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characteristics of hydrogen production and substrate consumption of rhodopseudomonas palustris cqk 01 in an immobilized-cell photobioreactor.effects of operation parameters on hydrogen production rate, substrate utilization efficiency and hydrogen bioconversion yield were investigated in a photobioreactor packed with sodium alginate/polyvinyl alcohol-124/carrageenan granules containing rhodopseudomonas palustris cqk 01. results demonstrate that an increase in influent glucose concentration and flow rate enhanced glucose transport from the bulk liquid into the granules, resulting in high hydrogen production. the bacteria mainly utiliz ...201020137910
genomics firms turn to other markets. 201020164890
a new small regulatory protein, hmup, modulates haemin acquisition in sinorhizobium meliloti.sinorhizobium meliloti has multiple systems for iron acquisition, including the use of haem as an iron source. haem internalization involves the shmr haem outer membrane receptor and the hmutuv locus, which participates in haem transport across the cytoplasmic membrane. previous studies have demonstrated that expression of the shmr gene is negatively regulated by iron through rira. here, we identify hmup in a genetic screen for mutants that displayed aberrant control of shmr. the normal inductio ...201020167620
enhanced bio-hydrogen production by the combination of dark- and photo-fermentation in batch culture.in this study, some key factors, for example, diluted ratio of effluents, the ratio of dark-photo bacteria, light intensity and light/dark cycle influencing hydrogen production by combining clostridium butyricum and immobilized rhodopseudomonas faecalis rld-53 in batch culture, were investigated. experimental results showed the photo-hydrogen yield decreased when increasing diluted ratio from 1:0.5 to 1:3, and it reached the maximum value of 4368 ml-h(2)/l-effluents at the ratio of 1:0.5. when t ...201020202826
microalgal cell surface carbohydrates as recognition sites for particle sorting in suspension-feeding bivalves.cell surface carbohydrates play important roles in cell recognition mechanisms. recently, we provided evidence that particle selection by suspension-feeding bivalves can be mediated by interactions between carbohydrates associated with the particle surface and lectins present in mucus covering bivalve feeding organs. in this study, we used lectins tagged with fluorescein isothiocyanate (fitc) to characterize carbohydrate moieties on the surface of microalgal species and evaluate the effect of oy ...201020203255
a high-throughput de novo sequencing approach for shotgun proteomics using high-resolution tandem mass spectrometry.high-resolution tandem mass spectra can now be readily acquired with hybrid instruments, such as ltq-orbitrap and ltq-ft, in high-throughput shotgun proteomics workflows. the improved spectral quality enables more accurate de novo sequencing for identification of post-translational modifications and amino acid polymorphisms.201020205730
formation and hydrogen production of photosynthetic bacterial biofilm under various illumination conditions.the application of immobilized-cell technology in photobioreactor for hydrogen production could offer improvements in photo-hydrogen production rate and light utilization efficiency. indigenous rhodopseudomonas palustris cqk 01 was attached to the surface of a cover glass slide in a flat-panel photobioreactor, to form biofilm under illumination with a range of intensities and wavelengths. the morphology and structure of mature photosynthetic bacterial (psb) biofilm were determined to elucidate t ...201020226657
responses of microbial community functional structures to pilot-scale uranium in situ bioremediation.a pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ u(vi) bioremediation at a us department of energy site, oak ridge, tn. the outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for u(vi) reduction/immobilization. after 2 years of biostimulation with ethanol, u(vi) levels were reduced to below drinking water standard (<30 microg l(-1)) in the inner loop monitoring ...201020237512
carbon dioxide fixation as a central redox cofactor recycling mechanism in bacteria.the calvin-benson-bassham cycle (calvin cycle) catalyzes virtually all primary productivity on earth and is the major sink for atmospheric co(2). a less appreciated function of co(2) fixation is as an electron-accepting process. it is known that anoxygenic phototrophic bacteria require the calvin cycle to accept electrons when growing with light as their sole energy source and organic substrates as their sole carbon source. however, it was unclear why and to what extent co(2) fixation is require ...201020558750
phototropic h2 production by a newly isolated strain of rhodopseudomonas palustris.rhodopseudomonas palustris tn1 was isolated from songkhla lake, thailand. it phototrophically generates h(2) from the predominant volatile fatty acids (vfas) produced from microbial dark-fermentations of palm oil milling effluent; yields from 20 mm butyrate, acetate and propionate were 4.7, 2.5, and 1.7 mol h(2) mol vfa(-1) with light efficiencies of 1.8, 1, and 0.2%, respectively. optimum conditions were ph 7 and 3000 lux, although production was reduced by only 33% at 1000 lux. co(2) evolution ...201020623317
excitation dynamics in phycoerythrin 545: modeling of steady-state spectra and transient absorption with modified redfield theory.we model the spectra and excitation dynamics in the phycobiliprotein antenna complex pe545 isolated from the unicellular photosynthetic cryptophyte algae rhodomonas cs24. the excitonic couplings between the eight bilins are calculated using the cis/6-31g method. the site energies are extracted from a simultaneous fit of the absorption, circular dichroism, fluorescence, and excitation anisotropy spectra together with the transient absorption kinetics using the modified redfield approach. quantita ...201020643051
heavy metal tolerant metalliresistens boonkerdii gen. nov., sp. nov., a new genus in the family bradyrhizobiaceae isolated from soil in thailand.bacterial strains from inoculated soybean field soil in thailand were directly isolated using bradyrhizobium japonicum selective medium (bjsm), on the basis of zn(2+) and co(2+) resistance of b. japonicum and b. elkanii. the isolates were classified into symbiotic and non-symbiotic groups by inoculation assays and southern hybridization of nod and nif genes. in this study, a nearly full-length 16s rrna gene sequence showed that the non-symbiotic isolates were more closely related to members of r ...201020663625
