediation Agent for Biological Wastewater Treatments

Directory of Open Access Journals (Sweden)

Stefania Costa

2017-02-01

Full Text Available The use of microorganisms to clean up wastewater provides a cheaper alternative to the conventional treatment plant. The efficiency of this method can be improved by the choice of microorganism with the potential of removing contaminants. One such group is photosynthetic bacteria. Rhodobacter capsulatus is a purple non-sulfur bacterium (PNSB found to be capable of different metabolic activities depending on the environmental conditions. Cell growth in different media and conditions was tested, obtaining a concentration of about 108 CFU/mL under aerobic-dark and 109 CFU/mL under anaerobic-light conditions. The biomass was then used as a bioremediation agent for denitrification and nitrification of municipal wastewater to evaluate the potential to be employed as an additive in biological wastewater treatment. Inoculating a sample of mixed liquor withdrawn from the municipal wastewater treatment plant with R. capsulatus grown in aerobic-dark and anaerobic-light conditions caused a significant decrease of N-NO3 (>95%, N-NH3 (70% and SCOD (soluble chemical oxygen demand (>69%, independent of the growth conditions. A preliminary evaluation of costs indicated that R. capsulatus grown in aerobic-dark conditions could be more convenient for industrial application.

The evolution of glutathione metabolism in phototrophic microorganisms

Science.gov (United States)

Fahey, R. C.; Buschbacher, R. M.; Newton, G. L.

1987-01-01

Of the many roles ascribed to glutathione (GSH) the one most clearly established is its role in the protection of higher eucaryotes against oxygen toxicity through destruction of thiol-reactive oxygen byproducts. If this is the primary function of GSH then GSH metabolism should have evolved during or after the evolution of oxygenic photosynthesis. That many bacteria do not produce GSH is consistent with this view. In the present study we have examined the low-molecular-weight thiol composition of a variety of phototrophic microorganisms to ascertain how evolution of GSH production is related to evolution of oxygenic photosynthesis. Cells were extracted in the presence of monobromobimane (mBBr) to convert thiols to fluorescent derivatives, which were analyzed by high-pressure liquid chromatography. Significant levels of GSH were not found in the green bacteria (Chlorobium thiosulfatophilum and Chloroflexus aurantiacus). Substantial levels of GSH were present in the purple bacteria (Chromatium vinosum, Rhodospirillum rubrum, Rhodobacter sphaeroides, and Rhodocyclus gelatinosa), the cyanobacteria [Anacystis nidulans, Microcoleus chthonoplastes S.G., Nostoc muscorum, Oscillatoria amphigranulata, Oscillatoria limnetica, Oscillatoria sp. (Stinky Spring, Utah), Oscillatoria terebriformis, Plectonema boryanum, and Synechococcus lividus], and eucaryotic algae (Chlorella pyrenoidsa, Chlorella vulgaris, Euglena gracilis, Scenedesmus obliquus, and Chlamydomonas reinhardtii). Other thiols measured included cysteine, gamma-glutamylcysteine, thiosulfate, coenzyme A, and sulfide; several unidentified thiols were also detected. Many of the organisms examined also exhibited a marked ability to reduce mBBr to syn-(methyl,methyl)bimane, an ability that was quenched by treatment with 2-pyridyl disulfide or 5,5'-bisdithio-(2-nitrobenzoic acid) prior to reaction with mBBr. These observations indicate the presence of a reducing system capable of electron transfer to mBBr and reduction of

Bridging the gap: linking molecular simulations and systemic descriptions of cellular compartments.

Directory of Open Access Journals (Sweden)

Tihamér Geyer

Full Text Available Metabolic processes in biological cells are commonly either characterized at the level of individual enzymes and metabolites or at the network level. Often these two paradigms are considered as mutually exclusive because concepts from neither side are suited to describe the complete range of scales. Additionally, when modeling metabolic or regulatory cellular systems, often a large fraction of the required kinetic parameters are unknown. This even applies to such simple and extensively studied systems like the photosynthetic apparatus of purple bacteria. Using the chromatophore vesicles of Rhodobacter sphaeroides as a model system, we show that a consistent kinetic model emerges when fitting the dynamics of a molecular stochastic simulation to a set of time dependent experiments even though about two thirds of the kinetic parameters in this system are not known from experiment. Those kinetic parameters that were previously known all came out in the expected range. The simulation model was built from independent protein units composed of elementary reactions processing single metabolites. This pools-and-proteins approach naturally compiles the wealth of available molecular biological data into a systemic model and can easily be extended to describe other systems by adding new protein or nucleic acid types. The automated parameter optimization, performed with an evolutionary algorithm, reveals the sensitivity of the model to the value of each parameter and the relative importances of the experiments used. Such an analysis identifies the crucial system parameters and guides the setup of new experiments that would add most knowledge for a systemic understanding of cellular compartments. The successful combination of the molecular model and the systemic parametrization presented here on the example of the simple machinery for bacterial photosynthesis shows that it is actually possible to combine molecular and systemic modeling. This framework can now

Reduction of chalcogen oxyanions and generation of nanoprecipitates by the photosynthetic bacterium Rhodobacter capsulatus

Energy Technology Data Exchange (ETDEWEB)

Borghese, Roberto, E-mail: roberto.borghese@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Baccolini, Chiara; Francia, Francesco [Department of Pharmacy and Biotechnology, University of Bologna (Italy); Sabatino, Piera [Department of Chemistry G. Ciamician, University of Bologna (Italy); Turner, Raymond J. [Department of Biological Sciences, University of Calgary, Calgary, Alberta (Canada); Zannoni, Davide, E-mail: davide.zannoni@unibo.it [Department of Pharmacy and Biotechnology, University of Bologna (Italy)

2014-03-01

Graphical abstract: - Highlights: • R. capsulatus cells produce extracellular chalcogens nanoprecipitates when lawsone is present. • Lawsone acts as a redox mediator from reducing equivalents to tellurite and selenite. • Nanoprecipitates production depends on carbon source and requires metabolically active cells. • Te{sup 0} and Se{sup 0} nanoprecipitates are identified by X-ray diffraction (XRD) spectroscopy. - Abstract: The facultative photosynthetic bacterium Rhodobacter capsulatus is characterized in its interaction with the toxic oxyanions tellurite (Te{sup IV}) and selenite (Se{sup IV}) by a highly variable level of resistance that is dependent on the growth mode making this bacterium an ideal organism for the study of the microbial interaction with chalcogens. As we have reported in the past, while the oxyanion tellurite is taken up by R. capsulatus cells via acetate permease and it is reduced to Te{sup 0} in the cytoplasm in the form of splinter-like black intracellular deposits no clear mechanism was described for Se{sup 0} precipitation. Here, we present the first report on the biotransformation of tellurium and selenium oxyanions into extracellular Te{sup 0} and Se{sup 0}nanoprecipitates (NPs) by anaerobic photosynthetically growing cultures of R. capsulatus as a function of exogenously added redox-mediator lawsone, i.e. 2-hydroxy-1,4-naphthoquinone. The NPs formation was dependent on the carbon source used for the bacterial growth and the rate of chalcogen reduction was constant at different lawsone concentrations, in line with a catalytic role for the redox mediator. X-ray diffraction (XRD) analysis demonstrated the Te{sup 0} and Se{sup 0} nature of the nanoparticles.

Solvation effect of bacteriochlorophyll excitons in light-harvesting complex LH2.

Science.gov (United States)

Urboniene, V; Vrublevskaja, O; Trinkunas, G; Gall, A; Robert, B; Valkunas, L

2007-09-15

We have characterized the influence of the protein environment on the spectral properties of the bacteriochlorophyll (Bchl) molecules of the peripheral light-harvesting (or LH2) complex from Rhodobacter sphaeroides. The spectral density functions of the pigments responsible for the 800 and 850 nm electronic transitions were determined from the temperature dependence of the Bchl absorption spectra in different environments (detergent micelles and native membranes). The spectral density function is virtually independent of the hydrophobic support that the protein experiences. The reorganization energy for the B850 Bchls is 220 cm(-1), which is almost twice that of the B800 Bchls, and its Huang-Rhys factor reaches 8.4. Around the transition point temperature, and at higher temperatures, both the static spectral inhomogeneity and the resonance interactions become temperature-dependent. The inhomogeneous distribution function of the transitions exhibits less temperature dependence when LH2 is embedded in membranes, suggesting that the lipid phase protects the protein. However, the temperature dependence of the fluorescence spectra of LH2 cannot be fitted using the same parameters determined from the analysis of the absorption spectra. Correct fitting requires the lowest exciton states to be additionally shifted to the red, suggesting the reorganization of the exciton spectrum.

Structural characterization of the thermostable Bradyrhizobium japonicumD-sorbitol dehydrogenase.

Science.gov (United States)

Fredslund, Folmer; Otten, Harm; Gemperlein, Sabrina; Poulsen, Jens Christian N; Carius, Yvonne; Kohring, Gert Wieland; Lo Leggio, Leila

2016-11-01

Bradyrhizobium japonicum sorbitol dehydrogenase is NADH-dependent and is active at elevated temperatures. The best substrate is D-glucitol (a synonym for D-sorbitol), although L-glucitol is also accepted, giving it particular potential in industrial applications. Crystallization led to a hexagonal crystal form, with crystals diffracting to 2.9 Å resolution. In attempts to phase the data, a molecular-replacement solution based upon PDB entry 4nbu (33% identical in sequence to the target) was found. The solution contained one molecule in the asymmetric unit, but a tetramer similar to that found in other short-chain dehydrogenases, including the search model, could be reconstructed by applying crystallographic symmetry operations. The active site contains electron density consistent with D-glucitol and phosphate, but there was not clear evidence for the binding of NADH. In a search for the features that determine the thermostability of the enzyme, the T m for the orthologue from Rhodobacter sphaeroides, for which the structure was already known, was also determined, and this enzyme proved to be considerably less thermostable. A continuous β-sheet is formed between two monomers in the tetramer of the B. japonicum enzyme, a feature not generally shared by short-chain dehydrogenases, and which may contribute to thermostability, as may an increased Pro/Gly ratio.

The Iron-Sulfur Cluster of Electron Transfer Flavoprotein-ubiquinone Oxidoreductase (ETF-QO) is the Electron Acceptor for Electron Transfer Flavoprotein†

Science.gov (United States)

Swanson, Michael A.; Usselman, Robert J.; Frerman, Frank E.; Eaton, Gareth R.; Eaton, Sandra S.

2011-01-01

Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) accepts electrons from electron-transfer flavoprotein (ETF) and reduces ubiquinone from the ubiquinone-pool. It contains one [4Fe-4S]2+,1+ and one FAD, which are diamagnetic in the isolated oxidized enzyme and can be reduced to paramagnetic forms by enzymatic donors or dithionite. In the porcine protein, threonine 367 is hydrogen bonded to N1 and O2 of the flavin ring of the FAD. The analogous site in Rhodobacter sphaeroides ETF-QO is asparagine 338. Mutations N338T and N338A were introduced into the R. sphaeroides protein by site-directed mutagenesis to determine the impact of hydrogen bonding at this site on redox potentials and activity. The mutations did not alter the optical spectra, EPR g-values, spin-lattice relaxation rates, or the [4Fe-4S]2+,1+ to FAD point-dipole interspin distances. The mutations had no impact on the reduction potential for the iron-sulfur cluster, which was monitored by changes in the continuous wave EPR signals of the [4Fe-4S]+ at 15 K. For the FAD semiquinone, significantly different potentials were obtained by monitoring the titration at 100 or 293 K. Based on spectra at 293 K the N338T mutation shifted the first and second midpoint potentials for the FAD from +47 mV and −30 mV for wild type to −11 mV and −19 mV, respectively. The N338A mutation decreased the potentials to −37 mV and −49 mV. Lowering the midpoint potentials resulted in a decrease in the quinone reductase activity and negligible impact on disproportionation of ETF1e− catalyzed by ETF-QO. These observations indicate that the FAD is involved in electron transfer to ubiquinone, but not in electron transfer from ETF to ETF-QO. Therefore the iron-sulfur cluster is the immediate acceptor from ETF. PMID:18672901

Reprint of “Extracellular production of tellurium nanoparticles by the photosynthetic bacterium Rhodobacter capsulatus”

Energy Technology Data Exchange (ETDEWEB)

Borghese, Roberto, E-mail: roberto.borghese@unibo.it [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy); Brucale, Marco [Institute for the Study of Nanostructured Materials (CNR-ISMN), Rome (Italy); Fortunato, Gianuario [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy); Lanzi, Massimiliano [Dept. of Industrial Chemistry “Toso Montanari”, University of Bologna (Italy); Mezzi, Alessio [Institute for the Study of Nanostructured Materials (CNR-ISMN), Rome (Italy); Valle, Francesco; Cavallini, Massimiliano [Institute for the Study of Nanostructured Materials (CNR-ISMN), Bologna (Italy); Zannoni, Davide [Dept. of Pharmacy and Biotechnology, University of Bologna (Italy)

2017-02-15

Highlights: • Tellurite is reduced by R. capsulatus as cytosolic tellurium nanoprecipitates TeNPs. • Lawsone allows R. capsulatus to produce extracellular TeNPs. • Extracellular TeNPs production depends on the carbon source used for cells growth. • Both lawsone concentration and the incubation time determine the TeNPs size. • Extracellular TeNPs are coated with extracellular polymeric substances (EPS). - Abstract: The toxic oxyanion tellurite (TeO{sub 3}{sup 2−}) is acquired by cells of Rhodobacter capsulatus grown anaerobically in the light, via acetate permease ActP2 and then reduced to Te{sup 0} in the cytoplasm as needle-like black precipitates. Interestingly, photosynthetic cultures of R. capsulatus can also generate Te{sup 0} nanoprecipitates (TeNPs) outside the cells upon addition of the redox mediator lawsone (2-hydroxy-1,4-naphtoquinone). TeNPs generation kinetics were monitored to define the optimal conditions to produce TeNPs as a function of various carbon sources and lawsone concentration. We report that growing cultures over a 10 days period with daily additions of 1 mM tellurite led to the accumulation in the growth medium of TeNPs with dimensions from 200 up to 600–700 nm in length as determined by atomic force microscopy (AFM). This result suggests that nucleation of TeNPs takes place over the entire cell growth period although the addition of new tellurium Te{sup 0} to pre-formed TeNPs is the main strategy used by R. capsulatus to generate TeNPs outside the cells. Finally, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FT-IR) analysis of TeNPs indicate they are coated with an organic material which keeps the particles in solution in aqueous solvents.

Sequential assembly of photosynthetic units in Rhodobacter sphaeroides as revealed by fast repetition rate analysis of variable bacteriochlorophyll a fluorescence

Czech Academy of Sciences Publication Activity Database

Koblížek, Michal; Shih, J. D.; Breitbart, S. I.; Ratcliffe, E. C.; Kolber, Z. S.; Hunter, C. N.; Niederman, R. A.

2005-01-01

Roč. 1706, - (2005), s. 220-231 ISSN 0006-3002 R&D Projects: GA ČR GP206/03/P079; GA MŠk LN00A141 Institutional research plan: CEZ:AV0Z50200510 Keywords : membrane development * light-harvesing complex * photosynthetic membrane Subject RIV: EE - Microbiology, Virology

The response of antioxidant systems in Nostoc sphaeroides against UV-B radiation and the protective effects of exogenous antioxidants

Science.gov (United States)

Wang, Gaohong; Hu, Chunxiang; Li, Dunhai; Zhang, Delu; Li, Xiaoyan; Chen, Kun; Liu, Yongding

UV radiation is one of many harmful factors found in space that are detrimental to organisms on earth in space exploration. In the present work, we examined the role of antioxidant system in Nostoc sphaeroides Kütz (Cyanobacterium) and the effects of exogenously applied antioxidant molecules on its photosynthetic rate under UV-B radiation. It was found that UV-B radiation promoted the activity of antioxidant system to protect photosystem II (PSII) and exogenously applied antioxidant: sodium nitroprusside (SNP) and N-acetylcysteine (NAC) had an obvious protection on PSII activity under UV-B radiation. The activity of superoxide dismutase (SOD, EC 1.15.1.1), catalase (CAT, EC 1.11.1.6), peroxidase (POD, EC 1.11.1.7) and content of MDA (malondialdehyde) and ASC (ascorbate) were improved by 0.5 mM and 1 mM SNP, but 0.1 mM SNP decreased the activity of antioxidant system. Addition of exogenous NAC decreased the activity of SOD, POD, CAT and the content MDA and ASC. In contrast, exogenously applied NAC increased GSH content. The results suggest that exogenous SNP and NAC may protect algae by different mechanisms: SNP may play double roles as both sources of reactive free radicals as well as ROS scavengers in mediating the protective role of PSII on algae under UV-B radiation. On the other hand, NAC functions as an antioxidant or precursor of glutathione, which could protect PSII directly from UV-B radiation.

Moessbauer spectroscopy on the reaction center of Rhodopseudomonas viridis

International Nuclear Information System (INIS)

Frolov, E.; Goldanskii, V.I.; Birk, A.; Parak, F.; Fritzsch, G.; Sinning, I.; Michel, H.

1992-01-01

Proteins called 'reaction centers' (RC) can be isolated from many photosynthetic bacteria. They have one non-heme iron in a quinone acceptor region. The RC of Rhodopseudomonas viridis contains an additional tightly bound tetra-heme cytochrome c subunit. The electronic configuration of both cytochrome and the non-heme iron has been studied in the crystallized protein by Moessbauer spectroscopy at different redox potentials, pH-values, and with an addition of o-phenanthroline. At high potentials (E h =+500 mV) all heme irons are in the low spin Fe 3+ -state, and at low potential (E h = 1 50 mV) they are low spin Fe 2+ with the same Moessbauer parameters for all hemes independent of pH. Redox titrations change the relative area of the reduced and oxidized states in agreement with other methods. The non-heme iron shows a high spin Fe 2+ configuration independent of E h and pH with parameters comparable to those of Rhodopseudomonas sphaeroides. Surprisingly, there is strong evidence for another non-heme iron species in part of the molecules with a Fe 2+ low spin configuration. Incubation with o-phenanthroline decreases the relative Fe 2+ hs-area and increases the contribution of Fe 2+ ls-area. Above 210 K the mean square displacement, 2 >, of the RC-crystals increases more than linearly with temperature. This may be correlated with the increase of the electron transfer rate and indicates that intramolecular mobility influences the functional activity of a protein. (orig.)

Synchronous Measurement of Ultrafast Anisotropy Decay of the B850 in Bacterial LH2 Complex

International Nuclear Information System (INIS)

Wang Yun-Peng; Du Lu-Chao; Zhu Gang-Bei; Wang Zhuan; Weng Yu-Xiang

2015-01-01

Ultrafast anisotropic decay is a prominent parameter revealing ultrafast energy and electron transfer; however, it is difficult to be determined reliably owing to the requirement of a simultaneous availability of the parallel and perpendicular polarized decay kinetics. Nowadays, any measurement of anisotropic decay is a kind of approach to the exact simultaneity. Here we report a novel method for a synchronous ultrafast anisotropy decay measurement, which can well determine the anisotropy, even at a very early time, as the rising phase of the excitation laser pulse. The anisotropic decay of the B850 in bacterial light harvesting antenna complex LH2 of Rhodobacter sphaeroides in solution at room temperature with coherent excitation is detected by this method, which shows a polarization response time of 30 fs, and the energy transfer from the initial excitation to the bacteriochlorophylls in B850 ring takes about 70 fs. The anisotropic decay that is probed at the red side of the absorption spectrum, such as 880 nm, has an initial value of 0.4, corresponding to simulated emission, while the blue side with an anisotropy of 0.1 contributes to the ground-state bleaching. Our results show that the coherent excitation covering the whole ring might not be realized owing to the symmetry breaking of LH2: from C_9 symmetry in membrane to C_2 symmetry in solution. (atomic and molecular physics)

Synchronous Measurement of Ultrafast Anisotropy Decay of the B850 in Bacterial LH2 Complex

Science.gov (United States)

Wang, Yun-Peng; Du, Lu-Chao; Zhu, Gang-Bei; Wang, Zhuan; Weng, Yu-Xiang

2015-02-01

Ultrafast anisotropic decay is a prominent parameter revealing ultrafast energy and electron transfer; however, it is difficult to be determined reliably owing to the requirement of a simultaneous availability of the parallel and perpendicular polarized decay kinetics. Nowadays, any measurement of anisotropic decay is a kind of approach to the exact simultaneity. Here we report a novel method for a synchronous ultrafast anisotropy decay measurement, which can well determine the anisotropy, even at a very early time, as the rising phase of the excitation laser pulse. The anisotropic decay of the B850 in bacterial light harvesting antenna complex LH2 of Rhodobacter sphaeroides in solution at room temperature with coherent excitation is detected by this method, which shows a polarization response time of 30 fs, and the energy transfer from the initial excitation to the bacteriochlorophylls in B850 ring takes about 70 fs. The anisotropic decay that is probed at the red side of the absorption spectrum, such as 880 nm, has an initial value of 0.4, corresponding to simulated emission, while the blue side with an anisotropy of 0.1 contributes to the ground-state bleaching. Our results show that the coherent excitation covering the whole ring might not be realized owing to the symmetry breaking of LH2: from C9 symmetry in membrane to C2 symmetry in solution.

A comparative spectroscopic and kinetic study of photoexcitations in detergent-isolated and membrane-embedded LH2 light-harvesting complexes.

Science.gov (United States)

Freiberg, Arvi; Rätsep, Margus; Timpmann, Kõu

2012-08-01

Integral membrane proteins constitute more than third of the total number of proteins present in organisms. Solubilization with mild detergents is a common technique to study the structure, dynamics, and catalytic activity of these proteins in purified form. However beneficial the use of detergents may be for protein extraction, the membrane proteins are often denatured by detergent solubilization as a result of native lipid membrane interactions having been modified. Versatile investigations of the properties of membrane-embedded and detergent-isolated proteins are, therefore, required to evaluate the consequences of the solubilization procedure. Herein, the spectroscopic and kinetic fingerprints have been established that distinguish excitons in individual detergent-solubilized LH2 light-harvesting pigment-protein complexes from them in the membrane-embedded complexes of purple photosynthetic bacteria Rhodobacter sphaeroides. A wide arsenal of spectroscopic techniques in visible optical range that include conventional broadband absorption-fluorescence, fluorescence anisotropy excitation, spectrally selective hole burning and fluorescence line-narrowing, and transient absorption-fluorescence have been applied over broad temperature range between physiological and liquid He temperatures. Significant changes in energetics and dynamics of the antenna excitons upon self-assembly of the proteins into intracytoplasmic membranes are observed, analyzed, and discussed. This article is part of a Special Issue entitled: Photosynthesis Research for Sustainability: from Natural to Artificial. Copyright © 2011. Published by Elsevier B.V.

Autodisplay of active sorbitol dehydrogenase (SDH) yields a whole cell biocatalyst for the synthesis of rare sugars.

Science.gov (United States)

Jose, Joachim; von Schwichow, Steffen

2004-04-02

Whole cell biocatalysts are attractive technological tools for the regio- and enantioselective synthesis of products, especially from substrates with several identical reactive groups. In the present study, a whole cell biocatalyst for the synthesis of rare sugars from polyalcohols was constructed. For this purpose, sorbitol dehydrogenase (SDH) from Rhodobacter sphaeroides, a member of the short-chain dehydrogenase/reductase (SDR) family, was expressed on the surface of Escherichia coli using Autodisplay. Autodisplay is an efficient surface display system for Gram-negative bacteria and is based on the autotransporter secretion pathway. Transport of SDH to the outer membrane was monitored by SDS-PAGE and Western blotting of different cell fractions. The surface exposure of the enzyme could be verified by immunofluorescence microscopy and fluorescence activated cell sorting (FACS). The activity of whole cells displaying SDH at the surface was determined in an optical test. Specific activities were found to be 12 mU per 3.3 x 10(8) cells for the conversion of D-glucitol (sorbitol) to D-fructose, 7 mU for the conversion D-galactitol to D-tagatose, and 17 mU for the conversion of L-arabitol to L-ribulose. The whole cell biocatalyst obtained by surface display of SDH could also produce D-glucitol from D-fructose (29 mU per 3.3 x 10(8) cells).

RpoH2 sigma factor controls the photooxidative stress response in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7.

Science.gov (United States)

Kumar, Santosh; Rai, Ashutosh Kumar; Mishra, Mukti Nath; Shukla, Mansi; Singh, Pradhyumna Kumar; Tripathi, Anil Kumar

2012-12-01

Bacteria belonging to the Alphaproteobacteria normally harbour multiple copies of the heat shock sigma factor (known as σ(32), σ(H) or RpoH). Azospirillum brasilense, a non-photosynthetic rhizobacterium, harbours five copies of rpoH genes, one of which is an rpoH2 homologue. The genes around the rpoH2 locus in A. brasilense show synteny with that found in rhizobia. The rpoH2 of A. brasilense was able to complement the temperature-sensitive phenotype of the Escherichia coli rpoH mutant. Inactivation of rpoH2 in A. brasilense results in increased sensitivity to methylene blue and to triphenyl tetrazolium chloride (TTC). Exposure of A. brasilense to TTC and the singlet oxygen-generating agent methylene blue induced several-fold higher expression of rpoH2. Comparison of the proteome of A. brasilense with its rpoH2 deletion mutant and with an A. brasilense strain overexpressing rpoH2 revealed chaperone GroEL, elongation factors (Ef-Tu and EF-G), peptidyl prolyl isomerase, and peptide methionine sulfoxide reductase as the major proteins whose expression was controlled by RpoH2. Here, we show that the RpoH2 sigma factor-controlled photooxidative stress response in A. brasilense is similar to that in the photosynthetic bacterium Rhodobacter sphaeroides, but that RpoH2 is not involved in the detoxification of methylglyoxal in A. brasilense.

Mutations That Alter the Bacterial Cell Envelope Increase Lipid Production

Energy Technology Data Exchange (ETDEWEB)

Lemmer, Kimberly C.; Zhang, Weiping; Langer, Samantha J.; Dohnalkova, Alice; Hu, Dehong; Lemke, Rachelle A.; Piotrowski, Jeff S.; Orr, Galya; Noguera, Daniel R.; Donohue, Timothy J.

2017-05-23

Lipids from microbes offer a promising source of renewable alternatives to petroleum-derived compounds. In particular, oleaginous microbes are of interest because they accumulate a large fraction of their biomass as lipids. In this study, we analyzed genetic changes that alter lipid accumulation inRhodobacter sphaeroides. By screening anR. sphaeroidesTn5mutant library for insertions that increased fatty acid content, we identified 10 high-lipid (HL) mutants for further characterization. These HL mutants exhibited increased sensitivity to drugs that target the bacterial cell envelope and changes in shape, and some had the ability to secrete lipids, with two HL mutants accumulating ~60% of their total lipids extracellularly. When one of the highest-lipid-secreting strains was grown in a fed-batch bioreactor, its lipid content was comparable to that of oleaginous microbes, with the majority of the lipids secreted into the medium. Based on the properties of these HL mutants, we conclude that alterations of the cell envelope are a previously unreported approach to increase microbial lipid production. We also propose that this approach may be combined with knowledge about biosynthetic pathways, in this or other microbes, to increase production of lipids and other chemicals.

IMPORTANCEThis paper reports on experiments to understand how to increase microbial lipid production. Microbial lipids are often cited as one renewable replacement for petroleum-based fuels and chemicals, but strategies to increase the yield of these compounds are needed to achieve this goal. While lipid biosynthesis is often well understood, increasing yields of these compounds to industrially relevant levels is a challenge, especially since genetic, synthetic biology, or engineering approaches are not feasible in many microbes. We show that altering the bacterial cell envelope can be used to increase

Effect of light-dark cycles on hydrogen and poly-β-hydroxybutyrate production by a photoheterotrophic culture and Rhodobacter capsulatus using a dark fermentation effluent as substrate.

Science.gov (United States)

Montiel Corona, Virginia; Le Borgne, Sylvie; Revah, Sergio; Morales, Marcia

2017-02-01

A Rhodobacter capsulatus strain and a photoheterotrophic culture (IZT) were cultivated to produce hydrogen under different light-dark cycles. A dark fermentation effluent (DFE) was used as substrate. It was found that IZT culture had an average cumulative hydrogen production (Paccum H 2 ) of 1300±43mLH 2 L -1 under continuous illumination and light-dark cycles of 30 or 60min. In contrast, R. capsulatus reduced its Paccum H 2 by 20% under 30:30min light-dark cycles, but tripled its poly-β-hydroxybutyrate (PHB) content (308±2mgPHB gdw -1 ) compared to continuous illumination. The highest PHB content by IZT culture was 178±10mgPHB gdw -1 under 15:15min light-dark cycles. PCR-DGGE analysis revealed that the IZT culture was mainly composed of Rhodopseudomonas palustris identified with high nucleotide similarity (99%). The evaluated cultures might be used for hydrogen and PHB production. They might provide energy savings by using light-dark cycles and DFE valorization. Copyright © 2016 Elsevier Ltd. All rights reserved.

Dietary Karaya Saponin and Rhodobacter capsulatus Exert Hypocholesterolemic Effects by Suppression of Hepatic Cholesterol Synthesis and Promotion of Bile Acid Synthesis in Laying Hens

Directory of Open Access Journals (Sweden)

Sadia Afrose

2010-01-01

Full Text Available This study was conducted to elucidate the mechanism underlying the hypolipidemic action of karaya saponin or Rhodobacter (R. capsulatus. A total of 40 laying hens (20-week-old were assigned into four dietary treatment groups and fed a basal diet (as a control or basal diets supplemented with either karaya saponin, R. capsulatus, or both for 60 days. The level of serum low-density-lipoprotein cholesterol and the levels of cholesterol and triglycerides in the serum, liver, and egg yolk were reduced by all the supplementations (<.05. Liver bile acid concentration and fecal concentrations of cholesterol, triacylglycerol, and bile acid were simultaneously increased by the supplementation of karaya saponin, R. capsulatus, and the combination of karaya saponin and R. capsulatus (<.05. The supplementation of karaya saponin, R. capsulatus, and the combination of karaya saponin and R. capsulatus suppressed the incorporation of 14C from 1-14C-palmitic acid into the fractions of total lipids, phospholipids, triacylglycerol, and cholesterol in the liver in vitro (<.05. These findings suggest that the hypocholesterolemic effects of karaya saponin and R. capsulatus are caused by the suppression of the cholesterol synthesis and the promotion of cholesterol catabolism in the liver.

B-side charge separation in bacterial photosynthetic reaction centers: nanosecond time scale electron transfer from HB- to QB.

Science.gov (United States)

Kirmaier, Christine; Laible, Philip D; Hanson, Deborah K; Holten, Dewey

2003-02-25

We report time-resolved optical measurements of the primary electron transfer reactions in Rhodobacter capsulatus reaction centers (RCs) having four mutations: Phe(L181) --> Tyr, Tyr(M208) --> Phe, Leu(M212) --> His, and Trp(M250) --> Val (denoted YFHV). Following direct excitation of the bacteriochlorophyll dimer (P) to its lowest excited singlet state P, electron transfer to the B-side bacteriopheophytin (H(B)) gives P(+)H(B)(-) in approximately 30% yield. When the secondary quinone (Q(B)) site is fully occupied, P(+)H(B)(-) decays with a time constant estimated to be in the range of 1.5-3 ns. In the presence of excess terbutryn, a competitive inhibitor of Q(B) binding, the observed lifetime of P(+)H(B)(-) is noticeably longer and is estimated to be in the range of 4-8 ns. On the basis of these values, the rate constant for P(+)H(B)(-) --> P(+)Q(B)(-) electron transfer is calculated to be between approximately (2 ns)(-)(1) and approximately (12 ns)(-)(1), making it at least an order of magnitude smaller than the rate constant of approximately (200 ps)(-)(1) for electron transfer between the corresponding A-side cofactors (P(+)H(A)(-) --> P(+)Q(A)(-)). Structural and energetic factors associated with electron transfer to Q(B) compared to Q(A) are discussed. Comparison of the P(+)H(B)(-) lifetimes in the presence and absence of terbutryn indicates that the ultimate (i.e., quantum) yield of P(+)Q(B)(-) formation relative to P is 10-25% in the YFHV RC.

The influence of quorum sensing in compartment II of the MELiSSA loop

Science.gov (United States)

Condori, Sandra; Mastroleo, Felice; Wattiez, Ruddy; Leys, Natalie

MELiSSA (Micro-Ecological Life Support System Alternative) has been conceived as a 5 compartments microorganisms and higher plants recycling system for long haul space flights. Rhodospirillum rubrum S1H colonizes compartment II. Previous work reported that continuous culture of the bacterium in a photobioreactor could lead to thick biofilm formation, leading to bioreactor arrest. Our aim is to investigate the unknown quorum sensing (QS) system of R. rubrum S1H, specifically under MELiSSA relevant culture conditions meaning light anaerobic (LAN) and using acetate as carbon source. In that purpose an autoinducer synthase gene (Rru_A3396) knockout mutant was constructed by allelic exchange generating strain M68. In addition phenotypic comparison between wild type (WT) and M68 was performed. Results of thin layer chromatography assay where Agrobacterium tumefaciens NT1 have been used as reporter strain showed that WT produces acyl-homoserine lactones (AHLs) from C4 to C12 acyl carbon chain length; however, in M68 no AHLs were detected confirming that gene Rru_A3396 (named rruI) encodes an autoinducer synthase. Interestingly under a low shear or static environment M68 showed cell aggregation similar as reported in a closely related bacterium Rhodobacter sphaeroides (cerI mutant). In contrast to WT, M68 did not form biofilm and exhibited a decreased motility and pigment content. M68 vs wild type transcriptomics results showed that 326 genes were statistically significant differentially expressed. Downregulation of genes related to photosynthesis e.g., reaction center subunits, light harvesting complex and photosynthetic assembly proteins was observed. Similar results were obtained for preliminary proteomic analysis. Results obtained showed that in R. rubrum S1H the AHL-based QS system regulates almost 8% of the genome which is linked to biofilm formation among other biological processes described above. Since strain M68 could not be used in compartment II due to its less

Impact of the lipid bilayer on energy transfer kinetics in the photosynthetic protein LH2† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc04814a

Science.gov (United States)

Ogren, John I.; Tong, Ashley L.; Gordon, Samuel C.; Chenu, Aurélia; Lu, Yue; Blankenship, Robert E.; Cao, Jianshu

2018-01-01

Photosynthetic purple bacteria convert solar energy to chemical energy with near unity quantum efficiency. The light-harvesting process begins with absorption of solar energy by an antenna protein called Light-Harvesting Complex 2 (LH2). Energy is subsequently transferred within LH2 and then through a network of additional light-harvesting proteins to a central location, termed the reaction center, where charge separation occurs. The energy transfer dynamics of LH2 are highly sensitive to intermolecular distances and relative organizations. As a result, minor structural perturbations can cause significant changes in these dynamics. Previous experiments have primarily been performed in two ways. One uses non-native samples where LH2 is solubilized in detergent, which can alter protein structure. The other uses complex membranes that contain multiple proteins within a large lipid area, which make it difficult to identify and distinguish perturbations caused by protein–protein interactions and lipid–protein interactions. Here, we introduce the use of the biochemical platform of model membrane discs to study the energy transfer dynamics of photosynthetic light-harvesting complexes in a near-native environment. We incorporate a single LH2 from Rhodobacter sphaeroides into membrane discs that provide a spectroscopically amenable sample in an environment more physiological than detergent but less complex than traditional membranes. This provides a simplified system to understand an individual protein and how the lipid–protein interaction affects energy transfer dynamics. We compare the energy transfer rates of detergent-solubilized LH2 with those of LH2 in membrane discs using transient absorption spectroscopy and transient absorption anisotropy. For one key energy transfer step in LH2, we observe a 30% enhancement of the rate for LH2 in membrane discs compared to that in detergent. Based on experimental results and theoretical modeling, we attribute this difference

Impact of the lipid bilayer on energy transfer kinetics in the photosynthetic protein LH2.

