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Sample records for oxygenic photosynthetic prokaryotes

  1. Proposal to consistently apply the International Code of Nomenclature of Prokaryotes (ICNP) to names of the oxygenic photosynthetic bacteria (cyanobacteria), including those validly published under the International Code of Botanical Nomenclature (ICBN)/International Code of Nomenclature for algae, fungi and plants (ICN), and proposal to change Principle 2 of the ICNP.

    Science.gov (United States)

    Pinevich, Alexander V

    2015-03-01

    This taxonomic note was motivated by the recent proposal [Oren & Garrity (2014) Int J Syst Evol Microbiol 64, 309-310] to exclude the oxygenic photosynthetic bacteria (cyanobacteria) from the wording of General Consideration 5 of the International Code of Nomenclature of Prokaryotes (ICNP), which entails unilateral coverage of these prokaryotes by the International Code of Nomenclature for algae, fungi, and plants (ICN; formerly the International Code of Botanical Nomenclature, ICBN). On the basis of key viewpoints, approaches and rules in the systematics, taxonomy and nomenclature of prokaryotes it is reciprocally proposed to apply the ICNP to names of cyanobacteria including those validly published under the ICBN/ICN. For this purpose, a change to Principle 2 of the ICNP is proposed to enable validation of cyanobacterial names published under the ICBN/ICN rules. © 2015 IUMS.

  2. Origin of photosynthetic oxygen

    International Nuclear Information System (INIS)

    Gerster, Richard; Dupuy, Jacques; Guerin de Montgareuil, Pierre

    From the comparison of isotopic exchange kinetics between C 18 O 2 and the water of algae suspensions or aerial leaves subjected to alternating darkness and light, it becomes possible to calculate the isotopic abundance of the CO 2 involved in the photochemical process; this value has been compared to those of the intracellular water and of the evolved O 2 . Kinetics of the appearance of 18 O in the oxygen produced by algae suspended in enriched water are also presented [fr

  3. Emerging experimental and computational technologies for purpose designed engineering of photosynthetic prokaryotes

    KAUST Repository

    Lindblad, Peter

    2016-01-01

    With recent advances in synthetic molecular tools to be used in photosynthetic prokaryotes, like cyanobacteria, it is possible to custom design and construct microbial cells for specific metabolic functions. This cross-disciplinary area of research

  4. Oxygen Concentration Inside a Functioning Photosynthetic Cell

    OpenAIRE

    Kihara, Shigeharu; Hartzler, Daniel A.; Savikhin, Sergei

    2014-01-01

    The excess oxygen concentration in the photosynthetic membranes of functioning oxygenic photosynthetic cells was estimated using classical diffusion theory combined with experimental data on oxygen production rates of cyanobacterial cells. The excess oxygen concentration within the plesiomorphic cyanobacterium Gloeobactor violaceus is only 0.025 μM, or four orders of magnitude lower than the oxygen concentration in air-saturated water. Such a low concentration suggests that the first oxygenic...

  5. Oxygen concentration inside a functioning photosynthetic cell.

    Science.gov (United States)

    Kihara, Shigeharu; Hartzler, Daniel A; Savikhin, Sergei

    2014-05-06

    The excess oxygen concentration in the photosynthetic membranes of functioning oxygenic photosynthetic cells was estimated using classical diffusion theory combined with experimental data on oxygen production rates of cyanobacterial cells. The excess oxygen concentration within the plesiomorphic cyanobacterium Gloeobactor violaceus is only 0.025 μM, or four orders of magnitude lower than the oxygen concentration in air-saturated water. Such a low concentration suggests that the first oxygenic photosynthetic bacteria in solitary form could have evolved ∼2.8 billion years ago without special mechanisms to protect them against reactive oxygen species. These mechanisms instead could have been developed during the following ∼500 million years while the oxygen level in the Earth's atmosphere was slowly rising. Excess oxygen concentrations within individual cells of the apomorphic cyanobacteria Synechocystis and Synechococcus are 0.064 and 0.25 μM, respectively. These numbers suggest that intramembrane and intracellular proteins in isolated oxygenic photosynthetic cells are not subjected to excessively high oxygen levels. The situation is different for closely packed colonies of photosynthetic cells. Calculations show that the excess concentration within colonies that are ∼40 μm or larger in diameter can be comparable to the oxygen concentration in air-saturated water, suggesting that species forming colonies require protection against reactive oxygen species even in the absence of oxygen in the surrounding atmosphere. Copyright © 2014 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  6. Melatonin immunoreactivity in the photosynthetic prokaryote Rhodospirillum rubrum: implications for an ancient antioxidant system.

    Science.gov (United States)

    Manchester, L C; Poeggeler, B; Alvares, F L; Ogden, G B; Reiter, R J

    1995-01-01

    Rhodospirillum rubrum is a spiral anoxygenic photosynthetic bacterium that can exist under either aerobic or anaerobic conditions. The organism thrives in the presence of light or complete darkness and represents one of the oldest species of living organisms, possibly 2-3.5 billion years old. The success of this prokaryotic species may be attributed to the evolution of certain indole compounds that offer protection against life-threatening oxygen radicals produced by an evolutionary harsh environment. Melatonin, N-acetyl-5-methoxytryptamine, is an indolic highly conserved molecule that exists in protists, plants, and animals. This study was undertaken to determine the presence of an immunoreactive melatonin in the kingdom Monera and particularly in the photosynthetic bacterium, R. rubrum, under conditions of prolonged darkness or prolonged light. Immunoreactive melatonin was measured during both the extended day and extended night. Significantly more melatonin was observed during the scotophase than the photophase. This study marks the first demonstration of melatonin in a bacterium. The high level of melatonin observed in bacteria may provide on-site protection of bacterial DNA against free radical attack.

  7. Emerging experimental and computational technologies for purpose designed engineering of photosynthetic prokaryotes

    KAUST Repository

    Lindblad, Peter

    2016-01-25

    With recent advances in synthetic molecular tools to be used in photosynthetic prokaryotes, like cyanobacteria, it is possible to custom design and construct microbial cells for specific metabolic functions. This cross-disciplinary area of research has emerged within the interfaces of advanced genetic engineering, computational science, and molecular biotechnology. We have initiated the development of a genetic toolbox, using a synthetic biology approach, to custom design, engineer and construct cyanobacteria for selected function and metabolism. One major bottleneck is a controlled transcription and translation of introduced genetic constructs. An additional major issue is genetic stability. I will present and discuss recent progress in our development of genetic tools for advanced cyanobacterial biotechnology. Progress on understanding the electron pathways in native and engineered cyanobacterial enzymes and heterologous expression of non-native enymzes in cyanobacterial cells will be highlighted. Finally, I will discuss our attempts to merge synthetic biology with synthetic chemistry to explore fundamantal questions of protein design and function.

  8. Construction of a phylogenetic tree of photosynthetic prokaryotes based on average similarities of whole genome sequences.

    Directory of Open Access Journals (Sweden)

    Soichirou Satoh

    Full Text Available Phylogenetic trees have been constructed for a wide range of organisms using gene sequence information, especially through the identification of orthologous genes that have been vertically inherited. The number of available complete genome sequences is rapidly increasing, and many tools for construction of genome trees based on whole genome sequences have been proposed. However, development of a reasonable method of using complete genome sequences for construction of phylogenetic trees has not been established. We have developed a method for construction of phylogenetic trees based on the average sequence similarities of whole genome sequences. We used this method to examine the phylogeny of 115 photosynthetic prokaryotes, i.e., cyanobacteria, Chlorobi, proteobacteria, Chloroflexi, Firmicutes and nonphotosynthetic organisms including Archaea. Although the bootstrap values for the branching order of phyla were low, probably due to lateral gene transfer and saturated mutation, the obtained tree was largely consistent with the previously reported phylogenetic trees, indicating that this method is a robust alternative to traditional phylogenetic methods.

  9. Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosynthetic organisms.

    Science.gov (United States)

    Bradbury, Louis M T; Shumskaya, Maria; Tzfadia, Oren; Wu, Shi-Biao; Kennelly, Edward J; Wurtzel, Eleanore T

    2012-07-03

    In photosynthetic organisms, carotenoids serve essential roles in photosynthesis and photoprotection. A previous report designated CruP as a secondary lycopene cyclase involved in carotenoid biosynthesis [Maresca J, et al. (2007) Proc Natl Acad Sci USA 104:11784-11789]. However, we found that cruP KO or cruP overexpression plants do not exhibit correspondingly reduced or increased production of cyclized carotenoids, which would be expected if CruP was a lycopene cyclase. Instead, we show that CruP aids in preventing accumulation of reactive oxygen species (ROS), thereby reducing accumulation of β-carotene-5,6-epoxide, a ROS-catalyzed autoxidation product, and inhibiting accumulation of anthocyanins, which are known chemical indicators of ROS. Plants with a nonfunctional cruP accumulate substantially higher levels of ROS and β-carotene-5,6-epoxide in green tissues. Plants overexpressing cruP show reduced levels of ROS, β-carotene-5,6-epoxide, and anthocyanins. The observed up-regulation of cruP transcripts under photoinhibitory and lipid peroxidation-inducing conditions, such as high light stress, cold stress, anoxia, and low levels of CO(2), fits with a role for CruP in mitigating the effects of ROS. Phylogenetic distribution of CruP in prokaryotes showed that the gene is only present in cyanobacteria that live in habitats characterized by large variation in temperature and inorganic carbon availability. Therefore, CruP represents a unique target for developing resilient plants and algae needed to supply food and biofuels in the face of global climate change.

  10. PHOTOINDUCED TRANSFER OF OXYGEN FROM WATER: AN ARTIFICAL PHOTOSYNTHETIC SYSTEM

    Energy Technology Data Exchange (ETDEWEB)

    Willner, Itamar; Otvos, John W.; Ford, William E.; Mettee, Howard; Calvin, Melvin

    1979-11-01

    The photoinduced splitting of water into hydrogen and oxygen has evoked great interest in recent years as a means for energy storag eand fuel production. Photoinduced reduction of water to hydrogen, using visible light, has been described using heterogeneous or homogeneous catalysts. However, the complementary part involving the oxidation of water to oxygen is required in order to create a cyclic artificial 'photosynthetic' fuel system. The major difficulty assocaited with the photooxidation of water involves the requirement for a four electron transfer to produce oxygen. A stepwise one-electron oxidation of water is unfavorable due to the implied formation of active hydroxyl radicals. Very recently, it has been reported that RuO{sub 2} can serve as a heterogeneous charge storage catalyst for oxygen production. On the basis of the limited knowledge about natural photosynthesis, in which manganese ions play an important role in oxygen evolution, synthetic manganese complexes, and in particular dimeric complexes, have been proposed as potential catalysts for oxygen production. So far, efforts directed toward this goal have been unsuccessful. Consequently, using a manganese complex, they attempted to perform a photoinduced oxidation of water whereby the active oxygen is transferred to a trapping substrate. In such a way, the requirement for a dimerization process to evolve molecular oxygen is avoided. They wish to report a photoinduced redox cycle sensitized by a manganese porphyrin, 5-(4{prime}-hexadecylpyridium)-10, 15, 20-tri (4{prime}-pyridyl)-porphinatomanganese(III) (abbreciated to Pn-Mn{sup III}) in which the resultant reaction is the oxidation of water and trapping of the single oxygen atom by a substrate (triphenylphosphine).

  11. How oxygen attacks [FeFe] hydrogenases from photosynthetic organisms

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    Stripp, Sven T.; Goldet, Gabrielle; Brandmayr, Caterina; Sanganas, Oliver; Vincent, Kylie A.; Haumann, Michael; Armstrong, Fraser A.; Happe, Thomas

    2009-01-01

    Green algae such as Chlamydomonas reinhardtii synthesize an [FeFe] hydrogenase that is highly active in hydrogen evolution. However, the extreme sensitivity of [FeFe] hydrogenases to oxygen presents a major challenge for exploiting these organisms to achieve sustainable photosynthetic hydrogen production. In this study, the mechanism of oxygen inactivation of the [FeFe] hydrogenase CrHydA1 from C. reinhardtii has been investigated. X-ray absorption spectroscopy shows that reaction with oxygen results in destruction of the [4Fe-4S] domain of the active site H-cluster while leaving the di-iron domain (2FeH) essentially intact. By protein film electrochemistry we were able to determine the order of events leading up to this destruction. Carbon monoxide, a competitive inhibitor of CrHydA1 which binds to an Fe atom of the 2FeH domain and is otherwise not known to attack FeS clusters in proteins, reacts nearly two orders of magnitude faster than oxygen and protects the enzyme against oxygen damage. These results therefore show that destruction of the [4Fe-4S] cluster is initiated by binding and reduction of oxygen at the di-iron domain—a key step that is blocked by carbon monoxide. The relatively slow attack by oxygen compared to carbon monoxide suggests that a very high level of discrimination can be achieved by subtle factors such as electronic effects (specific orbital overlap requirements) and steric constraints at the active site. PMID:19805068

  12. OxyGene: an innovative platform for investigating oxidative-response genes in whole prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    Barloy-Hubler Frédérique

    2008-12-01

    Full Text Available Abstract Background Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. To identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. Unfortunately, several problems persist in the annotation, classification and naming of these enzymes due mainly to some erroneous entries in databases, mistake propagation, absence of updating and disparity in function description. Description In order to improve the current annotation of oxidative stress subsystems, an innovative platform named OxyGene has been developed. It integrates an original database called OxyDB, holding thoroughly tested anchor-based signatures associated to subfamilies of oxidative stress enzymes, and a new anchor-driven annotator, for ab initio detection of ROS/RNS response genes. All complete Bacterial and Archaeal genomes have been re-annotated, and the results stored in the OxyGene repository can be interrogated via a Graphical User Interface. Conclusion OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes. It proposes a new classification that improves both the ontology and the annotation of the detoxification subsystems in prokaryotic whole genomes, while discovering new ORFs and attributing precise function to hypothetical annotated proteins. OxyGene is freely available at: http://www.umr6026.univ-rennes1.fr/english/home/research/basic/software

  13. Manganese in photosynthetic oxygen evolution: An edge and EXAFS study

    International Nuclear Information System (INIS)

    Yachandra, V.K.; Guiles, R.D.; McDermott, A.; Britt, R.D.; Dexheimer, S.L.; Saver, K.; Klein, M.P.

    1985-01-01

    The authors edge studies have previously shown that the Mn edges in photosynthetic samples in the S 1 and S 2 states fall into the range for Mn III and Mn IV complexes, and that the K-edge energy increases appreciably on advancing S 1 to S 2 . This was the first evidence that manganese is directly involved in the storage of oxidizing equivalents. More recently, they have extended this result with better quality data from both spinach and a thermophilic cyanobacterium. The newer results show an interesting structure to the edges, including a 1s to 3d transition. The EXAFS results for spinach membranes show that the salient features of the Mn structure are the same in the S 1 and S 2 states. These features are a Mn neighbor at approx. =2.7 A and O or N neighbors at approx. =1.75 A and approx. =2.0 A. The EXAFS spectrum of the S 1 state of the thermophilic blue green algae are strikingly similar to that of spinach

  14. Dynamics and controls of heterotrophic prokaryotic production in the western tropical South Pacific Ocean: links with diazotrophic and photosynthetic activity

    Science.gov (United States)

    Van Wambeke, France; Gimenez, Audrey; Duhamel, Solange; Dupouy, Cécile; Lefevre, Dominique; Pujo-Pay, Mireille; Moutin, Thierry

    2018-05-01

    Heterotrophic prokaryotic production (BP) was studied in the western tropical South Pacific (WTSP) using the leucine technique, revealing spatial and temporal variability within the region. Integrated over the euphotic zone, BP ranged from 58 to 120 mg C m-2 d-1 within the Melanesian Archipelago, and from 31 to 50 mg C m-2 d-1 within the western subtropical gyre. The collapse of a bloom was followed during 6 days in the south of Vanuatu using a Lagrangian sampling strategy. During this period, rapid evolution was observed in the three main parameters influencing the metabolic state: BP, primary production (PP) and bacterial growth efficiency. With N2 fixation being one of the most important fluxes fueling new production, we explored relationships between BP, PP and N2 fixation rates over the WTSP. The contribution of N2 fixation rates to bacterial nitrogen demand ranged from 3 to 81 %. BP variability was better explained by the variability of N2 fixation rates than by that of PP in surface waters of the Melanesian Archipelago, which were characterized by N-depleted layers and low DIP turnover times (TDIP 100 h), deeper in the Melanesian Archipelago, or within the entire euphotic zone in the subtropical gyre. The bacterial carbon demand to gross primary production ratio ranged from 0.75 to 3.1. These values are discussed in the framework of various assumptions and conversion factors used to estimate this ratio, including the methodological errors, the daily variability of BP, the bacterial growth efficiency and one bias so far not considered: the ability for Prochlorococcus to assimilate leucine in the dark.

  15. Photosynthetic oxygen production in a warmer ocean: the Sargasso Sea as a case study.

    Science.gov (United States)

    Richardson, Katherine; Bendtsen, Jørgen

    2017-09-13

    Photosynthetic O 2 production can be an important source of oxygen in sub-surface ocean waters especially in permanently stratified oligotrophic regions of the ocean where O 2 produced in deep chlorophyll maxima (DCM) is not likely to be outgassed. Today, permanently stratified regions extend across approximately 40% of the global ocean and their extent is expected to increase in a warmer ocean. Thus, predicting future ocean oxygen conditions requires a better understanding of the potential response of photosynthetic oxygen production to a warmer ocean. Based on our own and published observations of water column processes in oligotrophic regions, we develop a one-dimensional water column model describing photosynthetic oxygen production in the Sargasso Sea to quantify the importance of photosynthesis for the downward flux of O 2 and examine how it may be influenced in a warmer ocean. Photosynthesis is driven in the model by vertical mixing of nutrients (including eddy-induced mixing) and diazotrophy and is found to substantially increase the downward O 2 flux relative to physical-chemical processes alone. Warming (2°C) surface waters does not significantly change oxygen production at the DCM. Nor does a 15% increase in re-mineralization rate (assuming Q 10  = 2; 2°C warming) have significant effect on net sub-surface oxygen accumulation. However, changes in the relative production of particulate (POM) and dissolved organic material (DOM) generate relatively large changes in net sub-surface oxygen production. As POM/DOM production is a function of plankton community composition, this implies plankton biodiversity and food web structure may be important factors influencing O 2 production in a warmer ocean.This article is part of the themed issue 'Ocean ventilation and deoxygenation in a warming world'. © 2017 The Author(s).

  16. Dissolved natural organic matter (NOM) impacts photosynthetic oxygen production and electron transport in coontail Ceratophyllum demersum

    International Nuclear Information System (INIS)

    Pflugmacher, S.; Pietsch, C.; Rieger, W.; Steinberg, C.E.W.

    2006-01-01

    Dissolved natural organic matter (NOM) is dead organic matter exceeding, in freshwater systems, the concentration of organic carbon in all living organisms by far. 80-90% (w/w) of the NOM is made up of humic substances (HS). Although NOM possesses several functional groups, a potential effect on aquatic organisms has not been studied. In this study, direct effects of NOM from various origins on physiological and biochemical functions in the aquatic plant Ceratophyllum demersum are presented. Environmentally relevant concentrations of NOM cause inhibitory effects on the photosynthetic oxygen production of C. demersum. Various NOM sources and the synthetic humic substance HS1500 inhibit the photosynthetic oxygen production of the plant as observed with 1-amino-anthraquinone, a known inhibitor of plant photosynthesis. 1-Aminoanthraquinone may serve as an analogue for the quinoid structures in NOM and HS. Most likely, the effects of NOM may be related to quinoid structures and work downstream of photosynthesis at photosystem (PS) II

  17. Lycopene cyclase paralog CruP protects against reactive oxygen species in oxygenic photosynthetic organisms

    OpenAIRE

    Bradbury, Louis M. T.; Shumskaya, Maria; Tzfadia, Oren; Wu, Shi-Biao; Kennelly, Edward J.; Wurtzel, Eleanore T.

    2012-01-01

    In photosynthetic organisms, carotenoids serve essential roles in photosynthesis and photoprotection. A previous report designated CruP as a secondary lycopene cyclase involved in carotenoid biosynthesis [Maresca J, et al. (2007) Proc Natl Acad Sci USA 104:11784–11789]. However, we found that cruP KO or cruP overexpression plants do not exhibit correspondingly reduced or increased production of cyclized carotenoids, which would be expected if CruP was a lycopene cyclase. Instead, we show that...

  18. A time series of prokaryote secondary production in the oxygen minimum zone of the Humboldt current system, off central Chile

    Science.gov (United States)

    Levipan, H. A.; Quiñones, R. A.; Urrutia, H.

    2007-11-01

    Because the marine picoplanktonic communities are made up of phylogenetically different microbial groups, the re-evaluation of key processes such as bacterial secondary production (BSP) has become an important contemporary issue. The difficulty of differentiating the metabolic processes of Bacteria from the rest of the microorganisms in the water column (i.e., Archaea and Eukarya) has made it difficult to estimate in situ BSP. This work presents the seasonal variability of the prokaryote secondary production (PSP) measured by the incorporation of 14C-leucine in the oxygen minimum zone (OMZ) off central-southern Chile. The BSP and potential archaeal secondary production (PASP) were determined through the combined use of 14C-leucine and N1-guanyl-1, 7-diaminoheptane (GC 7), an efficient inhibitor of archaeal and eukaryote cell growth. BSP accounted for the majority of the PSP (total average, 59 ± 7.5%); maximum values were ∼600 μg C m -3 h -1 and, on several dates, BSP represented 100% of the PSP. Similarly, PASP was also an important fraction of the PSP (total average, 42.4 ± 8.5%), although with levels that ranged from not detectable (on given dates) to levels that represented up to ∼97% of PSP (winter 2003). Our results showed that both Bacteria and Archaea accounted for almost equal portions of the prokaryote heterotrophic metabolism in the OMZ, and that PASP is notoriously enhanced through temporal pulses of heterotrophy. This indicates that, at least in marine systems with high abundance of Archaea (e.g., mesopelagic realm), the secondary production obtained through methods measuring the uptake of radiolabeled substrates should be considered as PSP and not as BSP. If the latter is the target measurement, then the use of an inhibitor of both archaeal and eukaryote cell growth such as GC 7 is recommended.

  19. Isotopic exchange between CO2 and H2O and labelling kinetics of photosynthetic oxygen

    International Nuclear Information System (INIS)

    Gerster, Richard

    1971-01-01

    The reaction of carbon dioxide with water has been studied by measuring the rate of oxygen exchange between C 18 O 2 and H 2 16 O. The mathematical treatment of the kinetics allows to determine with accuracy the diffusion flow between the gas and the liquid phase, in the same way as the CO 2 hydration rate. The velocity constant of this last process, whose value gives the in situ enzymatic activity of carbonic anhydrase, has been established in the case of chloroplast and Euglena suspensions and of aerial leaves. The study of the isotopic exchange between C 18 O 2 and a vegetable submitted to alternations of dark and light has allowed to calculate the isotopic abundance of the metabolized CO 2 whose value has been compared to that of the intracellular water and that of photosynthetic oxygen. In addition, a new method using 13 C 18 O 2 gives the means to measure with accuracy eventual isotopic effects. The labelling kinetics of the oxygen evolved by Euglena suspensions whose water has been enriched with 18 O have been established at different temperatures. (author) [fr

  20. The Mechanisms of Oxygen Reduction in the Terminal Reducing Segment of the Chloroplast Photosynthetic Electron Transport Chain.

    Science.gov (United States)

    Kozuleva, Marina A; Ivanov, Boris N

    2016-07-01

    The review is dedicated to ascertainment of the roles of the electron transfer cofactors of the pigment-protein complex of PSI, ferredoxin (Fd) and ferredoxin-NADP reductase in oxygen reduction in the photosynthetic electron transport chain (PETC) in the light. The data regarding oxygen reduction in other segments of the PETC are briefly analyzed, and it is concluded that their participation in the overall process in the PETC under unstressful conditions should be insignificant. Data concerning the contribution of Fd to the oxygen reduction in the PETC are examined. A set of collateral evidence as well as results of direct measurements of the involvement of Fd in this process in the presence of isolated thylakoids led to the inference that this contribution in vivo is negligible. The increase in oxygen reduction rate in the isolated thylakoids in the presence of either Fd or Fd plus NADP + under increasing light intensity was attributed to the increase in oxygen reduction executed by the membrane-bound oxygen reductants. Data are presented which imply that a main reductant of the O 2 molecule in the terminal reducing segment of the PETC is the electron transfer cofactor of PSI, phylloquinone. The physiological significance of characteristic properties of oxygen reductants in this segment of the PETC is discussed. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  1. FtsZ-less prokaryotic cell division as well as FtsZ- and dynamin-less chloroplast and non-photosynthetic plastid division

    Directory of Open Access Journals (Sweden)

    Shin-Ya eMiyagishima

    2014-09-01

    Full Text Available The chloroplast division machinery is a mixture of a stromal FtsZ-based complex descended from a cyanobacterial ancestor of chloroplasts and a cytosolic dynamin-related protein (DRP 5B-based complex derived from the eukaryotic host. Molecular genetic studies have shown that each component of the division machinery is normally essential for normal chloroplast division. However, several exceptions have been found. In the absence of the FtsZ ring, nonphotosynthetic plastids are able to proliferate, likely by elongation and budding. Depletion of DRP5B impairs, but does not stop chloroplast division. Chloroplasts in glaucophytes, which possesses a peptidoglycan (PG layer, divide without DRP5B. Certain parasitic eukaryotes possess nonphotosynthetic plastids of secondary endosymbiotic origin, but neither FtsZ nor DRP5B is encoded in their genomes. Elucidation of the FtsZ- and/or DRP5B-less chloroplast division mechanism will lead to a better understanding of the function and evolution of the chloroplast division machinery and the finding of the as-yet-unknown mechanism that is likely involved in chloroplast division. Recent studies have shown that FtsZ was lost from a variety of prokaryotes, many of which lost PG by regressive evolution. In addition, even some of the FtsZ-bearing bacteria are able to divide when FtsZ and PG are depleted experimentally. In some cases, alternative mechanisms for cell division, such as budding by an increase of the cell surface-to-volume ratio, are proposed. Although PG is believed to have been lost from chloroplasts other than in glaucophytes, there is some indirect evidence for the existence of PG in chloroplasts. Such information is also useful for understanding how nonphotosynthetic plastids are able to divide in FtsZ-depleted cells and the reason for the retention of FtsZ in chloroplast division. Here we summarize information to facilitate analyses of FtsZ- and/or DRP5B-less chloroplast and nonphotosynthetic plastid

  2. Evaluation of the participation of ferredoxin in oxygen reduction in the photosynthetic electron transport chain of isolated pea thylakoids.

    Science.gov (United States)

    Kozuleva, Marina A; Ivanov, Boris N

    2010-07-01

    The contribution to reduction of oxygen by ferredoxin (Fd) to the overall reduction of oxygen in isolated pea thylakoids was studied in the presence of Fd versus Fd + NADP(+). The overall rate of electron transport was measured using a determination of Photosystem II quantum yield from chlorophyll fluorescence parameters, and the rate of oxidation of Fd was measured from the light-induced redox changes of Fd. At low light intensity, increasing Fd concentration from 5 to 30 microM in the absence of NADP(+) increased the proportion of oxygen reduction by Fd from 25-35 to 40-60% in different experiments. This proportion decreased with increasing light intensity. When NADP(+) was added in the presence of 15 microM Fd, which was optimal for the NADP(+) reduction rate, the participation of Fd in the reduction of oxygen was low, no more than 10%, and it also decreased with increasing light intensity. At high light intensity, the overall oxygen reduction rates in the presence of Fd + NADP(+) and in the presence of Fd alone were comparable. The significance of reduction of dioxygen either by water-soluble Fd or by the membrane-bound carriers of the photosynthetic electron transport chain for redox signaling under different light intensities is discussed.

  3. Surveying the expanding prokaryotic Rubisco multiverse.

    Science.gov (United States)

    Liu, Di; Ramya, Ramaswamy Chettiyan Seetharaman; Mueller-Cajar, Oliver

    2017-09-01

    The universal, but catalytically modest, CO2-fixing enzyme Rubisco is currently experiencing intense interest by researchers aiming to enhance crop photosynthesis. These efforts are mostly focused on the highly conserved hexadecameric enzyme found in land plants. In comparison, prokaryotic organisms harbor a far greater diversity in Rubisco forms. Recent work towards improving our appreciation of microbial Rubisco properties and harnessing their potential is surveyed. New structural models are providing informative glimpses into catalytic subtleties and diverse oligomeric states. Ongoing characterization is informing us about the conservation of constraints, such as sugar phosphate inhibition and the associated dependence on Rubisco activase helper proteins. Prokaryotic Rubiscos operate under a far wider range of metabolic contexts than the photosynthetic function of higher plant enzymes. Relaxed selection pressures may have resulted in the exploration of a larger volume of sequence space than permitted in organisms performing oxygenic photosynthesis. To tap into the potential of microbial Rubiscos, in vivo selection systems are being used to discover functional metagenomic Rubiscos. Various directed evolution systems to optimize their function have been developed. It is anticipated that this approach will provide access to biotechnologically valuable enzymes that cannot be encountered in the higher plant Rubisco space. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  4. Prokaryotic photosynthesis and phototrophy illuminated

    DEFF Research Database (Denmark)

    Bryant, Donald A; Frigaard, Niels-Ulrik

    2006-01-01

    Genome sequencing projects are revealing new information about the distribution and evolution of photosynthesis and phototrophy. Although coverage of the five phyla containing photosynthetic prokaryotes (Chlorobi, Chloroflexi, Cyanobacteria, Proteobacteria and Firmicutes) is limited and uneven...... components that have not yet been described. Metagenomics has already shown how the relatively simple phototrophy based upon rhodopsins has spread laterally throughout Archaea, Bacteria and eukaryotes. In this review, we present examples that reflect recent advances in phototroph biology as a result...

  5. Photosynthetic water splitting

    Energy Technology Data Exchange (ETDEWEB)

    Greenbaum, E.

    1981-01-01

    The photosynthetic unit of hydrogen evolution, the turnover time of photosynthetic hydrogen production, and hydrogenic photosynthesis are discussed in the section on previous work. Recent results are given on simultaneous photoproduction of hydrogen and oxygen, kinetic studies, microscopic marine algae-seaweeds, and oxygen profiles.

  6. Effects of dissolved oxygen concentration on photosynthetic bacteria wastewater treatment: Pollutants removal, cell growth and pigments production.

    Science.gov (United States)

    Meng, Fan; Yang, Anqi; Zhang, Guangming; Wang, Hangyao

    2017-10-01

    Dissolved oxygen (DO) is an important parameter in photosynthetic bacteria (PSB) wastewater treatment. This study set different DO levels and detected the pollutants removal, PSB growth and pigments production. Results showed that DO significantly influenced the performances of PSB wastewater treatment process. The highest COD (93%) and NH 3 -N removal (83%) was achieved under DO of 4-8mg/L, but DO of 2-4mg/L was recommended considering the aeration cost. PSB biomass reached 1645mg/L under DO of 4-8mg/L with satisfying co-enzyme Q10 content. The biomass yield was relatively stable at all DO levels. For bacteriochlorophyll and carotenoids, DO>1mg/L could satisfy their production. On the other hand, DOpigments production occurred at 24h; biomass reached peak at 48h; and the optimal time for pollutants removal was 72h. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Thiol biochemistry of prokaryotes

    Science.gov (United States)

    Fahey, Robert C.

    1986-01-01

    The present studies have shown that GSH metabolism arose in the purple bacteria and cyanobacteria where it functions to protect against oxygen toxicity. Evidence was obtained indicating that GSH metabolism was incorporated into eucaryotes via the endosymbiosis giving rise to mitochrondria and chloroplasts. Aerobic bacteria lacking GSH utilize other thiols for apparently similar functions, the thiol being coenzyme A in Gram positive bacteria and chi-glutamylcysteine in the halobacteria. The thiol biochemistry of prokaryotes is thus seen to be much more highly diversified than that of eucaryotes and much remains to be learned about this subject.

  8. Powered by light: Phototrophy and photosynthesis in prokaryotes and its evolution.

    Science.gov (United States)

    Nowicka, Beatrycze; Kruk, Jerzy

    2016-01-01

    Photosynthesis is a complex metabolic process enabling photosynthetic organisms to use solar energy for the reduction of carbon dioxide into biomass. This ancient pathway has revolutionized life on Earth. The most important event was the development of oxygenic photosynthesis. It had a tremendous impact on the Earth's geochemistry and the evolution of living beings, as the rise of atmospheric molecular oxygen enabled the development of a highly efficient aerobic metabolism, which later led to the evolution of complex multicellular organisms. The mechanism of photosynthesis has been the subject of intensive research and a great body of data has been accumulated. However, the evolution of this process is not fully understood, and the development of photosynthesis in prokaryota in particular remains an unresolved question. This review is devoted to the occurrence and main features of phototrophy and photosynthesis in prokaryotes. Hypotheses concerning the origin and spread of photosynthetic traits in bacteria are also discussed. Copyright © 2016 Elsevier GmbH. All rights reserved.

  9. Carbon and oxygen isotope analysis of leaf biomass reveals contrasting photosynthetic responses to elevated CO2 near geologic vents in Yellowstone National Park

    Directory of Open Access Journals (Sweden)

    D. G. Williams

    2009-01-01

    Full Text Available In this study we explore the use of natural CO2 emissions in Yellowstone National Park (YNP in Wyoming, USA to study responses of natural vegetation to elevated CO2 levels. Radiocarbon (14C analysis of leaf biomass from a conifer (Pinus contortus; lodgepole pine and an invasive, non-native herb (Linaria dalmatica; Dalmation toadflax was used to trace the inputs of vent CO2 and quantify assimilation-weighted CO2 concentrations experienced by individual plants near vents and in comparable locations with no geologic CO2 exposure. The carbon and oxygen isotopic composition and nitrogen percent of leaf biomass from the same plants was used to investigate photosynthetic responses of these plants to naturally elevated atmospheric CO2 concentrations. The coupled shifts in carbon and oxygen isotope values suggest that dalmation toadflax responded to elevated CO2 exposure by increasing stomatal conductance with no change in photosynthetic capacity and lodgepole pine apparently responded by decreasing stomatal conductance and photosynthetic capacity. Lodgepole pine saplings exposed to elevated levels of CO2 likewise had reduced leaf nitrogen concentrations compared to plants with no enhanced CO2 exposure, further suggesting widespread and dominant conifer down-regulated photosynthetic capacity under elevated CO2 levels near geologic vents.

  10. Photosynthetic oxygenation in waste water treatment lagoons; Oxigenacion fotosintetica en lagunas para la depuracion de aguas residuales

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, J.; Mujeriego, R. [Universitat Politecnica de Catalunya. (Spain)

    1999-07-01

    In order to reduce the costs of mechanical aeration in the treatment of waste waters the use of photosynthetic oxygenation (microalgae) in high capacity lagoons (100-200 kg/ha/day) providing a high alga biomass (200-500 mg/1) is suggested. Energy consumption is 0.01-0.03 W/m''3 of treated sewage. This method has been tried out in two pilot plants with a surface area of 1.54 m''2 a depth of 0.3 m and a volume of 0.47 m''3. each one has a central wall forming a channel and a wheel driving the water ar a rate of 9 cm/sec. By applying different operational regimes in each logoon, performance results were obtained for SS, COD, BOD and nutrients. These data were employed in designing the waste treatment plant for the village of Riudecanyes, which has about 1,000 inhabitants in winter and 2,000 in summer. This plant comprise a pre-treatment section, an Imhoff decanter, a 3500 m''2 lagoon (with 4 channels) and a secondary decanter. A subsurface flow wetland is planned for tertiary treatment. This is a totally new design in Spain that is capable of achieving results in line with Directive 91/271 with minimum exploitation costs. (Author) 8 refs.

  11. Nanophase Iron Oxides as an Ultraviolet Sunscreen for Ancient Photosynthetic Microbes: A Possible Link Between Early Organisms, Banded-Iron Formations, and the Oxygenation of the Atmosphere

    Science.gov (United States)

    Bishop, Janice L.; Rothschild, Lynn J.; Rothschild, Lynn J.; Rogoff, Dana A.

    2006-01-01

    We propose that nanophase iron oxide-bearing materials provided important niches for ancient photosynthetic microbes on the early Earth that ultimately led to the oxygenation of the Earth s atmosphere and the formation of iron oxide deposits. Atmospheric oxygen and ozone attenuate UV radiation on the Earth today providing substantial protection for photosynthetic organisms. With ultraviolet radiation fluxes likely to have been even higher on the early Earth than today, accessing solar radiation was particularly risky for early organisms. Yet, we know that photosynthesis arose then and played a critical role in subsequent evolution. Of primary importance was protection at approx.250-290 nm, where peak nucleic acid (approx.260 nm) and protein (approx.280 nm) absorptions occur. Nanophase ferric oxide/oxyhydroxide minerals absorb, and thus block, the lethal UV radiation, while transmitting light through much of the visible and near-infrared regions of interest to photosynthesis (400 to 1100 nm). Further, they were available in early environments, and are synthesized by many organisms. Based on ferric oxide/oxyhydroxide spectral properties, likely geologic processes, and the results of experiments with the photosynthetic organisms, Euglena sp. and Chlumydomonus reinhardtii, we propose a scenario where photosynthesis, and ultimately the oxygenation of the atmosphere, depended on the protection of early microbes by nanophase ferric oxides/oxyhydroxides. The results of this study are also applicable to other potentially habitable iron-bearing planetary bodies because of the evolutionary pressure to utilize solar radiation when available as an energy source.

  12. Association between minor loading vein architecture and light- and CO2-saturated rates of photosynthetic oxygen evolution among Arabidopsis thaliana ecotypes from different latitudes

    Directory of Open Access Journals (Sweden)

    Christopher M Cohu

    2013-07-01

    Full Text Available Through microscopic analysis of veins and assessment of light- and CO2-saturated rates of photosynthetic oxygen evolution, we investigated the relationship between minor loading vein anatomy and photosynthesis of mature leaves in three ecotypes of Arabidopsis thaliana grown under four different combinations of temperature and photon flux density (PFD. All three ecotypes exhibited greater numbers and cross-sectional area of phloem cells as well as higher photosynthesis rates in response to higher PFD and especially lower temperature. The Swedish ecotype exhibited the strongest response to these conditions, the Italian ecotype the weakest response, and the Col-0 ecotype exhibited an intermediate response. Among all three ecotypes, strong linear relationships were found between light- and CO2-saturated rates of photosynthetic oxygen evolution and the number and area of either sieve elements or of companion and phloem parenchyma cells in foliar minor loading veins, with the Swedish ecotype showing the highest number of cells in minor loading veins (and largest minor veins coupled with unprecedented high rates of photosynthesis. Linear, albeit less significant, relationships were also observed between number and cross-sectional area of tracheids per minor loading vein versus light- and CO2-saturated rates of photosynthetic oxygen evolution. We suggest that sugar distribution infrastructure in the phloem is co-regulated with other features that set the upper limit for photosynthesis. The apparent genetic differences among Arabidopsis ecotypes should allow for future identification of the gene(s involved in augmenting sugar-loading and -transporting phloem cells and maximal rates of photosynthesis.

  13. Novel thiols of prokaryotes.

    Science.gov (United States)

    Fahey, R C

    2001-01-01

    Glutathione metabolism is associated with oxygenic cyanobacteria and the oxygen-utilizing purple bacteria, but is absent in many other prokaryotes. This review focuses on novel thiols found in those bacteria lacking glutathione. Included are glutathione amide and its perthiol, produced by phototrophic purple sulfur bacteria and apparently involved in their sulfide metabolism. Among archaebacteria, coenzyme M (2-mercaptoethanesulfonic acid) and coenzyme B (7-mercaptoheptanoylthreonine phosphate) play central roles in the anaerobic production of CH4 and associated energy conversion by methanogens, whereas the major thiol in the aerobic phototrophic halobacteria is gamma-glutamylcysteine. The highly aerobic actinomycetes produce mycothiol, a conjugate of N-acetylcysteine with a pseudodisaccharide of glucosamine and myo-inositol, AcCys-GlcNalpha(1 --> 1)Ins, which appears to play an antioxidant role similar to glutathione. Ergothioneine, also produced by actinomycetes, remains a mystery despite many years of study. Available data on the biosynthesis and metabolism of these and other novel thiols is summarized and key areas for additional study are identified.

  14. Unicellular cyanobacteria with a new mode of life: the lack of photosynthetic oxygen evolution allows nitrogen fixation to proceed.

    Science.gov (United States)

    Bothe, Hermann; Tripp, H James; Zehr, Jonathan P

    2010-10-01

    Some unicellular N(2)-fixing cyanobacteria have recently been found to lack a functional photosystem II of photosynthesis. Such organisms, provisionally termed UCYN-A, of the oceanic picoplanktion are major contributors to the global marine N-input by N(2)-fixation. Since their photosystem II is inactive, they can perform N(2)-fixation during the day. UCYN-A organisms cannot be cultivated as yet. Their genomic analysis indicates that they lack genes coding for enzymes of the Calvin cycle, the tricarboxylic acid cycle and for the biosynthesis of several amino acids. The carbon source in the ocean that allows them to thrive in such high abundance has not been identified. Their genomic analysis implies that they metabolize organic carbon by a new mode of life. These unicellular N(2)-fixing cyanobacteria of the oceanic picoplankton are evolutionarily related to spheroid bodies present in diatoms of the family Epithemiaceae, such as Rhopalodia gibba. More recently, spheroid bodies were ultimately proven to be related to cyanobacteria and to express nitrogenase. They have been reported to be completely inactive in all photosynthetic reactions despite the presence of thylakoids. Sequence data show that R. gibba and its spheroid bodies are an evolutionarily young symbiosis that might serve as a model system to unravel early events in the evolution of chloroplasts. The cell metabolism of UCYN-A and the spheroid bodies may be related to that of the acetate photoassimilating green alga Chlamydobotrys.

  15. Thermodynamically accurate modeling of the catalytic cycle of photosynthetic oxygen evolution: a mathematical solution to asymmetric Markov chains.

    Science.gov (United States)

    Vinyard, David J; Zachary, Chase E; Ananyev, Gennady; Dismukes, G Charles

    2013-07-01

    Forty-three years ago, Kok and coworkers introduced a phenomenological model describing period-four oscillations in O2 flash yields during photosynthetic water oxidation (WOC), which had been first reported by Joliot and coworkers. The original two-parameter Kok model was subsequently extended in its level of complexity to better simulate diverse data sets, including intact cells and isolated PSII-WOCs, but at the expense of introducing physically unrealistic assumptions necessary to enable numerical solutions. To date, analytical solutions have been found only for symmetric Kok models (inefficiencies are equally probable for all intermediates, called "S-states"). However, it is widely accepted that S-state reaction steps are not identical and some are not reversible (by thermodynamic restraints) thereby causing asymmetric cycles. We have developed a mathematically more rigorous foundation that eliminates unphysical assumptions known to be in conflict with experiments and adopts a new experimental constraint on solutions. This new algorithm termed STEAMM for S-state Transition Eigenvalues of Asymmetric Markov Models enables solutions to models having fewer adjustable parameters and uses automated fitting to experimental data sets, yielding higher accuracy and precision than the classic Kok or extended Kok models. This new tool provides a general mathematical framework for analyzing damped oscillations arising from any cycle period using any appropriate Markov model, regardless of symmetry. We illustrate applications of STEAMM that better describe the intrinsic inefficiencies for photon-to-charge conversion within PSII-WOCs that are responsible for damped period-four and period-two oscillations of flash O2 yields across diverse species, while using simpler Markov models free from unrealistic assumptions. Copyright © 2013 Elsevier B.V. All rights reserved.

  16. X-ray induced inactivation of the capacity for photosynthetic oxygen evolution and nitrate reduction in blue-green algae

    International Nuclear Information System (INIS)

    Stevens, S.E. Jr.; Simic, M.G.; Rao, V.S.K.

    1975-01-01

    The level of inactivation of oxygen evolving photosynthesis in the green alga, Chlorella pyrenoidosa was 12 percent in N 2 at a dose of 100 krad of x irradiation. Under similar conditions, as well as under O 2 , there resulted a 20 percent inactivation of the same function in the blue-green algae, Agmenellum quadruplicatum, strains PR-6 and AQ-6. Nitrate reduction capacity in the mutant AQ-6 was inactivated to 40 percent in N 2 and to 7 percent in O 2 . Catalase and formate provided some protection from irradiation in O 2 , suggesting some inactivation by H 2 O 2 . Most of the damage to the nitrate reduction system resulted from the direct action of x irradiation on a constitutive subunit of the nitrate reductase complex. Moreover, the slight inactivation of the O 2 evolving system, a function which is associated with photosystem II, cannot account for the inactivation of nitrate reduction

  17. Characterization of xanthophyll pigments, photosynthetic performance, photon energy dissipation, reactive oxygen species generation and carbon isotope discrimination during artemisinin-induced stress in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    M Iftikhar Hussain

    Full Text Available Artemisinin, a potent antimalarial drug, is phytotoxic to many crops and weeds. The effects of artemisinin on stress markers, including fluorescence parameters, photosystem II photochemistry, photon energy dissipation, lipid peroxidation, reactive oxygen species generation and carbon isotope discrimination in Arabidopsis thaliana were studied. Arabidopsis ecotype Columbia (Col-0 seedlings were grown in perlite and watered with 50% Hoagland nutrient solution. Adult plants of Arabidopsis were treated with artemisinin at 0, 40, 80, 160 μM for one week. Artemisinin, in the range 40-160 μM, decreased the fresh biomass, chl a, b and leaf mineral contents. Photosynthetic efficiency, yield and electron transport rate in Arabidopsis were also reduced following exposure to 80 and 160 μM artemisinin. The ΦNPQ and NPQ were less than control. Artemisinin treatment caused an increase in root oxidizability and lipid peroxidation (MDA contents of Arabidopsis. Calcium and nitrogen contents decreased after 80 and 160 μM artemisinin treatment compared to control. δ13C values were less negative following treatment with artemisinin as compared to the control. Artemisinin also decreased leaf protein contents in Arabidopsis. Taken together, these data suggest that artemisinin inhibits many physiological and biochemical processes in Arabidopsis.

  18. Photosynthetic Pigments in Diatoms

    OpenAIRE

    Kuczynska, Paulina; Jemiola-Rzeminska, Malgorzata; Strzalka, Kazimierz

    2015-01-01

    Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvestin...

  19. X-ray absorption spectroscopy on the calcium cofactor to the manganese cluster in photosynthetic oxygen evolution

    Energy Technology Data Exchange (ETDEWEB)

    Cinco, Roehl M. [Univ. of California, Berkeley, CA (United States)

    1999-12-01

    Along with Mn, calcium and chloride ions are necessary cofactors for oxygen evolution in Photosystem II (PS II). To further test and verify whether Ca is close to the Mn cluster, the authors substituted strontium for Ca and probed from the Sr point of view for any nearby Mn. The extended X-ray absorption fine structure (EXAFS) of Sr-reactivated PS II indicates major differences between the intact and NH2OH-treated samples. In intact samples, the Fourier transform of the Sr EXAFS shows a Fourier peak that is missing in inactive samples. This peak II is best simulated by two Mn neighbors at a distance of 3.5 Angstrom, confirming the proximity of Ca (Sr) cofactor to the Mn cluster. In addition, polarized Sr EXAFS on oriented Sr-reactivated samples shows this peak II is dichroic: large magnitude at 10 degrees (angle between the PS II membrane normal and the x-ray electric field vector) and small at 80 degrees. Analysis of the dichroism yields the relative angle between the Sr-Mn vector and membrane normal (23 degrees ± 4 degrees), and the isotropic coordination number for these layered samples. X-ray absorption spectroscopy has also been employed to assess the degree of similarity between the manganese cluster in PS II and a family of synthetic manganese complexes containing the distorted cubane [Mn4O3X] core (X = benzoate, acetate, methoxide, hydroxide, azide, fluoride, chloride or bromide). In addition, Mn4O3Cl complexes containing three or six terminal Cl ligands at three of the Mn were included in this study. The EXAFS method detects the small changes in the core structures as X is varied in this series, and serves to exclude these distorted cubanes of C3v symmetry as a topological model for the Mn catalytic cluster. The sulfur K-edge x-ray absorption near-edge structure (XANES) spectra for the amino acids cysteine, methionine, their corresponding oxidized forms cystine and methionine sulfoxide, and

  20. Production and secretion of glucose in photosynthetic prokaryotes (cyanobacteria)

    Science.gov (United States)

    Nobles, Jr., David R. , Brown, Jr., R. Malcolm

    2010-09-28

    The present invention includes compositions and methods for making and using an isolated cyanobacterium that includes a portion of an exogenous bacterial cellulose operon sufficient to express bacterial cellulose, whereby the cyanobacterium produces extracellular glucose. The compositions and methods of the present invention may be used as a new global crop for the manufacture of cellulose, CO.sub.2 fixation, for the production of alternative sources of conventional cellulose as well as a biofuel and precursors thereof.

  1. Prokaryote metabolism activity

    OpenAIRE

    Biederman, Lori

    2017-01-01

    I wrote this activity to emphasize that prokaryotic organisms can carry out 6 different types of metabolisms (as presented in Freeman’s Biological Science textbook) and this contrasts to eukaryotes, which can only use 2 metabolism pathways (photoautotroph and heterotroph).    For in class materials I remove the  red box (upper right corner) and print slides 3-10, place them back-to-back and laminate them.  The students get a key (slide 2) and a two-sided organism sheet...

  2. Heterogeneous distribution of prokaryotes and viruses at the microscale in a tidal sediment

    DEFF Research Database (Denmark)

    Carreira, Cátia; Larsen, Morten; Glud, Ronnie

    2013-01-01

    In this study we show for the first time the microscale (mm) 2- and 3-dimensional spatial distribution and abundance of prokaryotes, viruses, and oxygen in a tidal sediment. Prokaryotes and viruses were highly heterogeneously distributed with patches of elevated abundances surrounded by areas of ...

  3. Halophilic & halotolerant prokaryotes in humans.

    Science.gov (United States)

    Seck, El Hadji; Dufour, Jean-Charles; Raoult, Didier; Lagier, Jean-Christophe

    2018-05-04

    Halophilic prokaryotes are described as microorganisms living in hypersaline environments. Here, we list the halotolerant and halophilic bacteria which have been isolated in humans. Of the 52 halophilic prokaryotes, 32 (61.54%) were moderately halophilic, 17 (32.69%) were slightly halophilic and three (5.76%) were extremely halophilic prokaryotes. At the phylum level, 29 (54.72%) belong to Firmicutes, 15 (28.84%) to Proteobacteria, four (7.69%) to Actinobacteria, three (5.78%) to Euryarchaeota and one (1.92%) belongs to Bacteroidetes. Halophilic prokaryotes are rarely pathogenic: of these 52 halophilic prokaryotes only two (3.92%) species were classified in Risk Group 2 (Vibrio cholerae, Vibrio parahaemolyticus) and one (1.96%), species in Risk Group 3 (Bacillus anthracis).

  4. Light-controlled motility in prokaryotes and the problem of directional light perception.

    Science.gov (United States)

    Wilde, Annegret; Mullineaux, Conrad W

    2017-11-01

    The natural light environment is important to many prokaryotes. Most obviously, phototrophic prokaryotes need to acclimate their photosynthetic apparatus to the prevailing light conditions, and such acclimation is frequently complemented by motility to enable cells to relocate in search of more favorable illumination conditions. Non-phototrophic prokaryotes may also seek to avoid light at damaging intensities and wavelengths, and many prokaryotes with diverse lifestyles could potentially exploit light signals as a rich source of information about their surroundings and a cue for acclimation and behavior. Here we discuss our current understanding of the ways in which bacteria can perceive the intensity, wavelength and direction of illumination, and the signal transduction networks that link light perception to the control of motile behavior. We discuss the problems of light perception at the prokaryotic scale, and the challenge of directional light perception in small bacterial cells. We explain the peculiarities and the common features of light-controlled motility systems in prokaryotes as diverse as cyanobacteria, purple photosynthetic bacteria, chemoheterotrophic bacteria and haloarchaea. © FEMS 2017.

  5. CEFLES2: the remote sensing component to quantify photosynthetic efficiency from the leaf to the region by measuring sun-induced fluorescence in the oxygen absorption bands

    Czech Academy of Sciences Publication Activity Database

    Rascher, U.; Agati, G.; Alonso, L.; Cecchi, G.; Champaigne, S.; Colombo, R.; Damm, A.; Daumard, F.; de Miguel, E.; Fernandez, G.; Franch, B.; Franke, J.; Gerbig, C.; Gioli, B.; Gomez, J.A.; Goulas, Y.; Guanter, L.; Gutierrez-de-la-Camara, O.; Hamdi, K.; Hostert, P.; Jimenez, M.; Košvancová, Martina; Lognoli, D.; Meroni, M.; Miglietta, F.; Moersch, A.; Moreno, J.; Moya, I.; Neininger, B.; Okujeni, A.; Ounis, A.; Palombi, L.; Raimondi, V.; Schickling, A.; Sobrino, J.A.; Stellmes, M.; Toci, G.; Toscano, P.; Udelhoven, T.; van der Linden, S.; Zaldei, A.

    2009-01-01

    Roč. 6, č. 7 (2009), s. 1181-1198 ISSN 1726-4170 Institutional research plan: CEZ:AV0Z60870520 Keywords : remote sensing * photosynthetic efficiency * fluorescence * CO2 flux * gross primary production * water-stress * steady-state Subject RIV: ED - Physiology Impact factor: 3.246, year: 2009 www.biogeosciences-discuss.net/6/2217/2009/

  6. Evolution of small prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    David José Martínez-Cano

    2015-01-01

    Full Text Available As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ~800 genes as well as endosymbiotic bacteria with as few as ~140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria; metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature.

  7. Photosynthetic Pigments in Diatoms.

    Science.gov (United States)

    Kuczynska, Paulina; Jemiola-Rzeminska, Malgorzata; Strzalka, Kazimierz

    2015-09-16

    Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvesting pigments such as chlorophyll a, chlorophyll c, and fucoxanthin, there is a group of photoprotective carotenoids which includes β-carotene and the xanthophylls, diatoxanthin, diadinoxanthin, violaxanthin, antheraxanthin, and zeaxanthin, which are engaged in the xanthophyll cycle. Additionally, some intermediate products of biosynthetic pathways have been identified in diatoms as well as unusual pigments, e.g., marennine. Marine algae have become widely recognized as a source of unique bioactive compounds for potential industrial, pharmaceutical, and medical applications. In this review, we summarize current knowledge on diatom photosynthetic pigments complemented by some new insights regarding their physico-chemical properties, biological role, and biosynthetic pathways, as well as the regulation of pigment level in the cell, methods of purification, and significance in industries.

  8. Photosynthetic Pigments in Diatoms

    Directory of Open Access Journals (Sweden)

    Paulina Kuczynska

    2015-09-01

    Full Text Available Photosynthetic pigments are bioactive compounds of great importance for the food, cosmetic, and pharmaceutical industries. They are not only responsible for capturing solar energy to carry out photosynthesis, but also play a role in photoprotective processes and display antioxidant activity, all of which contribute to effective biomass and oxygen production. Diatoms are organisms of a distinct pigment composition, substantially different from that present in plants. Apart from light-harvesting pigments such as chlorophyll a, chlorophyll c, and fucoxanthin, there is a group of photoprotective carotenoids which includes β-carotene and the xanthophylls, diatoxanthin, diadinoxanthin, violaxanthin, antheraxanthin, and zeaxanthin, which are engaged in the xanthophyll cycle. Additionally, some intermediate products of biosynthetic pathways have been identified in diatoms as well as unusual pigments, e.g., marennine. Marine algae have become widely recognized as a source of unique bioactive compounds for potential industrial, pharmaceutical, and medical applications. In this review, we summarize current knowledge on diatom photosynthetic pigments complemented by some new insights regarding their physico-chemical properties, biological role, and biosynthetic pathways, as well as the regulation of pigment level in the cell, methods of purification, and significance in industries.

  9. Capturing prokaryotic dark matter genomes.

    Science.gov (United States)

    Gasc, Cyrielle; Ribière, Céline; Parisot, Nicolas; Beugnot, Réjane; Defois, Clémence; Petit-Biderre, Corinne; Boucher, Delphine; Peyretaillade, Eric; Peyret, Pierre

    2015-12-01

    Prokaryotes are the most diverse and abundant cellular life forms on Earth. Most of them, identified by indirect molecular approaches, belong to microbial dark matter. The advent of metagenomic and single-cell genomic approaches has highlighted the metabolic capabilities of numerous members of this dark matter through genome reconstruction. Thus, linking functions back to the species has revolutionized our understanding of how ecosystem function is sustained by the microbial world. This review will present discoveries acquired through the illumination of prokaryotic dark matter genomes by these innovative approaches. Copyright © 2015 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

  10. The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

    Directory of Open Access Journals (Sweden)

    Miguel A. Hernández-Prieto

    2017-02-01

    Full Text Available Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels.

  11. The Complex Transcriptional Response of Acaryochloris marina to Different Oxygen Levels

    Science.gov (United States)

    Hernández-Prieto, Miguel A.; Lin, Yuankui; Chen, Min

    2016-01-01

    Ancient oxygenic photosynthetic prokaryotes produced oxygen as a waste product, but existed for a long time under an oxygen-free (anoxic) atmosphere, before an oxic atmosphere emerged. The change in oxygen levels in the atmosphere influenced the chemistry and structure of many enzymes that contained prosthetic groups that were inactivated by oxygen. In the genome of Acaryochloris marina, multiple gene copies exist for proteins that are normally encoded by a single gene copy in other cyanobacteria. Using high throughput RNA sequencing to profile transcriptome responses from cells grown under microoxic and hyperoxic conditions, we detected 8446 transcripts out of the 8462 annotated genes in the Cyanobase database. Two-thirds of the 50 most abundant transcripts are key proteins in photosynthesis. Microoxic conditions negatively affected the levels of expression of genes encoding photosynthetic complexes, with the exception of some subunits. In addition to the known regulation of the multiple copies of psbA, we detected a similar transcriptional pattern for psbJ and psbU, which might play a key role in the altered components of photosystem II. Furthermore, regulation of genes encoding proteins important for reactive oxygen species-scavenging is discussed at genome level, including, for the first time, specific small RNAs having possible regulatory roles under varying oxygen levels. PMID:27974439

  12. Nitrogen ligation to manganese in the photosynthetic oxygen-evolving complex: Continuous-wave and pulsed EPR studies of Photosystem II particles containing 14N or 15N

    International Nuclear Information System (INIS)

    DeRose, V.J.; Yachandra, V.K.; McDermott, A.E.; Britt, R.D.; Sauer, K.; Klein, M.P.

    1991-01-01

    The possibility of nitrogen ligation to the Mn in the oxygen-evolving complex from photosystem II was investigated with electron paramagnetic resonance (EPR) and electron spin echo envelope modulation (ESEEM) spectroscopies using 14 N- and 15 N-labeled preparations. Oxygen-evolving preparations were isolated from a thermophilic cyanobacterium, Synechococcus sp., grown on a medium containing either 14 NO 3 - or 15 NO - 3 as the sole source of nitrogen. The substructure on the multiline EPR signal, which arises from Mn in the S 2 state of the enzyme, was measured with continuous-wave EPR. No changes were detected in the substructure peak positions upon substitution of 15 N for 14 N, indicating that this substructure is not due to superhyperfine coupling from nitrogen ligands. To detect potential nitrogen ligands with superhyperfine couplings of lesser magnitude than could be observed with conventional EPR methods, electron spin-echo envelope modulation experiments were also performed on the multiline EPR signal. The Fourier transform of the light-minus-dark time domain ESEEM data shows a peak at 4.8 MHz in 14 N samples which is absent upon substitution with 15 N. This gives unambiguous evidence for weak hyperfine coupling of nitrogen to the Mn of the oxygen-evolving complex. Possible origins of this nitrogen interaction are discussed

  13. The Epigenomic Landscape of Prokaryotes.

    Directory of Open Access Journals (Sweden)

    Matthew J Blow

    2016-02-01

    Full Text Available DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93% organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases, doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active 'orphan' MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems.

  14. Translational selection is ubiquitous in prokaryotes.

    Directory of Open Access Journals (Sweden)

    Fran Supek

    2010-06-01

    Full Text Available Codon usage bias in prokaryotic genomes is largely a consequence of background substitution patterns in DNA, but highly expressed genes may show a preference towards codons that enable more efficient and/or accurate translation. We introduce a novel approach based on supervised machine learning that detects effects of translational selection on genes, while controlling for local variation in nucleotide substitution patterns represented as sequence composition of intergenic DNA. A cornerstone of our method is a Random Forest classifier that outperformed previous distance measure-based approaches, such as the codon adaptation index, in the task of discerning the (highly expressed ribosomal protein genes by their codon frequencies. Unlike previous reports, we show evidence that translational selection in prokaryotes is practically universal: in 460 of 461 examined microbial genomes, we find that a subset of genes shows a higher codon usage similarity to the ribosomal proteins than would be expected from the local sequence composition. These genes constitute a substantial part of the genome--between 5% and 33%, depending on genome size--while also exhibiting higher experimentally measured mRNA abundances and tending toward codons that match tRNA anticodons by canonical base pairing. Certain gene functional categories are generally enriched with, or depleted of codon-optimized genes, the trends of enrichment/depletion being conserved between Archaea and Bacteria. Prominent exceptions from these trends might indicate genes with alternative physiological roles; we speculate on specific examples related to detoxication of oxygen radicals and ammonia and to possible misannotations of asparaginyl-tRNA synthetases. Since the presence of codon optimizations on genes is a valid proxy for expression levels in fully sequenced genomes, we provide an example of an "adaptome" by highlighting gene functions with expression levels elevated specifically in

  15. Natural strategies for photosynthetic light harvesting

    NARCIS (Netherlands)

    Croce, R.; van Amerongen, H.

    2014-01-01

    Photosynthetic organisms are crucial for life on Earth as they provide food and oxygen and are at the basis of most energy resources. They have a large variety of light-harvesting strategies that allow them to live nearly everywhere where sunlight can penetrate. They have adapted their pigmentation

  16. Short Term INT-Formazan Production as a Proxy for Marine Prokaryote Respiration

    Science.gov (United States)

    Cajal-Medrano, R.; Villegas-Mendoza, J.; Maske, H.

    2016-02-01

    Prokaryotes are poisoned by the tetrazolium electron transport probe INT on time scales of less than one hour, invalidating the interpretation of the rate of in vivo INT reduction to formazan as a proxy for oxygen consumption rates (Villegas-Mendoza et al. 2015). We measured oxygen consumption rate (R; µM O2 hour-1) and electron transport activity with in vivo INT formazan production (IFP, mM formazan) at 0.5 mM INT during 1 hour exposure time of natural communities and cultures of the marine bacteria Vibrio harveyi growing in batch and continuous cultures. A strong exponential relationship R = 0.20 IFP2.15 (pgrowth rates under aerobic condition. We find that IFP and oxygen consumption increase with bacterial specific growth rates and temperature as expected from basic principles of physiology and biochemistry. Oxygen and nitrogen saturated batch cultures of V. harveyi showed that both, IFP and oxygen consumption increased for 0.8 hours but then stopped similar to natural bacterial communities supporting the above relationship of IFP to prokaryote respiration. Our method implies adding 0.5 mM INT to a plankton sample and incubating for less than 1 hour. After prokaryote separation by size filtration (0.8 mm), the formazan crystals are collected by filtration (0.2 mm) and dissolved in propanol. The absorbance at 485 nm per sample volume yields the formazan potential that is related to prokaryote respiration in the sample.

  17. Biofouling of marbles by oxygenic photosynthetic microorganisms.

    Science.gov (United States)

    Karaca, Zeki; Öztürk, Ayten; Çolak, Emel

    2015-08-01

    Phototrophic microorganisms disfigure the surfaces of different types of stone. Stone structure is damaged by the activity of photoautotrophic and other microorganisms. However, to date few, investigations have been undertaken into the relationship between microorganisms and the properties of different types of marble. In this study, biological activity of photoautotrophic microorganisms on three types of marble (Yatagan White, Giallo Anticato and Afyon White) was investigated under laboratory conditions over a short period of time. The three types of marble supported the growth of phototrophic microbial communities on their outer and inner layers, turning their original colour from white to a yellowish green colour. The porosity of the marble types facilitated filamentous microbial growth in the presence of water. Scanning electron microscope analysis revealed the accumulation of aggregates such as small spherical, fibrillar, calcified globular bodies on the inner surfaces of the marbles. This suggests that the microscopic characteristics of particular marble types may stimulate the growth of certain types of microorganisms.

  18. Advances in algal-prokaryotic wastewater treatment: A review of nitrogen transformations, reactor configurations and molecular tools.

    Science.gov (United States)

    Wang, Meng; Keeley, Ryan; Zalivina, Nadezhda; Halfhide, Trina; Scott, Kathleen; Zhang, Qiong; van der Steen, Peter; Ergas, Sarina J

    2018-07-01

    The synergistic activity of algae and prokaryotic microorganisms can be used to improve the efficiency of biological wastewater treatment, particularly with regards to nitrogen removal. For example, algae can provide oxygen through photosynthesis needed for aerobic degradation of organic carbon and nitrification and harvested algal-prokaryotic biomass can be used to produce high value chemicals or biogas. Algal-prokaryotic consortia have been used to treat wastewater in different types of reactors, including waste stabilization ponds, high rate algal ponds and closed photobioreactors. This review addresses the current literature and identifies research gaps related to the following topics: 1) the complex interactions between algae and prokaryotes in wastewater treatment; 2) advances in bioreactor technologies that can achieve high nitrogen removal efficiencies in small reactor volumes, such as algal-prokaryotic biofilm reactors and enhanced algal-prokaryotic treatment systems (EAPS); 3) molecular tools that have expanded our understanding of the activities of algal and prokaryotic communities in wastewater treatment processes. Copyright © 2018 Elsevier Ltd. All rights reserved.

  19. Evolving a photosynthetic organelle

    Directory of Open Access Journals (Sweden)

    Nakayama Takuro

    2012-04-01

    Full Text Available Abstract The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles. The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis - the conversion of solar energy into chemical energy - and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

  20. Evolving a photosynthetic organelle.

    Science.gov (United States)

    Nakayama, Takuro; Archibald, John M

    2012-04-24

    The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles.The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis--the conversion of solar energy into chemical energy--and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

  1. Genome resource utilization during prokaryotic development

    Czech Academy of Sciences Publication Activity Database

    Vohradský, Jiří; Ramsden, J. J.

    2001-01-01

    Roč. 15, - (2001), s. 2054-2056 ISSN 0892-6638 R&D Projects: GA ČR GA204/00/1253 Institutional research plan: CEZ:AV0Z5020903 Keywords : prokaryotic development Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 8.817, year: 2001

  2. How crowded is the prokaryotic cytoplasm?

    NARCIS (Netherlands)

    Spitzer, Jan; Poolman, Bert; Ferguson, Stuart

    2013-01-01

    We consider biomacromolecular crowding within the cytoplasm of prokaryotic cells as a two-phase system of 'supercrowded' cytogel and 'dilute' cytosol; we simplify and quantify this model for a coccoid cell over a wide range of biomacromolecular crowding. The key result shows that the supercrowded

  3. Plasmid and chromosome segregation in prokaryotes

    DEFF Research Database (Denmark)

    Møller-Jensen, Jakob; Bugge Jensen, Rasmus; Gerdes, Kenn

    2000-01-01

    Recent major advances in the understanding of prokaryotic DNA segregation have been achieved by using fluorescence microscopy to visualize the localization of cellular components. Plasmids and bacterial chromosomes are partitioned in a highly dynamic fashion, suggesting the presence of a mitotic...

  4. Diversity and activity in marine prokaryotes

    NARCIS (Netherlands)

    Arrieta López de Uralde, Jesús Maria

    2005-01-01

    Life on Earth epends on the endless recycling of elements as matter and energy are required to sustain life. The prokaryotes (Bacteria and Archaea) are the masters of the trade of life. After all, they were already responsible for the major biogeochemical cycles 3.000 million years ago, long before

  5. Getting out : protein traffic in prokaryotes

    NARCIS (Netherlands)

    Pugsley, A.P; Francetic, O; Driessen, A.J.M.; de Lorenzo, V.

    Protein secretion systems in prokaryotes are increasingly shifting from being considered as experimental models for 'more complex' processes (i.e. eukaryotes) to being a major source of key biological questions in their own right. The pathways by which proteins move between compartments or insert

  6. A novel potassium channel in photosynthetic cyanobacteria.

    Directory of Open Access Journals (Sweden)

    Manuela Zanetti

    Full Text Available Elucidation of the structure-function relationship of a small number of prokaryotic ion channels characterized so far greatly contributed to our knowledge on basic mechanisms of ion conduction. We identified a new potassium channel (SynK in the genome of the cyanobacterium Synechocystis sp. PCC6803, a photosynthetic model organism. SynK, when expressed in a K(+-uptake-system deficient E. coli strain, was able to recover growth of these organisms. The protein functions as a potassium selective ion channel when expressed in Chinese hamster ovary cells. The location of SynK in cyanobacteria in both thylakoid and plasmamembranes was revealed by immunogold electron microscopy and Western blotting of isolated membrane fractions. SynK seems to be conserved during evolution, giving rise to a TPK (two-pore K(+ channel family member which is shown here to be located in the thylakoid membrane of Arabidopsis. Our work characterizes a novel cyanobacterial potassium channel and indicates the molecular nature of the first higher plant thylakoid cation channel, opening the way to functional studies.

  7. Chlorosomes: antenna organelles in photosynthetic green bacteria

    DEFF Research Database (Denmark)

    Frigaard, N.-U.; Bryant, D. A.

    2006-01-01

    The new series "Microbiology Monographs" begins with two volumes on intracellular components in prokaryotes. In this second volume, "Complex Intracellular Structures in Prokaryotes", the components, labelled complex intracellular structures, encompass a multitude of important cellular functions. ...

  8. Effect of temperature and light intensity on growth and photosynthetic activity of Chlamydomonas Reinhardtii

    International Nuclear Information System (INIS)

    Alfonsel, M.; Fernandez Gonzalez, J.

    1986-01-01

    The effect of five temperatures (15, 20, 25, 30 and 35 0 C) and two levels of illumination on growth and photosynthetic activity of Chlamydomonas reinhardtii has been studied. The growth of the cultures was evaluated by optical density. Photosynthetic activity has been carried out studying either the assimilation rate of CO 2 labelled with C 14 or the oxygen evolution by means of polarographic measurements. The maximum photosynthetic rate has been obtained at 25 0 C for the lower lavel of illumination (2400 lux) and at 35 0 C for the higher one (13200 lux). These results suggest an interacton of temperature and illumination on photosynthetic activity. (author)

  9. INT (2-(4-Iodophenyl)-3-(4-Nitrophenyl)-5-(Phenyl) Tetrazolium Chloride) Is Toxic to Prokaryote Cells Precluding Its Use with Whole Cells as a Proxy for In Vivo Respiration.