progress toward a biomimetic leaf: 4,000 h of hydrogen production by coating-stabilized nongrowing photosynthetic rhodopseudomonas palustris.intact cells are the most stable form of nature's photosynthetic machinery. coating-immobilized microbes have the potential to revolutionize the design of photoabsorbers for conversion of sunlight into fuels. multi-layer adhesive polymer coatings could spatially combine photoreactive bacteria and algae (complementary biological irradiance spectra) creating high surface area, thin, flexible structures optimized for light trapping, and production of hydrogen (h(2)) from water, lignin, pollutants, ...201020730752
a pm6 study of rhodopseudomonas acidophila light harvesting center ii b800 bacteriochlorophylls in representative protein environment.bacterial light-harvesting ii (lh-ii) centers contain two types of bacteriochlorophylls (bchl). one is named b800 and found as a single molecule within one monomer of the complex while the other named b850 is found as a dimer. their names indicate their peak of uv absorbance around red spectrum. both types of molecules are attached to the protein chain via ligation of their central magnesium atom to an either histidine or deoxymethionine amino acid. they are also coordinated by peripheral hydrog ...201020814708
[biodegradation characteristics of o-chlorophenol with photosynthetic bacteria psb-1d].a strain of photosynthetic bacteria named psb-1d with degradation of o-chlorophenol (2-cp) was isolated and screened from the shallow substrate sludge in downstream side of the sewage outfall of an insecticide factory. the psb-1d is identified preliminarily as rhodopseudomonas sp. according to its colony and cell morphological properties, physiological biochemical characteristics and absorption spectrum analysis of living cells. the experiments results of relationship between psb-1d growth and o ...201020825044
regioselective oxidation of indole- and quinolinecarboxylic acids by cytochrome p450 cyp199a2.cyp199a2, a bacterial p450 monooxygenase from rhodopseudomonas palustris, was previously reported to oxidize 2-naphthoic acid and 4-ethylbenzoic acid. in this study, we examined the substrate specificity and regioselectivity of cyp199a2 towards indole- and quinolinecarboxylic acids. the cyp199a2 gene was coexpressed with palustrisredoxin gene from r. palustris and putidaredoxin reductase gene from pseudomonas putida to provide the redox partners of cyp199a2 in escherichia coli. following whole-c ...201020112454
production of hydrogen gas from light and the inorganic electron donor thiosulfate by rhodopseudomonas palustris.a challenge for photobiological production of hydrogen gas (h(2)) as a potential biofuel is to find suitable electron-donating feedstocks. here, we examined the inorganic compound thiosulfate as a possible electron donor for nitrogenase-catalyzed h(2) production by the purple nonsulfur phototrophic bacterium (pnsb) rhodopseudomonas palustris. thiosulfate is an intermediate of microbial sulfur metabolism in nature and is also generated in industrial processes. we found that r. palustris grew phot ...201020889777
primary reactions of bacteriophytochrome observed with ultrafast mid-infrared spectroscopy.phytochromes are red-light photoreceptor proteins that regulate a variety of responses and cellular processes in plants, bacteria, and fungi. the phytochrome light activation mechanism involves isomerization around the c(15)═c(16) double bond of an open-chain tetrapyrrole chromophore, resulting in a flip of its d-ring. in an important recent development, bacteriophytochrome (bph) has been engineered for use as a fluorescent marker in mammalian tissues. bphs covalently bind a biliverdin (bv) chro ...201021192725
mining bacterial genomes for novel arylesterase activity.one hundred and seventy-one genes encoding potential esterases from 11 bacterial genomes were cloned and overexpressed in escherichia coli; 74 of the clones produced soluble proteins. all 74 soluble proteins were purified and screened for esterase activity; 36 proteins showed carboxyl esterase activity on short-chain esters, 17 demonstrated arylesterase activity, while 38 proteins did not exhibit any activity towards the test substrates. esterases from rhodopseudomonas palustris (rpest-1, rpest- ...201021255363
performance of an experimental wastewater treatment high-rate algal pond in subarctic climate.a pilot-scale experimental high-rate algal pond (hrap) was investigated in the subarctic mid-sweden region, at latitude 63 degrees n. during autumn 2002, conditions included temperatures below 10 degrees c and photosynthetic active radiation below 200 microe/m2 x s. biochemical oxygen demand was reduced by approximately 90% (approximately 40 g/m3), chemical oxygen demand by 65% (approximately 80 g/m3), total phosphorus by 20% (approximately 1 g/m3), and total nitrogen by 46% (approximately 15 g/ ...201020942338
characterization of bacteriophytochromes from photosynthetic bacteria: histidine kinase signaling triggered by light and redox sensing.bacteria detect environmental changes, thanks to two-component signal-transduction systems, composed, in general, of a sensor coupled to a histidine kinase and a dna binding response regulator. anoxygenic photosynthetic bacteria like rhodopseudomonas (rps.) palustris, possess a highly versatile metabolism and can grow via photosynthesis using light energy or via respiration through oxygen consumption. for photosynthetic bacteria, detecting changes in light quality or quantity, or in oxygen conce ...201020946847
enhancement of photohydrogen production using phbc deficient mutant rhodopseudomonas palustris strain m23.this study used a dna recombination method to knock out the poly-β-hydroxybutyrate (phb) synthesis gene phbc in the photosynthetic bacterium rhodopseudomonas palustris wp3-5. the experimental results indicated that the mutant strain rps. palustris m23 could be successfully screened. fluorescent observation with nile blue staining showed no significant phb granule accumulation in the mutant cells. batch mode experiments using acetic acid as a carbon source revealed a 29.1% and 25.9% hydrogen gas ...201020961752
on the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins.tsien et al. (science, 2009, 324, 804-807) recently reported the creation of the first infrared fluorescent protein (ifp). it was engineered from bacterial phytochrome by removing the phy and histidine kinase-related domains, by optimizing the protein to prevent dimerization, and by limiting the biliverdins conformational freedom, especially around its d ring. we have used database analyses and molecular dynamics simulations with freely rotating chromophoric dihedrals in order to model the dihed ...201021047084
biochemical and physiological characterization of a bluf protein-eal protein complex involved in blue light-dependent degradation of cyclic diguanylate in the purple bacterium rhodopseudomonas palustris.organisms adapt their physiologies in response to the quality and quantity of environmental light. members of a recently identified photoreceptor protein family, bluf domain proteins, use a flavin chromophore to sense blue light. herein, we report that papb, which contains a bluf domain, controls the biofilm formation of the purple photosynthetic bacterium rhodopseudomonas palustris. purified papb undergoes a typical bluf-type photocycle, and light-excited papb enhances the phosphodiesterase act ...201021082778
