Reduction of Fe(III), Cr(VI), U(VI), and Tc(VII) by Deinococcus radiodurans R1

PubMed Central

Fredrickson, J. K.; Kostandarithes, H. M.; Li, S. W.; Plymale, A. E.; Daly, M. J.

2000-01-01

Deinococcus radiodurans is an exceptionally radiation-resistant microorganism capable of surviving acute exposures to ionizing radiation doses of 15,000 Gy and previously described as having a strictly aerobic respiratory metabolism. Under strict anaerobic conditions, D. radiodurans R1 reduced Fe(III)-nitrilotriacetic acid coupled to the oxidation of lactate to CO2 and acetate but was unable to link this process to growth. D. radiodurans reduced the humic acid analog anthraquinone-2,6-disulfonate (AQDS) to its dihydroquinone form, AH2DS, which subsequently transferred electrons to the Fe(III) oxides hydrous ferric oxide and goethite via a previously described electron shuttle mechanism. D. radiodurans reduced the solid-phase Fe(III) oxides in the presence of either 0.1 mM AQDS or leonardite humic acids (2 mg ml−1) but not in their absence. D. radiodurans also reduced U(VI) and Tc(VII) in the presence of AQDS. In contrast, Cr(VI) was directly reduced in anaerobic cultures with lactate although the rate of reduction was higher in the presence of AQDS. The results are the first evidence that D. radiodurans can reduce Fe(III) coupled to the oxidation of lactate or other organic compounds. Also, D. radiodurans, in combination with humic acids or synthetic electron shuttle agents, can reduce U and Tc and thus has potential applications for remediation of metal- and radionuclide-contaminated sites where ionizing radiation or other DNA-damaging agents may restrict the activity of more sensitive organisms. PMID:10788374

Computational protein design and protein-ligand interaction studies for the improvement of organophosphorus degrading potential of Deinococcus radiodurans.

PubMed

Manoharan, Prabu; Sridhar, J

2018-05-01

The organophosphorus hydrolase enzyme is involved in the catalyzing reaction that involve hydrolysis of organophosphate toxic compounds. An enzyme from Deinococcus radiodurans reported as homologous to phosphotriesterase and show activity against organophosphate. In the past activity of this enzyme is low and efforts made to improve the activity by experimental mutation study. However only very few organophosphates tested against very few catalytic site mutations. In order to improve the catalytic power of the organophosphorus hydrolase enzyme, we carried out systematic functional hotspot based protein engineering strategy. The mutants tested against 46 know organophosphate compounds using molecular docking study. Finally, we carried out an extensive molecular docking study to predict the binding of 46 organophosphate compounds to wild-type protein and mutant organophosphorus hydrolase enzyme. At the end we are able to improve the degrading potential of organophosphorus hydrolase enzyme against organophosphate toxic compounds. This preliminary study and the outcome would be useful guide for the experimental scientist involved in the bioremediation of toxic organophosphate compounds. Copyright © 2018 Elsevier Inc. All rights reserved.

DR2539 is a novel DtxR-like regulator of Mn/Fe ion homeostasis and antioxidant enzyme in Deinococcus radiodurans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Huan; Zhejiang Institute of Microbiology, Zhejiang Province, Hangzhou 310012; Wu, Rongrong

2010-05-28

Transcriptional regulators of the diphtheria toxin repressor (DtxR) family control the expression of genes involved in the uptake of iron and manganese, which is not only necessitous nutrients but also was suggested to be essential for intracellular redox cycling of microorganisms. We identified a unique DtxR homologue (DR2539) with special characteristics from Deinococcus radiodurans, which is known for its extreme resistance to radiation and oxidants. The dr2539 mutant showed higher resistance to hydrogen peroxide than the wild-type strain R1. Intracellular catalase activity assay and semiquantitative PCR analysis demonstrated that this DtxR is a negative regulator of catalase (katE). Furthermore, quantitativemore » real-time PCR, global transcription profile and inductively coupled plasma-mass spectrometry analysis showed that the DtxR is involved in the regulation of antioxidant system by maintaining the intracellular Mn/Fe ion homeostasis of D. radiodurans. However, unlike the other DtxR homologues, the DtxR of D. radiodurans acts as a negative regulator of a Mn transporter gene (dr2283) and as a positive regulator of Fe-dependent transporter genes (dr1219, drb0125) in D. radiodurans.« less

The emerging impact of genomics on the development of biological weapons. Threats and benefits posed by engineered extremophiles.

PubMed

Daly, M J

2001-09-01

During the past decades, representatives of Archaea, Bacteria, and Protista have been found thriving in many newly discovered extremely hostile habitats, which hitherto were regarded as too harsh to harbor life. To illustrate how an extremophile could be targeted for development as a biowarfare agent, an example is presented describing current advances in engineering Deinococcus radiodurans. Using a generally applicable combination of conventional genetic engineering and genomic informatics, this extremely radiation-resistant and environmentally robust bacterium is being developed for biotechnology.

Salt-mediated multicell formation in Deinococcus radiodurans.

PubMed Central

Chou, F I; Tan, S T

1991-01-01

The highly radiation-resistant tetracoccal bacterium Deinococcus radiodurans exhibited a reversible multi-cell-form transition which depended on the NaCl concentration in the medium. In response to 0.8% NaCl addition into the medium, the pair/tetrad (designated 2/4) cells in a young culture grew and divided but did not separate and became 8-, 16-, and 32-cell units successively. In exponential growth phase, the cells divided in a 16/32 pattern. Potassium ions were equally effective as Na+ in mediating this multicell-formation effect; Mg2+, Li+, and Ca2+ also worked but produced less multiplicity. This effect appears to be species specific. This-section micrographs revealed that in a 16/32-cell unit, eight 2/4 cells were encased in an orderly manner within a large peripheral wall, showing five cycles of septation. Our results suggest the presence of a salt-sensitive mechanism for controlling cell separation in D. radiodurans. Images PMID:2022617

Preserving genome integrity: the DdrA protein of Deinococcus radiodurans R1.

PubMed

Harris, Dennis R; Tanaka, Masashi; Saveliev, Sergei V; Jolivet, Edmond; Earl, Ashlee M; Cox, Michael M; Battista, John R

2004-10-01

The bacterium Deinococcus radiodurans can withstand extraordinary levels of ionizing radiation, reflecting an equally extraordinary capacity for DNA repair. The hypothetical gene product DR0423 has been implicated in the recovery of this organism from DNA damage, indicating that this protein is a novel component of the D. radiodurans DNA repair system. DR0423 is a homologue of the eukaryotic Rad52 protein. Following exposure to ionizing radiation, DR0423 expression is induced relative to an untreated control, and strains carrying a deletion of the DR0423 gene exhibit increased sensitivity to ionizing radiation. When recovering from ionizing-radiation-induced DNA damage in the absence of nutrients, wild-type D. radiodurans reassembles its genome while the mutant lacking DR0423 function does not. In vitro, the purified DR0423 protein binds to single-stranded DNA with an apparent affinity for 3' ends, and protects those ends from nuclease degradation. We propose that DR0423 is part of a DNA end-protection system that helps to preserve genome integrity following exposure to ionizing radiation. We designate the DR0423 protein as DNA damage response A protein.

Thioredoxin System from Deinococcus radiodurans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Obiero, Josiah; Pittet, Vanessa; Bonderoff, Sara A.

2010-05-03

This paper describes the cloning, purification, and characterization of thioredoxin (Trx) and thioredoxin reductase (TrxR) and the structure determination of TrxR from the ionizing radiation-tolerant bacterium Deinococcus radiodurans strain R1. The genes from D. radiodurans encoding Trx and TrxR were amplified by PCR, inserted into a pET expression vector, and overexpressed in Escherichia coli. The overexpressed proteins were purified by metal affinity chromatography, and their activity was demonstrated using well-established assays of insulin precipitation (for Trx), 5,5{prime}-dithiobis(2-nitrobenzoic acid) (DTNB) reduction, and insulin reduction (for TrxR). In addition, the crystal structure of oxidized TrxR was determined at 1.9-{angstrom} resolution. The overallmore » structure was found to be very similar to that of E. coli TrxR and homodimeric with both NADPH- and flavin adenine dinucleotide (FAD)-binding domains containing variants of the canonical nucleotide binding fold, the Rossmann fold. The K{sub m} (5.7 {micro}M) of D. radiodurans TrxR for D. radiodurans Trx was determined and is about twofold higher than that of the E. coli thioredoxin system. However, D. radiodurans TrxR has a much lower affinity for E. coli Trx (K{sub m}, 44.4 {micro}M). Subtle differences in the surface charge and shape of the Trx binding site on TrxR may account for the differences in recognition. Because it has been suggested that TrxR from D. radiodurans may have dual cofactor specificity (can utilize both NADH and NADPH), D. radiodurans TrxR was tested for its ability to utilize NADH as well. Our results show that D. radiodurans TrxR can utilize only NADPH for activity.« less

Deinococcus radiodurans RecA nucleoprotein filaments characterized at the single-molecule level with optical tweezers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pobegalov, Georgii, E-mail: george.pobegalov@nanobio.spbstu.ru; Cherevatenko, Galina; Alekseev, Aleksandr

2015-10-23

Deinococcus radiodurans can survive extreme doses of ionizing radiation due to the very efficient DNA repair mechanisms that are able to cope even with hundreds of double-strand breaks. RecA, the critical protein of homologous recombination in bacteria, is one of the key components of the DNA-repair system. Repair of double-strand breaks requires RecA binding to DNA and assembly of the RecA nucleoprotein helical filaments. The Escherichia coli RecA protein (EcRecA) and its interactions with DNA have been extensively studied using various approaches including single-molecule techniques, while the D. radiodurans RecA (DrRecA) remains much less characterized. However, DrRecA shows some remarkable differencesmore » from E. coli homolog. Here we combine microfluidics and single-molecule DNA manipulation with optical tweezers to follow the binding of DrRecA to long double-stranded DNA molecules and probe the mechanical properties of DrRecA nucleoprotein filaments at physiological pH. Our data provide a direct comparison of DrRecA and EcRecA binding to double-stranded DNA under identical conditions. We report a significantly faster filaments assembly as well as lower values of persistence length and contour length for DrRecA nucleoprotein filaments compared to EcRecA. Our results support the existing model of DrRecA forming more frequent and less continuous filaments relative to those of EcRecA. - Highlights: • We investigate Deinococcus radiodurans RecA interactions with long double-stranded DNA at the single-molecule level. • At physiological pH D. radiodurans RecA forms nucleoprotein filaments significantly faster relative to Escherichia coli RecA. • D. radiodurans RecA-dsDNA nucleoprotein filaments are more flexible and slightly shorter compared to those of E. coli RecA.« less

[Biosorption of Radionuclide Uranium by Deinococcus radiodurans].

PubMed

Yang, Jie; Dong, Fa-qin; Dai, Qun-wei; Liu, Ming-xue; Nie, Xiao-qin; Zhang, Dong; Ma, Jia-lin; Zhou, Xian

2015-04-01

As a biological adsorbent, Living Deinococcus radiodurans was used for removing radionuclide uranium in the aqueous solution. The effect factors on biosorption of radionuclide uranium were researched in the present paper, including solution pH values and initial uranium concentration. Meanwhile, the biosorption mechanism was researched by the method of FTIR and SEM/EDS. The results show that the optimum conditions for biosorption are as follows: pH = 5, co = 100 mg · L(-1) and the maximum biosorption capacity is up to 240 mgU · g(-1). According to the SEM results and EDXS analysis, it is indicated that the cell surface is attached by lots of sheet uranium crystals, and the main biosorpiton way of uranium is the ion exchange or surface complexation. Comparing FTIR spectra and FTIR fitting spectra before and after biosorption, we can find that the whole spectra has a certain change, particularly active groups (such as amide groups of the protein, hydroxy, carboxyl and phosphate group) are involved in the biosorption process. Then, there is a new peak at 906 cm(-1) and it is a stretching vibration peak of UO2(2+). Obviously, it is possible that as an anti radiation microorganism, Deinococcus radiodurans could be used for removing radionuclide uranium in radiation environment.

Responses of Mn2+ speciation in Deinococcus radiodurans and Escherichia coli to γ-radiation by advanced paramagnetic resonance methods

PubMed Central

Sharma, Ajay; Gaidamakova, Elena K.; Matrosova, Vera Y.; Bennett, Brian; Daly, Michael J.; Hoffman, Brian M.

2013-01-01

The remarkable ability of bacterium Deinococcus radiodurans to survive extreme doses of γ-rays (12,000 Gy), 20 times greater than Escherichia coli, is undiminished by loss of Mn-dependent superoxide dismutase (SodA). D. radiodurans radiation resistance is attributed to the accumulation of low-molecular-weight (LMW) “antioxidant” Mn2+–metabolite complexes that protect essential enzymes from oxidative damage. However, in vivo information about such complexes within D. radiodurans cells is lacking, and the idea that they can supplant reactive-oxygen-species (ROS)–scavenging enzymes remains controversial. In this report, measurements by advanced paramagnetic resonance techniques [electron-spin-echo (ESE)-EPR/electron nuclear double resonance/ESE envelope modulation (ESEEM)] reveal differential details of the in vivo Mn2+ speciation in D. radiodurans and E. coli cells and their responses to 10 kGy γ-irradiation. The Mn2+ of D. radiodurans exists predominantly as LMW complexes with nitrogenous metabolites and orthophosphate, with negligible EPR signal from Mn2+ of SodA. Thus, the extreme radiation resistance of D. radiodurans cells cannot be attributed to SodA. Correspondingly, 10 kGy irradiation causes no change in D. radiodurans Mn2+ speciation, despite the paucity of holo-SodA. In contrast, the EPR signal of E. coli is dominated by signals from low-symmetry enzyme sites such as that of SodA, with a minority pool of LMW Mn2+ complexes that show negligible coordination by nitrogenous metabolites. Nonetheless, irradiation of E. coli majorly changes LMW Mn2+ speciation, with extensive binding of nitrogenous ligands created by irradiation. We infer that E. coli is highly susceptible to radiation-induced ROS because it lacks an adequate supply of LMW Mn antioxidants. PMID:23536297

The three catalases in Deinococcus radiodurans: Only two show catalase activity

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jeong, Sun-Wook; Department of Biological Sciences, College of Biological Sciences and Biotechnology, Chungnam National University, Daejeon, 305-764; Jung, Jong-Hyun

2016-01-15

Deinococcus radiodurans, which is extremely resistant to ionizing radiation and oxidative stress, is known to have three catalases (DR1998, DRA0146, and DRA0259). In this study, to investigate the role of each catalase, we constructed catalase mutants (Δdr1998, ΔdrA0146, and ΔdrA0259) of D. radiodurans. Of the three mutants, Δdr1998 exhibited the greatest decrease in hydrogen peroxide (H{sub 2}O{sub 2}) resistance and the highest increase in intracellular reactive oxygen species (ROS) levels following H{sub 2}O{sub 2} treatments, whereas ΔdrA0146 showed no change in its H{sub 2}O{sub 2} resistance or ROS level. Catalase activity was not attenuated in ΔdrA0146, and none of the threemore » bands detected in an in-gel catalase activity assay disappeared in ΔdrA0146. The purified His-tagged recombinant DRA0146 did not show catalase activity. In addition, the phylogenetic analysis of the deinococcal catalases revealed that the DR1998-type catalase is common in the genus Deinococcus, but the DRA0146-type catalase was found in only 4 of 23 Deinococcus species. Taken together, these results indicate that DR1998 plays a critical role in the anti-oxidative system of D. radiodurans by detoxifying H{sub 2}O{sub 2}, but DRA0146 does not have catalase activity and is not involved in the resistance to H{sub 2}O{sub 2} stress. - Highlights: • The dr1998 mutant strain lost 90% of its total catalase activity. • Increased ROS levels and decreased H{sub 2}O{sub 2} resistance were observed in dr1998 mutants. • Lack of drA0146 did not affect any oxidative stress-related phenotypes. • The purified DRA0146 did not show catalase activity.« less

Preserving Genome Integrity: The DdrA Protein of Deinococcus radiodurans R1

PubMed Central

Harris, Dennis R; Tanaka, Masashi; Saveliev, Sergei V; Jolivet, Edmond; Earl, Ashlee M; Cox, Michael M

2004-01-01

The bacterium Deinococcus radiodurans can withstand extraordinary levels of ionizing radiation, reflecting an equally extraordinary capacity for DNA repair. The hypothetical gene product DR0423 has been implicated in the recovery of this organism from DNA damage, indicating that this protein is a novel component of the D. radiodurans DNA repair system. DR0423 is a homologue of the eukaryotic Rad52 protein. Following exposure to ionizing radiation, DR0423 expression is induced relative to an untreated control, and strains carrying a deletion of the DR0423 gene exhibit increased sensitivity to ionizing radiation. When recovering from ionizing-radiation-induced DNA damage in the absence of nutrients, wild-type D. radiodurans reassembles its genome while the mutant lacking DR0423 function does not. In vitro, the purified DR0423 protein binds to single-stranded DNA with an apparent affinity for 3′ ends, and protects those ends from nuclease degradation. We propose that DR0423 is part of a DNA end-protection system that helps to preserve genome integrity following exposure to ionizing radiation. We designate the DR0423 protein as DNA damage response A protein. PMID:15361932

Oxidative Stress Resistance in Deinococcus radiodurans†

PubMed Central

Slade, Dea; Radman, Miroslav

2011-01-01

Summary: Deinococcus radiodurans is a robust bacterium best known for its capacity to repair massive DNA damage efficiently and accurately. It is extremely resistant to many DNA-damaging agents, including ionizing radiation and UV radiation (100 to 295 nm), desiccation, and mitomycin C, which induce oxidative damage not only to DNA but also to all cellular macromolecules via the production of reactive oxygen species. The extreme resilience of D. radiodurans to oxidative stress is imparted synergistically by an efficient protection of proteins against oxidative stress and an efficient DNA repair mechanism, enhanced by functional redundancies in both systems. D. radiodurans assets for the prevention of and recovery from oxidative stress are extensively reviewed here. Radiation- and desiccation-resistant bacteria such as D. radiodurans have substantially lower protein oxidation levels than do sensitive bacteria but have similar yields of DNA double-strand breaks. These findings challenge the concept of DNA as the primary target of radiation toxicity while advancing protein damage, and the protection of proteins against oxidative damage, as a new paradigm of radiation toxicity and survival. The protection of DNA repair and other proteins against oxidative damage is imparted by enzymatic and nonenzymatic antioxidant defense systems dominated by divalent manganese complexes. Given that oxidative stress caused by the accumulation of reactive oxygen species is associated with aging and cancer, a comprehensive outlook on D. radiodurans strategies of combating oxidative stress may open new avenues for antiaging and anticancer treatments. The study of the antioxidation protection in D. radiodurans is therefore of considerable potential interest for medicine and public health. PMID:21372322

The N253F mutant structure of trehalose synthase from Deinococcus radiodurans reveals an open active-site topology.

PubMed

Chow, Sih Yao; Wang, Yung Lin; Hsieh, Yu Chiao; Lee, Guan Chiun; Liaw, Shwu Huey

2017-11-01

Trehalose synthase (TS) catalyzes the reversible conversion of maltose to trehalose and belongs to glycoside hydrolase family 13 (GH13). Previous mechanistic analysis suggested a rate-limiting protein conformational change, which is probably the opening and closing of the active site. Consistently, crystal structures of Deinococcus radiodurans TS (DrTS) in complex with the inhibitor Tris displayed an enclosed active site for catalysis of the intramoleular isomerization. In this study, the apo structure of the DrTS N253F mutant displays a new open conformation with an empty active site. Analysis of these structures suggests that substrate binding induces a domain rotation to close the active site. Such a substrate-induced domain rotation has also been observed in some other GH13 enzymes.

PprM is necessary for up-regulation of katE1, encoding the major catalase of Deinococcus radiodurans, under unstressed culture conditions.

PubMed

Jeong, Sun-Wook; Seo, Ho Seong; Kim, Min-Kyu; Choi, Jong-Il; Lim, Heon-Man; Lim, Sangyong

2016-06-01

Deinococcus radiodurans is a poly-extremophilic organism, capable of tolerating a wide variety of different stresses, such as gamma/ultraviolet radiation, desiccation, and oxidative stress. PprM, a cold shock protein homolog, is involved in the radiation resistance of D. radiodurans, but its role in the oxidative stress response has not been investigated. In this study, we investigated the effect of pprM mutation on catalase gene expression. pprM disruption decreased the mRNA and protein levels of KatE1, which is the major catalase in D. radiodurans, under normal culture conditions. A pprM mutant strain (pprM MT) exhibited decreased catalase activity, and its resistance to hydrogen peroxide (H2O2) decreased accordingly compared with that of the wild-type strain. We confirmed that RecG helicase negatively regulates katE1 under normal culture conditions. Among katE1 transcriptional regulators, the positive regulator drRRA was not altered in pprM (-), while the negative regulators perR, dtxR, and recG were activated more than 2.5-fold in pprM MT. These findings suggest that PprM is necessary for KatE1 production under normal culture conditions by down-regulation of katE1 negative regulators.

A PerR-like protein involved in response to oxidative stress in the extreme bacterium Deinococcus radiodurans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Chengzhi; Wang, Liangyan; Li, Tao

2014-07-18

Highlights: • We report a novel PerR-like protein of Fur family in D. radiodurans that is not annotated in the current database. • drperR responses to H{sub 2}O{sub 2} and functions as a negative regulator of katE and dps. • We provided implications on how to utilize sequenced genome data and the importance of genome data mining. • This study adds knowledge to complicated regulatory network that responds to ROS stress in D. radiodurans. - Abstract: Response and defense systems against reactive oxygen species (ROS) contribute to the remarkable resistance of Deinococcus radiodurans to oxidative stress induced by oxidants ormore » radiation. However, mechanisms involved in ROS response and defense systems of D. radiodurans are not well understood. Fur family proteins are important in ROS response. Only a single Fur homolog is predicted by sequence similarity in the current D. radiodurans genome database. Our bioinformatics analysis demonstrated an additional guanine nucleotide in the genome of D. radiodurans that is not in the database, leading to the discovery of another Fur homolog DrPerR. Gene disruption mutant of DrPerR showed enhanced resistance to hydrogen peroxide (H{sub 2}O{sub 2}) and increased catalase activity in cell extracts. Real-time PCR results indicated that DrPerR functions as a repressor of the catalase gene katE. Meanwhile, derepression of dps (DNA-binding proteins from starved cells) gene under H{sub 2}O{sub 2} stress by DrPerR point to its regulatory role in metal ions hemostasis. Thus, DrPerR might function as a Fur homolog protein which is involved in ROS response and defense. These results help clarify the complicated regulatory network that responds to ROS stress in D. radiodurans.« less

Comparative survival analysis of Deinococcus radiodurans and the haloarchaea Natrialba magadii and Haloferax volcanii exposed to vacuum ultraviolet irradiation.

PubMed

Abrevaya, Ximena C; Paulino-Lima, Ivan G; Galante, Douglas; Rodrigues, Fabio; Mauas, Pablo J D; Cortón, Eduardo; Lage, Claudia de Alencar Santos

2011-12-01

The haloarchaea Natrialba magadii and Haloferax volcanii, as well as the radiation-resistant bacterium Deinococcus radiodurans, were exposed to vacuum UV (VUV) radiation at the Brazilian Synchrotron Light Laboratory. Cell monolayers (containing 10(5) to 10(6) cells per sample) were prepared over polycarbonate filters and irradiated under high vacuum (10(-5) Pa) with polychromatic synchrotron radiation. N. magadii was remarkably resistant to high vacuum with a survival fraction of (3.77±0.76)×10(-2), which was larger than that of D. radiodurans (1.13±0.23)×10(-2). The survival fraction of the haloarchaea H. volcanii, of (3.60±1.80)×10(-4), was much smaller. Radiation resistance profiles were similar between the haloarchaea and D. radiodurans for fluences up to 150 J m(-2). For fluences larger than 150 J m(-2), there was a significant decrease in the survival of haloarchaea, and in particular H. volcanii did not survive. Survival for D. radiodurans was 1% after exposure to the higher VUV fluence (1350 J m(-2)), while N. magadii had a survival lower than 0.1%. Such survival fractions are discussed regarding the possibility of interplanetary transfer of viable microorganisms and the possible existence of microbial life in extraterrestrial salty environments such as the planet Mars and Jupiter's moon Europa. This is the first work to report survival of haloarchaea under simulated interplanetary conditions.

Deinococcus Mn2+ -Peptide Complex: A Novel Approach to Alphavirus Vaccine Development

DTIC Science & Technology

2016-08-05

immunogenicity loss due to oxidative damage to the surface proteins at the high doses of radiation required for complete virus inactivation. Thus, we...bacteria Deinococcus radiodurans) in the present study which selectively protects proteins but not the nucleic acid from the radiation - induced...presence of MDP have significant epitope preservation even at supra-lethal doses of radiation . Irradiated viruses were found to be completely

Modulating Radiation Resistance: Novel Protection Paradigms Based on Defenses against Ionizing Radiation in the Extrempohile Deinococcus radiodurans

DTIC Science & Technology

2013-07-01

USA (2013); 2) Many environmental yeast are extremely radiation-resistant, accumulate nitrogenous Mn2+-Pi complexes, and highly resistant to...5 important in aerobic environments . Numerous organisms which accumulate “compatible solutes” fit this model, including representative archaea...cyanobacteria, lichens, alpine yeast, and tardigrades. 4.3 Knowns and Unknowns of Deinococcus Mn2+ Complexes It is worth reminding the reader

Laboratory simulation of interplanetary ultraviolet radiation (broad spectrum) and its effects on Deinococcus radiodurans

NASA Astrophysics Data System (ADS)

Paulino-Lima, Ivan Gláucio; Pilling, Sérgio; Janot-Pacheco, Eduardo; de Brito, Arnaldo Naves; Barbosa, João Alexandre Ribeiro Gonçalves; Leitão, Alvaro Costa; Lage, Claudia de Alencar Santos

2010-08-01

The radiation-resistant bacterium Deinococcus radiodurans was exposed to a simulated interplanetary UV radiation at the Brazilian Synchrotron Light Laboratory (LNLS). Bacterial samples were irradiated on different substrates to investigate the influence of surface relief on cell survival. The effects of cell multi-layers were also investigated. The ratio of viable microorganisms remained virtually the same (average 2%) for integrated doses from 1.2 to 12 kJ m -2, corresponding to 16 h of irradiation at most. The asymptotic profiles of the curves, clearly connected to a shielding effect provided by multi-layering cells on a cavitary substrate (carbon tape), means that the inactivation rate may not change significantly along extended periods of exposure to radiation. Such high survival rates reinforce the possibility of an interplanetary transfer of viable microbes.

Impact of low-temperature plasmas on Deinococcus radiodurans and biomolecules

NASA Technical Reports Server (NTRS)

Mogul, Rakesh; Bol'shakov, Alexander A.; Chan, Suzanne L.; Stevens, Ramsey M.; Khare, Bishun N.; Meyyappan, M.; Trent, Jonathan D.

2003-01-01

The effects of cold plasma on Deinococcus radiodurans, plasmid DNA, and model proteins were assessed using microbiological, spectrometric, and biochemical techniques. In low power O(2) plasma (approximately 25 W, approximately 45 mTorr, 90 min), D. radiodurans, a radiation-resistant bacterium, showed a 99.999% reduction in bioburden. In higher power O(2) plasma (100 W and 500 mTorr), the reduction rate increased about 10-fold and observation by atomic force microscopy showed significant damage to the cell. Damage to cellular lipids, proteins, and chromosome was indicated by losses of infrared spectroscopic peaks at 2930, 1651, 1538, and 1245 cm(-1), respectively. In vitro experiments show that O(2) plasmas induce DNA strand scissions and cross-linking as well as reduction of enzyme activity. The observed degradation and removal of biomolecules was power-dependent. Exposures to 200 W at 500 mTorr removed biomolecules to below detection limits in 60 s. Emission spectroscopy indicated that D. radiodurans cells were volatilized into CO(2), CO, N(2), and H(2)O, confirming that these plasmas were removing complex biological matter from surfaces. A CO(2) plasma was not as effective as the O(2) plasma, indicating the importance of plasma composition and the dominant role of chemical degradation. Together, these findings have implications for NASA planetary protection schemes and for the contamination of Mars.

Expression, purification, crystallization and preliminary X-ray crystallographic studies of Deinococcus radiodurans thioredoxin reductase

DOE Office of Scientific and Technical Information (OSTI.GOV)

Obiero, Josiah; Bonderoff, Sara A.; Goertzen, Meghan M.

2006-08-01

Recombinant D. radiodurans TrxR with a His tag at the N-terminus was expressed in Escherichia coli and purified by metal-affinity chromatography. The protein was crystallized using the sitting-drop vapour-diffusion method in the presence of 35% PEG 4000, 0.2 M ammonium acetate and citric acid buffer pH 5.1 at 293 K. Deinococcus radiodurans, a Gram-positive bacterium capable of withstanding extreme ionizing radiation, contains two thioredoxins (Trx and Trx1) and a single thioredoxin reductase (TrxR) as part of its response to oxidative stress. Thioredoxin reductase is a member of the family of pyridine nucleotide-disulfide oxidoreductase flavoenzymes. Recombinant D. radiodurans TrxR with amore » His tag at the N-terminus was expressed in Escherichia coli and purified by metal-affinity chromatography. The protein was crystallized using the sitting-drop vapour-diffusion method in the presence of 35% PEG 4000, 0.2 M ammonium acetate and citric acid buffer pH 5.1 at 293 K. X-ray diffraction data were collected on a cryocooled crystal to a resolution of 1.9 Å using a synchrotron-radiation source. The space group was determined to be P3{sub 2}21, with unit-cell parameters a = b = 84.33, c = 159.88 Å. The structure of the enzyme has been solved by molecular-replacement methods and structure refinement is in progress.« less

Number, position, and significance of the pseudouridines in the large subunit ribosomal RNA of Haloarcula marismortui and Deinococcus radiodurans

PubMed Central

DEL CAMPO, MARK; RECINOS, CLAUDIA; YANEZ, GISCARD; POMERANTZ, STEVEN C.; GUYMON, REBECCA; CRAIN, PAMELA F.; MCCLOSKEY, JAMES A.; OFENGAND, JAMES

2005-01-01

The number and position of the pseudouridines of Haloarcula marismortui and Deinococcus radiodurans large subunit RNA have been determined by a combination of total nucleoside analysis by HPLC-mass spectrometry and pseudouridine sequencing by the reverse transcriptase method and by LC/MS/MS. Three pseudouridines were found in H. marismortui, located at positions 1956, 1958, and 2621 corresponding to Escherichia coli positions 1915, 1917, and 2586, respectively. The three pseudouridines are all in locations found in other organisms. Previous reports of a larger number of pseudouridines in this organism were incorrect. Three pseudouridines and one 3-methyl pseudouridine (m3Ψ) were found in D. radiodurans 23S RNA at positions 1894, 1898 (m3Ψ), 1900, and 2584, the m3Ψ site being determined by a novel application of mass spectrometry. These positions correspond to E. coli positions 1911, 1915, 1917, and 2605, which are also pseudouridines in E. coli (1915 is m3Ψ). The pseudouridines in the helix 69 loop, residues 1911, 1915, and 1917, are in positions highly conserved among all phyla. Pseudouridine 2584 in D. radiodurans is conserved in eubacteria and a chloroplast but is not found in archaea or eukaryotes, whereas pseudouridine 2621 in H. marismortui is more conserved in eukaryotes and is not found in eubacteria. All the pseudoridines are near, but not exactly at, nucleotides directly involved in various aspects of ribosome function. In addition, two D. radiodurans Ψ synthases responsible for the four Ψ were identified. PMID:15659360

The S-layer Protein DR_2577 Binds Deinoxanthin and under Desiccation Conditions Protects against UV-Radiation in Deinococcus radiodurans

PubMed Central

Farci, Domenica; Slavov, Chavdar; Tramontano, Enzo; Piano, Dario

2016-01-01

Deinococcus radiodurans has the puzzling ability to withstand over a broad range of extreme conditions including high doses of ultraviolet radiation and deep desiccation. This bacterium is surrounded by a surface layer (S-layer) built of a regular repetition of several proteins, assembled to form a paracrystalline structure. Here we report that the deletion of a main constituent of this S-layer, the gene DR_2577, causes a decrease in the UVC resistance, especially in desiccated cells. Moreover, we show that the DR_2577 protein binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium. A further spectroscopical characterization of the deinoxanthin-DR_2577 complex revealed features which could suggest a protective role of DR_2577. We propose that, especially under desiccation, the S-layer shields the bacterium from incident ultraviolet light and could behave as a first lane of defense against UV radiation. PMID:26909071

The S-layer Protein DR_2577 Binds Deinoxanthin and under Desiccation Conditions Protects against UV-Radiation in Deinococcus radiodurans.

PubMed

Farci, Domenica; Slavov, Chavdar; Tramontano, Enzo; Piano, Dario

2016-01-01

Deinococcus radiodurans has the puzzling ability to withstand over a broad range of extreme conditions including high doses of ultraviolet radiation and deep desiccation. This bacterium is surrounded by a surface layer (S-layer) built of a regular repetition of several proteins, assembled to form a paracrystalline structure. Here we report that the deletion of a main constituent of this S-layer, the gene DR_2577, causes a decrease in the UVC resistance, especially in desiccated cells. Moreover, we show that the DR_2577 protein binds the carotenoid deinoxanthin, a strong protective antioxidant specific of this bacterium. A further spectroscopical characterization of the deinoxanthin-DR_2577 complex revealed features which could suggest a protective role of DR_2577. We propose that, especially under desiccation, the S-layer shields the bacterium from incident ultraviolet light and could behave as a first lane of defense against UV radiation.

Effects of Low-Temperature Plasma-Sterilization on Mars Analog Soil Samples Mixed with Deinococcus radiodurans.

PubMed

Schirmack, Janosch; Fiebrandt, Marcel; Stapelmann, Katharina; Schulze-Makuch, Dirk

2016-05-26

We used Ar plasma-sterilization at a temperature below 80 °C to examine its effects on the viability of microorganisms when intermixed with tested soil. Due to a relatively low temperature, this method is not thought to affect the properties of a soil, particularly its organic component, to a significant degree. The method has previously been shown to work well on spacecraft parts. The selected microorganism for this test was Deinococcus radiodurans R1, which is known for its remarkable resistance to radiation effects. Our results showed a reduction in microbial counts after applying a low temperature plasma, but not to a degree suitable for a sterilization of the soil. Even an increase of the treatment duration from 1.5 to 45 min did not achieve satisfying results, but only resulted in in a mean cell reduction rate of 75% compared to the untreated control samples.

IrrE, a Global Regulator of Extreme Radiation Resistance in Deinococcus radiodurans, Enhances Salt Tolerance in Escherichia coli and Brassica napus

PubMed Central

Zhou, Zhengfu; Yan, Yongliang; Zhang, Wei; Lu, Wei; Ping, Shuzhen; Dai, Qilin; Yuan, Menglong; Feng, Bin; Hou, Xiaoguang; Zhang, Ying; Ruiqiang; Liu, Tingting; Feng, Lu; Wang, Lei; Chen, Ming; Lin, Min

2009-01-01

Background Globally, about 20% of cultivated land is now affected by salinity. Salt tolerance is a trait of importance to all crops in saline soils. Previous efforts to improve salt tolerance in crop plants have met with only limited success. Bacteria of the genus Deinococcus are known for their ability to survive highly stressful conditions, and therefore possess a unique pool of genes conferring extreme resistance. In Deinococcus radiodurans, the irrE gene encodes a global regulator responsible for extreme radioresistance. Methodology/Principal Findings Using plate assays, we showed that IrrE protected E. coli cells against salt shock and other abiotic stresses such as oxidative, osmotic and thermal shocks. Comparative proteomic analysis revealed that IrrE functions as a switch to regulate different sets of proteins such as stress responsive proteins, protein kinases, glycerol-degrading enzymes, detoxification proteins, and growth-related proteins in E. coli. We also used quantitative RT-PCR to investigate expression of nine selected stress-responsive genes in transgenic and wild-type Brassica napus plants. Transgenic B. napus plants expressing the IrrE protein can tolerate 350 mM NaCl, a concentration that inhibits the growth of almost all crop plants. Conclusions Expression of IrrE, a global regulator for extreme radiation resistance in D. radiodurans, confers significantly enhanced salt tolerance in both E. coli and B. napus. We thus propose that the irrE gene might be used as a potentially promising transgene to improve abiotic stress tolerances in crop plants. PMID:19204796

Biosynthesis of gold nanoparticles by the extreme bacterium Deinococcus radiodurans and an evaluation of their antibacterial properties.

PubMed

Li, Jiulong; Li, Qinghao; Ma, Xiaoqiong; Tian, Bing; Li, Tao; Yu, Jiangliu; Dai, Shang; Weng, Yulan; Hua, Yuejin

Deinococcus radiodurans is an extreme bacterium known for its high resistance to stresses including radiation and oxidants. The ability of D. radiodurans to reduce Au(III) and biosynthesize gold nanoparticles (AuNPs) was investigated in aqueous solution by ultraviolet and visible (UV/Vis) absorption spectroscopy, electron microscopy, X-ray diffraction (XRD), dynamic light scattering (DLS), Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). D. radiodurans efficiently synthesized AuNPs from 1 mM Au(III) solution in 8 h. The AuNPs were of spherical, triangular and irregular shapes with an average size of 43.75 nm and a polydispersity index of 0.23 as measured by DLS. AuNPs were distributed in the cell envelope, across the cytosol and in the extracellular space. XRD analysis confirmed the crystallite nature of the AuNPs from the cell supernatant. Data from the FTIR and XPS showed that upon binding to proteins or compounds through interactions with carboxyl, amine, phospho and hydroxyl groups, Au(III) may be reduced to Au(I), and further reduced to Au(0) with the capping groups to stabilize the AuNPs. Biosynthesis of AuNPs was optimized with respect to the initial concentration of gold salt, bacterial growth period, solution pH and temperature. The purified AuNPs exhibited significant antibacterial activity against both Gram-negative ( Escherichia coli ) and Gram-positive ( Staphylococcus aureus ) bacteria by damaging their cytoplasmic membrane. Therefore, the extreme bacterium D. radiodurans can be used as a novel bacterial candidate for efficient biosynthesis of AuNPs, which exhibited potential in biomedical application as an antibacterial agent.

FrnE, a Cadmium-Inducible Protein in Deinococcus radiodurans, Is Characterized as a Disulfide Isomerase Chaperone In Vitro and for Its Role in Oxidative Stress Tolerance In Vivo

PubMed Central

Khairnar, Nivedita P.; Joe, Min-Ho; Misra, H. S.; Lim, Sang-Yong

2013-01-01

Deinococcus radiodurans R1 exposed to a lethal dose of cadmium shows differential expression of a large number of genes, including frnE (drfrnE) and some of those involved in DNA repair and oxidative stress tolerance. The drfrnE::nptII mutant of D. radiodurans showed growth similar to that of the wild type, but its tolerance to 10 mM cadmium and 10 mM diamide decreased by ∼15- and ∼3-fold, respectively. These cells also showed nearly 6 times less resistance to gamma radiation at 12 kGy and ∼2-fold-higher sensitivity to 40 mM hydrogen peroxide than the wild type. In trans expression of drFrnE increased cytotoxicity of dithiothreitol (DTT) in the dsbA mutant of Escherichia coli. Recombinant drFrnE showed disulfide isomerase activity and could maintain insulin in its reduced form in the presence of DTT. While an equimolar ratio of wild-type protein could protect malate dehydrogenase completely from thermal denaturation at 42°C, the C22S mutant of drFrnE provided reduced protection to malate dehydrogenase from thermal inactivation. These results suggested that drFrnE is a protein disulfide isomerase in vitro and has a role in oxidative stress tolerance of D. radiodurans possibly by protecting the damaged cellular proteins from inactivation. PMID:23603741

The Essential Role of the Deinococcus radiodurans ssb Gene in Cell Survival and Radiation Tolerance

PubMed Central

Lockhart, J. Scott; DeVeaux, Linda C.

2013-01-01

Recent evidence has implicated single-stranded DNA-binding protein (SSB) expression level as an important factor in microbial radiation resistance. The genome of the extremely radiation resistant bacterium Deinococcus radiodurans contains genes for two SSB homologs: the homodimeric, canonical Ssb, encoded by the gene ssb, and a novel pentameric protein encoded by the gene ddrB. ddrB is highly induced upon exposure to radiation, and deletions result in decreased radiation-resistance, suggesting an integral role of the protein in the extreme resistance exhibited by this organism. Although expression of ssb is also induced after irradiation, Ssb is thought to be involved primarily in replication. In this study, we demonstrate that Ssb in D. radiodurans is essential for cell survival. The lethality of an ssb deletion cannot be complemented by providing ddrB in trans. In addition, the radiation-sensitive phenotype conferred by a ddrB deletion is not alleviated by providing ssb in trans. By altering expression of the ssb gene, we also show that lower levels of transcription are required for optimal growth than are necessary for high radiation resistance. When expression is reduced to that of E. coli, ionizing radiation resistance is similarly reduced. UV resistance is also decreased under low ssb transcript levels where growth is unimpaired. These results indicate that the expression of ssb is a key component of both normal cellular metabolism as well as pathways responsible for the high radiation tolerance of D. radiodurans. PMID:23951213

Coexisting properties of thermostability and ultraviolet radiation resistance in the main S-layer complex of Deinococcus radiodurans.

PubMed

Farci, Domenica; Slavov, Chavdar; Piano, Dario

2018-01-17

Deinococcus radiodurans is well known for its unusual resistance to different environmental stresses. Recently, we have described a novel complex composed of the surface (S)-layer protein DR_2577 and the carotenoid deinoxanthin. We also showed a role of this complex in the UV resistance under desiccation. Both these properties, UV and desiccation resistance, suggest a selective pressure generated by Sun irradiation. In order to confirm this hypothesis we checked whether this S-layer Deinoxanthin Binding Complex (SDBC) has features of thermo-resistance, a property also expected in proteins evolved under solar irradiative pressure. We performed the spectroscopic characterization of the SDBC by means of thermal shift assay, circular dichroism and related in silico analysis. Our findings identify a stability typical of thermo-adapted proteins and provide a new insight into the origin of specific S-layer types. The results are discussed in terms of co-evolutionary mechanisms related to Sun-induced desiccation and heat.

Nucleotide sequence analysis of the gene encoding the Deinococcus radiodurans surface protein, derived amino acid sequence, and complementary protein chemical studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peters, J.; Peters, M.; Lottspeich, F.

1987-11-01

The complete nucleotide sequence of the gene encoding the surface (hexagonally packed intermediate (HPI))-layer polypeptide of Deinococcus radiodurans Sark was determined and found to encode a polypeptide of 1036 amino acids. Amino acid sequence analysis of about 30% of the residues revealed that the mature polypeptide consists of at least 978 amino acids. The N terminus was blocked to Edman degradation. The results of proteolytic modification of the HPI layer in situ and M/sub r/ estimations of the HPI polypeptide expressed in Escherichia coli indicated that there is a leader sequence. The N-terminal region contained a very high percentage (29%)more » of threonine and serine, including a cluster of nine consecutive serine or threonine residues, whereas a stretch near the C terminus was extremely rich in aromatic amino acids (29%). The protein contained at least two disulfide bridges, as well as tightly bound reducing sugars and fatty acids.« less

Structural studies of the nudix hydrolase DR1025 from deinococcus radiodurans and its ligand complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ranatunga, Wasantha; Hill, Emma E.; Mooster, Jana L.

We have determined the crystal structure, at 1.4, of the Nudix hydrolase DR1025 from the extremely radiation resistant bacterium Deinococcus radiodurans. The protein forms an intertwined homodimer by exchanging N-terminal segments between chains. We have identified additional conserved elements of the Nudix fold, including the metal-binding motif, a kinked b-strand characterized by a proline two positions upstream of the Nudix consensus sequence, and participation of the N-terminal extension in the formation of the substrate-binding pocket. Crystal structures were also solved of DR1025 crystallized in the presence of magnesium and either a GTP analog or Ap4A (both at 1.6 resolution). Inmore » the Ap4Aco-crystal, the electron density indicated that the product of asymmetric hydrolysis, ATP, was bound to the enzyme. The GTP analog bound structure showed that GTP was bound almost identically as ATP. Neither nucleoside triphosphate was further cleaved.« less

Imposed Environmental Stresses Facilitate Cell-Free Nanoparticle Formation by Deinococcus radiodurans

PubMed Central

2017-01-01

ABSTRACT The biological synthesis of metal nanoparticles has been examined in a wide range of organisms, due to increased interest in green synthesis and environmental remediation applications involving heavy metal ion contamination. Deinococcus radiodurans is particularly attractive for environmental remediation involving metal reduction, due to its high levels of resistance to radiation and other environmental stresses. However, few studies have thoroughly examined the relationships between environmental stresses and the resulting effects on nanoparticle biosynthesis. In this work, we demonstrate cell-free nanoparticle production and study the effects of metal stressor concentrations and identity, temperature, pH, and oxygenation on the production of extracellular silver nanoparticles by D. radiodurans R1. We also report the synthesis of bimetallic silver and gold nanoparticles following the addition of a metal stressor (silver or gold), highlighting how production of these particles is enabled through the application of environmental stresses. Additionally, we found that both the morphology and size of monometallic and bimetallic nanoparticles were dependent on the environmental stresses imposed on the cells. The nanoparticles produced by D. radiodurans exhibited antimicrobial activity comparable to that of pure silver nanoparticles and displayed catalytic activity comparable to that of pure gold nanoparticles. Overall, we demonstrate that biosynthesized nanoparticle properties can be partially controlled through the tuning of applied environmental stresses, and we provide insight into how their application may affect nanoparticle production in D. radiodurans during bioremediation. IMPORTANCE Biosynthetic production of nanoparticles has recently gained prominence as a solution to rising concerns regarding increased bacterial resistance to antibiotics and a desire for environmentally friendly methods of bioremediation and chemical synthesis. To date, a range of organisms have been utilized for nanoparticle formation. The extremophile D. radiodurans, which can withstand significant environmental stresses and therefore is more robust for metal reduction applications, has yet to be exploited for this purpose. Thus, this work improves our understanding of the impact of environmental stresses on biogenic nanoparticle morphology and composition during metal reduction processes in this organism. This work also contributes to enhancing the controlled synthesis of nanoparticles with specific attributes and functions using biological systems. PMID:28687649

Imposed Environmental Stresses Facilitate Cell-Free Nanoparticle Formation by Deinococcus radiodurans.

PubMed

Chen, Angela; Contreras, Lydia M; Keitz, Benjamin K

2017-09-15

The biological synthesis of metal nanoparticles has been examined in a wide range of organisms, due to increased interest in green synthesis and environmental remediation applications involving heavy metal ion contamination. Deinococcus radiodurans is particularly attractive for environmental remediation involving metal reduction, due to its high levels of resistance to radiation and other environmental stresses. However, few studies have thoroughly examined the relationships between environmental stresses and the resulting effects on nanoparticle biosynthesis. In this work, we demonstrate cell-free nanoparticle production and study the effects of metal stressor concentrations and identity, temperature, pH, and oxygenation on the production of extracellular silver nanoparticles by D. radiodurans R1. We also report the synthesis of bimetallic silver and gold nanoparticles following the addition of a metal stressor (silver or gold), highlighting how production of these particles is enabled through the application of environmental stresses. Additionally, we found that both the morphology and size of monometallic and bimetallic nanoparticles were dependent on the environmental stresses imposed on the cells. The nanoparticles produced by D. radiodurans exhibited antimicrobial activity comparable to that of pure silver nanoparticles and displayed catalytic activity comparable to that of pure gold nanoparticles. Overall, we demonstrate that biosynthesized nanoparticle properties can be partially controlled through the tuning of applied environmental stresses, and we provide insight into how their application may affect nanoparticle production in D. radiodurans during bioremediation. IMPORTANCE Biosynthetic production of nanoparticles has recently gained prominence as a solution to rising concerns regarding increased bacterial resistance to antibiotics and a desire for environmentally friendly methods of bioremediation and chemical synthesis. To date, a range of organisms have been utilized for nanoparticle formation. The extremophile D. radiodurans , which can withstand significant environmental stresses and therefore is more robust for metal reduction applications, has yet to be exploited for this purpose. Thus, this work improves our understanding of the impact of environmental stresses on biogenic nanoparticle morphology and composition during metal reduction processes in this organism. This work also contributes to enhancing the controlled synthesis of nanoparticles with specific attributes and functions using biological systems. Copyright © 2017 American Society for Microbiology.

Crystal structure of the DNA polymerase III β subunit (β-clamp) from the extremophile Deinococcus radiodurans.

PubMed

Niiranen, Laila; Lian, Kjersti; Johnson, Kenneth A; Moe, Elin

2015-02-27

Deinococcus radiodurans is an extremely radiation and desiccation resistant bacterium which can tolerate radiation doses up to 5,000 Grays without losing viability. We are studying the role of DNA repair and replication proteins for this unusual phenotype by a structural biology approach. The DNA polymerase III β subunit (β-clamp) acts as a sliding clamp on DNA, promoting the binding and processivity of many DNA-acting proteins, and here we report the crystal structure of D. radiodurans β-clamp (Drβ-clamp) at 2.0 Å resolution. The sequence verification process revealed that at the time of the study the gene encoding Drβ-clamp was wrongly annotated in the genome database, encoding a protein of 393 instead of 362 amino acids. The short protein was successfully expressed, purified and used for crystallisation purposes in complex with Cy5-labeled DNA. The structure, which was obtained from blue crystals, shows a typical ring-shaped bacterial β-clamp formed of two monomers, each with three domains of identical topology, but with no visible DNA in electron density. A visualisation of the electrostatic surface potential reveals a highly negatively charged outer surface while the inner surface and the dimer forming interface have a more even charge distribution. The structure of Drβ-clamp was determined to 2.0 Å resolution and shows an evenly distributed electrostatic surface charge on the DNA interacting side. We hypothesise that this charge distribution may facilitate efficient movement on encircled DNA and help ensure efficient DNA metabolism in D. radiodurans upon exposure to high doses of ionizing irradiation or desiccation.

Expression of lycopene biosynthesis genes fused in line with Shine-Dalgarno sequences improves the stress-tolerance of Lactococcus lactis.

PubMed

Dong, Xiangrong; Wang, Yanping; Yang, Fengyuan; Zhao, Shanshan; Tian, Bing; Li, Tao

2017-01-01

Lycopene biosynthetic genes from Deinococcus radiodurans were co-expressed in Lactococcus lactis to produce lycopene and improve its tolerance to stress. Lycopene-related genes from D. radiodurans, DR1395 (crtE), DR0862 (crtB), and DR0861 (crtI), were fused in line with S hine-Dalgarno (SD) sequences and co-expressed in L. lactis. The recombinant strain produced 0.36 mg lycopene g -1  dry cell wt after 48 h fermentation. The survival rate to UV irradiation of the recombinant strain was higher than that of the non-transformed strain. The L. lactis with co-expressed genes responsible for lycopene biosynthesis from D. radiodurans produced lycopene and exhibited increased resistance to UV stress, suggesting that the recombinant strain has important application potential in food industry.

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Daly, Michael J.

2006-05-01

Ionizing Radiation (IR) Resistance in Bacteria. Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR) and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus & Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella & Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny,more » where very high and very low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR.« less

Characterizing the Catalytic Potential of Deinococcus, Arthrobacter and other Robust Bacteria in Contaminated Subsurface Environments of the Hanford Site

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredrickson, Jim K.; Daly, Michael J.

2006-06-01

Until recently, there have been no clear physiologic predictors of a cell's ability to recover from ionizing radiation (IR), desiccation, and other DOE-relevant oxidative stress conditions. In general, the most resistant bacteria have been Gram-positive (e.g., Deinococcus, Arthrobacter, Lactobacillus & Enterococcus spp.) and the most sensitive have been Gram-negative (e.g., Pseudomonas, Shewanella & Neisseria spp.). However, there are several reported exceptions to this paradigm, the Gram-negative cyanobacterium Chroococcidiopsis is extremely resistant to IR, whereas the Gram-positive Micrococcus luteus is sensitive. We have identified biomolecular signatures for radiation sensitivity and resistance which are independent of phylogeny, where very high and verymore » low intracellular Mn/Fe concentration ratios correlated with very high and very low resistances, respectively; and restricting Mn(II) in the famously resistant Deinococcus radiodurans sensitized this eubacterium to IR (http://cfyn.ifas.ufl.edu/radiation.pdf).« less

Spacecraft Sterilization Using Non-Equilibrium Atmospheric Pressure Plasma

NASA Technical Reports Server (NTRS)

Cooper, Moogega; Vaze, Nachiket; Anderson, Shawn; Fridman, Gregory; Vasilets, Victor N.; Gutsol, Alexander; Tsapin, Alexander; Fridman, Alexander

2007-01-01

As a solution to chemically and thermally destructive sterilization methods currently used for spacecraft, non-equilibrium atmospheric pressure plasmas are used to treat surfaces inoculated with Bacillus subtilis and Deinococcus radiodurans. Evidence of significant morphological changes and reduction in viability due to plasma exposure will be presented, including a 4-log reduction of B. subtilis after 2 minutes of dielectric barrier discharge treatment.

Low-Temperature Ionizing Radiation Resistance of Deinococcus radiodurans and Antarctic Dry Valley Bacteria

NASA Astrophysics Data System (ADS)

Dartnell, Lewis R.; Hunter, Stephanie J.; Lovell, Keith V.; Coates, Andrew J.; Ward, John M.

2010-09-01

The high flux of cosmic rays onto the unshielded surface of Mars poses a significant hazard to the survival of martian microbial life. Here, we determined the survival responses of several bacterial strains to ionizing radiation exposure while frozen at a low temperature characteristic of the martian near-subsurface. Novel psychrotolerant bacterial strains were isolated from the Antarctic Dry Valleys, an environmental analogue of the martian surface, and identified by 16S rRNA gene phylogeny as representatives of Brevundimonas, Rhodococcus, and Pseudomonas genera. These isolates, in addition to the known radioresistant extremophile Deinococcus radiodurans, were exposed to gamma rays while frozen on dry ice (-79°C). We found D. radiodurans to exhibit far greater radiation resistance when irradiated at -79°C than was observed in similar studies performed at higher temperatures. This greater radiation resistance has important implications for the estimation of potential survival times of microorganisms near the martian surface. Furthermore, the most radiation resistant of these Dry Valley isolates, Brevundimonas sp. MV.7, was found to show 99% 16S rRNA gene similarity to contaminant bacteria discovered in clean rooms at both Kennedy and Johnson Space Centers and so is of prime concern to efforts in the planetary protection of Mars from our lander probes. Results from this experimental irradiation, combined with previous radiation modeling, indicate that Brevundimonas sp. MV.7 emplaced only 30 cm deep in martian dust could survive the cosmic radiation for up to 100,000 years before suffering 106 population reduction.

Stress induction in the bacteria Shewanella oneidensis and Deinococcus radiodurans in response to below-background ionizing radiation.

PubMed

Castillo, Hugo; Schoderbek, Donald; Dulal, Santosh; Escobar, Gabriela; Wood, Jeffrey; Nelson, Roger; Smith, Geoffrey

2015-01-01

The 'Linear no-threshold' (LNT) model predicts that any amount of radiation increases the risk of organisms to accumulate negative effects. Several studies at below background radiation levels (4.5-11.4 nGy h(-1)) show decreased growth rates and an increased susceptibility to oxidative stress. The purpose of our study is to obtain molecular evidence of a stress response in Shewanella oneidensis and Deinococcus radiodurans grown at a gamma dose rate of 0.16 nGy h(-1), about 400 times less than normal background radiation. Bacteria cultures were grown at a dose rate of 0.16 or 71.3 nGy h(-1) gamma irradiation. Total RNA was extracted from samples at early-exponential and stationary phases for the rt-PCR relative quantification (radiation-deprived treatment/background radiation control) of the stress-related genes katB (catalase), recA (recombinase), oxyR (oxidative stress transcriptional regulator), lexA (SOS regulon transcriptional repressor), dnaK (heat shock protein 70) and SOA0154 (putative heavy metal efflux pump). Deprivation of normal levels of radiation caused a reduction in growth of both bacterial species, accompanied by the upregulation of katB, recA, SOA0154 genes in S. oneidensis and the upregulation of dnaK in D. radiodurans. When cells were returned to background radiation levels, growth rates recovered and the stress response dissipated. Our results indicate that below-background levels of radiation inhibited growth and elicited a stress response in two species of bacteria, contrary to the LNT model prediction.

Deinococcus frigens sp. nov., Deinococcus saxicola sp. nov., and Deinococcus marmoris sp. nov., low temperature and draught-tolerating, UV-resistant bacteria from continental Antarctica.

PubMed

Hirsch, Peter; Gallikowski, Claudia A; Siebert, Jörg; Peissl, Klaus; Kroppenstedt, Reiner; Schumann, Peter; Stackebrandt, Erko; Anderson, Robert

2004-11-01

Six Gram-positive, non-motile, UV- and draught-tolerant bacteria were isolated from antarctic soil and rock samples. The pink to orange cocci grew well on oligotrophic medium PYGV (pH 7.5) at 9-18 degrees C. They tolerated 0-10% NaCl, were aerobic to facultatively anaerobic and contained ornithine in their cell wall (type A3beta, Orn-Gly2). The lipid profiles of four strains were found to be typical for those of D. radiodurans. Major fatty acids were 16:1cis9, 15:1cis9, 17:1cis9 and i17:1cis9, the respiratory quinone of three strains was MK-8. Comparative 16S rDNA gene sequencing revealed phylogenetic relationships to the Deinococcus clade, especially to D. radiopugnans. The levels of 16S rRNA gene sequence similarity and DNA-DNA hybridisation data showed the six isolates represented new taxa. Phenotypic properties supported the description of three new species which were different from the eight known Deinococcus species and particularly from D. radiopugnans. Soil isolate AA-692T (DSM 12807T) is the type strain of Deinococcus frigens sp. nov., with AA-752 (DSM 15993) and AA-829 (DSM 15994) as additional strains from soil. The endolithic isolate AA-1444T, Deinococcus saxicola sp. nov., (DSM 15974T) came from antarctic sandstone, and Deinococcus marmoris sp. nov. (isolate AA-63T [DSM 12784T]) as well as AA-69 (DSM 15951) were isolated from antarctic marble.

Small-Molecule Antioxidant Proteome-Shields in Deinococcus Radiodurans

DTIC Science & Technology

2010-09-01

from oxidative damage and degradation. Nucleic Acids Res 31: 2995–3005. 48. Oren A, Gunde-Cimerman N (2007) Mycosporines and mycosporine - like amino ...TT-ultrafiltrates include Mn (Figure 2A), phosphate (Figure 2A), uridine, adenosine and uracil (Figure 2B and Table S1), and amino acids and peptides...which catalytically remove superoxide (O2 N2) via a disproportionation mechanism [23,24]; and amino acids and peptides, which scavenge HON very

Genetic analysis of stress responses in soil bacteria for enhanced bioremediation of mixed contaminants. 1997 annual progress report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, K.K.

'To provide increased knowledge of stress responses of indigenous microbes at contaminated sites as well as using microbes as molecular probes for monitoring the performance and effectiveness of bioremediation, the authors propose to identify the stress-inducible genes and promoters from two soil bacteria, Deinococcus radiodurans and Sphingomonas F199. These organisms represent two phylogenetically distinct groups of soil bacteria, each of which has specific features of interest for bioremediation. D. radiodurans exhibits high resistance to external stress; F199 is a deep subsurface (Savannah River Site) organism with unique degradative capabilities. Research Statement To realize the full potential of bioremediation, an understandingmore » of microbial community and individual bacterial responses to the stresses encountered at contaminated sites is needed. Knowledge about genetic responses of soil and subsurface bacteria to environmental stresses, which include low nutrients, low oxygen, and mixed pollutants, will allow extrapolation of basic principles to field applications either using indigenous bacteria or genetically engineered microorganisms. Defining bacterial responses to those stresses presents an opportunity for improving bioremediation strategies, and should contribute to environmental management and restoration actions that would reduce the cost and time required to achieve DOE''s cleanup goals.'« less

The structure of amylosucrase from Deinococcus radiodurans has an unusual open active-site topology.

PubMed

Skov, Lars K; Pizzut-Serin, Sandra; Remaud-Simeon, Magali; Ernst, Heidi A; Gajhede, Michael; Mirza, Osman

2013-09-01

Amylosucrases (ASes) catalyze the formation of an α-1,4-glucosidic linkage by transferring a glucosyl unit from sucrose onto an acceptor α-1,4-glucan. To date, several ligand-bound crystal structures of wild-type and mutant ASes from Neisseria polysaccharea and Deinococcus geothermalis have been solved. These structures all display a very similar overall conformation with a deep pocket leading to the site for transglucosylation, subsite -1. This has led to speculation on how sucrose enters the active site during glucan elongation. In contrast to previous studies, the AS structure from D. radiodurans presented here has a completely empty -1 subsite. This structure is strikingly different from other AS structures, as an active-site-lining loop comprising residues Leu214-Asn225 is found in a previously unobserved conformation. In addition, a large loop harbouring the conserved active-site residues Asp133 and Tyr136 is disordered. The result of the changed loop conformations is that the active-site topology is radically changed, leaving subsite -1 exposed and partially dismantled. This structure provides novel insights into the dynamics of ASes and comprises the first structural support for an elongation mechanism that involves considerable conformational changes to modulate accessibility to the sucrose-binding site and thereby allows successive cycles of glucosyl-moiety transfer to a growing glucan chain.

Untargeted Metabolite Profiling Reveals that Nitric Oxide Bioynthesis is an Endogenous Modulator of Carotenoid Biosynthesis in Deinococcus radiodurans and is Required for Extreme Ionizing Radiation Resistance

PubMed Central

Hansler, Alex; Chen, Qiuying; Ma, Yuliang; Gross, Steven S.

2015-01-01

Deinococcus radiodurans (Drad) is the most radioresistant organism known. Although mechanisms that underlie the extreme radioresistance of Drad are incompletely defined, resistance to UV irradiation-induced killing was found to be greatly attenuated in an NO synthase (NOS) knockout strain of Drad (Δnos). We now show that endogenous NO production is also critical for protection of Drad against γ-irradiation (3000 Gy), a result of accelerated growth recovery, not protection against killing. NO-donor treatment rescued radiosensitization in Δnos Drad but did not influence radiosensitivity in wild type Drad. To discover molecular mechanisms by which endogenous NO confers radioresistance, metabolite profiling studies were performed. Untargeted LC-MS-based metabolite profiling in Drad quantified relative abundances of 1,425 molecules and levels of 294 of these were altered by >5-fold (p< 0.01). Unexpectedly, these studies identified a dramatic perturbation in carotenoid biosynthetic intermediates in Δnos Drad, including a reciprocal switch in the pathway end-products from deoxydeinoxanthin to deinoxanthin. NO supplementation rescued these nos deletion-associated changes in carotenoid biosynthesis, and fully-restored radioresistance to wildtype levels. Because carotenoids were shown to be important contributors to radioprotection in Drad, our findings suggest that endogenously-produced NO serves to maintain a spectrum of carotenoids critical for Drad’s ability to withstand radiation insult. PMID:26550929

Identification and Characterization of uvrA, a DNA Repair Gene of Deinococcus radiodurans

DTIC Science & Technology

1996-01-01

and Classificalion I 2 . TheCellWall 4 3. Intracellular Molecules 7 4. Genetics _ _ _ _ _.. 8 a. DNA COntent. 8 b. Chromosomes 8 c. Plasmids 10 d...Summary 11 B. DNA Damaging Agenls 12 I. Visible Light and Low-Frequency UV Radiation 12 2 . High-frequency UV Radiation 13 a. Pyrimidine DiIners 13 b. The...23 a. Photoreactivation Repair 23 b. Repair of Spore Pholoproducts 27 2 . Repair by Methods Involving Single Proteins 27 a. Repair of

Biomolecular Effects of Cold Plasma Exposure

NASA Technical Reports Server (NTRS)

Mogul, Rakesh; Bolshakov, Alexander A.; Chan, Suzanne L.; Stevens, Ramsey D.; Khare, Bishun N.; Meyyappan, M.; Trent, Jonathan D.; DeVincenzi, D. (Technical Monitor)

2002-01-01

The effects of cold plasma exposure on Deinococcus radiodurans, plasmid DNA and model proteins were assessed using microbiological, spectrometric and biochemical techniques. Exposure of D. radiodurans, an extremely radiation resistant microbe, to O2 plasma (less than or equal to 25 W, approx. 45 mTorr, 90 min) yielded a approx. 99.999 % sterilization and the sterilization rate was increased approx. 10-fold at 100 W and 500 mTorr. AFM images shows that the exposed cells are significantly deformed and possess 50-70 nm concavities. IR analysis indicates the chemical degradation of lipids, proteins and carotenoids of the cell wall and membrane. Intracellular damage was indicated by major absorbance loss at 1245, 1651 and 1538/cm corresponding to degradation of DNA and proteins, respectively. Biochemical experiments demonstrate that plasmas induce strand scissions and crosslinking of plasmid DNA, and reduction of enzyme activity; the degradation is power dependent with total sample loss occurring in 60 s at 200 W and 500 mTorr. Emission spectroscopy shows that D. radiodurans is volatilized into CO2, CO, N2 and H2O confirming the removal of biological matter from contaminated surfaces. The O2 plasma impacts several cellular components predominantly through chemical degradation by atomic oxygen. A CO2, plasma, however, was not effective at degrading D. radiodurans, revealing the importance of plasma composition, which has implications for planetary protection and the contamination of Mars.

The possible interplanetary transfer of microbes: assessing the viability of Deinococcus spp. under the ISS Environmental conditions for performing exposure experiments of microbes in the Tanpopo mission.

PubMed

Kawaguchi, Yuko; Yang, Yinjie; Kawashiri, Narutoshi; Shiraishi, Keisuke; Takasu, Masako; Narumi, Issay; Satoh, Katsuya; Hashimoto, Hirofumi; Nakagawa, Kazumichi; Tanigawa, Yoshiaki; Momoki, Yoh-Hei; Tanabe, Maiko; Sugino, Tomohiro; Takahashi, Yuta; Shimizu, Yasuyuki; Yoshida, Satoshi; Kobayashi, Kensei; Yokobori, Shin-Ichi; Yamagishi, Akihiko

2013-10-01

To investigate the possible interplanetary transfer of life, numerous exposure experiments have been carried out on various microbes in space since the 1960s. In the Tanpopo mission, we have proposed to carry out experiments on capture and space exposure of microbes at the Exposure Facility of the Japanese Experimental Module of the International Space Station (ISS). Microbial candidates for the exposure experiments in space include Deinococcus spp.: Deinococcus radiodurans, D. aerius and D. aetherius. In this paper, we have examined the survivability of Deinococcus spp. under the environmental conditions in ISS in orbit (i.e., long exposure to heavy-ion beams, temperature cycles, vacuum and UV irradiation). A One-year dose of heavy-ion beam irradiation did not affect the viability of Deinococcus spp. within the detection limit. Vacuum (10(-1) Pa) also had little effect on the cell viability. Experiments to test the effects of changes in temperature from 80 °C to -80 °C in 90 min (± 80 °C/90 min cycle) or from 60 °C to -60 °C in 90 min (± 60 °C/90 min cycle) on cell viability revealed that the survival rate decreased severely by the ± 80 °C/90 min temperature cycle. Exposure of various thicknesses of deinococcal cell aggregates to UV radiation (172 nm and 254 nm, respectively) revealed that a few hundred micrometer thick aggregate of deinococcal cells would be able to withstand the solar UV radiation on ISS for 1 year. We concluded that aggregated deinococcal cells will survive the yearlong exposure experiments. We propose that microbial cells can aggregate as an ark for the interplanetary transfer of microbes, and we named it 'massapanspermia'.

Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans.

PubMed

Awile, Omar; Krisko, Anita; Sbalzarini, Ivo F; Zagrovic, Bojan

2010-07-15

The proteome of the radiation- and desiccation-resistant bacterium D. radiodurans features a group of proteins that contain significant intrinsically disordered regions that are not present in non-extremophile homologues. Interestingly, this group includes a number of housekeeping and repair proteins such as DNA polymerase III, nudix hydrolase and rotamase. Here, we focus on a member of the nudix hydrolase family from D. radiodurans possessing low-complexity N- and C-terminal tails, which exhibit sequence signatures of intrinsic disorder and have unknown function. The enzyme catalyzes the hydrolysis of oxidatively damaged and mutagenic nucleotides, and it is thought to play an important role in D. radiodurans during the recovery phase after exposure to ionizing radiation or desiccation. We use molecular dynamics simulations to study the dynamics of the protein, and study its hydration free energy using the GB/SA formalism. We show that the presence of disordered tails significantly decreases the hydration free energy of the whole protein. We hypothesize that the tails increase the chances of the protein to be located in the remaining water patches in the desiccated cell, where it is protected from the desiccation effects and can function normally. We extrapolate this to other intrinsically disordered regions in proteins, and propose a novel function for them: intrinsically disordered regions increase the "surface-properties" of the folded domains they are attached to, making them on the whole more hydrophilic and potentially influencing, in this way, their localization and cellular activity.