Science.gov (United States)

Ogren, John I; Tong, Ashley L; Gordon, Samuel C; Chenu, Aurélia; Lu, Yue; Blankenship, Robert E; Cao, Jianshu; Schlau-Cohen, Gabriela S

2018-03-28

Photosynthetic purple bacteria convert solar energy to chemical energy with near unity quantum efficiency. The light-harvesting process begins with absorption of solar energy by an antenna protein called Light-Harvesting Complex 2 (LH2). Energy is subsequently transferred within LH2 and then through a network of additional light-harvesting proteins to a central location, termed the reaction center, where charge separation occurs. The energy transfer dynamics of LH2 are highly sensitive to intermolecular distances and relative organizations. As a result, minor structural perturbations can cause significant changes in these dynamics. Previous experiments have primarily been performed in two ways. One uses non-native samples where LH2 is solubilized in detergent, which can alter protein structure. The other uses complex membranes that contain multiple proteins within a large lipid area, which make it difficult to identify and distinguish perturbations caused by protein-protein interactions and lipid-protein interactions. Here, we introduce the use of the biochemical platform of model membrane discs to study the energy transfer dynamics of photosynthetic light-harvesting complexes in a near-native environment. We incorporate a single LH2 from Rhodobacter sphaeroides into membrane discs that provide a spectroscopically amenable sample in an environment more physiological than detergent but less complex than traditional membranes. This provides a simplified system to understand an individual protein and how the lipid-protein interaction affects energy transfer dynamics. We compare the energy transfer rates of detergent-solubilized LH2 with those of LH2 in membrane discs using transient absorption spectroscopy and transient absorption anisotropy. For one key energy transfer step in LH2, we observe a 30% enhancement of the rate for LH2 in membrane discs compared to that in detergent. Based on experimental results and theoretical modeling, we attribute this difference to

Global Analysis of Photosynthesis Transcriptional Regulatory Networks

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Imam, Saheed; Noguera, Daniel R.; Donohue, Timothy J.

2014-01-01

Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888), which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis. PMID:25503406

Metabolic engineering of the Stevia rebaudiana ent-kaurene biosynthetic pathway in recombinant Escherichia coli.

Science.gov (United States)

Kong, Min Kyung; Kang, Hyun-Jun; Kim, Jin Ho; Oh, Soon Hwan; Lee, Pyung Cheon

2015-11-20

The ent-kaurene is a dedicated precursor pool and is responsible for synthesizing natural sweeteners such as steviol glycosides. In this study, to produce ent-kaurene in Escherichia coli, we modularly constructed and expressed two ent-kaurene genes encoding ent-copalyl diphosphate synthase (CPPS) and ent-kaurene synthase (KS) from Stevia rebaudiana known as a typical plant producing steviol glycoside. The CPPS and KS from S. rebaudiana were functionally expressed in a heterologous host E. coli. Furthermore, in order to enhance ent-kaurene production in E. coli, six geranylgeranyl diphosphate synthases (GGPPS) from various microorganisms and eight strains of E. coli as host were compared by measuring ent-kaurene production. The highest ent-kaurene production of approximately 41.1mg/L was demonstrated in E. coli strain MG1655 co-expressing synthetic CPPS-KS module and GGPPS from Rhodobacter sphaeroides. The ent-kaurene production was further increased up to 179.6 mg/L by overexpression of the three key enzymes for isoprenoid precursor, 1-deoxyxylulose-5-phosphate synthase (DXS), farnesyl diphosphate synthase (IspA) and isopentenyl diphosphate isomerase (IDI) from E. coli. Finally, the highest titer of ent-kaurene (578 mg/L) with a specific yield of ent-kaurene of 143.5mg/g dry cell weight was obtained by culturing E. coli strain MG1655 co-expressing the ent-kaurene module, DXS, IDI and IspA in 1L bioreactor containing 20 g/L glycerol. Copyright © 2015 Elsevier B.V. All rights reserved.

Communication: Broad manifold of excitonic states in light-harvesting complex 1 promotes efficient unidirectional energy transfer in vivo

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Sohail, Sara H.; Dahlberg, Peter D.; Allodi, Marco A.; Massey, Sara C.; Ting, Po-Chieh; Martin, Elizabeth C.; Hunter, C. Neil; Engel, Gregory S.

2017-10-01

In photosynthetic organisms, the pigment-protein complexes that comprise the light-harvesting antenna exhibit complex electronic structures and ultrafast dynamics due to the coupling among the chromophores. Here, we present absorptive two-dimensional (2D) electronic spectra from living cultures of the purple bacterium, Rhodobacter sphaeroides, acquired using gradient assisted photon echo spectroscopy. Diagonal slices through the 2D lineshape of the LH1 stimulated emission/ground state bleach feature reveal a resolvable higher energy population within the B875 manifold. The waiting time evolution of diagonal, horizontal, and vertical slices through the 2D lineshape shows a sub-100 fs intra-complex relaxation as this higher energy population red shifts. The absorption (855 nm) of this higher lying sub-population of B875 before it has red shifted optimizes spectral overlap between the LH1 B875 band and the B850 band of LH2. Access to an energetically broad distribution of excitonic states within B875 offers a mechanism for efficient energy transfer from LH2 to LH1 during photosynthesis while limiting back transfer. Two-dimensional lineshapes reveal a rapid decay in the ground-state bleach/stimulated emission of B875. This signal, identified as a decrease in the dipole strength of a strong transition in LH1 on the red side of the B875 band, is assigned to the rapid localization of an initially delocalized exciton state, a dephasing process that frustrates back transfer from LH1 to LH2.

Sequence Analysis of the Cryptic Plasmid pMG101 from Rhodopseudomonas palustris and Construction of Stable Cloning Vectors

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Inui, Masayuki; Roh, Jung Hyeob; Zahn, Kenneth; Yukawa, Hideaki

2000-01-01

A 15-kb cryptic plasmid was obtained from a natural isolate of Rhodopseudomonas palustris. The plasmid, designated pMG101, was able to replicate in R. palustris and in closely related strains of Bradyrhizobium japonicum and phototrophic Bradyrhizobium species. However, it was unable to replicate in the purple nonsulfur bacterium Rhodobacter sphaeroides and in Rhizobium species. The replication region of pMG101 was localized to a 3.0-kb SalI-XhoI fragment, and this fragment was stably maintained in R. palustris for over 100 generations in the absence of selection. The complete nucleotide sequence of this fragment revealed two open reading frames (ORFs), ORF1 and ORF2. The deduced amino acid sequence of ORF1 is similar to sequences of Par proteins, which mediate plasmid stability from certain plasmids, while ORF2 was identified as a putative rep gene, coding for an initiator of plasmid replication, based on homology with the Rep proteins of several other plasmids. The function of these sequences was studied by deletion mapping and gene disruptions of ORF1 and ORF2. pMG101-based Escherichia coli-R. palustris shuttle cloning vectors pMG103 and pMG105 were constructed and were stably maintained in R. palustris growing under nonselective conditions. The ability of plasmid pMG101 to replicate in R. palustris and its close phylogenetic relatives should enable broad application of these vectors within this group of α-proteobacteria. PMID:10618203

Global analysis of photosynthesis transcriptional regulatory networks.

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Saheed Imam

2014-12-01

Full Text Available Photosynthesis is a crucial biological process that depends on the interplay of many components. This work analyzed the gene targets for 4 transcription factors: FnrL, PrrA, CrpK and MppG (RSP_2888, which are known or predicted to control photosynthesis in Rhodobacter sphaeroides. Chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq identified 52 operons under direct control of FnrL, illustrating its regulatory role in photosynthesis, iron homeostasis, nitrogen metabolism and regulation of sRNA synthesis. Using global gene expression analysis combined with ChIP-seq, we mapped the regulons of PrrA, CrpK and MppG. PrrA regulates ∼34 operons encoding mainly photosynthesis and electron transport functions, while CrpK, a previously uncharacterized Crp-family protein, regulates genes involved in photosynthesis and maintenance of iron homeostasis. Furthermore, CrpK and FnrL share similar DNA binding determinants, possibly explaining our observation of the ability of CrpK to partially compensate for the growth defects of a ΔFnrL mutant. We show that the Rrf2 family protein, MppG, plays an important role in photopigment biosynthesis, as part of an incoherent feed-forward loop with PrrA. Our results reveal a previously unrealized, high degree of combinatorial regulation of photosynthetic genes and significant cross-talk between their transcriptional regulators, while illustrating previously unidentified links between photosynthesis and the maintenance of iron homeostasis.

Valencene synthase from the heartwood of Nootka cypress (Callitropsis nootkatensis) for biotechnological production of valencene.

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Beekwilder, Jules; van Houwelingen, Adèle; Cankar, Katarina; van Dijk, Aalt D J; de Jong, René M; Stoopen, Geert; Bouwmeester, Harro; Achkar, Jihane; Sonke, Theo; Bosch, Dirk

2014-02-01

Nootkatone is one of the major terpenes in the heartwood of the Nootka cypress Callitropsis nootkatensis. It is an oxidized sesquiterpene, which has been postulated to be derived from valencene. Both valencene and nootkatone are used for flavouring citrus beverages and are considered among the most valuable terpenes used at commercial scale. Functional evaluation of putative terpene synthase genes sourced by large-scale EST sequencing from Nootka cypress wood revealed a valencene synthase gene (CnVS). CnVS expression in different tissues from the tree correlates well with nootkatone content, suggesting that CnVS represents the first dedicated gene in the nootkatone biosynthetic pathway in C. nootkatensis The gene belongs to the gymnosperm-specific TPS-d subfamily of terpenes synthases and its protein sequence has low similarity to known citrus valencene synthases. In vitro, CnVS displays high robustness under different pH and temperature regimes, potentially beneficial properties for application in different host and physiological conditions. Biotechnological production of sesquiterpenes has been shown to be feasible, but productivity of microbial strains expressing valencene synthase from Citrus is low, indicating that optimization of valencene synthase activity is needed. Indeed, expression of CnVS in Saccharomyces cerevisiae indicated potential for higher yields. In an optimized Rhodobacter sphaeroides strain, expression of CnVS increased valencene yields 14-fold to 352 mg/L, bringing production to levels with industrial potential. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Dietary Effect of Selenium-enriched Radish Sprouts, Vitamin E, and Rhodobacter capsulatus on Hypocholesterolemia and Immunity of Broiler

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Tsujii H

2017-06-01

Full Text Available The study was designed to investigate the effects of dietary Selenium-enriched radish sprouts (Se-RS, Vitamin E (Vit E, and Rhodobacter capsulatus (RC on immunity, cholesterol concentration, and fatty acid composition in broiler meat. A total of 100 two-week-old male broiler chicks were randomly assigned into five dietary groups: I Control; II Se-RS (5 μg/kg Se-RS; III Se-RS+RC (5 μg/kg Se-RS + 0.2 g/kg RC; IV Se-RS+Vit E (5 μg/kg Se-RS + 50 mg/kg Vit E and V Se-RS+RC+Vit E (5 μg/kg Se-RS + 0.2 g/kg RC + 50 mg/kg Vit E. Diets and clean drinking water were offered ad libitum. After the end of 3-wk of feeding period, serum cholesterol and triglycerides concentrations were lower (P < 0.05 in broilers fed Se-RS + RC + Vit E supplemented diet compared to the control diet. At the end of the 6-wk feeding period, birds fed the Se-RS+RC+Vit E diet significantly (P < 0.05 reduced cholesterol and triglycerides concentrations and improved the ratio of unsaturated fatty acids to saturated fatty acids in broiler meat. The highest (P < 0.05 number of leukocytes was observed in broilers fed Se-RS+RC+Vit E supplemented diet. Foot web index and weights of spleen, bursa, and thymus were significantly (P < 0.05 higher in birds fed Se-RS+RC+Vit E compared to the control diet. Our findings suggest that there are dual benefits of supplementing broiler diets with Se-RS+RC+Vit E because of improvements in the bird’s immunity and meat quality that is important for health conscious consumers.

Ultrafast time-resolved carotenoid to-bacteriochlorophyll energy transfer in LH2 complexes from photosynthetic bacteria.

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Cong, Hong; Niedzwiedzki, Dariusz M; Gibson, George N; LaFountain, Amy M; Kelsh, Rhiannon M; Gardiner, Alastair T; Cogdell, Richard J; Frank, Harry A

2008-08-28

Steady-state and ultrafast time-resolved optical spectroscopic investigations have been carried out at 293 and 10 K on LH2 pigment-protein complexes isolated from three different strains of photosynthetic bacteria: Rhodobacter (Rb.) sphaeroides G1C, Rb. sphaeroides 2.4.1 (anaerobically and aerobically grown), and Rps. acidophila 10050. The LH2 complexes obtained from these strains contain the carotenoids, neurosporene, spheroidene, spheroidenone, and rhodopin glucoside, respectively. These molecules have a systematically increasing number of pi-electron conjugated carbon-carbon double bonds. Steady-state absorption and fluorescence excitation experiments have revealed that the total efficiency of energy transfer from the carotenoids to bacteriochlorophyll is independent of temperature and nearly constant at approximately 90% for the LH2 complexes containing neurosporene, spheroidene, spheroidenone, but drops to approximately 53% for the complex containing rhodopin glucoside. Ultrafast transient absorption spectra in the near-infrared (NIR) region of the purified carotenoids in solution have revealed the energies of the S1 (2(1)Ag-)-->S2 (1(1)Bu+) excited-state transitions which, when subtracted from the energies of the S0 (1(1)Ag-)-->S2 (1(1)Bu+) transitions determined by steady-state absorption measurements, give precise values for the positions of the S1 (2(1)Ag-) states of the carotenoids. Global fitting of the ultrafast spectral and temporal data sets have revealed the dynamics of the pathways of de-excitation of the carotenoid excited states. The pathways include energy transfer to bacteriochlorophyll, population of the so-called S* state of the carotenoids, and formation of carotenoid radical cations (Car*+). The investigation has found that excitation energy transfer to bacteriochlorophyll is partitioned through the S1 (1(1)Ag-), S2 (1(1)Bu+), and S* states of the different carotenoids to varying degrees. This is understood through a consideration of the

Comparative analysis of Mycobacterium and related Actinomycetes yields insight into the evolution of Mycobacterium tuberculosis pathogenesis.

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McGuire, Abigail Manson; Weiner, Brian; Park, Sang Tae; Wapinski, Ilan; Raman, Sahadevan; Dolganov, Gregory; Peterson, Matthew; Riley, Robert; Zucker, Jeremy; Abeel, Thomas; White, Jared; Sisk, Peter; Stolte, Christian; Koehrsen, Mike; Yamamoto, Robert T; Iacobelli-Martinez, Milena; Kidd, Matthew J; Maer, Andreia M; Schoolnik, Gary K; Regev, Aviv; Galagan, James

2012-03-28

The sequence of the pathogen Mycobacterium tuberculosis (Mtb) strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org), including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org.

Insights into the mechanisms on chemical reactions: reaction paths for chemical reactions

International Nuclear Information System (INIS)

Dunning, T.H. Jr.; Rosen, E.; Eades, R.A.

1987-01-01

We report reaction paths for two prototypical chemical reactions: Li + HF, an electron transfer reaction, and OH + H 2 , an abstraction reaction. In the first reaction we consider the connection between the energetic terms in the reaction path Hamiltonian and the electronic changes which occur upon reaction. In the second reaction we consider the treatment of vibrational effects in chemical reactions in the reaction path formalism. 30 refs., 9 figs

Comparative analysis of mycobacterium and related actinomycetes yields insight into the evolution of mycobacterium tuberculosis pathogenesis

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McGuire Abigail

2012-03-01

Full Text Available Abstract Background The sequence of the pathogen Mycobacterium tuberculosis (Mtb strain H37Rv has been available for over a decade, but the biology of the pathogen remains poorly understood. Genome sequences from other Mtb strains and closely related bacteria present an opportunity to apply the power of comparative genomics to understand the evolution of Mtb pathogenesis. We conducted a comparative analysis using 31 genomes from the Tuberculosis Database (TBDB.org, including 8 strains of Mtb and M. bovis, 11 additional Mycobacteria, 4 Corynebacteria, 2 Streptomyces, Rhodococcus jostii RHA1, Nocardia farcinia, Acidothermus cellulolyticus, Rhodobacter sphaeroides, Propionibacterium acnes, and Bifidobacterium longum. Results Our results highlight the functional importance of lipid metabolism and its regulation, and reveal variation between the evolutionary profiles of genes implicated in saturated and unsaturated fatty acid metabolism. It also suggests that DNA repair and molybdopterin cofactors are important in pathogenic Mycobacteria. By analyzing sequence conservation and gene expression data, we identify nearly 400 conserved noncoding regions. These include 37 predicted promoter regulatory motifs, of which 14 correspond to previously validated motifs, as well as 50 potential noncoding RNAs, of which we experimentally confirm the expression of four. Conclusions Our analysis of protein evolution highlights gene families that are associated with the adaptation of environmental Mycobacteria to obligate pathogenesis. These families include fatty acid metabolism, DNA repair, and molybdopterin biosynthesis. Our analysis reinforces recent findings suggesting that small noncoding RNAs are more common in Mycobacteria than previously expected. Our data provide a foundation for understanding the genome and biology of Mtb in a comparative context, and are available online and through TBDB.org.

Feedback control architecture and the bacterial chemotaxis network.

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Abdullah Hamadeh

2011-05-01

Full Text Available Bacteria move towards favourable and away from toxic environments by changing their swimming pattern. This response is regulated by the chemotaxis signalling pathway, which has an important feature: it uses feedback to 'reset' (adapt the bacterial sensing ability, which allows the bacteria to sense a range of background environmental changes. The role of this feedback has been studied extensively in the simple chemotaxis pathway of Escherichia coli. However it has been recently found that the majority of bacteria have multiple chemotaxis homologues of the E. coli proteins, resulting in more complex pathways. In this paper we investigate the configuration and role of feedback in Rhodobacter sphaeroides, a bacterium containing multiple homologues of the chemotaxis proteins found in E. coli. Multiple proteins could produce different possible feedback configurations, each having different chemotactic performance qualities and levels of robustness to variations and uncertainties in biological parameters and to intracellular noise. We develop four models corresponding to different feedback configurations. Using a series of carefully designed experiments we discriminate between these models and invalidate three of them. When these models are examined in terms of robustness to noise and parametric uncertainties, we find that the non-invalidated model is superior to the others. Moreover, it has a 'cascade control' feedback architecture which is used extensively in engineering to improve system performance, including robustness. Given that the majority of bacteria are known to have multiple chemotaxis pathways, in this paper we show that some feedback architectures allow them to have better performance than others. In particular, cascade control may be an important feature in achieving robust functionality in more complex signalling pathways and in improving their performance.

Improving photofermentative biohydrogen production by using intermittent ultrasonication and combined industrial effluents from palm oil, pulp and paper mills

International Nuclear Information System (INIS)

Budiman, Pretty Mori; Wu, Ta Yeong; Ramanan, Ramakrishnan Nagasundara; Md Jahim, Jamaliah

2017-01-01

Highlights: • Intermittent ultrasonication onto broth improved biohydrogen production. • A20T10 treatment produced 14.438 mL H_2/mL_m_e_d_i_u_m with 7.412% light efficiency. • Excessive ultrasonication (>306.1 J/mL) inhibited biohydrogen production. - Abstract: An ultrasonication technique was applied intermittently onto photofermentation broth during the first six hours of photofermentation to improve biohydrogen production by using Rhodobacter sphaeroides NCIMB8253. In this research, photofermentation broth consisted of a combination of palm oil (25%, v/v), pulp and paper (75%, v/v) mill effluents as well as liquid inoculum. The effects of amplitude (10, 20 and 30%, A) and ultrasonication duration (5, 10 and 15 min, T) were investigated in terms of their influences on photofermentative biohydrogen yield and total chemical oxygen demand (COD_t_o_t_a_l) removal. The recommended ultrasonication parameters were found at the middle range of amplitude and duration (A20T10). Using A20T10 intermittent treatment, the production of biohydrogen could be maximized up to 14.438 mL H_2/mL_m_e_d_i_u_m with a COD_t_o_t_a_l removal and light efficiency of 52.2% and 7.412%, respectively. By comparing the treatment without intermittent ultrasonication, an increase of biohydrogen yield by 44.6% was achieved in A20T10 treatment. A total energy input of 306.1 J/mL (A20T10 treatment) was supplied to improve substrate consumption and light distribution during the photofermentation, which led to the increase of biohydrogen yield.

[Improving Agricultural Safety of Soils Contaminated with Polycyclic Aromatic Hydrocarbons by In Situ Bioremediation].

Science.gov (United States)

Jiao, Hai-huan; Pan, Jian-gang; Xu, Shena-jun; Bai, Zhi-hui; Wang, Dong; Huang, Zhan-bin

2015-08-01

In order to reduce the risk of enrichment of polycyclic aromatic hydrocarbons (PAHs) in crops, reduce the potential hazards of food-sourced PAHs to human and increase the agricultural safety of PAHs contaminated soils, the bio-augmented removal of polycyclic aromatic hydrocarbons (PAHs) was investigated through in situ remediation by introducing Rhodobacter sphaeroides (RS) into the agricultural soil contaminated by PAHs. The 50-times diluted RS was sprayed on leaf surface (in area B) or irrigated to roots (in area D). The treatment of spraying water of the equal amount was taken as the control (A) and the wheat field without any treatment as the blank (CK). Treatments were conducted since wheat seeding. Soil and wheat samples were collected in the mature period to analyze the changes of community structure of the soil microorganisms and the concentration of PAHs in soils and investigate the strengthening and restoration effects of RS on PAHs contaminated soils. Compared to the CK Area, the areas B and D revealed that the variation ratio of phospholipid fatty acids (PLFAs) that were the biomarker of soil microorganisms was 29.6%, and the ratio of total PAHs removed was increased 1.59 times and 1.68 times, respectively. The dry weight of wheat grain of 50 spikes was increased by 8.95% and 12.5%, respectively, and the enrichment factor of total PAHs was decreased by 58.9% and 62.2% respectively in the wheat grains. All the results suggested that RS reduced enrichment of PAHs in wheat grains and increased wheat yield, which had great exploitation and utilization potentiality in repairing and improving the agricultural safety of the soils contaminated with PHAs.

Volume changes and electrostriction in the primary photoreactions of various photosynthetic systems: estimation of dielectric coefficient in bacterial reaction centers and of the observed volume changes with the Drude-Nernst equation.

Science.gov (United States)

Mauzerall, David; Hou, Jian-Min; Boichenko, Vladimir A

2002-01-01

Photoacoustics (PA) allows the determination of enthalpy and volume changes of photoreactions in photosynthetic reaction centers on the 0.1-10 mus time scale. These include the bacterial centers from Rb. sphaeroides, PS I and PS II centers from Synechocystis and in whole cells. In vitro and in vivo PA data on PS I and PS II revealed that both the volume change (-26 A(3)) and reaction enthalpy (-0.4 eV) in PS I are the same as those in the bacterial centers. However the volume change in PS II is small and the enthalpy far larger, -1 eV. Assigning the volume changes to electrostriction allows a coherent explanation of these observations. One can explain the large volume decrease in the bacterial centers with an effective dielectric coefficient of approximately 4. This is a unique approach to this parameter so important in estimation of protein energetics. The value of the volume contraction for PS I can only be explained if the acceptor is the super- cluster (Fe(4)S(4))(Cys(4)) with charge change from -1 to -2. The small volume change in PS II is explained by sub-mus electron transfer from Y(Z) anion to P(680) cation, in which charge is only moved from the Y(Z) anion to the Q(A) with no charge separation or with rapid proton transfer from oxidized Y(Z) to a polar region and thus very little change in electrostriction. At more acid pH equally rapid proton transfer from a neighboring histidine to a polar region may be caused by the electric field of the P(680) cation.

Functional assignment of gene AAC16202.1 from Rhodobacter capsulatus SB1003: new insights into the bacterial SDR sorbitol dehydrogenases family.

Science.gov (United States)

Sola-Carvajal, Agustín; García-García, María Inmaculada; Sánchez-Carrón, Guiomar; García-Carmona, Francisco; Sánchez-Ferrer, Alvaro

2012-11-01

Short-chain dehydrogenases/reductases (SDR) constitute one of the largest enzyme superfamilies with over 60,000 non-redundant sequences in the database, many of which need a correct functional assignment. Among them, the gene AAC16202.1 (NCBI) from Rhodobacter capsulatus SB1003 has been assigned in Uniprot both as a sorbitol dehydrogenase (#D5AUY1) and, as an N-acetyl-d-mannosamine dehydrogenase (#O66112), both enzymes being of biotechnological interest. When the gene was overexpressed in Escherichia coli Rosetta (DE3)pLys, the purified enzyme was not active toward N-acetyl-d-mannosamine, whereas it was active toward d-sorbitol and d-fructose. However, the relative activities toward xylitol and l-iditol (0.45 and 6.9%, respectively) were low compared with that toward d-sorbitol. Thus, the enzyme could be considered sorbitol dehydrogenase (SDH) with very low activity toward xylitol, which could increase its biotechnological interest for determining sorbitol without the unspecific cross-determination of added xylitol in food and pharma compositions. The tetrameric enzyme (120 kDa) showed similar catalytic efficiency (2.2 × 10(3) M(-1) s(-1)) to other sorbitol dehydrogenases for d-sorbitol, with an optimum pH of 9.0 and an optimum temperature of 37 °C. The enzyme was also more thermostable than other reported SDH, ammonium sulfate being the best stabilizer in this respect, increasing the melting temperature (T(m)) up to 52.9 °C. The enzyme can also be considered as a new member of the Zn(2+) independent SDH family since no effect on activity was detected in the presence of divalent cations or chelating agents. Finally, its in silico analysis enabled the specific conserved sequence blocks that are the fingerprints of bacterial sorbitol dehydrogenases and mainly located at C-terminal of the protein, to be determined for the first time. This knowledge will facilitate future data curation of present databases and a better functional assignment of newly described

Biomimetic Membranes for Multi-Redox Center Proteins

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Renate L. C. Naumann

2016-03-01

Full Text Available His-tag technology was applied for biosensing purposes involving multi-redox center proteins (MRPs. An overview is presented on various surfaces ranging from flat to spherical and modified with linker molecules with nitrile-tri-acetic acid (NTA terminal groups to bind his-tagged proteins in a strict orientation. The bound proteins are submitted to in situ dialysis in the presence of lipid micelles to form a so-called protein-tethered bilayer lipid membrane (ptBLM. MRPs, such as the cytochrome c oxidase (CcO from R. sphaeroides and P. denitrificans, as well as photosynthetic reactions centers (RCs from R. sphaeroides, were thus investigated. Electrochemical and surface-sensitive optical techniques, such as surface plasmon resonance, surface plasmon-enhanced fluorescence, surface-enhanced infrared absorption spectroscopy (SEIRAS and surface-enhanced resonance Raman spectroscopy (SERRS, were employed in the case of the ptBLM structure on flat surfaces. Spherical particles ranging from µm size agarose gel beads to nm size nanoparticles modified in a similar fashion were called proteo-lipobeads (PLBs. The particles were investigated by laser-scanning confocal fluorescence microscopy (LSM and UV/Vis spectroscopy. Electron and proton transfer through the proteins were demonstrated to take place, which was strongly affected by the membrane potential. MRPs can thus be used for biosensing purposes under quasi-physiological conditions.

WiseScaffolder: an algorithm for the semi-automatic scaffolding of Next Generation Sequencing data.

Science.gov (United States)

Farrant, Gregory K; Hoebeke, Mark; Partensky, Frédéric; Andres, Gwendoline; Corre, Erwan; Garczarek, Laurence

2015-09-03

The sequencing depth provided by high-throughput sequencing technologies has allowed a rise in the number of de novo sequenced genomes that could potentially be closed without further sequencing. However, genome scaffolding and closure require costly human supervision that often results in genomes being published as drafts. A number of automatic scaffolders were recently released, which improved the global quality of genomes published in the last few years. Yet, none of them reach the efficiency of manual scaffolding. Here, we present an innovative semi-automatic scaffolder that additionally helps with chimerae resolution and generates valuable contig maps and outputs for manual improvement of the automatic scaffolding. This software was tested on the newly sequenced marine cyanobacterium Synechococcus sp. WH8103 as well as two reference datasets used in previous studies, Rhodobacter sphaeroides and Homo sapiens chromosome 14 (http://gage.cbcb.umd.edu/). The quality of resulting scaffolds was compared to that of three other stand-alone scaffolders: SSPACE, SOPRA and SCARPA. For all three model organisms, WiseScaffolder produced better results than other scaffolders in terms of contiguity statistics (number of genome fragments, N50, LG50, etc.) and, in the case of WH8103, the reliability of the scaffolds was confirmed by whole genome alignment against a closely related reference genome. We also propose an efficient computer-assisted strategy for manual improvement of the scaffolding, using outputs generated by WiseScaffolder, as well as for genome finishing that in our hands led to the circularization of the WH8103 genome. Altogether, WiseScaffolder proved more efficient than three other scaffolders for both prokaryotic and eukaryotic genomes and is thus likely applicable to most genome projects. The scaffolding pipeline described here should be of particular interest to biologists wishing to take advantage of the high added value of complete genomes.

Impact of mutations on the midpoint potential of the [4Fe-4S]+1,+2 cluster and on catalytic activity in electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO).

Science.gov (United States)

Usselman, Robert J; Fielding, Alistair J; Frerman, Frank E; Watmough, Nicholas J; Eaton, Gareth R; Eaton, Sandra S

2008-01-08

Electron-transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is an iron-sulfur flavoprotein that accepts electrons from electron-transfer flavoprotein (ETF) and reduces ubiquinone from the Q-pool. ETF-QO contains a single [4Fe-4S]2+,1+ cluster and one equivalent of FAD, which are diamagnetic in the isolated oxidized enzyme and can be reduced to paramagnetic forms by enzymatic donors or dithionite. Mutations were introduced by site-directed mutagenesis of amino acids in the vicinity of the iron-sulfur cluster of Rhodobacter sphaeroides ETF-QO. Y501 and T525 are equivalent to Y533 and T558 in the porcine ETF-QO. In the porcine protein, these residues are within hydrogen-bonding distance of the Sgamma of the cysteine ligands to the iron-sulfur cluster. Y501F, T525A, and Y501F/T525A substitutions were made to determine the effects on midpoint potential, activity, and EPR spectral properties of the cluster. The integrity of the mutated proteins was confirmed by optical spectra, EPR g-values, and spin-lattice relaxation rates, and the cluster to flavin point-dipole distance was determined by relaxation enhancement. Potentiometric titrations were monitored by changes in the CW EPR signals of the cluster and semiquinone. Single mutations decreased the midpoint potentials of the iron-sulfur cluster from +37 mV for wild type to -60 mV for Y501F and T525A and to -128 mV for Y501F/T525A. Lowering the midpoint potential resulted in a decrease in steady-state ubiquinone reductase activity and in ETF semiquinone disproportionation. The decrease in activity demonstrates that reduction of the iron-sulfur cluster is required for activity. There was no detectable effect of the mutations on the flavin midpoint potentials.

Impact of Mutations on the Midpoint Potential of the [4Fe-4S]+1,+2 Cluster and on Catalytic Activity in Electron Transfer Flavoprotein-ubiquinone Oxidoreductase (ETF-QO)†

Science.gov (United States)

Usselman, Robert J.; Fielding, Alistair J.; Frerman, Frank E.; Watmough, Nicholas J.; Eaton, Gareth R.; Eaton, Sandra S.

2011-01-01

Electron transfer flavoprotein - ubiquinone oxidoreductase (ETF-QO) is an iron-sulfur flavoprotein that accepts electrons from electron-transfer flavoprotein (ETF) and reduces ubiquinone from the Q-pool. ETF-QO contains a single [4Fe-4S]2+,1+ cluster and one equivalent of FAD, which are diamagnetic in the isolated oxidized enzyme and can be reduced to paramagnetic forms by enzymatic donors or dithionite. Mutations were introduced by site-directed mutagenesis of amino acids in the vicinity of the iron-sulfur cluster of Rhodobacter sphaeroides ETF-QO. Y501 and T525 are equivalent to Y533 and T558 in the porcine ETF-QO. In the porcine protein, these residues are within hydrogen bonding distance of the Sγ of the cysteine ligands to the iron-sulfur cluster. Y501F, T525A, and Y501F/T525A substitutions were made to determine the effects on midpoint potential, activity, and EPR spectral properties of the cluster. The integrity of the mutated proteins was confirmed by optical spectra, EPR g-values, and spin-lattice relaxation rates, and the cluster to flavin point-dipole distance was determined by relaxation enhancement. Potentiometric titrations were monitored by changes in the CW EPR signals of the cluster and semiquinone. Single mutations decreased the mid-point potentials of the iron-sulfur cluster from +37 mV for wild type to −60 mV for Y501F and T525A and to −128 mV for Y501F/T525A. Lowering the midpoint potential resulted in a decrease in steady-state ubiquinone reductase activity and in ETF semiquinone disproportionation. The decrease in activity demonstrates that reduction of the iron-sulfur cluster is required for activity. There was no detectable effect of the mutations on the flavin midpoint potentials. PMID:18069858

Static and dynamic protein impact on electronic properties of light-harvesting complex LH2.