construction and characterization of a photosynthetic bacterium genetically engineered for hg2+ uptake.a recombinant photosynthetic bacterium, rhodopseudomonas palustris, was constructed to simultaneously express mercury transport system and metallothionein for hg(2+) removal from heavy metal wastewater. the effects of essential process parameters, including ph, ionic strength and presence of co-ions on hg(2+) uptake were evaluated. the results showed that compared with wild type r. palustris, recombinant strain displayed stronger resistance to toxic hg(2+), and its hg(2+) binding capacity was en ...201021094044
acetate-dependent photoheterotrophic growth and the differential requirement for the calvin-benson-bassham reductive pentose phosphate cycle in rhodobacter sphaeroides and rhodopseudomonas palustris.rhodobacter sphaeroides ribulose-1,5-bisphosphate carboxylase/oxygenase (rubisco)-deletion strain 16 was capable of photoheterotrophic growth with acetate, while rhodopseudomonas palustris rubisco-deletion strain 2040 could not grow under these conditions. the reason for this difference lies in the fact that rba. sphaeroides and rps. palustris use different pathways for acetate assimilation, the ethylmalonyl-coa pathway, and glyoxylate-bypass cycle, respectively. the ethylmalonyl-coa pathway is ...201021104179
regulation of the phototrophic iron oxidation (pio) genes in rhodopseudomonas palustris tie-1 is mediated by the global regulator, fixk.the pioabc operon is required for phototrophic iron oxidative (photoferrotrophic) growth by the α-proteobacterium rhodopseudomonas palustris tie-1. expression analysis of this operon showed that it was transcribed and translated during anaerobic growth, upregulation being observed only under photoferrotrophic conditions. very low levels of transcription were observed during aerobic growth, suggesting expression was induced by anoxia. the presence of two canonical fixk boxes upstream of the ident ...201021166894
differential effects of nutrient-limited primary production on primary, secondary or tertiary consumers.nutritional imbalances between predator and prey are the rule rather than the exception at the lower end of food webs. we investigated the role of different grazers in the propagation of nutritionally imbalanced primary production by using the same primary producers in a three-trophic-level food chain and a four-trophic-level food chain experimental setup. the three-trophic-level food chain consisted of a classic single-cell primary producer (rhodomonas salina), a metazoan grazer (the copepod ac ...201019784675
characteristics of a biofilm photobioreactor as applied to photo-hydrogen production.the application of a cell immobilization technique to a biofilm-based photobioreactor was developed to enhance its photo-hydrogen production rate and light conversion efficiency. rhodopseudomonas palustris cqk 01 was initially attached to the surface of packed glass beads to form a biofilm in this experiment. then, the biofilm photobioreactor (bpbr) was illuminated by light-emitting diodes with light wavelengths of 470, 590 and 630 nm and hydrogen was evolved with glucose being the sole carbon s ...201019818607
effect of treatment with probiotics as water additives on tilapia (oreochromis niloticus) growth performance and immune response.a feeding trial was conducted for 40 days to delineate the effect of treatment with probiotics as water additives on tilapia (oreochromis niloticus) growth performance and immune response. about 360 juveniles were randomly distributed into four treatment groups, each with three replicates. different probiotics (t-1, bacillus subtilis b10; t-2, bacillus coagulans b16; t-3, rhodopseudomonas palustris g06) were added to the water of tanks at final concentration of 1 x 10(7) cfu ml(-1) every 2 days, ...201019363655
a nitrite biosensor based on co-immobilization of nitrite reductase and viologen-modified chitosan on a glassy carbon electrode.an electrochemical nitrite biosensor based on co-immobilization of copper- containing nitrite reductase (cu-nir, from rhodopseudomonas sphaeroides forma sp. denitrificans) and viologen-modified chitosan (chit-v) on a glassy carbon electrode (gce) is presented. electron transfer (et) between a conventional gce and immobilized cu-nir was mediated by the co-immobilized chit-v. redox-active viologen was covalently linked to a chitosan backbone, and the thus produced chit-v was co-immobilized with cu ...201022219710
fluorescence blinking of the rc-lh1 complex from rhodopseudomonas palustris.we investigate fluorescence blinking of individual rc-lh1 (reaction-centre-light-harvesting 1) complexes from the photosynthetic purple bacterium rhodopseudomonas palustris. for both the on- and off-periods the telegraph-like intermittency of the fluorescence intensity follows power-law statistics with exponents between 1 and 2. yet, this behaviour was only observed for a small fraction of the complexes studied. we argue that the majority of the complexes reside in a prolonged on-state, due to a ...201021344600
production of biomass and extracellular 5-aminolevulinic acid by rhodopseudomonas palustris kg31 under light and dark conditions using volatile fatty acid.kinetic parameters for growth and extracellular 5-aminolevulinic acid (ala) production of rhodopseudomonas palustris kg31 under light and dark conditions in a medium containing volatile fatty acids (vfa) as the carbon sources were estimated using a gompertz model. the lag phase for growth and the maximum specific growth rate under microaerobic-light cultivations were 7.29-12.49 h and 0.038-0.094 h(-1), respectively, whereas under aerobic-dark cultivations, they were 2.03-14.25 h and 0.016-0.022 ...201121353636
thermostability of rhodopseudomonas viridis and rhodospirillum rubrum chromatophores reflecting physiological conditions.relationships between growth conditions and thermostability were examined for photosynthetic inner membranes (chromatophores) from rhodopseudomonas viridis and rhodospirillum rubrum of which morphology, lipid composition, and protein/lipid rate are rather mutually different. signals observed by differential scanning calorimetry of the chromatophores were correlated with thermal state transitions of the membrane components by reference to temperature dependencies of circular dichroism and absorpt ...201121354412