Detection of γ-radiation and heavy metals using electrochemical bacterial-based sensor

NASA Astrophysics Data System (ADS)

Al-Shanawa, M.; Nabok, A.; Hashim, A.; Smith, T.; Forder, S.

2013-06-01

The main aim of this work is to develop a simple electrochemical sensor for detection of γ-radiation and heavy metals using bacteria. A series of DC and AC electrical measurements were carried out on samples of two types of bacteria, namely Escherichia coli and Deinococcus radiodurans. As a first step, a correlation between DC and AC electrical conductivity and bacteria concentration in solution was established. The study of the effect of γ-radiation and heavy metal ions (Cd2+) on DC and AC electrical characteristics of bacteria revealed a possibility of pattern recognition of the above inhibition factors.

Extreme Ionizing-Radiation-Resistant Bacterium

NASA Technical Reports Server (NTRS)

Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

2012-01-01

There is a growing concern that desiccation and extreme radiation-resistant, non-spore-forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequent proliferation on another solar body. Such forward contamination would jeopardize future life detection or sample return technologies. The prime focus of NASA s planetary protection efforts is the development of strategies for inactivating resistance-bearing microorganisms. Eradification techniques can be designed to target resistance-conferring microbial populations by first identifying and understanding their physiologic and biochemical capabilities that confers its elevated tolerance (as is being studied in Deinococcus phoenicis, as a result of this description). Furthermore, hospitals, food, and government agencies frequently use biological indicators to ensure the efficacy of a wide range of radiation- based sterilization processes. Due to their resistance to a variety of perturbations, the non-spore forming D. phoenicis may be a more appropriate biological indicator than those currently in use. The high flux of cosmic rays during space travel and onto the unshielded surface of Mars poses a significant hazard to the survival of microbial life. Thus, radiation-resistant microorganisms are of particular concern that can survive extreme radiation, desiccation, and low temperatures experienced during space travel. Spore-forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate these extreme conditions. Since the Viking era, spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Members of the non-spore-forming bacterial community such as Deinococcus radiodurans can survive acute exposures to ionizing radiation (5 kGy), ultraviolet light (1 kJ/sq m), and desiccation (years). These resistive phenotypes of Deinococcus enhance the potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

Extreme Ionizing-Radiation-Resistant Bacterium

NASA Technical Reports Server (NTRS)

Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.; Schwendner, Petra

2013-01-01

There is a growing concern that desiccation and extreme radiation-resistant, non-spore-forming microorganisms associated with spacecraft surfaces can withstand space environmental conditions and subsequent proliferation on another solar body. Such forward contamination would jeopardize future life detection or sample return technologies. The prime focus of NASA s planetary protection efforts is the development of strategies for inactivating resistance-bearing micro-organisms. Eradi cation techniques can be designed to target resistance-conferring microbial populations by first identifying and understanding their physiologic and biochemical capabilities that confers its elevated tolerance (as is being studied in Deinococcus phoenicis, as a result of this description). Furthermore, hospitals, food, and government agencies frequently use biological indicators to ensure the efficacy of a wide range of radiation-based sterilization processes. Due to their resistance to a variety of perturbations, the nonspore forming D. phoenicis may be a more appropriate biological indicator than those currently in use. The high flux of cosmic rays during space travel and onto the unshielded surface of Mars poses a significant hazard to the survival of microbial life. Thus, radiation-resistant microorganisms are of particular concern that can survive extreme radiation, desiccation, and low temperatures experienced during space travel. Spore-forming bacteria, a common inhabitant of spacecraft assembly facilities, are known to tolerate these extreme conditions. Since the Viking era, spores have been utilized to assess the degree and level of microbiological contamination on spacecraft and their associated spacecraft assembly facilities. Members of the non-sporeforming bacterial community such as Deinococcus radiodurans can survive acute exposures to ionizing radiation (5 kGy), ultraviolet light (1 kJ/m2), and desiccation (years). These resistive phenotypes of Deinococcus enhance the potential for transfer, and subsequent proliferation, on another solar body such as Mars and Europa. These organisms are more likely to escape planetary protection assays, which only take into account presence of spores. Hence, presences of extreme radiation-resistant Deinococcus in the cleanroom facility where spacecraft are assembled pose a serious risk for integrity of life-detection missions. The microorganism described herein was isolated from the surfaces of the cleanroom facility in which the Phoenix Lander was assembled. The isolated bacterial strain was subjected to a comprehensive polyphasic analysis to characterize its taxonomic position. This bacterium exhibits very low 16SrRNA similarity with any other environmental isolate reported to date. Both phenotypic and phylogenetic analyses clearly indicate that this isolate belongs to the genus Deinococcus and represents a novel species. The name Deinococcus phoenicis was proposed after the Phoenix spacecraft, which was undergoing assembly, testing, and launch operations in the spacecraft assembly facility at the time of isolation. D. phoenicis cells exhibited higher resistance to ionizing radiation (cobalt-60; 14 kGy) than the cells of the D. radiodurans (5 kGy). Thus, it is in the best interest of NASA to thoroughly characterize this organism, which will further assess in determining the potential for forward contamination. Upon the completion of genetic and physiological characteristics of D. phoenicis, it will be added to a planetary protection database to be able to further model and predict the probability of forward contamination.

Diverse nucleotide compositions and sequence fluctuation in Rubisco protein genes

NASA Astrophysics Data System (ADS)

Holden, Todd; Dehipawala, S.; Cheung, E.; Bienaime, R.; Ye, J.; Tremberger, G., Jr.; Schneider, P.; Lieberman, D.; Cheung, T.

2011-10-01

The Rubisco protein-enzyme is arguably the most abundance protein on Earth. The biology dogma of transcription and translation necessitates the study of the Rubisco genes and Rubisco-like genes in various species. Stronger correlation of fractal dimension of the atomic number fluctuation along a DNA sequence with Shannon entropy has been observed in the studied Rubisco-like gene sequences, suggesting a more diverse evolutionary pressure and constraints in the Rubisco sequences. The strategy of using metal for structural stabilization appears to be an ancient mechanism, with data from the porphobilinogen deaminase gene in Capsaspora owczarzaki and Monosiga brevicollis. Using the chi-square distance probability, our analysis supports the conjecture that the more ancient Rubisco-like sequence in Microcystis aeruginosa would have experienced very different evolutionary pressure and bio-chemical constraint as compared to Bordetella bronchiseptica, the two microbes occupying either end of the correlation graph. Our exploratory study would indicate that high fractal dimension Rubisco sequence would support high carbon dioxide rate via the Michaelis- Menten coefficient; with implication for the control of the whooping cough pathogen Bordetella bronchiseptica, a microbe containing a high fractal dimension Rubisco-like sequence (2.07). Using the internal comparison of chi-square distance probability for 16S rRNA (~ E-22) versus radiation repair Rec-A gene (~ E-05) in high GC content Deinococcus radiodurans, our analysis supports the conjecture that high GC content microbes containing Rubisco-like sequence are likely to include an extra-terrestrial origin, relative to Deinococcus radiodurans. Similar photosynthesis process that could utilize host star radiation would not compete with radiation resistant process from the biology dogma perspective in environments such as Mars and exoplanets.

Deinococcus radiodurans RNA ligase exemplifies a novel ligase clade with a distinctive N-terminal module that is important for 5'-PO4 nick sealing and ligase adenylylation but dispensable for phosphodiester formation at an adenylylated nick.

PubMed

Raymond, Amy; Shuman, Stewart

2007-01-01

Deinococcus radiodurans RNA ligase (DraRnl) is a template-directed ligase that seals nicked duplexes in which the 3'-OH strand is RNA. DraRnl is a 342 amino acid polypeptide composed of a C-terminal adenylyltransferase domain fused to a distinctive 126 amino acid N-terminal module (a putative OB-fold). An alanine scan of the C domain identified 9 amino acids essential for nick ligation, which are located within nucleotidyltransferase motifs I, Ia, III, IIIa, IV and V. Seven mutants were dysfunctional by virtue of defects in ligase adenylylation: T163A, H167A, G168A, K186A, E230A, F281A and E305A. Four of these were also defective in phosphodiester formation at a preadenylylated nick: G168A, E230A, F281A and E305A. Two nick sealing-defective mutants were active in ligase adenylylation and sealing a preadenylylated nick, thereby implicating Ser185 and Lys326 in transfer of AMP from the enzyme to the nick 5'-PO(4). Whereas deletion of the N-terminal domain suppressed overall nick ligation and ligase adenylylation, it did not compromise sealing at a preadenylylated nick. Mutational analysis of 15 residues of the N domain identified Lys26, Gln31 and Arg79 as key constituents. Structure-activity relationships at the essential residues were determined via conservative substitutions. We propose that DraRnl typifies a new clade of polynucleotide ligases. DraRnl homologs are detected in several eukaryal proteomes.

Deinococcus radiodurans RNA ligase exemplifies a novel ligase clade with a distinctive N-terminal module that is important for 5′-PO4 nick sealing and ligase adenylylation but dispensable for phosphodiester formation at an adenylylated nick

PubMed Central

Raymond, Amy; Shuman, Stewart

2007-01-01

Deinococcus radiodurans RNA ligase (DraRnl) is a template-directed ligase that seals nicked duplexes in which the 3′-OH strand is RNA. DraRnl is a 342 amino acid polypeptide composed of a C-terminal adenylyltransferase domain fused to a distinctive 126 amino acid N-terminal module (a putative OB-fold). An alanine scan of the C domain identified 9 amino acids essential for nick ligation, which are located within nucleotidyltransferase motifs I, Ia, III, IIIa, IV and V. Seven mutants were dysfunctional by virtue of defects in ligase adenylylation: T163A, H167A, G168A, K186A, E230A, F281A and E305A. Four of these were also defective in phosphodiester formation at a preadenylylated nick: G168A, E230A, F281A and E305A. Two nick sealing-defective mutants were active in ligase adenylylation and sealing a preadenylylated nick, thereby implicating Ser185 and Lys326 in transfer of AMP from the enzyme to the nick 5′-PO4. Whereas deletion of the N-terminal domain suppressed overall nick ligation and ligase adenylylation, it did not compromise sealing at a preadenylylated nick. Mutational analysis of 15 residues of the N domain identified Lys26, Gln31 and Arg79 as key constituents. Structure–activity relationships at the essential residues were determined via conservative substitutions. We propose that DraRnl typifies a new clade of polynucleotide ligases. DraRnl homologs are detected in several eukaryal proteomes. PMID:17204483

Bacteriophytochrome controls carotenoid-independent response to photodynamic stress in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7

PubMed Central

Kumar, Santosh; Kateriya, Suneel; Singh, Vijay Shankar; Tanwar, Meenakshi; Agarwal, Shweta; Singh, Hina; Khurana, Jitendra Paul; Amla, Devinder Vijay; Tripathi, Anil Kumar

2012-01-01

Ever since the discovery of the role of bacteriophytochrome (BphP) in inducing carotenoid synthesis in Deinococcus radiodurans in response to light the role of BphPs in other non-photosynthetic bacteria is not clear yet. Azospirillum brasilense, a non-photosynthetic rhizobacterium, harbours a pair of BphPs out of which AbBphP1 is a homolog of AtBphP1 of Agrobacterium tumefaciens. By overexpression, purification, biochemical and spectral characterization we have shown that AbBphP1 is a photochromic bacteriophytochrome. Phenotypic study of the ΔAbBphP1 mutant showed that it is required for the survival of A. brasilense on minimal medium under red light. The mutant also showed reduced chemotaxis towards dicarboxylates and increased sensitivity to the photooxidative stress. Unlike D. radiodurans, AbBphP1 was not involved in controlling carotenoid synthesis. Proteome analysis of the ΔAbBphP1 indicated that AbBphP1 is involved in inducing a cellular response that enables A. brasilense in regenerating proteins that might be damaged due to photodynamic stress. PMID:23173079

Bacteriophytochrome controls carotenoid-independent response to photodynamic stress in a non-photosynthetic rhizobacterium, Azospirillum brasilense Sp7.

PubMed

Kumar, Santosh; Kateriya, Suneel; Singh, Vijay Shankar; Tanwar, Meenakshi; Agarwal, Shweta; Singh, Hina; Khurana, Jitendra Paul; Amla, Devinder Vijay; Tripathi, Anil Kumar

2012-01-01

Ever since the discovery of the role of bacteriophytochrome (BphP) in inducing carotenoid synthesis in Deinococcus radiodurans in response to light the role of BphPs in other non-photosynthetic bacteria is not clear yet. Azospirillum brasilense, a non-photosynthetic rhizobacterium, harbours a pair of BphPs out of which AbBphP1 is a homolog of AtBphP1 of Agrobacterium tumefaciens. By overexpression, purification, biochemical and spectral characterization we have shown that AbBphP1 is a photochromic bacteriophytochrome. Phenotypic study of the ΔAbBphP1 mutant showed that it is required for the survival of A. brasilense on minimal medium under red light. The mutant also showed reduced chemotaxis towards dicarboxylates and increased sensitivity to the photooxidative stress. Unlike D. radiodurans, AbBphP1 was not involved in controlling carotenoid synthesis. Proteome analysis of the ΔAbBphP1 indicated that AbBphP1 is involved in inducing a cellular response that enables A. brasilense in regenerating proteins that might be damaged due to photodynamic stress.

Mapping flexible protein domains at subnanometer resolution with the atomic force microscope.

PubMed

Müller, D J; Fotiadis, D; Engel, A

1998-06-23

The mapping of flexible protein domains with the atomic force microscope is reviewed. Examples discussed are the bacteriorhodopsin from Halobacterium salinarum, the head-tail-connector from phage phi29, and the hexagonally packed intermediate layer from Deinococcus radiodurans which all were recorded in physiological buffer solution. All three proteins undergo reversible structural changes that are reflected in standard deviation maps calculated from aligned topographs of individual protein complexes. Depending on the lateral resolution (up to 0.8 nm) flexible surface regions can ultimately be correlated with individual polypeptide loops. In addition, multivariate statistical classification revealed the major conformations of the protein surface.

Thickness determination of biological samples with a zeta-calibrated scanning tunneling microscope.

PubMed Central

Wang, Z H; Hartmann, T; Baumeister, W; Guckenberger, R

1990-01-01

A single-tube scanning tunneling microscope has been zeta-calibrated by using atomic steps of crystalline gold and was used for measuring the thickness of two biological samples, metal-coated as well as uncoated. The hexagonal surface layer of the bacterium Deinococcus radiodurans with an open network-type structure shows thickness values that are strongly influenced by the substrate and the preparation method. In contrast, the thickness of the purple membrane of Halobacterium halobium with its densely packed less-corrugated structure exhibits very little variation in thickness in coated preparations and the values obtained are in good agreement with x-ray data. Images PMID:2251276

Evaluation of microbial globin promoters for oxygen-limited processes using Escherichia coli.

PubMed

Lara, Alvaro R; Jaén, Karim E; Sigala, Juan-Carlos; Regestein, Lars; Büchs, Jochen

2017-01-01

Oxygen-responsive promoters can be useful for synthetic biology applications, however, information on their characteristics is still limited. Here, we characterized a group of heterologous microaerobic globin promoters in Escherichia coli . Globin promoters from Bacillus subtilis , Campylobacter jejuni , Deinococcus radiodurans , Streptomyces coelicolor , Salmonella typhi and Vitreoscilla stercoraria were used to express the FMN-binding fluorescent protein (FbFP), which is a non-oxygen dependent marker. FbFP fluorescence was monitored online in cultures at maximum oxygen transfer capacities (OTR max ) of 7 and 11 mmol L -1  h -1 . Different FbFP fluorescence intensities were observed and the OTR max affected the induction level and specific fluorescence emission rate (the product of the specific fluorescence intensity multiplied by the specific growth rate) of all promoters. The promoter from S. typhi displayed the highest fluorescence emission yields (the quotient of the fluorescence intensity divided by the scattered light intensity at every time-point) and rate, and together with the promoters from D. radiodurans and S. coelicolor , the highest induction ratios. These results show the potential of diverse heterologous globin promoters for oxygen-limited processes using E. coli .

Structural and functional characterization of two unusual endonuclease III enzymes from Deinococcus radiodurans.

PubMed

Sarre, Aili; Ökvist, Mats; Klar, Tobias; Hall, David R; Smalås, Arne O; McSweeney, Sean; Timmins, Joanna; Moe, Elin

2015-08-01

While most bacteria possess a single gene encoding the bifunctional DNA glycosylase Endonuclease III (EndoIII) in their genomes, Deinococcus radiodurans possesses three: DR2438 (DrEndoIII1), DR0289 (DrEndoIII2) and DR0982 (DrEndoIII3). Here we have determined the crystal structures of DrEndoIII1 and an N-terminally truncated form of DrEndoIII3 (DrEndoIII3Δ76). We have also generated a homology model of DrEndoIII2 and measured activity of the three enzymes. All three structures consist of two all α-helical domains, one of which exhibits a [4Fe-4S] cluster and the other a HhH-motif, separated by a DNA binding cleft, similar to previously determined structures of endonuclease III from Escherichia coli and Geobacillus stearothermophilus. However, both DrEndoIII1 and DrEndoIII3 possess an extended HhH motif with extra helical features and an altered electrostatic surface potential. In addition, the DNA binding cleft of DrEndoIII3 seems to be less accessible for DNA interactions, while in DrEndoIII1 it seems to be more open. Analysis of the enzyme activities shows that DrEndoIII2 is most similar to the previously studied enzymes, while DrEndoIII1 seems to be more distant with a weaker activity towards substrate DNA containing either thymine glycol or an abasic site. DrEndoIII3 is the most distantly related enzyme and displays no detectable activity towards these substrates even though the suggested catalytic residues are conserved. Based on a comparative structural analysis, we suggest that the altered surface potential, shape of the substrate-binding pockets and specific amino acid substitutions close to the active site and in the DNA interacting loops may underlie the unexpected differences in activity. Copyright © 2015 Elsevier Inc. All rights reserved.

Inhibition in a microgravity environment of the recovery of Escherichia coli cells damaged by heavy ion beams during the NASDA ISS phase I program of NASA Shuttle/Mir mission no. 6.

PubMed

Harada, K; Sugahara, T; Ohnishi, T; Ozaki, Y; Obiya, Y; Miki, S; Miki, T; Imamura, M; Kobayashi, Y; Watanabe, H; Akashi, M; Furusawa, Y; Mizuma, N; Yamanaka, H; Ohashi, E; Yamaoka, C; Yajima, M; Fukui, M; Nakano, T; Takahashi, S; Amano, T; Sekikawa, K; Yanagawa, K; Nagaoka, S

1998-05-01

We participated in a space experiment, part of the National Space Development Agency of Japan (NASDA) Phase I Space Radiation Environment Measurement Program, conducted during the National Aeronautics and Space Administration (NASA) Shuttle/Mir Mission No. 6 (S/MM-6) project. The aim of our study was to investigate the effects of microgravity on the DNA repair processes of living organisms in the in orbit. Heavy ion beam radiation- or ç-irradiation-damaged biological samples of Escherichia coli and the radioresistant bacterium Deinococcus radiodurans were prepared and placed in a biospecimen box, which was loaded into the RRMD III sensor unit of the Space Shuttle. Two identical sets of samples were left in the Spacehab's Payload Processing Facility (SPPF) in Florida, USA, as a control. (flight No. STS-84) was launched from NASA John F. Kennedy Space Center (KSC) in Florida, USA, on May 15, 1997. The mission duration was 9.22 days. An astronaut activated the biological samples in the biospecimen box in the Spacehab during orbit in order to start repair of the DNA damaged by heavy ion beams or ç-irradiation and the samples were incubated for 19 h 35 min at about 22ûC, the cabin temperature. The control specimens in the SPPF were subjected to the same treatment under terrestrial gravity. After returned to earth, we investigated cell recovery by comparing the repair of the radiation-damaged DNA of E. coli and D. radiodurans in the microgravity environment in space with that on Earth. The results indicated that the DNA repair process of E. coli, but not of D. radiodurans, cells was inhibited in a microgravity environment.

Destruction of Raman biosignatures by ionising radiation and the implications for life detection on Mars.

PubMed

Dartnell, Lewis R; Page, Kristian; Jorge-Villar, Susana E; Wright, Gary; Munshi, Tasnim; Scowen, Ian J; Ward, John M; Edwards, Howell G M

2012-04-01

Raman spectroscopy has proven to be a very effective approach for the detection of microorganisms colonising hostile environments on Earth. The ExoMars rover, due for launch in 2018, will carry a Raman laser spectrometer to analyse samples of the martian subsurface collected by the probe's 2-m drill in a search for similar biosignatures. The martian surface is unprotected from the flux of cosmic rays, an ionising radiation field that will degrade organic molecules and so diminish and distort the detectable Raman signature of potential martian microbial life. This study employs Raman spectroscopy to analyse samples of two model organisms, the cyanobacterium Synechocystis sp. PCC 6803 and the extremely radiation resistant polyextremophile Deinococcus radiodurans, that have been exposed to increasing doses of ionising radiation. The three most prominent peaks in the Raman spectra are from cellular carotenoids: deinoxanthin in D. radiodurans and β-carotene in Synechocystis. The degradative effect of ionising radiation is clearly seen, with significant diminishment of carotenoid spectral peak heights after 15 kGy and complete erasure of Raman biosignatures by 150 kGy of ionising radiation. The Raman signal of carotenoid in D. radiodurans diminishes more rapidly than that of Synechocystis, believed to be due to deinoxanthin acting as a superior scavenger of radiolytically produced reactive oxygen species, and so being destroyed more quickly than the less efficient antioxidant β-carotene. This study highlights the necessity for further experimental work on the manner and rate of degradation of Raman biosignatures by ionising radiation, as this is of prime importance for the successful detection of microbial life in the martian near subsurface.

Horizontal transfer of archaeal genes into the deinococcaceae: detection by molecular and computer-based approaches

NASA Technical Reports Server (NTRS)

Olendzenski, L.; Liu, L.; Zhaxybayeva, O.; Murphey, R.; Shin, D. G.; Gogarten, J. P.

2000-01-01

Members of the Deinococcaceae (e.g., Thermus, Meiothermus, Deinococcus) contain A/V-ATPases typically found in Archaea or Eukaryotes which were probably acquired by horizontal gene transfer. Two methods were used to quantify the extent to which archaeal or eukaryotic genes have been acquired by this lineage. Screening of a Meiothermus ruber library with probes made against Thermoplasma acidophilum DNA yielded a number of clones which hybridized more strongly than background. One of these contained the prolyl tRNA synthetase (RS) gene. Phylogenetic analysis shows the M. ruber and D. radiodurans prolyl RS to be more closely related to archaeal and eukaryal forms of this gene than to the typical bacterial type. Using a bioinformatics approach, putative open reading frames (ORFs) from the prerelease version of the D. radiodurans genome were screened for genes more closely related to archaeal or eukaryotic genes. Putative ORFs were searched against representative genomes from each of the three domains using automated BLAST. ORFs showing the highest matches against archaeal and eukaryotic genes were collected and ranked. Among the top-ranked hits were the A/V-ATPase catalytic and noncatalytic subunits and the prolyl RS genes. Using phylogenetic methods, ORFs were analyzed and trees assessed for evidence of horizontal gene transfer. Of the 45 genes examined, 20 showed topologies in which D. radiodurans homologues clearly group with eukaryotic or archaeal homologues, and 17 additional trees were found to show probable evidence of horizontal gene transfer. Compared to the total number of ORFs in the genome, those that can be identified as having been acquired from Archaea or Eukaryotes are relatively few (approximately 1%), suggesting that interdomain transfer is rare.

Phage Display on the Anti‐infective Target 1‐Deoxy‐d‐xylulose‐5‐phosphate Synthase Leads to an Acceptor–Substrate Competitive Peptidic Inhibitor

PubMed Central

Marcozzi, Alessio; Masini, Tiziana; Zhu, Di; Pesce, Diego; Illarionov, Boris; Fischer, Markus

2017-01-01

Abstract Enzymes of the 2‐C‐methyl‐d‐erythritol‐4‐phosphate pathway for the biosynthesis of isoprenoid precursors are validated drug targets. By performing phage display on 1‐deoxy‐d‐xylulose‐5‐phosphate synthase (DXS), which catalyzes the first step of this pathway, we discovered several peptide hits and recognized false‐positive hits. The enriched peptide binder P12 emerged as a substrate (d‐glyceraldehyde‐3‐phosphate)‐competitive inhibitor of Deinococcus radiodurans DXS. The results indicate possible overlap of the cofactor‐ and acceptor‐substrate‐binding pockets and provide inspiration for the design of inhibitors of DXS with a unique and novel mechanism of inhibition. PMID:29119720

Methanosarcina acetivorans 16S rRNA and transcription factor nucleotide fluctuation with implications in exobiology and pathology

NASA Astrophysics Data System (ADS)

Holden, Todd; Tremberger, G., Jr.; Cheung, E.; Subramaniam, R.; Sullivan, R.; Schneider, P.; Flamholz, A.; Marchese, P.; Hiciano, O.; Yao, H.; Lieberman, D.; Cheung, T.

2008-08-01

Cultures of the methane-producing archaea Methanosarcina, have recently been isolated from Alaskan sediments. It has been proposed that methanogens are strong candidates for exobiological life in extreme conditions. The spatial environmental gradients, such as those associated with the polygons on Mars' surface, could have been produced by past methanogenesis activity. The 16S rRNA gene has been used routinely to classify phenotypes. Using the fractal dimension of nucleotide fluctuation, a comparative study of the 16S rRNA nucleotide fluctuation in Methanosarcina acetivorans C2A, Deinococcus radiodurans, and E. coli was conducted. The results suggest that Methanosarcina acetivorans has the lowest fractal dimension, consistent with its ancestral position in evolution. Variation in fluctuation complexity was also detected in the transcription factors. The transcription factor B (TFB) was found to have a higher fractal dimension as compared to transcription factor E (TFE), consistent with the fact that a single TFB in Methanosarcina acetivorans can code three different TATA box proteins. The average nucleotide pair-wise free energy of the DNA repair genes was found to be highest for Methanosarcina acetivorans, suggesting a relatively weak bonding, which is consistent with its low prevalence in pathology. Multitasking capacity comparison of type-I and type-II topoisomerases has been shown to correlate with fractal dimension using the methicillin-resistant strain MRSA 252. The analysis suggests that gene adaptation in a changing chemical environment can be measured in terms of bioinformatics. Given that the radiation resistant Deinococcus radiodurans is a strong candidate for an extraterrestrial origin and that the cold temperature Psychrobacter cryohalolentis K5 can function in Siberian permafrost, the fractal dimension comparison in this study suggests that a chemical resistant methanogen could exist in extremely cold conditions (such as that which existed on early Mars) where demands on gene activity are low. In addition, the comparative study of the Methanococcoides burtonii cold shock domain sequence has provided further support for the correlation between multitasking capacity and fractal dimension.

Structure-Based and Random Mutagenesis Approaches Increase the Organophosphate-Degrading Activity of a Phosphotriesterase Homologue from Deinococcus radiodurans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hawwa, Renda; Larsen, Sonia D.; Ratia, Kiira

2010-11-09

An enzyme from the amidohydrolase family from Deinococcus radiodurans (Dr-OPH) with homology to phosphotriesterase has been shown to exhibit activity against both organophosphate (OP) and lactone compounds. We have characterized the physical properties of Dr-OPH and have found it to be a highly thermostable enzyme, remaining active after 3 h of incubation at 60 C and withstanding incubation at temperatures up to 70 C. In addition, it can withstand concentrations of at least 200 mg/mL. These properties make Dr-OPH a promising candidate for development in commercial applications. However, compared to the most widely studied OP-degrading enzyme, that from Pseudomonas diminuta,more » Dr-OPH has low hydrolytic activity against certain OP substrates. Therefore, we sought to improve the OP-degrading activity of Dr-OPH, specifically toward the pesticides ethyl and methyl paraoxon, using structure-based and random approaches. Site-directed mutagenesis, random mutagenesis, and site-saturation mutagenesis were utilized to increase the OP-degrading activity of Dr-OPH. Out of a screen of more than 30,000 potential mutants, a total of 26 mutant enzymes were purified and characterized kinetically. Crystal structures of w.t. Dr-OPH, of Dr-OPH in complex with a product analog, and of 7 mutant enzymes were determined to resolutions between 1.7 and 2.4 {angstrom}. Information from these structures directed the design and production of 4 additional mutants for analysis. In total, our mutagenesis efforts improved the catalytic activity of Dr-OPH toward ethyl and methyl paraoxon by 126- and 322-fold and raised the specificity for these two substrates by 557- and 183-fold, respectively. Our work highlights the importance of an iterative approach to mutagenesis, proving that large rate enhancements are achieved when mutations are made in already active mutants. In addition, the relationship between the kinetic parameters and the introduced mutations has allowed us to hypothesize on those factors most important for maintaining the structure and function of the enzyme.« less

Epigenetic changes of DNA repair genes in cancer.

PubMed

Lahtz, Christoph; Pfeifer, Gerd P

2011-02-01

'Every Hour Hurts, The Last One Kills'. That is an old saying about getting old. Every day, thousands of DNA damaging events take place in each cell of our body, but efficient DNA repair systems have evolved to prevent that. However, our DNA repair system and that of most other organisms are not as perfect as that of Deinococcus radiodurans, for example, which is able to repair massive amounts of DNA damage at one time. In many instances, accumulation of DNA damage has been linked to cancer, and genetic deficiencies in specific DNA repair genes are associated with tumor-prone phenotypes. In addition to mutations, which can be either inherited or somatically acquired, epigenetic silencing of DNA repair genes may promote tumorigenesis. This review will summarize current knowledge of the epigenetic inactivation of different DNA repair components in human cancer.

Microbial survival of space vacuum and extreme ultraviolet irradiation: strain isolation and analysis during a rocket flight.

PubMed

Saffary, Roya; Nandakumar, Renu; Spencer, Dennis; Robb, Frank T; Davila, Joseph M; Swartz, Marvin; Ofman, Leon; Thomas, Roger J; DiRuggiero, Jocelyne

2002-09-24

We have recovered new isolates from hot springs, in Yellowstone National Park and the Kamchatka Peninsula, after gamma-irradiation and exposure to high vacuum (10(-6) Pa) of the water and sediment samples. The resistance to desiccation and ionizing radiation of one of the isolates, Bacillus sp. strain PS3D, was compared to that of the mesophilic bacterium, Deinococcus radiodurans, a species well known for its extraordinary resistance to desiccation and high doses of ionizing radiation. Survival of these two microorganisms was determined in real and simulated space conditions, including exposure to extreme UV radiation (10-100 nm) during a rocket flight. We found that up to 15 days of desiccation alone had little effect on the viability of either bacterium. In contrast, exposure to space vacuum ( approximately 10(-6) Pa) decreased cell survival by two and four orders of magnitude for Bacillus sp. strain PS3D and D. radiodurans, respectively. Simultaneous exposure to space vacuum and extreme UV radiation further decreased the survival of both organisms, compared to unirradiated controls. This is the first report on the isolated effect of extreme UV at 30 nm on cell survival. Extreme UV can only be transmitted through high vacuum, therefore its penetration into the cells may only be superficial, suggesting that in contrast to near UV, membrane proteins rather than DNA were damaged by the radiation.

Essentiality of threonylcarbamoyladenosine (t6A), a universal tRNA modification, in bacteria

PubMed Central

Thiaville, Patrick C.; Yacoubi, Basma El; Köhrer, Caroline; Thiaville, Jennifer J.; Deutsch, Chris; Iwata-Reuyl, Dirk; Bacusmo, Jo Marie; Armengaud, Jean; Bessho, Yoshitaka; Wetzel, Collin; Cao, Xiaoyu; Limbach, Patrick A.; RajBhandary, Uttam L.; de Crécy-Lagard, Valérie

2016-01-01

Threonylcarbamoyladenosine (t6A) is a modified nucleoside universally conserved in tRNAs in all three kingdoms of life. The recently discovered genes for t6A synthesis, including tsaC and tsaD, are essential in model prokaryotes but not essential in yeast. These genes had been identified as antibacterial targets even before their functions were known. However, the molecular basis for this prokaryotic-specific essentiality has remained a mystery. Here, we show that t6A is a strong positive determinant for aminoacylation of tRNA by bacterial-type but not by eukaryotic-type isoleucyl-tRNA synthetases and might also be a determinant for the essential enzyme tRNAIle-lysidine synthetase. We confirm that t6A is essential in Escherichia coli and a survey of genome-wide essentiality studies shows that genes for t6A synthesis are essential in most prokaryotes. This essentiality phenotype is not universal in Bacteria as t6A is dispensable in Deinococcus radiodurans, Thermus thermophilus, Synechocystis PCC6803 and Streptococcus mutans. Proteomic analysis of t6A- D. radiodurans strains revealed an induction of the proteotoxic stress response and identified genes whose translation is most affected by the absence of t6A in tRNAs. Thus, although t6A is universally conserved in tRNAs, its role in translation might vary greatly between organisms. PMID:26337258

Biodegradation of naphthalene and anthracene by chemo-tactically active rhizobacteria of populus deltoides

PubMed Central

Bisht, Sandeep; Pandey, Piyush; Sood, Anchal; Sharma, Shivesh; Bisht, N. S.

2010-01-01

Several naphthalene and anthracene degrading bacteria were isolated from rhizosphere of Populus deltoides, which were growing in non-contaminated soil. Among these, four isolates, i.e. Kurthia sp., Micrococcus varians, Deinococcus radiodurans and Bacillus circulans utilized chrysene, benzene, toluene and xylene, in addition to anthracene and naphthalene. Kurthia sp and B. circulans showed positive chemotactic response for naphthalene and anthracene. The mean growth rate constant (K) of isolates were found to increase with successive increase in substrate concentration (0.5 to 1.0 mg/50ml). B. circulans SBA12 and Kurthia SBA4 degraded 87.5% and 86.6% of anthracene while, Kurthia sp. SBA4, B. circulans SBA12, and M. varians SBA8 degraded 85.3 %, 95.8 % and 86.8 % of naphthalene respectively after 6 days of incubation as determined by HPLC analysis. PMID:24031572

Mechanism for accurate, protein-assisted DNA annealing by Deinococcus radiodurans DdrB

PubMed Central

Sugiman-Marangos, Seiji N.; Weiss, Yoni M.; Junop, Murray S.

2016-01-01

Accurate pairing of DNA strands is essential for repair of DNA double-strand breaks (DSBs). How cells achieve accurate annealing when large regions of single-strand DNA are unpaired has remained unclear despite many efforts focused on understanding proteins, which mediate this process. Here we report the crystal structure of a single-strand annealing protein [DdrB (DNA damage response B)] in complex with a partially annealed DNA intermediate to 2.2 Å. This structure and supporting biochemical data reveal a mechanism for accurate annealing involving DdrB-mediated proofreading of strand complementarity. DdrB promotes high-fidelity annealing by constraining specific bases from unauthorized association and only releases annealed duplex when bound strands are fully complementary. To our knowledge, this mechanism provides the first understanding for how cells achieve accurate, protein-assisted strand annealing under biological conditions that would otherwise favor misannealing. PMID:27044084

Spectroelectrochemical insights into structural and redox properties of immobilized endonuclease III and its catalytically inactive mutant

NASA Astrophysics Data System (ADS)

Moe, Elin; Rollo, Filipe; Silveira, Célia M.; Sezer, Murat; Hildebrandt, Peter; Todorovic, Smilja

2018-01-01

Endonuclease III is a Fe-S containing bifunctional DNA glycosylase which is involved in the repair of oxidation damaged DNA. Here we employ surface enhanced IR spectroelectrochemistry and electrochemistry to study the enzyme from the highly radiation- and desiccation-resistant bacterium Deinococcus radiodurans (DrEndoIII2). The experiments are designed to shed more light onto specific parameters that are currently proposed to govern damage search and recognition by endonucleases III. We demonstrate that electrostatic interactions required for the redox activation of DrEndoIII2 may result in high electric fields that alter its structural and thermodynamic properties. Analysis of inactive DrEndoIII2 (K132A/D150A double mutant) interacting with undamaged DNA, and the active enzyme interacting with damaged DNA also indicate that the electron transfer is modulated by subtle differences in the protein-DNA complex.

Spectroelectrochemical insights into structural and redox properties of immobilized endonuclease III and its catalytically inactive mutant.

PubMed

Moe, Elin; Rollo, Filipe; Silveira, Célia M; Sezer, Murat; Hildebrandt, Peter; Todorovic, Smilja

2018-01-05

Endonuclease III is a Fe-S containing bifunctional DNA glycosylase which is involved in the repair of oxidation damaged DNA. Here we employ surface enhanced IR spectroelectrochemistry and electrochemistry to study the enzyme from the highly radiation- and desiccation-resistant bacterium Deinococcus radiodurans (DrEndoIII 2 ). The experiments are designed to shed more light onto specific parameters that are currently proposed to govern damage search and recognition by endonucleases III. We demonstrate that electrostatic interactions required for the redox activation of DrEndoIII 2 may result in high electric fields that alter its structural and thermodynamic properties. Analysis of inactive DrEndoIII 2 (K132A/D150A double mutant) interacting with undamaged DNA, and the active enzyme interacting with damaged DNA also indicate that the electron transfer is modulated by subtle differences in the protein-DNA complex. Copyright © 2017 Elsevier B.V. All rights reserved.

Inactivation, DNA double strand break induction and their rejoining in bacterial cells irradiated with heavy ions

NASA Technical Reports Server (NTRS)

Schaefer, M.; Zimmermann, H.; Schmitz, C.

1994-01-01

Besides inactivation one of the major interests in our experiments is to study the primary damage in the DNA double strand breaks (DSB) after heavy ion irradiation. These damages lead not only to cell death but also under repair activities to mutations. In further experiments we have investigated the inactivation with two different strains of Deinococcus radiodurans (R1, Rec 30) and the induction of DSB as well as the rejoining of DSB in stationary cells of E. coli (strain B/r) irradiated with radiations of different quality. In the latter case irradiations were done so that the cell survival was roughly at the same level. We measured the DSB using the pulse field gelelectrophoresis which allows to separate between intact (circular) and damaged (linear) DNA. The irradiated cells were transferred to NB medium and incubated for different times to allow rejoining.

Raman spectroscopic study of the photoprotection of extremophilic microbes against ultraviolet radiation

NASA Astrophysics Data System (ADS)

Edwards, H. G. M.; Moeller, R.; Jorge Villar, S. E.; Horneck, G.; Stackebrandt, E.

2006-12-01

Extremophiles use a range of pigments for protection against low-wavelength radiation in exposed terrestrial habitats and photoaccessory materials are synthesized for the effective harnessing of photosynthetically active radiation. Raman spectroscopy has been demonstrated to be a useful probe for information on the survival strategies employed by extremophilic bacteria through the identification of key biomolecular signatures of the suite of protective chemicals synthesized by the organisms in stressed environments. Raman spectroscopic analyses of Bacillus spp. spores, Bacillus atrophaeus (DSM 675: deep red) and Bacillus subtilis (DSM 5611: light grey and DSM 7264: dark grey), Deinococcus radiodurans (pink) and Natronomonas pharaonis (red), of visually different pigmentation showed the presence of different carotenoids and other protectant biomolecules, which assist microorganisms against UVA radiation. The implications for the survival of extremophilic microbes in extraterrestrial habitats and for the detection of the protectant biomolecules by remote, robotic Raman spectroscopic instrumentation in an astrobiological search for life context are discussed.

Structure determination of uracil-DNA N-glycosylase from Deinococcus radiodurans in complex with DNA.

PubMed

Pedersen, Hege Lynum; Johnson, Kenneth A; McVey, Colin E; Leiros, Ingar; Moe, Elin

2015-10-01

Uracil-DNA N-glycosylase (UNG) is a DNA-repair enzyme in the base-excision repair (BER) pathway which removes uracil from DNA. Here, the crystal structure of UNG from the extremophilic bacterium Deinococcus radiodurans (DrUNG) in complex with DNA is reported at a resolution of 1.35 Å. Prior to the crystallization experiments, the affinity between DrUNG and different DNA oligonucleotides was tested by electrophoretic mobility shift assays (EMSAs). As a result of this analysis, two 16 nt double-stranded DNAs were chosen for the co-crystallization experiments, one of which (16 nt AU) resulted in well diffracting crystals. The DNA in the co-crystal structure contained an abasic site (substrate product) flipped into the active site of the enzyme, with no uracil in the active-site pocket. Despite the high resolution, it was not possible to fit all of the terminal nucleotides of the DNA complex into electron density owing to disorder caused by a lack of stabilizing interactions. However, the DNA which was in contact with the enzyme, close to the active site, was well ordered and allowed detailed analysis of the enzyme-DNA interaction. The complex revealed that the interaction between DrUNG and DNA is similar to that in the previously determined crystal structure of human UNG (hUNG) in complex with DNA [Slupphaug et al. (1996). Nature (London), 384, 87-92]. Substitutions in a (here defined) variable part of the leucine loop result in a shorter loop (eight residues instead of nine) in DrUNG compared with hUNG; regardless of this, it seems to fulfil its role and generate a stabilizing force with the minor groove upon flipping out of the damaged base into the active site. The structure also provides a rationale for the previously observed high catalytic efficiency of DrUNG caused by high substrate affinity by demonstrating an increased number of long-range electrostatic interactions between the enzyme and the DNA. Interestingly, specific interactions between residues in the N-terminus of a symmetry-related molecule and the complementary DNA strand facing away from the active site were also observed which seem to stabilize the enzyme-DNA complex. However, the significance of this observation remains to be investigated. The results provide new insights into the current knowledge about DNA damage recognition and repair by uracil-DNA glycosylases.

Irradiation of Microbes from Spent Nuclear Fuel Storage Pool Environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Breckenridge, C.R.; Watkins, C.S.; Bruhn, D.F.

Microbes have been isolated and identified from spent nuclear fuel storage pools at the Idaho National Engineering and Environmental Laboratory (INEEL). Included among these are Corynebacterium aquaticum, Pseudomonas putida, Comamonas acidovorans, Gluconobacter cerinus, Micrococcus diversus, Rhodococcus rhodochrous, and two strains of sulfate-reducing bacteria (SRB). We examined the sensitivity of these microbes to a variety of total exposures of radiation generated by a 6-MeV linear accelerator (LINAC). The advantage of using a LINAC is that it provides a relatively quick screen of radiation tolerance. In the first set of experiments, we exposed each of the aforementioned microbes along with four additionalmore » microbes, pseudomonas aeruginosa, Micrococcus luteus, Escherchia coli, and Deinococcus radiodurans to exposures of 5 x 10{sup 3} and 6 x 10{sup 4} rad. All microbial specimens withstood the lower exposure with little or no reduction in cell population. Upon exposing the microbes to the larger dose of 6 x 10{sup 4} rad, we observed two distinct groupings: microbes that demonstrate resistance to radiation, and microbes that display intolerance through a dramatic reduction from their initial population. Microbes in the radiation tolerant grouping were exposed to 1.1 x 10{sup 5} rad to examine the extent of their resistance. We observe a correlation between radiation resistance and gram stain. The gram-positive species we examined seem to demonstrate a greater radiation resistance.« less

Below-Background Ionizing Radiation as an Environmental Cue for Bacteria

DOE PAGES

Castillo, Hugo; Smith, Geoffrey B.

2017-02-14

All organisms on earth grow under the influence of a natural and relatively constant dose of ionizing radiation referred to as background radiation, and so cells have different mechanisms to prevent the accumulation of damage caused by its different components. However, current knowledge of the deleterious effects of radiation on cells is based on the exposure to acute and high or to chronic, above background doses of radiation and therefore is not appropriate to explain the cellular and biochemical mechanisms that cells employ to sense and respond to chronic below-background levels. Studies at below-background radiation doses can provide insight intomore » the biological role of radiation, as suggested by several examples of what appears to be a stress response in cells grown at doses that range from 10 to 79 times lower than background. Here, we discuss some of the technical constraints to shield cells from radiation to below-background levels, as well as different approaches used to detect and measure responses to such unusual environmental conditions. Then, we present data from Shewanella oneidensis and Deinococcus radiodurans experiments that show how two taxonomically distant bacterial species sense and respond to unnaturally low levels of radiation. Finally, in brief, we grew S. oneidensis and D. radiodurans in liquid culture at dose rates of 72.05 (control) and 0.91 (treatment) nGy hr -1 (including radon) for up to 72 h and measured cell density and the expression of stress-related genes. Our results suggest that a stress response is triggered in the absence of normal levels of radiation.« less

S-layer proteins as a source of carotenoids: Isolation of the carotenoid cofactor deinoxanthin from its S-layer protein DR_2577.

PubMed

Farci, Domenica; Esposito, Francesca; El Alaoui, Sabah; Piano, Dario

2017-09-01

S-layers are regular paracrystalline arrays of proteins or glycoproteins that characterize the outer envelope of several bacteria and archaea. The auto-assembling properties of these proteins make them suitable for application in nanotechnologies. However, the bacterial cell wall and its S-layer are also an important binding sites for carotenoids and they may represent a potential source of these precious molecules for industrial purposes. The S-layer structure and its components were extensively studied in the radio-resistant bacterium Deinococcus radiodurans, which for long time represented one of the model organisms in this respect. The protein DR_2577 has been shown to be one of the naturally over-expressed S-layer components in this bacterium. The present report describes a high scale purification procedure of this protein in solution. The purity of the samples, assayed by native and denaturing electrophoresis, showed how this method leads to a selective and high efficient recovery of the pure DR_2577. Recently, we have found that the deinoxanthin, a carotenoid typical of D. radiodurans, is a cofactor non covalently bound to the protein DR_2577. The pure DR_2577 samples may be precipitated or lyophilized and used as a source of the carotenoid cofactor deinoxanthin by an efficient extraction using organic solvents. The procedure described in this work may represent a general approach for the isolation of S-layer proteins and their carotenoids with potentials for industrial applications. Copyright © 2016 Elsevier Ltd. All rights reserved.

Survival in Nuclear Waste, Extreme Resistance, and Potential Applications Gleaned from the Genome Sequence of Kineococcus radiotolerans SRS30216

PubMed Central

Bagwell, Christopher E.; Bhat, Swapna; Hawkins, Gary M.; Smith, Bryan W.; Biswas, Tapan; Hoover, Timothy R.; Saunders, Elizabeth; Han, Cliff S.; Tsodikov, Oleg V.; Shimkets, Lawrence J.

2008-01-01

Kineococcus radiotolerans SRS30216 was isolated from a high-level radioactive environment at the Savannah River Site (SRS) and exhibits γ-radiation resistance approaching that of Deinococcus radiodurans. The genome was sequenced by the U.S. Department of Energy's Joint Genome Institute which suggested the existence of three replicons, a 4.76 Mb linear chromosome, a 0.18 Mb linear plasmid, and a 12.92 Kb circular plasmid. Southern hybridization confirmed that the chromosome is linear. The K. radiotolerans genome sequence was examined to learn about the physiology of the organism with regard to ionizing radiation resistance, the potential for bioremediation of nuclear waste, and the dimorphic life cycle. K. radiotolerans may have a unique genetic toolbox for radiation protection as it lacks many of the genes known to confer radiation resistance in D. radiodurans. Additionally, genes involved in the detoxification of reactive oxygen species and the excision repair pathway are overrepresented. K. radiotolerans appears to lack degradation pathways for pervasive soil and groundwater pollutants. However, it can respire on two organic acids found in SRS high-level nuclear waste, formate and oxalate, which promote the survival of cells during prolonged periods of starvation. The dimorphic life cycle involves the production of motile zoospores. The flagellar biosynthesis genes are located on a motility island, though its regulation could not be fully discerned. These results highlight the remarkable ability of K radiotolerans to withstand environmental extremes and suggest that in situ bioremediation of organic complexants from high level radioactive waste may be feasible. PMID:19057647

Below-Background Ionizing Radiation as an Environmental Cue for Bacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castillo, Hugo; Smith, Geoffrey B.

All organisms on earth grow under the influence of a natural and relatively constant dose of ionizing radiation referred to as background radiation, and so cells have different mechanisms to prevent the accumulation of damage caused by its different components. However, current knowledge of the deleterious effects of radiation on cells is based on the exposure to acute and high or to chronic, above background doses of radiation and therefore is not appropriate to explain the cellular and biochemical mechanisms that cells employ to sense and respond to chronic below-background levels. Studies at below-background radiation doses can provide insight intomore » the biological role of radiation, as suggested by several examples of what appears to be a stress response in cells grown at doses that range from 10 to 79 times lower than background. Here, we discuss some of the technical constraints to shield cells from radiation to below-background levels, as well as different approaches used to detect and measure responses to such unusual environmental conditions. Then, we present data from Shewanella oneidensis and Deinococcus radiodurans experiments that show how two taxonomically distant bacterial species sense and respond to unnaturally low levels of radiation. Finally, in brief, we grew S. oneidensis and D. radiodurans in liquid culture at dose rates of 72.05 (control) and 0.91 (treatment) nGy hr -1 (including radon) for up to 72 h and measured cell density and the expression of stress-related genes. Our results suggest that a stress response is triggered in the absence of normal levels of radiation.« less

Microbial cells can cooperate to resist high-level chronic ionizing radiation.

PubMed

Shuryak, Igor; Matrosova, Vera Y; Gaidamakova, Elena K; Tkavc, Rok; Grichenko, Olga; Klimenkova, Polina; Volpe, Robert P; Daly, Michael J

2017-01-01

Understanding chronic ionizing radiation (CIR) effects is of utmost importance to protecting human health and the environment. Diverse bacteria and fungi inhabiting extremely radioactive waste and disaster sites (e.g. Hanford, Chernobyl, Fukushima) represent new targets of CIR research. We show that many microorganisms can grow under intense gamma-CIR dose rates of 13-126 Gy/h, with fungi identified as a particularly CIR-resistant group of eukaryotes: among 145 phylogenetically diverse strains tested, 78 grew under 36 Gy/h. Importantly, we demonstrate that CIR resistance can depend on cell concentration and that certain resistant microbial cells protect their neighbors (not only conspecifics, but even radiosensitive species from a different phylum), from high-level CIR. We apply a mechanistically-motivated mathematical model of CIR effects, based on accumulation/removal kinetics of reactive oxygen species (ROS) and antioxidants, in bacteria (3 Escherichia coli strains and Deinococcus radiodurans) and in fungi (Candida parapsilosis, Kazachstania exigua, Pichia kudriavzevii, Rhodotorula lysinophila, Saccharomyces cerevisiae, and Trichosporon mucoides). We also show that correlations between responses to CIR and acute ionizing radiation (AIR) among studied microorganisms are weak. For example, in D. radiodurans, the best molecular correlate for CIR resistance is the antioxidant enzyme catalase, which is dispensable for AIR resistance; and numerous CIR-resistant fungi are not AIR-resistant. Our experimental findings and quantitative modeling thus demonstrate the importance of investigating CIR responses directly, rather than extrapolating from AIR. Protection of radiosensitive cell-types by radioresistant ones under high-level CIR is a potentially important new tool for bioremediation of radioactive sites and development of CIR-resistant microbiota as radioprotectors.

Revisiting the structures of several antibiotics bound to the bacterial ribosome

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bulkley, David; Innis, C. Axel; Blaha, Gregor

2010-10-08

The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model.more » Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.« less

Revisiting the Structures of Several Antibiotics Bound to the Bacterial Ribosome

DOE Office of Scientific and Technical Information (OSTI.GOV)

D Bulkley; C Innis; G Blaha

2011-12-31

The increasing prevalence of antibiotic-resistant pathogens reinforces the need for structures of antibiotic-ribosome complexes that are accurate enough to enable the rational design of novel ribosome-targeting therapeutics. Structures of many antibiotics in complex with both archaeal and eubacterial ribosomes have been determined, yet discrepancies between several of these models have raised the question of whether these differences arise from species-specific variations or from experimental problems. Our structure of chloramphenicol in complex with the 70S ribosome from Thermus thermophilus suggests a model for chloramphenicol bound to the large subunit of the bacterial ribosome that is radically different from the prevailing model.more » Further, our structures of the macrolide antibiotics erythromycin and azithromycin in complex with a bacterial ribosome are indistinguishable from those determined of complexes with the 50S subunit of Haloarcula marismortui, but differ significantly from the models that have been published for 50S subunit complexes of the eubacterium Deinococcus radiodurans. Our structure of the antibiotic telithromycin bound to the T. thermophilus ribosome reveals a lactone ring with a conformation similar to that observed in the H. marismortui and D. radiodurans complexes. However, the alkyl-aryl moiety is oriented differently in all three organisms, and the contacts observed with the T. thermophilus ribosome are consistent with biochemical studies performed on the Escherichia coli ribosome. Thus, our results support a mode of macrolide binding that is largely conserved across species, suggesting that the quality and interpretation of electron density, rather than species specificity, may be responsible for many of the discrepancies between the models.« less

Microbial cells can cooperate to resist high-level chronic ionizing radiation

PubMed Central

Gaidamakova, Elena K.; Tkavc, Rok; Grichenko, Olga; Klimenkova, Polina; Volpe, Robert P.; Daly, Michael J.

2017-01-01

Understanding chronic ionizing radiation (CIR) effects is of utmost importance to protecting human health and the environment. Diverse bacteria and fungi inhabiting extremely radioactive waste and disaster sites (e.g. Hanford, Chernobyl, Fukushima) represent new targets of CIR research. We show that many microorganisms can grow under intense gamma-CIR dose rates of 13–126 Gy/h, with fungi identified as a particularly CIR-resistant group of eukaryotes: among 145 phylogenetically diverse strains tested, 78 grew under 36 Gy/h. Importantly, we demonstrate that CIR resistance can depend on cell concentration and that certain resistant microbial cells protect their neighbors (not only conspecifics, but even radiosensitive species from a different phylum), from high-level CIR. We apply a mechanistically-motivated mathematical model of CIR effects, based on accumulation/removal kinetics of reactive oxygen species (ROS) and antioxidants, in bacteria (3 Escherichia coli strains and Deinococcus radiodurans) and in fungi (Candida parapsilosis, Kazachstania exigua, Pichia kudriavzevii, Rhodotorula lysinophila, Saccharomyces cerevisiae, and Trichosporon mucoides). We also show that correlations between responses to CIR and acute ionizing radiation (AIR) among studied microorganisms are weak. For example, in D. radiodurans, the best molecular correlate for CIR resistance is the antioxidant enzyme catalase, which is dispensable for AIR resistance; and numerous CIR-resistant fungi are not AIR-resistant. Our experimental findings and quantitative modeling thus demonstrate the importance of investigating CIR responses directly, rather than extrapolating from AIR. Protection of radiosensitive cell-types by radioresistant ones under high-level CIR is a potentially important new tool for bioremediation of radioactive sites and development of CIR-resistant microbiota as radioprotectors. PMID:29261697

Ring-shaped architecture of RecR: implications for its role in homologous recombinational DNA repair

PubMed Central

Lee, Byung Il; Kim, Kyoung Hoon; Park, Soo Jeong; Eom, Soo Hyun; Song, Hyun Kyu; Suh, Se Won

2004-01-01

RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway of homologous recombinational DNA repair in procaryotes . The human Rad52 protein is a functional counterpart of RecFOR. We present here the crystal structure of RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a two-domain structure: the N-terminal domain with a helix–hairpin–helix (HhH) motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222 symmetry with a central hole of 30−35 Å diameter. In the crystal, two tetramers are concatenated, implying that the RecR tetramer is capable of opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA, and that its HhH motif is essential for DNA binding. PMID:15116069

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

DOE PAGES

Edlund, Petra; Takala, Heikki; Claesson, Elin; ...

2016-10-19

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Edlund, Petra; Takala, Heikki; Claesson, Elin

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

Structural basis for the interaction of antibiotics with peptidyl transferase center in eubacteria

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schlunzen, Frank; Zarivach, Raz; Harms, Jörg

2009-10-07

Ribosomes, the site of protein synthesis, are a major target for natural and synthetic antibiotics. Detailed knowledge of antibiotic binding sites is central to understanding the mechanisms of drug action. Conversely, drugs are excellent tools for studying the ribosome function. To elucidate the structural basis of ribosome-antibiotic interactions, we determined the high-resolution X-ray structures of the 50S ribosomal subunit of the eubacterium Deinococcus radiodurans, complexed with the clinically relevant antibiotics chloramphenicol, clindamycin and the three macrolides erythromycin, clarithromycin and roxithromycin. We found that antibiotic binding sites are composed exclusively of segments of 23S ribosomal RNA at the peptidyl transferase cavitymore » and do not involve any interaction of the drugs with ribosomal proteins. Here we report the details of antibiotic interactions with the components of their binding sites. Our results also show the importance of putative Mg{sup +2} ions for the binding of some drugs. This structural analysis should facilitate rational drug design.« less

Structural Determinants of Improved Fluorescence in a Family of Bacteriophytochrome-Based Infrared Fluorescent Proteins: Insights from Continuum Electrostatic Calculations and Molecular Dynamics Simulations.

PubMed

Feliks, Mikolaj; Lafaye, Céline; Shu, Xiaokun; Royant, Antoine; Field, Martin

2016-08-09

Using X-ray crystallography, continuum electrostatic calculations, and molecular dynamics simulations, we have studied the structure, protonation behavior, and dynamics of the biliverdin chromophore and its molecular environment in a series of genetically engineered infrared fluorescent proteins (IFPs) based on the chromophore-binding domain of the Deinococcus radiodurans bacteriophytochrome. Our study suggests that the experimentally observed enhancement of fluorescent properties results from the improved rigidity and planarity of the biliverdin chromophore, in particular of the first two pyrrole rings neighboring the covalent linkage to the protein. We propose that the increases in the levels of both motion and bending of the chromophore out of planarity favor the decrease in fluorescence. The chromophore-binding pocket in some of the studied proteins, in particular the weakly fluorescent parent protein, is shown to be readily accessible to water molecules from the solvent. These waters entering the chromophore region form hydrogen bond networks that affect the otherwise planar conformation of the first three rings of the chromophore. On the basis of our simulations, the enhancement of fluorescence in IFPs can be achieved either by reducing the mobility of water molecules in the vicinity of the chromophore or by limiting the interactions of the nearby protein residues with the chromophore. Finally, simulations performed at both low and neutral pH values highlight differences in the dynamics of the chromophore and shed light on the mechanism of fluorescence loss at low pH.

Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria—A Challenge for Life on Mars

PubMed Central

Bak, Ebbe N.; Larsen, Michael G.; Moeller, Ralf; Nissen, Silas B.; Jensen, Lasse R.; Nørnberg, Per; Jensen, Svend J. K.; Finster, Kai

2017-01-01

The habitability of Mars is determined by the physical and chemical environment. The effect of low water availability, temperature, low atmospheric pressure and strong UV radiation has been extensively studied in relation to the survival of microorganisms. In addition to these stress factors, it was recently found that silicates exposed to simulated saltation in a Mars-like atmosphere can lead to a production of reactive oxygen species. Here, we have investigated the stress effect induced by quartz and basalt abraded in Mars-like atmospheres by examining the survivability of the three microbial model organisms Pseudomonas putida, Bacillus subtilis, and Deinococcus radiodurans upon exposure to the abraded silicates. We found that abraded basalt that had not been in contact with oxygen after abrasion killed more than 99% of the vegetative cells while endospores were largely unaffected. Exposure of the basalt samples to oxygen after abrasion led to a significant reduction in the stress effect. Abraded quartz was generally less toxic than abraded basalt. We suggest that the stress effect of abraded silicates may be caused by a production of reactive oxygen species and enhanced by transition metal ions in the basalt leading to hydroxyl radicals through Fenton-like reactions. The low survivability of the usually highly resistant D. radiodurans indicates that the effect of abraded silicates, as is ubiquitous on the Martian surface, would limit the habitability of Mars as well as the risk of forward contamination. Furthermore, the reactivity of abraded silicates could have implications for future manned missions, although the lower effect of abraded silicates exposed to oxygen suggests that the effects would be reduced in human habitats. PMID:28955310

Silicates Eroded under Simulated Martian Conditions Effectively Kill Bacteria-A Challenge for Life on Mars.

PubMed

Bak, Ebbe N; Larsen, Michael G; Moeller, Ralf; Nissen, Silas B; Jensen, Lasse R; Nørnberg, Per; Jensen, Svend J K; Finster, Kai

2017-01-01

The habitability of Mars is determined by the physical and chemical environment. The effect of low water availability, temperature, low atmospheric pressure and strong UV radiation has been extensively studied in relation to the survival of microorganisms. In addition to these stress factors, it was recently found that silicates exposed to simulated saltation in a Mars-like atmosphere can lead to a production of reactive oxygen species. Here, we have investigated the stress effect induced by quartz and basalt abraded in Mars-like atmospheres by examining the survivability of the three microbial model organisms Pseudomonas putida, Bacillus subtilis , and Deinococcus radiodurans upon exposure to the abraded silicates. We found that abraded basalt that had not been in contact with oxygen after abrasion killed more than 99% of the vegetative cells while endospores were largely unaffected. Exposure of the basalt samples to oxygen after abrasion led to a significant reduction in the stress effect. Abraded quartz was generally less toxic than abraded basalt. We suggest that the stress effect of abraded silicates may be caused by a production of reactive oxygen species and enhanced by transition metal ions in the basalt leading to hydroxyl radicals through Fenton-like reactions. The low survivability of the usually highly resistant D. radiodurans indicates that the effect of abraded silicates, as is ubiquitous on the Martian surface, would limit the habitability of Mars as well as the risk of forward contamination. Furthermore, the reactivity of abraded silicates could have implications for future manned missions, although the lower effect of abraded silicates exposed to oxygen suggests that the effects would be reduced in human habitats.

Coccomyxa actinabiotis sp. nov. (Trebouxiophyceae, Chlorophyta), a new green microalga living in the spent fuel cooling pool of a nuclear reactor.

PubMed

Rivasseau, Corinne; Farhi, Emmanuel; Compagnon, Estelle; de Gouvion Saint Cyr, Diane; van Lis, Robert; Falconet, Denis; Kuntz, Marcel; Atteia, Ariane; Couté, Alain

2016-10-01

Life can thrive in extreme environments where inhospitable conditions prevail. Organisms which resist, for example, acidity, pressure, low or high temperature, have been found in harsh environments. Most of them are bacteria and archaea. The bacterium Deinococcus radiodurans is considered to be a champion among all living organisms, surviving extreme ionizing radiation levels. We have discovered a new extremophile eukaryotic organism that possesses a resistance to ionizing radiations similar to that of D. radiodurans. This microorganism, an autotrophic freshwater green microalga, lives in a peculiar environment, namely the cooling pool of a nuclear reactor containing spent nuclear fuels, where it is continuously submitted to nutritive, metallic, and radiative stress. We investigated its morphology and its ultrastructure by light, fluorescence and electron microscopy as well as its biochemical properties. Its resistance to UV and gamma radiation was assessed. When submitted to different dose rates of the order of some tens of mGy · h -1 to several thousands of Gy · h -1 , the microalga revealed to be able to survive intense gamma-rays irradiation, up to 2,000 times the dose lethal to human. The nuclear genome region spanning the genes for small subunit ribosomal RNA-Internal Transcribed Spacer (ITS) 1-5.8S rRNA-ITS2-28S rRNA (beginning) was sequenced (4,065 bp). The phylogenetic position of the microalga was inferred from the 18S rRNA gene. All the revealed characteristics make the alga a new species of the genus Coccomyxa in the class Trebouxiophyceae, which we name Coccomyxa actinabiotis sp. nov. © 2016 Phycological Society of America.

Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149.

PubMed

Tkavc, Rok; Matrosova, Vera Y; Grichenko, Olga E; Gostinčar, Cene; Volpe, Robert P; Klimenkova, Polina; Gaidamakova, Elena K; Zhou, Carol E; Stewart, Benjamin J; Lyman, Mathew G; Malfatti, Stephanie A; Rubinfeld, Bonnee; Courtot, Melanie; Singh, Jatinder; Dalgard, Clifton L; Hamilton, Theron; Frey, Kenneth G; Gunde-Cimerman, Nina; Dugan, Lawrence; Daly, Michael J

2017-01-01

Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans . However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites.

Prospects for Fungal Bioremediation of Acidic Radioactive Waste Sites: Characterization and Genome Sequence of Rhodotorula taiwanensis MD1149

PubMed Central

Tkavc, Rok; Matrosova, Vera Y.; Grichenko, Olga E.; Gostinčar, Cene; Volpe, Robert P.; Klimenkova, Polina; Gaidamakova, Elena K.; Zhou, Carol E.; Stewart, Benjamin J.; Lyman, Mathew G.; Malfatti, Stephanie A.; Rubinfeld, Bonnee; Courtot, Melanie; Singh, Jatinder; Dalgard, Clifton L.; Hamilton, Theron; Frey, Kenneth G.; Gunde-Cimerman, Nina; Dugan, Lawrence; Daly, Michael J.

2018-01-01

Highly concentrated radionuclide waste produced during the Cold War era is stored at US Department of Energy (DOE) production sites. This radioactive waste was often highly acidic and mixed with heavy metals, and has been leaking into the environment since the 1950s. Because of the danger and expense of cleanup of such radioactive sites by physicochemical processes, in situ bioremediation methods are being developed for cleanup of contaminated ground and groundwater. To date, the most developed microbial treatment proposed for high-level radioactive sites employs the radiation-resistant bacterium Deinococcus radiodurans. However, the use of Deinococcus spp. and other bacteria is limited by their sensitivity to low pH. We report the characterization of 27 diverse environmental yeasts for their resistance to ionizing radiation (chronic and acute), heavy metals, pH minima, temperature maxima and optima, and their ability to form biofilms. Remarkably, many yeasts are extremely resistant to ionizing radiation and heavy metals. They also excrete carboxylic acids and are exceptionally tolerant to low pH. A special focus is placed on Rhodotorula taiwanensis MD1149, which was the most resistant to acid and gamma radiation. MD1149 is capable of growing under 66 Gy/h at pH 2.3 and in the presence of high concentrations of mercury and chromium compounds, and forming biofilms under high-level chronic radiation and low pH. We present the whole genome sequence and annotation of R. taiwanensis strain MD1149, with a comparison to other Rhodotorula species. This survey elevates yeasts to the frontier of biology's most radiation-resistant representatives, presenting a strong rationale for a role of fungi in bioremediation of acidic radioactive waste sites. PMID:29375494

Normalization Approaches for Removing Systematic Biases Associated with Mass Spectrometry and Label-Free Proteomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Callister, Stephen J.; Barry, Richard C.; Adkins, Joshua N.

2006-02-01

Central tendency, linear regression, locally weighted regression, and quantile techniques were investigated for normalization of peptide abundance measurements obtained from high-throughput liquid chromatography-Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR MS). Arbitrary abundances of peptides were obtained from three sample sets, including a standard protein sample, two Deinococcus radiodurans samples taken from different growth phases, and two mouse striatum samples from control and methamphetamine-stressed mice (strain C57BL/6). The selected normalization techniques were evaluated in both the absence and presence of biological variability by estimating extraneous variability prior to and following normalization. Prior to normalization, replicate runs from each sample setmore » were observed to be statistically different, while following normalization replicate runs were no longer statistically different. Although all techniques reduced systematic bias, assigned ranks among the techniques revealed significant trends. For most LC-FTICR MS analyses, linear regression normalization ranked either first or second among the four techniques, suggesting that this technique was more generally suitable for reducing systematic biases.« less

Crystal Structure and Conformational Change Mechanism of a Bacterial Nramp-Family Divalent Metal Transporter.

PubMed

Bozzi, Aaron T; Bane, Lukas B; Weihofen, Wilhelm A; Singharoy, Abhishek; Guillen, Eduardo R; Ploegh, Hidde L; Schulten, Klaus; Gaudet, Rachelle

2016-12-06

The widely conserved natural resistance-associated macrophage protein (Nramp) family of divalent metal transporters enables manganese import in bacteria and dietary iron uptake in mammals. We determined the crystal structure of the Deinococcus radiodurans Nramp homolog (DraNramp) in an inward-facing apo state, including the complete transmembrane (TM) segment 1a (absent from a previous Nramp structure). Mapping our cysteine accessibility scanning results onto this structure, we identified the metal-permeation pathway in the alternate outward-open conformation. We investigated the functional impact of two natural anemia-causing glycine-to-arginine mutations that impaired transition metal transport in both human Nramp2 and DraNramp. The TM4 G153R mutation perturbs the closing of the outward metal-permeation pathway and alters the selectivity of the conserved metal-binding site. In contrast, the TM1a G45R mutation prevents conformational change by sterically blocking the essential movement of that helix, thus locking the transporter in an inward-facing state. Copyright © 2016 Elsevier Ltd. All rights reserved.

Physiological changes induced in four bacterial strains following oxidative stress.