    Science.gov (United States)

    Villegas-Mendoza, Josué; Cajal-Medrano, Ramón; Maske, Helmut

    2015-11-01

    Prokaryote respiration is expected to be responsible for more than half of the community respiration in the ocean, but the lack of a practical method to measure the rate of prokaryote respiration in the open ocean resulted in very few published data leaving the role of organotrophic prokaryotes open to debate. Oxygen consumption rates of oceanic prokaryotes measured with current methods may be biased due to pre-incubation size filtration and long incubation times both of which can change the physiological and taxonomic profile of the sample during the incubation period. In vivo INT reduction has been used in terrestrial samples to estimate respiration rates, and recently, the method was introduced and applied in aquatic ecology. We measured oxygen consumption rates and in vivo INT reduction to formazan in cultures of marine bacterioplankton communities, Vibrio harveyi and the eukaryote Isochrysis galbana. For prokaryotes, we observed a decrease in oxygen consumption rates with increasing INT concentrations between 0.05 and 1 mM. Time series after 0.5 mM INT addition to prokaryote samples showed a burst of in vivo INT reduction to formazan and a rapid decline of oxygen consumption rates to zero within less than an hour. Our data for non-axenic eukaryote cultures suggest poisoning of the eukaryote. Prokaryotes are clearly poisoned by INT on time scales of less than 1 h, invalidating the interpretation of in vivo INT reduction to formazan as a proxy for oxygen consumption rates.

  10. Coral bleaching independent of photosynthetic activity.

    Science.gov (United States)

    Tolleter, Dimitri; Seneca, François O; DeNofrio, Jan C; Krediet, Cory J; Palumbi, Stephen R; Pringle, John R; Grossman, Arthur R

    2013-09-23

    The global decline of reef-building corals is due in part to the loss of algal symbionts, or "bleaching," during the increasingly frequent periods of high seawater temperatures. During bleaching, endosymbiotic dinoflagellate algae (Symbiodinium spp.) either are lost from the animal tissue or lose their photosynthetic pigments, resulting in host mortality if the Symbiodinium populations fail to recover. The >1,000 studies of the causes of heat-induced bleaching have focused overwhelmingly on the consequences of damage to algal photosynthetic processes, and the prevailing model for bleaching invokes a light-dependent generation of toxic reactive oxygen species (ROS) by heat-damaged chloroplasts as the primary trigger. However, the precise mechanisms of bleaching remain unknown, and there is evidence for involvement of multiple cellular processes. In this study, we asked the simple question of whether bleaching can be triggered by heat in the dark, in the absence of photosynthetically derived ROS. We used both the sea anemone model system Aiptasia and several species of reef-building corals to demonstrate that symbiont loss can occur rapidly during heat stress in complete darkness. Furthermore, we observed damage to the photosynthetic apparatus under these conditions in both Aiptasia endosymbionts and cultured Symbiodinium. These results do not directly contradict the view that light-stimulated ROS production is important in bleaching, but they do show that there must be another pathway leading to bleaching. Elucidation of this pathway should help to clarify bleaching mechanisms under the more usual conditions of heat stress in the light. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Primary photosynthetic processes: from supercomplex to leaf

    NARCIS (Netherlands)

    Broess, K.

    2009-01-01

    This thesis describes fluorescence spectroscopy experiments on photosynthetic complexes that cover the primary photosynthetic processes, from the absorption of light by photosynthetic pigments to a charge separation (CS) in the reaction center (RC). Fluorescence spectroscopy is a useful tool in

  12. Relationship between viral and prokaryotic abundance on the Bajo O’Higgins 1 Seamount (Humboldt Current System off Chile

    Directory of Open Access Journals (Sweden)

    Oscar E. Chiang

    2007-03-01

    Full Text Available There is little known about the ecology of microbial communities living in the water column over seamounts. Here, for the first time, the spatial distribution and abundance of virus-like particles (VLP are described over a seamount. The association between VLP distribution, prokaryotic abundance, and environmental variables is also analyzed. Sampling was conducted in December 2004 on the Bajo O’Higgins 1 seamount (32°54’S, 73°53’W located in the Humboldt Current System off Chile. A oxygen minimum layer (OMZ was clearly present between 130 and 280 m in the water column over the seamount. Water samples were taken with Niskin bottles at 10 oceanographic stations over the seamount at depths of 5, 20, 50, 75, 100, and 150 m and at the benthic boundary layer (BBL; 5-12 m over the sediments. Temperature, salinity, oxygen, chlorophyll , and phaeopigments were measured at each station. Viral and prokaryotic abundances were determined with fluorochrome SYBR Green I. Viral abundance ranged from 1.53 x 109 VLP L-1 - 16.48 x 109 VLP L-1, whereas prokaryotic abundance ranged from 1.78 x 10 8 cell L-1 - 14.91 x 108 cell L-1. The virus-like particle/prokaryote ratio varied widely among the analyzed layers (i.e. surface, OMZ, and BBL, probably due to the presence of different prokaryotic and viral assemblages in each layer. Our results indicate that the environmental conditions, mainly the concentration of dissolved oxygen in the water column over Bajo O’Higgins 1 seamount, shape the association between viral and prokaryotic abundance.

  13. Prokaryotes versus Eukaryotes: Who is hosting whom?

    Directory of Open Access Journals (Sweden)

    Guillermo eTellez

    2014-10-01

    Full Text Available Microorganisms represent the largest component of biodiversity in our world. For millions of years, prokaryotic microorganisms have functioned as a major selective force shaping eukaryotic evolution. Microbes that live inside and on animals outnumber the animals’ actual somatic and germ cells by an estimated 10-fold. Collectively, the intestinal microbiome represents a ‘forgotten organ’, functioning as an organ inside another that can execute many physiological responsibilities. The nature of primitive eukaryotes was drastically changed due to the association with symbiotic prokaryotes facilitating mutual coevolution of host and microbe. Phytophagous insects have long been used to test theories of evolutionary diversification; moreover, the diversification of a number of phytophagous insect lineages has been linked to mutualisms with microbes. From termites and honey bees to ruminants and mammals, depending on novel biochemistries provided by the prokaryotic microbiome, the association helps to metabolize several nutrients that the host cannot digest and converting these into useful end products (such as short chain fatty acids, a process which has huge impact on the biology and homeostasis of metazoans. More importantly, in a direct and/or indirect way, the intestinal microbiota influences the assembly of gut-associated lymphoid tissue, helps to educate immune system, affects the integrity of the intestinal mucosal barrier, modulates proliferation and differentiation of its epithelial lineages, regulates angiogenesis, and modifies the activity of enteric as well as the central nervous system,. Despite these important effects, the mechanisms by which the gut microbial community influences the host’s biology remains almost entirely unknown. Our aim here is to encourage empirical inquiry into the relationship between mutualism and evolutionary diversification between prokaryotes and eukaryotes which encourage us to postulate: Who is

  14. Respiratory processes in non-photosynthetic plastids

    Science.gov (United States)

    Renato, Marta; Boronat, Albert; Azcón-Bieto, Joaquín

    2015-01-01

    Chlororespiration is a respiratory process located in chloroplast thylakoids which consists in an electron transport chain from NAD(P)H to oxygen. This respiratory chain involves the NAD(P)H dehydrogenase complex, the plastoquinone pool and the plastid terminal oxidase (PTOX), and it probably acts as a safety valve to prevent the over-reduction of the photosynthetic machinery in stress conditions. The existence of a similar respiratory activity in non-photosynthetic plastids has been less studied. Recently, it has been reported that tomato fruit chromoplasts present an oxygen consumption activity linked to ATP synthesis. Etioplasts and amyloplasts contain several electron carriers and some subunits of the ATP synthase, so they could harbor a similar respiratory process. This review provides an update on the study about respiratory processes in chromoplasts, identifying the major gaps that need to be addressed in future research. It also reviews the proteomic data of etioplasts and amyloplasts, which suggest the presence of a respiratory electron transport chain in these plastids. PMID:26236317

  15. Respiratory processes in non-photosynthetic plastids

    Directory of Open Access Journals (Sweden)

    Marta eRenato

    2015-07-01

    Full Text Available Chlororespiration is a respiratory process located in chloroplast thylakoids which consists in an electron transport chain from NAD(PH to oxygen. This respiratory chain involves the NAD(PH dehydrogenase complex, the plastoquinone pool and the plastid terminal oxidase (PTOX, and it probably acts as a safety valve to prevent the over-reduction of the photosynthetic machinery in stress conditions. The existence of a similar respiratory activity in non-photosynthetic plastids has been less studied. Recently, it has been reported that tomato fruit chromoplasts present an oxygen consumption activity linked to ATP synthesis. Etioplasts and amyloplasts contain several electron carriers and some subunits of the ATP synthase, so they could harbor a similar respiratory process. This review provides an update on the study about respiratory processes in chromoplasts, identifying the major gaps that need to be addressed in future research. It also reviews the proteomic data of etioplasts and amyloplasts, which suggest the presence of a respiratory electron transport chain in these plastids.

  16. Prokaryotic Heme Biosynthesis: Multiple Pathways to a Common Essential Product.

    Science.gov (United States)

    Dailey, Harry A; Dailey, Tamara A; Gerdes, Svetlana; Jahn, Dieter; Jahn, Martina; O'Brian, Mark R; Warren, Martin J

    2017-03-01

    The advent of heme during evolution allowed organisms possessing this compound to safely and efficiently carry out a variety of chemical reactions that otherwise were difficult or impossible. While it was long assumed that a single heme biosynthetic pathway existed in nature, over the past decade, it has become clear that there are three distinct pathways among prokaryotes, although all three pathways utilize a common initial core of three enzymes to produce the intermediate uroporphyrinogen III. The most ancient pathway and the only one found in the Archaea converts siroheme to protoheme via an oxygen-independent four-enzyme-step process. Bacteria utilize the initial core pathway but then add one additional common step to produce coproporphyrinogen III. Following this step, Gram-positive organisms oxidize coproporphyrinogen III to coproporphyrin III, insert iron to make coproheme, and finally decarboxylate coproheme to protoheme, whereas Gram-negative bacteria first decarboxylate coproporphyrinogen III to protoporphyrinogen IX and then oxidize this to protoporphyrin IX prior to metal insertion to make protoheme. In order to adapt to oxygen-deficient conditions, two steps in the bacterial pathways have multiple forms to accommodate oxidative reactions in an anaerobic environment. The regulation of these pathways reflects the diversity of bacterial metabolism. This diversity, along with the late recognition that three pathways exist, has significantly slowed advances in this field such that no single organism's heme synthesis pathway regulation is currently completely characterized. Copyright © 2017 American Society for Microbiology.

  17. Photosynthetic fuel for heterologous enzymes

    DEFF Research Database (Denmark)

    Mellor, Silas Busck; Vavitsas, Konstantinos; Nielsen, Agnieszka Janina Zygadlo

    2017-01-01

    of reducing power. Recent work on the metabolic engineering of photosynthetic organisms has shown that the electron carriers such as ferredoxin and flavodoxin can be used to couple heterologous enzymes to photosynthetic reducing power. Because these proteins have a plethora of interaction partners and rely...... on electrostatically steered complex formation, they form productive electron transfer complexes with non-native enzymes. A handful of examples demonstrate channeling of photosynthetic electrons to drive the activity of heterologous enzymes, and these focus mainly on hydrogenases and cytochrome P450s. However......, competition from native pathways and inefficient electron transfer rates present major obstacles, which limit the productivity of heterologous reactions coupled to photosynthesis. We discuss specific approaches to address these bottlenecks and ensure high productivity of such enzymes in a photosynthetic...

  18. Photosynthetic polyol production

    NARCIS (Netherlands)

    Savakis, P.E.

    2016-01-01

    In the combustion reaction, a fuel reacts with oxygen to carbon dioxide and water. The energy liberated in this process can then be harnessed to do work, e.g. to generate electricity or drive an engine. Excessive and increasing world-wide use of fossil fuels has led to increases in atmospheric

  19. Emerging spatial patterns in Antarctic prokaryotes

    Directory of Open Access Journals (Sweden)

    Chun Wie eChong

    2015-09-01

    Full Text Available Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote

  20. Emerging spatial patterns in Antarctic prokaryotes.

    Science.gov (United States)

    Chong, Chun-Wie; Pearce, David A; Convey, Peter

    2015-01-01

    Recent advances in knowledge of patterns of biogeography in terrestrial eukaryotic organisms have led to a fundamental paradigm shift in understanding of the controls and history of life on land in Antarctica, and its interactions over the long term with the glaciological and geological processes that have shaped the continent. However, while it has long been recognized that the terrestrial ecosystems of Antarctica are dominated by microbes and their processes, knowledge of microbial diversity and distributions has lagged far behind that of the macroscopic eukaryote organisms. Increasing human contact with and activity in the continent is leading to risks of biological contamination and change in a region whose isolation has protected it for millions of years at least; these risks may be particularly acute for microbial communities which have, as yet, received scant recognition and attention. Even a matter apparently as straightforward as Protected Area designation in Antarctica requires robust biodiversity data which, in most parts of the continent, remain almost completely unavailable. A range of important contributing factors mean that it is now timely to reconsider the state of knowledge of Antarctic terrestrial prokaryotes. Rapid advances in molecular biological approaches are increasingly demonstrating that bacterial diversity in Antarctica may be far greater than previously thought, and that there is overlap in the environmental controls affecting both Antarctic prokaryotic and eukaryotic communities. Bacterial dispersal mechanisms and colonization patterns remain largely unaddressed, although evidence for regional evolutionary differentiation is rapidly accruing and, with this, there is increasing appreciation of patterns in regional bacterial biogeography in this large part of the globe. In this review, we set out to describe the state of knowledge of Antarctic prokaryote diversity patterns, drawing analogy with those of eukaryote groups where appropriate

  1. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria

    OpenAIRE

    Maresca, Julia A.; Graham, Joel E.; Wu, Martin; Eisen, Jonathan A.; Bryant, Donald A.

    2007-01-01

    A fourth and large family of lycopene cyclases was identified in photosynthetic prokaryotes. The first member of this family, encoded by the cruA gene of the green sulfur bacterium Chlorobium tepidum, was identified in a complementation assay with a lycopene-producing strain of Escherichia coli. Orthologs of cruA are found in all available green sulfur bacterial genomes and in all cyanobacterial genomes that lack genes encoding CrtL- or CrtY-type lycopene cyclases. The cyanobacterium Synechoc...

  2. A framework for classification of prokaryotic protein kinases.

    Directory of Open Access Journals (Sweden)

    Nidhi Tyagi

    Full Text Available BACKGROUND: Overwhelming majority of the Serine/Threonine protein kinases identified by gleaning archaeal and eubacterial genomes could not be classified into any of the well known Hanks and Hunter subfamilies of protein kinases. This is owing to the development of Hanks and Hunter classification scheme based on eukaryotic protein kinases which are highly divergent from their prokaryotic homologues. A large dataset of prokaryotic Serine/Threonine protein kinases recognized from genomes of prokaryotes have been used to develop a classification framework for prokaryotic Ser/Thr protein kinases. METHODOLOGY/PRINCIPAL FINDINGS: We have used traditional sequence alignment and phylogenetic approaches and clustered the prokaryotic kinases which represent 72 subfamilies with at least 4 members in each. Such a clustering enables classification of prokaryotic Ser/Thr kinases and it can be used as a framework to classify newly identified prokaryotic Ser/Thr kinases. After series of searches in a comprehensive sequence database we recognized that 38 subfamilies of prokaryotic protein kinases are associated to a specific taxonomic level. For example 4, 6 and 3 subfamilies have been identified that are currently specific to phylum proteobacteria, cyanobacteria and actinobacteria respectively. Similarly subfamilies which are specific to an order, sub-order, class, family and genus have also been identified. In addition to these, we also identify organism-diverse subfamilies. Members of these clusters are from organisms of different taxonomic levels, such as archaea, bacteria, eukaryotes and viruses. CONCLUSION/SIGNIFICANCE: Interestingly, occurrence of several taxonomic level specific subfamilies of prokaryotic kinases contrasts with classification of eukaryotic protein kinases in which most of the popular subfamilies of eukaryotic protein kinases occur diversely in several eukaryotes. Many prokaryotic Ser/Thr kinases exhibit a wide variety of modular

  3. Net Community and Gross Photosynthetic Production Rates in the Eastern Tropical South Pacific, as Determined from O2/AR Ratios and Triple Oxygen Isotopic Composition of Dissolved O2

    Science.gov (United States)

    Prokopenko, M. G.; Yeung, L. Y.; Berelson, W.; Fleming, J.; Rollins, N.; Young, E. D.; Haskell, W. Z.; Hammond, D. E.; Capone, D. G.

    2010-12-01

    This study assesses the rates of ocean carbon production and its fate with respect to recycling or export in the Eastern Tropical South Pacific (ETSP). ETSP has been previously identified as a region where N2 fixation and denitrification may be spatially coupled; this is also a region of localized CO2 outgassing. Using an Equilibrated Inlet Mass Spectrometer (EIMS) system, we obtained continuous measurements of the biological O2 supersaturation in the mixed layer along the ship track encompassing a region bounded by 10-20° S and 80-100° W in January - March, 2010. Vertical profiles were also taken at selected stations and analyzed for dissolved O2/Ar ratios on EIMS and triple oxygen isotope composition (17O excess) on a multi-collector IRMS (Isotope Ratio Mass Spectrometer) at UCLA. Gas exchange rates were estimated using two approaches: the Rn-222 deficit method and the wind parameterization method, which utilized wind speeds extracted from ASCAT satellite database. Oxygen Net Community Production (O-NCP) rates calculated based on biological O2 supersaturation ranged from slightly negative to ~ 0.3 - 15 mmol/m2d, with higher rates along the northern part of the transect. Oxygen Gross Community Production (O-GPP) rates calculated from 17O excess were between 50 ± 20 and 200 ± 40 mmol/m2d, with higher rates observed along the northern cruise transect as well. Notably, the NCP/GPP ratios along the northern transect were higher by the factor of 2 to 3 than their southern counterparts. The O2/Ar-based NCP rates were comparable to POC flux measured with floating traps deployed at the southern stations, but exceeded by a factor of 5-10 the trap POC fluxes obtained at the northern stations. A one-dimensional box model has been constructed to quantify the magnitude of oxygen primary production below the mixed layer. The results of this work will be integrated with measurements of 15-N2 uptake that are in progress, to constrain the potential contribution of N2 fixation

  4. Bioinformatics analysis of disordered proteins in prokaryotes

    Directory of Open Access Journals (Sweden)

    Malkov Saša N

    2011-03-01

    Full Text Available Abstract Background A significant number of proteins have been shown to be intrinsically disordered, meaning that they lack a fixed 3 D structure or contain regions that do not posses a well defined 3 D structure. It has also been proven that a protein's disorder content is related to its function. We have performed an exhaustive analysis and comparison of the disorder content of proteins from prokaryotic organisms (i.e., superkingdoms Archaea and Bacteria with respect to functional categories they belong to, i.e., Clusters of Orthologous Groups of proteins (COGs and groups of COGs-Cellular processes (Cp, Information storage and processing (Isp, Metabolism (Me and Poorly characterized (Pc. We also analyzed the disorder content of proteins with respect to various genomic, metabolic and ecological characteristics of the organism they belong to. We used correlations and association rule mining in order to identify the most confident associations between specific modalities of the characteristics considered and disorder content. Results Bacteria are shown to have a somewhat higher level of protein disorder than archaea, except for proteins in the Me functional group. It is demonstrated that the Isp and Cp functional groups in particular (L-repair function and N-cell motility and secretion COGs of proteins in specific possess the highest disorder content, while Me proteins, in general, posses the lowest. Disorder fractions have been confirmed to have the lowest level for the so-called order-promoting amino acids and the highest level for the so-called disorder promoters. For each pair of organism characteristics, specific modalities are identified with the maximum disorder proteins in the corresponding organisms, e.g., high genome size-high GC content organisms, facultative anaerobic-low GC content organisms, aerobic-high genome size organisms, etc. Maximum disorder in archaea is observed for high GC content-low genome size organisms, high GC content

  5. Detecting uber-operons in prokaryotic genomes.

    Science.gov (United States)

    Che, Dongsheng; Li, Guojun; Mao, Fenglou; Wu, Hongwei; Xu, Ying

    2006-01-01

    We present a study on computational identification of uber-operons in a prokaryotic genome, each of which represents a group of operons that are evolutionarily or functionally associated through operons in other (reference) genomes. Uber-operons represent a rich set of footprints of operon evolution, whose full utilization could lead to new and more powerful tools for elucidation of biological pathways and networks than what operons have provided, and a better understanding of prokaryotic genome structures and evolution. Our prediction algorithm predicts uber-operons through identifying groups of functionally or transcriptionally related operons, whose gene sets are conserved across the target and multiple reference genomes. Using this algorithm, we have predicted uber-operons for each of a group of 91 genomes, using the other 90 genomes as references. In particular, we predicted 158 uber-operons in Escherichia coli K12 covering 1830 genes, and found that many of the uber-operons correspond to parts of known regulons or biological pathways or are involved in highly related biological processes based on their Gene Ontology (GO) assignments. For some of the predicted uber-operons that are not parts of known regulons or pathways, our analyses indicate that their genes are highly likely to work together in the same biological processes, suggesting the possibility of new regulons and pathways. We believe that our uber-operon prediction provides a highly useful capability and a rich information source for elucidation of complex biological processes, such as pathways in microbes. All the prediction results are available at our Uber-Operon Database: http://csbl.bmb.uga.edu/uber, the first of its kind.

  6. Special issue of photosynthetic research

    NARCIS (Netherlands)

    Okamura, M.; Wraight, C.A.; van Grondelle, R.

    2014-01-01

    This Special Issue of Photosynthesis Research honors Louis M. N. Duysens, Roderick K. Clayton, and George Feher, three pioneering researchers whose work on bacterial photosynthesis laid much of the groundwork for our understanding of the role of the reaction center in photosynthetic light energy

  7. Interactions Between Prokaryotes and Dissolved Organic Matter in Marine Waters

    DEFF Research Database (Denmark)

    Traving, Sachia Jo

    organic bound carbon equal in size to atmospheric carbon dioxide. Prokaryotes mediate the fate of a large part of marine DOM, which is their principal source of energy and substrate. However, a large fraction is also left behind in the water column persisting for millennia, and prokaryotes may hold...... the key to understanding the mechanisms controlling the cycling of DOM within marine waters. In the thesis presented here, the aim was to investigate the activity and composition of prokaryotes to determine their functional role in DOM utilization. The thesis incorporates a range of study systems...

  8. Photosynthetic characteristics of Lycoris aurea and monthly ...

    African Journals Online (AJOL)

    The leaf photosynthetic characteristics of Lycoris aurea, the monthly dynamics in lycorine and galantamine contents in its bulb and the correlation among the photosynthetic characteristics and the lycorine and galantamine during the annual growth period were studied by using LI-6400 portable photosynthetic measurement ...

  9. Two Tales of Prokaryotic Genomic Diversity: Escherichia coli and Halophiles

    Directory of Open Access Journals (Sweden)

    Lejla Pašić

    2014-01-01

    Full Text Available Prokaryotes are generally characterized by vast genomic diversity that has been shaped by mutations, horizontal gene transfer, bacteriocins and phage predation. Enormous genetic diversity has developed as a result of stresses imposed in harsh environments and the ability of microorganisms to adapt. Two examples of prokaryotic diversity are presented: on intraspecies level, exemplified by Escherichia coli, and the diversity of the hypersaline environment, with the discussion of food-related health issues and biotechnological potential.

  10. Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast

    DEFF Research Database (Denmark)

    Skjødt, Mette Louise; Snoek, Tim; Kildegaard, Kanchana Rueksomtawin

    2016-01-01

    ,cis-muconic acid at different levels, and found that reporter gene output correlated with production. The transplantation of prokaryotic transcriptional activators into the eukaryotic chassis illustrates the potential of a hitherto untapped biosensor resource useful for biotechnological applications....... real-time monitoring of production has attracted attention. Here we applied systematic engineering of multiple parameters to search for a general biosensor design in the budding yeast Saccharomyces cerevisiae based on small-molecule binding transcriptional activators from the prokaryote superfamily...

  11. Effects of viruses and predators on prokaryotic community composition.

    Science.gov (United States)

    Jardillier, Ludwig; Bettarel, Yvan; Richardot, Mathilde; Bardot, Corinne; Amblard, Christian; Sime-Ngando, Télesphore; Debroas, Didier

    2005-11-01

    Dialysis bags were used to examine the impact of predation and viral lysis on prokaryotic community composition (PCC) over a 5-day experiment in the oligomesotrophic Lake Pavin (France). The impact of the different predator communities (protists and metazoans) of prokaryotes was estimated by water fractionation (protists, which also affected PCC, whereas viruses seemed to be essentially responsible for profound changes in PCC via direct and indirect actions.

  12. Functional characterization of a prokaryotic Kir channel.

    Science.gov (United States)

    Enkvetchakul, Decha; Bhattacharyya, Jaya; Jeliazkova, Iana; Groesbeck, Darcy K; Cukras, Catherine A; Nichols, Colin G

    2004-11-05

    The Kir gene family encodes inward rectifying K+ (Kir) channels that are widespread and critical regulators of excitability in eukaryotic cells. A related gene family (KirBac) has recently been identified in prokaryotes. While a crystal structure of one member, Kir-Bac1.1, has been solved, there has been no functional characterization of any KirBac gene products. Here we present functional characterization of KirBac1.1 reconstituted in liposomes. Utilizing a 86Rb+ uptake assay, we demonstrate that KirBac1.1 generates a K+ -selective permeation path that is inhibited by extraliposomal Ba2+ and Ca2+ ions. In contrast to KcsA (an acid-activated bacterial potassium channel), KirBac1.1 is inhibited by extraliposomal acid (pKa approximately 6). This characterization of KirBac1.1 activity now paves the way for further correlation of structure and function in this model Kir channel.

  13. Phytochromes in photosynthetically competent plants

    Energy Technology Data Exchange (ETDEWEB)

    Pratt, L.H.

    1990-07-01

    Plants utilize light as a source of information in photomorphogenesis and of free energy in photosynthesis, two processes that are interrelated in that the former serves to increase the efficiency with which plants can perform the latter. Only one pigment involved in photomorphogenesis has been identified unequivocally, namely phytochrome. The thrust of this proposal is to investigate this pigment and its mode(s) of action in photosynthetically competent plants. Our long term objective is to characterize phytochrome and its functions in photosynthetically competent plants from molecular, biochemical and cellular perspectives. It is anticipated that others will continue to contribute indirectly to these efforts at the physiological level. The ultimate goal will be to develop this information from a comparative perspective in order to learn whether the different phytochromes have significantly different physicochemical properties, whether they fulfill independent functions and if so what these different functions are, and how each of the different phytochromes acts at primary molecular and cellular levels.

  14. Changes of Photosynthetic Behaviors in Kappaphycus alvarezii Infected by Epiphyte.

    Science.gov (United States)

    Pang, Tong; Liu, Jianguo; Liu, Qian; Lin, Wei

    2011-01-01

    Epiphytic filamentous algae (EFA) were noted as a serious problem to reduce the production and quality of K. alvarezii. The morphological studies revealed that the main epiphyte on K. alvarezii was Neosiphonia savatieri in China. Though the harmful effects of EFA on the production of K. alvarezii have been reported, the detailed mechanism of the N. savatieri in limiting the production of K. alvarezii has not been studied yet. The present paper studied the effects of N. savatieri infection on photosynthetic behaviors in K. alvarezii by detecting chlorophyll fluorescence transient in vivo. The results revealed that damage of oxygen-evolving complex (OEC), decrease of active reaction centers (RCs), and the plastoquinone (PQ) pool as well as significant reduction in the performance indexes (PI) of PSII were caused by the infection of N. savatieri. The influence of N. savatieri on photosynthetic activity of K. alvarezii should be one of the important reasons to reduce the production of K. alvarezii infected by N. savatieri.

  15. Pyrosequencing assessment of prokaryotic and eukaryotic diversity in biofilm communities from a French river.

    Science.gov (United States)

    Bricheux, Geneviève; Morin, Loïc; Le Moal, Gwenaël; Coffe, Gérard; Balestrino, Damien; Charbonnel, Nicolas; Bohatier, Jacques; Forestier, Christiane

    2013-06-01

    Despite the recent and significant increase in the study of aquatic microbial communities, little is known about the microbial diversity of complex ecosystems such as running waters. This study investigated the biodiversity of biofilm communities formed in a river with 454 Sequencing™. This river has the particularity of integrating both organic and microbiological pollution, as receiver of agricultural pollution in its upstream catchment area and urban pollution through discharges of the wastewater treatment plant of the town of Billom. Different regions of the small subunit (SSU) ribosomal RNA gene were targeted using nine pairs of primers, either universal or specific for bacteria, eukarya, or archaea. Our aim was to characterize the widest range of rDNA sequences using different sets of polymerase chain reaction (PCR) primers. A first look at reads abundance revealed that a large majority (47-48%) were rare sequences (<5 copies). Prokaryotic phyla represented the species richness, and eukaryotic phyla accounted for a small part. Among the prokaryotic phyla, Proteobacteria (beta and alpha) predominated, followed by Bacteroidetes together with a large number of nonaffiliated bacterial sequences. Bacillariophyta plastids were abundant. The remaining bacterial phyla, Verrucomicrobia and Cyanobacteria, made up the rest of the bulk biodiversity. The most abundant eukaryotic phyla were annelid worms, followed by Diatoms, and Chlorophytes. These latter phyla attest to the abundance of plastids and the importance of photosynthetic activity for the biofilm. These findings highlight the existence and plasticity of multiple trophic levels within these complex biological systems. © 2013 The Authors. Microbiology Open published by John Wiley & Sons Ltd.

  16. Effect of Temperature and light intensity on growth and Photosynthetic Activity of Chlamydomonas reinhard II

    International Nuclear Information System (INIS)

    Alfonsel Jaen, M.; Fernandez Gonzalez, J.

    1985-01-01

    The effect of five temperatures (15,20,25,30 and 35 degree centigree) and two levels of illumination on growth and photosynthetic activity of Chlamydomonas reinhard II has been studied. The growth of the cultures was evaluated by optical density. Photosynthetic activity has been carried out studying either the assimilation rate of C0 2 labelled with C-14 or the oxygen evolution by means of polarographic measurements. The maximum photosynthetic rate has been obtained at 25 degree centigree for the lower level of illumination (2400 lux) and at 35 degree centigree for the higher one (13200 lux) and at 35 degree centigree for the higher ono (13200 lux). These results suggest an interaction of temperature and illumination on photosynthetic activity. (Author) 37 refs

  17. Prokaryotic Argonautes - variations on the RNA interference theme

    Science.gov (United States)

    van der Oost, John; Swarts, Daan C.; Jore, Matthijs M.

    2014-01-01

    The discovery of RNA interference (RNAi) has been a major scientific breakthrough. This RNA-guided RNA interference system plays a crucial role in a wide range of regulatory and defense mechanisms in eukaryotes. The key enzyme of the RNAi system is Argonaute (Ago), an endo-ribonuclease that uses a small RNA guide molecule to specifically target a complementary RNA transcript. Two functional classes of eukaryotic Ago have been described: catalytically active Ago that cleaves RNA targets complementary to its guide, and inactive Ago that uses its guide to bind target RNA to down-regulate translation efficiency. A recent comparative genomics study has revealed that Argonaute-like proteins are also encoded by prokaryotic genomes. Interestingly, there is a lot of variation among these prokaryotic Argonaute (pAgo) proteins with respect to domain architecture: some resemble the eukaryotic Ago (long pAgo) containing a complete or disrupted catalytic site, while others are truncated versions (short pAgo) that generally contain an incomplete catalytic site. Prokaryotic Agos with an incomplete catalytic site often co-occur with (predicted) nucleases. Based on this diversity, and on the fact that homologs of other RNAi-related protein components (such as Dicer nucleases) have never been identified in prokaryotes, it has been predicted that variations on the eukaryotic RNAi theme may occur in prokaryotes. PMID:28357239

  18. Differential response of marine flagellate communities to prokaryotic food quality

    Science.gov (United States)

    De Corte, D.; Paredes, G.; Sintes, E.; Herndl, G. J.

    2016-02-01

    Marine prokaryotes play a major role in the biogeochemical cycles. The main predators of prokaryotes are heterotrophic nanoflagellates (HNF). HNF are thus a major link connecting dissolved organic material through prokaryotic grazing to the higher trophic levels. However, little is known about the grazing specificity of HNF on specific prokaryotic taxa. Bacterial and archaeal microbes may have different nutritive values for the HNF communities, thus affecting growth rates and community composition of HNFs. In this study we investigated the influence of prey food quality on Cafeteria roenbergensis and on a natural HNF community isolated in the northern Adriatic Sea. Two Nitrosopumilus maritimus-related strains isolated from the northern Adriatic Sea (Nitrosopumilus adriaticus, Nitrosopumilus piranensis), two Nitrosococcus strains and two fast growing marine Bacteria (Pseudomonas marina and Marinobacter algicola) were fed to the HNFs. The two fast growing bacterial strains resulted in high growth rates of Cafeteria roenbergensis and the mixed HNF community, while the two Nitrosococcus strains did not. Cafeteria roenbergensis fed on N. adriaticus but it did not graze N. piranensis, suggesting that the subtle metabolic and physiological differences between these two closely related thaumarchaeal strains affect the grazing pressure to which they are exposed. Our study also indicates that prokaryotic community composition influences the composition of the HNF community.

  19. Simple sequence proteins in prokaryotic proteomes

    Directory of Open Access Journals (Sweden)

    Ramachandran Srinivasan

    2006-06-01

    Full Text Available Abstract Background The structural and functional features associated with Simple Sequence Proteins (SSPs are non-globularity, disease states, signaling and post-translational modification. SSPs are also an important source of genetic and possibly phenotypic variation. Analysis of 249 prokaryotic proteomes offers a new opportunity to examine the genomic properties of SSPs. Results SSPs are a minority but they grow with proteome size. This relationship is exhibited across species varying in genomic GC, mutational bias, life style, and pathogenicity. Their proportion in each proteome is strongly influenced by genomic base compositional bias. In most species simple duplications is favoured, but in a few cases such as Mycobacteria, large families of duplications occur. Amino acid preference in SSPs exhibits a trend towards low cost of biosynthesis. In SSPs and in non-SSPs, Alanine, Glycine, Leucine, and Valine are abundant in species widely varying in genomic GC whereas Isoleucine and Lysine are rich only in organisms with low genomic GC. Arginine is abundant in SSPs of two species and in the non-SSPs of Xanthomonas oryzae. Asparagine is abundant only in SSPs of low GC species. Aspartic acid is abundant only in the non-SSPs of Halobacterium sp NRC1. The abundance of Serine in SSPs of 62 species extends over a broader range compared to that of non-SSPs. Threonine(T is abundant only in SSPs of a couple of species. SSPs exhibit preferential association with Cell surface, Cell membrane and Transport functions and a negative association with Metabolism. Mesophiles and Thermophiles display similar ranges in the content of SSPs. Conclusion Although SSPs are a minority, the genomic forces of base compositional bias and duplications influence their growth and pattern in each species. The preferences and abundance of amino acids are governed by low biosynthetic cost, evolutionary age and base composition of codons. Abundance of charged amino acids Arginine

  20. Biogeography of photosynthetic light-harvesting genes in marine phytoplankton.

    Directory of Open Access Journals (Sweden)

    Thomas S Bibby

    Full Text Available BACKGROUND: Photosynthetic light-harvesting proteins are the mechanism by which energy enters the marine ecosystem. The dominant prokaryotic photoautotrophs are the cyanobacterial genera Prochlorococcus and Synechococcus that are defined by two distinct light-harvesting systems, chlorophyll-bound protein complexes or phycobilin-bound protein complexes, respectively. Here, we use the Global Ocean Sampling (GOS Project as a unique and powerful tool to analyze the environmental diversity of photosynthetic light-harvesting genes in relation to available metadata including geographical location and physical and chemical environmental parameters. METHODS: All light-harvesting gene fragments and their metadata were obtained from the GOS database, aligned using ClustalX and classified phylogenetically. Each sequence has a name indicative of its geographic location; subsequent biogeographical analysis was performed by correlating light-harvesting gene budgets for each GOS station with surface chlorophyll concentration. CONCLUSION/SIGNIFICANCE: Using the GOS data, we have mapped the biogeography of light-harvesting genes in marine cyanobacteria on ocean-basin scales and show that an environmental gradient exists in which chlorophyll concentration is correlated to diversity of light-harvesting systems. Three functionally distinct types of light-harvesting genes are defined: (1 the phycobilisome (PBS genes of Synechococcus; (2 the pcb genes of Prochlorococcus; and (3 the iron-stress-induced (isiA genes present in some marine Synechococcus. At low chlorophyll concentrations, where nutrients are limited, the Pcb-type light-harvesting system shows greater genetic diversity; whereas at high chlorophyll concentrations, where nutrients are abundant, the PBS-type light-harvesting system shows higher genetic diversity. We interpret this as an environmental selection of specific photosynthetic strategy. Importantly, the unique light-harvesting system isiA is found

  1. Effect of chromone-substituted benzothiazolium halides on photosynthetic processes

    International Nuclear Information System (INIS)

    Kralova, K.; Sersen, F.; Gasparova, R.; Lacova, M.

    1998-01-01

    The effects of 3-R 2 -2[2-(6-R 1 -chromone-3-yl)ethenyl]benzothiazolium halides (CBH) on photosynthetic electron transport in spinach chloroplasts and in the legal suspension of Chlorella vulgaris were investigated. Using EPR spectroscopy it was confirmed that these compounds containing in their molecules two heterocyclic skeletons, namely benzothiazole and chromone, interact with the intermediate D + , corresponding to the tyrosine radical Tyr D situated in D 2 protein on the donor side of photosystem 2. Consequently, higher concentrations of CBH inhibited oxygen evolution rate in Chlorella vulgaris and the inhibitory effectiveness depended on the lipophilicity of the of the compound. (authors)

  2. The Role of Prokaryotes in Sediment Carbon Cycling

    DEFF Research Database (Denmark)

    Piil, Kristoffer

    in the sediment. In particular, the work has focused on estimating how rapidly amino acids derived from plankton are degraded and replaced by amino acids from prokaryotes and how extensive this reworking of amino acids is in surface sediments. Another part of my work has focused on establishing reliable estimates...... of cell specific amino acid and muramic acid concentrations in sediment bacteria. Such estimates are important tools when studying the reworking of amino acids by bacteria and the preservation of bacterial cell walls. In addition, it has been an aim of the work to investigate how abundant endospores...... are in marine sediment and how dynamic the endospore population is, as very little is known about this compartment of the prokaryotic community. Prokaryotic reworking of amino acids was investigated by two independent methods. The first approach involved estimating the amount of amino acids produced...

  3. Prokaryotic DNA segregation by an actin-like filament

    DEFF Research Database (Denmark)

    Møller-Jensen, Jakob; Bugge Jensen, Rasmus; Löwe, Jan

    2002-01-01

    The mechanisms responsible for prokaryotic DNA segregation are largely unknown. The partitioning locus (par) encoded by the Escherichia coli plasmid R1 actively segregates its replicon to daughter cells. We show here that the ParM ATPase encoded by par forms dynamic actin-like filaments with prop...... point for ParM polymerization. Hence, we provide evidence for a simple prokaryotic analogue of the eukaryotic mitotic spindle apparatus.......The mechanisms responsible for prokaryotic DNA segregation are largely unknown. The partitioning locus (par) encoded by the Escherichia coli plasmid R1 actively segregates its replicon to daughter cells. We show here that the ParM ATPase encoded by par forms dynamic actin-like filaments...

  4. Triplet–triplet energy transfer in artificial and natural photosynthetic antennas

    OpenAIRE

    Ho, Junming; Kish, Elizabeth; Méndez-Hernández, Dalvin D.; WongCarter, Katherine; Pillai, Smitha; Kodis, Gerdenis; Niklas, Jens; Poluektov, Oleg G.; Gust, Devens; Moore, Thomas A.; Moore, Ana L.; Batista, Victor S.; Robert, Bruno

    2017-01-01

    Rapid chlorophyll-to-carotenoid triplet–triplet energy transfer (T-TET) in photosynthetic organisms is crucial to photoprotection from singlet oxygen. Photosynthesis reengineered for increased efficiency will result in increased oxygen levels in the cells, and the need to ensure adequately rapid T-TET will arise. Using a combination of theoretical and experimental studies on artificial and natural carotenoid–chlorophyll complexes, we have identified spectroscopic markers indicative of specifi...

  5. Viral Diversity Threshold for Adaptive Immunity in Prokaryotes

    Science.gov (United States)

    Weinberger, Ariel D.; Wolf, Yuri I.; Lobkovsky, Alexander E.; Gilmore, Michael S.; Koonin, Eugene V.

    2012-01-01

    ABSTRACT Bacteria and archaea face continual onslaughts of rapidly diversifying viruses and plasmids. Many prokaryotes maintain adaptive immune systems known as clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (Cas). CRISPR-Cas systems are genomic sensors that serially acquire viral and plasmid DNA fragments (spacers) that are utilized to target and cleave matching viral and plasmid DNA in subsequent genomic invasions, offering critical immunological memory. Only 50% of sequenced bacteria possess CRISPR-Cas immunity, in contrast to over 90% of sequenced archaea. To probe why half of bacteria lack CRISPR-Cas immunity, we combined comparative genomics and mathematical modeling. Analysis of hundreds of diverse prokaryotic genomes shows that CRISPR-Cas systems are substantially more prevalent in thermophiles than in mesophiles. With sequenced bacteria disproportionately mesophilic and sequenced archaea mostly thermophilic, the presence of CRISPR-Cas appears to depend more on environmental temperature than on bacterial-archaeal taxonomy. Mutation rates are typically severalfold higher in mesophilic prokaryotes than in thermophilic prokaryotes. To quantitatively test whether accelerated viral mutation leads microbes to lose CRISPR-Cas systems, we developed a stochastic model of virus-CRISPR coevolution. The model competes CRISPR-Cas-positive (CRISPR-Cas+) prokaryotes against CRISPR-Cas-negative (CRISPR-Cas−) prokaryotes, continually weighing the antiviral benefits conferred by CRISPR-Cas immunity against its fitness costs. Tracking this cost-benefit analysis across parameter space reveals viral mutation rate thresholds beyond which CRISPR-Cas cannot provide sufficient immunity and is purged from host populations. These results offer a simple, testable viral diversity hypothesis to explain why mesophilic bacteria disproportionately lack CRISPR-Cas immunity. More generally, fundamental limits on the adaptability of biological

  6. Copahue Geothermal System: A Volcanic Environment with Rich Extreme Prokaryotic Biodiversity.

    Science.gov (United States)

    Urbieta, María Sofía; Porati, Graciana Willis; Segretín, Ana Belén; González-Toril, Elena; Giaveno, María Alejandra; Donati, Edgardo Rubén

    2015-07-08

    The Copahue geothermal system is a natural extreme environment located at the northern end of the Cordillera de los Andes in Neuquén province in Argentina. The geochemistry and consequently the biodiversity of the area are dominated by the activity of the Copahue volcano. The main characteristic of Copahue is the extreme acidity of its aquatic environments; ponds and hot springs of moderate and high temperature as well as Río Agrio. In spite of being an apparently hostile location, the prokaryotic biodiversity detected by molecular ecology techniques as well as cultivation shows a rich and diverse environment dominated by acidophilic, sulphur oxidising bacteria or archaea, depending on the conditions of the particular niche studied. In microbial biofilms, found in the borders of the ponds where thermal activity is less intense, the species found are completely different, with a high presence of cyanobacteria and other photosynthetic species. Our results, collected during more than 10 years of work in Copahue, have enabled us to outline geomicrobiological models for the different environments found in the ponds and Río Agrio. Besides, Copahue seems to be the habitat of novel, not yet characterised autochthonous species, especially in the domain Archaea.

  7. Copahue Geothermal System: A Volcanic Environment with Rich Extreme Prokaryotic Biodiversity

    Directory of Open Access Journals (Sweden)

    María Sofía Urbieta

    2015-07-01

    Full Text Available The Copahue geothermal system is a natural extreme environment located at the northern end of the Cordillera de los Andes in Neuquén province in Argentina. The geochemistry and consequently the biodiversity of the area are dominated by the activity of the Copahue volcano. The main characteristic of Copahue is the extreme acidity of its aquatic environments; ponds and hot springs of moderate and high temperature as well as Río Agrio. In spite of being an apparently hostile location, the prokaryotic biodiversity detected by molecular ecology techniques as well as cultivation shows a rich and diverse environment dominated by acidophilic, sulphur oxidising bacteria or archaea, depending on the conditions of the particular niche studied. In microbial biofilms, found in the borders of the ponds where thermal activity is less intense, the species found are completely different, with a high presence of cyanobacteria and other photosynthetic species. Our results, collected during more than 10 years of work in Copahue, have enabled us to outline geomicrobiological models for the different environments found in the ponds and Río Agrio. Besides, Copahue seems to be the habitat of novel, not yet characterised autochthonous species, especially in the domain Archaea.

  8. Photosynthetic light reactions at the gold interface

    NARCIS (Netherlands)

    Kamran, Muhammad

    2014-01-01

    In the project described in this thesis we studied a simple bio-electronic device for solar energy conversion by surface-assembly of photosynthetic pigment-protein complexes on a bare gold-electrode. Optical excitation of the photosynthetic pigments gives rise to charge separation in the so-called

  9. Use of in vivo chlorophyll fluorescence to estimate photosynthetic activity and biomass productivity in microalgae grown in different culture systems

    Directory of Open Access Journals (Sweden)

    Félix L Figueroa

    2013-11-01

    Full Text Available In vivo chlorophyll fluorescence associated to Photosystem II is being used to evaluate photosynthetic activity of microalgae grown in different types of photobioreactors; however, controversy on methodology is usual. Several recommendations on the use of chlorophyll fluorescence to estimate electron transport rate and productivity of microalgae grown in thin-layer cascade cultivators and methacrylate cylindrical vessels are included. Different methodologies related to the measure of photosynthetic activity in microalgae are discussed: (1 measurement of light absorption, (2 determination of electron transport rates versus irradiance and (3 use of simplified devices based on pulse amplitude modulated (PAM fluorescence as Junior PAM or Pocket PAM with optical fiber and optical head as measuring units, respectively. Data comparisons of in vivo chlorophyll fluorescence by using these devices and other PAM fluorometers as Water-PAM in the microalga Chlorella sp. (Chlorophyta are presented. Estimations of carbon production and productivity by transforming electron transport rate to gross photosynthetic rate (as oxygen evolution using reported oxygen produced per photons absorbed values and carbon photosynthetic yield based on reported oxygen/carbon ratio are also shown. The limitation of ETR as estimator of photosynthetic and biomass productivity is discussed. Low cost:quality PAMs can promote monitoring of chlorophyll fluorescence in algal biotechnology to estimate the photosynthetic activity and biomass productivity.

  10. R-prime site-directed transposon Tn7 mutagenesis of the photosynthetic apparatus in Rhodopseudomonas capsulata

    Energy Technology Data Exchange (ETDEWEB)

    Youvan, D C [Univ. of California, Berkeley; Elder, J T; Sandlin, D E; Zsebo, K; Alder, D P; Panopoulos, N J; Marrs, B L; Hearst, J E

    1982-01-01

    Site-directed mutagenesis of the photosynthetic apparatus (PSA) genes in Rhodopseudomonas capsulata is presented utilizing a transposon Tn7 mutagenized R-prime. The R-prime, pRPS404, bears most of the genes necessary for the differentiation of the photosynthetic apparatus. Mutagenesis of the R-prime with Tn7 in Escherichia coli, conjugation into R. capsulata, and homologous recombination with the wild-type alleles efficiently generates photosynthetic apparatus lesions. Wild-type alleles are lost spontaneously and the Tn7-induced lesions are revealed by subsequent intramolecular recombination between IS21 insertion elements that bracket the prime sequences in direct repeat. The molecular nature of the intermediates involved in the transposition, recombination and deletion have been investigated by Southern hybridization analysis. The spontaneous loss of wild-type alleles after homologous recombination with the chromosome may be of general use to other prokaryotic site-directed transposon mutagenesis schemes. The IS21-mediated deletion of the prime DNA is dependent on the RecA protein in E. coli, generating the parental R-factor bearing one IS21 element. A genetic-physical map exists for a portion of the prime photosynthetic apparatus DNA. When Tn7 is inserted into a bacteriochlorophyll gene in the R-prime and then crossed into R. capsulata, mutants are produced that accumulate a bacteriochlorophyll precursor, which is in excellent agreement with the existing genetic-physical map. This corroborates the mutagenesis scheme.

  11. Construction and prokaryotic expression of the fusion gene PRRSV ...

    African Journals Online (AJOL)

    ajl4

    2013-07-24

    Jul 24, 2013 ... The fusion expressing plasmid pET32-GP5-Hsp70 was constructed and expressed in ... 2004). Hsps, expressed by prokaryotes and eukaryotes and their action as molecular ..... Facts, thoughts, and dreams. Shock. 12(4): ...

  12. Top-Down Control of Diesel-Degrading Prokaryotic Communities.

    Science.gov (United States)

    Sauret, Caroline; Böttjer, Daniela; Talarmin, Agathe; Guigue, Catherine; Conan, Pascal; Pujo-Pay, Mireille; Ghiglione, Jean-François

    2015-08-01

    Biostimulation through the addition of inorganic nutrients has been the most widely practiced bioremediation strategy in oil-polluted marine waters. However, little attention has so far been paid to the microbial food web and the impact of top-down control that directly or indirectly influences the success of the bioremediation. We designed a mesocosm experiment using pre-filtered (diesel fuel. Prokaryotes, HNF and VLP abundances showed a predator-prey succession, with a co-development of HNF and VLP. In the polluted system, we observed a stronger impact of viral lysis on prokaryotic abundances than in the control. Analysis of the diversity revealed that a bloom of Vibrio sp. occurred in the polluted mesocosm. That bloom was rapidly followed by a less abundant and more even community of predation-resistant bacteria, including known hydrocarbon degraders such as Oleispira spp. and Methylophaga spp. and opportunistic bacteria such as Percisivirga spp., Roseobacter spp. and Phaeobacter spp. The shift in prokaryotic dominance in response to viral lysis provided clear evidence of the 'killing the winner' model. Nevertheless, despite clear effects on prokaryotic abundance, activity and diversity, the diesel degradation was not impacted by top-down control. The present study investigates for the first time the functioning of a complex microbial network (including VLP) using a nutrient-based biostimulation strategy and highlights some key processes useful for tailoring bioremediation.

  13. Small CRISPR RNAs guide antiviral defense in prokaryotes

    NARCIS (Netherlands)

    Brouns, S.J.J.; Jore, M.M.; Lundgren, M.; Westra, E.R.; Slijkhuis, R.J.; Snijders, A.P.; Dickman, M.J.; Makarova, K.S.; Koonin, E.V.; Oost, van der J.

    2008-01-01

    Prokaryotes acquire virus resistance by integrating short fragments of viral nucleic acid into clusters of regularly interspaced short palindromic repeats (CRISPRs). Here we show how virus-derived sequences contained in CRISPRs are used by CRISPR-associated (Cas) proteins from the host to mediate an

  14. Do marine natural products interfere with prokaryotic AHL regulatory systems?

    DEFF Research Database (Denmark)

    Kjelleberg, S.; Steinberg, P.; Givskov, Michael Christian

    1997-01-01

    Recent studies indicate that a taxonomically diverse range of marine eukaryotes produce metabolites which inhibit phenotypic traits in bacteria, with no or minimal effects on growth. In this review, we present evidence for the existence of such eukaryotic interference with a conserved prokaryotic...

  15. RNA in defense: CRISPRs protect prokaryotes against mobile genetic elements

    NARCIS (Netherlands)

    Jore, M.M.; Brouns, S.J.J.; Oost, van der J.

    2012-01-01

    The CRISPR/Cas system in prokaryotes provides resistance against invading viruses and plasmids. Three distinct stages in the mechanism can be recognized. Initially, fragments of invader DNA are integrated as new spacers into the repetitive CRISPR locus. Subsequently, the CRISPR is transcribed and

  16. Global diversity and biogeography of deep-sea pelagic prokaryotes

    KAUST Repository

    Salazar, Guillem

    2015-08-07

    The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean\\'s microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (∼3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.

  17. Global diversity and biogeography of deep-sea pelagic prokaryotes

    KAUST Repository

    Salazar, Guillem; Cornejo-Castillo, Francisco M.; Bení tez-Barrios, Veró nica; Fraile-Nuez, Eugenio; Á lvarez-Salgado, X. Antó n; Duarte, Carlos M.; Gasol, Josep M.; Acinas, Silvia G.

    2015-01-01

    The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (∼3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered.

  18. Gene duplications in prokaryotes can be associated with environmental adaptation.

    Science.gov (United States)

    Bratlie, Marit S; Johansen, Jostein; Sherman, Brad T; Huang, Da Wei; Lempicki, Richard A; Drabløs, Finn

    2010-10-20

    Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likely to be beneficial to the organism, e.g. in adaptation to new environmental conditions. The aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relating gene properties to life style of the corresponding prokaryotes. Paralogs were identified in a number of prokaryotes, and these paralogs were compared to singletons of persistent orthologs based on functional classification. This showed that the paralogs were associated with for example energy production, cell motility, ion transport, and defence mechanisms. A statistical overrepresentation analysis of gene and protein annotations was based on paralogs of the 200 prokaryotes with the highest fraction of paralog-forming genes. Biclustering of overrepresented gene ontology terms versus species was used to identify clusters of properties associated with clusters of species. The clusters were classified using similarity scores on properties and species to identify interesting clusters, and a subset of clusters were analysed by comparison to literature data. This analysis showed that paralogs often are associated with properties that are important for survival and proliferation of the specific organisms. This includes processes like ion transport, locomotion, chemotaxis and photosynthesis. However, the analysis also showed that the gene ontology terms sometimes were too general, imprecise or even misleading for automatic analysis. Properties described by gene ontology terms identified in the overrepresentation analysis are often consistent with individual prokaryote lifestyles and are likely to give a competitive advantage to the organism. Paralogs and singletons dominate

  19. Gene duplications in prokaryotes can be associated with environmental adaptation

    Directory of Open Access Journals (Sweden)

    Lempicki Richard A

    2010-10-01

    Full Text Available Abstract Background Gene duplication is a normal evolutionary process. If there is no selective advantage in keeping the duplicated gene, it is usually reduced to a pseudogene and disappears from the genome. However, some paralogs are retained. These gene products are likely to be beneficial to the organism, e.g. in adaptation to new environmental conditions. The aim of our analysis is to investigate the properties of paralog-forming genes in prokaryotes, and to analyse the role of these retained paralogs by relating gene properties to life style of the corresponding prokaryotes. Results Paralogs were identified in a number of prokaryotes, and these paralogs were compared to singletons of persistent orthologs based on functional classification. This showed that the paralogs were associated with for example energy production, cell motility, ion transport, and defence mechanisms. A statistical overrepresentation analysis of gene and protein annotations was based on paralogs of the 200 prokaryotes with the highest fraction of paralog-forming genes. Biclustering of overrepresented gene ontology terms versus species was used to identify clusters of properties associated with clusters of species. The clusters were classified using similarity scores on properties and species to identify interesting clusters, and a subset of clusters were analysed by comparison to literature data. This analysis showed that paralogs often are associated with properties that are important for survival and proliferation of the specific organisms. This includes processes like ion transport, locomotion, chemotaxis and photosynthesis. However, the analysis also showed that the gene ontology terms sometimes were too general, imprecise or even misleading for automatic analysis. Conclusions Properties described by gene ontology terms identified in the overrepresentation analysis are often consistent with individual prokaryote lifestyles and are likely to give a competitive

  20. Cyanobacteria: photosynthetic factories combining biodiversity, radiation resistance, and genetics to facilitate drug discovery.

    Science.gov (United States)

    Cassier-Chauvat, Corinne; Dive, Vincent; Chauvat, Franck

    2017-02-01

    Cyanobacteria are ancient, abundant, and widely diverse photosynthetic prokaryotes, which are viewed as promising cell factories for the ecologically responsible production of chemicals. Natural cyanobacteria synthesize a vast array of biologically active (secondary) metabolites with great potential for human health, while a few genetic models can be engineered for the (low level) production of biofuels. Recently, genome sequencing and mining has revealed that natural cyanobacteria have the capacity to produce many more secondary metabolites than have been characterized. The corresponding panoply of enzymes (polyketide synthases and non-ribosomal peptide synthases) of interest for synthetic biology can still be increased through gene manipulations with the tools available for the few genetically manipulable strains. In this review, we propose to exploit the metabolic diversity and radiation resistance of cyanobacteria, and when required the genetics of model strains, for the production and radioactive ( 14 C) labeling of bioactive products, in order to facilitate the screening for new drugs.

  1. Differential impact of lytic viruses on prokaryotic morphopopulations in a tropical estuarine system (Cochin estuary, India).

    Science.gov (United States)

    Jasna, Vijayan; Pradeep Ram, Angia Sriram; Parvathi, Ammini; Sime-Ngando, Telesphore

    2018-01-01

    Our understanding on the importance of viral lysis in the functioning of tropical estuarine ecosystem is limited. This study examines viral infection of prokaryotes and subsequent lysis of cells belonging to different morphotypes across a salinity gradient in monsoon driven estuarine ecosystem (Cochin estuary, India). High standing stock of viruses and prokaryotes accompanied by lytic infection rates in the euryhaline/mesohaline region of the estuary suggests salinity to have an influential role in driving interactions between prokaryotes and viruses. High prokaryotic mortality rates, up to 42% of prokaryote population in the pre-monsoon season is further substantiated by a high virus to prokaryote ratio (VPR), suggesting that maintenance of a high number of viruses is dependent on the most active fraction of bacterioplankton. Although myoviruses were the dominant viral morphotype (mean = 43%) throughout the study period, there was significant variation among prokaryotic morphotypes susceptible to viral infection. Among them, the viral infected short rod prokaryote morphotype with lower burst estimates (mean = 18 viruses prokaryote-1) was dominant (35%) in the dry seasons whereas a substantial increase in cocci forms (30%) infected by viruses with high burst size (mean = 31 viruses prokaryote-1) was evident during the monsoon season. Such preferential infections of prokaryotic morphopopulations with respect to seasons can have a strong and variable impact on the carbon and energy flow in this tropical ecosystem.

  2. Nitric Oxide is Required for Homeostasis of Oxygen and Reactive Oxygen Species in Barley Roots under Aerobic Conditions

    DEFF Research Database (Denmark)

    Gupta, Kapuganti J; Hebelstrup, Kim; Kruger, Nicholas J

    2014-01-01

    Oxygen, the terminal electron acceptor for mitochondrial electron transport, is vital for plants because of its role in the production of ATP by oxidative phosphorylation. While photosynthetic oxygen production contributes to the oxygen supply in leaves, reducing the risk of oxygen limitation of ...... electron transport chain (Gupta et al., 2011). Thus, NO could influence oxygen consumption under normal aerobic conditions in roots, and it is this specific function that is assessed here.......Oxygen, the terminal electron acceptor for mitochondrial electron transport, is vital for plants because of its role in the production of ATP by oxidative phosphorylation. While photosynthetic oxygen production contributes to the oxygen supply in leaves, reducing the risk of oxygen limitation...

  3. Geochemical Interactions and Viral-Prokaryote Relationships in Freshwater Environments

    Science.gov (United States)

    Kyle, J. E.; Ferris, G.

    2009-05-01

    Viral and prokaryotic abundances were surveyed throughout southern Ontario aquatic habitats to determine relationships with geochemical parameters in the natural environment. Surface water samples were collected from acid mine drainage in summer of 2007 and 2008 and from circum-neutral pH environments in October to November 2008. Site determination was based on collecting samples from various aquatic habitats (acid mine drainage, lakes, rivers, tributaries, wetlands) with differing bedrock geology (limestone and shale dominated vs granitic Canadian Shield) to obtain a range of geochemical conditions. At each site, measurements of temperature, pH, and Eh were conducted. Samples collected for microbial counts and electron imaging were preserved to a final concentration of 2.5 % (v/v) glutaraldehyde. Additional sample were filtered into 60 mL nalgene bottles and amber EPA certified 40 mL glass vials to determine chemical constituents and dissolved organic carbon (DOC), respectively. Water was also collected to determine additional physiochemical parameters (dissolved total iron, ferric iron, nitrate, sulfate, phosphate, alkalinity, and turbidity). All samples were stored at 4 °C until analysis. Viral and prokaryotic abundance was determined by staining samples with SYBR Green I and examining with a epifluorescence microscope under blue excitation. Multiple regression analysis using stepwise backwards regression and general linear models revealed that viral abundance was the most influential predictor of prokaryotic abundance. Additional predictors include pH, sulfate, phosphate, and magnesium. The strength of the model was very strong with 90 % of the variability explained (R2 = 0.90, p < 0.007). This is the first report, to our knowledge, of viruses exhibiting such strong controls over prokaryotic abundance in the natural environment. All relationships are positively correlated with the exception of Mg, which is negatively correlated. Iron was also noted as a

  4. Hybrid system of semiconductor and photosynthetic protein

    International Nuclear Information System (INIS)

    Kim, Younghye; Shin, Seon Ae; Lee, Jaehun; Yang, Ki Dong; Nam, Ki Tae

    2014-01-01

    Photosynthetic protein has the potential to be a new attractive material for solar energy absorption and conversion. The development of semiconductor/photosynthetic protein hybrids is an example of recent progress toward efficient, clean and nanostructured photoelectric systems. In the review, two biohybrid systems interacting through different communicating methods are addressed: (1) a photosynthetic protein immobilized semiconductor electrode operating via electron transfer and (2) a hybrid of semiconductor quantum dots and photosynthetic protein operating via energy transfer. The proper selection of materials and functional and structural modification of the components and optimal conjugation between them are the main issues discussed in the review. In conclusion, we propose the direction of future biohybrid systems for solar energy conversion systems, optical biosensors and photoelectric devices. (topical reviews)

  5. Separation, identification and quantification of photosynthetic ...

    African Journals Online (AJOL)

    Thirty one photosynthetic pigments (chlorophylls, carotenoids and degradation products) from the seaweeds, Codium dwarkense, (Chlorophyta), , Laurencia obtusa , (Rhodophyta) and , Lobophora variegata, (Phaeophyta), were separated in a single-step procedure by reversed phase high-performance liquid ...

  6. The adaptive response of lichens to mercury exposure involves changes in the photosynthetic machinery

    International Nuclear Information System (INIS)

    Nicolardi, Valentina; Cai, Giampiero; Parrotta, Luigi; Puglia, Michele; Bianchi, Laura; Bini, Luca; Gaggi, Carlo

    2012-01-01

    Lichens are an excellent model to study the bioaccumulation of heavy metals but limited information is available on the molecular mechanisms occurring during bioaccumulation. We investigated the changes of the lichen proteome during exposure to constant concentrations of mercury. We found that most of changes involves proteins of the photosynthetic pathway, such as the chloroplastic photosystem I reaction center subunit II, the oxygen-evolving protein and the chloroplastic ATP synthase β-subunit. This suggests that photosynthesis is a target of the toxic effects of mercury. These findings are also supported by changes in the content of photosynthetic pigments (chlorophyll a and b, and β-carotene). Alterations to the photosynthetic machinery also reflect on the structure of thylakoid membranes of algal cells. Response of lichens to mercury also involves stress-related proteins (such as Hsp70) but not cytoskeletal proteins. Results suggest that lichens adapt to mercury exposure by changing the metabolic production of energy. - Highlights: ► Lichens exposed to Hg° vapors accumulate this metal irreversibly. ► Hg° interferes with physiological processes of the epiphytic lichen Evernia prunastri. ► Hg° promotes changes in the concentration of photosynthetic pigments. ► Hg° treatment causes changes in the ultrastructure of the photobiont plastids. ► Hg° induces changes in the protein machinery involved in the photosynthesis pathway. - Mercury affects the photosynthetic protein machinery of lichens.

  7. Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways

    KAUST Repository

    Saidi, Rabie

    2017-08-28

    It is becoming more evident that computational methods are needed for the identification and the mapping of pathways in new genomes. We introduce an automatic annotation system (ARBA4Path Association Rule-Based Annotator for Pathways) that utilizes rule mining techniques to predict metabolic pathways across wide range of prokaryotes. It was demonstrated that specific combinations of protein domains (recorded in our rules) strongly determine pathways in which proteins are involved and thus provide information that let us very accurately assign pathway membership (with precision of 0.999 and recall of 0.966) to proteins of a given prokaryotic taxon. Our system can be used to enhance the quality of automatically generated annotations as well as annotating proteins with unknown function. The prediction models are represented in the form of human-readable rules, and they can be used effectively to add absent pathway information to many proteins in UniProtKB/TrEMBL database.

  8. Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways

    KAUST Repository

    Saidi, Rabie; Boudellioua, Imene; Martin, Maria J.; Solovyev, Victor

    2017-01-01

    It is becoming more evident that computational methods are needed for the identification and the mapping of pathways in new genomes. We introduce an automatic annotation system (ARBA4Path Association Rule-Based Annotator for Pathways) that utilizes rule mining techniques to predict metabolic pathways across wide range of prokaryotes. It was demonstrated that specific combinations of protein domains (recorded in our rules) strongly determine pathways in which proteins are involved and thus provide information that let us very accurately assign pathway membership (with precision of 0.999 and recall of 0.966) to proteins of a given prokaryotic taxon. Our system can be used to enhance the quality of automatically generated annotations as well as annotating proteins with unknown function. The prediction models are represented in the form of human-readable rules, and they can be used effectively to add absent pathway information to many proteins in UniProtKB/TrEMBL database.

  9. Patterns of prokaryotic lateral gene transfers affecting parasitic microbial eukaryotes

    DEFF Research Database (Denmark)

    Alsmark, Cecilia; Foster, Peter G; Sicheritz-Pontén, Thomas

    2013-01-01

    BACKGROUND: The influence of lateral gene transfer on gene origins and biology in eukaryotes is poorly understood compared with those of prokaryotes. A number of independent investigations focusing on specific genes, individual genomes, or specific functional categories from various eukaryotes have...... approach to systematically investigate lateral gene transfer affecting the proteomes of thirteen, mainly parasitic, microbial eukaryotes, representing four of the six eukaryotic super-groups. All of the genomes investigated have been significantly affected by prokaryote-to-eukaryote lateral gene transfers...... indicated that lateral gene transfer does indeed affect eukaryotic genomes. However, the lack of common methodology and criteria in these studies makes it difficult to assess the general importance and influence of lateral gene transfer on eukaryotic genome evolution. RESULTS: We used a phylogenomic...

  10. Trends and barriers to lateral gene transfer in prokaryotes.

    Science.gov (United States)

    Popa, Ovidiu; Dagan, Tal

    2011-10-01

    Gene acquisition by lateral gene transfer (LGT) is an important mechanism for natural variation among prokaryotes. Laboratory experiments show that protein-coding genes can be laterally transferred extremely fast among microbial cells, inherited to most of their descendants, and adapt to a new regulatory regime within a short time. Recent advance in the phylogenetic analysis of microbial genomes using networks approach reveals a substantial impact of LGT during microbial genome evolution. Phylogenomic networks of LGT among prokaryotes reconstructed from completely sequenced genomes uncover barriers to LGT in multiple levels. Here we discuss the kinds of barriers to gene acquisition in nature including physical barriers for gene transfer between cells, genomic barriers for the integration of acquired DNA, and functional barriers for the acquisition of new genes. Copyright © 2011 Elsevier Ltd. All rights reserved.

  11. Proteolytic enzymes in seawater: contribution of prokaryotes and protists

    Science.gov (United States)

    Obayashi, Y.; Suzuki, S.

    2016-02-01

    Proteolytic enzyme is one of the major catalysts of microbial processing of organic matter in biogeochemical cycle. Here we summarize some of our studies about proteases in seawater, including 1) distribution of protease activities in coastal and oceanic seawater, 2) responses of microbial community and protease activities in seawater to organic matter amending, and 3) possible contribution of heterotrophic protists besides prokaryotes to proteases in seawater, to clarify cleared facts and remaining questions. Activities of aminopeptidases, trypsin-type and chymotrypsin-type proteases were detected from both coastal and oceanic seawater by using MCA-substrate assay. Significant activities were detected from not only particulate (cell-associated) fraction but also dissolved fraction of seawater, especially for trypsin-type and chymotrypsin-type proteases. Hydrolytic enzymes in seawater have been commonly thought to be mainly derived from heterotrophic prokaryotes; however, it was difficult to determine actual source organisms of dissolved enzymes in natural seawater. Our experiment with addition of dissolved protein to subtropical oligotrophic Pacific water showed drastically enhancement of the protease activities especially aminopeptidases in seawater, and the prokaryotic community structure simultaneously changed to be dominant of Bacteroidetes, indicating that heterotrophic bacteria were actually one of the sources of proteases in seawater. Another microcosm experiment with free-living marine heterotrophic ciliate Paranophrys marina together with an associated bacterium showed that extracellular trypsin-type activity was mainly attributed to the ciliate. The protist seemed to work in organic matter digestion in addition to be a grazer. From the results, we propose a system of organic matter digestion by prokaryotes and protists in aquatic environments, although their actual contribution in natural environments should be estimated in future studies.

  12. A quantitative account of genomic island acquisitions in prokaryotes

    Directory of Open Access Journals (Sweden)

    Roos Tom E

    2011-08-01

    Full Text Available Abstract Background Microbial genomes do not merely evolve through the slow accumulation of mutations, but also, and often more dramatically, by taking up new DNA in a process called horizontal gene transfer. These innovation leaps in the acquisition of new traits can take place via the introgression of single genes, but also through the acquisition of large gene clusters, which are termed Genomic Islands. Since only a small proportion of all the DNA diversity has been sequenced, it can be hard to find the appropriate donors for acquired genes via sequence alignments from databases. In contrast, relative oligonucleotide frequencies represent a remarkably stable genomic signature in prokaryotes, which facilitates compositional comparisons as an alignment-free alternative for phylogenetic relatedness. In this project, we test whether Genomic Islands identified in individual bacterial genomes have a similar genomic signature, in terms of relative dinucleotide frequencies, and can therefore be expected to originate from a common donor species. Results When multiple Genomic Islands are present within a single genome, we find that up to 28% of these are compositionally very similar to each other, indicative of frequent recurring acquisitions from the same donor to the same acceptor. Conclusions This represents the first quantitative assessment of common directional transfer events in prokaryotic evolutionary history. We suggest that many of the resident Genomic Islands per prokaryotic genome originated from the same source, which may have implications with respect to their regulatory interactions, and for the elucidation of the common origins of these acquired gene clusters.

  13. [Experimental interaction of halophilic prokaryotes and opportunistic bacteria in brine].

    Science.gov (United States)

    Selivanova, E A; Nemtseva, N V

    2013-01-01

    Study the effect of extremely halophilic archaea and moderately halophilic bacteria on preservation of opportunistic bacteria in brine. 17 strains of moderately halophilic bacteria and 2 strains of extremely halophilic archaea were isolated from continental hypersaline lake Razval of Sol-Iletsk area of Orenburg Region. Identification of pure cultures of prokaryotes was carried out taking into account their phenotype properties and based on determination of 16S RNA gene sequence. The effect of halophilic prokaryote on elimination of Escherichia coli from brine was evaluated during co-cultivation. Antagonistic activity of cell extracts of the studied microorganisms was evaluated by photometric method. A more prolonged preservation of an E. coli strain in brine in the presence of live cells of extremely halophilic archaea Halorubrum tebenquichense and moderately halophilic bacteria Marinococcus halophilus was established. Extracts of cells of extremely halophilic archaea and moderately halophilic bacteria on the contrary displayed antagonistic activity. The protective effect of live cells of halophilic prokaryotes and antagonistic activity of their cell extracts change the period of conservation of opportunistic bacteria in brine that regulates inter-microbial interactions and changes the period of self-purification that reflects the sanitary condition of a hypersaline water body.