Science.gov (United States)

Zerlauskiene, O; Trinkunas, G; Gall, A; Robert, B; Urboniene, V; Valkunas, L

2008-12-11

A comparative analysis of the temperature dependence of the absorption spectra of the LH2 complexes from different species of photosynthetic bacteria, i.e., Rhodobacter sphaeroides, Rhodoblastus acidophilus, and Phaeospirillum molischianum, was performed in the temperature range from 4 to 300 K. Qualitatively, the temperature dependence is similar for all of the species studied. The spectral bandwidths of both B800 and B850 bands increases with temperature while the band positions shift in opposite directions: the B800 band shifts slightly to the red while the B850 band to the blue. These results were analyzed using the modified Redfield theory based on the exciton model. The main conclusion drawn from the analysis was that the spectral density function (SDF) is the main factor underlying the strength of the temperature dependence of the bandwidths for the B800 and B850 electronic transitions, while the bandwidths themselves are defined by the corresponding inhomogeneous distribution function (IDF). Slight variation of the slope of the temperature dependence of the bandwidths between species can be attributed to the changes of the values of the reorganization energies and characteristic frequencies determining the SDF. To explain the shift of the B850 band position with temperature, which is unusual for the conventional exciton model, a temperature dependence of the IDF must be postulated. This dependence can be achieved within the framework of the modified (dichotomous) exciton model. The slope of the temperature dependence of the B850 bandwidth is then defined by the value of the reorganization energy and by the difference between the transition energies of the dichotomous states of the pigment molecules. The equilibration factor between these dichotomous states mainly determines the temperature dependence of the peak shift.

Discovery of a Bacterial 5-Methylcytosine Deaminase

Science.gov (United States)

2015-01-01

5-Methylcytosine is found in all domains of life, but the bacterial cytosine deaminase from Escherichia coli (CodA) will not accept 5-methylcytosine as a substrate. Since significant amounts of 5-methylcytosine are produced in both prokaryotes and eukaryotes, this compound must eventually be catabolized and the fragments recycled by enzymes that have yet to be identified. We therefore initiated a comprehensive phylogenetic screen for enzymes that may be capable of deaminating 5-methylcytosine to thymine. From a systematic analysis of sequence homologues of CodA from thousands of bacterial species, we identified putative cytosine deaminases where a “discriminating” residue in the active site, corresponding to Asp-314 in CodA from E. coli, was no longer conserved. Representative examples from Klebsiella pneumoniae (locus tag: Kpn00632), Rhodobacter sphaeroides (locus tag: Rsp0341), and Corynebacterium glutamicum (locus tag: NCgl0075) were demonstrated to efficiently deaminate 5-methylcytosine to thymine with values of kcat/Km of 1.4 × 105, 2.9 × 104, and 1.1 × 103 M–1 s–1, respectively. These three enzymes also catalyze the deamination of 5-fluorocytosine to 5-fluorouracil with values of kcat/Km of 1.2 × 105, 6.8 × 104, and 2.0 × 102 M–1 s–1, respectively. The three-dimensional structure of Kpn00632 was determined by X-ray diffraction methods with 5-methylcytosine (PDB id: 4R85), 5-fluorocytosine (PDB id: 4R88), and phosphonocytosine (PDB id: 4R7W) bound in the active site. When thymine auxotrophs of E. coli express these enzymes, they are capable of growth in media lacking thymine when supplemented with 5-methylcytosine. Expression of these enzymes in E. coli is toxic in the presence of 5-fluorocytosine, due to the efficient transformation to 5-fluorouracil. PMID:25384249

Reconstruction of the core and extended regulons of global transcription factors.

Directory of Open Access Journals (Sweden)

Yann S Dufour

2010-07-01

Full Text Available The processes underlying the evolution of regulatory networks are unclear. To address this question, we used a comparative genomics approach that takes advantage of the large number of sequenced bacterial genomes to predict conserved and variable members of transcriptional regulatory networks across phylogenetically related organisms. Specifically, we developed a computational method to predict the conserved regulons of transcription factors across alpha-proteobacteria. We focused on the CRP/FNR super-family of transcription factors because it contains several well-characterized members, such as FNR, FixK, and DNR. While FNR, FixK, and DNR are each proposed to regulate different aspects of anaerobic metabolism, they are predicted to recognize very similar DNA target sequences, and they occur in various combinations among individual alpha-proteobacterial species. In this study, the composition of the respective FNR, FixK, or DNR conserved regulons across 87 alpha-proteobacterial species was predicted by comparing the phylogenetic profiles of the regulators with the profiles of putative target genes. The utility of our predictions was evaluated by experimentally characterizing the FnrL regulon (a FNR-type regulator in the alpha-proteobacterium Rhodobacter sphaeroides. Our results show that this approach correctly predicted many regulon members, provided new insights into the biological functions of the respective regulons for these regulators, and suggested models for the evolution of the corresponding transcriptional networks. Our findings also predict that, at least for the FNR-type regulators, there is a core set of target genes conserved across many species. In addition, the members of the so-called extended regulons for the FNR-type regulators vary even among closely related species, possibly reflecting species-specific adaptation to environmental and other factors. The comparative genomics approach we developed is readily applicable to other

Improved biohydrogen production and treatment of pulp and paper mill effluent through ultrasonication pretreatment of wastewater

International Nuclear Information System (INIS)

Hay, Jacqueline Xiao Wen; Wu, Ta Yeong; Juan, Joon Ching; Md Jahim, Jamaliah

2015-01-01

Highlights: • Ultrasonication facilitated the reuse of PPME in biohydrogen production. • Ultrasonication at an amplitude of 60% for 45 min produced the highest biohydrogen. • Ultrasonication increased the solubilization of PPME. • Higher net savings were obtained in pretreated PPME compared to raw PPME. - Abstract: Pulp and paper mill effluent (PPME), a rich cellulosic material, was found to have great potential for biohydrogen production through a photofermentation process. However, pretreatments were needed for degrading the complex structure of PPME before biohydrogen production. The aim of this study was to gain further insight into the effect of an ultrasonication process on PPME as a pretreatment method and on photofermentative biohydrogen production using Rhodobacter sphaeroides NCIMB. The ultrasonication amplitudes and times were varied between 30–90% and 15–60 min, respectively, and no dilution or nutrient supplementation was introduced during the biohydrogen production process. A higher biohydrogen yield, rate, light efficiency and COD removal efficiency were attained in conditions using ultrasonicated PPME. Among these different pretreatment conditions, PPME with ultrasonication pretreatment employing an amplitude of 60% and time of 45 min (A60:T45) gave the highest yield and rate of 5.77 mL H_2/mL medium and 0.077 mL H_2/mL h, respectively, while the raw PPME without ultrasonication showed a significantly lower yield and rate of 1.10 mL H_2/mL medium and 0.015 mL H_2/mL h, respectively. The results of this study demonstrated the potential of using ultrasonication as a pretreatment for PPME because the yield and rate of biohydrogen production were highly enhanced compared to the raw PPME. Economic analysis was also performed in this study, and in comparison with raw PPME, the highest net saving was $0.2132 for A60:T45.

光合成細菌の塩ストレス応答に関する研究

OpenAIRE

都築, 稔

2005-01-01

地球上の自然環境は極めて多様であり、生命が生きていくには過酷とも思える環境においても適応可能な生物がおり、その適応機構は非常に興味深い問題である。環境中の高塩濃度を感知して生育するために、細菌はいくつかの恒常的かつ誘導的な適応機構を有している。例えば、塩ストレスに応答して細胞内に低分子有機化合物(適合溶質)を蓄積することが知られている。一方、塩ストレス環境に適応するために働いているいくつかの誘導タンパク質に関する報告もなされている。しかし、シグナル伝達経路はもちろん、制御および適応機構全般に関しても未だに分かっていないことが多い。　Rhodobacter sphaeroides (R. sphaeroides)はα-3subdivisionに属するグラム陰性細菌であり、極めて多様な環境で生育できることが知られている。好気条件では酸素呼吸により、嫌気条件では光合成をエネルギーとして生育することが可能である。塩ストレスへの適応としては、本菌は淡水より単離されたものの、培地NaCl濃度が4%(0.68M)まで生育が可能である。また、塩ストレスに応答してトレハロースを細胞内に適合溶質とし...

Biotransformation of isoeugenol to vanillin by Pseudomonas putida IE27 cells.

Science.gov (United States)

Yamada, Mamoru; Okada, Yukiyoshi; Yoshida, Toyokazu; Nagasawa, Toru

2007-01-01

The ability to produce vanillin and/or vanillic acid from isoeugenol was screened using resting cells of various bacteria. The vanillin- and/or vanillic-acid-producing activities were observed in strains belonging to the genera Achromobacter, Aeromonas, Agrobacerium, Alcaligenes, Arthrobacter, Bacillus, Micrococcus, Pseudomonas, Rhodobacter, and Rhodococcus. Strain IE27, a soil isolate showing the highest vanillin-producing activity, was identified as Pseudomonas putida. We optimized the culture and reaction conditions for vanillin production from isoeugenol using P. putida IE27 cells. The vanillin-producing activity was induced by adding isoeugenol to the culture medium but not vanillin or eugenol. Under the optimized reaction conditions, P. putida IE27 cells produced 16.1 g/l vanillin from 150 mM isoeugenol, with a molar conversion yield of 71% at 20 degrees C after a 24-h incubation in the presence of 10% (v/v) dimethyl sulfoxide.

Genetically Modified Bacteria for Fuel Production: Development of Rhodobacteria as a Versatile Platform for Fuels Production

Energy Technology Data Exchange (ETDEWEB)

None

2010-07-01

Electrofuels Project: Penn State is genetically engineering bacteria called Rhodobacter to use electricity or electrically generated hydrogen to convert carbon dioxide into liquid fuels. Penn State is taking genes from oil-producing algae called Botryococcus braunii and putting them into Rhodobacter to produce hydrocarbon molecules, which closely resemble gasoline. Penn State is developing engineered tanks to support microbial fuel production and determining the most economical way to feed the electricity or hydrogen to the bacteria, including using renewable sources of power like solar energy.

Reaction time for trimolecular reactions in compartment-based reaction-diffusion models

Science.gov (United States)

Li, Fei; Chen, Minghan; Erban, Radek; Cao, Yang

2018-05-01

Trimolecular reaction models are investigated in the compartment-based (lattice-based) framework for stochastic reaction-diffusion modeling. The formulae for the first collision time and the mean reaction time are derived for the case where three molecules are present in the solution under periodic boundary conditions. For the case of reflecting boundary conditions, similar formulae are obtained using a computer-assisted approach. The accuracy of these formulae is further verified through comparison with numerical results. The presented derivation is based on the first passage time analysis of Montroll [J. Math. Phys. 10, 753 (1969)]. Montroll's results for two-dimensional lattice-based random walks are adapted and applied to compartment-based models of trimolecular reactions, which are studied in one-dimensional or pseudo one-dimensional domains.

Reaction Decoder Tool (RDT): extracting features from chemical reactions.

Science.gov (United States)

Rahman, Syed Asad; Torrance, Gilliean; Baldacci, Lorenzo; Martínez Cuesta, Sergio; Fenninger, Franz; Gopal, Nimish; Choudhary, Saket; May, John W; Holliday, Gemma L; Steinbeck, Christoph; Thornton, Janet M

2016-07-01

Extracting chemical features like Atom-Atom Mapping (AAM), Bond Changes (BCs) and Reaction Centres from biochemical reactions helps us understand the chemical composition of enzymatic reactions. Reaction Decoder is a robust command line tool, which performs this task with high accuracy. It supports standard chemical input/output exchange formats i.e. RXN/SMILES, computes AAM, highlights BCs and creates images of the mapped reaction. This aids in the analysis of metabolic pathways and the ability to perform comparative studies of chemical reactions based on these features. This software is implemented in Java, supported on Windows, Linux and Mac OSX, and freely available at https://github.com/asad/ReactionDecoder : asad@ebi.ac.uk or s9asad@gmail.com. © The Author 2016. Published by Oxford University Press.

Quinone reduction via secondary B-branch electron transfer in mutant bacterial reaction centers.

Science.gov (United States)

Laible, Philip D; Kirmaier, Christine; Udawatte, Chandani S M; Hofman, Samuel J; Holten, Dewey; Hanson, Deborah K

2003-02-18

Symmetry-related branches of electron-transfer cofactors-initiating with a primary electron donor (P) and terminating in quinone acceptors (Q)-are common features of photosynthetic reaction centers (RC). Experimental observations show activity of only one of them-the A branch-in wild-type bacterial RCs. In a mutant RC, we now demonstrate that electron transfer can occur along the entire, normally inactive B-branch pathway to reduce the terminal acceptor Q(B) on the time scale of nanoseconds. The transmembrane charge-separated state P(+)Q(B)(-) is created in this manner in a Rhodobacter capsulatus RC containing the F(L181)Y-Y(M208)F-L(M212)H-W(M250)V mutations (YFHV). The W(M250)V mutation quantitatively blocks binding of Q(A), thereby eliminating Q(B) reduction via the normal A-branch pathway. Full occupancy of the Q(B) site by the native UQ(10) is ensured (without the necessity of reconstitution by exogenous quinone) by purification of RCs with the mild detergent, Deriphat 160-C. The lifetime of P(+)Q(B)(-) in the YFHV mutant RC is >6 s (at pH 8.0, 298 K). This charge-separated state is not formed upon addition of competitive inhibitors of Q(B) binding (terbutryn or stigmatellin). Furthermore, this lifetime is much longer than the value of approximately 1-1.5 s found when P(+)Q(B)(-) is produced in the wild-type RC by A-side activity alone. Collectively, these results demonstrate that P(+)Q(B)(-) is formed solely by activity of the B-branch carriers in the YFHV RC. In comparison, P(+)Q(B)(-) can form by either the A or B branches in the YFH RC, as indicated by the biexponential lifetimes of approximately 1 and approximately 6-10 s. These findings suggest that P(+)Q(B)(-) states formed via the two branches are distinct and that P(+)Q(B)(-) formed by the B side does not decay via the normal (indirect) pathway that utilizes the A-side cofactors when present. These differences may report on structural and energetic factors that further distinguish the functional

Nuclear reactions

International Nuclear Information System (INIS)

Lane, A.M.

1980-01-01

In reviewing work at Harwell over the past 25 years on nuclear reactions it is stated that a balance has to be struck in both experiment and theory between work on cross-sections of direct practical relevance to reactors and on those relevant to an overall understanding of reaction processes. The compound nucleus and direct process reactions are described. Having listed the contributions from AERE, Harwell to developments in nuclear reaction research in the period, work on the optical model, neutron capture theory, reactions at doorway states with fine structure, and sum-rules for spectroscopic factors are considered in more detail. (UK)

Extent of reaction in open systems with multiple heterogeneous reactions

Science.gov (United States)

Friedly, John C.

1991-01-01

The familiar batch concept of extent of reaction is reexamined for systems of reactions occurring in open systems. Because species concentrations change as a result of transport processes as well as reactions in open systems, the extent of reaction has been less useful in practice in these applications. It is shown that by defining the extent of the equivalent batch reaction and a second contribution to the extent of reaction due to the transport processes, it is possible to treat the description of the dynamics of flow through porous media accompanied by many chemical reactions in a uniform, concise manner. This approach tends to isolate the reaction terms among themselves and away from the model partial differential equations, thereby enabling treatment of large problems involving both equilibrium and kinetically controlled reactions. Implications on the number of coupled partial differential equations necessary to be solved and on numerical algorithms for solving such problems are discussed. Examples provided illustrate the theory applied to solute transport in groundwater flow.

ReactionMap: an efficient atom-mapping algorithm for chemical reactions.

Science.gov (United States)

Fooshee, David; Andronico, Alessio; Baldi, Pierre

2013-11-25

Large databases of chemical reactions provide new data-mining opportunities and challenges. Key challenges result from the imperfect quality of the data and the fact that many of these reactions are not properly balanced or atom-mapped. Here, we describe ReactionMap, an efficient atom-mapping algorithm. Our approach uses a combination of maximum common chemical subgraph search and minimization of an assignment cost function derived empirically from training data. We use a set of over 259,000 balanced atom-mapped reactions from the SPRESI commercial database to train the system, and we validate it on random sets of 1000 and 17,996 reactions sampled from this pool. These large test sets represent a broad range of chemical reaction types, and ReactionMap correctly maps about 99% of the atoms and about 96% of the reactions, with a mean time per mapping of 2 s. Most correctly mapped reactions are mapped with high confidence. Mapping accuracy compares favorably with ChemAxon's AutoMapper, versions 5 and 6.1, and the DREAM Web tool. These approaches correctly map 60.7%, 86.5%, and 90.3% of the reactions, respectively, on the same data set. A ReactionMap server is available on the ChemDB Web portal at http://cdb.ics.uci.edu .

Reaction path analysis of sodium-water reaction phenomena in support of chemical reaction model development

International Nuclear Information System (INIS)

Kikuchi, Shin; Ohshima, Hiroyuki; Hashimoto, Kenro

2011-01-01

Computational study of the sodium-water reaction at the gas (water) - liquid (sodium) interface has been carried out using ab initio (first-principle) method. A possible reaction channel has been identified for the stepwise OH bond dissociations of a single water molecule. The energetics including the binding energy of a water molecule to the sodium surface, the activation energies of the bond cleavages, and the reaction energies, have been evaluated, and the rate constants of the first and second OH bond-breakings have been compared. The results are used as the basis for constructing the chemical reaction model used in a multi-dimensional sodium-water reaction code, SERAPHIM, being developed by JAEA toward the safety assessment of the steam generator (SG) in a sodium-cooled fast reactor (SFR). (author)

Studies in the reaction dynamics of beam-gas chemiluminescent reactions

International Nuclear Information System (INIS)

Prisant, M.G.

1984-01-01

This thesis develops techniques for the analysis and interpretation of data obtained from beam-gas chemiluminescence experiments. These techniques are applied to experimental studies of atom transfer reactions of the type A + BC → AB + C. A procedure is developed for determining the product rotational alignment in the center-of-mass frame from polarization measurements of chemiluminescent atom-diatom exchange reactions under beam-gas conditions. Knowledge of a vector property of a reaction, such as product alignment, provides information on the disposition of angular momentum by a chemical reaction. Fluorescence polarization and hence product alignment are measured for two prototype reactions. The reaction of metastable calcium atoms with hydrogen-chloride gas yields highly aligned calcium-chloride product which exhibits little variation of alignment with vibrational state. The reaction of ground-state calcium with fluorine gas yields moderately aligned product which shows strong variation of alignment with vibration. A multi-surface direct-interaction model is developed to interpret product alignment and population data. The predictions of this model for the reaction of calcium with fluorine show reasonable agreement with experiment

Procedures for Decomposing a Redox Reaction into Half-Reaction

Science.gov (United States)

Fishtik, Ilie; Berka, Ladislav H.

2005-01-01

A simple algorithm for a complete enumeration of the possible ways a redox reaction (RR) might be uniquely decomposed into half-reactions (HRs) using the response reactions (RERs) formalism is presented. A complete enumeration of the possible ways a RR may be decomposed into HRs is equivalent to a complete enumeration of stoichiometrically…

Microbial treatment of aqueous wastes

International Nuclear Information System (INIS)

Lee, Kang Suk; Chun, Ki Jung; Kim, Kug Chan; Choi, Yong Ho; Kim, Jin Kyu; Kim, In Gyu; Park, Hyo Koo; Lee, Keun Bae

1992-01-01

Uranium accumulated extracellularly on the surface of Rhodobacter capsulata and Rhodospirillum rubrum cells. The rate and extent accumulation were subject to environmental parameter such as pH, temperature, carbon source, trace element and interference by certain cations. Uranium accumulation by the cells was rapid and metabolism was not required for uranium uptake by both organism. Cell-bound uranium reached concentration of 22% (Rhodospirillum rubrum) and 24% (Rhdobacter capsulata)of the dry cell weight, but in the cells grown in the presence of inhibitory concentration of CoCl 2 , cell-bound uranium reached concentration of 27% (Rhodospirillum rubrum) and 29% (Rhodobacter capsulata) of dry cell weight. (Author)

Chemical kinetics and reaction mechanism

International Nuclear Information System (INIS)

Jung, Ou Sik; Park, Youn Yeol

1996-12-01

This book is about chemical kinetics and reaction mechanism. It consists of eleven chapters, which deal with reaction and reaction speed on reaction mechanism, simple reaction by rate expression, reversible reaction and simultaneous reaction, successive reaction, complicated reaction mechanism, assumption for reaction mechanism, transition state theory, successive reaction and oscillating reaction, reaction by solution, research method high except kinetics on reaction mechanism, high reaction of kinetics like pulsed radiolysis.

Reaction energetics on long-range corrected density functional theory: Diels-Alder reactions.

Science.gov (United States)

Singh, Raman K; Tsuneda, Takao

2013-02-15

The possibility of quantitative reaction analysis on the orbital energies of long-range corrected density functional theory (LC-DFT) is presented. First, we calculated the Diels-Alder reaction enthalpies that have been poorly given by conventional functionals including B3LYP functional. As a result, it is found that the long-range correction drastically improves the reaction enthalpies. The barrier height energies were also computed for these reactions. Consequently, we found that dispersion correlation correction is also crucial to give accurate barrier height energies. It is, therefore, concluded that both long-range exchange interactions and dispersion correlations are essentially required in conventional functionals to investigate Diels-Alder reactions quantitatively. After confirming that LC-DFT accurately reproduces the orbital energies of the reactant and product molecules of the Diels-Alder reactions, the global hardness responses, the halves of highest occupied molecular orbital (HOMO)-lowest unoccupied molecular orbital (LUMO) energy gaps, along the intrinsic reaction coordinates of two Diels-Alder reactions were computed. We noticed that LC-DFT results satisfy the maximum hardness rule for overall reaction paths while conventional functionals violate this rule on the reaction pathways. Furthermore, our results also show that the HOMO-LUMO gap variations are close to the reaction enthalpies for these Diels-Alder reactions. Based on these results, we foresee quantitative reaction analysis on the orbital energies. Copyright © 2012 Wiley Periodicals, Inc.

Experimental and numerical reaction analysis on sodium-water chemical reaction field

International Nuclear Information System (INIS)

Deguchi, Yoshihiro; Takata, Takashi; Yamaguchi, Akira; Kikuchi, Shin; Ohshima, Hiroyuki

2015-01-01

In a sodium-cooled fast reactor (SFR), liquid sodium is used as a heat transfer fluid because of its excellent heat transport capability. On the other hand, it has strong chemical reactivity with water vapor. One of the design basis accidents of the SFR is the water leakage into the liquid sodium flow by a breach of heat transfer tubes. This process ends up damages on the heat transport equipment in the SFR. Therefore, the study on sodium-water chemical reactions is of paramount importance for security reasons. This study aims to clarify the sodium-water reaction mechanisms using an elementary reaction analysis. A quasi one-dimensional flame model is applied to a sodium-water counter-flow reaction field. The analysis contains 25 elementary reactions, which consist of 17 H_2-O_2 and 8 Na-H_2O reactions. Temperature and species concentrations in the counter-flow reaction field were measured using laser diagnostics such as LIF and CARS. The main reaction in the experimental conditions is Na+H_2O → NaOH+H and OH is produced by H_2O+H → H_2+OH. It is demonstrated that the reaction model in this study well explains the structure of the sodium-water counter-flow diffusion flame. (author)

Stability of integral membrane proteins under high hydrostatic pressure: the LH2 and LH3 antenna pigment-protein complexes from photosynthetic bacteria.

Science.gov (United States)

Kangur, Liina; Timpmann, Kõu; Freiberg, Arvi

2008-07-03

The bacteriochlorophyll a-containing LH2 and LH3 antenna complexes are the integral membrane proteins that catalyze the photosynthetic process in purple photosynthetic bacteria. The LH2 complex from Rhodobacter sphaeroides shows characteristic strong absorbance at 800 and 850 nm due to the pigment molecules confined in two separate areas of the protein. In the LH3 complex from Rhodopesudomonas acidophila the corresponding bands peak at 800 and 820 nm. Using the bacteriochlorophyll a cofactors as intrinsic probes to monitor local changes in the protein structure, we investigate spectral responses of the antenna complexes to very high hydrostatic pressures up to 2.5 GPa when embedded into natural membrane environment or extracted with detergent. We first demonstrate that high pressure does induce significant alterations to the tertiary structure of the proteins not only in proximity of the 800 nm-absorbing bacteriochlorophyll a molecules known previously (Gall, A.; et al. Biochemistry 2003, 42, 13019) but also of the 850 nm- and 820 nm-absorbing molecules, including breakage of the hydrogen bond they are involved in. The membrane-protected complexes appear more resilient to damaging effects of the compression compared with the complexes extracted into mixed detergent-buffer environment. Increased resistance of the isolated complexes is observed at high protein concentration resulting aggregation as well as when cosolvent (glycerol) is added into the solution. These stability variations correlate with ability of penetration of the surrounding polar solvent (water) into the hydrophobic protein interiors, being thus the principal reason of the pressure-induced denaturation of the proteins. Considerable variability of elastic properties of the isolated complexes was also observed, tentatively assigned to heterogeneous protein packing in detergent micelles. While a number of the isolated complexes release most of their bacteriochlorophyll a content under high pressure

Comparison normal composting with composting using effective microorganisms for poultry carcasses disposal in poultry farms

Directory of Open Access Journals (Sweden)

D. M. Taher

2009-01-01

Full Text Available Composting offers a convenient and environmentally acceptable safe, effective method for the disposal of carcasses as an alternative method to burning, burial and rendering. This study was conducted to evaluate the effects of a natural biological products containing an effective microorganisms namily; Lactic acid bacill (Lactobacillus plantarum; L. casei Streptococcus Lactis., Photosynthetic bacteria (Rhodopseudomonas palustris; Rhodobacter sphaeroides,Yeast (Saccharomyces cerevisiae; Candida utilis Toula, Pichia Jadinii, Actinomycetes (Streptomyces albus; S. griseus., and Fermenting fungi (Aspergillus oryzae; Mucor hiemalis in the composting activity of poultry carcasses. The composting stacks constitute multi alternative layers of wood shaves, hay, poultry carcasses and then wood shaves and so on. The layers have been bypassed with plastic tubes for oxygen supply. Moreover, a petri dishes of salmonella and E. coli colonies were introduced within poultry carcasses layer. After 8 days of the experimental period this study follows the physical properties of the composting process according to its odor intesity, color and pH level as well as the bacterial reisolation from the stored colonies. Results indicate that the biological products increase the temperature of the composting stack (66-68° C with a minimal odors as the pH meters recording 5.4 as compared to the control composting stack (52-64° C and pH 6.8 with offender odors. On the other hand ,the biological product inhibit the bacterial reisolation offers since the 10the day of the experiment, however, in the normal composting stack that periods will prolonged till the 17 days of the experiment. Interestingly, the biological product induce high and rapid digestable rate for the poultry carcasses which shown within 25 days of the experiment, in comparison to the normal composting stack which induce that effects in 60 days. In conclusion, the addition of effective microorganism to the

Thermonuclear reaction listing

International Nuclear Information System (INIS)

Fukai, Yuzo

1993-01-01

The following 10 elements, including T, are well known as nuclear fusion fuels: p, D, T, 3 He, 4 He, 6 Li, 7 Li, 9 Be, 10 B, 11 B, ( 12 C, 13 C), where 12 C and 13 C are considered only in the calculation of Q value. Accordingly the number of the thermonuclear reactions is 55, and 78, if including carbon elements. The reactions have some branches. For the branches having two and three reaction products, the reaction products, Q value and threshold energy are calculated by using a computer. We have investigated those of the branches having more than three products from the papers of Ajzenberg-Selove and so on. And also, by the same papers, we check whether the above mentioned branch has been observed or not. The results are as follows: (I) the number of reactions which have Q 0 branches only with γ ray production, and Q 0 and neutron production is 36(17), and (IV) that of reactions whose branch with Q > 0 does not produce neutrons is 9(3). The value in the parentheses shows the number of the case of the carbon elements. For 55 thermonuclear reactions induced by lighter nuclides than 11 B, the reaction products, the values of Q and threshold energy, and the papers with reaction cross section data are presented in the tables. (author)

Reaction Hamiltonian and state-to-state description of chemical reactions

International Nuclear Information System (INIS)

Ruf, B.A.; Kresin, V.Z.; Lester, W.A. Jr.

1985-08-01

A chemical reaction is treated as a quantum transition from reactants to products. A specific reaction Hamiltonian (in second quantization formalism) is introduced. The approach leads to Franck-Condon-like factor, and adiabatic method in the framework of the nuclear motion problems. The influence of reagent vibrational state on the product energy distribution has been studied following the reaction Hamiltonian method. Two different cases (fixed available energy and fixed translational energy) are distinguished. Results for several biomolecular reactions are presented. 40 refs., 5 figs

Fusion chain reaction - a chain reaction with charged particles

International Nuclear Information System (INIS)

Peres, A.; Shvarts, D.

1975-01-01

When a DT-plasma is compressed to very high density, the particles resulting from nuclear reactions give their energy mostly to D and T ions, by nuclear collisions, rather than to electrons as usual. Fusion can thus proceed as a chain reaction, without the need of thermonuclear temperatures. In this paper, we derive relations for the suprathermal ion population created by a fusion reaction. Numerical integration of these equations shows that a chain reaction can proceed in a cold infinite DT-plasma at densities above 8.4x10 27 ions.cm -3 . Seeding the plasma with a small amount of 6 Li reduces the critical density to 7.2x10 27 ions.cm -3 (140000times the normal solid density). (author)

A dynamical theory of incomplete fusion reactions: The breakup-fusion reaction approach

International Nuclear Information System (INIS)

Udagawa, T.

1984-01-01

A dynamical theory of partial fusion reactions is presented, which may fill the gap between direct and compound nuclear reaction theories. With the new theory one can calculate partial fusion taking place in three-body (and many more) channels reached via direct reactions, e.g., breakup and knockout reactions. The authors present first the results for the cross section for such reactions, taking as an example breakup followed by fusion. They then discuss a physical picture which emerges from their theory, namely that the partial fusion reactions, particularly of the massive-transfer type, take place in a so-called deep peripheral region. It is also shown that the deep peripheral character of such processes diminishes as the mass of the fused system decreases, so that the reactions essentially evolve to the usual peripheral character. Finally, comparisons are made of results of numerical calculations with experimental data, taking as an example the /sup 159/Tb(/sup 14/N,α) reaction with E/sub lab/ = 95 MeV

Discussion of the Investigation Method on the Reaction Kinetics of Metallurgical Reaction Engineering

Science.gov (United States)

Du, Ruiling; Wu, Keng; Zhang, Jiazhi; Zhao, Yong

Reaction kinetics of metallurgical physical chemistry which was successfully applied in metallurgy (as ferrous metallurgy, non-ferrous metallurgy) became an important theoretical foundation for subject system of traditional metallurgy. Not only the research methods were very perfect, but also the independent structures and systems of it had been formed. One of the important tasks of metallurgical reaction engineering was the simulation of metallurgical process. And then, the mechanism of reaction process and the conversion time points of different control links should be obtained accurately. Therefore, the research methods and results of reaction kinetics in metallurgical physical chemistry were not very suitable for metallurgical reaction engineering. In order to provide the definite conditions of transmission, reaction kinetics parameters and the conversion time points of different control links for solving the transmission and reaction equations in metallurgical reaction engineering, a new method for researching kinetics mechanisms in metallurgical reaction engineering was proposed, which was named stepwise attempt method. Then the comparison of results between the two methods and the further development of stepwise attempt method were discussed in this paper. As a new research method for reaction kinetics in metallurgical reaction engineering, stepwise attempt method could not only satisfy the development of metallurgical reaction engineering, but also provide necessary guarantees for establishing its independent subject system.

Integrating reaction and analysis: investigation of higher-order reactions by cryogenic trapping

Directory of Open Access Journals (Sweden)

Skrollan Stockinger

2013-09-01

Full Text Available A new approach for the investigation of a higher-order reaction by on-column reaction gas chromatography is presented. The reaction and the analytical separation are combined in a single experiment to investigate the Diels–Alder reaction of benzenediazonium-2-carboxylate as a benzyne precursor with various anthracene derivatives, i.e. anthracene, 9-bromoanthracene, 9-anthracenecarboxaldehyde and 9-anthracenemethanol. To overcome limitations of short reaction contact times at elevated temperatures a novel experimental setup was developed involving a cooling trap to achieve focusing and mixing of the reactants at a defined spot in a fused-silica capillary. This trap functions as a reactor within the separation column in the oven of a gas chromatograph. The reactants are sequentially injected to avoid undefined mixing in the injection port. An experimental protocol was developed with optimized injection intervals and cooling times to achieve sufficient conversions at short reaction times. Reaction products were rapidly identified by mass spectrometric detection. This new approach represents a practical procedure to investigate higher-order reactions at an analytical level and it simultaneously provides valuable information for the optimization of the reaction conditions.

Organocatalytic aza-Michael/retro-aza-Michael reaction: pronounced chirality amplification in aza-Michael reaction and racemization via retro-aza-Michael reaction.

Science.gov (United States)

Cai, Yong-Feng; Li, Li; Luo, Meng-Xian; Yang, Ke-Fang; Lai, Guo-Qiao; Jiang, Jian-Xiong; Xu, Li-Wen

2011-05-01

A detailed experimental investigation of an aza-Michael reaction of aniline and chalcone is presented. A series of Cinchona alkaloid-derived organocatalysts with different functional groups were prepared and used in the aza-Michael and retro-aza-Michael reaction. There was an interesting finding that a complete reversal of stereoselectivity when a benzoyl group was introduced to the cinchonine and cinchonidine. The chirality amplification vs. time proceeds in the quinine-derived organocatalyst containing silicon-based bulky group, QN-TBS, -catalyzed aza-Michael reaction under solvent-free conditions. In addition, we have demonstrated for the first time that racemization was occurred in suitable solvents under mild conditions due to retro-aza-Michael reaction of the Michael adduct of aniline with chalcone. These indicate the equilibrium of retro-aza-Michael reaction and aza-Michael reaction produce the happening of chirality amplification in aza-Michael reaction and racemization via retro-aza-Michael reaction under different conditions, which would be beneficial to the development of novel chiral catalysts for the aza-Michael reactions. Copyright © 2011 Wiley-Liss, Inc.