PubMed

Baatout, S; De Boever, P; Mergeay, M

2006-01-01

In order to study the behaviour and resistance of bacteria under extreme conditions, physiological changes associated with oxidative stress were monitored using flow cytometry. The study was conducted to assess the maintenance of membrane integrity and potential as well as the esterase activity, the intracellular pH and the production of superoxide anions in four bacterial strains (Ralstonia metallidurans, Escherichia coli, Shewanella oneidensis and Deinococcus radiodurans). The strains were chosen for their potential usefulness in bioremediation. Suspensions of R. metallidurans, E. coli, S. oneidensis and D. radiodurans were submitted to 1 h oxidative stress (H2O2 at various concentrations from 0 to 880 mM). Cell membrane permeability (propidium iodide) and potential (rhodamine-123, 3,3'-dihexyloxacarbocyanine iodide), intracellular esterase activity (fluorescein diacetate), intracellular reactive oxygen species concentration (hydroethidine) and intracellular pH (carboxyflurorescein diacetate succinimidyl ester (5(6)) were monitored to evaluate the physiological state and the overall fitness of individual bacterial cells under oxidative stress. The four bacterial strains exhibited varying sensitivities towards H2O2. However, for all bacterial strains, some physiological damage could already be observed from 13.25 mM H2O2 onwards, in particular with regard to their membrane permeability. Depending on the bacterial strains, moderate to high physiological damage could be observed between 13.25 mM and 220 mM H2O2. Membrane potential, esterase activity, intracellular pH and production of superoxide anion production were considerably modified at high H2O2 concentrations in all four strains. In conclusion, we show that a range of significant physiological alterations occurs when bacteria are challenged with H2O2 and fluorescent staining methods coupled with flow cytometry are useful for monitoring the changes induced not only by oxidative stress but also by other stresses like temperature, radiation, pressure, pH, etc....

A probabilistic framework for microarray data analysis: fundamental probability models and statistical inference.

PubMed

Ogunnaike, Babatunde A; Gelmi, Claudio A; Edwards, Jeremy S

2010-05-21

Gene expression studies generate large quantities of data with the defining characteristic that the number of genes (whose expression profiles are to be determined) exceed the number of available replicates by several orders of magnitude. Standard spot-by-spot analysis still seeks to extract useful information for each gene on the basis of the number of available replicates, and thus plays to the weakness of microarrays. On the other hand, because of the data volume, treating the entire data set as an ensemble, and developing theoretical distributions for these ensembles provides a framework that plays instead to the strength of microarrays. We present theoretical results that under reasonable assumptions, the distribution of microarray intensities follows the Gamma model, with the biological interpretations of the model parameters emerging naturally. We subsequently establish that for each microarray data set, the fractional intensities can be represented as a mixture of Beta densities, and develop a procedure for using these results to draw statistical inference regarding differential gene expression. We illustrate the results with experimental data from gene expression studies on Deinococcus radiodurans following DNA damage using cDNA microarrays. Copyright (c) 2010 Elsevier Ltd. All rights reserved.

Deinococcus Mn2+-peptide complex: A novel approach to alphavirus vaccine development.

PubMed

Gayen, Manoshi; Gupta, Paridhi; Morazzani, Elaine M; Gaidamakova, Elena K; Knollmann-Ritschel, Barbara; Daly, Michael J; Glass, Pamela J; Maheshwari, Radha K

2017-06-22

Over the last ten years, Chikungunya virus (CHIKV), an Old World alphavirus has caused numerous outbreaks in Asian and European countries and the Americas, making it an emerging pathogen of great global health importance. Venezuelan equine encephalitis virus (VEEV), a New World alphavirus, on the other hand, has been developed as a bioweapon in the past due to its ease of preparation, aerosol dispersion and high lethality in aerosolized form. Currently, there are no FDA approved vaccines against these viruses. In this study, we used a novel approach to develop inactivated vaccines for VEEV and CHIKV by applying gamma-radiation together with a synthetic Mn-decapeptide-phosphate complex (MnDpPi), based on manganous-peptide-orthophosphate antioxidants accumulated in the extremely radiation-resistant bacterium Deinococcus radiodurans. Classical gamma-irradiated vaccine development approaches are limited by immunogenicity-loss due to oxidative damage to the surface proteins at the high doses of radiation required for complete virus-inactivation. However, addition of MnDpPi during irradiation process selectively protects proteins, but not the nucleic acids, from the radiation-induced oxidative damage, as required for safe and efficacious vaccine development. Previously, this approach was used to develop a bacterial vaccine. In the present study, we show that this approach can successfully be applied to protecting mice against viral infections. Irradiation of VEEV and CHIKV in the presence of MnDpPi resulted in substantial epitope preservation even at supra-lethal doses of gamma-rays (50,000Gy). Irradiated viruses were found to be completely inactivated and safe in vivo (neonatal mice). Upon immunization, VEEV inactivated in the presence of MnDpPi resulted in drastically improved protective efficacy. Thus, the MnDpPi-based gamma-inactivation approach described here can readily be applied to developing vaccines against any pathogen of interest in a fast and cost-effective manner. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

The complete genome and proteome of Laribacter hongkongensis reveal potential mechanisms for adaptations to different temperatures and habitats.

PubMed

Woo, Patrick C Y; Lau, Susanna K P; Tse, Herman; Teng, Jade L L; Curreem, Shirly O T; Tsang, Alan K L; Fan, Rachel Y Y; Wong, Gilman K M; Huang, Yi; Loman, Nicholas J; Snyder, Lori A S; Cai, James J; Huang, Jian-Dong; Mak, William; Pallen, Mark J; Lok, Si; Yuen, Kwok-Yung

2009-03-01

Laribacter hongkongensis is a newly discovered Gram-negative bacillus of the Neisseriaceae family associated with freshwater fish-borne gastroenteritis and traveler's diarrhea. The complete genome sequence of L. hongkongensis HLHK9, recovered from an immunocompetent patient with severe gastroenteritis, consists of a 3,169-kb chromosome with G+C content of 62.35%. Genome analysis reveals different mechanisms potentially important for its adaptation to diverse habitats of human and freshwater fish intestines and freshwater environments. The gene contents support its phenotypic properties and suggest that amino acids and fatty acids can be used as carbon sources. The extensive variety of transporters, including multidrug efflux and heavy metal transporters as well as genes involved in chemotaxis, may enable L. hongkongensis to survive in different environmental niches. Genes encoding urease, bile salts efflux pump, adhesin, catalase, superoxide dismutase, and other putative virulence factors-such as hemolysins, RTX toxins, patatin-like proteins, phospholipase A1, and collagenases-are present. Proteomes of L. hongkongensis HLHK9 cultured at 37 degrees C (human body temperature) and 20 degrees C (freshwater habitat temperature) showed differential gene expression, including two homologous copies of argB, argB-20, and argB-37, which encode two isoenzymes of N-acetyl-L-glutamate kinase (NAGK)-NAGK-20 and NAGK-37-in the arginine biosynthesis pathway. NAGK-20 showed higher expression at 20 degrees C, whereas NAGK-37 showed higher expression at 37 degrees C. NAGK-20 also had a lower optimal temperature for enzymatic activities and was inhibited by arginine probably as negative-feedback control. Similar duplicated copies of argB are also observed in bacteria from hot springs such as Thermus thermophilus, Deinococcus geothermalis, Deinococcus radiodurans, and Roseiflexus castenholzii, suggesting that similar mechanisms for temperature adaptation may be employed by other bacteria. Genome and proteome analysis of L. hongkongensis revealed novel mechanisms for adaptations to survival at different temperatures and habitats.

Degradation of microbial fluorescence biosignatures by solar ultraviolet radiation on Mars

NASA Astrophysics Data System (ADS)

Dartnell, Lewis R.; Patel, Manish R.

2014-04-01

Recent and proposed robotic missions to Mars are equipped with implements to expose or excavate fresh material from beneath the immediate surface. Once brought into the open, any organic molecules or potential biosignatures of present or past life will be exposed to the unfiltered solar ultraviolet (UV) radiation and face photolytic degradation over short time courses. The key question, then, is what is the window of opportunity for detection of recently exposed samples during robotic operations? Detection of autofluorescence has been proposed as a simple method for surveying or triaging samples for organic molecules. Using a Mars simulation chamber we conduct UV exposures on thin frozen layers of two model microorganisms, the radiation-resistant polyextremophile Deinococcus radiodurans and the cyanobacterium Synechocystis sp. PCC 6803. Excitation-emission matrices (EEMs) are generated of the full fluorescence response to quantify the change in signal of different cellular fluorophores over Martian equivalent time. Fluorescence of Deinococcus cells, protected by a high concentration of carotenoid pigments, was found to be relatively stable over 32 h of Martian UV irradiation, with around 90% of the initial signal remaining. By comparison, fluorescence from protein-bound tryptophan in Synechocystis is much more sensitive to UV photodegradation, declining to 50% after 64 h exposure. The signal most readily degraded by UV irradiation is fluorescence of the photosynthetic pigments - diminished to only 35% after 64 h. This sensitivity may be expected as the biological function of chlorophyll and phycocyanin is to optimize the harvesting of light energy and so they are readily photobleached. A significant increase in a ~450 nm emission feature is interpreted as accumulation of fluorescent cellular degradation products from photolysis. Accounting for diurnal variation in Martian sunlight, this study calculates that frozen cellular biosignatures would remain detectable by fluorescence for at least several sols; offering a sufficient window for robotic exploration operations.

Effects of Deinococcus spp. supplement on egg quality traits in laying hens.

PubMed

Li, I-Chen; Wu, Szu-Yin; Liou, Jenn-Fa; Liu, Hsiao-Hui; Chen, Jiau-Hua; Chen, Chin-Chu

2018-01-01

To counter the ill effects of synthetic dyes, bacterial pigment production as an alternative is now one of the promising and emerging fields of research. This study was conducted to evaluate the applicability of Deinococcus genus on the egg quality traits in laying hens. In study I, 24 single comb White Leghorn layers were fed with various 1 wt % Deinococcus bacterial strains for 10 d. In study II, 84 brown Hendrix layers were fed with one of 4 diets containing 0, 0.2, 1, or 5 wt % Deinococcus sp. GKB-Aid 1995 powder for 12 wk. In study III, 60 White Leghorn laying hens were fed either with or without 1 wt % Deinococcus sp. GKB-Aid 1995 powder, 1 wt % Deinococcus sp. GKB-Aid 1995 granules, or 1 wt % Deinococcus sp. GKB-Aid 1995 oily granules for 10 successive d. In all of the experiments, feeding Deinococcus powder did not affect egg quality traits except for the yolk color. In particular, supplementation with all Deinococcus powder treatments changed the yolk color (P < 0.05) in study I, with the best pigmentation score obtained by D. grandis and Deinococcus sp. GKB-Aid 1995. Moreover, longer supplementation of Deinococcus sp. GKB-Aid 1995 in study II had a significant effect on feed conversion ratio. With these findings under consideration, the present study suggests that the Deinococcus species, especially Deinococcus sp. GKB-Aid 1995, can be an excellent candidate for improving egg yolk color in laying hens. © 2017 Poultry Science Association Inc.

D-MATRIX: A web tool for constructing weight matrix of conserved DNA motifs

PubMed Central

Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

2009-01-01

Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D­MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co­regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos­box cis­regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D­MATRIX tool is accessible through the CIMAP domain network. Availability http://203.190.147.116/dmatrix/ PMID:19759861

D-MATRIX: a web tool for constructing weight matrix of conserved DNA motifs.

PubMed

Sen, Naresh; Mishra, Manoj; Khan, Feroz; Meena, Abha; Sharma, Ashok

2009-07-27

Despite considerable efforts to date, DNA motif prediction in whole genome remains a challenge for researchers. Currently the genome wide motif prediction tools required either direct pattern sequence (for single motif) or weight matrix (for multiple motifs). Although there are known motif pattern databases and tools for genome level prediction but no tool for weight matrix construction. Considering this, we developed a D-MATRIX tool which predicts the different types of weight matrix based on user defined aligned motif sequence set and motif width. For retrieval of known motif sequences user can access the commonly used databases such as TFD, RegulonDB, DBTBS, Transfac. D-MATRIX program uses a simple statistical approach for weight matrix construction, which can be converted into different file formats according to user requirement. It provides the possibility to identify the conserved motifs in the co-regulated genes or whole genome. As example, we successfully constructed the weight matrix of LexA transcription factor binding site with the help of known sos-box cis-regulatory elements in Deinococcus radiodurans genome. The algorithm is implemented in C-Sharp and wrapped in ASP.Net to maintain a user friendly web interface. D-MATRIX tool is accessible through the CIMAP domain network. http://203.190.147.116/dmatrix/

Detoxification of toxins by bacillithiol in Staphylococcus aureus

PubMed Central

Newton, Gerald L.; Fahey, Robert C.

2012-01-01

Bacillithiol (BSH), an α-anomeric glycoside of l-cysteinyl-d-glucosaminyl-l-malate, is a major low-molecular-mass thiol found in bacteria such as Bacillus sp., Staphylococcus aureus and Deinococcus radiodurans. Like other low-molecular-mass thiols such as glutathione and mycothiol, BSH is likely to be involved in protection against environmental toxins including thiol-reactive antibiotics. We report here a BSH-dependent detoxification mechanism in S. aureus. When S. aureus Newman strain was treated with monobromobimane and monochlorobimane, the cellular BSH was converted to the fluorescent S-conjugate BS-bimane. A bacillithiol conjugate amidase activity acted upon the BS-bimane to produce Cys-bimane, which was then acetylated by an N-acetyltransferase to generate N-acetyl-Cys-bimane, a mercapturic acid. An S. aureus mutant lacking BSH did not produce mercapturic acid when treated with monobromobimane and monochlorobimane, confirming the involvement of bacillithiol. Furthermore, treatment of S. aureus Newman with rifamycin, the parent compound of the first-line anti-tuberculosis drug, rifampicin, indicated that this thiol-reactive antibiotic is also detoxified in a BSH-dependent manner, since mercapturic acids of rifamycin were observed in the culture medium. These data indicate that toxins and thiol-reactive antibiotics are detoxified to less potent mercapturic acids in a BSH-dependent manner and then exported out of the cell in S. aureus. PMID:22262099

Characterization of a novel eukaryal nick-sealing RNA ligase from Naegleria gruberi

PubMed Central

Unciuleac, Mihaela-Carmen; Shuman, Stewart

2015-01-01

The proteome of the amoebo-flagellate protozoan Naegleria gruberi is rich in candidate RNA repair enzymes, including 15 putative RNA ligases, one of which, NgrRnl, is a eukaryal homolog of Deinococcus radiodurans RNA ligase, DraRnl. Here we report that purified recombinant NgrRnl seals nicked 3′-OH/5′-PO4 duplexes in which the 3′-OH strand is RNA. It does so via the “classic” ligase pathway, entailing reaction with ATP to form a covalent NgrRnl–AMP intermediate, transfer of AMP to the nick 5′-PO4, and attack of the RNA 3′-OH on the adenylylated nick to form a 3′–5′ phosphodiester. Unlike members of the four known families of ATP-dependent RNA ligases, NgrRnl lacks a carboxy-terminal appendage to its nucleotidyltransferase domain. Instead, it contains a defining amino-terminal domain that we show is important for 3′-OH/5′-PO4 nick-sealing and ligase adenylylation, but dispensable for phosphodiester synthesis at a preadenylylated nick. We propose that NgrRnl, DraRnl, and their homologs from diverse bacteria, viruses, and unicellular eukarya comprise a new “Rnl5 family” of nick-sealing ligases with a signature domain organization. PMID:25740837

Advanced Mass Spectrometric Methods for the Rapid and Quantitative Characterization of Proteomes

DOE PAGES

Smith, Richard D.

2002-01-01

Progress is reviewedmore » towards the development of a global strategy that aims to extend the sensitivity, dynamic range, comprehensiveness and throughput of proteomic measurements based upon the use of high performance separations and mass spectrometry. The approach uses high accuracy mass measurements from Fourier transform ion cyclotron resonance mass spectrometry (FTICR) to validate peptide ‘accurate mass tags’ (AMTs) produced by global protein enzymatic digestions for a specific organism, tissue or cell type from ‘potential mass tags’ tentatively identified using conventional tandem mass spectrometry (MS/MS). This provides the basis for subsequent measurements without the need for MS/ MS. High resolution capillary liquid chromatography separations combined with high sensitivity, and high resolution accurate FTICR measurements are shown to be capable of characterizing peptide mixtures of more than 10 5 components. The strategy has been initially demonstrated using the microorganisms Saccharomyces cerevisiae and Deinococcus radiodurans. Advantages of the approach include the high confidence of protein identification, its broad proteome coverage, high sensitivity, and the capability for stableisotope labeling methods for precise relative protein abundance measurements. Abbreviations : LC, liquid chromatography; FTICR, Fourier transform ion cyclotron resonance; AMT, accurate mass tag; PMT, potential mass tag; MMA, mass measurement accuracy; MS, mass spectrometry; MS/MS, tandem mass spectrometry; ppm, parts per million.« less

Enhancement of bioelectricity generation via heterologous expression of IrrE in Pseudomonas aeruginosa-inoculated MFCs.

PubMed

Luo, Jianmei; Wang, Tingting; Li, Xiao; Yang, Yanan; Zhou, Minghua; Li, Ming; Yan, Zhongli

2018-05-30

Low electricity power output (EPT) is still the main bottleneck limited the industrial application of microbial fuel cells (MFCs). Herein, EPT enhancement by introducing an exogenous global regulator IrrE derived from Deinococcus radiodurans into electrochemically active bacteria (EAB) was explored using Pseudomonas aeruginosa PAO1 as a model strain, achieving a power density 71% higher than that of the control strain. Moreover, IrrE-expressing strain exhibited a remarkable increase in the total amount of electron shuttles (majorly phenazines compounds) and a little decrease in internal resistance, which should underlie the enhancement in extracellular electron transfer (EET) efficiency and EPT. Strikingly, IrrE significantly affected substrate utilization profiling, improved cell growth characterization and cell tolerance to various stresses. Further quantitative RT-PCR analysis revealed that IrrE led to many differentially expressed genes, which were responsible for phenazines core biosynthesis, biofilm formation, QS systems, transcriptional regulation, glucose metabolism and general stress response. The results substantiated that targeting cellular regulatory network by the introduction of exogenous global regulators could be a facile and promising approach for the enhancement of bioelectricity generation and cell multiple phenotypes, and thus would be of great potential application in the practical MFCs. Copyright © 2018 Elsevier B.V. All rights reserved.

Survival of thermophilic and hyperthermophilic microorganisms after exposure to UV-C, ionizing radiation and desiccation.

PubMed

Beblo, Kristina; Douki, Thierry; Schmalz, Gottfried; Rachel, Reinhard; Wirth, Reinhard; Huber, Harald; Reitz, Günther; Rettberg, Petra

2011-11-01

In this study, we investigated the ability of several (hyper-) thermophilic Archaea and phylogenetically deep-branching thermophilic Bacteria to survive high fluences of monochromatic UV-C (254 nm) and high doses of ionizing radiation, respectively. Nine out of fourteen tested microorganisms showed a surprisingly high tolerance against ionizing radiation, and two species (Aquifex pyrophilus and Ignicoccus hospitalis) were even able to survive 20 kGy. Therefore, these species had a comparable survivability after exposure to ionizing radiation such as Deinococcus radiodurans. In contrast, there was nearly no difference in survival of the tested strains after exposure to UV-C under anoxic conditions. If the cells had been dried in advance of UV-C irradiation, they were more sensitive to UV-C radiation compared with cells irradiated in liquid suspension; this effect could be reversed by the addition of protective material like sulfidic ores before irradiation. By exposure to UV-C, photoproducts were formed in the DNA of irradiated Archaea and Bacteria. The distribution of the main photoproducts was species specific, but the amount of the photoproducts was only partly dependent on the applied fluence. Overall, our results show that tolerance to radiation seems to be a common phenomenon among thermophilic and hyperthermophilic microorganisms.

Exploration of Deinococcus-Thermus molecular diversity by novel group-specific PCR primers

PubMed Central

Theodorakopoulos, Nicolas; Bachar, Dipankar; Christen, Richard; Alain, Karine; Chapon, Virginie

2013-01-01

The deeply branching Deinococcus-Thermus lineage is recognized as one of the most extremophilic phylum of bacteria. In previous studies, the presence of Deinococcus-related bacteria in the hot arid Tunisian desert of Tataouine was demonstrated through combined molecular and culture-based approaches. Similarly, Thermus-related bacteria have been detected in Tunisian geothermal springs. The present work was conducted to explore the molecular diversity within the Deinococcus-Thermus phylum in these extreme environments. A set of specific primers was designed in silico on the basis of 16S rRNA gene sequences, validated for the specific detection of reference strains, and used for the polymerase chain reaction (PCR) amplification of metagenomic DNA retrieved from the Tataouine desert sand and Tunisian hot spring water samples. These analyses have revealed the presence of previously undescribed Deinococcus-Thermus bacterial sequences within these extreme environments. The primers designed in this study thus represent a powerful tool for the rapid detection of Deinococcus-Thermus in environmental samples and could also be applicable to clarify the biogeography of the Deinococcus-Thermus phylum. PMID:23996915

Urate is a ligand for the transcriptional regulator PecS.

PubMed

Perera, Inoka C; Grove, Anne

2010-09-24

PecS is a member of the MarR (multiple antibiotic resistance regulator) family, which has been shown in Erwinia to regulate the expression of virulence genes. MarR homologs typically bind a small molecule ligand, resulting in attenuated DNA binding. For PecS, the natural ligand has not been identified. We have previously shown that urate is a ligand for the Deinococcus radiodurans-encoded MarR homolog HucR (hypothetical uricase regulator) and identified residues responsible for ligand binding. We show here that all four residues involved in urate binding and propagation of conformational changes to DNA recognition helices are conserved in PecS homologs, suggesting that urate is the ligand for PecS. Consistent with this prediction, Agrobacterium tumefaciens PecS specifically binds urate, and urate attenuates DNA binding in vitro. PecS binds two operator sites in the intergenic region between the divergent pecS gene and pecM genes, one of which features two partially overlapping repeats to which PecS binds as a dimer on opposite faces of the duplex. Notably, urate dissociates PecS from cognate DNA, allowing transcription of both genes in vivo. Taken together, our data show that urate is a ligand for PecS and suggest that urate serves a novel function in signaling the colonization of a host plant. Copyright © 2010 Elsevier Ltd. All rights reserved.

Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes

PubMed Central

Vicedo, Esmeralda; Schlessinger, Avner; Rost, Burkhard

2015-01-01

Many prokaryotic organisms have adapted to incredibly extreme habitats. The genomes of such extremophiles differ from their non-extremophile relatives. For example, some proteins in thermophiles sustain high temperatures by being more compact than homologs in non-extremophiles. Conversely, some proteins have increased volumes to compensate for freezing effects in psychrophiles that survive in the cold. Here, we revealed that some differences in organisms surviving in extreme habitats correlate with a simple single feature, namely the fraction of proteins predicted to have long disordered regions. We predicted disorder with different methods for 46 completely sequenced organisms from diverse habitats and found a correlation between protein disorder and the extremity of the environment. More specifically, the overall percentage of proteins with long disordered regions tended to be more similar between organisms of similar habitats than between organisms of similar taxonomy. For example, predictions tended to detect substantially more proteins with long disordered regions in prokaryotic halophiles (survive high salt) than in their taxonomic neighbors. Another peculiar environment is that of high radiation survived, e.g. by Deinococcus radiodurans. The relatively high fraction of disorder predicted in this extremophile might provide a shield against mutations. Although our analysis fails to establish causation, the observed correlation between such a simplistic, coarse-grained, microscopic molecular feature (disorder content) and a macroscopic variable (habitat) remains stunning. PMID:26252577

Bacillithiol, a New Player in Bacterial Redox Homeostasis

PubMed Central

2011-01-01

Abstract Bacillithiol (BSH), the α-anomeric glycoside of l-cysteinyl-d-glucosamine with l-malic acid, plays a dominant role in the cytosolic thiol redox chemistry of the low guanine and cytosine (GC) Gram-positive bacteria (phylum Firmicutes). BSH is functionally analogous to glutathione (GSH) but differs sufficiently in chemical structure that cells have evolved a distinct set of enzymes that use BSH as cofactor. BSH was discovered in Bacillus subtilis as a mixed disulfide with the redox-sensing repressor OhrR and in B. anthracis by biochemical analysis of pools of labeled thiols. The structure of BSH was determined after purification from Deinococcus radiodurans. Similarities in structure between BSH and mycothiol (MSH) facilitated the identification of biosynthetic genes for BSH in the model organism B. subtilis. Phylogenomic analyses have identified several candidate BSH-using or associated proteins, including a BSH reductase, glutaredoxin-like thiol-dependent oxidoreductases (bacilliredoxins), and a BSH-S-transferase (FosB) involved in resistance to the epoxide antibiotic fosfomycin. Preliminary results implicate BSH in cellular processes to maintain cytosolic redox balance and for adaptation to reactive oxygen, nitrogen, and electrophilic species. BSH also is predicted to chelate metals avidly, in part due to the appended malate moiety, although the implications of BSH for metal ion homeostasis have yet to be explored in detail. Antioxid. Redox Signal. 15, 123–133. PMID:20712413

Deinococcus daejeonensis sp. nov., isolated from sludge in a sewage disposal plant.

PubMed

Srinivasan, Sathiyaraj; Kim, Myung Kyum; Lim, Sangyong; Joe, Minho; Lee, Myungjin

2012-06-01

A Gram-stain-positive, strictly aerobic, spherical, non-motile red-pigmented bacterial strain, designated MJ27(T), was isolated from a sludge sample of the Daejeon sewage disposal plant in South Korea. A polyphasic approach was used to study the taxonomic position of strain MJ27(T). Strain MJ27(T) shared highest 16S rRNA gene sequence similarity with Deinococcus grandis DSM 3963(T) (98.8 %), Deinococcus caeni Ho-08(T) (97.5 %) and Deinococcus aquaticus PB314(T) (96.6 %.); levels of sequence similarity with the type strains of other Deinococcus species were less than 96.0 %. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain MJ27(T) belonged to the clade formed by members of the genus Deinococcus in the family Deinococcaceae. The G+C content of the genomic DNA of strain MJ27(T) was 67.6 mol%. The chemotaxonomic characteristics of strain MJ27(T) were typical of members of the genus Deinococcus, with MK-8 as the predominant respiratory quinone, C(16:1)ω7c, C(15:1)ω6c, C(16:0) and C(15:0) as major fatty acids (>12 %), ornithine as the diamino acid in the cell-wall peptidoglycan and resistance to gamma radiation [D(10) (dose required to reduce the bacterial population by tenfold) >9 kGy]. The low levels of DNA-DNA relatedness reported here (5.3±1.5-29.2±2.3 %) indicate that strain MJ27(T) represents a species that is separate from its closest relatives in the genus Deinococcus. On the basis of phylogenetic inference, fatty acid profile and other phenotypic properties, strain MJ27(T) is considered to represent a novel species of the genus Deinococcus, for which the name Deinococcus daejeonensis sp. nov. is proposed. The type strain is MJ27(T) ( = KCTC 13751(T) = JCM 16918(T)).

Deinococcus multiflagellatus sp. nov., isolated from a car air-conditioning system.

PubMed

Kim, Dong-Uk; Lee, Hyosun; Lee, Suyeon; Park, Sooyeon; Yoon, Jung-Hoon; Zhao, Lei; Kim, Min-Kyu; Ahn, Jae-Hyung; Ka, Jong-Ok

2018-04-01

A gamma radiation-resistant and pink-to-red pigmented bacterial strain, designated ID1504 T , was isolated from a car air-conditioning system sampled in Korea. The cells were observed to be Gram-stain negative, aerobic, motile with peritrichous flagella and short rod-shaped. Phylogenetically, the strain groups with the members of the genus Deinococcus and exhibits high 16S rRNA gene sequence similarities with Deinococcus arenae SA1 T (94.0%), Deinococcus actinosclerus BM2 T (93.9%) and Deinococcus soli N5 T (93.5%). The predominant fatty acids were identified as C 17:0 , C 16:0 , summed feature 3 (C 16:1 ω7c and/or C 16:1 ω6c) and iso-C 17:0 . The major respiratory quinone was identified as MK-8. The polar lipids were found to be comprised of unidentified phospholipids, unidentified glycolipids, an unidentified aminophospholipid and an unidentified lipid. The DNA G+C content of the strain was determined to be 68.3 mol%. On the basis of the phenotypic, genotypic and chemotaxonomic characteristics, strain ID1504 T should be classified in a novel species in the genus Deinococcus, for which the name Deinococcus multiflagellatus sp. nov. (= KACC 19287 T  = NBRC 112888 T ) is proposed.

NMR structure and Mg2+ binding of an RNA segment that underlies the L7/L12 stalk in the E.coli 50S ribosomal subunit

PubMed Central

Zhao, Qin; Nagaswamy, Uma; Lee, Hunjoong; Xia, Youlin; Huang, Hung-Chung; Gao, Xiaolian; Fox, George E.

2005-01-01

Helix 42 of Domain II of Escherichia coli 23S ribosomal RNA underlies the L7/L12 stalk in the ribosome and may be significant in positioning this feature relative to the rest of the 50S ribosomal subunit. Unlike the Haloarcula marismortui and Deinococcus radiodurans examples, the lower portion of helix 42 in E.coli contains two consecutive G•A oppositions with both adenines on the same side of the stem. Herein, the structure of an analog of positions 1037–1043 and 1112–1118 in the helix 42 region is reported. NMR spectra and structure calculations support a cis Watson–Crick/Watson–Crick (cis W.C.) G•A conformation for the tandem (G•A)2 in the analog and a minimally perturbed helical duplex stem. Mg2+ titration studies imply that the cis W.C. geometry of the tandem (G•A)2 probably allows O6 of G20 and N1 of A4 to coordinate with a Mg2+ ion as indicated by the largest chemical shift changes associated with the imino group of G20 and the H8 of G20 and A4. A cross-strand bridging Mg2+ coordination has also been found in a different sequence context in the crystal structure of H.marismortui 23S rRNA, and therefore it may be a rare but general motif in Mg2+ coordination. PMID:15939932

Fluorescence imaging of microbe-containing particles shot from a two-stage Light-gas gun into an aerogel.

PubMed

Kawaguchi, Yuko; Sugino, Tomohiro; Tabata, Makoto; Okudaira, Kyoko; Imai, Eichi; Yano, Hajime; Hasegawa, Sunao; Hashimoto, Hirofumi; Yabuta, Hikaru; Kobayashi, Kensei; Kawai, Hideyuki; Mita, Hajime; Yokobori, Shin-ichi; Yamagishi, Akihiko

2014-02-01

We have proposed an experiment (the Tanpopo mission) to capture microbes on the Japan Experimental Module of the International Space Station. An ultra low-density silica aerogel will be exposed to space for more than 1 year. After retrieving the aerogel, particle tracks and particles found in it will be visualized by fluorescence microscopy after staining it with a DNA-specific fluorescence dye. In preparation for this study, we simulated particle trapping in an aerogel so that methods could be developed to visualize the particles and their tracks. During the Tanpopo mission, particles that have an orbital velocity of ~8 km/s are expected to collide with the aerogel. To simulate these collisions, we shot Deinococcus radiodurans-containing Lucentite particles into the aerogel from a two-stage light-gas gun (acceleration 4.2 km/s). The shapes of the captured particles, and their tracks and entrance holes were recorded with a microscope/camera system for further analysis. The size distribution of the captured particles was smaller than the original distribution, suggesting that the particles had fragmented. We were able to distinguish between microbial DNA and inorganic compounds after staining the aerogel with the DNA-specific fluorescence dye SYBR green I as the fluorescence of the stained DNA and the autofluorescence of the inorganic particles decay at different rates. The developed methods are suitable to determine if microbes exist at the International Space Station altitude.

Enhanced Radiation Resistance of Methanosarcina soligelidi SMA-21, a New Methanogenic Archaeon Isolated from a Siberian Permafrost-Affected Soil in Direct Comparison to Methanosarcina barkeri.

PubMed

Morozova, Daria; Moeller, Ralf; Rettberg, Petra; Wagner, Dirk

2015-11-01

Permafrost-affected soils are characterized by a high abundance and diversity of methanogenic communities, which are considered suitable model organisms for potential life on Mars. Methanogens from Siberian permafrost have been proven to be highly resistant against divers stress conditions such as subzero temperatures, desiccation, and simulated thermophysical martian conditions. Here, we studied the radiation resistance of the currently described new species Methanosarcina soligelidi SMA-21, which was isolated from a Siberian permafrost-affected soil, in comparison to Methanosarcina barkeri, which is used as a reference organism from a nonpermafrost soil environment. Both strains were exposed to solar UV and ionizing radiation to assess their limits of survival. Methanosarcina soligelidi exhibit an increase in radiation resistance to UV (2.5- to 13.8-fold) and ionizing radiation (46.6-fold) compared to M. barkeri. The F10 (UVC) and D10 (X-rays) values of M. soligelidi are comparable to values for the well-known, highly radioresistant species Deinococcus radiodurans. In contrast, the radiation response of M. barkeri was highly sensitive to UV and ionizing radiation comparably to Escherichia coli and other radiosensitive microorganisms. This study showed that species of the same genus respond differently to UV and ionizing radiation, which might reflect the adaptation of Methanosarcina soligelidi SMA-21 to the harsh environmental conditions of the permafrost habitat. Methanogenic archaea-Environmental UV-Ionizing radiation-Permafrost-Radiation resistance-Mars.

Antibiotic Sensitivity of Micrococcus radiodurans

PubMed Central

Hawiger, J.; Jeljaszewicz, J.

1967-01-01

A wild-type strain of Micrococcus radiodurans and its nonpigmented mutant W1 were tested for sensitivity to 10 antibiotics selected from the standpoint of their mechanism of action. Representatives of groups of antibiotics inhibiting deoxyribonucleic acid (DNA) synthesis, DNA-dependent ribonucleic acid synthesis, protein synthesis, and cell wall synthesis were selected. M. radiodurans and its mutant exhibited full susceptibility to all antibiotics tested (mitomycin C, actinomycin D, chloramphenicol, dihydrostreptomycin, erythromycin, neomycin, kanamycin, benzylpenicillin, bacitracin, and vancomycin), the degree of susceptibility being of the same order as that of a standard strain of Staphylococcus aureus 209 P, with the exception of dihydrostreptomycin. PMID:4166078

Structure-guided design and functional characterization of an artificial red light-regulated guanylate/adenylate cyclase for optogenetic applications.

PubMed

Etzl, Stefan; Lindner, Robert; Nelson, Matthew D; Winkler, Andreas

2018-06-08

Genetically targeting biological systems to control cellular processes with light is the concept of optogenetics. Despite impressive developments in this field, underlying molecular mechanisms of signal transduction of the employed photoreceptor modules are frequently not sufficiently understood to rationally design new optogenetic tools. Here, we investigate the requirements for functional coupling of red light-sensing phytochromes with non-natural enzymatic effectors by creating a series of constructs featuring the Deinococcus radiodurans bacteriophytochrome linked to a Synechocystis guanylate/adenylate cyclase. Incorporating characteristic structural elements important for cyclase regulation in our designs, we identified several red light-regulated fusions with promising properties. We provide details of one light-activated construct with low dark-state activity and high dynamic range that outperforms previous optogenetic tools in vitro and expands our in vivo toolkit, as demonstrated by manipulation of Caenorhabditis elegans locomotor activity. The full-length crystal structure of this phytochrome-linked cyclase revealed molecular details of photoreceptor-effector coupling, highlighting the importance of the regulatory cyclase element. Analysis of conformational dynamics by hydrogen-deuterium exchange in different functional states enriched our understanding of phytochrome signaling and signal integration by effectors. We found that light-induced conformational changes in the phytochrome destabilize the coiled-coil sensor-effector linker, which releases the cyclase regulatory element from an inhibited conformation, increasing cyclase activity of this artificial system. Future designs of optogenetic functionalities may benefit from our work, indicating that rational considerations for the effector improve the rate of success of initial designs to obtain optogenetic tools with superior properties. © 2018 Etzl et al.

Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria.

PubMed

Ilag, Leopold L; Videler, Hortense; McKay, Adam R; Sobott, Frank; Fucini, Paola; Nierhaus, Knud H; Robinson, Carol V

2005-06-07

Ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. These properties pose considerable challenges for modern-day structural biology. Despite these obstacles, high-resolution x-ray structures of the 30S and 50S subunits have revealed the RNA architecture and its interactions with proteins for ribosomes from Thermus thermophilus, Deinococcus radiodurans, and Haloarcula marismortui. Some regions, however, remain inaccessible to these high-resolution approaches because of their high conformational dynamics and potential heterogeneity, specifically the so-called L7/L12 stalk complex. This region plays a vital role in protein synthesis by interacting with GTPase factors in translation. Here, we apply tandem MS, an approach widely applied to peptide sequencing for proteomic applications but not previously applied to MDa complexes. Isolation and activation of ions assigned to intact 30S and 50S subunits releases proteins S6 and L12, respectively. Importantly, this process reveals, exclusively while attached to ribosomes, a phosphorylation of L12, the protein located in multiple copies at the tip of the stalk complex. Moreover, through tandem MS we discovered a stoichiometry for the stalk protuberance on Thermus thermophilus and other thermophiles and contrast this assembly with the analogous one on ribosomes from mesophiles. Together with evidence for a potential interaction with the degradosome, these results show that important findings on ribosome structure, interactions, and modifications can be discovered by tandem MS, even on well studied ribosomes from Thermus thermophilus.

Heptameric (L12)6/L10 rather than canonical pentameric complexes are found by tandem MS of intact ribosomes from thermophilic bacteria

PubMed Central

Ilag, Leopold L.; Videler, Hortense; McKay, Adam R.; Sobott, Frank; Fucini, Paola; Nierhaus, Knud H.; Robinson, Carol V.

2005-01-01

Ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. These properties pose considerable challenges for modern-day structural biology. Despite these obstacles, high-resolution x-ray structures of the 30S and 50S subunits have revealed the RNA architecture and its interactions with proteins for ribosomes from Thermus thermophilus, Deinococcus radiodurans, and Haloarcula marismortui. Some regions, however, remain inaccessible to these high-resolution approaches because of their high conformational dynamics and potential heterogeneity, specifically the so-called L7/L12 stalk complex. This region plays a vital role in protein synthesis by interacting with GTPase factors in translation. Here, we apply tandem MS, an approach widely applied to peptide sequencing for proteomic applications but not previously applied to MDa complexes. Isolation and activation of ions assigned to intact 30S and 50S subunits releases proteins S6 and L12, respectively. Importantly, this process reveals, exclusively while attached to ribosomes, a phosphorylation of L12, the protein located in multiple copies at the tip of the stalk complex. Moreover, through tandem MS we discovered a stoichiometry for the stalk protuberance on Thermus thermophilus and other thermophiles and contrast this assembly with the analogous one on ribosomes from mesophiles. Together with evidence for a potential interaction with the degradosome, these results show that important findings on ribosome structure, interactions, and modifications can be discovered by tandem MS, even on well studied ribosomes from Thermus thermophilus. PMID:15923259

Natural transfer of viable microbes in space

NASA Technical Reports Server (NTRS)

Mileikowsky, C.; Cucinotta, F. A.; Wilson, J. W.; Gladman, B.; Horneck, G.; Lindegren, L.; Melosh, J.; Rickman, H.; Valtonen, M.; Zheng, J. Q.

2000-01-01

The possibility and probability of natural transfer of viable microbes from Mars to Earth and Earth to Mars traveling in meteoroids during the first 0.5 Ga and the following 4 Ga are investigated, including: --radiation protection against the galactic cosmic ray nuclei and the solar rays, dose rates as a function of the meteorite's radial column mass (radius x density), combined with dose rates generated by natural radioactivity within the meteorite; and survival curves for some bacterial species using NASA's HZETRN transport code --other factors affecting microbe survival: vacuum; central meteorite temperatures at launch, orbiting, and arrival; pressure and acceleration at launch; spontaneous DNA decay; metal ion migration --mean sizes and numbers of unshocked meteorites ejected and percentage falling on Earth, using current semiempirical results --viable flight times for the microbe species Bacillus subtilis and Deinococcus radiodurans R1 --the approximate fraction of microbes (with properties like the two species studied) viably arriving on Earth out of those ejected from Mars during the period 4 Ga BP to the present time, and during the 700 Ma from 4.5 to 3.8 Ga. Similarly, from Earth to Mars. The conclusion is that if microbes existed or exist on Mars, viable transfer to Earth is not only possible but also highly probable, due to microbes' impressive resistance to the dangers of space transfer and to the dense traffic of billions of martian meteorites which have fallen on Earth since the dawn of our planetary system. Earth-to-Mars transfer is also possible but at a much lower frequency.

Natural transfer of viable microbes in space.

PubMed

Mileikowsky, C; Cucinotta, F A; Wilson, J W; Gladman, B; Horneck, G; Lindegren, L; Melosh, J; Rickman, H; Valtonen, M; Zheng, J Q

2000-06-01

The possibility and probability of natural transfer of viable microbes from Mars to Earth and Earth to Mars traveling in meteoroids during the first 0.5 Ga and the following 4 Ga are investigated, including: --radiation protection against the galactic cosmic ray nuclei and the solar rays, dose rates as a function of the meteorite's radial column mass (radius x density), combined with dose rates generated by natural radioactivity within the meteorite; and survival curves for some bacterial species using NASA's HZETRN transport code --other factors affecting microbe survival: vacuum; central meteorite temperatures at launch, orbiting, and arrival; pressure and acceleration at launch; spontaneous DNA decay; metal ion migration --mean sizes and numbers of unshocked meteorites ejected and percentage falling on Earth, using current semiempirical results --viable flight times for the microbe species Bacillus subtilis and Deinococcus radiodurans R1 --the approximate fraction of microbes (with properties like the two species studied) viably arriving on Earth out of those ejected from Mars during the period 4 Ga BP to the present time, and during the 700 Ma from 4.5 to 3.8 Ga. Similarly, from Earth to Mars. The conclusion is that if microbes existed or exist on Mars, viable transfer to Earth is not only possible but also highly probable, due to microbes' impressive resistance to the dangers of space transfer and to the dense traffic of billions of martian meteorites which have fallen on Earth since the dawn of our planetary system. Earth-to-Mars transfer is also possible but at a much lower frequency.

Complete fluorescent fingerprints of extremophilic and photosynthetic microbes

NASA Astrophysics Data System (ADS)

Dartnell, Lewis R.; Storrie-Lombardi, Michael C.; Ward, John M.

2010-10-01

The work reported here represents a study into the total fluorescence exhibited by a broad selection of model, extremophilic and photosynthetic bacterial strains, over a great range of excitation and emission wavelengths from ultraviolet (UV) through visible to near infrared. The aim is to identify distinctive fluorescent features that may serve as detectable biosignatures of remnant microbial life on the Martian surface. A lab-bench fluorescence spectrometer was used to generate an excitation-emission matrix (EEM) for the unpigmented Escherichia coli, radiation-resistant Deinococcus radiodurans, Antarctic Dry Valley isolates Brevundimonas sp. MV.7 and Rhodococcus sp. MV.10, and the cyanobacterium Synechocystis sp. PCC 6803. Detailed EEMs, representing the fluorescence signature of each organism, are presented, and the most significant features suitable for biosignature surveys are identified, including small-molecule cellular metabolites, light-harvesting photosynthetic pigments and extracellular UV-screening compounds. E. coli exhibits the most intense emission from tryptophan, presumably due to the absence of UV-screening pigments that would shield the organism from short-wavelength light-exciting intracellular fluorescence. The efficacy of commonly available laser diodes for exciting cellular fluorescence is treated, along with the most appropriate filter wavelengths for imaging systems. The best combination of available laser diodes and PanCam filters aboard the ExoMars probe is proposed. The possibility of detecting fluorescence excited by solar UV radiation in freshly exposed surface samples by imaging when both sunlit and shadowed, perhaps by the body of the rover itself, is discussed. We also study how these biological fluorophore molecules may be degraded, and thus the potential biosignatures erased, by the high flux of far-ultraviolet light on Mars.

Binding modes of phosphotriesterase-like lactonase complexed with δ-nonanoic lactone and paraoxon using molecular dynamics simulations.

PubMed

Guan, Shanshan; Zhao, Li; Jin, Hanyong; Shan, Ning; Han, Weiwei; Wang, Song; Shan, Yaming

2017-02-01

Phosphotriesterase-like lactonases (PLLs) have received much attention because of their physical and chemical properties. They may have widespread applications in various fields. For example, they show potential for quorum-sensing signaling pathways and organophosphorus (OP) detoxification in agricultural science. However, the mechanism by which PLLs hydrolyze, which involves OP compounds and lactones and a variety of distinct catalytic efficiencies, has only rarely been explored. In the present study, molecular dynamics (MD) simulations were performed to characterize and contrast the structural dynamics of DrPLL, a member of the PLL superfamily in Deinococcus radiodurans, bound to two substrates, δ-nonanoic lactone and paraoxon. It has been observed that there is a 16-fold increase in the catalytic efficiency of the two mutant strains of DrPLL (F26G/C72I) vs. the wild-type enzyme toward the hydrolysis of paraoxon, but an explanation for this behavior is currently lacking. The analysis of the molecular trajectories of DrPLL bound to δ-nonanoic lactone indicated that lactone-induced conformational changes take place in loop 8, which is near the active site. Binding to paraoxon may lead to conformational displacement of loop 1 residues, which could lead to the deformation of the active site and so trigger the entry of the paraoxon into the active site. The efficiency of the F26G/C72I mutant was increased by decreasing the displacement of loop 1 residues and increasing the flexibility of loop 8 residues. These results provide a molecular-level explanation for the experimental behavior.

Dose modification in e.coli by a constitutive radioprotective agent isolated from m. radiodurans

DOE Office of Scientific and Technical Information (OSTI.GOV)

Goldstein, Lawrence S.

1972-01-01

A constitutive low molecular weight radioprotective agent has been isolated from a colorless mutant of Micrococcus radiodurans. The effect of radioprotective extract was also investigated in three mutant strains of E.coli B/r differing from one another at a given locus concerned with the repair of radiation induced damage/

Deinococcus metallilatus sp. nov. and Deinococcus carri sp. nov., isolated from a car air-conditioning system.

PubMed

Kim, Dong-Uk; Lee, Hyosun; Lee, Ji-Hyeong; Ahn, Jae-Hyung; Lim, Sangyong; Jeong, Sunwook; Park, So Yoon; Seong, Chi Nam; Ka, Jong-Ok

2015-09-01

Two bacterial strains, designated MA1002(T) and MA1003(T), were isolated from the air-conditioning system of a car. Cells of both strains were Gram-reaction-positive, non-motile, non-spore-forming coccoids, catalase- and oxidase-positive and UV-radiation resistant. The major fatty acids of strain MA1002(T) were iso-C17 : 0 and iso-C15 : 0 and those of strain MA1003(T) were iso-C16 : 0 and iso-C16 : 1 H. The polar lipid profile of MA1002(T) contained phosphatidylethanolamine, two unidentified phosphoglycolipids, an unidentified phospholipid, an unidentified aminophospholipid, an unidentified aminolipid and an unidentified lipid. MA1003(T) had three unidentified phosphoglycolipids, six unidentified phospholipids, two unidentified glycolipids and two unidentified polar lipids as the polar lipids. The G+C contents of the genomic DNA of MA1002(T) and MA1003(T) were 70.5 and 76.0 mol%, respectively. MK-8 was the predominant respiratory quinone for both strains. 16S rRNA gene sequence analysis showed that strain MA1002(T) was phylogenetically related to Deinococcus apachensis DSM 19763(T), D. geothermalis DSM 11300(T), D. aerius TR0125(T) and D. aetherius ST0316(T) (92.9, 92.6, 92.0 and 91.9% sequence similarity, respectively), and MA1003(T) showed the highest sequence similarity to Deinococcus hopiensis KR-140(T) (92.9%) and D. xinjiangensis X-82(T) (91.4%). The results of genotypic and phenotypic characterizations showed that both strains could be distinguished from phylogenetically related species, and that the strains represented novel species within the genus Deinococcus, for which we propose the names Deinococcus metallilatus sp. nov. (type strain MA1002(T) = KACC 17964(T) = NBRC 110141(T)) and Deinococcus carri sp. nov. (type strain is MA1003(T) = KACC 17965(T) = NBRC 110142(T)).

Deinococcus mumbaiensis sp. nov., a radiation-resistant pleomorphic bacterium isolated from Mumbai, India.

PubMed

Shashidhar, Ravindranath; Bandekar, Jayant R

2006-01-01

A radiation-resistant, Gram-negative and pleomorphic bacterium (CON-1) was isolated from a contaminated tryptone glucose yeast extract agar plate in the laboratory. It was red pigmented, nonmotile, nonsporulating, and aerobic, and contained MK-8 as respiratory quinone. The cell wall of this bacterium contained ornithine. The major fatty acids were C16:0, C16:1, C17:0, C18:1 and iso C18:0. The DNA of CON-1 had a G+C content of 70 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that CON-1 exhibited a maximum similarity (94.72%) with Deinococcus grandis. Based on the genotypic, phenotypic and chemotaxonomic characteristics, the bacterium CON-1 was identified as a new species of the genus Deinococcus, for which the name Deinococcus mumbaiensis sp. nov. is proposed. The type strain of D. mumbaiensis is CON-1 (MTCC 7297(T)=DSM 17424(T)).

Distinctive Protein Signatures Provide Molecular Markers and Evidence for the Monophyletic Nature of the Deinococcus-Thermus Phylum

PubMed Central

Griffiths, Emma; Gupta, Radhey S.

2004-01-01

The Deinococcus-Thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16S rRNA trees. No unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. In this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the Deinococcus-Thermus phylum but are not found in any other group of bacteria. The identified signatures include a 7-amino-acid (aa) insert in threonyl-tRNA synthetase, 1- and 3-aa inserts in the RNA polymerase β′ subunit, a 5-aa deletion in signal recognition particle (Ffh/SR54), a 2-aa insert in major sigma factor 70 (σ70), a 2-aa insert in seryl-tRNA synthetase (SerRS), a 1-aa insert in ribosomal protein L1, and a 2-aa insert in UvrA homologs. By using PCR primers for conserved regions, fragments of these genes were amplified from a number of Deinococcus-Thermus species, and all such fragments (except SerRS in Deinococcus proteolyticus) were found to contain the indicated signatures. The presence of these signatures in various species from all three known genera within this phylum, viz., Deinococcus, Thermus, and Meiothermus, provide evidence that they are likely distinctive characteristics of the entire phylum which were introduced in a common ancestor of this group. The signature in SerRS, which is absent in D. proteolyticus, was likely introduced after the branching of this species. Phylogenetic studies as well as the nature of the inserts in some of these proteins (viz., σ70 and SerRS) also support a sister group relationship between the Thermus and the Meiothermus genera. The identified signatures provide strong evidence for the monophyletic nature of the Deinococcus-Thermus phylum. These molecular markers should prove very useful in the identification of new species related to this group. PMID:15126471

Manganese Complexes: Diverse Metabolic Routes to Oxidative Stress Resistance in Prokaryotes and Yeast

PubMed Central

2013-01-01

Abstract Significance: Antioxidant enzymes are thought to provide critical protection to cells against reactive oxygen species (ROS). However, many organisms can fully compensate for the loss of such enzymatic defenses by accumulating metabolites and Mn2+, which can form catalytic Mn-antioxidants. Accumulated metabolites can direct reactivity of Mn2+ with superoxide and specifically shield proteins from oxidative damage. Recent Advances: There is mounting evidence that Mn-Pi (orthophosphate) complexes act as potent scavengers of superoxide in all three branches of life. Moreover, it is evident that Mn2+ in complexes with carbonates, peptides, nucleosides, and organic acids can also form catalytic Mn-antioxidants, pointing to diverse metabolic routes to oxidative stress resistance. Critical Issues: What conditions favor utility of Mn-metabolites versus enzymatic means for removing ROS? Mn2+-metabolite defenses are critical for preserving the activity of repair enzymes in Deinococcus radiodurans exposed to intense radiation stress, and in Lactobacillus plantarum, which lacks antioxidant enzymes. In other microorganisms, Mn-antioxidants can serve as an auxiliary protection when enzymatic antioxidants are insufficient or fail. These findings of a critical role of Mn-antioxidants in the survival of prokaryotes under oxidative stress parallel the trends developing for the simple eukaryote Saccharomyces cerevisiae. Future Directions: Phosphates, peptides and organic acids are just a snapshot of the types of anionic metabolites that promote such reactivity of Mn2+. Their probable roles in pathogen defense against the host immune response and in ROS-mediated signaling pathways are also areas that are worthy of serious investigation. Moreover, it is clear that these protective chemical processes can be harnessed for practical purposes. Antioxid. Redox Signal. 19, 933–944. PMID:23249283

Geomicrobiology of High-Level Nuclear Waste-Contaminated Vadose Sediments at the Hanford Site, Washington State

PubMed Central

Fredrickson, James K.; Zachara, John M.; Balkwill, David L.; Kennedy, David; Li, Shu-mei W.; Kostandarithes, Heather M.; Daly, Michael J.; Romine, Margaret F.; Brockman, Fred J.

2004-01-01

Sediments from a high-level nuclear waste plume were collected as part of investigations to evaluate the potential fate and migration of contaminants in the subsurface. The plume originated from a leak that occurred in 1962 from a waste tank consisting of high concentrations of alkali, nitrate, aluminate, Cr(VI), 137Cs, and 99Tc. Investigations were initiated to determine the distribution of viable microorganisms in the vadose sediment samples, probe the phylogeny of cultivated and uncultivated members, and evaluate the ability of the cultivated organisms to survive acute doses of ionizing radiation. The populations of viable aerobic heterotrophic bacteria were generally low, from below detection to ∼104 CFU g−1, but viable microorganisms were recovered from 11 of 16 samples, including several of the most radioactive ones (e.g., >10 μCi of 137Cs/g). The isolates from the contaminated sediments and clone libraries from sediment DNA extracts were dominated by members related to known gram-positive bacteria. Gram-positive bacteria most closely related to Arthrobacter species were the most common isolates among all samples, but other phyla high in G+C content were also represented, including Rhodococcus and Nocardia. Two isolates from the second-most radioactive sample (>20 μCi of 137Cs g−1) were closely related to Deinococcus radiodurans and were able to survive acute doses of ionizing radiation approaching 20 kGy. Many of the gram-positive isolates were resistant to lower levels of gamma radiation. These results demonstrate that gram-positive bacteria, predominantly from phyla high in G+C content, are indigenous to Hanford vadose sediments and that some are effective at surviving the extreme physical and chemical stress associated with radioactive waste. PMID:15240306

Growth of Serratia liquefaciens under 7 mbar, 0°C, and CO2-Enriched Anoxic Atmospheres

PubMed Central

Ulrich, Richard; Berry, Bonnie J.; Nicholson, Wayne L.

2013-01-01

Abstract Twenty-six strains of 22 bacterial species were tested for growth on trypticase soy agar (TSA) or sea-salt agar (SSA) under hypobaric, psychrophilic, and anoxic conditions applied singly or in combination. As each factor was added to multi-parameter assays, the interactive stresses decreased the numbers of strains capable of growth and, in general, reduced the vigor of the strains observed to grow. Only Serratia liquefaciens strain ATCC 27592 exhibited growth at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres. To discriminate between the effects of desiccation and hypobaria, vegetative cells of Bacillus subtilis strain 168 and Escherichia coli strain K12 were grown on TSA surfaces and simultaneously in liquid Luria-Bertani (LB) broth media. Inhibition of growth under hypobaria for 168 and K12 decreased in similar ways for both TSA and LB assays as pressures were reduced from 100 to 25 mbar. Results for 168 and K12 on TSA and LB are interpreted to indicate a direct low-pressure effect on microbial growth with both species and do not support the hypothesis that desiccation alone on TSA was the cause of reduced growth at low pressures. The growth of S. liquefaciens at 7 mbar, 0°C, and CO2-enriched anoxic atmospheres was surprising since S. liquefaciens is ecologically a generalist that occurs in terrestrial plant, fish, animal, and food niches. In contrast, two extremophiles tested in the assays, Deinococcus radiodurans strain R1 and Psychrobacter cryohalolentis strain K5, failed to grow under hypobaric (25 mbar; R1 only), psychrophilic (0°C; R1 only), or anoxic (<0.1% ppO2; both species) conditions. Key Words: Habitable zone—Hypobaria—Extremophiles—Special regions—Planetary protection. Astrobiology 13, 115–131. PMID:23289858

Bacterial and archaeal resistance to ionizing radiation

NASA Astrophysics Data System (ADS)

Confalonieri, F.; Sommer, S.

2011-01-01

Organisms living in extreme environments must cope with large fluctuations of temperature, high levels of radiation and/or desiccation, conditions that can induce DNA damage ranging from base modifications to DNA double-strand breaks. The bacterium Deinococcus radiodurans is known for its resistance to extremely high doses of ionizing radiation and for its ability to reconstruct a functional genome from hundreds of radiation-induced chromosomal fragments. Recently, extreme ionizing radiation resistance was also generated by directed evolution of an apparently radiation-sensitive bacterial species, Escherichia coli. Radioresistant organisms are not only found among the Eubacteria but also among the Archaea that represent the third kingdom of life. They present a set of particular features that differentiate them from the Eubacteria and eukaryotes. Moreover, Archaea are often isolated from extreme environments where they live under severe conditions of temperature, pressure, pH, salts or toxic compounds that are lethal for the large majority of living organisms. Thus, Archaea offer the opportunity to understand how cells are able to cope with such harsh conditions. Among them, the halophilic archaeon Halobacterium sp and several Pyrococcus or Thermococcus species, such as Thermococcus gammatolerans, were also shown to display high level of radiation resistance. The dispersion, in the phylogenetic tree, of radioresistant prokaryotes suggests that they have independently acquired radioresistance. Different strategies were selected during evolution including several mechanisms of radiation byproduct detoxification and subtle cellular metabolism modifications to help cells recover from radiation-induced injuries, protection of proteins against oxidation, an efficient DNA repair tool box, an original pathway of DNA double-strand break repair, a condensed nucleoid that may prevent the dispersion of the DNA fragments and specific radiation-induced proteins involved in radioresistance. Here, we compare mechanisms and discuss hypotheses suggested to contribute to radioresistance in several Archaea and Eubacteria.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Patel, Asmita; Shuman, Stewart; Mondragon, Alfonso

Type IB DNA topoisomerases are found in all eukarya, two families of eukaryotic viruses (poxviruses and mimivirus), and many genera of bacteria. They alter DNA topology by cleaving and resealing one strand of duplex DNA via a covalent DNA-(3-phosphotyrosyl)-enzyme intermediate. Bacterial type IB enzymes were discovered recently and are described as poxvirus-like with respect to their small size, primary structures, and bipartite domain organization. Here we report the 1.75-{angstrom} crystal structure of Deinococcus radiodurans topoisomerase IB (DraTopIB), a prototype of the bacterial clade. DraTopIB consists of an amino-terminal (N) {beta}-sheet domain (amino acids 1-90) and a predominantly {alpha}-helical carboxyl-terminal (C)more » domain (amino acids 91-346) that closely resemble the corresponding domains of vaccinia virus topoisomerase IB. The five amino acids of DraTopIB that comprise the catalytic pentad (Arg-137, Lys-174, Arg-239, Asn-280, and Tyr-289) are preassembled into the active site in the absence of DNA in a manner nearly identical to the pentad configuration in human topoisomerase I bound to DNA. This contrasts with the apoenzyme of vaccinia topoisomerase, in which three of the active site constituents are either displaced or disordered. The N and C domains of DraTopIB are splayed apart in an 'open' conformation, in which the surface of the catalytic domain containing the active site is exposed for DNA binding. A comparison with the human topoisomerase I-DNA cocrystal structure suggests how viral and bacterial topoisomerase IB enzymes might bind DNA circumferentially via movement of the N domain into the major groove and clamping of a disordered loop of the C domain around the helix.« less

Multiplicity of genome equivalents in the radiation-resistant bacterium Micrococcus radiodurans.

PubMed Central

Hansen, M T

1978-01-01

The complexity of the genome of Micrococcus radiodurans was determined to be (2.0 +/- 0.3) X 10(9) daltons by DNA renaturation kinetics. The number of genome equivalents of DNA per cell was calculated from the complexity and the content of DNA. A lower limit of four genome equivalents per cell was approached with decreasing growth rate. Thus, no haploid stage appeared to be realized in this organism. The replication time was estimated from the kinetics and amount of residual DNA synthesis after inhibiting initiation of new rounds of replication. From this, the redundancy of terminal genetic markers was calculated to vary with growth rate from four to approximately eight copies per cell. All genetic material, including the least abundant, is thus multiply represented in each cell. The potential significance of the maintenance in each cell of multiple gene copies is discussed in relation to the extreme radiation resistance of M. radiodurans. PMID:649572

Dormancy in Deinococcus sp. UDEC-P1 as a survival strategy to escape from deleterious effects of carbon starvation and temperature.

PubMed

Guerra, Matías; González, Karina; González, Carlos; Parra, Boris; Martínez, Miguel

2015-09-01

Dormancy is characterized by low metabolism and absence of protein synthesis and cellular division enabling bacterial cells to survive under stress. The aim was to determine if carbon starvation and low temperature are factors that modify the proportion of dormant/active cells in Deinococcus sp. UDEC-P1. By flow cytometry, RedoxSensor Green (RSG) was used to quantify metabolic activity and Propidium Iodide (PI) to evaluate membrane integrity in order to determine the percentage of dormant cells. Cell size and morphology were determined using scanning electronic microscopy. Under carbon starvation at 30°C, Deinococcus sp. UDEC-P1 increased its proportion of dormant cells from 0.1% to 20%, decreased the count of culturable cells and average cell volume decreased 7.1 times. At 4°C, however, the proportion of dormant cells increased only to 6%, without a change in the count of culturable cells and an average cellular volume decrease of 4.1 times and 3% of the dormant cells were able to be awakened. Results indicate a greater proportion of dormant Deinococcus sp. UDEC-P1 cells at 30ºC and it suggests that carbon starvation is more deleterious condition at 30ºC than 4ºC. For this reason Deinococcus sp. UDEC-P1 cells are more likely to enter into dormancy at higher temperature as a strategy to survive. Copyright© by the Spanish Society for Microbiology and Institute for Catalan Studies.

Protein Oxidation Implicated as the Primary Determinant of Bacterial Radioresistance

DTIC Science & Technology

2007-04-01

the facultative anaerobic, radio- resistant bacterium Lactobacillus plantarum [1,22] accumulates 20–25 mM Mn(II) [23]. For an irradiated cell...in dH2O at 0 8C and pre-conditioned to be anaerobic, H2O2 was released by D. radiodurans (;23 105 M) and L. plantarum (;6 3 105 M), in which the...non-irradiated D. radiodurans or L. plantarum control samples, nor by irradiated S. oneidensis (Figure 5A), which accumulates substantially more Fe

Deinococcus petrolearius sp. nov. isolated from crude oil recovery water in China.

PubMed

Xi, Lijun; Qiao, Nenghu; Zhang, Jingjing; Li, Jing; Liu, Dejian; You, Jing; Liu, Jianguo

2018-03-01

A Gram-stain positive, non-motile, spherical, red-pigmented and facultatively anaerobic bacterium, designated strain 6.1 T , was isolated from a crude oil recovery water sample from the Huabei oil field in China. The novel strain exhibited tolerance of UV irradiation (> 1000 J m -2 ). Based on 16S rRNA gene sequence comparisons, strain 6.1 T shows high similarity to Deinococcus citri DSM 24791 T (98.1%) and Deinococcus gobiensis I-0 T (97.8%), with less than 93.5% similarity to other closely related taxa. The major cellular fatty acids were identified as summed feature 3 (C 16:1 ω7c and/or iso-C 15:0 2-OH), followed by iso-C 17:1 ω9c and C 16:0 . The polar lipid profile was found to contain phospholipids, glycolipids, phosphoglycolipids and aminophospholipids. The predominant respiratory quinone was identified as MK-8. The DNA G + C content was determined to be 68.3 mol %. DNA-DNA hybridization between strain 6.1 T and D. citri DSM 24791 T was 45.6 ± 7.1% and with D. gobiensis I-O T was 36.6 ± 4.7%. On the basis of phylogenetic, chemotaxonomic and phenotypic data, we conclude strain 6.1 T represents a novel species of the genus Deinococcus, for which we propose the name Deinococcus petrolearius sp. nov. The type strain is 6.1 T (= CGMCC 1.15053 T  = KCTC 33744 T ).

Draft Genome Sequence of the Deinococcus-Thermus Bacterium Meiothermus ruber Strain A

DOE PAGES

Thiel, Vera; Tomsho, Lynn P.; Burhans, Richard; ...

2015-03-26

The draft genome sequence of the Deinococcus-Thermus group bacterium Meiothermus ruber strain A, isolated from a cyanobacterial enrichment culture obtained from Octopus Spring (Yellowstone National Park, WY), comprises 2,968,099 bp in 170 contigs. It is predicted to contain 2,895 protein-coding genes, 44 tRNA-coding genes, and 2 rRNA operons.

Draft Genome Sequence of Deinococcus sp. Strain RL Isolated from Sediments of a Hot Water Spring

PubMed Central

Mahato, Nitish Kumar; Tripathi, Charu; Verma, Helianthous; Singh, Neha

2014-01-01

Deinococcus sp. strain RL, a moderately thermophilic bacterium, was isolated from sediments of a hot water spring in Manikaran, India. Here, we report the draft genome (2.79 Mbp) of this strain, which contains 62 contigs and 2,614 coding DNA sequences, with an average G+C content of 69.4%. PMID:25035332

Deinococcus aluminii sp. nov., isolated from an automobile air conditioning system.

PubMed

Kim, Dong-Uk; Lee, Hyosun; Lee, Suyeon; Park, Sooyeon; Yoon, Jung-Hoon; Zhao, Lei; Kim, Min-Kyu; Ahn, Jae-Hyung; Ka, Jong-Ok

2018-01-16

A Gram-stain-positive and pale pink-pigmented bacterial strain, designated ID0501 T , was isolated from an automobile evaporator core collected in the Republic of Korea. The cells were aerobic and coccoidal. The strain grew at 15-40 ˚C (optimum, 37 ˚C), at pH 6.0-7.0 (optimum, pH 6.5), and in the presence of 0-1.5 % (w/v) NaCl. Phylogenetically, the strain was related to members of the genus Deinococcus and showed the highest sequence similarity, of 96.9 %, with Deinococcus metallilatus MA1002 T . The major fatty acids of the strain were iso-C17 : 0, iso-C15 : 0 and iso-C13 : 0. The predominant respiratory quinone was MK-8. The polar lipids profile revealed the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidylcholine, diphosphatidylglycerol, unidentified phospholipids, an unidentified aminolipid and unidentified glycolipids. The DNA G+C content of the strain was 68.3 mol%. On the basis of phenotypic, genotypic and chemotaxonomic data, strain ID0501 T represents a novel species of the genus Deinococcus, for which the name Deinococcusaluminii sp. nov. (=KACC 19286 T =NBRC 112889 T ) is proposed.

Microbial Isolates from the Upper Atmosphere Support Panspermia Hypothesis

NASA Astrophysics Data System (ADS)

Yang, Yinjie; Yokobori, Shin-Ichi; Yamagishi, Akihiko

Terrestrial microbes may be transported into the upper atmosphere via various means. Due to the environmental similarity of the upper atmosphere to outer space, knowledge of microbes in the upper atmosphere would be valuable for assessing the chances and limits of microbial transfer from the earth to extraterrestrial bodies (i.e., Panspermia of terrestrial microbes). We collected air dust samples in the upper troposphere and the stratosphere over Japan by using aircrafts or balloons. Microbial isolates from the samples were endospore-forming species (Bacillus, Paenibacillus, Streptomyces) and non-spore-forming Deinococci. Besides the evidence of microbial presence in the upper atmosphere, we show the possible presence of terrestrial microbes in space by extrapolated height-dependent distribution of microbes. High resistance to radiation and desiccation was common for our upper-atmospheric isolates and likely the most important feature enabled their survival in the environment of elevated radiation and desiccation. In this regard, Panspermia of viable Deinococci and endospores would be more likely than other terrestrial microbes. Specifically, the Deinococcus isolates exhibited extreme resistance to radiation (several times higher than bacterial endospores), the principle threat for microbial survival during interplanetary transfer. Based on detailed characterization of the Deinococcus isolates, we proposed two new species Deinococcus aerius sp. nov. and Deinococcus aetherius sp. nov., which are now candidate microbes for exposure experiment in space.

Limit for the Survivability from Potassium Decay of Bacterial Spores in Halite Fluid Inclusions

NASA Astrophysics Data System (ADS)

Kminek, G.; Bada, J. L.