  14. Prokaryotic cells: structural organisation of the cytoskeleton and organelles

    Directory of Open Access Journals (Sweden)

    Wanderley de Souza

    2012-05-01

    Full Text Available For many years, prokaryotic cells were distinguished from eukaryotic cells based on the simplicity of their cytoplasm, in which the presence of organelles and cytoskeletal structures had not been discovered. Based on current knowledge, this review describes the complex components of the prokaryotic cell cytoskeleton, including (i tubulin homologues composed of FtsZ, BtuA, BtuB and several associated proteins, which play a fundamental role in cell division, (ii actin-like homologues, such as MreB and Mb1, which are involved in controlling cell width and cell length, and (iii intermediate filament homologues, including crescentin and CfpA, which localise on the concave side of a bacterium and along its inner curvature and associate with its membrane. Some prokaryotes exhibit specialised membrane-bound organelles in the cytoplasm, such as magnetosomes and acidocalcisomes, as well as protein complexes, such as carboxysomes. This review also examines recent data on the presence of nanotubes, which are structures that are well characterised in mammalian cells that allow direct contact and communication between cells.

  15. The prokaryote-eukaryote dichotomy: meanings and mythology.

    Science.gov (United States)

    Sapp, Jan

    2005-06-01

    Drawing on documents both published and archival, this paper explains how the prokaryote-eukaryote dichotomy of the 1960s was constructed, the purposes it served, and what it implied in terms of classification and phylogeny. In doing so, I first show how the concept was attributed to Edouard Chatton and the context in which he introduced the terms. Following, I examine the context in which the terms were reintroduced into biology in 1962 by Roger Stanier and C. B. van Niel. I study the discourse over the subsequent decade to understand how the organizational dichotomy took on the form of a natural classification as the kingdom Monera or superkingdom Procaryotae. Stanier and van Niel admitted that, in regard to constructing a natural classification of bacteria, structural characteristics were no more useful than physiological properties. They repeatedly denied that bacterial phylogenetics was possible. I thus examine the great historical irony that the "prokaryote," in both its organizational and phylogenetic senses, was defined (negatively) on the basis of structure. Finally, we see how phylogenetic research based on 16S rRNA led by Carl Woese and his collaborators confronted the prokaryote concept while moving microbiology to the center of evolutionary biology.

  16. A computational genomics pipeline for prokaryotic sequencing projects.

    Science.gov (United States)

    Kislyuk, Andrey O; Katz, Lee S; Agrawal, Sonia; Hagen, Matthew S; Conley, Andrew B; Jayaraman, Pushkala; Nelakuditi, Viswateja; Humphrey, Jay C; Sammons, Scott A; Govil, Dhwani; Mair, Raydel D; Tatti, Kathleen M; Tondella, Maria L; Harcourt, Brian H; Mayer, Leonard W; Jordan, I King

    2010-08-01

    New sequencing technologies have accelerated research on prokaryotic genomes and have made genome sequencing operations outside major genome sequencing centers routine. However, no off-the-shelf solution exists for the combined assembly, gene prediction, genome annotation and data presentation necessary to interpret sequencing data. The resulting requirement to invest significant resources into custom informatics support for genome sequencing projects remains a major impediment to the accessibility of high-throughput sequence data. We present a self-contained, automated high-throughput open source genome sequencing and computational genomics pipeline suitable for prokaryotic sequencing projects. The pipeline has been used at the Georgia Institute of Technology and the Centers for Disease Control and Prevention for the analysis of Neisseria meningitidis and Bordetella bronchiseptica genomes. The pipeline is capable of enhanced or manually assisted reference-based assembly using multiple assemblers and modes; gene predictor combining; and functional annotation of genes and gene products. Because every component of the pipeline is executed on a local machine with no need to access resources over the Internet, the pipeline is suitable for projects of a sensitive nature. Annotation of virulence-related features makes the pipeline particularly useful for projects working with pathogenic prokaryotes. The pipeline is licensed under the open-source GNU General Public License and available at the Georgia Tech Neisseria Base (http://nbase.biology.gatech.edu/). The pipeline is implemented with a combination of Perl, Bourne Shell and MySQL and is compatible with Linux and other Unix systems.

  17. Depth Dependent Relationships between Temperature and Ocean Heterotrophic Prokaryotic Production

    KAUST Repository

    Lønborg, Christian

    2016-06-07

    Marine prokaryotes play a key role in cycling of organic matter and nutrients in the ocean. Using a unique dataset (>14,500 samples), we applied a space-for-time substitution analysis to assess the temperature dependence of prokaryotic heterotrophic production (PHP) in epi- (0-200 m), meso- (201-1000 m) and bathypelagic waters (1001-4000 m) of the global ocean. Here, we show that the temperature dependence of PHP is fundamentally different between these major oceanic depth layers, with an estimated ecosystem-level activation energy (E) of 36 ± 7 kJ mol for the epipelagic, 72 ± 15 kJ mol for the mesopelagic and 274 ± 65 kJ mol for the bathypelagic realm. We suggest that the increasing temperature dependence with depth is related to the parallel vertical gradient in the proportion of recalcitrant organic compounds. These Ea predict an increased PHP of about 5, 12, and 55% in the epi-, meso-, and bathypelagic ocean, respectively, in response to a water temperature increase by 1°C. Hence, there is indication that a major thus far underestimated feedback mechanism exists between future bathypelagic ocean warming and heterotrophic prokaryotic activity.

  18. Depth Dependent Relationships between Temperature and Ocean Heterotrophic Prokaryotic Production

    KAUST Repository

    Lø nborg, Christian; Cuevas, L. Antonio; Reinthaler, Thomas; Herndl, Gerhard J.; Gasol, Josep M.; Moran, Xose Anxelu G.; Bates, Nicholas R.; á lvarez-Salgado, Xosé A.

    2016-01-01

    Marine prokaryotes play a key role in cycling of organic matter and nutrients in the ocean. Using a unique dataset (>14,500 samples), we applied a space-for-time substitution analysis to assess the temperature dependence of prokaryotic heterotrophic production (PHP) in epi- (0-200 m), meso- (201-1000 m) and bathypelagic waters (1001-4000 m) of the global ocean. Here, we show that the temperature dependence of PHP is fundamentally different between these major oceanic depth layers, with an estimated ecosystem-level activation energy (E) of 36 ± 7 kJ mol for the epipelagic, 72 ± 15 kJ mol for the mesopelagic and 274 ± 65 kJ mol for the bathypelagic realm. We suggest that the increasing temperature dependence with depth is related to the parallel vertical gradient in the proportion of recalcitrant organic compounds. These Ea predict an increased PHP of about 5, 12, and 55% in the epi-, meso-, and bathypelagic ocean, respectively, in response to a water temperature increase by 1°C. Hence, there is indication that a major thus far underestimated feedback mechanism exists between future bathypelagic ocean warming and heterotrophic prokaryotic activity.

  19. Photoelectrochemical cells based on photosynthetic systems: a review

    Directory of Open Access Journals (Sweden)

    Roman A. Voloshin

    2015-06-01

    Full Text Available Photosynthesis is a process which converts light energy into energy contained in the chemical bonds of organic compounds by photosynthetic pigments such as chlorophyll (Chl a, b, c, d, f or bacteriochlorophyll. It occurs in phototrophic organisms, which include higher plants and many types of photosynthetic bacteria, including cyanobacteria. In the case of the oxygenic photosynthesis, water is a donor of both electrons and protons, and solar radiation serves as inexhaustible source of energy. Efficiency of energy conversion in the primary processes of photosynthesis is close to 100%. Therefore, for many years photosynthesis has attracted the attention of researchers and designers looking for alternative energy systems as one of the most efficient and eco-friendly pathways of energy conversion. The latest advances in the design of optimal solar cells include the creation of converters based on thylakoid membranes, photosystems, and whole cells of cyanobacteria immobilized on nanostructured electrode (gold nanoparticles, carbon nanotubes, nanoparticles of ZnO and TiO2. The mode of solar energy conversion in photosynthesis has a great potential as a source of renewable energy while it is sustainable and environmentally safety as well. Application of pigments such as Chl f and Chl d (unlike Chl a and Chl b, by absorbing the far red and near infrared region of the spectrum (in the range 700-750 nm, will allow to increase the efficiency of such light transforming systems. This review article presents the last achievements in the field of energy photoconverters based on photosynthetic systems.

  20. Species selection for the design of gold nanobioreactor by photosynthetic organisms

    Energy Technology Data Exchange (ETDEWEB)

    Dahoumane, Si Amar [Universite Paris Diderot, Interfaces, Traitements, Organisation et Dynamique des Systemes (ITODYS), UMR 7086, CNRS, Sorbonne Paris Cite (France); Djediat, Chakib; Yepremian, Claude; Coute, Alain [Museum National d' Histoire Naturelle, Departement RDDM, FRE 3206, USM 505 (France); Fievet, Fernand [Universite Paris Diderot, Interfaces, Traitements, Organisation et Dynamique des Systemes (ITODYS), UMR 7086, CNRS, Sorbonne Paris Cite (France); Coradin, Thibaud, E-mail: thibaud.coradin@upmc.fr [UPMC Universites Paris 06, CNRS, Chimie de la Matiere Condensee de Paris (LCMCP), College de France (France); Brayner, Roberta, E-mail: roberta.brayner@univ-paris-diderot.fr [Universite Paris Diderot, Interfaces, Traitements, Organisation et Dynamique des Systemes (ITODYS), UMR 7086, CNRS, Sorbonne Paris Cite (France)

    2012-06-15

    The design of cell-based bioreactors for inorganic particles formation requires both a better understanding of the underlying processes and the identification of most suitable organisms. With this purpose, the process of Au{sup 3+} incorporation, intracellular reduction, and Au{sup 0} nanoparticle release in the culture medium was compared for four photosynthetic microorganisms, Klebsormidium flaccidum and Cosmarium impressulum green algae, Euglena gracilis euglenoid and Anabaena flos-aquae cyanobacteria. At low gold content, the two green algae show maintained photosynthetic activity and recovered particles (ca. 10 nm in size) are similar to internal colloids, indicating a full biological control over the whole process. In similar conditions, the euglenoid exhibits a rapid loss of biological activity, due to the absence of protective extracellular polysaccharide, but could grow again after an adaptation period. This results in a larger particle size dispersity but larger reduction yield. The cyanobacteria undergo rapid cell death, due to their prokaryotic nature, leading to high gold incorporation rate but poor control over released particle size. Similar observations can be made after addition of a larger gold salt concentration when all organisms rapidly die, suggesting that part of the process is not under biological control anymore but also involves extracellular chemical reactions. Overall, fruitful information on the whole biocrystallogenesis process is gained and most suitable species for further bioreactor design can be identified, i.e., green algae with external coating.

  1. Design, engineering, and construction of photosynthetic microbial cell factories for renewable solar fuel production.

    Science.gov (United States)

    Lindblad, Peter; Lindberg, Pia; Oliveira, Paulo; Stensjö, Karin; Heidorn, Thorsten

    2012-01-01

    There is an urgent need to develop sustainable solutions to convert solar energy into energy carriers used in the society. In addition to solar cells generating electricity, there are several options to generate solar fuels. This paper outlines and discusses the design and engineering of photosynthetic microbial systems for the generation of renewable solar fuels, with a focus on cyanobacteria. Cyanobacteria are prokaryotic microorganisms with the same type of photosynthesis as higher plants. Native and engineered cyanobacteria have been used by us and others as model systems to examine, demonstrate, and develop photobiological H(2) production. More recently, the production of carbon-containing solar fuels like ethanol, butanol, and isoprene have been demonstrated. We are using a synthetic biology approach to develop efficient photosynthetic microbial cell factories for direct generation of biofuels from solar energy. Present progress and advances in the design, engineering, and construction of such cyanobacterial cells for the generation of a portfolio of solar fuels, e.g., hydrogen, alcohols, and isoprene, are presented and discussed. Possibilities and challenges when introducing and using synthetic biology are highlighted.

  2. Species selection for the design of gold nanobioreactor by photosynthetic organisms

    International Nuclear Information System (INIS)

    Dahoumane, Si Amar; Djediat, Chakib; Yéprémian, Claude; Couté, Alain; Fiévet, Fernand; Coradin, Thibaud; Brayner, Roberta

    2012-01-01

    The design of cell-based bioreactors for inorganic particles formation requires both a better understanding of the underlying processes and the identification of most suitable organisms. With this purpose, the process of Au 3+ incorporation, intracellular reduction, and Au 0 nanoparticle release in the culture medium was compared for four photosynthetic microorganisms, Klebsormidium flaccidum and Cosmarium impressulum green algae, Euglena gracilis euglenoid and Anabaena flos-aquae cyanobacteria. At low gold content, the two green algae show maintained photosynthetic activity and recovered particles (ca. 10 nm in size) are similar to internal colloids, indicating a full biological control over the whole process. In similar conditions, the euglenoid exhibits a rapid loss of biological activity, due to the absence of protective extracellular polysaccharide, but could grow again after an adaptation period. This results in a larger particle size dispersity but larger reduction yield. The cyanobacteria undergo rapid cell death, due to their prokaryotic nature, leading to high gold incorporation rate but poor control over released particle size. Similar observations can be made after addition of a larger gold salt concentration when all organisms rapidly die, suggesting that part of the process is not under biological control anymore but also involves extracellular chemical reactions. Overall, fruitful information on the whole biocrystallogenesis process is gained and most suitable species for further bioreactor design can be identified, i.e., green algae with external coating.

  3. Progress of CRISPR-Cas Based Genome Editing in Photosynthetic Microbes.

    Science.gov (United States)

    Naduthodi, Mihris Ibnu Saleem; Barbosa, Maria J; van der Oost, John

    2018-02-03

    The carbon footprint caused by unsustainable development and its environmental and economic impact has become a major concern in the past few decades. Photosynthetic microbes such as microalgae and cyanobacteria are capable of accumulating value-added compounds from carbon dioxide, and have been regarded as environmentally friendly alternatives to reduce the usage of fossil fuels, thereby contributing to reducing the carbon footprint. This light-driven generation of green chemicals and biofuels has triggered the research for metabolic engineering of these photosynthetic microbes. CRISPR-Cas systems are successfully implemented across a wide range of prokaryotic and eukaryotic species for efficient genome editing. However, the inception of this genome editing tool in microalgal and cyanobacterial species took off rather slowly due to various complications. In this review, we elaborate on the established CRISPR-Cas based genome editing in various microalgal and cyanobacterial species. The complications associated with CRISPR-Cas based genome editing in these species are addressed along with possible strategies to overcome these issues. It is anticipated that in the near future this will result in improving and expanding the microalgal and cyanobacterial genome engineering toolbox. © 2018 The Authors. Biotechnology Journal Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  4. Design, Engineering, and Construction of Photosynthetic Microbial Cell Factories for Renewable Solar Fuel Production

    Energy Technology Data Exchange (ETDEWEB)

    Lindblad, Peter; Lindberg, Pia; Stensjoe, Karin (Photochemistry and Molecular Science, Dept. of Chemistry-Aangstroem Laboratory, Uppsala Univ., Uppsala (Sweden)), E-mail: Peter.Lindblad@kemi.uu.se; Oliveira, Paulo (Instituto de Biologia Molecular e Celular, Porto (Portugal)); Heidorn, Thorsten (Bioforsk-Norwegian Inst. for Agricultural and Environmental Research, Aas Oslo, (Norway))

    2012-03-15

    There is an urgent need to develop sustainable solutions to convert solar energy into energy carriers used in the society. In addition to solar cells generating electricity, there are several options to generate solar fuels. This paper outlines and discusses the design and engineering of photosynthetic microbial systems for the generation of renewable solar fuels, with a focus on cyanobacteria. Cyanobacteria are prokaryotic microorganisms with the same type of photosynthesis as higher plants. Native and engineered cyanobacteria have been used by us and others as model systems to examine, demonstrate, and develop photobiological H{sub 2} production. More recently, the production of carbon-containing solar fuels like ethanol, butanol, and isoprene have been demonstrated. We are using a synthetic biology approach to develop efficient photosynthetic microbial cell factories for direct generation of biofuels from solar energy. Present progress and advances in the design, engineering, and construction of such cyanobacterial cells for the generation of a portfolio of solar fuels, e.g., hydrogen, alcohols, and isoprene, are presented and discussed. Possibilities and challenges when introducing and using synthetic biology are highlighted

  5. Species selection for the design of gold nanobioreactor by photosynthetic organisms

    Science.gov (United States)

    Dahoumane, Si Amar; Djediat, Chakib; Yéprémian, Claude; Couté, Alain; Fiévet, Fernand; Coradin, Thibaud; Brayner, Roberta

    2012-06-01

    The design of cell-based bioreactors for inorganic particles formation requires both a better understanding of the underlying processes and the identification of most suitable organisms. With this purpose, the process of Au3+ incorporation, intracellular reduction, and Au0 nanoparticle release in the culture medium was compared for four photosynthetic microorganisms, Klebsormidium flaccidum and Cosmarium impressulum green algae, Euglena gracilis euglenoid and Anabaena flos- aquae cyanobacteria. At low gold content, the two green algae show maintained photosynthetic activity and recovered particles (ca. 10 nm in size) are similar to internal colloids, indicating a full biological control over the whole process. In similar conditions, the euglenoid exhibits a rapid loss of biological activity, due to the absence of protective extracellular polysaccharide, but could grow again after an adaptation period. This results in a larger particle size dispersity but larger reduction yield. The cyanobacteria undergo rapid cell death, due to their prokaryotic nature, leading to high gold incorporation rate but poor control over released particle size. Similar observations can be made after addition of a larger gold salt concentration when all organisms rapidly die, suggesting that part of the process is not under biological control anymore but also involves extracellular chemical reactions. Overall, fruitful information on the whole biocrystallogenesis process is gained and most suitable species for further bioreactor design can be identified, i.e., green algae with external coating.

  6. Changes of Photosynthetic Behaviors in Kappaphycus alvarezii Infected by Epiphyte

    Directory of Open Access Journals (Sweden)

    Tong Pang

    2011-01-01

    Full Text Available Epiphytic filamentous algae (EFA were noted as a serious problem to reduce the production and quality of K. alvarezii. The morphological studies revealed that the main epiphyte on K. alvarezii was Neosiphonia savatieri in China. Though the harmful effects of EFA on the production of K. alvarezii have been reported, the detailed mechanism of the N. savatieri in limiting the production of K. alvarezii has not been studied yet. The present paper studied the effects of N. savatieri infection on photosynthetic behaviors in K. alvarezii by detecting chlorophyll fluorescence transient in vivo. The results revealed that damage of oxygen-evolving complex (OEC, decrease of active reaction centers (RCs, and the plastoquinone (PQ pool as well as significant reduction in the performance indexes (PI of PSII were caused by the infection of N. savatieri. The influence of N. savatieri on photosynthetic activity of K. alvarezii should be one of the important reasons to reduce the production of K. alvarezii infected by N. savatieri.

  7. Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria

    Directory of Open Access Journals (Sweden)

    Hou Jing

    2006-04-01

    Full Text Available Abstract Background Chloroplasts descended from cyanobacteria and have a drastically reduced genome following an endosymbiotic event. Many genes of the ancestral cyanobacterial genome have been transferred to the plant nuclear genome by horizontal gene transfer. However, a selective set of metabolism pathways is maintained in chloroplasts using both chloroplast genome encoded and nuclear genome encoded enzymes. As an organelle specialized for carrying out photosynthesis, does the chloroplast metabolic network have properties adapted for higher efficiency of photosynthesis? We compared metabolic network properties of chloroplasts and prokaryotic photosynthetic organisms, mostly cyanobacteria, based on metabolic maps derived from genome data to identify features of chloroplast network properties that are different from cyanobacteria and to analyze possible functional significance of those features. Results The properties of the entire metabolic network and the sub-network that consists of reactions directly connected to the Calvin Cycle have been analyzed using hypergraph representation. Results showed that the whole metabolic networks in chloroplast and cyanobacteria both possess small-world network properties. Although the number of compounds and reactions in chloroplasts is less than that in cyanobacteria, the chloroplast's metabolic network has longer average path length, a larger diameter, and is Calvin Cycle -centered, indicating an overall less-dense network structure with specific and local high density areas in chloroplasts. Moreover, chloroplast metabolic network exhibits a better modular organization than cyanobacterial ones. Enzymes involved in the same metabolic processes tend to cluster into the same module in chloroplasts. Conclusion In summary, the differences in metabolic network properties may reflect the evolutionary changes during endosymbiosis that led to the improvement of the photosynthesis efficiency in higher plants. Our

  8. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

    Science.gov (United States)

    Puigbò, Pere; Lobkovsky, Alexander E; Kristensen, David M; Wolf, Yuri I; Koonin, Eugene V

    2014-08-21

    Genomes of bacteria and archaea (collectively, prokaryotes) appear to exist in incessant flux, expanding via horizontal gene transfer and gene duplication, and contracting via gene loss. However, the actual rates of genome dynamics and relative contributions of different types of event across the diversity of prokaryotes are largely unknown, as are the sizes of microbial supergenomes, i.e. pools of genes that are accessible to the given microbial species. We performed a comprehensive analysis of the genome dynamics in 35 groups (34 bacterial and one archaeal) of closely related microbial genomes using a phylogenetic birth-and-death maximum likelihood model to quantify the rates of gene family gain and loss, as well as expansion and reduction. The results show that loss of gene families dominates the evolution of prokaryotes, occurring at approximately three times the rate of gain. The rates of gene family expansion and reduction are typically seven and twenty times less than the gain and loss rates, respectively. Thus, the prevailing mode of evolution in bacteria and archaea is genome contraction, which is partially compensated by the gain of new gene families via horizontal gene transfer. However, the rates of gene family gain, loss, expansion and reduction vary within wide ranges, with the most stable genomes showing rates about 25 times lower than the most dynamic genomes. For many groups, the supergenome estimated from the fraction of repetitive gene family gains includes about tenfold more gene families than the typical genome in the group although some groups appear to have vast, 'open' supergenomes. Reconstruction of evolution for groups of closely related bacteria and archaea reveals an extremely rapid and highly variable flux of genes in evolving microbial genomes, demonstrates that extensive gene loss and horizontal gene transfer leading to innovation are the two dominant evolutionary processes, and yields robust estimates of the supergenome size.

  9. Characterization of prokaryotic and eukaryotic promoters usinghidden Markov models

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Baldi, Pierre; Brunak, Søren

    1996-01-01

    In this paper we utilize hidden Markov models (HMMs) and information theory to analyze prokaryotic and eukaryotic promoters. We perform this analysis with special emphasis on the fact that promoters are divided into a number of different classes, depending on which polymerase-associated factors...... that bind to them. We find that HMMs trained on such subclasses of Escherichia coli promoters (specifically, the so-called sigma-70 and sigma-54 classes) give an excellent classification of unknown promoters with respect to sigma-class. HMMs trained on eukaryotic sequences from human genes also model nicely...

  10. Characterization of prokaryotic and eukaryotic promoters using hidden Markov models

    DEFF Research Database (Denmark)

    Pedersen, Anders Gorm; Baldi, P.; Chauvin, Y.

    1996-01-01

    In this paper we utilize hidden Markov models (HMMs) and information theory to analyze prokaryotic and eukaryotic promoters. We perform this analysis with special emphasis on the fact that promoters are divided into a number of different classes, depending on which polymerase-associated factors...... that bind to them. We find that HMMs trained on such subclasses of Escherichia coli promoters (specifically, the so-called sigma 70 and sigma 54 classes) give an excellent classification of unknown promoters with respect to sigma-class. HMMs trained on eukaryotic sequences from human genes also model nicely...

  11. BLAST Ring Image Generator (BRIG: simple prokaryote genome comparisons

    Directory of Open Access Journals (Sweden)

    Beatson Scott A

    2011-08-01

    Full Text Available Abstract Background Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. Results BLAST Ring Image Generator (BRIG can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons

  12. BLAST Ring Image Generator (BRIG): simple prokaryote genome comparisons.

    Science.gov (United States)

    Alikhan, Nabil-Fareed; Petty, Nicola K; Ben Zakour, Nouri L; Beatson, Scott A

    2011-08-08

    Visualisation of genome comparisons is invaluable for helping to determine genotypic differences between closely related prokaryotes. New visualisation and abstraction methods are required in order to improve the validation, interpretation and communication of genome sequence information; especially with the increasing amount of data arising from next-generation sequencing projects. Visualising a prokaryote genome as a circular image has become a powerful means of displaying informative comparisons of one genome to a number of others. Several programs, imaging libraries and internet resources already exist for this purpose, however, most are either limited in the number of comparisons they can show, are unable to adequately utilise draft genome sequence data, or require a knowledge of command-line scripting for implementation. Currently, there is no freely available desktop application that enables users to rapidly visualise comparisons between hundreds of draft or complete genomes in a single image. BLAST Ring Image Generator (BRIG) can generate images that show multiple prokaryote genome comparisons, without an arbitrary limit on the number of genomes compared. The output image shows similarity between a central reference sequence and other sequences as a set of concentric rings, where BLAST matches are coloured on a sliding scale indicating a defined percentage identity. Images can also include draft genome assembly information to show read coverage, assembly breakpoints and collapsed repeats. In addition, BRIG supports the mapping of unassembled sequencing reads against one or more central reference sequences. Many types of custom data and annotations can be shown using BRIG, making it a versatile approach for visualising a range of genomic comparison data. BRIG is readily accessible to any user, as it assumes no specialist computational knowledge and will perform all required file parsing and BLAST comparisons automatically. There is a clear need for a user

  13. Ultrafast fluorescence of photosynthetic crystals and light-harvesting complexes

    NARCIS (Netherlands)

    Oort, van B.F.

    2008-01-01

    This thesis focuses on the study of photosynthetic pigment protein complexes using time resolved fluorescence techniques. Fluorescence spectroscopy often requires attaching fluorescent labels to the proteins under investigation. With photosynthetic proteins this is not necessary, because these

  14. Difference in photosynthetic performance among three peach ...

    African Journals Online (AJOL)

    The effects of low photosynthetic photon flux density (PPFD) on greenhouse grown peach trees ('Qingfeng': Prunus persica L. Batsch, 'NJN76': Prunus persica L. Batsch and 'Maixiang': P. persica var. nectarine) were investigated. Difference in photosynthesis rate (Pn) and stoma morphology among cultivars were studied.

  15. Photosynthetic carbon metabolism in freshwater phytoplankton

    International Nuclear Information System (INIS)

    Groeger, A.W.

    1986-01-01

    Photosynthetic carbon metabolism of natural assemblages of freshwater phytoplankton was measured by following the flow of inorganic 14 C into the photosynthetic end products polysaccharide protein, lipid, and soluble metabolites. Data were collected from a wide range of physical, chemical, and trophic conditions in six southern United States reservoirs, with the primary environmental variables of interest being light intensity and nutrient supply. Polysaccharide and protein were consistently the primary products of photosynthetic carbon metabolism, comprising an average of 70% of the total carbon fixation over a wide range of light intensities. Polysaccharide was quantitatively more important at higher light intensities, and protein at lower light intensities, as light intensity varied both with depth within the water column and over diurnal cycles. Polysaccharide synthesis was more variable over the diurnal period than was protein synthesis. Phytoplankton in the downlake epilimnion of Normandy Lake, a central Tennessee reservoir, responded to summer nitrogen (N) deficiency by increasing relative rates of lipid synthesis from 10-15% to 20-25% of the total photosynthetic carbon fixation. Phytoplankton in more nitrogen-sufficient areas of the reservoir maintained lower rates of lipid synthesis throughout the summer. These results document the occurrence in nature of a relationship between N-deficiency and increased lipid synthesis previously observed only in laboratory algal culture studies

  16. Excitons in intact cells of photosynthetic bacteria.

    Science.gov (United States)

    Freiberg, Arvi; Pajusalu, Mihkel; Rätsep, Margus

    2013-09-26

    Live cells and regular crystals seem fundamentally incompatible. Still, effects characteristic to ideal crystals, such as coherent sharing of excitation, have been recently used in many studies to explain the behavior of several photosynthetic complexes, especially the inner workings of the light-harvesting apparatus of the oldest known photosynthetic organisms, the purple bacteria. To this date, there has been no concrete evidence that the same effects are instrumental in real living cells, leaving a possibility that this is an artifact of unnatural study conditions, not a real effect relevant to the biological operation of bacteria. Hereby, we demonstrate survival of collective coherent excitations (excitons) in intact cells of photosynthetic purple bacteria. This is done by using excitation anisotropy spectroscopy for tracking the temperature-dependent evolution of exciton bands in light-harvesting systems of increasing structural complexity. The temperature was gradually raised from 4.5 K to ambient temperature, and the complexity of the systems ranged from detergent-isolated complexes to complete bacterial cells. The results provide conclusive evidence that excitons are indeed one of the key elements contributing to the energetic and dynamic properties of photosynthetic organisms.

  17. Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors

    Directory of Open Access Journals (Sweden)

    Tatiana Tatarinova

    2015-01-01

    Full Text Available Proteins of the same functional family (for example, kinases may have significantly different lengths. It is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. The main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. We believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome rank and genome property, is a reasonable approach in revealing such evolutionary driving factors. As we demonstrated earlier, our chosen approach, Bubble-sort, combines stability, accuracy, and computational efficiency as compared to other ranking methods. Application of Bubble Sort to the set of 1390 prokaryotic genomes confirmed that genes of Archaeal species are generally shorter than Bacterial ones. We observed that gene lengths are affected by various factors: within each domain, different phyla have preferences for short or long genes; thermophiles tend to have shorter genes than the soil-dwellers; halophiles tend to have longer genes. We also found that species with overrepresentation of cytosines and guanines in the third position of the codon (GC3 content tend to have longer genes than species with low GC3 content.

  18. Lengths of Orthologous Prokaryotic Proteins Are Affected by Evolutionary Factors.

    Science.gov (United States)

    Tatarinova, Tatiana; Salih, Bilal; Dien Bard, Jennifer; Cohen, Irit; Bolshoy, Alexander

    2015-01-01

    Proteins of the same functional family (for example, kinases) may have significantly different lengths. It is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. The main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. We believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome rank and genome property, is a reasonable approach in revealing such evolutionary driving factors. As we demonstrated earlier, our chosen approach, Bubble-sort, combines stability, accuracy, and computational efficiency as compared to other ranking methods. Application of Bubble Sort to the set of 1390 prokaryotic genomes confirmed that genes of Archaeal species are generally shorter than Bacterial ones. We observed that gene lengths are affected by various factors: within each domain, different phyla have preferences for short or long genes; thermophiles tend to have shorter genes than the soil-dwellers; halophiles tend to have longer genes. We also found that species with overrepresentation of cytosines and guanines in the third position of the codon (GC3 content) tend to have longer genes than species with low GC3 content.

  19. Primer design for a prokaryotic differential display RT-PCR.

    Science.gov (United States)

    Fislage, R; Berceanu, M; Humboldt, Y; Wendt, M; Oberender, H

    1997-05-01

    We have developed a primer set for a prokaryotic differential display of mRNA in the Enterobacteriaceae group. Each combination of ten 10mer and ten 11mer primers generates up to 85 bands from total Escherichia coli RNA, thus covering expressed sequences of a complete bacterial genome. Due to the lack of polyadenylation in prokaryotic RNA the type T11VN anchored oligonucleotides for the reverse transcriptase reaction had to be replaced with respect to the original method described by Liang and Pardee [ Science , 257, 967-971 (1992)]. Therefore, the sequences of both the 10mer and the new 11mer oligonucleotides were determined by a statistical evaluation of species-specific coding regions extracted from the EMBL database. The 11mer primers used for reverse transcription were selected for localization in the 3'-region of the bacterial RNA. The 10mer primers preferentially bind to the 5'-end of the RNA. None of the primers show homology to rRNA or other abundant small RNA species. Randomly sampled cDNA bands were checked for their bacterial origin either by re-amplification, cloning and sequencing or by re-amplification and direct sequencing with 10mer and 11mer primers after asymmetric PCR.

  20. Insights into structural variations and genome rearrangements in prokaryotic genomes.

    Science.gov (United States)

    Periwal, Vinita; Scaria, Vinod

    2015-01-01

    Structural variations (SVs) are genomic rearrangements that affect fairly large fragments of DNA. Most of the SVs such as inversions, deletions and translocations have been largely studied in context of genetic diseases in eukaryotes. However, recent studies demonstrate that genome rearrangements can also have profound impact on prokaryotic genomes, leading to altered cell phenotype. In contrast to single-nucleotide variations, SVs provide a much deeper insight into organization of bacterial genomes at a much better resolution. SVs can confer change in gene copy number, creation of new genes, altered gene expression and many other functional consequences. High-throughput technologies have now made it possible to explore SVs at a much refined resolution in bacterial genomes. Through this review, we aim to highlight the importance of the less explored field of SVs in prokaryotic genomes and their impact. We also discuss its potential applicability in the emerging fields of synthetic biology and genome engineering where targeted SVs could serve to create sophisticated and accurate genome editing. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

  1. Transcriptome dynamics-based operon prediction in prokaryotes.

    Science.gov (United States)

    Fortino, Vittorio; Smolander, Olli-Pekka; Auvinen, Petri; Tagliaferri, Roberto; Greco, Dario

    2014-05-16

    Inferring operon maps is crucial to understanding the regulatory networks of prokaryotic genomes. Recently, RNA-seq based transcriptome studies revealed that in many bacterial species the operon structure vary with the change of environmental conditions. Therefore, new computational solutions that use both static and dynamic data are necessary to create condition specific operon predictions. In this work, we propose a novel classification method that integrates RNA-seq based transcriptome profiles with genomic sequence features to accurately identify the operons that are expressed under a measured condition. The classifiers are trained on a small set of confirmed operons and then used to classify the remaining gene pairs of the organism studied. Finally, by linking consecutive gene pairs classified as operons, our computational approach produces condition-dependent operon maps. We evaluated our approach on various RNA-seq expression profiles of the bacteria Haemophilus somni, Porphyromonas gingivalis, Escherichia coli and Salmonella enterica. Our results demonstrate that, using features depending on both transcriptome dynamics and genome sequence characteristics, we can identify operon pairs with high accuracy. Moreover, the combination of DNA sequence and expression data results in more accurate predictions than each one alone. We present a computational strategy for the comprehensive analysis of condition-dependent operon maps in prokaryotes. Our method can be used to generate condition specific operon maps of many bacterial organisms for which high-resolution transcriptome data is available.

  2. ProOpDB: Prokaryotic Operon DataBase.

    Science.gov (United States)

    Taboada, Blanca; Ciria, Ricardo; Martinez-Guerrero, Cristian E; Merino, Enrique

    2012-01-01

    The Prokaryotic Operon DataBase (ProOpDB, http://operons.ibt.unam.mx/OperonPredictor) constitutes one of the most precise and complete repositories of operon predictions now available. Using our novel and highly accurate operon identification algorithm, we have predicted the operon structures of more than 1200 prokaryotic genomes. ProOpDB offers diverse alternatives by which a set of operon predictions can be retrieved including: (i) organism name, (ii) metabolic pathways, as defined by the KEGG database, (iii) gene orthology, as defined by the COG database, (iv) conserved protein domains, as defined by the Pfam database, (v) reference gene and (vi) reference operon, among others. In order to limit the operon output to non-redundant organisms, ProOpDB offers an efficient method to select the most representative organisms based on a precompiled phylogenetic distances matrix. In addition, the ProOpDB operon predictions are used directly as the input data of our Gene Context Tool to visualize their genomic context and retrieve the sequence of their corresponding 5' regulatory regions, as well as the nucleotide or amino acid sequences of their genes.

  3. Prokaryote genome fluidity: toward a system approach of the mobilome.

    Science.gov (United States)

    Toussaint, Ariane; Chandler, Mick

    2012-01-01

    The importance of horizontal/lateral gene transfer (LGT) in shaping the genomes of prokaryotic organisms has been recognized in recent years as a result of analysis of the increasing number of available genome sequences. LGT is largely due to the transfer and recombination activities of mobile genetic elements (MGEs). Bacterial and archaeal genomes are mosaics of vertically and horizontally transmitted DNA segments. This generates reticulate relationships between members of the prokaryotic world that are better represented by networks than by "classical" phylogenetic trees. In this review we summarize the nature and activities of MGEs, and the problems that presently limit their analysis on a large scale. We propose routes to improve their annotation in the flow of genomic and metagenomic sequences that currently exist and those that become available. We describe network analysis of evolutionary relationships among some MGE categories and sketch out possible developments of this type of approach to get more insight into the role of the mobilome in bacterial adaptation and evolution.

  4. From Plant Infectivity to Growth Patterns: The Role of Blue-Light Sensing in the Prokaryotic World

    Directory of Open Access Journals (Sweden)

    Aba Losi

    2014-01-01

    Full Text Available Flavin-based photoreceptor proteins of the LOV (Light, Oxygen, and Voltage and BLUF (Blue Light sensing Using Flavins superfamilies are ubiquitous among the three life domains and are essential blue-light sensing systems, not only in plants and algae, but also in prokaryotes. Here we review their biological roles in the prokaryotic world and their evolution pathways. An unexpected large number of bacterial species possess flavin-based photosensors, amongst which are important human and plant pathogens. Still, few cases are reported where the activity of blue-light sensors could be correlated to infectivity and/or has been shown to be involved in the activation of specific genes, resulting in selective growth patterns. Metagenomics and bio-informatic analysis have only recently been initiated, but signatures are beginning to emerge that allow definition of a bona fide LOV or BLUF domain, aiming at better selection criteria for novel blue-light sensors. We also present here, for the first time, the phylogenetic tree for archaeal LOV domains that have reached a statistically significant number but have not at all been investigated thus far.

  5. Effects of gold nanoparticles on the photophysical and photosynthetic parameters of leaves and chloroplasts.

    Science.gov (United States)

    Torres, Rocio; Diz, Virginia E; Lagorio, M Gabriela

    2018-04-18

    Effects of gold nanoparticles (average diameter: 10-14 nm) on leaves and chloroplasts have been studied. Gold nanoparticles (AuNPs) quenched significantly chlorophyll fluorescence when introduced both in intact leaves and isolated chloroplasts. Additionally, the fluorescence spectra corrected for light re-absorption processes showed a net decrease in the fluorescence ratio calculated as the quotient between the maximum fluorescence at 680 and 735 nm. This fact gave evidence for a reduction in the fluorescence emission of the PSII relative to that of the PSI. Strikingly, the photosynthetic parameters derived from the analysis of the slow phase of Kautsky's kinetics, the rate of oxygen evolution and the rate of photo-reduction of 2,6-dichlorophenolindophenol were increased in the presence of AuNPs indicating an apparent greater photosynthetic capacity. The observed results were consistent with an electron transfer process from the excited PSII, which was thermodynamically possible, and which competed with both the electron transport process that initiated photosynthesis and the deactivation of the excited PSII by fluorescence emission. Additionally, it is here explained, in terms of a completely rational kinetic scheme and their corresponding algebraic expressions, why the photosynthetic parameters and the variable and non-variable fluorescence of chlorophyll are modified in a photosynthetic tissue containing gold nanoparticles.

  6. Links between viruses and prokaryotes throughout the water column along a North Atlantic latitudinal transect

    NARCIS (Netherlands)

    De Corte, Daniele; Sintes, Eva; Yokokawa, Taichi; Reinthaler, Thomas; Herndl, Gerhard J.

    Viruses are an abundant, diverse and dynamic component of marine ecosystems and have a key role in the biogeochemical processes of the ocean by controlling prokaryotic and phytoplankton abundance and diversity. However, most of the studies on virus-prokaryote interactions in marine environments have

  7. A proposed genus boundary for the prokaryotes based on genomic insights.

    Science.gov (United States)

    Qin, Qi-Long; Xie, Bin-Bin; Zhang, Xi-Ying; Chen, Xiu-Lan; Zhou, Bai-Cheng; Zhou, Jizhong; Oren, Aharon; Zhang, Yu-Zhong

    2014-06-01

    Genomic information has already been applied to prokaryotic species definition and classification. However, the contribution of the genome sequence to prokaryotic genus delimitation has been less studied. To gain insights into genus definition for the prokaryotes, we attempted to reveal the genus-level genomic differences in the current prokaryotic classification system and to delineate the boundary of a genus on the basis of genomic information. The average nucleotide sequence identity between two genomes can be used for prokaryotic species delineation, but it is not suitable for genus demarcation. We used the percentage of conserved proteins (POCP) between two strains to estimate their evolutionary and phenotypic distance. A comprehensive genomic survey indicated that the POCP can serve as a robust genomic index for establishing the genus boundary for prokaryotic groups. Basically, two species belonging to the same genus would share at least half of their proteins. In a specific lineage, the genus and family/order ranks showed slight or no overlap in terms of POCP values. A prokaryotic genus can be defined as a group of species with all pairwise POCP values higher than 50%. Integration of whole-genome data into the current taxonomy system can provide comprehensive information for prokaryotic genus definition and delimitation. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  8. Temperature regulation of marine heterotrophic prokaryotes increases latitudinally as a breach between bottom-up and top-down controls

    KAUST Repository

    Moran, Xose Anxelu G.; Gasol, Josep M.; Pernice, Massimo C.; Mangot, Jean-Franç ois; Massana, Ramon; Lara, Elena; Vaqué , Dolors; Duarte, Carlos M.

    2017-01-01

    Planktonic heterotrophic prokaryotes make up the largest living biomass and process most organic matter in the ocean. Determining when and where the biomass and activity of heterotrophic prokaryotes are controlled by resource availability (bottom

  9. Effect of Azospirillum brasilense and Burkholderia unamae Bacteria on Maize Photosynthetic Activity Evaluated Using the Photoacoustic Technique

    Science.gov (United States)

    Gordillo-Delgado, F.; Marín, E.; Calderón, A.

    2016-09-01

    In this work, the photosynthetic process of maize plants ( Zea mays), which were grown using seeds inoculated with plant growth promoting bacteria Azospirillum brasilense and Burkholderia unamae, was monitored. Photothermal and photobaric signals obtained by a time-resolved photoacoustic measurement configuration were used for measuring the oxygen evolution rate in situ. A frequency-resolved configuration of the method was utilized to determine the oxygen diffusion coefficient and the thermal diffusivity of the maize leaves. The latter parameters, which can be used as indicators of the photosynthetic activity of maize, are found to vary according to the plant-microbe interaction. Treatment with plant growth promoting bacteria induced a decrease in the oxygen diffusion coefficient of about 20 %.

  10. Tetrapyrroles as Endogenous TSPO Ligands in Eukaryotes and Prokaryotes: Comparisons with Synthetic Ligands

    Directory of Open Access Journals (Sweden)

    Leo Veenman

    2016-06-01

    Full Text Available The 18 kDa translocator protein (TSPO is highly 0conserved in eukaryotes and prokaryotes. Since its discovery in 1977, numerous studies established the TSPO’s importance for life essential functions. For these studies, synthetic TSPO ligands typically are applied. Tetrapyrroles present endogenous ligands for the TSPO. Tetrapyrroles are also evolutionarily conserved and regulate multiple functions. TSPO and tetrapyrroles regulate each other. In animals TSPO-tetrapyrrole interactions range from effects on embryonic development to metabolism, programmed cell death, response to stress, injury and disease, and even to life span extension. In animals TSPOs are primarily located in mitochondria. In plants TSPOs are also present in plastids, the nuclear fraction, the endoplasmic reticulum, and Golgi stacks. This may contribute to translocation of tetrapyrrole intermediates across organelles’ membranes. As in animals, plant TSPO binds heme and protoporphyrin IX. TSPO-tetrapyrrole interactions in plants appear to relate to development as well as stress conditions, including salt tolerance, abscisic acid-induced stress, reactive oxygen species homeostasis, and finally cell death regulation. In bacteria, TSPO is important for switching from aerobic to anaerobic metabolism, including the regulation of photosynthesis. As in mitochondria, in bacteria TSPO is located in the outer membrane. TSPO-tetrapyrrole interactions may be part of the establishment of the bacterial-eukaryote relationships, i.e., mitochondrial-eukaryote and plastid-plant endosymbiotic relationships.

  11. Diversity of sulfur isotope fractionations by sulfate-reducing prokaryotes

    DEFF Research Database (Denmark)

    Detmers, Jan; Brüchert, Volker; Habicht, K S

    2001-01-01

    Batch culture experiments were performed with 32 different sulfate-reducing prokaryotes to explore the diversity in sulfur isotope fractionation during dissimilatory sulfate reduction by pure cultures. The selected strains reflect the phylogenetic and physiologic diversity of presently known...... sulfate reducers and cover a broad range of natural marine and freshwater habitats. Experimental conditions were designed to achieve optimum growth conditions with respect to electron donors, salinity, temperature, and pH. Under these optimized conditions, experimental fractionation factors ranged from 2.......0 to 42.0 per thousand. Salinity, incubation temperature, pH, and phylogeny had no systematic effect on the sulfur isotope fractionation. There was no correlation between isotope fractionation and sulfate reduction rate. The type of dissimilatory bisulfite reductase also had no effect on fractionation...

  12. Functional Implications of Domain Organization Within Prokaryotic Rhomboid Proteases.

    Science.gov (United States)

    Panigrahi, Rashmi; Lemieux, M Joanne

    2015-01-01

    Intramembrane proteases are membrane embedded enzymes that cleave transmembrane substrates. This interesting class of enzyme and its water mediated substrate cleavage mechanism occurring within the hydrophobic lipid bilayer has drawn the attention of researchers. Rhomboids are a family of ubiquitous serine intramembrane proteases. Bacterial forms of rhomboid proteases are mainly composed of six transmembrane helices that are preceded by a soluble N-terminal domain. Several crystal structures of the membrane domain of the E. coli rhomboid protease ecGlpG have been solved. Independently, the ecGlpG N-terminal cytoplasmic domain structure was solved using both NMR and protein crystallography. Despite these structures, we still do not know the structure of the full-length protein, nor do we know the functional role of these domains in the cell. This chapter will review the structural and functional roles of the different domains associated with prokaryotic rhomboid proteases. Lastly, we will address questions remaining in the field.

  13. Cloning and prokaryotic expression of the porcine lipasin gene.

    Science.gov (United States)

    Li, M M; Geng, J; Guo, Y J; Jiao, X Q; Lu, W F; Zhu, H S; Wang, Y Y; Yang, G Y

    2015-11-23

    Lipasin has recently been demonstrated to be involved in lipid metabolism. In this study, two specific primers were used to amplify the lipasin open reading frame from porcine liver tissue. The polymerase chain reaction product was cloned to a pGEM®-T Easy Vector, digested by SalI and NotI, and sequenced. The lipasin fragment was then cloned to a pET21(b) vector and digested by the same restriction enzyme. The recombinant plasmid was transferred to Escherichia coli (BL21), and the lipasin protein was induced with isopropyl-β-D-thiogalactopyranoside. The protein obtained was identified by sodium dodecyl sulfate polyacrylamide gel electrophoresis and western blotting. A pET-lipasin prokaryotic recombinant expression vector was successfully constructed, and a 25.2-kDa protein was obtained. This study provides a basis for further research on the biological function of porcine lipasin.

  14. Metabolic Compensation and Circadian Resilience in Prokaryotic Cyanobacteria

    Science.gov (United States)

    Johnson, Carl Hirschie; Egli, Martin

    2014-01-01

    For a biological oscillator to function as a circadian pacemaker that confers a fitness advantage, its timing functions must be stable in response to environmental and metabolic fluctuations. One such stability enhancer, temperature compensation, has long been a defining characteristic of these timekeepers. However, an accurate biological timekeeper must also resist changes in metabolism, and this review suggests that temperature compensation is actually a subset of a larger phenomenon, namely metabolic compensation, which maintains the frequency of circadian oscillators in response to a host of factors that impinge on metabolism and would otherwise destabilize these clocks. The circadian system of prokaryotic cyanobacteria is an illustrative model because it is composed of transcriptional and nontranscriptional oscillators that are coupled to promote resilience. Moreover, the cyanobacterial circadian program regulates gene activity and metabolic pathways, and it can be manipulated to improve the expression of bioproducts that have practical value. PMID:24905782

  15. Known knowns, known unknowns and unknown unknowns in prokaryotic transposition.

    Science.gov (United States)

    Siguier, Patricia; Gourbeyre, Edith; Chandler, Michael

    2017-08-01

    Although the phenomenon of transposition has been known for over 60 years, its overarching importance in modifying and streamlining genomes took some time to recognize. In spite of a robust understanding of transposition of some TE, there remain a number of important TE groups with potential high genome impact and unknown transposition mechanisms and yet others, only recently identified by bioinformatics, yet to be formally confirmed as mobile. Here, we point to some areas of limited understanding concerning well established important TE groups with DDE Tpases, to address central gaps in our knowledge of characterised Tn with other types of Tpases and finally, to highlight new potentially mobile DNA species. It is not exhaustive. Examples have been chosen to provide encouragement in the continued exploration of the considerable prokaryotic mobilome especially in light of the current threat to public health posed by the spread of multiple Ab R . Copyright © 2017 Elsevier Ltd. All rights reserved.

  16. Prokaryotic communities differ along a geothermal soil photic gradient.

    Science.gov (United States)

    Meadow, James F; Zabinski, Catherine A

    2013-01-01

    Geothermal influenced soils exert unique physical and chemical limitations on resident microbial communities but have received little attention in microbial ecology research. These environments offer a model system in which to investigate microbial community heterogeneity and a range of soil ecological concepts. We conducted a 16S bar-coded pyrosequencing survey of the prokaryotic communities in a diatomaceous geothermal soil system and compared communities across soil types and along a conspicuous photic depth gradient. We found significant differences between the communities of the two different soils and also predictable differences between samples taken at different depths. Additionally, we targeted three ecologically relevant bacterial phyla, Cyanobacteria, Planctomycetes, and Verrucomicrobia, for clade-wise comparisons with these variables and found strong differences in their abundances, consistent with the autecology of these groups.

  17. [Engineering photosynthetic cyanobacterial chassis: a review].

    Science.gov (United States)

    Wu, Qin; Chen, Lei; Wang, Jiangxin; Zhang, Weiwen

    2013-08-01

    Photosynthetic cyanobacteria possess a series of good properties, such as their abilities to capture solar energy for CO2 fixation, low nutritional requirements for growth, high growth rate, and relatively simple genetic background. Due to the high oil price and increased concern of the global warming in recent years, cyanobacteria have attracted widespread attention because they can serve as an 'autotrophic microbial factory' for producing renewable biofuels and fine chemicals directly from CO2. Particularly, significant progress has been made in applying synthetic biology techniques and strategies to construct and optimize cyanobacteria chassis. In this article, we critically summarized recent advances in developing new methods to optimize cyanobacteria chassis, improving cyanobacteria photosynthetic efficiency, and in constructing cyanobacteria chassis tolerant to products or environmental stresses. In addition, various industrial applications of cyanobacteria chassis are also discussed.

  18. Photosynthetic Rates of Citronella and Lemongrass 1

    Science.gov (United States)

    Herath, H. M. Walter; Ormrod, Douglas P.

    1979-01-01

    Ten selections of citronella (Cymbopogon nardus [L.] Rendle) were grown at 32/27, 27/21, or 15/10 C day/night temperatures, and plants from three populations of lemongrass (Cymbopogon citratus [D.C.] Stapf from Japan or Sri Lanka and Cymbopogon flexuosus [D.C.] Stapf from India) were grown at 8- or 15-hour photoperiods. Net photosynthetic rates of mature leaves were measured in a controlled environment at 25 C and 260 microeinsteins per meter2 per second. Rates declined with increasing leaf age, and from the tip to the base of the leaf blade. Rates for citronella leaves grown at 15/10 C were extremely low for all selections. Highest rates of net photosynthesis were recorded for four selections grown at 27/21 C and for two selections grown at 32/27 C. Lemongrass grown at 8-hour photoperiod had higher photosynthetic rates than that grown at 15-hour photoperiod. PMID:16660737

  19. BOREAS TE-9 NSA Photosynthetic Response Data

    Science.gov (United States)

    Hall, Forrest G.; Curd, Shelaine (Editor); Dang, Qinglai; Margolis, Hank; Coyea, Marie

    2000-01-01

    The Boreal Ecosystem-Atmospheric Study (BOREAS) TE-9 (Terrestrial Ecology) team collected several data sets related to chemical and photosynthetic properties of leaves. This data set describes: (1) the response of leaf and shoot-level photosynthesis to ambient and intercellular CO2 concentration, temperature, and incident photosynthetically active radiation (PAR) for black spruce, jack pine, and aspen during the three intensive field campaigns (IFCs) in 1994 in the Northern Study Area (NSA); (2) the response of stomatal conductance to vapor pressure difference throughout the growing season of 1994; and (3) a range of shoot water potentials (controlled in the laboratory) for black spruce and jack pine. The data are stored in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  20. Reconstruction of phylogenetic trees of prokaryotes using maximal common intervals.

    Science.gov (United States)

    Heydari, Mahdi; Marashi, Sayed-Amir; Tusserkani, Ruzbeh; Sadeghi, Mehdi

    2014-10-01

    One of the fundamental problems in bioinformatics is phylogenetic tree reconstruction, which can be used for classifying living organisms into different taxonomic clades. The classical approach to this problem is based on a marker such as 16S ribosomal RNA. Since evolutionary events like genomic rearrangements are not included in reconstructions of phylogenetic trees based on single genes, much effort has been made to find other characteristics for phylogenetic reconstruction in recent years. With the increasing availability of completely sequenced genomes, gene order can be considered as a new solution for this problem. In the present work, we applied maximal common intervals (MCIs) in two or more genomes to infer their distance and to reconstruct their evolutionary relationship. Additionally, measures based on uncommon segments (UCS's), i.e., those genomic segments which are not detected as part of any of the MCIs, are also used for phylogenetic tree reconstruction. We applied these two types of measures for reconstructing the phylogenetic tree of 63 prokaryotes with known COG (clusters of orthologous groups) families. Similarity between the MCI-based (resp. UCS-based) reconstructed phylogenetic trees and the phylogenetic tree obtained from NCBI taxonomy browser is as high as 93.1% (resp. 94.9%). We show that in the case of this diverse dataset of prokaryotes, tree reconstruction based on MCI and UCS outperforms most of the currently available methods based on gene orders, including breakpoint distance and DCJ. We additionally tested our new measures on a dataset of 13 closely-related bacteria from the genus Prochlorococcus. In this case, distances like rearrangement distance, breakpoint distance and DCJ proved to be useful, while our new measures are still appropriate for phylogenetic reconstruction. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  1. Ionizing radiation and photosynthetic ability of cyanobacteria

    International Nuclear Information System (INIS)

    Agarwal, Rachna; Sainis, Jayashree K.

    2006-01-01

    Unicellular photoautotrophic cyanobacteria, Anacystis nidulans when exposed to lethal dose of 1.5 kGy of 60 Co γ- radiation (D 10 = 257.32 Gy) were as effective photosynthetical as unirradiated controls immediately after irradiation although level of ROS was higher by several magnitudes in these irradiated cells. The results suggested the preservation of the functional integrity of thylakoids even after exposure to lethal dose of ionizing radiation. (author)

  2. Nitrogen control of photosynthetic protein synthesis

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, G.W.

    1986-09-01

    Plant growth is severely affected by impaired photosynthesis resulting from nitrogen deficiency. The molecular aspects of this effect are being studied in the green alga Chlamydomonas grown in continuous culture systems. Photosynthetic membranes of nitrogen-limited cells are dramatically depleted in chlorophylls, xanthophylls and proteins of the light-harvesting complexes. In contrast, enzymes of the reductive pentose phosphate cycle and electron transport chain complexes are reduced only 40 to 65% on a per cell basis comparison with nitrogen-sufficient cultures. From analyses of mRNA levels by in vitro translation and hybridization analyses with cloned DNA sequences for photosynthetic proteins, we have found there are rather minor effects of nitrogen deficiency on nuclear or chloroplast gene transcription. Maturation of a transcript of the nuclear-encoded small subunit of ribulose 1,5-bisphosphate carboxylase is inhibited in nitrogen-deficient cells and causes accumulation of large amounts of mRNA precursors. Most of the effects of nitrogen deficiency on photosynthetic proteins appear to result from posttranscriptional regulatory processes: light-harvesting protein synthesis may be sustained but their import into chloroplasts or translocation to photosynthetic membranes is impaired. Nitrogen-deficient cells lack violaxanthin, a pigment that is essential for the structure, function and biogenesis of the major antenna complexes. The absence of this pigment may be a causative factor for the deficiency of light harvesting complexes. Finally, the accumulation of massive amounts of starch and triglycerides in nitrogen-limited cells indicate there are some genes whose maximal expression is dependent upon nitrogen-limiting conditions. 10 refs.

  3. Zooxanthellae Harvested by Ciliates Associated with Brown Band Syndrome of Corals Remain Photosynthetically Competent▿

    Science.gov (United States)

    Ulstrup, Karin E.; Kühl, Michael; Bourne, David G.

    2007-01-01

    Brown band syndrome is a new coral affliction characterized by a local accumulation of yet-unidentified ciliates migrating as a band along the branches of coral colonies. In the current study, morphologically intact zooxanthellae (= Symbiodinium) were observed in great numbers inside the ciliates (>50 dinoflagellates per ciliate). Microscale oxygen measurements and variable chlorophyll a fluorescence analysis along with microscopic observations demonstrated that zooxanthellae within the ciliates are photosynthetically competent and do not become compromised during the progression of the brown band zone. Zooxanthellae showed similar trends in light acclimation in a comparison of rapid light curve and steady-state light curve measures of variable chlorophyll a fluorescence. Extended light exposure of steady-state light curves resulted in higher quantum yields of photosystem II. The brown band tissue exhibited higher photosynthetically active radiation absorptivity, indicating more efficient light absorption due to a higher density of zooxanthellae in the ciliate-dominated zone. This caused relatively higher gross photosynthesis rates in the zone with zooxanthella-containing ciliates compared to healthy coral tissue. The observation of photosynthetically active intracellular zooxanthellae in the ciliates suggests that the latter can benefit from photosynthates produced by ingested zooxanthellae and from photosynthetic oxygen production that alleviates diffusion limitation of oxic respiration in the densely populated brown band tissue. It remains to be shown whether the zooxanthellae form a stable symbiotic association with the ciliate or are engulfed incidentally during grazing on coral tissue and then maintained as active inside the ciliate for a period before being digested and replaced by new zooxanthellae. PMID:17259357

  4. Zooxanthellae harvested by ciliates associated with brown band syndrome of corals remain photosynthetically competent.

    Science.gov (United States)

    Ulstrup, Karin E; Kühl, Michael; Bourne, David G

    2007-03-01

    Brown band syndrome is a new coral affliction characterized by a local accumulation of yet-unidentified ciliates migrating as a band along the branches of coral colonies. In the current study, morphologically intact zooxanthellae (= Symbiodinium) were observed in great numbers inside the ciliates (>50 dinoflagellates per ciliate). Microscale oxygen measurements and variable chlorophyll a fluorescence analysis along with microscopic observations demonstrated that zooxanthellae within the ciliates are photosynthetically competent and do not become compromised during the progression of the brown band zone. Zooxanthellae showed similar trends in light acclimation in a comparison of rapid light curve and steady-state light curve measures of variable chlorophyll a fluorescence. Extended light exposure of steady-state light curves resulted in higher quantum yields of photosystem II. The brown band tissue exhibited higher photosynthetically active radiation absorptivity, indicating more efficient light absorption due to a higher density of zooxanthellae in the ciliate-dominated zone. This caused relatively higher gross photosynthesis rates in the zone with zooxanthella-containing ciliates compared to healthy coral tissue. The observation of photosynthetically active intracellular zooxanthellae in the ciliates suggests that the latter can benefit from photosynthates produced by ingested zooxanthellae and from photosynthetic oxygen production that alleviates diffusion limitation of oxic respiration in the densely populated brown band tissue. It remains to be shown whether the zooxanthellae form a stable symbiotic association with the ciliate or are engulfed incidentally during grazing on coral tissue and then maintained as active inside the ciliate for a period before being digested and replaced by new zooxanthellae.

  5. Oxygen toxicity

    Directory of Open Access Journals (Sweden)

    C. A. van der Westhuizen

    1990-07-01

    Full Text Available Oxygen has been discovered about 200 years ago. Since then the vital physiological involvement of oxygen in various biologi­cal processes, mainly energy production, has been established. However, in the body molecular oxygen can be converted to toxic oxygen metabolites such as superoxide anion, hydrogen peroxide, the hydroxyl radical and singlet oxygen. These toxic metabolites are produced mainly in the mitochondria, plasma membranes and endoplasmic reticulum.

  6. Biodegradation of Emiliania huxleyi Aggregates by natural Prokaryotic Communities under Increasing Hydrostatic Pressure.

    Science.gov (United States)

    Riou, V.; Para, J.; Garel, M.; Guigue, C.; Al Ali, B.; Santinelli, C.; Lefèvre, D.; Gattuso, J. P.; Goutx, M.; Panagiotopoulos, C.; Beaufort, L.; Jacquet, S.; Le Moigne, F. A. C.; Tachikawa, K.; Tamburini, C.

    2016-02-01

    Fluxes of particulate organic carbon (POC) and minerals are positively correlated, suggesting that minerals could enhance the flux of POC into the deep ocean. The so called "ballast effect" posits that minerals could increase sinking particle densities and/or protect the organic matter from heterotrophic degradation. Laboratory controlled experiments on coccolithophorid aggregates under atmospheric pressure show that biogenic calcite both increases particle settling velocities and preserves the organic matter. However, such experiments have yet to include genuine prokaryote rates indicators as well as the effect of increasing pressure. Here, we used the PArticle Sinking Simulator (PASS) to investigate the effect of the increasing pressure on the degradation of Emiliania huxleyi (calcifiers) aggregates. Extra care was taken to obtain culture aggregates with low prokaryotic abundance prior to exposure to natural mesopelagic prokaryotic communities. Particulate organic and inorganic carbon and dissolved organic carbon concentrations were monitored along with the lipid and carbohydrate compositions, as well as prokaryotic community abundance and specific diversity. A control experiment, without natural prokaryotic community addition, indicates that the pressure increase did not have any effect on calcite dissolution observed after ten days. In contrast, the addition of natural prokaryotic community accelerates calcite dissolution under conditions of increasing pressure. Prokaryotic community development and the lipid fraction of E. huxleyi particulate organic carbon are enhanced under increasing pressure. These results suggest that hydrostatic pressure denatures the structural integrity of the carbonate skeleton that protects the cellular organic matter.

  7. Development of a Photosynthetic Microbial Electrochemical Cell (PMEC Reactor Coupled with Dark Fermentation of Organic Wastes: Medium Term Perspectives

    Directory of Open Access Journals (Sweden)

    Samir Bensaid

    2015-01-01

    Full Text Available In this article the concept, the materials and the exploitation potential of a photosynthetic microbial electrochemical cell for the production of hydrogen driven by solar power are investigated. In a photosynthetic microbial electrochemical cell, which is based on photosynthetic microorganisms confined to an anode and heterotrophic bacteria confined to a cathode, water is split by bacteria hosted in the anode bioactive film. The generated electrons are conveyed through external “bio-appendages” developed by the bacteria to transparent nano-pillars made of indium tin oxide (ITO, Fluorine-doped tin oxide (FTO or other conducting materials, and then transferred to the cathode. On the other hand, the generated protons diffuse to the cathode via a polymer electrolyte membrane, where they are reduced by the electrons by heterotrophic bacteria growing attached to a similar pillared structure as that envisaged for the anode and supplemented with a specific low cost substrate (e.g., organic waste, anaerobic digestion outlet. The generated oxygen is released to the atmosphere or stored, while the produced pure hydrogen leaves the electrode through the porous layers. In addition, the integration of the photosynthetic microbial electrochemical cell system with dark fermentation as acidogenic step of anaerobic digester, which is able to produce additional H2, and the use of microbial fuel cell, feed with the residues of dark fermentation (mainly volatile fatty acids, to produce the necessary extra-bias for the photosynthetic microbial electrochemical cell is here analyzed to reveal the potential benefits to this novel integrated technology.

  8. Oceanographic temperature, salinity and oxygen profiles and other measurements from CTD casts by the National Park Service (NPS) and United States Geological Survey (USGS) for the Inventory and Monitoring Program of the Southeast Alaska Network (SEAN) from multiple platforms in Glacier Bay, Alaska from 1993-07-01 to 2016-10-04 (NODC Accession 0074611)

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This dataset contains temperature, salinity, pressure, photosynthetically active radiation (PAR), optical backscatterance (OBS turbidity), dissolved oxygen, and...

  9. Effects of sodium azide on the abundance of prokaryotes and viruses in marine samples.

    Directory of Open Access Journals (Sweden)

    Christian Winter

    Full Text Available Flow cytometry is set to become the standard method for enumerating prokaryotes and viruses in marine samples. However, the samples need to be flash-frozen in liquid nitrogen directly after aldehyde fixation. Because liquid nitrogen may not always be available, we tested the potential of sodium azide as a preservative for prokaryotes and viruses in marine samples as a possible alternative. For that we conducted incubation experiments with untreated and sodium azide treated marine water samples at 4°C and room temperature. The data indicate that sodium azide cannot be used to maintain marine samples used for the enumeration of prokaryotes and viruses.

  10. Biophysical model of prokaryotic diversity in geothermal hot springs.

    Science.gov (United States)

    Klales, Anna; Duncan, James; Nett, Elizabeth Janus; Kane, Suzanne Amador

    2012-02-01

    Recent studies of photosynthetic bacteria living in geothermal hot spring environments have revealed surprisingly complex ecosystems with an unexpected level of genetic diversity. One case of particular interest involves the distribution along hot spring thermal gradients of genetically distinct bacterial strains that differ in their preferred temperatures for reproduction and photosynthesis. In such systems, a single variable, temperature, defines the relevant environmental variation. In spite of this, each region along the thermal gradient exhibits multiple strains of photosynthetic bacteria adapted to several distinct thermal optima, rather than a single thermal strain adapted to the local environmental temperature. Here we analyze microbiology data from several ecological studies to show that the thermal distribution data exhibit several universal features independent of location and specific bacterial strain. These include the distribution of optimal temperatures of different thermal strains and the functional dependence of the net population density on temperature. We present a simple population dynamics model of these systems that is highly constrained by biophysical data and by physical features of the environment. This model can explain in detail the observed thermal population distributions, as well as certain features of population dynamics observed in laboratory studies of the same organisms. © 2012 American Physical Society

  11. Effect of nitrate addition on prokaryotic diversity and the activity of sulfate-reducing prokaryotes in high-temperature oil production systems

    DEFF Research Database (Denmark)

    Gittel, Antje; Wieczorek, Adam; Sørensen, Ketil

    Adding nitrate to injection water is a possible strategy to control the activity of sulfate-reducing prokaryotes (SRP) in oil production system. To assess the effects of nitrate addition, prokaryotic diversity (Bacteria, Archaea, SRP) and SRP activity were studied in the production waters......-treated site was additionally supported by demonstrating their potential activity at 58°C, indicating that the troublesome SRP were pipeline-derived. Consistent with the low frequency of SRP in the clone libraries, no activity could be shown for samples from the nitrate-treated system suggesting that SRP were...... inhibited by nitrate addition. Visualization and quantification of the identified troublesome prokaryotes and potential competitors using the CARD-FISH technique will be performed on production water from both sites....

  12. Identification of a fourth family of lycopene cyclases in photosynthetic bacteria.

    Science.gov (United States)

    Maresca, Julia A; Graham, Joel E; Wu, Martin; Eisen, Jonathan A; Bryant, Donald A

    2007-07-10

    A fourth and large family of lycopene cyclases was identified in photosynthetic prokaryotes. The first member of this family, encoded by the cruA gene of the green sulfur bacterium Chlorobium tepidum, was identified in a complementation assay with a lycopene-producing strain of Escherichia coli. Orthologs of cruA are found in all available green sulfur bacterial genomes and in all cyanobacterial genomes that lack genes encoding CrtL- or CrtY-type lycopene cyclases. The cyanobacterium Synechococcus sp. PCC 7002 has two homologs of CruA, denoted CruA and CruP, and both were shown to have lycopene cyclase activity. Although all characterized lycopene cyclases in plants are CrtL-type proteins, genes orthologous to cruP also occur in plant genomes. The CruA- and CruP-type carotenoid cyclases are members of the FixC dehydrogenase superfamily and are distantly related to CrtL- and CrtY-type lycopene cyclases. Identification of these cyclases fills a major gap in the carotenoid biosynthetic pathways of green sulfur bacteria and cyanobacteria.

  13. Connectivity between surface and deep waters determines prokaryotic diversity in the North Atlantic Deep Water.

    Science.gov (United States)

    Frank, Alexander H; Garcia, Juan A L; Herndl, Gerhard J; Reinthaler, Thomas

    2016-06-01

    To decipher the influence of depth stratification and surface provincialism on the dark ocean prokaryotic community composition, we sampled the major deep-water masses in the eastern North Atlantic covering three biogeographic provinces. Their diversity was evaluated using ordination and canonical analysis of 454 pyrotag sequences. Variance partitioning suggested that 16% of the variation in the bacterial community composition was based on depth stratification while 9% of the variation was due to geographic location. General linear mixed effect models showed that the community of the subsurface waters was connected to the dark ocean prokaryotic communities in different biogeographic provinces. Cluster analysis indicated that some prokaryotic taxa are specific to distinct regions in bathypelagic water masses. Taken together, our data suggest that the dark ocean prokaryotic community composition of the eastern North Atlantic is primed by the formation and the horizontal transport of water masses. © 2016 Society for Applied Microbiology and John Wiley & Sons Ltd.

  14. Magnetic irone oxide nanoparticles in photosynthetic systems

    International Nuclear Information System (INIS)

    Khalilov, R.I.; Nasibova, A.N.; Khomutov, G.B.

    2014-01-01

    Full text : It was found and studied the effect of biogenic formation of magnetic inclusions in photosynthetic systems - in various higher plants under the influence of some external stress factors (radiation impact, moisture deficit) and in a model system - a suspension of chloroplasts. For registration and characterization of magnetic nanoparticles in the samples used EPR spectrometer because superparamagnetic and ferromagnetic nanoparticles have a chcracteristic signals of electron magnetic resonance. For direct visualization of magnetic nanoparticles it was used the method of transmission electron microscopy

  15. Engineering cyanobacteria as photosynthetic feedstock factories.

    Science.gov (United States)

    Hays, Stephanie G; Ducat, Daniel C

    2015-03-01

    Carbohydrate feedstocks are at the root of bioindustrial production and are needed in greater quantities than ever due to increased prioritization of renewable fuels with reduced carbon footprints. Cyanobacteria possess a number of features that make them well suited as an alternative feedstock crop in comparison to traditional terrestrial plant species. Recent advances in genetic engineering, as well as promising preliminary investigations of cyanobacteria in a number of distinct production regimes have illustrated the potential of these aquatic phototrophs as biosynthetic chassis. Further improvements in strain productivities and design, along with enhanced understanding of photosynthetic metabolism in cyanobacteria may pave the way to translate cyanobacterial theoretical potential into realized application.