unravelling the regulatory twist--regulation of co2 fixation in rhodopseudomonas palustris cga010 mediated by atypical response regulator(s).in rhodopseudomonas palustris cga010, the lysr type regulator, cbbr, specifically controls transcription of the cbbls genes encoding form i rubisco. previous genetic and physiological studies had indicated that a unique two-component (cbbrrs) system influences cbbr-mediated cbbls transcription under conditions where co(2) is the sole carbon source. in this study, we have established direct protein-protein interactions between the response regulators of the cbbrrs system and cbbr, using a variety ...201121362064
activity of the rhodopseudomonas palustris p-coumaroyl-homoserine lactone-responsive transcription factor rpar.the rhodopseudomonas palustris transcriptional regulator rpar responds to the rpai-synthesized quorum-sensing signal p-coumaroyl-homoserine lactone (pc-hsl). other characterized rpar homologs respond to fatty acyl-hsls. we show here that rpar functions as a transcriptional activator, which binds directly to the rpai promoter. we developed an rnaseq method that does not require a ribosome depletion step to define a set of transcripts regulated by pc-hsl and rpar. the transcripts include several n ...201121378182
probing the enantioselectivity of a diverse group of purified cobalt-centred nitrile hydratases.in this study a diverse range of purified cobalt containing nitrile hydratases (nhases, ec 4.2.1.84) from rhodopseudomonas palustris haa2 (haa2), rhodopseudomonas palustris cga009 (009), sinorhizobium meliloti 1021 (1021), and nitriliruptor alkaliphilus (iso2), were screened for the first time for their enantioselectivity towards a broad range of chiral nitriles. enantiomeric ratios of >100 were found for the nhases from haa2 and cga009 on 2-phenylpropionitrile. in contrast, the fe-containing nh ...201121380438
ab inito study on triplet excitation energy transfer in photosynthetic light-harvesting complexes.we have studied the triplet energy transfer (tet) for photosynthetic light-harvesting complexes, the bacterial light-harvesting complex ii (lh2) of rhodospirillum molischianum and rhodopseudomonas acidophila, and the peridinin-chlorophyll a protein (pcp) from amphidinium carterae. the electronic coupling factor was calculated with the recently developed fragment spin difference scheme (you and hsu, j. chem. phys. 2010, 133, 074105), which is a general computational scheme that yields the overall ...201121410281
enhanced hydrogen production by rhodopseudomonas palustris cqk 01 with ultra-sonication pretreatment in batch culture.in the present study, the photo-hydrogen production performances by rhodopseudomonas palustris cqk 01 growing from the inoculated cells with ultra-sonication pretreatment (r. palustris cqk 01-usp) were experimentally investigated in batch culture and compared with that without pretreatment (r. palustris cqk 01-np). it was found that the ultra-sonication pretreatment modified membrane morphology and broke up part of the cells, resulting in improvement of membrane permeability and bacterial activi ...201121411314
energy transfer in an lh4-like light harvesting complex from the aerobic purple photosynthetic bacterium roseobacter denitrificans.a peripheral light-harvesting complex from the aerobic purple bacterium roseobacter (r.) denitrificans was purified and its photophysical properties characterized. the complex contains two types of pigments, bacteriochlorophyll (bchl) a and the carotenoid (car) spheroidenone and possesses unique spectroscopic properties. it appears to lack the b850 bacteriochlorophyll a q(y) band that is typical for similar light-harvesting complex 2 antennas. circular dichroism and low temperature steady-state ...201121419098
calvin cycle flux, pathway constraints, and substrate oxidation state together determine the h2 biofuel yield in photoheterotrophic bacteria.hydrogen gas (h(2)) is a possible future transportation fuel that can be produced by anoxygenic phototrophic bacteria via nitrogenase. the electrons for h(2) are usually derived from organic compounds. thus, one would expect more h(2) to be produced when anoxygenic phototrophs are supplied with increasingly reduced (electron-rich) organic compounds. however, the h(2) yield does not always differ according to the substrate oxidation state. to understand other factors that influence the h(2) yield ...201121427286
quantum chemical simulations of excited-state absorption spectra of photosynthetic bacterial reaction center and antenna complexes.the semiempirical zindo/s cis configuration interaction method has been used to study the ground- and excited-state absorption spectra of wild type and heterodimer m202hl reaction centers from purple bacterium rhodobacter sphaeroides as well as of peripheral lh2 and lh3 light harvesting complexes from purple bacterium rhodopseudomonas acidophila. the calculations well reproduce the experimentally observed excited-state absorption spectra between 1000 and 17,000 cm(-1), despite the necessarily li ...201121466178
aryl-homoserine lactone quorum sensing in stem-nodulating photosynthetic bradyrhizobia.many proteobacteria possess luxi-luxr-type quorum-sensing systems that produce and detect fatty acyl-homoserine lactone (hsl) signals. the photoheterotroph rhodopseudomonas palustris is unusual in that it produces and detects an aryl-hsl, p-coumaroyl-hsl, and signal production requires an exogenous source of p-coumarate. a photosynthetic stem-nodulating member of the genus bradyrhizobium produces a small molecule signal that elicits an r. palustris quorum-sensing response. here, we show that thi ...201121471459
excitation-emission polarization spectroscopy of single light harvesting complexes.excitation and emission polarization dependence of fluorescence intensity of single lh2 complexes from rhodopseudomonas acidophila 10050 and rhodobacter sphaeroides is reported. the results are presented as two-dimensional polarization plots and interpreted in terms of tilted light harvesting complexes indicating that sample preparation leads to partially oriented lh2 cylinders. an alternative explanation of the observation can be structural deformation. fluorescence intensity of the complexes h ...201121486039
bradyrhizobium canariense and bradyrhizobium japonicum are the two dominant rhizobium species in root nodules of lupin and serradella plants growing in europe.forty three bradyrhizobium strains isolated in poland from root nodules of lupin species (lupinus albus, l. angustifolius and l. luteus), and pink serradella (ornithopus sativus) were examined based on phylogenetic analyses of three housekeeping (atpd, glnii and reca) and nodulation (noda) gene sequences. additionally, seven strains originating from root-nodules of yellow serradella (o. compressus) from asinara island (italy) were included in this study. phylogenetic trees revealed that 15 serra ...201121514760