2001-12-01

Vreeland et al.1 recently claimed to have isolated and cultured a viable spore forming halotolerant bacterium from a 250 million year old brine inclusion present in a salt crystal from the Salado formation. An earlier report suggested that viable bacterial spores could be revived from samples obtained from insects entombed in 25-40 million year old Dominican amber2. On the bases of these reports, Parkes3 raised the question of whether bacterial spores under some conditions might be effectively immortal. Sporulation, induced by an adverse change in the environmental conditions, is able to stabilize the DNA primarily against hydrolytic depurination for extended periods of time4. However, the organism is still exposed to ionizing radiation from the environment. Dormant spores have a reduced sensitivity to ionizing radiation per se, but unlike active organisms are unable to repair DNA damage encountered during long-term exposure to ionizing radiation. The accumulated damage may overwhelm any repair mechanism that starts in the early stage of spore germination5. The main radionuclide in a halite fluid inclusion is 40K, which accounts for 0.0117% of natural potassium. 40K decays via beta decay to 40Ca and via electron capture to 40Ar, releasing a primary gamma-ray. About 83.3 % of the beta's emitted are in the energy range of 0.3-1.3 MeV. We assume 7 g/l for an average concentration of natural potassium in a halite fluid inclusion, which means that the amount of 40K in a 10 μ l fluid inclusion is 8.19 ng. We have chosen a 10 μ l because this volume is typical of that used to obtain chemical data and in the attempts to extract bacteria. Less than a percent of the gamma decay energy is absorbed in a fluid inclusion of 10 μ l. Thus, we will not take the gamma decay energy into account for the further discussion. Almost all the beta energy is absorbed in the fluid inclusion. The total decay energy absorbed in a time period of 250 million years is about 87 kGy. The most DNA damage-tolerant organism known today is Deinococcus radiodurans. The viability of D. radiodurans falls to undetectable levels6 at about 18 kGy. The survival curve of dry Bacillus megaterium spores shows a 4-log reduction at about 8-10 kGy7,8. These numbers can be compared to the 87 kGy in the case for a Permian fluid inclusion. The ability to tolerate radiation induced damage lies in the efficient repair mechanism employed by D. radiodurans, which is not operative in a dormant spore. It would thus be highly unusual for a bacterial spore to survive intact for 100's of millions of years unless these bacteria are extremely radiation tolerant. Based on these considerations and without active DNA repair mechanisms, viability of a dormant bacterial spore and the survival of viable genetic material over extended periods of geologic time is probably limited by exposure to natural background radiation. 1. Vreeland, R. H., Rosenzweig, W. D., Powers, D. W. Nature 407, 897-900 (2000) 2. Cano, P. J., Borucki, M. K. Science 268, 1060-1064 (1995) 3. Parkes, R. J.Nature, 407, 844-845 (2000) 4. Lindahl, T. Nature 362, 709-715 (1993) 5. Setlow, P. J. Bacteriol., 174 (9), 2737-2741 (1992) 6. Battista, J. R. Annu. Rev. Micriobiol. 51, 203-224 (1997) 7. Powers, E. L., Kaleta, B. F. Science 132, 959-960 (1960) 8. Ewing, D., Powers, E. L. Science 194, 1049-1051 (1976)

Infrared Detection of Evidence for Microscopic Organisms on Europa

NASA Astrophysics Data System (ADS)

Dalton, J. B.; Mogul, R.

2002-12-01

The infrared detection of evidence for microorganisms on surfaces of icy satellites requires four conditions: (1) the emplacement of microorganisms at the surface, (2) the survival of biotic material in the hostile conditions of space, (3) that the biotic material exhibit diagnostic infrared absorption features and (4) spectra with sufficient resolution and signal-to-noise ratios. This paper will focus on each topic with respect to cryogenic data recently collected on model microorganisms. Several studies suggest that materials from a Europan interior ocean have been emplaced in disrupted regions[1-10]. If the Europan ocean at one time contained Life and its associated biomolecules, then it is possible that surface materials may still harbor some remnant of these structures. Such remnant material must be capable of surviving the low pressure, low temperature and high radiation environment. The terrestrial extremophile Deinococcus radiodurans has been found viable after exposure both to vacuum at temperatures as low as 80 K [11] and to 60 Gy/h of radiation[12]. The chemical degradation of D. radiodurans has also been shown to be dependent on plasma composition (O2 {>>} CO2)[13]. Hence, it is reasonable to assume that some degree of sterilization and degradation would be occurring at the surface of Europa. However, given the sputtering rate at Europa of approximately a few cm every few million years [14], it is possible that fresh material may be continually exposed from depths to which little radiation penetrates. Remote sensing of the surface, therefore, would not be dependent on the survival of the microorganism but on the endurance of the particular biomolecules that give rise to the spectral signature. This endurance is not unreasonable since previous studies have detected hydrated salts, which contain labile bonds to water, on Europa [3,15]. Cryogenic reflectance spectra of hydrated sulfate salts have broad (150-300 nm), asymmetric absorption features due to bound water of hydration, as well as narrow features on the order of 10 to 20 nm. Cryogenic reflectance spectra of D. radiodurans are similarly dominated by asymmetric, water-related absorption features but also have two sharp (5-10 nm) features arising from amide bonds within the cells. These amide bonds are two orders of magnitude stronger than the hydration bonds in the salts [16]. Thus, the features arising from the amides could be exploited for remote-sensing investigations. In comparison, the Europa spectra from Galileo NIMS also contain the broad, asymmetric absorption features attributed to water and several other weaker absorptions. Together, the narrow features are suggestive of a mixture of materials. The NIMS data are consistent with the presence of water ice, with up to 50% sulfuric acid octahydrate, 20-45% hydrated salts, and possibly as much as 0.2 mg /cm3 carbonaceous material which may be of biological origin. However, inherent noise in the observations and limitations of spectral resolution must be taken into account when discussing these findings. References:[1]Greenberg et al.,Icarus 141,1999. [2]Pappalardo et al., JGR 104, 1999. [3]McCord et al., Science 280, 1998. [4]McCord et al., LPSC XXX,1508,1999a.[5]McCord et al., LPSC XXX,1510,1999b.[6]McCord et al., JGR 104,1999c. [7]McCord et al., DPS 31,1171,1999d.[8]McCordet al., JGR 104,1999e.[9]McCord et al., JGR 106,2001.[10]McCord et al.,JGR 107,E1-4,2002.[11]Dalton et al., NAI AstroBiol. Sci. Con. 2,2002.[12]Ventkataswaran et al., Appl Environ Microbiol. 66, 2000.[13]Mogul et al., PNAS, subm., 2002.[14]Cooper et al., Icarus 149, 2000.[15]Dalton, PhD Diss., U. Colorado,Boulder,2000.[16]Darwent, Nat. Bur. Stand., NSRDS-NBS 31,1970.

Characterization and safety evaluation of a Deinococcus member as feed additive for hens.

PubMed

Wu, Szu-Yin; Li, I-Chen; Lin, Yi-Chin; Chen, Chin-Chu

2016-04-01

As previous studies mainly focus on understanding the mechanisms of radioresistance in Deinococcus bacteria, the present study aimed at characterizing and verifying the safety use of the GKB-Aid 1995 strain, a member of the radiation-resistant bacterial genus Deinococcus, as an ingredient in feed supplements. Using Vitek 2 system and 16S rRNA gene sequencing, GKB-Aid 1995 most resembles Deinococcus grandis. The Ames test, in vitro chromosomal test, in vivo micronucleus test and acute toxicity test were performed subsequently for its safety evaluation. As there is a possibility that the pigment of GKB-Aid 1995 can pass from feed to eggs intended for human consumption, an acute toxicity test was also carried out in pigmented egg yolk. The results confirmed that GKB-Aid 1995 was non-genotoxic in three genotoxicity experiments, and the LD50 of GKB-Aid 1995 and the pigmented egg yolk in ICR mice was greater than 10 and 12 g kg(-1) body weight, respectively. Overall, these data indicate that GKB-Aid 1995 is a non-toxic substance with no genotoxicity and is therefore safe to be used as a feed supplement or feed additive. This study suggests there is potential in developing GKB-Aid 1995 as an animal feed additive intended to enhance yolk coloration to meet the demand of consumers. Copyright © 2016 Elsevier Inc. All rights reserved.

On the Stability of Deinoxanthin Exposed to Mars Conditions during a Long-Term Space Mission and Implications for Biomarker Detection on Other Planets

PubMed Central

Leuko, Stefan; Bohmeier, Maria; Hanke, Franziska; Böettger, Ute; Rabbow, Elke; Parpart, Andre; Rettberg, Petra; de Vera, Jean-Pierre P.

2017-01-01

Outer space, the final frontier, is a hostile and unforgiving place for any form of life as we know it. The unique environment of space allows for a close simulation of Mars surface conditions that cannot be simulated as accurately on the Earth. For this experiment, we tested the resistance of Deinococcus radiodurans to survive exposure to simulated Mars-like conditions in low-Earth orbit for a prolonged period of time as part of the Biology and Mars experiment (BIOMEX) project. Special focus was placed on the integrity of the carotenoid deinoxanthin, which may serve as a potential biomarker to search for remnants of life on other planets. Survival was investigated by evaluating colony forming units, damage inflicted to the 16S rRNA gene by quantitative PCR, and the integrity and detectability of deinoxanthin by Raman spectroscopy. Exposure to space conditions had a strong detrimental effect on the survival of the strains and the 16S rRNA integrity, yet results show that deinoxanthin survives exposure to conditions as they prevail on Mars. Solar radiation is not only strongly detrimental to the survival and 16S rRNA integrity but also to the Raman signal of deinoxanthin. Samples not exposed to solar radiation showed only minuscule signs of deterioration. To test whether deinoxanthin is able to withstand the tested parameters without the protection of the cell, it was extracted from cell homogenate and exposed to high/low temperatures, vacuum, germicidal UV-C radiation, and simulated solar radiation. Results obtained by Raman investigations showed a strong resistance of deinoxanthin against outer space and Mars conditions, with the only exception of the exposure to simulated solar radiation. Therefore, deinoxanthin proved to be a suitable easily detectable biomarker for the search of Earth-like organic pigment-containing life on other planets. PMID:28966605

The International Journal of Astrobiology

NASA Astrophysics Data System (ADS)

Wynn-Williams, David D.

2002-01-01

The launch of a new journal is appropriately like a space mission. It is the result of a scientific need, the inspiration of a group of committed scientists and technologists, a series of draft proposals, an approved mission protocol, and a launch. Today is the launch day for a journal whose remit has only recently consolidated from diverse disciplines. Cambridge University Press has an international reputation for astronomy. To this we add extreme biology and its associated environmental research to integrate astrobiology as: 'the study of the origin, evolution, adaptation and distribution of past and present life in the Universe'. Astrobiology has three main themes: (1) Origin, evolution and limits of life on Earth; (2) Future of life, both on Earth and elsewhere; (3) Search for habitats, biomolecules and life in the Solar System and elsewhere. These fundamental concepts require the integration of various disciplines, including biology (especially microbiology), chemistry, geology, palaeontology, and the physics of atmospheres, planets and stars. We must also keep our minds wide open about the nature and limits of life. We can safely assume a carbon-based system within Solar Systems as we know them, but our concept of habitable zones expands yearly. We were taught that only the spores of certain bacilli could survive temperatures above the boiling point of water, and yet we now know that the deep-sea vent microbe Pyrolobus can survive an hour at 121 °C, which is the temperature used for sterilising medical instruments. We know of cyanobacteria which can not only live inside deep-frozen Antarctic rocks but also survive on roof-tops in Jerusalem at 80 °C. The bacterium Deinococcus radiodurans tolerates lethal doses of nuclear radiation, and cyanobacteria inside Antarctic desert sandstone receive so little moisture that their carbon turnover time (from its fixation by photosynthesis to its release as carbon dioxide during respiration) is 10,000 years. Life is tolerant, adaptable and tenacious.

Phosphinothricin Acetyltransferases Identified Using In Vivo, In Vitro, and Bioinformatic Analyses

PubMed Central

VanDrisse, Chelsey M.; Hentchel, Kristy L.

2016-01-01

ABSTRACT Acetylation of small molecules is widespread in nature, and in some cases, cells use this process to detoxify harmful chemicals. Streptomyces species utilize a Gcn5 N-acetyltransferase (GNAT), known as Bar, to acetylate and detoxify a self-produced toxin, phosphinothricin (PPT), a glutamate analogue. Bar homologues, such as MddA from Salmonella enterica, acetylate methionine analogues such as methionine sulfoximine (MSX) and methionine sulfone (MSO), but not PPT, even though Bar homologues are annotated as PPT acetyltransferases. S. enterica was used as a heterologous host to determine whether or not putative PPT acetyltransferases from various sources could acetylate PPT, MSX, and MSO. In vitro and in vivo analyses identified substrates acetylated by putative PPT acetyltransferases from Deinococcus radiodurans (DR_1057 and DR_1182) and Geobacillus kaustophilus (GK0593 and GK2920). In vivo, synthesis of DR_1182, GK0593, and GK2920 blocked the inhibitory effects of PPT, MSX, and MSO. In contrast, DR_1057 did not detoxify any of the above substrates. Results of in vitro studies were consistent with the in vivo results. In addition, phylogenetic analyses were used to predict the functionality of annotated PPT acetyltransferases in Burkholderia xenovorans, Bacillus subtilis, Staphylococcus aureus, Acinetobacter baylyi, and Escherichia coli. IMPORTANCE The work reported here provides an example of the use of a heterologous system for the identification of enzyme function. Many members of this superfamily of proteins do not have a known function, or it has been annotated solely on the basis of sequence homology to previously characterized enzymes. The critical role of Gcn5 N-acetyltransferases (GNATs) in the modulation of central metabolic processes, and in controlling metabolic stress, necessitates approaches that can reveal their physiological role. The combination of in vivo, in vitro, and bioinformatics approaches reported here identified GNATs that can acetylate and detoxify phosphinothricin. PMID:27694229

On the Stability of Deinoxanthin Exposed to Mars Conditions during a Long-Term Space Mission and Implications for Biomarker Detection on Other Planets.

PubMed

Leuko, Stefan; Bohmeier, Maria; Hanke, Franziska; Böettger, Ute; Rabbow, Elke; Parpart, Andre; Rettberg, Petra; de Vera, Jean-Pierre P

2017-01-01

Outer space, the final frontier, is a hostile and unforgiving place for any form of life as we know it. The unique environment of space allows for a close simulation of Mars surface conditions that cannot be simulated as accurately on the Earth. For this experiment, we tested the resistance of Deinococcus radiodurans to survive exposure to simulated Mars-like conditions in low-Earth orbit for a prolonged period of time as part of the Biology and Mars experiment (BIOMEX) project. Special focus was placed on the integrity of the carotenoid deinoxanthin, which may serve as a potential biomarker to search for remnants of life on other planets. Survival was investigated by evaluating colony forming units, damage inflicted to the 16S rRNA gene by quantitative PCR, and the integrity and detectability of deinoxanthin by Raman spectroscopy. Exposure to space conditions had a strong detrimental effect on the survival of the strains and the 16S rRNA integrity, yet results show that deinoxanthin survives exposure to conditions as they prevail on Mars. Solar radiation is not only strongly detrimental to the survival and 16S rRNA integrity but also to the Raman signal of deinoxanthin. Samples not exposed to solar radiation showed only minuscule signs of deterioration. To test whether deinoxanthin is able to withstand the tested parameters without the protection of the cell, it was extracted from cell homogenate and exposed to high/low temperatures, vacuum, germicidal UV-C radiation, and simulated solar radiation. Results obtained by Raman investigations showed a strong resistance of deinoxanthin against outer space and Mars conditions, with the only exception of the exposure to simulated solar radiation. Therefore, deinoxanthin proved to be a suitable easily detectable biomarker for the search of Earth-like organic pigment-containing life on other planets.

DNA Recombinase Proteins, their Function and Structure in the Active Form, a Computational Study

NASA Technical Reports Server (NTRS)

Carra, Claudio; Cucinotta, Francis A.

2007-01-01

Homologous recombination is a crucial sequence of reactions in all cells for the repair of double strand DNA (dsDNA) breaks. While it was traditionally considered as a means for generating genetic diversity, it is now known to be essential for restart of collapsed replication forks that have met a lesion on the DNA template (Cox et al., 2000). The central stage of this process requires the presence of the DNA recombinase protein, RecA in bacteria, RadA in archaea, or Rad51 in eukaryotes, which leads to an ATP-mediated DNA strand-exchange process. Despite many years of intense study, some aspects of the biochemical mechanism, and structure of the active form of recombinase proteins are not well understood. Our theoretical study is an attempt to shed light on the main structural and mechanistic issues encountered on the RecA of the e-coli, the RecA of the extremely radio resistant Deinococcus Radiodurans (promoting an inverse DNA strand-exchange repair), and the homolog human Rad51. The conformational changes are analyzed for the naked enzymes, and when they are linked to ATP and ADP. The average structures are determined over 2ns time scale of Langevian dynamics using a collision frequency of 1.0 ps(sup -1). The systems are inserted in an octahedron periodic box with a 10 Angstrom buffer of water molecules explicitly described by the TIP3P model. The corresponding binding free energies are calculated in an implicit solvent using the Poisson-Boltzmann solvent accessible surface area, MM-PBSA model. The role of the ATP is not only in stabilizing the interaction RecA-DNA, but its hydrolysis is required to allow the DNA strand-exchange to proceed. Furthermore, we extended our study, using the hybrid QM/MM method, on the mechanism of this chemical process. All the calculations were performed using the commercial code Amber 9.

The deoxyribonucleic acid of Micrococcus radiodurans

PubMed Central

Schein, Arnold H.

1966-01-01

The DNA of Micrococcus radiodurans was prepared by three methods. Although the recovery of DNA varied considerably, the percentage molar base ratios of the DNA from the three preparations were essentially the same: guanine, 33±2; adenine, 18±1; cytosine, 33±2; thymine, 17±1. Base compositions calculated from Tm values and from density in caesium chloride gradients also yielded guanine+cytosine contents of 66 and 68% of total bases respectively. No unusual bases were observed. The S20,w values were characteristic of high-molecular-weight DNA. Electron microscopy showed the purified DNA in long strands; occasionally these were coiled. Images(a)(b)(c)(d)(e)Fig. 1. PMID:16742439

Deinococcus hibisci sp. nov., isolated from rhizosphere of Hibiscus syriacus L. (mugunghwa flower).

PubMed

Moya, Gabriela; Yan, Zheng-Fei; Chu, Dong-Hun; Won, KyungHwa; Yang, Jung-Eun; Wang, Qi-Jun; Kook, Moo-Chang; Yi, Tae-Hoo

2018-01-01

A Gram-stain-positive, pink-pigmented, coccus-shaped, strictly aerobic, non-motile bacterium, strain THG-AG1.5 T , was isolated from rhizosphere of Hibiscus syriacus L. (Mugunghwa flower) located in Kyung Hee University, Yongin, Gyeonggi, Republic of Korea. The isolated strain grew optimally at 25-30 °C, at pH 6.0-7.5 and in the presence of additional 0-1.5 % (w/v) NaCl. Strain THG-AG1.5 T exhibited tolerance to UV radiation (>1500 J m -2 ) and to gamma radiation (>12 kGy). Based on 16S rRNA gene sequence comparisons, strain THG-AG1.5 T was closely related to Deinococcus daejeonensis MJ27 T (98.03 %), Deinococcus radiotolerans C1 T (97.61 %) and Deinococcus grandis DSM 3963 T (97.32 %). The genomic DNA G+C content of strain THG-AG1.5 T was 74.8 mol%. The DNA-DNA hybridization values between strain THG-AG1.5 T and its closest phylogenetically neighbours were below 63.0 %. The peptidoglycan amino acids were alanine, valine, glutamic acid, glycine, ornithine, lysine and aspartic acid. Strain THG-AG1.5 T contained ribose, mannose and glucose as whole-cell-wall sugars and menaquinone-8 (MK-8) as the only isoprenoid quinone. The major component in the polyamine pattern was spermidine. The major polar lipids of strain THG-AG1.5 T were a phosphoglycolipid, six unidentified glycolipids and an unidentified aminophospholipid. The major fatty acids were identified as iso-C15 : 0, C15 : 1ω6c, C16 : 0, iso-C17 : 0, C17 : 0, C18 : 0 and summed feature 3. On the basis of our polyphasic taxonomy study, strain THG-AG1.5 T represents a novel species within the genus Deinococcus, for which the name Deinococcushibisci sp. nov. is proposed. The type strain is THG-AG1.5 T (=KACC 18850 T =CCTCC AB 2016078 T ).

Effect of physiological age on radiation resistance of some bacteria that are highly radiation resistant. [Micrococcus radiodurans; Micrococcus sp. isolate C-3; Moraxella sp isolate 4; Escherichia coli

DOE Office of Scientific and Technical Information (OSTI.GOV)

Keller, L.C.; Maxcy, R.B.

1984-05-01

Physiological age-dependent variation in radiation resistance was studied for three bacteria that are highly radiation resistant: Micrococcus radiodurans, Micrococcus sp. isolate C-3, and Moraxella sp. isolate 4. Stationary-phase cultures of M. radiodurans and isolate C-3 were much more resistant to gamma radiation than were log-phase cultures. This pattern of relative resistance was reversed for isolate 4. Resistance of isolate 4 to UV light was also greater during log phase, although heat resistance and NaCl tolerance after heat stresses were greater during stationary phase. Radiation-induced injury of isolate 4 compared with injury of Escherichia coli B suggested that the injury process,more » as well as the lethal process, was affected by growth phase. The hypothesis that growth rate affects radiation resistance was tested, and results were interpreted in light of the probable confounding effect of methods used to alter growth rates of bacteria. These results indicate that dose-response experiments should be designed to measure survival during the most resistant growth phase of the organism under study. The timing is particularly important when extrapolations of survival results might be made to potential irradiation processes for foods. 17 references.« less

Inactivation of the Radiation-Resistant Spoilage Bacterium Micrococcus radiodurans

PubMed Central

Duggan, D. E.; Anderson, A. W.; Elliker, P. R.

1963-01-01

A simplified technique permitting the pipetting of raw puréed meats for quantitative bacteriological study is described for use in determining survival of these non-sporing bacteria, which are exceptionally resistant to radiation. Survival curves, using gamma radiation as the sterilizing agent, were determined in raw beef with four strains of Micrococcus radiodurans. Survival curves of the R1 strain in other meat substrates showed that survival was significantly greater in raw beef and raw chicken than in raw fish or in cooked beef. Resistance was lowest in the buffer. Cells grown in broth (an artificial growth medium) and resuspended in beef did not differ in resistance from cells that had been grown and irradiated in beef. Survival rate was statistically independent of the initial cell concentration, even though there appeared to be a correlation between lower death rate and lower initial cell concentrations. The initial viable count of this culture of the domesticated R1 strain in beef was reduced by a factor of about 10-5 by 3.0 megarad, and 4.0 megarad reduced the initial count by a factor of more than 10-9. Data suggest that M. radiodurans R1 is more resistant to radiation than spore-forming spoilage bacteria for which inactivation rates have been published. PMID:14063780

Bacterial Diversity in Bentonites, Engineered Barrier for Deep Geological Disposal of Radioactive Wastes.

PubMed

Lopez-Fernandez, Margarita; Cherkouk, Andrea; Vilchez-Vargas, Ramiro; Jauregui, Ruy; Pieper, Dietmar; Boon, Nico; Sanchez-Castro, Ivan; Merroun, Mohamed L

2015-11-01

The long-term disposal of radioactive wastes in a deep geological repository is the accepted international solution for the treatment and management of these special residues. The microbial community of the selected host rocks and engineered barriers for the deep geological repository may affect the performance and the safety of the radioactive waste disposal. In this work, the bacterial population of bentonite formations of Almeria (Spain), selected as a reference material for bentonite-engineered barriers in the disposal of radioactive wastes, was studied. 16S ribosomal RNA (rRNA) gene-based approaches were used to study the bacterial community of the bentonite samples by traditional clone libraries and Illumina sequencing. Using both techniques, the bacterial diversity analysis revealed similar results, with phylotypes belonging to 14 different bacterial phyla: Acidobacteria, Actinobacteria, Armatimonadetes, Bacteroidetes, Chloroflexi, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes, Proteobacteria, Nitrospirae, Verrucomicrobia and an unknown phylum. The dominant groups of the community were represented by Proteobacteria and Bacteroidetes. A high diversity was found in three of the studied samples. However, two samples were less diverse and dominated by Betaproteobacteria.

Influence of Culture Media on the Radiation Resistance of Micrococcus radiodurans

PubMed Central

Krabbenhoft, K. L.; Anderson, A. W.; Elliker, P. R.

1967-01-01

The addition of NZ-case (a tryptic digest of casein) to a growth medium (PC) consisting of tryptone, glucose, and yeast extract caused a significant decrease in γ radiation resistance of Micrococcus radiodurans. The level of radiation resistance was inversely related to the concentration of NZ-case. The ld50 for this organism was approximately 700 krad when grown in tryptone, glucose, yeast extract, and dl-methionine (TGYM) broth, but it was approximately one-half as resistant when grown in a PC medium containing 0.5% NZ-case (PCNZ). The resistance to ultraviolet light was also reduced. Cultures transferred from PCNZ to TGYM media regained the high level of resistance. Images Fig. 2 Fig. 3 PMID:5340165

Culturable bacterial diversity at the Princess Elisabeth Station (Utsteinen, Sør Rondane Mountains, East Antarctica) harbours many new taxa.

PubMed

Peeters, Karolien; Ertz, Damien; Willems, Anne

2011-07-01

We studied the culturable heterotrophic bacterial diversity present at the site of the new Princess Elisabeth Station at Utsteinen (Dronning Maud Land, East Antarctica) before construction. About 800 isolates were picked from two terrestrial microbial mat samples after incubation on several growth media at different temperatures. They were grouped using rep-PCR fingerprinting and partial 16S rRNA gene sequencing. Phylogenetic analysis of the complete 16S rRNA gene sequences of 93 representatives showed that the isolates belonged to five major phyla: Actinobacteria, Bacteroidetes, Proteobacteria, Firmicutes and Deinococcus-Thermus. Isolates related to the genus Arthrobacter were the most prevalent whereas the genera Hymenobacter, Deinococcus, Cryobacterium and Sphingomonas were also recovered in high numbers in both samples. A total of 35 different genera were found, the majority of which has previously been reported from Antarctica. For the genera Aeromicrobium, Aurantimonas, Rothia, Subtercola, Tessaracoccus and Xylophilus, this is the first report in Antarctica. In addition, numerous potential new species and new genera were recovered; many of them currently restricted to Antarctica, particularly in the phyla Bacteroidetes and Deinococcus-Thermus. Copyright © 2011 Elsevier GmbH. All rights reserved.

The microbe capture experiment in space: Fluorescence microscopic detection of microbes captured by aerogel

NASA Astrophysics Data System (ADS)

Sugino, Tomohiro; Yokobori, Shin-Ichi; Yang, Yinjie; Kawaguchi, Yuko; Okudaira, Kyoko; Tabata, Makoto; Kawai, Hideyuki; Hasegawa, Sunao; Yamagishi, Akihiko

Microbes have been collected at the altitude up to about 70 km in the sampling experiment done by several groups[1]. We have also collected high altitude microbes, by using an airplane and balloons[2][3][4][5]. We collected new deinococcal strain (Deinococcus aetherius and Deinococ-cus aerius) and several strains of spore-forming bacilli from stratosphere[2][4][5]. However, microbe sampling in space has never been reported. On the other hand, "Panspermia" hy-pothesis, where terrestrial life is originated from outside of Earth, has been proposed[6][7][8][9]. Recent report suggesting existence of the possible microbe fossils in the meteorite of Mars origin opened the serious debate on the possibility of migration of life embedded in meteorites (and cosmic dusts)[10][11]. If we were able to find terrestrial microbes in space, it would suggest that the terrestrial life can travel between astronomical bodies. We proposed a mission "Tanpopo: Astrobiology Exposure and Micrometeoroid Capture Experiments" to examine possible inter-planetary migration of microbes, organic compounds and meteoroids on Japan Experimental Module of the International Space Station (ISS)[12]. Two of six sub themes in this mission are directly related to interplanetary migration of microbes. One is the direct capturing experi-ment of microbes (probably within the particles such as clay) in space by the exposed ultra-low density aerogel. Another is the exposure experiment to examine survivability of the microbes in harsh space environment. They will tell us the possibility of interplanetary migration of microbes (life) from Earth to outside of Earth (or vise versa). In this report, we will report whether aerogel that have been used for the collection of space debris and cosmic dusts can be used for microbe sampling in space. We will discuss how captured particles by aerogel can be detected with DNA-specific fluorescent dye, and how to distinguish microbes from other mate-rials (i.e. aerogel and particles such as clay). The surface of micro-particles captured by aerogel is often vitrified. The non-specific fluorescent light is often observed from vitrified materials. Therefore, we need to distinguish fluorescent light of stained microbes from that of vitrified ma-terials. We are going to use two types of differences (wavelength dependence and attenuation rate of fluorescent) between stained microbes with DNA-specific fluorescent dye and other ma-terials such as clay and aerogel. Fluorescent light of stained microbes shows attenuation faster than that of vitrified materials. Fluorescent light of vitrified materials shows broader range of emission spectra than that of stained microbes. In addition, we simulated the high-speed collision experiment of micro-particles to the aerogel with the two stage light gas gun (ca. 4 km/s). The micro-particles containing pre-stained and dried cells of Deinococcus radiodurans mixed with clay material were used for the collision experiment, and the captured particles were observed with fluorescence microscope. This experiment suggests that the captured microbes can be detected and be distinguished from clay materials. Reference [1] Yang, Y. et al. (2009) Biol. Sci. Space, 23, 151-163. [2] Yang, Y., et al. (2008) Biol. Sci. Space 22:18-25. [3] Yang, Y., et al. (2008) JAXA-RR-08-001: 34-42. [4] Yang, Y., et al. (2009) Internatl. J. Syst. Evol. Bacteriol., 59: 1862-1866. [5] Yang, Y. et al. (2010) Internatl. J. Syst. Evol. Bacteriol. (in press). [6] Arrhenius, S. (1908) Worlds in the Making-the Evolution of the Universe (translation to English by H. Borns) Harper and Brothers Publishers, New York. [7]Crick, F. (1981) Life Itself. Simon Schuster, New York. [8] W.L. Nicholson et al., Microbiol. Mol. Biol. Rev. 64 (2000) 548. [9] G. Horneck et al., Orig. Life Evol. Biosph. 31 (2001) 527. [10] Chyba, C. and C. Sagan (1992) Nature 355: 125-132. [11] Sandford, S. A., et al. (2006) Science 314: 1720-1724. [12] Yamagishi, A., et al. (2008) International Symposium on Space Technology and Science (ISTS) Web Paper Archives. 2008-k-05.

Structure and nature of manganese(II) imidazole complexes in frozen aqueous solutions.

PubMed

Un, Sun

2013-04-01

A common feature of a large majority of the manganese metalloenzymes, as well as many synthetic biomimetic complexes, is the bonding between the manganese ion and imidazoles. This interaction was studied by examining the nature and structure of manganese(II) imidazole complexes in frozen aqueous solutions using 285 GHz high magnet-field continuous-wave electron paramagnetic resonance (cw-HFEPR) and 95 GHz pulsed electron-nuclear double resonance (ENDOR) and pulsed electron-double resonance detected nuclear magnetic resonance (PELDOR-NMR). The (55)Mn hyperfine coupling and isotropic g values of Mn(II) in frozen imidazole solutions continuously decreased with increasing imidazole concentration. ENDOR and PELDOR-NMR measurements demonstrated that the structural basis for this behavior arose from the imidazole concentration-dependent distribution of three six-coordinate and two four-coordinate species: [Mn(H2O)6](2+), [Mn(imidazole)(H2O)5](2+), [Mn(imidazole)2(H2O)4](2+), [Mn(imidazole)3(H2O)](2+), and [Mn(imidazole)4](2+). The hyperfine and g values of manganese proteins were also fully consistent with this imidazole effect. Density functional theory methods were used to calculate the structures, spin and charge densities, and hyperfine couplings of a number of different manganese imidazole complexes. The use of density functional theory with large exact-exchange admixture calculations gave isotropic (55)Mn hyperfine couplings that were semiquantitative and of predictive value. The results show that the covalency of the Mn-N bonds play an important role in determining not only magnetic spin parameters but also the structure of the metal binding site. The relationship between the isotropic (55)Mn hyperfine value and the number of imidazole ligands provides a quick and easy test for determining whether a protein binds an Mn(II) ion using histidine residues and, if so, how many are involved. Application of this method shows that as much as 40% of the Mn(II) ions in Deinococcus radiodurans are ligated to two histidines (Tabares, L. C.; Un, S. J. Biol. Chem 2013, in press).

Assessing fluctuating evolutionary pressure in yeast and mammal evolutionary rate covariation using bioinformatics of meiotic protein genetic sequences

NASA Astrophysics Data System (ADS)

Dehipawala, Sunil; Nguyen, A.; Tremberger, G.; Cheung, E.; Holden, T.; Lieberman, D.; Cheung, T.

2013-09-01

The evolutionary rate co-variation in meiotic proteins has been reported for yeast and mammal using phylogenic branch lengths which assess retention, duplication and mutation. The bioinformatics of the corresponding DNA sequences could be classified as a diagram of fractal dimension and Shannon entropy. Results from biomedical gene research provide examples on the diagram methodology. The identification of adaptive selection using entropy marker and functional-structural diversity using fractal dimension would support a regression analysis where the coefficient of determination would serve as evolutionary pathway marker for DNA sequences and be an important component in the astrobiology community. Comparisons between biomedical genes such as EEF2 (elongation factor 2 human, mouse, etc), WDR85 in epigenetics, HAR1 in human specificity, clinical trial targeted cancer gene CD47, SIRT6 in spermatogenesis, and HLA-C in mosquito bite immunology demonstrate the diagram classification methodology. Comparisons to the SEPT4-XIAP pair in stem cell apoptosis, testesexpressed taste genes TAS1R3-GNAT3 pair, and amyloid beta APLP1-APLP2 pair with the yeast-mammal DNA sequences for meiotic proteins RAD50-MRE11 pair and NCAPD2-ICK pair have accounted for the observed fluctuating evolutionary pressure systematically. Regression with high R-sq values or a triangular-like cluster pattern for concordant pairs in co-variation among the studied species could serve as evidences for the possible location of common ancestors in the entropy-fractal dimension diagram, consistent with an example of the human-chimp common ancestor study using the FOXP2 regulated genes reported in human fetal brain study. The Deinococcus radiodurans R1 Rad-A could be viewed as an outlier in the RAD50 diagram and also in the free energy versus fractal dimension regression Cook's distance, consistent with a non-Earth source for this radiation resistant bacterium. Convergent and divergent fluctuating evolutionary pressure could be studied with extension to genetic sequences in organisms in possible astrobiology conditions, with the assumption that the continuation of a book of life would require meiotic proteins everywhere in the universe.

Remote Sensing of Potential Biosignatures from Rocky, Liquid, or Icy (Exo)Planetary Surfaces.

PubMed

Poch, Olivier; Frey, Joachim; Roditi, Isabel; Pommerol, Antoine; Jost, Bernhard; Thomas, Nicolas

2017-03-01

To detect signs of life by remote sensing on objects of our Solar System and on exoplanets, the characterization of light scattered by surface life material could complement possible clues given by the atmospheric composition. We reviewed the reflectance spectra of a broad selection of major biomolecules that constitute terrestrial carbon-based life from 0.4 to 2.4 μm, and we discuss their detectability through atmospheric spectral windows. Biomolecule features in the near-infrared (0.8-2.4 μm) will likely be obscured by water spectral features and some atmospheric gases. The visible range (0.4-0.8 μm), including the strong spectral features of pigments, is the most favorable. We investigated the detectability of a pigmented microorganism (Deinococcus radiodurans) when mixed with silica sand, liquid water, and water-ice particles representative of diverse surfaces of potentially habitable worlds. We measured the visible to near-infrared reflectance spectra (0.4-2.4 μm) and the visible phase curves (at 0.45 and 0.75 μm) of the mixtures to assess how the surface medium and the viewing geometry affect the detectability of the microorganisms. The results show that ice appears to be the most favorable medium for the detection of pigments. Water ice is bright and featureless from 0.4 to 0.8 μm, allowing the absorption of any pigment present in the ice to be well noticeable. We found that the visible phase curve of water ice is the most strongly affected by the presence of pigments, with variations of the spectral slope by more than a factor of 3 with phase angles. Finally, we show that the sublimation of the ice results in the concentration of the biological material onto the surface and the consequent increase of its signal. These results have applications to the search for life on icy worlds, such as Europa or Enceladus. Key Words: Remote sensing-Biosignatures-Reflectance spectroscopy-Exoplanets-Spectroscopic biosignatures-Pigments. Astrobiology 17, 231-252.

Ultraviolet radiation and the photobiology of earth's early oceans.

PubMed

Cockell, C S

2000-10-01

During the Archean era (3.9-2.5 Ga ago) the earth was dominated by an oceanic lithosphere. Thus, understanding how life arose and persisted in the Archean oceans constitutes a major challenge in understanding early life on earth. Using a radiative transfer model of the late Archean oceans, the photobiological environment of the photic zone and the surface microlayer is explored at the time before the formation of a significant ozone column. DNA damage rates might have been approximately three orders of magnitude higher in the surface layer of the Archean oceans than on the present-day oceans, but at 30 m depth, damage may have been similar to the surface of the present-day oceans. However at this depth the risk of being transported to surface waters in the mixed layer was high. The mixed layer may have been inhabited by a low diversity UV-resistant biota. But it could have been numerically abundant. Repair capabilities similar to Deinococcus radiodurans would be sufficient to survive in the mixed layer. Diversity may have been greater in the region below the mixed layer and above the light compensation point corresponding to today's 'deep chlorophyll maximum'. During much of the Archean the air-water interface was probably an uninhabitable extreme environment for neuston. The habitability of some regions of the photic zone is consistent with the evidence embodied in the geologic record, which suggests an oxygenated upper layer in the Archean oceans. During the early Proterozoic, as ozone concentrations increased to a column abundance above 1 x 10(17) cm-2, UV stress would have been reduced and possibly a greater diversity of organisms could have inhabited the mixed layer. However, nutrient upwelling from newly emergent continental crusts may have been more significant in increasing total planktonic abundance in the open oceans and coastal regions than photobiological factors. The phohobiological environment of the Archean oceans has implications for the potential cross-transfer of life between other water bodies of the early Solar System, possibly on early Mars or the water bodies of a wet, early Venus.

Low-energy electron-beam treatment as alternative for on-site sterilization of highly functionalized medical products - A feasibility study

NASA Astrophysics Data System (ADS)

Gotzmann, G.; Portillo, J.; Wronski, S.; Kohl, Y.; Gorjup, E.; Schuck, H.; Rögner, F. H.; Müller, M.; Chaberny, I. F.; Schönfelder, J.; Wetzel, C.

2018-09-01

Over the last decades, the medical device industry has grown significantly. Complex and highly functionalized medical devices and implants are being developed to improve patient treatment and to enhance their health-related quality of life. However, medical devices from this new generation often cannot be sterilized by standard methods such as autoclaving or sterilizing gases, as they are temperature sensitive, containing electronic components like sensors and microchips, or consist of polymers. Gamma irradiation for sterilization of such products is also problematic due to long processing times under highly reactive conditions resulting in material degradation or loss of functionality. Low-energy electron-beam treatment could enable irradiation sterilization of medical surfaces within seconds. This method is very fast in comparison to gamma irradiation because of its high dose rate and therefore degradation processes of polymers can be reduced or even prevented. Additionally, electron penetration depth can be precisely controlled to prevent damage of sensitive components like electronics and semiconductors. The presented study focuses on two key aspects: 1.) Can new and highly functionalized medical products in future be sterilized using low-energy electron-beam irradiation; and 2.) Is the low-energy electron-beam technology suitable to be set up on-site to speed up sterilization processing or make it available "just-in-time". To address these questions, different test specimens were chosen with complex geometry or electronic functional parts to gather information about the limitations and chances for this new approach. The test specimens were inoculated with clinical relevant test organisms (Pseudomonas aeruginosa) as well as with approved radiation resistant organisms (Deinococcus radiodurans and Bacillus pumilus) to prove the suitability of low-energy electron-beam treatment for the above-mentioned medical products. The calculation of the D10 value for B. pumilus revealed equal efficacy when compared to standard high-energy irradiation sterilization. All of the above-mentioned germs were successfully inactivated by low-energy electron-beam treatment when test specimens were inoculated with a germ load > 10^6 CFU and treated with doses ≥ 10 kGy (for B. pumilus and P. aeruginosa) and > 300 kGy (for D. radiodurans) respectively. As an example, for specialized electronic components to be sterilized, an impedance sensor for cell culture applications was sterilized and unimpaired functionality was demonstrated even after five repeated sterilization cycles to a total dose of 50 kGy. To address the second aspect of on-site suitability of this technology, the product handling for low-energy electron-beam treatment had to be adapted to minimize the size of the electron-beam facility. Therefore, a mini electron-beam source was used and a specialized sample holder and 3D-handling regime were developed to allow reproducible surface treatment for complex product geometries. Inactivation of B. pumilus inoculated medical screws (> 10^6 CFU) was successful using the developed handling procedure. In addition, a packaging material (PET12/PE50) for medical products was investigated for its suitability for low-energy irradiation sterilization. Biocompatibility assessment revealed the material to be eligible for this application as even overdoses did not impair the biocompatibility of the material. With these results, the principal suitability of low-energy electron-beam treatment for sterilization of medical products containing electronics like sensors is demonstrated. The low-energy technology and the specialized 3D-handling regime allow the on-site setup of the technology in hospitals, medical practices or any other point of care.

Repair of Ultraviolet Radiation Damage in Sensitive Mutants of Micrococcus radiodurans

PubMed Central

Moseley, B. E. B.

1969-01-01

Various aspects of the repair of ultraviolet (UV) radiation-induced damage were compared in wild-type Micrococcus radiodurans and two UV-sensitive mutants. Unlike the wild type, the mutants are more sensitive to radiation at 265 nm than at 280 nm. The delay in deoxyribonucleic acid (DNA) synthesis following exposure to UV is about seven times as long in the mutants as in the wild type. All three strains excise UV-induced pyrimidine dimers from their DNA, although the rate at which cytosine-thymine dimers are excised is slower in the mutants. The three strains also mend the single-strand breaks that appear in the irradiated DNA as a result of dimer excision, although the process is less efficient in the mutants. It is suggested that the increased sensitivity of the mutants to UV radiation may be caused by a partial defect in the second step of dimer excision. PMID:5773016

Genetic Analysis of Stress Responses in Soil Bacteria for Enhanced Bioremediation of Mixed Contaminants

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wong, Kwong-Kwok

In order to realize the full potential of bioremediation, an understanding of microbial community and individual bacterial responses to the stresses encountered at contaminated sites is needed. Knowledge about genetic responses of soil and subsurface bacteria to environmental stresses, which include low nutrients, low oxygen, and mixed pollutants, will allow extrapolation of basic principles to field applications, either using indigenous bacteria or genetically engineered microorganisms. Defining bacterial responses to those stresses presents an opportunity for improving bioremediation strategies, both with indigenous populations and genetically-engineered microbes, and should contribute to environmental management and restoration actions that would reduce the cost andmore » time required to achieve OEM's clean up goals. Stress-inducible genes identified in this project can be used as molecular probes for monitoring performance of indigenous bacteria as well as the effectiveness of bioremediation strategies being employed. Knowledge of survival and catabolic plasmid stability of indigenous bacteria will be needed for devising the most effective bioremediation strategy. In addition, stress-inducible regulatory elements identified in this project will be useful for creating genetically-engineered microorganisms which are able to degrade hazardous wastes under stress conditions at contaminated sites. One of the model organisms, Deinococcus radiodurans, is a stress-resistant bacterium. Thus, in addition to serving as a model for gene regulation in Gram-positive organisms, it may have specific application at aerobic DOE sites where combinations of contaminants produce a particularly stressful environment. Similarly, the use of Sphingomonas F199, isolated from a depth of 407 m at the Savannah River site (Fredrickson et al., 1991), may have relevance to deep subsurface bioremediation applications, where indigenous or engineered microorganisms adapted to the that environment are needed. In addition, F199 contains aromatic oxygenases that are relevant to degradation of contaminants at that site and is representative of a large class of similar organisms from Savannah River Identification of the genes responsive to different stresses encountered at contaminated sites will provide a basic understanding of stress responses in soil bacteria and can lead to improved strategies for bioremediation. Enhanced in situ removal of hazardous wastes by stimulating growth of indigenous bacteria with nutrients or electron acceptors such as oxygen has been demonstrated. However, how much and how often to apply these supplements has largely been determined empirically. As a result, a controlled, reproducible, and properly managed degradation of pollutants in the environment is difficult to achieve. Genes inducible by low nutrient and low oxygen conditions can serve as markers for determining the minimal amount of supplements needed. The disappearance and reappearance of such stress responses will determine how much and when nutrients and oxygen are needed to be applied or reapplied. Similar applications of stress-inducible markers are already being applied in bacterial cultures in solution (Selifonova and Eaton, 1996). Stress responses induced by pollutants also have potential use as a biological index for the performance of indigenous bacteria during bioremediation as well as a microbiological risk assessment index for environmental pollutants. For instance, measurement of the stress responses of contaminant-degrading microorganisms would provide information complementary to measurement of enzymatic activity. This more complete picture of the physiological state of the desired organisms can be used to predict their performance. Finally, prior knowledge of the stress responses of competing bacteria could be used to predict their environmental competitiveness. Promoters from stress inducible genes will facilitate the construction of genetically engineered microorganisms in which the expression of the catabolic genes is uncoupled from both microbial growth and the utilization of the pollutant as the carbon source. The application of genetically engineered organisms in bioremediation requires the design of gene expression systems that function under environmental conditions and are cost effective. The promoter, the genetic regulatory element that directs the use of the gene, plays the central role in gene expression systems. The ideal promoter for environmental applications should possess two qualities: (1) it does not require the addition of exogenous compounds for activation, and (2) it is active under nutrient-limited conditions and not dependent on cell growth for activity. Promoters that are expressed constitutively meet the first quality. However, such promoters usually require active cell growth for expression and thus incur the increased cost of constant nutrient addition.« less

Astrobiological Significance of Microbial Extremophiles

NASA Technical Reports Server (NTRS)

Pikuta, Elena V.; Hoover, Richard B.

2007-01-01

The microflora of the cryosphere of planet Earth provides the best analogs for life forms that might be found in the permafrost or polar ice caps of Mars, near the surface of the cometary nuclei, or in the liquid water beneath and the ice crusts of icy moons of Jupiter and Saturn. The importance of study alkaliphilic microorganisms for astrobiology was enhanced by the findings of abundant carbonates and carbonate globules rimmed with possibly biogenic magnetites in association with the putative microfossils in the ALH84001 meteorite. Although the ALH84001 "nanofossils" were to small and simple to be unambiguously recognized as biogenic, they stimulated Astrobiology research and studies of microbial extremophiles and biomarkers in ancient rocks and meteorites. Recent studies of CI and CM carbonaceous meteorites have resulted in the detection of the well-preserved mineralized remains of coccoidal and filamentous microorganisms in cyanobacterial mats. Energy Dispersive X-ray Analysis has shown anomalous biogenic element ratios clearly indicating they are not recent biological contaminants. This paper reviews microbial extremophiles in context of their significance to Astrobiology. The study of halophilic microorganisms was started from work with saline soils and lakes, and one of the record of good growth for Haloferax mediterranei was shown at 30 percent NaC1. Although alkali-tolerant nitrifying bacteria had previously been reported, the first described alkaliphilic microorganism was the bacterium Streptococcus faecalis. Halophilic and alkaliphilic forms are relevant to conditions that might be found in closed impact basins and craters on Mars filled with evaporite deposits. The first obligately acidophilic bacterium described was Acidithiobacillus ferrooxydans (formally Thiobacillus ferrooxidans). Later thermophilic lithotrophic acidophiles were found, and the hyperacidophilic moderately thermophilic species of the genus Picrophilus were found to grow at negative pH. The epoch of study of thermophilic microorganisms starts with the discovery of Thermus aquaticus, and presently the maximum temperature for growth at 113 C was found for Pyrolobus fumarii. The microorganisms capable of growth at high temperatures and in hyperacidic environments on Earth are good analogs for life that might be able to survive in hot acidic droplets in the upper regimes of the atmosphere of Venus. The study of barophiles was made possible by engineering achievements leading to the development of the submersible crafts used to study the Black Smokers of the Deep-sea Hydrothermal vents. The first described radioresistant bacterium Deinococcus radiodurans can survive ionizing irradiation and other DNA-damaging assaults at doses that are lethal to all other organisms. These microbes are models for life that might endure high radiation environments in the ice near the surface of comets or on the icy moons of Jupiter and Saturn and in the seafloor deep beneath icy crusts Europa and Enceladus. This paper presents ESEM and FESEM images showing intact microbes preserved in the deep ice cores extracted from just above Lake Vostok, Antarctica that are considered analogs for life forms that might survive on comets and icy moons.

Radiation and Heat Resistance of Moraxella-Acinetobacter in Meats

DTIC Science & Technology

1978-01-23

Parrish, and D. Duggan. 1956. Studies on a radiation-resistant Micrococcus . I. Isolation, morphology, cul- tural characteristics, and resistance to...Anderson, and P. R. Elliker. 1965. Ecology of Micrococcus radiodurans. Appl. Microbiol. 13: 1030. Lewis, N. F. 1973. Radio-resistant Micrococcus

Heterologous Expression of Der Homologs in an Escherichia coli der Mutant and Their Functional Complementation

PubMed Central

Choi, Eunsil; Kang, Nalae; Jeon, Young; Pai, Hyun-Sook

2016-01-01

ABSTRACT The unique Escherichia coli GTPase Der (double Era-like GTPase), which contains tandemly repeated GTP-binding domains, has been shown to play an essential role in 50S ribosomal subunit biogenesis. The depletion of Der results in the accumulation of precursors of 50S ribosomal subunits that are structurally unstable at low Mg2+ concentrations. Der homologs are ubiquitously found in eubacteria. Conversely, very few are conserved in eukaryotes, and none is conserved in archaea. In the present study, to verify their conserved role in bacterial 50S ribosomal subunit biogenesis, we cloned Der homologs from two gammaproteobacteria, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium; two pathogenic bacteria, Staphylococcus aureus and Neisseria gonorrhoeae; and the extremophile Deinococcus radiodurans and then evaluated whether they could functionally complement the E. coli der-null phenotype. Only K. pneumoniae and S. Typhimurium Der proteins enabled the E. coli der-null strain to grow under nonpermissive conditions. Sucrose density gradient experiments revealed that the expression of K. pneumoniae and S. Typhimurium Der proteins rescued the structural instability of 50S ribosomal subunits, which was caused by E. coli Der depletion. To determine what allows their complementation, we constructed Der chimeras. We found that only Der chimeras harboring both the linker and long C-terminal regions could reverse the growth defects of the der-null strain. Our findings suggest that ubiquitously conserved essential GTPase Der is involved in 50S ribosomal subunit biosynthesis in various bacteria and that the linker and C-terminal regions may participate in species-specific recognition or interaction with the 50S ribosomal subunit. IMPORTANCE In Escherichia coli, Der (double Era-like GTPase) is an essential GTPase that is important for the production of mature 50S ribosomal subunits. However, to date, its precise role in ribosome biogenesis has not been clarified. In this study, we used five Der homologs from gammaproteobacteria, pathogenic bacteria, and an extremophile to elucidate their conserved function in 50S ribosomal subunit biogenesis. Among them, Klebsiella pneumoniae and Salmonella enterica serovar Typhimurium Der homologs implicated the participation of Der in ribosome assembly in E. coli. Our results show that the linker and C-terminal regions of Der homologs are correlated with its functional complementation in E. coli der mutants, suggesting that they are involved in species-specific recognition or interaction with 50S ribosomal subunits. PMID:27297882

The Deinococcus-Thermus phylum and the effect of rRNA composition on phylogenetic tree construction

NASA Technical Reports Server (NTRS)

Weisburg, W. G.; Giovannoni, S. J.; Woese, C. R.

1989-01-01

Through comparative analysis of 16S ribosomal RNA sequences, it can be shown that two seemingly dissimilar types of eubacteria Deinococcus and the ubiquitous hot spring organism Thermus are distantly but specifically related to one another. This confirms an earlier report based upon 16S rRNA oligonucleotide cataloging studies (Hensel et al., 1986). Their two lineages form a distinctive grouping within the eubacteria that deserved the taxonomic status of a phylum. The (partial) sequence of T. aquaticus rRNA appears relatively close to those of other thermophilic eubacteria. e.g. Thermotoga maritima and Thermomicrobium roseum. However, this closeness does not reflect a true evolutionary closeness; rather it is due to a "thermophilic convergence", the result of unusually high G+C composition in the rRNAs of thermophilic bacteria. Unless such compositional biases are taken into account, the branching order and root of phylogenetic trees can be incorrectly inferred.

Characterization of Thermostable Cellulases Produced by Bacillus and Geobacillus Strains

USDA-ARS?s Scientific Manuscript database

Bacterial community composition of thermophilic (60 deg C) mixed cellulose-enrichment cultures was examined by constructing a 16S rDNA clone library which demonstrated major lineages affiliated to Actinobacteria, Bacteroidetes, Chloroflexi, Deinococcus-Thermus, Firmicutes, and Proteobacteria. A tot...

Identification of pink-pigmented bacteria isolated from environmental water samples and their biofilm formation abilities.

PubMed

Furuhata, Katsunori; Kato, Yuko; Goto, Keiichi; Saitou, Keiko; Sugiyama, Jun-Ichi; Hara, Motonobu; Fukuyama, Masahumi

2008-06-01

Sixty-seven strains of pink-pigmented bacteria, which were isolated from environmental water samples collected nationwide, were identified by partial 16S rDNA sequence analysis. In addition, the biofilm formation ability of the isolates was experimentally investigated. We could identify only 2 strains at the species level: Pedobacter roseus HS-38 and Runella slithyformis HS-77. The results showed that of the strains tested, 22 strains (32.8%) were Pedobacter spp., which was most frequently identified, followed by 19 strains (28.4%) of Arcicella spp., 16 strains (23.9%) of Deinococcus spp., 5 strains (7.5%) of Roseomonas spp., 4 strains (6.0%) of Flectobacillus spp. and 1 strain (1.5%) of Runella sp. Most isolates showed low similarity values to previously known species, and they were found to be novel species. At a result, it was difficult to identify environmental water-derived pink-pigmented bacteria at the species level. On the other hand, when we measured the absorbance by the crystal violet staining to examine the quantities of biofilm formation of these strains, fifty-five (82.0%) of the 67 isolates formed biofilm. The absorbance of Deinococcus sp. HS-75 was the highest (3.56). When comparing the absorbance values among the genera, Roseomonas spp. showed the highest absorbance (mean:1.62), followed by Deinococcus spp. (mean: 1.03), and Arcicella spp. (mean: 1.01). Strains of Flectobacillus spp. (mean: 0.48) and Pedobacter spp. (mean: 0.42) showed lower absorbance values. As above, it was shown that, at the species level, the pink-pigmented bacteria in the water in the Japanese environment had various levels of ability to form biofilm.

Crystal Structure of Deinococcus Phytochrome in the Photoactivated State Reveals a Cascade of Structural Rearrangements during Photoconversion.

PubMed

Burgie, E Sethe; Zhang, Junrui; Vierstra, Richard D

2016-03-01

Phytochromes are photochromic photoreceptors responsible for a myriad of red/far-red light-dependent processes in plants and microorganisms. Interconversion is initially driven by photoreversible isomerization of bilin, but how this alteration directs the photostate-dependent changes within the protein to actuate signaling is poorly understood. Here, we describe the structure of the Deinococcus phytochrome photosensory module in its near complete far-red light-absorbing Pfr state. In addition to confirming the 180° rotation of the D-pyrrole ring, the dimeric structure clearly identifies downstream rearrangements that trigger large-scale conformational differences between the dark-adapted and photoactivated states. Mutational analyses verified the importance of residues surrounding the bilin in Pfr stabilization, and protease sensitivity assays corroborated photostate alterations that propagate along the dimeric interface. Collectively, these data support a cooperative "toggle" model for phytochrome photoconversion and advance our understanding of the allosteric connection between the photosensory and output modules. Copyright © 2016 Elsevier Ltd. All rights reserved.

The protein PprI provides protection against radiation injury in human and mouse cells

PubMed Central

Shi, Yi; Wu, Wei; Qiao, Huiping; Yue, Ling; Ren, Lili; Zhang, Shuyu; Yang, Wei; Yang, Zhanshan

2016-01-01

Severe acute radiation injuries are both very lethal and exceptionally difficult to treat. Though the radioresistant bacterium D. radiodurans was first characterized in 1956, genes and proteins key to its radioprotection have not yet to be applied in radiation injury therapy for humans. In this work, we express the D. radiodurans protein PprI in Pichia pastoris yeast cells transfected with the designed vector plasmid pHBM905A-pprI. We then treat human umbilical endothelial vein cells and BALB/c mouse cells with the yeast-derived PprI and elucidate the radioprotective effects the protein provides upon gamma irradiation. We see that PprI significantly increases the survival rate, antioxidant viability, and DNA-repair capacity in irradiated cells and decreases concomitant apoptosis rates and counts of damage-indicative γH2AX foci. Furthermore, we find that PprI reduces mortality and enhances bone marrow cell clone formation and white blood cell and platelet counts in irradiated mice. PprI also seems to alleviate pathological injuries to multiple organs and improve antioxidant viability in some tissues. Our results thus suggest that PprI has crucial radioprotective effects on irradiated human and mouse cells. PMID:27222438

Origins and Evolution of Life

NASA Astrophysics Data System (ADS)

Gargaud, Muriel; López-García, Purificación; Martin, Hervé

2011-01-01

Part I. What Is Life?: 1. Problems raised by a definition of life M. Morange; 2. Some remarks about uses of cosmological anthropic 'principles' D. Lambert; 3. Minimal cell: the biologist point of view C. Brochier-Armanet; 4. Minimal cell: the computer scientist point of view H. Bersini; 5. Origins of life: computing and simulation approaches B. Billoud; Part II. Astronomical and Geophysical Context of the Emergence of Life: 6. Organic molecules in interstellar medium C. Ceccarelli and C. Cernicharo; 7. Cosmochemical evolution and the origin of life: insights from meteorites S. Pizzarello; 8. Astronomical constraints on the emergence of life M. Gounelle and T. Montmerle; 9. Formation of habitable planets J. Chambers; 10. The concept of galactic habitable zone N. Prantzos; 11. The young Sun and its influence on planetary atmospheres M. Güdel and J. Kasting; 12. Climates of the Earth G. Ramstein; Part III. Role of Water in the Emergence of Life: 13. Liquid water: a necessary condition to all forms of life K. Bartik, G. Bruylants, E. Locci and J. Reisse; 14. The role of water in the formation and evolution of planets T. Encrenaz; 15. Water on Mars J. P. Bibring; Part IV. From Non-Living Systems to Life: 16. Energetic constraints on prebiotic pathways: application to the emergence of translation R. Pascal and L. Boiteau; 17. Comparative genomics and early cell evolution A. Lazcano; 18. Origin and evolution of metabolisms J. Peretó; Part V. Mechanisms for Life Evolution: 19. Molecular phylogeny: inferring the patterns of evolution E. Douzery; 20. Horizontal gene transfer: mechanisms and evolutionary consequences D. Moreira; 21. The role of symbiosis in eukaryotic evolution A. Latorre, A. Durbán, A. Moya and J. Peretó; Part VI. Life in Extreme Conditions: 22. Life in extreme conditions: Deinococcus radiodurans, an organism able to survive prolonged desiccation and high doses of ionising radiation S. Sommer and M. Toueille; 23. Molecular effects of UV and ionizing radiations on DNA J. Cadet and T. Douki; 24. Molecular adaptations to life at high salt: lessons from Haloarcula marismortui G. Zaccai; Part VII. Traces of Life and Biosignatures: 25. Early life: nature, distribution and evolution F. Westall; 26. Early eukaryotes in precambrian oceans E. Javaux; 27. Biomineralisation mechanisms K. Benzerara and J. Miot; 28. Limits of life and biosphere: lesson from detection of microorganisms in deep sea and deep subsurface in the Earth K. Takai; Part VIII. Life Elsewhere?: 29. Titan and the Cassini-Huygens mission J. Lunine and F. Raulin; 30. The role of terrestrial analogue environments in astrobiology R. Léveillé; Index.

Interaction of Uranium with Bacterial Cell Surfaces: Inferences from Phosphatase-Mediated Uranium Precipitation.

PubMed

Kulkarni, Sayali; Misra, Chitra Seetharam; Gupta, Alka; Ballal, Anand; Apte, Shree Kumar

2016-08-15

Deinococcus radiodurans and Escherichia coli expressing either PhoN, a periplasmic acid phosphatase, or PhoK, an extracellular alkaline phosphatase, were evaluated for uranium (U) bioprecipitation under two specific geochemical conditions (GCs): (i) a carbonate-deficient condition at near-neutral pH (GC1), and (ii) a carbonate-abundant condition at alkaline pH (GC2). Transmission electron microscopy revealed that recombinant cells expressing PhoN/PhoK formed cell-associated uranyl phosphate precipitate under GC1, whereas the same cells displayed extracellular precipitation under GC2. These results implied that the cell-bound or extracellular location of the precipitate was governed by the uranyl species prevalent at that particular GC, rather than the location of phosphatase. MINTEQ modeling predicted the formation of predominantly positively charged uranium hydroxide ions under GC1 and negatively charged uranyl carbonate-hydroxide complexes under GC2. Both microbes adsorbed 6- to 10-fold more U under GC1 than under GC2, suggesting that higher biosorption of U to the bacterial cell surface under GC1 may lead to cell-associated U precipitation. In contrast, at alkaline pH and in the presence of excess carbonate under GC2, poor biosorption of negatively charged uranyl carbonate complexes on the cell surface might have resulted in extracellular precipitation. The toxicity of U observed under GC1 being higher than that under GC2 could also be attributed to the preferential adsorption of U on cell surfaces under GC1. This work provides a vivid description of the interaction of U complexes with bacterial cells. The findings have implications for the toxicity of various U species and for developing biological aqueous effluent waste treatment strategies. The present study provides illustrative insights into the interaction of uranium (U) complexes with recombinant bacterial cells overexpressing phosphatases. This work demonstrates the effects of aqueous speciation of U on the biosorption of U and the localization pattern of uranyl phosphate precipitated as a result of phosphatase action. Transmission electron microscopy revealed that location of uranyl phosphate (cell associated or extracellular) was primarily influenced by aqueous uranyl species present under the given geochemical conditions. The data would be useful for understanding the toxicity of U under different geochemical conditions. Since cell-associated precipitation of metal facilitates easy downstream processing by simple gravity-based settling down of metal-loaded cells, compared to cumbersome separation techniques, the results from this study are of considerable relevance to effluent treatment using such cells. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Interaction of Uranium with Bacterial Cell Surfaces: Inferences from Phosphatase-Mediated Uranium Precipitation

PubMed Central

Kulkarni, Sayali; Misra, Chitra Seetharam; Gupta, Alka; Ballal, Anand

2016-01-01

ABSTRACT Deinococcus radiodurans and Escherichia coli expressing either PhoN, a periplasmic acid phosphatase, or PhoK, an extracellular alkaline phosphatase, were evaluated for uranium (U) bioprecipitation under two specific geochemical conditions (GCs): (i) a carbonate-deficient condition at near-neutral pH (GC1), and (ii) a carbonate-abundant condition at alkaline pH (GC2). Transmission electron microscopy revealed that recombinant cells expressing PhoN/PhoK formed cell-associated uranyl phosphate precipitate under GC1, whereas the same cells displayed extracellular precipitation under GC2. These results implied that the cell-bound or extracellular location of the precipitate was governed by the uranyl species prevalent at that particular GC, rather than the location of phosphatase. MINTEQ modeling predicted the formation of predominantly positively charged uranium hydroxide ions under GC1 and negatively charged uranyl carbonate-hydroxide complexes under GC2. Both microbes adsorbed 6- to 10-fold more U under GC1 than under GC2, suggesting that higher biosorption of U to the bacterial cell surface under GC1 may lead to cell-associated U precipitation. In contrast, at alkaline pH and in the presence of excess carbonate under GC2, poor biosorption of negatively charged uranyl carbonate complexes on the cell surface might have resulted in extracellular precipitation. The toxicity of U observed under GC1 being higher than that under GC2 could also be attributed to the preferential adsorption of U on cell surfaces under GC1. This work provides a vivid description of the interaction of U complexes with bacterial cells. The findings have implications for the toxicity of various U species and for developing biological aqueous effluent waste treatment strategies. IMPORTANCE The present study provides illustrative insights into the interaction of uranium (U) complexes with recombinant bacterial cells overexpressing phosphatases. This work demonstrates the effects of aqueous speciation of U on the biosorption of U and the localization pattern of uranyl phosphate precipitated as a result of phosphatase action. Transmission electron microscopy revealed that location of uranyl phosphate (cell associated or extracellular) was primarily influenced by aqueous uranyl species present under the given geochemical conditions. The data would be useful for understanding the toxicity of U under different geochemical conditions. Since cell-associated precipitation of metal facilitates easy downstream processing by simple gravity-based settling down of metal-loaded cells, compared to cumbersome separation techniques, the results from this study are of considerable relevance to effluent treatment using such cells. PMID:27287317

Growth of the extremophilic Deinococcus geothermalis DSM 11302 using co-substrate fed-batch culture.

PubMed

Bornot, Julie; Molina-Jouve, Carole; Uribelarrea, Jean-Louis; Gorret, Nathalie

2014-02-01

Deinococcus geothermalis metabolism has been scarcely studied to date, although new developments on its utilization for bioremediation have been carried out. So, large-scale production of this strain and a better understanding of its physiology are required. A fed-batch experiment was conducted to achieve a high cell density non-limiting culture of D. geothermalis DSM 11302. A co-substrate nutritional strategy using glucose and yeast extract was carried out in a 20-L bioreactor in order to maintain a non-limited growth at a maximal growth rate of 1 h(-1) at 45 °C. Substrate supplies were adjusted by monitoring online culture parameters and physiological data (dissolved oxygen, gas analyses, respiratory quotient, biomass concentration). The results showed that yeast extract could serve as both carbon and nitrogen sources, although glucose and ammonia were consumed too. Yeast extract carbon-specific uptake rate reached a value 4.5 times higher than glucose carbon-specific uptake rate. Cell concentration of 9.6 g L(-1) dry cell weight corresponding to 99 g of biomass was obtained using glucose and yeast extract as carbon and nitrogen sources.

The first evidence of deinoxanthin from Deinococcus sp. Y35 with strong algicidal effect on the toxic dinoflagellate Alexandrium tamarense.

PubMed

Li, Yi; Zhu, Hong; Lei, Xueqian; Zhang, Huajun; Guan, Chengwei; Chen, Zhangran; Zheng, Wei; Xu, Hong; Tian, Yun; Yu, Zhiming; Zheng, Tianling

2015-06-15

Harmful algal blooms (HABs) could be deemed hazardous materials in aquatic environment. Alexandrium tamarense is a toxic HAB causing alga, which causes serious economic losses and health problems. In this study, the bacterium Deinococcus xianganensis Y35 produced a new algicide, showing a high algicidal effect on A. tamarense. The algicidal compound was identified as deinoxanthin, a red pigment, based on high resolution mass spectrometry and NMR after the active compound was isolated and purified. Deinoxanthin exhibited an obvious inhibitory effect on algal growth, and showed algicidal activity against A. tamarense with an EC50 of 5.636 μg/mL with 12h treatment time. Based on the unique structure and characteristics of deinoxanthin, the content of reactive oxygen species (ROS) increased after 0.5h exposure, the structure of organelles including chloroplasts and mitochondria were seriously damaged. All these results firstly confirmed that deinoxanthin as the efficient and eco-environmental algicidal compound has potential to be used for controlling harmful algal blooms through overproduction of ROS. Copyright © 2015 Elsevier B.V. All rights reserved.

Description of Deinococcus oregonensis sp. nov., from biological soil crusts in the Southwestern arid lands of the United States of America.