  16. Culturing photosynthetic bacteria through surface plasmon resonance

    Energy Technology Data Exchange (ETDEWEB)

    Ooms, Matthew D.; Bajin, Lauren; Sinton, David [Department of Mechanical and Industrial Engineering and Centre for Sustainable Energy, University of Toronto, Toronto M5S 3G8 (Canada)

    2012-12-17

    In this work, cultivation of photosynthetic microbes in surface plasmon enhanced evanescent fields is demonstrated. Proliferation of Synechococcus elongatus was obtained on gold surfaces excited with surface plasmons. Excitation over three days resulted in 10 {mu}m thick biofilms with maximum cell volume density of 20% vol/vol (2% more total accumulation than control experiments with direct light). Collectively, these results indicate the ability to (1) excite surface-bound cells using plasmonic light fields, and (2) subsequently grow thick biofilms by coupling light from the surface. Plasmonic light delivery presents opportunities for high-density optofluidic photobioreactors for microalgal analysis and solar fuel production.

  17. A molecular genetic analysis of carotenoid biosynthesis and the effects of carotenoid mutations on other photosynthetic genes in Rhodobacter capsulatus

    International Nuclear Information System (INIS)

    Armstrong, G.A.

    1989-04-01

    The nine known R. capsulatus carotenoid genes are contained within the 46 kilobase (kb) photosynthesis gene cluster. An 11 kb subcluster containing eight of these genes has been cloned and its nucleotide sequence determined. A new gene, crtK, has been located in the middle of the subcluster. The carotenoid gene cluster contains sequences homologous to Escherichia coli ω 70 promoters, rho-independent transcription terminators, and prokaryotic transcriptional factor binding sites. The phenotypes and genotypes of ten transposon Tn5.7 insertion mutations within the carotenoid gene cluster have been analyzed, by characterization of the carotenoids accumulated and high resolution mapping of the Tn5.7 insertions. The enzymatic blockages in previously uncharacterized early carotenoid mutants have been determined using a new in vitro synthesis system, suggesting specific roles for the CrtB and CrtE gene products. The expression of six of the eight carotenoid genes in the cluster is induced upon the shift from dark chemoheterotrophic to anaerobic photosynthetic growth. The magnitude of the induction is equivalent to that of genes encoding structural photosynthesis polypeptides, although the carotenoid genes are induced earlier after the growth shift. Different means of regulating photosynthesis genes in R. capsulatus are discussed, and a rationale for the temporal pattern of expression of the carotenoid genes during photosynthetic adaptation is presented. Comparison of the deduced amino acid sequences of the two dehydrogenases of the R. capsulatus carotenoid biosynthesis pathway reveals two regions of strong similarity. The effect of carotenoid mutations on the photosynthetic phenotype has been studied by examining growth rates, pigments, pigment-protein complexes and gene expression for a complete set of carotenoid mutants. 161 refs

  18. A molecular genetic analysis of carotenoid biosynthesis and the effects of carotenoid mutations on other photosynthetic genes in Rhodobacter capsulatus

    Energy Technology Data Exchange (ETDEWEB)

    Armstrong, G.A.

    1989-04-01

    The nine known R. capsulatus carotenoid genes are contained within the 46 kilobase (kb) photosynthesis gene cluster. An 11 kb subcluster containing eight of these genes has been cloned and its nucleotide sequence determined. A new gene, crtK, has been located in the middle of the subcluster. The carotenoid gene cluster contains sequences homologous to Escherichia coli ..omega../sup 70/ promoters, rho-independent transcription terminators, and prokaryotic transcriptional factor binding sites. The phenotypes and genotypes of ten transposon Tn5.7 insertion mutations within the carotenoid gene cluster have been analyzed, by characterization of the carotenoids accumulated and high resolution mapping of the Tn5.7 insertions. The enzymatic blockages in previously uncharacterized early carotenoid mutants have been determined using a new in vitro synthesis system, suggesting specific roles for the CrtB and CrtE gene products. The expression of six of the eight carotenoid genes in the cluster is induced upon the shift from dark chemoheterotrophic to anaerobic photosynthetic growth. The magnitude of the induction is equivalent to that of genes encoding structural photosynthesis polypeptides, although the carotenoid genes are induced earlier after the growth shift. Different means of regulating photosynthesis genes in R. capsulatus are discussed, and a rationale for the temporal pattern of expression of the carotenoid genes during photosynthetic adaptation is presented. Comparison of the deduced amino acid sequences of the two dehydrogenases of the R. capsulatus carotenoid biosynthesis pathway reveals two regions of strong similarity. The effect of carotenoid mutations on the photosynthetic phenotype has been studied by examining growth rates, pigments, pigment-protein complexes and gene expression for a complete set of carotenoid mutants. 161 refs.

  19. Microscopic Identification of Prokaryotes in Modern and Ancient Halite, Saline Valley and Death Valley, California

    Science.gov (United States)

    Schubert, Brian A.; Lowenstein, Tim K.; Timofeeff, Michael N.

    2009-06-01

    Primary fluid inclusions in halite crystallized in Saline Valley, California, in 1980, 2004-2005, and 2007, contain rod- and coccoid-shaped microparticles the same size and morphology as archaea and bacteria living in modern brines. Primary fluid inclusions from a well-dated (0-100,000 years), 90 m long salt core from Badwater Basin, Death Valley, California, also contain microparticles, here interpreted as halophilic and halotolerant prokaryotes. Prokaryotes are distinguished from crystals on the basis of morphology, optical properties (birefringence), and uniformity of size. Electron micrographs of microparticles from filtered modern brine (Saline Valley), dissolved modern halite crystals (Saline Valley), and dissolved ancient halite crystals (Death Valley) support in situ microscopic observations that prokaryotes are present in fluid inclusions in ancient halite. In the Death Valley salt core, prokaryotes in fluid inclusions occur almost exclusively in halite precipitated in perennial saline lakes 10,000 to 35,000 years ago. This suggests that trapping and preservation of prokaryotes in fluid inclusions is influenced by the surface environment in which the halite originally precipitated. In all cases, prokaryotes in fluid inclusions in halite from the Death Valley salt core are miniaturized (<1 μm diameter cocci, <2.5 μm long, very rare rod shapes), which supports interpretations that the prokaryotes are indigenous to the halite and starvation survival may be the normal response of some prokaryotes to entrapment in fluid inclusions for millennia. These results reinforce the view that fluid inclusions in halite and possibly other evaporites are important repositories of microbial life and should be carefully examined in the search for ancient microorganisms on Earth, Mars, and elsewhere in the Solar System.

  20. Modeling the winter-to-summer transition of prokaryotic and viral abundance in the Arctic Ocean.

    Science.gov (United States)

    Winter, Christian; Payet, Jérôme P; Suttle, Curtis A

    2012-01-01

    One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations.

  1. Modeling the Winter–to–Summer Transition of Prokaryotic and Viral Abundance in the Arctic Ocean

    Science.gov (United States)

    Winter, Christian; Payet, Jérôme P.; Suttle, Curtis A.

    2012-01-01

    One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis. Here, we developed ANN-based models of prokaryotic and viral abundances in the Arctic Ocean. The models were used to identify the best predictors for prokaryotic and viral abundances including cytometrically-distinguishable populations of prokaryotes (high and low nucleic acid cells) and viruses (high- and low-fluorescent viruses) among salinity, temperature, depth, day length, and the concentration of Chlorophyll-a. The best performing ANNs to model the abundances of high and low nucleic acid cells used temperature and Chl-a as input parameters, while the abundances of high- and low-fluorescent viruses used depth, Chl-a, and day length as input parameters. Decreasing viral abundance with increasing depth and decreasing system productivity was captured well by the ANNs. Despite identifying the same predictors for the two populations of prokaryotes and viruses, respectively, the structure of the best performing ANNs differed between high and low nucleic acid cells and between high- and low-fluorescent viruses. Also, the two prokaryotic and viral groups responded differently to changes in the predictor parameters; hence, the cytometric distinction between these populations is ecologically relevant. The models imply that temperature is the main factor explaining most of the variation in the abundances of high nucleic acid cells and total prokaryotes and that the mechanisms governing the reaction to changes in the environment are distinctly different among the prokaryotic and viral populations. PMID:23285186

  2. Viral infections stimulate the metabolism and shape prokaryotic assemblages in submarine mud volcanoes.

    Science.gov (United States)

    Corinaldesi, Cinzia; Dell'Anno, Antonio; Danovaro, Roberto

    2012-06-01

    Mud volcanoes are geological structures in the oceans that have key roles in the functioning of the global ecosystem. Information on the dynamics of benthic viruses and their interactions with prokaryotes in mud volcano ecosystems is still completely lacking. We investigated the impact of viral infection on the mortality and assemblage structure of benthic prokaryotes of five mud volcanoes in the Mediterranean Sea. Mud volcano sediments promote high rates of viral production (1.65-7.89 × 10(9) viruses g(-1) d(-1)), viral-induced prokaryotic mortality (VIPM) (33% cells killed per day) and heterotrophic prokaryotic production (3.0-8.3 μgC g(-1) d(-1)) when compared with sediments outside the mud volcano area. The viral shunt (that is, the microbial biomass converted into dissolved organic matter as a result of viral infection, and thus diverted away from higher trophic levels) provides 49 mgC m(-2) d(-1), thus fuelling the metabolism of uninfected prokaryotes and contributing to the total C budget. Bacteria are the dominant components of prokaryotic assemblages in surface sediments of mud volcanoes, whereas archaea dominate the subsurface sediment layers. Multivariate multiple regression analyses show that prokaryotic assemblage composition is not only dependant on the geochemical features and processes of mud volcano ecosystems but also on synergistic interactions between bottom-up (that is, trophic resources) and top-down (that is, VIPM) controlling factors. Overall, these findings highlight the significant role of the viral shunt in sustaining the metabolism of prokaryotes and shaping their assemblage structure in mud volcano sediments, and they provide new clues for our understanding of the functioning of cold-seep ecosystems.

  3. Oxygen Therapy

    Science.gov (United States)

    ... their breathing to dangerously low levels. Will I need oxygen when I sleep? Usually if you use supplemental oxygen during the ... your health care provider tells you you only need to use oxygen for exercise or sleep. Even if you feel “fine” off of your ...

  4. RNA function and phosphorus use by photosynthetic organisms

    Directory of Open Access Journals (Sweden)

    John Albert Raven

    2013-12-01

    Full Text Available Phosphorus (P in RNA accounts for half or more of the total non-storage P in oxygenic photolithotrophs grown in either P-replete or P-limiting growth conditions. Since many natural environments are P-limited for photosynthetic primary productivity, and peak phosphorus fertilizer production is forecast for the next few decades, the paper analyses what economies in P allocation to RNA could, in principle, increase P use efficiency of growth (rate of dry matter production per unit organism P. The possibilities of decreasing P allocation to RNA without decreasing growth rate include a more widespread down-regulation of RNA production in P-limited organisms (as in the growth rate hypothesis, optimal allocation of P to RNA spatially among cell compartments and organs, and temporally depending on the stage of growth, and, for exponentially growing organisms with a constant fraction of P in RNA, a constant rate of protein synthesis through the diel cycle. Acting on these suggestions would be technically demanding, and could have unintended consequences for other aspect of metabolism.

  5. NMR comparison of prokaryotic and eukaryotic cytochromes c

    International Nuclear Information System (INIS)

    Chau, Meihing; Cai, Meng Li; Timkovich, R.

    1990-01-01

    1 H NMR spectroscopy has been used to examine ferrocytochrome c-551 from Pseudomonas aeruginosa (ATCC 19429) over the pH range 3.5-10.6 and the temperature range 4-60 degree C. Resonance assignments are proposed for main-chain and side-chain protons. Comparison of results for cytochrome c-551 to recently assigned spectra for horse cytochrome c and mutants of yeast iso-1 cytochrome reveals some unique resonances with unusual chemical shifts in all cytochromes that may serve as markers for the heme region. Results for cytochrome c-551 indicate that in the smaller prokaryotic cytochrome, all benzoid side chains are rapidly flipping on the NMR time scale. In contrast, in eukaryotic cytochromes there are some rings flipping slowly on the NMR time scale. The ferrocytochrome c-551 undergoes a transition linked to pH with a pK around 7. The pH behavior of assigned resonances provides evidence that the site of protonation is the inner or buried 17-propionic acid heme substituent (IUPAC-IUB porphyrin nomenclature). Conformational heterogeneity has been observed for segments near the inner heme propionate substituent

  6. Structural similarities between prokaryotic and eukaryotic 5S ribosomal RNAs

    International Nuclear Information System (INIS)

    Welfle, H.; Boehm, S.; Damaschun, G.; Fabian, H.; Gast, K.; Misselwitz, R.; Mueller, J.J.; Zirwer, D.; Filimonov, V.V.; Venyaminov, S.Yu.; Zalkova, T.N.

    1986-01-01

    5S RNAs from rat liver and E. coli have been studied by diffuse X-ray and dynamic light scattering and by infrared and Raman spectroscopy. Identical structures at a resolution of 1 nm can be deduced from the comparison of the experimental X-ray scattering curves and electron distance distribution functions and from the agreement of the shape parameters. A flat shape model with a compact central region and two protruding arms was derived. Double helical stems are eleven-fold helices with a mean base pair distance of 0.28 nm. The number of base pairs (26 GC, 9 AU for E. coli; 27 GC, 9 AU for rat liver) and the degree of base stacking are the same within the experimental error. A very high regularity in the ribophosphate backbone is indicated for both 5S RNAs. The observed structural similarity and the consensus secondary structure pattern derived from comparative sequence analyses suggest the conclusion that prokaryotic and eukaryotic 5S RNAs are in general very similar with respect to their fundamental structural features. (author)

  7. Current Developments in Prokaryotic Single Cell Whole Genome Amplification

    Energy Technology Data Exchange (ETDEWEB)

    Goudeau, Danielle; Nath, Nandita; Ciobanu, Doina; Cheng, Jan-Fang; Malmstrom, Rex

    2014-03-14

    Our approach to prokaryotic single-cell Whole Genome Amplification at the JGI continues to evolve. To increase both the quality and number of single-cell genomes produced, we explore all aspects of the process from cell sorting to sequencing. For example, we now utilize specialized reagents, acoustic liquid handling, and reduced reaction volumes eliminate non-target DNA contamination in WGA reactions. More specifically, we use a cleaner commercial WGA kit from Qiagen that employs a UV decontamination procedure initially developed at the JGI, and we use the Labcyte Echo for tip-less liquid transfer to set up 2uL reactions. Acoustic liquid handling also dramatically reduces reagent costs. In addition, we are exploring new cell lysis methods including treatment with Proteinase K, lysozyme, and other detergents, in order to complement standard alkaline lysis and allow for more efficient disruption of a wider range of cells. Incomplete lysis represents a major hurdle for WGA on some environmental samples, especially rhizosphere, peatland, and other soils. Finding effective lysis strategies that are also compatible with WGA is challenging, and we are currently assessing the impact of various strategies on genome recovery.

  8. Prokaryotic phylogenetic diversity of Hungarian deep subsurface geothermal well waters.

    Science.gov (United States)

    Németh, Andrea; Szirányi, Barbara; Krett, Gergely; Janurik, Endre; Kosáros, Tünde; Pekár, Ferenc; Márialigeti, Károly; Borsodi, Andrea K

    2014-09-01

    Geothermal wells characterized by thermal waters warmer than 30°C can be found in more than 65% of the area of Hungary. The examined thermal wells located nearby Szarvas are used for heating industrial and agricultural facilities because of their relatively high hydrocarbon content. The aim of this study was to reveal the prokaryotic community structure of the water of SZR18, K87 and SZR21 geothermal wells using molecular cloning methods and Denaturing Gradient Gel Electrophoresis (DGGE). Water samples from the outflow pipes were collected in 2012 and 2013. The phylogenetic distribution of archaeal molecular clones was very similar in each sample, the most abundant groups belonged to the genera Methanosaeta, Methanothermobacter and Thermofilum. In contrast, the distribution of bacterial molecular clones was very diverse. Many of them showed the closest sequence similarities to uncultured clone sequences from similar thermal environments. From the water of the SZR18 well, phylotypes closely related to genera Fictibacillus and Alicyclobacillus (Firmicutes) were only revealed, while the bacterial diversity of the K87 well water was much higher. Here, the members of the phyla Thermodesulfobacteria, Proteobacteria, Nitrospira, Chlorobi, OP1 and OPB7 were also detected besides Firmicutes.

  9. VU-B radiation inhibits the photosynthetic electron transport chain in chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    Cai, W.; Li, X.; Chen, L.

    2016-01-01

    UV radiation of sunlight is one of harmful factors for earth organisms, especially for photoautotrophs because they require light for energy and biomass production. A number of works have already been done regarding the effects of UV-B radiation at biochemical and molecular level, which showed that UV-B radiation could inhibit photosynthesis activity and reduce photosynthetic electron transport. However quite limited information can accurately make out inhibition site of UV-B radiation on photosynthetic electron transport. In this study, this issue was investigated through measuring oxygen evolution activity, chlorophyll a fluorescence and gene expression in a model unicellular green alga Chlamydomonas reinhardtii. Our results indicated that UV-B radiation could evidently decrease photosynthesis activity and inhibit electron transport by blocking electron transfer process from the first plastoquinone electron acceptors QA to second plastoquinone electron acceptors QB, but not impair electron transfer from the water oxidizing complex to QA. The psbA gene expression was also altered by UV-B radiation, where up-regulation occurred at 2, 4 and 6h after exposure and down-regulation happened at 12 and 24 h after exposure. These results suggested that UV-B could affects D1 protein normal turnover, so there was not enough D1 for binding with QB, which may affect photosynthetic electron transport and photosynthesis activity. (author)

  10. Competition for inorganic carbon between oxygenic and anoxygenic phototrophs in a hypersaline microbial mat, Guerrero Negro, Mexico

    DEFF Research Database (Denmark)

    Finke, Niko; Hoehler, Tori M.; Polerecky, Lubos

    2013-01-01

    While most oxygenic phototrophs harvest light only in the visible range (400-700 nm, VIS), anoxygenic phototrophs can harvest near infrared light (> 700 nm, NIR). To study interactions between the photosynthetic guilds we used microsensors to measure oxygen and gross oxygenic photosynthesis (gOP)...

  11. Redox regulation of photosynthetic gene expression.

    Science.gov (United States)

    Queval, Guillaume; Foyer, Christine H

    2012-12-19

    Redox chemistry and redox regulation are central to the operation of photosynthesis and respiration. However, the roles of different oxidants and antioxidants in the regulation of photosynthetic or respiratory gene expression remain poorly understood. Leaf transcriptome profiles of a range of Arabidopsis thaliana genotypes that are deficient in either hydrogen peroxide processing enzymes or in low molecular weight antioxidant were therefore compared to determine how different antioxidant systems that process hydrogen peroxide influence transcripts encoding proteins targeted to the chloroplasts or mitochondria. Less than 10 per cent overlap was observed in the transcriptome patterns of leaves that are deficient in either photorespiratory (catalase (cat)2) or chloroplastic (thylakoid ascorbate peroxidase (tapx)) hydrogen peroxide processing. Transcripts encoding photosystem II (PSII) repair cycle components were lower in glutathione-deficient leaves, as were the thylakoid NAD(P)H (nicotinamide adenine dinucleotide (phosphate)) dehydrogenases (NDH) mRNAs. Some thylakoid NDH mRNAs were also less abundant in tAPX-deficient and ascorbate-deficient leaves. Transcripts encoding the external and internal respiratory NDHs were increased by low glutathione and low ascorbate. Regulation of transcripts encoding specific components of the photosynthetic and respiratory electron transport chains by hydrogen peroxide, ascorbate and glutathione may serve to balance non-cyclic and cyclic electron flow pathways in relation to oxidant production and reductant availability.

  12. Photosynthetic pathways of some aquatic plants

    Energy Technology Data Exchange (ETDEWEB)

    Hough, R A [Wayne State Univ., Detroit; Wetzel, R G

    1977-12-01

    Over 40 species of aquatic angiosperms, including submersed, floating and emergent types, have been examined for photosynthetic status as part of a search for possible aquatic C/sub 4/ species. The C/sub 4/ system is viewed as potentially of adaptive value in certain aquatic situations, although evidence for its occurrence there is not conclusive. Emphasis was on plants from North-temperate softwater and hardwater lakes to explore both possibilities of CO/sub 2/ limitation, i.e., low total inorganic carbon in softwater vs. low free CO/sub 2/ in hardwater lakes. On the basis of leaf cross-section anatomy, all plants examined, with one exception, clearly did not show evidence of C/sub 4/ ''Krantz anatomy.'' In the submersed plant Potamogeton praelongus Wulf, large starch-producing chloroplasts were concentrated in cells surrounding vascular bundles and in a narrow band of cells between vascular bundles. The in situ photosynthetic rate of this plant was twice that of a related species, but other evidence including PEP carboxylase content and photorespiratory response to high O/sub 2/ did not confirm the presence of the C/sub 4/ photosynthesis.

  13. Diversity, abundance and niche differentiation of ammonia-oxidizing prokaryotes in mud deposits of the eastern China marginal seas

    Directory of Open Access Journals (Sweden)

    Shaolan eYu

    2016-02-01

    Full Text Available The eastern China marginal seas are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA and bacteria (AOB were investigated in mud deposits of the South Yellow Sea (SYS and the East China Sea (ECS by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia and silicate (SiO32-, was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ15NTN and SiO32-, and nitrate and δ13C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO32-. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits.

  14. Diversity, Abundance, and Niche Differentiation of Ammonia-Oxidizing Prokaryotes in Mud Deposits of the Eastern China Marginal Seas.

    Science.gov (United States)

    Yu, Shaolan; Yao, Peng; Liu, Jiwen; Zhao, Bin; Zhang, Guiling; Zhao, Meixun; Yu, Zhigang; Zhang, Xiao-Hua

    2016-01-01

    The eastern China marginal seas (ECMS) are prominent examples of river-dominated ocean margins, whose most characteristic feature is the existence of isolated mud patches on sandy sediments. Ammonia-oxidizing prokaryotes play a crucial role in the nitrogen cycles of many marine environments, including marginal seas. However, few studies have attempted to address the distribution patterns of ammonia-oxidizing prokaryotes in mud deposits of these seas. The horizontal and vertical community composition and abundance of ammonia-oxidizing archaea (AOA) and bacteria (AOB) were investigated in mud deposits of the South Yellow Sea (SYS) and the East China Sea (ECS) by using amoA clone libraries and quantitative PCR. The diversity of AOB was comparable or higher in the mud zone of SYS and lower in ECS when compared with AOA. Vertically, surface sediments had generally higher diversity of AOA and AOB than middle and bottom layers. Diversity of AOA and AOB showed significant correlation with latitude. Nitrosopumilus and Nitrosospira lineages dominated AOA and AOB communities, respectively. Both AOA and AOB assemblages exhibited greater variations across different sites than those among various depths at one site. The abundance of bacterial amoA was generally higher than that of archaeal amoA, and both of them decreased with depth. Niche differentiation, which was affected by dissolved oxygen, salinity, ammonia, and silicate (SiO[Formula: see text]), was observed between AOA and AOB and among different groups of them. The spatial distribution of AOA and AOB was significantly correlated with δ(15)NTN and SiO[Formula: see text], and nitrate and δ(13)C, respectively. Both archaeal and bacterial amoA abundance correlated strongly with SiO[Formula: see text]. This study improves our understanding of spatial distribution of AOA and AOB in ecosystems featuring oceanic mud deposits.

  15. Mn K-edge XANES spectroscopy of photosynthetic water oxidation enzyme in the S0-, S1-, S2- and S3-states induced by flash excitation

    International Nuclear Information System (INIS)

    Ono, Taka-aki; Noguchi, Takumi; Inoue, Yorinao; Kusunoki, Masami; Matsushita, Tadashi; Oyanagi, Hiroyuki.

    1993-01-01

    Electronic and structural rearrangement of the Mn-cluster during the four step oxidation of water in photosynthetic oxygen evolution was studied by XANES spectroscopy. The Mn K-edge energy of the spectrum was changed with flash number to show a clear quadruple oscillation, indicating a periodic change in oxidation and electronic state of the Mn-cluster depending on Joliot and Kok's oxygen clock. (author)

  16. Oxygen Therapy

    Directory of Open Access Journals (Sweden)

    Bonnie Solmes

    2000-01-01

    Full Text Available LTOT is prescribed for people with chronic lung disease in whom there is a decrease in the ability of the lungs to supply enough oxygen to the body. The heart is obliged to pump faster to meet the body's oxygen requirements. This may place undue stress on the heart, resulting in palpitations, dizziness and fatigue. A low oxygen level in arterial blood is also harmful to the heart, the brain and the pulmonary blood vessels. Oxygen therapy is used to break this cycle. A person with low blood oxygen will often be able to accomplish more with less fatigue with the help of supplemental oxygen therapy. Shortness of breath is a mechanical problem resulting from the effects of chronic obstructive pulmonary disease. Oxygen therapy may or may not reduce shortness of breath, but it will help the lungs and heart to function with less stress.

  17. Hybrid artificial photosynthetic systems comprising semiconductors as light harvesters and biomimetic complexes as molecular cocatalysts.

    Science.gov (United States)

    Wen, Fuyu; Li, Can

    2013-11-19

    Solar fuel production through artificial photosynthesis may be a key to generating abundant and clean energy, thus addressing the high energy needs of the world's expanding population. As the crucial components of photosynthesis, the artificial photosynthetic system should be composed of a light harvester (e.g., semiconductor or molecular dye), a reduction cocatalyst (e.g., hydrogenase mimic, noble metal), and an oxidation cocatalyst (e.g., photosystem II mimic for oxygen evolution from water oxidation). Solar fuel production catalyzed by an artificial photosynthetic system starts from the absorption of sunlight by the light harvester, where charge separation takes place, followed by a charge transfer to the reduction and oxidation cocatalysts, where redox reaction processes occur. One of the most challenging problems is to develop an artificial photosynthetic solar fuel production system that is both highly efficient and stable. The assembly of cocatalysts on the semiconductor (light harvester) not only can facilitate the charge separation, but also can lower the activation energy or overpotential for the reactions. An efficient light harvester loaded with suitable reduction and oxidation cocatalysts is the key for high efficiency of artificial photosynthetic systems. In this Account, we describe our strategy of hybrid photocatalysts using semiconductors as light harvesters with biomimetic complexes as molecular cocatalysts to construct efficient and stable artificial photosynthetic systems. We chose semiconductor nanoparticles as light harvesters because of their broad spectral absorption and relatively robust properties compared with a natural photosynthesis system. Using biomimetic complexes as cocatalysts can significantly facilitate charge separation via fast charge transfer from the semiconductor to the molecular cocatalysts and also catalyze the chemical reactions of solar fuel production. The hybrid photocatalysts supply us with a platform to study the

  18. Genes, Genomes, and Assemblages of Modern Anoxygenic Photosynthetic Cyanobacteria as Proxies for Ancient Cyanobacteria

    Science.gov (United States)

    Grim, S. L.; Dick, G.

    2015-12-01

    Oxygenic photosynthetic (OP) cyanobacteria were responsible for the production of O2 during the Proterozoic. However, the extent and degree of oxygenation of the atmosphere and oceans varied for over 2 Ga after OP cyanobacteria first appeared in the geologic record. Cyanobacteria capable of anoxygenic photosynthesis (AP) may have altered the trajectory of oxygenation, yet the scope of their role in the Proterozoic is not well known. Modern cyanobacterial populations from Middle Island Sinkhole (MIS), Michigan and a handful of cultured cyanobacterial strains, are capable of OP and AP. With their metabolic versatility, these microbes may approximate ancient cyanobacterial assemblages that mediated Earth's oxygenation. To better characterize the taxonomic and genetic signatures of these modern AP/OP cyanobacteria, we sequenced 16S rRNA genes and conducted 'omics analyses on cultured strains, lab mesocosms, and MIS cyanobacterial mat samples collected over multiple years from May to September. Diversity in the MIS cyanobacterial mat is low, with one member of Oscillatoriales dominating at all times. However, Planktothrix members are more abundant in the cyanobacterial community in late summer and fall. The shift in cyanobacterial community composition may be linked to seasonally changing light intensity. In lab mesocosms of MIS microbial mat, we observed a shift in dominant cyanobacterial groups as well as the emergence of Chlorobium, bacteria that specialize in AP. These shifts in microbial community composition and metabolism are likely in response to changing environmental parameters such as the availability of light and sulfide. Further research is needed to understand the impacts of the changing photosynthetic community on oxygen production and the entire microbial consortium. Our study connects genes and genomes of AP cyanobacteria to their environment, and improves understanding of cyanobacterial metabolic strategies that may have shaped Earth's redox evolution.

  19. ATGC: a database of orthologous genes from closely related prokaryotic genomes and a research platform for microevolution of prokaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Novichkov, Pavel S.; Ratnere, Igor; Wolf, Yuri I.; Koonin, Eugene V.; Dubchak, Inna

    2009-07-23

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov.

  20. 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

  1. Influence of the quantity and quality of light on photosynthetic periodicity in coral endosymbiotic algae.

    Directory of Open Access Journals (Sweden)

    Michal Sorek

    Full Text Available Symbiotic corals, which are benthic organisms intimately linked with their environment, have evolved many ways to deal with fluctuations in the local marine environment. One possible coping mechanism is the endogenous circadian clock, which is characterized as free running, maintaining a ~24 h periodicity of circuits under constant stimuli or in the absence of external cues. The quantity and quality of light were found to be the most influential factors governing the endogenous clock for plants and algae. Unicellular dinoflagellate algae are among the best examples of organisms that exhibit circadian clocks using light as the dominant signal. This study is the first to examine the effects of light intensity and quality on the rhythmicity of photosynthesis in the symbiotic dinoflagellate Symbiodinium sp., both as a free-living organism and in symbiosis with the coral Stylophora pistillata. Oxygen production measurements in Symbiodinium cultures exhibited rhythmicity with a periodicity of approximately 24 h under constant high light (LL, whereas under medium and low light, the cycle time increased. Exposing Symbiodinium cultures and corals to spectral light revealed different effects of blue and red light on the photosynthetic rhythm, specifically shortening or increasing the cycle time respectively. These findings suggest that the photosynthetic rhythm is entrained by different light cues, which are wired to an endogenous circadian clock. Furthermore, we provide evidence that mRNA expression was higher under blue light for two potential cryptochrome genes and higher under red light for a phytochrome gene isolated from Symbiodinium. These results offer the first evidence of the impact of the intensity and quality of light on the photosynthetic rhythm in algal cells living freely or as part of a symbiotic association. Our results indicate the presence of a circadian oscillator in Symbiodinium governing the photosynthetic apparatus through a light

  2. The effect of nitrogen on the development and photosynthetic activity ...

    African Journals Online (AJOL)

    Whole plant net photosynthetic rates appeared to vary according to the units in which the activity is expressed. The optimum levels of photosynthetic activity differed with the stage of development, depending on the basis of expression. The form and concentration of nitrogen applied influenced morphological development ...

  3. Research on spatial distribution of photosynthetic characteristics of Winter Wheat

    Science.gov (United States)

    Yan, Q. Q.; Zhou, Q. Y.; Zhang, B. Z.; Han, X.; Han, N. N.; Li, S. M.

    2018-03-01

    In order to explore the spatial distribution of photosynthetic characteristics of winter wheat leaf, the photosynthetic rate on different parts of leaf (leaf base-leaf middle-leaf apex) and that on each canopy (top layer-middle layer-bottom layer) leaf during the whole growth period of winter wheat were measured. The variation of photosynthetic rate with PAR and the spatial distribution of winter wheat leaf during the whole growth periods were analysed. The results showed that the photosynthetic rate of different parts of winter wheat increased with the increase of PAR, which was showed as leaf base>leaf middle>leaf apex. In the same growth period, photosynthetic rate in different parts of the tablet was showed as leaf middle>leaf base>leaf apex. For the different canopy layer of winter wheat, the photosynthetic rate of the top layer leaf was significantly greater than that of the middle layer and lower layer leaf. The photosynthetic rate of the top layer leaf was the largest in the leaf base position. The photosynthetic rate of leaf of the same canopy layer at different growth stages were showed as tasseling stage >grain filling stage > maturation stage.

  4. Effects of proline on photosynthesis, root reactive oxygen species ...

    African Journals Online (AJOL)

    Effects of 0.2 mM proline applied to saline nutrient solution on biomass, chlorophyll content, photosynthetic parameters, reactive oxygen species and antioxidant enzymes activities of two melon cultivars (cv. Yuhuang and cv. Xuemei) were examined. Results indicate that exogenous proline increased the fresh and dry ...

  5. Microbial eukaryote diversity in the marine oxygen minimum zone off northern Chile

    OpenAIRE

    Parris, Darren J.; Ganesh, Sangita; Edgcomb, Virginia P.; Stewart, Frank J.; DeLong, Edward

    2014-01-01

    Molecular surveys are revealing diverse eukaryotic assemblages in oxygen-limited ocean waters. These communities may play pivotal ecological roles through autotrophy, feeding, and a wide range of symbiotic associations with prokaryotes. We used 18S rRNA gene sequencing to provide the first snapshot of pelagic microeukaryotic community structure in two cellular size fractions (0.2-1.6 µm, >1.6 µm) from seven depths through the anoxic oxygen minimum zone (OMZ) off northern Chile. Sequencing ...

  6. Seasonal response of photosynthetic electron transport and energy dissipation in the eighth year of exposure to elevated atmospheric CO2 (FACE) in Pinus taeda (loblolly pine)

    International Nuclear Information System (INIS)

    Logan, B.A.; Combs, A.; Kent, R.; Stanley, L.; Myers, K.; Tissue, D.T.; Western Sydney Univ., Richmond, NSW

    2009-01-01

    This study investigated the biological adaptation of loblolly pine following long-term seasonal exposure to elevated carbon dioxide (CO 2 ) partial pressures (pCO 2 ). Exposure to elevated atmospheric CO 2 (pCO 2 ) usually results in significant stimulation in light-saturated rates of photosynthetic CO 2 assimilation. Plants are protected against photoinhibition by biochemical processes known as photoprotection, including energy dissipation, which converts excess absorbed light energy into heat. This study was conducted in the eighth year of exposure to elevated pCO 2 at the Duke FACE site. The effect of elevated pCO 2 on electron transport and energy dissipation in the pine trees was examined by coupling the analyses of the capacity for photosynthetic oxygen (O 2 ) evolution, chlorophyll fluorescence emission and photosynthetic pigment composition with measurements of net photosynthetic CO 2 assimilation (Asat). During the summer growing season, Asat was 50 per cent higher in current-year needles and 24 per cent higher in year-old needles in elevated pCO 2 in comparison with needles of the same age cohort in ambient pCO 2 . Thus, older needles exhibited greater photosynthetic down-regulation than younger needles in elevated pCO 2 . In the winter, Asat was not significantly affected by growth pCO 2 . Asat was lower in winter than in summer. Growth at elevated pCO 2 had no significant effect on the capacity for photosynthetic oxygen evolution, photosystem 2 efficiencies, chlorophyll content or the size and conversion state of the xanthophyll cycle, regardless of season or needle age. There was no evidence that photosynthetic electron transport or photoprotective energy dissipation responded to compensate for the effects of elevated pCO 2 on Calvin cycle activity. 73 refs., 4 figs

  7. Oxidation of inorganic sulfur compounds in acidophilic prokaryotes

    Energy Technology Data Exchange (ETDEWEB)

    Rohwerder, T.; Sand, W. [Universitaet Duisburg-Essen, Biofilm Centre, Aquatic Biotechnology, Duisburg (Germany)

    2007-07-15

    The oxidation of reduced inorganic sulfur compounds to sulfuric acid is of great importance for biohydrometallurgical technologies as well as the formation of acidic (below pH 3) and often heavy metal-contaminated environments. The use of elemental sulfur as an electron donor is the predominant energy-yielding process in acidic natural sulfur-rich biotopes but also at mining sites containing sulfidic ores. Contrary to its significant role in the global sulfur cycle and its biotechnological importance, the microbial fundamentals of acidophilic sulfur oxidation are only incompletely understood. Besides giving an overview of sulfur-oxidizing acidophiles, this review describes the so far known enzymatic reactions related to elemental sulfur oxidation in acidophilic bacteria and archaea. Although generally similar reactions are employed in both prokaryotic groups, the stoichiometry of the key enzymes is different. Bacteria oxidize elemental sulfur by a sulfur dioxygenase to sulfite whereas in archaea, a sulfur oxygenase reductase is used forming equal amounts of sulfide and sulfite. In both cases, the activation mechanism of elemental sulfur is not known but highly reactive linear sulfur forms are assumed to be the actual substrate. Inhibition as well as promotion of these biochemical steps is highly relevant in bioleaching operations. An efficient oxidation can prevent the formation of passivating sulfur layers. In other cases, a specific inhibition of sulfur biooxidation may be beneficial for reducing cooling and neutralization costs. In conclusion, the demand for a better knowledge of the biochemistry of sulfur-oxidizing acidophiles is underlined. (Abstract Copyright [2007], Wiley Periodicals, Inc.)

  8. Porphyrin and fullerene-based artificial photosynthetic materials for photovoltaics

    International Nuclear Information System (INIS)

    Imahori, Hiroshi; Kashiwagi, Yukiyasu; Hasobe, Taku; Kimura, Makoto; Hanada, Takeshi; Nishimura, Yoshinobu; Yamazaki, Iwao; Araki, Yasuyuki; Ito, Osamu; Fukuzumi, Shunichi

    2004-01-01

    We have developed artificial photosynthetic systems in which porphyrins and fullerenes are self-assembled as building blocks into nanostructured molecular light-harvesting materials and photovoltaic devices. Multistep electron transfer strategy has been combined with our finding that porphyrin and fullerene systems have small reorganization energies, which are suitable for the construction of light energy conversion systems as well as artificial photosynthetic models. Highly efficient photosynthetic electron transfer reactions have been realized at ITO electrodes modified with self-assembled monolayers of porphyrin oligomers as well as porphyrin-fullerene linked systems. Porphyrin-modified gold nanoclusters have been found to have potential as artificial photosynthetic materials. These results provide basic information for the development of nanostructured artificial photosynthetic systems

  9. Morning reduction of photosynthetic capacity before midday depression.

    Science.gov (United States)

    Koyama, Kohei; Takemoto, Shuhei

    2014-03-17

    Midday depression of photosynthesis has important consequences for ecosystem carbon exchange. Recent studies of forest trees have demonstrated that latent reduction of photosynthetic capacity can begin in the early morning, preceding the midday depression. We investigated whether such early morning reduction also occurs in an herbaceous species, Oenothera biennis. Diurnal changes of the photosynthetic light response curve (measured using a light-emitting diode) and incident sunlight intensity were measured under field conditions. The following results were obtained: (1) the light-saturated photosynthetic rate decreased beginning at sunrise; (2) the incident sunlight intensity on the leaves increased from sunrise; and (3) combining (1) and (2), the net photosynthetic rate under natural sunlight intensity increased from sunrise, reached a maximum at mid-morning, and then showed midday depression. Our results demonstrate that the latent morning reduction of photosynthetic capacity begins at sunrise, preceding the apparent midday depression, in agreement with previous studies of forest trees.

  10. Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi indicated by metagenomics

    Science.gov (United States)

    Li, Zhi-Yong; Wang, Yue-Zhu; He, Li-Ming; Zheng, Hua-Jun

    2014-01-01

    The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi. PMID:24463735

  11. Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Neamphius huxleyi [corrected]. indicated by metagenomics.

    Science.gov (United States)

    Li, Zhi-Yong; Wang, Yue-Zhu; He, Li-Ming; Zheng, Hua-Jun

    2014-01-27

    The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Neamphius huxleyi [corrected] . at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Neamphius huxleyi [corrected]. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Neamphius huxleyi [corrected].

  12. Metabolic profiles of prokaryotic and eukaryotic communities in deep-sea sponge Lamellomorpha sp. indicated by metagenomics

    Science.gov (United States)

    Li, Zhi-Yong; Wang, Yue-Zhu; He, Li-Ming; Zheng, Hua-Jun

    2014-01-01

    The whole metabolism of a sponge holobiont and the respective contributions of prokaryotic and eukaryotic symbionts and their associations with the sponge host remain largely unclear. Meanwhile, compared with shallow water sponges, deep-sea sponges are rarely understood. Here we report the metagenomic exploration of deep-sea sponge Lamellomorpha sp. at the whole community level. Metagenomic data showed phylogenetically diverse prokaryotes and eukaryotes in Lamellomorpha sp.. MEGAN and gene enrichment analyses indicated different metabolic potentials of prokaryotic symbionts from eukaryotic symbionts, especially in nitrogen and carbon metabolisms, and their molecular interactions with the sponge host. These results supported the hypothesis that prokaryotic and eukaryotic symbionts have different ecological roles and relationships with sponge host. Moreover, vigorous denitrification, and CO2 fixation by chemoautotrophic prokaryotes were suggested for this deep-sea sponge. The study provided novel insights into the respective potentials of prokaryotic and eukaryotic symbionts and their associations with deep-sea sponge Lamellomorpha sp..

  13. Titania may produce abiotic oxygen atmospheres on habitable exoplanets

    OpenAIRE

    Norio Narita; Takafumi Enomoto; Shigeyuki Masaoka; Nobuhiko Kusakabe

    2015-01-01

    The search for habitable exoplanets in the Universe is actively ongoing in the field of astronomy. The biggest future milestone is to determine whether life exists on such habitable exoplanets. In that context, oxygen in the atmosphere has been considered strong evidence for the presence of photosynthetic organisms. In this paper, we show that a previously unconsidered photochemical mechanism by titanium (IV) oxide (titania) can produce abiotic oxygen from liquid water under near ultraviolet ...

  14. Diversity and abundance of photosynthetic sponges in temperate Western Australia

    Directory of Open Access Journals (Sweden)

    Brümmer Franz

    2009-02-01

    Full Text Available Abstract Background Photosynthetic sponges are important components of reef ecosystems around the world, but are poorly understood. It is often assumed that temperate regions have low diversity and abundance of photosynthetic sponges, but to date no studies have investigated this question. The aim of this study was to compare the percentages of photosynthetic sponges in temperate Western Australia (WA with previously published data on tropical regions, and to determine the abundance and diversity of these associations in a range of temperate environments. Results We sampled sponges on 5 m belt transects to determine the percentage of photosynthetic sponges and identified at least one representative of each group of symbionts using 16S rDNA sequencing together with microscopy techniques. Our results demonstrate that photosynthetic sponges are abundant in temperate WA, with an average of 63% of sponge individuals hosting high levels of photosynthetic symbionts and 11% with low to medium levels. These percentages of photosynthetic sponges are comparable to those found on tropical reefs and may have important implications for ecosystem function on temperate reefs in other areas of the world. A diverse range of symbionts sometimes occurred within a small geographic area, including the three "big" cyanobacterial clades, Oscillatoria spongeliae, "Candidatus Synechococcus spongiarum" and Synechocystis species, and it appears that these clades all occur in a wide range of sponges. Additionally, spongin-permeating red algae occurred in at least 7 sponge species. This study provides the first investigation of the molecular phylogeny of rhodophyte symbionts in sponges. Conclusion Photosynthetic sponges are abundant and diverse in temperate WA, with comparable percentages of photosynthetic to non-photosynthetic sponges to tropical zones. It appears that there are three common generalist clades of cyanobacterial symbionts of sponges which occur in a wide

  15. The Arabidopsis ppi1 Mutant Is Specifically Defective in the Expression, Chloroplast Import, and Accumulation of Photosynthetic ProteinsW⃞

    Science.gov (United States)

    Kubis, Sybille; Baldwin, Amy; Patel, Ramesh; Razzaq, Azam; Dupree, Paul; Lilley, Kathryn; Kurth, Joachim; Leister, Dario; Jarvis, Paul

    2003-01-01

    The import of nucleus-encoded proteins into chloroplasts is mediated by translocon complexes in the envelope membranes. A component of the translocon in the outer envelope membrane, Toc34, is encoded in Arabidopsis by two homologous genes, atTOC33 and atTOC34. Whereas atTOC34 displays relatively uniform expression throughout development, atTOC33 is strongly upregulated in rapidly growing, photosynthetic tissues. To understand the reason for the existence of these two related genes, we characterized the atTOC33 knockout mutant ppi1. Immunoblotting and proteomics revealed that components of the photosynthetic apparatus are deficient in ppi1 chloroplasts and that nonphotosynthetic chloroplast proteins are unchanged or enriched slightly. Furthermore, DNA array analysis of 3292 transcripts revealed that photosynthetic genes are moderately, but specifically, downregulated in ppi1. Proteome differences in ppi1 could be correlated with protein import rates: ppi1 chloroplasts imported the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit and 33-kD oxygen-evolving complex precursors at significantly reduced rates, but the import of a 50S ribosomal subunit precursor was largely unaffected. The ppi1 import defect occurred at the level of preprotein binding, which is consistent with a role for atToc33 during preprotein recognition. The data suggest that atToc33 is involved preferentially in the import of photosynthetic proteins and, by extension, that atToc34 is involved in the import of nonphotosynthetic chloroplast proteins. PMID:12897258

  16. Changes in photosynthetic performance and antioxidative strategies during maturation of Norway maple (Acer platanoides L.) leaves.

    Science.gov (United States)

    Lepeduš, Hrvoje; Gaća, Vlatka; Viljevac, Marija; Kovač, Spomenka; Fulgosi, Hrvoje; Simić, Domagoj; Jurković, Vlatka; Cesar, Vera

    2011-04-01

    Different structural and functional changes take place during leaf development. Since some of them are highly connected to oxidative metabolism, regulation of reactive oxygen species (ROS) abundance is required. Most of the reactive oxygen species ROS in plant cells are produced in chloroplasts as a result of highly energetic reactions of photosynthesis. The aim of our study was to examine the changes in concentration of oxidative stress parameters (TBARS - thiobarbituric acid-reacting substances and protein carbonyls) as well as antioxidative strategies during development of maple (Acer platanoides L.) leaves in the light of their enhanced photosynthetic performance. We reveal that biogenesis of the photosynthetic apparatus during maple leaf maturation corresponded with oxidative damage of lipids, but not proteins. In addition, antioxidative responses in young leaves differed from that in older leaves. Young leaves had high values of non-photochemical quenching (NPQ) and catalase (CAT, EC 1.11.1.6) activity which declined during the maturation process. Developing leaves were characterized by an increase in TBARS level, the content of non-enzymatic antioxidants as well as ascorbate peroxidase activity (APX, EC 1.11.1.11), while the content of protein carbonyls decreased with leaf maturation. Fully developed leaves had the highest lipid peroxidation level accompanied by a maximum in ascorbic acid content and superoxide dismutase activity (SOD, EC1.15.1.1). These observations imply completely different antioxidative strategies during leaf maturation enabling them to perform their basic function. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

  17. PSSRdb: a relational database of polymorphic simple sequence repeats extracted from prokaryotic genomes.

    Science.gov (United States)

    Kumar, Pankaj; Chaitanya, Pasumarthy S; Nagarajaram, Hampapathalu A

    2011-01-01

    PSSRdb (Polymorphic Simple Sequence Repeats database) (http://www.cdfd.org.in/PSSRdb/) is a relational database of polymorphic simple sequence repeats (PSSRs) extracted from 85 different species of prokaryotes. Simple sequence repeats (SSRs) are the tandem repeats of nucleotide motifs of the sizes 1-6 bp and are highly polymorphic. SSR mutations in and around coding regions affect transcription and translation of genes. Such changes underpin phase variations and antigenic variations seen in some bacteria. Although SSR-mediated phase variation and antigenic variations have been well-studied in some bacteria there seems a lot of other species of prokaryotes yet to be investigated for SSR mediated adaptive and other evolutionary advantages. As a part of our on-going studies on SSR polymorphism in prokaryotes we compared the genome sequences of various strains and isolates available for 85 different species of prokaryotes and extracted a number of SSRs showing length variations and created a relational database called PSSRdb. This database gives useful information such as location of PSSRs in genomes, length variation across genomes, the regions harboring PSSRs, etc. The information provided in this database is very useful for further research and analysis of SSRs in prokaryotes.

  18. Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge

    Science.gov (United States)

    Hirakata, Yuga; Oshiki, Mamoru; Kuroda, Kyohei; Hatamoto, Masashi; Kubota, Kengo; Yamaguchi, Takashi; Harada, Hideki; Araki, Nobuo

    2016-01-01

    Predation by protists is top-down pressure that regulates prokaryotic abundance, community function, structure, and diversity in natural and artificial ecosystems. Although the effects of predation by protists have been studied in aerobic ecosystems, they are poorly understood in anoxic environments. We herein studied the influence of predation by Metopus and Caenomorpha ciliates—ciliates frequently found in anoxic ecosystems—on prokaryotic community function, structure, and diversity. Metopus and Caenomorpha ciliates were cocultivated with prokaryotic assemblages (i.e., anaerobic granular sludge) in an up-flow anaerobic sludge blanket (UASB) reactor for 171 d. Predation by these ciliates increased the methanogenic activities of granular sludge, which constituted 155% of those found in a UASB reactor without the ciliates (i.e., control reactor). Sequencing of 16S rRNA gene amplicons using Illumina MiSeq revealed that the prokaryotic community in the UASB reactor with the ciliates was more diverse than that in the control reactor; 2,885–3,190 and 2,387–2,426 operational taxonomic units (>97% sequence similarities), respectively. The effects of predation by protists in anaerobic engineered systems have mostly been overlooked, and our results show that the influence of predation by protists needs to be examined and considered in the future for a better understanding of prokaryotic community structure and function. PMID:27431197

  19. Evolution of glutamate dehydrogenase genes: evidence for lateral gene transfer within and between prokaryotes and eukaryotes

    Directory of Open Access Journals (Sweden)

    Roger Andrew J

    2003-06-01

    Full Text Available Abstract Background Lateral gene transfer can introduce genes with novel functions into genomes or replace genes with functionally similar orthologs or paralogs. Here we present a study of the occurrence of the latter gene replacement phenomenon in the four gene families encoding different classes of glutamate dehydrogenase (GDH, to evaluate and compare the patterns and rates of lateral gene transfer (LGT in prokaryotes and eukaryotes. Results We extend the taxon sampling of gdh genes with nine new eukaryotic sequences and examine the phylogenetic distribution pattern of the various GDH classes in combination with maximum likelihood phylogenetic analyses. The distribution pattern analyses indicate that LGT has played a significant role in the evolution of the four gdh gene families. Indeed, a number of gene transfer events are identified by phylogenetic analyses, including numerous prokaryotic intra-domain transfers, some prokaryotic inter-domain transfers and several inter-domain transfers between prokaryotes and microbial eukaryotes (protists. Conclusion LGT has apparently affected eukaryotes and prokaryotes to a similar extent within the gdh gene families. In the absence of indications that the evolution of the gdh gene families is radically different from other families, these results suggest that gene transfer might be an important evolutionary mechanism in microbial eukaryote genome evolution.

  20. Effects of Predation by Protists on Prokaryotic Community Function, Structure, and Diversity in Anaerobic Granular Sludge.

    Science.gov (United States)

    Hirakata, Yuga; Oshiki, Mamoru; Kuroda, Kyohei; Hatamoto, Masashi; Kubota, Kengo; Yamaguchi, Takashi; Harada, Hideki; Araki, Nobuo

    2016-09-29

    Predation by protists is top-down pressure that regulates prokaryotic abundance, community function, structure, and diversity in natural and artificial ecosystems. Although the effects of predation by protists have been studied in aerobic ecosystems, they are poorly understood in anoxic environments. We herein studied the influence of predation by Metopus and Caenomorpha ciliates-ciliates frequently found in anoxic ecosystems-on prokaryotic community function, structure, and diversity. Metopus and Caenomorpha ciliates were cocultivated with prokaryotic assemblages (i.e., anaerobic granular sludge) in an up-flow anaerobic sludge blanket (UASB) reactor for 171 d. Predation by these ciliates increased the methanogenic activities of granular sludge, which constituted 155% of those found in a UASB reactor without the ciliates (i.e., control reactor). Sequencing of 16S rRNA gene amplicons using Illumina MiSeq revealed that the prokaryotic community in the UASB reactor with the ciliates was more diverse than that in the control reactor; 2,885-3,190 and 2,387-2,426 operational taxonomic units (>97% sequence similarities), respectively. The effects of predation by protists in anaerobic engineered systems have mostly been overlooked, and our results show that the influence of predation by protists needs to be examined and considered in the future for a better understanding of prokaryotic community structure and function.

  1. PSP: rapid identification of orthologous coding genes under positive selection across multiple closely related prokaryotic genomes.

    Science.gov (United States)

    Su, Fei; Ou, Hong-Yu; Tao, Fei; Tang, Hongzhi; Xu, Ping

    2013-12-27

    With genomic sequences of many closely related bacterial strains made available by deep sequencing, it is now possible to investigate trends in prokaryotic microevolution. Positive selection is a sub-process of microevolution, in which a particular mutation is favored, causing the allele frequency to continuously shift in one direction. Wide scanning of prokaryotic genomes has shown that positive selection at the molecular level is much more frequent than expected. Genes with significant positive selection may play key roles in bacterial adaption to different environmental pressures. However, selection pressure analyses are computationally intensive and awkward to configure. Here we describe an open access web server, which is designated as PSP (Positive Selection analysis for Prokaryotic genomes) for performing evolutionary analysis on orthologous coding genes, specially designed for rapid comparison of dozens of closely related prokaryotic genomes. Remarkably, PSP facilitates functional exploration at the multiple levels by assignments and enrichments of KO, GO or COG terms. To illustrate this user-friendly tool, we analyzed Escherichia coli and Bacillus cereus genomes and found that several genes, which play key roles in human infection and antibiotic resistance, show significant evidence of positive selection. PSP is freely available to all users without any login requirement at: http://db-mml.sjtu.edu.cn/PSP/. PSP ultimately allows researchers to do genome-scale analysis for evolutionary selection across multiple prokaryotic genomes rapidly and easily, and identify the genes undergoing positive selection, which may play key roles in the interactions of host-pathogen and/or environmental adaptation.

  2. Alternative photosynthetic electron transport pathways during anaerobiosis in the green alga Chlamydomonas reinhardtii.

    Science.gov (United States)

    Hemschemeier, Anja; Happe, Thomas

    2011-08-01

    Oxygenic photosynthesis uses light as energy source to generate an oxidant powerful enough to oxidize water into oxygen, electrons and protons. Upon linear electron transport, electrons extracted from water are used to reduce NADP(+) to NADPH. The oxygen molecule has been integrated into the cellular metabolism, both as the most efficient electron acceptor during respiratory electron transport and as oxidant and/or "substrate" in a number of biosynthetic pathways. Though photosynthesis of higher plants, algae and cyanobacteria produces oxygen, there are conditions under which this type of photosynthesis operates under hypoxic or anaerobic conditions. In the unicellular green alga Chlamydomonas reinhardtii, this condition is induced by sulfur deficiency, and it results in the production of molecular hydrogen. Research on this biotechnologically relevant phenomenon has contributed largely to new insights into additional pathways of photosynthetic electron transport, which extend the former concept of linear electron flow by far. This review summarizes the recent knowledge about various electron sources and sinks of oxygenic photosynthesis besides water and NADP(+) in the context of their contribution to hydrogen photoproduction by C. reinhardtii. This article is part of a Special Issue entitled: Regulation of Electron Transport in Chloroplasts. Copyright © 2011 Elsevier B.V. All rights reserved.

  3. An Excel tool for deriving key photosynthetic parameters from combined gas exchange and chlorophyll fluorescence: theory and practice.

    Science.gov (United States)

    Bellasio, Chandra; Beerling, David J; Griffiths, Howard

    2016-06-01

    Combined photosynthetic gas exchange and modulated fluorometres are widely used to evaluate physiological characteristics associated with phenotypic and genotypic variation, whether in response to genetic manipulation or resource limitation in natural vegetation or crops. After describing relatively simple experimental procedures, we present the theoretical background to the derivation of photosynthetic parameters, and provide a freely available Excel-based fitting tool (EFT) that will be of use to specialists and non-specialists alike. We use data acquired in concurrent variable fluorescence-gas exchange experiments, where A/Ci and light-response curves have been measured under ambient and low oxygen. From these data, the EFT derives light respiration, initial PSII (photosystem II) photochemical yield, initial quantum yield for CO2 fixation, fraction of incident light harvested by PSII, initial quantum yield for electron transport, electron transport rate, rate of photorespiration, stomatal limitation, Rubisco (ribulose 1·5-bisphosphate carboxylase/oxygenase) rate of carboxylation and oxygenation, Rubisco specificity factor, mesophyll conductance to CO2 diffusion, light and CO2 compensation point, Rubisco apparent Michaelis-Menten constant, and Rubisco CO2 -saturated carboxylation rate. As an example, a complete analysis of gas exchange data on tobacco plants is provided. We also discuss potential measurement problems and pitfalls, and suggest how such empirical data could subsequently be used to parameterize predictive photosynthetic models. © 2015 John Wiley & Sons Ltd.

  4. Minimal tool set for a prokaryotic circadian clock.

    Science.gov (United States)

    Schmelling, Nicolas M; Lehmann, Robert; Chaudhury, Paushali; Beck, Christian; Albers, Sonja-Verena; Axmann, Ilka M; Wiegard, Anika

    2017-07-21

    Circadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear. Using a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs. Our analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems

  5. Prokaryotic caspase homologs: phylogenetic patterns and functional characteristics reveal considerable diversity.

    Directory of Open Access Journals (Sweden)

    Johannes Asplund-Samuelsson

    Full Text Available Caspases accomplish initiation and execution of apoptosis, a programmed cell death process specific to metazoans. The existence of prokaryotic caspase homologs, termed metacaspases, has been known for slightly more than a decade. Despite their potential connection to the evolution of programmed cell death in eukaryotes, the phylogenetic distribution and functions of these prokaryotic metacaspase sequences are largely uncharted, while a few experiments imply involvement in programmed cell death. Aiming at providing a more detailed picture of prokaryotic caspase homologs, we applied a computational approach based on Hidden Markov Model search profiles to identify and functionally characterize putative metacaspases in bacterial and archaeal genomes. Out of the total of 1463 analyzed genomes, merely 267 (18% were identified to contain putative metacaspases, but their taxonomic distribution included most prokaryotic phyla and a few archaea (Euryarchaeota. Metacaspases were particularly abundant in Alphaproteobacteria, Deltaproteobacteria and Cyanobacteria, which harbor many morphologically and developmentally complex organisms, and a distinct correlation was found between abundance and phenotypic complexity in Cyanobacteria. Notably, Bacillus subtilis and Escherichia coli, known to undergo genetically regulated autolysis, lacked metacaspases. Pfam domain architecture analysis combined with operon identification revealed rich and varied configurations among the metacaspase sequences. These imply roles in programmed cell death, but also e.g. in signaling, various enzymatic activities and protein modification. Together our data show a wide and scattered distribution of caspase homologs in prokaryotes with structurally and functionally diverse sub-groups, and with a potentially intriguing evolutionary role. These features will help delineate future characterizations of death pathways in prokaryotes.

  6. Evolution and Diversity of the Ras Superfamily of Small GTPases in Prokaryotes

    Science.gov (United States)

    Wuichet, Kristin; Søgaard-Andersen, Lotte

    2015-01-01

    The Ras superfamily of small GTPases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. Originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain GTPases also control complex functions such as cell polarity, motility, predation, development and antibiotic resistance in bacteria. Here, we used a computational genomics approach to understand the abundance, diversity, and evolution of small GTPases in prokaryotes. We collected 520 small GTPase sequences present in 17% of 1,611 prokaryotic genomes analyzed that cover diverse lineages. We identified two discrete families of small GTPases in prokaryotes that show evidence of three distinct catalytic mechanisms. The MglA family includes MglA homologs, which are typically associated with the MglB GTPase activating protein, whereas members of the Rup (Ras superfamily GTPase of unknown function in prokaryotes) family are not predicted to interact with MglB homologs. System classification and genome context analyses support the involvement of small GTPases in diverse prokaryotic signal transduction pathways including two component systems, laying the foundation for future experimental characterization of these proteins. Phylogenetic analysis of prokaryotic and eukaryotic GTPases supports that the last universal common ancestor contained ancestral MglA and Rup family members. We propose that the MglA family was lost from the ancestral eukaryote and that the Ras superfamily members in extant eukaryotes are the result of vertical and horizontal gene transfer events of ancestral Rup GTPases. PMID:25480683

  7. Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea

    NARCIS (Netherlands)

    Stief, Peter; Fuchs-Ocklenburg, Silvia; Kamp, Anja; Manohar, Cathrine-Sumathi; Houbraken, Jos; Boekhout, Teun; de Beer, Dirk; Stoeck, Thorsten

    2014-01-01

    BACKGROUND: A wealth of microbial eukaryotes is adapted to life in oxygen-deficient marine environments. Evidence is accumulating that some of these eukaryotes survive anoxia by employing dissimilatory nitrate reduction, a strategy that otherwise is widespread in prokaryotes. Here, we report on the

  8. The swimming polarity of multicellular magnetotactic prokaryotes can change during an isolation process employing magnets: evidence of a relation between swimming polarity and magnetic moment intensity.

    Science.gov (United States)

    de Melo, Roger Duarte; Acosta-Avalos, Daniel

    2017-09-01

    Magnetotactic microorganisms are characterized by swimming in the direction of an applied magnetic field. In nature, two types of swimming polarity have been observed: north-seeking microorganisms that swim in the same direction as the magnetic field, and south-seeking microorganisms that swim in the opposite direction. The present work studies the reversal in the swimming polarity of the multicellular magnetotactic prokaryote Candidatus Magnetoglobus multicellularis following an isolation process using high magnetic fields from magnets. The proportion of north- and south-seeking organisms was counted as a function of the magnetic field intensity used during the isolation of the organisms from sediment. It was observed that the proportion of north-seeking organisms increased when the magnetic field was increased. The magnetic moment for north- and south-seeking populations was estimated using the U-turn method. The average magnetic moment was higher for north- than south-seeking organisms. The results suggest that the reversal of swimming polarity must occur during the isolation process in the presence of high magnetic fields and magnetic field gradients. It is shown for the first time that the swimming polarity reversal depends on the magnetic moment intensity of multicellular magnetotactic prokaryotes, and new studies must be undertaken to understand the role of magnetic moment polarity and oxygen gradients in determination of swimming polarity.

  9. Design, Engineering, and Characterization of Prokaryotic Ligand-Binding Transcriptional Activators as Biosensors in Yeast

    DEFF Research Database (Denmark)

    Ambri, Francesca; Snoek, Tim; Skjødt, Mette Louise

    2018-01-01

    process. In the yeast Saccharomyces cerevisiae, implementation of allosterically regulated transcription factors from prokaryotes as metabolite biosensors has proven a valuable strategy to alleviate this screening bottleneck. Here, we present a protocol to select and incorporate prokaryotic...... transcriptional activators as metabolite biosensors in S. cerevisiae. As an example, we outline the engineering and characterization of the LysR-type transcriptional regulator (LTTR) family member BenM from Acetinobacter sp. ADP1 for monitoring accumulation of cis,cis-muconic acid, a bioplast precursor, in yeast...

  10. Once in a lifetime: strategies for preventing re-replication in prokaryotic and eukaryotic cells

    DEFF Research Database (Denmark)

    Nielsen, Olaf; Løbner-Olesen, Anders

    2008-01-01

    DNA replication is an extremely accurate process and cells have evolved intricate control mechanisms to ensure that each region of their genome is replicated only once during S phase. Here, we compare what is known about the processes that prevent re-replication in prokaryotic and eukaryotic cells...... prokaryotes and eukaryotes are inactivated until the next cell cycle. Furthermore, in both systems the beta-clamp of the replicative polymerase associates with enzymatic activities that contribute to the inactivation of the helicase loaders. Finally, recent studies suggest that the control mechanism...

  11. Photoprotection Conferred by Changes in Photosynthetic Protein Levels and Organization during Dehydration of a Homoiochlorophyllous Resurrection Plant1

    Science.gov (United States)

    Charuvi, Dana; Nevo, Reinat; Shimoni, Eyal; Naveh, Leah; Zia, Ahmad; Adam, Zach; Farrant, Jill M.; Kirchhoff, Helmut; Reich, Ziv

    2015-01-01

    During desiccation, homoiochlorophyllous resurrection plants retain most of their photosynthetic apparatus, allowing them to resume photosynthetic activity quickly upon water availability. These plants rely on various mechanisms to prevent the formation of reactive oxygen species and/or protect their tissues from the damage they inflict. In this work, we addressed the issue of how homoiochlorophyllous resurrection plants deal with the problem of excessive excitation/electron pressures during dehydration using Craterostigma pumilum as a model plant. To investigate the alterations in the supramolecular organization of photosynthetic protein complexes, we examined cryoimmobilized, freeze-fractured leaf tissues using (cryo)scanning electron microscopy. These examinations revealed rearrangements of photosystem II (PSII) complexes, including a lowered density during moderate dehydration, consistent with a lower level of PSII proteins, as shown by biochemical analyses. The latter also showed a considerable decrease in the level of cytochrome f early during dehydration, suggesting that initial regulation of the inhibition of electron transport is achieved via the cytochrome b6f complex. Upon further dehydration, PSII complexes are observed to arrange into rows and semicrystalline arrays, which correlates with the significant accumulation of sucrose and the appearance of inverted hexagonal lipid phases within the membranes. As opposed to PSII and cytochrome f, the light-harvesting antenna complexes of PSII remain stable throughout the course of dehydration. Altogether, these results, along with photosynthetic activity measurements, suggest that the protection of retained photosynthetic components is achieved, at least in part, via the structural rearrangements of PSII and (likely) light-harvesting antenna complexes into a photochemically quenched state. PMID:25713340

  12. ENHANCED PRACTICAL PHOTOSYNTHETIC CO2 MITIGATION

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Gregory Kremer; Dr. David J. Bayless; Dr. Morgan Vis; Dr. Michael Prudich; Dr. Keith Cooksey; Dr. Jeff Muhs

    2001-07-25

    This quarterly report documents significant achievements in the Enhanced Practical Photosynthetic CO{sub 2} Mitigation project during the period from 4/03/2001 through 7/02/2001. Most of the achievements are milestones in our efforts to complete the tasks and subtasks that constitute the project objectives. Note that this version of the quarterly technical report is a revision to add the reports from subcontractors Montana State and Oak Ridge National Laboratories The significant accomplishments for this quarter include: Development of an experimental plan and initiation of experiments to create a calibration curve that correlates algal chlorophyll levels with carbon levels (to simplify future experimental procedures); Completion of debugging of the slug flow reactor system, and development of a plan for testing the pressure drop of the slug flow reactor; Design and development of a new bioreactor screen design which integrates the nutrient delivery drip system and the harvesting system; Development of an experimental setup for testing the new integrated drip system/harvesting system; Completion of model-scale bioreactor tests examining the effects of CO{sub 2} concentration levels and lighting levels on Nostoc 86-3 growth rates; Completion of the construction of a larger model-scale bioreactor to improve and expand testing capabilities and initiation of tests; Substantial progress on construction of a pilot-scale bioreactor; and Preliminary economic analysis of photobioreactor deployment. Plans for next quarter's work are included in the conclusions. A preliminary economic analysis is included as an appendix.

  13. ENHANCED PRACTICAL PHOTOSYNTHETIC CO2 MITIGATION

    Energy Technology Data Exchange (ETDEWEB)

    Dr. David J. Bayless; Dr. Morgan Vis; Dr. Gregory Kremer; Dr. Michael Prudich; Dr. Keith Cooksey; Dr. Jeff Muhs

    2001-01-16

    This is the first quarterly report of the project Enhanced Practical Photosynthetic CO{sub 2} Mitigation. The official project start date, 10/02/2000, was delayed until 10/31/2000 due to an intellectual property dispute that was resolved. However, the delay forced a subsequent delay in subcontracting with Montana State University, which then delayed obtaining a sampling permit from Yellowstone National Park. However, even with these delays, the project moved forward with some success. Accomplishments for this quarter include: Culturing of thermophilic organisms from Yellowstone; Testing of mesophilic organisms in extreme CO{sub 2} conditions; Construction of a second test bed for additional testing; Purchase of a total carbon analyzer dedicated to the project; Construction of a lighting container for Oak Ridge National Laboratory optical fiber testing; Modified lighting of existing test box to provide more uniform distribution; Testing of growth surface adhesion and properties; Experimentation on water-jet harvesting techniques; and Literature review underway regarding uses of biomass after harvesting. Plans for next quarter's work and an update on the project's web page are included in the conclusions.

  14. Photosynthetic efficiency of Chlamydomonas reinhardtii in flashing light

    NARCIS (Netherlands)

    Vejrazka, C.; Janssen, M.G.J.; Streefland, M.; Wijffels, R.H.

    2011-01-01

    Efficient light to biomass conversion in photobioreactors is crucial for economically feasible microalgae production processes. It has been suggested that photosynthesis is enhanced in short light path photobioreactors by mixing-induced flashing light regimes. In this study, photosynthetic

  15. Dynamics of photosynthetic activity of cyanobacteria after gut ...

    African Journals Online (AJOL)

    African Journal of Biotechnology ... carp and goldfish, whereas there was a significant stimulation of photosynthetic activity of diatom and green algae following the depressed cyanobacteria during cultivation. The mainly stimulated eukaryotic algae species were Fragilariaceae and Scenedesmus obliquus by microscopy.

  16. Effects of 1-butanol, neomycin and calcium on the photosynthetic ...

    African Journals Online (AJOL)

    ajl yemi

    2011-10-31

    Oct 31, 2011 ... (Shanghai Jierui Bio-Engineering Co., Ltd.) were used in the total. RNA extraction of ..... PC and reverse through calcium removal agent. EGTA indicating .... Photosynthetic characteristics and tolerance to photo- oxidation of ...

  17. Photosynthetic responses of pea plants (Pisum sativum L. cv. Little ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-08-04

    Aug 4, 2008 ... (O3) have fundamental effects on CO2 exchange by plants. ... produce responses such as reduced photosynthetic rates and earlier senescence .... quality localities treatments and two soil regimes in Riyadh city, KSA. Pn rates.

  18. Photosynthetic and nitrogen fixation capability in several soybean mutant lines

    International Nuclear Information System (INIS)

    Gandanegara, S.; Hendratno, K.

    1987-01-01

    Photosynthetic and nitrogen fixation capability in several soybean mutant lines. A greenhouse experiment has been carried out to study photosynthetic and nitrogen fixation capability of five mutant lines and two soybean varieties. An amount of 330 uCi of 14 CO 2 was fed to the plants including of the non-fixing reference crop (Chippewa non-nodulating isoline). Nitrogen fixation measurements was carried out using 15 N isotope dilution technique according to A-value concept. Results showed that beside variety/mutant lines, plant growth also has important role in photosynthetic and N fixing capability. Better growth and a higher photosynthetic capability in Orba, mutant lines nos. 63 and 65 resulted in a greater amount of N 2 fixed (mg N/plant) than other mutant lines. (author). 12 refs.; 5 figs

  19. Counting viruses and bacteria in photosynthetic microbial mats

    NARCIS (Netherlands)

    Carreira, C; Staal, M.; Middelboe, M.; Brussaard, C.P.D.