arsenic biotransformation and volatilization in transgenic rice.• biotransformation of arsenic includes oxidation, reduction, methylation, and conversion to more complex organic arsenicals. members of the class of arsenite (as(iii)) s-adenosylmethyltransferase enzymes catalyze as(iii) methylation to a variety of mono-, di-, and trimethylated species, some of which are less toxic than as(iii) itself. however, no methyltransferase gene has been identified in plants. • here, an arsm gene from the soil bacterium rhodopseudomonas palustris was expressed in japoni ...201121517874
effects of flow rate and substrate concentration on the formation and h(2) production of photosynthetic bacterial biofilms.photosynthetic bacteria (psb), rhodopseudomonas palustris cqk 01, were immobilized on the surface of a thin glass slide in a lab-scale flat panel photobioreactor under different flow rates and substrate concentrations. the morphology, dry weight and thickness of the mature psb biofilms were determined to reveal the relationship between biofilm formation and hydrogen production performance. the mature biofilm formed at a low flow rate and a high substrate concentration showed a looser structure, ...201121531551
[biological characteristics and phylogenetic analysis of a denitrifying photosynthetic bacterium].nitrite accumulation in aquaculture water is toxic to reared animals. one of the solutions to this problem is to apply denitrifying bacteria. this paper is intended to get a strain of phototrophic bacteria for efficient removal of nitrite from aquaculture water.201121574387
enhancement of photo-hydrogen production in a biofilm photobioreactor using optical fiber with additional rough surface.in this study, a biofilm photobioreactor with optical fibers that have additional rough surface (ofbp-r) was developed and it was shown that additional rough surface greatly enhanced the biofilm formation and thus increased the cell concentration, leading to an improvement in the hydrogen production performance. the effects of operational conditions, including the influent substrate concentration, flow rate, temperature and influent medium ph, on the performance of ofbp-r were also investigated. ...201121596561
reconstitution of bacterial photosynthetic unit in a lipid bilayer studied by single-molecule spectroscopy at 5 k.as a model of photosynthetic unit (psu), self-assembled aggregates of pigment-protein complexes from photosynthetic bacteria were prepared in a lipid bilayer by reconstitution of the light-harvesting 2 (lh2) complex and light-harvesting 1-reaction center (lh1-rc) complex through detergent removal of their micelles in the presence of lipids. by performing polarization-controlled fluorescence and fluorescence-excitation spectroscopy on single aggregates at a temperature of 5 k, the composition of ...201121597611
hydrogen production by rhodopseudomonas palustris wp 3-5 in a serial photobioreactor fed with hydrogen fermentation effluent.in this study, a lab-scale serial photobioreactor composed of three column reactors was constructed and continuously operated to investigate several parameters influencing photohydrogen production when using the synthetic wastewater and the anaerobic hydrogen fermentation effluents as the influents. the results indicated that better hydrogen production rate was obtained when the serial photobioreactor was operated under cellular recycling at a short hrt of 8h. the serial photobioreactor maintain ...201121600763
in silico predictions of lh2 ring sizes from the crystal structure of a single subunit using molecular dynamics simulations.most of the currently known light-harvesting complexes 2 (lh2) rings are formed by 8 or 9 subunits. as of now, questions like "what factors govern the lh2 ring size?" and "are there other ring sizes possible?" remain largely unanswered. here, we investigate by means of molecular dynamics (md) simulations and stochastic modeling the possibility of predicting the size of an lh2 ring from the sole knowledge of the high resolution crystal structure of a single subunit. starting with single subunits ...201121604304
fluorescence quantum yield and photochemistry of bacteriophytochrome constructs.bacteriophytochromes (bphs) are red-light photoreceptor proteins with a photosensory core that consists of three distinct domains, pas, gaf and phy, and covalently binds biliverdin (bv) to a conserved cysteine in the pas domain. in a recent development, pas-gaf variants were engineered for use as a near-infrared fluorescent marker in mammalian tissues (tsien and co-workers, science, 2009, 324, 804-807). here, we report the fluorescence quantum yield and photochemistry of two highly-related bphs ...201121611667
environment sensing and response mediated by abc transporters.transporter proteins are one of an organism's primary interfaces with the environment. the expressed set of transporters mediates cellular metabolic capabilities and influences signal transduction pathways and regulatory networks. the functional annotation of most transporters is currently limited to general classification into families. the development of capabilities to map ligands with specific transporters would improve our knowledge of the function of these proteins, improve the annotation ...201121810210
molecular origins and consequences of high-800 lh2 in roseobacter denitrificans.roseobacter denitrificans is a marine bacterium capable of using a wide variety of different metabolic schemes and in particular is an anoxygenic aerobic photosynthetic bacterium. in the work reported here we use a deletion mutant that we have constructed to investigate the structural origin of the unusual high-800 light-harvesting complex absorption in this bacterium. we suggest that the structure is essentially unaltered when compared to the usual nonameric complexes but that a change in the e ...201121739946
theoretical study of the excited states of the photosynthetic reaction center in photosystem ii: electronic structure, interactions, and their origin.the excited states of the chlorophyll 6-mer in the photosystem ii (psii) reaction center (rc) were investigated theoretically using ab initio quantum chemical calculations, and the results are compared with those of the bacterial reaction center (brc). a significant difference in the peak at the lowest energy in the absorption spectra arises from the structural asymmetry of the special pair (sp). the origin can be traced back to the structural difference in the cd helix. the low-lying excited st ...201121816534
mode of action of membrane-disruptive lytic compounds from the marine dinoflagellate alexandrium tamarense.certain allelochemicals of the marine dinoflagellate alexandrium tamarense cause lysis of a broad spectrum of target protist cells but the lytic mechanism is poorly defined. we first hypothesized that membrane sterols serve as molecular targets of these lytic compounds, and that differences in sterol composition among donor and target cells may cause insensitivity of alexandrium and sensitivity of targets to lytic compounds. we investigated ca(2+) influx after application of lytic fractions to a ...201121741395