PubMed

Gundlapally, Sathyanarayana Reddy; Garcia-Pichel, Ferran

2017-01-01

Biological soil crusts are distinct habitats, harbor unique prokaryotic diversity and gave an impetus to isolate novel species. In the present study, a pink-pigmented bacterium, (OR316-6 T ), was isolated from biological soil crusts using oligotrophic BG11-PGY medium. Strain OR316-6 T was Gram-positive, short rods, non-motile and non-spore forming. Cells were positive for catalase, oxidase and β-galactosidase and negative for most of the enzymatic activities. The major fatty acids present were C 16:0 , C 17:0 , and C 16:1 ω7c and contained MK-8 and MK-10 as the predominant menaquinones. The cell wall peptidoglycan was of A3β variant with L-ornithine as the diamino acid. Based on the above characteristics, strain OR316-6 T was assigned to the genus Deinococcus. The phylogenetic analysis indicated that strain OR316-6 T was closely related to D. aquatilis DSM 23025 T with a 16S rRNA gene similarity of 99.3 % and clustered with a bootstrap value of 100 %. DNA-DNA similarity between strain OR316-6 T and D. aquatilis DSM 23025 T was 37.0 % indicating that strain OR316-6 T was a novel species. Further, DNA fingerprinting of stains OR316-6 T and D. aquatilis DSM 23035 T demonstrated that both strains were related to each other with a similarity coefficient of only 0.32 and supported the species status to strain OR316-6 T . In addition, phenotypic characteristics distinguished strain OR316-6 T from D. aquatilis DSM 23025 T . Based on the cumulative differences, strain OR316-16 T exhibited with its closely related species, it was identified as a novel species and proposed the name Deinococcus oregonensis sp. nov. The type strain is D. oregonensis sp. nov. (OR316-6 T  = JCM 13503 T  = DSM 17762 T ).

Metagenomic Evaluation of Bacterial and Archaeal Diversity in the Geothermal Hot Springs of Manikaran, India

PubMed Central

Pathak, Ashish; Green, Stefan J.; Joshi, Amit; Chauhan, Ashvini

2015-01-01

Bacterial and archaeal diversity in geothermal spring water were investigated using 16S rRNA gene amplicon metagenomic sequencing. This revealed the dominance of Firmicutes, Aquificae, and the Deinococcus-Thermus group in this thermophilic environment. A number of sequences remained taxonomically unresolved, indicating the presence of potentially novel microbes in this unique habitat. PMID:25700403

Wind driven saltation: a hitherto overlooked challenge for life on Mars

NASA Astrophysics Data System (ADS)

Bak, Ebbe; Goul, Michael; Rasmussen, Martin; Moeller, Ralf; Nørnberg, Per; Knak Jensen, Svend; Finster, Kai

2017-04-01

The Martian surface is a hostile environment characterized by low water availability, low atmospheric pressure and high UV and ionizing radiation. Furthermore, wind-driven saltation leads to abrasion of silicates with a production of reactive surface sites and, through triboelectric charging, a release of electrical discharges with a concomitant production of reactive oxygen species. While the effects of low water availability, low pressure and radiation have been extensively studied in relation to the habitability of the Martian surface and the preservation of organic biosignatures, the effects of wind-driven saltation have hitherto been ignored. In this study, we have investigated the effect of exposing bacteria to wind-abraded silicates and directly to wind-driven saltation on Mars in controlled laboratory simulation experiments. Wind-driven saltation was simulated by tumbling mineral samples in a Mars-like atmosphere in sealed quartz ampoules. The effects on bacterial survival and structure were evaluated by colony forming unit counts in combination with scanning electron microscopy, quantitative polymerase chain reaction and life/dead-staining with flow cytometry. The viability of vegetative cells of P. putida, B. subtilis and D. radiodurans in aqueous suspensions was reduced by more than 99% by exposure to abraded basalt, while the viability of B. subtilis endospores was unaffected. B. subtilis mutants lacking different spore components were likewise highly resistant to the exposure to abraded basalt, which indicates that the resistance of spores is not associated with any specific spore component. We found a significant but reduced effect of abraded quartz and we suggest that the stress effect of abraded silicates is induced by a production of reactive oxygen species and hydroxyl radicals produced by Fenton-like reactions in the presence of transition metals. Direct exposure to simulated saltation had a dramatic effect on both D. radiodurans cells and B. subtilis spore with a more than 99.9% decrease in survival after 17 days. The high susceptibility of the usually multi-resistant D. radiodurans cells and B. sublitis spores to the effects of wind-driven saltation indicates that wind abraded silicates as well as direct exposure to saltation represent a considerable stress for microorganisms at the Martian surface, which may have limited the chance of indigenous life, could limit the risk of forward contamination and may have degraded potential organic biosignatures.

Scanning Tunneling Microscopy, Atomic Force Microscopy, and Related Techniques.

DTIC Science & Technology

1992-06-15

images of the heaoal ekdprotein monolayer pressed powder samples of pismO claim and sea urchin shells found ~ ~ sx inteotrcelwl fDincoccu radioduran...can be in- Semiconductor Substrates. The atomic structure of sem - vastigated using AFM but has not been as extensively re- iconductor-detal interfaces...from SEM mage (D99). Komaica and p-type Si(00) and p-n junctions formed by implantation of ANALYTICAL CHEMISTRY. VOL 84, NO. 12. JILNE 18. 1992 121R

Investigation of detection conditions of captured microbes in space with PCR Microbes capture experiment on ISS proposed in "Tanpopo" mission

NASA Astrophysics Data System (ADS)

Kawaguchi, Yuko; Sugino, Tomohiro; Yang, Yinjie; Yoshimura, Yoshitaka; Tsuji, Takashi; Kobayashi, Kensei; Tabata, Makoto; Hashimoto, Hirofumi; Mita, Hajime; Imai, Eiichi; Kawai, Hideyuki; Okudaira, Kyoko; Hasegawa, Sunao; Yamashita, Masamichi; Yano, Hajime; Yokobori, Shin-Ichi; Yamagishi, Akihiko

Terrestrial life may fly off into outer space by volcanic eruption meteorological impacts, and so on. Microbes have been collected from high altitude up to 70 km since 1936 [1]. We also isolated microbes at high altitude up to 35 km using an airplane and balloons [2, 3]. The two isolates of these microbes are new species, one of which shows higher UV ray tolerance than Deinococcus radiodurans [2, 3]. On the other hand, there is a hypothesis on the origin of terrestrial life called panspermia [4, 5], in which terrestrial life is thought to have come from space (or astronomical bodies other than Earth). This hypothesis suggests that life may migrate between Earth and other planets. If microbes were to exist at the high altitude of low earth orbit (400 km), it would endorse the possibility of interplanetary migration of terrestrial lifeWe proposed, the Tanpopo mission to examine interplanetary migration of microbes and organic compounds on Japan Experimental Module (JEM) of the International Space Station (ISS). We will capture micro-particles including microbes and micro-meteoroids at the altitude of ISS orbit (400 km) with ultra low-density aerogel exposed to space for a given period of time. After retreaving the aerogel, we will investigate captured micro particles and tracks followed by microbiological, organic chemical and mineralogical analyses.Captured particles will be analyzed after the initial curation of the aerogel and tracks. Particles potentially containing microbes will be used for PCR amplification of small subunit (ss) rRNA gene followed by DNA sequencing. Comparision between the determined sequences and known ss rRNA gene sequences of terrestrial organisms will suggest the origin and properties of the organism.The density of microbes at the ISS altitude might be quite low, and microbe cell number on each captured particle may be quite limited. Therefore, it is necessary to establish the effective PCR procedure for quite small amount of DNA template in the presence of other materials such as clay and aerogel.We will report current status of the PCR identification of microbes from test samples. The PCR conditions to amplify ss rRNA gene from quite small number of cells and quite low concentration of genomic DNA with/without clay and aerogel are examined. References. [1] Y. Yang et al. (2009) Biol. Sci. in Space, 23, 151-163[2] Y. Yang et al. (2009) Int. J. Syst. Evol. Microbiol, 59, 1862-1866[3] Y. Yang et al. (2010) Int. J. Syst. Evol. Microbiol, (in press)[4] S. Arrhenius (1908) Worlds in the Making-the Evolution of the Universe. Harper and Brothers Publishers.[5] F. Crick (1981) Life Itself. Simon Schuster.

A Metagenomic Analysis of Microbial Contamination in Aviation Fuels

DTIC Science & Technology

2009-03-01

classification by the RDP Classifier, sequences similar to members of the Acidobacteria, Actinobacteria , Bacteroidetes, Chloroflexi, Cyanobacteria... Actinobacteria 85 63 4 152 Bacteroidetes 5 0 0 5 Chloroflexi 7 0 0 7 Cyanobacteria 56 0 0 56 Deinococcus-Thermus 2 0 0 2 Firmicutes 83 99 2 184...Members of the Proteobacteria, Firmicutes and Actinobacteria were represented in all three fuel types; in Jet A and Biodiesel they were the only

Microbiological investigations on the water of a thermal bath at Budapest.

PubMed

Szuróczki, Sára; Kéki, Zsuzsa; Káli, Szandra; Lippai, Anett; Márialigeti, Károly; Tóth, Erika

2016-06-01

Thermal baths are unique aquatic environments combining a wide variety of natural and anthropogenic ecological factors, which also appear in their microbiological state. There is limited information on the microbiology of thermal baths in their complexity, tracking community shifts from the thermal wells to the pools. In the present study, the natural microbial community of well and pool waters in Gellért bath was studied in detail by cultivation-based techniques. To isolate bacteria, 10% R2A and minimal synthetic media (with "bath water") with agar-agar and gellan gum were used after prolonged incubation time; moreover, polyurethane blocks covered with media were also applied. Strains were identified by sequencing their 16S rRNA gene after grouping them by amplified rDNA restriction analysis. From each sample, the dominance of Alphaproteobacteria was characteristic though their diversity differed among samples. Members of Actinobacteria, Firmicutes, Beta- and Gamma-proteobacteria, Deinococcus-Thermus, and Bacteroidetes were also identified. Representatives of Deinococcus-Thermus phylum appeared only in the pool water. The largest groups in the pool water belonged to the Tistrella and Chelatococcus genera. The most dominant member in the well water was a new taxon, its similarity to Hartmannibacter diazotrophicus as closest relative was 93.93%.

The death mechanism of the harmful algal bloom species Alexandrium tamarense induced by algicidal bacterium Deinococcus sp. Y35

PubMed Central

Li, Yi; Zhu, Hong; Lei, Xueqian; Zhang, Huajun; Cai, Guanjing; Chen, Zhangran; Fu, Lijun; Xu, Hong; Zheng, Tianling

2015-01-01

Harmful algal blooms (HABs) cause a variety of deleterious effects on aquatic ecosystems, especially the toxic dinoflagellate Alexandrium tamarense, which poses a serious threat to marine economic and human health based on releasing paralytic shellfish poison into the environment. The algicidal bacterium Deinococcus sp. Y35 which can induce growth inhibition on A. tamarense was used to investigate the functional mechanism. The growth status, reactive oxygen species (ROS) content, photosynthetic system and the nuclear system of algal cells were determined under algicidal activity. A culture of strain Y35 not only induced overproduction of ROS in algal cells within only 0.5 h of treatment, also decrease the total protein content as well as the response of the antioxidant enzyme. Meanwhile, lipid peroxidation was induced and cell membrane integrity was lost. Photosynthetic pigments including chlorophyll a and carotenoid decreased along with the photosynthetic efficiency being significantly inhibited. At the same time, photosynthesis-related gene expression showed down-regulation. More than, the destruction of cell nuclear structure and inhibition of proliferating cell nuclear antigen (PCNA) related gene expression were confirmed. The potential functional mechanism of the algicidal bacterium on A. tamarense was investigated and provided a novel viewpoint which could be used in HABs control. PMID:26441921

The death mechanism of the harmful algal bloom species Alexandrium tamarense induced by algicidal bacterium Deinococcus sp. Y35.

PubMed

Li, Yi; Zhu, Hong; Lei, Xueqian; Zhang, Huajun; Cai, Guanjing; Chen, Zhangran; Fu, Lijun; Xu, Hong; Zheng, Tianling

2015-01-01

Harmful algal blooms (HABs) cause a variety of deleterious effects on aquatic ecosystems, especially the toxic dinoflagellate Alexandrium tamarense, which poses a serious threat to marine economic and human health based on releasing paralytic shellfish poison into the environment. The algicidal bacterium Deinococcus sp. Y35 which can induce growth inhibition on A. tamarense was used to investigate the functional mechanism. The growth status, reactive oxygen species (ROS) content, photosynthetic system and the nuclear system of algal cells were determined under algicidal activity. A culture of strain Y35 not only induced overproduction of ROS in algal cells within only 0.5 h of treatment, also decrease the total protein content as well as the response of the antioxidant enzyme. Meanwhile, lipid peroxidation was induced and cell membrane integrity was lost. Photosynthetic pigments including chlorophyll a and carotenoid decreased along with the photosynthetic efficiency being significantly inhibited. At the same time, photosynthesis-related gene expression showed down-regulation. More than, the destruction of cell nuclear structure and inhibition of proliferating cell nuclear antigen (PCNA) related gene expression were confirmed. The potential functional mechanism of the algicidal bacterium on A. tamarense was investigated and provided a novel viewpoint which could be used in HABs control.

Plants of the fynbos biome harbour host species-specific bacterial communities.

PubMed

Miyambo, Tsakani; Makhalanyane, Thulani P; Cowan, Don A; Valverde, Angel

2016-08-01

The fynbos biome in South Africa is globally recognised as a plant biodiversity hotspot. However, very little is known about the bacterial communities associated with fynbos plants, despite interactions between primary producers and bacteria having an impact on the physiology of both partners and shaping ecosystem diversity. This study reports on the structure, phylogenetic composition and potential roles of the endophytic bacterial communities located in the stems of three fynbos plants (Erepsia anceps, Phaenocoma prolifera and Leucadendron laureolum). Using Illumina MiSeq 16S rRNA sequencing we found that different subpopulations of Deinococcus-Thermus, Alphaproteobacteria, Acidobacteria and Firmicutes dominated the endophytic bacterial communities. Alphaproteobacteria and Actinobacteria were prevalent in P. prolifera, whereas Deinococcus-Thermus dominated in L. laureolum, revealing species-specific host-bacteria associations. Although a high degree of variability in the endophytic bacterial communities within hosts was observed, we also detected a core microbiome across the stems of the three plant species, which accounted for 72% of the sequences. Altogether, it seems that both deterministic and stochastic processes shaped microbial communities. Endophytic bacterial communities harboured putative plant growth-promoting bacteria, thus having the potential to influence host health and growth. © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Cryogenic X-Ray Diffraction Microscopy for Biological Samples

NASA Astrophysics Data System (ADS)

Lima, Enju; Wiegart, Lutz; Pernot, Petra; Howells, Malcolm; Timmins, Joanna; Zontone, Federico; Madsen, Anders

2009-11-01

X-ray diffraction microscopy (XDM) is well suited for nondestructive, high-resolution biological imaging, especially for thick samples, with the high penetration power of x rays and without limitations imposed by a lens. We developed nonvacuum, cryogenic (cryo-) XDM with hard x rays at 8 keV and report the first frozen-hydrated imaging by XDM. By preserving samples in amorphous ice, the risk of artifacts associated with dehydration or chemical fixation is avoided, ensuring the imaging condition closest to their natural state. The reconstruction shows internal structures of intact D. radiodurans bacteria in their natural contrast.

Metagenomic analysis of bacterial and archaeal assemblages in the soil-mousse surrounding a geothermal spring.

PubMed

Bhatia, Sonu; Batra, Navneet; Pathak, Ashish; Joshi, Amit; Souza, Leila; Almeida, Paulo; Chauhan, Ashvini

2015-09-01

The soil-mousse surrounding a geothermal spring was analyzed for bacterial and archaeal diversity using 16S rRNA gene amplicon metagenomic sequencing which revealed the presence of 18 bacterial phyla distributed across 109 families and 219 genera. Firmicutes, Actinobacteria, and the Deinococcus-Thermus group were the predominant bacterial assemblages with Crenarchaeota and Thaumarchaeota as the main archaeal assemblages in this largely understudied geothermal habitat. Several metagenome sequences remained taxonomically unassigned suggesting the presence of a repertoire of hitherto undescribed microbes in this geothermal soil-mousse econiche.

Compositions containing nucleosides and manganese and their uses

DOEpatents

Daly, Michael J.; Gaidamakova, Elena K.; Matrosova, Vera Y.; Levine, Rodney L.; Wehr, Nancy B.

2015-11-17

This invention encompasses methods of preserving protein function by contacting a protein with a composition comprising one or more purine or pyrimidine nucleosides (such as e.g., adenosine or uridine) and an antioxidant (such as e.g., manganese). In addition, the invention encompasses methods of treating and/or preventing a side effect of radiation exposure and methods of preventing a side effect of radiotherapy comprising administration of a pharmaceutically effective amount of a composition comprising one or more purine or pyrimidine nucleosides (such as e.g., adenosine or uridine) and an antioxidant (such as e.g., manganese) to a subject in need thereof. The compositions may comprise D. radiodurans extracts.

Metagenomic analysis of bacterial and archaeal assemblages in the soil-mousse surrounding a geothermal spring

PubMed Central

Bhatia, Sonu; Batra, Navneet; Pathak, Ashish; Joshi, Amit; Souza, Leila; Almeida, Paulo; Chauhan, Ashvini

2015-01-01

The soil-mousse surrounding a geothermal spring was analyzed for bacterial and archaeal diversity using 16S rRNA gene amplicon metagenomic sequencing which revealed the presence of 18 bacterial phyla distributed across 109 families and 219 genera. Firmicutes, Actinobacteria, and the Deinococcus-Thermus group were the predominant bacterial assemblages with Crenarchaeota and Thaumarchaeota as the main archaeal assemblages in this largely understudied geothermal habitat. Several metagenome sequences remained taxonomically unassigned suggesting the presence of a repertoire of hitherto undescribed microbes in this geothermal soil-mousse econiche. PMID:26484255

Cryogenic x-ray diffraction microscopy utilizing high-pressure cryopreservation

NASA Astrophysics Data System (ADS)

Lima, Enju; Chushkin, Yuriy; van der Linden, Peter; Kim, Chae Un; Zontone, Federico; Carpentier, Philippe; Gruner, Sol M.; Pernot, Petra

2014-10-01

We present cryo x-ray diffraction microscopy of high-pressure-cryofixed bacteria and report high-convergence imaging with multiple image reconstructions. Hydrated D. radiodurans cells were cryofixed at 200 MPa pressure into ˜10-μm-thick water layers and their unstained, hydrated cellular environments were imaged by phasing diffraction patterns, reaching sub-30-nm resolutions with hard x-rays. Comparisons were made with conventional ambient-pressure-cryofixed samples, with respect to both coherent small-angle x-ray scattering and the image reconstruction. The results show a correlation between the level of background ice signal and phasing convergence, suggesting that phasing difficulties with frozen-hydrated specimens may be caused by high-background ice scattering.

Quantitative Characterization of the Growth of Deinococcus geothermalis DSM-11302: Effect of Inoculum Size, Growth Medium and Culture Conditions.

PubMed

Bornot, Julie; Molina-Jouve, Carole; Uribelarrea, Jean-Louis; Gorret, Nathalie

2015-08-20

Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great interest to biotechnological prospects. However, the physiology of the extremophile strain Deinococcus geothermalis has scarcely been studied and is not well understood. The physiological behaviour was then studied in well-controlled conditions in flask and bioreactor cultures. The growth of D. geothermalis type strains was compared. Among the strains tested, the strain from the German Collection of Microorganisms (Deutsche Sammlung von Mikroorganismen DSM) DSM-11302 was found to give the highest biomass concentration and growth rate: in a complex medium with glucose, the growth rate reached 0.75 h(-1) at 45 °C. Yeast extract concentration in the medium had significant constitutive and catalytic effects. Furthermore, the results showed that the physiological descriptors were not affected by the inoculum preparation steps. A batch culture of D. geothermalis DSM-11302 on defined medium was carried out: cells grew exponentially with a maximal growth rate of 0.28 h(-1) and D. geothermalis DSM-11302 biomass reached 1.4 g·L(-1) in 20 h. Then, 1.4 gDryCellWeight of biomass (X) was obtained from 5.6 g glucose (Glc) consumed as carbon source, corresponding to a yield of 0.3 CmolX·CmolGlc(-1); cell specific oxygen uptake and carbon dioxide production rates reached 216 and 226 mmol.CmolX(-1)·h(-1), respectively, and the respiratory quotient (QR) value varied from 1.1 to 1.7. This is the first time that kinetic parameters and yields are reported for D. geothermalis DSM-11302 grown on a mineral medium in well-controlled batch culture.

Quantitative Characterization of the Growth of Deinococcus geothermalis DSM-11302: Effect of Inoculum Size, Growth Medium and Culture Conditions

PubMed Central

Bornot, Julie; Molina-Jouve, Carole; Uribelarrea, Jean-Louis; Gorret, Nathalie

2015-01-01

Due to their remarkable resistance to extreme conditions, Deinococcaceae strains are of great interest to biotechnological prospects. However, the physiology of the extremophile strain Deinococcus geothermalis has scarcely been studied and is not well understood. The physiological behaviour was then studied in well-controlled conditions in flask and bioreactor cultures. The growth of D. geothermalis type strains was compared. Among the strains tested, the strain from the German Collection of Microorganisms (Deutsche Sammlung von Mikroorganismen DSM) DSM-11302 was found to give the highest biomass concentration and growth rate: in a complex medium with glucose, the growth rate reached 0.75 h−1 at 45 °C. Yeast extract concentration in the medium had significant constitutive and catalytic effects. Furthermore, the results showed that the physiological descriptors were not affected by the inoculum preparation steps. A batch culture of D. geothermalis DSM-11302 on defined medium was carried out: cells grew exponentially with a maximal growth rate of 0.28 h−1 and D. geothermalis DSM-11302 biomass reached 1.4 g·L−1 in 20 h. Then, 1.4 gDryCellWeight of biomass (X) was obtained from 5.6 g glucose (Glc) consumed as carbon source, corresponding to a yield of 0.3 CmolX·CmolGlc−1; cell specific oxygen uptake and carbon dioxide production rates reached 216 and 226 mmol.CmolX−1·h−1, respectively, and the respiratory quotient (QR) value varied from 1.1 to 1.7. This is the first time that kinetic parameters and yields are reported for D. geothermalis DSM-11302 grown on a mineral medium in well-controlled batch culture. PMID:27682099

Thermophilic bacterial communities inhabiting the microbial mats of "indifferent" and chalybeate (iron-rich) thermal springs: Diversity and biotechnological analysis.

PubMed

Selvarajan, Ramganesh; Sibanda, Timothy; Tekere, Memory

2018-04-01

Microbial mats are occasionally reported in thermal springs and information on such mats is very scarce. In this study, microbial mats were collected from two hot springs (Brandvlei (BV) and Calitzdorp (CA)), South Africa and subjected to scanning electron microscopy (SEM) and targeted 16S rRNA gene amplicon analysis using Next Generation Sequencing (NGS). Spring water temperature was 55°C for Brandvlei and 58°C for Calitzdorp while the pH of both springs was slightly acidic, with an almost identical pH range (6.2-6.3). NGS analysis resulted in a total of 4943 reads, 517 and 736 OTUs for BV and CA at, respectively, a combined total of 14 different phyla in both samples, 88 genera in CA compared to 45 in BV and 37.64% unclassified sequences in CA compared to 27.32% recorded in BV. Dominant bacterial genera in CA microbial mat were Proteobacteria (29.19%), Bacteroidetes (9.41%), Firmicutes (9.01%), Cyanobacteria (6.89%), Actinobacteria (2.65%), Deinococcus-Thermus (2.57%), and Planctomycetes (1.94%) while the BV microbial mat was dominated by Bacteroidetes (47.3%), Deinococcus-Thermus (12.35%), Proteobacteria (7.98%), and Planctomycetes (2.97%). Scanning electron microscopy results showed the presence of microbial filaments possibly resembling cyanobacteria, coccids, rod-shaped bacteria and diatoms in both microbial mats. Dominant genera that were detected in this study have been linked to different biotechnological applications including hydrocarbon degradation, glycerol fermentation, anoxic-fermentation, dehalogenation, and biomining processes. Overall, the results of this study exhibited thermophilic bacterial community structures with high diversity in microbial mats, which have a potential for biotechnological exploitation. © 2017 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Compositional profile of α/β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites

PubMed Central

Jiménez, Diego Javier; Dini-Andreote, Francisco; Ottoni, Júlia Ronzella; de Oliveira, Valéria Maia; van Elsas, Jan Dirk; Andreote, Fernando Dini

2015-01-01

The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; < 5%). Detailed analysis of the genes predicted to encode proteins of the abH08 superfamily revealed a high proportion related to epoxide hydrolases and haloalkane dehalogenases in polluted mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes. PMID:25171437

Survival of Deinococcus geothermalis in Biofilms under Desiccation and Simulated Space and Martian Conditions

NASA Astrophysics Data System (ADS)

Frösler, Jan; Panitz, Corinna; Wingender, Jost; Flemming, Hans-Curt; Rettberg, Petra

2017-05-01

Biofilm formation represents a successful survival strategy for bacteria. In biofilms, cells are embedded in a matrix of extracellular polymeric substances (EPS). As they are often more stress-tolerant than single cells, biofilm cells might survive the conditions present in space and on Mars. To investigate this topic, the bacterium Deinococcus geothermalis was chosen as a model organism due to its tolerance toward desiccation and radiation. Biofilms cultivated on membranes and, for comparison, planktonically grown cells deposited on membranes were air-dried and exposed to individual stressors that included prolonged desiccation, extreme temperatures, vacuum, simulated martian atmosphere, and UV irradiation, and they were exposed to combinations of stressors that simulate space (desiccation + vacuum + UV) or martian (desiccation + Mars atmosphere + UV) conditions. The effect of sulfatic Mars regolith simulant on cell viability during stress was investigated separately. The EPS produced by the biofilm cells contained mainly polysaccharides and proteins. To detect viable but nonculturable (VBNC) cells, cultivation-independent viability indicators (membrane integrity, ATP, 16S rRNA) were determined in addition to colony counts. Desiccation for 2 months resulted in a decrease of culturability with minor changes of membrane integrity in biofilm cells and major loss of membrane integrity in planktonic bacteria. Temperatures between -25°C and +60°C, vacuum, and Mars atmosphere affected neither culturability nor membrane integrity in both phenotypes. Monochromatic (254 nm; ≥1 kJ m-2) and polychromatic (200-400 nm; >5.5 MJ m-2 for planktonic cells and >270 MJ m-2 for biofilms) UV irradiation significantly reduced the culturability of D. geothermalis but did not affect cultivation-independent viability markers, indicating the induction of a VBNC state in UV-irradiated cells. In conclusion, a substantial proportion of the D. geothermalis population remained viable under all stress conditions tested, and in most cases the biofilm form proved advantageous for surviving space and Mars-like conditions.

A freeze-thaw method for disintegration of Escherichia coli cells producing T7 lysozyme used in pBAD expression systems.

PubMed

Wanarska, Marta; Hildebrandt, Piotr; Kur, Józef

2007-01-01

The pLysN plasmid containing the T7 lysozyme gene under control of the lac promoter was constructed to facilitate cell disintegration after expression of recombinant proteins in arabinose-induced expression systems. The usefulness of this plasmid was tested in Escherichia coli TOP10 and E. coli LMG194 cells carrying pBADMHADgeSSB plasmid containing Deinococcus geothermalis SSB protein gene under control of the araBAD promoter. The results showed that low-level expression of T7 lysozyme did not interfere with the target SSB protein production, and that the freezing-thawing treatment was sufficient for disruption of the E. coli cells producing low amounts of T7 lysozyme.

Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites.

PubMed

Jiménez, Diego Javier; Dini-Andreote, Francisco; Ottoni, Júlia Ronzella; de Oliveira, Valéria Maia; van Elsas, Jan Dirk; Andreote, Fernando Dini

2015-05-01

The occurrence of genes encoding biotechnologically relevant α/β-hydrolases in mangrove soil microbial communities was assessed using data obtained by whole-metagenome sequencing of four mangroves areas, denoted BrMgv01 to BrMgv04, in São Paulo, Brazil. The sequences (215 Mb in total) were filtered based on local amino acid alignments against the Lipase Engineering Database. In total, 5923 unassembled sequences were affiliated with 30 different α/β-hydrolase fold superfamilies. The most abundant predicted proteins encompassed cytosolic hydrolases (abH08; ∼ 23%), microsomal hydrolases (abH09; ∼ 12%) and Moraxella lipase-like proteins (abH04 and abH01; < 5%). Detailed analysis of the genes predicted to encode proteins of the abH08 superfamily revealed a high proportion related to epoxide hydrolases and haloalkane dehalogenases in polluted mangroves BrMgv01-02-03. This suggested selection and putative involvement in local degradation/detoxification of the pollutants. Seven sequences that were annotated as genes for putative epoxide hydrolases and five for putative haloalkane dehalogenases were found in a fosmid library generated from BrMgv02 DNA. The latter enzymes were predicted to belong to Actinobacteria, Deinococcus-Thermus, Planctomycetes and Proteobacteria. Our integrated approach thus identified 12 genes (complete and/or partial) that may encode hitherto undescribed enzymes. The low amino acid identity (< 60%) with already-described genes opens perspectives for both production in an expression host and genetic screening of metagenomes. © 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.

Patterns of cell division, DNA base compositions, and fine structures of some radiation-resistant vegetative bacteria found in food

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanders, S.W.; Maxcy, R.B.

1979-01-01

Representative highly radiation-resistant Moraxella-Acinetobacter (M-A), Pseudomonas radiora, Micrococcus radiodurans, and Micrococcus radiophilus exhibited a wide variety of division systems and cell wall characteristics. However, the more resistant M-A possessed unusually thick cell walls, indicating a possible role of the cell wall in radiation resistance in the M-A. Thick septation was present in most of the bacteria studied, but was absent in P. radiora, thus excluding this as a necessity for high resistance. Reliable determination of the number of division planes of the M-A for use as a taxonomic criterion was achieved by the direct observation of dividing cells. The highlymore » resistant M-A were found to divide in multiple planes and had base compositions of 54.0 to 57.5%, unlike typical Moraxella and/or Acinetobacter species. The taxonomic position of most highly resistant bacteria remains unclear.« less

Biofilms and planktonic cells of Deinococcus geothermalis in extreme environments

NASA Astrophysics Data System (ADS)

Panitz, Corinna; Reitz, Guenther; Rabbow, Elke; Rettberg, Petra; Flemming, Hans-Curt; Wingender, Jost; Froesler, Jan

In addition to the several extreme environments on Earth, Space can be considered as just another exceptional environment with a unique mixture of stress factors comprising UV radiation, vacuum, desiccation, temperature, ionizing radiation and microgravity. Life that processes in these environments can depend on the life forms and their state of living. The question is whether there are different strategies for individual microorganisms compared to communities of the same organisms to cope with the different factors of their surroundings. Comparative studies of the survi-val of these communities called biofilms and planktonic cell samples of Deinococcus geothermalis stand at the focal point of the presented investigations. A biofilm is a structured community of microorganisms that live encapsulated in a matrix of extracellular polymeric substances on a surface. Microorganisms living in a biofilm usually have significantly different properties to cooperate than individually living microorganisms of the same species. An advantage of the biofilm is increased resistance to various chemical and physical effects, while the dense extracellular matrix and the outer layer of the cells protect the interior of the microbial consortium. The space experiment BOSS (Biofilm organisms surfing Space) as part the ESA experimental unit EXPOSE R-2 with a planned launch date in July 2014 will be subsequently mounted on the Russian Svesda module outside the ISS. An international team of scientists coordinated by Dr. P. Rettberg will investigate the hypothesis whether microorganisms organized as biofilm outmatch the same microorganisms exposed individually in the long-term survival of the harsh environmental conditions as they occur in space and on Mars. Another protective function in the samples could be dust par-ticles for instance Mars regolith simulant contained inside the biofilms or mixed with the planktonic cells, as additional shelter especially against the extraterrestrial UV radiation. D. geothermalis besides others, like co-cultures of Halomonas muralis and Halococcus morrhuae, Bacillus horneckiae, Chroococcidiopsis CCMEE 029 and Streptomyces + Polaromonas and Arthrobacter strains from volcanic rocks, was involved in the several preparatory test runs at the Planetary and Space Simulation facilities at the German Aerospace Center in Cologne. Results of the already carried out EVTs (Experiment Verification Test) and the SVT (Science verification test) as EXPOSE-R2 mission pre-paration tests, where investigated parameters like dehydration, temperature extremes, extraterrestrial UV radiation, simulated Martian atmosphere, and a Mars-like UV climate were tested individually as well as in combination will be presented. Following exposure to the parameters listed above, the survival of both biofilms and planktonic cells of D. geothermalis was assessed in terms of (i) culturability by colony counts on R2A medium, (ii) membrane integrity by using the Live/Dead differential staining kit, (iii) ATP content by using a commercial luminometric assay, and (iv) the presence of 16S rRNA by fluorescence in situ hybridization. So far, the results suggest that Deinococcus geothermalis remains viable in the desiccated state over weeks to months, whereas culturability, intracellular ATP levels, and membrane integrity were preserved in biofilm cells at a significantly higher level than in planktonic cells. Furthermore, cells of both sample types were able to survive simulated space and Martian conditions and showed high resistance after irradiation with monochromatic and polychromatic UV. The results will contribute to the fundamental understanding of the opportunities and limitations of viability of microorganisms organized in biofilms or as planktonic cells under the extreme environ-mental conditions of space or other planets.

Dose Limits for Man do not Adequately Protect the Ecosystem

DOE Office of Scientific and Technical Information (OSTI.GOV)

Higley, Kathryn A.; Alexakhin, Rudolf M.; McDonald, Joseph C.

2004-08-01

It has been known for quite some time that different organisms display differing degrees of sensitivity to the effects of ionizing radiations. Some microorganisms such as the bacterium Micrococcus radiodurans, along with many species of invertebrates, are extremely radio-resistant. Humans might be categorized as being relatively sensitive to radiation, and are a bit more resistant than some pine trees. Therefore, it could be argued that maintaining the dose limits necessary to protect humans will also result in the protection of most other species of flora and fauna. This concept is usually referred to as the anthropocentric approach. In other words,more » if man is protected then the environment is also adequately protected. The ecocentric approach might be stated as; the health of humans is effectively protected only when the environment is not unduly exposed to radiation. The ICRP is working on new recommendations dealing with the protection of the environment, and this debate should help to highlight a number of relevant issues concerning that topic.« less

Diversity of bacteria in surface ice of Austre Lovénbreen glacier, Svalbard.

PubMed

Zeng, Yin-Xin; Yan, Ming; Yu, Yong; Li, Hui-Rong; He, Jian-Feng; Sun, Kun; Zhang, Fang

2013-05-01

Two 16S rRNA gene clone libraries Cores 1U and 2U were constructed using two ice core samples collected from Austre Lovénbreen glacier in Svalbard. The two libraries yielded a total of 262 clones belonging to 59 phylotypes. Sequences fell into 10 major lineages of the domain Bacteria, including Proteobacteria (alpha, beta, gamma and delta subdivisions), Bacteroidetes, Actinobacteria, Firmicutes, Acidobacteria, Deinococcus-Thermus, Chloroflexi, Planctomycetes, Cyanobacteria and candidate division TM7. Among them, Bacteroidetes, Actinobacteria, Alphaproteobacteria and Cyanobacteria were most abundant. UniFrac data showed no significant differences in community composition between the two ice cores. A total of nineteen bacterial strains from the genera Pseudoalteromonas and Psychrobacter were isolated from the ice cores. Phylogenetic and phenotypic analyses revealed a close relationship between the ice core isolates and bacteria in marine environments, indicating a wide distribution of some bacterial phylotypes in both terrestrial and marine ecosystems.

Putative carotenoid genes expressed under the regulation of Shine-Dalgarno regions in Escherichia coli for efficient lycopene production.

PubMed

Jin, Weiyue; Xu, Xian; Jiang, Ling; Zhang, Zhidong; Li, Shuang; Huang, He

2015-11-01

Putative genes crtE, crtB, and crtI from Deinococcus wulumiqiensis R12, a novel species, were identified by genome mining and were co-expressed using the optimized Shine-Dalgarno (SD) regions to improve lycopene yield. A lycopene biosynthesis pathway was constructed by co-expressing these three genes in Escherichia coli. After optimizing the upstream SD regions and the culture medium, the recombinant strain EDW11 produced 88 mg lycopene g(-1) dry cell wt (780 mg lycopene l(-1)) after 40 h fermentation without IPTG induction, while the strain EDW without optimized SD regions only produced 49 mg lycopene g(-1) dry cell wt (417 mg lycopene l(-1)). Based on the optimization of the upstream SD regions and culture medium, the yield of the strain EDW11 reached a high level during microbial lycopene production until now.

[Phylogenetic diversity of airborne microbes in Qingdao downtown in autumn].

PubMed

Wang, Lin; Song, Zhi-wen; Xu, Ai-ling; Wu, Deng-deng; Xia, Yan

2015-04-01

To determine the community structure of airborne microbes in Qingdao downtown in autumn, the airborne bacteria and fungi were collected by the KC-6120 air sampler and analyzed using the 16S/18S rDNA gene clone library method. Phylogenetic analysis of airborne bacteria showed that they belonged to six major phylogenetic groups: Proteobacteria (78. 8%), Firmicutes (14.6%), Actinobacteria (4.0%), Planctomycetes (1.3%), Cyanobacteria (0.7%), and Deinococcus-Thermus (0.7%). The dominant genera of airborne bacteria included Acinetobacter (39.7%), Staphylococcus (11.3%), Sphingomonas (8.6%), Paracoccus (6.0%) and Massilia (5.3%). The main types of airborne fungi were Ascomycota (97.5%) and Basidiomycota (2.5%). Dominant genera of airborne fungi included Pyrenophora (76.5%), Xylaria (13.6%) and Exophiala (2.5%). The pathogens or conditioned pathogens, such as Acinetobacter, Staphylococcus, or Sphingomonas were detected in the airborne bacteria, whereas certain kinds of fungi, such as P. graminea, X. hypoxylon and Zasmidium angulare that could cause a variety of crop diseases were also detected.

Unexpected diversity during community succession in the apple flower microbiome.

PubMed

Shade, Ashley; McManus, Patricia S; Handelsman, Jo

2013-02-26

Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management. Flowering plants (angiosperms) represent a diverse group of an estimated 400,000 species, and their successful cultivation is essential to agriculture. Yet fundamental knowledge of flower-associated microbiotas remains largely unknown. Even less well understood are the changes that flower microbial communities experience through time. Flowers are particularly conducive to comprehensive temporal studies because they are, by nature, ephemeral organs. Here, we present the first culture-independent time series of bacterial and archaeal communities associated with the flowers of apple, an economically important crop. We found unexpected diversity on apple flowers, including a preponderance of taxa affiliated with Deinococcus-Thermus and TM7, phyla that are understudied but thought to be tolerant to an array of environmental stresses. Our results also suggest that changes in microbial community structure on the apple flower may be predictable over the life of the flower, providing the basis for ecological understanding and disease management.

Protein Oxidation: Key to Bacterial Desiccation Resistance?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fredrickson, Jim K.; Li, Shu-Mei W.; Gaidamakova, E.

For extremely ionizing radiation resistant bacteria, survival has been attributed to protection of proteins from oxidative damage during irradiation, with the result that repair systems survive and function with far greater efficiency during recovery than in sensitive bacteria. Here we examined the relationship between survival of dry-climate soil bacteria and the level of cellular protein oxidation induced by desiccation. Bacteria were isolated from surface soils of the shrub-steppe of the U.S. Department of Energy’s Hanford Site in Washington state. A total of 63 isolates were used for phylogenetic analysis. The majority of isolates were closely related to members of themore » genus Deinococcus, with Chelatococcus, Methylobacterium and Bosea also among the genera identified. Desiccation-resistant isolates accumulated high intracellular manganese and low iron concentrations compared to sensitive bacteria. In vivo, proteins of desiccation-resistant bacteria were protected from oxidative modifications that introduce carbonyl groups in sensitive bacteria during drying. We present the case that survival of bacteria that inhabit dry-climate soils are highly dependent on mechanisms which limit protein oxidation during dehydration.« less

Revealing the gut bacteriome of Dendroctonus bark beetles (Curculionidae: Scolytinae): diversity, core members and co-evolutionary patterns.

PubMed

Hernández-García, Juan Alfredo; Briones-Roblero, Carlos Iván; Rivera-Orduña, Flor N; Zúñiga, Gerardo

2017-10-24

Dendroctonus bark beetles comprise 20 taxonomically recognized species, which are one of the most destructive pine forest pests in North and Central America, and Eurasia. The aims of this study were to characterize the gut bacterial diversity, to determine the core bacteriome and to explore the ecological association between these bacteria and bark beetles. A total of five bacterial phyla were identified in the gut of 13 Dendroctonus species; Proteobacteria was the most abundant, followed by Firmicutes, Fusobacteria, Actinobacteria and Deinococcus-Thermus. The α-diversity was low as demonstrated in previous studies and significant differences in β-diversity were observed. The core bacteriome was composed of Enterobacter, Pantoea, Pseudomonas, Rahnella, Raoultella, and Serratia. The tanglegram between bacteria and bark beetles suggests that members of bacterial community are acquired from the environment, possibly from the host tree. These findings improve the knowledge about the bacterial community composition, and provide the bases to study the metabolic functions of these bacteria, as well as their interaction with these bark beetles.

Molecular mechanism and evolution of guanylate kinase regulation by (p)ppGpp

DOE PAGES

Liu, Kuanqing; Myers, Angela R.; Pisithkul, Tippapha; ...

2015-02-05

The nucleotide (p)ppGpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. In this paper, we characterize the molecular interaction between (p)ppGpp and guanylate kinase (GMK), revealing the importance of this interaction in adaptation to starvation. Combining structural and kinetic analyses, we show that (p)ppGpp binds the GMK active site and competitively inhibits the enzyme. The (p)ppGpp-GMK interaction prevents the conversion of GMP to GDP, resulting in GMP accumulation upon amino acid downshift. Abolishing this interaction leads to excess (p)ppGpp and defective adaptation to amino acid starvation. A surveymore » of GMKs from phylogenetically diverse bacteria shows that the (p)ppGpp-GMK interaction is conserved in members of Firmicutes, Actinobacteria, and Deinococcus-Thermus, but not in Proteobacteria, where (p)ppGpp regulates RNA polymerase (RNAP). Finally, we propose that GMK is an ancestral (p)ppGpp target and RNAP evolved more recently as a direct target in Proteobacteria.« less

Microbial mat of the thermal springs Kuchiger Republic of Buryatia: species composition, biochemical properties and electrogenic activity in biofuel cell

NASA Astrophysics Data System (ADS)

Aleksandrovich Yuriev, Denis; Viktorovna Zaitseva, Svetlana; Olegovna Zhdanova, Galina; Yurievich Tolstoy, Mikhail; Dondokovna Barkhutova, Darima; Feodorovna Vyatchina, Olga; Yuryevna Konovalova, Elena; Iosifovich Stom, Devard

2018-02-01

Electrogenic, molecular and some other properties of a microbial mat isolated from the Kuchiger hot spring (Kurumkansky District, Republic of Buryatia) were studied. Molecular analysis showed that representatives of Proteobacteria (85.5 % of the number of classified bacterial sequences) prevailed in the microbial mat of the Kuchiger springs, among which sulfur bacteria of the genus Thiothrix were the most numerous. In the microbial mat there were bacteria from the families Rhodocyclaceae, Comamonadaceae and Flavobacteriaceae. Phylum Bacteroidetes, Cyanobacteria/Chloroplast, Fusobacteria, Fibrobacteres, Acidobacteria, Chlorobi, Spirochaetes, Verrucomicrobia, Firmicutes, Deinococcus-Thermus, Chloroflexi and Actinobacteria are also noted in the composition of the microbial mat. Under the experimental conditions using Kuchiger-mat 16 as bioagents, glucose and peptone as substrates, the power of BFC was 240 and 221 mW / m2, respectively. When replacing the substrate with sodium acetate, the efficiency of the BFC was reduced by a factor of 10 (20 mW / m2). The prospects of using a microbial mat “Kuchiger-16” as an electrogen in BFC when utilizing alkaline waste water components to generate electricity are discussed.

Injury and destruction of Moraxella-Acinetobacter in the radappertization process. Final Report Apr 78-1 May 80

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maxcy, R.B.; Rowley, D.B.

1981-02-01

Some highly radiation-resistant Moraxella-Acinetobacter (M-A) may survive the radappertization process for meat preservation, because these vegetative bacteria are more resistant than spores to radiation. They are, however, more susceptible than spores to other destructive factors. This work was to determine the effect of some environmental factors that influence the radappertization process. M-A, M. radiodurans, and B. cereus spores varied greatly in their response to changes in temperature of radiation and menstruum in which they were suspended. Available water was critical in response of vegetative cells to radiation. Salts at the level incorporated into meat for the radappertization process suppressed growthmore » of both injured and uninjured M-A. This effect was attributed to reduction in water activity of the menstruum. Freezing and thawing of M-A indicated some destruction and some injury. The injured cells recovered during subsequent incubation. Thus, specific food products and conditions of radappertization must be considered for setting processing parameters. When all the factors of injury, destruction, and suppression of microbial growth are considered in the radappertization process, it is apparent there is little likelihood any of the low number of naturally occurring M-A cells would survive.« less

Community variability of bacteria in alpine snow (Mont Blanc) containing Saharan dust deposition and their snow colonisation potential.

PubMed

Chuvochina, Maria S; Marie, Dominique; Chevaillier, Servanne; Petit, Jean-Robert; Normand, Philippe; Alekhina, Irina A; Bulat, Sergey A

2011-01-01

Microorganisms uplifted during dust storms survive long-range transport in the atmosphere and could colonize high-altitude snow. Bacterial communities in alpine snow on a Mont Blanc glacier, associated with four depositions of Saharan dust during the period 2006-2009, were studied using 16S rRNA gene sequencing and flow cytometry. Also, sand from the Tunisian Sahara, Saharan dust collected in Grenoble and Mont Blanc snow containing no Saharan dust (one sample of each) were analyzed. The bacterial community composition varied significantly in snow containing four dust depositions over a 3-year period. Out of 61 phylotypes recovered from dusty snow, only three phylotypes were detected in more than one sample. Overall, 15 phylotypes were recognized as potential snow colonizers. For snow samples, these phylotypes belonged to Actinobacteria, Proteobacteria and Cyanobacteria, while for Saharan sand/dust samples they belonged to Actinobacteria, Bacteroidetes, Deinococcus-Thermus and Proteobacteria. Thus, regardless of the time-scale, Saharan dust events can bring different microbiota with no common species set to alpine glaciers. This seems to be defined more by event peculiarities and aeolian transport conditions than by the bacterial load from the original dust source.

Spatial distribution of microbial communities in the shallow submarine alkaline hydrothermal field of the Prony Bay, New Caledonia.

PubMed

Quéméneur, Marianne; Bes, Méline; Postec, Anne; Mei, Nan; Hamelin, Jérôme; Monnin, Christophe; Chavagnac, Valérie; Payri, Claude; Pelletier, Bernard; Guentas-Dombrowsky, Linda; Gérard, Martine; Pisapia, Céline; Gérard, Emmanuelle; Ménez, Bénédicte; Ollivier, Bernard; Erauso, Gaël

2014-12-01

The shallow submarine hydrothermal field of the Prony Bay (New Caledonia) discharges hydrogen- and methane-rich fluids with low salinity, temperature (< 40°C) and high pH (11) produced by the serpentinization reactions of the ultramafic basement into the lagoon seawater. They are responsible for the formation of carbonate chimneys at the lagoon seafloor. Capillary electrophoresis single-strand conformation polymorphism fingerprinting, quantitative polymerase chain reaction and sequence analysis of 16S rRNA genes revealed changes in microbial community structure, abundance and diversity depending on the location, water depth, and structure of the carbonate chimneys. The low archaeal diversity was dominated by few uncultured Methanosarcinales similar to those found in other serpentinization-driven submarine and subterrestrial ecosystems (e.g. Lost City, The Cedars). The most abundant and diverse bacterial communities were mainly composed of Chloroflexi, Deinococcus-Thermus, Firmicutes and Proteobacteria. Functional gene analysis revealed similar abundance and diversity of both Methanosarcinales methanoarchaea, and Desulfovibrionales and Desulfobacterales sulfate-reducers in the studied sites. Molecular studies suggest that redox reactions involving hydrogen, methane and sulfur compounds (e.g. sulfate) are the energy driving forces of the microbial communities inhabiting the Prony hydrothermal system.

Characterization of 15 selected coccal bacteria isolated from Antarctic rock and soil samples from the McMurdo-Dry Valleys (South-Victoria Land)

NASA Technical Reports Server (NTRS)

Siebert, J.; Hirsch, P.; Friedmann, E. I. (Principal Investigator)

1988-01-01

Approximately 1500 cultures of microorganisms were isolated from rocks and soils of the Ross Desert (McMurdo-Dry Valleys). From these, 15 coccoid strains were chosen for more detailed investigation. They were characterized by morphological, physiological and chemotaxonomical properties. All isolates were Gram-positive, catalase-positive and nonmotile. Six strains showed red pigmentation and could be identified as members of the genera Micrococcus (M. roseus, M. agilis) or Deinococcus. In spite of their coccoid morphology, the remaining nine strains had to be associated with coryneform bacteria (Arthrobacter, Brevibacterium), because of their cell wall composition and G+C ratios. Most of the strains were psychrotrophic, but one strain was even obligately psychrophilic, with a temperature maximum below 20 degrees C. Red cocci had in vitro pH optima above 9.0 although they generally originated from acid samples. Most isolates showed a preference for sugar alcohols and organic acids, compounds which are commonly known to be released by lichens, molds and algae, the other components of the cryptoendolithic ecosystem. These properties indicate that our strains are autochthonous members of the natural Antarctic microbial population.

Correlated motion of protein subdomains and large-scale conformational flexibility of RecA protein filament

NASA Astrophysics Data System (ADS)

Yu, Garmay; A, Shvetsov; D, Karelov; D, Lebedev; A, Radulescu; M, Petukhov; V, Isaev-Ivanov

2012-02-01

Based on X-ray crystallographic data available at Protein Data Bank, we have built molecular dynamics (MD) models of homologous recombinases RecA from E. coli and D. radiodurans. Functional form of RecA enzyme, which is known to be a long helical filament, was approximated by a trimer, simulated in periodic water box. The MD trajectories were analyzed in terms of large-scale conformational motions that could be detectable by neutron and X-ray scattering techniques. The analysis revealed that large-scale RecA monomer dynamics can be described in terms of relative motions of 7 subdomains. Motion of C-terminal domain was the major contributor to the overall dynamics of protein. Principal component analysis (PCA) of the MD trajectories in the atom coordinate space showed that rotation of C-domain is correlated with the conformational changes in the central domain and N-terminal domain, that forms the monomer-monomer interface. Thus, even though C-terminal domain is relatively far from the interface, its orientation is correlated with large-scale filament conformation. PCA of the trajectories in the main chain dihedral angle coordinate space implicates a co-existence of a several different large-scale conformations of the modeled trimer. In order to clarify the relationship of independent domain orientation with large-scale filament conformation, we have performed analysis of independent domain motion and its implications on the filament geometry.

Bacterial communities in pigmented biofilms formed on the sandstone bas-relief walls of the Bayon Temple, Angkor Thom, Cambodia.

PubMed

Kusumi, Asako; Li, Xianshu; Osuga, Yu; Kawashima, Arata; Gu, Ji-Dong; Nasu, Masao; Katayama, Yoko

2013-01-01

The Bayon temple in Angkor Thom, Cambodia has shown serious deterioration and is subject to the formation of various pigmented biofilms. Because biofilms are damaging the bas-reliefs, low reliefs engraved on the surface of sandstone, information about the microbial community within them is indispensable to control biofilm colonization. PCR-denaturing gradient gel electrophoresis (DGGE) analysis of biofilm samples from the pigmented sandstone surfaces showed that the bacterial community members in the biofilms differed clearly from those in the air and had low sequence similarity to database sequences. Non-destructive sampling of biofilm revealed novel bacterial groups of predominantly Rubrobacter in salmon pink biofilm, Cyanobacteria in chrome green biofilm, Cyanobacteria and Chloroflexi in signal violet biofilm, Chloroflexi in black gray biofilm, and Deinococcus-Thermus, Cyanobacteria, and Rubrobacter in blue green biofilm. Serial peeling-off of a thick biofilm by layers with adhesive sheets revealed a stratified structure: the blue-green biofilm, around which there was serious deterioration, was very rich in Cyanobacteria near the surface and Chloroflexi in deep layer below. Nitrate ion concentrations were high in the blue-green biofilm. The characteristic distribution of bacteria at different biofilm depths provides valuable information on not only the biofilm formation process but also the sandstone weathering process in the tropics.

Complete Genome of the Starch-Degrading Myxobacteria Sandaracinus amylolyticus DSM 53668T

PubMed Central

Sharma, Gaurav; Khatri, Indu; Subramanian, Srikrishna

2016-01-01

Myxobacteria are members of δ-proteobacteria and are typified by large genomes, well-coordinated social behavior, gliding motility, and starvation-induced fruiting body formation. Here, we report the 10.33 Mb whole genome of a starch-degrading myxobacterium Sandaracinus amylolyticus DSM 53668T that encodes 8,962 proteins, 56 tRNA, and two rRNA operons. Phylogenetic analysis, in silico DNA-DNA hybridization and average nucleotide identity reveal its divergence from other myxobacterial species and support its taxonomic characterization into a separate family Sandaracinaceae, within the suborder Sorangiineae. Sequence similarity searches using the Carbohydrate-active enzymes (CAZyme) database help identify the enzyme repertoire of S. amylolyticus involved in starch, agar, chitin, and cellulose degradation. We identified 16 α-amylases and two γ-amylases in the S. amylolyticus genome that likely play a role in starch degradation. While many of the amylases are seen conserved in other δ-proteobacteria, we notice several novel amylases acquired via horizontal transfer from members belonging to phylum Deinococcus-Thermus, Acidobacteria, and Cyanobacteria. No agar degrading enzyme(s) were identified in the S. amylolyticus genome. Interestingly, several putative β-glucosidases and endoglucanases proteins involved in cellulose degradation were identified. However, the absence of cellobiohydrolases/exoglucanases corroborates with the lack of cellulose degradation by this bacteria. PMID:27358428

Microbial and viral-like rhodopsins present in coastal marine sediments from four polar and subpolar regions

DOE Office of Scientific and Technical Information (OSTI.GOV)

López, José L.; Golemba, Marcelo; Hernández, Edgardo

Rhodopsins are broadly distributed. In this work, we analyzed 23 metagenomes corresponding to marine sediment samples from four regions that share cold climate conditions (Norway; Sweden; Argentina and Antarctica). In order to investigate the genes evolution of viral rhodopsins, an initial set of 6224 bacterial rhodopsin sequences according to COG5524 were retrieved from the 23 metagenomes. After selection by the presence of transmembrane domains and alignment, 123 viral (51) and non-viral (72) sequences (>50 amino acids) were finally included in further analysis. Viral rhodopsin genes were homologs of Phaeocystis globosa virus and Organic lake Phycodnavirus. Non-viral microbial rhodopsin genes weremore » ascribed to Bacteroidetes, Planctomycetes, Firmicutes, Actinobacteria, Cyanobacteria, Proteobacteria, Deinococcus-Thermus and Cryptophyta and Fungi. A rescreening using Blastp, using as queries the viral sequences previously described, retrieved 30 sequences (>100 amino acids). Phylogeographic analysis revealed a geographical clustering of the sequences affiliated to the viral group. This clustering was not observed for the microbial non-viral sequences. The phylogenetic reconstruction allowed us to propose the existence of a putative ancestor of viral rhodopsin genes related to Actinobacteria and Chloroflexi. This is the first report about the existence of a phylogeographic association of the viral rhodopsin sequences from marine sediments.« less

Changes in the Bacterial Community of Soil from a Neutral Mine Drainage Channel

PubMed Central

Pereira, Letícia Bianca; Vicentini, Renato; Ottoboni, Laura M. M.

2014-01-01

Mine drainage is an important environmental disturbance that affects the chemical and biological components in natural resources. However, little is known about the effects of neutral mine drainage on the soil bacteria community. Here, a high-throughput 16S rDNA pyrosequencing approach was used to evaluate differences in composition, structure, and diversity of bacteria communities in samples from a neutral drainage channel, and soil next to the channel, at the Sossego copper mine in Brazil. Advanced statistical analyses were used to explore the relationships between the biological and chemical data. The results showed that the neutral mine drainage caused changes in the composition and structure of the microbial community, but not in its diversity. The Deinococcus/Thermus phylum, especially the Meiothermus genus, was in large part responsible for the differences between the communities, and was positively associated with the presence of copper and other heavy metals in the environmental samples. Other important parameters that influenced the bacterial diversity and composition were the elements potassium, sodium, nickel, and zinc, as well as pH. The findings contribute to the understanding of bacterial diversity in soils impacted by neutral mine drainage, and demonstrate that heavy metals play an important role in shaping the microbial population in mine environments. PMID:24796430

Microbiological studies of hot springs in India: a review.

PubMed

Poddar, Abhijit; Das, Subrata K

2018-01-01

The earliest microbiological studies on hot springs in India date from 2003, a much later date compared to global attention in this striking field of study. As of today, 28 out of 400 geothermal springs have been explored following both culturable and non-culturable approaches. The temperatures and pH of the springs are 37-99 °C and 6.8-10, respectively. Several studies have been performed on the description of novel genera and species, characterization of different bio-resources, metagenomics of hot spring microbiome and whole genome analysis of few isolates. 17 strains representing novel species and many thermostable enzymes, including lipase, protease, chitinase, amylase, etc. with potential biotechnological applications have been reported by several authors. Influence of physico-chemical conditions, especially that of temperature, on shaping the hot spring microbiome has been established by metagenomic investigations. Bacteria are the predominant life forms in all the springs with an abundance of phyla Firmicutes, Proteobacteria, Actinobacteria, Thermi, Bacteroidetes, Deinococcus-Thermus and Chloroflexi. In this review, we have discussed the findings on all microbiological studies that have been carried out to date, on the 28 hot springs. Further, the possibilities of extrapolating these studies for practical applications and environmental impact assessment towards protection of natural ecosystem of hot springs have also been discussed.

Phylogeny of Rieske/cytb Complexes with a Special Focus on the Haloarchaeal Enzymes

PubMed Central

Baymann, Frauke; Schoepp-Cothenet, Barbara; Lebrun, Evelyne; van Lis, Robert; Nitschke, Wolfgang

2012-01-01

Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. Haloarchaea are the only organisms found so far that acquired Rieske/cytb complexes via interdomain lateral gene transfer. They encode two Rieske/cytb complexes in their genomes; one of them is found in genetic context with nitrate reductase genes and has its closest relatives among Actinobacteria and the Thermus/Deinococcus group. It is likely to function in nitrate respiration. The second Rieske/cytb complex of Haloarchaea features a split cytochrome b sequence as do Cyanobacteria, chloroplasts, Heliobacteria, and Bacilli. It seems that Haloarchaea acquired this complex from an ancestor of the above-mentioned phyla. Its involvement in the bioenergetic reaction chains of Haloarchaea is unknown. We present arguments in favor of the hypothesis that the ancestor of Haloarchaea, which relied on a highly specialized bioenergetic metabolism, that is, methanogenesis, and was devoid of quinones and most enzymes of anaerobic or aerobic bioenergetic reaction chains, integrated laterally transferred genes into its genome to respond to a change in environmental conditions that made methanogenesis unfavorable. PMID:22798450

Bacterial and archaeal diversities in Yunnan and Tibetan hot springs, China.

PubMed

Song, Zhao-Qi; Wang, Feng-Ping; Zhi, Xiao-Yang; Chen, Jin-Quan; Zhou, En-Min; Liang, Feng; Xiao, Xiang; Tang, Shu-Kun; Jiang, Hong-Chen; Zhang, Chuanlun L; Dong, Hailiang; Li, Wen-Jun

2013-04-01

Thousands of hot springs are located in the north-eastern part of the Yunnan-Tibet geothermal zone, which is one of the most active geothermal areas in the world. However, a comprehensive and detailed understanding of microbial diversity in these hot springs is still lacking. In this study, bacterial and archaeal diversities were investigated in 16 hot springs (pH 3.2-8.6; temperature 47-96°C) in Yunnan Province and Tibet, China by using a barcoded 16S rRNA gene-pyrosequencing approach. Aquificae, Proteobacteria, Firmicutes, Deinococcus-Thermus and Bacteroidetes comprised the large portion of the bacterial communities in acidic hot springs. Non-acidic hot springs harboured more and variable bacterial phyla than acidic springs. Desulfurococcales and unclassified Crenarchaeota were the dominated groups in archaeal populations from most of the non-acidic hot springs; whereas, the archaeal community structure in acidic hot springs was simpler and characterized by Sulfolobales and Thermoplasmata. The phylogenetic analyses showed that Aquificae and Crenarchaeota were predominant in the investigated springs and possessed many phylogenetic lineages that have never been detected in other hot springs in the world. Thus findings from this study significantly improve our understanding of microbial diversity in terrestrial hot springs. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Characterization of Early Microbial Communities on Volcanic Deposits along a Vegetation Gradient on the Island of Miyake, Japan

PubMed Central

Guo, Yong; Fujimura, Reiko; Sato, Yoshinori; Suda, Wataru; Kim, Seok-won; Oshima, Kenshiro; Hattori, Masahira; Kamijo, Takashi; Narisawa, Kazuhiko; Ohta, Hiroyuki

2014-01-01

The 2000 eruption of Mount Oyama on the island of Miyake (Miyake-jima) created a unique opportunity to study the early ecosystem development on newly exposed terrestrial substrates. In this study, bacterial and fungal communities on 9- and 11-year-old volcanic deposits at poorly to fully vegetation-recovered sites in Miyake-jima, Japan, were characterized by conventional culture-based methods and pyrosequencing of 16S rRNA and 18S rRNA genes. Despite the differences in the vegetation cover, the upper volcanic deposit layer samples displayed low among-site variation for chemical properties (pH, total organic carbon, and total nitrogen) and microbial population densities (total direct count and culturable count). Statistical analyses of pyrosequencing data revealed that the microbial communities of volcanic deposit samples were phylogenetically diverse, in spite of very low-carbon environmental conditions, and their diversity was comparable to that in the lower soil layer (buried soil) samples. Comparing with the microbial communities in buried soil, the volcanic deposit communities were characterized by the presence of Betaproteobacteria and Gammaproteobacteria as the main bacterial class, Deinococcus- Thermus as the minor bacterial phyla, and Ascomycota as the major fungal phyla. Multivariate analysis revealed that several bacterial families and fungal classes correlated positively or negatively with plant species. PMID:24463576

Single molecule analysis of Thermus thermophilus SSB protein dynamics on single-stranded DNA.

PubMed

Zhang, Jichuan; Zhou, Ruobo; Inoue, Jin; Mikawa, Tsutomu; Ha, Taekjip

2014-04-01

Single-stranded (ss) DNA binding (SSB) proteins play central roles in DNA replication, recombination and repair in all organisms. We previously showed that Escherichia coli (Eco) SSB, a homotetrameric bacterial SSB, undergoes not only rapid ssDNA-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssDNA. Whereas the majority of bacterial SSB family members function as homotetramers, dimeric SSB proteins were recently discovered in a distinct bacterial lineage of extremophiles, the Thermus-Deinococcus group. Here we show, using single-molecule fluorescence resonance energy transfer (FRET), that homodimeric bacterial SSB from Thermus thermophilus (Tth) is able to diffuse spontaneously along ssDNA over a wide range of salt concentrations (20-500 mM NaCl), and that TthSSB diffusion can help transiently melt the DNA hairpin structures. Furthermore, we show that two TthSSB molecules undergo transitions among different DNA-binding modes while remaining bound to ssDNA. Our results extend our previous observations on homotetrameric SSBs to homodimeric SSBs, indicating that the dynamic features may be shared among different types of SSB proteins. These dynamic features of SSBs may facilitate SSB redistribution and removal on/from ssDNA, and help recruit other SSB-interacting proteins onto ssDNA for subsequent DNA processing in DNA replication, recombination and repair.

Molecular characterization of natural biofilms from household taps with different materials: PVC, stainless steel, and cast iron in drinking water distribution system.

PubMed

Lin, Wenfang; Yu, Zhisheng; Chen, Xi; Liu, Ruyin; Zhang, Hongxun

2013-09-01

Microorganism in drinking water distribution system may colonize in biofilms. Bacterial 16S rRNA gene diversities were analyzed in both water and biofilms grown on taps with three different materials (polyvinyl chloride (PVC), stainless steel, and cast iron) from a local drinking water distribution system. In total, five clone libraries (440 sequences) were obtained. The taxonomic composition of the microbial communities was found to be dominated by members of Proteobacteria (65.9-98.9 %), broadly distributed among the classes Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria. Other bacterial groups included Firmicutes, Acidobacteria, Bacteroidetes, Cyanobacteria, and Deinococcus-Thermus. Moreover, a small proportion of unclassified bacteria (3.5-10.6 %) were also found. This investigation revealed that the bacterial communities in biofilms appeared much more diversified than expected and more care should be taken to the taps with high bacterial diversity. Also, regular monitor of outflow water would be useful as potentially pathogenic bacteria were detected. In addition, microbial richness and diversity in taps ranked in the order as: PVC < stainless steel < cast iron. All the results interpreted that PVC would be a potentially suitable material for use as tap component in drinking water distribution system.

Ribosome reinitiation at leader peptides increases translation of bacterial proteins.

PubMed

Korolev, Semen A; Zverkov, Oleg A; Seliverstov, Alexandr V; Lyubetsky, Vassily A

2016-04-16

Short leader genes usually do not encode stable proteins, although their importance in expression control of bacterial genomes is widely accepted. Such genes are often involved in the control of attenuation regulation. However, the abundance of leader genes suggests that their role in bacteria is not limited to regulation. Specifically, we hypothesize that leader genes increase the expression of protein-coding (structural) genes via ribosome reinitiation at the leader peptide in the case of a short distance between the stop codon of the leader gene and the start codon of the structural gene. For instance, in Actinobacteria, the frequency of leader genes at a distance of 10-11 bp is about 70 % higher than the mean frequency within the 1 to 65 bp range; and it gradually decreases as the range grows longer. A pronounced peak of this frequency-distance relationship is also observed in Proteobacteria, Bacteroidetes, Spirochaetales, Acidobacteria, the Deinococcus-Thermus group, and Planctomycetes. In contrast, this peak falls to the distance of 15-16 bp and is not very pronounced in Firmicutes; and no such peak is observed in cyanobacteria and tenericutes. Generally, this peak is typical for many bacteria. Some leader genes located close to a structural gene probably play a regulatory role as well.

Bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong, China.

PubMed

Pagaling, Eulyn; Grant, William D; Cowan, Don A; Jones, Brian E; Ma, Yanhe; Ventosa, Antonio; Heaphy, Shaun

2012-07-01

We investigated the bacterial and archaeal diversity in two hot spring microbial mats from the geothermal region of Tengchong in the Yunnan Province, China, using direct molecular analyses. The Langpu (LP) laminated mat was found by the side of a boiling pool with temperature of 60-65 °C and a pH of 8.5, while the Tengchong (TC) streamer mat consisted of white streamers in a slightly acidic (pH 6.5) hot pool outflow with a temperature of 72 °C. Four 16S rRNA gene clone libraries were constructed and restriction enzyme analysis of the inserts was used to identify unique sequences and clone frequencies. From almost 200 clones screened, 55 unique sequences were retrieved. Phylogenetic analysis showed that the LP mat consisted of a diverse bacterial population [Cyanobacteria, Chloroflexi, Chlorobia, Nitrospirae, 'Deinococcus-Thermus', Proteobacteria (alpha, beta and delta subdivisions), Firmicutes, Bacteroidetes and Actinobacteria], while the archaeal population was dominated by methanogenic Euryarchaeota and Crenarchaeota. In contrast, the TC streamer mat consisted of a bacterial population dominated by Aquificae, while the archaeal population also contained Korarchaeota as well as Crenarchaeota and methanogenic Euryarchaeota. These mats harboured clone sequences affiliated to unidentified lineages, suggesting that they are a potential source for discovering novel bacteria and archaea.

Microbial communities established on Mont Blanc summit with Saharan dust deposition

NASA Astrophysics Data System (ADS)

Chuvochina, M.; Alekhina, I.; Normand, P.; Petit, J. R.; Bulat, S.