Chemical transport reactions

CERN Document Server

Schäfer, Harald

2013-01-01

Chemical Transport Reactions focuses on the processes and reactions involved in the transport of solid or liquid substances to form vapor phase reaction products. The publication first offers information on experimental and theoretical principles and the transport of solid substances and its special applications. Discussions focus on calculation of the transport effect of heterogeneous equilibria for a gas motion between equilibrium spaces; transport effect and the thermodynamic quantities of the transport reaction; separation and purification of substances by means of material transport; and

The dynamics of the Hg + Br2 reaction: elucidation of the reaction mechanism for the Br exchange reaction.

Science.gov (United States)

Jambrina, P G; Menéndez, M; Aoiz, F J

2017-06-28

In spite of its importance in the Hg atmospheric chemistry, the dynamics of the Hg + Br 2 → HgBr + Br reaction is poorly understood. In this article, we have carried out a comprehensive study of the reaction mechanism of this reaction by means of quasiclassical trajectories (QCTs) on an existing ab initio potential energy surface (PES). The reaction has a non trivial dynamics, as a consequence of its large endothermicity, the presence of a deep potential well, and the competition between the Br exchange and the collision induced dissociation processes. Our calculations demonstrate that insertion is only relevant at energies just above the reaction threshold and that, at energies above 2.3 eV, HgBr formation typically takes place via a sort of frustrated dissociation. In order to compare directly with the results obtained in extensive cross molecular beam experiments for the homologous reaction with I 2 , angular distributions in the laboratory frame for Hg + Br 2 have been simulated under similar experimental conditions. The lack of agreement at the highest energies considered suggests that either the two reactions have substantially different mechanisms or that calculations on a single PES cannot account for the dynamics at those energies.

Explore the reaction mechanism of the Maillard reaction: a density functional theory study.

Science.gov (United States)

Ren, Ge-Rui; Zhao, Li-Jiang; Sun, Qiang; Xie, Hu-Jun; Lei, Qun-Fang; Fang, Wen-Jun

2015-05-01

The mechanism of Maillard reaction has been investigated by means of density functional theory calculations in the gaseous phase and aqueous solution. The Maillard reaction is a cascade of consecutive and parallel reaction. In the present model system study, glucose and glycine were taken as the initial reactants. On the basis of previous experimental results, the mechanisms of Maillard reaction have been proposed, and the possibility for the formation of different compounds have been evaluated through calculating the relative energy changes for different steps of reaction under different pH conditions. Our calculations reveal that the TS3 in Amadori rearrangement reaction is the rate-determining step of Maillard reaction with the activation barriers of about 66.7 and 68.8 kcal mol(-1) in the gaseous phase and aqueous solution, respectively. The calculation results are in good agreement with previous studies and could provide insights into the reaction mechanism of Maillard reaction, since experimental evaluation of the role of intermediates in the Maillard reaction is quite complicated.

Synthesis and Reactions of Acenaphthenequinones-Part-2. The Reactions of Acenaphthenequinones

Directory of Open Access Journals (Sweden)

Mahmoud Shoukry

2002-02-01

Full Text Available The reactions of acenaphthenequinone and its derivatives with different nucleophiles, organic and inorganic reagents are reviewed. This survey also covers their oxidation and reduction reactions, in addition to many known reactions such as Friedel Crafts, Diels-Alder, bromination and thiolation.

Progress in microscopic direct reaction modeling of nucleon induced reactions

Energy Technology Data Exchange (ETDEWEB)

Dupuis, M.; Bauge, E.; Hilaire, S.; Lechaftois, F.; Peru, S.; Pillet, N.; Robin, C. [CEA, DAM, DIF, Arpajon (France)

2015-12-15

A microscopic nuclear reaction model is applied to neutron elastic and direct inelastic scatterings, and pre-equilibrium reaction. The JLM folding model is used with nuclear structure information calculated within the quasi-particle random phase approximation implemented with the Gogny D1S interaction. The folding model for direct inelastic scattering is extended to include rearrangement corrections stemming from both isoscalar and isovector density variations occurring during a transition. The quality of the predicted (n,n), (n,n{sup '}), (n,xn) and (n,n{sup '}γ) cross sections, as well as the generality of the present microscopic approach, shows that it is a powerful tool that can help improving nuclear reactions data quality. Short- and long-term perspectives are drawn to extend the present approach to more systems, to include missing reactions mechanisms, and to consistently treat both structure and reaction problems. (orig.)

Microbial production of hydrogen from starch-manufacturing wastes

Energy Technology Data Exchange (ETDEWEB)

Yokoi, H.; Maki, R.; Hirose, J.; Hayashi, S. [Miyazaki Univ. (Japan). Dept. of Applied Chemistry

2002-05-01

Effective hydrogen production from starch-manufacturing wastes by microorganisms was investigated. Continuous hydrogen production in high yield of 2.7 mol H{sub 2} mol{sup -1} glucose was attained by a mixed culture of Clostridium butyricum and Enterobacter aerogenes HO-39 in the starch waste medium consisting of sweet potato starch residue as a carbon source and corn steep liquor as a nitrogen source in a repeated batch culture. Rhodobacter sp. M-19 could produce hydrogen from the supernatant of the culture broth obtained in the repeated batch culture of C. butyricum and E. aerogenes HO-39. Hydrogen yield of 4.5 mol H{sub 2} mol{sup -1} glucose was obtained by culturing Rhodobacter sp. M-19 in the supernatant supplemented with 20{mu}gl{sup -1} Na{sub 2}MoO{sub 4} 2H{sub 2}O and 10mgl{sup -1} EDTA in a repeated batch culture with pH control at 7.5. Therefore, continuous hydrogen production with total hydrogen yield of 7.2 mol H{sub 2} mol{sup -1} glucose from the starch remaining in the starch residue was attained by the repeated batch culture with C. butyricum and E. aerogenes HO-39 and by the successive repeated batch culture with Rhodobacter sp. M-19. (Author)

Sleeve reaction chamber system

Science.gov (United States)

Northrup, M Allen [Berkeley, CA; Beeman, Barton V [San Mateo, CA; Benett, William J [Livermore, CA; Hadley, Dean R [Manteca, CA; Landre, Phoebe [Livermore, CA; Lehew, Stacy L [Livermore, CA; Krulevitch, Peter A [Pleasanton, CA

2009-08-25

A chemical reaction chamber system that combines devices such as doped polysilicon for heating, bulk silicon for convective cooling, and thermoelectric (TE) coolers to augment the heating and cooling rates of the reaction chamber or chambers. In addition the system includes non-silicon-based reaction chambers such as any high thermal conductivity material used in combination with a thermoelectric cooling mechanism (i.e., Peltier device). The heat contained in the thermally conductive part of the system can be used/reused to heat the device, thereby conserving energy and expediting the heating/cooling rates. The system combines a micromachined silicon reaction chamber, for example, with an additional module/device for augmented heating/cooling using the Peltier effect. This additional module is particularly useful in extreme environments (very hot or extremely cold) where augmented heating/cooling would be useful to speed up the thermal cycling rates. The chemical reaction chamber system has various applications for synthesis or processing of organic, inorganic, or biochemical reactions, including the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction.

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

Energy Technology Data Exchange (ETDEWEB)

Li, Wenjin; Ma, Ao, E-mail: aoma@uic.edu [Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607 (United States)

2016-03-21

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C{sub 7eq} → C{sub 7ax} transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.

Reaction mechanism and reaction coordinates from the viewpoint of energy flow

International Nuclear Information System (INIS)

Li, Wenjin; Ma, Ao

2016-01-01

Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C 7eq → C 7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.

Nuclear Astrophysics and Neutron Induced Reactions: Quasi-Free Reactions and RIBs

International Nuclear Information System (INIS)

Cherubini, S.; Spitaleri, C.; Crucilla, V.; Gulino, M.; La Cognata, M.; Lamia, L.; Pizzone, R. G.; Puglia, S.; Rapisarda, G. G.; Romano, S.; Sergi, M. L.; Coc, A.; Kubono, S.; Binh, D. N.; Hayakawa, S.; Wakabayashi, Y.; Yamaguchi, H.; Burjan, V.; Kroha, V.; De Sereville, N.

2010-01-01

The use of quasi-free reactions in studying nuclear reactions between charged particles of astrophysical interest has received much attention over the last two decades. The Trojan Horse Method is based on this approach and it has been used to study a number of reactions relevant for Nuclear Astrophysics. Recently we applied this method to the study of nuclear reactions that involve radioactive species, namely to the study of the 18 F+p→ 15 O+α process at temperatures corresponding to the energies available in the classical novae scenario. Quasi-free reactions can also be exploited to study processes induced by neutrons. This technique is particularly interesting when applied to reaction induced by neutrons on unstable short-lived nuclei. Such processes are very important in the nucleosynthesis of elements in the sand r-processes scenarios and this technique can give hints for solving key questions in nuclear astrophysics where direct measurements are practically impossible.

Enhancing chemical reactions

Science.gov (United States)

Morrey, John R.

1978-01-01

Methods of enhancing selected chemical reactions. The population of a selected high vibrational energy state of a reactant molecule is increased substantially above its population at thermal equilibrium by directing onto the molecule a beam of radiant energy from a laser having a combination of frequency and intensity selected to pump the selected energy state, and the reaction is carried out with the temperature, pressure, and concentrations of reactants maintained at a combination of values selected to optimize the reaction in preference to thermal degradation by transforming the absorbed energy into translational motion. The reaction temperature is selected to optimize the reaction. Typically a laser and a frequency doubler emit radiant energy at frequencies of .nu. and 2.nu. into an optical dye within an optical cavity capable of being tuned to a wanted frequency .delta. or a parametric oscillator comprising a non-centrosymmetric crystal having two indices of refraction, to emit radiant energy at the frequencies of .nu., 2.nu., and .delta. (and, with a parametric oscillator, also at 2.nu.-.delta.). Each unwanted frequency is filtered out, and each desired frequency is focused to the desired radiation flux within a reaction chamber and is reflected repeatedly through the chamber while reactants are fed into the chamber and reaction products are removed therefrom.

ReactionPredictor: prediction of complex chemical reactions at the mechanistic level using machine learning.

Science.gov (United States)

Kayala, Matthew A; Baldi, Pierre

2012-10-22

Proposing reasonable mechanisms and predicting the course of chemical reactions is important to the practice of organic chemistry. Approaches to reaction prediction have historically used obfuscating representations and manually encoded patterns or rules. Here we present ReactionPredictor, a machine learning approach to reaction prediction that models elementary, mechanistic reactions as interactions between approximate molecular orbitals (MOs). A training data set of productive reactions known to occur at reasonable rates and yields and verified by inclusion in the literature or textbooks is derived from an existing rule-based system and expanded upon with manual curation from graduate level textbooks. Using this training data set of complex polar, hypervalent, radical, and pericyclic reactions, a two-stage machine learning prediction framework is trained and validated. In the first stage, filtering models trained at the level of individual MOs are used to reduce the space of possible reactions to consider. In the second stage, ranking models over the filtered space of possible reactions are used to order the reactions such that the productive reactions are the top ranked. The resulting model, ReactionPredictor, perfectly ranks polar reactions 78.1% of the time and recovers all productive reactions 95.7% of the time when allowing for small numbers of errors. Pericyclic and radical reactions are perfectly ranked 85.8% and 77.0% of the time, respectively, rising to >93% recovery for both reaction types with a small number of allowed errors. Decisions about which of the polar, pericyclic, or radical reaction type ranking models to use can be made with >99% accuracy. Finally, for multistep reaction pathways, we implement the first mechanistic pathway predictor using constrained tree-search to discover a set of reasonable mechanistic steps from given reactants to given products. Webserver implementations of both the single step and pathway versions of Reaction

Kinetics of Bio-Reactions

DEFF Research Database (Denmark)

Villadsen, John

2015-01-01

his chapter predicts the specific rates of reaction by means of a mathematical expression, the kinetics of the reaction. This expression can be derived through a mechanistic interpretation of an enzymatically catalyzed reaction, but it is essentially of empirical nature for cell reactions. The mo...

Application of Enzyme Coupling Reactions to Shift Thermodynamically Limited Biocatalytic Reactions

DEFF Research Database (Denmark)

Abu, Rohana; Woodley, John M.

2015-01-01

, it can be challenging to combine several engineered enzymes in vitro for the conversion of non-natural substrates. In this mini-review we focus on enzyme coupling reactions as a tool to alleviate thermodynamic constraints in synthetically useful biocatalytic reactions. The implications of thermodynamic...... shift the equilibrium of otherwise thermodynamically unfavourable reactions to give a higher conversion of the target product. By coupling an energetically unfavourable reaction with a more favourable one, the multi-enzyme cascade mimics the approach taken in nature in metabolic pathways. Nevertheless...

Calculation of reaction energies and adiabatic temperatures for waste tank reactions

International Nuclear Information System (INIS)

Burger, L.L.

1995-10-01

Continual concern has been expressed over potentially hazardous exothermic reactions that might occur in Hanford Site underground waste storage tanks. These tanks contain many different oxidizable compounds covering a wide range of concentrations. The chemical hazards are a function of several interrelated factors, including the amount of energy (heat) produced, how fast it is produced, and the thermal absorption and heat transfer properties of the system. The reaction path(s) will determine the amount of energy produced and kinetics will determine the rate that it is produced. The tanks also contain many inorganic compounds inert to oxidation. These compounds act as diluents and can inhibit exothermic reactions because of their heat capacity and thus, in contrast to the oxidizable compounds, provide mitigation of hazardous reactions. In this report the energy that may be released when various organic and inorganic compounds react is computed as a function of the reaction-mix composition and the temperature. The enthalpy, or integrated heat capacity, of these compounds and various reaction products is presented as a function of temperature; the enthalpy of a given mixture can then be equated to the energy release from various reactions to predict the maximum temperature which may be reached. This is estimated for several different compositions. Alternatively, the amounts of various diluents required to prevent the temperature from reaching a critical value can be estimated. Reactions taking different paths, forming different products such as N 2 O in place of N 2 are also considered, as are reactions where an excess of caustic is present. Oxidants other than nitrate and nitrite are considered briefly

Calculation of reaction energies and adiabatic temperatures for waste tank reactions

Energy Technology Data Exchange (ETDEWEB)

Burger, L.L.

1995-10-01

Continual concern has been expressed over potentially hazardous exothermic reactions that might occur in Hanford Site underground waste storage tanks. These tanks contain many different oxidizable compounds covering a wide range of concentrations. The chemical hazards are a function of several interrelated factors, including the amount of energy (heat) produced, how fast it is produced, and the thermal absorption and heat transfer properties of the system. The reaction path(s) will determine the amount of energy produced and kinetics will determine the rate that it is produced. The tanks also contain many inorganic compounds inert to oxidation. These compounds act as diluents and can inhibit exothermic reactions because of their heat capacity and thus, in contrast to the oxidizable compounds, provide mitigation of hazardous reactions. In this report the energy that may be released when various organic and inorganic compounds react is computed as a function of the reaction-mix composition and the temperature. The enthalpy, or integrated heat capacity, of these compounds and various reaction products is presented as a function of temperature; the enthalpy of a given mixture can then be equated to the energy release from various reactions to predict the maximum temperature which may be reached. This is estimated for several different compositions. Alternatively, the amounts of various diluents required to prevent the temperature from reaching a critical value can be estimated. Reactions taking different paths, forming different products such as N{sub 2}O in place of N{sub 2} are also considered, as are reactions where an excess of caustic is present. Oxidants other than nitrate and nitrite are considered briefly.

Cross-section and reaction rates for some reactions involved in explosive nucleosynthesis

International Nuclear Information System (INIS)

Cheng, C.W.

1979-03-01

Total proton-induced and alpha-induced reaction cross sections have been determined for the 24 Mg(α,n), 25 Mg(p,n), 26 Mg(p,n), 27 Al(p,n), 28 Si(α,n), 42 Ca(p,γ), 42 Ca(α,n) and 44 Ca(p,n) reactions from energies near threshold (except the exothermic (p,γ) reaction) to about 3 to 4 MeV above threshold. The product nuclei are all positron emitters with half-lives ranging from about 3 sec to about 4 hours. From the measured cross sections reaction rates have been calculated in the temperature range 1 9 9 =1, at which the discrepancy is large. Included also are analytic forms for (p,n), (α,n), and (p,γ) reactions which can be used to describe the reaction rate within the temperature range 1 9 <=6 and which agree with the experimental rates at the discrete temperatures where the reaction rates have been calculated

Quasielastic reactions

International Nuclear Information System (INIS)

Henning, W.

1979-01-01

Quasielastic reaction studies, because of their capability to microscopically probe nuclear structure, are still of considerable interest in heavy-ion reactions. The recent progress in understanding various aspects of the reaction mechanism make this aim appear closer. The relation between microscopic and macroscopic behavior, as suggested, for example, by the single proton transfer data to individual final states or averaged excitation energy intervals, needs to be explored. It seems particularly useful to extend measurements to higher incident energies, to explore and understand nuclear structure aspects up to the limit of the energy range where they are important

Ion-Molecule Reaction Dynamics.

Science.gov (United States)

Meyer, Jennifer; Wester, Roland

2017-05-05

We review the recent advances in the investigation of the dynamics of ion-molecule reactions. During the past decade, the combination of single-collision experiments in crossed ion and neutral beams with the velocity map ion imaging detection technique has enabled a wealth of studies on ion-molecule reactions. These methods, in combination with chemical dynamics simulations, have uncovered new and unexpected reaction mechanisms, such as the roundabout mechanism and the subtle influence of the leaving group in anion-molecule nucleophilic substitution reactions. For this important class of reactions, as well as for many fundamental cation-molecule reactions, the information obtained with crossed-beam imaging is discussed. The first steps toward understanding micro-solvation of ion-molecule reaction dynamics are presented. We conclude with the presentation of several interesting directions for future research.

Maillard Reaction: review

Directory of Open Access Journals (Sweden)

Júlia d'Almeida Francisquini

2017-11-01

Full Text Available Maillard reaction is an important subject of study in food science and technology and different areas of knowledge are involved such as chemistry, food engineering, nutrition and food technology. The objective of this paper is to present the basic concepts of the Maillard reaction, such as the reaction stages, the main compounds producced and some technological consequences for dairy products.

Mining chemical reactions using neighborhood behavior and condensed graphs of reactions approaches.

Science.gov (United States)

de Luca, Aurélie; Horvath, Dragos; Marcou, Gilles; Solov'ev, Vitaly; Varnek, Alexandre

2012-09-24

This work addresses the problem of similarity search and classification of chemical reactions using Neighborhood Behavior (NB) and Condensed Graphs of Reaction (CGR) approaches. The CGR formalism represents chemical reactions as a classical molecular graph with dynamic bonds, enabling descriptor calculations on this graph. Different types of the ISIDA fragment descriptors generated for CGRs in combination with two metrics--Tanimoto and Euclidean--were considered as chemical spaces, to serve for reaction dissimilarity scoring. The NB method has been used to select an optimal combination of descriptors which distinguish different types of chemical reactions in a database containing 8544 reactions of 9 classes. Relevance of NB analysis has been validated in generic (multiclass) similarity search and in clustering with Self-Organizing Maps (SOM). NB-compliant sets of descriptors were shown to display enhanced mapping propensities, allowing the construction of better Self-Organizing Maps and similarity searches (NB and classical similarity search criteria--AUC ROC--correlate at a level of 0.7). The analysis of the SOM clusters proved chemically meaningful CGR substructures representing specific reaction signatures.

Chemical potential and reaction electronic flux in symmetry controlled reactions.

Science.gov (United States)

Vogt-Geisse, Stefan; Toro-Labbé, Alejandro

2016-07-15

In symmetry controlled reactions, orbital degeneracies among orbitals of different symmetries can occur along a reaction coordinate. In such case Koopmans' theorem and the finite difference approximation provide a chemical potential profile with nondifferentiable points. This results in an ill-defined reaction electronic flux (REF) profile, since it is defined as the derivative of the chemical potential with respect to the reaction coordinate. To overcome this deficiency, we propose a new way for the calculation of the chemical potential based on a many orbital approach, suitable for reactions in which symmetry is preserved. This new approach gives rise to a new descriptor: symmetry adapted chemical potential (SA-CP), which is the chemical potential corresponding to a given irreducible representation of a symmetry group. A corresponding symmetry adapted reaction electronic flux (SA-REF) is also obtained. Using this approach smooth chemical potential profiles and well defined REFs are achieved. An application of SA-CP and SA-REF is presented by studying the Cs enol-keto tautomerization of thioformic acid. Two SA-REFs are obtained, JA'(ξ) and JA'' (ξ). It is found that the tautomerization proceeds via an in-plane delocalized 3-center 4-electron O-H-S hypervalent bond which is predicted to exist only in the transition state (TS) region. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Nuclear reaction studies

International Nuclear Information System (INIS)

Alexander, J.M.; Lacey, R.A.

1994-01-01

Research focused on the statistical and dynamical properties of ''hot'' nuclei formed in symmetric heavy-ion reactions. Theses included ''flow'' measurements and the mechanism for multifragment disassembly. Model calculations are being performed for the reactions C+C, Ne+Al, Ar+Sc, Kr+Nb, and Xe+La. It is planned to study 40 Ar reactions from 27 to 115 MeV/nucleon. 2 figs., 41 refs

Exchange Reactions. Proceedings of the Symposium on Exchange Reactions

International Nuclear Information System (INIS)

1965-01-01

The mechanisms and kinetics of chemical reactions are of great interest to chemists. The study of exchange reactions in particular helps to shed light on the dynamics of chemical change, providing an insight into the structures and the reactivities of the chemical species involved. The main theme of this meeting was the subject of oxidation-reduction reactions in which the net result is the transfer of one or more electrons between the different oxidation states of the same element. Other studies reported included the transfer of protons, atoms, complex ligands or organic radicals between molecules. Heterogeneous exchange, which is of importance in many cases of catalytic action, was also considered. For a long time isotopic tracers have formed the most convenient means of studying exchange reactions and today a considerable amount of work continues to be done with their aid. Consequently, several papers presented at this Symposium reported on work carried out by purely radiochemical tracer methods. In recognition, however, of the important role which nuclear magnetic resonance and electron spin resonance play in this field, in particular in the study of fast reactions, a number of reports on investigations in which these techniques had been used was included in the programme. By kind invitation of the United States Government the Symposium on Exchange Reactions was held from 31 May to 4 June at the Brookhaven National Laboratory, Upton, Long Island, N.Y., USA. It was attended by 46 participants from nine countries and one inter-governmental organization. The publication of these Proceedings makes the contents of the papers and the discussion available to a wider audience

RxnFinder: biochemical reaction search engines using molecular structures, molecular fragments and reaction similarity.

Science.gov (United States)

Hu, Qian-Nan; Deng, Zhe; Hu, Huanan; Cao, Dong-Sheng; Liang, Yi-Zeng

2011-09-01

Biochemical reactions play a key role to help sustain life and allow cells to grow. RxnFinder was developed to search biochemical reactions from KEGG reaction database using three search criteria: molecular structures, molecular fragments and reaction similarity. RxnFinder is helpful to get reference reactions for biosynthesis and xenobiotics metabolism. RxnFinder is freely available via: http://sdd.whu.edu.cn/rxnfinder. qnhu@whu.edu.cn.

Global Controllability of Chemical Reactions

OpenAIRE

Drexler, Dániel András; Tóth, János

2015-01-01

Controllability of chemical reactions is an important problem in chemical engineering science. In control theory, analysis of the controllability of linear systems is well-founded, however the dynamics of chemical reactions is usually nonlinear. Global controllability properties of chemical reactions are analyzed here based on the Lie-algebra of the vector fields associated to elementary reactions. A chemical reaction is controllable almost everywhere if all the reaction rate coefficients can...

Introduction to chemical reaction engineering

International Nuclear Information System (INIS)

Kim, Yeong Geol

1990-10-01

This deals with chemical reaction engineering with thirteen chapters. The contents of this book are introduction on reaction engineering, chemical kinetics, thermodynamics and chemical reaction, abnormal reactor, non-isothermal reactor, nonideal reactor, catalysis in nonuniform system, diffusion and reaction in porosity catalyst, design catalyst heterogeneous reactor in solid bed, a high molecule polymerization, bio reaction engineering, reaction engineering in material process, control multi-variable reactor process using digital computer.

Nonequilibrium thermodynamics and a fluctuation theorem for individual reaction steps in a chemical reaction network

International Nuclear Information System (INIS)

Pal, Krishnendu; Das, Biswajit; Banerjee, Kinshuk; Gangopadhyay, Gautam

2015-01-01

We have introduced an approach to nonequilibrium thermodynamics of an open chemical reaction network in terms of the propensities of the individual elementary reactions and the corresponding reverse reactions. The method is a microscopic formulation of the dissipation function in terms of the relative entropy or Kullback-Leibler distance which is based on the analogy of phase space trajectory with the path of elementary reactions in a network of chemical process. We have introduced here a fluctuation theorem valid for each opposite pair of elementary reactions which is useful in determining the contribution of each sub-reaction on the nonequilibrium thermodynamics of overall reaction. The methodology is applied to an oligomeric enzyme kinetics at a chemiostatic condition that leads the reaction to a nonequilibrium steady state for which we have estimated how each step of the reaction is energy driven or entropy driven to contribute to the overall reaction. (paper)

Direct Reactions

Energy Technology Data Exchange (ETDEWEB)

Austern, N. [University of Pittsburgh, Pittsburgh, PA (United States)

1963-01-15

In order to give a unified presentation of one point of view, these lectures are devoted only to a detailed development of the standard theories of direct reactions, starting from basic principles. Discussion is given of the present status of the theories, of the techniques used for practical calculation, and of possible future developments. The direct interaction (DI) aspects of a reaction are those which involve only a few of the many degrees of freedom of a nucleus. In fact the minimum number of degrees of freedom which must be involved in a reaction are those required to describe the initial and final channels, and DI studies typically consider these degrees of freedom and no others. Because of this simplicity DI theories may be worked out in painstaking detail. DI processes concern only part of the wave function for a problem. The other part involves complicated excitations of many degrees of freedom, and gives the compound nucleus (CN) effects. While it is extremely interesting to learn how to separate DI and CN effects in an orderly manner, if they are both present in a reaction, no suitable method has yet been found. Instead, current work stresses the kinds of reactions and the kinds of final states in which DI effects dominate and in which CN effects may almost be forgotten. The DI cross-sections which are studied are often extremely large, comparable to elastic scattering cross-sections. (author)

Knock-out reactions

International Nuclear Information System (INIS)

de Forest, T. Jr.

1977-01-01

It is pointed out that the primary motivation for performing high energy single nucleon knock-out reactions is based on the concept of quasi-elastic scattering. The validity of and corrections to the partial wave impulse approximation and kinematical invariance of knock-out reactions and tests of the reaction mechanism are treated. The effect of distortions on the momentum distribution in the effective momentum approximation for given parameters are plotted. 12 references

Phosphite radicals and their reactions. Examples of redox, substitution, and addition reactions

International Nuclear Information System (INIS)

Schaefer, K.; Asmus, K.D.

1980-01-01

Phosphite radicals HPO 3 - and PO 3 2 -, which exist in an acid-base equilibrium with pK = 5.75, are shown to take part in various types of reactions. In the absence of scavengers, they disappear mainly by second-order disproportionation and combination; a first-order contribution to the decay is also indicated. HPO 3 - and PO 3 2 - are good reductants toward electron acceptors such as tetranitromethane. In this reaction phosphate and C(NO 2 ) 3 - are formed. Phosphite radicals can, however, also act as good oxidants, e.g., toward thiols and thiolate ions. These reactions lead to the formation of RS. radicals which were identified either directly, as in the case of penicillamine, through the optical absorption of PenS. or more indirectly through equilibration of RS. with RS- to the optically absorbing RSSR-. disulfide radical anion. A homolytic substitution reaction (S/sub H/2) occurs in the reaction of the phosphite radicals with aliphatic disulfides, yielding RS. radicals and phosphate thioester RSPO 3 2 -. Lipoic acid, as an example of a cyclic disulfide, is reduced to the corresponding RSSR-. radical anion and also undergoes the S/sub H/2 reaction with about equal probability. An addition reaction is observed between phosphite radicals and molecular oxygen. The resulting peroxo phosphate radicals establish an acid-base equilibrium HPO 5 - . reversible PO 5 2- . + H+ with a pK = 3.4. Absolute rate constants were determined for all reactions discussed

Heavy ion transfer reactions

International Nuclear Information System (INIS)

Weisser, D.C.

1977-06-01

To complement discussions on the role of γ rays in heavy ion induced reactions, the author discusses the role played by particle detection. Transfer reactions are part of this subject and are among those in which one infers the properties of the residual nucleus in a reaction by observing the emerging light nucleus. Inelastic scattering ought not be excluded from this subject, although no particles are transferred, because of the role it plays in multistep reactions and in fixing O.M. parameters describing the entrance channel of the reaction. Heavy ion transfer reaction studies have been under study for some years and yet this research is still in its infancy. The experimental techniques are difficult and the demands on theory rigorous. One of the main products of heavy ion research has been the thrust to re-examine the assumptions of reaction theory and now include many effects neglected for light ion analysis. This research has spurred the addition of multistep processes to simple direct processes and coupled channel calculations. (J.R.)

Noncanonical Reactions of Flavoenzymes

Directory of Open Access Journals (Sweden)

Pablo Sobrado

2012-11-01

Full Text Available Enzymes containing flavin cofactors are predominantly involved in redox reactions in numerous cellular processes where the protein environment modulates the chemical reactivity of the flavin to either transfer one or two electrons. Some flavoenzymes catalyze reactions with no net redox change. In these reactions, the protein environment modulates the reactivity of the flavin to perform novel chemistries. Recent mechanistic and structural data supporting novel flavin functionalities in reactions catalyzed by chorismate synthase, type II isopentenyl diphosphate isomerase, UDP-galactopyranose mutase, and alkyl-dihydroxyacetonephosphate synthase are presented in this review. In these enzymes, the flavin plays either a direct role in acid/base reactions or as a nucleophile or electrophile. In addition, the flavin cofactor is proposed to function as a “molecular scaffold” in the formation of UDP-galactofuranose and alkyl-dihydroxyacetonephosphate by forming a covalent adduct with reaction intermediates.

Confining Domains Lead to Reaction Bursts: Reaction Kinetics in the Plasma Membrane

Science.gov (United States)

Kalay, Ziya; Fujiwara, Takahiro K.; Kusumi, Akihiro

2012-01-01

Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity. PMID:22479350

Confining domains lead to reaction bursts: reaction kinetics in the plasma membrane.

Directory of Open Access Journals (Sweden)

Ziya Kalay

Full Text Available Confinement of molecules in specific small volumes and areas within a cell is likely to be a general strategy that is developed during evolution for regulating the interactions and functions of biomolecules. The cellular plasma membrane, which is the outermost membrane that surrounds the entire cell, was considered to be a continuous two-dimensional liquid, but it is becoming clear that it consists of numerous nano-meso-scale domains with various lifetimes, such as raft domains and cytoskeleton-induced compartments, and membrane molecules are dynamically trapped in these domains. In this article, we give a theoretical account on the effects of molecular confinement on reversible bimolecular reactions in a partitioned surface such as the plasma membrane. By performing simulations based on a lattice-based model of diffusion and reaction, we found that in the presence of membrane partitioning, bimolecular reactions that occur in each compartment proceed in bursts during which the reaction rate is sharply and briefly increased even though the asymptotic reaction rate remains the same. We characterized the time between reaction bursts and the burst amplitude as a function of the model parameters, and discussed the biological significance of the reaction bursts in the presence of strong inhibitor activity.

Model Experiment of Thermal Runaway Reactions Using the Aluminum-Hydrochloric Acid Reaction

Science.gov (United States)

Kitabayashi, Suguru; Nakano, Masayoshi; Nishikawa, Kazuyuki; Koga, Nobuyoshi

2016-01-01

A laboratory exercise for the education of students about thermal runaway reactions based on the reaction between aluminum and hydrochloric acid as a model reaction is proposed. In the introductory part of the exercise, the induction period and subsequent thermal runaway behavior are evaluated via a simple observation of hydrogen gas evolution and…

Infrared laser-induced chemical reactions

International Nuclear Information System (INIS)

Katayama, Mikio

1978-01-01

The experimental means which clearly distinguishes between infrared ray-induced reactions and thermal reactions has been furnished for the first time when an intense monochromatic light source has been obtained by the development of infrared laser. Consequently, infrared laser-induced chemical reactions have started to develop as one field of chemical reaction researches. Researches of laser-induced chemical reactions have become new means for the researches of chemical reactions since they were highlighted as a new promising technique for isotope separation. Specifically, since the success has been reported in 235 U separation using laser in 1974, comparison of this method with conventional separation techniques from the economic point of view has been conducted, and it was estimated by some people that the laser isotope separation is cheaper. This report briefly describes on the excitation of oscillation and reaction rate, and introduces the chemical reactions induced by CW laser and TEA CO 2 laser. Dependence of reaction yield on laser power, measurement of the absorbed quantity of infrared ray and excitation mechanism are explained. Next, isomerizing reactions are reported, and finally, isotope separation is explained. It was found that infrared laser-induced chemical reactions have the selectivity for isotopes. Since it is evident that there are many examples different from thermal and photo-chemical reactions, future collection of the data is expected. (Wakatsuki, Y.)

Chemical kinetics of gas reactions

CERN Document Server

Kondrat'Ev, V N

2013-01-01

Chemical Kinetics of Gas Reactions explores the advances in gas kinetics and thermal, photochemical, electrical discharge, and radiation chemical reactions. This book is composed of 10 chapters, and begins with the presentation of general kinetic rules for simple and complex chemical reactions. The next chapters deal with the experimental methods for evaluating chemical reaction mechanisms and some theories of elementary chemical processes. These topics are followed by discussions on certain class of chemical reactions, including unimolecular, bimolecular, and termolecular reactions. The rema

[Reaction mechanism studies of heavy ion induced nuclear reactions]: Annual progress report, October 1987

International Nuclear Information System (INIS)

Mignerey, A.C.

1987-10-01

The experiments which this group has been working on seek to define the reaction mechanisms responsible for complex fragment emission in heavy ion reactions. The reactions studied are La + La, La + Al, and La + Cu at 46.8 MeV/u; and Ne + Ag and Ne + Au reactions at 250 MeV/u. Another experimental program at the Oak Ridge Hollifield Heavy Ion Research Facility (HHIRF) is designed to measure the excitation energy division between reaction products in asymmetric deep inelastic reactions. A brief description is given of progress to date, the scientific goals of this experiment and the plastic phoswich detectors developed for this experiment

The Glaser–Hay reaction

DEFF Research Database (Denmark)

Vilhelmsen, Mie Højer; Jensen, Jonas; Tortzen, Christian

2013-01-01

The oxidative Glaser–Hay coupling of two terminal alkynes to furnish a butadiyne is a key reaction for acetylenic scaffolding. Although the reaction is performed under rather simple conditions [CuCl/TMEDA/O2 (air)], the mechanism is still under debate. Herein we present detailed studies...... on the scope of this reaction by using both 13C NMR and UV/Vis spectroscopic methods. The former method was used to study the kinetics of the coupling of aryl-substituted alkynes as the aryl carbon resonances of the reactants and products have similar NOEs and relaxation times. The reaction was found...... to be zero-order with respect to the terminal alkyne reactant under standard preparative conditions. Moreover, as the reaction proceeded, a clear change to slower reaction kinetics was observed, but it was still apparently zero-order. The onset of this change was found to depend on the catalyst loading...