Polarization single complex imaging of circular photosynthetic antenna.Single complex fluorescence polarization spectroscopy is applied to study the peripheral light harvesting antenna (LH2) from photosynthetic purple bacterium Rhodopseudomonas (Rps.) acidophila. The measured two-dimensional excitation-emission polarization plots are used to construct geometric representation for the absorbing B800 and emitting B850 as ellipses. The shape and orientation of the ellipses is discussed in terms of tilted LH2 complexes where emission occurs from energetically disordere ...201121830142
alga-derived substrates select for distinct betaproteobacterial lineages and contribute to niche separation in limnohabitans strains.we examined the proportions of major betaproteobacteria subgroups within bacterial communities in diverse nonaxenic, monospecific cultures of algae or cyanobacteria: four species of cryptophyta (genera cryptomonas and rhodomonas), four species of chlorophyta (genera pediastrum, staurastrum, and chlamydomonas), and two species of cyanobacteria (genera dolichospermum and aphanizomenon). in the cryptophyta cultures, betaproteobacteria represented 48 to 71% of total bacteria, the genus limnohabitans ...201121873481
Isovaleryl-homoserine lactone, an unusual branched-chain quorum-sensing signal from the soybean symbiont Bradyrhizobium japonicum.Many species of Proteobacteria communicate by using LuxI-LuxR-type quorum-sensing systems that produce and detect acyl-homoserine lactone (acyl-HSL) signals. Most of the known signals are straight-chain fatty acyl-HSLs, and evidence indicates that LuxI homologs prefer fatty acid-acyl carrier protein (ACP) over fatty acyl-CoA as the acyl substrate for signal synthesis. Two related LuxI homologs, RpaI and BtaI from Rhodopseudomonas palustris and photosynthetic stem-nodulating bradyrhizobia, direct ...201121949379
the rnd-family transporter, hpnn, is required for hopanoid localization to the outer membrane of rhodopseudomonas palustris tie-1.rhodopseudomonas palustris tie-1 is a gram-negative bacterium that produces structurally diverse hopanoid lipids that are similar to eukaryotic steroids. its genome encodes several homologues to proteins involved in eukaryotic steroid trafficking. in this study, we explored the possibility that two of these proteins are involved in intracellular hopanoid transport. r. palustris has a sophisticated membrane system comprising outer, cytoplasmic, and inner cytoplasmic membranes. it also divides asy ...201121873238
nano-tio2 enhanced photofermentative hydrogen produced from the dark fermentation liquid of waste activated sludge.after anaerobic dark fermentation of waste activated sludge (was) for hydrogen production, there are a large number of organic compounds including protein, polysaccharide, and volatile fatty acids left in the dark fermentation liquid, which can be further bioconverted to hydrogen by photofermentation techniquea. in this study, the enhancement of photofermentative hydrogen produced from was dark fermentation liquid by using nano-tio2 is reported. first, high concentration of nh(4)(+)-n in the dar ...201121851074
revealing the functions of the transketolase enzyme isoforms in rhodopseudomonas palustris using a systems biology approach.rhodopseudomonas palustris (r. palustris) is a purple non-sulfur anoxygenic phototrophic bacterium that belongs to the class of proteobacteria. it is capable of absorbing atmospheric carbon dioxide and converting it to biomass via the process of photosynthesis and the calvin-benson-bassham (cbb) cycle. transketolase is a key enzyme involved in the cbb cycle. here, we reveal the functions of transketolase isoforms i and ii in r. palustris using a systems biology approach.201122174789
isolation and pigment composition of the reaction centers from purple photosynthetic bacterium rhodopseudomonas palustris species.the reaction centers (rcs) from several species of a purple photosynthetic bacterium, rhodopseudomonas palustris, were first isolated by ammonium-sulfate fractionation of the isolated core complexes, and were successfully purified by anion-exchange and gel-filtration chromatography as well as sucrose-density gradient centrifugation. the rcs were characterized by spectroscopic and biochemical analyses, indicating that they were sufficiently pure and had conserved their redox activity. the pigment ...201122182773
characterization of microbial communities during anode biofilm reformation in a two-chambered microbial electrolysis cell (mec).geochip (ii) and single strand conformation polymorphism (sscp) were used to characterize anode microbial communities of a microbial electrolysis cell (mec). biofilm communities, enriched in a two-chamber mec (r1, 0.6v applied) having a coulombic efficiency (ce) of 35±4% and a hydrogen yield [formula: see text] of 31±3%, were used as the inoculum for a new reactor (r2). after three months r2 achieved stable performance with ce=38±4% and [formula: see text] few changes in the predominant populati ...201121939699
the electronically excited states of lh2 complexes from rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic monte carlo simulations. i: isolated, non-interacting lh2 complexes.we have employed time-resolved spectroscopy on the picosecond time scale in combination with dynamic monte carlo simulations to investigate the photophysical properties of light-harvesting 2 (lh2) complexes from the purple photosynthetic bacterium <i>rhodopseudomonas acidophila</i>. the variations of the fluorescence transients were studied as a function of the excitation fluence, the repetition rate of the excitation and the sample preparation conditions. here we present the results obtained on ...201121648465
the electronically excited states of lh2 complexes from rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic monte carlo simulations. ii. homo-arrays of lh2 complexes reconstituted into phospholipid model membranes.we performed time-resolved spectroscopy on homoarrays of lh2 complexes from the photosynthetic purple bacterium rhodopseudomonas acidophila. variations of the fluorescence transients were monitored as a function of the excitation fluence and the repetition rate of the excitation. these parameters are directly related to the excitation density within the array and to the number of lh2 complexes that still carry a triplet state prior to the next excitation. comparison of the experimental observati ...201121650216
the light intensity at which cells are grown controls the type of peripheral light-harvesting complexes that are assembled in a purple photosynthetic bacterium.the differing composition of peripheral light harvesting complexes (lh2) present in rhodopseudomonas (rps.) palustris 2.1.6 have been investigated when cells are grown at progressively decreasing light intensity. detailed analysis of their absorption spectra reveals that there must be more than two types of lh2 complexes present. purified high-light (hl) and low-light (ll) lh2 complexes have mixed apoprotein compositions. the hl complexes contain pucaba and pucabb apoproteins. the ll complexes c ...201121793805