2009-04-01

Dust originating from the Sahara desert can be uplifted during storms, transported across the Mediterranean towards the Alpine region and deposited during snowfalls. The microbes associated with dust particles can be involved in establishing microbiota in icy environments as well as affect ecosystem and human health. Our objective was to use a culture-free DNA-based approach to assess bacterial content and diversity and furthermore, to identify ‘icy' microbes which could be brought on the Mont Blanc (MtBl) summit with Saharan dust and became living in the snow. Saharan dust fallout on MtBl summit from one event (MB5, event June 2006) vs. control libraries and that from another event (May 2008) were collected in Grenoble (SD, 200 m a.s.l.) and at Col du Dome (MB-SD, 4250 m a.s.l.). Soil from Ksar Ghilane (SS, Saharan desert, Tunisia, March 2008) was taken for overall comparison as a possible source population. Fresh snow falling in Grenoble (85) was collected as example of diversity in this area. To assess the microbial diversity 16S rRNA gene libraries (v3-v5 region) were constructed for corresponding dust-snow samples (MB5, SS, SD, 85 and MB-SD) along with clear snow samples and several controls. For both MB5 and MB-SD samples full-gene technique was evoked in attempt to differentiate reproduced bacteria from damaged DNA. Before sequencing the clones were rybotyped. All clone libraries were distinct in community composition except for some single phylotypes (or closely related groups) overlap. Thus, clone libraries from two different events that were collected at Col du Dome area within 2 year interval (MB5 and MB-SD) were different in community composition except one of the abundant phylotype from MB-SD library (Geodermatophilus sp.) which was shared (98% sequence similarity) with single representative from MB-5 library. These bacteria are pigmented and radiation-resistant, so it could be an indicator of desert origin for our sequences. For MB5 library two Deinococcus-Thermus phylotypes (46.2%) along with A-Proteobacteria and CFB were dominated while for MB-SD library two Actinobacteria phylotypes (29%) with another A-Proteobacteria phylotype were copious. This testify that two dust events are principally different in species composition meaning that any other events can also be different in microbes transferred from Sahara to MtBl summit. Of three other gene libraries (SD, SS and 85) selected as ‘supporting' gene pools for MB-SD two libraries (SD and 85) were strictly different from MB-SD while SS library showed two phylotype groups shared with MB-SD. Among them, one A-Proteobacteria phylotype have been detected in unrelated dust event (Polymenakou et al., 2008). It's worth noticing that one numerous A-Proteobacteria phylotype from MB5 library was closely related (97%) to another numerous phylotype from 85 (Grenoble snow fallout) library despite the events were separated geographically and split in time. Such phylotypes could be present in atmosphere elsewhere. Amongst microbes detected in MtBl dust layers libraries four separate minor phylotypes (three cyanobacteria and Deinococcus sp1) were found in MB5 and two minor phylotypes (uncultured actinobacteria, uncultured alphaproteobacteria) - in MB-SD which could be living (keep safe) in ice and snow. All of them were early discovered in cold ecosystems. Seems to be despite the dominant phylotypes recovered in both dust event gene libraries might have a high chance to be established in a snow as populations the minor phylotypes in the dust microbial load are more important in habiting the snow with dust-providing nutrients. In order to recover the cultures of ‘icy' microbes identified by sequence the attempt was done with Deinococci but we didn't succeed. The full gene and partial gene sub-libraries of the MB5 sample showed different results with respect to observed phylotypes. For example, ‘cold-loving' Cyanobacteria phylotypes were detected only in full gene library while one phylotype related to abundant Deinococcus sp was detected mostly by partial gene PCR approach. This provides extra evidence for microbes (Cyanobacteria spp.) which indeed can be living in snow that follows from their full-size gene sequences. When microbes are dead (DNA is degraded in snow with time like ancient DNA) someone has more possibility to be recovered by partial gene sequences. Several phylotypes related to human (Streptococcus sanguinis, Acinetobacter johnsonii and Helcococcus sp.) and plants pathogens (Sphingomonas melonis, Pseudomonas sp) were detected in association with studied dust events. Based on these primary results another view concerning the microbial transport from Sahara desert to the terrestrial glacier can be drawn. The dust fallout could provide just nutrients than dominant microbial seeds while minor phylotypes can be brought from elsewhere.

Bacterial Composition and Survival on Sahara Dust Particles Transported to the European Alps

PubMed Central

Meola, Marco; Lazzaro, Anna; Zeyer, Josef

2015-01-01

Deposition of Sahara dust (SD) particles is a frequent phenomenon in Europe, but little is known about the viability and composition of the bacterial community transported with SD. The goal of this study was to characterize SD-associated bacteria transported to the European Alps, deposited and entrapped in snow. During two distinct events in February and May 2014, SD particles were deposited and promptly covered by falling snow, thus preserving them in distinct ochre layers within the snowpack. In June 2014, we collected samples at different depths from a snow profile at the Jungfraujoch (Swiss Alps; 3621 m a.s.l.). After filtration, we performed various microbiological and physicochemical analyses of the snow and dust particles therein that originated in Algeria. Our results show that bacteria survive and are metabolically active after the transport to the European Alps. Using high throughput sequencing, we observed distinct differences in bacterial community composition and structure in SD-layers as compared to clean snow layers. Sporulating bacteria were not enriched in the SD-layers; however, phyla with low abundance such as Gemmatimonadetes and Deinococcus-Thermus appeared to be specific bio-indicators for SD. Since many members of these phyla are known to be adapted to arid oligotrophic environments and UV radiation, they are well suited to survive the harsh conditions of long-range airborne transport. PMID:26733988

Biofilm-forming bacteria with varying tolerance to peracetic acid from a paper machine.

PubMed

Rasimus, Stiina; Kolari, Marko; Rita, Hannu; Hoornstra, Douwe; Salkinoja-Salonen, Mirja

2011-09-01

Biofilms cause runnability problems in paper machines and are therefore controlled with biocides. Peracetic acid is usually effective in preventing bulky biofilms. This study investigated the microbiological status of a paper machine where low concentrations (≤ 15 ppm active ingredient) of peracetic acid had been used for several years. The paper machine contained a low amount of biofilms. Biofilm-forming bacteria from this environment were isolated and characterized by 16S rRNA gene sequencing, whole-cell fatty acid analysis, biochemical tests, and DNA fingerprinting. Seventy-five percent of the isolates were identified as members of the subclades Sphingomonas trueperi and S. aquatilis, and the others as species of the genera Burkholderia (B. cepacia complex), Methylobacterium, and Rhizobium. Although the isolation media were suitable for the common paper machine biofoulers Deinococcus, Meiothermus, and Pseudoxanthomonas, none of these were found, indicating that peracetic acid had prevented their growth. Spontaneous, irreversible loss of the ability to form biofilm was observed during subculturing of certain isolates of the subclade S. trueperi. The Sphingomonas isolates formed monoculture biofilms that tolerated peracetic acid at concentrations (10 ppm active ingredient) used for antifouling in paper machines. High pH and low conductivity of the process waters favored the peracetic acid tolerance of Sphingomonas sp. biofilms. This appears to be the first report on sphingomonads as biofilm formers in warm water using industries.

Metagenomic analyses of the dominant bacterial community in the Fildes Peninsula, King George Island (South Shetland Islands)

NASA Astrophysics Data System (ADS)

Foong, Choon Pin; Wong Vui Ling, Clemente Michael; González, Marcelo

2010-08-01

There is little information on the bacterial diversity of the Fildes Peninsula, King George Island. Hence, this study was conducted to determine the bacterial population of sediments and soils from the lakes, river, glacier and an abandoned oil tank area in the Fildes Peninsula, using a metagenomic approach. DNA was extracted from the sediment and soil samples, and analyzed using the 16S rDNA polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). A total of 299 DNA fragments resolved using the DGGE were sequenced. The results of the analysis provided an overview of the predominant groups of bacteria and the diversity of the bacterial communities. The most abundant phyla of bacteria in Fildes Peninsula were Bacteroidetes, Proteobacteria, Acidobacteria, Gemmatimonadetes, Nitrospira, Firmicutes, Actinobacteria, Chloroflexi, Cyanobacteria, Spirochaetes, Deinococcus-Thermus, WS3 and BRC1. All of the sediment samples from the lakes had different representatives of dominant bacterial species. Interestingly, 15% of the operational taxonomic units (OTUs) did not group into any of the existing phyla in the Ribosomal Database Project (RDP). One of the OTUs had a similarity of <0.90 when compared to the GenBank sequences and probably was a novel bacterium specific to that location. The majority of the bacterial 16S rDNA sequences were found to be closely related to those found elsewhere.

Tissue age and plant genotype affect the microbiota of apple and pear bark.

PubMed

Arrigoni, Elena; Antonielli, Livio; Pindo, Massimo; Pertot, Ilaria; Perazzolli, Michele

2018-06-01

Plant tissues host complex fungal and bacterial communities, and their composition is determined by host traits such as tissue age, plant genotype and environmental conditions. Despite the importance of bark as a possible reservoir of plant pathogenic microorganisms, little is known about the associated microbial communities. In this work, we evaluated the composition of fungal and bacterial communities in the pear (Abate and Williams cultivars) and apple (Golden Delicious and Gala cultivars) bark of three/four-year-old shoots (old bark) or one-year-old shoots (young bark), using a meta-barcoding approach. The results showed that both fungal and bacterial communities are dominated by genera with ubiquitous attitudes, such as Aureobasidium, Cryptococcus, Deinococcus and Hymenobacter, indicating intense microbial migration to surrounding environments. The shoot age, plant species and plant cultivar influenced the composition of bark fungal and bacterial communities. In particular, bark communities included potential biocontrol agents that could maintain an equilibrium with potential plant pathogens. The abundance of fungal (e.g. Alternaria, Penicillium, Rosellinia, Stemphylium and Taphrina) and bacterial (e.g. Curtobacterium and Pseudomonas) plant pathogens was affected by bark age and host genotype, as well as those of fungal genera (e.g. Arthrinium, Aureobasidium, Rhodotorula, Sporobolomyces) and bacterial genera (e.g. Bacillus, Brevibacillus, Methylobacterium, Sphingomonas and Stenotrophomonas) with possible biocontrol and plant growth promotion properties. Copyright © 2018 Elsevier GmbH. All rights reserved.

Substrate-Specific Development of Thermophilic Bacterial Consortia by Using Chemically Pretreated Switchgrass.

PubMed

Eichorst, Stephanie A; Joshua, Chijioke; Sathitsuksanoh, Noppadon; Singh, Seema; Simmons, Blake A; Singer, Steven W

2014-12-01

Microbial communities that deconstruct plant biomass have broad relevance in biofuel production and global carbon cycling. Biomass pretreatments reduce plant biomass recalcitrance for increased efficiency of enzymatic hydrolysis. We exploited these chemical pretreatments to study how thermophilic bacterial consortia adapt to deconstruct switchgrass (SG) biomass of various compositions. Microbial communities were adapted to untreated, ammonium fiber expansion (AFEX)-pretreated, and ionic-liquid (IL)-pretreated SG under aerobic, thermophilic conditions using green waste compost as the inoculum to study biomass deconstruction by microbial consortia. After microbial cultivation, gravimetric analysis of the residual biomass demonstrated that both AFEX and IL pretreatment enhanced the deconstruction of the SG biomass approximately 2-fold. Two-dimensional nuclear magnetic resonance (2D-NMR) experiments and acetyl bromide-reactive-lignin analysis indicated that polysaccharide hydrolysis was the dominant process occurring during microbial biomass deconstruction, and lignin remaining in the residual biomass was largely unmodified. Small-subunit (SSU) rRNA gene amplicon libraries revealed that although the dominant taxa across these chemical pretreatments were consistently represented by members of the Firmicutes, the Bacteroidetes, and Deinococcus-Thermus, the abundance of selected operational taxonomic units (OTUs) varied, suggesting adaptations to the different substrates. Combining the observations of differences in the community structure and the chemical and physical structure of the biomass, we hypothesize specific roles for individual community members in biomass deconstruction. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Doping Polypyrrole Films with 4-N-Pentylphenylboronic Acid to Enhance Affinity towards Bacteria and Dopamine

PubMed Central

Padiolleau, Laurence; Chen, Xi; Jafari, Mohammad Javad; Sheikhzadeh, Elham; Turner, Anthony P. F.; Jager, Edwin W. H.; Beni, Valerio

2016-01-01

Here we demonstrate the use of a functional dopant as a fast and simple way to tune the chemical affinity and selectivity of polypyrrole films. More specifically, a boronic-functionalised dopant, 4-N-Pentylphenylboronic Acid (PBA), was used to provide to polypyrrole films with enhanced affinity towards diols. In order to prove the proposed concept, two model systems were explored: (i) the capture and the electrochemical detection of dopamine and (ii) the adhesion of bacteria onto surfaces. The chemisensor, based on overoxidised polypyrrole boronic doped film, was shown to have the ability to capture and retain dopamine, thus improving its detection; furthermore the chemisensor showed better sensitivity in comparison with overoxidised perchlorate doped films. The adhesion of bacteria, Deinococcus proteolyticus, Escherichia coli, Streptococcus pneumoniae and Klebsiella pneumoniae, onto the boric doped polypyrrole film was also tested. The presence of the boronic group in the polypyrrole film was shown to favour the adhesion of sugar-rich bacterial cells when compared with a control film (Dodecyl benzenesulfonate (DBS) doped film) with similar morphological and physical properties. The presented single step synthesis approach is simple and fast, does not require the development and synthesis of functional monomers, and can be easily expanded to the electrochemical, and possibly chemical, fabrication of novel functional surfaces and interfaces with inherent pre-defined sensing and chemical properties. PMID:27875555

Comparative metagenomic analysis of the microbial communities in the surroundings of Iheya north and Iheya ridge hydrothermal fields reveals insights into the survival strategy of microorganisms in deep-sea environments

NASA Astrophysics Data System (ADS)

Wang, Hai-liang; Sun, Li

2018-04-01

In this study, metagenomic analysis was performed to investigate the taxonomic compositions and metabolic profiles of the microbial communities inhabiting the sediments in the surroundings of Iheya North and Iheya Ridge hydrothermal fields. The microbial communities in four different samples were found to be dominated by bacteria and, to a much lesser extent, archaea belonging to the phyla Proteobacteria, Actinobacteria, Planctomycetes, Firmicutes, Deinococcus-Thermus, and Nitrospirae, which play important roles in the cycling of carbon, nitrogen, and sulfur. All four microbial communities (i) contained chemoautotrophs and heterotrophs, the former probably fixed CO2 via various carbon fixation pathways, and the latter may degrade organic matters using nitrate and sulfate as electron acceptors, (ii) exhibited an abundance of DNA repair genes and bacterial sulfur oxidation mediated by reverse sulfate reduction, and (iii) harbored bacteria and archaea involved in anaerobic methane oxidation via intra-aerobic denitrification and reverse methanogenesis, which were found for the first time in hydrothermal areas. Furthermore, genes involved in DNA repair, reductive acetyl-CoA pathway, and ammonia metabolism were possibly affected by distance to the vent fields. These findings facilitate our understanding of the strategies of the microbial communities to adapt to the environments in deep sea areas associated with hydrothermal vents.

Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins.

PubMed

Kwon, Soon-Kyeong; Kim, Byung Kwon; Song, Ju Yeon; Kwak, Min-Jung; Lee, Choong Hoon; Yoon, Jung-Hoon; Oh, Tae Kwang; Kim, Jihyun F

2013-01-01

Rhodopsin-containing marine microbes such as those in the class Flavobacteriia play a pivotal role in the biogeochemical cycle of the euphotic zone (Fuhrman JA, Schwalbach MS, Stingl U. 2008. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol. 6:488-494). Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins are important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in the oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a species of Cytophagia, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.

Unexpected Diversity during Community Succession in the Apple Flower Microbiome

PubMed Central

Shade, Ashley; McManus, Patricia S.; Handelsman, Jo

2013-01-01

ABSTRACT Despite its importance to the host, the flower microbiome is poorly understood. We report a culture-independent, community-level assessment of apple flower microbial diversity and dynamics. We collected flowers from six apple trees at five time points, starting before flowers opened and ending at petal fall. We applied streptomycin to half of the trees when flowers opened. Assessment of microbial diversity using tag pyrosequencing of 16S rRNA genes revealed that the apple flower communities were rich and diverse and dominated by members of TM7 and Deinococcus-Thermus, phyla about which relatively little is known. From thousands of taxa, we identified six successional groups with coherent dynamics whose abundances peaked at different times before and after bud opening. We designated the groups Pioneer, Early, Mid, Late, Climax, and Generalist communities. The successional pattern was attributed to a set of prevalent taxa that were persistent and gradually changing in abundance. These taxa had significant associations with other community members, as demonstrated with a cooccurrence network based on local similarity analysis. We also detected a set of less-abundant, transient taxa that contributed to general tree-to-tree variability but not to the successional pattern. Communities on trees sprayed with streptomycin had slightly lower phylogenetic diversity than those on unsprayed trees but did not differ in structure or succession. Our results suggest that changes in apple flower microbial community structure are predictable over the life of the flower, providing a basis for ecological understanding and disease management. PMID:23443006

Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes.

PubMed

Gupta, R S

1998-12-01

The presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes.

Protein Phylogenies and Signature Sequences: A Reappraisal of Evolutionary Relationships among Archaebacteria, Eubacteria, and Eukaryotes

PubMed Central

Gupta, Radhey S.

1998-01-01

The presence of shared conserved insertion or deletions (indels) in protein sequences is a special type of signature sequence that shows considerable promise for phylogenetic inference. An alternative model of microbial evolution based on the use of indels of conserved proteins and the morphological features of prokaryotic organisms is proposed. In this model, extant archaebacteria and gram-positive bacteria, which have a simple, single-layered cell wall structure, are termed monoderm prokaryotes. They are believed to be descended from the most primitive organisms. Evidence from indels supports the view that the archaebacteria probably evolved from gram-positive bacteria, and I suggest that this evolution occurred in response to antibiotic selection pressures. Evidence is presented that diderm prokaryotes (i.e., gram-negative bacteria), which have a bilayered cell wall, are derived from monoderm prokaryotes. Signature sequences in different proteins provide a means to define a number of different taxa within prokaryotes (namely, low G+C and high G+C gram-positive, Deinococcus-Thermus, cyanobacteria, chlamydia-cytophaga related, and two different groups of Proteobacteria) and to indicate how they evolved from a common ancestor. Based on phylogenetic information from indels in different protein sequences, it is hypothesized that all eukaryotes, including amitochondriate and aplastidic organisms, received major gene contributions from both an archaebacterium and a gram-negative eubacterium. In this model, the ancestral eukaryotic cell is a chimera that resulted from a unique fusion event between the two separate groups of prokaryotes followed by integration of their genomes. PMID:9841678

The Role of +4U as an Extended Translation Termination Signal in Bacteria

PubMed Central

Wei, Yulong; Xia, Xuhua

2017-01-01

Termination efficiency of stop codons depends on the first 3′ flanking (+4) base in bacteria and eukaryotes. In both Escherichia coli and Saccharomyces cerevisiae, termination read-through is reduced in the presence of +4U; however, the molecular mechanism underlying +4U function is poorly understood. Here, we perform comparative genomics analysis on 25 bacterial species (covering Actinobacteria, Bacteriodetes, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Proteobacteria, and Spirochaetae) with bioinformatics approaches to examine the influence of +4U in bacterial translation termination by contrasting highly- and lowly-expressed genes (HEGs and LEGs, respectively). We estimated gene expression using the recently formulated Index of Translation Elongation, ITE, and identified stop codon near-cognate transfer RNAs (tRNAs) from well-annotated genomes. We show that +4U was consistently overrepresented in UAA-ending HEGs relative to LEGs. The result is consistent with the interpretation that +4U enhances termination mainly for UAA. Usage of +4U decreases in GC-rich species where most stop codons are UGA and UAG, with few UAA-ending genes, which is expected if UAA usage in HEGs drives up +4U usage. In HEGs, +4U usage increases significantly with abundance of UAA nc_tRNAs (near-cognate tRNAs that decode codons differing from UAA by a single nucleotide), particularly those with a mismatch at the first stop codon site. UAA is always the preferred stop codon in HEGs, and our results suggest that UAAU is the most efficient translation termination signal in bacteria. PMID:27903612

Temporal and spatial variation in the mechanisms used by microorganisms to form methylmercury in the water column of Changshou Lake.

PubMed

Xing, Zhilin; Zhao, Tiantao; Bai, Weiyang; Yang, Xu; Liu, Shuai; Zhang, Lijie

2018-09-30

The microbiome in artificial lake water and its impact on mercury (Hg) methylation remain largely unknown. We selected the largest artificial lake in southeastern china, Changshou Lake (CSL), which has high background levels of Hg, for our investigation of Hg transformation microorganisms. Five different sections of the water column of CSL were sampled during four seasons. The water samples were subjected to analysis of geochemical parameters, various Hg species and microbiome information. High concentrations of total mercury (THg) were detected in CSL in comparison with those found in natural lakes. Significant differences in microbial community structure and Hg species abundance existed among seasons. High dissolved methyl mercury (DMeHg) formation and high bacterial richness and diversity occurred in the fall. The microbiome was dominated by Proteobacteria, Actinobacteria, Bacteroidetes, Deinococcus-Thermus and many unclassified bacteria. Significant correlations were found between seasonal bacterial communities and Hg levels. Hg methylation was strongly linked to the abundance of Cyanobacteria. Methylators, including Syntrophus, Desulfovibrio and Desulfomonile species, were detected only in samples collected in the fall. The results of enzyme functional analyses revealed that many unknown types of bacteria could also be responsible for Hg transformation. This study was the first to investigate the impact of various Hg species on the microbiome of artificial lake water. The findings of this study illuminate the role of seasonal bacteria in Hg transformation. Copyright © 2018 Elsevier Inc. All rights reserved.

Diversity of ionizing radiation-resistant bacteria obtained from the Taklimakan Desert.

PubMed

Yu, Li Zhi-Han; Luo, Xue-Song; Liu, Ming; Huang, Qiaoyun

2015-01-01

So far, little is known about the diversity of the radiation-resistant microbes of the hyperarid Taklimakan Desert. In this study, ionizing radiation (IR)-resistant bacteria from two sites in Xinjiang were investigated. After exposing the arid (water content of 0.8 ± 0.3%) and non-arid (water content of 21.3 ± 0.9%) sediment samples to IR of 3000 Gy using a (60)Co source, a total of 52 γ-radiation-resistant bacteria were isolated from the desert sample. The 16S rRNA genes of all isolates were sequenced. The phylogenetic tree places these isolates into five groups: Cytophaga-Flavobacterium-Bacteroides, Proteobacteria, Deinococcus-Thermus, Firmicutes, and Actinobacteria. Interestingly, this is the first report of radiation-resistant bacteria belonging to the genera Knoellia, Lysobacter, Nocardioides, Paracoccus, Pontibacter, Rufibacter and Microvirga. The 16s rRNA genes of four isolates showed low sequence similarities to those of the published species. Phenotypic analysis showed that all bacteria in this study are able to produce catalase, suggesting that these bacteria possess reactive oxygen species (ROS)-scavenging enzymes. These radiation-resistant bacteria also displayed diverse metabolic properties. Moreover, their radiation resistances were found to differ. The diversity of the radiation-resistant bacteria in the desert provides further ecological support for the hypothesis that the ionizing-radiation resistance phenotype is a consequence of the evolution of ROS-scavenging systems that protect cells against oxidative damage caused by desiccation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular tools to track bacteria responsible for fuel deterioration and microbiologically influenced corrosion.

PubMed

Suflita, Joseph M; Aktas, Deniz F; Oldham, Athenia L; Perez-Ibarra, Beatriz Monica; Duncan, Kathleen

2012-01-01

Investigating the susceptibility of various fuels to anaerobic biodegradation has become complicated with the recognition that the fuels themselves are not sterile. Bacterial DNA could be obtained when various fuels were filtered through a hydrophobic teflon (0.22 μm) membrane filter. Bacterial 16S rRNA genes from these preparations were PCR amplified, cloned, and the resulting libraries sequenced to identify the fuel-borne bacterial communities. The most common sequence, found in algal- and camelina-based biofuels as well as in ultra-low sulfur diesel (ULSD) and F76 diesel, was similar to that of a Tumebacillus. The next most common sequence was similar to Methylobacterium and was found in the biofuels and ULSD. Higher level phylogenetic groups included representatives of the Firmicutes (Bacillus, Lactobacillus and Streptococcus), several Actinobacteria, Deinococcus-Thermus, Chloroflexi, Cyanobacteria, Bacteroidetes, Alphaproteobacteria (Methylobacterium and Sphingomonadales), Betaproteobacteria (Oxalobacteraceae and Burkholderiales) and Deltaproteobacteria. All of the fuel-associated bacterial sequences, except those obtained from a few facultative microorganisms, were from aerobes and only remotely affiliated with sequences that resulted from anaerobic successional events evident when ULSD was incubated with a coastal seawater and sediment inoculum. Thus, both traditional and alternate fuel formulations harbor a characteristic microflora, but these microorganisms contributed little to the successional patterns that ultimately resulted in fuel decomposition, sulfide formation and metal biocorrosion. The findings illustrate the value of molecular approaches to track the fate of bacteria that might come in contact with fuels and potentially contribute to corrosion problems throughout the energy value chain.

Bacterial community in ancient permafrost alluvium at the Mammoth Mountain (Eastern Siberia).

PubMed

Brouchkov, Anatoli; Kabilov, Marsel; Filippova, Svetlana; Baturina, Olga; Rogov, Victor; Galchenko, Valery; Mulyukin, Andrey; Fursova, Oksana; Pogorelko, Gennady

2017-12-15

Permanently frozen (approx. 3.5Ma) alluvial Neogene sediments exposed in the Aldan river valley at the Mammoth Mountain (Eastern Siberia) are unique, ancient, and poorly studied permafrost environments. So far, the structure of the indigenous bacterial community has remained unknown. Use of 16S metagenomic analysis with total DNA isolation using DNA Spin Kit for Soil (MO-Bio) and QIAamp DNA Stool Mini Kit (Qiagen) has revealed the major and minor bacterial lineages in the permafrost alluvium sediments. In sum, 61 Operational Taxonomic Units (OTUs) with 31,239 reads (Qiagen kit) and 15,404 reads (Mo-Bio kit) could be assigned to the known taxa. Only three phyla, Bacteroidetes, Proteobacteria and Firmicutes, comprised >5% of the OTUs abundance and accounted for 99% of the total reads. OTUs pertaining to the top families (Chitinophagaceae, Caulobacteraceae, Sphingomonadaceae, Bradyrhizobiaceae, Halomonadaceae) held >90% of reads. The abundance of Actinobacteria was less (0.7%), whereas members of other phyla (Deinococcus-Thermus, Cyanobacteria/Chloroplast, Fusobacteria, and Acidobacteria) constituted a minor fraction of reads. The bacterial community in the studied ancient alluvium differs from other permafrost sediments, mainly by predominance of Bacteroidetes (>52%). The diversity of this preserved bacterial community has the potential to cause effects unknown if prompted to thaw and spread with changing climate. Therefore, this study elicits further reason to study how reintroduction of these ancient bacteria could affect the surrounding ecosystem, including current bacterial species. Copyright © 2017 Elsevier B.V. All rights reserved.

Reactive Oxygen Species on the Early Earth and Survival of Bacteria

NASA Technical Reports Server (NTRS)

Balk, Melikea; Mason, Paul; Stams, Alfons J. M.; Smidt, Hauke; Freund, Friedemann; Rothschild, Lynn

2011-01-01

An oxygen-rich atmosphere appears to have been a prerequisite for complex, multicellular life to evolve on Earth and possibly elsewhere in the Universe. However it remains unclear how free oxygen first became available on the early Earth. A potentially important, and as yet poorly constrained pathway, is the production of oxygen through the weathering of rocks and release into the near-surface environment. Reactive Oxygen Species (ROS), as precursors to molecular oxygen, are a key step in this process, and may have had a decisive impact on the evolution of life, present and past. ROS are generated from minerals in igneous rocks during hydrolysis of peroxy defects, which consist of pairs of oxygen anions oxidized to the valence state -1 and during (bio) transformations of iron sulphide minerals. ROS are produced and consumed by intracellular and extracellular reactions of Fe, Mn, C, N, and S species. We propose that, despite an overall reducing or neutral oxidation state of the macroenvironment and the absence of free O2 in the atmosphere, organisms on the early Earth had to cope with ROS in their microenvironments. They were thus under evolutionary pressure to develop enzymatic and other defences against the potentially dangerous, even lethal effects of oxygen and its derived ROS. Conversely it appears that microorganisms learned to take advantage of the enormous reactive potential and energy gain provided by nascent oxygen. We investigate how oxygen might be released through weathering. We test microorganisms in contact with rock surfaces and iron sulphides. We model bacteria such as Deionococcus radiodurans and Desulfotomaculum, Moorella and Bacillus species for their ability to grow or survive in the presence of ROS. We examine how early Life might have adapted to oxygen.

Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls.

PubMed

Mei, Qi-Xiang; Huang, Chun-Lan; Luo, Sheng-Zheng; Zhang, Xue-Mei; Zeng, Yue; Lu, Ying-Ying

2018-06-01

An increasing number of reports have demonstrated that there is an association between the presence of pathogenic microorganisms and pancreatic cancer. However, the role of the duodenal microbiota in pancreatic carcinogenesis remains unknown. In this study, duodenal mucosal microbiota was analyzed in 14 patients with pancreatic head cancer and 14 healthy controls using 16S rRNA gene pyrosequencing methods. Plasma endotoxin activity and the concentrations of the proinflammatory cytokine IL-6 and C-reactive protein (CRP) were measured in blood samples. The urea breath test was used to detect Helicobacter pylori infections. Endoscopic duodenal mucosal biopsies were evaluated by histological examinations. Statistical comparisons of inflammatory factors revealed significantly higher levels of CRP and IL-6 in the pancreatic cancer group as compared to healthy controls. Patients with pancreatic cancer also had a higher incidence of H. pylori infections and showed mucosal changes, including villous abnormalities and diffuse inflammatory cell infiltration in the lamina propria. The sequences analysis showed that based on linear discriminant analysis effect size (LEfSe) analysis at the genus level, Acinetobacter, Aquabacterium, Oceanobacillus, Rahnella, Massilia, Delftia, Deinococcus, and Sphingobium were more abundant in the duodenal mucosa of pancreatic cancer patients, whereas the duodenal microbiotas of healthy controls were enriched with Porphyromonas, Paenibacillus, Enhydrobacter, Escherichia, Shigella, and Pseudomonas. These results reveal a picture of duodenal microbiota in pancreatic head cancer patients that could be useful in future trials investigating the role of gut microbiota in pancreatic cancer. Copyright © 2018 IAP and EPC. Published by Elsevier B.V. All rights reserved.

Isolation, characterization, and diversity of novel radiotolerant carotenoid-producing bacteria.

PubMed

Asker, Dalal; Awad, Tarek S; Beppu, Teruhiko; Ueda, Kenji

2012-01-01

Carotenoids are natural pigments that exhibit many biological functions, such as antioxidants (i.e., promote oxidative stress resistance), membrane stabilizers, and precursors for vitamin A. The link between these biological activities and many health benefits (e.g., anticarcinogenic activity, prevention of chronic diseases, etc.) has raised the interest of several industrial sectors, especially in the cosmetics and pharmaceutical industries. The use of microorganisms in biotechnology to produce carotenoids is favorable by consumer and can help meet the growing demand for these bioactive compounds in the food, feed, and pharmaceutical industries. This methodological chapter details the development of a rapid and selective screening method for isolation and identification of carotenoid-producing microorganisms based on UV treatment, sequencing analysis of 16S rRNA genes, and carotenoids' analysis using rapid and effective High-Performance Liquid Chromatography-Diodearray-MS methods. The results of a comprehensive 16S rRNA gene-based phylogenetic analysis revealed a diversity of carotenoid-producing microorganisms (104 isolates) that were isolated at a high frequency from water samples collected at Misasa (Tottori, Japan), a region known for its high natural radioactivity content. These carotenoid-producing isolates were classified into 38 different species belonging to 7 bacterial classes (Flavobacteria, Sphingobacteria, α-Proteobacteria, γ-Proteobacteria, Deinococci, Actinobacteria, and Bacilli). The carotenoids produced by the isolates were zeaxanthin (6 strains), dihydroxyastaxanthin (24 strains), astaxanthin (27 strains), canthaxanthin (10 strains), and unidentified molecular species that were produced by the isolates related to Deinococcus, Exiguobacterium, and Flectobacillus. Here, we describe the methods used to isolate and classify these microorganisms.

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India

PubMed Central

Badhai, Jhasketan; Ghosh, Tarini S.; Das, Subrata K.

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40–58°C; pH: 7.2–7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria. PMID:26579081

Effect of postharvest practices including degreening on citrus carpoplane microbial biomes.

PubMed

Gomba, A; Chidamba, L; Korsten, L

2017-04-01

To investigate the effect of commercial citrus packhouse processing steps on the fruit surface microbiome of Clementines and Palmer navel oranges. Viable bacteria, yeast and fungi counts, and the pyrosequencing analysis of the 16S rRNA and ITS were used to evaluate the community structure and population dynamics of phylloepiphytic bacteria and fungi associated with commercial postharvest processing. Drenching significantly reduced microbial counts in all cases except for yeasts on navels, while the extent of degreening effects varied between the citrus varieties. Pyrosequencing analysis showed a total of 4409 bacteria and 5792 fungi nonchimeric unique sequences with an average of 1102 bacteria and 1448 fungi reads per sample. Dominant phyla on the citrus carpoplane were Proteobacteria (53·5%), Actinobacteria (19·9%), Bacteroidetes (5·6%) and Deinococcus-Thermus (5·4%) for bacteria and Ascomycota (80·5%) and Basidiomycota (9·8%) for fungi. Beginning with freshly harvested fruit fungal diversity declined significantly after drenching, but had little effect on bacteria and populations recovered during degreening treatments, including those for Penicillium sp. Packhouse processing greatly influences microbial communities on the citrus carpoplane. A broad orange biome was described with pyrosequencing and gave insight into the likely survival and persistence of pathogens, especially as they may affect the quality and safety of the packed product. A close examination of the microbiota of fruit and the impact of intervention strategies on the ecological balance may provide a more durable approach to reduce losses and spoilage. © 2017 The Society for Applied Microbiology.

Taxonomic and functional characteristics of microbial communities and their correlation with physicochemical properties of four geothermal springs in Odisha, India.

PubMed

Badhai, Jhasketan; Ghosh, Tarini S; Das, Subrata K

2015-01-01

This study describes microbial diversity in four tropical hot springs representing moderately thermophilic environments (temperature range: 40-58°C; pH: 7.2-7.4) with discrete geochemistry. Metagenome sequence data showed a dominance of Bacteria over Archaea; the most abundant phyla were Chloroflexi and Proteobacteria, although other phyla were also present, such as Acetothermia, Nitrospirae, Acidobacteria, Firmicutes, Deinococcus-Thermus, Bacteroidetes, Thermotogae, Euryarchaeota, Verrucomicrobia, Ignavibacteriae, Cyanobacteria, Actinobacteria, Planctomycetes, Spirochaetes, Armatimonadetes, Crenarchaeota, and Aquificae. The distribution of major genera and their statistical correlation analyses with the physicochemical parameters predicted that the temperature, aqueous concentrations of ions (such as sodium, chloride, sulfate, and bicarbonate), total hardness, dissolved solids and conductivity were the main environmental variables influencing microbial community composition and diversity. Despite the observed high taxonomic diversity, there were only little variations in the overall functional profiles of the microbial communities in the four springs. Genes involved in the metabolism of carbohydrates and carbon fixation were the most abundant functional class of genes present in these hot springs. The distribution of genes involved in carbon fixation predicted the presence of all the six known autotrophic pathways in the metagenomes. A high prevalence of genes involved in membrane transport, signal transduction, stress response, bacterial chemotaxis, and flagellar assembly were observed along with genes involved in the pathways of xenobiotic degradation and metabolism. The analysis of the metagenomic sequences affiliated to the candidate phylum Acetothermia from spring TB-3 provided new insight into the metabolism and physiology of yet-unknown members of this lineage of bacteria.

Anoxic biodegradation of BTEX in a biotrickling filter.

PubMed

Akmirza, Ilker; Pascual, Celia; Carvajal, Andrea; Pérez, Rebeca; Muñoz, Raúl; Lebrero, Raquel

2017-06-01

Emissions of BTEX (benzene, toluene, ethylbenzene and xylene) from the petrochemical industry are characterized by a low pollutants concentration and the absence of oxygen. Biodegradation of these pollutants using nitrate as the electron acceptor is of key interest to reuse the residual gas for inertization purposes. However, the biological mineralization of BTEX is often limited by their recalcitrant nature and the toxicity of the secondary metabolites produced. The potential of an anoxic biotrickling filter for the treatment of a model O 2 -free BTEX-laden emission at inlet individual concentrations of ~700mgm -3 was here evaluated. A UV oxidation step was also tested both in the recycling liquid and in the inlet gas emission prior to biofiltration. Removal efficiencies >90% were achieved for both toluene and ethylbenzene, corresponding to elimination capacities (ECs) of 1.4±0.2gm -3 h -1 and 1.5±0.3gm -3 h -1 , respectively, while ~45% of xylene (EC=0.6±0.1g m -3 h -1 ) was removed at a liquid recycling rate of 2mh -1 . Benzene biodegradation was however limited by the accumulation of toxic metabolites in the liquid phase. The oxidation of these intermediates in the recycling liquid by UV photolysis boosted benzene abatement, achieving an average EC of 0.5±0.2gm -3 h -1 and removals of ~40%. However, the implementation of UV oxidation as a pretreatment step in the inlet gas emission resulted in the deterioration of the BTEX biodegradation capacity of the biotrickling filter. Finally, a high bacterial diversity was observed throughout the entire experiment, the predominant phyla being Proteobacteria and Deinococcus-thermus. Copyright © 2017 Elsevier B.V. All rights reserved.

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites

PubMed Central

Toneatti, Diego M.; Albarracín, Virginia H.; Flores, Maria R.; Polerecky, Lubos; Farías, María E.

2017-01-01

At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H2S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5–7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth. PMID:28446906

Stratified Bacterial Diversity along Physico-chemical Gradients in High-Altitude Modern Stromatolites.

PubMed

Toneatti, Diego M; Albarracín, Virginia H; Flores, Maria R; Polerecky, Lubos; Farías, María E

2017-01-01

At an altitude of 3,570 m, the volcanic lake Socompa in the Argentinean Andes is presently the highest site where actively forming stromatolite-like structures have been reported. Interestingly, pigment and microsensor analyses performed through the different layers of the stromatolites (50 mm-deep) showed steep vertical gradients of light and oxygen, hydrogen sulfide and pH in the porewater. Given the relatively good characterization of these physico-chemical gradients, the aim of this follow-up work was to specifically address how the bacterial diversity stratified along the top six layers of the stromatolites which seems the most metabolically important and diversified zone of the whole microbial community. We herein discussed how, in only 7 mm, a drastic succession of metabolic adaptations occurred: i.e., microbial communities shift from a UV-high/oxic world to an IR-low/anoxic/high H 2 S environment which force stratification and metabolic specialization of the bacterial community, thus, modulating the chemical faces of the Socompa stromatolites. The oxic zone was dominated by Deinococcus sp. at top surface (0.3 mm), followed by a second layer of Coleofasciculus sp. (0.3 to ∼2 mm). Sequences from anoxygenic phototrophic Alphaproteobacteria, along with an increasing diversity of phyla including Bacteroidetes, Spirochaetes were found at middle layers 3 and 4. Deeper layers (5-7 mm) were mostly occupied by sulfate reducers of Deltaproteobacteria, Bacteroidetes and Firmicutes, next to a high diversity and equitable community of rare, unclassified and candidate phyla. This analysis showed how microbial communities stratified in a physicochemical vertical profile and according to the light source. It also gives an insight of which bacterial metabolic capabilities might operate and produce a microbial cooperative strategy to thrive in one of the most extreme environments on Earth.

The oral and conjunctival microbiotas in cats with and without feline immunodeficiency virus infection.

PubMed

Weese, Scott J; Nichols, Jamieson; Jalali, Mohammad; Litster, Annette

2015-03-03

The oral and conjunctival microbiotas likely play important roles in protection from opportunistic infections, while also being the source of potential pathogens. Yet, there has been limited investigation in cats, and the impact of comorbidities such as feline immunodeficiency virus (FIV) infection has not been reported. Oral and conjunctival swabs were collected from cats with FIV infection and FIV-uninfected controls, and subjected to 16S rRNA gene (V4) PCR and next generation sequencing. 9,249 OTUs were identified from conjunctival swabs, yet the most common 20 (0.22%) OTUs accounted for 76% of sequences. The two most abundant OTUs both belonged to Staphylococcus, and accounted for 37% of sequences. Cats with FIV infection had significantly lower relative abundances of Verrucomicrobia, Fibrobacteres, Spirochaetes, Bacteroidetes and Tenericutes, and a higher relative abundance of Deinococcus-Thermus. There were significant differences in both community membership (P = 0.006) and community structure (P = 0.02) between FIV-infected and FIV-uninfected cats. FIV-infected cats had significantly higher relative abundances of Fusobacteria and Actinobacteria in the oral cavity, and significantly higher relative abundances of several bacterial classes including Fusobacteria (0.022 vs 0.007, P = 0.006), Actinobacteria (0.017 vs 0.003, P = 0.003), Sphingobacteria (0.00015 vs 0.00003, P = 0.0013) and Flavobacteria (0.0073 vs 0.0034, P = 0.030). The feline conjunctival and oral microbiotas are complex polymicrobial communities but dominated by a limited number of genera. There is an apparent impact of FIV infection on various components of the microbiota, and assessment of the clinical relevance of these alterations in required.

Phylogenetic Diversity Analysis of Subterranean Hot Springs in Iceland

PubMed Central

Marteinsson, Viggó Thór; Hauksdóttir, Sigurbjörg; Hobel, Cédric F. V.; Kristmannsdóttir, Hrefna; Hreggvidsson, Gudmundur Oli; Kristjánsson, Jakob K.

2001-01-01

Geothermal energy has been harnessed and used for domestic heating in Iceland. In wells that are typically drilled to a depth of 1,500 to 2,000 m, the temperature of the source water is 50 to 130°C. The bottoms of the boreholes can therefore be regarded as subterranean hot springs and provide a unique opportunity to study the subterranean biosphere. Large volumes of geothermal fluid from five wells and a mixture of geothermal water from 50 geothermal wells (hot tap water) were sampled and concentrated through a 0.2-μm-pore-size filter. Cells were observed in wells RG-39 (91.4°C) and MG-18 (71.8°C) and in hot tap water (76°C), but no cells were detected in wells SN-4, SN-5 (95 to 117°C), and RV-5 (130°C). Archaea and Bacteria were detected by whole-cell fluorescent in situ hybridization. DNAs were extracted from the biomass, and small-subunit rRNA genes (16S rDNAs) were amplified by PCR using primers specific for the Archaea and Bacteria domains. The PCR products were cloned and sequenced. The sequence analysis showed 11 new operational taxonomic units (OTUs) out of 14, 3 of which were affiliated with known surface OTUs. Samples from RG-39 and hot tap water were inoculated into enrichment media and incubated at 65 and 85°C. Growth was observed only in media based on geothermal water. 16S rDNA analysis showed enrichments dominated with Desulfurococcales relatives. Two strains belonging to Desulfurococcus mobilis and to the Thermus/Deinococcus group were isolated from borehole RG-39. The results indicate that subsurface volcanic zones are an environment that provides a rich subsurface for novel thermophiles. PMID:11526029

Polybacterial community analysis in human conjunctiva through 16S rRNA gene libraries.

PubMed

Deepthi, KrishnanNair Geetha; Jayasudha, Rajagopalaboopathi; Girish, Rameshan Nair; Manikandan, Palanisamy; Ram, Rammohan; Narendran, Venkatapathy; Prabagaran, Solai Ramatchandirane

2018-05-14

The conjunctival sac of healthy human harbours a variety of microorganisms. When the eye is compromised, an occasional inadvertent spread happens to the adjacent tissue, resulting in bacterial ocular infections. Microbiological investigation of the conjunctival swab is one of the broadly used modality to study the aetiological agent of conjunctiva. However, most of the time such methods yield unsatisfactory results. Hence, the present study intends to identify the bacterial community in human conjunctiva of pre-operative subjects through 16S rRNA gene libraries. Out of 45 samples collected from preoperative patients undergoing cataract surgery, 36 libraries were constructed with bacterial nested-PCR-positive samples. The representative clones with unique restriction pattern were generated through Amplified Ribosomal DNA Restriction Analysis (ARDRA) which were sequenced for phylogenetic affiliation. A total of 211 representative clones were obtained which were distributed in phyla Actinobacteria, Firmicutes, α-Proteobacteria, β-Proteobacteria, γ-Proteobacteria, Bacteroidetes, and Deinococcus-Thermus. Findings revealed the presence of polybacterial community, especially in some cases even though no bacterium or a single bacterium alone was identified through cultivable method. Remarkably, we identified 17 species which have never been reported in any ocular infections. The sequencing data reported 6 unidentified bacteria suggesting the possibility of novel organisms in the sample. Since, polybacterial community has been identified consisting of both gram positive and gram negative bacteria, a broad spectrum antibiotic therapy is advisable to the patients who are undergoing cataract surgery. Consolidated effort would significantly improve a clear understanding of the nature of microbial community in the human conjunctiva which will promote administration of appropriate antibiotic regimen and also help in the development of oligonucleotide probes to screen the predominant pathogens for early predisposition. Copyright © 2018 Elsevier Ltd. All rights reserved.

Profile Changes in the Soil Microbial Community When Desert Becomes Oasis

PubMed Central

Li, Chen-hua; Tang, Li-song; Jia, Zhong-jun; Li, Yan

2015-01-01

The conversion of virgin desert into oasis farmland creates two contrasting types of land-cover. During oasis formation with irrigation and fertilizer application, however, the changes in the soil microbial population, which play critical roles in the ecosystem, remain poorly understood. We applied high-throughput pyrosequencing to investigate bacterial and archaeal communities throughout the profile (0–3 m) in an experimental field, where irrigation and fertilization began in 1990 and cropped with winter wheat since then. To assess the effects of cultivation, the following treatments were compared with the virgin desert: CK (no fertilizer), PK, NK, NP, NPK, NPKR, and NPKM (R: straw residue; M: manure fertilizer). Irrigation had a greater impact on the overall microbial community than fertilizer application. The greatest impact occurred in topsoil (0–0.2 m), e.g., Cyanobacteria (25% total abundance) were most abundant in desert soil, while Actinobacteria (26%) were most abundant in oasis soil. The proportions of extremophilic and photosynthetic groups (e.g., Deinococcus-Thermus and Cyanobacteria) decreased, while the proportions of R-strategy (e.g., Gammaproteobacteria including Xanthomonadales), nitrifying (e.g., Nitrospirae), and anaerobic bacteria (e.g., Anaerolineae) increased throughout the oasis profile. Archaea occurred only in oasis soil. The impact of fertilizer application was mainly reflected in the non-dominant communities or finer taxonomic divisions. Oasis formation led to a dramatic shift in microbial community and enhanced soil enzyme activities. The rapidly increased soil moisture and decreased salt caused by irrigation were responsible for this shift. Furthermore, difference in fertilization and crop growth altered the organic carbon contents in the soil, which resulted in differences of microbial communities within oasis. PMID:26426279

Phylogenetic diversity analysis of subterranean hot springs in Iceland.

PubMed

Marteinsson, V T; Hauksdóttir, S; Hobel, C F; Kristmannsdóttir, H; Hreggvidsson, G O; Kristjánsson, J K

2001-09-01

Geothermal energy has been harnessed and used for domestic heating in Iceland. In wells that are typically drilled to a depth of 1,500 to 2,000 m, the temperature of the source water is 50 to 130 degrees C. The bottoms of the boreholes can therefore be regarded as subterranean hot springs and provide a unique opportunity to study the subterranean biosphere. Large volumes of geothermal fluid from five wells and a mixture of geothermal water from 50 geothermal wells (hot tap water) were sampled and concentrated through a 0.2-microm-pore-size filter. Cells were observed in wells RG-39 (91.4 degrees C) and MG-18 (71.8 degrees C) and in hot tap water (76 degrees C), but no cells were detected in wells SN-4, SN-5 (95 to 117 degrees C), and RV-5 (130 degrees C). Archaea and Bacteria were detected by whole-cell fluorescent in situ hybridization. DNAs were extracted from the biomass, and small-subunit rRNA genes (16S rDNAs) were amplified by PCR using primers specific for the Archaea and Bacteria domains. The PCR products were cloned and sequenced. The sequence analysis showed 11 new operational taxonomic units (OTUs) out of 14, 3 of which were affiliated with known surface OTUs. Samples from RG-39 and hot tap water were inoculated into enrichment media and incubated at 65 and 85 degrees C. Growth was observed only in media based on geothermal water. 16S rDNA analysis showed enrichments dominated with Desulfurococcales relatives. Two strains belonging to Desulfurococcus mobilis and to the Thermus/Deinococcus group were isolated from borehole RG-39. The results indicate that subsurface volcanic zones are an environment that provides a rich subsurface for novel thermophiles.

Exploring bacterial diversity in hospital environments by GS-FLX Titanium pyrosequencing.

PubMed

Poza, Margarita; Gayoso, Carmen; Gómez, Manuel J; Rumbo-Feal, Soraya; Tomás, María; Aranda, Jesús; Fernández, Ana; Bou, Germán

2012-01-01

Understanding microbial populations in hospital environments is crucial for improving human health. Hospital-acquired infections are an increasing problem in intensive care units (ICU). In this work we present an exploration of bacterial diversity at inanimate surfaces of the ICU wards of the University Hospital A Coruña (Spain), as an example of confined hospital environment subjected to selective pressure, taking the entrance hall of the hospital, an open and crowded environment, as reference. Surface swab samples were collected from both locations and recovered DNA used as template to amplify a hypervariable region of the bacterial 16S rRNA gene. Sequencing of the amplicons was performed at the Roche 454 Sequencing Center using GS-FLX Titanium procedures. Reads were pre-processed and clustered into OTUs (operational taxonomic units), which were further classified. A total of 16 canonical bacterial phyla were detected in both locations. Members of the phyla Firmicutes (mainly Staphylococcus and Streptococcus) and Actinobacteria (mainly Micrococcaceae, Corynebacteriaceae and Brevibacteriaceae) were over-represented in the ICU with respect to the Hall. The phyllum Proteobacteria was also well represented in the ICU, mainly by members of the families Enterobacteriaceae, Methylobacteriaceae and Sphingomonadaceae. In the Hall sample, the phyla Proteobacteria, Bacteroidetes, Deinococcus-Thermus and Cyanobacteria were over-represented with respect to the ICU. Over-representation of Proteobacteria was mainly due to the high abundance of Enterobacteriaceae members. The presented results demonstrate that bacterial diversity differs at the ICU and entrance hall locations. Reduced diversity detected at ICU, relative to the entrance hall, can be explained by its confined character and by the existence of antimicrobial selective pressure. This is the first study using deep sequencing techniques made in hospital wards showing substantial hospital microbial diversity.

Bacterial diversity at different stages of the composting process

PubMed Central

2010-01-01

Background Composting is an aerobic microbiological process that is facilitated by bacteria and fungi. Composting is also a method to produce fertilizer or soil conditioner. Tightened EU legislation now requires treatment of the continuously growing quantities of organic municipal waste before final disposal. However, some full-scale composting plants experience difficulties with the efficiency of biowaste degradation and with the emission of noxious odours. In this study we examine the bacterial species richness and community structure of an optimally working pilot-scale compost plant, as well as a full-scale composting plant experiencing typical problems. Bacterial species composition was determined by isolating total DNA followed by amplifying and sequencing the gene encoding the 16S ribosomal RNA. Results Over 1500 almost full-length 16S rRNA gene sequences were analysed and of these, over 500 were present only as singletons. Most of the sequences observed in either one or both of the composting processes studied here were similar to the bacterial species reported earlier in composts, including bacteria from the phyla Actinobacteria, Bacteroidetes, Firmicutes, Proteobacteria and Deinococcus-Thermus. In addition, a number of previously undetected bacterial phylotypes were observed. Statistical calculations estimated a total bacterial diversity of over 2000 different phylotypes in the studied composts. Conclusions Interestingly, locally enriched or evolved bacterial variants of familiar compost species were observed in both composts. A detailed comparison of the bacterial diversity revealed a large difference in composts at the species and strain level from the different composting plants. However, at the genus level, the difference was much smaller and illustrated a delay of the composting process in the full-scale, sub-optimally performing plants. PMID:20350306

Bacterial communities in soil samples from the Mingyong Glacier of southwestern China.

PubMed

Li, Haoyu; Taj, Muhammad Kamran; Ji, Xiuling; Zhang, Qi; Lin, Liangbing; Zhou, Zhimei; Wei, Yunlin

2017-05-01

The present study was an effort to determine the bacterial diversity of soils in Mingyong Glacier located at the Meili Snow Mountains of southwestern China. Mingyong Glacier has different climatic zones within a very narrow area, and bacterial community diversity in this low temperature area remains largely unknown. In this study, soil samples were collected from four different climatic zones: M11A (dry warm valley), M14 (forest), M15 (grass land), and M16 (glacier zones). Phylogenetic analysis based on 16S rRNA gene V6 hypervariable region showed high bacterial abundance in the glacier. The number of Operational Taxonomic Units ranged from 2.24×10 3 to 5.56×10 3 in soil samples. Statistical analysis of 16S rRNA gene clone libraries results showed that bacterial diversity in zones M11A，M14 and M16 are higher than in zone M15. The bacterial community structures are clearly distinguishable, and phylogenetic analysis showed that the predominant phyla were Proteobacteria, Deinococcus-Thermus, Firmicutes, Actinobacteria, and Nitrospirae in Mingyong Glacier. Seventy-nine different orders from four zones have been isolated. Bacterial diversity and distribution of bacterial communities related to the anthropogenic perturbations in zone (M15) were confirmed by diversity index analysis, and the diversity index of other three zones was satisfactory through this analysis software. The results suggest that bacterial diversity and distribution analyses using bacterial 16S rRNA gene V6 hypervariable region were successful, and bacterial communities in this area not only had the same bacterial phyla compared to other glaciers but also had their own rare species.

Transcription activation mediated by a cyclic AMP receptor protein from Thermus thermophilus HB8.

PubMed

Shinkai, Akeo; Kira, Satoshi; Nakagawa, Noriko; Kashihara, Aiko; Kuramitsu, Seiki; Yokoyama, Shigeyuki

2007-05-01

The extremely thermophilic bacterium Thermus thermophilus HB8, which belongs to the phylum Deinococcus-Thermus, has an open reading frame encoding a protein belonging to the cyclic AMP (cAMP) receptor protein (CRP) family present in many bacteria. The protein named T. thermophilus CRP is highly homologous to the CRP family proteins from the phyla Firmicutes, Actinobacteria, and Cyanobacteria, and it forms a homodimer and interacts with cAMP. CRP mRNA and intracellular cAMP were detected in this strain, which did not drastically fluctuate during cultivation in a rich medium. The expression of several genes was altered upon disruption of the T. thermophilus CRP gene. We found six CRP-cAMP-dependent promoters in in vitro transcription assays involving DNA fragments containing the upstream regions of the genes exhibiting decreased expression in the CRP disruptant, indicating that the CRP is a transcriptional activator. The consensus T. thermophilus CRP-binding site predicted upon nucleotide sequence alignment is 5'-(C/T)NNG(G/T)(G/T)C(A/C)N(A/T)NNTCACAN(G/C)(G/C)-3'. This sequence is unique compared with the known consensus binding sequences of CRP family proteins. A putative -10 hexamer sequence resides at 18 to 19 bp downstream of the predicted T. thermophilus CRP-binding site. The CRP-regulated genes found in this study comprise clustered regularly interspaced short palindromic repeat (CRISPR)-associated (cas) ones, and the genes of a putative transcriptional regulator, a protein containing the exonuclease III-like domain of DNA polymerase, a GCN5-related acetyltransferase homolog, and T. thermophilus-specific proteins of unknown function. These results suggest a role for cAMP signal transduction in T. thermophilus and imply the T. thermophilus CRP is a cAMP-responsive regulator.

Bacterial host and reporter gene optimization for genetically encoded whole cell biosensors.

PubMed

Brutesco, Catherine; Prévéral, Sandra; Escoffier, Camille; Descamps, Elodie C T; Prudent, Elsa; Cayron, Julien; Dumas, Louis; Ricquebourg, Manon; Adryanczyk-Perrier, Géraldine; de Groot, Arjan; Garcia, Daniel; Rodrigue, Agnès; Pignol, David; Ginet, Nicolas

2017-01-01

Whole-cell biosensors based on reporter genes allow detection of toxic metals in water with high selectivity and sensitivity under laboratory conditions; nevertheless, their transfer to a commercial inline water analyzer requires specific adaptation and optimization to field conditions as well as economical considerations. We focused here on both the influence of the bacterial host and the choice of the reporter gene by following the responses of global toxicity biosensors based on constitutive bacterial promoters as well as arsenite biosensors based on the arsenite-inducible P ars promoter. We observed important variations of the bioluminescence emission levels in five different Escherichia coli strains harboring two different lux-based biosensors, suggesting that the best host strain has to be empirically selected for each new biosensor under construction. We also investigated the bioluminescence reporter gene system transferred into Deinococcus deserti, an environmental, desiccation- and radiation-tolerant bacterium that would reduce the manufacturing costs of bacterial biosensors for commercial water analyzers and open the field of biodetection in radioactive environments. We thus successfully obtained a cell survival biosensor and a metal biosensor able to detect a concentration as low as 100 nM of arsenite in D. deserti. We demonstrated that the arsenite biosensor resisted desiccation and remained functional after 7 days stored in air-dried D. deserti cells. We also report here the use of a new near-infrared (NIR) fluorescent reporter candidate, a bacteriophytochrome from the magnetotactic bacterium Magnetospirillum magneticum AMB-1, which showed a NIR fluorescent signal that remained optimal despite increasing sample turbidity, while in similar conditions, a drastic loss of the lux-based biosensors signal was observed.

Optimization of the liquid biofertilizer production in batch fermentation with by-product from MSG

NASA Astrophysics Data System (ADS)

Namfon, Panjanapongchai; Ratchanok, Sahaworarak; Chalida, Daengbussade

2017-03-01

The long term use of chemical fertilizers destroyed the friability of soil which obviously decreased quantity and quality of crops and especially affect microorganisms living in soils. The bio-fertilizer with microbial consortium is an environmental friendly alternative to solve this bottleneck due to harboring soil microorganisms such as Bacillus sp., Micrococcus sp., Pseudomonas sp., Staphylococcus sp. and Deinococcus sp. produced with natural by-product or waste from industries that is alternative and sustainable such as nutrient-rich (by-product) from Mono Sodium Glutamate (MSG) for producing liquid biofertilizer by batch fermentation. In this work, the concentration of reducing sugar from substrate as main carbon source was evaluated in shake flask with mixed cultures. The optimal conditions were studied comparing with two levels of reducing sugar concentration (10, 20 g/L) and inoculums concentration (10, 20 %v/v) with using (2×2) full factorial design. The results indicated that the by-product from monosodium glutamate is feasible for fermentation and inoculums concentration is mainly influenced the batch fermentation process. Moreover, the combined 20 g/L and 10%v/v were considerably concluded as an optimal condition, of which the concentration of vegetative cells and spores attained at 8.29×109 CFU/mL and 1.97×105 CFU/mL, respectively. Their spores cell yields from reducing sugar (Yx/s) were obtained at 1.22×106 and 3.34×105 CFU/g were markedly different. In conclusion, the liquid Biofertilizer was produced satisfactorily at 20 g/L reducing sugar and 10% v/v inoculums in shake flask culture. Moreover, these results suggested that the by-product from monosodium glutamate is feasible for low-cost substrate in economical scale and environmental-friendly.

The Effect of Different Oceanic Abiotic Factors on Prokaryotic Body Sizes

NASA Astrophysics Data System (ADS)

Pidathala, S.; Bellon, M.; Heim, N.; Payne, J.

2016-12-01

We are studying the impact of abiotic factors in the Pacific and Atlantic on prokaryotic body sizes and genome sizes because we are interested in the manner in which abiotic factors influence genome sizes independent of their influence on body sizes. Some research has been done in the past on marine bacterial evolution, including data collection on marine ecology in relation to bacterial body sizes (Straza 2009). We are using the abiotic factors: temperature, salinity, and pH to compare the biovolumes/genome sizes of different phyla by using R. We made 9 scatter plots to model these relationships. Regardless of the phyla or the ocean, we found that there is no relation between pH, temperature, and body size, with several exceptions: Deinococcus. thermus has an indirect relationship with size in respect to temperature; size only correlates to temperature for phyla that are thermophiles. We also found that bacteria like D. thermus and Thermotogae are taxa only found in higher temperatures. Additionally, almost all phyla have genome sizes restricted by certain pH levels:, Proteobacteria only reach genomes with acidity levels greater than 6. In terms of salinity levels, certain bacteria are only found within a small range, and others, like Proteobacteria, can only reach genomes at low salinity levels. Finally, Proteobacteria have large genome sizes between 30 and 40 °, and Crenarchaeota have constant genome sizes in higher temperatures. Conclusively, we discovered that these abiotic factors generally do not affect body size, with the exception of D. thermus' indirect relationship to temperature due to its small biovolume in high temperatures. However, we determined that these abiotic factors have a great impact on genome sizes. This is due to genome size independence from body size. Also, genome size could have served as an adaptive feature for bacteria in marine environments, explaining why different phyla may have diverged to accommodate their lifestyles.

The discovery of stromatolites developing at 3570 m above sea level in a high-altitude volcanic lake Socompa, Argentinean Andes.

PubMed

Farías, María E; Rascovan, Nicolás; Toneatti, Diego M; Albarracín, Virginia H; Flores, María R; Poiré, Daniel G; Collavino, Mónica M; Aguilar, O Mario; Vazquez, Martin P; Polerecky, Lubos

2013-01-01

We describe stromatolites forming at an altitude of 3570 m at the shore of a volcanic lake Socompa, Argentinean Andes. The water at the site of stromatolites formation is alkaline, hypersaline, rich in inorganic nutrients, very rich in arsenic, and warm (20-24°C) due to a hydrothermal input. The stromatolites do not lithify, but form broad, rounded and low-domed bioherms dominated by diatom frustules and aragonite micro-crystals agglutinated by extracellular substances. In comparison to other modern stromatolites, they harbour an atypical microbial community characterized by highly abundant representatives of Deinococcus-Thermus, Rhodobacteraceae, Desulfobacterales and Spirochaetes. Additionally, a high proportion of the sequences that could not be classified at phylum level showed less than 80% identity to the best hit in the NCBI database, suggesting the presence of novel distant lineages. The primary production in the stromatolites is generally high and likely dominated by Microcoleus sp. Through negative phototaxis, the location of these cyanobacteria in the stromatolites is controlled by UV light, which greatly influences their photosynthetic activity. Diatoms, dominated by Amphora sp., are abundant in the anoxic, sulfidic and essentially dark parts of the stromatolites. Although their origin in the stromatolites is unclear, they are possibly an important source of anaerobically degraded organic matter that induces in situ aragonite precipitation. To the best of our knowledge, this is so far the highest altitude with documented actively forming stromatolites. Their generally rich, diverse and to a large extent novel microbial community likely harbours valuable genetic and proteomic reserves, and thus deserves active protection. Furthermore, since the stromatolites flourish in an environment characterized by a multitude of extremes, including high exposure to UV radiation, they can be an excellent model system for studying microbial adaptations under conditions that, at least in part, resemble those during the early phase of life evolution on Earth.

The distribution of active β-glucosidase-producing microbial communities in composting.

PubMed

Zang, Xiangyun; Liu, Meiting; Wang, Han; Fan, Yihong; Zhang, Haichang; Liu, Jiawen; Xing, Enlu; Xu, Xiuhong; Li, Hongtao

2017-12-01

The composting ecosystem is a suitable source for the discovery of novel microorganisms and secondary metabolites. Cellulose degradation is an important part of the global carbon cycle, and β-glucosidases complete the final step of cellulose hydrolysis by converting cellobiose to glucose. This work analyzes the succession of β-glucosidase-producing microbial communities that persist throughout cattle manure - rice straw composting, and evaluates their metabolic activities and community advantage during the various phases of composting. Fungal and bacterial β-glucosidase genes belonging to glycoside hydrolase families 1 and 3 (GH1 and GH3) amplified from DNA were classified and gene abundance levels were analyzed. The major reservoirs of β-glucosidase genes were the fungal phylum Ascomycota and the bacterial phyla Firmicutes, Actinobacteria, Proteobacteria, and Deinococcus-Thermus. This indicates that a diverse microbial community utilizes cellobiose. The succession of dominant bacteria was also detected during composting. Firmicutes was the dominant bacteria in the thermophilic phase of composting; there was a shift to Actinomycetes in the maturing stage. Proteobacteria accounted for the highest proportions during the heating and thermophilic phases of composting. By contrast, the fungal phylum Ascomycota was a minor microbial community constituent in thermophilic phase of composting. Combined with the analysis of the temperature, cellulose degradation rate and the carboxymethyl cellulase and β-glucosidase activities showed that the bacterial GH1 family β-glucosidase genes make greater contribution in cellulose degradation at the later thermophilic stage of composting. In summary, even GH1 bacteria families β-glucosidase genes showing low abundance in DNA may be functionally important in the later thermophilic phase of composting. The results indicate that a complex community of bacteria and fungi expresses β-glucosidases in compost. Several β-glucosidase-producing bacteria and fungi identified in this study may represent potential indicators of composting in cellulose degradation.

Desert farming benefits from microbial potential in arid soils and promotes diversity and plant health.

PubMed

Köberl, Martina; Müller, Henry; Ramadan, Elshahat M; Berg, Gabriele

2011-01-01

To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems.

The Discovery of Stromatolites Developing at 3570 m above Sea Level in a High-Altitude Volcanic Lake Socompa, Argentinean Andes

PubMed Central

Farías, María E.; Rascovan, Nicolás; Toneatti, Diego M.; Albarracín, Virginia H.; Flores, María R.; Poiré, Daniel G.; Collavino, Mónica M.; Aguilar, O. Mario; Vazquez, Martin P.; Polerecky, Lubos

2013-01-01

We describe stromatolites forming at an altitude of 3570 m at the shore of a volcanic lake Socompa, Argentinean Andes. The water at the site of stromatolites formation is alkaline, hypersaline, rich in inorganic nutrients, very rich in arsenic, and warm (20–24°C) due to a hydrothermal input. The stromatolites do not lithify, but form broad, rounded and low-domed bioherms dominated by diatom frustules and aragonite micro-crystals agglutinated by extracellular substances. In comparison to other modern stromatolites, they harbour an atypical microbial community characterized by highly abundant representatives of Deinococcus-Thermus, Rhodobacteraceae, Desulfobacterales and Spirochaetes. Additionally, a high proportion of the sequences that could not be classified at phylum level showed less than 80% identity to the best hit in the NCBI database, suggesting the presence of novel distant lineages. The primary production in the stromatolites is generally high and likely dominated by Microcoleus sp. Through negative phototaxis, the location of these cyanobacteria in the stromatolites is controlled by UV light, which greatly influences their photosynthetic activity. Diatoms, dominated by Amphora sp., are abundant in the anoxic, sulfidic and essentially dark parts of the stromatolites. Although their origin in the stromatolites is unclear, they are possibly an important source of anaerobically degraded organic matter that induces in situ aragonite precipitation. To the best of our knowledge, this is so far the highest altitude with documented actively forming stromatolites. Their generally rich, diverse and to a large extent novel microbial community likely harbours valuable genetic and proteomic reserves, and thus deserves active protection. Furthermore, since the stromatolites flourish in an environment characterized by a multitude of extremes, including high exposure to UV radiation, they can be an excellent model system for studying microbial adaptations under conditions that, at least in part, resemble those during the early phase of life evolution on Earth. PMID:23308236

Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context

PubMed Central

2008-01-01

Background The phosphoenolpyruvate phosphotransferase system (PTS) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. The PTS couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (PEP) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme II complexes which catalyze the uptake and phosphorylation of solutes. Previous studies have suggested that the evolution of the constituents of the enzyme II complexes has been driven largely by horizontal gene transfer whereas vertical inheritance has been prevalent in the general phosphoryl transfer proteins in some bacterial groups. The aim of this work is to test this hypothesis by studying the evolution of the phosphoryl transfer proteins of the PTS. Results We have analyzed the evolutionary history of the PTS phosphoryl transfer chain (PTS-ptc) components in 222 complete genomes by combining phylogenetic methods and analysis of genomic context. Phylogenetic analyses alone were not conclusive for the deepest nodes but when complemented with analyses of genomic context and functional information, the main evolutionary trends of this system could be depicted. Conclusion The PTS-ptc evolved in bacteria after the divergence of early lineages such as Aquificales, Thermotogales and Thermus/Deinococcus. The subsequent evolutionary history of the PTS-ptc varied in different bacterial lineages: vertical inheritance and lineage-specific gene losses mainly explain the current situation in Actinobacteria and Firmicutes whereas horizontal gene transfer (HGT) also played a major role in Proteobacteria. Most remarkably, we have identified a HGT event from Firmicutes or Fusobacteria to the last common ancestor of the Enterobacteriaceae, Pasteurellaceae, Shewanellaceae and Vibrionaceae. This transfer led to extensive changes in the metabolic and regulatory networks of these bacteria including the development of a novel carbon catabolite repression system. Hence, this example illustrates that HGT can drive major physiological modifications in bacteria. PMID:18485189

Metagenomics of an Alkaline Hot Spring in Galicia (Spain): Microbial Diversity Analysis and Screening for Novel Lipolytic Enzymes.