The Paterno-Buchi reaction

DEFF Research Database (Denmark)

Brogaard, Rasmus Yding; Schalk, Oliver; Boguslavskiy, Andrey E.

2012-01-01

The Paternò-Büchi (PB) reaction between an excited carbonyl compound and an alkene has been widely studied, but so far little is known about the excited-state dynamics of the reaction. In this investigation, we used a compound in which a formyl and a vinyl group are attached to a [2.......2]paracyclophane in order to obtain a model system in pre-reactive conformation for the PB reaction. We studied the excited-state dynamics of the isolated molecule in a molecular beam using femtosecond time-resolved photoelectron spectroscopy and ab initio calculations. The results show that inter-system crossing...... within two picoseconds competes efficiently with the reaction in the singlet manifold. Thus, the PB reaction in this model system takes place in the triplet state on a time scale of nanoseconds. This result stresses the importance of triplet states in the excited-state pathway of the PB reaction...

Metal-catalyzed asymmetric aldol reactions

Energy Technology Data Exchange (ETDEWEB)

Dias, Luiz C.; Lucca Junior, Emilio C. de; Ferreira, Marco A. B.; Polo, Ellen C., E-mail: ldias@iqm.unicamp.br [Universidade de Campinas (UNICAMP), SP (Brazil). Inst. de Quimica

2012-12-15

The aldol reaction is one of the most powerful and versatile methods for the construction of C-C bonds. Traditionally, this reaction was developed in a stoichiometric version; however, great efforts in the development of chiral catalysts for aldol reactions were performed in recent years. Thus, in this review article, the development of metal-mediated chiral catalysts in Mukaiyama-type aldol reaction, reductive aldol reaction and direct aldol reaction are discussed. Moreover, the application of these catalysts in the total synthesis of complex molecules is discussed. (author)

Reaction Qualifications Revisited

DEFF Research Database (Denmark)

Lippert-Rasmussen, Kasper

2009-01-01

  When, in a competitive sphere, people are selected on the basis of qualifications only, their chances of acquiring positions of advantage may seem to depend entirely upon their abilities, not discriminatory bias. However, if reaction qualifications - i.e. characteristics which contribute...... to a person's effectiveness by causing a favourable reaction in customers, co-workers etc. (for short: recipients) - are involved, this assumption is false. Building on work by Wertheimer, Mason, and Miller, this paper proposes an account of the reaction qualifications that count, from the point of view...... of merit. Specifically, it preserves symmetry between negative evaluations of antimeritocratic bases of selection and negative evaluations of qualifications rooted in comparable antimeritocratic reactions. So if employers should not select among applicants on the basis of their (the employers') racial...

Reaction Qualifications Revisited

DEFF Research Database (Denmark)

Lippert-Rasmussen, Kasper

2009-01-01

to a person's effectiveness by causing a favourable reaction in customers, co-workers etc. (for short: recipients) - are involved, this assumption is false. Building on work by Wertheimer, Mason, and Miller, this paper proposes an account of the reaction qualifications that count, from the point of view...... preferences, recipients should not respond to the applicant actually hired on the basis of their (the recipients') racial preferences. My account decomposes the meritocratic ideal into four separate norms, one of which applies to recipients rather than to selectors. Finally, it defends the view that reaction...... qualifications based on antimeritocratic reactions, while not unproblematic, are not entirely irrelevant from the point of view of merit. Notably, selectors need not discount them when no one - including the targets of the objectionable preferences - is unfairly disadvantaged. Because not all problematic...

Calculation of reaction energies and adiabatic temperatures for waste tank reactions

International Nuclear Information System (INIS)

Burger, L.L.

1993-03-01

Continual concern has been expressed over potentially hazardous exothermic reactions that might occur in underground Hanford waste tanks. These tanks contain many different oxidizable compounds covering a wide range of concentrations. Several may be in concentrations and quantities great enough to be considered a hazard in that they could undergo rapid and energetic chemical reactions with nitrate and nitrite salts that are present. The tanks also contain many inorganic compounds inert to oxidation. In this report the computed energy that may be released when various organic and inorganic compounds react is computed as a function of the reaction mix composition and the temperature. The enthalpy, or integrated heat capacity, of these compounds and various reaction products is presented as a function of temperature, and the enthalpy of a given mixture can then be equated to the energy release from various reactions to predict the maximum temperature that may be reached. This is estimated for several different compositions. Alternatively, the amounts of various diluents required to prevent the temperature from reaching a critical value can be estimated

Effects of reaction-kinetic parameters on modeling reaction pathways in GaN MOVPE growth

Science.gov (United States)

Zhang, Hong; Zuo, Ran; Zhang, Guoyi

2017-11-01

In the modeling of the reaction-transport process in GaN MOVPE growth, the selections of kinetic parameters (activation energy Ea and pre-exponential factor A) for gas reactions are quite uncertain, which cause uncertainties in both gas reaction path and growth rate. In this study, numerical modeling of the reaction-transport process for GaN MOVPE growth in a vertical rotating disk reactor is conducted with varying kinetic parameters for main reaction paths. By comparisons of the molar concentrations of major Ga-containing species and the growth rates, the effects of kinetic parameters on gas reaction paths are determined. The results show that, depending on the values of the kinetic parameters, the gas reaction path may be dominated either by adduct/amide formation path, or by TMG pyrolysis path, or by both. Although the reaction path varies with different kinetic parameters, the predicted growth rates change only slightly because the total transport rate of Ga-containing species to the substrate changes slightly with reaction paths. This explains why previous authors using different chemical models predicted growth rates close to the experiment values. By varying the pre-exponential factor for the amide trimerization, it is found that the more trimers are formed, the lower the growth rates are than the experimental value, which indicates that trimers are poor growth precursors, because of thermal diffusion effect caused by high temperature gradient. The effective order for the contribution of major species to growth rate is found as: pyrolysis species > amides > trimers. The study also shows that radical reactions have little effect on gas reaction path because of the generation and depletion of H radicals in the chain reactions when NH2 is considered as the end species.

Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

Science.gov (United States)

Latino, Diogo A R S; Aires-de-Sousa, João

2014-01-01

The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1)H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants) and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1)H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps) produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF), the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure elucidation of

Automatic NMR-based identification of chemical reaction types in mixtures of co-occurring reactions.

Directory of Open Access Journals (Sweden)

Diogo A R S Latino

Full Text Available The combination of chemoinformatics approaches with NMR techniques and the increasing availability of data allow the resolution of problems far beyond the original application of NMR in structure elucidation/verification. The diversity of applications can range from process monitoring, metabolic profiling, authentication of products, to quality control. An application related to the automatic analysis of complex mixtures concerns mixtures of chemical reactions. We encoded mixtures of chemical reactions with the difference between the (1H NMR spectra of the products and the reactants. All the signals arising from all the reactants of the co-occurring reactions were taken together (a simulated spectrum of the mixture of reactants and the same was done for products. The difference spectrum is taken as the representation of the mixture of chemical reactions. A data set of 181 chemical reactions was used, each reaction manually assigned to one of 6 types. From this dataset, we simulated mixtures where two reactions of different types would occur simultaneously. Automatic learning methods were trained to classify the reactions occurring in a mixture from the (1H NMR-based descriptor of the mixture. Unsupervised learning methods (self-organizing maps produced a reasonable clustering of the mixtures by reaction type, and allowed the correct classification of 80% and 63% of the mixtures in two independent test sets of different similarity to the training set. With random forests (RF, the percentage of correct classifications was increased to 99% and 80% for the same test sets. The RF probability associated to the predictions yielded a robust indication of their reliability. This study demonstrates the possibility of applying machine learning methods to automatically identify types of co-occurring chemical reactions from NMR data. Using no explicit structural information about the reactions participants, reaction elucidation is performed without structure

The redox-Mannich reaction.

Science.gov (United States)

Chen, Weijie; Seidel, Daniel

2014-06-06

A complement to the classic three-component Mannich reaction, the redox-Mannich reaction, utilizes the same starting materials but incorporates an isomerization step that enables the facile preparation of ring-substituted β-amino ketones. Reactions occur under relatively mild conditions and are facilitated by benzoic acid.

Investigation of Na-CO2 Reaction with Initial Reaction in Various Reacting Surface

International Nuclear Information System (INIS)

Kim, Hyun Su; Park, Gunyeop; Kim, Soo Jae; Park, Hyun Sun; Kim, Moo Hwan; Wi, Myung-Hwan

2015-01-01

The reaction products that cause oxidation and erosion are threaten the heat transfer tubes so that it is necessary to investigate Na-CO 2 reaction according to various experimental parameter. Unlike SWR, Na-CO 2 reaction is more complex to deal with reaction kinetics. Since a comprehensive understanding of Na-CO 2 reaction mechanism is crucial for the safety analysis, the reaction phenomenon under the various conditions was investigated. The current issue is to make a database for developing computational code for CO 2 gas leak situation because it is experimentally difficult to analyze the actual accident situation. Most studies on Na-CO 2 interaction reports that chemical reaction is getting vigorous as temperature increased and reactivity is sensitive as temperature change between 400 .deg. C and 600 .deg. C. Therefore, temperature range is determined based on the operating condition (450 - 500 .deg. C) of KALIMER-600 employed as supercritical CO 2 brayton cycle energy conversion system for Na-CO 2 heat exchanger. And next parameter is sodium surface area which contact between sodium and CO 2 when CO 2 is injected into sodium pool in the accident situation. So, the fundamental surface reaction is experimentally studied in the range of 8 - 12cm 2 . Additionally, it has been reported in recent years that CO 2 Flow rate affects reactivity less significantly and CO 2 flow rate is assumed that 5 SLPM (standard liter per minute) is suitable as a basis for a small leakage. The finally selected control parameters is sodium temperature and reacting surface area with constant CO 2 flow rate. Na-CO 2 reaction test is performed for investigating risk of potential accident which contacts with liquid sodium and CO 2 . Amount of reaction is saturated as time passed because of kept a balance between production of solid phase reaction products and amount of diffusivity. These results contribute to make a database for the SFR safety analysis and additional experiments are needed

Preequilibrium Nuclear Reactions

International Nuclear Information System (INIS)

Strohmaier, B.

1988-01-01

After a survey on existing experimental data on precompound reactions and a description of preequilibrium reactions, theoretical models and quantum mechanical theories of preequilibrium emission are presented. The 25 papers of this meeting are analyzed separately

Extension of a Kinetic-Theory Approach for Computing Chemical-Reaction Rates to Reactions with Charged Particles

Science.gov (United States)

Liechty, Derek S.; Lewis, Mark J.

2010-01-01

Recently introduced molecular-level chemistry models that predict equilibrium and nonequilibrium reaction rates using only kinetic theory and fundamental molecular properties (i.e., no macroscopic reaction rate information) are extended to include reactions involving charged particles and electronic energy levels. The proposed extensions include ionization reactions, exothermic associative ionization reactions, endothermic and exothermic charge exchange reactions, and other exchange reactions involving ionized species. The extensions are shown to agree favorably with the measured Arrhenius rates for near-equilibrium conditions.

1,3,5-Triethylbenzene Transformation Reactions Compared to Its Transalkylation Reaction with Ethylbenzene

KAUST Repository

Akhtar, M. Naseem; Sulaiman, Al Khattaf

2009-01-01

The transalkylation of 1,3,5-triethylbenzene (1,3,5-TEB) with ethylbenzene (EB) has been studied over USYtype catalysts using a riser simulator that mimics the operation of a fluidized-bed reactor. The reaction mixture EB and 1,3,5-TEB was used at a molar ratio of 1:1, which is equivalent to 40:60 wt % of EB/1,3,5-TEB, respectively. The reaction temperature was varied from 350 to 500 °C with a time on stream ranging from 3-15 s. The effect of reaction conditions on 1,3,5-TEB conversion, DEB selectivity, and isomerization of 1,3,5-TEB is reported. The transalkylation of 1,3,5-TEB with EB has been compared to the transformation reaction of pure 1,3,5-TEB and EB. The experimental results have revealed that reactivity of 1,3,5-TEB and selectivity of DEB is increased during the transalkylation reaction (EB + 1,3,5-TEB) as compared to the transformation reaction of pure EB or 1,3,5-TEB. The 1,3,5-TEB undergoes isomerization and a cracking reaction to produce DEB and EB but does not undergo any appreciable disproportionation reaction. The isomerization of 1,3,5-TEB is more active at low temperatures, while cracking is more active at high temperatures. © 2009 American Chemical Society.

1,3,5-Triethylbenzene Transformation Reactions Compared to Its Transalkylation Reaction with Ethylbenzene

KAUST Repository

Akhtar, M. Naseem

2009-08-20

The transalkylation of 1,3,5-triethylbenzene (1,3,5-TEB) with ethylbenzene (EB) has been studied over USYtype catalysts using a riser simulator that mimics the operation of a fluidized-bed reactor. The reaction mixture EB and 1,3,5-TEB was used at a molar ratio of 1:1, which is equivalent to 40:60 wt % of EB/1,3,5-TEB, respectively. The reaction temperature was varied from 350 to 500 °C with a time on stream ranging from 3-15 s. The effect of reaction conditions on 1,3,5-TEB conversion, DEB selectivity, and isomerization of 1,3,5-TEB is reported. The transalkylation of 1,3,5-TEB with EB has been compared to the transformation reaction of pure 1,3,5-TEB and EB. The experimental results have revealed that reactivity of 1,3,5-TEB and selectivity of DEB is increased during the transalkylation reaction (EB + 1,3,5-TEB) as compared to the transformation reaction of pure EB or 1,3,5-TEB. The 1,3,5-TEB undergoes isomerization and a cracking reaction to produce DEB and EB but does not undergo any appreciable disproportionation reaction. The isomerization of 1,3,5-TEB is more active at low temperatures, while cracking is more active at high temperatures. © 2009 American Chemical Society.

Liquid-Crystalline Ionic Liquids as Ordered Reaction Media for the Diels-Alder Reaction.

Science.gov (United States)

Bruce, Duncan W; Gao, Yanan; Canongia Lopes, José Nuno; Shimizu, Karina; Slattery, John M

2016-11-02

Liquid-crystalline ionic liquids (LCILs) are ordered materials that have untapped potential to be used as reaction media for synthetic chemistry. This paper investigates the potential for the ordered structures of LCILs to influence the stereochemical outcome of the Diels-Alder reaction between cyclopentadiene and methyl acrylate. The ratio of endo- to exo-product from this reaction was monitored for a range of ionic liquids (ILs) and LCILs. Comparison of the endo:exo ratios in these reactions as a function of cation, anion and liquid crystallinity of the reaction media, allowed for the effects of liquid crystallinity to be distinguished from anion effects or cation alkyl chain length effects. These data strongly suggest that the proportion of exo-product increases as the reaction media is changed from an isotropic IL to a LCIL. A detailed molecular dynamics (MD) study suggests that this effect is related to different hydrogen bonding interactions between the reaction media and the exo- and endo-transition states in solvents with layered, smectic ordering compared to those that are isotropic. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron transfer reactions

CERN Document Server

Cannon, R D

2013-01-01

Electron Transfer Reactions deals with the mechanisms of electron transfer reactions between metal ions in solution, as well as the electron exchange between atoms or molecules in either the gaseous or solid state. The book is divided into three parts. Part 1 covers the electron transfer between atoms and molecules in the gas state. Part 2 tackles the reaction paths of oxidation states and binuclear intermediates, as well as the mechanisms of electron transfer. Part 3 discusses the theories and models of the electron transfer process; theories and experiments involving bridged electron transfe

The Electronic Flux in Chemical Reactions. Insights on the Mechanism of the Maillard Reaction

Science.gov (United States)

Flores, Patricio; Gutiérrez-Oliva, Soledad; Herrera, Bárbara; Silva, Eduardo; Toro-Labbé, Alejandro

2007-11-01

The electronic transfer that occurs during a chemical process is analysed in term of a new concept, the electronic flux, that allows characterizing the regions along the reaction coordinate where electron transfer is actually taking place. The electron flux is quantified through the variation of the electronic chemical potential with respect to the reaction coordinate and is used, together with the reaction force, to shed light on reaction mechanism of the Schiff base formation in the Maillard reaction. By partitioning the reaction coordinate in regions in which different process might be taking place, electronic reordering associated to polarization and transfer has been identified and found to be localized at specific transition state regions where most bond forming and breaking occur.

Identifying Understudied Nuclear Reactions by Text-mining the EXFOR Experimental Nuclear Reaction Library

Energy Technology Data Exchange (ETDEWEB)

Hirdt, J.A. [Department of Mathematics and Computer Science, St. Joseph' s College, Patchogue, NY 11772 (United States); Brown, D.A., E-mail: dbrown@bnl.gov [National Nuclear Data Center, Brookhaven National Laboratory, Upton, NY 11973-5000 (United States)

2016-01-15

The EXFOR library contains the largest collection of experimental nuclear reaction data available as well as the data's bibliographic information and experimental details. We text-mined the REACTION and MONITOR fields of the ENTRYs in the EXFOR library in order to identify understudied reactions and quantities. Using the results of the text-mining, we created an undirected graph from the EXFOR datasets with each graph node representing a single reaction and quantity and graph links representing the various types of connections between these reactions and quantities. This graph is an abstract representation of the connections in EXFOR, similar to graphs of social networks, authorship networks, etc. We use various graph theoretical tools to identify important yet understudied reactions and quantities in EXFOR. Although we identified a few cross sections relevant for shielding applications and isotope production, mostly we identified charged particle fluence monitor cross sections. As a side effect of this work, we learn that our abstract graph is typical of other real-world graphs.

Identifying Understudied Nuclear Reactions by Text-mining the EXFOR Experimental Nuclear Reaction Library

International Nuclear Information System (INIS)

Hirdt, J.A.; Brown, D.A.

2016-01-01

The EXFOR library contains the largest collection of experimental nuclear reaction data available as well as the data's bibliographic information and experimental details. We text-mined the REACTION and MONITOR fields of the ENTRYs in the EXFOR library in order to identify understudied reactions and quantities. Using the results of the text-mining, we created an undirected graph from the EXFOR datasets with each graph node representing a single reaction and quantity and graph links representing the various types of connections between these reactions and quantities. This graph is an abstract representation of the connections in EXFOR, similar to graphs of social networks, authorship networks, etc. We use various graph theoretical tools to identify important yet understudied reactions and quantities in EXFOR. Although we identified a few cross sections relevant for shielding applications and isotope production, mostly we identified charged particle fluence monitor cross sections. As a side effect of this work, we learn that our abstract graph is typical of other real-world graphs.

Substrate-Directed Catalytic Selective Chemical Reactions.

Science.gov (United States)

Sawano, Takahiro; Yamamoto, Hisashi

2018-05-04

The development of highly efficient reactions at only the desired position is one of the most important subjects in organic chemistry. Most of the reactions in current organic chemistry are reagent- or catalyst-controlled reactions, and the regio- and stereoselectivity of the reactions are determined by the inherent nature of the reagent or catalyst. In sharp contrast, substrate-directed reaction determines the selectivity of the reactions by the functional group on the substrate and can strictly distinguish sterically and electronically similar multiple reaction sites in the substrate. In this Perspective, three topics of substrate-directed reaction are mainly reviewed: (1) directing group-assisted epoxidation of alkenes, (2) ring-opening reactions of epoxides by various nucleophiles, and (3) catalytic peptide synthesis. Our newly developed synthetic methods with new ligands including hydroxamic acid derived ligands realized not only highly efficient reactions but also pinpointed reactions at the expected position, demonstrating the substrate-directed reaction as a powerful method to achieve the desired regio- and stereoselective functionalization of molecules from different viewpoints of reagent- or catalyst-controlled reactions.

Microfabricated sleeve devices for chemical reactions

Science.gov (United States)

Northrup, M. Allen

2003-01-01

A silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and non-silicon based materials to provide the thermal properties desired. For example, the chamber may combine a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

What Is a Reaction Rate?

Science.gov (United States)

Schmitz, Guy

2005-01-01

The definition of reaction rate is derived and demonstrations are made for the care to be taken while using the term. Reaction rate can be in terms of a reaction property, the extent of reaction and thus it is possible to give a definition applicable in open and closed systems.

A Green Multicomponent Reaction for the Organic Chemistry Laboratory: The Aqueous Passerini Reaction

Science.gov (United States)

Hooper, Matthew M.; DeBoef, Brenton

2009-01-01

Water is the ideal green solvent for organic reactions. However, most organic molecules are insoluble in it. Herein, we report a laboratory module that takes advantage of this property. The Passerini reaction, a three-component coupling involving an isocyanide, aldehyde, and carboxylic acid, typically requires [similar to] 24 h reaction times in…

Fluorogenic organocatalytic reactions

NARCIS (Netherlands)

Raeisolsadati Oskouei, M.

2017-01-01

In this thesis, we introduce fluorescence spectroscopy as a new tool to gain insight into the interactions between the substrates and catalyst during organocatalytic reactions. The ultimate goal is to resolve the kinetics of the binding and reaction steps and obtain detailed understanding of the

Final technical report for award NO. DE-FG02-95ER20206

Energy Technology Data Exchange (ETDEWEB)

James P. Shapleigh

2010-02-23

ABSTRACT Initial work focused on the regulation of nitrite reductase, the defining reaction of denitrification as well as nitric oxide (NO) reductase. Expression of the genes encoding both proteins was controlled by NnrR. This regulator was shown to be responsive to NO. More recent work has shown NnrR function is also likely inhibited by oxygen. Therefore, it is this protein that sets the oxygen level at which nitrate respiration takes over from aerobic respiration. The gene encoding NO reductase appears to only require NnrR for expression. Expression of the gene encoding nitrite reductase is more complex. In addition to NnrR, a two component sensor regulator complex termed PrrA and PrrB is also required for expression. These proteins are global regulators and serve to link denitrification with other bioenergetic processes in the cell. They also provide an additional layer of oxygen dependent regulation. The sequencing of the R. sphaeroides 2.4.3 genome allowed us to identify several other genes regulated by NnrR. Surprisingly, most of the genes were not essential for denitrification. Their high level of conservation in related denitrifiers suggests they do provide a selectable benefit to the bacterium, however. We also examined the role of nitrate reductase in contributing to denitrification in R. sphaeroides. Strain 2.4.3 is unusual in having two distinct, but related clusters of genes encoding nitrate reductase. One of these genes clusters is expressed under high oxygen conditions but is repressed, likely by PrrB-PrrA, under low oxygen conditions. The other cluster is expressed only under low oxygen conditions. This cluster expresses the nitrate reductase used during denitrification. The high oxygen expressed cluster encodes a protein used for redox homeostasis. Surprisingly, both clusters are fully expressed even in the absence of nitrate. During the course of this work we found that the type strain of R. sphaeroides, 2.4.1, is a partial denitrifier because it

Polymer reaction engineering, an integrated approach

NARCIS (Netherlands)

Meyer, T.; Keurentjes, J.T.F.; Meyer, T.; Keurentjes, J.T.F.

2005-01-01

Summary This chapter contains sections titled: Polymer Materials A Short History of Polymer Reaction Engineering The Position of Polymer Reaction Engineering Toward Integrated Polymer Reaction Engineering The Disciplines in Polymer Reaction Engineering The Future: Product-inspired Polymer Reaction

High-precision (p,t) reactions to determine reaction rates of explosive stellar processes

NARCIS (Netherlands)

Matić, Andrija

2007-01-01

The aim of my study was to investigate the nuclear structure of 22Mg and 26Si. These two nuclei play a significant role in stellar reaction processes at high temperatures. On base of the obtained nuclear structure we calculated the stellar reaction rates for the following reactions: 18Ne(α,p)21Na,

Thermonuclear reaction rates. III

International Nuclear Information System (INIS)

Harris, M.J.; Fowler, W.A.; Caughlan, G.R.; Zimmerman, B.A.

1983-01-01

Stellar thermonuclear reaction rates are revised and updated, adding a number of new important reaction rates. Several reactions with large negative Q-values are included, and examples of them are discussed. The importance of the decay rates for Mg-26(p,n) exp 26 Al and Al-26(n,p) exp 26 Mg for stellar studies is emphasized. 19 references

Resonant thermonuclear reaction rate

International Nuclear Information System (INIS)

Haubold, H.J.; Mathai, A.M.

1986-01-01

Basic physical principles for the resonant and nonresonant thermonuclear reaction rates are applied to find their standard representations for nuclear astrophysics. Closed-form representations for the resonant reaction rate are derived in terms of Meijer's G-function. Analytic representations of the resonant and nonresonant nuclear reaction rates are compared and the appearance of Meijer's G-function is discussed in physical terms

Reaction mechanisms of metal complexes

CERN Document Server

Hay, R W

2000-01-01

This text provides a general background as a course module in the area of inorganic reaction mechanisms, suitable for advanced undergraduate and postgraduate study and/or research. The topic has important research applications in the metallurgical industry and is of interest in the science of biochemistry, biology, organic, inorganic and bioinorganic chemistry. In addition to coverage of substitution reactions in four-, five- and six-coordinate complexes, the book contains further chapters devoted to isomerization and racemization reactions, to the general field of redox reactions, and to the reactions of coordinated ligands. It is relevant in other fields such as organic, bioinorganic and biological chemistry, providing a bridge to organic reaction mechanisms. The book also contains a chapter on the kinetic background to the subject with many illustrative examples which should prove useful to those beginning research. Provides a general background as a course module in the area of inorganic reaction mechanis...

Dechlorinating reaction of organic chlorides

Energy Technology Data Exchange (ETDEWEB)

Yahata, Taneaki; Kihara, Shinji [Japan Atomic Energy Research Inst., Oarai, Ibaraki (Japan). Oarai Research Establishment; Ohuchi, Misao

1996-06-01

Dechlorination has been examined by the reaction between iron, aluminum powder or CaO and organic chlorides such as C{sub 2}HCl{sub 3} and CH{sub 2}Cl{sub 2}. Progress of the reaction was analyzed with mass spectrometer. The reaction between iron and organic chloride was rapidly occurred at the temperature between 350 and 440degC in an atmosphere of argon. Above 380degC, more than 99.5% of C{sub 2}HCl{sub 3} was decomposed within approximately 100 minutes. At 440degC, approximately 60% of C{sub 2}HCl{sub 3} was decomposed by the reaction with aluminium powder within approximately 100 minutes. At 440degC, reaction between C{sub 2}HCl{sub 3} and CaO powder were occurred rapidly in an atmosphere of argon to form CaCl{sub 2} and free carbon. Also in an atmosphere of air, nearly the same result was obtained. In this reaction, CaCl{sub 2}, CO and CO{sub 2} were formed. CH{sub 2}Cl{sub 2} was also decomposed by the reaction with iron at the temperature between 380 and 440degC. In the reaction, FeCl{sub 2}, carbon and hydrogen were formed. CH{sub 3}{sup +} and CH{sub 4} were observed during the dechlorinating reaction of CH{sub 2}Cl{sub 2}. Variation in particle size of iron powder such as 100, 150 and 250 mesh did not affect the reaction rate. (author)

Firefighter Nozzle Reaction

DEFF Research Database (Denmark)

Chin, Selena K.; Sunderland, Peter B.; Jomaas, Grunde

2017-01-01

Nozzle reaction and hose tension are analyzed using conservation of fluid momentum and assuming steady, inviscid flow and a flexible hose in frictionless contact with the ground. An expression that is independent of the bend angle is derived for the hose tension. If this tension is exceeded owing...... to anchor forces, the hose becomes straight. The nozzle reaction is found to equal the jet momentum flow rate, and it does not change when an elbow connects the hose to the nozzle. A forward force must be exerted by a firefighter or another anchor that matches the forward force that the jet would exert...... on a perpendicular wall. Three reaction expressions are derived, allowing it to be determined in terms of hose diameter, jet diameter, flow rate, and static pressure upstream of the nozzle. The nozzle reaction predictions used by the fire service are 56% to 90% of those obtained here for typical firefighting hand...

Reaction product imaging

Energy Technology Data Exchange (ETDEWEB)

Chandler, D.W. [Sandia National Laboratories, Livermore, CA (United States)

1993-12-01

Over the past few years the author has investigated the photochemistry of small molecules using the photofragment imaging technique. Bond energies, spectroscopy of radicals, dissociation dynamics and branching ratios are examples of information obtained by this technique. Along with extending the technique to the study of bimolecular reactions, efforts to make the technique as quantitative as possible have been the focus of the research effort. To this end, the author has measured the bond energy of the C-H bond in acetylene, branching ratios in the dissociation of HI, the energetics of CH{sub 3}Br, CD{sub 3}Br, C{sub 2}H{sub 5}Br and C{sub 2}H{sub 5}OBr dissociation, and the alignment of the CD{sub 3} fragment from CD{sub 3}I photolysis. In an effort to extend the technique to bimolecular reactions the author has studied the reaction of H with HI and the isotopic exchange reaction between H and D{sub 2}.

Theory of nuclear reactions, with applications to heavy ion scattering reactions

International Nuclear Information System (INIS)

Youssef, M.S.A.

1981-01-01

Nuclear science to day, has gained its stature through the pioneer work of both theorists and experimentalists within its two main divisions, Nuclear Reaction and Nuclear Structure theories. Our main interest in this theoretical work in nuclear reaction theory is focused on three topics, come under the headings of three parts which are the constituents of the present paper. Part 1 is concerned with ''Contributions to the theory of Threshold phenomena in nuclear reactions; cluster threshold states in heavy ion reactions''. Part II is devoted to ''Hermiticity of the Laplacian operator, R-matrix theories and direct interaction theory'', while part xII is ascribed to ''Heavy ion transfer reactions and scattering''. The aforementioned selected topics are the backbones of this thesis, which starts with general introduction giving a brief account about the material included in. In each part, investiqations are given in an extended manner through several chapters. Finally, the thesis is ended eith the chapter on ''General Discussions and Conclusions''. Appendices, references, and figure captions are found at the end of each part, the matter which we believe to facilitate much the reading through of the thesis. The first two parts are based (to some extent) on the same formal background (R-matrix, Kapur-Peierls-theories) and they converge to solve some physical problems originating from flux conservation laws in nuclear reactions, while the third part is indirect related to the first two; in principle it joins the other two parts under computational aspects. All of them after all, form the solidarity of the material included in the thesis. (author)

Estimating the Backup Reaction Wheel Orientation Using Reaction Wheel Spin Rates Flight Telemetry from a Spacecraft

Science.gov (United States)

Rizvi, Farheen

2013-01-01

A report describes a model that estimates the orientation of the backup reaction wheel using the reaction wheel spin rates telemetry from a spacecraft. Attitude control via the reaction wheel assembly (RWA) onboard a spacecraft uses three reaction wheels (one wheel per axis) and a backup to accommodate any wheel degradation throughout the course of the mission. The spacecraft dynamics prediction depends upon the correct knowledge of the reaction wheel orientations. Thus, it is vital to determine the actual orientation of the reaction wheels such that the correct spacecraft dynamics can be predicted. The conservation of angular momentum is used to estimate the orientation of the backup reaction wheel from the prime and backup reaction wheel spin rates data. The method is applied in estimating the orientation of the backup wheel onboard the Cassini spacecraft. The flight telemetry from the March 2011 prime and backup RWA swap activity on Cassini is used to obtain the best estimate for the backup reaction wheel orientation.

Allergic reactions seen in orthodontic treatment

Directory of Open Access Journals (Sweden)

Hande Görücü Coşkuner

2016-01-01

Full Text Available Allergy can be defined as inappropriate and harmful response to harmless and ordinary materials. Allergic reactions, like in other fields of dentistry, can also be seen in the field of orthodontics. The reactions that occur against orthodontic materials can be seen as irritant or hypersensitivity reactions. The main reason of the irritant reactions is friction between soft tissues and orthodontic appliances. However, the reason of the hypersensitivity reactions is usually the antigenicity of the materials. Hypersensitivity reactions are usually seen as allergic contact dermatitis on face and neck; the occurrence of mucosal-gingival reactions and dermal and systemic reactions are rare. Latex, metal and acrylic resins are the most common allergens in orthodontics. Apart from these materials, allergic reactions can occur against bonding materials, extraoral appliances, disinfectants and antimicrobial agents. The reactions that occur against extraoral appliances usually result from metallic and elastic parts of the appliances or the appliance parts that are in contact with skin. Orthodontists should be aware of the allergic reactions to protect their patients’ health. The aim of this review was to evaluate the allergic reactions seen in orthodontic patients and discuss the cautions that orthodontists can take.

Tattoo reaction: Case series

Directory of Open Access Journals (Sweden)

Muneer Mohamed

2018-04-01

Full Text Available Tattoo is going to be a very common practice especially among young people and we are witnessing a gradual increase of numerous potential complications to tattoo placement which are often seen by physicians, but generally unknown to the public. The most common skin reactions to tattoo include a transient acute inflammatory reaction due to trauma of the skin with needles and medical complications such as superficial and deep local infections, systemic infections, allergic contact dermatitis, photodermatitis, granulomatous and lichenoid reactions, and skin diseases localized on tattooed area (eczema, psoriasis, lichen, and morphea. In this series we present three cases of tattoo reaction.

Direct interaction between linear electron transfer chains and solute transport systems in bacteria

NARCIS (Netherlands)

Elferink, Marieke G.L.; Hellingwerf, Klaas J.; Belkum, Marco J. van; Poolman, Bert; Konings, Wil N.

1984-01-01

In studies on alanine and lactose transport in Rhodopseudomonas sphaeroides we have demonstrated that the rate of solute uptake in this phototrophic bacterium is regulated by the rate of light-induced cyclic electron transfer. In the present paper the interaction between linear electron transfer

Firefighter Nozzle Reaction

DEFF Research Database (Denmark)

Chin, Selena K.; Sunderland, Peter B.; Jomaas, Grunde

2017-01-01

to anchor forces, the hose becomes straight. The nozzle reaction is found to equal the jet momentum flow rate, and it does not change when an elbow connects the hose to the nozzle. A forward force must be exerted by a firefighter or another anchor that matches the forward force that the jet would exert...... on a perpendicular wall. Three reaction expressions are derived, allowing it to be determined in terms of hose diameter, jet diameter, flow rate, and static pressure upstream of the nozzle. The nozzle reaction predictions used by the fire service are 56% to 90% of those obtained here for typical firefighting hand...