    2015-01-01

    Viral abundances in benthic environments are the highest found in aquatic systems. Photosynthetic microbial mats represent benthic environments with high microbial activity and possibly high viral densities, yet viral abundances have not been examined in such systems. Existing extraction procedures

  20. Effect of space mutation on photosynthetic characteristics of soybean varieties

    International Nuclear Information System (INIS)

    Liu Xinlei; Ma Yansong; Luan Xiaoyan; Man Weiqun; Xu Dechun; Meng Lifen; Fu Lixin; Zhao Xiaonan; Liu Qi

    2011-01-01

    In order to elucidate the response of the photosynthetic traits of soybean to space mutation, three soybean varieties (lines) of Heinong 48, Heinong 44 and Ha 2291-Y were carried by artificial satellite in 2006 and the net photosynthetic rate (Pn), stomatal conductance (Cond), intercellular CO 2 concentration (Ci) and stomatal resistance (Rs) from SP 1 to SP 4 generation were determined. The results showed that space mutation affected photosynthesis traits of soybean. The photosynthetic rate of soybean varieties by space mutation occurred different levels of genetic variation and the positive mutation rate were higher. Coefficient of variation among generations were SP 2 > SP 3 > SP 4 > CK. Results suggest that space mutation can effectively create soybean materials with higher photosynthetic rate. (authors)

  1. Carotenoids are essential for the assembly of cyanobacterial photosynthetic complexes

    NARCIS (Netherlands)

    Tóth, T.N.; Chukhutsina, Volha; Domonkos, Ildikó; Knoppová, Jana; Komenda, Josef; Kis, Mihály; Lénárt, Zsófia; Garab, Gyozo; Kovács, László; Gombos, Zoltán; Amerongen, Van Herbert

    2015-01-01

    In photosynthetic organisms, carotenoids (carotenes and xanthophylls) are important for light harvesting, photoprotection and structural stability of a variety of pigment-protein complexes. Here, we investigated the consequences of altered carotenoid composition for the functional organization of

  2. Variability of photosynthetic pigments in the Colombian Pacific ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Picture series of surface chlorophyll,. SST, wind ... photosynthetic pigments during the time of inten- sification of ... calculation of Ekman pumping (We) using finite- differencing to ..... Legeckis R 1986 A satellite time series sea surface tempera-.

  3. Photosynthetic and Ultrastructure Parameters of Maize Plants are Affected During the Phyto-Rhizoremediation Process of Degraded Metal Working Fluids.

    Science.gov (United States)

    Grijalbo, Lucía; Gutierrez Mañero, Francisco Javier; Fernandez-Pascual, Mercedes; Lucas, Jose Antonio

    2015-01-01

    A phyto-rhizoremediation system using corn and esparto fiber as rooting support to remediate degraded metal working fluids (dMWFs) has been developed in the present study. In order to improve the process, plants were inoculated at the root level with bacteria either individually, and with a consortium of strains. All strains used were able to grow with MWFs. The results show that this system significantly lowers the Chemical Oxygen Demand below legal limits within 5 days. However, results were only improved with the bacterial consortium. Despite the effectiveness of the phyto-rhizoremediation process, plants are damaged at the photosynthetic level according to the photosynthetic parameters measured, as well as at the ultrastructure of the vascular cylinder and the Bundle Sheath Cells. Interestingly, the bacterial inoculation protects against this damage. Therefore, it seems that that the inoculation with bacteria can protect the plants against these harmful effects.

  4. On the photosynthetic potential in the very Early Archean oceans.

    Science.gov (United States)

    Avila, Daile; Cardenas, Rolando; Martin, Osmel

    2013-02-01

    In this work we apply a mathematical model of photosynthesis to quantify the potential for photosynthetic life in the very Early Archean oceans. We assume the presence of oceanic blockers of ultraviolet radiation, specifically ferrous ions. For this scenario, our results suggest a potential for photosynthetic life greater than or similar to that in later eras/eons, such as the Late Archean and the current Phanerozoic eon.

  5. Ultrafast fluorescence of photosynthetic crystals and light-harvesting complexes

    OpenAIRE

    Oort, van, B.F.

    2008-01-01

    This thesis focuses on the study of photosynthetic pigment protein complexes using time resolved fluorescence techniques. Fluorescence spectroscopy often requires attaching fluorescent labels to the proteins under investigation. With photosynthetic proteins this is not necessary, because these proteins contain fluorescent pigments. Each pigment’s fluorescence is influenced by its environment, and thereby may provide information on structure and dynamics of pigment protein complexes in vitro a...

  6. Tree Species with Photosynthetic Stems Have Greater Nighttime Sap Flux

    Directory of Open Access Journals (Sweden)

    Xia Chen

    2018-01-01

    Full Text Available An increasing body of evidence has shown that nighttime sap flux occurs in most plants, but the physiological implications and regulatory mechanism are poorly known. The significance of corticular photosynthesis has received much attention during the last decade, however, the knowledge of the relationship between corticular photosynthesis and nocturnal stem sap flow is limited at present. In this study, we divided seven tree species into two groups according to different photosynthetic capabilities: trees of species with (Castanopsis hystrix, Michelia macclurei, Eucalyptus citriodora, and Eucalyptus grandis × urophylla and without (Castanopsis fissa, Schima superba, and Acacia auriculiformis photosynthetic stems, and the sap flux (Js and chlorophyll fluorescence parameters for these species were measured. One-way ANOVA analysis showed that the Fv/Fm (Maximum photochemical quantum yield of PSII and ΦPSII (effective photochemical quantum yield of PSII values were lower in non-photosynthetic stem species compared to photosynthetic stem species. The linear regression analysis showed that Js,d (daytime sap flux and Js,n (nighttime sap flux of non-photosynthetic stem species was 87.7 and 60.9% of the stem photosynthetic species. Furthermore, for a given daytime transpiration water loss, total nighttime sap flux was higher in species with photosynthetic stems (SlopeSMA = 2.680 than in non-photosynthetic stems species (SlopeSMA = 1.943. These results mean that stem corticular photosynthesis has a possible effect on the nighttime water flow, highlighting the important eco-physiological relationship between nighttime sap flux and corticular photosynthesis.

  7. Tree Species with Photosynthetic Stems Have Greater Nighttime Sap Flux.

    Science.gov (United States)

    Chen, Xia; Gao, Jianguo; Zhao, Ping; McCarthy, Heather R; Zhu, Liwei; Ni, Guangyan; Ouyang, Lei

    2018-01-01

    An increasing body of evidence has shown that nighttime sap flux occurs in most plants, but the physiological implications and regulatory mechanism are poorly known. The significance of corticular photosynthesis has received much attention during the last decade, however, the knowledge of the relationship between corticular photosynthesis and nocturnal stem sap flow is limited at present. In this study, we divided seven tree species into two groups according to different photosynthetic capabilities: trees of species with ( Castanopsis hystrix, Michelia macclurei, Eucalyptus citriodora , and Eucalyptus grandis × urophylla ) and without ( Castanopsis fissa, Schima superba , and Acacia auriculiformis ) photosynthetic stems, and the sap flux ( J s ) and chlorophyll fluorescence parameters for these species were measured. One-way ANOVA analysis showed that the F v / F m (Maximum photochemical quantum yield of PSII) and Φ PSII (effective photochemical quantum yield of PSII) values were lower in non-photosynthetic stem species compared to photosynthetic stem species. The linear regression analysis showed that J s,d (daytime sap flux) and J s,n (nighttime sap flux) of non-photosynthetic stem species was 87.7 and 60.9% of the stem photosynthetic species. Furthermore, for a given daytime transpiration water loss, total nighttime sap flux was higher in species with photosynthetic stems (Slope SMA = 2.680) than in non-photosynthetic stems species (Slope SMA = 1.943). These results mean that stem corticular photosynthesis has a possible effect on the nighttime water flow, highlighting the important eco-physiological relationship between nighttime sap flux and corticular photosynthesis.

  8. Tree Species with Photosynthetic Stems Have Greater Nighttime Sap Flux

    Science.gov (United States)

    Chen, Xia; Gao, Jianguo; Zhao, Ping; McCarthy, Heather R.; Zhu, Liwei; Ni, Guangyan; Ouyang, Lei

    2018-01-01

    An increasing body of evidence has shown that nighttime sap flux occurs in most plants, but the physiological implications and regulatory mechanism are poorly known. The significance of corticular photosynthesis has received much attention during the last decade, however, the knowledge of the relationship between corticular photosynthesis and nocturnal stem sap flow is limited at present. In this study, we divided seven tree species into two groups according to different photosynthetic capabilities: trees of species with (Castanopsis hystrix, Michelia macclurei, Eucalyptus citriodora, and Eucalyptus grandis × urophylla) and without (Castanopsis fissa, Schima superba, and Acacia auriculiformis) photosynthetic stems, and the sap flux (Js) and chlorophyll fluorescence parameters for these species were measured. One-way ANOVA analysis showed that the Fv/Fm (Maximum photochemical quantum yield of PSII) and ΦPSII (effective photochemical quantum yield of PSII) values were lower in non-photosynthetic stem species compared to photosynthetic stem species. The linear regression analysis showed that Js,d (daytime sap flux) and Js,n (nighttime sap flux) of non-photosynthetic stem species was 87.7 and 60.9% of the stem photosynthetic species. Furthermore, for a given daytime transpiration water loss, total nighttime sap flux was higher in species with photosynthetic stems (SlopeSMA = 2.680) than in non-photosynthetic stems species (SlopeSMA = 1.943). These results mean that stem corticular photosynthesis has a possible effect on the nighttime water flow, highlighting the important eco-physiological relationship between nighttime sap flux and corticular photosynthesis. PMID:29416547

  9. 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

  10. Effect of Temperature and light intensity on growth and Photosynthetic Activity of Chlamydomonas reinhard II; Efecto de la temperatura e intensidad luminosa sobre el crecimiento y actividad fotosintetica del alga Chlamydomonas Reinhardt II

    Energy Technology Data Exchange (ETDEWEB)

    Alfonsel Jaen, M; Fernandez Gonzalez, J

    1985-07-01

    The effect of five temperatures (15,20,25,30 and 35 degree centigree) and two levels of illumination on growth and photosynthetic activity of Chlamydomonas reinhard II has been studied. The growth of the cultures was evaluated by optical density. Photosynthetic activity has been carried out studying either the assimilation rate of C0{sub 2} labelled with C-14 or the oxygen evolution by means of polarographic measurements. The maximum photosynthetic rate has been obtained at 25 degree centigree for the lower level of illumination (2400 lux) and at 35 degree centigree for the higher one (13200 lux) and at 35 degree centigree for the higher ono (13200 lux). These results suggest an interaction of temperature and illumination on photosynthetic activity. (Author) 37 refs.

  11. Rice Photosynthetic Productivity and PSII Photochemistry under Nonflooded Irrigation

    Directory of Open Access Journals (Sweden)

    Haibing He

    2014-01-01

    Full Text Available Nonflooded irrigation is an important water-saving rice cultivation technology, but little is known on its photosynthetic mechanism. The aims of this work were to investigate photosynthetic characteristics of rice during grain filling stage under three nonflooded irrigation treatments: furrow irrigation with plastic mulching (FIM, furrow irrigation with nonmulching (FIN, and drip irrigation with plastic mulching (DI. Compared with the conventional flooding (CF treatment, those grown in the nonflooded irrigation treatments showed lower net photosynthetic rate (PN, lower maximum quantum yield (Fv/Fm, and lower effective quantum yield of PSII photochemistry (ΦPSII. And the poor photosynthetic characteristics in the nonflooded irrigation treatments were mainly attributed to the low total nitrogen content (TNC. Under non-flooded irrigation, the PN, Fv/Fm, and ΦPSII significantly decreased with a reduction in the soil water potential, but these parameters were rapidly recovered in the DI and FIM treatments when supplementary irrigation was applied. Moreover, The DI treatment always had higher photosynthetic productivity than the FIM and FIN treatments. Grain yield, matter translocation, and dry matter post-anthesis (DMPA were the highest in the CF treatment, followed by the DI, FIM, and FIN treatments in turn. In conclusion, increasing nitrogen content in leaf of rice plants could be a key factor to improve photosynthetic capacity in nonflooded irrigation.

  12. 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

  13. Dissimilatory nitrate reduction by Aspergillus terreus isolated from the seasonal oxygen minimum zone in the Arabian Sea

    OpenAIRE

    Stief, Peter; Fuchs-Ocklenburg, Silvia; Kamp, Anja; Manohar, Cathrine-Sumathi; Houbraken, Jos; Boekhout, Teun; de Beer, Dirk; Stoeck, Thorsten

    2014-01-01

    Background A wealth of microbial eukaryotes is adapted to life in oxygen-deficient marine environments. Evidence is accumulating that some of these eukaryotes survive anoxia by employing dissimilatory nitrate reduction, a strategy that otherwise is widespread in prokaryotes. Here, we report on the anaerobic nitrate metabolism of the fungus Aspergillus terreus (isolate An-4) that was obtained from sediment in the seasonal oxygen minimum zone in the Arabian Sea, a globally important site of oce...

  14. Multilayer models of photosynthetic membranes. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Brocklehurst, J R; Flanagan, M T

    1982-01-01

    The primary aim of this project has been to build an artificial membrane in which is incorporated, in a functional state, the protein bacteriorhodopsin responsible for generating an electrical potential difference across the membrane of the photosynthetic bacterium, halobacterium halobium, and to investigate the use of this artificial system as the basis of a solar cell. the bacteriorhodopsin has been incorporated into Langmuir-Blodgett multilayers. If ths supporting filter is then illuminated, a potential difference is generated between the two compartments. The lipid in the filter appears to act as a charge carrier for protons, the charge species that forms the electrochemical gradient generated by the bacteriorhodopsin when this molecule absorbs light. The internal resistances of such solar cells were determined and found to be so high that the cells could not be seriously considered as competitors with classical semiconductor cells. Multilayerswere deposited onto filters in which ion carriers that make the filters permeable to sodium ions had been dissolved in the paraffin. The photovoltage obtained indicated that protons transferred from one side of the filter to the other by the action of the bacteriorhodopsin were bing exchanged for sodium ions. A secondary aim of the project has been to examine the possibility of depositing mixed multilayers of a dye and a long chain quinone onto a semiconductor surface. A sensitizing multilayer has been prepared and the mobility of long chain quinones within the layers is high enough to warrant further research. However, it was found that, with the dyes and quinones used, quenched complexes were formed which would not act as sensitizers.

  15. Anaerobic energy metabolism in unicellular photosynthetic eukaryotes.

    Science.gov (United States)

    Atteia, Ariane; van Lis, Robert; Tielens, Aloysius G M; Martin, William F

    2013-02-01

    Anaerobic metabolic pathways allow unicellular organisms to tolerate or colonize anoxic environments. Over the past ten years, genome sequencing projects have brought a new light on the extent of anaerobic metabolism in eukaryotes. A surprising development has been that free-living unicellular algae capable of photoautotrophic lifestyle are, in terms of their enzymatic repertoire, among the best equipped eukaryotes known when it comes to anaerobic energy metabolism. Some of these algae are marine organisms, common in the oceans, others are more typically soil inhabitants. All these species are important from the ecological (O(2)/CO(2) budget), biotechnological, and evolutionary perspectives. In the unicellular algae surveyed here, mixed-acid type fermentations are widespread while anaerobic respiration, which is more typical of eukaryotic heterotrophs, appears to be rare. The presence of a core anaerobic metabolism among the algae provides insights into its evolutionary origin, which traces to the eukaryote common ancestor. The predicted fermentative enzymes often exhibit an amino acid extension at the N-terminus, suggesting that these proteins might be compartmentalized in the cell, likely in the chloroplast or the mitochondrion. The green algae Chlamydomonas reinhardtii and Chlorella NC64 have the most extended set of fermentative enzymes reported so far. Among the eukaryotes with secondary plastids, the diatom Thalassiosira pseudonana has the most pronounced anaerobic capabilities as yet. From the standpoints of genomic, transcriptomic, and biochemical studies, anaerobic energy metabolism in C. reinhardtii remains the best characterized among photosynthetic protists. This article is part of a Special Issue entitled: The evolutionary aspects of bioenergetic systems. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. ENHANCED PRACTICAL PHOTOSYNTHETIC CO2 MITIGATION

    Energy Technology Data Exchange (ETDEWEB)

    Dr. David J. Bayless; Dr. Morgan Vis; Dr. Gregory Kremer; Dr. Michael Prudich; Dr. Keith Cooksey; Dr. Jeff Muhs

    2001-04-16

    This quarterly report documents significant achievements in the Enhanced Practical Photosynthetic CO{sub 2} Mitigation project during the period from 1/03/2001 through 4/02/2001. Many of the activities and accomplishments are continuations of work initiated and reported in last quarter's status report. Major activities and accomplishments for this quarter include: Three sites in Yellowstone National Park have been identified that may contain suitable organisms for use in a bioreactor; Full-scale culturing of one thermophilic organism from Yellowstone has progressed to the point that there is a sufficient quantity to test this organism in the model-scale bioreactor; The effects of the additive monoethanolamine on the growth of one thermophilic organism from Yellowstone has been tested; Testing of growth surface adhesion and properties is continuing; Construction of a larger model-scale bioreactor to improve and expand testing capabilities is completed and the facility is undergoing proof tests; Model-scale bioreactor tests examining the effects of CO{sub 2} concentration levels and lighting levels on organism growth rates are continuing; Alternative fiber optic based deep-penetration light delivery systems for use in the pilot-scale bioreactor have been designed, constructed and tested; An existing slug flow reactor system has been modified for use in this project, and a proof-of-concept test plan has been developed for the slug flow reactor; Research and testing of water-jet harvesting techniques is continuing, and a harvesting system has been designed for use in the model-scale bioreactor; and The investigation of comparative digital image analysis as a means for determining the ''density'' of algae on a growth surface is continuing Plans for next quarter's work and an update on the project's web page are included in the conclusions.

  17. Read length and repeat resolution: exploring prokaryote genomes using next-generation sequencing technologies.

    Directory of Open Access Journals (Sweden)

    Matt J Cahill

    Full Text Available BACKGROUND: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. METHODOLOGY/PRINCIPAL FINDINGS: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. CONCLUSIONS: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length.

  18. Exploring cultivable Bacteria from the prokaryotic community associated with the carnivorous sponge Asbestopluma hypogea.

    Science.gov (United States)

    Dupont, Samuel; Carre-Mlouka, Alyssa; Domart-Coulon, Isabelle; Vacelet, Jean; Bourguet-Kondracki, Marie-Lise

    2014-04-01

    Combining culture-dependent and independent approaches, we investigated for the first time the cultivable fraction of the prokaryotic community associated with the carnivorous sponge Asbestopluma hypogea. The heterotrophic prokaryotes isolated from this tiny sponge were compared between specimens freshly collected from cave and maintained in aquarium. Overall, 67 isolates obtained in pure culture were phylogenetically affiliated to the bacterial phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. This cultivable diversity was lower than the prokaryotic diversity obtained by previous pyrosequencing study and comparable to that of another Mediterranean demosponge, the filter-feeding Phorbas tenacior. Furthermore, using fluorescence in situ hybridization, we visualized bacterial and archaeal cells, confirming the presence of both prokaryotes in A. hypogea tissue. Approximately 16% of the bacterial isolates tested positive for chitinolytic activity, suggesting potential microbial involvement in the digestion processes of crustacean prey by this carnivorous sponge. Additionally, 6% and 16% of bacterial isolates revealed antimicrobial and antioxidant activities, respectively. One Streptomyces sp. S1CA strain was identified as a promising candidate for the production of antimicrobial and antioxidant secondary metabolites as well as chitinolytic enzymes. Implications in the context of the sponge biology and prey-feeding strategy are discussed. © 2014 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

  19. Horizontal transfer, not duplication, drives the expansion of protein families in prokaryotes.

    Directory of Open Access Journals (Sweden)

    Todd J Treangen

    2011-01-01

    Full Text Available Gene duplication followed by neo- or sub-functionalization deeply impacts the evolution of protein families and is regarded as the main source of adaptive functional novelty in eukaryotes. While there is ample evidence of adaptive gene duplication in prokaryotes, it is not clear whether duplication outweighs the contribution of horizontal gene transfer in the expansion of protein families. We analyzed closely related prokaryote strains or species with small genomes (Helicobacter, Neisseria, Streptococcus, Sulfolobus, average-sized genomes (Bacillus, Enterobacteriaceae, and large genomes (Pseudomonas, Bradyrhizobiaceae to untangle the effects of duplication and horizontal transfer. After removing the effects of transposable elements and phages, we show that the vast majority of expansions of protein families are due to transfer, even among large genomes. Transferred genes--xenologs--persist longer in prokaryotic lineages possibly due to a higher/longer adaptive role. On the other hand, duplicated genes--paralogs--are expressed more, and, when persistent, they evolve slower. This suggests that gene transfer and gene duplication have very different roles in shaping the evolution of biological systems: transfer allows the acquisition of new functions and duplication leads to higher gene dosage. Accordingly, we show that paralogs share most protein-protein interactions and genetic regulators, whereas xenologs share very few of them. Prokaryotes invented most of life's biochemical diversity. Therefore, the study of the evolution of biology systems should explicitly account for the predominant role of horizontal gene transfer in the diversification of protein families.

  20. PePPER : a webserver for prediction of prokaryote promoter elements and regulons

    NARCIS (Netherlands)

    de Jong, Anne; Pietersma, Hilco; Cordes, Martijn; Kuipers, Oscar P.; Kok, Jan

    2012-01-01

    Background: Accurate prediction of DNA motifs that are targets of RNA polymerases, sigma factors and transcription factors (TFs) in prokaryotes is a difficult mission mainly due to as yet undiscovered features in DNA sequences or structures in promoter regions. Improved prediction and comparison

  1. Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

    KAUST Repository

    Cahill, Matt J.

    2010-07-12

    Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

  2. Rumen prokaryotic communities of ruminants under different feeding paradigms on the Qinghai-Tibetan Plateau.

    Science.gov (United States)

    Xue, Dan; Chen, Huai; Zhao, Xinquan; Xu, Shixiao; Hu, Linyong; Xu, Tianwei; Jiang, Lin; Zhan, Wei

    2017-06-01

    Yak and Tibetan sheep are the major indigenous ruminants on the Qinghai-Tibetan Plateau in China. The aim of this work was to study the differences in ruminal fermentation parameters and rumen prokaryotic community composition between hosts and feeding paradigms. The 16S rRNA genes targeting bacteria and archaea were sequenced using the MiSeq platform. The results showed that the prokaryotic community structure between yak and Tibetan sheep was significantly different (PTibetan sheep of the two groups (P=0.026). The core prokaryotic populations that existed in the rumen mostly dominated the structure. There was an obvious correlation of the prokaryotic community composition at the phylum and genus levels with the host or the feeding pattern. In addition, Tibetan sheep showed significantly higher yields of volatile fatty acids (VFAs) than yak, as did the NG group compared with the TMR group. In conclusion, both the host and feeding pattern may influence rumen microbial ecology system, with host effects being more important than those of the feeding pattern. Copyright © 2017 Elsevier GmbH. All rights reserved.

  3. Focus on Membrane Differentiation and Membrane Domains in the Prokaryotic Cell

    NARCIS (Netherlands)

    Boekema, Egbert J.; Scheffers, Dirk-Jan; van Bezouwen, Laura S.; Bolhuis, Henk; Folea, I. Mihaela

    2013-01-01

    A summary is presented of membrane differentiation in the prokaryotic cell, with an emphasis on the organization of proteins in the plasma/cell membrane. Many species belonging to the Eubacteria and Archaea have special membrane domains and/or membrane proliferation, which are vital for different

  4. Global identification of prokaryotic glycoproteins based on an Escherichia coli proteome microarray.

    Directory of Open Access Journals (Sweden)

    Zong-Xiu Wang

    Full Text Available Glycosylation is one of the most abundant protein posttranslational modifications. Protein glycosylation plays important roles not only in eukaryotes but also in prokaryotes. To further understand the roles of protein glycosylation in prokaryotes, we developed a lectin binding assay to screen glycoproteins on an Escherichia coli proteome microarray containing 4,256 affinity-purified E.coli proteins. Twenty-three E.coli proteins that bound Wheat-Germ Agglutinin (WGA were identified. PANTHER protein classification analysis showed that these glycoprotein candidates were highly enriched in metabolic process and catalytic activity classes. One sub-network centered on deoxyribonuclease I (sbcB was identified. Bioinformatics analysis suggests that prokaryotic protein glycosylation may play roles in nucleotide and nucleic acid metabolism. Fifteen of the 23 glycoprotein candidates were validated by lectin (WGA staining, thereby increasing the number of validated E. coli glycoproteins from 3 to 18. By cataloguing glycoproteins in E.coli, our study greatly extends our understanding of protein glycosylation in prokaryotes.

  5. Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

    Science.gov (United States)

    Koonin, Eugene V.; Wolf, Yuri I.

    2008-01-01

    The first bacterial genome was sequenced in 1995, and the first archaeal genome in 1996. Soon after these breakthroughs, an exponential rate of genome sequencing was established, with a doubling time of approximately 20 months for bacteria and approximately 34 months for archaea. Comparative analysis of the hundreds of sequenced bacterial and dozens of archaeal genomes leads to several generalizations on the principles of genome organization and evolution. A crucial finding that enables functional characterization of the sequenced genomes and evolutionary reconstruction is that the majority of archaeal and bacterial genes have conserved orthologs in other, often, distant organisms. However, comparative genomics also shows that horizontal gene transfer (HGT) is a dominant force of prokaryotic evolution, along with the loss of genetic material resulting in genome contraction. A crucial component of the prokaryotic world is the mobilome, the enormous collection of viruses, plasmids and other selfish elements, which are in constant exchange with more stable chromosomes and serve as HGT vehicles. Thus, the prokaryotic genome space is a tightly connected, although compartmentalized, network, a novel notion that undermines the ‘Tree of Life’ model of evolution and requires a new conceptual framework and tools for the study of prokaryotic evolution. PMID:18948295

  6. Energy Coupling Factor-Type ABC Transporters for Vitamin Uptake in Prokaryotes

    NARCIS (Netherlands)

    Erkens, Guus B.; Dosz-Majsnerowska, Maria; ter Beek, Josy; Slotboom, Dirk Jan

    2012-01-01

    Energy coupling factor (ECF) transporters are a subgroup of ATP-binding cassette (ABC) transporters involved in the uptake of vitamins and micronutrients in prokaryotes. In contrast to classical ABC importers, ECF transporters do not make use of water-soluble substrate binding proteins or domains

  7. Lateral gene transfer between prokaryotes and multicellular eukaryotes: ongoing and significant?

    NARCIS (Netherlands)

    Ros, V.I.D.; Hurst, G.D.D.

    2009-01-01

    The expansion of genome sequencing projects has produced accumulating evidence for lateral transfer of genes between prokaryotic and eukaryotic genomes. However, it remains controversial whether these genes are of functional importance in their recipient host. Nikoh and Nakabachi, in a recent paper

  8. Prokaryotic diversity of the Saccharomyces cerevisiae Atx1p-mediated copper pathway.

    NARCIS (Netherlands)

    Bakel, H. van; Huynen, M.A.; Wijmenga, C.

    2004-01-01

    MOTIVATION: Several genes involved in the cellular import of copper and its subsequent incorporation into the high-affinity iron transport complex in Saccharomyces cerevisiae are known to be conserved between eukaryotes and prokaryotes. However, the degree to which these genes share their functional

  9. Use of prokaryotic transcriptional activators as metabolite biosensors in eukaryotic cells

    DEFF Research Database (Denmark)

    2018-01-01

    The present invention relates to the use of transcriptional activators from prokaryotic organisms for use in eukaryotic cells, such as yeast as sensors of intracellular and extracellular accumulation of a ligand or metabolite specifically activating this transcriptional activator in a eukaryot...

  10. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engelbrecht, Jacob; Brunak, Søren

    1997-01-01

    We have developed a new method for the identification of signal peptides and their cleavage based on neural networks trained on separate sets of prokaryotic and eukaryotic sequence. The method performs significantly better than previous prediction schemes and can easily be applied on genome...

  11. Read length and repeat resolution: Exploring prokaryote genomes using next-generation sequencing technologies

    KAUST Repository

    Cahill, Matt J.; Kö ser, Claudio U.; Ross, Nicholas E.; Archer, John A.C.

    2010-01-01

    Background: There are a growing number of next-generation sequencing technologies. At present, the most cost-effective options also produce the shortest reads. However, even for prokaryotes, there is uncertainty concerning the utility of these technologies for the de novo assembly of complete genomes. This reflects an expectation that short reads will be unable to resolve small, but presumably abundant, repeats. Methodology/Principal Findings: Using a simple model of repeat assembly, we develop and test a technique that, for any read length, can estimate the occurrence of unresolvable repeats in a genome, and thus predict the number of gaps that would need to be closed to produce a complete sequence. We apply this technique to 818 prokaryote genome sequences. This provides a quantitative assessment of the relative performance of various lengths. Notably, unpaired reads of only 150nt can reconstruct approximately 50% of the analysed genomes with fewer than 96 repeat-induced gaps. Nonetheless, there is considerable variation amongst prokaryotes. Some genomes can be assembled to near contiguity using very short reads while others require much longer reads. Conclusions: Given the diversity of prokaryote genomes, a sequencing strategy should be tailored to the organism under study. Our results will provide researchers with a practical resource to guide the selection of the appropriate read length. 2010 Cahill et al.

  12. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

    Science.gov (United States)

    Battistuzzi, Fabia U.; Feijao, Andreia; Hedges, S. Blair

    2004-01-01

    BACKGROUND: The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (approximately 7600 amino acids) common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. RESULTS: Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria) that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5-3.2 billion years ago (Ga) while those for archaebacteria are mostly between 3.1-4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga), an early origin of methanogenesis (3.8-4.1 Ga), an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8-3.1 Ga, and an origin of aerobic methanotrophy 2.5-2.8 Ga. CONCLUSIONS: Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8-2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically produced, were made by

  13. A genomic timescale of prokaryote evolution: insights into the origin of methanogenesis, phototrophy, and the colonization of land

    Directory of Open Access Journals (Sweden)

    Hedges S Blair

    2004-11-01

    Full Text Available Abstract Background The timescale of prokaryote evolution has been difficult to reconstruct because of a limited fossil record and complexities associated with molecular clocks and deep divergences. However, the relatively large number of genome sequences currently available has provided a better opportunity to control for potential biases such as horizontal gene transfer and rate differences among lineages. We assembled a data set of sequences from 32 proteins (~7600 amino acids common to 72 species and estimated phylogenetic relationships and divergence times with a local clock method. Results Our phylogenetic results support most of the currently recognized higher-level groupings of prokaryotes. Of particular interest is a well-supported group of three major lineages of eubacteria (Actinobacteria, Deinococcus, and Cyanobacteria that we call Terrabacteria and associate with an early colonization of land. Divergence time estimates for the major groups of eubacteria are between 2.5–3.2 billion years ago (Ga while those for archaebacteria are mostly between 3.1–4.1 Ga. The time estimates suggest a Hadean origin of life (prior to 4.1 Ga, an early origin of methanogenesis (3.8–4.1 Ga, an origin of anaerobic methanotrophy after 3.1 Ga, an origin of phototrophy prior to 3.2 Ga, an early colonization of land 2.8–3.1 Ga, and an origin of aerobic methanotrophy 2.5–2.8 Ga. Conclusions Our early time estimates for methanogenesis support the consideration of methane, in addition to carbon dioxide, as a greenhouse gas responsible for the early warming of the Earths' surface. Our divergence times for the origin of anaerobic methanotrophy are compatible with highly depleted carbon isotopic values found in rocks dated 2.8–2.6 Ga. An early origin of phototrophy is consistent with the earliest bacterial mats and structures identified as stromatolites, but a 2.6 Ga origin of cyanobacteria suggests that those Archean structures, if biologically

  14. Impact of Lowland Rainforest Transformation on Diversity and Composition of Soil Prokaryotic Communities in Sumatra (Indonesia)

    Science.gov (United States)

    Schneider, Dominik; Engelhaupt, Martin; Allen, Kara; Kurniawan, Syahrul; Krashevska, Valentyna; Heinemann, Melanie; Nacke, Heiko; Wijayanti, Marini; Meryandini, Anja; Corre, Marife D.; Scheu, Stefan; Daniel, Rolf

    2015-01-01

    Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use systems comprised rubber agroforests (jungle rubber), rubber plantations and oil palm plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 16,413 bacterial and 1679 archaeal operational taxonomic units at species level (97% genetic identity). Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota) dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to N ratio

  15. PairWise Neighbours database: overlaps and spacers among prokaryote genomes

    Directory of Open Access Journals (Sweden)

    Garcia-Vallvé Santiago

    2009-06-01

    Full Text Available Abstract Background Although prokaryotes live in a variety of habitats and possess different metabolic and genomic complexity, they have several genomic architectural features in common. The overlapping genes are a common feature of the prokaryote genomes. The overlapping lengths tend to be short because as the overlaps become longer they have more risk of deleterious mutations. The spacers between genes tend to be short too because of the tendency to reduce the non coding DNA among prokaryotes. However they must be long enough to maintain essential regulatory signals such as the Shine-Dalgarno (SD sequence, which is responsible of an efficient translation. Description PairWise Neighbours is an interactive and intuitive database used for retrieving information about the spacers and overlapping genes among bacterial and archaeal genomes. It contains 1,956,294 gene pairs from 678 fully sequenced prokaryote genomes and is freely available at the URL http://genomes.urv.cat/pwneigh. This database provides information about the overlaps and their conservation across species. Furthermore, it allows the wide analysis of the intergenic regions providing useful information such as the location and strength of the SD sequence. Conclusion There are experiments and bioinformatic analysis that rely on correct annotations of the initiation site. Therefore, a database that studies the overlaps and spacers among prokaryotes appears to be desirable. PairWise Neighbours database permits the reliability analysis of the overlapping structures and the study of the SD presence and location among the adjacent genes, which may help to check the annotation of the initiation sites.

  16. An integrative and applicable phylogenetic footprinting framework for cis-regulatory motifs identification in prokaryotic genomes.

    Science.gov (United States)

    Liu, Bingqiang; Zhang, Hanyuan; Zhou, Chuan; Li, Guojun; Fennell, Anne; Wang, Guanghui; Kang, Yu; Liu, Qi; Ma, Qin

    2016-08-09

    Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP(3)). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, we collected orthologous genes from available prokaryotic genomes and built the orthologous regulatory regions based on sequence similarity of promoter regions. This procedure made full use of the large-scale genomic data and taxonomy information and filtered out the promoters with limited contribution to produce a high quality orthologous promoter set. The promoter scoring and pruning is implemented through motif voting by a set of complementary predicting tools that mine as many motif candidates as possible and simultaneously eliminate the effect of random noise. We have applied the framework to Escherichia coli k12 genome and evaluated the prediction performance through comparison with seven existing programs. This evaluation was systematically carried out at the nucleotide and binding site level, and the results showed that MP(3) consistently outperformed other popular motif finding tools. We have integrated MP(3) into our motif identification and analysis server DMINDA, allowing users to efficiently identify and analyze motifs in 2,072 completely sequenced prokaryotic genomes. The performance evaluation indicated that MP(3) is effective for predicting regulatory motifs in prokaryotic genomes. Its application may enhance

  17. Impact of lowland rainforest transformation on diversity and composition of soil prokaryotic communities in Sumatra (Indonesia

    Directory of Open Access Journals (Sweden)

    Dominik eSchneider

    2015-12-01

    Full Text Available Prokaryotes are the most abundant and diverse group of microorganisms in soil and mediate virtually all biogeochemical cycles in terrestrial ecosystems. Thereby, they influence aboveground plant productivity and diversity. In this study, the impact of rainforest transformation to intensively managed cash crop systems on soil prokaryotic communities was investigated. The studied managed land use system comprised rubber agroforests (jungle rubber, rubber plantation and oil plantations within two Indonesian landscapes Bukit Duabelas and Harapan. Soil prokaryotic community composition and diversity were assessed by pyrotag sequencing of bacterial and archaeal 16S rRNA genes. The curated dataset contained 20,494 bacterial and 1,762 archaeal Operational Taxonomic Units at species level (97% genetic identity. Analysis revealed changes in indigenous taxon-specific patterns of soil prokaryotic communities accompanying lowland rainforest transformation to jungle rubber, and intensively managed rubber and oil palm plantations. Distinct clustering of the rainforest soil communities indicated that these are different from the communities in the studied managed land use systems. The predominant bacterial taxa in all investigated soils were Acidobacteria, Actinobacteria, Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Overall, the bacterial community shifted from proteobacterial groups in rainforest soils to Acidobacteria in managed soils. The archaeal soil communities were mainly represented by Thaumarchaeota and Euryarchaeota. Members of the Terrestrial Group and South African Gold Mine Group 1 (Thaumarchaeota dominated in the rainforest and members of Thermoplasmata in the managed land use systems. The alpha and beta diversity of the soil prokaryotic communities was higher in managed land use systems than in rainforest. In the case of bacteria, this was related to soil characteristics such as pH value, exchangeable Ca and Fe content, C to

  18. Analysis of intra-genomic GC content homogeneity within prokaryotes

    DEFF Research Database (Denmark)

    Bohlin, J; Snipen, L; Hardy, S.P.

    2010-01-01

    the GC content varies within microbial genomes to assess whether this property can be associated with certain biological functions related to the organism's environment and phylogeny. We utilize a new quantity GCVAR, the intra-genomic GC content variability with respect to the average GC content......Bacterial genomes possess varying GC content (total guanines (Gs) and cytosines (Cs) per total of the four bases within the genome) but within a given genome, GC content can vary locally along the chromosome, with some regions significantly more or less GC rich than on average. We have examined how...... both aerobic and facultative microbes. Although an association has previously been found between mean genomic GC content and oxygen requirement, our analysis suggests that no such association exits when phylogenetic bias is accounted for. A significant association between GCVAR and mean GC content...

  19. Molecular Evolution of the Oxygen-Binding Hemerythrin Domain.

    Directory of Open Access Journals (Sweden)

    Claudia Alvarez-Carreño

    Full Text Available The evolution of oxygenic photosynthesis during Precambrian times entailed the diversification of strategies minimizing reactive oxygen species-associated damage. Four families of oxygen-carrier proteins (hemoglobin, hemerythrin and the two non-homologous families of arthropodan and molluscan hemocyanins are known to have evolved independently the capacity to bind oxygen reversibly, providing cells with strategies to cope with the evolutionary pressure of oxygen accumulation. Oxygen-binding hemerythrin was first studied in marine invertebrates but further research has made it clear that it is present in the three domains of life, strongly suggesting that its origin predated the emergence of eukaryotes.Oxygen-binding hemerythrins are a monophyletic sub-group of the hemerythrin/HHE (histidine, histidine, glutamic acid cation-binding domain. Oxygen-binding hemerythrin homologs were unambiguously identified in 367/2236 bacterial, 21/150 archaeal and 4/135 eukaryotic genomes. Overall, oxygen-binding hemerythrin homologues were found in the same proportion as single-domain and as long protein sequences. The associated functions of protein domains in long hemerythrin sequences can be classified in three major groups: signal transduction, phosphorelay response regulation, and protein binding. This suggests that in many organisms the reversible oxygen-binding capacity was incorporated in signaling pathways. A maximum-likelihood tree of oxygen-binding hemerythrin homologues revealed a complex evolutionary history in which lateral gene transfer, duplications and gene losses appear to have played an important role.Hemerythrin is an ancient protein domain with a complex evolutionary history. The distinctive iron-binding coordination site of oxygen-binding hemerythrins evolved first in prokaryotes, very likely prior to the divergence of Firmicutes and Proteobacteria, and spread into many bacterial, archaeal and eukaryotic species. The later evolution of the

  20. Probing the Energy Transfer Dynamics of Photosynthetic Reaction Center Complexes Through Hole-Burning and Single-Complex Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Riley, Kerry Joseph [Iowa State Univ., Ames, IA (United States)

    2007-01-01

    Photosynthesis is the process by which light energy is used to drive reactions that generate sugars to supply energy for cellular processes. It is one of the most important fundamental biological reactions and occurs in both prokaryotic (e.g. bacteria) and eukaryotic (e.g. plants and algae) organisms. Photosynthesis is also remarkably intricate, requiring the coordination of many different steps and reactions in order to successfully transform absorbed solar energy into a biochemical usable form of energy. However, the net reaction for all photosynthetic organisms can be reduced to the following, deceptively general, equation developed by Van Niel[1] H2 - D + Aimplieshv A - H2 + D where H2-D is the electron donor, e.g. H2O, H2S. A is the electron acceptor, e.g. CO2, and A-H2 is the synthesized sugar. Amazingly, this simple net equation is responsible for creating the oxidizing atmosphere of Earth and the recycling of CO2, both of which are necessary for the sustainment of the global ecosystem.

  1. Oxygen safety

    Science.gov (United States)

    ... sure you have working smoke detectors and a working fire extinguisher in your home. If you move around the house with your oxygen, you may need more than one fire extinguisher in different locations. Smoking can be very dangerous. No one should smoke ...

  2. Carotenoid Photoprotection in Artificial Photosynthetic Antennas

    Energy Technology Data Exchange (ETDEWEB)

    Kloz, Miroslav [VU Univ., Amsterdam (Netherlands); Pillai, Smitha [Arizona State Univ., Tempe, AZ (United States); Kodis, Gerdenis [Arizona State Univ., Tempe, AZ (United States); Gust, Devens [Arizona State Univ., Tempe, AZ (United States); Moore, Thomas A. [Arizona State Univ., Tempe, AZ (United States); Moore, Ana L. [Arizona State Univ., Tempe, AZ (United States); van Grondelle, Rienk [VU Univ., Amsterdam (Netherlands); Kennis, John T. M. [VU Univ., Amsterdam (Netherlands)

    2011-04-14

    . These synthetic systems are providing a deeper understanding of structural and environmental effects on the interactions between carotenoids and tetrapyrroles and thereby better defining their role in controlling natural photosynthetic systems.

  3. A Survey into Taxonomic and Physiological Differences of Symbiodinium sp., the Photosynthetic Symbiont of Reef-building Corals

    KAUST Repository

    Gong, Xianzhe

    2012-11-01

    The dinoflagellate genus Symbiodinium is a popular research topic in the coral reef molecular biology field. Primarily because these organisms serve as the coral holobiont’s primary source of energy, carrying out photosynthesis, and providing hydrocarbons to the coral host. Previous studies have shown the difficulty of isolating Symbiodinium as well as the inherent problems in trying to quantify the diversity of this genus and to qualify the distinct reactions of different Symbiodinium sp. to changing environmental conditions. The main goals of this study are: (1) to detail the relationship between the genetic classification of the organism and its physiology in regard to photosynthesis with a number of established Symbiodinium cultures; and (2) to isolate Symbiodinium from coral of the central Red Sea. To evaluate the photosynthetic physiology of Symbiodinium, a microsensor was used to measure oxygen concentrations along with a phytoplankton analyzer system that used pulse-amplitude-modulation (Phyto-PAM) to measure fluorescence. In order to identify the particular clade that the isolates belonged to, denaturing gradient gel electrophoresis (PCR-DGGE) was used to identify Symbiodinium based on their internal transcribed spacer 2 (ITS2) region. These techniques helped us to achieve our goals in the following ways: Symbiodinium sp. from a culture collection were classified to the subclade level; species-specific and clade-specific photosynthetic profiles were generated; and a Symbiodinium sp. was isolated from the central Red Sea. This study provided preliminary correlation between the photosynthetic difference and Symbiodinium genetic classification; showed the probable existence of a self-protection system inside the Symbiodinium cells by comparing the difference between the initial oxygen production at the beginning of each light step and the oxygen production after light adaptation; and confirmed the possibility of the isolation of Symbiodinium.

  4. Oxygen therapy - infants

    Science.gov (United States)

    ... breathe increased amounts of oxygen to get normal levels of oxygen in their blood. Oxygen therapy provides babies with the extra oxygen. Information Oxygen is a gas that the cells in your body need to work properly. The ...

  5. Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline-Alkaline Soils.

    Science.gov (United States)

    Liu, Kaihui; Ding, Xiaowei; Tang, Xiaofei; Wang, Jianjun; Li, Wenjun; Yan, Qingyun; Liu, Zhenghua

    2018-01-01

    Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline-alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity ( P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi ( P analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi.

  6. Macro and Microelements Drive Diversity and Composition of Prokaryotic and Fungal Communities in Hypersaline Sediments and Saline–Alkaline Soils

    Science.gov (United States)

    Liu, Kaihui; Ding, Xiaowei; Tang, Xiaofei; Wang, Jianjun; Li, Wenjun; Yan, Qingyun; Liu, Zhenghua

    2018-01-01

    Understanding the effects of environmental factors on microbial communities is critical for microbial ecology, but it remains challenging. In this study, we examined the diversity (alpha diversity) and community compositions (beta diversity) of prokaryotes and fungi in hypersaline sediments and salinized soils from northern China. Environmental variables were highly correlated, but they differed significantly between the sediments and saline soils. The compositions of prokaryotic and fungal communities in the hypersaline sediments were different from those in adjacent saline–alkaline soils, indicating a habitat-specific microbial distribution pattern. The macroelements (S, P, K, Mg, and Fe) and Ca were, respectively, correlated closely with the alpha diversity of prokaryotes and fungi, while the macronutrients (e.g., Na, S, P, and Ca) were correlated with the prokaryotic and fungal beta-diversity (P ≤ 0.05). And, the nine microelements (e.g., Al, Ba, Co, Hg, and Mn) and micronutrients (Ba, Cd, and Sr) individually shaped the alpha diversity of prokaryotes and fungi, while the six microelements (e.g., As, Ba, Cr, and Ge) and only the trace elements (Cr and Cu), respectively, influenced the beta diversity of prokaryotes and fungi (P analysis (VPA) showed that environmental variables jointly explained 55.49% and 32.27% of the total variation for the prokaryotic and fungal communities, respectively. Together, our findings demonstrate that the diversity and community composition of the prokaryotes and fungi were driven by different macro and microelements in saline habitats, and that geochemical elements could more widely regulate the diversity and community composition of prokaryotes than these of fungi. PMID:29535703

  7. Climate controls photosynthetic capacity more than leaf nitrogen contents

    Science.gov (United States)

    Ali, A. A.; Xu, C.; McDowell, N. G.

    2013-12-01

    Global vegetation models continue to lack the ability to make reliable predictions because the photosynthetic capacity varies a lot with growth conditions, season and among species. It is likely that vegetation models link photosynthetic capacity to concurrent changes in leaf nitrogen content only. To improve the predictions of the vegetation models, there is an urgent need to review species growth conditions and their seasonal response to changing climate. We sampled the global distribution of the Vcmax (maximum carboxylation rates) data of various species across different environmental gradients from the literature and standardized its value to 25 degree Celcius. We found that species explained the largest variation in (1) the photosynthetic capacity and (2) the proportion of nitrogen allocated for rubisco (PNcb). Surprisingly, climate variables explained more variations in photosynthetic capacity as well as PNcb than leaf nitrogen content and/or specific leaf area. The chief climate variables that explain variation in photosynthesis and PNcb were radiation, temperature and daylength. Our analysis suggests that species have the greatest control over photosynthesis and PNcb. Further, compared to leaf nitrogen content and/or specific leaf area, climate variables have more control over photosynthesis and PNcb. Therefore, climate variables should be incorporated in the global vegetation models when making predictions about the photosynthetic capacity.

  8. Photosynthetic water oxidation: binding and activation of substrate waters for O-O bond formation.

    Science.gov (United States)

    Vinyard, David J; Khan, Sahr; Brudvig, Gary W

    2015-01-01

    Photosynthetic water oxidation occurs at the oxygen-evolving complex (OEC) of Photosystem II (PSII). The OEC, which contains a Mn4CaO5 inorganic cluster ligated by oxides, waters and amino-acid residues, cycles through five redox intermediates known as S(i) states (i = 0-4). The electronic and structural properties of the transient S4 intermediate that forms the O-O bond are not well understood. In order to gain insight into how water is activated for O-O bond formation in the S4 intermediate, we have performed a detailed analysis of S-state dependent substrate water binding kinetics taking into consideration data from Mn coordination complexes. This analysis supports a model in which the substrate waters are both bound as terminal ligands and react via a water-nucleophile attack mechanism.

  9. Effects of temperature and irradiance on a benthic microalgal community: A combined two-dimensional oxygen and fluorescence imaging approach

    DEFF Research Database (Denmark)

    Hancke, Kasper; Sorrell, Brian Keith; Lund-Hansen, Lars Chresten

    2014-01-01

    The effects of temperature and light on both oxygen (O2) production and gross photosynthesis were resolved in a benthic microalgae community by combining two-dimensional (2D) imaging of O2 and variable chlorophyll a (Chl a) fluorescence. Images revealed a photosynthetically active community...... microbial community, at different temperatures. The present imaging approach demonstrates a great potential to study consequences of environmental effects on photosynthetic activity and O2 turnover in complex phototrophic benthic communities....

  10. Deriving C4 photosynthetic parameters from combined gas exchange and chlorophyll fluorescence using an Excel tool: theory and practice.

    Science.gov (United States)

    Bellasio, Chandra; Beerling, David J; Griffiths, Howard

    2016-06-01

    The higher photosynthetic potential of C4 plants has led to extensive research over the past 50 years, including C4 -dominated natural biomes, crops such as maize, or for evaluating the transfer of C4 traits into C3 lineages. Photosynthetic gas exchange can be measured in air or in a 2% Oxygen mixture using readily available commercial gas exchange and modulated PSII fluorescence systems. Interpretation of these data, however, requires an understanding (or the development) of various modelling approaches, which limit the use by non-specialists. In this paper we present an accessible summary of the theory behind the analysis and derivation of C4 photosynthetic parameters, and provide a freely available Excel Fitting Tool (EFT), making rigorous C4 data analysis accessible to a broader audience. Outputs include those defining C4 photochemical and biochemical efficiency, the rate of photorespiration, bundle sheath conductance to CO2 diffusion and the in vivo biochemical constants for PEP carboxylase. The EFT compares several methodological variants proposed by different investigators, allowing users to choose the level of complexity required to interpret data. We provide a complete analysis of gas exchange data on maize (as a model C4 organism and key global crop) to illustrate the approaches, their analysis and interpretation. © 2015 John Wiley & Sons Ltd. © 2016 John Wiley & Sons Ltd.

  11. Balancing photosynthetic light-harvesting and light-utilization capacities in potato leaf tissue during acclimation to different growth temperatures

    Science.gov (United States)

    Steffen, K. L.; Wheeler, R. M.; Arora, R.; Palta, J. P.; Tibbitts, T. W.

    1995-01-01

    We investigated the effect of temperature during growth and development on the relationship between light-harvesting capacity, indicated by chlorophyll concentration, and light-utilization potential, indicated by light- and bicarbonate-saturated photosynthetic oxygen evolution, in Solanum tuberosum L. cv. Norland. Clonal plantlets were transplanted and grown at 20 degrees C for 2 weeks before transfer to 12, 16, 20, 24 and 28 degrees C for 6 weeks. After 4 weeks of the temperature treatments, leaf tissue fresh weights per area were one-third higher in plants grown at 12 degrees C vs those grown at 28 degrees C. Conversely, chlorophyll content per area in tissue grown at 12 degrees C was less than one-half of that of tissue grown at 28 degrees C at 4 weeks. Photosynthetic capacity measured at a common temperature of 20 degrees C and expressed on a chlorophyll basis was inversely proportional to growth temperature. Leaf tissue from plants grown at 12 degrees C for 4 weeks had photosynthetic rates that were 3-fold higher on a chlorophyll basis than comparable tissue from plants grown at 28 degrees C. These results suggest that the relationship between light-harvesting capacity and light-utilization potential varies 3-fold in response to the growth temperatures examined. The role of this response in avoidance of photoinhibition is discussed.

  12. Okadaic acid inhibits cell growth and photosynthetic electron transport in the alga Dunaliella tertiolecta

    Energy Technology Data Exchange (ETDEWEB)

    Perreault, Francois; Matias, Marcelo Seleme; Oukarroum, Abdallah [Department of Chemistry, Universite du Quebec a Montreal, 2101, Rue Jeanne Mance, Montreal, QC, Canada H2X 2J6 (Canada); Matias, William Gerson [Department of Chemistry, Universite du Quebec a Montreal, 2101, Rue Jeanne Mance, Montreal, QC, Canada H2X 2J6 (Canada); Laboratorio de Toxicologia Ambiental, LABTOX, Depto. de Engenharia Sanitaria e Ambiental, Universidade Federal de Santa Catarina, Campus Universitario, CEP: 88040-970, Florianopolis, SC (Brazil); Popovic, Radovan, E-mail: popovic.radovan@uqam.ca [Department of Chemistry, Universite du Quebec a Montreal, 2101, Rue Jeanne Mance, Montreal, QC, Canada H2X 2J6 (Canada)

    2012-01-01

    Okadaic acid (OA), which is produced by several dinoflagellate species, is a phycotoxin known to induce a decrease of biomass production in phytoplankton. However, the mechanisms of OA cytotoxicity are still unknown in microalgae. In this study, we exposed the green microalga Dunaliella tertiolecta to OA concentrations of 0.05 to 0.5 {mu}M in order to evaluate its effects on cell division, reactive oxygen species production and photosynthetic electron transport. After 72 h of treatment under continuous illumination, OA concentrations higher than 0.10 {mu}M decreased culture cell density, induced oxidative stress and inhibited photosystem II electron transport capacity. OA effect in D. tertiolecta was strongly light dependent since no oxidative stress was observed when D. tertiolecta was exposed to OA in the dark. In the absence of light, the effect of OA on culture cell density and photosystem II activity was also significantly reduced. Therefore, light appears to have a significant role in the toxicity of OA in microalgae. Our results indicate that the site of OA interaction on photosynthetic electron transport is likely to be at the level of the plastoquinone pool, which can lead to photo-oxidative stress when light absorbed by the light-harvesting complex of photosystem II cannot be dissipated via photochemical pathways. These findings allowed for a better understanding of the mechanisms of OA toxicity in microalgae. - Highlights: Black-Right-Pointing-Pointer Exposition of Dunaliella tertiolecta to okadaic acid in light conditions results in reactive oxygen species formation. Black-Right-Pointing-Pointer Inhibition of photosystem II is dependent on oxidative stress and effects of okadaic acid on the plastoquinone pool. Black-Right-Pointing-Pointer Oxidative stress and inhibition of photosynthesis increase okadaic acid effect on cell density in light conditions. Black-Right-Pointing-Pointer Okadaic acid induces toxicity in algae via both light-dependent and light

  13. Biological optimization systems for enhancing photosynthetic efficiency and methods of use

    Science.gov (United States)

    Hunt, Ryan W.; Chinnasamy, Senthil; Das, Keshav C.; de Mattos, Erico Rolim

    2012-11-06

    Biological optimization systems for enhancing photosynthetic efficiency and methods of use. Specifically, methods for enhancing photosynthetic efficiency including applying pulsed light to a photosynthetic organism, using a chlorophyll fluorescence feedback control system to determine one or more photosynthetic efficiency parameters, and adjusting one or more of the photosynthetic efficiency parameters to drive the photosynthesis by the delivery of an amount of light to optimize light absorption of the photosynthetic organism while providing enough dark time between light pulses to prevent oversaturation of the chlorophyll reaction centers are disclosed.

  14. Effect of space mutation of photosynthetic characteristics of soybean varieties

    International Nuclear Information System (INIS)

    Liu Xinlei; Ma Yansong; Luan Xiaoyan; Man Weiqun; Xu Dechun; Meng Lifen; Fu Lixin; Zhao Xiao'nan; Liu Qi

    2012-01-01

    In order to elucidate the response of the photosynthetic traits of soybean to space mutation, three soybean varieties (lines) of Heinong 48, Heinong 44 and Ha 2291-Y were carried by artificial satellite in 2006 and the net photo synthetic rate (Pn), stomatal conductance (Cond), intercellular CO 2 concentration (Ci) and stomatal resistance (Rs) from SP 1 to SP 4 generation were determined. The results showed that space mutation affected photosynthesis traits of soy bean. The photosynthetic rate of soybean varieties by space mutation occurred different levels of genetic variation and the positive mutation rate were higher. Coefficient of variation among generations were SP 2 >SP 3 >SP 4 >CK. Results suggest that space mutation can effectively create soybean materials with higher photosynthetic rate. (authors)

  15. Cyanobacteria as photosynthetic biocatalysts: a systems biology perspective.

    Science.gov (United States)

    Gudmundsson, Steinn; Nogales, Juan

    2015-01-01

    The increasing need to replace oil-based products and to address global climate change concerns has triggered considerable interest in photosynthetic microorganisms. Cyanobacteria, in particular, have great potential as biocatalysts for fuels and fine-chemicals. During the last few years the biotechnological applications of cyanobacteria have experienced an unprecedented increase and the use of these photosynthetic organisms for chemical production is becoming a tangible reality. However, the field is still immature and many concerns about the economic feasibility of the biotechnological potential of cyanobacteria remain. In this review we describe recent successes in biofuel and fine-chemical production using cyanobacteria. We discuss the role of the photosynthetic metabolism and highlight the need for systems-level metabolic optimization in order to achieve the true potential of cyanobacterial biocatalysts.

  16. Superradiance Transition and Nonphotochemical Quenching in Photosynthetic Complexes

    Energy Technology Data Exchange (ETDEWEB)

    Berman, Gennady Petrovich [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nesterov, Alexander [Universidad de Guadalajara, Departamento de Fısica, Jalisco (Mexico); Lopez, Gustavo [Universidad de Guadalajara, Departamento de Fısica, Jalisco (Mexico); Sayre, Richard Thomas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-04-23

    Photosynthetic organisms have evolved protective strategies to allow them to survive in cases of intense sunlight fluctuation with the development of nonphotochemical quenching (NPQ). This process allows light harvesting complexes to transfer the excess sunlight energy to non-damaging quenching channels. This report compares the NPQ process with the superradiance transition (ST). We demonstrated that the maximum of the NPQ efficiency is caused by the ST to the sink associated with the CTS. However, experimental verifications are required in order to determine whether or not the NPQ regime is associated with the ST transition for real photosynthetic complexes. Indeed, it can happen that, in the photosynthetic apparatus, the NPQ regime occurs in the “non-optimal” region of parameters, and it could be independent of the ST.

  17. ENHANCED PRACTICAL PHOTOSYNTHETIC CO2 MITIGATION

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Gregory Kremer; Dr. David J. Bayless; Dr. Morgan Vis; Dr. Michael Prudich; Dr. Keith Cooksey; Dr. Jeff Muhs

    2002-07-15

    This quarterly report documents significant achievements in the Enhanced Practical Photosynthetic CO{sub 2} Mitigation project during the period from 4/2/2001 through 7/01/2002. Most of the achievements are milestones in our efforts to complete the tasks and subtasks that constitute the project objectives, and we are currently on schedule to complete Phase I activities by 10/2002, the milestone date from the original project timeline. As indicated in the list of accomplishments below, our efforts are focused on improving the design of the bioreactor test system, evaluating candidate organisms and growth surfaces, and scaling-up the test facilities from bench scale to pilot scale. Specific results and accomplishments for the second quarter of 2002 include: Organisms and Growth Surfaces: (1) Our collection of cyanobacteria, isolated in YNP was increased to 15 unialgal cultures. (2) Illumination rate about 50 {micro}E/m{sup 2}/sec is not saturated for the growth of 1.2 s.c. (2) isolate. The decrease of illumination rate led to the decrease of doubling time of this isolate. (3) The positive effect of Ca{sup 2+} on the growth of isolate 1.2 s.c. (2) without Omnisil was revealed, though Ca{sup 2+} addition was indifferent for the growth of this isolate at the presence of Omnisil. (4) Calcium addition had a positive effect on the generation of cyanobacterial biofilm on Omnisil surface. (5) The survivability problems with the Tr9.4 organism on Omnisil screens in the CRF2 model-scale bioreactor have been solved. The problems were related to the method used to populate the growth surfaces. When pre-populated screens were placed in the bioreactor the microalgae died within 72 hours, but when the microalgae were cultured while in place in the bioreactor using a continuous-population method they grew well inside of the CRF2 test system and survived for the full 7-day test duration. CRF2 tests will continue as soon as the new combined drip system/harvesting system header pipe

  18. Energy transfer in real and artificial photosynthetic systems

    Energy Technology Data Exchange (ETDEWEB)

    Hindman, J.C.; Hunt, J.E.; Katz, J.J.

    1995-02-01

    Fluorescence emission from the photosynthetic organisms Tribonema aequale, Anacystis nidulau, and Chlorelia vulgais and from some chlorophyll model systems have been recorded as a function of excitation wavelength and temperature. Considerable similarity was observed in the effects of excitation wavelength and temperature on the fluorescence from intact photosynthetic organisms and the model systems. The parallelism in behavior suggest that self-assembly processes may occur in both the in vivo and in vitro systems that give rise to chlorophyll species at low temperature that may differ significantly from those present at ambient temperatures.

  19. Photoinhibition-like damage to the photosynthetic apparatus in plant leaves induced by submergence treatment in the dark.

    Directory of Open Access Journals (Sweden)

    Xingli Fan

    Full Text Available Submergence is a common type of environmental stress for plants. It hampers survival and decreases crop yield, mainly by inhibiting plant photosynthesis. The inhibition of photosynthesis and photochemical efficiency by submergence is primarily due to leaf senescence and excess excitation energy, caused by signals from hypoxic roots and inhibition of gas exchange, respectively. However, the influence of mere leaf-submergence on the photosynthetic apparatus is currently unknown. Therefore, we studied the photosynthetic apparatus in detached leaves from four plant species under dark-submergence treatment (DST, without influence from roots and light. Results showed that the donor and acceptor sides, the reaction center of photosystem II (PSII and photosystem I (PSI in leaves were significantly damaged after 36 h of DST. This is a photoinhibition-like phenomenon similar to the photoinhibition induced by high light, as further indicated by the degradation of PsaA and D1, the core proteins of PSI and PSII. In contrast to previous research, the chlorophyll content remained unchanged and the H2O2 concentration did not increase in the leaves, implying that the damage to the photosynthetic apparatus was not caused by senescence or over-accumulation of reactive oxygen species (ROS. DST-induced damage to the photosynthetic apparatus was aggravated by increasing treatment temperature. This type of damage also occurred in the anaerobic environment (N2 without water, and could be eliminated or restored by supplying air to the water during or after DST. Our results demonstrate that DST-induced damage was caused by the hypoxic environment. The mechanism by which DST induces the photoinhibition-like damage is discussed below.

  20. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes

    NARCIS (Netherlands)

    Al-Attar, S.; Westra, E.R.; Oost, van der J.; Brouns, S.J.J.

    2011-01-01

    Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences

  1. Footprints of Optimal Protein Assembly Strategies in the Operonic Structure of Prokaryotes

    Directory of Open Access Journals (Sweden)

    Jan Ewald

    2015-04-01

    Full Text Available In this work, we investigate optimality principles behind synthesis strategies for protein complexes using a dynamic optimization approach. We show that the cellular capacity of protein synthesis has a strong influence on optimal synthesis strategies reaching from a simultaneous to a sequential synthesis of the subunits of a protein complex. Sequential synthesis is preferred if protein synthesis is strongly limited, whereas a simultaneous synthesis is optimal in situations with a high protein synthesis capacity. We confirm the predictions of our optimization approach through the analysis of the operonic organization of protein complexes in several hundred prokaryotes. Thereby, we are able to show that cellular protein synthesis capacity is a driving force in the dissolution of operons comprising the subunits of a protein complex. Thus, we also provide a tested hypothesis explaining why the subunits of many prokaryotic protein complexes are distributed across several operons despite the presumably less precise co-regulation.

  2. SURVIVAL AND EVOLUTION OF CRISPR-CAS SYSTEM IN PROKARYOTES AND ITS APPLICATIONS

    Directory of Open Access Journals (Sweden)

    Muhammad Abu Bakr Shabbir

    2016-09-01

    Full Text Available Prokaryotes have developed numerous innate immune mechanisms in order to fend off bacteriophage or plasmid attack. One of these immune systems is Clustered regularly interspaced short palindromic repeats (CRISPR. CRISPR associated proteins play a key role in survival of prokaryotes against invaders, as these systems cleave DNA of foreign genetic elements. Beyond providing immunity, these systems have significant impact in altering the bacterial physiology in term of its virulence and pathogenicity, as well as evolution. Also, due to their diverse nature of functionality, cas9 endoribonuclease can be easily reprogrammed with the help of guide RNAs, showing unprecedented potential and significance for gene editing in treating genetic diseases. Here, we also discuss the use of NgAgo-gDNA system in genome editing of human cells.

  3. Survival and Evolution of CRISPR–Cas System in Prokaryotes and Its Applications

    Science.gov (United States)

    Shabbir, Muhammad Abu Bakr; Hao, Haihong; Shabbir, Muhammad Zubair; Hussain, Hafiz Iftikhar; Iqbal, Zahid; Ahmed, Saeed; Sattar, Adeel; Iqbal, Mujahid; Li, Jun; Yuan, Zonghui

    2016-01-01

    Prokaryotes have developed numerous innate immune mechanisms in order to fend off bacteriophage or plasmid attack. One of these immune systems is clustered regularly interspaced short palindromic repeats (CRISPR). CRISPR-associated proteins play a key role in survival of prokaryotes against invaders, as these systems cleave DNA of foreign genetic elements. Beyond providing immunity, these systems have significant impact in altering the bacterial physiology in term of its virulence and pathogenicity, as well as evolution. Also, due to their diverse nature of functionality, cas9 endoribonuclease can be easily reprogrammed with the help of guide RNAs, showing unprecedented potential and significance for gene editing in treating genetic diseases. Here, we also discuss the use of NgAgo–gDNA system in genome editing of human cells. PMID:27725818

  4. [Description of the phylogenetic structure of hydrolytic prokaryotic complex in the soils].

    Science.gov (United States)

    Lukacheva, E G; Chernov, T I; Bykova, E M; Vlasenko, A N; Manucharova, N A

    2013-01-01

    With the help of the molecular-biological method of cell hybridization in situ (FISH), the abundance of a physiologically active hydrolytic prokaryotic complex in chernozem and gley-podzolic soils is determined. The total proportion of metabolically active cells, which were detected by hybridization with universal probes as representatives of the domains Bacteria and Archaea, in samples of the studied soil, was from 38% for chernozem up to 78% for gley-podzolic soil of the total number of cells. The differences in the structure of chitinolytic and pectinolytic prokaryotic soil complexes are detected. Along with the high abundance of Actinobacteria and Firmicutes in the soils with chitin, an increase in phylogenetic groups such as Alphaproteobacteria and Bacteroidetes is observed.

  5. ConSpeciFix: Classifying prokaryotic species based on gene flow.

    Science.gov (United States)

    Bobay, Louis-Marie; Ellis, Brian Shin-Hua; Ochman, Howard

    2018-05-16

    Classification of prokaryotic species is usually based on sequence similarity thresholds, which are easy to apply but lack a biologically-relevant foundation. Here, we present ConSpeciFix, a program that classifies prokaryotes into species using criteria set forth by the Biological Species Concept, thereby unifying species definition in all domains of life. ConSpeciFix's webserver is freely available at www.conspecifix.com. The local version of the program can be freely downloaded from https://github.com/Bobay-Ochman/ConSpeciFix. ConSpeciFix is written in Python 2.7 and requires the following dependencies: Usearch, MCL, MAFFT and RAxML. ljbobay@uncg.edu.

  6. Abundance and distribution of the highly iterated palindrome 1 (HIP1) among prokaryotes

    OpenAIRE

    Delaye, Luis; Moya, Andrés

    2011-01-01

    We have studied the abundance and phylogenetic distribution of the Highly Iterated Palindrome 1 (HIP1) among sequenced prokaryotic genomes. We show that an overrepresentation of HIP1 is exclusive of some lineages of cyanobacteria, and that this abundance was gained only once during evolution and was subsequently lost in the lineage leading to marine pico-cyanobacteria. We show that among cyanobacterial protein sequences with annotated Pfam domains, only OpcA (glucose 6-phosphate dehydrogenase...

  7. Biodiversity of prokaryotic communities associated with the ectoderm of Ectopleura crocea (Cnidaria, Hydrozoa.

    Directory of Open Access Journals (Sweden)

    Cristina Gioia Di Camillo

    Full Text Available The surface of many marine organisms is colonized by complex communities of microbes, yet our understanding of the diversity and role of host-associated microbes is still limited. We investigated the association between Ectopleura crocea (a colonial hydroid distributed worldwide in temperate waters and prokaryotic assemblages colonizing the hydranth surface. We used, for the first time on a marine hydroid, a combination of electron and epifluorescence microscopy and 16S rDNA tag pyrosequencing to investigate the associated prokaryotic diversity. Dense assemblages of prokaryotes were associated with the hydrant surface. Two microbial morphotypes were observed: one horseshoe-shaped and one fusiform, worm-like. These prokaryotes were observed on the hydrozoan epidermis, but not in the portions covered by the perisarcal exoskeleton, and their abundance was higher in March while decreased in late spring. Molecular analyses showed that assemblages were dominated by Bacteria rather than Archaea. Bacterial assemblages were highly diversified, with up to 113 genera and 570 Operational Taxonomic Units (OTUs, many of which were rare and contributed to <0.4%. The two most abundant OTUs, likely corresponding to the two morphotypes present on the epidermis, were distantly related to Comamonadaceae (genus Delftia and to Flavobacteriaceae (genus Polaribacter. Epibiontic bacteria were found on E. crocea from different geographic areas but not in other hydroid species in the same areas, suggesting that the host-microbe association is species-specific. This is the first detailed report of bacteria living on the hydrozoan epidermis, and indeed the first study reporting bacteria associated with the epithelium of E. crocea. Our results provide a starting point for future studies aiming at clarifying the role of this peculiar hydrozoan-bacterial association.

  8. Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

    KAUST Repository

    Salazar, Guillem; Cornejo-Castillo, Francisco M.; Borrull, Encarna; Dí ez-Vives, Cristina; Lara, Elena; Vaqué , Dolors; Arrieta, J M; Duarte, Carlos M.; Gasol, Josep M.; Acinas, Silvia G.

    2015-01-01

    The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been proved to differ in their diversity and composition in the photic ocean and also recently in the bathypelagic ocean at a global scale. However, although high taxonomic ranks exhibit preferences for a PA or FL mode of life, it remains poorly understood whether two clear lifestyles do exist and how these are distributed across the prokaryotic phylogeny. We studied the FL (<0.8 μm) and PA (0.8 – 20 μm) prokaryotes at 30 stations distributed worldwide within the bathypelagic oceanic realm (2,150 – 4,000 m depth) using high throughput sequencing of the small subunit ribosomal RNA gene (16S rRNA). A high proportion of the bathypelagic prokaryotes were mostly found either attached to particles or freely in the surrounding water but rarely in both types of environments. In particular, this trait was deeply conserved through their phylogeny suggesting that the deep-ocean particles and the surrounding water constitute two highly distinct niches and that transitions from one to the other have been rare at an evolutionary time-scale. As a consequence, PA and FL communities had clear alpha- and beta-diversity differences that exceeded the global-scale geographical variation. Our study organizes the bathypelagic prokaryotic diversity into a reasonable number of ecologically coherent taxa regarding their association to particles, a first step for understanding which are the microbes responsible for the processing of the dissolved and particulate pools of organic matter that have a very different biogeochemical role in the deep ocean.