PubMed

López-López, Olalla; Knapik, Kamila; Cerdán, Maria-Esperanza; González-Siso, María-Isabel

2015-01-01

A fosmid library was constructed with the metagenomic DNA from the water of the Lobios hot spring (76°C, pH = 8.2) located in Ourense (Spain). Metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 Mbp. 23,207 ORFs (Open Reading Frames) were predicted from the assembly. Biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. The six most abundant bacterial phyla were Deinococcus-Thermus, Proteobacteria, Firmicutes, Acidobacteria, Aquificae, and Chloroflexi. Within the archaeal superkingdom, the phylum Thaumarchaeota was predominant with the dominant species "Candidatus Caldiarchaeum subterraneum." Functional classification revealed the genes associated to one-carbon metabolism as the most abundant. Both taxonomic and functional classifications showed a mixture of different microbial metabolic patterns: aerobic and anaerobic, chemoorganotrophic and chemolithotrophic, autotrophic and heterotrophic. Remarkably, the presence of genes encoding enzymes with potential biotechnological interest, such as xylanases, galactosidases, proteases, and lipases, was also revealed in the metagenomic library. Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. Six genes conferring lipolytic activity were identified and one was cloned and characterized. This gene was named LOB4Est and it was expressed in a yeast mesophilic host. LOB4Est codes for a novel esterase of family VIII, with sequence similarity to β-lactamases, but with unusual wide substrate specificity. When the enzyme was purified from the mesophilic host it showed half-life of 1 h and 43 min at 50°C, and maximal activity at 40°C and pH 7.5 with p-nitrophenyl-laurate as substrate. Interestingly, the enzyme retained more than 80% of maximal activity in a broad range of pH from 6.5 to 8.

High taxonomic diversity of cultivation-recalcitrant endophytic bacteria in grapevine field shoots, their in vitro introduction, and unsuspected persistence.

PubMed

Thomas, Pious; Sekhar, Aparna C; Shaik, Sadiq Pasha

2017-11-01

Molecular and microscopic analyses reveal enormous non-cultivable endophytic bacteria in grapevine field shoots with functional significance. Diverse bacteria enter tissue cultures through surface-sterilized tissues and survive surreptitiously with varying taxonomic realignments. The study was envisaged to assess the extent of endophytic bacterial association with field shoot tissues of grapevine and the likelihood of introduction of such internally colonizing bacteria in vitro adopting molecular techniques targeting the non-cultivable bacterial community. PowerFood ® -kit derived DNA from surface-sterilized field shoot tips of grapevine Flame Seedless was employed in a preliminary bacterial class-specific PCR screening proving positive for major prokaryotic taxa including Archaea. Taxonomic and functional diversity were analyzed through whole metagenome profiling (WMG) which revealed predominantly phylum Actinobacteria, Proteobacteria, and minor shares of Firmicutes, Bacteroidetes, and Deinococcus-Thermus with varying functional roles ascribable to the whole bacterial community. Field shoot tip tissues and callus derived from stem segments were further employed in 16S rRNA V3-V4 amplicon taxonomic profiling. This revealed elevated taxonomic diversity in field shoots over WMG, predominantly Proteobacteria succeeded by Actinobacteria, Firmicutes, Bacteroidetes, and 15 other phyla including several candidate phyla (135 families, 179 genera). Callus stocks also displayed broad bacterial diversity (16 phyla; 96 families; 141 genera) bearing resemblance to field tissues with Proteobacterial dominance but a reduction in its share, enrichment of Actinobacteria and Firmicutes, disappearance of some field-associated phyla and detection of a few additional taxonomic groups over field community. Similar results were documented during 16S V3-V4 amplicon taxonomic profiling on Thompson Seedless field shoot tip and callus tissues. Video microscopy on tissue homogenates corroborated enormous endophytic bacteria. This study elucidates a vast diversity of cultivation-recalcitrant endophytic bacteria prevailing in grapevine field shoots, their in vitro introduction, and unsuspecting sustenance with possible silent participation in tissue culture processes.

Microbial community of a hydrothermal mud vent underneath the deep-sea anoxic brine lake Urania (eastern Mediterranean).

PubMed

Yakimov, Michail M; Giuliano, Laura; Cappello, Simone; Denaro, Renata; Golyshin, Peter N

2007-04-01

The composition of a metabolically active prokaryotic community thriving in hydrothermal mud fluids of the deep-sea hypersaline anoxic Western Urania Basin was characterized using rRNA-based phylogenetic analysis of a clone library. The physiologically active prokaryotic assemblage in this extreme environment showed a great genetic diversity. Most members of the microbial community appeared to be affiliated to yet uncultured organisms from similar ecosystems, i.e., deep-sea hypersaline basins and hydrothermal vents. The bacterial clone library was dominated by phylotypes affiliated with the epsilon-Proteobacteria subdivision recognized as an ecologically significant group of bacteria inhabiting deep-sea hydrothermal environments. Almost 18% of all bacterial clones were related to delta-Proteobacteria, suggesting that sulfate reduction is one of the dominant metabolic processes occurring in warm mud fluids. The remaining bacterial phylotypes were related to alpha- and beta-Proteobacteria, Actinobacteria, Bacteroides, Deinococcus-Thermus, KB1 and OP-11 candidate divisions. Moreover, a novel monophyletic clade, deeply branched with unaffiliated 16S rDNA clones was also retrieved from deep-sea sediments and halocline of Urania Basin. Archaeal diversity was much lower and detected phylotypes included organisms affiliated exclusively with the Euryarchaeota. More than 96% of the archaeal clones belonged to the MSBL-1 candidate order recently found in hypersaline anoxic environments, such as endoevaporitic microbial mats, Mediterranean deep-sea mud volcanoes and anoxic basins. Two phylotypes, represented by single clones were related to uncultured groups DHVE-1 and ANME-1. Thus, the hydrothermal mud of hypersaline Urania Basin seems to contain new microbial diversity. The prokaryotic community was significantly different from that occurring in the upper layers of the Urania Basin since 60% of all bacterial and 40% of all archaeal phylotypes were obtained only from mud fluids. The uniqueness of the composition of the active prokaryotic community could be explained by the complex environmental conditions at the site. The interaction of oxygenated warm mud fluids with the cold hypersaline brine of the Urania Basin seems to simultaneously select for various metabolic processes, such as aerobic and anaerobic heterotrophy, sulfide- and methane-dependent chemotrophy along with anaerobic oxidation of methane, sulfate- and metal-reduction.

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman.

PubMed

Rempfert, Kaitlin R; Miller, Hannah M; Bompard, Nicolas; Nothaft, Daniel; Matter, Juerg M; Kelemen, Peter; Fierer, Noah; Templeton, Alexis S

2017-01-01

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite ("gabbro," "alkaline peridotite," "hyperalkaline peridotite," and "gabbro/peridotite contact") that vary strongly in pH and the concentrations of H 2 , CH 4 , Ca 2+ , Mg 2+ , [Formula: see text], [Formula: see text], trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus , candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira , Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. These data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.

Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H 2, CH 4, Ca 2+, Mg 2+, NO 3 more » $-$, SO$$2-\\atop{4}$$, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. As a result, these data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.« less

Geological and Geochemical Controls on Subsurface Microbial Life in the Samail Ophiolite, Oman

PubMed Central

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas; Nothaft, Daniel; Matter, Juerg M.; Kelemen, Peter; Fierer, Noah; Templeton, Alexis S.

2017-01-01

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H2, CH4, Ca2+, Mg2+, NO3-, SO42-, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. These data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites. PMID:28223966

Study of the Microbial Diversity of a Newly Discovered East Antarctic Freshwater Lake, L27C, and of a Perennially Ice-Covered Lake Untersee

NASA Technical Reports Server (NTRS)

Huang, Jonathan P.; Hoover, Richard B.; Andersen, Dale; Bej, Asim K.

2010-01-01

The microbial communities that reside within freshwater lakes of Schirmacher and Untersee Oases in East Antarctica must cope with extreme conditions that may include cold temperature, annual freeze-thaw cycles, exposure to UV radiation, especially during the austral summer months, low light beneath thick ice-cover, followed by seasonal darkness. The objective of this study was to assess the microbial biodiversity and distribution from samples taken from two freshwater lakes (L27C and Lake Untersee) that were collected during the Tawani 2008 International Antarctic Expedition that conducted research in this region of Antarctica. L27C is a small, previously unreported lake residing 2 km WNW of Maitri Station at Schirmacher Oasis. Biodiversity and distribution of microorganisms within the lake were studied using both culture-independent and culture-dependent methodologies based upon the analysis of eubacterial 16S rRNA gene sequences. Lake Untersee, a perennially ice-covered, ultra-oligotrophic, lake in the Otto-von-Gruber-Gebirge (Gruber Mountains) of central Dronning Maud Land was also sampled and the microbial diversity was analyzed by eubacterial 16S rRNA gene sequences derived from pure cultures. Direct culturing of water samples from each lake on separate R2A growth medium exhibited a variety of microorganisms including: Janthinobacterium, Hymenobacter, Sphingamonas, Subtercola, Deinococcus, Arthrobacter, Flavobacterium, Polaromonas, Rhodoferax and Duganella. The evaluation of samples from L27C through culture-independent methodology identified a rich microbial diversity consisting of six different phyla of bacteria. The culture-independent analysis also displayed the majority of bacteria (56%) belonged to the Class gamma-proteobacteria within the phylum Proteobacteria. Within the Class gamma-proteobacteria, Acinetobacter dominated (48%) the total microbial load. Overall, L27C exhibited 7 different phyla of bacteria and 20 different genera. Statistical analysis (Shannon-Weaver Diversity Index and Simpson Diversity Index) of the biodiversity of L27C displayed a moderately rich and diverse community. Investigations of the biodiversity and distribution of microorganisms in these lakes will help further our understanding of how the physical environment impact the structure and function within these microbially dominated ecosystems.

Desert Farming Benefits from Microbial Potential in Arid Soils and Promotes Diversity and Plant Health

PubMed Central

Köberl, Martina; Müller, Henry; Ramadan, Elshahat M.; Berg, Gabriele

2011-01-01

Background To convert deserts into arable, green landscapes is a global vision, and desert farming is a strong growing area of agriculture world-wide. However, its effect on diversity of soil microbial communities, which are responsible for important ecosystem services like plant health, is still not known. Methodology/Principal Findings We studied the impact of long-term agriculture on desert soil in one of the most prominent examples for organic desert farming in Sekem (Egypt). Using a polyphasic methodological approach to analyse microbial communities in soil as well as associated with cultivated plants, drastic effects caused by 30 years of agriculture were detected. Analysing bacterial fingerprints, we found statistically significant differences between agricultural and native desert soil of about 60%. A pyrosequencing-based analysis of the 16S rRNA gene regions showed higher diversity in agricultural than in desert soil (Shannon diversity indices: 11.21/7.90), and displayed structural differences. The proportion of Firmicutes in field soil was significantly higher (37%) than in the desert (11%). Bacillus and Paenibacillus play the key role: they represented 96% of the antagonists towards phytopathogens, and identical 16S rRNA sequences in the amplicon library and for isolates were detected. The proportion of antagonistic strains was doubled in field in comparison to desert soil (21.6%/12.4%); disease-suppressive bacteria were especially enriched in plant roots. On the opposite, several extremophilic bacterial groups, e.g., Acidimicrobium, Rubellimicrobium and Deinococcus-Thermus, disappeared from soil after agricultural use. The N-fixing Herbaspirillum group only occurred in desert soil. Soil bacterial communities were strongly driven by the a-biotic factors water supply and pH. Conclusions/Significance After long-term farming, a drastic shift in the bacterial communities in desert soil was observed. Bacterial communities in agricultural soil showed a higher diversity and a better ecosystem function for plant health but a loss of extremophilic bacteria. Interestingly, we detected that indigenous desert microorganisms promoted plant health in desert agro-ecosystems. PMID:21912695

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis

PubMed Central

Santana, Margarida M.; Gonzalez, Juan M.; Cruz, Cristina

2017-01-01

Many publications highlight the importance of nitric oxide (NO) in plant–bacteria interactions, either in the promotion of health and plant growth or in pathogenesis. However, the role of NO in the signaling between bacteria and plants and in the fate of their interaction, as well as the reconstruction of their interactive evolution, remains largely unknown. Despite the complexity of the evolution of life on Earth, we explore the hypothesis that denitrification and aerobic respiration were responsible for local NO accumulation, which triggered primordial antagonistic biotic interactions, namely the first phytopathogenic interactions. N-oxides, including NO, could globally accumulate via lightning synthesis in the early anoxic ocean and constitute pools for the evolution of denitrification, considered an early step of the biological nitrogen cycle. Interestingly, a common evolution may be proposed for components of denitrification and aerobic respiration pathways, namely for NO and oxygen reductases, a theory compatible with the presence of low amounts of oxygen before the great oxygenation event (GOE), which was generated by Cyanobacteria. During GOE, the increase in oxygen caused the decrease of Earth’s temperature and the consequent increase of oxygen dissolution and availability, making aerobic respiration an increasingly dominant trait of the expanding mesophilic lifestyle. Horizontal gene transfer was certainly important in the joint expansion of mesophily and aerobic respiration. First denitrification steps lead to NO formation through nitrite reductase activity, and NO may further accumulate when oxygen binds NO reductase, resulting in denitrification blockage. The consequent transient NO surplus in an oxic niche could have been a key factor for a successful outcome of an early denitrifying prokaryote able to scavenge oxygen by NO/oxygen reductase or by an independent heterotrophic aerobic respiration pathway. In fact, NO surplus could result in toxicity causing “the first disease” in oxygen-producing Cyanobacteria. We inspected in bacteria the presence of sequences similar to the NO-producing nitrite reductase nirS gene of Thermus thermophilus, an extreme thermophilic aerobe of the Thermus/Deinococcus group, which constitutes an ancient lineage related to Cyanobacteria. In silico analysis revealed the relationship between the presence of nirS genes and phytopathogenicity in Gram-negative bacteria. PMID:29067010

Geological and geochemical controls on subsurface microbial life in the Samail Ophiolite, Oman

DOE PAGES

Rempfert, Kaitlin R.; Miller, Hannah M.; Bompard, Nicolas; ...

2017-02-07

Microbial abundance and diversity in deep subsurface environments is dependent upon the availability of energy and carbon. However, supplies of oxidants and reductants capable of sustaining life within mafic and ultramafic continental aquifers undergoing low-temperature water-rock reaction are relatively unknown. We conducted an extensive analysis of the geochemistry and microbial communities recovered from fluids sampled from boreholes hosted in peridotite and gabbro in the Tayin block of the Samail Ophiolite in the Sultanate of Oman. The geochemical compositions of subsurface fluids in the ophiolite are highly variable, reflecting differences in host rock composition and the extent of fluid-rock interaction. Principal component analysis of fluid geochemistry and geologic context indicate the presence of at least four fluid types in the Samail Ophiolite (“gabbro,” “alkaline peridotite,” “hyperalkaline peridotite,” and “gabbro/peridotite contact”) that vary strongly in pH and the concentrations of H 2, CH 4, Ca 2+, Mg 2+, NO 3 more » $-$, SO$$2-\\atop{4}$$, trace metals, and DIC. Geochemistry of fluids is strongly correlated with microbial community composition; similar microbial assemblages group according to fluid type. Hyperalkaline fluids exhibit low diversity and are dominated by taxa related to the Deinococcus-Thermus genus Meiothermus, candidate phyla OP1, and the family Thermodesulfovibrionaceae. Gabbro- and alkaline peridotite- aquifers harbor more diverse communities and contain abundant microbial taxa affiliated with Nitrospira, Nitrosospharaceae, OP3, Parvarcheota, and OP1 order Acetothermales. Wells that sit at the contact between gabbro and peridotite host microbial communities distinct from all other fluid types, with an enrichment in betaproteobacterial taxa. Together the taxonomic information and geochemical data suggest that several metabolisms may be operative in subsurface fluids, including methanogenesis, acetogenesis, and fermentation, as well as the oxidation of methane, hydrogen and small molecular weight organic acids utilizing nitrate and sulfate as electron acceptors. Dynamic nitrogen cycling may be especially prevalent in gabbro and alkaline peridotite fluids. As a result, these data suggest water-rock reaction, as controlled by lithology and hydrogeology, constrains the distribution of life in terrestrial ophiolites.« less

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

NASA Technical Reports Server (NTRS)

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 anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations.

Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi).

PubMed

Kylie, Jennifer; Weese, J Scott; Turner, Patricia V

2018-04-27

Rabbits are cecotrophic, hindgut-fermenters that rely heavily on their gastrointestinal microbiota for optimal digestion of plant-based diets. Dysbiosis, caused by disruption of the gastrointestinal microbiota, is known to predispose rabbits to rabbit enteritis complex (REC), a major cause of morbidity and mortality. The objectives of this study were to describe the fecal microbiota of domestic rabbits from a variety of settings (commercial meat, companion, laboratory, and shelter) and to identify how factors such as age, season, and routine antimicrobial use affect the fecal microbiota composition. A total of 86 pooled commercial meat, 54 companion, 14 pooled laboratory, and 14 shelter rabbit fecal samples were evaluated using 16S rRNA gene sequencing of the V4 region. In all sample types, the predominant bacterial phylum was Firmicutes. Other commonly identified phyla (composing ≥ 1% of the total microbiota composition) were Verrucomicrobia, Proteobacteria, and Bacteroidetes. Significant differences in composition were noted between commercial, companion, laboratory, and shelter rabbit samples for proportions of Verrucomicrobia (P < 0.01), Proteobacteria (P < 0.01), and Lentisphaerae (P = 0.01) within the total microbiota. Within the commercial meat rabbit samples, significant differences between the microbiota composition of growers (n = 42) and does (n = 44) were limited to one unclassified Firmicutes (P = 0.03) and no differences were identified at the phylum level. Significant differences were present between fecal samples taken from rabbits during the summer (n = 44) compared to the winter (n = 42), with Firmicutes (P = 0.04), Verrucomicrobia (P = 0.03), Proteobacteria (P = 0.02), Deinococcus-Thermus (P = 0.04), Armatimonadates (P = 0.003), and Actinobacteria (P = 0.03) forming significantly different proportions of the microbiota. The only significant difference in composition between those farms that routinely reported antimicrobial use and those that did not was in one unclassified Bacteroidetes (P < 0.05) and no differences were identified at the phylum level. Rabbit husbandry and diet, in addition to season, significantly influence the fecal microbiota composition of domestic rabbits, while age of the rabbit post-weaning has minimal impact.

Data Documentation for Navy Civilian Manpower Study,

DTIC Science & Technology

1986-09-01

Engineering 0830 Mechanical Engineer 0840 Nuclear Engineering 0850 Electrical Engineering 0855 Electronics Engineering 0856 Electronics ...OCCUPATIONAL LEVEL (DONOL) CODES DONOL code Title 1060 Engineering Drafting 1061 Electronics Technician w 1062 Engineering Technician 1063 Industrial...Architect 2314 Electrical Engineer 2315 Electronic Engineer 2316 Industrial Engineer 2317 Mechanical Engineer 2318

40 CFR 90.116 - Certification procedure-determining engine displacement, engine class, and engine families.

Code of Federal Regulations, 2014 CFR

2014-07-01

... engine displacement, engine class, and engine families. 90.116 Section 90.116 Protection of Environment... Certification procedure—determining engine displacement, engine class, and engine families. (a) Engine displacement must be calculated using nominal engine values and rounded to the nearest whole cubic centimeter...

40 CFR 90.116 - Certification procedure-determining engine displacement, engine class, and engine families.

Code of Federal Regulations, 2013 CFR

2013-07-01

... engine displacement, engine class, and engine families. 90.116 Section 90.116 Protection of Environment... Certification procedure—determining engine displacement, engine class, and engine families. (a) Engine displacement must be calculated using nominal engine values and rounded to the nearest whole cubic centimeter...

40 CFR 90.116 - Certification procedure-determining engine displacement, engine class, and engine families.

Code of Federal Regulations, 2012 CFR

2012-07-01

... engine displacement, engine class, and engine families. 90.116 Section 90.116 Protection of Environment... Certification procedure—determining engine displacement, engine class, and engine families. (a) Engine displacement must be calculated using nominal engine values and rounded to the nearest whole cubic centimeter...

40 CFR 90.116 - Certification procedure-determining engine displacement, engine class, and engine families.

Code of Federal Regulations, 2011 CFR

2011-07-01

... engine displacement, engine class, and engine families. 90.116 Section 90.116 Protection of Environment... Certification procedure—determining engine displacement, engine class, and engine families. (a) Engine displacement must be calculated using nominal engine values and rounded to the nearest whole cubic centimeter...

40 CFR 90.116 - Certification procedure-determining engine displacement, engine class, and engine families.

Code of Federal Regulations, 2010 CFR

2010-07-01

... engine displacement, engine class, and engine families. 90.116 Section 90.116 Protection of Environment... Certification procedure—determining engine displacement, engine class, and engine families. (a) Engine displacement must be calculated using nominal engine values and rounded to the nearest whole cubic centimeter...

Engineering Ethics in the Subject of Engineering History

NASA Astrophysics Data System (ADS)

Isohata, Hiroshi

Engineering ethics has been focused in the field of engineering education since the introduction of accreditation system of engineering education. In this paper, contents of the subject of engineering history are examined and discussed from the viewpoints of education of engineering ethics through a practical case of civil engineering history in a college. For the first step, codes of engineering ethics regulated in various engineering organizations are analyzed and the common contents are extracted to set the requirements for the education of engineering ethics. Then contents of the subject of engineering history are examined according to the requirements. Finally, conditions of engineering history for engineering ethics are discussed.

Perturbing engine performance measurements to determine optimal engine control settings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Li; Lee, Donghoon; Yilmaz, Hakan

Methods and systems for optimizing a performance of a vehicle engine are provided. The method includes determining an initial value for a first engine control parameter based on one or more detected operating conditions of the vehicle engine, determining a value of an engine performance variable, and artificially perturbing the determined value of the engine performance variable. The initial value for the first engine control parameter is then adjusted based on the perturbed engine performance variable causing the engine performance variable to approach a target engine performance variable. Operation of the vehicle engine is controlled based on the adjusted initialmore » value for the first engine control parameter. These acts are repeated until the engine performance variable approaches the target engine performance variable.« less

Key Reliability Drivers of Liquid Propulsion Engines and A Reliability Model for Sensitivity Analysis

NASA Technical Reports Server (NTRS)

Huang, Zhao-Feng; Fint, Jeffry A.; Kuck, Frederick M.

2005-01-01

This paper is to address the in-flight reliability of a liquid propulsion engine system for a launch vehicle. We first establish a comprehensive list of system and sub-system reliability drivers for any liquid propulsion engine system. We then build a reliability model to parametrically analyze the impact of some reliability parameters. We present sensitivity analysis results for a selected subset of the key reliability drivers using the model. Reliability drivers identified include: number of engines for the liquid propulsion stage, single engine total reliability, engine operation duration, engine thrust size, reusability, engine de-rating or up-rating, engine-out design (including engine-out switching reliability, catastrophic fraction, preventable failure fraction, unnecessary shutdown fraction), propellant specific hazards, engine start and cutoff transient hazards, engine combustion cycles, vehicle and engine interface and interaction hazards, engine health management system, engine modification, engine ground start hold down with launch commit criteria, engine altitude start (1 in. start), Multiple altitude restart (less than 1 restart), component, subsystem and system design, manufacturing/ground operation support/pre and post flight check outs and inspection, extensiveness of the development program. We present some sensitivity analysis results for the following subset of the drivers: number of engines for the propulsion stage, single engine total reliability, engine operation duration, engine de-rating or up-rating requirements, engine-out design, catastrophic fraction, preventable failure fraction, unnecessary shutdown fraction, and engine health management system implementation (basic redlines and more advanced health management systems).

Engineering Review Information System

NASA Technical Reports Server (NTRS)

Grems, III, Edward G. (Inventor); Henze, James E. (Inventor); Bixby, Jonathan A. (Inventor); Roberts, Mark (Inventor); Mann, Thomas (Inventor)

2015-01-01

A disciplinal engineering review computer information system and method by defining a database of disciplinal engineering review process entities for an enterprise engineering program, opening a computer supported engineering item based upon the defined disciplinal engineering review process entities, managing a review of the opened engineering item according to the defined disciplinal engineering review process entities, and closing the opened engineering item according to the opened engineering item review.

Concurrently adjusting interrelated control parameters to achieve optimal engine performance

DOEpatents

Jiang, Li; Lee, Donghoon; Yilmaz, Hakan; Stefanopoulou, Anna

2015-12-01

Methods and systems for real-time engine control optimization are provided. A value of an engine performance variable is determined, a value of a first operating condition and a value of a second operating condition of a vehicle engine are detected, and initial values for a first engine control parameter and a second engine control parameter are determined based on the detected first operating condition and the detected second operating condition. The initial values for the first engine control parameter and the second engine control parameter are adjusted based on the determined value of the engine performance variable to cause the engine performance variable to approach a target engine performance variable. In order to cause the engine performance variable to approach the target engine performance variable, adjusting the initial value for the first engine control parameter necessitates a corresponding adjustment of the initial value for the second engine control parameter.

Component improvement of free-piston Stirling engine key technology for space power

NASA Technical Reports Server (NTRS)

Alger, Donald L.

1988-01-01

The successful performance of the 25 kW Space Power Demonstrator (SPD) engine during an extensive testing period has provided a baseline of free piston Stirling engine technology from which future space Stirling engines may evolve. Much of the success of the engine was due to the initial careful selection of engine materials, fabrication and joining processes, and inspection procedures. Resolution of the few SPD engine problem areas that did occur has resulted in the technological advancement of certain key free piston Stirling engine components. Derivation of two half-SPD, single piston engines from the axially opposed piston SPD engine, designated as Space Power Research (SPR) engines, has made possible the continued improvement of these engine components. The two SPR engines serve as test bed engines for testing of engine components. Some important fabrication and joining processes are reviewed. Also, some component deficiencies that were discovered during SPD engine testing are described and approaches that were taken to correct these deficiencies are discussed. Potential component design modifications, based upon the SPD and SPR engine testing, are also reported.

Engine systems analysis results of the Space Shuttle Main Engine redesigned powerhead initial engine level testing

NASA Technical Reports Server (NTRS)

Sander, Erik J.; Gosdin, Dennis R.

1992-01-01

Engineers regularly analyze SSME ground test and flight data with respect to engine systems performance. Recently, a redesigned SSME powerhead was introduced to engine-level testing in part to increase engine operational margins through optimization of the engine internal environment. This paper presents an overview of the MSFC personnel engine systems analysis results and conclusions reached from initial engine level testing of the redesigned powerhead, and further redesigns incorporated to eliminate accelerated main injector baffle and main combustion chamber hot gas wall degradation. The conclusions are drawn from instrumented engine ground test data and hardware integrity analysis reports and address initial engine test results with respect to the apparent design change effects on engine system and component operation.

Engine having multiple pumps driven by a single shaft

DOEpatents

Blass, James R.

2001-01-01

An engine comprises an engine housing. A first engine fluid sub-system that includes a first pump and the engine housing defining a first fluid passage is also included in the engine. The engine also includes at least one additional engine fluid sub-system that includes a second pump and the engine housing defining a second fluid passage. A rotating shaft is at least partially positioned in the engine housing, the first pump and the second pump.

Engineering Education for a New Era

NASA Astrophysics Data System (ADS)

Ohgaki, Shinichiro

Engineering education is composed of five components, the idea what engineering education ought to be, the knowledge in engineering fields, those who learn engineering, those who teach engineering and the stakeholders in engineering issues. The characteristics of all these five components are changing with the times. When we consider the engineering education for the next era, we should analyze the changes of all five components. Especially the knowledge and tools in engineering fields has been expanding, and advanced science and technology is casting partly a dark shadow on the modern convenient life. Moral rules or ethics for developing new products and engineering systems are now regarded as most important in engineering fields. All those who take the responsibility for engineering education should understand the change of all components in engineering education and have a clear grasp of the essence of engineering for sustainable society.

78 FR 5710 - Airworthiness Directives; Engine Alliance Turbofan Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-28

... Airworthiness Directives; Engine Alliance Turbofan Engines AGENCY: Federal Aviation Administration (FAA), DOT... all Engine Alliance GP7270 and GP7277 turbofan engines. This AD requires initial and repetitive...) Applicability This AD applies to all Engine Alliance GP7270 and GP7277 turbofan engines with a high-pressure...

78 FR 775 - Goodman Networks, Inc. Core Network Engineering (Deployment Engineering) Division Alpharetta, GA...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-04

...,846B; TA-W-81,846C; TA-W-81,846D] Goodman Networks, Inc. Core Network Engineering (Deployment Engineering) Division Alpharetta, GA; Goodman Networks, Inc. Core Network Engineering (Deployment Engineering) Division Hunt Valley, MD; Goodman Networks, Inc. Core Network Engineering (Deployment Engineering) Division...

40 CFR 91.115 - Certification procedure-determining engine power and engine families.

Code of Federal Regulations, 2010 CFR

2010-07-01

... engine power and engine families. 91.115 Section 91.115 Protection of Environment ENVIRONMENTAL... ENGINES Emission Standards and Certification Provisions § 91.115 Certification procedure—determining engine power and engine families. (a) Engine power must be calculated using SAE J1228. This procedure has...

14 CFR 23.777 - Cockpit controls.

Code of Federal Regulations, 2013 CFR

2013-01-01

... powerplant controls for each engine must be located to prevent confusion as to the engines they control. (1... engines(s) and the right control(s) operates the right engine(s). (2) On twin-engine airplanes with front and rear engine locations (tandem), the left powerplant controls must operate the front engine and the...

14 CFR 23.777 - Cockpit controls.

Code of Federal Regulations, 2014 CFR

2014-01-01

... powerplant controls for each engine must be located to prevent confusion as to the engines they control. (1... engines(s) and the right control(s) operates the right engine(s). (2) On twin-engine airplanes with front and rear engine locations (tandem), the left powerplant controls must operate the front engine and the...

Biocatalysis engineering: the big picture.

PubMed

Sheldon, Roger A; Pereira, Pedro C

2017-05-22

In this tutorial review we describe a holistic approach to the invention, development and optimisation of biotransformations utilising isolated enzymes. Increasing attention to applied biocatalysis is motivated by its numerous economic and environmental benefits. Biocatalysis engineering concerns the development of enzymatic systems as a whole, which entails engineering its different components: substrate engineering, medium engineering, protein (enzyme) engineering, biocatalyst (formulation) engineering, biocatalytic cascade engineering and reactor engineering.

Technician Career Opportunities in Engineering Technology.

ERIC Educational Resources Information Center

Engineers' Council for Professional Development, New York, NY.

Career opportunities for engineering technicians are available in the technologies relating to air conditioning, heating, and refrigeration, aviation and aerospace, building construction, chemical engineering, civil engineering, electrical engineering, electronics, industrial engineering, instrumentation, internal combustion engines, mechanical…

The responsibilities of engineers.

PubMed

Smith, Justin; Gardoni, Paolo; Murphy, Colleen

2014-06-01

Knowledge of the responsibilities of engineers is the foundation for answering ethical questions about the work of engineers. This paper defines the responsibilities of engineers by considering what constitutes the nature of engineering as a particular form of activity. Specifically, this paper focuses on the ethical responsibilities of engineers qua engineers. Such responsibilities refer to the duties acquired in virtue of being a member of a group. We examine the practice of engineering, drawing on the idea of practices developed by philosopher Alasdair MacIntyre, and show how the idea of a practice is important for identifying and justifying the responsibilities of engineers. To demonstrate the contribution that knowledge of the responsibilities of engineers makes to engineering ethics, a case study from structural engineering is discussed. The discussion of the failure of the Sleipner A Platform off the coast of Norway in 1991 demonstrates how the responsibilities of engineers can be derived from knowledge of the nature of engineering and its context.

Globalization and Organizational Change: Engineers' Experiences and Their Implications for Engineering Education

ERIC Educational Resources Information Center

Lucena, Juan C.

2006-01-01

The demand for flexible engineers presents significant challenges to engineering education. Among these is the need for engineers to be prepared to understand and deal with organizational change. Yet engineering education and research on engineers have overlooked the impact of organizational change on engineering work. After outlining the impact…

Staged combustion with piston engine and turbine engine supercharger

DOEpatents

Fischer, Larry E [Los Gatos, CA; Anderson, Brian L [Lodi, CA; O'Brien, Kevin C [San Ramon, CA

2006-05-09

A combustion engine method and system provides increased fuel efficiency and reduces polluting exhaust emissions by burning fuel in a two-stage combustion system. Fuel is combusted in a piston engine in a first stage producing piston engine exhaust gases. Fuel contained in the piston engine exhaust gases is combusted in a second stage turbine engine. Turbine engine exhaust gases are used to supercharge the piston engine.

Staged combustion with piston engine and turbine engine supercharger

DOEpatents

Fischer, Larry E [Los Gatos, CA; Anderson, Brian L [Lodi, CA; O'Brien, Kevin C [San Ramon, CA

2011-11-01

A combustion engine method and system provides increased fuel efficiency and reduces polluting exhaust emissions by burning fuel in a two-stage combustion system. Fuel is combusted in a piston engine in a first stage producing piston engine exhaust gases. Fuel contained in the piston engine exhaust gases is combusted in a second stage turbine engine. Turbine engine exhaust gases are used to supercharge the piston engine.

Wave rotor demonstrator engine assessment

NASA Technical Reports Server (NTRS)

Snyder, Philip H.

1996-01-01

The objective of the program was to determine a wave rotor demonstrator engine concept using the Allison 250 series engine. The results of the NASA LERC wave rotor effort were used as a basis for the wave rotor design. A wave rotor topped gas turbine engine was identified which incorporates five basic requirements of a successful demonstrator engine. Predicted performance maps of the wave rotor cycle were used along with maps of existing gas turbine hardware in a design point study. The effects of wave rotor topping on the engine cycle and the subsequent need to rematch compressor and turbine sections in the topped engine were addressed. Comparison of performance of the resulting engine is made on the basis of wave rotor topped engine versus an appropriate baseline engine using common shaft compressor hardware. The topped engine design clearly demonstrates an impressive improvement in shaft horsepower (+11.4%) and SFC (-22%). Off design part power engine performance for the wave rotor topped engine was similarly improved including that at engine idle conditions. Operation of the engine at off design was closely examined with wave rotor operation at less than design burner outlet temperatures and rotor speeds. Challenges identified in the development of a demonstrator engine are discussed. A preliminary design was made of the demonstrator engine including wave rotor to engine transition ducts. Program cost and schedule for a wave rotor demonstrator engine fabrication and test program were developed.

Wave Engine Topping Cycle Assessment

NASA Technical Reports Server (NTRS)

Welch, Gerard E.

1996-01-01

The performance benefits derived by topping a gas turbine engine with a wave engine are assessed. The wave engine is a wave rotor that produces shaft power by exploiting gas dynamic energy exchange and flow turning. The wave engine is added to the baseline turboshaft engine while keeping high-pressure-turbine inlet conditions, compressor pressure ratio, engine mass flow rate, and cooling flow fractions fixed. Related work has focused on topping with pressure-exchangers (i.e., wave rotors that provide pressure gain with zero net shaft power output); however, more energy can be added to a wave-engine-topped cycle leading to greater engine specific-power-enhancement The energy addition occurs at a lower pressure in the wave-engine-topped cycle; thus the specific-fuel-consumption-enhancement effected by ideal wave engine topping is slightly lower than that effected by ideal pressure-exchanger topping. At a component level, however, flow turning affords the wave engine a degree-of-freedom relative to the pressure-exchanger that enables a more efficient match with the baseline engine. In some cases, therefore, the SFC-enhancement by wave engine topping is greater than that by pressure-exchanger topping. An ideal wave-rotor-characteristic is used to identify key wave engine design parameters and to contrast the wave engine and pressure-exchanger topping approaches. An aerodynamic design procedure is described in which wave engine design-point performance levels are computed using a one-dimensional wave rotor model. Wave engines using various wave cycles are considered including two-port cycles with on-rotor combustion (valved-combustors) and reverse-flow and through-flow four-port cycles with heat addition in conventional burners. A through-flow wave cycle design with symmetric blading is used to assess engine performance benefits. The wave-engine-topped turboshaft engine produces 16% more power than does a pressure-exchanger-topped engine under the specified topping constraints. Positive and negative aspects of wave engine topping in gas turbine engines are identified.

Problem Decomposition and Recomposition in Engineering Design: A Comparison of Design Behavior between Professional Engineers, Engineering Seniors, and Engineering Freshmen

ERIC Educational Resources Information Center

Song, Ting; Becker, Kurt; Gero, John; DeBerard, Scott; DeBerard, Oenardi; Reeve, Edward

2016-01-01

The authors investigated the differences in using problem decomposition and problem recomposition between dyads of engineering experts, engineering seniors, and engineering freshmen. Participants worked in dyads to complete an engineering design challenge within 1 hour. The entire design process was video and audio recorded. After the design…

Automotive Stirling Engine Mod 1 Design Review, Volume 1

NASA Technical Reports Server (NTRS)

1982-01-01

Risk assessment, safety analysis of the automotive stirling engine (ASE) mod I, design criteria and materials properties for the ASE mod I and reference engines, combustion are flower development, and the mod I engine starter motor are discussed. The stirling engine system, external heat system, hot engine system, cold engine system, and engine drive system are also discussed.

77 FR 42724 - Agency Information Collection Activities; Submission to OMB for Review and Approval; Comment...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-20

... Nonroad Spark-Ignited Engines, New Nonroad Compression-Ignited Engines, and New On-Road Heavy Duty Engines... Compression-ignited Engines, and New On-road Heavy Duty Engines (Renewal). ICR numbers: EPA ICR No. 1852.05... engines, new nonroad compression-ignited engines, and new on- road heavy duty engines. Estimated Number of...

Civil engineering reference guide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Merritt, F.S.

1986-01-01

The civil engineering reference guide contains the following: Structural theory. Structural steel design. Concrete design and construction. Wood design and construction. Bridge engineering. Geotechnical engineering. Water engineering. Environmental engineering. Surveying.

Understanding the Role of Academic Language on Conceptual Understanding in an Introductory Materials Science and Engineering Course

NASA Astrophysics Data System (ADS)

Kelly, Jacquelyn

Students may use the technical engineering terms without knowing what these words mean. This creates a language barrier in engineering that influences student learning. Previous research has been conducted to characterize the difference between colloquial and scientific language. Since this research had not yet been applied explicitly to engineering, conclusions from the area of science education were used instead. Various researchers outlined strategies for helping students acquire scientific language. However, few examined and quantified the relationship it had on student learning. A systemic functional linguistics framework was adopted for this dissertation which is a framework that has not previously been used in engineering education research. This study investigated how engineering language proficiency influenced conceptual understanding of introductory materials science and engineering concepts. To answer the research questions about engineering language proficiency, a convenience sample of forty-one undergraduate students in an introductory materials science and engineering course was used. All data collected was integrated with the course. Measures included the Materials Concept Inventory, a written engineering design task, and group observations. Both systemic functional linguistics and mental models frameworks were utilized to interpret data and guide analysis. A series of regression analyses were conducted to determine if engineering language proficiency predicts group engineering term use, if conceptual understanding predicts group engineering term use, and if conceptual understanding predicts engineering language proficiency. Engineering academic language proficiency was found to be strongly linked to conceptual understanding in the context of introductory materials engineering courses. As the semester progressed, this relationship became even stronger. The more engineering concepts students are expected to learn, the more important it is that they are proficient in engineering language. However, exposure to engineering terms did not influence engineering language proficiency. These results stress the importance of engineering language proficiency for learning, but warn that simply exposing students to engineering terms does not promote engineering language proficiency.

Performance and driveline analyses of engine capacity in range extender engine hybrid vehicle

NASA Astrophysics Data System (ADS)

Praptijanto, Achmad; Santoso, Widodo Budi; Nur, Arifin; Wahono, Bambang; Putrasari, Yanuandri

2017-01-01

In this study, range extender engine designed should be able to meet the power needs of a power generator of hybrid electrical vehicle that has a minimum of 18 kW. Using this baseline model, the following range extenders will be compared between conventional SI piston engine (Baseline, BsL), engine capacity 1998 cm3, and efficiency-oriented SI piston with engine capacity 999 cm3 and 499 cm3 with 86 mm bore and stroke square gasoline engine in the performance, emission prediction of range extender engine, standard of charge by using engine and vehicle simulation software tools. In AVL Boost simulation software, range extender engine simulated from 1000 to 6000 rpm engine loads. The highest peak engine power brake reached up to 38 kW at 4500 rpm. On the other hand the highest torque achieved in 100 Nm at 3500 rpm. After that using AVL cruise simulation software, the model of range extended electric vehicle in series configuration with main components such as internal combustion engine, generator, electric motor, battery and the arthemis model rural road cycle was used to simulate the vehicle model. The simulation results show that engine with engine capacity 999 cm3 reported the economical performances of the engine and the emission and the control of engine cycle parameters.

40 CFR 1048.330 - May I sell engines from an engine family with a suspended certificate of conformity?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false May I sell engines from an engine... ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW, LARGE NONROAD SPARK-IGNITION ENGINES Testing Production-line Engines § 1048.330 May I sell engines from an engine...

A Feasibility Study for Advanced Technology Integration for General Aviation.

DTIC Science & Technology

1980-05-01

154 4.5.9.4 Stratified Charge Reciprocating Engine ..... .. 155 4.5.9.5 Advanced Diesel Engine . ... 158 4.5.9.6 Liquid Cooling ... ........ 159... diesel , rotary combustion engine, advanced reciprocating engine concepts. (7) Powerplant control - integrated controls, microprocessor- based controls...Research Center Topics. (1) GATE (2) Positive displacement engines (a) Advanced reciprocating engines. (b) Alternative engine systems Diesel engines

Entropy-Based Performance Analysis of Jet Engines; Methodology and Application to a Generic Single-Spool Turbojet

NASA Astrophysics Data System (ADS)

Abbas, Mohammad

Recently developed methodology that provides the direct assessment of traditional thrust-based performance of aerospace vehicles in terms of entropy generation (i.e., exergy destruction) is modified for stand-alone jet engines. This methodology is applied to a specific single-spool turbojet engine configuration. A generic compressor performance map along with modeled engine component performance characterizations are utilized in order to provide comprehensive traditional engine performance results (engine thrust, mass capture, and RPM), for on and off-design engine operation. Details of exergy losses in engine components, across the entire engine, and in the engine wake are provided and the engine performance losses associated with their losses are discussed. Results are provided across the engine operating envelope as defined by operational ranges of flight Mach number, altitude, and fuel throttle setting. The exergy destruction that occurs in the engine wake is shown to be dominant with respect to other losses, including all exergy losses that occur inside the engine. Specifically, the ratio of the exergy destruction rate in the wake to the exergy destruction rate inside the engine itself ranges from 1 to 2.5 across the operational envelope of the modeled engine.

40 CFR 1065.401 - Test engine selection.

Code of Federal Regulations, 2010 CFR

2010-07-01

... CONTROLS ENGINE-TESTING PROCEDURES Engine Selection, Preparation, and Maintenance § 1065.401 Test engine selection. While all engine configurations within a certified engine family must comply with the applicable... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Test engine selection. 1065.401...

Enhancing Engineering Education through Engineering Management

ERIC Educational Resources Information Center

Pence, Kenneth R.; Rowe, Christopher J.

2012-01-01

Engineering Management courses are added to a traditional engineering curriculum to enhance the value of an undergraduate's engineering degree. A four-year engineering degree often leaves graduates lacking in business and management acumen. Engineering management education covers topics enhancing the value of new graduates by teaching management…

78 FR 12359 - Goodman Networks, Inc., Core Network Engineering (Deployment Engineering) Division Including...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-22

...., Core Network Engineering (Deployment Engineering) Division Including Workers in the Core Network Engineering (Deployment Engineering) Division in Alpharetta, GA, Hunt Valley, MD, Naperville, IL, and St... Reconsideration applicable to workers and former workers of Goodman Networks, Inc., Core Network Engineering...

40 CFR 1042.825 - Baseline determination.

Code of Federal Regulations, 2010 CFR

2010-07-01

... a used engine to be the emission-data engine for the engine family for testing. Using good engineering judgment, select the engine configuration expected to represent the most common configuration in... adjust it differently, consistent with good engineering judgment. (d) Test the baseline engine four times...

40 CFR 1042.825 - Baseline determination.

Code of Federal Regulations, 2011 CFR

2011-07-01

... a used engine to be the emission-data engine for the engine family for testing. Using good engineering judgment, select the engine configuration expected to represent the most common configuration in... adjust it differently, consistent with good engineering judgment. (d) Test the baseline engine four times...

40 CFR 1065.401 - Test engine selection.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Test engine selection. 1065.401... CONTROLS ENGINE-TESTING PROCEDURES Engine Selection, Preparation, and Maintenance § 1065.401 Test engine selection. While all engine configurations within a certified engine family must comply with the applicable...

40 CFR 1065.401 - Test engine selection.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false Test engine selection. 1065.401... CONTROLS ENGINE-TESTING PROCEDURES Engine Selection, Preparation, and Maintenance § 1065.401 Test engine selection. While all engine configurations within a certified engine family must comply with the applicable...

40 CFR 1065.401 - Test engine selection.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Test engine selection. 1065.401... CONTROLS ENGINE-TESTING PROCEDURES Engine Selection, Preparation, and Maintenance § 1065.401 Test engine selection. While all engine configurations within a certified engine family must comply with the applicable...

Multi-fuel rotary engine for general aviation aircraft

NASA Technical Reports Server (NTRS)

Jones, C.; Ellis, D. R.; Meng, P. R.

1983-01-01

Design studies of advanced multifuel general aviation and commuter aircraft rotary stratified charge engines are summarized. Conceptual design studies were performed at two levels of technology, on advanced general aviation engines sized to provide 186/250 shaft kW/hp under cruise conditions at 7620 (25000 m/ft) altitude. A follow on study extended the results to larger (2500 hp max.) engine sizes suitable for applications such as commuter transports and helicopters. The study engine designs were derived from relevant engine development background including both prior and recent engine test results using direct injected unthrottled rotary engine technology. Aircraft studies, using these resultant growth engines, define anticipated system effects of the performance and power density improvements for both single engine and twin engine airplanes. The calculated results indicate superior system performance and 27 to 33 percent fuel economy improvement for the rotary engine airplanes as compared to equivalent airframe concept designs with current baseline engines. The research and technology activities required to attain the projected engine performance levels are also discussed.

Virtual Collaborative Environments for System of Systems Engineering and Applications for ISAT

NASA Technical Reports Server (NTRS)

Dryer, David A.

2002-01-01

This paper describes an system of systems or metasystems approach and models developed to help prepare engineering organizations for distributed engineering environments. These changes in engineering enterprises include competition in increasingly global environments; new partnering opportunities caused by advances in information and communication technologies, and virtual collaboration issues associated with dispersed teams. To help address challenges and needs in this environment, a framework is proposed that can be customized and adapted for NASA to assist in improved engineering activities conducted in distributed, enhanced engineering environments. The approach is designed to prepare engineers for such distributed collaborative environments by learning and applying e-engineering methods and tools to a real-world engineering development scenario. The approach consists of two phases: an e-engineering basics phase and e-engineering application phase. The e-engineering basics phase addresses skills required for e-engineering. The e-engineering application phase applies these skills in a distributed collaborative environment to system development projects.

Analysis of a topping-cycle, aircraft, gas-turbine-engine system which uses cryogenic fuel

NASA Technical Reports Server (NTRS)

Turney, G. E.; Fishbach, L. H.

1984-01-01

A topping-cycle aircraft engine system which uses a cryogenic fuel was investigated. This system consists of a main turboshaft engine that is mechanically coupled (by cross-shafting) to a topping loop, which augments the shaft power output of the system. The thermodynamic performance of the topping-cycle engine was analyzed and compared with that of a reference (conventional) turboshaft engine. For the cycle operating conditions selected, the performance of the topping-cycle engine in terms of brake specific fuel consumption (bsfc) was determined to be about 12 percent better than that of the reference turboshaft engine. Engine weights were estimated for both the topping-cycle engine and the reference turboshaft engine. These estimates were based on a common shaft power output for each engine. Results indicate that the weight of the topping-cycle engine is comparable with that of the reference turboshaft engine.

Study of LH2-fueled topping cycle engine for aircraft propulsion

NASA Technical Reports Server (NTRS)

Turney, G. E.; Fishbach, L. H.

1983-01-01

An analytical investigation was made of a topping cycle aircraft engine system which uses a cryogenic fuel. This system consists of a main turboshaft engine which is mechanically coupled (by cross-shafting) to a topping loop which augments the shaft power output of the system. The thermodynamic performance of the topping cycle engine was analyzed and compared with that of a reference (conventional-type) turboshaft engine. For the cycle operating conditions selected, the performance of the topping cycle engine in terms of brake specific fuel consumption (bsfc) was determined to be about 12 percent better than that of the reference turboshaft engine. Engine weights were estimated for both the topping cycle engine and the reference turboshaft engine. These estimates were based on a common shaft power output for each engine. Results indicate that the weight of the topping cycle engine is comparable to that of the reference turboshaft engine.

Adjusting the specificity of an engine map based on the sensitivity of an engine control parameter relative to a performance variable

DOEpatents

Jiang, Li; Lee, Donghoon; Yilmaz, Hakan; Stefanopoulou, Anna

2014-10-28

Methods and systems for engine control optimization are provided. A first and a second operating condition of a vehicle engine are detected. An initial value is identified for a first and a second engine control parameter corresponding to a combination of the detected operating conditions according to a first and a second engine map look-up table. The initial values for the engine control parameters are adjusted based on a detected engine performance variable to cause the engine performance variable to approach a target value. A first and a second sensitivity of the engine performance variable are determined in response to changes in the engine control parameters. The first engine map look-up table is adjusted when the first sensitivity is greater than a threshold, and the second engine map look-up table is adjusted when the second sensitivity is greater than a threshold.

Performance and efficiency evaluation and heat release study of a direct-injection stratified-charge rotary engine

NASA Technical Reports Server (NTRS)

Nguyen, H. L.; Addy, H. E.; Bond, T. H.; Lee, C. M.; Chun, K. S.

1987-01-01

A computer simulation which models engine performance of the Direct Injection Stratified Charge (DISC) rotary engines was used to study the effect of variations in engine design and operating parameters on engine performance and efficiency of an Outboard Marine Corporation (OMC) experimental rotary combustion engine. Engine pressure data were used in a heat release analysis to study the effects of heat transfer, leakage, and crevice flows. Predicted engine data were compared with experimental test data over a range of engine speeds and loads. An examination of methods to improve the performance of the rotary engine using advanced heat engine concepts such as faster combustion, reduced leakage, and turbocharging is also presented.

Advanced General Aviation Turbine Engine (GATE) study

NASA Technical Reports Server (NTRS)

Smith, R.; Benstein, E. H.

1979-01-01

The small engine technology requirements suitable for general aviation service in the 1987 to 1988 time frame were defined. The market analysis showed potential United States engines sales of 31,500 per year providing that the turbine engine sales price approaches current reciprocating engine prices. An optimum engine design was prepared for four categories of fixed wing aircraft and for rotary wing applications. A common core approach was derived from the optimum engines that maximizes engine commonality over the power spectrum with a projected price competitive with reciprocating piston engines. The advanced technology features reduced engine cost, approximately 50 percent compared with current technology.

14 CFR Appendix D to Part 147 - Powerplant Curriculum Subjects

Code of Federal Regulations, 2013 CFR

2013-01-01

... a. reciprocating engines (1) 1. Inspect and repair a radial engine. (2) 2. Overhaul reciprocating.... Install, troubleshoot, and remove reciprocating engines. b. turbine engines (2) 5. Overhaul turbine engine. (3) 6. Inspect, check, service, and repair turbine engines and turbine engine installations. (3) 7...

14 CFR Appendix D to Part 147 - Powerplant Curriculum Subjects

Code of Federal Regulations, 2012 CFR

2012-01-01

... a. reciprocating engines (1) 1. Inspect and repair a radial engine. (2) 2. Overhaul reciprocating.... Install, troubleshoot, and remove reciprocating engines. b. turbine engines (2) 5. Overhaul turbine engine. (3) 6. Inspect, check, service, and repair turbine engines and turbine engine installations. (3) 7...

14 CFR Appendix D to Part 147 - Powerplant Curriculum Subjects

Code of Federal Regulations, 2014 CFR

2014-01-01

... a. reciprocating engines (1) 1. Inspect and repair a radial engine. (2) 2. Overhaul reciprocating.... Install, troubleshoot, and remove reciprocating engines. b. turbine engines (2) 5. Overhaul turbine engine. (3) 6. Inspect, check, service, and repair turbine engines and turbine engine installations. (3) 7...

14 CFR Appendix D to Part 147 - Powerplant Curriculum Subjects

Code of Federal Regulations, 2011 CFR

2011-01-01

... a. reciprocating engines (1) 1. Inspect and repair a radial engine. (2) 2. Overhaul reciprocating.... Install, troubleshoot, and remove reciprocating engines. b. turbine engines (2) 5. Overhaul turbine engine. (3) 6. Inspect, check, service, and repair turbine engines and turbine engine installations. (3) 7...

Be a Professional - Be Licensed! - Take the agricultural engineering professional engineering exam

USDA-ARS?s Scientific Manuscript database

Between October 2005 and October 2007, only 78 Agricultural Engineers took the professional engineering (PE) exam in the field of Agricultural Engineering, while the other 406 registered Agricultural Engineering Examinees took tests offer by other engineering disciplines. With the decline in partic...

Opportunities in Civil Engineering. [VGM Career Horizons Series].

ERIC Educational Resources Information Center

Hagerty, D. Joseph; Heer, John E., Jr.

This book presents information on career opportunities in civil engineering. Chapter 1 focuses on the scope of civil engineering, discussing: role of scientist, engineer, and technologists; engineering and engineering technology; civil engineer's role and obligations; and other information. Chapter 2 considers such aspects of the education for…

Federal Funding of Engineering Research and Development, 1980-1984.

ERIC Educational Resources Information Center

American Society of Mechanical Engineers, Washington, DC.

Data on the sources, amounts, and trends of federal funding for engineering research and development (R&D) are presented for 1980-1984. Narrative highlights are provided for: the total federal funding obligations for engineering R&D, mechanical engineering, astronautical engineering, aeronautical engineering, chemical engineering, civil…

Engine control techniques to account for fuel effects

DOEpatents

Kumar, Shankar; Frazier, Timothy R.; Stanton, Donald W.; Xu, Yi; Bunting, Bruce G.; Wolf, Leslie R.

2014-08-26

A technique for engine control to account for fuel effects including providing an internal combustion engine and a controller to regulate operation thereof, the engine being operable to combust a fuel to produce an exhaust gas; establishing a plurality of fuel property inputs; establishing a plurality of engine performance inputs; generating engine control information as a function of the fuel property inputs and the engine performance inputs; and accessing the engine control information with the controller to regulate at least one engine operating parameter.

40 CFR 1042.101 - Exhaust emission standards for Category 1 engines and Category 2 engines.

Code of Federal Regulations, 2014 CFR

2014-07-01

... from research engines or similar engine models that are already in production. Your demonstration must... Category 1 engines and Category 2 engines. 1042.101 Section 1042.101 Protection of Environment... MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Emission Standards and Related Requirements § 1042.101...

14 CFR 33.84 - Engine overtorque test.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Engine overtorque test. 33.84 Section 33.84... STANDARDS: AIRCRAFT ENGINES Block Tests; Turbine Aircraft Engines § 33.84 Engine overtorque test. (a) If approval of a maximum engine overtorque is sought for an engine incorporating a free power turbine...

40 CFR 1054.140 - What is my engine's maximum engine power and displacement?

Code of Federal Regulations, 2010 CFR

2010-07-01

... power and displacement? 1054.140 Section 1054.140 Protection of Environment ENVIRONMENTAL PROTECTION... engine power and displacement? This section describes how to quantify your engine's maximum engine power and displacement for the purposes of this part. (a) An engine configuration's maximum engine power is...

40 CFR 1054.140 - What is my engine's maximum engine power and displacement?

Code of Federal Regulations, 2011 CFR

2011-07-01

... power and displacement? 1054.140 Section 1054.140 Protection of Environment ENVIRONMENTAL PROTECTION... engine power and displacement? This section describes how to quantify your engine's maximum engine power and displacement for the purposes of this part. (a) An engine configuration's maximum engine power is...

40 CFR 1054.140 - What is my engine's maximum engine power and displacement?

Code of Federal Regulations, 2012 CFR

2012-07-01

... power and displacement? 1054.140 Section 1054.140 Protection of Environment ENVIRONMENTAL PROTECTION... engine power and displacement? This section describes how to quantify your engine's maximum engine power and displacement for the purposes of this part. (a) An engine configuration's maximum engine power is...

40 CFR 1054.140 - What is my engine's maximum engine power and displacement?

Code of Federal Regulations, 2014 CFR

2014-07-01

... power and displacement? 1054.140 Section 1054.140 Protection of Environment ENVIRONMENTAL PROTECTION... engine power and displacement? This section describes how to quantify your engine's maximum engine power and displacement for the purposes of this part. (a) An engine configuration's maximum engine power is...

40 CFR 1054.140 - What is my engine's maximum engine power and displacement?

Code of Federal Regulations, 2013 CFR

2013-07-01

... power and displacement? 1054.140 Section 1054.140 Protection of Environment ENVIRONMENTAL PROTECTION... engine power and displacement? This section describes how to quantify your engine's maximum engine power and displacement for the purposes of this part. (a) An engine configuration's maximum engine power is...

40 CFR 1039.140 - What is my engine's maximum engine power?

Code of Federal Regulations, 2014 CFR

2014-07-01

...) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE NONROAD COMPRESSION-IGNITION ENGINES... 1065, based on the manufacturer's design and production specifications for the engine. This information... power values for an engine are based on maximum engine power. For example, the group of engines with...

40 CFR 1039.140 - What is my engine's maximum engine power?

Code of Federal Regulations, 2011 CFR

2011-07-01

...) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE NONROAD COMPRESSION-IGNITION ENGINES... 1065, based on the manufacturer's design and production specifications for the engine. This information... power values for an engine are based on maximum engine power. For example, the group of engines with...

40 CFR 1039.140 - What is my engine's maximum engine power?

Code of Federal Regulations, 2010 CFR

2010-07-01

...) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE NONROAD COMPRESSION-IGNITION ENGINES... 1065, based on the manufacturer's design and production specifications for the engine. This information... power values for an engine are based on maximum engine power. For example, the group of engines with...

40 CFR 1039.140 - What is my engine's maximum engine power?

Code of Federal Regulations, 2012 CFR

2012-07-01

...) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE NONROAD COMPRESSION-IGNITION ENGINES... 1065, based on the manufacturer's design and production specifications for the engine. This information... power values for an engine are based on maximum engine power. For example, the group of engines with...

14 CFR 23.777 - Cockpit controls.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Identical powerplant controls for each engine must be located to prevent confusion as to the engines they...) operates the left engines(s) and the right control(s) operates the right engine(s). (2) On twin-engine airplanes with front and rear engine locations (tandem), the left powerplant controls must operate the front...

Remembering the Giants: Apollo Rocket Propulsion Development

NASA Technical Reports Server (NTRS)

Fisher, Steven C. (Editor); Rahman, Shamim A. (Editor)

2009-01-01

Topics discussed include: Rocketdyne - F-1 Saturn V First Stage Engine; Rocketdyne - J-2 Saturn V 2nd & 3rd Stage Engine; Rocketdyne - SE-7 & SE-8 Engines; Aerojet - AJ10-137 Apollo Service Module Engine; Aerojet - Attitude Control Engines; TRW - Lunar Descent Engine; and Rocketdyne - Lunar Ascent Engine.

78 FR 70216 - Airworthiness Directives; Thielert Aircraft Engines GmbH Reciprocating Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-25

... Airworthiness Directives; Thielert Aircraft Engines GmbH Reciprocating Engines AGENCY: Federal Aviation... all Thielert Aircraft Engines GmbH TAE 125-01 reciprocating engines. This AD requires applying sealant... directive (AD): 2013-24-06 Thielert Aircraft Engines GmbH: Amendment 39-17680; Docket No. FAA-2013-0561...

Comparison of China-US Engineering Ethics Educations in Sino-Western Philosophies of Technology.

PubMed

Cao, Gui Hong

2015-12-01

Ethics education has become essential in modern engineering. Ethics education in engineering has been increasingly implemented worldwide. It can improve ethical behaviors in technology and engineering design under the guidance of the philosophy of technology. Hence, this study aims to compare China-US engineering ethics education in Sino-Western philosophies of technology by using literature studies, online surveys, observational researches, textual analyses, and comparative methods. In my original theoretical framework and model of input and output for education, six primary variables emerge in the pedagogy: disciplinary statuses, educational goals, instructional contents, didactic models, teaching methods, and edificatory effects. I focus on the similarities and differences of engineering ethics educations between China and the U.S. in Chinese and Western philosophies of technology. In the field of engineering, the U.S. tends toward applied ethics training, whereas China inclines toward practical moral education. The U.S. is the leader, particularly in the amount of money invested and engineering results. China has quickened its pace, focusing specifically on engineering labor input and output. Engineering ethics is a multiplayer game effected at various levels among (a) lower level technicians and engineers, engineering associations, and stockholders; (b) middle ranking engineering ethics education, the ministry of education, the academy of engineering, and the philosophy of technology; and (c) top national and international technological policies. I propose that professional engineering ethics education can play many important roles in reforming engineering social responsibility by international cooperation in societies that are becoming increasingly reliant on engineered devices and systems. Significantly, my proposals contribute to improving engineering ethics education and better-solving engineering ethics issues, thereby maximizing engineering sustainability.

Engineers' Responsibilities for Global Electronic Waste: Exploring Engineering Student Writing Through a Care Ethics Lens.

PubMed

Campbell, Ryan C; Wilson, Denise

2017-04-01

This paper provides an empirically informed perspective on the notion of responsibility using an ethical framework that has received little attention in the engineering-related literature to date: ethics of care. In this work, we ground conceptual explorations of engineering responsibility in empirical findings from engineering student's writing on the human health and environmental impacts of "backyard" electronic waste recycling/disposal. Our findings, from a purposefully diverse sample of engineering students in an introductory electrical engineering course, indicate that most of these engineers of tomorrow associated engineers with responsibility for the electronic waste (e-waste) problem in some way. However, a number of responses suggested attempts to deflect responsibility away from engineers towards, for example, the government or the companies for whom engineers work. Still other students associated both engineers and non-engineers with responsibility, demonstrating the distributed/collective nature of responsibility that will be required to achieve a solution to the global problem of excessive e-waste. Building upon one element of a framework for care ethics adopted from the wider literature, these empirical findings are used to facilitate a preliminary, conceptual exploration of care-ethical responsibility within the context of engineering and e-waste recycling/disposal. The objective of this exploration is to provide a first step toward understanding how care-ethical responsibility applies to engineering. We also hope to seed dialogue within the engineering community about its ethical responsibilities on the issue. We conclude the paper with a discussion of its implications for engineering education and engineering ethics that suggests changes for educational policy and the practice of engineering.

Diving Deep: A Comparative Study of Educator Undergraduate and Graduate Backgrounds and Their Effect on Student Understanding of Engineering and Engineering Careers, Utilizing an Underwater Robotics Program

NASA Astrophysics Data System (ADS)

Scribner, J. Adam

Numerous studies have demonstrated that educators having degrees in their subjects significantly enhances student achievement, particularly in secondary mathematics and science (Chaney, 1995; Goe, 2007; Rowan, Chiang, & Miller, 1997; Wenglinsky, 2000). Yet, science teachers in states that adopt the Next Generation Science Standards will be facilitating classroom engineering activities despite the fact that few have backgrounds in engineering. This quantitative study analyzed ex-post facto WaterBotics (an innovative underwater robotics curriculum for middle and high school students) data to determine if educators having backgrounds in engineering (i.e., undergraduate and graduate degrees in engineering) positively affected student learning on two engineering outcomes: 1) the engineering design process, and 2) understanding of careers in engineering (who engineers are and what engineers do). The results indicated that educators having backgrounds in engineering did not significantly affect student understanding of the engineering design process or careers in engineering when compared to educators having backgrounds in science, mathematics, technology education, or other disciplines. There were, however, statistically significant differences between the groups of educators. Students of educators with backgrounds in technology education had the highest mean score on assessments pertaining to the engineering design process while students of educators with disciplines outside of STEM had the highest mean scores on instruments that assess for student understanding of careers in engineering. This might be due to the fact that educators who lack degrees in engineering but who teach engineering do a better job of "sticking to the script" of engineering curricula.

Structural engineering masters level education framework of knowledge for the needs of initial professional practice

NASA Astrophysics Data System (ADS)

Balogh, Zsuzsa Enriko

For at least the last decade, engineering, civil engineering, along with structural engineering as a profession within civil engineering, have and continue to face an emerging need for "Raising the Bar" of preparedness of young engineers seeking to become practicing professional engineers. The present consensus of the civil engineering profession is that the increasing need for broad and in-depth knowledge should require the young structural engineers to have at least a Masters-Level education. This study focuses on the Masters-Level preparedness in the structural engineering area within the civil engineering field. It follows much of the methodology used in the American Society of Civil Engineers (ASCE) Body of Knowledge determination for civil engineering and extends this type of study to better define the portion of the young engineers preparation beyond the undergraduate program for one specialty area of civil engineering. The objective of this research was to create a Framework of Knowledge for the young engineer which identifies and recognizes the needs of the profession, along with the profession's expectations of how those needs can be achieved in the graduate-level academic setting, in the practice environment, and through lifelong learning opportunities with an emphasis on the initial five years experience past completion of a Masters program in structural engineering. This study applied a modified Delphi method to obtain the critical information from members of the structural engineering profession. The results provide a Framework of Knowledge which will be useful to several groups seeking to better ensure the preparedness of the future young structural engineers at the Masters-Level.

21. Engine identified as a 'single cylinder vacuum assist engine ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

21. Engine identified as a 'single cylinder vacuum assist engine for Tod tandem compound engine' showing compressor. - Carnegie Steel-Ohio Works, Steam Engines, 912 Salt Springs Road, Youngstown, Mahoning County, OH

Apparatus for sensor failure detection and correction in a gas turbine engine control system

NASA Technical Reports Server (NTRS)

Spang, H. A., III; Wanger, R. P. (Inventor)

1981-01-01

A gas turbine engine control system maintains a selected level of engine performance despite the failure or abnormal operation of one or more engine parameter sensors. The control system employs a continuously updated engine model which simulates engine performance and generates signals representing real time estimates of the engine parameter sensor signals. The estimate signals are transmitted to a control computational unit which utilizes them in lieu of the actual engine parameter sensor signals to control the operation of the engine. The estimate signals are also compared with the corresponding actual engine parameter sensor signals and the resulting difference signals are utilized to update the engine model. If a particular difference signal exceeds specific tolerance limits, the difference signal is inhibited from updating the model and a sensor failure indication is provided to the engine operator.

Key Future Engineering Capabilities for Human Capital Retention

NASA Astrophysics Data System (ADS)

Sivich, Lorrie

Projected record retirements of Baby Boomer generation engineers have been predicted to result in significant losses of mission-critical knowledge in space, national security, and future scientific ventures vital to high-technology corporations. No comprehensive review or analysis of engineering capabilities has been performed to identify threats related to the specific loss of mission-critical knowledge posed by the increasing retirement of tenured engineers. Archival data from a single diversified Fortune 500 aerospace manufacturing engineering company's engineering career database were analyzed to ascertain whether relationships linking future engineering capabilities, engineering disciplines, and years of engineering experience could be identified to define critical knowledge transfer models. Chi square, logistic, and linear regression analyses were used to map patterns of discipline-specific, mission-critical knowledge using archival data of engineers' perceptions of engineering capabilities, key developmental experiences, and knowledge learned from their engineering careers. The results from the study were used to document key engineering future capabilities. The results were then used to develop a proposed human capital retention plan to address specific key knowledge gaps of younger engineers as veteran engineers retire. The potential for social change from this study involves informing leaders of aerospace engineering corporations on how to build better quality mentoring or succession plans to fill the void of lost knowledge from retiring engineers. This plan can secure mission-critical knowledge for younger engineers for current and future product development and increased global competitiveness in the technology market.

A novel paradigm for engineering education: virtual internships with individualized mentoring and assessment of engineering thinking.

PubMed

Chesler, Naomi C; Ruis, A R; Collier, Wesley; Swiecki, Zachari; Arastoopour, Golnaz; Williamson Shaffer, David

2015-02-01

Engineering virtual internships are a novel paradigm for providing authentic engineering experiences in the first-year curriculum. They are both individualized and accommodate large numbers of students. As we describe in this report, this approach can (a) enable students to solve complex engineering problems in a mentored, collaborative environment; (b) allow educators to assess engineering thinking; and (c) provide an introductory experience that students enjoy and find valuable. Furthermore, engineering virtual internships have been shown to increase students'-and especially women's-interest in and motivation to pursue engineering degrees. When implemented in first-year engineering curricula more broadly, the potential impact of engineering virtual internships on the size and diversity of the engineering workforce could be dramatic.