A cellular automata approach to chemical reactions : 1 reaction controlled systems

NARCIS (Netherlands)

Korte, de A.C.J.; Brouwers, H.J.H.

2013-01-01

A direct link between the chemical reaction controlled (shrinking core) model and cellular automata, to study the dissolution of particles, is derived in this paper. Previous research on first and second order reactions is based on the concentration of the reactant. The present paper describes the

Substitution reactions of technetium complexes

International Nuclear Information System (INIS)

Omori, T.

1997-01-01

Substitution reactions of a series of technetium complexes are considered in comparison with corresponding reactions of rhenium. Rhenium and technetium complexes are rather inert in substitution reactions, the latter are characterized by greater rate constants when they proceed according to dissociative mechanism. In rare cases when k Tc /k Re id little it is assumed that the reaction proceeds according to the associative mechanism. (author)

Differences between Drug-Induced and Contrast Media-Induced Adverse Reactions Based on Spontaneously Reported Adverse Drug Reactions.

Science.gov (United States)

Ryu, JiHyeon; Lee, HeeYoung; Suh, JinUk; Yang, MyungSuk; Kang, WonKu; Kim, EunYoung

2015-01-01

We analyzed differences between spontaneously reported drug-induced (not including contrast media) and contrast media-induced adverse reactions. Adverse drug reactions reported by an in-hospital pharmacovigilance center (St. Mary's teaching hospital, Daejeon, Korea) from 2010-2012 were classified as drug-induced or contrast media-induced. Clinical patterns, frequency, causality, severity, Schumock and Thornton's preventability, and type A/B reactions were recorded. The trends among causality tools measuring drug and contrast-induced adverse reactions were analyzed. Of 1,335 reports, 636 drug-induced and contrast media-induced adverse reactions were identified. The prevalence of spontaneously reported adverse drug reaction-related admissions revealed a suspected adverse drug reaction-reporting rate of 20.9/100,000 (inpatient, 0.021%) and 3.9/100,000 (outpatients, 0.004%). The most common adverse drug reaction-associated drug classes included nervous system agents and anti-infectives. Dermatological and gastrointestinal adverse drug reactions were most frequently and similarly reported between drug and contrast media-induced adverse reactions. Compared to contrast media-induced adverse reactions, drug-induced adverse reactions were milder, more likely to be preventable (9.8% vs. 1.1%, p contrast media-induced adverse reactions (56.6%, p = 0.066). Causality patterns differed between the two adverse reaction classes. The World Health Organization-Uppsala Monitoring Centre causality evaluation and Naranjo algorithm results significantly differed from those of the Korean algorithm version II (p contrast media-induced adverse reactions. The World Health Organization-Uppsala Monitoring Centre and Naranjo algorithm causality evaluation afforded similar results.

Effective dynamics along given reaction coordinates, and reaction rate theory.

Science.gov (United States)

Zhang, Wei; Hartmann, Carsten; Schütte, Christof

2016-12-22

In molecular dynamics and related fields one considers dynamical descriptions of complex systems in full (atomic) detail. In order to reduce the overwhelming complexity of realistic systems (high dimension, large timescale spread, limited computational resources) the projection of the full dynamics onto some reaction coordinates is examined in order to extract statistical information like free energies or reaction rates. In this context, the effective dynamics that is induced by the full dynamics on the reaction coordinate space has attracted considerable attention in the literature. In this article, we contribute to this discussion: we first show that if we start with an ergodic diffusion process whose invariant measure is unique then these properties are inherited by the effective dynamics. Then, we give equations for the effective dynamics, discuss whether the dominant timescales and reaction rates inferred from the effective dynamics are accurate approximations of such quantities for the full dynamics, and compare our findings to results from approaches like Mori-Zwanzig, averaging, or homogenization. Finally, by discussing the algorithmic realization of the effective dynamics, we demonstrate that recent algorithmic techniques like the "equation-free" approach and the "heterogeneous multiscale method" can be seen as special cases of our approach.

Wang-Landau Reaction Ensemble Method: Simulation of Weak Polyelectrolytes and General Acid-Base Reactions.

Science.gov (United States)

Landsgesell, Jonas; Holm, Christian; Smiatek, Jens

2017-02-14

We present a novel method for the study of weak polyelectrolytes and general acid-base reactions in molecular dynamics and Monte Carlo simulations. The approach combines the advantages of the reaction ensemble and the Wang-Landau sampling method. Deprotonation and protonation reactions are simulated explicitly with the help of the reaction ensemble method, while the accurate sampling of the corresponding phase space is achieved by the Wang-Landau approach. The combination of both techniques provides a sufficient statistical accuracy such that meaningful estimates for the density of states and the partition sum can be obtained. With regard to these estimates, several thermodynamic observables like the heat capacity or reaction free energies can be calculated. We demonstrate that the computation times for the calculation of titration curves with a high statistical accuracy can be significantly decreased when compared to the original reaction ensemble method. The applicability of our approach is validated by the study of weak polyelectrolytes and their thermodynamic properties.

A Multilevel Adaptive Reaction-splitting Simulation Method for Stochastic Reaction Networks

KAUST Repository

Moraes, Alvaro; Tempone, Raul; Vilanova, Pedro

2016-01-01

In this work, we present a novel multilevel Monte Carlo method for kinetic simulation of stochastic reaction networks characterized by having simultaneously fast and slow reaction channels. To produce efficient simulations, our method adaptively classifies the reactions channels into fast and slow channels. To this end, we first introduce a state-dependent quantity named level of activity of a reaction channel. Then, we propose a low-cost heuristic that allows us to adaptively split the set of reaction channels into two subsets characterized by either a high or a low level of activity. Based on a time-splitting technique, the increments associated with high-activity channels are simulated using the tau-leap method, while those associated with low-activity channels are simulated using an exact method. This path simulation technique is amenable for coupled path generation and a corresponding multilevel Monte Carlo algorithm. To estimate expected values of observables of the system at a prescribed final time, our method bounds the global computational error to be below a prescribed tolerance, TOL, within a given confidence level. This goal is achieved with a computational complexity of order O(TOL-2), the same as with a pathwise-exact method, but with a smaller constant. We also present a novel low-cost control variate technique based on the stochastic time change representation by Kurtz, showing its performance on a numerical example. We present two numerical examples extracted from the literature that show how the reaction-splitting method obtains substantial gains with respect to the standard stochastic simulation algorithm and the multilevel Monte Carlo approach by Anderson and Higham. © 2016 Society for Industrial and Applied Mathematics.

A Multilevel Adaptive Reaction-splitting Simulation Method for Stochastic Reaction Networks

KAUST Repository

Moraes, Alvaro

2016-07-07

In this work, we present a novel multilevel Monte Carlo method for kinetic simulation of stochastic reaction networks characterized by having simultaneously fast and slow reaction channels. To produce efficient simulations, our method adaptively classifies the reactions channels into fast and slow channels. To this end, we first introduce a state-dependent quantity named level of activity of a reaction channel. Then, we propose a low-cost heuristic that allows us to adaptively split the set of reaction channels into two subsets characterized by either a high or a low level of activity. Based on a time-splitting technique, the increments associated with high-activity channels are simulated using the tau-leap method, while those associated with low-activity channels are simulated using an exact method. This path simulation technique is amenable for coupled path generation and a corresponding multilevel Monte Carlo algorithm. To estimate expected values of observables of the system at a prescribed final time, our method bounds the global computational error to be below a prescribed tolerance, TOL, within a given confidence level. This goal is achieved with a computational complexity of order O(TOL-2), the same as with a pathwise-exact method, but with a smaller constant. We also present a novel low-cost control variate technique based on the stochastic time change representation by Kurtz, showing its performance on a numerical example. We present two numerical examples extracted from the literature that show how the reaction-splitting method obtains substantial gains with respect to the standard stochastic simulation algorithm and the multilevel Monte Carlo approach by Anderson and Higham. © 2016 Society for Industrial and Applied Mathematics.

Study of the (p,d3He) reaction as a quasi-free reaction process

International Nuclear Information System (INIS)

Cowley, A.A.; Roos, P.G.; Chant, N.S.; Woody, R. III; Holmgren, H.D.; Goldberg, D.A.

1976-11-01

The (p,d 3 He) reaction on 6 Li, 7 Li, 9 Be, and 12 C has been investigated in conjunction with studies of the (p,pα) reaction on the same targets. Coincident data for all four targets were obtained at a bombarding energy of 100 MeV for numerous angle pairs in order to test the reaction mechanism. Comparisons of the (p,d 3 He) data to both (p,pα) data and distorted wave impulse approximation calculations (DWIA) indicate a dominance of the direct quasi-free reaction process (p + alpha yields d + 3 He). The absolute alpha-particle spectroscopic factors extracted using DWIA analysis are in agreement with the values obtained in the (p,pα) reaction

Diels-Alder reactions: The effects of catalyst on the addition reaction

Science.gov (United States)

Yilmaz, Özgür; Kus, Nermin Simsek; Tunç, Tuncay; Sahin, Ertan

2015-10-01

The reaction between 2,3-dimethyl-1,3-butadiene and dimethyl 7-oxabicyclo[2.2.1]hepta-2,5-diene-2,3-dicarboxylate is efficiently achieved with small amounts of catalyst, i.e. phenol, AcOH, nafion, and β-cyclodextrin. Exo-diastereoselective cycloaddition reactions were observed both without catalyst and different catalysts for 48 days. As a result, different products (tricyclicmolecule 5, retro-Diels-Alder product 6, and oxidation product 7) were obtained with different catalysts. In addition, we synthesized Diels-Alders product 8 and tricyclocyclitol 10 via Diels-Alder reaction. The structures of these products were characterized by 1H NMR, 13C NMR, MS and IR spectroscopy.

Nuclear Reaction Data File for Astrophysics (NRDF/A) in Hokkaido University Nuclear Reaction Data Center

International Nuclear Information System (INIS)

Kato, Kiyoshi; Kimura, Masaaki; Furutachi, Naoya; Makinaga, Ayano; Togashi, Tomoaki; Otuka, Naohiko

2010-01-01

The activities of the Japan Nuclear Reaction Data Centre is explained. The main task of the centre is data compilation of Japanese nuclear reaction data in collaboration of the International Network of Nuclear Reaction Data Centres. As one of recent activities, preparation of a new database (NRDF/A) and evaluation of astronuclear reaction data are reported. Collaboration in the nuclear data activities among Asian countries is proposed.

Limits for Stochastic Reaction Networks

DEFF Research Database (Denmark)

Cappelletti, Daniele

Reaction systems have been introduced in the 70s to model biochemical systems. Nowadays their range of applications has increased and they are fruitfully used in dierent elds. The concept is simple: some chemical species react, the set of chemical reactions form a graph and a rate function...... is associated with each reaction. Such functions describe the speed of the dierent reactions, or their propensities. Two modelling regimes are then available: the evolution of the dierent species concentrations can be deterministically modelled through a system of ODE, while the counts of the dierent species...... at a certain time are stochastically modelled by means of a continuous-time Markov chain. Our work concerns primarily stochastic reaction systems, and their asymptotic properties. In Paper I, we consider a reaction system with intermediate species, i.e. species that are produced and fast degraded along a path...

Metal-free bioconjugation reactions.

Science.gov (United States)

van Berkel, Sander S; van Delft, Floris L

2013-01-01

The recent strategy to apply chemical reactions to address fundamental biological questions has led to the emergence of entirely new conjugation reactions that are fast and irreversible, yet so mild and selective that they can be performed even in living cells or organisms. These so-called bioorthogonal reactions open novel avenues, not only in chemical biology research, but also in many other life sciences applications, including the modulation of biopharmaceuticals by site-specific modification approaches.

Reaction of hydrogen atoms with acrylaldehyde

International Nuclear Information System (INIS)

Koda, Seiichiro; Nakamura, Kazumoto; Hoshino, Takashi; Hikita, Tsutomu

1978-01-01

The reaction of hydrogen atoms with acrylaldehyde was investigated in a fast flow reactor equipped with a time-of-flight type mass spectrometer under reduced pressure. Main reaction products were carbon monoxide, ethylene, ethane, methane, and propanal. Consideration of the distributions of the reaction products under various reaction conditions showed that hydrogen atoms attacked the C=C double bond, especially its inner carbon side under reduced pressure. Resulting hot radicals caused subsequent reactions. The relative value of the apparent bimolecular rate constant of the reaction against that of trans-2-butene with hydrogen atoms was 1.6+-0.2, which supported the above-mentioned initial reaction. (auth.)

SOLVENTLESS MIGRATORY-INSERTION REACTIONS OF ...

African Journals Online (AJOL)

Preferred Customer

The product formed by reaction of an alkyl or aryl cyclopentadienyl metal carbonyl .... (as also observed from the NMR tube experiments) that the solventless reaction between ... As can be seen from Figure 3, the reaction rate in the melt.

Investigation of Na-CO{sub 2} Reaction with Initial Reaction in Various Reacting Surface

Energy Technology Data Exchange (ETDEWEB)

Kim, Hyun Su; Park, Gunyeop; Kim, Soo Jae; Park, Hyun Sun; Kim, Moo Hwan [POSTECH, Pohang (Korea, Republic of); Wi, Myung-Hwan [KAERI, Daejeon (Korea, Republic of)

2015-10-15

The reaction products that cause oxidation and erosion are threaten the heat transfer tubes so that it is necessary to investigate Na-CO{sub 2} reaction according to various experimental parameter. Unlike SWR, Na-CO{sub 2} reaction is more complex to deal with reaction kinetics. Since a comprehensive understanding of Na-CO{sub 2} reaction mechanism is crucial for the safety analysis, the reaction phenomenon under the various conditions was investigated. The current issue is to make a database for developing computational code for CO{sub 2} gas leak situation because it is experimentally difficult to analyze the actual accident situation. Most studies on Na-CO{sub 2} interaction reports that chemical reaction is getting vigorous as temperature increased and reactivity is sensitive as temperature change between 400 .deg. C and 600 .deg. C. Therefore, temperature range is determined based on the operating condition (450 - 500 .deg. C) of KALIMER-600 employed as supercritical CO{sub 2} brayton cycle energy conversion system for Na-CO{sub 2} heat exchanger. And next parameter is sodium surface area which contact between sodium and CO{sub 2} when CO{sub 2} is injected into sodium pool in the accident situation. So, the fundamental surface reaction is experimentally studied in the range of 8 - 12cm{sup 2}. Additionally, it has been reported in recent years that CO{sub 2} Flow rate affects reactivity less significantly and CO{sub 2} flow rate is assumed that 5 SLPM (standard liter per minute) is suitable as a basis for a small leakage. The finally selected control parameters is sodium temperature and reacting surface area with constant CO{sub 2} flow rate. Na-CO{sub 2} reaction test is performed for investigating risk of potential accident which contacts with liquid sodium and CO{sub 2}. Amount of reaction is saturated as time passed because of kept a balance between production of solid phase reaction products and amount of diffusivity. These results contribute to make a

Transfusion reactions in pediatric compared with adult patients: a look at rate, reaction type, and associated products.

Science.gov (United States)

Oakley, Fredrick D; Woods, Marcella; Arnold, Shanna; Young, Pampee P

2015-03-01

The majority of reports on transfusion reactions address adult patients. Less is known about the types, incidence, and other clinical details of transfusion reactions in pediatric populations. Furthermore, to our knowledge, there have been no previous reports directly comparing these aspects between adults and pediatric patient populations to assess if there are differences. Between the period of January 1, 2011, and February 1, 2013, all reported adult and pediatric transfusion reactions at Vanderbilt University Medical Center (VUMC) were evaluated by transfusion medicine clinical service. The information was subsequently shared with the hemovigilance database. Data provided to hemovigilance included age, sex, blood product associated with the reaction, severity of the reaction, and the type of transfusion reactions. These were collated with hospital and blood bank information system-acquired data on overall admission and product transfusion. A total of 133,671 transfusions were performed at VUMC during the study period including 20,179 platelet (PLT) transfusions, 31,605 plasma transfusions, 79,933 red blood cell (RBC) transfusions, and 2154 cryoprecipitate transfusions. Over the same period, 108 pediatric and 277 adult transfusion reactions were recorded. This corresponds to an incidence of 6.2 reactions per 1000 transfusions within the pediatric (age reactions per 1000 transfusions within the adult population. In both adult and pediatric populations, transfusion reactions were most commonly associated with PLT, followed by RBC, and then plasma transfusions. Within the pediatric population, subset analysis identified multiple differences when compared to the adult population, including an increased incidence of allergic transfusion reactions (2.7/1000 vs. 1.1/1000, p reactions (1.9/1000 vs. 0.47/1000, p reactions (0.29/1000 vs. 0.078/1000, p reaction incidence was the same between sexes in adults, in pediatric patients, reactions were more common in male

Reaction-Map of Organic Chemistry

Science.gov (United States)

Murov, Steven

2007-01-01

The Reaction-Map of Organic Chemistry lists all the most commonly studied reactions in organic chemistry on one page. The discussed Reaction-Map will act as another learning aide for the students, making the study of organic chemistry much easier.

The oxygen evolution reaction on cobalt Part I. Reaction order experiments and impedance measurements

NARCIS (Netherlands)

Kobussen, A.G.C.; Willems, H.; Wit, J.H.W. de; Broers, G.H.J.

1984-01-01

It was found that the oxygen evolution reaction on cobalt in concentrated KOH solutions can be described differently for low and high overpotentials. In the overpotential range from 150 to 280 mV, the reaction has a Tafel slope of approximately 40 mV and a reaction order with respect to the KOH

The reaction mechanism of the (3HE,T) reaction and applications to nuclear structure

NARCIS (Netherlands)

1986-01-01

In this thesis we present a study on the reaction meachanism of the (3He,t) reaction at 70-80 MeV bombarding energy and on structures of the residual nuclei excited in this reaction: 24-Al, 26-Al, 28-P, 32-Cl, 40-Sc, 42-Sc and 58-Cu... Zie: Summary

Reaction of Aldehydes/Ketones with Electron-Deficient 1,3,5-Triazines Leading to Functionalized Pyrimidines as Diels-Alder/Retro-Diels-Alder Reaction Products: Reaction Development and Mechanistic Studies.

Science.gov (United States)

Yang, Kai; Dang, Qun; Cai, Pei-Jun; Gao, Yang; Yu, Zhi-Xiang; Bai, Xu

2017-03-03

Catalytic inverse electron demand Diels-Alder (IEDDA) reactions of heterocyclic aza-dienes are rarely reported since highly reactive and electron-rich dienophiles are often found not compatible with strong acids such as Lewis acids. Herein, we disclose that TFA-catalyzed reactions of electron-deficient 1,3,5-triazines and electron-deficient aldehydes/ketones can take place. These reactions led to highly functionalized pyrimidines as products in fair to good yields. The reaction mechanism was carefully studied by the combination of experimental and computational studies. The reactions involve a cascade of stepwise inverse electron demand hetero-Diels-Alder (ihDA) reactions, followed by retro-Diels-Alder (rDA) reactions and elimination of water. An acid was required for both ihDA and rDA reactions. This mechanism was further verified by comparing the relative reactivity of aldehydes/ketones and their corresponding vinyl ethers in the current reaction system.

Hypersensitivity reactions in patients receiving hemodialysis.

Science.gov (United States)

Butani, Lavjay; Calogiuri, Gianfranco

2017-06-01

To describe hypersensitivity reactions in patients receiving maintenance hemodialysis. PubMed search of articles published during the past 30 years with an emphasis on publications in the past decade. Case reports and review articles describing hypersensitivity reactions in the context of hemodialysis. Pharmacologic agents are the most common identifiable cause of hypersensitivity reactions in patients receiving hemodialysis. These include iron, erythropoietin, and heparin, which can cause anaphylactic or pseudoallergic reactions, and topical antibiotics and anesthetics, which lead to delayed-type hypersensitivity reactions. Many hypersensitivity reactions are triggered by complement activation and increased bradykinin resulting from contact system activation, especially in the context of angiotensin-converting enzyme inhibitor use. Several alternative pharmacologic preparations and dialyzer membranes are available, such that once an etiology for the reaction is established, recurrences can be prevented without affecting the quality of care provided to patients. Although hypersensitivity reactions are uncommon in patients receiving hemodialysis, they can be life-threatening. Moreover, considering the large prevalence of the end-stage renal disease population, the implications of such reactions are enormous. Most reactions are pseudoallergic and not mediated by immunoglobulin E. The multiplicity of potential exposures and the complexity of the environment to which patients on dialysis are exposed make it challenging to identify the precise cause of these reactions. Great diligence is needed to investigate hypersensitivity reactions to avoid recurrence in this high-risk population. Copyright © 2017 American College of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

Silicon-based sleeve devices for chemical reactions

Science.gov (United States)

Northrup, M. Allen; Mariella, Jr., Raymond P.; Carrano, Anthony V.; Balch, Joseph W.

1996-01-01

A silicon-based sleeve type chemical reaction chamber that combines heaters, such as doped polysilicon for heating, and bulk silicon for convection cooling. The reaction chamber combines a critical ratio of silicon and silicon nitride to the volume of material to be heated (e.g., a liquid) in order to provide uniform heating, yet low power requirements. The reaction chamber will also allow the introduction of a secondary tube (e.g., plastic) into the reaction sleeve that contains the reaction mixture thereby alleviating any potential materials incompatibility issues. The reaction chamber may be utilized in any chemical reaction system for synthesis or processing of organic, inorganic, or biochemical reactions, such as the polymerase chain reaction (PCR) and/or other DNA reactions, such as the ligase chain reaction, which are examples of a synthetic, thermal-cycling-based reaction. The reaction chamber may also be used in synthesis instruments, particularly those for DNA amplification and synthesis.

Characterising Complex Enzyme Reaction Data.

Directory of Open Access Journals (Sweden)

Handan Melike Dönertaş

Full Text Available The relationship between enzyme-catalysed reactions and the Enzyme Commission (EC number, the widely accepted classification scheme used to characterise enzyme activity, is complex and with the rapid increase in our knowledge of the reactions catalysed by enzymes needs revisiting. We present a manual and computational analysis to investigate this complexity and found that almost one-third of all known EC numbers are linked to more than one reaction in the secondary reaction databases (e.g., KEGG. Although this complexity is often resolved by defining generic, alternative and partial reactions, we have also found individual EC numbers with more than one reaction catalysing different types of bond changes. This analysis adds a new dimension to our understanding of enzyme function and might be useful for the accurate annotation of the function of enzymes and to study the changes in enzyme function during evolution.

Nuclear reactions as structure probes

International Nuclear Information System (INIS)

Fernandez, Bernard; Cugnon, Joseph; Roussel-Chomaz, Patricia; Sparenberg, Jean-Marc; Oliveira Santos, Francois de; Bauge, Eric; Poves, Alfredo; Keeley, Nicholas; Simenel, Cedric; Avez, Benoit; Lacroix, Denis; Baye, Daniel; Cortina-Gil, Dolores; Pons, Alexandre

2007-09-01

This publication gathers courses which aim at giving a view on new experiments which are performed by using radioactive beams, notably low intensity beams, in different accelerators, and allow the structure of very exotic nuclei to be characterized. Experimental as well as theoretical aspects are thus addressed. The contributions propose: a brief history of nuclear reactions and of instruments used to study them from the discovery of nucleus to the DWBA (Distorted Wave Born Approximation); an overview of nuclear reactions; experimental techniques; the theory of collisions at low energy; resonant elastic scattering, inelastic scattering and astrophysical reactions; to probe nuclear structure with nucleons; shell model and spectroscopic factors; analysis of transfer reactions and determination of spectroscopic factors; microscopic approaches of nuclear dynamics; theoretical aspects of dissociation reactions; experimental aspects of knockout reactions; research in oenology with the chemical characterisation of defective ageing of dry white wines

Microfluidic chemical reaction circuits

Science.gov (United States)

Lee, Chung-cheng [Irvine, CA; Sui, Guodong [Los Angeles, CA; Elizarov, Arkadij [Valley Village, CA; Kolb, Hartmuth C [Playa del Rey, CA; Huang, Jiang [San Jose, CA; Heath, James R [South Pasadena, CA; Phelps, Michael E [Los Angeles, CA; Quake, Stephen R [Stanford, CA; Tseng, Hsian-rong [Los Angeles, CA; Wyatt, Paul [Tipperary, IE; Daridon, Antoine [Mont-Sur-Rolle, CH

2012-06-26

New microfluidic devices, useful for carrying out chemical reactions, are provided. The devices are adapted for on-chip solvent exchange, chemical processes requiring multiple chemical reactions, and rapid concentration of reagents.

Chemical reactions in solvents and melts

CERN Document Server

Charlot, G

1969-01-01

Chemical Reactions in Solvents and Melts discusses the use of organic and inorganic compounds as well as of melts as solvents. This book examines the applications in organic and inorganic chemistry as well as in electrochemistry. Organized into two parts encompassing 15 chapters, this book begins with an overview of the general properties and the different types of reactions, including acid-base reactions, complex formation reactions, and oxidation-reduction reactions. This text then describes the properties of inert and active solvents. Other chapters consider the proton transfer reactions in

Sodium concrete reaction - Structural considerations

International Nuclear Information System (INIS)

Ferskakis, G.N.

1984-01-01

An overview of the sodium concrete reaction phenomenon, with emphasis on structural considerations, is presented. Available test results for limestone, basalt, and magnetite concrete with various test article configurations are reviewed. Generally, tests indicate reaction is self limiting before all sodium is used. Uncertainties, however, concerning the mechanism for penetration of sodium into concrete have resulted in different theories about a reaction model. Structural behavior may be significant in the progression of the reaction due to thermal-structuralchemical interactions involving tensile cracking, compressive crushing, or general deterioration of concrete and the exposure of fresh concrete surfaces to react with sodium. Structural behavior of test articles and potential factors that could enhance the progression of the reaction are discussed

Low energy ion-molecule reactions

Energy Technology Data Exchange (ETDEWEB)

Farrar, J.M. [Univ. of Rochester, NY (United States)

1993-12-01

This project is concerned with elucidating the dynamics of elementary ion-molecule reactions at collision energies near and below 1 eV. From measurements of the angular and energy distributions of the reaction products, one can infer intimathe details about the nature of collisions leading to chemical reaction, the geometries and lifetimes of intermediate complexes that govern the reaction dynamics, and the collision energy dependence of these dynamical features. The author employs crossed-beam low energy mass spectrometry technology developed over the last several years, with the focus of current research on proton transfer and hydrogen atom transfer reactions of te O{sup {minus}} ion with species such as HF, H{sub 2}O, and NH{sub 3}.

Multiresponse modelling of the caramelisation reaction

OpenAIRE

Quintas, Mafalda; Guimarães, Carla; Baylina, João; Brandão, Teresa R. S.; Silva, Cristina L.M.

2007-01-01

Multiresponse modelling is a powerful tool for studying complex kinetics of reactions occurring in food products. This modelling technique uses information of reactants and products involved, allowing insightful kinetic parameters estimation and helping in clarifying reaction mechanisms. One example of a complex reaction that occurs in food processing is the caramelisation reaction. Caramelisation is the common name for a group of reactions observed when carbohydrates are exposed to high temp...

Correlations between reaction product yields as a tool for probing heavy-ion reaction scenarios

International Nuclear Information System (INIS)

Gawlikowicz, W.; Agnihotri, D. K.; Baldwin, S. A.; Schroeder, W. U.; Toke, J.; Charity, R. J.; Sarantites, D. G.; Sobotka, L. G.; Souza, R. T. de; Barczyk, T.; Grotowski, K.; Micek, S.; Planeta, R.; Sosin, Z.

2010-01-01

Experimental multidimensional joint distributions of neutrons and charged reaction products were analyzed for 136 Xe + 209 Bi reactions at E/A=28, 40, and 62 MeV and were found to exhibit several different types of prominent correlation patterns. Some of these correlations have a simple explanation in terms of the system excitation energy and pose little challenge to most statistical decay theories. However, several other types of correlation patterns are difficult to reconcile with some, but not other, possible reaction scenarios. In this respect, correlations between the average atomic numbers of intermediate-mass fragments, on the one hand, and light particle multiplicities, on the other, are notable. This kind of multiparticle correlation provides a useful tool for probing reaction scenarios, which is different from the traditional approach of interpreting inclusive yields of individual reaction products.

Evolutionary change in continuous reaction norms

DEFF Research Database (Denmark)

Murren, Courtney J; Maclean, Heidi J; Diamond, Sarah E

2014-01-01

Understanding the evolution of reaction norms remains a major challenge in ecology and evolution. Investigating evolutionary divergence in reaction norm shapes between populations and closely related species is one approach to providing insights. Here we use a meta-analytic approach to compare...... divergence in reaction norms of closely related species or populations of animals and plants across types of traits and environments. We quantified mean-standardized differences in overall trait means (Offset) and reaction norm shape (including both Slope and Curvature). These analyses revealed...... contributed to the best-fitting models, especially for Offset, Curvature, and the total differences (Total) between reaction norms. Congeneric species had greater differences in reaction norms than populations, and novel environmental conditions increased the differences in reaction norms between populations...

Treatment and Managing Reactions

Science.gov (United States)

... of reactions. Learn more here. Milk Egg Peanut Tree Nuts Soy Wheat Fish Shellfish Sesame Other Food ... a severe reaction. Consider wearing an emergency medical identification (e.g., bracelet, other jewelry). What to Read ...

An Improved Protocol for the Aldehyde Olefination Reaction Using (bmim ( as Reaction Medium

Directory of Open Access Journals (Sweden)

Vivek Srivastava

2013-01-01

Full Text Available [Ru(CODCl2]/CuCl2·2H2O/LiCl catalytic system works efficiently in ionic liquid media for aldehyde olefination reaction. It offers good yield and selectivity with the added advantage of 5 times recyclability for [Ru(CODCl2] /CuCl2·2H2O/LiCl catalytic system. We also successfully reduced the reaction time from 12 hours to 9 hours for the aldehyde olefination reaction.

Improved predictions of nuclear reaction rates with the TALYS reaction code for astrophysical applications

International Nuclear Information System (INIS)

Goriely, S.; Hilaire, S.; Koning, A.J

2008-01-01

Context. Nuclear reaction rates of astrophysical applications are traditionally determined on the basis of Hauser-Feshbach reaction codes. These codes adopt a number of approximations that have never been tested, such as a simplified width fluctuation correction, the neglect of delayed or multiple-particle emission during the electromagnetic decay cascade, or the absence of the pre-equilibrium contribution at increasing incident energies. Aims. The reaction code TALYS has been recently updated to estimate the Maxwellian-averaged reaction rates that are of astrophysical relevance. These new developments enable the reaction rates to be calculated with increased accuracy and reliability and the approximations of previous codes to be investigated. Methods. The TALYS predictions for the thermonuclear rates of relevance to astrophysics are detailed and compared with those derived by widely-used codes for the same nuclear ingredients. Results. It is shown that TALYS predictions may differ significantly from those of previous codes, in particular for nuclei for which no or little nuclear data is available. The pre-equilibrium process is shown to influence the astrophysics rates of exotic neutron-rich nuclei significantly. For the first time, the Maxwellian- averaged (n, 2n) reaction rate is calculated for all nuclei and its competition with the radiative capture rate is discussed. Conclusions. The TALYS code provides a new tool to estimate all nuclear reaction rates of relevance to astrophysics with improved accuracy and reliability. (authors)

Resonant elastic scattering, inelastic scattering and astrophysical reactions; Diffusion elastique resonante, diffusion inelastique et reactions astrophysiques

Energy Technology Data Exchange (ETDEWEB)

De Oliveira Santos, F. [Grand Accelerateur National d' Ions Lourds, UMR 6415, 14 - Caen (France)

2007-07-01

Nuclear reactions can occur at low kinetic energy. Low-energy reactions are characterized by a strong dependence on the structure of the compound nucleus. It turns out that it is possible to study the nuclear structure by measuring these reactions. In this course, three types of reactions are treated: Resonant Elastic Scattering (such as N{sup 14}(p,p)N{sup 14}), Inelastic Scattering (such as N{sup 14}(p,p')N{sup 14*}) and Astrophysical reactions (such as N{sup 14}(p,{gamma})O{sup 15}). (author)

Reaction mechanisms

International Nuclear Information System (INIS)

Nguyen Trong Anh

1988-01-01

The 1988 progress report of the Reaction Mechanisms laboratory (Polytechnic School, France), is presented. The research topics are: the valence bond methods, the radical chemistry, the modelling of the transition states by applying geometric constraints, the long range interactions (ion - molecule) in gaseous phase, the reaction sites in gaseous phase and the mass spectroscopy applications. The points of convergence between the investigations of the mass spectroscopy and the theoretical chemistry teams, as well as the purposes guiding the research programs, are discussed. The published papers, the conferences, the congress communications and the thesis, are also reported [fr

Sodium-concrete reaction model development

International Nuclear Information System (INIS)

Nguyen, D.H.; Muhlestein, L.D.; Postma, A.K.

1982-07-01

Major observations have been formulated after reviewing test results for over 100 sodium-concrete reaction tests. The observations form the basis for developing a mechanistic model to predict the transient behavior of sodium-concrete reactions. The major observations are listed. Mechanisms associated with sodium and water transport to the reaction zone are identified, and represented by appropriate mathematical expressions. The model attempts to explain large-scale, long-term (100 h) test results were sodium-concrete reactions terminated even in the presence of unreacted sodium and concrete

Photobiological hydrogen production and carbon dioxide sequestration

Science.gov (United States)

Berberoglu, Halil

Photobiological hydrogen production is an alternative to thermochemical and electrolytic technologies with the advantage of carbon dioxide sequestration. However, it suffers from low solar to hydrogen energy conversion efficiency due to limited light transfer, mass transfer, and nutrient medium composition. The present study aims at addressing these limitations and can be divided in three parts: (1) experimental measurements of the radiation characteristics of hydrogen producing and carbon dioxide consuming microorganisms, (2) solar radiation transfer modeling and simulation in photobioreactors, and (3) parametric experiments of photobiological hydrogen production and carbon dioxide sequestration. First, solar radiation transfer in photobioreactors containing microorganisms and bubbles was modeled using the radiative transport equation (RTE) and solved using the modified method of characteristics. The study concluded that Beer-Lambert's law gives inaccurate results and anisotropic scattering must be accounted for to predict the local irradiance inside a photobioreactor. The need for accurate measurement of the complete set of radiation characteristics of microorganisms was established. Then, experimental setup and analysis methods for measuring the complete set of radiation characteristics of microorganisms have been developed and successfully validated experimentally. A database of the radiation characteristics of representative microorganisms have been created including the cyanobacteria Anabaena variabilis, the purple non-sulfur bacteria Rhodobacter sphaeroides and the green algae Chlamydomonas reinhardtii along with its three genetically engineered strains. This enabled, for the first time, quantitative assessment of the effect of genetic engineering on the radiation characteristics of microorganisms. In addition, a parametric experimental study has been performed to model the growth, CO2 consumption, and H 2 production of Anabaena variabilis as functions of

HMGB1 Contributes to the Expression of P-Glycoprotein in Mouse Epileptic Brain through Toll-Like Receptor 4 and Receptor for Advanced Glycation End Products.