  9. SIS: a program to generate draft genome sequence scaffolds for prokaryotes

    Directory of Open Access Journals (Sweden)

    Dias Zanoni

    2012-05-01

    Full Text Available Abstract Background Decreasing costs of DNA sequencing have made prokaryotic draft genome sequences increasingly common. A contig scaffold is an ordering of contigs in the correct orientation. A scaffold can help genome comparisons and guide gap closure efforts. One popular technique for obtaining contig scaffolds is to map contigs onto a reference genome. However, rearrangements that may exist between the query and reference genomes may result in incorrect scaffolds, if these rearrangements are not taken into account. Large-scale inversions are common rearrangement events in prokaryotic genomes. Even in draft genomes it is possible to detect the presence of inversions given sufficient sequencing coverage and a sufficiently close reference genome. Results We present a linear-time algorithm that can generate a set of contig scaffolds for a draft genome sequence represented in contigs given a reference genome. The algorithm is aimed at prokaryotic genomes and relies on the presence of matching sequence patterns between the query and reference genomes that can be interpreted as the result of large-scale inversions; we call these patterns inversion signatures. Our algorithm is capable of correctly generating a scaffold if at least one member of every inversion signature pair is present in contigs and no inversion signatures have been overwritten in evolution. The algorithm is also capable of generating scaffolds in the presence of any kind of inversion, even though in this general case there is no guarantee that all scaffolds in the scaffold set will be correct. We compare the performance of sis, the program that implements the algorithm, to seven other scaffold-generating programs. The results of our tests show that sis has overall better performance. Conclusions sis is a new easy-to-use tool to generate contig scaffolds, available both as stand-alone and as a web server. The good performance of sis in our tests adds evidence that large

  10. Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

    KAUST Repository

    Salazar, Guillem

    2015-10-13

    The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been proved to differ in their diversity and composition in the photic ocean and also recently in the bathypelagic ocean at a global scale. However, although high taxonomic ranks exhibit preferences for a PA or FL mode of life, it remains poorly understood whether two clear lifestyles do exist and how these are distributed across the prokaryotic phylogeny. We studied the FL (<0.8 μm) and PA (0.8 – 20 μm) prokaryotes at 30 stations distributed worldwide within the bathypelagic oceanic realm (2,150 – 4,000 m depth) using high throughput sequencing of the small subunit ribosomal RNA gene (16S rRNA). A high proportion of the bathypelagic prokaryotes were mostly found either attached to particles or freely in the surrounding water but rarely in both types of environments. In particular, this trait was deeply conserved through their phylogeny suggesting that the deep-ocean particles and the surrounding water constitute two highly distinct niches and that transitions from one to the other have been rare at an evolutionary time-scale. As a consequence, PA and FL communities had clear alpha- and beta-diversity differences that exceeded the global-scale geographical variation. Our study organizes the bathypelagic prokaryotic diversity into a reasonable number of ecologically coherent taxa regarding their association to particles, a first step for understanding which are the microbes responsible for the processing of the dissolved and particulate pools of organic matter that have a very different biogeochemical role in the deep ocean.

  11. New insights into the structural organization of eukaryotic and prokaryotic cytoskeletons using cryo-electron tomography

    International Nuclear Information System (INIS)

    Kuerner, Julia; Medalia, Ohad; Linaroudis, Alexandros A.; Baumeister, Wolfgang

    2004-01-01

    Cryo-electron tomography (cryo-ET) is an emerging imaging technology that combines the potential of three-dimensional (3-D) imaging at molecular resolution (<5 nm) with a close-to-life preservation of the specimen. In conjunction with pattern recognition techniques, it enables us to map the molecular landscape inside cells. The application of cryo-ET to intact cells provides novel insights into the structure and the spatial organization of the cytoskeleton in prokaryotic and eukaryotic cells

  12. Colorimetric sensor for triphosphates and their application as a viable staining agent for prokaryotes and eukaryotes.

    Science.gov (United States)

    Ghosh, Amrita; Shrivastav, Anupama; Jose, D Amilan; Mishra, Sanjiv K; Chandrakanth, C K; Mishra, Sandhya; Das, Amitava

    2008-07-15

    The chromogenic complex 1 x Zn (where 1 is (E)-4-(4-dimethylamino-phenylazo)-N,N-bispyridin-2-ylmethyl-benzenesulfonamide) showed high affinity toward the phosphate ion in tetrabutylammonium phosphate in acetonitrile solution and could preferentially bind to adenosine triphosphate (ATP) in aqueous solution at physiological pH. This binding caused a visual change in color, whereas no such change was noticed with other related anions (adenosine monophosphate, adenosine diphosphate, pyrophosphate, and phosphate) of biological significance. Thus, 1 x Zn could be used as a staining agent for different biological cells through binding to the ATP, generated in situ by the mitochondria (in eukaryotes). For prokaryotes (bacteria) the cell membrane takes care of the cells' energy conversion, since they lack mitochondria. ATP is produced in their unique cell structure on the cell membrane, which is not found in any eukaryotes. These stained cells could be viewed with normal light microscopy. This reagent could even be used for distinguishing the gram-positive and the gram-negative bacteria (prokaryotes). This dye was found to be nonlipophilic in nature and nontoxic to living microbes (eukaryotes and prokaryotes). Further, stained cells were found to grow in their respective media, and this confirmed the maintenance of viability of the microbes even after staining, unlike with many other dyes available commercially.

  13. The current status of cyanobacterial nomenclature under the "prokaryotic" and the "botanical" code.

    Science.gov (United States)

    Oren, Aharon; Ventura, Stefano

    2017-10-01

    Cyanobacterial taxonomy developed in the botanical world because Cyanobacteria/Cyanophyta have traditionally been identified as algae. However, they possess a prokaryotic cell structure, and phylogenetically they belong to the Bacteria. This caused nomenclature problems as the provisions of the International Code of Nomenclature for algae, fungi, and plants (ICN; the "Botanical Code") differ from those of the International Code of Nomenclature of Prokaryotes (ICNP; the "Prokaryotic Code"). While the ICN recognises names validly published under the ICNP, Article 45(1) of the ICN has not yet been reciprocated in the ICNP. Different solutions have been proposed to solve the current problems. In 2012 a Special Committee on the harmonisation of the nomenclature of Cyanobacteria was appointed, but its activity has been minimal. Two opposing proposals to regulate cyanobacterial nomenclature were recently submitted, one calling for deletion of the cyanobacteria from the groups of organisms whose nomenclature is regulated by the ICNP, the second to consistently apply the rules of the ICNP to all cyanobacteria. Following a general overview of the current status of cyanobacterial nomenclature under the two codes we present five case studies of genera for which nomenclatural aspects have been discussed in recent years: Microcystis, Planktothrix, Halothece, Gloeobacter and Nostoc.

  14. Non-Random Inversion Landscapes in Prokaryotic Genomes Are Shaped by Heterogeneous Selection Pressures.

    Science.gov (United States)

    Repar, Jelena; Warnecke, Tobias

    2017-08-01

    Inversions are a major contributor to structural genome evolution in prokaryotes. Here, using a novel alignment-based method, we systematically compare 1,651 bacterial and 98 archaeal genomes to show that inversion landscapes are frequently biased toward (symmetric) inversions around the origin-terminus axis. However, symmetric inversion bias is not a universal feature of prokaryotic genome evolution but varies considerably across clades. At the extremes, inversion landscapes in Bacillus-Clostridium and Actinobacteria are dominated by symmetric inversions, while there is little or no systematic bias favoring symmetric rearrangements in archaea with a single origin of replication. Within clades, we find strong but clade-specific relationships between symmetric inversion bias and different features of adaptive genome architecture, including the distance of essential genes to the origin of replication and the preferential localization of genes on the leading strand. We suggest that heterogeneous selection pressures have converged to produce similar patterns of structural genome evolution across prokaryotes. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

  15. Comparative evaluation of prokaryotic 16S rDNA clone libraries and SSCP in groundwater samples.

    Science.gov (United States)

    Larentis, Michael; Alfreider, Albin

    2011-06-01

    A comparison of ribosomal RNA sequence analysis methods based on clone libraries and single-strand conformational polymorphism technique (SSCP) was performed with groundwater samples obtained between 523-555 meters below surface. The coverage of analyzed clones by phylotype-richness estimates was between 88-100%, confirming that the clone libraries were adequately examined. Analysis of individual bands retrieved from SSCP gels identified 1-6 different taxonomic units per band, suggesting that a single SSCP band does often represent more than one single prokaryotic species. The prokaryotic diversity obtained by both methods showed an overall difference of 42-80%. In comparison to SSCP, clone libraries underestimated the phylogenetic diversity and only 36-66% of the phylotypes observed with SSCP were also detected with the clone libraries. An exception was a sample where the SSCP analysis of Archaea identified only half of the phylotypes retrieved by the clone library. Overall, this study suggests that the clone library and the SSCP approach do not provide an identical picture of the prokaryotic diversity in groundwater samples. The results clearly show that the SSCP method, although this approach is prone to generate methodological artifacts, was able to detect significantly more phylotypes than microbial community analysis based on clone libraries. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  16. Cellular Viscosity in Prokaryotes and Thermal Stability of Low Molecular Weight Biomolecules.

    Science.gov (United States)

    Cuecas, Alba; Cruces, Jorge; Galisteo-López, Juan F; Peng, Xiaojun; Gonzalez, Juan M

    2016-08-23

    Some low molecular weight biomolecules, i.e., NAD(P)H, are unstable at high temperatures. The use of these biomolecules by thermophilic microorganisms has been scarcely analyzed. Herein, NADH stability has been studied at different temperatures and viscosities. NADH decay increased at increasing temperatures. At increasing viscosities, NADH decay rates decreased. Thus, maintaining relatively high cellular viscosity in cells could result in increased stability of low molecular weight biomolecules (i.e., NADH) at high temperatures, unlike what was previously deduced from studies in diluted water solutions. Cellular viscosity was determined using a fluorescent molecular rotor in various prokaryotes covering the range from 10 to 100°C. Some mesophiles showed the capability of changing cellular viscosity depending on growth temperature. Thermophiles and extreme thermophiles presented a relatively high cellular viscosity, suggesting this strategy as a reasonable mechanism to thrive under these high temperatures. Results substantiate the capability of thermophiles and extreme thermophiles (growth range 50-80°C) to stabilize and use generally considered unstable, universal low molecular weight biomolecules. In addition, this study represents a first report, to our knowledge, on cellular viscosity measurements in prokaryotes and it shows the dependency of prokaryotic cellular viscosity on species and growth temperature. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. A Preliminary List of Horizontally Transferred Genes in Prokaryotes Determined by Tree Reconstruction and Reconciliation

    Directory of Open Access Journals (Sweden)

    Hyeonsoo Jeong

    2017-08-01

    Full Text Available Genome-wide global detection of genes involved in horizontal gene transfer (HGT remains an active area of research in medical microbiology and evolutionary genomics. Utilizing the explicit evolutionary method of comparing topologies of a total of 154,805 orthologous gene trees against corresponding 16S rRNA “reference” trees, we previously detected a total of 660,894 candidate HGT events in 2,472 completely-sequenced prokaryotic genomes. Here, we report an HGT-index for each individual gene-reference tree pair reconciliation, representing the total number of detected HGT events on the gene tree divided by the total number of genomes (taxa member of that tree. HGT-index is thus a simple measure indicating the sensitivity of prokaryotic genes to participate (or not participate in HGT. Our preliminary list provides HGT-indices for a total of 69,365 genes (detected in >10 and <50% available prokaryotic genomes that are involved in a wide range of biological processes such as metabolism, information, and bacterial response to environment. Identification of horizontally-derived genes is important to combat antibiotic resistance and is a step forward toward reconstructions of improved phylogenies describing the history of life. Our effort is thus expected to benefit ongoing research in the fields of clinical microbiology and evolutionary biology.

  18. Prokaryotic diversity and community composition in the Salar de Uyuni, a large scale, chaotropic salt flat.

    Science.gov (United States)

    dC Rubin, Sergio S; Marín, Irma; Gómez, Manuel J; Morales, Eduardo A; Zekker, Ivar; San Martín-Uriz, Patxi; Rodríguez, Nuria; Amils, Ricardo

    2017-09-01

    Salar de Uyuni (SdU), with a geological history that reflects 50 000 years of climate change, is the largest hypersaline salt flat on Earth and is estimated to be the biggest lithium reservoir in the world. Its salinity reaches saturation levels for NaCl, a kosmotropic salt, and high concentrations of MgCL 2 and LiCl, both salts considered important chaotrophic stressors. In addition, extreme temperatures, anoxic conditions, high UV irradiance, high albedo and extremely low concentrations of phosphorous, make SdU a unique natural extreme environment in which to contrast hypotheses about limiting factors of life diversification. Geophysical studies of brines from different sampling stations show that water activity is rather constant along SdU. Geochemical measurements show significant differences in magnesium concentration, ranging from 0.2 to 2M. This work analyses the prokaryotic diversity and community structure at four SdU sampling stations, selected according to their location and ionic composition. Prokaryotic communities were composed of both Archaea (with members of the classes Halobacteria, Thermoplasmata and Nanohaloarchaea, from the Euryarchaeota and Nanohaloarcheota phyla respectively) and Bacteria (mainly belonging to Bacteroidetes and Proteobacteria phyla). The important differences in composition of microbial communities inversely correlate with Mg 2+ concentration, suggesting that prokaryotic diversity at SdU is chaotropic dependent. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

  19. Differences in Prokaryotic Species Between Primary and Logged-Over Deep Peat Forest in Sarawak, Malaysia

    International Nuclear Information System (INIS)

    Mohd Shawal Thakib Maidin; Sakinah Safari; Nur Aziemah Ghani; Sharifah Azura Syed Ibrahim; Shamsilawani Ahamed Bakeri; Mohamed Mazmira Mohd Masri; Siti Ramlah Ahmad Ali

    2016-01-01

    Peat land has an important role in environmental sustainability which can be used for agricultural purposes. However, deforestation in the logged-over forest may disrupt the diversity of microbial population in peat soil. Therefore, this study focuses on the differences of microbial populations in Maludam primary forest and Cermat Ceria logged-over forest in Sarawak, Malaysia. The prokaryotic 16S rDNA region was amplified followed by denaturing gradient gel electrophoresis (16S PCR-DGGE) analysis. Berger-Parker and Shannon-Weaver Biodiversity Index showed that Maludam (0.11, 7.75) was more diverse compared to Cermat Ceria (0.19, 7.63). Sequence analysis showed that the bacterial community in Maludam and Cermat Ceria were dominated by unclassified bacteria, followed by Acidobacteria, Actinobacteria, Firmicutes and a-Proteobacteria. Based on the findings, the distinct species that can be found in Maludam were Acidobacterium capsulatum, Solibacter sp., Mycobacterium intracellulare, Rhodoplanes sp., Clostridia bacterium, Exiguobacterium sp. and Lysinibacillus fusiformis. While, the distinct species that can be found in Cermat Ceria were Telmatobacter, Mycobacterium tuberculosis and Bacillus tequilensis. Overall, the findings showed that microbial population in the logged-over forest are less diverse compared to primary forest. Higher prokaryotic diversity identified in the primary forest compared to logged-over forest showed that deforestation might cause prokaryotic population changes to both ecosystems. (author)

  20. Contrasting Responses of Marine and Freshwater Photosynthetic Organisms to UVB Radiation: A Meta-Analysis

    KAUST Repository

    Jin, Peng; Duarte, Carlos M.; Agusti, Susana

    2017-01-01

    artificial lamps. We found that marine photosynthetic organisms tend to be more sensitive than freshwater photosynthetic organisms to UVB radiation; responses to either decreased or increased UVB radiation vary among taxa; the mortality rate is the most

  1. On the photosynthetic and devlopmental responses of leaves to the spectral composition of light

    NARCIS (Netherlands)

    Hogewoning, S.W.

    2010-01-01

    Key words: action spectrum, artificial solar spectrum, blue light, Cucumis sativus, gas-exchange, light-emitting diodes (LEDs), light interception, light quality, non-photosynthetic pigments, photo-synthetic capacity, photomorphogenesis, photosystem excitation balance, quantum yield, red light.

  2. Spatiotemporal and species variations in prokaryotic communities associated with sediments from surface-flow constructed wetlands for treating swine wastewater.

    Science.gov (United States)

    Jia, Fen; Lai, Cui; Chen, Liang; Zeng, Guangming; Huang, Danlian; Liu, Feng; Li, Xi; Luo, Pei; Wu, Jinshui; Qin, Lei; Zhang, Chen; Cheng, Min; Xu, Piao

    2017-10-01

    Microorganisms are the main mechanisms of pollutants removals in constructed wetlands (CWs) used for wastewater treatment. However, the different biological processes and variations of prokaryotic community in CWs remain poorly understood. In this study, we applied a high-throughput sequencing technique to investigate the prokaryotic communities associated with sediments from pilot-scale surface-flow constructed wetlands (SFCWs) treating swine wastewater (SW) of varying strengths. Our results revealed that highly diverse prokaryotic communities were present in the SFCWs, with Proteobacteria (16.44-44.44%), Acidobacteria (3.25-24.40%), and Chloroflexi (5.77-14.43%) being the major phyla, and Nitrospira (4.14-12.02%), the most dominant genus. The prokaryotic communities in the sediments varied greatly with location and season, which markedly altered the microenvironmental conditions. Principal co-ordinates analysis indicated that SW strength significantly influenced the community structure in sediments of the SFCWs, and canonical correspondence analysis illustrated that the shifts in prokaryotic communities were strongly related to NO 3 - -N and TN in winter; and in summer with NH 4 + N, NO 3 - -N, NO 2 - -N, TN, TP, SOM, and pH. In conclusion, the use of high-throughput sequencing greatly enhanced our understanding of prokaryotic communities with different functional groups in SFCWs. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. EPR spectroscopic evidence for a tetranuclear manganese cluster as the site for photosynthetic oxygen evolution

    Energy Technology Data Exchange (ETDEWEB)

    Dismukes, G C; Ferris, K; Watnick, P

    1982-01-01

    It has been shown that EPR observations of a polynuclear Mn cluster in spinach chloroplasts can be interpreted in terms of a cluster containing three Mn(III) ions and one Mn(IV) ion within a tetranuclear complex. Both ferromagnetic and antiferromagnetic interactions appear to exist between the Mn ions, which exhibit deeply trapped discrete oxidation states, at least in this EPR active state. These results are discussed in terms of what is currently known about the polypeptide composition of the enzyme. A model of the oxidation state changes in the enzyme is proposed which is consistent with the EPR and protein isolation studies. Finally, a comparison between the electron-transporting metalloenzymes and the electron-storing metalloenzymes shows that the facile electron transfer kinetics observed in the former class and the slow kinetics observed in the latter class are consistent with the distinctly different electronic structures of these enzymes and their functional roles.

  4. X-ray spectroscopy of the photosynthetic oxygen-evolving complex

    Energy Technology Data Exchange (ETDEWEB)

    Sauer, Ken; Yano, Junko; Yachandra, Vittal K

    2007-04-05

    Water oxidation to dioxygen in photosynthesis is catalyzed by a Mn4Ca cluster with O bridging in Photosystem II (PS II) of plants, algae and cyanobacteria. A variety of spectroscopic methods have been applied to analyzing the participation of the complex. X-ray spectroscopy is particularly useful because it is element-specific, and because it can reveal important structural features of the complex with high accuracy and identify the participation of Mn in the redox chemistry. Following a brief history of the application of X-ray spectroscopy to PS II, an overview of newer results will be presented and a description of the present state of our knowledge based on this approach.

  5. Photosynthetic efficiency and oxygen evolution of Chlamydomonas reinhardtii under continuous and flashing light.

    NARCIS (Netherlands)

    Vejrazka, C.; Janssen, M.; Benvenuti, G.; Streefland, M.; Wijffels, R.H.

    2013-01-01

    As a result of mixing and light attenuation in a photobioreactor (PBR), microalgae experience light/dark (L/D) cycles that can enhance PBR efficiency. One parameter which characterizes L/D cycles is the duty cycle; it determines the time fraction algae spend in the light. The objective of this study

  6. Enhanced Practical Photosynthetic CO2 Mitigation

    Energy Technology Data Exchange (ETDEWEB)

    Gregory Kremer; David J. Bayless; Morgan Vis; Michael Prudich; Keith Cooksey; Jeff Muhs

    2006-01-15

    This final report highlights significant achievements in the Enhanced Practical Photosynthetic CO{sub 2} Mitigation Project during the period from 10/1/2001 through 01/02/2006. As indicated in the list of accomplishments below, our efforts during this project were focused on the selection of candidate organisms and growth surfaces and initiating long-term tests in the bench-scale and pilot-scale bioreactor test systems. Specific results and accomplishments for the program include: (1) CRF-2 test system: (a) Sampling test results have shown that the initial mass of algae loaded into the Carbon Recycling Facility Version 2 (CRF-2) system can be estimated with about 3% uncertainty using a statistical sampling procedure. (b) The pressure shim header pipe insert design was shown to have better flow for harvesting than the drilled-hole design. (c) The CRF-2 test system has undergone major improvements to produce the high flow rates needed for harvesting (as determined by previous experiments). The main changes to the system are new stainless steel header/frame units, with increased flow capacity and a modified pipe-end-sealing method to improve flow uniformity, and installation and plumbing for a new high flow harvesting pump. Qualitative system tests showed that the harvesting system performed wonderfully, cleaning the growth surfaces within a matter of seconds. (d) Qualitative tests have shown that organisms can be repopulated on a harvested section of a bioreactor screen, demonstrating that continuous bioreactor operation is feasible, with continuous cycles of harvesting and repopulating screens. (e) Final preparations are underway for quantitative, long-term tests in the CRF-2 with weekly harvesting. (2) Pilot-scale test system: (a) The construction of the pilot-scale bioreactor was completed, including the solar collector and light distribution system. Over the course of the project, the solar collector used in the light delivery system showed some degradation, but

  7. Effects of gibberellic acid on growth and photosynthetic pigments of ...

    African Journals Online (AJOL)

    The aim of this study was to improve growth performance by enhancing the photosynthetic pigments and enzyme carbonic anhydrase (CA) activity of Hibiscus sabdariffa L. (cv. Sabahia 17) under NaCl stress. Under non-saline condition, application of GA3 enhanced growth parameters (shoot length, shoot fresh weight (FW) ...

  8. 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)....

  9. Effect of Photosynthetic Photon Flux Density on Carboxylation Efficiency 1

    Science.gov (United States)

    Weber, James A.; Tenhunen, John D.; Gates, David M.; Lange, Otto L.

    1987-01-01

    The effect of photosynthetic photon flux density (PPFD) on photosynthetic response (A) to CO2 partial pressures between 35 pascals and CO2 compensation point (Γ) was investigated, especially below PPFD saturation. Spinacia oleracea cv `Atlanta,' Glycine max cv `Clark,' and Arbutus unedo were studied in detail. The initial slope of the photosynthetic response to CO2 (∂A/∂C[Γ]) was constant above a PPFD of about 500 to 600 micromoles per square meter per second for all three species; but declined rapidly with PPFD below this critical level. For Γ there was also a critical PPFD (approximately 200 micromoles per square meter per second for S. oleracea and G. max; 100 for A. unedo) above which Γ was essentially constant, but below which Γ increased with decreasing PPFD. All three species showed a dependence of ∂A/∂C(Γ) on PPFD at low PPFD. Simulated photosynthetic responses obtained with a biochemically based model of whole-leaf photosynthesis were similar to measured responses. PMID:16665640

  10. Coherent memory functions for finite systems: hexagonal photosynthetic unit

    International Nuclear Information System (INIS)

    Barvik, I.; Herman, P.

    1990-10-01

    Coherent memory functions entering the Generalized Master Equation are presented for an hexagonal model of a photosynthetic unit. Influence of an energy heterogeneity on an exciton transfer is an antenna system as well as to a reaction center is investigated. (author). 9 refs, 3 figs

  11. Effects of 1-butanol, neomycin and calcium on the photosynthetic ...

    African Journals Online (AJOL)

    ajl yemi

    Institute of Food Crops, Jiangsu High Quality Rice R&D Center, Jiangsu Academy of Agricultural Sciences, Nanjing,. Jiangsu Province, 210014, China. Accepted 31 October, 2011. The effects .... and blue light source under the open system, with the following conditions: 1200 µmol m-2s-1 photosynthetic photon flux density.

  12. Photosynthetic behaviour of Arabidopsis thaliana (Pa-1 accession ...

    African Journals Online (AJOL)

    The growth reduction observed in many plants caused by salinity is often associated with a decrease in their photosynthetic capacity. This effect could be associated with the partial stomatal closure and/or the non-stomatal limitation which involves the decrease in ribulose-1,5-bisphosphate carboxylase oxygenase ...

  13. Variability of photosynthetic pigments in the Colombian Pacific ...

    Indian Academy of Sciences (India)

    Home; Journals; Journal of Earth System Science; Volume 111; Issue 3. Variability of photosynthetic pigments in the Colombian Pacific Ocean and its relationship with the wind field using ADEOS-I data. Efrain Rodriguez-Rubio Jose Stuardo. Volume 111 Issue 3 September 2002 pp 227-236 ...

  14. Photosynthetic Responses of Seedlings of two Indigenous Plants ...

    African Journals Online (AJOL)

    Bheema

    ABSTRACT. The potential role of exotic tree plantations in facilitating successional processes on degraded areas was evaluated in southern Ethiopia, Munessa-Shashemene forest, by examining photosynthetic responses of Bersamaabyssinica Fres. and Croton macrostachyusDel. seedlings naturally grown inside ...

  15. Abscisic acid effects on water and photosynthetic characteristics of ...

    African Journals Online (AJOL)

    The aim of this study is to compare the water and photosynthetic characteristics of two xerophilic ecotypes of Atriplex halimus (L.). Seeds collected from two different sites Djelfa and Oran are germinated in controlled greenhouse. After 6 months, the plantlets were treated 21 days with increasing concentrations of abscisic ...

  16. An Improved Method for Extraction and Separation of Photosynthetic Pigments

    Science.gov (United States)

    Katayama, Nobuyasu; Kanaizuka, Yasuhiro; Sudarmi, Rini; Yokohama, Yasutsugu

    2003-01-01

    The method for extracting and separating hydrophobic photosynthetic pigments proposed by Katayama "et al." ("Japanese Journal of Phycology," 42, 71-77, 1994) has been improved to introduce it to student laboratories at the senior high school level. Silica gel powder was used for removing water from fresh materials prior to…

  17. Photosynthetic incorporation of 14C by Stevia rebaudiana

    International Nuclear Information System (INIS)

    Ferraresi, M. de L.; Ferraresi Filho, O.; Bracht, A.

    1985-01-01

    The photosynthetic incorporation of 14 by Stevia rebaudiana specimens was investigated. The 14 C incorporation, when the isotope was furnished to the plant in form of 14 CO 2 , was rapid. After 24 hours, the radioactivity has been incorporated into a great number of compounds including pigments, terpenes, glucose, cellulose and also stevioside and its derivatives. (M.A.C.) [pt

  18. The role of energy losses in photosynthetic light harvesting

    NARCIS (Netherlands)

    Kruger, T. P. J.; van Grondelle, R.

    2017-01-01

    Photosynthesis operates at the bottom of the food chain to convert the energy of light into carbohydrates at a remarkable global rate of about 130 TW. Nonetheless, the overall photosynthetic process has a conversion efficiency of a few percent at best, significantly less than bottom-up photovoltaic

  19. effect of ambient levels of ozone on photosynthetic components

    African Journals Online (AJOL)

    ACSS

    To clarify the long-term effects of ambient levels of tropospheric ozone (O3) on ... (Rubisco), thus contributing to the reduction in net photosynthetic rate at the .... USA). During the measurements, atmospheric. CO2 concentrations, air ...... productivity and implications for climate change. Annual Review of Plant Biology 63:.

  20. Effect of ambient levels of ozone on photosynthetic components and ...

    African Journals Online (AJOL)

    Effect of ambient levels of ozone on photosynthetic components and radical scavenging system in leaves of African cowpea varieties. ... The O3-induced significant reduction in catalase activity was observed in Blackeye at vegetative and reproductive growth stages; and in Asontem at reproductive growth stage. On the other ...

  1. Non-photosynthetic plastids as hosts for metabolic engineering.

    Science.gov (United States)

    Mellor, Silas Busck; Behrendorff, James B Y H; Nielsen, Agnieszka Zygadlo; Jensen, Poul Erik; Pribil, Mathias

    2018-04-13

    Using plants as hosts for production of complex, high-value compounds and therapeutic proteins has gained increasing momentum over the past decade. Recent advances in metabolic engineering techniques using synthetic biology have set the stage for production yields to become economically attractive, but more refined design strategies are required to increase product yields without compromising development and growth of the host system. The ability of plant cells to differentiate into various tissues in combination with a high level of cellular compartmentalization represents so far the most unexploited plant-specific resource. Plant cells contain organelles called plastids that retain their own genome, harbour unique biosynthetic pathways and differentiate into distinct plastid types upon environmental and developmental cues. Chloroplasts, the plastid type hosting the photosynthetic processes in green tissues, have proven to be suitable for high yield protein and bio-compound production. Unfortunately, chloroplast manipulation often affects photosynthetic efficiency and therefore plant fitness. In this respect, plastids of non-photosynthetic tissues, which have focused metabolisms for synthesis and storage of particular classes of compounds, might prove more suitable for engineering the production and storage of non-native metabolites without affecting plant fitness. This review provides the current state of knowledge on the molecular mechanisms involved in plastid differentiation and focuses on non-photosynthetic plastids as alternative biotechnological platforms for metabolic engineering. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

  2. Effect of maize seed laser irradiation on plant photosynthetic activity

    International Nuclear Information System (INIS)

    Antonov, M.; Stanev, V.; Velichkov, D.; Tsonev, Ts.

    1986-01-01

    Investigations were made with the two hybrids, H-708 and P x -20. The seeds were irradiated by a helium-neon quantum generator (L'vov-1 Electronica) with output power of 24 MW and 632.8 nm wave length. Once and twice irradiated seeds were sown on the 2nd, 5th and 10th day post irradiation. Changes in leaf area, chlorophyll content in the leaves, photosynthetic rate and its dependence on temperature and light, transpiration, stomatal resistance to CO 2 and total dry matter of the overground plant part were traced. Seed irradiation with laser rays did not affect the chlorophyll content of the leaves. The photosynthetic rate did not depend on the cultivar characteristics of the crop. Single and repeated irradiation of the hybrid H-708 in most case enhanced photosynthetic rate, but a similar effect was not observed in P x -20. Transpiration and CO 2 stomatal resistance were not equally affected by radiation. Laser rays enhanced the ability of the photosynthetic apparatus of the entire plants to use more efficiently high light intensities. The leaf area and the total plant dry matter increased in case of sowing on the 2nd and 5th day and a single irradiation and in case of sowing on the 5th and 10th day and twice repeated irradiations

  3. Proteomic Analysis of Metabolic Responses to Biofuels and Chemicals in Photosynthetic Cyanobacteria.

    Science.gov (United States)

    Sun, T; Chen, L; Zhang, W

    2017-01-01

    Recent progresses in various "omics" technologies have enabled quantitative measurements of biological molecules in a high-throughput manner. Among them, high-throughput proteomics is a rapidly advancing field that offers a new means to quantify metabolic changes at protein level, which has significantly facilitated our understanding of cellular process, such as protein synthesis, posttranslational modifications, and degradation in responding to environmental perturbations. Cyanobacteria are autotrophic prokaryotes that can perform oxygenic photosynthesis and have recently attracted significant attentions as one promising alternative to traditionally biomass-based "microbial cell factories" to produce green fuels and chemicals. However, early studies have shown that the low tolerance to toxic biofuels and chemicals represented one major hurdle for further improving productivity of the cyanobacterial production systems. To address the issue, metabolic responses and their regulation of cyanobacterial cells to toxic end-products need to be defined. In this chapter, we discuss recent progresses in interpreting cyanobacterial responses to biofuels and chemicals using high-throughput proteomics approach, aiming to provide insights and guidelines on how to enhance tolerance and productivity of biofuels or chemicals in the renewable cyanobacteria systems in the future. © 2017 Elsevier Inc. All rights reserved.

  4. Evolution of the F0F1 ATP synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes.

    Directory of Open Access Journals (Sweden)

    Vassiliki Lila Koumandou

    2014-09-01

    Full Text Available Bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. Apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. Most bioenergetic pathways have a similar general structure, with an electron transport chain composed of protein complexes acting as electron donors and acceptors, as well as a central cytochrome complex, mobile electron carriers, and an ATP synthase. While each pathway has been studied in considerable detail in isolation, not much is known about their relative evolutionary relationships. Wanting to address how this metabolic diversity evolved, we mapped the distribution of nine bioenergetic modes on a phylogenetic tree based on 16S rRNA sequences from 272 species representing the full diversity of prokaryotic lineages. This highlights the patchy distribution of many pathways across different lineages, and suggests either up to 26 independent origins or 17 horizontal gene transfer events. Next, we used comparative genomics and phylogenetic analysis of all subunits of the F0F1 ATP synthase, common to most bacterial lineages regardless of their bioenergetic mode. Our results indicate an ancient origin of this protein complex, and no clustering based on bioenergetic mode, which suggests that no special modifications are needed for the ATP synthase to work with different electron transport chains. Moreover, examination of the ATP synthase genetic locus indicates various gene rearrangements in the different bacterial lineages, ancient duplications of atpI and of the beta subunit of the F0 subcomplex, as well as more recent stochastic lineage-specific and species-specific duplications of all subunits. We

  5. Molecular fossils of prokaryotes in ancient authigenic minerals: archives of microbial activity in reefs and mounds?

    Science.gov (United States)

    Heindel, Katrin; Birgel, Daniel; Richoz, Sylvain; Westphal, Hildegard; Peckmann, Jörn

    2016-04-01

    Molecular fossils (lipid biomarkers) are commonly used as proxies in organic-rich sediments of various sources, including eukaryotes and prokaryotes. Usually, molecular fossils of organisms transferred from the water column to the sediment are studied to monitor environmental changes (e.g., temperature, pH). Apart from these 'allochthonous' molecular fossils, prokaryotes are active in sediments and mats on the seafloor and leave behind 'autochthonous' molecular fossils in situ. In contrast to many phototrophic organisms, most benthic sedimentary prokaryotes are obtaining their energy from oxidation or reduction of organic or inorganic substrates. A peculiarity of some of the sediment-thriving prokaryotes is their ability to trigger in situ mineral precipitation, often but not only due to metabolic activity, resulting in authigenic rocks (microbialites). During that process, prokaryotes are rapidly entombed in the mineral matrix, where the molecular fossils are protected from early (bio)degradation. In contrast to other organic compounds (DNA, proteins etc.), molecular fossils can be preserved over very long time periods (millions of years). Thus, molecular fossils in authigenic mineral phases are perfectly suitable to trace microbial activity back in time. Among the best examples of molecular fossils, which are preserved in authigenic rocks are various microbialites, forming e.g. in phototrophic microbial mats and at cold seeps. Microbialite formation is reported throughout earth history. We here will focus on reefal microbialites form the Early Triassic and the Holocene. After the End-Permian mass extinction, microbialites covered wide areas on the ocean margins. In microbialites from the Griesbachian in Iran and Turkey (both Neotethys), molecular fossils of cyanobacteria, archaea, anoxygenic phototrophs, and sulphate-reducing bacteria indicate the presence of layered microbial mats on the seafloor, in which carbonate precipitation was induced. In association with

  6. Carotenoids, versatile components of oxygenic photosynthesis.

    Science.gov (United States)

    Domonkos, Ildikó; Kis, Mihály; Gombos, Zoltán; Ughy, Bettina

    2013-10-01

    Carotenoids (CARs) are a group of pigments that perform several important physiological functions in all kingdoms of living organisms. CARs serve as protective agents, which are essential structural components of photosynthetic complexes and membranes, and they play an important role in the light harvesting mechanism of photosynthesizing plants and cyanobacteria. The protection against reactive oxygen species, realized by quenching of singlet oxygen and the excited states of photosensitizing molecules, as well as by the scavenging of free radicals, is one of the main biological functions of CARs. X-ray crystallographic localization of CARs revealed that they are present at functionally and structurally important sites of both the PSI and PSII reaction centers. Characterization of a CAR-less cyanobacterial mutant revealed that while the absence of CARs prevents the formation of PSII complexes, it does not abolish the assembly and function of PSI. CAR molecules assist in the formation of protein subunits of the photosynthetic complexes by gluing together their protein components. In addition to their aforementioned indispensable functions, CARs have a substantial role in the formation and maintenance of proper cellular architecture, and potentially also in the protection of the translational machinery under stress conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

  7. Sun and Shade leaves, SIF, and Photosynthetic Capacity

    Science.gov (United States)

    Berry, J. A.; Badgley, G.

    2016-12-01

    Recent advances in retrieval of solar induced chlorophyll fluorescence (SIF) have opened up new possibilities for remote sensing of canopy physiology and structure. To date most of the emphasis has been placed on SIF as an indicator of stress and photosynthetic capacity. However, it is clear that canopy structure can also have an influence. To this point, simulations of SIF in land surface models tend to under predict observed variation in SIF. Also, large, systematic differences in SIF from different canopy types seem to correlate well with the photosynthetic capacity of these canopies. SIF emissions from pampered crops can be several-fold that from evergreen, needle-leaf forests. Yet, these may have similar vegetation indices and absorb a similar fraction of incident PAR. SIF photons produced in a conifer canopy do have a lower probability of escaping its dense, clumped foliage. However, this does not explain the correlated differences in photosynthetic rate and SIF. It is useful, in this regard, to consider the separate contributions of sun and shade leaves to the SIF emitted by a canopy. Sun leaves tend to be displayed to intercept the direct solar beam, and these highly illuminated leaves are often visible from above the canopy. Sun leaves produce more SIF and a large fraction of it escapes. Therefore, the intensity of SIF may be a sensitive indicator of the partitioning of absorbed PAR to sun and shade leaves. Many models account tor the different photosynthetic capacity of sun and shade leaves in calculating canopy responses. However, the fraction of leaves in each category is usually parameterized by an assumed leaf angle distribution (e.g. spherical). In reality, the sun/shade fraction can vary over a wide range, and it has been difficult to measure. SIF and possibly near-IR reflectance of canopies can be used to specify this key parameter with obvious importance to understanding photosynthetic rate.

  8. Photosynthetic carbon metabolism in the submerged aquatic angiosperm Scirpus subterminalis

    Energy Technology Data Exchange (ETDEWEB)

    Beer, S; Wetzel, R G

    1981-01-01

    Scirpus subterminalis Torr., a submerged angiosperm abundant in many hardwater lakes of the Great Lakes region, was investigated for various photosynthetic carbon fixation properties in relation to available inorganic carbon and levels of carbon fixing enzymes. Photosynthetic experiments were CO/sub 2/ and HCO/sub 3//sup -/ were supplied at various concentrations showed that Scirpus was able to utilize HCO/sub 3//sup -/ at those concentrations close to natural conditions. However, when CO/sub 2/ concentrations were increased above ambient, photosynthetic rates increased markedly. It was concluded that the photosynthetic potential of this plant in many natural situations may be limited by inorganic carbon uptake in the light. Phosphoenolpyruvate carboxylase (PEPcase)/ribulose-1,5-bisphosphate carboxylase (ruBPcase) ratios of the leaves varied between 0.5 and 0.9 depending on substrate concentration during assay. The significance of PEP-mediated carbon fixation of Scirpus (basically a C/sub 3/ plant) in the dark was investigated. Malate accumulated in the leaves during the dark period of a 24-h cycle and malate levels decreased significantly during the following light period. The accumulation was not due to transport of malate from the roots. Carbon uptake rates in the dark by the leaves of Scirpus were lower than malate accumulation rates. Therefore, part of the malate was likely derived from respired CO/sub 2/. Carbon uptake rates in the light were much higher than malate turnover rates. It was estimated that carbon fixation via malate could contribute up to 12% to net photosynthetic rates. The ecological significance of this type of metabolism in submerged aquatics is discussed.

  9. Functions of tocopherols in the cells of plants and other photosynthetic organisms.

    Science.gov (United States)

    Mokrosnop, V M

    2014-01-01

    Tocopherol synthesis has only been observed in photosynthetic organisms (plants, algae and some cyanobacteria). Tocopherol is synthesized in the inner membrane of chloroplasts and distributed between chloroplast membranes, thylakoids and plastoglobules. Physiological significance of tocopherols for human and animal is well-studied, but relatively little is known about their function in plant organisms. Among the best characterized functions oftocopherols in cells is their ability to scavenge and quench reactive oxygen species and fat-soluble by-products of oxidative stress. There are the data on the participation of different mechanisms of α-tocopherol action in protecting photosystem II (PS II) from photoinhibition both by deactivation of singlet oxygen produced by PSII and by reduction of proton permeability of thylakoid membranes, leading to acidification of lumen under high light conditions and activation of violaxanthin de-epoxidase. Additional biological activity of tocopherols, independent of its antioxidant functions have been demonstrated. Basic mechanisms for these effects are connected with the modulation of signal transduction pathways by specific tocopherols and, in some instances, by transcriptional activation of gene expression.

  10. Inhibition of photosynthetic CO₂ fixation in the coral Pocillopora damicornis and its relationship to thermal bleaching.

    Science.gov (United States)

    Hill, Ross; Szabó, Milán; ur Rehman, Ateeq; Vass, Imre; Ralph, Peter J; Larkum, Anthony W D

    2014-06-15

    Two inhibitors of the Calvin-Benson cycle [glycolaldehyde (GA) and potassium cyanide (KCN)] were used in cultured Symbiodinium cells and in nubbins of the coral Pocillopora damicornis to test the hypothesis that inhibition of the Calvin-Benson cycle triggers coral bleaching. Inhibitor concentration range-finding trials aimed to determine the appropriate concentration to generate inhibition of the Calvin-Benson cycle, but avoid other metabolic impacts to the symbiont and the animal host. Both 3 mmol l(-1) GA and 20 μmol l(-1) KCN caused minimal inhibition of host respiration, but did induce photosynthetic impairment, measured by a loss of photosystem II function and oxygen production. GA did not affect the severity of bleaching, nor induce bleaching in the absence of thermal stress, suggesting inhibition of the Calvin-Benson cycle by GA does not initiate bleaching in P. damicornis. In contrast, KCN did activate a bleaching response through symbiont expulsion, which occurred in the presence and absence of thermal stress. While KCN is an inhibitor of the Calvin-Benson cycle, it also promotes reactive oxygen species formation, and it is likely that this was the principal agent in the coral bleaching process. These findings do not support the hypothesis that temperature-induced inhibition of the Calvin-Benson cycle alone induces coral bleaching. © 2014. Published by The Company of Biologists Ltd.

  11. Photosynthetic Microbial Mats are Exemplary Sources of Diverse Biosignatures (Invited)

    Science.gov (United States)

    Des Marais, D. J.; Jahnke, L. L.

    2013-12-01

    Marine cyanobacterial microbial mats are widespread, compact, self-contained ecosystems that create diverse biosignatures and have an ancient fossil record. Within the mats, oxygenic photosynthesis provides organic substrates and O2 to the community. Both the absorption and scattering of light change the intensity and spectral composition of incident radiation as it penetrates a mat. Some phototrophs utilize infrared light near the base of the photic zone. A mat's upper layers can become highly reduced and sulfidic at night. Counteracting gradients of O2 and sulfide shape the chemical environment and provide daily-contrasting microenvironments separated on a scale of a few mm. Radiation hazards (UV, etc.), O2 and sulfide toxicity elicit motility and other physiological responses. This combination of benefits and hazards of light, O2 and sulfide promotes the allocation of various essential mat processes between light and dark periods and to various depths in the mat. Associated nonphotosynthetic communities, including anaerobes, strongly influence many of the ecosystem's overall characteristics, and their processes affect any biosignatures that enter the fossil record. A biosignature is an object, substance and/or pattern whose origin specifically requires a biological agent. The value of a biosignature depends not only on the probability of life creating it, but also on the improbability of nonbiological processes producing it. Microbial mats create biosignatures that identify particular groups of organisms and also reveal attributes of the mat ecosystem. For example, branched hydrocarbons and pigments can be diagnostic of cyanobacteria and other phototrophic bacteria, and isoprenoids can indicate particular groups of archea. Assemblages of lipid biosignatures change with depth due to changes in microbial populations and diagenetic transformations of organic matter. The 13C/12C values of organic matter and carbonates reflect isotopic discrimination by particular

  12. Protein Based Molecular Markers Provide Reliable Means to Understand Prokaryotic Phylogeny and Support Darwinian Mode of Evolution

    Directory of Open Access Journals (Sweden)

    Vaibhav eBhandari

    2012-07-01

    Full Text Available The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning whether the Darwinian model of evolution is applicable to the prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs and conserved signature proteins (CSPs for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical

  13. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.

    Science.gov (United States)

    Bhandari, Vaibhav; Naushad, Hafiz S; Gupta, Radhey S

    2012-01-01

    The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.

  14. Prokaryotic communities in pit mud from different-aged cellars used for the production of Chinese strong-flavored liquor.

    Science.gov (United States)

    Tao, Yong; Li, Jiabao; Rui, Junpeng; Xu, Zhancheng; Zhou, Yan; Hu, Xiaohong; Wang, Xiang; Liu, Menghua; Li, Daping; Li, Xiangzhen

    2014-04-01

    Chinese strong-flavored liquor (CSFL) accounts for more than 70% of all Chinese liquor production. Microbes in pit mud play key roles in the fermentation cellar for the CSFL production. However, microbial diversity, community structure, and cellar-age-related changes in pit mud are poorly understood. Here, we investigated the prokaryotic community structure and diversity in pit-mud samples with different cellar ages (1, 10, 25, and 50 years) using the pyrosequencing technique. Results indicated that prokaryotic diversity increased with cellar age until the age reached 25 years and that prokaryotic community structure changed significantly between three cellar ages (1, 10, and 25 years). Significant correlations between prokaryotic communities and environmental variables (pH, NH4(+), lactic acid, butyric acid, and caproic acid) were observed. Overall, our study results suggested that the long-term brewing operation shapes unique prokaryotic community structure and diversity as well as pit-mud chemistry. We have proposed a three-phase model to characterize the changes of pit-mud prokaryotic communities. (i) Phase I is an initial domestication period. Pit mud is characterized by abundant Lactobacillus and high lactic acid and low pH levels. (ii) Phase II is a transition period. While Lactobacillus abundance decreases dramatically, that of Bacteroidetes and methanogens increases. (iii) Phase III is a relative mature period. The prokaryotic community shows the highest diversity and capability to produce more caproic acid as a precursor for synthesis of ethyl caproate, the main flavor component in CSFL. This research provides scientific evidence to support the practical experience that old fermentation cellars produce high-quality liquor.

  15. Microbial biomass and viral infections of heterotrophic prokaryotes in the sub-surface layer of the central Arctic Ocean

    Science.gov (United States)

    Steward, Grieg F.; Fandino, Laura B.; Hollibaugh, James T.; Whitledge, Terry E.; Azam, Farooq

    2007-10-01

    Seawater samples were collected for microbial analyses between 55 and 235 m depth across the Arctic Ocean during the SCICEX 97 expedition (03 September-02 October 1997) using a nuclear submarine as a research platform. Abundances of prokaryotes (range 0.043-0.47×10 9 dm -3) and viruses (range 0.68-11×10 9 dm -3) were correlated ( r=0.66, n=150) with an average virus:prokaryote ratio of 26 (range 5-70). Biomass of prokaryotes integrated from 55 to 235 m ranged from 0.27 to 0.85 g C m -2 exceeding that of phytoplankton (0.005-0.2 g C m -2) or viruses (0.02-0.05 g C m -2) over the same depth range by an order of magnitude on average. Using transmission electron microscopy (TEM), we estimated that 0.5% of the prokaryote community on average (range 0-1.4%) was visibly infected with viruses, which suggests that very little of prokaryotic secondary production was lost due to viral lysis. Intracellular viruses ranged from 5 to >200/cell, with an average apparent burst size of 45±38 (mean±s.d.; n=45). TEM also revealed the presence of putative metal-precipitating bacteria in 8 of 13 samples, which averaged 0.3% of the total prokaryote community (range 0-1%). If these prokaryotes are accessible to protistan grazers, the Fe and Mn associated with their capsules might be an important source of trace metals to the planktonic food web. After combining our abundance and mortality data with data from the literature, we conclude that the biomass of prokaryoplankton exceeds that of phytoplankton when averaged over the upper 250 m of the central Arctic Ocean and that the fate of this biomass is poorly understood.

  16. Flow of light energy in benthic photosynthetic microbial mats

    Energy Technology Data Exchange (ETDEWEB)

    Al-Najjar, Mohammad Ahmad A.

    2010-12-15

    The work in this thesis demonstrates the assessment of the energy budget inside microbial mat ecosystems, and the factors affecting light utilization efficiency. It presents the first balanced light energy budget for benthic microbial mat ecosystems, and shows how the budget and the spatial distribution of the local photosynthetic efficiencies within the euphotic zone depend on the absorbed irradiance (Jabs). The energy budget was dominated by heat dissipation on the expense of photosynthesis. The maximum efficiency of photosynthesis was at light limiting conditions When comparing three different marine benthic photosynthetic ecosystems (originated from Abu-Dhabi, Arctic, and Exmouth Gulf in Western Australia), differences in the efficiencies were calculated. The results demonstrated that the maximum efficiency depended on mat characteristics affecting light absorption and scattering; such as, photopigments ratio and distribution, and the structural organization of the photosynthetic organisms relative to other absorbing components of the ecosystem (i.e., EPS, mineral particles, detritus, etc.). The maximum efficiency decreased with increasing light penetration depth, and increased with increasing the accessory pigments (phycocyanin and fucoxanthin)/chlorophyll ratio. Spatial heterogeneity in photosynthetic efficiency, pigment distribution, as well as light acclimation in microbial mats originating from different geographical locations was investigated. We used a combined pigment imaging approach (variable chlorophyll fluorescence and hyperspectral imaging), and fingerprinting approach. For each mat, the photosynthetic activity was proportional to the local pigment concentration in the photic zone, but not for the deeper layers and between different mats. In each mat, yield of PSII and E1/2 (light acclimation) generally decreased in parallel with depth, but the gradients in both parameters varied greatly between samples. This mismatch between pigments concentration

  17. The mechanism of anthracene interaction with photosynthetic apparatus: A study using intact cells, thylakoid membranes and PS II complexes isolated from Chlamydomonas reinhardtii

    International Nuclear Information System (INIS)

    Aksmann, Anna; Shutova, Tatiana; Samuelsson, Goeran; Tukaj, Zbigniew

    2011-01-01

    Intact cells of Chlamydomonas reinhardtii as well as isolated thylakoid membranes and photosystem II complexes were used to examine a possible mechanism of anthracene (ANT) interaction with the photosynthetic apparatus. Since ANT concentrations above 1 mM were required to significantly inhibit the rate of oxygen evolution in PS II membrane fragments it may indicate that the toxicant did not directly interact with this photosystem. On the other hand, stimulation of oxygen uptake by ANT-treated thylakoids suggested that ANT could either act as an artificial electron acceptor in the photosynthetic electron transport chain or function as an uncoupler. Electron transfer from excited chlorophyll to ANT is impossible due to the very low reduction potential of ANT and therefore we propose that toxic concentrations of ANT increase the thylakoid membrane permeability and thereby function as an uncoupler, enhancing electron transport in vitro. Hence, its unspecific interference with photosynthetic membranes in vitro suggests that the inhibitory effect observed on intact cell photosynthesis is caused by uncoupling of phosphorylation.

  18. Genotypic variations in photosynthetic and physiological adjustment to potassium deficiency in cotton (Gossypium hirsutum).

    Science.gov (United States)

    Wang, Ning; Hua, Hanbai; Eneji, A Egrinya; Li, Zhaohu; Duan, Liusheng; Tian, Xiaoli

    2012-05-02

    A hydroponic culture experiment was conducted to determine genotypic variation in photosynthetic rate and the associated physiological changes in response to potassium (K) deficiency in cotton (Gossypium hirsutum L.) seedlings with contrasting two cotton cultivars in K efficiency. The K-efficient Liaomian18 produced 66.7% more biomass than the K-inefficient NuCOTN99(B) under K deficiency, despite their similar biomass under K sufficiency. Compared with NuCOTN99(B), Liaomian18 showed 19.4% higher net photosynthetic rate (P(n), per unit leaf area) under K deficient solutions and this was associated with higher photochemical efficiency and faster export of soluble sugars from the phloem. The lower net P(n) of NuCOTN99(B) was attributed to higher capacity for nitrate assimilation and lower export of soluble sugars. Furthermore, NuCOTN99(B) showed 38.4% greater ETR/P(n) than Liaomian18 under K deficiency, indicating that more electrons were driven to other sinks. Higher superoxide dismutase (SOD) and lower catalase (CAT) and ascorbate peroxidase (APX) activities resulted in higher levels of reactive oxygen species (ROS; e.g. O(2)(-)and H(2)O(2)) in NuCOTN99(B) relative to Liaomian18. Thus, the K inefficiency of NuCOTN99(B), indicated by lower biomass and net P(n) under K deficiency, was associated with excessively high nitrogen assimilation, lower export of carbon assimilates, and greater ROS accumulation in the leaf. Crown Copyright © 2012. Published by Elsevier B.V. All rights reserved.

  19. Determination of Oxygen Production by Cyanobacteria in Desert Environment Soil

    Science.gov (United States)

    Bueno Prieto, J. E.

    2009-12-01

    The cyanobacteria have been characterized for being precursor in the production of oxygen. By means of photosynthetic reactions, they provide oxygen to the environment that surrounds them and they capture part of surrounding dioxide of carbon. This way it happened since the primitive Earth until today. Besides, these microorganisms can support the harmful effects of ultraviolet radiation. The presence of cyanobacterias in an environment like a dry tropical bioma, such as the geographical location called Desert of The Tatacoa (Huila - Colombia), is determinant to establish parameters in the search of biological origin of atmospheric oxygen detected in Mars. In that case, I work with a random sample of not rhizospheric soil, taken to 15 cm of depth. After determining the presence of cyanobacterias in the sample, this one was in laboratory to stimulate the oxygen production. The presence of oxygen in Mars is very interesting. Since oxygen gas is very reactive, it disappear if it is not renewed; the possibility that this renovation of oxygen has a biological origin is encouraging, bearing in mind that in a dry environment and high radiation such as the studied one, the production of oxygen by cyanobacterias is notable. Also it is necessary to keep in mind that the existence of cyanobacterias would determine water presence in Mars subsoil and the nutrients cycles renovation. An interesting exploration possibility for some future space probe to Mars might be the study of worldwide distribution of oxygen concentration in this planet and this way, indentify zones suitable for microbian life.

  20. Apparatus and method for measuring single cell and sub-cellular photosynthetic efficiency

    Science.gov (United States)

    Davis, Ryan Wesley; Singh, Seema; Wu, Huawen

    2013-07-09

    Devices for measuring single cell changes in photosynthetic efficiency in algal aquaculture are disclosed that include a combination of modulated LED trans-illumination of different intensities with synchronized through objective laser illumination and confocal detection. Synchronization and intensity modulation of a dual illumination scheme were provided using a custom microcontroller for a laser beam block and constant current LED driver. Therefore, single whole cell photosynthetic efficiency, and subcellular (diffraction limited) photosynthetic efficiency measurement modes are permitted. Wide field rapid light scanning actinic illumination is provided for both by an intensity modulated 470 nm LED. For the whole cell photosynthetic efficiency measurement, the same LED provides saturating pulses for generating photosynthetic induction curves. For the subcellular photosynthetic efficiency measurement, a switched through objective 488 nm laser provides saturating pulses for generating photosynthetic induction curves. A second near IR LED is employed to generate dark adapted states in the system under study.

  1. Anoxygenic photosynthesis modulated Proterozoic oxygen and sustained Earth's middle age

    Science.gov (United States)

    Johnston, D. T.; Wolfe-Simon, F.; Pearson, A.; Knoll, A. H.

    2009-01-01

    Molecular oxygen (O2) began to accumulate in the atmosphere and surface ocean ca. 2,400 million years ago (Ma), but the persistent oxygenation of water masses throughout the oceans developed much later, perhaps beginning as recently as 580–550 Ma. For much of the intervening interval, moderately oxic surface waters lay above an oxygen minimum zone (OMZ) that tended toward euxinia (anoxic and sulfidic). Here we illustrate how contributions to primary production by anoxygenic photoautotrophs (including physiologically versatile cyanobacteria) influenced biogeochemical cycling during Earth's middle age, helping to perpetuate our planet's intermediate redox state by tempering O2 production. Specifically, the ability to generate organic matter (OM) using sulfide as an electron donor enabled a positive biogeochemical feedback that sustained euxinia in the OMZ. On a geologic time scale, pyrite precipitation and burial governed a second feedback that moderated sulfide availability and water column oxygenation. Thus, we argue that the proportional contribution of anoxygenic photosynthesis to overall primary production would have influenced oceanic redox and the Proterozoic O2 budget. Later Neoproterozoic collapse of widespread euxinia and a concomitant return to ferruginous (anoxic and Fe2+ rich) subsurface waters set in motion Earth's transition from its prokaryote-dominated middle age, removing a physiological barrier to eukaryotic diversification (sulfide) and establishing, for the first time in Earth's history, complete dominance of oxygenic photosynthesis in the oceans. This paved the way for the further oxygenation of the oceans and atmosphere and, ultimately, the evolution of complex multicellular organisms. PMID:19805080

  2. Viruses and Protists Induced-mortality of Prokaryotes around the Antarctic Peninsula during the Austral Summer

    KAUST Repository

    Vaque, Dolors; Boras, Julia A.; Torrent-Llagostera, Francesc; Agusti, Susana; Arrieta, J M; Lara, Elena; Castillo, Yaiza M.; Duarte, Carlos M.; Sala, Maria M.

    2017-01-01

    During the Austral summer 2009 we studied three areas surrounding the Antarctic Peninsula: the Bellingshausen Sea, the Bransfield Strait and the Weddell Sea. We aimed to investigate, whether viruses or protists were the main agents inducing prokaryotic mortality rates, and the sensitivity to temperature of prokaryotic heterotrophic production and mortality based on the activation energy (Ea) for each process. Seawater samples were taken at seven depths (0.1-100 m) to quantify viruses, prokaryotes and protists abundances, and heterotrophic prokaryotic production (PHP). Viral lytic production, lysogeny, and mortality rates of prokaryotes due to viruses and protists were estimated at surface (0.1-1 m) and at the Deep Fluorescence Maximum (DFM, 12-55 m) at eight representative stations of the three areas. The average viral lytic production ranged from 1.0 +/- 0.3 x 10(7) viruses ml(-1) d(-1) in the Bellingshausen Sea to1.3 +/- 0.7 x 10(7) viruses ml(-1) d(-1) in the Bransfield Strait, while lysogeny, when detectable, recorded the lowest value in the Bellingshausen Sea (0.05 +/- 0.05 x 10(7) viruses ml(-1) d(-1)) and the highest in the Weddell Sea (4.3 +/- 3.5 x 10(7) viruses ml(-1) d(-1)). Average mortality rates due to viruses ranged from 9.7 +/- 6.1 x 10(4) cells ml(-1) d(-1) in the Weddell Sea to 14.3 +/- 4.0 x 10(4) cells ml(-1) d(-1) in the Bellingshausen Sea, and were higher than averaged grazing rates in the Weddell Sea (5.9 +/- 1.1 x 10(4) cells ml(-1) d(-1)) and in the Bellingshausen Sea (6.8 +/- 0.9 x 10(4) cells ml-1 d(-1)). The highest impact on prokaryotes by viruses and main differences between viral and protists activities were observed in surface samples: 17.8 +/- 6.8 x 10(4) cells ml(-1) d(-1) and 6.5 +/- 3.9 x 10(4) cells ml(-1) d(-1) in the Weddell Sea; 22.1 +/- 9.6 x 10(4) cells ml(-1) d(-1) and 11.6 +/- 1.4 x 10(4) cells ml(-1) d(-1) in the Bransfield Strait; and 16.1 +/- 5.7 x 10(4) cells ml(-1) d(-1) and 7.9 +/- 2.6 x 10(4) cells ml(-1) d(-1) in

  3. Viruses and Protists Induced-mortality of Prokaryotes around the Antarctic Peninsula during the Austral Summer

    KAUST Repository

    Vaque, Dolors

    2017-03-27

    During the Austral summer 2009 we studied three areas surrounding the Antarctic Peninsula: the Bellingshausen Sea, the Bransfield Strait and the Weddell Sea. We aimed to investigate, whether viruses or protists were the main agents inducing prokaryotic mortality rates, and the sensitivity to temperature of prokaryotic heterotrophic production and mortality based on the activation energy (Ea) for each process. Seawater samples were taken at seven depths (0.1-100 m) to quantify viruses, prokaryotes and protists abundances, and heterotrophic prokaryotic production (PHP). Viral lytic production, lysogeny, and mortality rates of prokaryotes due to viruses and protists were estimated at surface (0.1-1 m) and at the Deep Fluorescence Maximum (DFM, 12-55 m) at eight representative stations of the three areas. The average viral lytic production ranged from 1.0 +/- 0.3 x 10(7) viruses ml(-1) d(-1) in the Bellingshausen Sea to1.3 +/- 0.7 x 10(7) viruses ml(-1) d(-1) in the Bransfield Strait, while lysogeny, when detectable, recorded the lowest value in the Bellingshausen Sea (0.05 +/- 0.05 x 10(7) viruses ml(-1) d(-1)) and the highest in the Weddell Sea (4.3 +/- 3.5 x 10(7) viruses ml(-1) d(-1)). Average mortality rates due to viruses ranged from 9.7 +/- 6.1 x 10(4) cells ml(-1) d(-1) in the Weddell Sea to 14.3 +/- 4.0 x 10(4) cells ml(-1) d(-1) in the Bellingshausen Sea, and were higher than averaged grazing rates in the Weddell Sea (5.9 +/- 1.1 x 10(4) cells ml(-1) d(-1)) and in the Bellingshausen Sea (6.8 +/- 0.9 x 10(4) cells ml-1 d(-1)). The highest impact on prokaryotes by viruses and main differences between viral and protists activities were observed in surface samples: 17.8 +/- 6.8 x 10(4) cells ml(-1) d(-1) and 6.5 +/- 3.9 x 10(4) cells ml(-1) d(-1) in the Weddell Sea; 22.1 +/- 9.6 x 10(4) cells ml(-1) d(-1) and 11.6 +/- 1.4 x 10(4) cells ml(-1) d(-1) in the Bransfield Strait; and 16.1 +/- 5.7 x 10(4) cells ml(-1) d(-1) and 7.9 +/- 2.6 x 10(4) cells ml(-1) d(-1) in

  4. Viruses and Protists Induced-mortality of Prokaryotes around the Antarctic Peninsula during the Austral Summer.

    Science.gov (United States)

    Vaqué, Dolors; Boras, Julia A; Torrent-Llagostera, Francesc; Agustí, Susana; Arrieta, Jesús M; Lara, Elena; Castillo, Yaiza M; Duarte, Carlos M; Sala, Maria M

    2017-01-01

    During the Austral summer 2009 we studied three areas surrounding the Antarctic Peninsula: the Bellingshausen Sea, the Bransfield Strait and the Weddell Sea. We aimed to investigate, whether viruses or protists were the main agents inducing prokaryotic mortality rates, and the sensitivity to temperature of prokaryotic heterotrophic production and mortality based on the activation energy (Ea) for each process. Seawater samples were taken at seven depths (0.1-100 m) to quantify viruses, prokaryotes and protists abundances, and heterotrophic prokaryotic production (PHP). Viral lytic production, lysogeny, and mortality rates of prokaryotes due to viruses and protists were estimated at surface (0.1-1 m) and at the Deep Fluorescence Maximum (DFM, 12-55 m) at eight representative stations of the three areas. The average viral lytic production ranged from 1.0 ± 0.3 × 10 7 viruses ml -1 d -1 in the Bellingshausen Sea to1.3 ± 0.7 × 10 7 viruses ml -1 d -1 in the Bransfield Strait, while lysogeny, when detectable, recorded the lowest value in the Bellingshausen Sea (0.05 ± 0.05 × 10 7 viruses ml -1 d -1 ) and the highest in the Weddell Sea (4.3 ± 3.5 × 10 7 viruses ml -1 d -1 ). Average mortality rates due to viruses ranged from 9.7 ± 6.1 × 10 4 cells ml -1 d -1 in the Weddell Sea to 14.3 ± 4.0 × 10 4 cells ml -1 d -1 in the Bellingshausen Sea, and were higher than averaged grazing rates in the Weddell Sea (5.9 ± 1.1 × 10 4 cells ml -1 d -1 ) and in the Bellingshausen Sea (6.8 ± 0.9 × 10 4 cells ml -1 d -1 ). The highest impact on prokaryotes by viruses and main differences between viral and protists activities were observed in surface samples: 17.8 ± 6.8 × 10 4 cells ml -1 d -1 and 6.5 ± 3.9 × 10 4 cells ml -1 d -1 in the Weddell Sea; 22.1 ± 9.6 × 10 4 cells ml -1 d -1 and 11.6 ± 1.4 × 10 4 cells ml -1 d -1 in the Bransfield Strait; and 16.1 ± 5.7 × 10 4 cells ml -1 d -1 and 7.9 ± 2.6 × 10 4 cells ml -1 d -1 in the Bellingshausen Sea, respectively

  5. Conversion Efficiency of Photosynthetically Active Radiation Into Acacia mearnsii Biomass

    Directory of Open Access Journals (Sweden)

    Elder Eloy

    2018-02-01

    Full Text Available ABSTRACT The objective of this experiment was to determine the conversion efficiency of intercepted photosynthetically active radiation into biomass of Acacia mearnsii De Wild. seedlings. A forest species, plastic tubes (90 cm3, and 11 evaluation periods (up to 180 days after emergence were used in this study. The leaf area index (LAI, total dry biomass (BIO, global solar radiation (GSR, cumulative intercepted photosynthetically active radiation (PARic, and conversion efficiency of radiation (εb were determined using a pyranometer (LI200X, LICOR. The value of εb in BIO seedlings of Acacia mearnsii was 7.76 g MJ-1. LAI was directly related to the efficiency of PARic, and this influenced the development, production potential and accumulation of BIO. The value of GSR flow was 11.81 MJ m-2 day-1, while the value inside the greenhouse was 6.26 MJ m-2 day-1.

  6. A theoretical approach to photosynthetically active radiation silicon sensor

    International Nuclear Information System (INIS)

    Tamasi, M.J.L.; Martínez Bogado, M.G.

    2013-01-01

    This paper presents a theoretical approach for the development of low cost radiometers to measure photosynthetically active radiation (PAR). Two alternatives are considered: a) glass optical filters attached to a silicon sensor, and b) dielectric coating on a silicon sensor. The devices proposed are based on radiometers previously developed by the Argentine National Atomic Energy Commission. The objective of this work is to adapt these low cost radiometers to construct reliable instruments for measuring PAR. The transmittance of optical filters and sensor response have been analyzed for different dielectric materials, number of layers deposited, and incidence angles. Uncertainties in thickness of layer deposition were evaluated. - Highlights: • Design of radiometers to measure photosynthetically active radiation • The study has used a filter and a Si sensor to modify spectral response. • Dielectric multilayers on glass and silicon sensor • Spectral response related to different incidence angles, materials and spectra

  7. Photosynthetic planulae and planktonic hydroids: contrasting strategies of propagule survival

    Directory of Open Access Journals (Sweden)

    Patrizia Pagliara

    2000-12-01

    Full Text Available Settlement delays can be important to prevent propagule waste when proper settling substrates are not immediately available. Under laboratory conditions, the planulae of Clytia viridicans underwent two alternative developmental patterns. Some settled on the bottom, forming a hydranth-gonotheca complex that produced up to four medusae and later either degenerated or gave rise to a hydroid colony. Other planulae settled right below the air-water interface, forming floating colonies that eventually fell to the bottom and settled. Halecium nanum released planulae with a rich population of symbiotic zooxanthellae that survived into a rearing jar for three months. After a long period of apparent quiescence (possibly fuelled by photosynthetic activities of zooxanthellae the planulae produced new colonies. Both photosynthetic planulae and settlement at the interface air-water allow a delay in the passage from a planktonic to a fully functional benthic life.

  8. Photosynthetic Energy Transfer at the Quantum/Classical Border.

    Science.gov (United States)

    Keren, Nir; Paltiel, Yossi

    2018-06-01

    Quantum mechanics diverges from the classical description of our world when very small scales or very fast processes are involved. Unlike classical mechanics, quantum effects cannot be easily related to our everyday experience and are often counterintuitive to us. Nevertheless, the dimensions and time scales of the photosynthetic energy transfer processes puts them close to the quantum/classical border, bringing them into the range of measurable quantum effects. Here we review recent advances in the field and suggest that photosynthetic processes can take advantage of the sensitivity of quantum effects to the environmental 'noise' as means of tuning exciton energy transfer efficiency. If true, this design principle could be a base for 'nontrivial' coherent wave property nano-devices. Copyright © 2018 Elsevier Ltd. All rights reserved.

  9. Non-photosynthetic plastids as hosts for metabolic engineering

    DEFF Research Database (Denmark)

    Mellor, Silas Busck; Behrendorff, James Bruce Yarnton H; Nielsen, Agnieszka Janina Zygadlo

    2018-01-01

    Using plants as hosts for production of complex, high-value compounds and therapeutic proteins has gained increasing momentum over the past decade. Recent advances in metabolic engineering techniques using synthetic biology have set the stage for production yields to become economically attractive......, but more refined design strategies are required to increase product yields without compromising development and growth of the host system. The ability of plant cells to differentiate into various tissues in combination with a high level of cellular compartmentalization represents so far the most...... in green tissues, have proven to be suitable for high yield protein and bio-compound production. Unfortunately, chloroplast manipulation often affects photosynthetic efficiency and therefore plant fitness. In this respect, plastids of non-photosynthetic tissues, which have focused metabolisms for synthesis...

  10. Influence of thermal light correlations on photosynthetic structures

    Science.gov (United States)

    de Mendoza, Adriana; Manrique, Pedro; Caycedo-Soler, Felipe; Johnson, Neil F.; Rodríguez, Ferney J.; Quiroga, Luis

    2014-03-01

    The thermal light from the sun is characterized by both classical and quantum mechanical correlations. These correlations have left a fingerprint on the natural harvesting structures developed through five billion years of evolutionary pressure, specially in photosynthetic organisms. In this work, based upon previous extensive studies of spatio-temporal correlations of light fields, we hypothesize that structures involving photosensitive pigments like those present in purple bacteria vesicles emerge as an evolutionary response to the different properties of incident light. By using burstiness and memory as measures that quantify higher moments of the photon arrival statistics, we generate photon-time traces. They are used to simulate absorption on detectors spatially extended over regions comparable to these light fields coherence length. Finally, we provide some insights into the connection between these photo-statistical features with the photosynthetic membrane architecture and the lights' spatial correlation. Facultad de Ciencias Uniandes.