20. Engine identified as a 'single cylinder vacuum assist engine ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

20. Engine identified as a 'single cylinder vacuum assist engine for the Tod tandem compound engine' showing crank end. - Carnegie Steel-Ohio Works, Steam Engines, 912 Salt Springs Road, Youngstown, Mahoning County, OH

Biomedical Engineering | Classification | College of Engineering & Applied

Science.gov Websites

Engineering, Biomedical Engineering(414) 229-6614wjchang@uwm.eduEng & Math Sciences 1113 profile photo Malkoc, Ph.D.Visiting Assistant ProfessorBiomedical Engineering414-229-6919malkoc@uwm.eduEng & Math Engineering / Electrical Engineering(414) 229-3327misra@uwm.eduEng & Math Sciences E-314 profile photo

Students' Changing Images of Engineering and Engineers. Research Brief

ERIC Educational Resources Information Center

Jocuns, Andrew; Stevens, Reed; Garrison, Lari; Amos, Daniel

2008-01-01

This study analyzes the images of engineers and engineering that students construct over the course of their undergraduate engineering educations. Students in their first year of study to become engineers knew very little about the work they would be doing as an engineer and their expectations were more specific, hopeful, and high status than…

78 FR 22168 - Airworthiness Directives; International Aero Engines AG Turbofan Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-15

... Airworthiness Directives; International Aero Engines AG Turbofan Engines AGENCY: Federal Aviation Administration... International Aero Engines AG (IAE), V2525-D5 and V2528-D5 turbofan engines, with a certain No. 4 bearing... turbofan engines, serial numbers V20001 through V20285, with No. 4 bearing internal scavenge tube, part...

40 CFR 1042.101 - Exhaust emission standards for Category 1 engines and Category 2 engines.

Code of Federal Regulations, 2013 CFR

2013-07-01

... information equivalent to such in-use data, such as data from research engines or similar engine models that... Category 1 engines and Category 2 engines. 1042.101 Section 1042.101 Protection of Environment... MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Emission Standards and Related Requirements § 1042.101...

40 CFR 1042.101 - Exhaust emission standards for Category 1 engines and Category 2 engines.

Code of Federal Regulations, 2012 CFR

2012-07-01

... information equivalent to such in-use data, such as data from research engines or similar engine models that... Category 1 engines and Category 2 engines. 1042.101 Section 1042.101 Protection of Environment... MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Emission Standards and Related Requirements § 1042.101...

40 CFR 1042.101 - Exhaust emission standards for Category 1 engines and Category 2 engines.

Code of Federal Regulations, 2011 CFR

2011-07-01

... information equivalent to such in-use data, such as data from research engines or similar engine models that... Category 1 engines and Category 2 engines. 1042.101 Section 1042.101 Protection of Environment... MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Emission Standards and Related Requirements § 1042.101...

76 FR 82110 - Airworthiness Directives; Thielert Aircraft Engines GmbH Reciprocating Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-30

... Airworthiness Directives; Thielert Aircraft Engines GmbH Reciprocating Engines AGENCY: Federal Aviation...) for Thielert Aircraft Engines GmbH models TAE 125-02-99 and TAE 125-01 reciprocating engines. That AD... flight hours to within 600 flight hours for TAE 125-01 reciprocating engines. This AD was prompted by the...

76 FR 40219 - Airworthiness Directives; Various Aircraft Equipped With Rotax Aircraft Engines 912 A Series Engine

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-08

... Airworthiness Directives; Various Aircraft Equipped With Rotax Aircraft Engines 912 A Series Engine AGENCY... installed on a limited number of engines. No defective washers have been shipped as spare parts. This... consequent ignition failure, possibly resulting in damage to the engine, in- flight engine shutdown and...

40 CFR 1042.140 - Maximum engine power, displacement, power density, and maximum in-use engine speed.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Maximum engine power, displacement... Maximum engine power, displacement, power density, and maximum in-use engine speed. This section describes how to determine the maximum engine power, displacement, and power density of an engine for the...

40 CFR 1042.140 - Maximum engine power, displacement, power density, and maximum in-use engine speed.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Maximum engine power, displacement... Maximum engine power, displacement, power density, and maximum in-use engine speed. This section describes how to determine the maximum engine power, displacement, and power density of an engine for the...

Multi-fuel rotary engine for general aviation aircraft

NASA Technical Reports Server (NTRS)

Jones, C.; Ellis, D. R.; Meng, P. R.

1983-01-01

Design studies of advanced multifuel general aviation and commuter aircraft rotary stratified charge engines are summarized. Conceptual design studies were performed at two levels of technology, an advanced general aviation engines sized to provide 186/250 shaft kW/hp under cruise conditions at 7620 (25,000 m/ft) altitude. A follow on study extended the results to larger (2500 hp max.) engine sizes suitable for applications such as commuter transports and helicopters. The study engine designs were derived from relevant engine development background including both prior and recent engine test results using direct injected unthrottled rotary engine technology. Aircraft studies, using these resultant growth engines, define anticipated system effects of the performance and power density improvements for both single engine and twin engine airplanes. The calculated results indicate superior system performance and 27 to 33 percent fuel economy improvement for the rotary engine airplanes as compared to equivalent airframe concept designs with current baseline engines. The research and technology activities required to attain the projected engine performance levels are also discussed. Previously announced in STAR as N83-18910

A Method for Search Engine Selection using Thesaurus for Selective Meta-Search Engine

NASA Astrophysics Data System (ADS)

Goto, Shoji; Ozono, Tadachika; Shintani, Toramatsu

In this paper, we propose a new method for selecting search engines on WWW for selective meta-search engine. In selective meta-search engine, a method is needed that would enable selecting appropriate search engines for users' queries. Most existing methods use statistical data such as document frequency. These methods may select inappropriate search engines if a query contains polysemous words. In this paper, we describe an search engine selection method based on thesaurus. In our method, a thesaurus is constructed from documents in a search engine and is used as a source description of the search engine. The form of a particular thesaurus depends on the documents used for its construction. Our method enables search engine selection by considering relationship between terms and overcomes the problems caused by polysemous words. Further, our method does not have a centralized broker maintaining data, such as document frequency for all search engines. As a result, it is easy to add a new search engine, and meta-search engines become more scalable with our method compared to other existing methods.

A simple method of calculating Stirling engines for engine design optimization

NASA Technical Reports Server (NTRS)

Martini, W. R.

1978-01-01

A calculation method is presented for a rhombic drive Stirling engine with a tubular heater and cooler and a screen type regenerator. Generally the equations presented describe power generation and consumption and heat losses. It is the simplest type of analysis that takes into account the conflicting requirements inherent in Stirling engine design. The method itemizes the power and heat losses for intelligent engine optimization. The results of engine analysis of the GPU-3 Stirling engine are compared with more complicated engine analysis and with engine measurements.

Stennis certifies final shuttle engine

NASA Image and Video Library

2008-10-22

Steam blasts out of the A-2 Test Stand at Stennis Space Center on Oct. 22 as engineers begin a certification test on engine 2061, the last space shuttle main flight engine scheduled to be built. Since 1975, Stennis has tested every space shuttle main engine used in the program - about 50 engines in all. Those engines have powered more than 120 shuttle missions - and no mission has failed as a result of engine malfunction. For the remainder of 2008 and throughout 2009, Stennis will continue testing of various space shuttle main engine components.

Orbit Transfer Vehicle (OTV) engine phase A study

NASA Technical Reports Server (NTRS)

Mellish, J. A.

1978-01-01

Requirements for the orbit transfer vehicle engine were examined. Engine performance/weight sensitivities, the effect of a service life of 300 start/shutdown cycles between overalls on the maximum engine operating pressure, and the sensitivity of the engine design point (i.e., thrust chamber pressure and nozzle area ratio) to the performance requirements specified are among the factors studied. Preliminary engine systems analyses were conducted on the stage combustion, expander, and gas generator engine cycles. Hydrogen and oxygen pump discharge pressure requirements are shown for various engine cycles. Performance of the engine cycles is compared.

Study of a LH2-fueled topping cycle engine for aircraft propulsion

NASA Technical Reports Server (NTRS)

Turney, G. E.; Fishbach, L. H.

1983-01-01

An analytical investigation was made of a topping cycle aircraft engine system which uses a cryogenic fuel. This system consists of a main turboshaft engine which is mechanically coupled (by cross-shafting) to a topping loop which augments the shaft power output of the system. The thermodynamic performance of the topping cycle engine was analyzed and compared with that of a reference (conventional-type) turboshaft engine. For the cycle operating conditions selected, the performance of the topping cycle engine in terms of brake specific fuel consumption (bsfc) was determined to be about 12 percent better than that of the reference turboshaft engine. Engine weights were estimated for both the topping cycle engine and the reference turboshaft engine. These estimates were based on a common shaft power output for each engine. Results indicate that the weight of the topping cycle engine is comparable to that of the reference turboshaft engine. Previously announced in STAR as N83-34942

Analysis of automobile engine cylinder pressure and rotation speed from engine body vibration signal

NASA Astrophysics Data System (ADS)

Wang, Yuhua; Cheng, Xiang; Tan, Haishu

2016-01-01

In order to improve the engine vibration signal process method for the engine cylinder pressure and engine revolution speed measurement instrument, the engine cylinder pressure varying with the engine working cycle process has been regarded as the main exciting force for the engine block forced vibration. The forced vibration caused by the engine cylinder pressure presents as a low frequency waveform which varies with the cylinder pressure synchronously and steadily in time domain and presents as low frequency high energy discrete humorous spectrum lines in frequency domain. The engine cylinder pressure and the rotation speed can been extract form the measured engine block vibration signal by low-pass filtering analysis in time domain or by FFT analysis in frequency domain, the low-pass filtering analysis in time domain is not only suitable for the engine in uniform revolution condition but also suitable for the engine in uneven revolution condition. That provides a practical and convenient way to design motor revolution rate and cylinder pressure measurement instrument.

Engineering Lessons Learned and Systems Engineering Applications

NASA Technical Reports Server (NTRS)

Gill, Paul S.; Garcia, Danny; Vaughan, William W.

2005-01-01

Systems Engineering is fundamental to good engineering, which in turn depends on the integration and application of engineering lessons learned. Thus, good Systems Engineering also depends on systems engineering lessons learned from within the aerospace industry being documented and applied. About ten percent of the engineering lessons learned documented in the NASA Lessons Learned Information System are directly related to Systems Engineering. A key issue associated with lessons learned datasets is the communication and incorporation of this information into engineering processes. As part of the NASA Technical Standards Program activities, engineering lessons learned datasets have been identified from a number of sources. These are being searched and screened for those having a relation to Technical Standards. This paper will address some of these Systems Engineering Lessons Learned and how they are being related to Technical Standards within the NASA Technical Standards Program, including linking to the Agency's Interactive Engineering Discipline Training Courses and the life cycle for a flight vehicle development program.

Evolving social responsibility understandings, motivations, and career goals of undergraduate students initially pursuing engineering degrees

NASA Astrophysics Data System (ADS)

Rulifson, Gregory A.

Engineers impact the lives of every person every day, and need to have a strong sense of social responsibility. Understanding what students think about social responsibility in engineering and their futures is very important. Further, by identifying influences that change these ideas and shape their conceptualizations, we can intervene to help prepare students for their responsibilities as part of the profession in the future. This thesis presents the experiences, in their own words, of 34 students who started in engineering. The study is composed of three parts: (i) engineering students' ideas about socially responsible engineering and what influenced these ideas, (ii) how students see themselves as future socially responsible engineers and how this idea changes over their first three years of college, and (iii) what social responsibility-related reasons students who leave engineering have for choosing a new major. Results show that students are complicated and have varied paths through and out of engineering studies. Students came up with their own ideas about socially responsible engineering that converged over the years on legal and safety related aspects of the profession. Relatedly, students identified with the engineering profession through internships and engineering courses, and rarely described socially responsible aspirations that could be accomplished with engineering. More often, those students who desired to help the disadvantaged through their engineering work left engineering. Their choice to leave was a combination of an unsupportive climate, disinterest in their classes, and a desire to combine their personal and professional social responsibility ambitions. If we want engineering students to push the engineering profession forward to be more socially responsible, we can identify the effective influences and develop a curriculum that encourages critical thinking about the social context and impacts of engineering. Additionally, a social responsibility-related curriculum could provide more opportunities for engagement that keeps those socially-motivated students in engineering. The engineering profession must also reflect these values to keep the new engineers working towards social responsibility and pushing the profession forward.

Annual Conference Abstracts

ERIC Educational Resources Information Center

Journal of Engineering Education, 1972

1972-01-01

Includes abstracts of papers presented at the 80th Annual Conference of the American Society for Engineering Education. The broad areas include aerospace, affiliate and associate member council, agricultural engineering, biomedical engineering, continuing engineering studies, chemical engineering, civil engineering, computers, cooperative…

40 CFR 1033.625 - Special certification provisions for non-locomotive-specific engines.

Code of Federal Regulations, 2014 CFR

2014-07-01

... name of the engine manufacturer and engine family identifier for the engines. (ii) A brief engineering... proprietary engine software. Note that this allowance to separately submit some of the information required by...

40 CFR 1033.625 - Special certification provisions for non-locomotive-specific engines.

Code of Federal Regulations, 2012 CFR

2012-07-01

... name of the engine manufacturer and engine family identifier for the engines. (ii) A brief engineering... proprietary engine software. Note that this allowance to separately submit some of the information required by...

40 CFR 1033.625 - Special certification provisions for non-locomotive-specific engines.

Code of Federal Regulations, 2013 CFR

2013-07-01

... name of the engine manufacturer and engine family identifier for the engines. (ii) A brief engineering... proprietary engine software. Note that this allowance to separately submit some of the information required by...

Paired peer learning through engineering education outreach

NASA Astrophysics Data System (ADS)

Fogg-Rogers, Laura; Lewis, Fay; Edmonds, Juliet

2017-01-01

Undergraduate education incorporating active learning and vicarious experience through education outreach presents a critical opportunity to influence future engineering teaching and practice capabilities. Engineering education outreach activities have been shown to have multiple benefits; increasing interest and engagement with science and engineering for school children, providing teachers with expert contributions to engineering subject knowledge, and developing professional generic skills for engineers such as communication and teamwork. This pilot intervention paired 10 pre-service teachers and 11 student engineers to enact engineering outreach in primary schools, reaching 269 children. A longitudinal mixed methods design was employed to measure change in attitudes and Education Outreach Self-Efficacy in student engineers; alongside attitudes, Teaching Engineering Self-Efficacy and Engineering Subject Knowledge Confidence in pre-service teachers. Highly significant improvements were noted in the pre-service teachers' confidence and self-efficacy, while both the teachers and engineers qualitatively described benefits arising from the paired peer mentor model.

GENENG 2: A program for calculating design and off-design performance of two- and three-spool turbofans with as many as three nozzles

NASA Technical Reports Server (NTRS)

Fishbach, L. H.; Koenig, R. W.

1972-01-01

A computer program which calculates steady-state design and off-design jet engine performance for two- or three-spool turbofans with one, two, or three nozzles is described. Included in the report are complete FORTRAN 4 listings of the program with sample results for nine basic turbofan engines that can be calculated: (1) three-spool, three-stream engine; (2) two-spool, three-stream, boosted-fan engine; (3) two-spool, three-stream, supercharged-compressor engine; (4) three-spool, two-stream engine; (5) two-spool, two-stream engine; (6) three-spool, three-stream, aft-fan engine; (7) two-spool, three-stream, aft-fan engine; (8) two-spool, two-stream, aft-engine; and (9) three-spool, two-stream, aft-fan engine. The simulation of other engines by using logical variables built into the program is also described.

Ecosystem engineering effects on species diversity across ecosystems: a meta-analysis.

PubMed

Romero, Gustavo Q; Gonçalves-Souza, Thiago; Vieira, Camila; Koricheva, Julia

2015-08-01

Ecosystem engineering is increasingly recognized as a relevant ecological driver of diversity and community composition. Although engineering impacts on the biota can vary from negative to positive, and from trivial to enormous, patterns and causes of variation in the magnitude of engineering effects across ecosystems and engineer types remain largely unknown. To elucidate the above patterns, we conducted a meta-analysis of 122 studies which explored effects of animal ecosystem engineers on species richness of other organisms in the community. The analysis revealed that the overall effect of ecosystem engineers on diversity is positive and corresponds to a 25% increase in species richness, indicating that ecosystem engineering is a facilitative process globally. Engineering effects were stronger in the tropics than at higher latitudes, likely because new or modified habitats provided by engineers in the tropics may help minimize competition and predation pressures on resident species. Within aquatic environments, engineering impacts were stronger in marine ecosystems (rocky shores) than in streams. In terrestrial ecosystems, engineers displayed stronger positive effects in arid environments (e.g. deserts). Ecosystem engineers that create new habitats or microhabitats had stronger effects than those that modify habitats or cause bioturbation. Invertebrate engineers and those with lower engineering persistence (<1 year) affected species richness more than vertebrate engineers which persisted for >1 year. Invertebrate species richness was particularly responsive to engineering impacts. This study is the first attempt to build an integrative framework of engineering effects on species diversity; it highlights the importance of considering latitude, habitat, engineering functional group, taxon and persistence of their effects in future theoretical and empirical studies. © 2014 The Authors. Biological Reviews © 2014 Cambridge Philosophical Society.

Green engineering education through a U.S. EPA/academia collaboration.

PubMed

Shonnard, David R; Allen, David T; Nguyen, Nhan; Austin, Sharon Weil; Hesketh, Robert

2003-12-01

The need to use resources efficiently and reduce environmental impacts of industrial products and processes is becoming increasingly important in engineering design; therefore, green engineering principles are gaining prominence within engineering education. This paper describes a general framework for incorporating green engineering design principles into engineering curricula, with specific examples for chemical engineering. The framework for teaching green engineering discussed in this paper mirrors the 12 Principles of Green Engineering proposed by Anastas and Zimmerman (Environ. Sci. Technol. 2003, 37, 94A-101A), especially in methods for estimating the hazardous nature of chemicals, strategies for pollution prevention, and approaches leading to efficient energy and material utilization. The key elements in green engineering education, which enlarge the "box" for engineering design, are environmental literacy, environmentally conscious design, and beyond-the-plant boundary considerations.

Fuel quantity modulation in pilot ignited engines

DOEpatents

May, Andrew

2006-05-16

An engine system includes a first fuel regulator adapted to control an amount of a first fuel supplied to the engine, a second fuel regulator adapted to control an amount of a second fuel supplied to the engine concurrently with the first fuel being supplied to the engine, and a controller coupled to at least the second fuel regulator. The controller is adapted to determine the amount of the second fuel supplied to the engine in a relationship to the amount of the first fuel supplied to the engine to operate in igniting the first fuel at a specified time in steady state engine operation and adapted to determine the amount of the second fuel supplied to the engine in a manner different from the relationship at steady state engine operation in transient engine operation.

Quiet engine program flight engine design study

NASA Technical Reports Server (NTRS)

Klapproth, J. F.; Neitzel, R. E.; Seeley, C. T.

1974-01-01

The results are presented of a preliminary flight engine design study based on the Quiet Engine Program high-bypass, low-noise turbofan engines. Engine configurations, weight, noise characteristics, and performance over a range of flight conditions typical of a subsonic transport aircraft were considered. High and low tip speed engines in various acoustically treated nacelle configurations were included.

The Engineer of 2020: Visions of Engineering in the New Century

ERIC Educational Resources Information Center

National Academies Press, 2004

2004-01-01

To enhance the nation's economic productivity and improve the quality of life worldwide, engineering education in the United States must anticipate and adapt to the dramatic changes of engineering practice. The Engineer of 2020 urges the engineering profession to recognize what engineers can build for the future through a wide range of leadership…

Software engineering as an engineering discipline

NASA Technical Reports Server (NTRS)

Berard, Edward V.

1988-01-01

The following topics are discussed in the context of software engineering: early use of the term; the 1968 NATO conference; Barry Boehm's definition; four requirements fo software engineering; and additional criteria for software engineering. Additionally, the four major requirements for software engineering--computer science, mathematics, engineering disciplines, and excellent communication skills--are discussed. The presentation is given in vugraph form.

78 FR 1776 - Airworthiness Directives; International Aero Engines AG Turbofan Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-09

... Engines AG Turbofan Engines AGENCY: Federal Aviation Administration (FAA), DOT. ACTION: Notice of proposed... Aero Engines AG (IAE), V2525-D5 and V2528-D5 turbofan engines, with a certain number (No.) 4 bearing... proposed AD. Discussion We received a report of a fire warning on an IAE V2525 turbofan engine shortly...

I "Still" Wanna Be an Engineer! Women, Education and the Engineering Profession

ERIC Educational Resources Information Center

Gill, Judith; Sharp, Rhonda; Mills, Julie; Franzway, Suzanne

2008-01-01

Women's low enrolment in post-school engineering degrees continues to be a problem for engineering faculties and the profession generally. A qualitative interview-based study of Australian women engineers across the range of engineering disciplines showed the relevance of success in math and science at school to their enrolling in engineering at…

40 CFR 1042.310 - Engine selection for Category 1 and Category 2 engines.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Category 2 engines. (a) Determine minimum sample sizes as follows: (1) For Category 1 engines, the minimum sample size is one engine or one percent of the projected U.S.-directed production volume for all your Category 1 engine families, whichever is greater. (2) For Category 2 engines, the minimum sample size is...

76 FR 56637 - Airworthiness Directives; Lycoming Engines Model IO-720-A1B Reciprocating Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2011-09-14

... Airworthiness Directives; Lycoming Engines Model IO-720-A1B Reciprocating Engines AGENCY: Federal Aviation... directive (AD) for certain model IO-720-A1B Lycoming Engines reciprocating engines. This AD requires a... crankshaft due to incorrect parts installed. We are issuing this AD to prevent engine crankshaft failure and...

14 CFR 63.42 - Flight engineer certificate issued on basis of a foreign flight engineer license.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 14 Aeronautics and Space 2 2013-01-01 2013-01-01 false Flight engineer certificate issued on basis of a foreign flight engineer license. 63.42 Section 63.42 Aeronautics and Space FEDERAL AVIATION... PILOTS Flight Engineers § 63.42 Flight engineer certificate issued on basis of a foreign flight engineer...

14 CFR 63.42 - Flight engineer certificate issued on basis of a foreign flight engineer license.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 14 Aeronautics and Space 2 2011-01-01 2011-01-01 false Flight engineer certificate issued on basis of a foreign flight engineer license. 63.42 Section 63.42 Aeronautics and Space FEDERAL AVIATION... PILOTS Flight Engineers § 63.42 Flight engineer certificate issued on basis of a foreign flight engineer...

14 CFR 63.42 - Flight engineer certificate issued on basis of a foreign flight engineer license.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 14 Aeronautics and Space 2 2012-01-01 2012-01-01 false Flight engineer certificate issued on basis of a foreign flight engineer license. 63.42 Section 63.42 Aeronautics and Space FEDERAL AVIATION... PILOTS Flight Engineers § 63.42 Flight engineer certificate issued on basis of a foreign flight engineer...

14 CFR 63.42 - Flight engineer certificate issued on basis of a foreign flight engineer license.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 2 2014-01-01 2014-01-01 false Flight engineer certificate issued on basis of a foreign flight engineer license. 63.42 Section 63.42 Aeronautics and Space FEDERAL AVIATION... PILOTS Flight Engineers § 63.42 Flight engineer certificate issued on basis of a foreign flight engineer...

14 CFR 63.42 - Flight engineer certificate issued on basis of a foreign flight engineer license.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 2 2010-01-01 2010-01-01 false Flight engineer certificate issued on basis of a foreign flight engineer license. 63.42 Section 63.42 Aeronautics and Space FEDERAL AVIATION... PILOTS Flight Engineers § 63.42 Flight engineer certificate issued on basis of a foreign flight engineer...

Engineering Encounters: Teaching Educators about Engineering

ERIC Educational Resources Information Center

Tank, Kristina M.; Raman, D. Raj; Lamm, Monica H.; Sundararajan, Sriram; Estapa, Anne

2017-01-01

This column presents ideas and techniques to enhance science teaching. This month's issue describes preservice elementary teachers learning engineering principles from engineers. Few elementary teachers have experience with implementing engineering into the classroom. While engineering professional development opportunities for inservice teachers…

46 CFR 10.109 - Classification of endorsements.

Code of Federal Regulations, 2013 CFR

2013-10-01

...) Professional nurse; (41) Marine physician assistant; (42) Hospital corpsman; and (43) Radar observer. (b) The... engineer (limited-near-coastal); (22) First assistant engineer; (23) Second assistant engineer; (24) Third assistant engineer; (25) Assistant engineer (limited); (26) Designated duty engineer (DDE); (27) Chief...

46 CFR 70.20-1 - Marine engineering details.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 3 2011-10-01 2011-10-01 false Marine engineering details. 70.20-1 Section 70.20-1... General Marine Engineering Requirements § 70.20-1 Marine engineering details. All marine engineering... subchapter F (Marine Engineering) of this chapter. ...

46 CFR 70.20-1 - Marine engineering details.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 3 2013-10-01 2013-10-01 false Marine engineering details. 70.20-1 Section 70.20-1... General Marine Engineering Requirements § 70.20-1 Marine engineering details. All marine engineering... subchapter F (Marine Engineering) of this chapter. ...

46 CFR 70.20-1 - Marine engineering details.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 3 2014-10-01 2014-10-01 false Marine engineering details. 70.20-1 Section 70.20-1... General Marine Engineering Requirements § 70.20-1 Marine engineering details. All marine engineering... subchapter F (Marine Engineering) of this chapter. ...

46 CFR 70.20-1 - Marine engineering details.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 3 2010-10-01 2010-10-01 false Marine engineering details. 70.20-1 Section 70.20-1... General Marine Engineering Requirements § 70.20-1 Marine engineering details. All marine engineering... subchapter F (Marine Engineering) of this chapter. ...

46 CFR 70.20-1 - Marine engineering details.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 3 2012-10-01 2012-10-01 false Marine engineering details. 70.20-1 Section 70.20-1... General Marine Engineering Requirements § 70.20-1 Marine engineering details. All marine engineering... subchapter F (Marine Engineering) of this chapter. ...

Space engine safety system

NASA Technical Reports Server (NTRS)

Maul, William A.; Meyer, Claudia M.

1991-01-01

A rocket engine safety system was designed to initiate control procedures to minimize damage to the engine or vehicle or test stand in the event of an engine failure. The features and the implementation issues associated with rocket engine safety systems are discussed, as well as the specific concerns of safety systems applied to a space-based engine and long duration space missions. Examples of safety system features and architectures are given, based on recent safety monitoring investigations conducted for the Space Shuttle Main Engine and for future liquid rocket engines. Also, the general design and implementation process for rocket engine safety systems is presented.

PROFESSIONAL REGISTRATION OF GOVERNMENT ENGINEERS.

USGS Publications Warehouse

Buchanan, Thomas J.

1985-01-01

The American Society of Civil Engineers views professional registration as an appropriate requirement for engineers, including those in government. The National Society of Professional Engineers makes registration a requirement for the grade of member and full privileges in the society. Some Federal agencies require engineering registration for certain positions in their agencies. Engineers in government service should consider the value of engineering registration to themselves and to their agencies and take pride in their professions and in their own capabilities by becoming registered engineers. They should also take steps to encourage their agencies to give more attention to engineering registration.

Conversion of a micro, glow-ignition, two-stroke engine from nitromethane-methanol blend fuel to military jet propellant (JP-8)

NASA Astrophysics Data System (ADS)

Wiegand, Andrew L.

The goal of the thesis "Conversion of a Micro, Glow-Ignition, Two-Stroke Engine from Nitromethane-Methanol Blend Fuel to Military Jet Propellant (JP-8)" was to demonstrate the ability to operate a small engine on JP-8 and was completed in two phases. The first phase included choosing, developing a test stand for, and baseline testing a nitromethane-methanol-fueled engine. The chosen engine was an 11.5 cc, glow-ignition, two-stroke engine designed for remote-controlled helicopters. A micro engine test stand was developed to load and motor the engine. Instrumentation specific to the low flow rates and high speeds of the micro engine was developed and used to document engine behavior. The second phase included converting the engine to operate on JP-8, completing JP-8-fueled steady-state testing, and comparing the performance of the JP-8-fueled engine to the nitromethane-methanol-fueled engine. The conversion was accomplished through a novel crankcase heating method; by heating the crankcase for an extended period of time, a flammable fuel-air mixture was generated in the crankcase scavenged engine, which greatly improved starting times. To aid in starting and steady-state operation, yttrium-zirconia impregnated resin (i.e. ceramic coating) was applied to the combustion surfaces. This also improved the starting times of the JP-8-fueled engine and ultimately allowed for a 34-second starting time. Finally, the steady-state data from both the nitromethane-methanol and JP-8-fueled micro engine were compared. The JP-8-fueled engine showed signs of increased engine friction while having higher indicated fuel conversion efficiency and a higher overall system efficiency. The minimal ability of JP-8 to cool the engine via evaporative effects, however, created the necessity of increased cooling air flow. The conclusion reached was that JP-8-fueled micro engines could be viable in application, but not without additional research being conducted on combustion phenomenon and cooling requirements.

40 CFR 1048.325 - What happens if an engine family fails the production-line testing requirements?

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false What happens if an engine family fails... SPARK-IGNITION ENGINES Testing Production-line Engines § 1048.325 What happens if an engine family fails... engine family if it fails under § 1048.315. The suspension may apply to all facilities producing engines...

40 CFR 1048.325 - What happens if an engine family fails the production-line testing requirements?

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false What happens if an engine family fails... SPARK-IGNITION ENGINES Testing Production-line Engines § 1048.325 What happens if an engine family fails... engine family if it fails under § 1048.315. The suspension may apply to all facilities producing engines...

Impact of an Engineering Case Study in a High School Pre-Engineering Course

ERIC Educational Resources Information Center

Rutz, Eugene; Shafer, Michelle

2011-01-01

Students at an all-girls high school who were enrolled in an introduction to engineering course were presented an engineering case study to determine if the case study affected their attitudes toward engineering and their abilities to solve engineering problems. A case study on power plants was implemented during a unit on electrical engineering.…

40 CFR 1045.330 - May I sell engines from an engine family with a suspended certificate of conformity?

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false May I sell engines from an engine... ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM SPARK-IGNITION PROPULSION MARINE ENGINES AND VESSELS Testing Production-line Engines § 1045.330 May I sell engines from an...

Motivational Factors of Professional Engineers and Non-Professional Engineers in Applying for License as Professional Engineer: A Comparative Study

ERIC Educational Resources Information Center

Khamis, Nor Kamaliana; Harun, Zambri; Tahir, Mohd Faizal Mat; Wahid, Zaliha; Sabri, Mohd Anas Mohd

2013-01-01

All engineering faculties in Malaysia are required to have at least three academics who have engineering competency for each program. Having an engineering competency means academics has obtained the compulsory endorsements from the Boards of Engineers, Malaysia, BEM. Upon approval, academics seeking such competency could carry the suffix Ir. to…

75 FR 39803 - Airworthiness Directives; Thielert Aircraft Engines GmbH Model TAE 125-01 Reciprocating Engines

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-13

... Airworthiness Directives; Thielert Aircraft Engines GmbH Model TAE 125-01 Reciprocating Engines AGENCY: Federal...-18300R5, may cause a blow-by gas pressure increase inside the crankcase of the engine in excess of the oil seal design pressure limits. Leaking engine oil may adversely affect the gearbox clutch or the engine...

40 CFR 1048.325 - What happens if an engine family fails the production-line testing requirements?

Code of Federal Regulations, 2010 CFR

2010-07-01

... steps you must take to remedy the cause of the engine family's production-line failure. All the engines... 40 Protection of Environment 32 2010-07-01 2010-07-01 false What happens if an engine family fails... SPARK-IGNITION ENGINES Testing Production-line Engines § 1048.325 What happens if an engine family fails...

40 CFR 1045.325 - What happens if an engine family fails the production-line testing requirements?

Code of Federal Regulations, 2010 CFR

2010-07-01

... steps you must take to remedy the cause of the engine family's production-line failure. All the engines... 40 Protection of Environment 32 2010-07-01 2010-07-01 false What happens if an engine family fails... PROPULSION MARINE ENGINES AND VESSELS Testing Production-line Engines § 1045.325 What happens if an engine...

Engineering Design Handbook. Helicopter Engineering. Part One. Preliminary Design

DTIC Science & Technology

1974-08-30

1.3 ENGINE REPLACEMENT .............. ......................... 8-1 8-1.4 ENGINE AIR INDUCTION SYSTEM .............................. 8-2 8-1.5 ENGINE ...8-5 8-2.2 ENGINE AIR INDUCTION SYSTEM .............................. 8-5 8-2.2.1 G eneral Design...8-5 8-2.2.2 Air Induction System Inlet Location ............................... 8-6 8-2.2.3 Engine Air Induction System Pressure Losses

Engineering the future with America's high school students

NASA Technical Reports Server (NTRS)

Farrance, M. A.; Jenner, J. W.

1993-01-01

The number of students enrolled in engineering is declining while the need for engineers is increasing. One contributing factor is that most high school students have little or no knowledge about what engineering is, or what engineers do. To teach young students about engineering, engineers need good tools. This paper presents a course of study developed and used by the authors in a junior college course for high school students. Students learned about engineering through independent student projects, in-class problem solving, and use of career information resources. Selected activities from the course can be adapted to teach students about engineering in other settings. Among the most successful techniques were the student research paper assignments, working out a solution to an engineering problem as a class exercise, and the use of technical materials to illustrate engineering concepts and demonstrate 'tools of the trade'.

Orbit transfer vehicle engine study, phase A extension. Volume 2A: Study results

NASA Technical Reports Server (NTRS)

1980-01-01

Engine trade studies and systems analyses leading to a baseline engine selection for advanced expander cycle engine are discussed with emphasis on: (1) performance optimization of advanced expander cycle engines in the 10 to 20K pound thrust range; (2) selection of a recommended advanced expander engine configuration based on maximized performance and minimized mission risk, and definition of the components for this configuration; (3) characterization of the low thrust adaptation requirements and performance for the staged combustion engine; (4) generation of a suggested safety and reliability approach for OTV engines independent of engine cycle; (5) definition of program risk relationships between expander and staged combustion cycle engines; and (6) development of schedules and costs for the DDT&E, production, and operation phases of the 10K pound thrust expander engine program.

40 CFR 1042.230 - Engine families.

Code of Federal Regulations, 2010 CFR

2010-07-01

... degree). (19) The type of smoke control system. (d) For Category 3 engines, group engines into engine....230 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Certifying Engine...

40 CFR 1042.230 - Engine families.

Code of Federal Regulations, 2014 CFR

2014-07-01

... degree). (19) The type of smoke control system. (d) For Category 3 engines, group engines into engine....230 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Certifying Engine...

40 CFR 1042.230 - Engine families.

Code of Federal Regulations, 2011 CFR

2011-07-01

... degree). (19) The type of smoke control system. (d) For Category 3 engines, group engines into engine....230 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Certifying Engine...

40 CFR 1042.230 - Engine families.

Code of Federal Regulations, 2012 CFR

2012-07-01

... degree). (19) The type of smoke control system. (d) For Category 3 engines, group engines into engine....230 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR POLLUTION CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE MARINE COMPRESSION-IGNITION ENGINES AND VESSELS Certifying Engine...

40 CFR 1036.230 - Selecting engine families.

Code of Federal Regulations, 2014 CFR

2014-07-01

... CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE HEAVY-DUTY HIGHWAY ENGINES Certifying Engine Families... sold into non-vocational tractor applications. You may assign the numbers and configurations of engines...). (d) Engine configurations within an engine family must use equivalent greenhouse gas emission...

40 CFR 1036.230 - Selecting engine families.

Code of Federal Regulations, 2012 CFR

2012-07-01

... CONTROLS CONTROL OF EMISSIONS FROM NEW AND IN-USE HEAVY-DUTY HIGHWAY ENGINES Certifying Engine Families... sold into non-vocational tractor applications. You may assign the numbers and configurations of engines...). (d) Engine configurations within an engine family must use equivalent greenhouse gas emission...

The Nutating Engine-Prototype Engine Progress Report and Test Results

NASA Technical Reports Server (NTRS)

Meitner, Peter L.; Boruta, Mike

2006-01-01

A prototype of a new, internal combustion (IC) engine concept has been completed. The Nutating Engine features an internal disk nutating (wobbling) on a Z-shaped power shaft. The engine is exceedingly compact, and several times more power dense than any conventional (reciprocating or rotary) IC engine. This paper discusses lessons learned during the prototype engine's development and provides details of its construction. In addition, results of the initial performance tests of the various components, as well as the complete engine, are summarized.

Engine dynamic analysis with general nonlinear finite element codes

NASA Technical Reports Server (NTRS)

Adams, M. L.; Padovan, J.; Fertis, D. G.

1991-01-01

A general engine dynamic analysis as a standard design study computational tool is described for the prediction and understanding of complex engine dynamic behavior. Improved definition of engine dynamic response provides valuable information and insights leading to reduced maintenance and overhaul costs on existing engine configurations. Application of advanced engine dynamic simulation methods provides a considerable cost reduction in the development of new engine designs by eliminating some of the trial and error process done with engine hardware development.

14. INTERIOR OF ENGINE ROOM, CONTAINING MESTACORLISS CROSSCOMPOUND ENGINE, FOR ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

14. INTERIOR OF ENGINE ROOM, CONTAINING MESTA-CORLISS CROSS-COMPOUND ENGINE, FOR 40" BLOOMING MILL. THIS VIEW HIGHLIGHTS THE CRANK AND 24' DIAMETER FLYWHEEL. THE ENGINE IS A 7,940 HP MESTA-CORLISS CROSS-COMPOUND STEAM ENGINE ITS BORE AND STROKE ARE 32"X84"X60". NOTE FLY BALL GOVERNOR ON ENGINE. MILL DRIVE SHAFT ATTACHED TO PULLEY ON LOCATED ON CRANK. - Republic Iron & Steel Company, Youngstown Works, Blooming Mill & Blooming Mill Engines, North of Poland Avenue, Youngstown, Mahoning County, OH

Study of Bird Ingestions into Small Inlet Area Aircraft Turbine Engines

DTIC Science & Technology

1990-12-01

engines (ALF502, TFE731 , TPE331, and JTI5D) included in the study. This includes 24 months of operations for the first three engines and 12 months of...through the National Teclical Bird Ingestion- TFE731 Information Service, Springfield, 4 Tuibine Engine,’ TPt331 Virginia 22161 Turbofan Engine...ALF502 Engine 7 2.2 Operations, TFE731 Engine 8 2.3 Operations, TPE331 Engine 9 3.1 Distribution of Bird Weights 13 3.2 Aircraft Ingestions by Month

Qualitative and temporal reasoning in engine behavior analysis

NASA Technical Reports Server (NTRS)

Dietz, W. E.; Stamps, M. E.; Ali, M.

1987-01-01

Numerical simulation models, engine experts, and experimental data are used to generate qualitative and temporal representations of abnormal engine behavior. Engine parameters monitored during operation are used to generate qualitative and temporal representations of actual engine behavior. Similarities between the representations of failure scenarios and the actual engine behavior are used to diagnose fault conditions which have already occurred, or are about to occur; to increase the surveillance by the monitoring system of relevant engine parameters; and to predict likely future engine behavior.

Sequence of the hyperplastic genome of the naturally competent Thermus scotoductus SA-01

PubMed Central

2011-01-01

Background Many strains of Thermus have been isolated from hot environments around the world. Thermus scotoductus SA-01 was isolated from fissure water collected 3.2 km below surface in a South African gold mine. The isolate is capable of dissimilatory iron reduction, growth with oxygen and nitrate as terminal electron acceptors and the ability to reduce a variety of metal ions, including gold, chromate and uranium, was demonstrated. The genomes from two different Thermus thermophilus strains have been completed. This paper represents the completed genome from a second Thermus species - T. scotoductus. Results The genome of Thermus scotoductus SA-01 consists of a chromosome of 2,346,803 bp and a small plasmid which, together are about 11% larger than the Thermus thermophilus genomes. The T. thermophilus megaplasmid genes are part of the T. scotoductus chromosome and extensive rearrangement, deletion of nonessential genes and acquisition of gene islands have occurred, leading to a loss of synteny between the chromosomes of T. scotoductus and T. thermophilus. At least nine large inserts of which seven were identified as alien, were found, the most remarkable being a denitrification cluster and two operons relating to the metabolism of phenolics which appear to have been acquired from Meiothermus ruber. The majority of acquired genes are from closely related species of the Deinococcus-Thermus group, and many of the remaining genes are from microorganisms with a thermophilic or hyperthermophilic lifestyle. The natural competence of Thermus scotoductus was confirmed experimentally as expected as most of the proteins of the natural transformation system of Thermus thermophilus are present. Analysis of the metabolic capabilities revealed an extensive energy metabolism with many aerobic and anaerobic respiratory options. An abundance of sensor histidine kinases, response regulators and transporters for a wide variety of compounds are indicative of an oligotrophic lifestyle. Conclusions The genome of Thermus scotoductus SA-01 shows remarkable plasticity with the loss, acquisition and rearrangement of large portions of its genome compared to Thermus thermophilus. Its ability to naturally take up foreign DNA has helped it adapt rapidly to a subsurface lifestyle in the presence of a dense and diverse population which acted as source of nutrients. The genome of Thermus scotoductus illustrates how rapid adaptation can be achieved by a highly dynamic and plastic genome. PMID:22115438

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

PubMed Central

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 (~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 anoxygenic photosynthesizers. The resistance to desiccation of Terrabacteria and their elaboration of photoprotective compounds suggests that the common ancestor of this group inhabited land. If true, then oxygenic photosynthesis may owe its origin to terrestrial adaptations. PMID:15535883

[Hospital clinical engineer orientation and function in the maintenance system of hospital medical equipment].

PubMed

Li, Bin; Zheng, Yunxin; He, Dehua; Jiang, Ruiyao; Chen, Ying; Jing, Wei

2012-03-01

The quantity of medical equipment in hospital rise quickly recent year. It provides the comprehensive support to the clinical service. The maintenance of medical equipment becomes more important than before. It is necessary to study on the orientation and function of clinical engineer in medical equipment maintenance system. Refer to three grade health care system, the community doctors which is called General practitioner, play an important role as the gatekeeper of health care system to triage and cost control. The paper suggests that hospital clinical engineer should play similar role as the gatekeeper of medical equipment maintenance system which composed by hospital clinical engineer, manufacture engineer and third party engineer. The hospital clinical engineer should be responsible of guard a pass of medical equipment maintenance quality and cost control. As the gatekeeper, hospital clinical engineer should take the responsibility of "General engineer" and pay more attention to safety and health of medical equipment. The responsibility description and future transition? development of clinical engineer as "General Engineer" is discussed. More attention should be recommended to the team building of hospital clinical engineer as "General Engineer".

Engineering: Defining and differentiating its unique culture

NASA Astrophysics Data System (ADS)

Pilotte, Mary K.

The world of work for engineering professionals is changing. At a rapid pace, experienced engineers are exiting the workforce due to retirement of the Baby Boomer generation, while at the same time the problems facing engineers are increasingly complex and frequently global in nature. For firms to protect their knowledge assets, they must ensure that acquired understandings are shared among their engineering work groups. Engineering teaching and learning in the workplace (i.e., knowledge sharing), is a social activity that resides in a social context governed by the professional engineering culture. This quantitative study uses Hofstede's Organizational Cultural Values Model (Hofstede, Neuijen, Ohayv, & Sanders, 1990) to examine dimensions of engineering culture in the workplace, producing a central tendency profile of engineering's cultural practices. Further, it explores through hypotheses if demographic differentiators, including birth generation, gender, race, industry sector of employment, and engineering discipline, play roles in forming engineering cultural practices. Results both corroborate aspects of Hofstede's model and assert new understandings relative to factors influencing dimensions of engineering practice. Outcomes are discussed in terms of their potential impact on industrial knowledge sharing and formation of beneficial engineering cultures.

Development of natural gas rotary engines

NASA Astrophysics Data System (ADS)

Mack, J. R.

1991-08-01

Development of natural gas-fueled rotary engines was pursued on the parallel paths of converted Mazda automotive engines and of establishing technology and demonstration of a test model of a larger John Deer Technologies Incorporated (JDTI) rotary engine with power capability of 250 HP per power section for future production of multi-rotor engines with power ratings 250, 500, and 1000 HP and upward. Mazda engines were converted to natural gas and were characterized by a laboratory which was followed by nearly 12,000 hours of testing in three different field installations. To develop technology for the larger JDTI engine, laboratory and engine materials testing was accomplished. Extensive combustion analysis computer codes were modified, verified, and utilized to predict engine performance, to guide parameters for actual engine design, and to identify further improvements. A single rotor test engine of 5.8 liter displacement was designed for natural gas operation based on the JDTI 580 engine series. This engine was built and tested. It ran well and essentially achieved predicted performance. Lean combustion and low NOW emission were demonstrated.

Engineers’ Responsibilities for Global Electronic Waste: Exploring Engineering Student Writing Through a Care Ethics Lens

PubMed Central

Campbell, Ryan C.; Wilson, Denise

2016-01-01

This paper provides an empirically informed perspective on the notion of responsibility using an ethical framework that has received little attention in the engineering-related literature to date: ethics of care. In this work, we ground conceptual explorations of engineering responsibility in empirical findings from engineering student’s writing on the human health and environmental impacts of “backyard” electronic waste recycling/disposal. Our findings, from a purposefully diverse sample of engineering students in an introductory electrical engineering course, indicate that most of these engineers of tomorrow associated engineers with responsibility for the electronic waste (e-waste) problem in some way. However, a number of responses suggested attempts to deflect responsibility away from engineers towards, for example, the government or the companies for whom engineers work. Still other students associated both engineers and non-engineers with responsibility, demonstrating the distributed/collective nature of responsibility that will be required to achieve a solution to the global problem of excessive e-waste. Building upon one element of a framework for care ethics adopted from the wider literature, these empirical findings are used to facilitate a preliminary, conceptual exploration of care-ethical responsibility within the context of engineering and e-waste recycling/disposal. The objective of this exploration is to provide a first step toward understanding how care-ethical responsibility applies to engineering. We also hope to seed dialogue within the engineering community about its ethical responsibilities on the issue. We conclude the paper with a discussion of its implications for engineering education and engineering ethics that suggests changes for educational policy and the practice of engineering. PMID:27368195

First-year engineering students' views of the nature of engineering

NASA Astrophysics Data System (ADS)

Karatas, Faik O.

The changing nature of engineering problems and new challenges that result from globalization and new ways of doing business have triggered calls for a revolutionary shift in engineering education. To respond to these challenges, the engineering education paradigm has been revised by adding more design and humanities/social sciences components to it. Philosophy, sociology, and history of engineering are more often cited as a major part of engineering education in this movement. Research on the nature of engineering (NOE), which is derived from philosophy, sociology, and the history of engineering, could have as much potential impact on engineering education as research on the nature of science (NOS) has had on science education. Thus, it is surprising that there has been no noteworthy research on this topic. The purpose of this study is to describe and determine first-year engineering students' views of the NOE and how these students differentiate engineering from science. In this research, an open-ended Views of the Nature of Engineering questionnaire (VNOE) was employed to collect baseline data. Semi-structured interviews based on the VNOE questionnaire were conducted with the second cohort of the participants. Data analysis was guided by a traditional phenomenographic approach, which is a branch of the hermeneutic tradition, coupled to constant comparison technique. The results of this study indicated that the participants' overall views of the nature of engineering were not ill-developed, but rather unarticulated. Moreover, the relationship between engineering and science was considered unidirectional rather than bidirectional. The results of this study could be used to inform engineering educators, first-year engineering coordinators, and policy makers as well as serving as the base for further research and potential implications for future first-year and K-12 engineering education.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kevin Young

In this paper, the author describes how engineers can increase the number of future engineers by volunteering as guest speakers in the elementary school classroom. The paper is divided into three main subjects. First, the importance of engineers speaking directly with young students is discussed. Next, several best practice techniques for speaking with young students are described. Finally, information on getting started as a guest speaker is presented, and a list of resources available to guest speakers is provided. The guest engineer speaking to an elementary school audience (ages 6-11) performs a critical role in encouraging young students to pursuemore » a career in engineering. Often, he or she is the first engineer these students meet in person, providing a crucial first impression of the engineering career field and a positive visual image of what an engineer really looks like. A dynamic speaker presenting a well-delivered talk creates a lasting, positive impression on students, influencing their future decisions to pursue careers in engineering. By reaching these students early in life, the guest speaker will help dispel the many prevailing stereotypes about engineers which discourage so many students, especially young women, from considering this career. The guest speaker can ensure young students gain a positive first impression of engineers and the engineering career field by following some best practice techniques in preparing for and delivering their presentation. The author, an electrical engineer, developed these best practice techniques over the past 10 years while presenting over 350 talks on engineering subjects to elementary school students as a volunteer speaker with the U.S. Department of Energy, Idaho National Laboratory’s Speakers Bureau. Every engineer can make a meaningful contribution toward reversing the predicted shortfall of future engineers by volunteering to speak with young students at the elementary school level. Elementary school teachers typically have a limited education in engineering and are eager to have career engineers speak with their students. As an engineer, there are many opportunities to get involved with guest speaking at the elementary school level. If you have a young child, start by meeting with her or his teacher and volunteering to give a presentation on engineering to the class. Many organizations have formal speakers bureaus. If your organization does not have one, consider starting one. There are several excellent resources on the Internet, such as the IEEE Center for Pre-University Engineering Education’s TryEngineering.org Web site. This site is designed for young students, teachers and parents, giving information on engineering careers and engineering activities the guest speaker can use to prepare a dynamic and informative presentation. Young students who have experienced a positive interaction with an engineer are more likely to pursue a career in engineering. Effective guest speaking by engineers in elementary school classrooms today will increase the likelihood these young students will become the desperately needed engineers of our future.« less

The Effects of Cylinder Head Gasket Opening on Engine Temperature Distribution for a Water-Cooled Engine

NASA Astrophysics Data System (ADS)

Jang, J. Y.; Chi, G. X.

2017-02-01

In a liquid-cooled engine, coolant is pumped throughout the water jacket of the engine, drawing heat from the cylinder head, pistons, combustion chambers, cylinder walls, and valves, etc. If the engine temperature is too high or too low, various problems will occur. These include overheating of the lubricating oil and engine parts, excessive stresses between engine parts, loss of power, incomplete burning of fuel, etc. Thus, the engine should be maintained at the proper operating temperature. This study investigated the effects of different cylinder head gasket opening on the engine temperature distributions in a water-cooled motorcycle engine. The numerical predictions for the temperature distribution are in good agreement with the experimental data within 20%.

Collaborative Systems Thinking: A Response to the Problems Faced by Systems Engineering's 'Middle Tier'

NASA Technical Reports Server (NTRS)

Phfarr, Barbara B.; So, Maria M.; Lamb, Caroline Twomey; Rhodes, Donna H.

2009-01-01

Experienced systems engineers are adept at more than implementing systems engineering processes: they utilize systems thinking to solve complex engineering problems. Within the space industry demographics and economic pressures are reducing the number of experienced systems engineers that will be available in the future. Collaborative systems thinking within systems engineering teams is proposed as a way to integrate systems engineers of various experience levels to handle complex systems engineering challenges. This paper uses the GOES-R Program Systems Engineering team to illustrate the enablers and barriers to team level systems thinking and to identify ways in which performance could be improved. Ways NASA could expand its engineering training to promote team-level systems thinking are proposed.

Two-stroke S.I. engine competitive to four-stroke engine in terms of the exhaust emission

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pavletic, R.; Trenc, F.

1994-09-01

A model engine with disintegrated working cycle was built. Its operation is not autonomous; compression of the working air is performed separately outside the engine by the compressed-air line supply. Pre-compressed charge together with the injected fuel is introduced in the combustion chamber. The model engine makes possible to determine indicated performance characteristics and its emission capability. Effective measured engine characteristics are of course not comparable with those obtained by a practical engine. The model presented is a two-stroke cycle engine. Exhaust emission picture of the presented engine is comparable with the emission of a modern four-stroke engine. 2 refs.,more » 13 figs., 2 tabs.« less

Interactive-graphic flowpath plotting for turbine engines

NASA Technical Reports Server (NTRS)

Corban, R. R.

1981-01-01

An engine cycle program capable of simulating the design and off-design performance of arbitrary turbine engines, and a computer code which, when used in conjunction with the cycle code, can predict the weight of the engines are described. A graphics subroutine was added to the code to enable the engineer to visualize the designed engine with more clarity by producing an overall view of the designed engine for output on a graphics device using IBM-370 graphics subroutines. In addition, with the engine drawn on a graphics screen, the program allows for the interactive user to make changes to the inputs to the code for the engine to be redrawn and reweighed. These improvements allow better use of the code in conjunction with the engine program.

The history and evolution of optically accessible research engines and their impact on our understanding of engine combustion

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miles, Paul C.

2015-03-01

The development and application of optically accessible engines to further our understanding of in-cylinder combustion processes is reviewed, spanning early efforts in simplified engines to the more recent development of high-pressure, high-speed engines that retain the geometric complexities of modern production engines. Limitations of these engines with respect to the reproduction of realistic metal test engine characteristics and performance are identified, as well as methods that have been used to overcome these limitations. Finally, the role of the work performed in these engines on clarifying the fundamental physical processes governing the combustion process and on laying the foundation for predictivemore » engine simulation is summarized.« less

A 150 and 300 kW lightweight diesel aircraft engine design study

NASA Technical Reports Server (NTRS)

Brouwers, A. P.

1980-01-01

The diesel engine was reinvestigated as an aircraft powerplant through design study conducted to arrive at engine configurations and applicable advanced technologies. Two engines are discussed, a 300 kW six-cylinder engine for twin engine general aviation aircraft and a 150 kW four-cylinder engine for single engine aircraft. Descriptions of each engine include concept drawings, a performance analysis, stress and weight data, and a cost study. This information was used to develop two airplane concepts, a six-place twin and a four-place single engine aircraft. The aircraft study consists of installation drawings, computer generated performance data, aircraft operating costs, and drawings of the resulting airplanes. The performance data show a vast improvement over current gasoline-powered aircraft.

Small Engine Component Technology (SECT) study

NASA Technical Reports Server (NTRS)

Singh, B.

1986-01-01

Small advanced (450 to 850 pounds thrust, 2002 to 3781 N) gas turbine engines were studied for a subsonic strategic cruise missile application, using projected year 2000 technology. An aircraft, mission characteristics, and baseline (state-of-the-art) engine were defined to evaluate technology benefits. Engine performance and configuration analyses were performed for two and three spool turbofan and propfan engine concepts. Mission and Life Cycle Cost (LCC) analyses were performed in which the candidate engines were compared to the baseline engines over a prescribed mission. The advanced technology engines reduced system LCC up to 41 percent relative to the baseline engine. Critical aerodynamic, materials, and mechanical systems turbine engine technologies were identified and program plans were defined for each identified critical technology.

Correlation tests of the engine performance parameter by using the detrended cross-correlation coefficient

NASA Astrophysics Data System (ADS)

Dong, Keqiang; Gao, You; Jing, Liming

2015-02-01

The presence of cross-correlation in complex systems has long been noted and studied in a broad range of physical applications. We here focus on an aero-engine system as an example of a complex system. By applying the detrended cross-correlation (DCCA) coefficient method to aero-engine time series, we investigate the effects of the data length and the time scale on the detrended cross-correlation coefficients ρ DCCA ( T, s). We then show, for a twin-engine aircraft, that the engine fuel flow time series derived from the left engine and the right engine exhibit much stronger cross-correlations than the engine exhaust-gas temperature series derived from the left engine and the right engine do.

The gate studies: Assessing the potential of future small general aviation turbine engines

NASA Technical Reports Server (NTRS)

Strack, W. C.

1979-01-01

Four studies were completed that explore the opportunities for future General Aviation turbine engines (GATE) in the 150-1000 SHP class. These studies forecasted the potential impact of advanced technology turbine engines in the post-1988 market, identified important aircraft and missions, desirable engine sizes, engine performance, and cost goals. Parametric evaluations of various engine cycles, configurations, design features, and advanced technology elements defined baseline conceptual engines for each of the important missions identified by the market analysis. Both fixed-wing and helicopter aircraft, and turboshaft, turboprop, and turbofan engines were considered. Sizable performance gains (e.g., 20% SFC decrease), and large engine cost reductions of sufficient magnitude to challenge the reciprocating engine in the 300-500 SHP class were predicted.

40 CFR 1033.130 - Instructions for engine remanufacturing or engine installation.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 32 2010-07-01 2010-07-01 false Instructions for engine remanufacturing or engine installation. 1033.130 Section 1033.130 Protection of Environment ENVIRONMENTAL... and Related Requirements § 1033.130 Instructions for engine remanufacturing or engine installation. (a...

14 CFR 29.903 - Engines.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Engines. 29.903 Section 29.903 Aeronautics... STANDARDS: TRANSPORT CATEGORY ROTORCRAFT Powerplant General § 29.903 Engines. (a) Engine type certification. Each engine must have an approved type certificate. Reciprocating engines for use in helicopters must...

78 FR 13030 - Board on Coastal Engineering Research

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-26

... DEPARTMENT OF DEFENSE Department of the Army; Corps of Engineers Board on Coastal Engineering... following committee meeting: Name of Committee: Board on Coastal Engineering Research. Date of Meeting... coastal engineering field and the objectives of the Chief of Engineers. Proposed Agenda: On Monday, March...

77 FR 52701 - Board on Coastal Engineering Research

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-30

... DEPARTMENT OF DEFENSE Department of the Army; Corps of Engineers Board on Coastal Engineering... following committee meeting: Name of Committee: Board on Coastal Engineering Research. Date of Meeting... consonance with the needs of the coastal engineering field and the objectives of the Chief of Engineers...

Industrial Education. "Small Engines".

ERIC Educational Resources Information Center

Parma City School District, OH.

Part of a series of curriculum guides dealing with industrial education in junior high schools, this guide provides the student with information and manipulative experiences on small gasoline engines. Included are sections on shop adjustment, safety, small engines, internal combustion, engine construction, four stroke engines, two stroke engines,…

14 CFR 29.903 - Engines.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 14 Aeronautics and Space 1 2011-01-01 2011-01-01 false Engines. 29.903 Section 29.903 Aeronautics... STANDARDS: TRANSPORT CATEGORY ROTORCRAFT Powerplant General § 29.903 Engines. (a) Engine type certification. Each engine must have an approved type certificate. Reciprocating engines for use in helicopters must...

40 CFR 1033.130 - Instructions for engine remanufacturing or engine installation.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 34 2012-07-01 2012-07-01 false Instructions for engine remanufacturing or engine installation. 1033.130 Section 1033.130 Protection of Environment ENVIRONMENTAL... and Related Requirements § 1033.130 Instructions for engine remanufacturing or engine installation. (a...

40 CFR 1033.130 - Instructions for engine remanufacturing or engine installation.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 34 2013-07-01 2013-07-01 false Instructions for engine remanufacturing or engine installation. 1033.130 Section 1033.130 Protection of Environment ENVIRONMENTAL... and Related Requirements § 1033.130 Instructions for engine remanufacturing or engine installation. (a...

40 CFR 1033.130 - Instructions for engine remanufacturing or engine installation.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 33 2014-07-01 2014-07-01 false Instructions for engine remanufacturing or engine installation. 1033.130 Section 1033.130 Protection of Environment ENVIRONMENTAL... and Related Requirements § 1033.130 Instructions for engine remanufacturing or engine installation. (a...

40 CFR 1033.130 - Instructions for engine remanufacturing or engine installation.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 33 2011-07-01 2011-07-01 false Instructions for engine remanufacturing or engine installation. 1033.130 Section 1033.130 Protection of Environment ENVIRONMENTAL... and Related Requirements § 1033.130 Instructions for engine remanufacturing or engine installation. (a...

14 CFR 29.903 - Engines.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 14 Aeronautics and Space 1 2012-01-01 2012-01-01 false Engines. 29.903 Section 29.903 Aeronautics... STANDARDS: TRANSPORT CATEGORY ROTORCRAFT Powerplant General § 29.903 Engines. (a) Engine type certification. Each engine must have an approved type certificate. Reciprocating engines for use in helicopters must...

14 CFR 29.903 - Engines.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 14 Aeronautics and Space 1 2013-01-01 2013-01-01 false Engines. 29.903 Section 29.903 Aeronautics... STANDARDS: TRANSPORT CATEGORY ROTORCRAFT Powerplant General § 29.903 Engines. (a) Engine type certification. Each engine must have an approved type certificate. Reciprocating engines for use in helicopters must...

14 CFR 29.903 - Engines.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 14 Aeronautics and Space 1 2014-01-01 2014-01-01 false Engines. 29.903 Section 29.903 Aeronautics... STANDARDS: TRANSPORT CATEGORY ROTORCRAFT Powerplant General § 29.903 Engines. (a) Engine type certification. Each engine must have an approved type certificate. Reciprocating engines for use in helicopters must...

Aerospike Engine Post-Test Diagnostic System Delivered to Rocketdyne

NASA Technical Reports Server (NTRS)

Meyer, Claudia M.

2000-01-01

The NASA Glenn Research Center at Lewis Field, in cooperation with Rocketdyne, has designed, developed, and implemented an automated Post-Test Diagnostic System (PTDS) for the X-33 linear aerospike engine. The PTDS was developed to reduce analysis time and to increase the accuracy and repeatability of rocket engine ground test fire and flight data analysis. This diagnostic system provides a fast, consistent, first-pass data analysis, thereby aiding engineers who are responsible for detecting and diagnosing engine anomalies from sensor data. It uses analytical methods modeled after the analysis strategies used by engineers. Glenn delivered the first version of PTDS in September of 1998 to support testing of the engine s power pack assembly. The system was used to analyze all 17 power pack tests and assisted Rocketdyne engineers in troubleshooting both data acquisition and test article anomalies. The engine version of PTDS, which was delivered in June of 1999, will support all single-engine, dual-engine, and flight firings of the aerospike engine.

Analysis of Performance of Jet Engine from Characteristics of Components II : Interaction of Components as Determined from Engine Operation

NASA Technical Reports Server (NTRS)

Goldstein, Arthur W; Alpert, Sumner; Beede, William; Kovach, Karl

1949-01-01

In order to understand the operation and the interaction of jet-engine components during engine operation and to determine how component characteristics may be used to compute engine performance, a method to analyze and to estimate performance of such engines was devised and applied to the study of the characteristics of a research turbojet engine built for this investigation. An attempt was made to correlate turbine performance obtained from engine experiments with that obtained by the simpler procedure of separately calibrating the turbine with cold air as a driving fluid in order to investigate the applicability of component calibration. The system of analysis was also applied to prediction of the engine and component performance with assumed modifications of the burner and bearing characteristics, to prediction of component and engine operation during engine acceleration, and to estimates of the performance of the engine and the components when the exhaust gas was used to drive a power turbine.

Performance Benefits for Wave Rotor-Topped Gas Turbine Engines

NASA Technical Reports Server (NTRS)

Jones, Scott M.; Welch, Gerard E.

1996-01-01

The benefits of wave rotor-topping in turboshaft engines, subsonic high-bypass turbofan engines, auxiliary power units, and ground power units are evaluated. The thermodynamic cycle performance is modeled using a one-dimensional steady-state code; wave rotor performance is modeled using one-dimensional design/analysis codes. Design and off-design engine performance is calculated for baseline engines and wave rotor-topped engines, where the wave rotor acts as a high pressure spool. The wave rotor-enhanced engines are shown to have benefits in specific power and specific fuel flow over the baseline engines without increasing turbine inlet temperature. The off-design steady-state behavior of a wave rotor-topped engine is shown to be similar to a conventional engine. Mission studies are performed to quantify aircraft performance benefits for various wave rotor cycle and weight parameters. Gas turbine engine cycles most likely to benefit from wave rotor-topping are identified. Issues of practical integration and the corresponding technical challenges with various engine types are discussed.

Multi-Fuel Rotary Engine for General Aviation Aircraft

NASA Technical Reports Server (NTRS)

Jones, C.; Ellis, D. R.; Meng, P. R.

1983-01-01

Design studies, conducted for NASA, of Advanced Multi-fuel General Aviation and Commuter Aircraft Rotary Stratified Charge Engines are summarized. Conceptual design studies of an advanced engine sized to provide 186/250 shaft KW/HP under cruise conditions at 7620/25,000 m/ft. altitude were performed. Relevant engine development background covering both prior and recent engine test results of the direct injected unthrottled rotary engine technology, including the capability to interchangeably operate on gasoline, diesel fuel, kerosene, or aviation jet fuel, are presented and related to growth predictions. Aircraft studies, using these resultant growth engines, define anticipated system effects of the performance and power density improvements for both single engine and twin engine airplanes. The calculated results indicate superior system performance and 30 to 35% fuel economy improvement for the Rotary-engine airplanes as compared to equivalent airframe concept designs with current baseline engines. The research and technology activities required to attain the projected engine performance levels are also discussed.

A New Method to Measure Temperature and Burner Pattern Factor Sensing for Active Engine Control

NASA Technical Reports Server (NTRS)

Ng, Daniel

1999-01-01

The determination of the temperatures of extended surfaces which exhibit non-uniform temperature variation is very important for a number of applications including the "Burner Pattern Factor" (BPF) of turbine engines. Exploratory work has shown that use of BPF to control engine functions can result in many benefits, among them reduction in engine weight, reduction in operating cost, increase in engine life, while attaining maximum engine efficiency. Advanced engines are expected to operate at very high temperature to achieve high efficiency. Brief exposure of engine components to higher than design temperatures due to non-uniformity in engine burner pattern can reduce engine life. The engine BPF is a measure of engine temperature uniformity. Attainment of maximum temperature uniformity and high temperatures is key to maximum efficiency and long life. A new approach to determine through the measurement of just one radiation spectrum by a multiwavelength pyrometer is possible. This paper discusses a new temperature sensing approach and its application to determine the BPF.

Integration of Engineering Education by High School Teachers to Meet Standards in the Physics Classroom

NASA Astrophysics Data System (ADS)

Kersten, Jennifer Anna

In recent years there has been increasing interest in engineering education at the K-12 level, which has resulted in states adopting engineering standards as a part of their academic science standards. From a national perspective, the basis for research into engineering education at the K-12 level is the belief that it is of benefit to student learning, including to "improve student learning and achievement in science and mathematics; increase awareness of engineering and the work of engineers; boost youth interest in pursuing engineering as a career; and increase the technological literacy of all students" (National Research Council, 2009a, p. 1). The above has led to a need to understand how teachers are currently implementing engineering education in their classrooms. High school physics teachers have a history of implementing engineering design projects in their classrooms, thus providing an appropriate setting to look for evidence of quality engineering education at the high school level. Understanding the characteristics of quality engineering integration can inform curricular and professional development efforts for teachers asked to implement engineering in their classrooms. Thus, the question that guided this study is: How, and to what extent, do physics teachers represent quality engineering in a physics unit focused on engineering? A case study research design was implemented for this project. Three high school physics teachers were participants in this study focused on the integration of engineering education into the physics classroom. The data collected included observations, interviews, and classroom documents that were analyzed using the Framework for Quality K-12 Engineering Education (Moore, Glancy et al., 2013). The results provided information about the areas of the K-12 engineering framework addressed during these engineering design projects, and detailed the quality of these lesson components. The results indicate that all of the design projects contained components of the indicators central to engineering education, although with varied degrees of success. In addition, each design project contained aspects important to the development of students' understanding of engineering and that promote important professional skills used by engineers. The implications of this work are discussed at the teacher, school, professional development, and policy levels.

4. INTERIOR OF ENGINE ROOM, CONTAINING UNITEDTOD TWINTANDEM ENGINE, FOR ...

Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

4. INTERIOR OF ENGINE ROOM, CONTAINING UNITED-TOD TWIN-TANDEM ENGINE, FOR 40" BLOOMING MILL; AS SEEN FROM THE UPPER LEVEL BRIDGE CRANE, THIS ENGINE WAS THE DIRECT DRIVE TO THE 40" BLOOMING MILL LOCATED IN THE ADJACENT ROOM TO THE LEFT. THE UNITED-TOD ENGINE, A TWIN TANDEM COMPOUND STEAM ENGINE, WAS RATED AT 20,000 MP. IN 1946 NEW HIGH PRESSURE CYLINDERS WERE INSTALLED AND THE ENGINE RAN ON 200 PSI STEAM, WITH A 44"X76"X60" STROKE, TO A BUILT-UP COUNTER-BALANCED CENTER CRANK. - Republic Iron & Steel Company, Youngstown Works, Blooming Mill & Blooming Mill Engines, North of Poland Avenue, Youngstown, Mahoning County, OH