Directory of Open Access Journals (Sweden)

Yan Chen

Full Text Available The objective of the present study was to investigate the role of high-mobility group box-1 (HMGB1 in the seizure-induced P-glycoprotein (P-gp overexpression and the underlying mechanism. Kainic acid (KA-induced mouse seizure model was used for in vivo experiments. Male C57BL/6 mice were divided into four groups: normal saline control (NS group, KA-induced epileptic seizure (EP group, and EP group pretreated with HMGB1 (EP+HMGB1 group or BoxA (HMGB1 antagonist, EP+BoxA group. Compared to the NS group, increased levels of HMGB1 and P-gp in the brain were observed in the EP group. Injection of HMGB1 before the induction of KA further increased the expression of P-gp while pre-treatment with BoxA abolished this up-regulation. Next, the regulatory role of HMGB1 and its potential involved signal pathways were investigated in mouse microvascular endothelial bEnd.3 cells in vitro. Cells were treated with HMGB1, HMGB1 plus lipopolysaccharide from Rhodobacter sphaeroides (LPS-RS [toll-like receptor 4 (TLR4 antagonist], HMGB1 plus FPS-ZM1 [receptor for advanced glycation end products (RAGE inhibitor], HMGB1 plus SN50 [nuclear factor-kappa B (NF-κB inhibitor], or vehicle. Treatment with HMGB1 increased the expression levels of P-gp, TLR4, RAGE and the activation of NF-κB in bEnd.3 cells. These effects were inhibited by the pre-treatment with either LPS-RS or FPS-ZM1, and were abolished by the pre-treatment of SN50 or a combination treatment of both LPS-RS and FPS-ZM1. Luciferase reporter assays showed that exogenous expression of NF-κB p65 increased the promoter activity of multidrug resistance 1a (P-gp-encoding gene in endothelial cells. These data indicate that HMGB1 contributes to the overexpression of P-gp in mouse epileptic brain tissues via activation of TLR4/RAGE receptors and the downstream transcription factor NF-κB in brain microvascular endothelial cells.

Comparative Study Between Ethylbenzene Disproportionation Reaction and its Ethylation Reaction with Ethanol over ZSM-5

KAUST Repository

Tukur, N. M.

2009-06-23

Ethylation of ethylbenzene with ethanol has been studied over ZSM-5 catalyst in a riser simulator that mimics the operation of a fluidized-bed reactor. The feed molar ratio of ethylbenzene:ethanol is 1:1. The study was carried out at 350, 400, 450, and 500°C for reaction times of 3, 5, 7, 10, 13, and 15 s. Comparisons are made between the results of the ethylbenzene ethylation reaction with that of ethylbenzene disproportionation reaction earlier reported. The effect of reaction conditions on ethylbenzene reactivity, p-diethylbenzene selectivity, total diethylbenzene (DEB) isomers selectivity, p-DEB-to-m-DEB ratio, benzene-to-DEB molar ratio, and benzene selectivity, are reported. Benzene selectivity is about 10 times more in the EB disproportion reaction as compared to its ethylation reaction with ethanol at 350°C. In addition, the results showed a p-DEB/m-DEB ratio for the EB ethylation reaction varying between 1.2-1.7, which is greater than the equilibrium values. Increase in temperature shifts the alkylation/dealkylation equilibrium towards dealkylation, thereby decreasing conversion and selectivity to DEB. © Springer Science+Business Media, LLC 2009.

Palladium-catalyzed coupling reactions

CERN Document Server

Molnár, Árpád

2013-01-01

This handbook and ready reference brings together all significant issues of practical importance for interested readers in one single volume. While covering homogeneous and heterogeneous catalysis, the text is unique in focusing on such important aspects as using different reaction media, microwave techniques or catalyst recycling. It also provides a comprehensive treatment of modern-day coupling reactions and emphasizes those topics that show potential for future development, such as continuous flow systems, water as a reaction medium, and catalyst immobilization, among others. With i

Managing Your Emotional Reactions

Science.gov (United States)

... Videos for Educators Search English Español Managing Your Emotional Reactions KidsHealth / For Teens / Managing Your Emotional Reactions ... Think about what you might do next time. Emotions 101 The skills we use to manage our ...

Heavy ion transfer reactions

Indian Academy of Sciences (India)

array (CLARA), extensive investigations of nuclear structure and reaction dynamics have been carried out. In the present paper aspects of these studies will be presented, focussing more closely on the reaction mechanism, in particular on the ...

Analysis of reaction products formed in the gas phase reaction of E,E-2,4-hexadienal with atmospheric oxidants: Reaction mechanisms and atmospheric implications

Science.gov (United States)

Colmenar, I.; Martin, P.; Cabañas, B.; Salgado, S.; Martinez, E.

2018-03-01

An analysis of reaction products for the reaction of E,E-2,4-hexadienal with chlorine atoms (Cl) and OH and NO3 radicals has been carried out at the first time with the aim of obtaining a better understanding of the tropospheric reactivity of α,β-unsaturated carbonyl compounds. Fourier Transform Infrared (FTIR) spectroscopy and Gas Chromatography-Mass Spectrometry with a Time of Flight detector (GC-TOFMS) were used to carry out the qualitative and/or quantitative analyses. Reaction products in gas and particulate phase were observed from the reactions of E,E-2,4- hexadienal with all oxidants. E/Z-Butenedial and maleic anhydride were the main products identified in gas phase. E-butenedial calculated molar yield ranging from 4 to 10%. A significant amount of multifunctional compounds (chloro and hydroxy carbonyls) was identified. These compounds could be formed in particulate phase explaining the ∼90% of unaccounted carbon in gas phase. The reaction with Cl atoms in the presence of NOx with a long reaction time gave Peroxy Acetyl Nitrate (PAN) as an additional product, which is known for being an important specie in the generation of the photochemical smog. Nitrated compounds were the major organic products from the reaction with the NO3 radical. Based on the identified products, the reaction mechanisms have been proposed. In these mechanisms a double bond addition of the atmospheric oxidant at C4/C5 of E,E-2,4-hexadienal is the first step for tropospheric degradation.

Thermodynamics of Enzyme-Catalyzed Reactions Database

Science.gov (United States)

SRD 74 Thermodynamics of Enzyme-Catalyzed Reactions Database (Web, free access)   The Thermodynamics of Enzyme-Catalyzed Reactions Database contains thermodynamic data on enzyme-catalyzed reactions that have been recently published in the Journal of Physical and Chemical Reference Data (JPCRD). For each reaction the following information is provided: the reference for the data, the reaction studied, the name of the enzyme used and its Enzyme Commission number, the method of measurement, the data and an evaluation thereof.

Kiss-induced severe anaphylactic reactions

Directory of Open Access Journals (Sweden)

Atanasković-Marković Marina

2010-01-01

Full Text Available Introduction. Ingestion is the principal route for food allergens to trigger allergic reaction in atopic persons. However, in some highly sensitive patients severe symptoms may develop upon skin contact and by inhalation. The clinical spectrum ranges from mild facial urticaria and angioedema to life-threatening anaphylactic reactions. Outline of Cases. We describe cases of severe anaphylactic reactions by skin contact, induced by kissing in five children with prior history of severe anaphylaxis caused by food ingestion. These cases were found to have the medical history of IgE mediated food allergy, a very high total and specific serum IgE level and very strong family history of allergy. Conclusion. The presence of tiny particles of food on the kisser's lips was sufficient to trigger an anaphylactic reaction in sensitized children with prior history of severe allergic reaction caused by ingestion of food. Allergic reaction provoked with food allergens by skin contact can be a risk factor for generalized reactions. Therefore, extreme care has to be taken in avoiding kissing allergic children after eating foods to which they are highly allergic. Considering that kissing can be a cause of severe danger for the food allergic patient, such persons should inform their partners about the risk factor for causing their food hypersensitivity.

Charged-particle thermonuclear reaction rates: II. Tables and graphs of reaction rates and probability density functions

International Nuclear Information System (INIS)

Iliadis, C.; Longland, R.; Champagne, A.E.; Coc, A.; Fitzgerald, R.

2010-01-01

Numerical values of charged-particle thermonuclear reaction rates for nuclei in the A=14 to 40 region are tabulated. The results are obtained using a method, based on Monte Carlo techniques, that has been described in the preceding paper of this issue (Paper I). We present a low rate, median rate and high rate which correspond to the 0.16, 0.50 and 0.84 quantiles, respectively, of the cumulative reaction rate distribution. The meaning of these quantities is in general different from the commonly reported, but statistically meaningless expressions, 'lower limit', 'nominal value' and 'upper limit' of the total reaction rate. In addition, we approximate the Monte Carlo probability density function of the total reaction rate by a lognormal distribution and tabulate the lognormal parameters μ and σ at each temperature. We also provide a quantitative measure (Anderson-Darling test statistic) for the reliability of the lognormal approximation. The user can implement the approximate lognormal reaction rate probability density functions directly in a stellar model code for studies of stellar energy generation and nucleosynthesis. For each reaction, the Monte Carlo reaction rate probability density functions, together with their lognormal approximations, are displayed graphically for selected temperatures in order to provide a visual impression. Our new reaction rates are appropriate for bare nuclei in the laboratory. The nuclear physics input used to derive our reaction rates is presented in the subsequent paper of this issue (Paper III). In the fourth paper of this issue (Paper IV) we compare our new reaction rates to previous results.

Reactor for exothermic reactions

Science.gov (United States)

Smith, L.A. Jr.; Hearn, D.; Jones, E.M. Jr.

1993-03-02

A liquid phase process is described for oligomerization of C[sub 4] and C[sub 5] isoolefins or the etherification thereof with C[sub 1] to C[sub 6] alcohols wherein the reactants are contacted in a reactor with a fixed bed acid cation exchange resin catalyst at an LHSV of 5 to 20, pressure of 0 to 400 psig and temperature of 120 to 300 F. Wherein the improvement is the operation of the reactor at a pressure to maintain the reaction mixture at its boiling point whereby at least a portion but less than all of the reaction mixture is vaporized. By operating at the boiling point and allowing a portion of the reaction mixture to vaporize, the exothermic heat of reaction is dissipated by the formation of more boil up and the temperature in the reactor is controlled.

Sequential charged particle reaction

International Nuclear Information System (INIS)

Hori, Jun-ichi; Ochiai, Kentaro; Sato, Satoshi; Yamauchi, Michinori; Nishitani, Takeo

2004-01-01

The effective cross sections for producing the sequential reaction products in F82H, pure vanadium and LiF with respect to the 14.9-MeV neutron were obtained and compared with the estimation ones. Since the sequential reactions depend on the secondary charged particles behavior, the effective cross sections are corresponding to the target nuclei and the material composition. The effective cross sections were also estimated by using the EAF-libraries and compared with the experimental ones. There were large discrepancies between estimated and experimental values. Additionally, we showed the contribution of the sequential reaction on the induced activity and dose rate in the boundary region with water. From the present study, it has been clarified that the sequential reactions are of great importance to evaluate the dose rates around the surface of cooling pipe and the activated corrosion products. (author)

The Reaction Wheel Pendulum

CERN Document Server

Block, Daniel J; Spong, Mark W

2007-01-01

This monograph describes the Reaction Wheel Pendulum, the newest inverted-pendulum-like device for control education and research. We discuss the history and background of the reaction wheel pendulum and other similar experimental devices. We develop mathematical models of the reaction wheel pendulum in depth, including linear and nonlinear models, and models of the sensors and actuators that are used for feedback control. We treat various aspects of the control problem, from linear control of themotor, to stabilization of the pendulum about an equilibrium configuration using linear control, t

Kinetic studies of elementary chemical reactions

Energy Technology Data Exchange (ETDEWEB)

Durant, J.L. Jr. [Sandia National Laboratories, Livermore, CA (United States)

1993-12-01

This program concerning kinetic studies of elementary chemical reactions is presently focussed on understanding reactions of NH{sub x} species. To reach this goal, the author is pursuing experimental studies of reaction rate coefficients and product branching fractions as well as using electronic structure calculations to calculate transition state properties and reaction rate calculations to relate these properties to predicted kinetic behavior. The synergy existing between the experimental and theoretical studies allow one to gain a deeper insight into more complex elementary reactions.

Optimizing Chemical Reactions with Deep Reinforcement Learning.

Science.gov (United States)

Zhou, Zhenpeng; Li, Xiaocheng; Zare, Richard N

2017-12-27

Deep reinforcement learning was employed to optimize chemical reactions. Our model iteratively records the results of a chemical reaction and chooses new experimental conditions to improve the reaction outcome. This model outperformed a state-of-the-art blackbox optimization algorithm by using 71% fewer steps on both simulations and real reactions. Furthermore, we introduced an efficient exploration strategy by drawing the reaction conditions from certain probability distributions, which resulted in an improvement on regret from 0.062 to 0.039 compared with a deterministic policy. Combining the efficient exploration policy with accelerated microdroplet reactions, optimal reaction conditions were determined in 30 min for the four reactions considered, and a better understanding of the factors that control microdroplet reactions was reached. Moreover, our model showed a better performance after training on reactions with similar or even dissimilar underlying mechanisms, which demonstrates its learning ability.

Reaction kinetics of polybutylene terephthalate polycondensation reaction

NARCIS (Netherlands)

Darda, P. J.; Hogendoorn, J. A.; Versteeg, G. F.; Souren, F.

2005-01-01

The kinetics of the forward polycondensation reaction of polybutylene terephthalate (PBT) has been investigated using thermogravimetric analysis (TGA). PBT - prepolymer with an initial degree of polymerization of 5.5 was used as starting material. The PBT prepolymer was prepared from dimethyl

Thermodynamics of random reaction networks.

Science.gov (United States)

Fischer, Jakob; Kleidon, Axel; Dittrich, Peter

2015-01-01

Reaction networks are useful for analyzing reaction systems occurring in chemistry, systems biology, or Earth system science. Despite the importance of thermodynamic disequilibrium for many of those systems, the general thermodynamic properties of reaction networks are poorly understood. To circumvent the problem of sparse thermodynamic data, we generate artificial reaction networks and investigate their non-equilibrium steady state for various boundary fluxes. We generate linear and nonlinear networks using four different complex network models (Erdős-Rényi, Barabási-Albert, Watts-Strogatz, Pan-Sinha) and compare their topological properties with real reaction networks. For similar boundary conditions the steady state flow through the linear networks is about one order of magnitude higher than the flow through comparable nonlinear networks. In all networks, the flow decreases with the distance between the inflow and outflow boundary species, with Watts-Strogatz networks showing a significantly smaller slope compared to the three other network types. The distribution of entropy production of the individual reactions inside the network follows a power law in the intermediate region with an exponent of circa -1.5 for linear and -1.66 for nonlinear networks. An elevated entropy production rate is found in reactions associated with weakly connected species. This effect is stronger in nonlinear networks than in the linear ones. Increasing the flow through the nonlinear networks also increases the number of cycles and leads to a narrower distribution of chemical potentials. We conclude that the relation between distribution of dissipation, network topology and strength of disequilibrium is nontrivial and can be studied systematically by artificial reaction networks.

Ozone-surface reactions in five homes: surface reaction probabilities, aldehyde yields, and trends.

Science.gov (United States)

Wang, H; Morrison, G

2010-06-01

Field experiments were conducted in five homes during three seasons (summer 2005, summer 2006 and winter 2007) to quantify ozone-initiated secondary aldehyde yields, surface reaction probabilities, and trends any temporal over a 1.5-year interval. Surfaces examined include living room carpets, bedroom carpets, kitchen floors, kitchen counters, and living room walls. Reaction probabilities for all surfaces for all seasons ranged from 9.4 x 10(-8) to 1.0 x 10(-4). There were no significant temporal trends in reaction probabilities for any surfaces from summer 2005 to summer 2006, nor over the entire 1.5-year period, indicating that it may take significantly longer than this period for surfaces to exhibit any 'ozone aging' or lowering of ozone-surface reactivity. However, all surfaces in three houses exhibited a significant decrease in reaction probabilities from summer 2006 to winter 2007. The total yield of aldehydes for the summer of 2005 were nearly identical to that for summer of 2006, but were significantly higher than for winter 2007. We also observed that older carpets were consistently less reactive than in newer carpets, but that countertops remained consistently reactive, probably because of occupant activities such as cooking and cleaning. Ozone reactions taking place at indoor surfaces significantly influence personal exposure to ozone and volatile reaction products. These field studies show that indoor surfaces only slowly lose their ability to react with ozone over several year time frames, and that this is probably because of a combination of large reservoirs of reactive coatings and periodic additions of reactive coatings in the form of cooking, cleaning, and skin-oil residues. When considering exposure to ozone and its reaction products and in the absence of dramatic changes in occupancy, activities or furnishings, indoor surface reactivity is expected to change very slowly.

Multistep processes in nuclear reactions

International Nuclear Information System (INIS)

Hodgson, P.E.

1988-01-01

The theories of nuclear reactions are reviewed with particular attention to the recent work on multistep processes. The evidence for compound nucleus and direct interaction reactions is described together with the results of comparisons between theories and experimental data. These theories have now proved inadequate, and there is evidence for multistep processes that take place after the initial direct stage but long before the attainment of the statistical equilibrium characteristic of compound nucleus processes. The theories of these reactions are described and it is shown how they can account for the experimental data and thus give a comprehensive understanding of nuclear reactions. (author)

Chemical burn or reaction

Science.gov (United States)

Chemicals that touch skin can lead to a reaction on the skin, throughout the body, or both. ... leave the person alone and watch carefully for reactions affecting the entire body. Note: If a chemical gets into the eyes, the eyes should be ...

Precompound Reactions: Basic Concepts

International Nuclear Information System (INIS)

Weidenmueller, H. A.

2008-01-01

Because of the non-zero nuclear equilibration time, the compound-nucleus scattering model fails when the incident energy exceeds 10 or 20 MeV, and precompound reactions become important. Basic ideas used in the quantum-statistical approaches to these reactions are described

Thermally multiplexed polymerase chain reaction.

Science.gov (United States)

Phaneuf, Christopher R; Pak, Nikita; Saunders, D Curtis; Holst, Gregory L; Birjiniuk, Joav; Nagpal, Nikita; Culpepper, Stephen; Popler, Emily; Shane, Andi L; Jerris, Robert; Forest, Craig R

2015-07-01

Amplification of multiple unique genetic targets using the polymerase chain reaction (PCR) is commonly required in molecular biology laboratories. Such reactions are typically performed either serially or by multiplex PCR. Serial reactions are time consuming, and multiplex PCR, while powerful and widely used, can be prone to amplification bias, PCR drift, and primer-primer interactions. We present a new thermocycling method, termed thermal multiplexing, in which a single heat source is uniformly distributed and selectively modulated for independent temperature control of an array of PCR reactions. Thermal multiplexing allows amplification of multiple targets simultaneously-each reaction segregated and performed at optimal conditions. We demonstrate the method using a microfluidic system consisting of an infrared laser thermocycler, a polymer microchip featuring 1 μl, oil-encapsulated reactions, and closed-loop pulse-width modulation control. Heat transfer modeling is used to characterize thermal performance limitations of the system. We validate the model and perform two reactions simultaneously with widely varying annealing temperatures (48 °C and 68 °C), demonstrating excellent amplification. In addition, to demonstrate microfluidic infrared PCR using clinical specimens, we successfully amplified and detected both influenza A and B from human nasopharyngeal swabs. Thermal multiplexing is scalable and applicable to challenges such as pathogen detection where patients presenting non-specific symptoms need to be efficiently screened across a viral or bacterial panel.

Improved predictions of nuclear reaction rates for astrophysics applications with the TALYS reaction code

International Nuclear Information System (INIS)

Goriely, S.; Hilaire, S.; Koning, A.J.

2008-01-01

Nuclear reaction rates for astrophysics applications are traditionally determined on the basis of Hauser-Feshbach reaction codes, like MOST. These codes use simplified schemes to calculate the capture reaction cross section on a given target nucleus, not only in its ground state but also on the different thermally populated states of the stellar plasma at a given temperature. Such schemes include a number of approximations that have never been tested, such as an approximate width fluctuation correction, the neglect of delayed particle emission during the electromagnetic decay cascade or the absence of the pre-equilibrium contribution at increasing incident energies. New developments have been brought to the reaction code TALYS to estimate the Maxwellian-averaged reaction rates of astrophysics relevance. These new developments give us the possibility to calculate with an improved accuracy the reaction cross sections and the corresponding astrophysics rates. The TALYS predictions for the thermonuclear rates of astrophysics relevance are presented and compared with those obtained with the MOST code on the basis of the same nuclear ingredients for nuclear structure properties, optical model potential, nuclear level densities and γ-ray strength. It is shown that, in particular, the pre-equilibrium process significantly influences the astrophysics rates of exotic neutron-rich nuclei. The reciprocity theorem traditionally used in astrophysics to determine photo-rates is also shown no to be valid for exotic nuclei. The predictions obtained with different nuclear inputs are also analyzed to provide an estimate of the theoretical uncertainties still affecting the reaction rate prediction far away from the experimentally known regions. (authors)

Simulation of square wave voltammetry of three electrode reactions coupled by two reversible chemical reactions

OpenAIRE

Lovrić, Milivoj

2017-01-01

Three fast and reversible electrode reactions that are connected by two reversible chemical reactions that are permanently in the equilibrium are analysed theoretically for square wave voltammetry. The dependence of peak potentials on the dimensionless equilibrium constants of chemical reactions is calculated. The influence of the basic thermodynamic parameters on the square wave voltammetric responses is analysed.

Reaction

African Journals Online (AJOL)

abp

19 oct. 2017 ... Reaction to Mohamed Said Nakhli et al. concerning the article: "When the axillary block remains the only alternative in a 5 year old child". .... Bertini L1, Savoia G, De Nicola A, Ivani G, Gravino E, Albani A et al ... 2010;7(2):101-.

Reaction of Titanocene Alkyls with Pyridines; A Novel Type of Cyclometallation Reaction

NARCIS (Netherlands)

Klei, E.; Teuben, J.H.

1981-01-01

Reaction of Cp2TiR (R = alkyl) with 2-substituted-pyridines and with quinolines leads to α-metallation of these ligands with formation of triangular titanocycles containing TiIII. Proof of the metallation at the α-position comes from reactions of the complexes formed with I2 and D2O/DCl which yield

A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions

International Nuclear Information System (INIS)

Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C.; Brooks, Scott C; Pace, Molly; Kim, Young Jin; Jardine, Philip M.; Watson, David B.

2007-01-01

This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M. partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M. species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing NE equilibrium reactions and a set of reactive transport equations of M-NE kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions

A reaction-based paradigm to model reactive chemical transport in groundwater with general kinetic and equilibrium reactions.

Science.gov (United States)

Zhang, Fan; Yeh, Gour-Tsyh; Parker, Jack C; Brooks, Scott C; Pace, Molly N; Kim, Young-Jin; Jardine, Philip M; Watson, David B

2007-06-16

This paper presents a reaction-based water quality transport model in subsurface flow systems. Transport of chemical species with a variety of chemical and physical processes is mathematically described by M partial differential equations (PDEs). Decomposition via Gauss-Jordan column reduction of the reaction network transforms M species reactive transport equations into two sets of equations: a set of thermodynamic equilibrium equations representing N(E) equilibrium reactions and a set of reactive transport equations of M-N(E) kinetic-variables involving no equilibrium reactions (a kinetic-variable is a linear combination of species). The elimination of equilibrium reactions from reactive transport equations allows robust and efficient numerical integration. The model solves the PDEs of kinetic-variables rather than individual chemical species, which reduces the number of reactive transport equations and simplifies the reaction terms in the equations. A variety of numerical methods are investigated for solving the coupled transport and reaction equations. Simulation comparisons with exact solutions were performed to verify numerical accuracy and assess the effectiveness of various numerical strategies to deal with different application circumstances. Two validation examples involving simulations of uranium transport in soil columns are presented to evaluate the ability of the model to simulate reactive transport with complex reaction networks involving both kinetic and equilibrium reactions.

Interfacial reactions in intermetallic matrix composites

International Nuclear Information System (INIS)

Cantrell, L.B.; Clevenger, E.M.; Perepezko, J.H.

1993-01-01

The thermal stability of advanced composites is dominated by the behavior of internal interfaces. Analysis of these internal interfaces often involves consideration of at least ternary order phase equilibria. Limited thermodynamic data exists for ternary and higher order systems. However, a combined approach based upon the use of binary data to estimate ternary phase equilibria and experimentally determined reaction pathways is effective in the analysis of interface reactions in composite systems. In blended powder samples, thermal analysis was used to find possible reaction temperatures, while X-ray analysis, EDS, and EPMA of diffusion couples were used to assess interdiffusion reaction pathways. The approach is illustrated by compatibility studies between TiAl and TiSi 2 at 1,100 C, and in-situ reactions between B 4 C and TiAl at 1300 C where multiple reaction sequences have been analyzed to provide guidance for the design of in-situ reaction processing of composites

Thermodynamics of random reaction networks.

Directory of Open Access Journals (Sweden)

Jakob Fischer

Full Text Available Reaction networks are useful for analyzing reaction systems occurring in chemistry, systems biology, or Earth system science. Despite the importance of thermodynamic disequilibrium for many of those systems, the general thermodynamic properties of reaction networks are poorly understood. To circumvent the problem of sparse thermodynamic data, we generate artificial reaction networks and investigate their non-equilibrium steady state for various boundary fluxes. We generate linear and nonlinear networks using four different complex network models (Erdős-Rényi, Barabási-Albert, Watts-Strogatz, Pan-Sinha and compare their topological properties with real reaction networks. For similar boundary conditions the steady state flow through the linear networks is about one order of magnitude higher than the flow through comparable nonlinear networks. In all networks, the flow decreases with the distance between the inflow and outflow boundary species, with Watts-Strogatz networks showing a significantly smaller slope compared to the three other network types. The distribution of entropy production of the individual reactions inside the network follows a power law in the intermediate region with an exponent of circa -1.5 for linear and -1.66 for nonlinear networks. An elevated entropy production rate is found in reactions associated with weakly connected species. This effect is stronger in nonlinear networks than in the linear ones. Increasing the flow through the nonlinear networks also increases the number of cycles and leads to a narrower distribution of chemical potentials. We conclude that the relation between distribution of dissipation, network topology and strength of disequilibrium is nontrivial and can be studied systematically by artificial reaction networks.

Modeling chemical reactions for drug design.

Science.gov (United States)

Gasteiger, Johann

2007-01-01

Chemical reactions are involved at many stages of the drug design process. This starts with the analysis of biochemical pathways that are controlled by enzymes that might be downregulated in certain diseases. In the lead discovery and lead optimization process compounds have to be synthesized in order to test them for their biological activity. And finally, the metabolism of a drug has to be established. A better understanding of chemical reactions could strongly help in making the drug design process more efficient. We have developed methods for quantifying the concepts an organic chemist is using in rationalizing reaction mechanisms. These methods allow a comprehensive modeling of chemical reactivity and thus are applicable to a wide variety of chemical reactions, from gas phase reactions to biochemical pathways. They are empirical in nature and therefore allow the rapid processing of large sets of structures and reactions. We will show here how methods have been developed for the prediction of acidity values and of the regioselectivity in organic reactions, for designing the synthesis of organic molecules and of combinatorial libraries, and for furthering our understanding of enzyme-catalyzed reactions and of the metabolism of drugs.

Microdosimetric concepts for indirect radiation reactions

International Nuclear Information System (INIS)

Pohlit, W.

1976-01-01

It is the aim of microdosimetric models to get information about the influence of microscopic energy deposition by radiation on radiation reactions. Two parameters are always of interest: the energy necessary to produce a certain reaction and the volume in which this energy has to be desposited. In the simple case of an aqueous solution with point targets a complete description of radiation reactions in targets with various concentrations can be given. This model takes into consideration the distinct energy deposition on the particle track, diffusion of radicals and a mean energy necessary for a certain reaction at the target. Typical dose effect curves are obtained which allow the determination of all these quantities from experiments. The model has been tested with the oxydation of iron atoms in aqueous solutions and has been applied for more complex targets such as different alcohols and amino acids. The oxygen consumption in these reactions is used as an easy method for continuous measurement of these indirect reactions. It is the aim of such experiments to get enough quantitative microscopic data on indirect radiation reactions that these reactions can also be followed in living cells

Intramolecular Diels-Alder Reactions in Organic Synthesis

OpenAIRE

Sizemore, Nicholas Blandford Luke

2014-01-01

Intramolecular Diels-Alder (IMDA) reactions are an important class of reactions in synthetic organic chemistry for the rapid construction of polycyclic frameworks. Three classes of IMDA reactions were investigated synthetically and computationally: 1) all-carbon type 1 IMDA reactions, 2) N-acylnitroso type 2 IMDA reactions, and 3) cyano-azadiene IMDA reactions. The first class was implemented in research toward the total synthesis of maoecrystal Z and isopalhinine A. The second class was stud...

Substrate dependent reaction channels of the Wolff–Kishner reduction reaction: A theoretical study

Directory of Open Access Journals (Sweden)

Shinichi Yamabe

2014-01-01

Full Text Available Wolff–Kishner reduction reactions were investigated by DFT calculations for the first time. B3LYP/6-311+G(d,p SCRF=(PCM, solvent = 1,2-ethanediol optimizations were carried out. To investigate the role of the base catalyst, the base-free reaction was examined by the use of acetone, hydrazine (H2N–NH2 and (H2O8. A ready reaction channel of acetone → acetone hydrazine (Me2C=N–NH2 was obtained. The channel involves two likely proton-transfer routes. However, it was found that the base-free reaction was unlikely at the N2 extrusion step from the isopropyl diimine intermediate (Me2C(H–N=N–H. Two base-catalyzed reactions were investigated by models of the ketone, H2N–NH2 and OH−(H2O7. Here, ketones are acetone and acetophenone. While routes of the ketone → hydrazone → diimine are similar, those from the diimines are different. From the isopropyl diimine, the N2 extrusion and the C–H bond formation takes place concomitantly. The concomitance leads to the propane product concertedly. From the (1-phenylethyl substituted diimine, a carbanion intermediate is formed. The para carbon of the phenyl ring of the anion is subject to the protonation, which leads to a 3-ethylidene-1,4-cyclohexadiene intermediate. Its [1,5]-hydrogen migration gives the ethylbenzene product. For both ketone substrates, the diimines undergoing E2 reactions were found to be key intermediates.

Catalyst Initiation in the Oscillatory Carbonylation Reaction

Directory of Open Access Journals (Sweden)

Katarina Novakovic

2011-01-01

Full Text Available Palladium(II iodide is used as a catalyst in the phenylacetylene oxidative carbonylation reaction that has demonstrated oscillatory behaviour in both pH and heat of reaction. In an attempt to extract the reaction network responsible for the oscillatory nature of this reaction, the system was divided into smaller parts and they were studied. This paper focuses on understanding the reaction network responsible for the initial reactions of palladium(II iodide within this oscillatory reaction. The species researched include methanol, palladium(II iodide, potassium iodide, and carbon monoxide. Several chemical reactions were considered and applied in a modelling study. The study revealed the significant role played by traces of water contained in the standard HPLC grade methanol used.

Spallation reactions - physics and applications

International Nuclear Information System (INIS)

Kelic, A.; Ricciardi, M.; Schmidt, K-H.

2009-01-01

Spallation reactions have become an ideal tool for studying the equation of state and thermal instabilities of nuclear matter. In astrophysics, the interactions of cosmic rays with the interstellar medium have to be understood in detail for deducing their original composition and their production mechanisms. Renewed interest in spallation reactions with protons around 1 GeV came up recently with the developments of spallation neutron sources. The project of an accelerator-driven system (ADS) as a technological solution for incinerating the radioactive waste even intensified the efforts for better understanding the physics involved in the spallation process. Experiments on spallation reactions were performed for determining the production cross sections and properties of particles, fragments and heavy residues. Traditional experiments on heavy residues, performed in direct kinematics, were limited to the direct observation of long-lived radioactive nuclides and did not provide detailed information on the kinematics of the reaction. Therefore, an innovative experimental method has been developed, based on inverse kinematics, which allowed to identify all reaction residues in-flight, using the high resolution magnetic spectrometer FRS of GSL Darmstadt. It also gives direct access to the reaction kinematics. An experimental campaign has been carried out in a Europe-wide collaboration, investigating the spallation of several nuclei ranging from 56 Fe to 238 U Complementary experiments were performed with a full-acceptance detection system, yielding total fission cross sections. Recently, another detection system using the large acceptance ALADIN dipole and the LAND neutron detector was introduced to measure light particles in coincidence with the heavy residues. Another intense activity was dedicated to developing codes, which cover nuclear reactions occurring in an ADS. The first phase of the reaction is successfully described by a sequence of quasi-free nucleon

Spallation reactions: calculations

International Nuclear Information System (INIS)

Bertini, H.W.

1975-01-01

Current methods for calculating spallation reactions over various energy ranges are described and evaluated. Recent semiempirical fits to existing data will probably yield the most accurate predictions for these reactions in general. However, if the products in question have binding energies appreciably different from their isotropic neighbors and if the cross section is approximately 30 mb or larger, then the intranuclear-cascade-evaporation approach is probably better suited. (6 tables, 12 figures, 34 references) (U.S.)

Copper-Mediated Reactions of Nitriles with Nitromethanes: Aza-Henry Reactions and Nitrile Hydrations.

Science.gov (United States)

Kuwabara, Jun; Sawada, Yoshiharu; Yoshimatsu, Mitsuhiro

2018-02-16

In this study, the first aza-Henry reaction of nitriles with nitromethane in a CuI/Cs 2 CO 3 /DBU system is described. The process was conveniently and directly used for the synthesis of β-aminonitroalkenes 2a-x and tolerated aryl-, alkyl-, hetaryl-, alkenyl-, and alkynylnitriles. The resulting aminonitroalkenes 2 could be successfully transformed to the corresponding 2-nitroacetophenones, 2-amino-1-halonitroalkenes, 2-alkylaminonitroalkenes, or 3-nitropyridines. In the presence of H 2 O, the aza-Henry reaction turned the reaction path to the nitrile hydration to exclusively yield the amides 3a-s.