  11. Quantum measurement corrections to CIDNP in photosynthetic reaction centers

    International Nuclear Information System (INIS)

    Kominis, Iannis K

    2013-01-01

    Chemically induced dynamic nuclear polarization is a signature of spin order appearing in many photosynthetic reaction centers. Such polarization, significantly enhanced above thermal equilibrium, is known to result from the nuclear spin sorting inherent in the radical pair mechanism underlying long-lived charge-separated states in photosynthetic reaction centers. We will show here that the recently understood fundamental quantum dynamics of radical-ion-pair reactions open up a new and completely unexpected pathway toward obtaining chemically induced dynamic nuclear polarization signals. The fundamental decoherence mechanism inherent in the recombination process of radical pairs is shown to produce nuclear spin polarizations of the order of 10 4 times (or more) higher than the thermal equilibrium value at the Earth's magnetic field relevant to natural photosynthesis. This opens up the possibility of a fundamentally new exploration of the biological significance of high nuclear polarizations in photosynthesis. (paper)

  12. Photosynthetic carbon reduction by seagrasses exposed to ultraviolet A radiation

    Science.gov (United States)

    1979-01-01

    The seagrasses Halophila engelmannii, Halodule wrightii, and Syringodium filiforme were examined for their intrinsic sensitivity to ultraviolet-A-UV-A and ultraviolet-B-UV-B radiation. The effect of UV-A on photosynthetically active radiation (PAR) was also determined. Ultraviolet-A and ultraviolet-B were studied with emphasis on the greater respective environmental consequence in terms of seagrass distribution and abundance. Results indicate that an intrinsic sensitivity to UV-A alone is apparent only in Halophila, while net photosynthesis in Halodule and Syringodium seems unaffected by the level of UV-A provided. The sensitivity of Halophila to UV-A in the absense of (PAR) indicates that the photosynthetic reaction does not need to be in operation for damage to occur. Other significant results are reported.

  13. BOREAS TE-9 NSA Photosynthetic Capacity and Foliage Nitrogen Data

    Science.gov (United States)

    Hall, Forrest G. (Editor); Curd, Shelaine (Editor); Dang, Qinglai; Margolis, Hank; Coyea, Marie

    2000-01-01

    The Boreal Ecosystem-Atmospheric Study (BOREAS) TE-9 (Terrestrial Ecology) team collected several data sets related to chemical and photosynthetic properties of leaves in boreal forest tree species. This data set describes the spatial and temporal relationship between foliage nitrogen concentration and photosynthetic capacity in the canopies of black spruce, jack pine, and aspen located within the Northern Study Area (NSA). The data were collected from June to September 1994 and are useful for modeling the vertical distribution of carbon fixation for different forest types in the boreal forest. The data are available in tabular ASCII files. The data files are available on a CD-ROM (see document number 20010000884), or from the Oak Ridge National Laboratory (ORNL) Distributed Active Archive Center (DAAC).

  14. Relationships between meiofaunal biodiversity and prokaryotic heterotrophic production in different tropical habitats and oceanic regions.

    Science.gov (United States)

    Pusceddu, Antonio; Gambi, Cristina; Corinaldesi, Cinzia; Scopa, Mariaspina; Danovaro, Roberto

    2014-01-01

    Tropical marine ecosystems are among the most diverse of the world oceans, so that assessing the linkages between biodiversity and ecosystem functions (BEF) is a crucial step to predict consequences of biodiversity loss. Most BEF studies in marine ecosystems have been carried out on macrobenthic diversity, whereas the influence of the meiofauna on ecosystem functioning has received much less attention. We compared meiofaunal and nematode biodiversity and prokaryotic heterotrophic production across seagrass, mangrove and reef sediments in the Caribbean, Celebes and Red Seas. For all variables we report the presence of differences among habitats within the same region, and among regions within the same habitat. In all regions, the richness of meiofaunal taxa in reef and seagrass sediments is higher than in mangrove sediments. The sediments of the Celebes Sea show the highest meiofaunal biodiversity. The composition of meiofaunal assemblages varies significantly among habitats in the same region. The nematode beta diversity among habitats within the same region is higher than the beta diversity among regions. Although one site per habitat was considered in each region, these results suggest that the composition of meiofaunal assemblages varies primarily among biogeographic regions, whereas the composition of nematode assemblages varies more considerably among habitats. Meiofauna and nematode biodiversity and prokaryotic heterotrophic production, even after the removal of covariate effects linked with longitude and the quantity and nutritional quality of organic matter, are positively and linearly linked both across regions and within each habitat type. Our results confirm that meiofauna and nematode biodiversity may influence benthic prokaryotic activity, which, in turn, implies that diversity loss could have negative impacts on ecosystem functioning in these systems.

  15. Relationships between meiofaunal biodiversity and prokaryotic heterotrophic production in different tropical habitats and oceanic regions.

    Directory of Open Access Journals (Sweden)

    Antonio Pusceddu

    Full Text Available Tropical marine ecosystems are among the most diverse of the world oceans, so that assessing the linkages between biodiversity and ecosystem functions (BEF is a crucial step to predict consequences of biodiversity loss. Most BEF studies in marine ecosystems have been carried out on macrobenthic diversity, whereas the influence of the meiofauna on ecosystem functioning has received much less attention. We compared meiofaunal and nematode biodiversity and prokaryotic heterotrophic production across seagrass, mangrove and reef sediments in the Caribbean, Celebes and Red Seas. For all variables we report the presence of differences among habitats within the same region, and among regions within the same habitat. In all regions, the richness of meiofaunal taxa in reef and seagrass sediments is higher than in mangrove sediments. The sediments of the Celebes Sea show the highest meiofaunal biodiversity. The composition of meiofaunal assemblages varies significantly among habitats in the same region. The nematode beta diversity among habitats within the same region is higher than the beta diversity among regions. Although one site per habitat was considered in each region, these results suggest that the composition of meiofaunal assemblages varies primarily among biogeographic regions, whereas the composition of nematode assemblages varies more considerably among habitats. Meiofauna and nematode biodiversity and prokaryotic heterotrophic production, even after the removal of covariate effects linked with longitude and the quantity and nutritional quality of organic matter, are positively and linearly linked both across regions and within each habitat type. Our results confirm that meiofauna and nematode biodiversity may influence benthic prokaryotic activity, which, in turn, implies that diversity loss could have negative impacts on ecosystem functioning in these systems.

  16. Prokaryotic Diversity in the Rhizosphere of Organic, Intensive, and Transitional Coffee Farms in Brazil.

    Science.gov (United States)

    Caldwell, Adam Collins; Silva, Lívia Carneiro Fidéles; da Silva, Cynthia Canêdo; Ouverney, Cleber Costa

    2015-01-01

    Despite a continuous rise in consumption of coffee over the past 60 years and recent studies showing positive benefits linked to human health, intensive coffee farming practices have been associated with environmental damage, risks to human health, and reductions in biodiversity. In contrast, organic farming has become an increasingly popular alternative, with both environmental and health benefits. This study aimed to characterize and determine the differences in the prokaryotic soil microbiology of three Brazilian coffee farms: one practicing intensive farming, one practicing organic farming, and one undergoing a transition from intensive to organic practices. Soil samples were collected from 20 coffee plant rhizospheres (soil directly influenced by the plant root exudates) and 10 control sites (soil 5 m away from the coffee plantation) at each of the three farms for a total of 90 samples. Profiling of 16S rRNA gene V4 regions revealed high levels of prokaryotic diversity in all three farms, with thousands of species level operational taxonomic units identified in each farm. Additionally, a statistically significant difference was found between each farm's coffee rhizosphere microbiome, as well as between coffee rhizosphere soils and control soils. Two groups of prokaryotes associated with the nitrogen cycle, the archaeal genus Candidatus Nitrososphaera and the bacterial order Rhizobiales were found to be abundant and statistically different in composition between the three farms and in inverse relationship to each other. Many of the nitrogen-fixing genera known to enhance plant growth were found in low numbers (e.g. Rhizobium, Agrobacter, Acetobacter, Rhodospirillum, Azospirillum), but the families in which they belong had some of the highest relative abundance in the dataset, suggesting many new groups may exist in these samples that can be further studied as potential plant growth-promoting bacteria to improve coffee production while diminishing negative

  17. [Prokaryotic expression of Leptospira interrogans groEL gene and immunoprotection of its products in hamsters].

    Science.gov (United States)

    Li, Xiaoyu; Wang, Yinhuan; Yan, Jie; Cheng, Dongqing

    2013-03-01

    To construct a prokaryotic expression system of groEL gene of Leptospira interrogans serogroup Icterohaemorrhagia serovar Lai strain Lai, and to determine the immunoprotective effect of recombinant GroEL protein (rGroEL) in LVG hamsters. The groEL gene was amplified by high fidelity PCR and the amplification products were then sequenced. A prokaryotic expression system of groEL gene was constructed using routine genetic engineering technique. SDS-PAGE plus Bio-Rad Gel Image Analyzer was applied to examine the expression and dissolubility of rGroEL protein while Ni-NTA affinity chromatography was used to extract the expressed rGroEL. The immunoprotective rate in rGroEL-immunized LVG hamsters was determined after challenge with L.interrogans strain Lai. The cross agglutination titers of sera from immunized hamsters with different L.interrogans serogroups were detected using MAT. The nucleotide and amino acid sequences of the cloned groEL gene were the same as those reported in GenBank. The constructed prokaryotic expression system of groEL gene expressed soluble rGroEL. The immunoprotective rates of 100 and 200 μg rGroEL in LVG hamsters were 50.0 % and 75.0%, respectively. The sera from the rGroEL-immunized LVG hamsters agglutinated all the L.interrogans serogroups tested with different levels. The GroEL protein is a genus-specific immunoprotective antigen of L.interrogans and can be used to develop an universal genetically engineering vaccine of Leptospira.

  18. Analyzing the Differences and Preferences of Pathogenic and Nonpathogenic Prokaryote Species

    Science.gov (United States)

    Nolen, L.; Duong, K.; Heim, N. A.; Payne, J.

    2015-12-01

    A limited amount of knowledge exists on the large-scale characteristics and differences of pathogenic species in comparison to all prokaryotes. Pathogenic species, like other prokaryotes, have attributes specific to their environment and lifestyles. However, because they have evolved to coexist inside their hosts, the conditions they occupy may be more limited than those of non-pathogenic species. In this study we investigate the possibility of divergent evolution between pathogenic and non-pathogenic species by examining differences that may have evolved as a result of the need to adapt to their host. For this research we analyzed data collected from over 1900 prokaryotic species and performed t-tests using R to quantify potential differences in preferences. To examine the possible divergences from nonpathogenic bacteria, we focused on three variables: cell biovolume, preferred environmental pH, and preferred environmental temperature. We also looked at differences between pathogenic and nonpathogenic species belonging to the same phylum. Our results suggest a strong divergence in abiotic preferences between the two groups, with pathogens occupying a much smaller range of temperatures and pHs than their non-pathogenic counterparts. However, while the median biovolume is different when comparing pathogens and nonpathogens, we cannot conclude that the mean values are significantly different from each other. In addition, we found evidence of convergent evolution, as the temperature and pH preferences of pathogenic bacteria species from different phlya all approach the same values. Pathogenic species do not, however, all approach the same biovolume values, suggesting that specific pH and temperature preferences are more characteristic of pathogens than certain biovolumes.

  19. Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine–Dalgarno sequence in prokaryotes

    KAUST Repository

    Nakagawa, So

    2017-02-15

    In prokaryotes, translation initiation is believed to occur through an interaction between the 3\\' tail of a 16S rRNA and a corresponding Shine-Dalgarno (SD) sequence in the 5\\' untranslated region (UTR) of an mRNA. However, some genes lack SD sequences (non-SD genes), and the fraction of non-SD genes in a genome varies depending on the prokaryotic species. To elucidate non-SD translation initiation mechanisms in prokaryotes from an evolutionary perspective, we statistically examined the nucleotide frequencies around the initiation codons in non-SD genes from 260 prokaryotes (235 bacteria and 25 archaea). We identified distinct nucleotide frequency biases upstream of the initiation codon in bacteria and archaea, likely because of the presence of leaderless mRNAs lacking a 5\\' UTR. Moreover, we observed overall similarities in the nucleotide patterns between upstream and downstream regions of the initiation codon in all examined phyla. Symmetric nucleotide frequency biases might facilitate translation initiation by preventing the formation of secondary structures around the initiation codon. These features are more prominent in species\\' genomes that harbor large fractions of non-SD sequences, suggesting that a reduced stability around the initiation codon is important for efficient translation initiation in prokaryotes.

  20. Comparative genomic analysis of translation initiation mechanisms for genes lacking the Shine–Dalgarno sequence in prokaryotes

    KAUST Repository

    Nakagawa, So; Niimura, Yoshihito; Gojobori, Takashi

    2017-01-01

    In prokaryotes, translation initiation is believed to occur through an interaction between the 3' tail of a 16S rRNA and a corresponding Shine-Dalgarno (SD) sequence in the 5' untranslated region (UTR) of an mRNA. However, some genes lack SD sequences (non-SD genes), and the fraction of non-SD genes in a genome varies depending on the prokaryotic species. To elucidate non-SD translation initiation mechanisms in prokaryotes from an evolutionary perspective, we statistically examined the nucleotide frequencies around the initiation codons in non-SD genes from 260 prokaryotes (235 bacteria and 25 archaea). We identified distinct nucleotide frequency biases upstream of the initiation codon in bacteria and archaea, likely because of the presence of leaderless mRNAs lacking a 5' UTR. Moreover, we observed overall similarities in the nucleotide patterns between upstream and downstream regions of the initiation codon in all examined phyla. Symmetric nucleotide frequency biases might facilitate translation initiation by preventing the formation of secondary structures around the initiation codon. These features are more prominent in species' genomes that harbor large fractions of non-SD sequences, suggesting that a reduced stability around the initiation codon is important for efficient translation initiation in prokaryotes.

  1. Enhanced Practical Photosynthetic CO2 Mitigation. Quarterly Technical Report

    International Nuclear Information System (INIS)

    Gregory Kremer; David J. Bayless; Morgan Vis; Michael Prudich; Keith Cooksey; Jeff Muhs

    2005-01-01

    This report highlights significant achievements in the Enhanced Practical Photosynthetic CO 2 Mitigation Project during the ending 12/31/2004. Specific results and accomplishments for the program include review of pilot scale testing and design of a new bioreactor. Testing confirmed that algae can be grown in a sustainable fashion in the pilot bioreactor, even with intermittent availability of sunlight. The pilot-scale tests indicated that algal growth rate followed photon delivery during productivity testing

  2. Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production

    OpenAIRE

    Lai, Martin C.; Lan, Ethan I.

    2015-01-01

    Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central metabolism and rerouting carbon flux towards desirable compound production, cyanobacteria are engineered to directly convert CO2 into various chemicals. This review discusses the d...

  3. Microbiological Hydrogen Production by Anaerobic Fermentation and Photosynthetic Process

    International Nuclear Information System (INIS)

    Asada, Y.; Ohsawa, M.; Nagai, Y.; Fukatsu, M.; Ishimi, K.; Ichi-ishi, S.

    2009-01-01

    Hydrogen gas is a clean and renewable energy carrier. Microbiological hydrogen production from glucose or starch by combination used of an anaerobic fermenter and a photosynthetic bacterium, Rhodobacter spheroides RV was studied. In 1984, the co-culture of Clostridium butyricum and RV strain to convert glucose to hydrogen was demonstrated by Miyake et al. Recently, we studied anaerobic fermentation of starch by a thermophilic archaea. (Author)

  4. Microbial diversity from chlorophyll maximum, oxygen minimum and bottom zones in the southwestern Atlantic Ocean

    Science.gov (United States)

    Medina-Silva, Renata; de Oliveira, Rafael R.; Pivel, Maria A. G.; Borges, Luiz G. A.; Simão, Taiz L. L.; Pereira, Leandro M.; Trindade, Fernanda J.; Augustin, Adolpho H.; Valdez, Fernanda P.; Eizirik, Eduardo; Utz, Laura R. P.; Groposo, Claudia; Miller, Dennis J.; Viana, Adriano R.; Ketzer, João M. M.; Giongo, Adriana

    2018-02-01

    Conspicuous physicochemical vertical stratification in the deep sea is one of the main forces driving microbial diversity in the oceans. Oxygen and sunlight availability are key factors promoting microbial diversity throughout the water column. Ocean currents also play a major role in the physicochemical stratification, carrying oxygen down to deeper zones as well as moving deeper water masses up towards shallower depths. Water samples within a 50-km radius in a pockmark location of the southwestern Atlantic Ocean were collected and the prokaryotic communities from different water depths - chlorophyll maximum, oxygen minimum and deep-sea bottom (down to 1355 m) - were described. At phylum level, Proteobacteria were the most frequent in all water depths, Cyanobacteria were statistically more frequent in chlorophyll maximum zone, while Thaumarchaeota were significantly more abundant in both oxygen minimum and bottom waters. The most frequent microorganism in the chlorophyll maximum and oxygen minimum zones was a Pelagibacteraceae operational taxonomic unit (OTU). At the bottom, the most abundant genus was the archaeon Nitrosopumilus. Beta diversity analysis of the 16S rRNA gene sequencing data uncovered in this study shows high spatial heterogeneity among water zones communities. Our data brings important contribution for the characterisation of oceanic microbial diversity, as it consists of the first description of prokaryotic communities occurring in different oceanic water zones in the southwestern Atlantic Ocean.

  5. Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

    DEFF Research Database (Denmark)

    Kim, Hyun Uk; Charusanti, Pep; Lee, Sang Yup

    2016-01-01

    Metabolic engineering using systems biology tools is increasingly applied to overproduce secondary metabolites for their potential industrial production. In this Highlight, recent relevant metabolic engineering studies are analyzed with emphasis on host selection and engineering approaches...... for the optimal production of various prokaryotic secondary metabolites: native versus heterologous hosts (e.g., Escherichia coli) and rational versus random approaches. This comparative analysis is followed by discussions on systems biology tools deployed in optimizing the production of secondary metabolites....... The potential contributions of additional systems biology tools are also discussed in the context of current challenges encountered during optimization of secondary metabolite production....

  6. Keeping the wolves at bay: antitoxins of prokaryotic type II toxin-antitoxin systems

    Directory of Open Access Journals (Sweden)

    Wai Ting eChan

    2016-03-01

    Full Text Available In their initial stages of discovery, prokaryotic toxin-antitoxin (TA systems were confined to bacterial plasmids where they function to mediate the maintenance and stability of usually low- to medium-copy number plasmids through the post-segregational killing of any plasmid-free daughter cells that developed. Their eventual discovery as nearly ubiquitous and repetitive elements in bacterial chromosomes led to a wealth of knowledge and scientific debate as to their diversity and functionality in the prokaryotic lifestyle. Currently categorized into six different types designated types I – VI, type II TA systems are the best characterized. These generally comprised of two genes encoding a proteic toxin and its corresponding proteic antitoxin, respectively. Under normal growth conditions, the stable toxin is prevented from exerting its lethal effect through tight binding with the less stable antitoxin partner, forming a non-lethal TA protein complex. Besides binding with its cognate toxin, the antitoxin also plays a role in regulating the expression of the type II TA operon by binding to the operator site, thereby repressing transcription from the TA promoter. In most cases, full repression is observed in the presence of the TA complex as binding of the toxin enhances the DNA binding capability of the antitoxin. TA systems have been implicated in a gamut of prokaryotic cellular functions such as being mediators of programmed cell death as well as persistence or dormancy, biofilm formation, as defensive weapons against bacteriophage infections and as virulence factors in pathogenic bacteria. It is thus apparent that these antitoxins, as DNA-binding proteins, play an essential role in modulating the prokaryotic lifestyle whilst at the same time preventing the lethal action of the toxins under normal growth conditions, i.e., keeping the proverbial wolves at bay. In this review, we will cover the diversity and characteristics of various type II TA

  7. Mesopelagic Prokaryotes Alter Surface Phytoplankton Production during Simulated Deep Mixing Experiments in Eastern Mediterranean Sea Waters

    Directory of Open Access Journals (Sweden)

    Or Hazan

    2018-01-01

    Full Text Available Mesopelagic prokaryotes (archaea and bacteria, which are transported together with nutrient-rich intermediate-water to the surface layer by deep convection in the oceans (e.g., winter mixing, upwelling systems, can interact with surface microbial populations. This interaction can potentially affect production rates and biomass of surface microbial populations, and thus play an important role in the marine carbon cycle and oceanic carbon sequestration. The Eastern Mediterranean Sea (EMS is one of the most oligotrophic and warm systems in the world's oceans, with usually very shallow winter mixing (<200 m and lack of large-size spring algal blooms. In this study, we collected seawater (0–1,500 m in 9 different cruises at the open EMS during both the stratified and the mixed seasons. We show that the EMS is a highly oligotrophic regime, resulting in low autotrophic biomass and primary productivity and relatively high heterotrophic prokaryotic biomass and production. Further, we simulated deep water mixing in on-board microcosms using Levantine surface (LSW, ~0.5 m and intermediate (LIW, ~400 m waters at a 9:1 ratio, respectively and examined the responses of the microbial populations to such a scenario. We hypothesized that the LIW, being nutrient-rich (e.g., N, P and a “hot-spot” for microbial activity (due to the warm conditions that prevail in these depths, may supply the LSW with not only key-limiting nutrients but also with viable and active heterotrophic prokaryotes that can interact with the ambient surface microbial population. Indeed, we show that LIW heterotrophic prokaryotes negatively affected the surface phytoplankton populations, resulting in lower chlorophyll-a levels and primary production rates. This may be due to out-competition of phytoplankton by LIW populations for resources and/or by a phytoplankton cell lysis via viral infection. Our results suggest that phytoplankton in the EMS may not likely form blooms, even after

  8. [Prokaryotic expression of trigeminy artificial fusion gene of Leptospira interrogans and the immunogenicity of its products].

    Science.gov (United States)

    Luo, Dong-jiao; Qiu, Xiao-feng; Wang, Jiang; Yan, Jin; Wang, Hai-bin; Zhou, Jin-cheng; Yan, Jie

    2008-11-01

    To construct lipL32/1-lipL21-OmpL1/2 fusion gene of Leptospira interrogans and its prokaryotic expression system, and to identify the immunogenicity of its products. PCR using linking primers was applied to construct lipL32/1-lipL21-OmpL1/2 fusion gene and a prokaryotic expression system of the fusion gene was then established using routine genetic engineering technique. SDS-PAGE was used to examine output of the target recombinant protein rLipL32/1-LipL21-OmpL1/2. Double immunodiffusion and Western Blot assay were applied to identify immunogenicity of rLipL32/1-LipL21-OmpL1/2. lipL32/1-lipL21-OmpL1/2 fusion gene with correct sequence and its prokaryotic expression system E.coli BL21DE3pET42a-lipL32/1-lipL21-ompL1/2 was obtained in this study. The output of rLipL32/1-LipL21- OmpL1/2 after optimisation was 37.78 mg/L. The immunodiffusion titer of rabbit antiserum against rLipL32/1-LipL21-OmpL1/2 was 1:4. The rLipL32/1-LipL21-OmpL1/2 antiserum was able to recognize rLipL32/1-LipL21-OmpL1/2, rLipL32/1, rLipL21 and rOmpL1/2. Positive Western hybridization signals were found among rLipL32/1-LipL21-OmpL1/2 and rabbit antiserum against whole cell of strain 56601 and serum from patients infected with L.interrogans serogroups Icterohaemorrhagiae, Grippotyphosa, Autumnalis and Pomona. The fusion gene lipL32/1-lipL21-OmpL1/2 and its prokaryotic expression system were successfully constructed in this study. The expressed fusion protein can be used as the antigen for developing universal genetic engineering vaccine and universal serological tests of leptospirosis.

  9. Continuous cultivation of photosynthetic microorganisms: Approaches, applications and future trends.

    Science.gov (United States)

    Fernandes, Bruno D; Mota, Andre; Teixeira, Jose A; Vicente, Antonio A

    2015-11-01

    The possibility of using photosynthetic microorganisms, such as cyanobacteria and microalgae, for converting light and carbon dioxide into valuable biochemical products has raised the need for new cost-efficient processes ensuring a constant product quality. Food, feed, biofuels, cosmetics and pharmaceutics are among the sectors that can profit from the application of photosynthetic microorganisms. Biomass growth in a photobioreactor is a complex process influenced by multiple parameters, such as photosynthetic light capture and attenuation, nutrient uptake, photobioreactor hydrodynamics and gas-liquid mass transfer. In order to optimize productivity while keeping a standard product quality, a permanent control of the main cultivation parameters is necessary, where the continuous cultivation has shown to be the best option. However it is of utmost importance to recognize the singularity of continuous cultivation of cyanobacteria and microalgae due to their dependence on light availability and intensity. In this sense, this review provides comprehensive information on recent breakthroughs and possible future trends regarding technological and process improvements in continuous cultivation systems of microalgae and cyanobacteria, that will directly affect cost-effectiveness and product quality standardization. An overview of the various applications, techniques and equipment (with special emphasis on photobioreactors) in continuous cultivation of microalgae and cyanobacteria are presented. Additionally, mathematical modeling, feasibility, economics as well as the applicability of continuous cultivation into large-scale operation, are discussed. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Quantum transport in the FMO photosynthetic light-harvesting complex.

    Science.gov (United States)

    Karafyllidis, Ioannis G

    2017-06-01

    The very high light-harvesting efficiency of natural photosynthetic systems in conjunction with recent experiments, which showed quantum-coherent energy transfer in photosynthetic complexes, raised questions regarding the presence of non-trivial quantum effects in photosynthesis. Grover quantum search, quantum walks, and entanglement have been investigated as possible effects that lead to this efficiency. Here we explain the near-unit photosynthetic efficiency without invoking non-trivial quantum effects. Instead, we use non-equilibrium Green's functions, a mesoscopic method used to study transport in nano-conductors to compute the transmission function of the Fenna-Matthews-Olson (FMO) complex using an experimentally derived exciton Hamiltonian. The chlorosome antenna and the reaction center play the role of input and output contacts, connected to the FMO complex. We show that there are two channels for which the transmission is almost unity. Our analysis also revealed a dephasing-driven regulation mechanism that maintains the efficiency in the presence of varying dephasing potentials.

  11. The role of energy losses in photosynthetic light harvesting

    Science.gov (United States)

    Krüger, T. P. J.; van Grondelle, R.

    2017-07-01

    Photosynthesis operates at the bottom of the food chain to convert the energy of light into carbohydrates at a remarkable global rate of about 130 TW. Nonetheless, the overall photosynthetic process has a conversion efficiency of a few percent at best, significantly less than bottom-up photovoltaic cells. The primary photosynthetic steps, consisting of light harvesting and charge separation, are often presented as having near-unity quantum efficiency but this holds only true under ideal conditions. In this review, we discuss the importance of energy loss mechanisms to establish robustness in photosynthetic light harvesting. Thermal energy dissipation of light-harvesting complexes (LHCs) in different environments is investigated and the relationships and contrasts between concentration quenching of high pigment concentrations, photoprotection (non-photochemical quenching), quenching due to protein aggregation, and fluorescence blinking are discussed. The role of charge-transfer states in light harvesting and energy dissipation is highlighted and the importance of controlled protein structural disorder to switch the light-harvesting antennae between effective light harvesters and efficient energy quenchers is underscored. The main LHC of plants, LHCII, is used as a prime example.

  12. Photosynthetic efficiency of Pedunculate oak seedlings under simulated water stress

    Directory of Open Access Journals (Sweden)

    Popović Zorica

    2010-01-01

    Full Text Available Photosynthetic performance of seedlings of Quercus robur exposed to short-term water stress in the laboratory conditions was assessed through the method of induced fluorometry. The substrate for seedlings was clayey loam, with the dominant texture fraction made of silt, followed by clay and fine sand, with total porosity 68.2%. Seedlings were separated in two groups: control (C (soil water regime in pots was maintained at the level of field water capacity and treated (water-stressed, WS (soil water regime was maintained in the range of wilting point and lentocapillary capacity. The photosynthetic efficiency was 0.642±0.25 and 0.522±0.024 (WS and C, respectively, which was mostly due to transplantation disturbances and sporadic leaf chlorosis. During the experiment Fv/Fm decreased in both groups (0.551±0.0100 and 0.427±0.018 in C and WS, respectively. Our results showed significant differences between stressed and control group, in regard to both observed parameters (Fv/Fm and T½. Photosynthetic efficiency of pedunculate oak seedlings was significantly affected by short-term water stress, but to a lesser extent than by sufficient watering.

  13. The role of energy losses in photosynthetic light harvesting

    International Nuclear Information System (INIS)

    Krüger, T P J; Van Grondelle, R

    2017-01-01

    Photosynthesis operates at the bottom of the food chain to convert the energy of light into carbohydrates at a remarkable global rate of about 130 TW. Nonetheless, the overall photosynthetic process has a conversion efficiency of a few percent at best, significantly less than bottom-up photovoltaic cells. The primary photosynthetic steps, consisting of light harvesting and charge separation, are often presented as having near-unity quantum efficiency but this holds only true under ideal conditions. In this review, we discuss the importance of energy loss mechanisms to establish robustness in photosynthetic light harvesting. Thermal energy dissipation of light-harvesting complexes (LHCs) in different environments is investigated and the relationships and contrasts between concentration quenching of high pigment concentrations, photoprotection (non-photochemical quenching), quenching due to protein aggregation, and fluorescence blinking are discussed. The role of charge-transfer states in light harvesting and energy dissipation is highlighted and the importance of controlled protein structural disorder to switch the light-harvesting antennae between effective light harvesters and efficient energy quenchers is underscored. The main LHC of plants, LHCII, is used as a prime example. (topical review)

  14. Photosynthetic Reaction Centres-from Basic Research to Application

    Directory of Open Access Journals (Sweden)

    László NAGY

    2010-06-01

    Full Text Available There is no doubt that studying the photosynthetic conversion of light into chemical energy is extremely important in many points of view; e.g., 1 technical-in order to improve the utilization of the solar energy; 2 food production-to improve the photosynthetic production of plants in agriculture; 3 ecology-keeping the primer production in ecosystems in the biosphere balanced, etc. In the photosynthetic reaction centre protein, RC, light energy is converted by a quantum yield of almost unity. There is no such a system designed by human which is able to do that. The RC purified from purple bacteria provides an extremely unique system for studying the requirements for high efficiency conversion of light into electrochemical energy. Thanks to the recent structural (e.g. crystallography (Nobel prize to Michel, Deisenhofer, Huber and functional (Nobel prize to Marcus results together with the works of molecular biology, computer- and electro-techniques, a wealth of information made a relatively clear picture about the kinetics, energetics and stabilization of electron transport within this protein that opens possibilities for new generation practical applications. In this paper we provide a short summary of fields in which the reaction centre protein can be important from practical points of view.

  15. Photovoltaic concepts inspired by coherence effects in photosynthetic systems

    KAUST Repository

    Bredas, Jean-Luc

    2016-12-20

    The past decade has seen rapid advances in our understanding of how coherent and vibronic phenomena in biological photosynthetic systems aid in the efficient transport of energy from light-harvesting antennas to photosynthetic reaction centres. Such coherence effects suggest strategies to increase transport lengths even in the presence of structural disorder. Here we explore how these principles could be exploited in making improved solar cells. We investigate in depth the case of organic materials, systems in which energy and charge transport stand to be improved by overcoming challenges that arise from the effects of static and dynamic disorder-structural and energetic-and from inherently strong electron-vibration couplings. We discuss how solar-cell device architectures can evolve to use coherence-exploiting materials, and we speculate as to the prospects for a coherent energy conversion system. We conclude with a survey of the impacts of coherence and bioinspiration on diverse solar-energy harvesting solutions, including artificial photosynthetic systems.

  16. DAILY BUDGETS OF PHOTOSYNTHETICALLY FIXED CARBON IN SYMBIOTIC ZOANTHIDS.

    Science.gov (United States)

    Steen, R Grant; Muscatine, L

    1984-10-01

    We tested the hypothesis that some zoanthids are able to meet a portion of their daily respiratory carbon requirement with photosynthetic carbon from symbiotic algal cells (= zooxanthellae). A daily budget was constructed for carbon (C) photosynthetically fixed by zooxanthellae of the Bermuda zoanthids Zoanthus sociatus and Palythoa variabilis. Zooxanthellae have an average net photosynthetic C fixation of 7.48 and 15.56 µgC·polyp -1 ·day -1 for Z. sociatus and P. variabilis respectively. The C-specific growth rate (µ c ) was 0.215·day -1 for Z. sociatus and 0.152·day -1 for P. variabilis. The specific growth rate (µ) of zooxanthellae in the zoanthids was measured to be 0.011 and 0.017·day -1 for Z. sociatus and P. variabilis zooxanthellae respectively. Z. sociatus zooxanthellae translocated 95.1% of the C assimilated in photosynthesis, while P. variabilis zooxanthellae translocated 88.8% of their fixed C. As the animal tissue of a polyp of Z. sociatus required 14.75 µgC·day -1 for respiration, and one of P. variabiis required 105.54 µgC·day -1 , the contribution of zooxanthellae to animal respiration (CZAR) was 48.2% for Z. sociatus and 13.1% for P. variabilis.

  17. Calculation of the radiative properties of photosynthetic microorganisms

    International Nuclear Information System (INIS)

    Dauchet, Jérémi; Blanco, Stéphane; Cornet, Jean-François; Fournier, Richard

    2015-01-01

    A generic methodological chain for the predictive calculation of the light-scattering and absorption properties of photosynthetic microorganisms within the visible spectrum is presented here. This methodology has been developed in order to provide the radiative properties needed for the analysis of radiative transfer within photobioreactor processes, with a view to enable their optimization for large-scale sustainable production of chemicals for energy and chemistry. It gathers an electromagnetic model of light-particle interaction along with detailed and validated protocols for the determination of input parameters: morphological and structural characteristics of the studied microorganisms as well as their photosynthetic-pigment content. The microorganisms are described as homogeneous equivalent-particles whose shape and size distribution is characterized by image analysis. The imaginary part of their refractive index is obtained thanks to a new and quite extended database of the in vivo absorption spectra of photosynthetic pigments (that is made available to the reader). The real part of the refractive index is then calculated by using the singly subtractive Kramers–Krönig approximation, for which the anchor point is determined with the Bruggeman mixing rule, based on the volume fraction of the microorganism internal-structures and their refractive indices (extracted from a database). Afterwards, the radiative properties are estimated using the Schiff approximation for spheroidal or cylindrical particles, as a first step toward the description of the complexity and diversity of the shapes encountered within the microbial world. Finally, these predictive results are confronted to experimental normal-hemispherical transmittance spectra for validation. This entire procedure is implemented for Rhodospirillum rubrum, Arthrospira platensis and Chlamydomonas reinhardtii, each representative of the main three kinds of photosynthetic microorganisms, i.e. respectively

  18. Calculation of the radiative properties of photosynthetic microorganisms

    Science.gov (United States)

    Dauchet, Jérémi; Blanco, Stéphane; Cornet, Jean-François; Fournier, Richard

    2015-08-01

    A generic methodological chain for the predictive calculation of the light-scattering and absorption properties of photosynthetic microorganisms within the visible spectrum is presented here. This methodology has been developed in order to provide the radiative properties needed for the analysis of radiative transfer within photobioreactor processes, with a view to enable their optimization for large-scale sustainable production of chemicals for energy and chemistry. It gathers an electromagnetic model of light-particle interaction along with detailed and validated protocols for the determination of input parameters: morphological and structural characteristics of the studied microorganisms as well as their photosynthetic-pigment content. The microorganisms are described as homogeneous equivalent-particles whose shape and size distribution is characterized by image analysis. The imaginary part of their refractive index is obtained thanks to a new and quite extended database of the in vivo absorption spectra of photosynthetic pigments (that is made available to the reader). The real part of the refractive index is then calculated by using the singly subtractive Kramers-Krönig approximation, for which the anchor point is determined with the Bruggeman mixing rule, based on the volume fraction of the microorganism internal-structures and their refractive indices (extracted from a database). Afterwards, the radiative properties are estimated using the Schiff approximation for spheroidal or cylindrical particles, as a first step toward the description of the complexity and diversity of the shapes encountered within the microbial world. Finally, these predictive results are confronted to experimental normal-hemispherical transmittance spectra for validation. This entire procedure is implemented for Rhodospirillum rubrum, Arthrospira platensis and Chlamydomonas reinhardtii, each representative of the main three kinds of photosynthetic microorganisms, i.e. respectively

  19. Adaptation of the short intergenic spacers between co-directional genes to the Shine-Dalgarno motif among prokaryote genomes

    DEFF Research Database (Denmark)

    Caro, Albert Pallejà; García-Vallvé, Santiago; Romeu, Antoni

    2009-01-01

    ABSTRACT: BACKGROUND: In prokaryote genomes most of the co-directional genes are in close proximity. Even the coding sequence or the stop codon of a gene can overlap with the Shine-Dalgarno (SD) sequence of the downstream co-directional gene. In this paper we analyze how the presence of SD may...... influence the stop codon usage or the spacing lengths between co-directional genes. RESULTS: The SD sequences for 530 prokaryote genomes have been predicted using computer calculations of the base-pairing free energy between translation initiation regions and the 16S rRNA 3' tail. Genomes with a large...... to the discussion of which factors affect the intergenic lengths, which cannot be totally explained by the pressure to compact the prokaryote genomes....

  20. Photosynthetic performance of restored and natural mangroves under different environmental constraints

    International Nuclear Information System (INIS)

    Rovai, André Scarlate; Barufi, José Bonomi; Pagliosa, Paulo Roberto; Scherner, Fernando; Torres, Moacir Aluísio; Horta, Paulo Antunes

    2013-01-01

    We hypothesized that the photosynthetic performance of mangrove stands restored by the single planting of mangroves species would be lowered due to residual stressors. The photosynthetic parameters of the vegetation of three planted mangrove stands, each with a different disturbance history, were compared to reference sites and correlated with edaphic environmental variables. A permutational analysis of variance showed significant interaction when the factors were compared, indicating that the photosynthetic parameters of the restoration areas differed from the reference sites. A univariate analysis of variance showed that all the photosynthetic parameters differed between sites and treatments, except for photosynthetic efficiency (α ETR ). The combination of environmental variables that best explained the variations observed in the photosynthetic performance indicators were Cu, Pb and elevation disruptions. Fluorescence techniques proved efficient in revealing important physiological differences, representing a powerful tool for rapid analysis of the effectiveness of initiatives aimed at restoring coastal environments. -- Highlights: •Photosynthetic efficiency of natural and restored mangroves are compared. •Natural stands present higher photosynthetic performance. •Photosynthetic performance of mangroves is reduced due to Cu and Pb contamination. •Chlorophyll a fluorescence is a useful indicator to assess short-term restoration. -- Photosynthetic performance of mangroves is reduced due to Cu and Pb contamination

  1. Photosynthetic performance of restored and natural mangroves under different environmental constraints

    Energy Technology Data Exchange (ETDEWEB)

    Rovai, André Scarlate, E-mail: rovaias@hotmail.com [Universidade Federal de Santa Catarina, Departamento de Ecologia e Zoologia, Campus Universitário, Trindade, 88040-900 Florianópolis, SC (Brazil); Barufi, José Bonomi, E-mail: jose.bonomi@gmail.com [Universidade Federal de Santa Catarina, Departamento de Botânica, Campus Universitário, Trindade, 88040-900 Florianópolis, SC (Brazil); Pagliosa, Paulo Roberto, E-mail: paulo.pagliosa@ufsc.br [Universidade Federal de Santa Catarina, Departamento de Geociências, Campus Universitário, Trindade, 88040-900 Florianópolis, SC (Brazil); Scherner, Fernando [Universidade Federal Rural de Pernambuco, Laboratório de Ficologia, Campus Universitário, Dois Irmãos, 52171-900 Recife, PE (Brazil); Torres, Moacir Aluísio, E-mail: moatorres@cav.udesc.br [Universidade do Estado de Santa Catarina, Departamento de Engenharia Ambiental, Centro de Ciências Agroveterinárias, Av Luiz de Camões 2090, Conta Dinheiro, 88520-000 Lages, SC (Brazil); Horta, Paulo Antunes, E-mail: pahorta@ccb.ufsc.br [Universidade Federal de Santa Catarina, Departamento de Botânica, Campus Universitário, Trindade, 88040-900 Florianópolis, SC (Brazil); others, and

    2013-10-15

    We hypothesized that the photosynthetic performance of mangrove stands restored by the single planting of mangroves species would be lowered due to residual stressors. The photosynthetic parameters of the vegetation of three planted mangrove stands, each with a different disturbance history, were compared to reference sites and correlated with edaphic environmental variables. A permutational analysis of variance showed significant interaction when the factors were compared, indicating that the photosynthetic parameters of the restoration areas differed from the reference sites. A univariate analysis of variance showed that all the photosynthetic parameters differed between sites and treatments, except for photosynthetic efficiency (α{sub ETR}). The combination of environmental variables that best explained the variations observed in the photosynthetic performance indicators were Cu, Pb and elevation disruptions. Fluorescence techniques proved efficient in revealing important physiological differences, representing a powerful tool for rapid analysis of the effectiveness of initiatives aimed at restoring coastal environments. -- Highlights: •Photosynthetic efficiency of natural and restored mangroves are compared. •Natural stands present higher photosynthetic performance. •Photosynthetic performance of mangroves is reduced due to Cu and Pb contamination. •Chlorophyll a fluorescence is a useful indicator to assess short-term restoration. -- Photosynthetic performance of mangroves is reduced due to Cu and Pb contamination.

  2. How well do growing season dynamics of photosynthetic capacity correlate with leaf biochemistry and climate fluctuations?

    Science.gov (United States)

    Way, Danielle A; Stinziano, Joseph R; Berghoff, Henry; Oren, Ram

    2017-07-01

    Accurate values of photosynthetic capacity are needed in Earth System Models to predict gross primary productivity. Seasonal changes in photosynthetic capacity in these models are primarily driven by temperature, but recent work has suggested that photoperiod may be a better predictor of seasonal photosynthetic capacity. Using field-grown kudzu (Pueraria lobata (Willd.) Ohwi), a nitrogen-fixing vine species, we took weekly measurements of photosynthetic capacity, leaf nitrogen, and pigment and photosynthetic protein concentrations and correlated these with temperature, irradiance and photoperiod over the growing season. Photosynthetic capacity was more strongly correlated with photoperiod than with temperature or daily irradiance, while the growing season pattern in photosynthetic capacity was uncoupled from changes in leaf nitrogen, chlorophyll and Rubisco. Daily estimates of the maximum carboxylation rate of Rubisco (Vcmax) based on either photoperiod or temperature were correlated in a non-linear manner, but Vcmax estimates from both approaches that also accounted for diurnal temperature fluctuations were similar, indicating that differences between these models depend on the relevant time step. We advocate for considering photoperiod, and not just temperature, when estimating photosynthetic capacity across the year, particularly as climate change alters temperatures but not photoperiod. We also caution that the use of leaf biochemical traits as proxies for estimating photosynthetic capacity may be unreliable when the underlying relationships between proxy leaf traits and photosynthetic capacity are established outside of a seasonal framework. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  3. Direct measurements of the light dependence of gross photosynthesis and oxygen consumption in the ocean

    Science.gov (United States)

    Bailleul, B.; Park, J.; Brown, C. M.; Bidle, K. D.; Lee, S.; Falkowski, P. G.

    2016-02-01

    For decades, a lack of understanding of how respiration is influenced by light has been stymying our ability to quantitatively analyze how phytoplankton allocate carbon in situ and the biological mechanisms that participate to the fate of blooms. Using membrane inlet mass spectrometry (MIMS), the light dependencies of gross photosynthesis and oxygen uptake rates were measured during the bloom demises of two prymnesiophytes, in two open ocean regions. In the North Atlantic, dominated by Emiliania huxleyi, respiration was independent of irradiance and was higher than the gross photosynthetic rate at all irradiances. In the Amundsen Sea (Antarctica), dominated by Phaeocystis antarctica, the situation was very different. Dark respiration was one order of magnitude lower than the maximal gross photosynthetic rate. ut the oxygen uptake rate increased by 10 fold at surface irradiances, where it becomes higher than gross photosynthesis. Our results suggest that the light dependence of oxygen uptake in P. antarctica has two sources: one is independent of photosynthesis, and is possibly associated with the photo-reduction of O2 mediated by dissolved organic matter; the second reflects the activity of an oxidase fueled in the light with photosynthetic electron flow. Interestingly, these dramatic light-dependent changes in oxygen uptake were not reproduced in nutrient-replete P. antarctica cultures, in the laboratory. Our measurements highlight the importance of improving our understanding of oxygen consuming reactions in the euphotic zone, which is critical to investigating the physiology of phytoplankton and tracing the fate of phytoplankton blooms.

  4. Diversity, evolution, and therapeutic applications of small RNAs in prokaryotic and eukaryotic immune systems

    Science.gov (United States)

    Cooper, Edwin L.; Overstreet, Nicola

    2014-03-01

    Recent evidence supports that prokaryotes exhibit adaptive immunity in the form of CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) and Cas (CRISPR associated proteins). The CRISPR-Cas system confers resistance to exogenous genetic elements such as phages and plasmids by allowing for the recognition and silencing of these genetic elements. Moreover, CRISPR-Cas serves as a memory of past exposures. This suggests that the evolution of the immune system has counterparts among the prokaryotes, not exclusively among eukaryotes. Mathematical models have been proposed which simulate the evolutionary patterns of CRISPR, however large gaps in our understanding of CRISPR-Cas function and evolution still exist. The CRISPR-Cas system is analogous to small RNAs involved in resistance mechanisms throughout the tree of life, and a deeper understanding of the evolution of small RNA pathways is necessary before the relationship between these convergent systems is to be determined. Presented in this review are novel RNAi therapies based on CRISPR-Cas analogs and the potential for future therapies based on CRISPR-Cas system components.

  5. Establishing homology between mitochondrial calcium uniporters, prokaryotic magnesium channels and chlamydial IncA proteins.

    Science.gov (United States)

    Lee, Andre; Vastermark, Ake; Saier, Milton H

    2014-08-01

    Mitochondrial calcium uniporters (MCUs) (TC no. 1.A.77) are oligomeric channel proteins found in the mitochondrial inner membrane. MCUs have two well-conserved transmembrane segments (TMSs), connected by a linker, similar to bacterial MCU homologues. These proteins and chlamydial IncA proteins (of unknown function; TC no. 9.B.159) are homologous to prokaryotic Mg(2+) transporters, AtpI and AtpZ, based on comparison scores of up to 14.5 sds. A phylogenetic tree containing all of these proteins showed that the AtpZ proteins cluster coherently as a subset within the large and diverse AtpI cluster, which branches separately from the MCUs and IncAs, both of which cluster coherently. The MCUs and AtpZs share the same two TMS topology, but the AtpIs have four TMSs, and IncAs can have either two (most frequent) or four (less frequent) TMSs. Binary alignments, comparison scores and motif analyses showed that TMSs 1 and 2 align with TMSs 3 and 4 of the AtpIs, suggesting that the four TMS AtpI proteins arose via an intragenic duplication event. These findings establish an evolutionary link interconnecting eukaryotic and prokaryotic Ca(2+) and Mg(2+) transporters with chlamydial IncAs, and lead us to suggest that all members of the MCU superfamily, including IncAs, function as divalent cation channels. © 2014 The Authors.

  6. [Characterization of the Structure of the Prokaryotic Complex of Antarctic Permafrost by Molecular Genetic Techniques].

    Science.gov (United States)

    Manucharova, N A; Trosheva, E V; Kol'tsova, E M; Demkina, E V; Karaevskaya, E V; Rivkina, E M; Mardanov, A V; El'-Registan, G I

    2016-01-01

    A prokaryotic mesophilic organotrophic community responsible for 10% of the total microbial number determined by epifluorescence microscopy was reactivated in the samples ofAntarctic permafrost retrieved from the environment favoring long-term preservation of microbial communities (7500 years). No culturable forms were obtained without resuscitation procedures (CFU = 0). Proteobacteria, Actinobacteria, and Firmicutes were the dominant microbial groups in the complex. Initiation of the reactivated microbial complex by addition of chitin (0.1% wt/vol) resulted in an increased share of metabolically active biomass (up to 50%) due to the functional domination of chitinolytics caused by the target resource. Thus, sequential application of resuscitation procedures and initiation of a specific physiological group (in this case, chitinolytics) to a permafrost-preserved microbial community made it possible to reveal a prokaryotic complex capable of reversion of metabolic activity (FISH data), to determine its phylogenetic structure by metagenomic anal-ysis, and to isolate a pure culture of the dominant microorganism with high chitinolytic activity.

  7. Prokaryotic Phylogenies Inferred from Whole-Genome Sequence and Annotation Data

    Directory of Open Access Journals (Sweden)

    Wei Du

    2013-01-01

    Full Text Available Phylogenetic trees are used to represent the evolutionary relationship among various groups of species. In this paper, a novel method for inferring prokaryotic phylogenies using multiple genomic information is proposed. The method is called CGCPhy and based on the distance matrix of orthologous gene clusters between whole-genome pairs. CGCPhy comprises four main steps. First, orthologous genes are determined by sequence similarity, genomic function, and genomic structure information. Second, genes involving potential HGT events are eliminated, since such genes are considered to be the highly conserved genes across different species and the genes located on fragments with abnormal genome barcode. Third, we calculate the distance of the orthologous gene clusters between each genome pair in terms of the number of orthologous genes in conserved clusters. Finally, the neighbor-joining method is employed to construct phylogenetic trees across different species. CGCPhy has been examined on different datasets from 617 complete single-chromosome prokaryotic genomes and achieved applicative accuracies on different species sets in agreement with Bergey's taxonomy in quartet topologies. Simulation results show that CGCPhy achieves high average accuracy and has a low standard deviation on different datasets, so it has an applicative potential for phylogenetic analysis.

  8. Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining

    KAUST Repository

    Boudellioua, Imene; Saidi, Rabie; Hoehndorf, Robert; Martin, Maria J.; Solovyev, Victor

    2016-01-01

    The widening gap between known proteins and their functions has encouraged the development of methods to automatically infer annotations. Automatic functional annotation of proteins is expected to meet the conflicting requirements of maximizing annotation coverage, while minimizing erroneous functional assignments. This trade-off imposes a great challenge in designing intelligent systems to tackle the problem of automatic protein annotation. In this work, we present a system that utilizes rule mining techniques to predict metabolic pathways in prokaryotes. The resulting knowledge represents predictive models that assign pathway involvement to UniProtKB entries. We carried out an evaluation study of our system performance using cross-validation technique. We found that it achieved very promising results in pathway identification with an F1-measure of 0.982 and an AUC of 0.987. Our prediction models were then successfully applied to 6.2 million UniProtKB/TrEMBL reference proteome entries of prokaryotes. As a result, 663,724 entries were covered, where 436,510 of them lacked any previous pathway annotations.

  9. A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs

    Directory of Open Access Journals (Sweden)

    Guoqin Mai

    2016-01-01

    Full Text Available Motivation. Clustered regularly interspaced short palindromic repeat (CRISPR is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals. Results. This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition is proposed to cover all the CRISPRs. The comprehensive comparison of CRISPR numbers on the taxonomic levels of both domains and genus shows high variations for closely related species even in the same genus. The detailed investigation of how CRISPRs are evolutionarily manipulated in the 8 completely sequenced species in the genus Thermoanaerobacter demonstrates that transposons act as a frequent tool for splitting long CRISPRs into shorter ones along a long evolutionary history.

  10. Prokaryotic community composition in alkaline-fermented skate (Raja pulchra).

    Science.gov (United States)

    Jang, Gwang Il; Kim, Gahee; Hwang, Chung Yeon; Cho, Byung Cheol

    2017-02-01

    Prokaryotes were extracted from skates and fermented skates purchased from fish markets and a local manufacturer in South Korea. The prokaryotic community composition of skates and fermented skates was investigated using 16S rRNA pyrosequencing. The ranges for pH and salinity of the grinded tissue extract from fermented skates were 8.4-8.9 and 1.6-6.6%, respectively. Urea and ammonia concentrations were markedly low and high, respectively, in fermented skates compared to skates. Species richness was increased in fermented skates compared to skates. Dominant and predominant bacterial groups present in the fermented skates belonged to the phylum Firmicutes, whereas those in skates belonged to Gammaproteobacteria. The major taxa found in Firmicutes were Atopostipes (Carnobacteriaceae, Lactobacillales) and/or Tissierella (Tissierellaceae, Tissierellales). A combination of RT-PCR and pyrosequencing for active bacterial composition showed that the dominant taxa i.e., Atopostipes and Tissierella, were active in fermented skate. Those dominant taxa are possibly marine lactic acid bacteria. Marine bacteria of the taxa Lactobacillales and/or Clostridia seem to be important in alkaline fermentation of skates. Copyright © 2016 Elsevier Ltd. All rights reserved.

  11. Resilience of the prokaryotic microbial community of Acropora digitifera to elevated temperature.

    Science.gov (United States)

    Gajigan, Andrian P; Diaz, Leomir A; Conaco, Cecilia

    2017-08-01

    The coral is a holobiont formed by the close interaction between the coral animal and a diverse community of microorganisms, including dinoflagellates, bacteria, archaea, fungi, and viruses. The prokaryotic symbionts of corals are important for host fitness but are also highly sensitive to changes in the environment. In this study, we used 16S ribosomal RNA (rRNA) sequencing to examine the response of the microbial community associated with the coral, Acropora digitifera, to elevated temperature. The A. digitifera microbial community is dominated by operational taxonomic unit (OTUs) affiliated with classes Alphaproteobacteria and Gammaproteobacteria. The prokaryotic community in the coral tissue is distinct from that of the mucus and the surrounding seawater. Remarkably, the overall microbial community structure of A. digitifera remained stable for 10 days of continuous exptosure at 32°C compared to corals maintained at 27°C. However, the elevated temperature regime resulted in a decrease in the abundance of OTUs affiliated with certain groups of bacteria, such as order Rhodobacterales. On the other hand, some OTUs affiliated with the orders Alteromonadales, Vibrionales, and Flavobacteriales, which are often associated with diseased and stressed corals, increased in abundance. Thus, while the A. digitifera bacterial community structure appears resilient to higher temperature, prolonged exposure and intensified stress results in changes in the abundance of specific microbial community members that may affect the overall metabolic state and health of the coral holobiont. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

  12. Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes

    Directory of Open Access Journals (Sweden)

    Wang Guang-Zhong

    2010-08-01

    Full Text Available Abstract Background Among bacteria and archaea, amino acid usage is correlated with habitat temperatures. In particular, protein surfaces in species thriving at higher temperatures appear to be enriched in amino acids that stabilize protein structure and depleted in amino acids that decrease thermostability. Does this observation reflect a causal relationship, or could the apparent trend be caused by phylogenetic relatedness among sampled organisms living at different temperatures? And do proteins from endothermic and exothermic vertebrates show similar differences? Results We find that the observed correlations between the frequencies of individual amino acids and prokaryotic habitat temperature are strongly influenced by evolutionary relatedness between the species analysed; however, a proteome-wide bias towards increased thermostability remains after controlling for phylogeny. Do eukaryotes show similar effects of thermal adaptation? A small shift of amino acid usage in the expected direction is observed in endothermic ('warm-blooded' mammals and chicken compared to ectothermic ('cold-blooded' vertebrates with lower body temperatures; this shift is not simply explained by nucleotide usage biases. Conclusion Protein homologs operating at different temperatures have different amino acid composition, both in prokaryotes and in vertebrates. Thus, during the transition from ectothermic to endothermic life styles, the ancestors of mammals and of birds may have experienced weak genome-wide positive selection to increase the thermostability of their proteins.

  13. New Insight Into the Diversity of SemiSWEET Sugar Transporters and the Homologs in Prokaryotes

    Directory of Open Access Journals (Sweden)

    Baolei Jia

    2018-05-01

    Full Text Available Sugars will eventually be exported transporters (SWEETs and SemiSWEETs represent a family of sugar transporters in eukaryotes and prokaryotes, respectively. SWEETs contain seven transmembrane helices (TMHs, while SemiSWEETs contain three. The functions of SemiSWEETs are less studied. In this perspective article, we analyzed the diversity and conservation of SemiSWEETs and further proposed the possible functions. 1,922 SemiSWEET homologs were retrieved from the UniProt database, which is not proportional to the sequenced prokaryotic genomes. However, these proteins are very diverse in sequences and can be classified into 19 clusters when >50% sequence identity is required. Moreover, a gene context analysis indicated that several SemiSWEETs are located in the operons that are related to diverse carbohydrate metabolism. Several proteins with seven TMHs can be found in bacteria, and sequence alignment suggested that these proteins in bacteria may be formed by the duplication and fusion. Multiple sequence alignments showed that the amino acids for sugar translocation are still conserved and coevolved, although the sequences show diversity. Among them, the functions of a few amino acids are still not clear. These findings highlight the challenges that exist in SemiSWEETs and provide future researchers the foundation to explore these uncharted areas.

  14. Deep-biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts.

    Science.gov (United States)

    Bengtson, S; Ivarsson, M; Astolfo, A; Belivanova, V; Broman, C; Marone, F; Stampanoni, M

    2014-11-01

    The deep biosphere of the subseafloor crust is believed to contain a significant part of Earth's biomass, but because of the difficulties of directly observing the living organisms, its composition and ecology are poorly known. We report here a consortium of fossilized prokaryotic and eukaryotic micro-organisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 m below seafloor (mbsf). Fungal hyphae provide the framework on which prokaryote-like organisms are suspended like cobwebs and iron-oxidizing bacteria form microstromatolites (Frutexites). The spatial inter-relationships show that the organisms were living at the same time in an integrated fashion, suggesting symbiotic interdependence. The community is contemporaneous with secondary mineralizations of calcite partly filling the cavities. The fungal hyphae frequently extend into the calcite, indicating that they were able to bore into the substrate through mineral dissolution. A symbiotic relationship with chemoautotrophs, as inferred for the observed consortium, may be a pre-requisite for the eukaryotic colonization of crustal rocks. Fossils thus open a window to the extant as well as the ancient deep biosphere. © 2014 The Authors. Geobiology Published by John Wiley & Sons Ltd.

  15. Prokaryotic diversity, composition structure, and phylogenetic analysis of microbial communities in leachate sediment ecosystems.

    Science.gov (United States)

    Liu, Jingjing; Wu, Weixiang; Chen, Chongjun; Sun, Faqian; Chen, Yingxu

    2011-09-01

    In order to obtain insight into the prokaryotic diversity and community in leachate sediment, a culture-independent DNA-based molecular phylogenetic approach was performed with archaeal and bacterial 16S rRNA gene clone libraries derived from leachate sediment of an aged landfill. A total of 59 archaeal and 283 bacterial rDNA phylotypes were identified in 425 archaeal and 375 bacterial analyzed clones. All archaeal clones distributed within two archaeal phyla of the Euryarchaeota and Crenarchaeota, and well-defined methanogen lineages, especially Methanosaeta spp., are the most numerically dominant species of the archaeal community. Phylogenetic analysis of the bacterial library revealed a variety of pollutant-degrading and biotransforming microorganisms, including 18 distinct phyla. A substantial fraction of bacterial clones showed low levels of similarity with any previously documented sequences and thus might be taxonomically new. Chemical characteristics and phylogenetic inferences indicated that (1) ammonium-utilizing bacteria might form consortia to alleviate or avoid the negative influence of high ammonium concentration on other microorganisms, and (2) members of the Crenarchaeota found in the sediment might be involved in ammonium oxidation. This study is the first to report the composition of the microbial assemblages and phylogenetic characteristics of prokaryotic populations extant in leachate sediment. Additional work on microbial activity and contaminant biodegradation remains to be explored.

  16. Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining

    KAUST Repository

    Boudellioua, Imene

    2016-07-08

    The widening gap between known proteins and their functions has encouraged the development of methods to automatically infer annotations. Automatic functional annotation of proteins is expected to meet the conflicting requirements of maximizing annotation coverage, while minimizing erroneous functional assignments. This trade-off imposes a great challenge in designing intelligent systems to tackle the problem of automatic protein annotation. In this work, we present a system that utilizes rule mining techniques to predict metabolic pathways in prokaryotes. The resulting knowledge represents predictive models that assign pathway involvement to UniProtKB entries. We carried out an evaluation study of our system performance using cross-validation technique. We found that it achieved very promising results in pathway identification with an F1-measure of 0.982 and an AUC of 0.987. Our prediction models were then successfully applied to 6.2 million UniProtKB/TrEMBL reference proteome entries of prokaryotes. As a result, 663,724 entries were covered, where 436,510 of them lacked any previous pathway annotations.

  17. Comparative genomic analyses of copper transporters and cuproproteomes reveal evolutionary dynamics of copper utilization and its link to oxygen.

    Directory of Open Access Journals (Sweden)

    Perry G Ridge

    2008-01-01

    Full Text Available Copper is an essential trace element in many organisms and is utilized in all domains of life. It is often used as a cofactor of redox proteins, but is also a toxic metal ion. Intracellular copper must be carefully handled to prevent the formation of reactive oxygen species which pose a threat to DNA, lipids, and proteins. In this work, we examined patterns of copper utilization in prokaryotes by analyzing the occurrence of copper transporters and copper-containing proteins. Many organisms, including those that lack copper-dependent proteins, had copper exporters, likely to protect against copper ions that inadvertently enter the cell. We found that copper use is widespread among prokaryotes, but also identified several phyla that lack cuproproteins. This is in contrast to the use of other trace elements, such as selenium, which shows more scattered and reduced usage, yet larger selenoproteomes. Copper transporters had different patterns of occurrence than cuproproteins, suggesting that the pathways of copper utilization and copper detoxification are independent of each other. We present evidence that organisms living in oxygen-rich environments utilize copper, whereas the majority of anaerobic organisms do not. In addition, among copper users, cuproproteomes of aerobic organisms were larger than those of anaerobic organisms. Prokaryotic cuproproteomes were small and dominated by a single protein, cytochrome c oxidase. The data are consistent with the idea that proteins evolved to utilize copper following the oxygenation of the Earth.

  18. Photosynthetic performance of restored and natural mangroves under different environmental constraints.

    Science.gov (United States)

    Rovai, André Scarlate; Barufi, José Bonomi; Pagliosa, Paulo Roberto; Scherner, Fernando; Torres, Moacir Aluísio; Horta, Paulo Antunes; Simonassi, José Carlos; Quadros, Daiane Paula Cunha; Borges, Daniel Lázaro Gallindo; Soriano-Sierra, Eduardo Juan

    2013-10-01

    We hypothesized that the photosynthetic performance of mangrove stands restored by the single planting of mangroves species would be lowered due to residual stressors. The photosynthetic parameters of the vegetation of three planted mangrove stands, each with a different disturbance history, were compared to reference sites and correlated with edaphic environmental variables. A permutational analysis of variance showed significant interaction when the factors were compared, indicating that the photosynthetic parameters of the restoration areas differed from the reference sites. A univariate analysis of variance showed that all the photosynthetic parameters differed between sites and treatments, except for photosynthetic efficiency (αETR). The combination of environmental variables that best explained the variations observed in the photosynthetic performance indicators were Cu, Pb and elevation disruptions. Fluorescence techniques proved efficient in revealing important physiological differences, representing a powerful tool for rapid analysis of the effectiveness of initiatives aimed at restoring coastal environments. Copyright © 2013 Elsevier Ltd. All rights reserved.

  19. Cyanobacteria in sulfidic spring microbial mats can perform oxygenic and anoxygenic photosynthesis simultaneously during an entire diurnal period

    Directory of Open Access Journals (Sweden)

    Judith M Klatt

    2016-12-01

    Full Text Available We used microsensors to study the regulation of oxygenic and anoxygenic photosynthesis by light and sulfide in a cyanobacterium dominating microbial mats from cold sulfidic springs. Both photosynthetic modes were performed simultaneously over all H2S concentrations (1–2200 µM and irradiances (4–52 µmol photons m-2 s-1 tested. Anoxygenic photosynthesis increased with H2S concentration while the sum of oxygenic and anoxygenic photosynthetic rates was constant at each light intensity. Thus, the total photosynthetically driven electron transport rate was solely controlled by the irradiance level. The partitioning between the rates of these two photosynthetic modes was regulated by both light and H2S concentration. The plastoquinone pool (PQ receives electrons from sulfide:quinone:reductase (SQR in anoxygenic photosynthesis and from photosystem II (PSII in oxygenic photosynthesis. It is thus the link in the electron transport chain where both pathways intersect, and the compound that controls their partitioning. We fitted our data with a model of the photosynthetic electron transport that includes the kinetics of plastoquinone reduction and oxidation. The model results confirmed that the observed partitioning between photosynthetic modes can be explained by a simple kinetic control based on the affinity of SQR and PSII towards PQ. The SQR enzyme and PSII have similar affinities towards PQ, which explains the concurrent oxygenic and anoxygenic photosynthesis over an astonishingly wide range of H2S concentrations and irradiances. The elegant kinetic control of activity makes the cyanobacterium successful in the fluctuating spring environment. We discuss how these specific regulation mechanisms may have played a role in ancient H2S-rich oceans.

  20. Functional Mitochondrial Complex I Is Required by Tobacco Leaves for Optimal Photosynthetic Performance in Photorespiratory Conditions and during Transients1

    Science.gov (United States)

    Dutilleul, Christelle; Driscoll, Simon; Cornic, Gabriel; De Paepe, Rosine; Foyer, Christine H.; Noctor, Graham

    2003-01-01

    The importance of the mitochondrial electron transport chain in photosynthesis was studied using the tobacco (Nicotiana sylvestris) mutant CMSII, which lacks functional complex I. Rubisco activities and oxygen evolution at saturating CO2 showed that photosynthetic capacity in the mutant was at least as high as in wild-type (WT) leaves. Despite this, steady-state photosynthesis in the mutant was reduced by 20% to 30% at atmospheric CO2 levels. The inhibition of photosynthesis was alleviated by high CO2 or low O2. The mutant showed a prolonged induction of photosynthesis, which was exacerbated in conditions favoring photorespiration and which was accompanied by increased extractable NADP-malate dehydrogenase activity. Feeding experiments with leaf discs demonstrated that CMSII had a lower capacity than the WT for glycine (Gly) oxidation in the dark. Analysis of the postillumination burst in CO2 evolution showed that this was not because of insufficient Gly decarboxylase capacity. Despite the lower rate of Gly metabolism in CMSII leaves in the dark, the Gly to Ser ratio in the light displayed a similar dependence on photosynthesis to the WT. It is concluded that: (a) Mitochondrial complex I is required for optimal photosynthetic performance, despite the operation of alternative dehydrogenases in CMSII; and (b) complex I is necessary to avoid redox disruption of photosynthesis in conditions where leaf mitochondria must oxidize both respiratory and photorespiratory substrates simultaneously. PMID:12529534

  1. PS2013 Satellite Workshop on Photosynthetic Light-Harvesting Systems

    Energy Technology Data Exchange (ETDEWEB)

    Niederman, Robert A. [Rutgers Univ., New Brunswick, NJ (United States); Blankenship, Robert E. [Washington Univ., St. Louis, MO (United States); Frank, Harry A. [Univ. of Connecticut, Storrs, CT (United States)

    2015-02-07

    These funds were used for partial support of the PS2013 Satellite Workshop on Photosynthetic Light-Harvesting Systems, that was held on 8-11 August, 2013, at Washington University, St. Louis, MO. This conference, held in conjunction with the 16th International Congress on Photosynthesis/St. Louis, continued a long tradition of light-harvesting satellite conferences that have been held prior to the previous six international photosynthesis congresses. In this Workshop, the basis was explored for the current interest in replacing fossil fuels with energy sources derived form direct solar radiation, coupled with light-driven electron transport in natural photosynthetic systems and how they offer a valuable blueprint for conversion of sunlight to useful energy forms. This was accomplished through sessions on the initial light-harvesting events in the biological conversion of solar energy to chemically stored energy forms, and how these natural photosynthetic processes serve as a guide to the development of robust bio-hybrid and artificial systems for solar energy conversion into both electricity or chemical fuels. Organized similar to a Gordon Research Conference, a lively, informal and collegial setting was established, highlighting the exchange of exciting new data and unpublished results from ongoing studies. A significant amount of time was set aside for open discussion and interactive poster sessions, with a special session devoted to oral presentations by talented students and postdoctoral fellows judged to have the best posters. This area of research has seen exceptionally rapid progress in recent years, with the availability of a number of antenna protein structures at atomic resolution, elucidation of the molecular surface architecture of native photosynthetic membranes by atomic force microscopy and the maturing of ultrafast spectroscopic and molecular biological techniques for the investigation and manipulation of photosynthetic systems. The conferees

  2. Revealing Linear Aggregates of Light Harvesting Antenna Proteins in Photosynthetic Membranes

    OpenAIRE

    He, Yufan; Zeng, Xiaohua; Mukherjee, Saptarshi; Rajapaksha, Suneth; Kaplan, Samuel; Lu, H. Peter

    2010-01-01

    How light energy is harvested in a natural photosynthetic membrane through energy transfer is closely related to the stoichiometry and arrangement of light harvesting antenna proteins in the membrane. The specific photosynthetic architecture facilitates a rapid and efficient energy transfer among the light harvesting proteins (LH2 and LH1) and to the reaction center. Here we report the identification of linear aggregates of light harvesting proteins, LH2, in the photosynthetic membranes under...

  3. Photoperiodic controls on ecosystem-level photosynthetic capacity

    Science.gov (United States)

    Stoy, P. C.; Trowbridge, A. M.; Bauerle, W.

    2012-12-01

    Most models of photosynthesis at the leaf or canopy level assume that temperature is the dominant control on the variability of photosynthetic parameters. Recent studies, however, have found that photoperiod is a better descriptor of the seasonal variability of photosynthetic function at the leaf and plant scale, and that spectral indices of leaf functionality are poor descriptors of this seasonality. We explored the variability of photosynthesic parameters at the ecosystem scale using over 100 site-years of air temperature and gross primary productivity (GPP) data from non-tropical forested sites in the Free/Fair Use LaThuille FLUXNET database (www.fluxdata.org), excluding sites that were classified as dry and/or with savanna vegetation, where we expected GPP to be driven by moisture availability. Both GPP and GPP normalized by daily photosynthetic photon flux density (GPPn) were considered, and photoperiod was calculated from eddy covariance tower coordinates. We performed a Granger causality analysis, a method based on the understanding that causes precede effects, on both the GPP and GPPn. Photoperiod Granger-caused GPP (GPPn) in 95% (87%) of all site-years. While temperature Granger-caused GPP in a mere 23% of site years, it Granger-caused GPPn 73% of the time. Both temperature values are significantly less than the percent of cases in which day length Granger-caused GPP (p<0.05, Student's t-test). An inverse analysis was performed for completeness, and it was found that GPP Granger-caused photoperiod (temperature) in 39% (78%) of all site years. Results demonstrate that incorporating simple photoperiod controls may be a logical step in improving ecosystem and global model output.

  4. Cyanobacteria in sulfidic spring microbial mats can perform oxygenic and anoxygenic photosynthesis simultaneously during an entire diurnal period

    NARCIS (Netherlands)

    Klatt, Judith M.; de Beer, Dirk; Häusler, Stefan; Polerecky, Lubos|info:eu-repo/dai/nl/370827929

    2016-01-01

    We used microsensors to study the regulation of anoxygenic and oxygenic photosynthesis (AP and OP, respectively) by light and sulfide in a cyanobacterium dominating microbial mats from cold sulfidic springs. Both photosynthetic modes were performed simultaneously over all H2S concentrations (1–2200

  5. Effects of ultraviolet radiation (UVA+UVB) on young gametophytes of Gelidium floridanum: growth rate, photosynthetic pigments, carotenoids, photosynthetic performance, and ultrastructure.