an integrated semiconductor device enabling non-optical genome sequencing.the seminal importance of dna sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. here we describe a dna sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical dna sequencing of genomes. sequence data are obtained by directly sensing the ions produced by template-directed dna polymerase synthesis using all-natural ...201121776081
genome-scale analysis of anaerobic benzoate and phenol metabolism in the hyperthermophilic archaeon ferroglobus placidus.insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (>80°?c) environments and to identify enzymes that might have biotechnological applications. analysis of the f. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as having a role in benzoate and phenol metabolism in mesophilic bacteria. su ...201121776029
anaerobic utilization of phenanthrene by rhodopseudomonas palustris.a phenanthrene-utilizing bacterium was anaerobically isolated and identified as rhodopseudomonas palustris. it tolerated up to 100 mg phenanthrene l(-1) and degraded 50% of 50 mg phenanthrene l(-1) over 10 days. the presence of phenanthrene caused a prolonged lag phase (2-3 days) in cell growth and affected the photopigments biosynthesis, while dmso (the solvent for phenanthrene) had no impact on cell growth. the cell surface hydrophobicity of the isolate was also increased.201121748363
stoichiometric conversion of biodiesel derived crude glycerol to hydrogen: response surface methodology study of the effects of light intensity and crude glycerol and glutamate concentration.photofermentation by the photosynthetic bacterium rhodopseudomonas palustris has been used to convert the crude glycerol fraction from biodiesel production to hydrogen as a means of converting this large resource to useful energy. in the present study response surface methodology was applied to investigate the interactive effects among several important process parameters; light intensity, and the concentrations of crude glycerol and glutamate, on the stoichiometric conversion of crude glycerol ...201122206915
[rhodomonas salina (cryptophyta) pastes as feed for brachionus plicatilis (rotifera)].rotifers are an important live feed for first feeding larvae of many fish species. the use of concentrated algae cells in the mass culture of the rotifer brachionus plicatilis (brachionidae) has opened new horizons for research on this organism. pastes of rhodomonas salina (pyrenomonadaceae) obtained either by centrifugation or flocculation with chitosan were preserved, with or without vitamin c, at -20 degrees c for four weeks and were evaluated biochemically (proteins, lipids, pigments and fat ...201122208069
Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria.Purple nonsulfur bacteria (PNSB) are facultative photosynthetic bacteria and exhibit an extremely versatile metabolism. A central focus of research on PNSB dealt with the elucidation of mechanisms by which they manage to balance cellular redox under diverse conditions, in particular under photoheterotrophic growth.201121943387
How post-translational modification of nitrogenase is circumvented in Rhodopseudomonas palustris strains that produce hydrogen gas constitutively.Nitrogenase catalyzes the conversion of dinitrogen gas (N(2)) and protons to ammonia and hydrogen gas (H(2)). This is a catalytically difficult reaction that requires large amounts of ATP and reducing power. Thus nitrogenase is not normally expressed or active in bacteria grown with a readily utilized nitrogen source like ammonium. nifA* mutants of the purple nonsulfur phototrophic bacterium Rhodopseudomonas palustris have been described that express nitrogenase genes constitutively and produce ...201122179236
functional annotation analytics of rhodopseudomonas palustris genomes.rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. the availability of the finished genome sequences of six r. palustris strains (bisa53, bisb18, bisb5, cga009, haa2 and tie-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological l ...201122084572
long-term field fertilization alters the diversity of autotrophic bacteria based on the ribulose-1,5-biphosphate carboxylase/oxygenase (rubisco) large-subunit genes in paddy soil.carbon dioxide (co(2)) assimilation by autotrophic bacteria is an important process in the soil carbon cycle with major environmental implications. the long-term impact of fertilizer on co(2) assimilation in the bacterial community of paddy soils remains poorly understood. to narrow this knowledge gap, the composition and abundance of co(2)-assimilating bacteria were investigated using terminal restriction fragment length polymorphism and quantitative pcr of the cbbl gene [that encodes ribulose- ...201122159889
monitoring of environmental arsenic by cultures of the photosynthetic bacterial sensor illuminated with a near-infrared light emitting diode array.recombinant rhodopseudomonas palustris, harboring the carotenoid-metabolizing gene crti (crtibs), and whose color changes from greenish yellow to red in response to inorganic as(iii), was cultured in transparent microplate wells illuminated with a light emitting diode (led) array. the cells were seen to grow better under near-infrared light, when compared with cells illuminated with blue or green leds. the absorbance ratio of 525 to 425 nm after cultivation for 24 h, which reflects red carotenoi ...201122210618
description of rhodopseudomonas parapalustris sp. nov., rhodopseudomonas harwoodiae sp. nov., rhodopseudomonas pseudopalustris sp. nov. and emended description of rhodopseudomonas palustris.four strains (ja310(t) ja531(t) ja447 and ja490) of red to reddish brown pigmented, rod shaped, motile and budding phototrophic bacteria were isolated from soil and fresh water sediment samples from different geographic regions of india. all strains contain bchl-a and carotenoids of spirilloxanthin series. major cellular fatty acid of strains ja310(t) and ja531(t) was c(18:1)ω7c, quinone is q10 and polar lipids, diphosphatidyl glycerol (dpg), phosphatidyl glycerol (pg), phosphatidyl ethanolamine ...201121986724
biohydrogen production from cheese whey wastewater in a two-step anaerobic process.cheese whey-based biohydrogen production was seen in batch experiments via dark fermentation by free and immobilized enterobacter aerogenes mtcc 2822 followed by photofermentation of vfas (mainly acetic and butyric acid) in the spent medium by rhodopseudomonas bhu 01 strain. e. aerogenes free cells grown on cheese whey diluted to 10 g lactose/l, had maximum lactose consumption (∼79%), high production of acetic acid (1,900 mg/l), butyric acid (537.2 mg/l) and h(2) yield (2.04 mol/mol lactose; rat ...201122183564