Hydrogen evolution reaction catalyst

Science.gov (United States)

Subbaraman, Ram; Stamenkovic, Vojislav; Markovic, Nenad; Tripkovic, Dusan

2016-02-09

Systems and methods for a hydrogen evolution reaction catalyst are provided. Electrode material includes a plurality of clusters. The electrode exhibits bifunctionality with respect to the hydrogen evolution reaction. The electrode with clusters exhibits improved performance with respect to the intrinsic material of the electrode absent the clusters.

Radiation reactions and care of the patient

International Nuclear Information System (INIS)

Lochhead, J.N.M.

1983-01-01

Many of the radiation reactions which may occur in patients following radiotherapy and the care of these reactions are described. These include the systemic reaction, reactions of the blood and skin, reactions occurring after treatment of the breast and chest wall, reactions after irradiation of the mouth and throat, intrathoracic tumours, the abdominal alimentary tract and pelvis, bone, the CNS and the eye. Patient care during the treatment of children and also during treatment using small sealed sources is also described. (U.K.)

On the mechanism of effective chemical reactions with turbulent mixing of reactants and finite rate of molecular reactions

Energy Technology Data Exchange (ETDEWEB)

Vorotilin, V. P., E-mail: VPVorotilin@yandex.ru [Russian Academy of Sciences, Institute of Applied Mechanics (Russian Federation)

2017-01-15

A generalization of the theory of chemical transformation processes under turbulent mixing of reactants and arbitrary values of the rate of molecular reactions is presented that was previously developed for the variant of an instantaneous reaction [13]. The use of the features of instantaneous reactions when considering the general case, namely, the introduction of the concept of effective reaction for the reactant volumes and writing a closing conservation equation for these volumes, became possible due to the partition of the whole amount of reactants into “active” and “passive” classes; the reactants of the first class are not mixed and react by the mechanism of instantaneous reactions, while the reactants of the second class approach each other only through molecular diffusion, and therefore their contribution to the reaction process can be neglected. The physical mechanism of reaction for the limit regime of an ideal mixing reactor (IMR) is revealed and described. Although formally the reaction rate in this regime depends on the concentration of passive fractions of the reactants, according to the theory presented, the true (hidden) mechanism of the reaction is associated only with the reaction of the active fractions of the reactants with vanishingly small concentration in the volume of the reactor. It is shown that the rate constant of fast chemical reactions can be evaluated when the mixing intensity of reactants is much less than that needed to reach the mixing conditions in an IMR.

Reaction chemistry of nitrogen species in hydrothermal systems: Simple reactions, waste simulants, and actual wastes

International Nuclear Information System (INIS)

Dell'Orco, P.; Luan, L.; Proesmans, P.; Wilmanns, E.

1995-01-01

Results are presented from hydrothermal reaction systems containing organic components, nitrogen components, and an oxidant. Reaction chemistry observed in simple systems and in simple waste simulants is used to develop a model which presents global nitrogen chemistry in these reactive systems. The global reaction path suggested is then compared with results obtained for the treatment of an actual waste stream containing only C-N-0-H species

Connecting localized DNA strand displacement reactions

Science.gov (United States)

Mullor Ruiz, Ismael; Arbona, Jean-Michel; Lad, Amitkumar; Mendoza, Oscar; Aimé, Jean-Pierre; Elezgaray, Juan

2015-07-01

Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions.Logic circuits based on DNA strand displacement reactions have been shown to be versatile enough to compute the square root of four-bit numbers. The implementation of these circuits as a set of bulk reactions faces difficulties which include leaky reactions and intrinsically slow, diffusion-limited reaction rates. In this paper, we consider simple examples of these circuits when they are attached to platforms (DNA origamis). As expected, constraining distances between DNA strands leads to faster reaction rates. However, it also induces side-effects that are not detectable in the solution-phase version of this circuitry. Appropriate design of the system, including protection and asymmetry between input and fuel strands, leads to a reproducible behaviour, at least one order of magnitude faster than the one observed under bulk conditions. Electronic supplementary information (ESI) available. See DOI: 10.1039/C5NR02434J

cycloaddition reactions

Indian Academy of Sciences (India)

Unknown

Molecular Modeling Group, Organic Chemical Sciences, Indian Institute of Chemical Technology,. Hyderabad ... thus obtained are helpful to model the regioselectivity ... compromise to model Diels–Alder reactions involving ...... acceptance.

Nuclear Reactions for Astrophysics and Other Applications

Energy Technology Data Exchange (ETDEWEB)

Escher, J E; Burke, J T; Dietrich, F S; Scielzo, N D; Ressler, J J

2011-03-01

Cross sections for compound-nuclear reactions are required for many applications. The surrogate nuclear reactions method provides an indirect approach for determining cross sections for reactions on unstable isotopes, which are difficult or impossible to measure otherwise. Current implementations of the method provide useful cross sections for (n,f) reactions, but need to be improved upon for applications to capture reactions.

A New Road to Reaction, Part 3. Teaching the Heat Effect of Reaction.

Science.gov (United States)

de Vos, Wobbe; Verdonk, Adri H.

1986-01-01

Addresses the need to present beginning chemistry students with a variety of experiences dealing with chemical reactions to develop the individual student's concept of these processes. Presents information and experiments dealing with the heat effect of chemical reactions. Includes a discussion on exothermic and endothermic processes in laboratory…

Reciprocity theory of homogeneous reactions

Science.gov (United States)

Agbormbai, Adolf A.

1990-03-01

The reciprocity formalism is applied to the homogeneous gaseous reactions in which the structure of the participating molecules changes upon collision with one another, resulting in a change in the composition of the gas. The approach is applied to various classes of dissociation, recombination, rearrangement, ionizing, and photochemical reactions. It is shown that for the principle of reciprocity to be satisfied it is necessary that all chemical reactions exist in complementary pairs which consist of the forward and backward reactions. The backward reaction may be described by either the reverse or inverse process. The forward and backward processes must satisfy the same reciprocity equation. Because the number of dynamical variables is usually unbalanced on both sides of a chemical equation, it is necessary that this balance be established by including as many of the dynamical variables as needed before the reciprocity equation can be formulated. Statistical transformation models of the reactions are formulated. The models are classified under the titles free exchange, restricted exchange and simplified restricted exchange. The special equations for the forward and backward processes are obtained. The models are consistent with the H theorem and Le Chatelier's principle. The models are also formulated in the context of the direct simulation Monte Carlo method.

Palaeobiology of Mesoproterozoic Salkhan Limestone, Semri Group ...

Indian Academy of Sciences (India)

Eoentophysalis cumulus Butterfield et al revised. 1994. Description: Cells polygonal, sphaeroidal, ellip- soidal, occur in solitary or in pairs, planar tetrads, irregular clusters and colonies, occasionally dis- torted due to mutual compression. The size of cells varies from 3–10µm across (with the aver- age of 4µm, 100 cells ...

Cross sections and thermonuclear reaction rates of proton-induced reactions on 37Cl

International Nuclear Information System (INIS)

Weber, R.O.; Tingwell, C.I.W.; Mitchell, L.W.; Sevior, M.E.; Sargood, D.G.

1984-01-01

The yields of γ-rays from the reactions of 37 Cl(p,γ) 38 Ar and 37 Cl(p,αγ) 34 S have been measured as a of bombarding energy over the ranges 0.65 - 2.15 MeV and 1.25 -2.15 MeV respectively, and the yield of neutrons from 37 Cl(p,n) 37 Ar from threshold to 2.50 MeV. The results are compared with global statistical-model calculations and thermonuclear reaction rates are calculated for the temperature range 5 x 10 8 - 10 10 K. The significance of these thermonuclear reaction rates for stellar nucleosynthesis calculations is discussed

Comparison of Sprint Reaction and Visual Reaction Times of Athletes in Different Branches

Science.gov (United States)

Akyüz, Murat; Uzaldi, Basar Basri; Akyüz, Öznur; Dogru, Yeliz

2017-01-01

The aims of this study are to analyse sprint reaction and visual reaction times of female athletes of different branches competing in Professional leagues and to show the differences between them. 42 voluntary female athletes from various branches of Professional leagues of Istanbul (volleyball, basketball, handball) were included in the…

Catalysis of Nuclear Reactions by Electrons

Science.gov (United States)

Lipoglavšek, Matej

2018-01-01

Electron screening enhances nuclear reaction cross sections at low energies. We studied the nuclear reaction 1H(19F,αγ)16O in inverse kinematics in different solid hydrogen targets. Measured resonance strengths differed by up to a factor of 10 in different targets. We also studied the 2H(p,γ)3He fusion reaction and observed electrons emitted as reaction products instead of γ rays. In this case electron screening greatly enhances internal conversion probability.

Clozapine-associated extrapyramidal reaction.

Science.gov (United States)

Elliott, E S; Marken, P A; Ruehter, V L

2000-05-01

To report a case of extrapyramidal reaction associated with a dosage increase of clozapine. A 44-year-old white man with a 20-year history of chronic paranoid schizophrenia was admitted to an inpatient psychiatric facility. His prior medications restarted on admission were clozapine 650 mg at bedtime, haloperidol 10 mg at bedtime, clonazepam 2 mg/d, and aspirin 325 mg/d. Two days after admission (hospital day 3), clozapine and clonazepam were discontinued, and he was prescribed haloperidol 5 mg every morning and 10 mg every evening. Stabilization occurred over the following 24 days, with progressively lower dosages of haloperidol and increasing dosages of clozapine. Haloperidol was discontinued on day 24. On day 47, the patient was agitated and making bizarre statements; thus, the morning dose of clozapine was increased by 50 mg (total 450 mg/d). On day 48 at 2200, a dystonic reaction was diagnosed; he received intramuscular diphenhydramine 50 mg, which caused the reaction to subside. At the time of the adverse reaction, he was prescribed clozapine 450 mg/d, vitamin E 400 IU three times daily, aspirin 325 mg/d, and acetaminophen, milk of magnesia, and Maalox as needed. Although the risk of extrapyramidal symptoms (EPS) is significantly lower with clozapine than with conventional agents, elevated clozapine blood concentrations have been reported to cause EPS; other reports have cited severe dystonias and dyskinesias on abrupt clozapine withdrawal. Considering the medications prescribed at the time and the discontinuation of haloperidol 24 days before the event, clozapine was the most likely cause of the extrapyramidal reaction. Regardless of anticipated safety associated with novel antipsychotics such as clozapine, reports of dystonic reactions must be taken into account and patients monitored appropriately.

Applications of Reaction Rate

Science.gov (United States)

Cunningham, Kevin

2007-01-01

This article presents an assignment in which students are to research and report on a chemical reaction whose increased or decreased rate is of practical importance. Specifically, students are asked to represent the reaction they have chosen with an acceptable chemical equation, identify a factor that influences its rate and explain how and why it…

Verification of cold nuclear fusion reaction, (1)

International Nuclear Information System (INIS)

Yoshida, Zenko; Aratono, Yasuyuki; Hirabayashi, Takakuni

1991-01-01

Can cold nuclear fusion reaction occur as is expected? If it occurs, what extent is its reaction probability? At present after 2 years elapsed since its beginning, the clear solution of these questions is not yet obtained. In many reaction systems employing different means, the experiments to confirm the cold nuclear fusion reaction have been attempted. In order to confirm that the nuclear fusion reaction of deuterium mutually has occurred, the neutrons, He-3, protons, tritium or generated heat, which were formed by the reaction and released from the system, are measured. Since it is considered that the frequency of the occurrence at normal temperature of the reaction is very low, it is necessary to select the most suitable method upon evaluating the limit of detection peculiar to the measuring methods. The methods of measuring neutrons, protons, gamma ray and generated heat, and the reaction systems by electrolytic process and dry process are explained. The detection of plural kinds of the reaction products and the confirmation of synchronism of signals are important. (K.I.)

The unified theory of nuclear reactions

International Nuclear Information System (INIS)

Tobocman, W.

A unified nuclear reaction theory is a formalism for the scattering reactions of many-body nuclear systems which is capable of describing both direct interaction and compound nucleus formation processes. The Feshbach projection operator formalism is the original unified nuclear reaction theory. An alternative unified nuclear reaction theory called the X-matrix formalism is described. The X-matrix formalism is a generalization of the Brown-de Dominicis formalism. It does not require projection operators and is readly applied to rearrangement collisions

Degradations and Rearrangement Reactions

Science.gov (United States)

Zhang, Jianbo

This section deals with recent reports concerning degradation and rearrangement reactions of free sugars as well as some glycosides. The transformations are classified in chemical and enzymatic ways. In addition, the Maillard reaction will be discussed as an example of degradation and rearrangement transformation and its application in current research in the fields of chemistry and biology.

Combustion kinetics and reaction pathways

Energy Technology Data Exchange (ETDEWEB)

Klemm, R.B.; Sutherland, J.W. [Brookhaven National Laboratory, Upton, NY (United States)

1993-12-01

This project is focused on the fundamental chemistry of combustion. The overall objectives are to determine rate constants for elementary reactions and to elucidate the pathways of multichannel reactions. A multitechnique approach that features three independent experiments provides unique capabilities in performing reliable kinetic measurements over an exceptionally wide range in temperature, 300 to 2500 K. Recent kinetic work has focused on experimental studies and theoretical calculations of the methane dissociation system (CH{sub 4} + Ar {yields} CH{sub 3} + H + Ar and H + CH{sub 4} {yields} CH{sub 3} + H{sub 2}). Additionally, a discharge flow-photoionization mass spectrometer (DF-PIMS) experiment is used to determine branching fractions for multichannel reactions and to measure ionization thresholds of free radicals. Thus, these photoionization experiments generate data that are relevant to both reaction pathways studies (reaction dynamics) and fundamental thermochemical research. Two distinct advantages of performing PIMS with high intensity, tunable vacuum ultraviolet light at the National Synchrotron Light Source are high detection sensitivity and exceptional selectivity in monitoring radical species.

Enantio- and Stereoselective Construction of Atisane Scaffold via Organocatalytic Intramolecular Michael Reaction and Diels-Alder Reaction.

Science.gov (United States)

Sekita, Hiroko; Adachi, Kyohei; Kobayashi, Ippei; Sato, Yusuke; Nakada, Masahisa

2017-05-05

An enantio- and stereoselective construction of the atisane scaffold via organocatalytic intramolecular Michael reaction and Diels-Alder reaction is described. The organocatalytic intramolecular Michael reaction has been found to stereoselectively generate a trans-stereodiad comprising an all-carbon quaternary and a tertiary stereogenic centers. Use of the chiral secondary amine bearing thiourea with benzoic acid as additive is the key to obtaining the desired product with excellent ee in synthetically acceptable yield. The prepared chiral building block has been successfully converted to the compound including the atisane scaffold via the highly stereoselective intramolecular Diels-Alder reaction.

Delayed reactions to reusable protective gloves.

Science.gov (United States)

Pontén, Ann; Dubnika, Inese

2009-04-01

The materials in plastic protective gloves are thought to cause less contact allergy than rubber gloves. Our aim was to estimate the frequency of delayed reactions to different types of reusable protective gloves among dermatitis patients. 2 x 2 cm pieces of polyvinyl chloride (PVC) gloves, nitrile gloves, and natural rubber latex (NRL) gloves were tested as is in consecutive dermatitis patients tested with the baseline series. Among 658 patients, 6 patients reacted to PVC gloves and 6 patients to the NRL gloves. None reacted to both these types of gloves. Five of six patients with reactions to rubber gloves reacted to thiuram mix in the baseline series. Delayed reactions to reusable PVC gloves may be as common as to reusable NRL gloves. In contrast to most reactions to the NRL glove, the reactions to the PVC glove had no obvious association with reactions to any allergen(s) in the baseline series.

Surface-Activated Coupling Reactions Confined on a Surface.

Science.gov (United States)

Dong, Lei; Liu, Pei Nian; Lin, Nian

2015-10-20

Chemical reactions may take place in a pure phase of gas or liquid or at the interface of two phases (gas-solid or liquid-solid). Recently, the emerging field of "surface-confined coupling reactions" has attracted intensive attention. In this process, reactants, intermediates, and products of a coupling reaction are adsorbed on a solid-vacuum or a solid-liquid interface. The solid surface restricts all reaction steps on the interface, in other words, the reaction takes place within a lower-dimensional, for example, two-dimensional, space. Surface atoms that are fixed in the surface and adatoms that move on the surface often activate the surface-confined coupling reactions. The synergy of surface morphology and activity allow some reactions that are inefficient or prohibited in the gas or liquid phase to proceed efficiently when the reactions are confined on a surface. Over the past decade, dozens of well-known "textbook" coupling reactions have been shown to proceed as surface-confined coupling reactions. In most cases, the surface-confined coupling reactions were discovered by trial and error, and the reaction pathways are largely unknown. It is thus highly desirable to unravel the mechanisms, mechanisms of surface activation in particular, of the surface-confined coupling reactions. Because the reactions take place on surfaces, advanced surface science techniques can be applied to study the surface-confined coupling reactions. Among them, scanning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) are the two most extensively used experimental tools. The former resolves submolecular structures of individual reactants, intermediates, and products in real space, while the latter monitors the chemical states during the reactions in real time. Combination of the two methods provides unprecedented spatial and temporal information on the reaction pathways. The experimental findings are complemented by theoretical modeling. In particular, density

A Networks Approach to Modeling Enzymatic Reactions.

Science.gov (United States)

Imhof, P

2016-01-01

Modeling enzymatic reactions is a demanding task due to the complexity of the system, the many degrees of freedom involved and the complex, chemical, and conformational transitions associated with the reaction. Consequently, enzymatic reactions are not determined by precisely one reaction pathway. Hence, it is beneficial to obtain a comprehensive picture of possible reaction paths and competing mechanisms. By combining individually generated intermediate states and chemical transition steps a network of such pathways can be constructed. Transition networks are a discretized representation of a potential energy landscape consisting of a multitude of reaction pathways connecting the end states of the reaction. The graph structure of the network allows an easy identification of the energetically most favorable pathways as well as a number of alternative routes. © 2016 Elsevier Inc. All rights reserved.

An experimental and theoretical study of reaction steps relevant to the methanol-to-hydrocarbons reaction

Energy Technology Data Exchange (ETDEWEB)

Svelle, Stian

2004-07-01

The primary objective of the present work is to obtain new insight into the reaction mechanism of the zeolite catalyzed methanol-to-hydrocarbons (MTH) reaction. It was decided to use both experimental and computational techniques to reach this goal. An investigation of the n-butene + methanol system was therefore initiated. Over time, it became apparent that it was possible to determine the rate for the methylation of n-butene by methanol. The ethene and propene systems were therefore reexamined in order to collect kinetic information also for those cases. With the development of user-friendly quantum chemistry programs such as the Gaussian suite of programs, the possibility of applying quantum chemical methods to many types of problems has become readily available even for non-experts. When performing mechanistic studies, there is quite often a considerable synergy effect when combining experimental and computational approaches. The methylation reactions mentioned above turned out to be an issue well suited for quantum chemical investigations. The incentive for examining the halomethane reactivity was the clear analogy to the MTH reaction system. Alkene dimerization was also a reaction readily examined with quantum chemistry. As discussed in the introduction of this thesis, polymethylbenzenes, or their cationic counterparts, are suspected to be key intermediates in the MTH reaction. It was therefore decided to investigate the intrinsic reactivity of these species in the gas-phase by employing sophisticated mass spectrometric (MS) techniques in collaboration with the MS group at the Department of Chemistry, University of Oslo The data thus obtained will also be compared with results from an ongoing computational study on gas phase polymethylbenzenium reactivity. 6 papers presenting various studies are included. The titles are: 1) A Theoretical Investigation of the Methylation of Alkenes with Methanol over Acidic Zeolites. 2) A Theoretical Investigation of the

Catalytic Wittig and aza-Wittig reactions

Directory of Open Access Journals (Sweden)

Zhiqi Lao

2016-11-01

Full Text Available This review surveys the literature regarding the development of catalytic versions of the Wittig and aza-Wittig reactions. The first section summarizes how arsenic and tellurium-based catalytic Wittig-type reaction systems were developed first due to the relatively easy reduction of the oxides involved. This is followed by a presentation of the current state of the art regarding phosphine-catalyzed Wittig reactions. The second section covers the field of related catalytic aza-Wittig reactions that are catalyzed by both phosphine oxides and phosphines.

Charge-exchange reactions on 36 S

International Nuclear Information System (INIS)

Fifield, L.K.; Catford, W.N.; Orr, N.A.; Ophel, T.R.; Etchegoyen, A.; Etchegoyen, M.C.

1992-11-01

A series of charge-exchange reactions on 36 S targets have been investigated at beam energies ∼7 MeV/A. Pronounced selectivities to different final states in 36 P are observed which depend on the projectile employed. An interpretation of the data in terms of one- and two-step pictures of the reaction mechanism is presented. At least two, and probably all, of the reactions have a significant 1-step contribution to the reaction mechanism at these energies. 22 refs., 5 tabs., 5 figs

Direct catalytic asymmetric aldol-Tishchenko reaction.

Science.gov (United States)

Gnanadesikan, Vijay; Horiuchi, Yoshihiro; Ohshima, Takashi; Shibasaki, Masakatsu

2004-06-30

A direct catalytic asymmetric aldol reaction of propionate equivalent was achieved via the aldol-Tishchenko reaction. Coupling an irreversible Tishchenko reaction to a reversible aldol reaction overcame the retro-aldol reaction problem and thereby afforded the products in high enantio and diastereoselectivity using 10 mol % of the asymmetric catalyst. A variety of ketones and aldehydes, including propyl and butyl ketones, were coupled efficiently, yielding the corresponding aldol-Tishchenko products in up to 96% yield and 95% ee. Diastereoselectivity was generally below the detection limit of 1H NMR (>98:2). Preliminary studies performed to clarify the mechanism revealed that the aldol products were racemic with no diastereoselectivity. On the other hand, the Tishchenko products were obtained in a highly enantiocontrolled manner.

Multiparticle production in heavy-ion reactions

International Nuclear Information System (INIS)

Pelte, D.

1980-01-01

This lecture is concerned with the question how many particles and what kind of them are produced in heavy-ion collisions at energies about 10 MeV/n. We tend to assume that heavy-ion reactions at this energy are binary reactions. The experimental set consisting of two large ionization chambers serving to detection, in coincidence, the reaction fragments is described. With this set-up a number of reactions induced on 27 Al, 28 Si and 40 Ca by the 32 S beam of 135 and 190 MeV energy has been studied. Two-fragments inclusive and exclusive reactions were investigated. The assumption of a sequential statistical decay gives the best agreement with the data for all analyzed cases. (H.M.)

Learning to predict chemical reactions.

Science.gov (United States)

Kayala, Matthew A; Azencott, Chloé-Agathe; Chen, Jonathan H; Baldi, Pierre

2011-09-26

Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles, respectively, are not high throughput, are not generalizable or scalable, and lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry data set consisting of 1630 full multistep reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top-ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of nonproductive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

Learning to Predict Chemical Reactions

Science.gov (United States)

Kayala, Matthew A.; Azencott, Chloé-Agathe; Chen, Jonathan H.

2011-01-01

Being able to predict the course of arbitrary chemical reactions is essential to the theory and applications of organic chemistry. Approaches to the reaction prediction problems can be organized around three poles corresponding to: (1) physical laws; (2) rule-based expert systems; and (3) inductive machine learning. Previous approaches at these poles respectively are not high-throughput, are not generalizable or scalable, or lack sufficient data and structure to be implemented. We propose a new approach to reaction prediction utilizing elements from each pole. Using a physically inspired conceptualization, we describe single mechanistic reactions as interactions between coarse approximations of molecular orbitals (MOs) and use topological and physicochemical attributes as descriptors. Using an existing rule-based system (Reaction Explorer), we derive a restricted chemistry dataset consisting of 1630 full multi-step reactions with 2358 distinct starting materials and intermediates, associated with 2989 productive mechanistic steps and 6.14 million unproductive mechanistic steps. And from machine learning, we pose identifying productive mechanistic steps as a statistical ranking, information retrieval, problem: given a set of reactants and a description of conditions, learn a ranking model over potential filled-to-unfilled MO interactions such that the top ranked mechanistic steps yield the major products. The machine learning implementation follows a two-stage approach, in which we first train atom level reactivity filters to prune 94.00% of non-productive reactions with a 0.01% error rate. Then, we train an ensemble of ranking models on pairs of interacting MOs to learn a relative productivity function over mechanistic steps in a given system. Without the use of explicit transformation patterns, the ensemble perfectly ranks the productive mechanism at the top 89.05% of the time, rising to 99.86% of the time when the top four are considered. Furthermore, the system

Adverse reactions associated with acetylcysteine.

Science.gov (United States)

Sandilands, E A; Bateman, D N

2009-02-01

Paracetamol (acetaminophen) is one of the most common agents deliberately ingested in self-poisoning episodes and a leading cause of acute liver failure in the western world. Acetylcysteine is widely acknowledged as the antidote of choice for paracetamol poisoning, but its use is not without risk. Adverse reactions, often leading to treatment delay, are frequently associated with both intravenous and oral acetylcysteine and are a common source of concern among treating physicians. A systematic literature review investigating the incidence, clinical features, and mechanisms of adverse effects associated with acetylcysteine. A variety of adverse reactions to acetylcysteine have been described ranging from nausea to death, most of the latter due to incorrect dosing. The pattern of reactions differs with oral and intravenous dosing, but reported frequency is at least as high with oral as intravenous. The reactions to the intravenous preparation result in similar clinical features to true anaphylaxis, including rash, pruritus, angioedema, bronchospasm, and rarely hypotension, but are caused by nonimmunological mechanisms. The precise nature of this reaction remains unclear. Histamine now seems to be an important mediator of the response, and there is evidence of variability in patient susceptibility, with females, and those with a history of asthma or atopy are particularly susceptible. Quantity of paracetamol ingestion, measured through serum paracetamol concentration, is also important as higher paracetamol concentrations protect patients against anaphylactoid effects. Most anaphylactoid reactions occur at the start of acetylcysteine treatment when concentrations are highest. Acetylcysteine also affects clotting factor activity, and this affects the interpretation of minor disturbances in the International Normalized Ratio in the context of paracetamol overdose. This review discusses the incidence, clinical features, underlying pathophysiological mechanisms, and

Uranium/water vapor reactions in gaseous atmospheres

International Nuclear Information System (INIS)

Jackson, R.L.; Condon, J.B.; Steckel, L.M.

1977-07-01

Experiments have been performed to determine the effect of varying humidities, gaseous atmospheres, and temperatures on the uranium/water vapor reaction. A balance, which allowed continuous in-system weighings, was used to determine the rates of the uranium/water vapor reactions at water vapor pressures of 383, 1586, and 2853 Pa and at temperatures of 80, 100, and 150 0 C in atmospheres of hydrogen, argon, or argon/oxygen mixtures. Based on rate data, the reactions were characterized as hydriding or nonhydriding. Hydriding reactions were found to be preferred in moist hydrogen systems at the higher temperatures and the lower humidities. The presence of hydrogen in hydriding systems was found to initially inhibit the reaction, but causes an acceleration of the rate in the final stages. In general, reaction rates of hydriding systems approached the hydriding rates calculated and observed in dry hydrogen. Hydriding and nonhydriding reaction rates showed a positive correlation to temperature and water vapor pressure. Final reaction rates in moist argon/oxygen mixtures of 1.93, 4.57, and 9.08 mole percent oxygen were greater than the rates observed in moist hydrogen or argon. Final reaction rates were negatively correlated to the oxygen concentration

Effect of Solvents on the Product Distribution and Reaction Rate of a Buchwald-Hartwig Amination Reaction

DEFF Research Database (Denmark)

Christensen, H.; Kiil, Søren; Dam-Johansen, Kim

2006-01-01

The Buchwald-Hartwig amination reaction between p-bromotoluene and piperazine in the presence of the homogeneous catalytic system Pd(dba)(2)/(+/-)-BINAP and the base NaO-t-Bu was investigated in two different classes of solvents: aprotic, nonpolar and aprotic, polar. The reaction was carried out...... solvent for the Buchwald-Hartwig amination reaction under the conditions applied was m-xylene....

On the ambiguity of the reaction rate constants in multivariate curve resolution for reversible first-order reaction systems.

Science.gov (United States)

Schröder, Henning; Sawall, Mathias; Kubis, Christoph; Selent, Detlef; Hess, Dieter; Franke, Robert; Börner, Armin; Neymeyr, Klaus

2016-07-13

If for a chemical reaction with a known reaction mechanism the concentration profiles are accessible only for certain species, e.g. only for the main product, then often the reaction rate constants cannot uniquely be determined from the concentration data. This is a well-known fact which includes the so-called slow-fast ambiguity. This work combines the question of unique or non-unique reaction rate constants with factor analytic methods of chemometrics. The idea is to reduce the rotational ambiguity of pure component factorizations by considering only those concentration factors which are possible solutions of the kinetic equations for a properly adapted set of reaction rate constants. The resulting set of reaction rate constants corresponds to those solutions of the rate equations which appear as feasible factors in a pure component factorization. The new analysis of the ambiguity of reaction rate constants extends recent research activities on the Area of Feasible Solutions (AFS). The consistency with a given chemical reaction scheme is shown to be a valuable tool in order to reduce the AFS. The new methods are applied to model and experimental data. Copyright © 2016 Elsevier B.V. All rights reserved.

Experimental Study of Serpentinization Reactions

Science.gov (United States)

Cohen, B. A.; Brearley, A. J.; Ganguly, J.; Liermann, H.-P.; Keil, K.

2004-01-01

Current carbonaceous chondrite parent-body thermal models [1-3] produce scenarios that are inconsistent with constraints on aqueous alteration conditions based on meteorite mineralogical evidence, such as phase stability relationships within the meteorite matrix minerals [4] and isotope equilibration arguments [5, 6]. This discrepancy arises principally because of the thermal runaway effect produced by silicate hydration reactions (here loosely called serpentinization, as the principal products are serpentine minerals), which are so exothermic as to produce more than enough heat to melt more ice and provide a self-sustaining chain reaction. One possible way to dissipate the heat of reaction is to use a very small parent body [e.g., 2] or possibly a rubble pile model. Another possibility is to release this heat more slowly, which depends on the alteration reaction path and kinetics.

Reaction mechanisms for the synthesis of the heaviest elements from heavy ion reactions

International Nuclear Information System (INIS)

Gaeggeler, H.W.

1988-10-01

This review paper concerns fusion reactions with light heavy-ions, cold fusion, transfer reactions using light heavy-ions or heavy ions. In two appendices, methods for the separation and detection of nuclides in the domain of heaviest elements are described and a comment on the discovery of the element 104 is given. 51 figs., 10 tabs., 335 refs

Application of multi-step direct reaction theory to 14 MeV neutron reaction, 3 (n,. cap alpha. )

Energy Technology Data Exchange (ETDEWEB)

Kumabe, I.; Matoba, M.; Fukuda, K. [Kyushu Univ., Fukuoka (Japan). Faculty of Engineering; Ikegami, H.; Muraoka, M [eds.

1980-01-01

Multi-step direct-reaction theory proposed by Tamura et al. has been applied to continuous spectra of the 14 MeV (n, ..cap alpha..) reaction with some modifications. Calculated results reproduce well the experimental energy and angular distributions of the 14 MeV (n, ..cap alpha..) reactions.

The nuclear reaction model code MEDICUS

International Nuclear Information System (INIS)

Ibishia, A.I.

2008-01-01

The new computer code MEDICUS has been used to calculate cross sections of nuclear reactions. The code, implemented in MATLAB 6.5, Mathematica 5, and Fortran 95 programming languages, can be run in graphical and command line mode. Graphical User Interface (GUI) has been built that allows the user to perform calculations and to plot results just by mouse clicking. The MS Windows XP and Red Hat Linux platforms are supported. MEDICUS is a modern nuclear reaction code that can compute charged particle-, photon-, and neutron-induced reactions in the energy range from thresholds to about 200 MeV. The calculation of the cross sections of nuclear reactions are done in the framework of the Exact Many-Body Nuclear Cluster Model (EMBNCM), Direct Nuclear Reactions, Pre-equilibrium Reactions, Optical Model, DWBA, and Exciton Model with Cluster Emission. The code can be used also for the calculation of nuclear cluster structure of nuclei. We have calculated nuclear cluster models for some nuclei such as 177 Lu, 90 Y, and 27 Al. It has been found that nucleus 27 Al can be represented through the two different nuclear cluster models: 25 Mg + d and 24 Na + 3 He. Cross sections in function of energy for the reaction 27 Al( 3 He,x) 22 Na, established as a production method of 22 Na, are calculated by the code MEDICUS. Theoretical calculations of cross sections are in good agreement with experimental results. Reaction mechanisms are taken into account. (author)

Nuclear Reaction Data Centers

International Nuclear Information System (INIS)

McLane, V.; Nordborg, C.; Lemmel, H.D.; Manokhin, V.N.

1988-01-01

The cooperating Nuclear Reaction Data Centers are involved in the compilation and exchange of nuclear reaction data for incident neutrons, charged particles and photons. Individual centers may also have services in other areas, e.g., evaluated data, nuclear structure and decay data, reactor physics, nuclear safety; some of this information may also be exchanged between interested centers. 20 refs., 1 tab

Explorations into Chemical Reactions and Biochemical Pathways.

Science.gov (United States)

Gasteiger, Johann

2016-12-01

A brief overview of the work in the research group of the present author on extracting knowledge from chemical reaction data is presented. Methods have been developed to calculate physicochemical effects at the reaction site. It is shown that these physicochemical effects can quite favourably be used to derive equations for the calculation of data on gas phase reactions and on reactions in solution such as aqueous acidity of alcohols or carboxylic acids or the hydrolysis of amides. Furthermore, it is shown that these physicochemical effects are quite effective for assigning reactions into reaction classes that correspond to chemical knowledge. Biochemical reactions constitute a particularly interesting and challenging task for increasing our understanding of living species. The BioPath.Database is a rich source of information on biochemical reactions and has been used for a variety of applications of chemical, biological, or medicinal interests. Thus, it was shown that biochemical reactions can be assigned by the physicochemical effects into classes that correspond to the classification of enzymes by the EC numbers. Furthermore, 3D models of reaction intermediates can be used for searching for novel enzyme inhibitors. It was shown in a combined application of chemoinformatics and bioinformatics that essential pathways of diseases can be uncovered. Furthermore, a study showed that bacterial flavor-forming pathways can be discovered. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A comprehensive survey of nuclear reactions; Panorama des reactions nucleaires