    Science.gov (United States)

    Simioni, Carmen; Schmidt, Eder C; Felix, Marthiellen R de L; Polo, Luz Karime; Rover, Ticiane; Kreusch, Marianne; Pereira, Debora T; Chow, Fungyi; Ramlov, Fernanda; Maraschin, Marcelo; Bouzon, Zenilda L

    2014-01-01

    This study investigated the effects of radiation (PAR+UVA+UVB) on the development and growth rates (GRs) of young gametophytes of Gelidium floridanum. In addition, photosynthetic pigments were quantified, carotenoids identified, and photosynthetic performance assessed. Over a period of 3 days, young gametophytes were cultivated under laboratory conditions and exposed to photosynthetically active radiation (PAR) at 80 μmol photons m(-2) s(-1) and PAR+UVA (0.70 W m(-2))+UVB (0.35 W m(-2)) for 3 h per day. The samples were processed for light and electron microscopy to analyze the ultrastructure features, as well as carry out metabolic studies of GRs, quantify the content of photosynthetic pigments, identify carotenoids and assess photosynthetic performance. PAR+UVA+UVB promoted increase in cell wall thickness, accumulation of floridean starch grains in the cytoplasm and disruption of chloroplast internal organization. Algae exposed to PAR+UVA+UVB also showed a reduction in GR of 97%. Photosynthetic pigments, in particular, phycoerythrin and allophycocyanin contents, decreased significantly from UV radiation exposure. This result agrees with the decrease in photosynthetic performance observed after exposure to ultraviolet radiation, as measured by a decrease in the electron transport rate (ETR), where values of ETRmax declined approximately 44.71%. It can be concluded that radiation is a factor that affects the young gametophytes of G. floridanum at this stage of development. © 2014 The American Society of Photobiology.

  6. Response of Lemna minor L. to short-term cobalt exposure: The effect on photosynthetic electron transport chain and induction of oxidative damage

    Energy Technology Data Exchange (ETDEWEB)

    Begović, Lidija, E-mail: lbegovic@biologija.unios.hr [Josip Juraj Strossmayer University of Osijek, Department of Biology, Ulica cara Hadrijana 8/A, H R -31000 Osijek (Croatia); Mlinarić, Selma, E-mail: smlinaric@biologija.unios.hr [Josip Juraj Strossmayer University of Osijek, Department of Biology, Ulica cara Hadrijana 8/A, H R -31000 Osijek (Croatia); Antunović Dunić, Jasenka, E-mail: jantunovic@biologija.unios.hr [Josip Juraj Strossmayer University of Osijek, Department of Biology, Ulica cara Hadrijana 8/A, H R -31000 Osijek (Croatia); Katanić, Zorana, E-mail: zkatanic@biologija.unios.hr [Josip Juraj Strossmayer University of Osijek, Department of Biology, Ulica cara Hadrijana 8/A, H R -31000 Osijek (Croatia); Lončarić, Zdenko, E-mail: zdenko.loncaric@pfos.hr [Faculty of Agriculture, Josip Juraj Strossmayer University of Osijek, Ulica kralja Petra Svačića 1d, H R -31000 Osijek (Croatia); Lepeduš, Hrvoje, E-mail: hlepedus@yahoo.com [Faculty of Humanities and Social Sciences, Josip Juraj Strossmayer University of Osijek, Lorenza Jägera 9, HR-31000 Osijek (Croatia); Cesar, Vera, E-mail: vcesarus@yahoo.com [Josip Juraj Strossmayer University of Osijek, Department of Biology, Ulica cara Hadrijana 8/A, H R -31000 Osijek (Croatia)

    2016-06-15

    Highlights: • Cobalt (Co{sup 2+}) impaired the function of oxygen evolving complex (OEC) in L. minor L. • Electron transport through PSII components varied depending on Co{sup 2+} concentration. • K-band was proven to be suitable parameter for investigation of Co{sup 2+} toxicity. • Increased lipid peroxidation level showed early oxidative damage induced by Co{sup 2+}. - Abstract: The effect of two concentrations of cobalt (Co{sup 2+}) on photosynthetic activity and antioxidative response in Lemna minor L. were assessed 24, 48 and 72 h after the start of the exposure. Higher concentration of cobalt (1 mM) induced growth inhibition while lower concentration (0.01 mM) increased photosynthetic pigments content. Analysis of chlorophyll a fluorescence transients revealed high sensitivity of photosystem II primary photochemistry to excess of Co{sup 2+} especially at the higher concentration where decreased electron transport beyond primary quinone acceptor Q{sub A}{sup −} and impaired function of oxygen evolving complex (OEC) was observed. Due to impairment of OEC, oxygen production was decreased at higher Co{sup 2+} concentration. Activity of superoxide dismutase was mainly inhibited while lipid peroxidation increased, at both concentrations, indicating that cobalt-induced oxidative damage after short exposure and moreover, susceptibility of the membranes in the cell to cobalt toxicity. Results obtained in this study suggest possible application of used parameters as tools in assessment of early damage caused by metals.

  7. Response of Lemna minor L. to short-term cobalt exposure: The effect on photosynthetic electron transport chain and induction of oxidative damage

    International Nuclear Information System (INIS)

    Begović, Lidija; Mlinarić, Selma; Antunović Dunić, Jasenka; Katanić, Zorana; Lončarić, Zdenko; Lepeduš, Hrvoje; Cesar, Vera

    2016-01-01

    Highlights: • Cobalt (Co"2"+) impaired the function of oxygen evolving complex (OEC) in L. minor L. • Electron transport through PSII components varied depending on Co"2"+ concentration. • K-band was proven to be suitable parameter for investigation of Co"2"+ toxicity. • Increased lipid peroxidation level showed early oxidative damage induced by Co"2"+. - Abstract: The effect of two concentrations of cobalt (Co"2"+) on photosynthetic activity and antioxidative response in Lemna minor L. were assessed 24, 48 and 72 h after the start of the exposure. Higher concentration of cobalt (1 mM) induced growth inhibition while lower concentration (0.01 mM) increased photosynthetic pigments content. Analysis of chlorophyll a fluorescence transients revealed high sensitivity of photosystem II primary photochemistry to excess of Co"2"+ especially at the higher concentration where decreased electron transport beyond primary quinone acceptor Q_A"− and impaired function of oxygen evolving complex (OEC) was observed. Due to impairment of OEC, oxygen production was decreased at higher Co"2"+ concentration. Activity of superoxide dismutase was mainly inhibited while lipid peroxidation increased, at both concentrations, indicating that cobalt-induced oxidative damage after short exposure and moreover, susceptibility of the membranes in the cell to cobalt toxicity. Results obtained in this study suggest possible application of used parameters as tools in assessment of early damage caused by metals.

  8. Reductive evolution of chloroplasts in non-photosynthetic plants, algae and protists.

    Science.gov (United States)

    Hadariová, Lucia; Vesteg, Matej; Hampl, Vladimír; Krajčovič, Juraj

    2018-04-01

    Chloroplasts are generally known as eukaryotic organelles whose main function is photosynthesis. They perform other functions, however, such as synthesizing isoprenoids, fatty acids, heme, iron sulphur clusters and other essential compounds. In non-photosynthetic lineages that possess plastids, the chloroplast genomes have been reduced and most (or all) photosynthetic genes have been lost. Consequently, non-photosynthetic plastids have also been reduced structurally. Some of these non-photosynthetic or "cryptic" plastids were overlooked or unrecognized for decades. The number of complete plastid genome sequences and/or transcriptomes from non-photosynthetic taxa possessing plastids is rapidly increasing, thus allowing prediction of the functions of non-photosynthetic plastids in various eukaryotic lineages. In some non-photosynthetic eukaryotes with photosynthetic ancestors, no traces of plastid genomes or of plastids have been found, suggesting that they have lost the genomes or plastids completely. This review summarizes current knowledge of non-photosynthetic plastids, their genomes, structures and potential functions in free-living and parasitic plants, algae and protists. We introduce a model for the order of plastid gene losses which combines models proposed earlier for land plants with the patterns of gene retention and loss observed in protists. The rare cases of plastid genome loss and complete plastid loss are also discussed.

  9. Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data

    Directory of Open Access Journals (Sweden)

    Lespinet Olivier

    2007-11-01

    Full Text Available Abstract Background Comparison of completely sequenced microbial genomes has revealed how fluid these genomes are. Detecting synteny blocks requires reliable methods to determining the orthologs among the whole set of homologs detected by exhaustive comparisons between each pair of completely sequenced genomes. This is a complex and difficult problem in the field of comparative genomics but will help to better understand the way prokaryotic genomes are evolving. Results We have developed a suite of programs that automate three essential steps to study conservation of gene order, and validated them with a set of 107 bacteria and archaea that cover the majority of the prokaryotic taxonomic space. We identified the whole set of shared homologs between two or more species and computed the evolutionary distance separating each pair of homologs. We applied two strategies to extract from the set of homologs a collection of valid orthologs shared by at least two genomes. The first computes the Reciprocal Smallest Distance (RSD using the PAM distances separating pairs of homologs. The second method groups homologs in families and reconstructs each family's evolutionary tree, distinguishing bona fide orthologs as well as paralogs created after the last speciation event. Although the phylogenetic tree method often succeeds where RSD fails, the reverse could occasionally be true. Accordingly, we used the data obtained with either methods or their intersection to number the orthologs that are adjacent in for each pair of genomes, the Positional Orthologous Genes (POGs, and to further study their properties. Once all these synteny blocks have been detected, we showed that POGs are subject to more evolutionary constraints than orthologs outside synteny groups, whichever the taxonomic distance separating the compared organisms. Conclusion The suite of programs described in this paper allows a reliable detection of orthologs and is useful for evaluating gene

  10. PSAT: A web tool to compare genomic neighborhoods of multiple prokaryotic genomes

    Directory of Open Access Journals (Sweden)

    Wasnick Michael

    2008-03-01

    Full Text Available Abstract Background The conservation of gene order among prokaryotic genomes can provide valuable insight into gene function, protein interactions, or events by which genomes have evolved. Although some tools are available for visualizing and comparing the order of genes between genomes of study, few support an efficient and organized analysis between large numbers of genomes. The Prokaryotic Sequence homology Analysis Tool (PSAT is a web tool for comparing gene neighborhoods among multiple prokaryotic genomes. Results PSAT utilizes a database that is preloaded with gene annotation, BLAST hit results, and gene-clustering scores designed to help identify regions of conserved gene order. Researchers use the PSAT web interface to find a gene of interest in a reference genome and efficiently retrieve the sequence homologs found in other bacterial genomes. The tool generates a graphic of the genomic neighborhood surrounding the selected gene and the corresponding regions for its homologs in each comparison genome. Homologs in each region are color coded to assist users with analyzing gene order among various genomes. In contrast to common comparative analysis methods that filter sequence homolog data based on alignment score cutoffs, PSAT leverages gene context information for homologs, including those with weak alignment scores, enabling a more sensitive analysis. Features for constraining or ordering results are designed to help researchers browse results from large numbers of comparison genomes in an organized manner. PSAT has been demonstrated to be useful for helping to identify gene orthologs and potential functional gene clusters, and detecting genome modifications that may result in loss of function. Conclusion PSAT allows researchers to investigate the order of genes within local genomic neighborhoods of multiple genomes. A PSAT web server for public use is available for performing analyses on a growing set of reference genomes through any

  11. Evolutionary consequences of polyploidy in prokaryotes and the origin of mitosis and meiosis.

    Science.gov (United States)

    Markov, Alexander V; Kaznacheev, Ilya S

    2016-06-08

    The origin of eukaryote-specific traits such as mitosis and sexual reproduction remains disputable. There is growing evidence that both mitosis and eukaryotic sex (i.e., the alternation of syngamy and meiosis) may have already existed in the basal eukaryotes. The mating system of the halophilic archaeon Haloferax volcanii probably represents an intermediate stage between typical prokaryotic and eukaryotic sex. H. volcanii is highly polyploid, as well as many other Archaea. Here, we use computer simulation to explore genetic and evolutionary outcomes of polyploidy in amitotic prokaryotes and its possible role in the origin of mitosis, meiosis and eukaryotic sex. Modeling suggests that polyploidy can confer strong short-term evolutionary advantage to amitotic prokaryotes. However, it also promotes the accumulation of recessive deleterious mutations and the risk of extinction in the long term, especially in highly mutagenic environment. There are several possible strategies that amitotic polyploids can use in order to reduce the genetic costs of polyploidy while retaining its benefits. Interestingly, most of these strategies resemble different components or aspects of eukaryotic sex. They include asexual ploidy cycles, equalization of genome copies by gene conversion, high-frequency lateral gene transfer between relatives, chromosome exchange coupled with homologous recombination, and the evolution of more accurate chromosome distribution during cell division (mitosis). Acquisition of mitosis by an amitotic polyploid results in chromosome diversification and specialization. Ultimately, it transforms a polyploid cell into a functionally monoploid one with multiple unique, highly redundant chromosomes. Specialization of chromosomes makes the previously evolved modes of promiscuous chromosome shuffling deleterious. This can result in selective pressure to develop accurate mechanisms of homolog pairing, and, ultimately, meiosis. Emergence of mitosis and the first

  12. The stereochemistry of chlorophyll-c₃ from the haptophyte Emiliania huxleyi: the (13²R)-enantiomers of chlorophylls-c are exclusively selected as the photosynthetically active pigments in chromophyte algae.

    Science.gov (United States)

    Mizoguchi, Tadashi; Kimura, Yuki; Yoshitomi, Taichi; Tamiaki, Hitoshi

    2011-11-01

    Chlorophyll(Chl)-c pigments in algae, diatoms and some prokaryotes are characterized by the fully conjugated porphyrin π-system as well as the acrylate residue at the 17-position. The precise structural characterization of Chl-c(3) from the haptophyte Emiliania huxleyi was performed. The conformations of the π-conjugated peripheral substituents, the 3-/8-vinyl, 7-methoxycarbonyl and 17-acrylate moieties were evaluated, in a solution, using nuclear Overhauser enhancement correlations and molecular modeling calculations. The rotation of the 17-acrylate residue was considerably restricted, whereas the other three substituents readily rotated at ambient temperature. Moreover, the stereochemistry at the 13²-position was determined by combination of chiral high-performance liquid chromatography (HPLC) with circular dichroism (CD) spectroscopy. Compared with the CD spectra of the structurally related, synthetic (13²R)- and (13²S)-protochlorophyllide(PChlide)-a, naturally occurring Chl-c₃ had exclusively the (13²R)-configuration. To elucidate this natural selection of a single enantiomer, we analyzed the three major Chl-c pigments (Chl-c₁, c₂ and c₃) in four phylogenetically distinct classes of Chl-c containing algae, i.e., heterokontophyta, dinophyta, cryptophyta and haptophyta using chiral HPLC. All the photosynthetic organisms contained only the (13²R)-enantiomerically pure Chls-c, and lacked the corresponding enantiomeric (13²S)-forms. Additionally, Chl-c₂ was found in all the organisms as the common Chl-c. These results throw a light on the biosynthesis as well as photosynthetic function of Chl-c pigments: Chl-c₂ is derived from 8-vinyl-PChlide-a by dehydrogenation of the 17-propionate to acrylate residues as generally proposed, and the (13²R)-enantiomers of Chls-c function as photosynthetically active, light-harvesting pigments together with the principal Chl-a and carotenoids. 2011 Elsevier B.V. All rights reserved.

  13. Artificial oxygen transport protein

    Science.gov (United States)

    Dutton, P. Leslie

    2014-09-30

    This invention provides heme-containing peptides capable of binding molecular oxygen at room temperature. These compounds may be useful in the absorption of molecular oxygen from molecular oxygen-containing atmospheres. Also included in the invention are methods for treating an oxygen transport deficiency in a mammal.

  14. Adaptive changes in chlorophyll content and photosynthetic features to low light in Physocarpus amurensis Maxim and Physocarpus opulifolius "Diabolo".

    Science.gov (United States)

    Zhang, Huihui; Zhong, Haixiu; Wang, Jifeng; Sui, Xin; Xu, Nan

    2016-01-01

    Physocarpus cultivars, and that the low light intensity significantly inhibited electron transfer on the acceptor side of PS II and reduced the activity of the oxygen-evolving complex (OEC) in the leaves of both Physocarpus cultivars. The PS II function in P. opulifolius "Diabolo" was higher than that in P. amurensis Maxim in response to low light. Under low light, the composition of photosynthetic pigments was altered in the leaves of P. opulifolius "Diabolo" in order to maintain a relatively high activity of primary photochemical reactions, and this is the basis of the greater photosynthetic carbon assimilation capacity and one of the main reasons for the better shade-tolerance in P. opulifolius "Diabolo."

  15. Biochemical factors affecting the quantum efficiency of hydrogen production by membranes of green photosynthetic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Bernstein, J.D.; Olson, J.M.

    1981-01-01

    Photohydrogen production, 200-700 ..mu..mol H/sub 2/ h/sup -1/ (mg bacteriochlorophyll a)/sup -1/ has been obtained in a system containing unit membrane vesicles (Complex I) from the green photosynthetic bacterium Chlorobium limicola f. thiosulfatophilum, ascorbate, N,N,N',N'-tetramethyl-p-phenylenediamine, dithioerythritol, an oxygen scavenging mixture, either methyl viologen (MV) or clostridial ferredoxin (CPS Fd) as electron carrier, and either CPS hydrogenase or platinum asbestos as catalyst. All components are necessary for maximum activity, and spinach Fd cannot be substituted for CPS Fd. Higher rates of photohydrogen production are obtained using MV or CPS Fd with hydrogenase than with MV and Pt asbestos. The highest quantum efficiencies (7-10% at 0.2-0.9 mW absorbed light and over 20% at lower light) were obtained with CPS Fd, hydrogenase and non-saturating 812 nm light. With saturating white light, however, rates of photohydrogen production varied relatively little among the various combinations of electron carrier and catalyst tested. The reaction rate is unaffected by 0.03% Triton X-100, and is insensitive to treatment with antimycin a or m-chloro-carbonyl cyanide phenylhydrazone.This indicates that neither electron flow through an endogenous cyclic chain, nor maintenance of a proton gradient are involved in this process.

  16. Reduced graphene oxide induces cytotoxicity and inhibits photosynthetic performance of the green alga Scenedesmus obliquus.

    Science.gov (United States)

    Du, Shaoting; Zhang, Peng; Zhang, Ranran; Lu, Qi; Liu, Lin; Bao, Xiaowei; Liu, Huijun

    2016-12-01

    Increased use of graphene materials might ultimately lead to their release into the environment. However, only a few studies have investigated the impact of graphene-based materials on green plants. In this study, the impact of reduced graphene oxide (RGO) on the microalgae Scenedesmus obliquus was evaluated to determine its phytotoxicity. Treatment with RGO suppressed the growth of the microalgae. The 72-h IC 50 values of RGO evaluated using the logistic and Gompertz models were 148 and 151 mg L -1 , respectively. RGO significantly inhibited Chl a and Chl a/b levels in the algal cells. Chlorophyll a fluorescence analysis showed that RGO significantly down-regulated photosystem II activity. The mechanism of how RGO inhibited algal growth and photosynthetic performance was determined by analyzing the alterations in ultrastructural morphology. RGO adhered to the algal cell surface as a semitranslucent coating. Cell wall damage and membrane integrity loss occurred in the treated cells. Moreover, nuclear chromatin clumping and starch grain number increase were noted. These changes might be attributed to the increase in malondialdehyde and reactive oxygen species levels, which might have exceeded the scavenging ability of antioxidant enzymes (including peroxidase and superoxide dismutase). RGO impaired the extra- and intra-cellular morphology and increased oxidative stress and thus inhibited algal growth and photosynthesis. Copyright © 2016 Elsevier Ltd. All rights reserved.

  17. Combined effects of graphene oxide and Cd on the photosynthetic capacity and survival of Microcystis aeruginosa

    Energy Technology Data Exchange (ETDEWEB)

    Tang, Yulin, E-mail: tangyulin@tongji.edu.cn; Tian, Jinglin; Li, Shuyan; Xue, Chonghua; Xue, Zhehua; Yin, Daqiang; Yu, Shuili

    2015-11-01

    In this work, the combined effects of graphene oxide (GO) and Cd{sup 2+} solution on Microcystis aeruginosa were investigated. Chlorophyll fluorescence parameters were measured by a pulse-amplitude modulated fluorometer. GO at low concentrations exhibited no significant toxicity. The presence of GO at low concentrations significantly enhanced Cd{sup 2+} toxicity as the 96 h half maximal effective concentration of the Cd{sup 2+} reduced from 0.51 ± 0.01 to 0.474 ± 0.01 mg/L. However, concentrations of GO above 5 mg/L did not significantly increase the toxicity of the Cd{sup 2+}/GO system. Observations through scanning and transmission electron microscopy revealed that GO, with Cd{sup 2+}, easily attached to and entered into the algae. Reactive oxygen species and malondialdehyde were measured to explain the toxicity mechanism. The photosynthetic parameters were useful in measuring the combined toxicity of the nanoparticles and heavy metals. - Highlights: • Combined effects of graphene oxide and Cd{sup 2+} to M. aeruginosa were investigated. • Chlorophyll fluorescence parameters were obtained by PAM. • OS and MDA were measured to evaluate algae toxicity. • GO at low concentration enhanced Cd{sup 2+} toxicity.

  18. [Biodegradation characteristics of o-chlorophenol with photosynthetic bacteria PSB-1D].

    Science.gov (United States)

    Hu, Xiao-min; Dong, Yi-hu; Li, Liang; Lu, Juan; He, Ying-dian; Gao, Yang

    2010-07-01

    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-chlorophenol degradation showed that the degradation rate of o-chlorophenol was up to 57.26% after 7 days cultural time. The main environmental factors including way of illumination and oxygen, initial pH, cultural temperature, illumination intensity had distinctly influenced on the o-chlorophenol degradation with PSB-1D. The results showed that the optimum conditions were as following: an anaerobic light, pH 7.0, temperature 30 degrees C, illumination intensity 4000 lx,initial o-chlorophenol concentration 50 mg/L. Under that cultural condition, the degradation rate of o-chlorophenol could reach to 62.08%. The degradation kinetic data fitted the Andrews model well. In addition, the biodegradation process of o-chlorophenol can be well described by enzymatic reaction of high concentration inhibition, with the maximum substrate utilization rate 0.309 d(-1), Michaelis-Menten constant 2.733 mg/L, inhibitory constant 230.15 mg/L respectively.

  19. Ferredoxin-thioredoxin reductase: a catalytically active dithiol group links photoreduced ferredoxin to thioredoxin functional in photosynthetic enzyme regulation

    International Nuclear Information System (INIS)

    Droux, M.; Miginiac-Maslow, M.; Jacquot, J.P.; Gadal, P.; Crawford, N.A.; Kosower, N.S.; Buchanan, B.B.

    1987-01-01

    The mechanism by which the ferredoxin-thioredoxin system activates the target enzyme, NADP-malate dehydrogenase, was investigated by analyzing the sulfhydryl status of individual protein components with [ 14 C]iodoacetate and monobromobimane. The data indicate that ferredoxin-thioredoxin reductase (FTR)--an iron-sulfur enzyme present in oxygenic photosynthetic organisms--is the first member of a thiol chain that links light to enzyme regulation. FTR possesses a catalytically active dithiol group localized on the 13 kDa (similar) subunit, that occurs in all species investigated and accepts reducing equivalents from photoreduced ferredoxin and transfers them stoichiometrically to the disulfide form of thioredoxin m. The reduced thioredoxin m, in turn, reduces NADP-malate dehydrogenase, thereby converting it from an inactive (S-S) to an active (SH) form. The means by which FTR is able to combine electrons (from photoreduced ferredoxin) with protons (from the medium) to reduce its active disulfide group remains to be determined

  20. Clustered regularly interspaced short palindromic repeats (CRISPRs): the hallmark of an ingenious antiviral defense mechanism in prokaryotes.

    Science.gov (United States)

    Al-Attar, Sinan; Westra, Edze R; van der Oost, John; Brouns, Stan J J

    2011-04-01

    Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences (repeats), interspaced by highly variable sequences referred to as spacers. The spacers originate from either phages or plasmids and comprise the prokaryotes' 'immunological memory'. CRISPR-associated (cas) genes encode conserved proteins that together with CRISPRs make-up the CRISPR/Cas system, responsible for defending the prokaryotic cell against invaders. CRISPR-mediated resistance has been proposed to involve three stages: (i) CRISPR-Adaptation, the invader DNA is encountered by the CRISPR/Cas machinery and an invader-derived short DNA fragment is incorporated in the CRISPR array. (ii) CRISPR-Expression, the CRISPR array is transcribed and the transcript is processed by Cas proteins. (iii) CRISPR-Interference, the invaders' nucleic acid is recognized by complementarity to the crRNA and neutralized. An application of the CRISPR/Cas system is the immunization of industry-relevant prokaryotes (or eukaryotes) against mobile-genetic invasion. In addition, the high variability of the CRISPR spacer content can be exploited for phylogenetic and evolutionary studies. Despite impressive progress during the last couple of years, the elucidation of several fundamental details will be a major challenge in future research.

  1. Rational development of an attenuated recombinant cyprinid herpesvirus 3 vaccine using prokaryotic mutagenesis and in vivo bioluminescent imaging

    Science.gov (United States)

    Cyprinid herpesvirus 3 (CyHV-3) is causing severe economic losses worldwide in the carp industry, and a safe and efficacious attenuated vaccine compatible with mass vaccination is needed. We produced single deleted recombinants using prokaryotic mutagenesis. When producing a recombinant lacking open...

  2. Metagenomic Sequence of Prokaryotic Microbiota from an Intermediate-Salinity Pond of a Saltern in Isla Cristina, Spain

    OpenAIRE

    Fernández, Ana B.; León, María José; Vera, Blanca; Sánchez-Porro, Cristina; Ventosa, Antonio

    2014-01-01

    Marine salterns are artificial multipond systems designed for the commercial production of salt by evaporation of seawater. We report here the metagenomic sequence of the prokaryotic microbiota of a pond with intermediate salinity (21% total salts) of a saltern located in Isla Cristina, Huelva, southwest Spain.

  3. Metagenomic sequence of prokaryotic microbiota from an intermediate-salinity pond of a saltern in isla cristina, Spain.

    Science.gov (United States)

    Fernández, Ana B; León, María José; Vera, Blanca; Sánchez-Porro, Cristina; Ventosa, Antonio

    2014-02-13

    Marine salterns are artificial multipond systems designed for the commercial production of salt by evaporation of seawater. We report here the metagenomic sequence of the prokaryotic microbiota of a pond with intermediate salinity (21% total salts) of a saltern located in Isla Cristina, Huelva, southwest Spain.

  4. A neural network method for identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites

    DEFF Research Database (Denmark)

    Nielsen, Henrik; Engelbrecht, Jacob; Brunak, Søren

    1997-01-01

    We have developed a new method for the identication of signal peptides and their cleavage sites based on neural networks trained on separate sets of prokaryotic and eukaryotic sequences. The method performs signicantly better than previous prediction schemes, and can easily be applied to genome...

  5. Cloning, expression, and purification of recombinant protein MPT-64 from a virulent strain of Mycobacterium bovis in a prokaryotic system

    Directory of Open Access Journals (Sweden)

    Maryam Mohammadi Tashakkori

    2016-01-01

    Conclusion: These results indicated successful expression and purification of recombinant MPT-64 protein in a prokaryotic system. This protein can be used for serological diagnosis, improved detection of pathogenicity and non-pathogenicity between infected cattle, and for verification of suspected cases of bovine TB.

  6. THE STATE OF MANGANESE IN THE PHOTOSYNTHETIC APPARATUS. I. EXAFS STUDIES ON CHLOROPLASTS AND di-u-oxo BRIDGED di-MANGANESE MODEL COMPOUNDS

    Energy Technology Data Exchange (ETDEWEB)

    Kirby, J. A.; Robertson, A. S.; Smith, J. P.; Thompson, A. C.; Thompson, A. C.; Klein, M. P.

    1980-11-01

    Extended X-ray Absorption Fine Structure (EXAFS) studies on the manganese contained in spinach chloroplasts and on certain di-u-oxo bridged manganese dimers of the form (X{sub 2}Mn)O{sub 2}(MnX{sub 2} (X=2,2'-bypyridine and 1,10-phenanthroline) are reported. From these studies, the manganese associated with photosynthetic oxygen evolution is suggested to occur as a bridged transition metal dimer with most likely another manganese. Extensive details on the analysis are included.

  7. Production of isotopically labeled heterologous proteins in non-E. coli prokaryotic and eukaryotic cells

    International Nuclear Information System (INIS)

    Takahashi, Hideo; Shimada, Ichio

    2010-01-01

    The preparation of stable isotope-labeled proteins is necessary for the application of a wide variety of NMR methods, to study the structures and dynamics of proteins and protein complexes. The E. coli expression system is generally used for the production of isotope-labeled proteins, because of the advantages of ease of handling, rapid growth, high-level protein production, and low cost for isotope-labeling. However, many eukaryotic proteins are not functionally expressed in E. coli, due to problems related to disulfide bond formation, post-translational modifications, and folding. In such cases, other expression systems are required for producing proteins for biomolecular NMR analyses. In this paper, we review the recent advances in expression systems for isotopically labeled heterologous proteins, utilizing non-E. coli prokaryotic and eukaryotic cells.

  8. Binding site of ribosomal proteins on prokaryotic 5S ribonucleic acids: a study with ribonucleases

    DEFF Research Database (Denmark)

    Douthwaite, S; Christensen, A; Garrett, R A

    1982-01-01

    The binding sites of ribosomal proteins L18 and L25 on 5S RNA from Escherichia coli were probed with ribonucleases A, T1, and T2 and a double helix specific cobra venom endonuclease. The results for the protein-RNA complexes, which were compared with those for the free RNA [Douthwaite, S...... stearothermophilus 5S RNA. Several protein-induced changes in the RNA structures were identified; some are possibly allosteric in nature. The two prokaryotic 5S RNAs were also incubated with total 50S subunit proteins from E. coli and B. stearothermophilus ribosomes. Homologous and heterologous reconstitution....... stearothermophilus 5S RNA, which may have been due to a third ribosomal protein L5....

  9. [Prokaryote diversity in water environment of land-ocean ecotone of Zhuhai City].

    Science.gov (United States)

    Huang, Xiao-Lan; Chen, Jian-Yao; Zhou, Shi-Ning; Xie, Li-Chun; Fu, Cong-Sheng

    2010-02-01

    By constructing 16S rDNA clone library with PCR-RFLP, the prokaryote diversity in the seawater and groundwater of land-ocean ecotone of Zhuhai City was investigated, and the similarity and cluster analyses were implemented with the database of the sequences in Genbank. In the seawater, Proteobacteria was dominant, followed by Archaeon, Gemmatimonadetes, Candidate division OP3 and OP8, and Planctomycetes, etc.; while in the groundwater, Archaeon was dominant, followed by Proteobacteria, Sphingobacteria, Candidate division OP3, Actinobacterium, and Pseudomonas. The dominant taxa in the groundwater had high similarity to the unculturable groups of marine microorganisms. Large amount of bacteria capable of degrading organic matter and purifying water body existed in the groundwater, suggesting that after long-term evolution, the land-ocean ecotone of Zhuhai City had the characteristics of both land and ocean.

  10. [A study of recombinant human sestrin 1 and sestrin 2 proteins produced in a prokaryotic system].

    Science.gov (United States)

    Rai, N; Kumar, R; Haque, Md A; Hassan, Md I; Dey, S

    2017-01-01

    Sestrins are highly conserved stress-inducible proteins capable of suppressing the production of ROS and signalling through mTORC1. Here we report a study of human sestrin1 (sesn1) and sestrin2 (sesn2) proteins produced in a pET28^(+) vector based prokaryotic system. Mass spectrometry analysis, western blot and surface plasmon resonance (SPR) of affinity purified sesn1 and sesn2 proteins confirmed their identity; biophysical characteristics were observed using circular dichroism (CD) showing that sesn1 and sesn2 have a predominant α-helical structure. Here we describe a simple, one step purification process to purify a large amount of sestrin proteins with significant yield. Further study of recombinant human sestrins may further facilitate the understanding of their roles in eukaryotic cells.

  11. [Ultrastructural basis of interactions between prokaryotes and eukaryotes in different symbiotic models].

    Science.gov (United States)

    Sacchi, L

    2004-06-01

    This paper reviews the Author's contribution to the knowledge of the ultrastructural basis of the prokaryote-eukaryote interactions in different models assessed by an ultrastructural approach. In agreement with the hypothesis of the origin of eukaryotic cells, which are chimeras of several prokaryotes with different morpho-functional specializations, symbiosis had major consequence for evolution of life. In Arthropods, one of the most successful lifestyles, the presence of endosymbiotic prokaryotes, plays an important role in their metabolism. In some cases, genome integration has occurred in the endosymbiotic relationships with the host, proving that intracellular symbiosis is not merely a nutritional supplement. Intracellular symbiotic bacteria are also described in nematodes. In particular, the presence of intracellular Wolbachia in filariae, even if its function is not yet completely known, influences positively the reproductive biology and the survival of the host, as proved by antibiotic treatment against this bacterium. The ultrastructural images reported in this review were obtained using different species of cockroaches, termites, ticks and filarial nematodes. The traditional methods of transmission (TEM), scansion (SEM) and immuno electron microscopy were used. In addition, also freeze-fracture and deep-etching techniques were employed. The cockroaches and the primitive termite Mastotermes darwiniensis host symbiotic bacteria in the ovary and in specialized cells (bacteriocytes) of the fat body. These bacteria have the typical cell boundary profile of gram-negative bacteria and are enveloped in a vacuolar membrane produced by the host cell. Molecular sequence data of 16S rDNA of endosymbionts of five species of cockroaches and M. darwiniensis indicate that they are members of the Flavobacteria-bacteroides group and that the infection occurred in an ancestor common to cockroaches and termites probably after the end of the Paleozoic (250 Ma BP). The

  12. Pangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.

    Directory of Open Access Journals (Sweden)

    Mikhail A. Moldovan

    2018-03-01

    Full Text Available The pangenome is the collection of all groups of orthologous genes (OGGs from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria Prochlorococcus marinus should be divided into two species. As a control we have confirmed the paraphyletic origin of Yersinia pseudotuberculosis (with embedded, monophyletic Y. pestis and Burkholderia pseudomallei (with B. mallei. We also demonstrate that by our definition and in accordance with recent studies Escherichia coli and Shigella spp. are one species.

  13. Nitrate addition has minimal short-term impacts on greenland ice sheet supraglacial prokaryotes

    DEFF Research Database (Denmark)

    Cameron, Karen A.; Stibal, Marek; Chrismas, Nathan

    2017-01-01

    Tropospheric nitrate levels are predicted to increase throughout the 21st century, with potential effects on terrestrial ecosystems, including the Greenland ice sheet (GrIS). This study considers the impacts of elevated nitrate concentrations on the abundance and composition of dominant bulk...... and active prokaryotic communities sampled from in situ nitrate fertilization plots on the GrIS surface. Nitrate concentrations were successfully elevated within sediment-filled meltwater pools, known as cryoconite holes; however, nitrate additions applied to surface ice did not persist. Estimated bulk...... cryoconite communities were not nitrate limited at the time of sampling. Instead, temporal changes in biomass and community composition were more pronounced. As these in situ incubations were short (6 weeks), and the community composition across GrIS surface ice is highly variable, we suggest that further...

  14. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    Directory of Open Access Journals (Sweden)

    Katelyn McNair

    2015-06-01

    Full Text Available As more and more prokaryotic sequencing takes place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

  15. Genome-based analysis of heme biosynthesis and uptake in prokaryotic systems.

    Science.gov (United States)

    Cavallaro, Gabriele; Decaria, Leonardo; Rosato, Antonio

    2008-11-01

    Heme is the prosthetic group of many proteins that carry out a variety of key biological functions. In addition, for many pathogenic organisms, heme (acquired from the host) may constitute a very important source of iron. Organisms can meet their heme demands by taking it up from external sources, by producing the cofactor through a dedicated biosynthetic pathway, or both. Here we analyzed the distribution of proteins specifically involved in the processes of heme biosynthesis and heme uptake in 474 prokaryotic organisms. These data allowed us to identify which organisms are capable of performing none, one, or both processes, based on the similarity to known systems. Some specific instances where one or more proteins along the pathways had unusual modifications were singled out. For two key protein domains involved in heme uptake, we could build a series of structural models, which suggested possible alternative modes of heme binding. Future directions for experimental work are given.

  16. Light Driven Energy Research at LCLS: Planned Pump-Probe X-ray Spectroscopy Studies on Photosynthetic Water Splitting

    Science.gov (United States)

    Bergmann, Uwe

    2010-02-01

    Arguably the most important chemical reaction on earth is the photosynthetic splitting of water to molecular oxygen by the Mn-containing oxygen-evolving complex (Mn-OEC) in the protein known as photosystem II (PSII). It is this reaction which has, over the course of some 3.8 billion years, gradually filled our atmosphere with O2 and consequently enabled and sustained the evolution of complex aerobic life. Coupled to the reduction of carbon dioxide, biological photosynthesis contributes foodstuffs for nutrition while recycling CO2 from the atmosphere and replacing it with O2. By utilizing sunlight to power these energy-requiring reactions, photosynthesis also serves as a model for addressing societal energy needs as we enter an era of diminishing fossil hydrocarbon resources. Understanding, at the molecular level, the dynamics and mechanism of how nature has solved this problem is of fundamental importance and could be critical to aid in the design of manufactured devices to accomplish the conversion of sunlight into useful electrochemical energy and transportable fuel in the foreseeable future. In order to understand the photosynthetic splitting of water by the Mn-OEC we need to be able to follow the reaction in real time at an atomic level. A powerful probe to study the electronic and molecular structure of the Mn-OEC is x-ray spectroscopy. Here, in particular x-ray emission spectroscopy (XES) has two crucial qualities for LCLS based time-dependent pump-probe studies of the Mn-OEC: a) it directly probes the Mn oxidation state and ligation, b) it can be performed with wavelength dispersive optics to avoid the necessity of scanning in pump probe experiments. Recent results and the planned time dependent experiments at LCLS will be discussed. )

  17. Prokaryotic Abundance and Activity in Permafrost of the Northern Victoria Land and Upper Victoria Valley (Antarctica).

    Science.gov (United States)

    La Ferla, Rosabruna; Azzaro, Maurizio; Michaud, Luigi; Caruso, Gabriella; Lo Giudice, Angelina; Paranhos, Rodolfo; Cabral, Anderson S; Conte, Antonella; Cosenza, Alessandro; Maimone, Giovanna; Papale, Maria; Rappazzo, Alessandro Ciro; Guglielmin, Mauro

    2017-08-01

    Victoria Land permafrost harbours a potentially large pool of cold-affected microorganisms whose metabolic potential still remains underestimated. Three cores (BC-1, BC-2 and BC-3) drilled at different depths in Boulder Clay (Northern Victoria Land) and one sample (DY) collected from a core in the Dry Valleys (Upper Victoria Valley) were analysed to assess the prokaryotic abundance, viability, physiological profiles and potential metabolic rates. The cores drilled at Boulder Clay were a template of different ecological conditions (different temperature regime, ice content, exchanges with atmosphere and with liquid water) in the same small basin while the Dry Valleys site was very similar to BC-2 conditions but with a complete different geological history and ground ice type. Image analysis was adopted to determine cell abundance, size and shape as well as to quantify the potential viable and respiring cells by live/dead and 5-cyano-2,3-ditolyl-tetrazolium chloride staining, respectively. Subpopulation recognition by apparent nucleic acid contents was obtained by flow cytometry. Moreover, the physiological profiles at community level by Biolog-Ecoplate™ as well as the ectoenzymatic potential rates on proteinaceous (leucine-aminopeptidase) and glucidic (ß-glucosidase) organic matter and on organic phosphates (alkaline-phosphatase) by fluorogenic substrates were tested. The adopted methodological approach gave useful information regarding viability and metabolic performances of microbial community in permafrost. The occurrence of a multifaceted prokaryotic community in the Victoria Land permafrost and a large number of potentially viable and respiring cells (in the order of 10 4 -10 5 ) were recognised. Subpopulations with a different apparent DNA content within the different samples were observed. The physiological profiles stressed various potential metabolic pathways among the samples and intense utilisation rates of polymeric carbon compounds and carbohydrates

  18. Diversity of 23S rRNA genes within individual prokaryotic genomes.

    Directory of Open Access Journals (Sweden)

    Anna Pei

    Full Text Available BACKGROUND: The concept of ribosomal constraints on rRNA genes is deduced primarily based on the comparison of consensus rRNA sequences between closely related species, but recent advances in whole-genome sequencing allow evaluation of this concept within organisms with multiple rRNA operons. METHODOLOGY/PRINCIPAL FINDINGS: Using the 23S rRNA gene as an example, we analyzed the diversity among individual rRNA genes within a genome. Of 184 prokaryotic species containing multiple 23S rRNA genes, diversity was observed in 113 (61.4% genomes (mean 0.40%, range 0.01%-4.04%. Significant (1.17%-4.04% intragenomic variation was found in 8 species. In 5 of the 8 species, the diversity in the primary structure had only minimal effect on the secondary structure (stem versus loop transition. In the remaining 3 species, the diversity significantly altered local secondary structure, but the alteration appears minimized through complex rearrangement. Intervening sequences (IVS, ranging between 9 and 1471 nt in size, were found in 7 species. IVS in Deinococcus radiodurans and Nostoc sp. encode transposases. T. tengcongensis was the only species in which intragenomic diversity >3% was observed among 4 paralogous 23S rRNA genes. CONCLUSIONS/SIGNIFICANCE: These findings indicate tight ribosomal constraints on individual 23S rRNA genes within a genome. Although classification using primary 23S rRNA sequences could be erroneous, significant diversity among paralogous 23S rRNA genes was observed only once in the 184 species analyzed, indicating little overall impact on the mainstream of 23S rRNA gene-based prokaryotic taxonomy.

  19. Prokaryotic diversity in one of the largest hypersaline coastal lagoons in the world.

    Science.gov (United States)

    Clementino, M M; Vieira, R P; Cardoso, A M; Nascimento, A P A; Silveira, C B; Riva, T C; Gonzalez, A S M; Paranhos, R; Albano, R M; Ventosa, A; Martins, O B

    2008-07-01

    Araruama Lagoon is an environment characterized by high salt concentrations. The low raining and high evaporation rates in this region favored the development of many salty ponds around the lagoon. In order to reveal the microbial composition of this system, we performed a 16S rRNA gene survey. Among archaea, most clones were related to uncultured environmental Euryarchaeota. In lagoon water, we found some clones related to Methanomicrobia and Methanothermococcus groups, while in the saline pond water members related to the genus Haloarcula were detected. Bacterial community was dominated by clones related to Gamma-proteobacteria, Actinobacteria, and Synechococcus in lagoon water, while Salinibacter ruber relatives dominated in saline pond. We also detected the presence of Alpha-proteobacteria, Pseudomonas-like bacteria and Verrucomicrobia. Only representatives of the genus Ralstonia were cosmopolitan, being observed in both systems. The detection of a substantial number of clones related to uncultured archaea and bacteria suggest that the hypersaline waters of Araruama harbor a pool of novel prokaryotic phylotypes, distinct from those observed in other similar systems. We also observed clones related to halophilic genera of cyanobacteria that are specific for each habitat studied. Additionally, two bacterioplankton molecular markers with ecological relevance were analyzed, one is linked to nitrogen fixation (nifH) and the other is linked to carbon fixation by bacterial photosynthesis, the protochlorophyllide genes, revealing a specific genetic distribution in this ecosystem. This is the first study of the biogeography and community structure of microbial assemblages in Brazilian tropical hypersaline environments. This work is directed towards a better understanding of the free-living prokaryotic diversity adapted to life in hypersaline waters.

  20. Phylogenetic and Comparative Sequence Analysis of Thermostable Alpha Amylases of kingdom Archea, Prokaryotes and Eukaryotes.

    Science.gov (United States)

    Huma, Tayyaba; Maryam, Arooma; Rehman, Shahid Ur; Qamar, Muhammad Tahir Ul; Shaheen, Tayyaba; Haque, Asma; Shaheen, Bushra

    2014-01-01

    Alpha amylase family is generally defined as a group of enzymes that can hydrolyse and transglycosylase α-(1, 4) or α-(1, 6) glycosidic bonds along with the preservation of anomeric configuration. For the comparative analysis of alpha amylase family, nucleotide sequences of seven thermo stable organisms of Kingdom Archea i.e. Pyrococcus furiosus (100-105°C), Kingdom Prokaryotes i.e. Bacillus licheniformis (90-95°C), Geobacillus stearothermophilus (75°C), Bacillus amyloliquefaciens (72°C), Bacillus subtilis (70°C) and Bacillus KSM K38 (55°C) and Eukaryotes i.e. Aspergillus oryzae (60°C) were selected from NCBI. Primary structure composition analysis and Conserved sequence analysis were conducted through Bio Edit tools. Results from BioEdit shown only three conserved regions of base pairs and least similarity in MSA of the above mentioned alpha amylases. In Mega 5.1 Phylogeny of thermo stable alpha amylases of Kingdom Archea, Prokaryotes and Eukaryote was handled by Neighbor-Joining (NJ) algorithm. Mega 5.1 phylogenetic results suggested that alpha amylases of thermo stable organisms i.e. Pyrococcus furiosus (100-105°C), Bacillus licheniformis (90-95°C), Geobacillus stearothermophilus (75°C) and Bacillus amyloliquefaciens (72°C) are more distantly related as compared to less thermo stable organisms. By keeping in mind the characteristics of most thermo stable alpha amylases novel and improved features can be introduced in less thermo stable alpha amylases so that they become more thermo tolerant and productive for industry.

  1. Towards quantification of vibronic coupling in photosynthetic antenna complexes

    Energy Technology Data Exchange (ETDEWEB)

    Singh, V. P.; Westberg, M.; Wang, C.; Gellen, T.; Engel, G. S., E-mail: gsengel@uchicago.edu [Department of Chemistry, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637 (United States); Dahlberg, P. D. [Graduate Program in the Biophysical Sciences, The James Franck Institute and The Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637 (United States); Gardiner, A. T.; Cogdell, R. J. [Department of Botany, Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow, Scotland (United Kingdom)

    2015-06-07

    Photosynthetic antenna complexes harvest sunlight and efficiently transport energy to the reaction center where charge separation powers biochemical energy storage. The discovery of existence of long lived quantum coherence during energy transfer has sparked the discussion on the role of quantum coherence on the energy transfer efficiency. Early works assigned observed coherences to electronic states, and theoretical studies showed that electronic coherences could affect energy transfer efficiency—by either enhancing or suppressing transfer. However, the nature of coherences has been fiercely debated as coherences only report the energy gap between the states that generate coherence signals. Recent works have suggested that either the coherences observed in photosynthetic antenna complexes arise from vibrational wave packets on the ground state or, alternatively, coherences arise from mixed electronic and vibrational states. Understanding origin of coherences is important for designing molecules for efficient light harvesting. Here, we give a direct experimental observation from a mutant of LH2, which does not have B800 chromophores, to distinguish between electronic, vibrational, and vibronic coherence. We also present a minimal theoretical model to characterize the coherences both in the two limiting cases of purely vibrational and purely electronic coherence as well as in the intermediate, vibronic regime.

  2. Managing the cellular redox hub in photosynthetic organisms.

    Science.gov (United States)

    Foyer, Christine H; Noctor, Graham

    2012-02-01

    Light-driven redox chemistry is a powerful source of redox signals that has a decisive input into transcriptional control within the cell nucleus. Like photosynthetic electron transport pathways, the respiratory electron transport chain exerts a profound control over gene function, in order to balance energy (reductant and ATP) supply with demand, while preventing excessive over-reduction or over-oxidation that would be adversely affect metabolism. Photosynthetic and respiratory redox chemistries are not merely housekeeping processes but they exert a controlling influence over every aspect of plant biology, participating in the control of gene transcription and translation, post-translational modifications and the regulation of assimilatory reactions, assimilate partitioning and export. The number of processes influenced by redox controls and signals continues to increase as do the components that are recognized participants in the associated signalling pathways. A step change in our understanding of the overall importance of the cellular redox hub to plant cells has occurred in recent years as the complexity of the management of the cellular redox hub in relation to metabolic triggers and environmental cues has been elucidated. This special issue describes aspects of redox regulation and signalling at the cutting edge of current research in this dynamic and rapidly expanding field. © 2011 Blackwell Publishing Ltd.

  3. Chlorophyll Fluorescence Imaging Uncovers Photosynthetic Fingerprint of Citrus Huanglongbing

    Directory of Open Access Journals (Sweden)

    Haiyan Cen

    2017-08-01

    Full Text Available Huanglongbing (HLB is one of the most destructive diseases of citrus, which has posed a serious threat to the global citrus production. This research was aimed to explore the use of chlorophyll fluorescence imaging combined with feature selection to characterize and detect the HLB disease. Chlorophyll fluorescence images of citrus leaf samples were measured by an in-house chlorophyll fluorescence imaging system. The commonly used chlorophyll fluorescence parameters provided the first screening of HLB disease. To further explore the photosynthetic fingerprint of HLB infected leaves, three feature selection methods combined with the supervised classifiers were employed to identify the unique fluorescence signature of HLB and perform the three-class classification (i.e., healthy, HLB infected, and nutrient deficient leaves. Unlike the commonly used fluorescence parameters, this novel data-driven approach by using the combination of the mean fluorescence parameters and image features gave the best classification performance with the accuracy of 97%, and presented a better interpretation for the spatial heterogeneity of photochemical and non-photochemical components in HLB infected citrus leaves. These results imply the potential of the proposed approach for the citrus HLB disease diagnosis, and also provide a valuable insight for the photosynthetic response to the HLB disease.

  4. Phylogeny and photosynthetic pathway distribution in Anticharis Endl. (Scrophulariaceae).

    Science.gov (United States)

    Khoshravesh, Roxana; Hossein, Akhani; Sage, Tammy L; Nordenstam, Bertil; Sage, Rowan F

    2012-09-01

    C(4) photosynthesis independently evolved >62 times, with the majority of origins within 16 dicot families. One origin occurs in the poorly studied genus Anticharis Endl. (Scrophulariaceae), which consists of ~10 species from arid regions of Africa and southwest Asia. Here, the photosynthetic pathway of 10 Anticharis species and one species from each of the sister genera Aptosimum and Peliostomum was identified using carbon isotope ratios (δ(13)C). The photosynthetic pathway was then mapped onto an internal transcribed spacer (ITS) phylogeny of Anticharis and its sister genera. Leaf anatomy was examined for nine Anticharis species and plants from Aptosimum and Peliostomum. Leaf ultrastructure, gas exchange, and enzyme distributions were assessed in Anticharis glandulosa collected in SE Iran. The results demonstrate that C(3) photosynthesis is the ancestral condition, with C(4) photosynthesis occurring in one clade containing four species. C(4) Anticharis species exhibit the atriplicoid type of C(4) leaf anatomy and the NAD-malic enzyme biochemical subtype. Six Anticharis species had C(3) or C(3)-C(4) δ(13)C values and branched at phylogenetic nodes that were sister to the C(4) clade. The rest of Anticharis species had enlarged bundle sheath cells, close vein spacing, and clusters of chloroplasts along the centripetal (inner) bundle sheath walls. These traits indicate that basal-branching Anticharis species are evolutionary intermediates between the C(3) and C(4) conditions. Anticharis appears to be an important new group in which to study the dynamics of C(4) evolution.

  5. Enzymes involved in organellar DNA replication in photosynthetic eukaryotes.

    Science.gov (United States)

    Moriyama, Takashi; Sato, Naoki

    2014-01-01

    Plastids and mitochondria possess their own genomes. Although the replication mechanisms of these organellar genomes remain unclear in photosynthetic eukaryotes, several organelle-localized enzymes related to genome replication, including DNA polymerase, DNA primase, DNA helicase, DNA topoisomerase, single-stranded DNA maintenance protein, DNA ligase, primer removal enzyme, and several DNA recombination-related enzymes, have been identified. In the reference Eudicot plant Arabidopsis thaliana, the replication-related enzymes of plastids and mitochondria are similar because many of them are dual targeted to both organelles, whereas in the red alga Cyanidioschyzon merolae, plastids and mitochondria contain different replication machinery components. The enzymes involved in organellar genome replication in green plants and red algae were derived from different origins, including proteobacterial, cyanobacterial, and eukaryotic lineages. In the present review, we summarize the available data for enzymes related to organellar genome replication in green plants and red algae. In addition, based on the type and distribution of replication enzymes in photosynthetic eukaryotes, we discuss the transitional history of replication enzymes in the organelles of plants.

  6. Biomaterials based on photosynthetic membranes as potential sensors for herbicides.

    Science.gov (United States)

    Ventrella, Andrea; Catucci, Lucia; Placido, Tiziana; Longobardi, Francesco; Agostiano, Angela

    2011-08-15

    In this study, ultrathin film multilayers of Photosystem II-enriched photosynthetic membranes (BBY) were prepared and immobilized on quartz substrates by means of a Layer by Layer procedure exploiting electrostatic interactions with poly(ethylenimine) as polyelectrolyte. The biomaterials thus obtained were characterized by means of optical techniques and Atomic Force Microscopy, highlighting the fact that the Layer by Layer approach allowed the BBYs to be immobilized with satisfactory results. The activity of these hybrid materials was evaluated by means of optical assays based on the Hill Reaction, indicating that the biosamples, which preserved about 65% of their original activity even ten weeks after preparation, were both stable and active. Furthermore, an investigation of the biochips' sensitivity to the herbicide terbutryn, as a model analyte, gave interesting results: inhibition of photosynthetic activity was observed at terbutryn concentrations higher than 10(-7)M, thus evidencing the potential of such biomaterials in the environmental biosensor field. Copyright © 2011 Elsevier B.V. All rights reserved.

  7. Dynamic reorganization of photosynthetic supercomplexes during environmental acclimation

    Directory of Open Access Journals (Sweden)

    Jun eMinagawa

    2013-12-01

    Full Text Available Plants and algae have acquired the ability to acclimate to ever-changing environments in order to survive. During photosynthesis, light energy is converted by several membrane protein supercomplexes into electrochemical energy, which is eventually used to assimilate CO2. The efficiency of photosynthesis is modulated by many environmental factors such as quality and quantity of light, temperature, drought, and CO2 concentration, among others. Accumulating evidence indicates that photosynthetic supercomplexes undergo supramolecular reorganization within a short timeframe during acclimation to an environmental change. This reorganization includes state transitions that balance the excitation of photosystem I and II by shuttling peripheral antenna proteins between the two, thermal energy dissipation that occurs at energy-quenching sites within the light-harvesting antenna generated for negative feedback when excess light is absorbed, and cyclic electron flow that is facilitated between photosystem I and the cytochrome bf complex when cells demand more ATP and/or need to activate energy dissipation. This review will highlight the recent findings regarding these environmental acclimation events in model organisms with particular attention to the unicellular green alga C. reinhardtii and with reference to the vascular plant A. thaliana, which offers a glimpse into the dynamic behavior of photosynthetic machineries in nature.

  8. The independent prokaryotic origins of eukaryotic fructose-1, 6-bisphosphatase and sedoheptulose-1, 7-bisphosphatase and the implications of their origins for the evolution of eukaryotic Calvin cycle

    Directory of Open Access Journals (Sweden)

    Jiang Yong-Hai

    2012-10-01

    Full Text Available Abstract Background In the Calvin cycle of eubacteria, the dephosphorylations of both fructose-1, 6-bisphosphate (FBP and sedoheptulose-1, 7-bisphosphate (SBP are catalyzed by the same bifunctional enzyme: fructose-1, 6-bisphosphatase/sedoheptulose-1, 7-bisphosphatase (F/SBPase, while in that of eukaryotic chloroplasts by two distinct enzymes: chloroplastic fructose-1, 6-bisphosphatase (FBPase and sedoheptulose-1, 7-bisphosphatase (SBPase, respectively. It was proposed that these two eukaryotic enzymes arose from the divergence of a common ancestral eubacterial bifunctional F/SBPase of mitochondrial origin. However, no specific affinity between SBPase and eubacterial FBPase or F/SBPase can be observed in the previous phylogenetic analyses, and it is hard to explain why SBPase and/or F/SBPase are/is absent from most extant nonphotosynthetic eukaryotes according to this scenario. Results Domain analysis indicated that eubacterial F/SBPase of two different resources contain distinct domains: proteobacterial F/SBPases contain typical FBPase domain, while cyanobacterial F/SBPases possess FBPase_glpX domain. Therefore, like prokaryotic FBPase, eubacterial F/SBPase can also be divided into two evolutionarily distant classes (Class I and II. Phylogenetic analysis based on a much larger taxonomic sampling than previous work revealed that all eukaryotic SBPase cluster together and form a close sister group to the clade of epsilon-proteobacterial Class I FBPase which are gluconeogenesis-specific enzymes, while all eukaryotic chloroplast FBPase group together with eukaryotic cytosolic FBPase and form another distinct clade which then groups with the Class I FBPase of diverse eubacteria. Motif analysis of these enzymes also supports these phylogenetic correlations. Conclusions There are two evolutionarily distant classes of eubacterial bifunctional F/SBPase. Eukaryotic FBPase and SBPase do not diverge from either of them but have two independent origins

  9. Evolutionary origins, molecular cloning and expression of carotenoid hydroxylases in eukaryotic photosynthetic algae

    Science.gov (United States)

    2013-01-01

    Background Xanthophylls, oxygenated derivatives of carotenes, play critical roles in photosynthetic apparatus of cyanobacteria, algae, and higher plants. Although the xanthophylls biosynthetic pathway of algae is largely unknown, it is of particular interest because they have a very complicated evolutionary history. Carotenoid hydroxylase (CHY) is an important protein that plays essential roles in xanthophylls biosynthesis. With the availability of 18 sequenced algal genomes, we performed a comprehensive comparative analysis of chy genes and explored their distribution, structure, evolution, origins, and expression. Results Overall 60 putative chy genes were identified and classified into two major subfamilies (bch and cyp97) according to their domain structures. Genes in the bch subfamily were found in 10 green algae and 1 red alga, but absent in other algae. In the phylogenetic tree, bch genes of green algae and higher plants share a common ancestor and are of non-cyanobacterial origin, whereas that of red algae is of cyanobacteria. The homologs of cyp97a/c genes were widespread only in green algae, while cyp97b paralogs were seen in most of algae. Phylogenetic analysis on cyp97 genes supported the hypothesis that cyp97b is an ancient gene originated before the formation of extant algal groups. The cyp97a gene is more closely related to cyp97c in evolution than to cyp97b. The two cyp97 genes were isolated from the green alga Haematococcus pluvialis, and transcriptional expression profiles of chy genes were observed under high light stress of different wavelength. Conclusions Green algae received a β-xanthophylls biosynthetic pathway from host organisms. Although red algae inherited the pathway from cyanobacteria during primary endosymbiosis, it remains unclear in Chromalveolates. The α-xanthophylls biosynthetic pathway is a common feature in green algae and higher plants. The origination of cyp97a/c is most likely due to gene duplication before divergence of

  10. Evolutionary origins, molecular cloning and expression of carotenoid hydroxylases in eukaryotic photosynthetic algae.

    Science.gov (United States)

    Cui, Hongli; Yu, Xiaona; Wang, Yan; Cui, Yulin; Li, Xueqin; Liu, Zhaopu; Qin, Song

    2013-07-08

    Xanthophylls, oxygenated derivatives of carotenes, play critical roles in photosynthetic apparatus of cyanobacteria, algae, and higher plants. Although the xanthophylls biosynthetic pathway of algae is largely unknown, it is of particular interest because they have a very complicated evolutionary history. Carotenoid hydroxylase (CHY) is an important protein that plays essential roles in xanthophylls biosynthesis. With the availability of 18 sequenced algal genomes, we performed a comprehensive comparative analysis of chy genes and explored their distribution, structure, evolution, origins, and expression. Overall 60 putative chy genes were identified and classified into two major subfamilies (bch and cyp97) according to their domain structures. Genes in the bch subfamily were found in 10 green algae and 1 red alga, but absent in other algae. In the phylogenetic tree, bch genes of green algae and higher plants share a common ancestor and are of non-cyanobacterial origin, whereas that of red algae is of cyanobacteria. The homologs of cyp97a/c genes were widespread only in green algae, while cyp97b paralogs were seen in most of algae. Phylogenetic analysis on cyp97 genes supported the hypothesis that cyp97b is an ancient gene originated before the formation of extant algal groups. The cyp97a gene is more closely related to cyp97c in evolution than to cyp97b. The two cyp97 genes were isolated from the green alga Haematococcus pluvialis, and transcriptional expression profiles of chy genes were observed under high light stress of different wavelength. Green algae received a β-xanthophylls biosynthetic pathway from host organisms. Although red algae inherited the pathway from cyanobacteria during primary endosymbiosis, it remains unclear in Chromalveolates. The α-xanthophylls biosynthetic pathway is a common feature in green algae and higher plants. The origination of cyp97a/c is most likely due to gene duplication before divergence of green algae and higher plants

  11. Comparison of Methods for Estimating Fractional Cover of Photosynthetic and Non-Photosynthetic Vegetation in the Otindag Sandy Land Using GF-1 Wide-Field View Data

    OpenAIRE

    Xiaosong Li; Guoxiong Zheng; Jinying Wang; Cuicui Ji; Bin Sun; Zhihai Gao

    2016-01-01

    Photosynthetic vegetation (PV) and non-photosynthetic vegetation (NPV) are important ground cover types for desertification monitoring and land management. Hyperspectral remote sensing has been proven effective for separating NPV from bare soil, but few studies determined fractional cover of PV (fpv) and NPV (fnpv) using multispectral information. The purpose of this study is to evaluate several spectral unmixing approaches for retrieval of fpv and fnpv in the Otindag Sandy Land using GF-1 wi...

  12. Photosynthetic control of electron transport and the regulation of gene expression

    NARCIS (Netherlands)

    Foyer, C.H.; Neukermans, J.; Queval, G.; Noctor, G.; Harbinson, J.

    2012-01-01

    The term ‘photosynthetic control’ describes the short- and long-term mechanisms that regulate reactions in the photosynthetic electron transport (PET) chain so that the rate of production of ATP and NADPH is coordinated with the rate of their utilization in metabolism. At low irradiances these

  13. Influence of stomatic aperture on photosynthetic activity of bean-seedlings leaves

    International Nuclear Information System (INIS)

    Suarez Moya, J.; Fernandez Gonzalez, J.

    1984-01-01

    The present paper contains the data of photosynthetic activity and stomatic aperture of bean-seedlings Ieaves, and the relations obtained with both results. It has been observed that the product of photosynthetic activity by the resistance; to transpiration measured by a promoter ia a constant, between some limits. (Author) 45 refs

  14. Interactions between heavy metals and photosynthetic materials studied by optical techniques.

    Science.gov (United States)

    Ventrella, Andrea; Catucci, Lucia; Piletska, Elena; Piletsky, Sergey; Agostiano, Angela

    2009-11-01

    In this work studies on rapid inhibitory interactions between heavy metals and photosynthetic materials at different organization levels were carried out by optical assay techniques, investigating the possibility of applications in the heavy metal detection field. Spinach chloroplasts, thylakoids and Photosystem II proteins were employed as biotools in combination with colorimetric assays based on dichlorophenol indophenole (DCIP) photoreduction and on fluorescence emission techniques. It was found that copper and mercury demonstrated a strong and rapid photosynthetic activity inhibition, that varied from proteins to membranes, while other metals like nickel, cobalt and manganese produced only slight inhibition effects on all tested photosynthetic materials. By emission measurements, only copper was found to rapidly influence the photosynthetic material signals. These findings give interesting information about the rapid effects of heavy metals on isolated photosynthetic samples, and are in addition to the literature data concerning the effects of growth in heavy metal enriched media.

  15. A cost-effective microbial fuel cell to detect and select for photosynthetic electrogenic activity in algae and cyanobacteria

    NARCIS (Netherlands)

    Luimstra, V.M.; Kennedy, S.J.; Güttler, J.; Wood, S.A.; Williams, D.E.; Packer, M.A.

    2014-01-01

    This work describes the development of an easily constructed, cost-effective photosynthetic microbial fuel cell design with highly reproducible electrochemical characteristics that can be used to screen algae and cyanobacteria for photosynthetic electrogenic activity. It is especially suitable for

  16. Seasonal photosynthetic activity in evergreen conifer leaves monitored with spectral reflectance

    Science.gov (United States)

    Wong, C. Y.; Gamon, J. A.

    2013-12-01

    Boreal evergreen conifers must maintain photosynthetic systems in environments where temperatures vary greatly across seasons from high temperatures in the summer to freezing levels in the winter. This involves seasonal downregulation and photoprotection during periods of extreme temperatures. To better understand this downregulation, seasonal dynamics of photosynthesis of lodgepole (Pinus contorta D.) and ponderosa pine (Pinus ponderosa D.) were monitored in Edmonton, Canada over two years. Spectral reflectance at the leaf and stand scales was measured weekly and the Photochemical Reflectance Index (PRI), often used as a proxy for chlorophyll and carotenoid pigment levels and photosynthetic light-use efficiency (LUE), was used to track the seasonal dynamics of photosynthetic activity. Additional physiological measurements included leaf pigment content, chlorophyll fluorescence, and gas exchange. All the metrics indicate large seasonal changes in photosynthetic activity, with a sharp transition from winter downregulation to active photosynthesis in the spring and a more gradual fall transition into winter. The PRI was a good indicator of several other variables including seasonally changing photosynthetic activity, chlorophyll fluorescence, photosynthetic LUE, and pigment pool sizes. Over the two-year cycle, PRI was primarily driven by changes in constitutive (chlorophyll:carotenoid) pigment levels correlated with seasonal photosynthetic activity, with a much smaller variation caused by diurnal changes in xanthophyll cycle activity (conversion between violaxanthin & zeaxanthin). Leaf and canopy scale PRI measurements exhibited parallel responses during the winter-spring transition. Together, our findings indicate that evergreen conifers photosynthetic system possesses a remarkable degree of resilience in response to large temperature changes across seasons, and that optical remote sensing can be used to observe the seasonal effects on photosynthesis and

  17. Photosynthetic antennae systems: energy transport and optical absorption

    International Nuclear Information System (INIS)

    Reineker, P.; Supritz, Ch.; Warns, Ch.; Barvik, I.

    2004-01-01

    The energy transport and the optical line shape of molecular aggregates, modeling bacteria photosynthetic light-harvesting systems (chlorosomes in the case of Chlorobium tepidum or Chloroflexus aurantiacus and LH2 in the case of Rhodopseudomonas acidophila) is investigated theoretically. The molecular units are described by two-level systems with an average excitation energy ε and interacting with each other through nearest-neighbor interactions. For LH2 an elliptical deformation of the ring is also allowed. Furthermore, dynamic and in the case of LH2 also quasi-static fluctuations of the local excitation energies are taken into account, simulating fast molecular vibrations and slow motions of the protein backbone, respectively. The fluctuations are described by Gaussian Markov processes in the case of the chlorosomes and by colored dichotomic Markov processes, with exponentially decaying correlation functions, with small (λ s ) and large (λ) decay constants, in the case of LH2

  18. Mathematical Modeling of Acclimation Processes of the Photosynthetic Chain

    Directory of Open Access Journals (Sweden)

    S Heidari

    2016-10-01

    Full Text Available Introduction Photosynthetic energy conversion efficiency is characteristic of a system which is determined by interactions between various components of the system. The complex process of photosynthesis has been studied as a whole system which enables in silico examination of a large number of candidate genes for genetic engineering for a higher photosynthetic energy conversion efficiency. One of the most important environmental factors which influence the photosynthesis efficiency is light regime which can cause producing ROS components. To acclimate to such fluctuations, plants have evolved adaptive mechanisms to minimize damage of the photosynthetic apparatus excess light. A fast compatibility response to high light stresses is non-photochemical quenching process (NPQ, dissipating excessive energy to heat. Light harvested state switches into a quenched state by a conformational change of light harvesting complex (LHCII that regulated by xanthophylls and the PsbS protein within seconds. Low lumen pH activates xanthophyll synthesis via a xanthophyll cycle which consists of the de-epoxidation of violaxanthin to zeaxanthin by violaxanthin de-epoxidase in high light and inversely by zeaxanthin epoxidase in low light which occurs more slowly. Materials and Methods Thale cress (Arabidopsis thaliana (Chlombia-0 were grown on soil at 25/22 °C day/night temperature, with a 16/8 h photoperiod, and 40-70% (depend of plant species relative humidity. The light intensity was 150–200 µE m-2s-1 white light. Intensity of chlorophyll fluorescence was measured with PAM-2000 fluorometer (Heinz Walz, Germany and the manufacturer’s software (PamWin v.2. Results and Discussion In the present study, a dynamic kinetics amplified mathematical model was developed based on differential equations in order to predict short-term changes in NPQ in the process of adaptation to different light conditions. We investigated the stationary and dynamic behavior of the model

  19. Single Molecule Spectroscopy on Photosynthetic Pigment-Protein Complexes

    CERN Document Server

    Jelezko, F; Schuler, S; Thews, E; Tietz, C; Wechsler, A; Wrachtrup, J

    2001-01-01

    Single molecule spectroscopy was applied to unravel the energy transfer pathway in photosynthetic pigment-protein complexes. Detailed analysis of excitation and fluorescence emission spectra has been made for peripheral plant antenna LHC II and Photosystem I from cyanobacterium Synechococcus elongatus. Optical transitions of individual pigments were resolved under nonselective excitation of antenna chlorophylls. High-resolution fluorescence spectroscopy of individual plant antenna LHC II indicates that at low temperatures, the excitation energy is localized on the red-most Chl a pool absorbing at 680 nm. More than one pigment molecule is responsible for the fluorescence emission of the LHC II trimer. The spectral lines of single Chl a molecules absorbing at 675 nm are broadened because of the Foerster energy transfer towards the red-most pigments. Low-temperature spectroscopy on single PS I trimers indicates that two subgroups of pigments, which are present in the red antenna pool, differ by the strength of t...

  20. C4 photosynthetic machinery: insights from maize chloroplast proteomics

    Directory of Open Access Journals (Sweden)

    Qi eZhao

    2013-04-01

    Full Text Available C4 plants exhibit much higher CO2 assimilation rates than C3 plants. The specialized differentiation of mesophyll cell (M and bundle sheath cell (BS type chloroplasts is unique to C4 plants and improves photosynthesis efficiency. Maize (Zea mays is an important crop and model with C4 photosynthetic machinery. Current high-throughput quantitative proteomics approaches (e.g., 2DE, iTRAQ, and shotgun proteomics have been employed to investigate maize chloroplast structure and function. These proteomic studies have provided valuable information on C4 chloroplast protein components, photosynthesis, and other metabolic mechanisms underlying chloroplast biogenesis, stromal and membrane differentiation, as well as response to salinity, high/low temperature, and light stress. This review presents an overview of proteomics advances in maize chloroplast biology.