manifestations of native topology in the denatured state ensemble of rhodopseudomonas palustris cytochrome c'.to provide insight into the role of local sequence in the nonrandom coil behavior of the denatured state, we have extended our measurements of histidine-heme loop formation equilibria for cytochrome c' to 6 m guanidine hydrochloride. we observe that there is some reduction in the scatter about the best fit line of loop stability versus loop size data in 6 m versus 3 m guanidine hydrochloride, but the scatter is not eliminated. the scaling exponent, ν(3), of 2.5 ± 0.2 is also similar to that foun ...201121190388
dynamics of exciton relaxation in lh2 antenna probed by multipulse nonlinear spectroscopy.we explain the relaxation dynamics in the lh2-b850 antenna as revealed by multipulse pump-dump-probe spectroscopy (th. a. cohen stuart, m. vengris, v. i. novoderezhkin, r. j. cogdell, c. n. hunter, r. van grondelle, submitted). the theory of pump-dump-probe response is evaluated using the doorway-window approach in combination with the modified redfield theory. we demonstrate that a simultaneous fit of linear spectra, pump-probe, and pump-dump-probe kinetics can be obtained at a quantitative lev ...201121265578
photosynthetic light-harvesting is tuned by the heterogeneous polarizable environment of the protein.in photosynthesis, special antenna proteins that contain multiple light-absorbing molecules (chromophores) are able to capture sunlight and transfer the excitation energy to reaction centers with almost 100% quantum efficiencies. the critical role of the protein scaffold in holding the appropriate arrangement of the chromophores is well established and can be intuitively understood given the need to keep optimal dipole-dipole interactions between the energy-transferring chromophores, as describe ...201121322565
do inactivated microbial preparations improve life history traits of the copepod acartia tonsa?we have tested a microbial preparation with probiotic effects (psi; sorbial a/s danisco) on the calanoid copepod acartia tonsa (dana) development time and reproduction effectiveness in culture. the hypotheses were that psi increases the productivity and quality of copepods in culture (increased egg production and hatching success, hs). this was carried out because the use of copepods as live prey in aquaculture could increase the number of fish successfully raised through their entire life cycle ...201121213117
bacterial genome chimaerism and the origin of mitochondria.many studies have sought to determine the origin and evolution of mitochondria. although the alphaproteobacteria are thought to be the closest relatives of the mitochondrial progenitor, there is dispute as to what its particular sister group is. some have argued that mitochondria originated from ancestors of the order rickettsiales, or more specifically of the rickettsiaceae family, while others believe that ancestors of the family rhodospirillaceae are also equally likely the progenitors. to re ...201121217797
a quantum mechanical analysis of the light-harvesting complex 2 (lh2) from purple photosynthetic bacteria: insights into the electrostatic effects of transmembrane helices.we perform a quantum mechanical study of the peptides that are part of the lh2 complex from rhodopseudomonas acidophila, a non-sulfur purple bacteria that has the ability of producing chemical energy from photosynthesis. the electronic structure calculations indicate that the transmembrane helices of these peptides are characterized by dipole moments with a magnitude of about 150d. when the full nonamer assembly made of 18 peptides is considered, then a macrodipole of magnitude 806d is built up ...201120837095
effects of ethanol, formaldehyde, and gentle heat fixation in confocal resonance raman microscopy of purple nonsulfur bacteria.resonance raman microscopy is well suited to examine living bacterial samples without further preparation. therefore, comparatively little thought has been given to its compatibility with common fixation methods. however, fixation of cell samples is a very important tool in the microbiological sciences, allowing the preservation of samples in a specific condition for further examination, future measurements, transport, or later reference. we examined the effects of three common fixatives-ethanol ...201120544803
further unravelling the regulatory twist - metabolic coinducer-mediated cbbr-cbbi promoter interactions in rhodopseudomonas palustris cga010.the cbb(i) region of rhodopseudomonas palustris contains the cbbls genes encoding form i ribulose -1, 5 -bisphosphate (rubp) carboxylase oxygenase (rubisco) along with a divergently transcribed regulator gene, cbbr. juxtaposed between cbbr and cbbls are the cbbrrs genes encoding an unusual three protein two-component (cbbrrs) system that modulates the ability of cbbr to influence cbbls expression. the nature of the metabolic signals that rps. palustris cbbr perceives to regulate cbbls transcript ...201222247506
identification and characterization of rhodopseudomonas palustris tie-1 hopanoid biosynthesis mutants.hopanes preserved in both modern and ancient sediments are recognized as the molecular fossils of bacteriohopanepolyols, pentacyclic hopanoid lipids. based on the phylogenetic distribution of hopanoid production by extant bacteria, hopanes have been used as indicators of specific bacterial groups and/or their metabolisms. however, our ability to interpret them ultimately depends on understanding the physiological roles of hopanoids in modern bacteria. toward this end, we set out to identify gene ...201222221333
Effects of Karenia brevis on clearance rates and bioaccumulation of brevetoxins in benthic suspension feeding invertebrates.Blooms of the toxic alga Karenia brevis occur along coastlines where sessile suspension feeding invertebrates are common components of benthic communities. We studied the effects of K. brevis on four benthic suspension feeding invertebrates common to the coast of the SE United States: the sponge Haliclona tubifera, the bryozoan Bugula neritina, the bivalve Mercenaria mercenaria, and the tunicate Styela plicata. In controlled laboratory experiments, we determined the rate at which K. brevis was c ...201222115907
Efficient electricity generation from sewage sludge usingbiocathode microbial fuel cell.Microbial fuel cells (MFCs) with abiotic cathodes require expensive catalyst (such as Pt) or catholyte (such as hexacynoferrate) to facilitate oxidation reactions. This study incorporated biocathodes into a three-chamber MFC to yield electricity from sewage sludge at maximum power output of 13.2±1.7W/m(3) during polarization, much higher than those previously reported. After 15d operation, the total chemical oxygen demand (TCOD) removal and coulombic efficiency (CE) of cell reached 40.8±9.0% and ...201222078254
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