Genome Sequence of the Fleming Strain of Micrococcus luteus, a Simple Free-Living Actinobacterium▿ †‡

PubMed Central

Young, Michael; Artsatbanov, Vladislav; Beller, Harry R.; Chandra, Govind; Chater, Keith F.; Dover, Lynn G.; Goh, Ee-Been; Kahan, Tamar; Kaprelyants, Arseny S.; Kyrpides, Nikos; Lapidus, Alla; Lowry, Stephen R.; Lykidis, Athanasios; Mahillon, Jacques; Markowitz, Victor; Mavromatis, Konstantinos; Mukamolova, Galina V.; Oren, Aharon; Rokem, J. Stefan; Smith, Margaret C. M.; Young, Danielle I.; Greenblatt, Charles L.

2010-01-01

Micrococcus luteus (NCTC2665, “Fleming strain”) has one of the smallest genomes of free-living actinobacteria sequenced to date, comprising a single circular chromosome of 2,501,097 bp (G+C content, 73%) predicted to encode 2,403 proteins. The genome shows extensive synteny with that of the closely related organism, Kocuria rhizophila, from which it was taxonomically separated relatively recently. Despite its small size, the genome harbors 73 insertion sequence (IS) elements, almost all of which are closely related to elements found in other actinobacteria. An IS element is inserted into the rrs gene of one of only two rrn operons found in M. luteus. The genome encodes only four sigma factors and 14 response regulators, a finding indicative of adaptation to a rather strict ecological niche (mammalian skin). The high sensitivity of M. luteus to β-lactam antibiotics may result from the presence of a reduced set of penicillin-binding proteins and the absence of a wblC gene, which plays an important role in the antibiotic resistance in other actinobacteria. Consistent with the restricted range of compounds it can use as a sole source of carbon for energy and growth, M. luteus has a minimal complement of genes concerned with carbohydrate transport and metabolism and its inability to utilize glucose as a sole carbon source may be due to the apparent absence of a gene encoding glucokinase. Uniquely among characterized bacteria, M. luteus appears to be able to metabolize glycogen only via trehalose and to make trehalose only via glycogen. It has very few genes associated with secondary metabolism. In contrast to most other actinobacteria, M. luteus encodes only one resuscitation-promoting factor (Rpf) required for emergence from dormancy, and its complement of other dormancy-related proteins is also much reduced. M. luteus is capable of long-chain alkene biosynthesis, which is of interest for advanced biofuel production; a three-gene cluster essential for this metabolism has been identified in the genome. PMID:19948807

Molecular Characterization of the Calvin Cycle Enzyme Phosphoribulokinase in the Stramenopile Alga Vaucheria litorea and the Plastid Hosting Mollusc Elysia chlorotica

PubMed Central

Rumpho, Mary E.; Pochareddy, Sirisha; Worful, Jared M.; Summer, Elizabeth J.; Bhattacharya, Debashish; Pelletreau, Karen N.; Tyler, Mary S.; Lee, Jungho; Manhart, James R.; Soule, Kara M.

2009-01-01

Phosphoribulokinase (PRK), a nuclear-encoded plastid-localized enzyme unique to the photosynthetic carbon reduction (Calvin) cycle, was cloned and characterized from the stramenopile alga Vaucheria litorea. This alga is the source of plastids for the mollusc (sea slug) Elysia chlorotica which enable the animal to survive for months solely by photoautotrophic CO2 fixation. The 1633-bp V. litorea prk gene was cloned and the coding region, found to be interrupted by four introns, encodes a 405-amino acid protein. This protein contains the typical bipartite target sequence expected of nuclear-encoded proteins that are directed to complex (i.e. four membrane-bound) algal plastids. De novo synthesis of PRK and enzyme activity were detected in E. chlorotica in spite of having been starved of V. litorea for several months. Unlike the algal enzyme, PRK in the sea slug did not exhibit redox regulation. Two copies of partial PRK-encoding genes were isolated from both sea slug and aposymbiotic sea slug egg DNA using PCR. Each copy contains the nucleotide region spanning exon 1 and part of exon 2 of V. litorea prk, including the bipartite targeting peptide. However, the larger prk fragment also includes intron 1. The exon and intron sequences of prk in E. chlorotica and V. litorea are nearly identical. These data suggest that PRK is differentially regulated in V. litorea and E. chlorotica and at least a portion of the V. litorea nuclear PRK gene is present in sea slugs that have been starved for several months. PMID:19995736

Identification and in vitro characterization of a Marek’s disease virus encoded ribonucleotide reductase

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus (MDV) encodes a ribonucleotide reductase (RR), a key regulatory enzyme in the DNA synthesis pathway. The gene coding for the RR of MDV is located in the unique long (UL) region of the genome. The large subunit is encoded by UL39 (RR1) and is predicted to comprise 860 amino acid...

SPARKy-Spring Ankle with Regenerative Kinematics

DTIC Science & Technology

2011-09-01

fiber keel. In our design considerations, we kept the passive carbon fiber keel to allow for walking in the event of battery failure. b. Test...used include a motor encoder, ankle encoder, and a heel switch. 7. Energy efficient carbon fiber keel is integrated into the device. Figure 6... Isometric and side views of SPARKy Phase 1 as modeled in SolidWorks. The Robotic Tendon actuator provides a dynamic moment about the ankle joint. Lever

The Arabidopsis thaliana RNA editing factor SLO2, which affects the mitochondrial electron transport chain, participates in multiple stress and hormone responses.

PubMed

Zhu, Qiang; Dugardeyn, Jasper; Zhang, Chunyi; Mühlenbock, Per; Eastmond, Peter J; Valcke, Roland; De Coninck, Barbara; Oden, Sevgi; Karampelias, Michael; Cammue, Bruno P A; Prinsen, Els; Van Der Straeten, Dominique

2014-02-01

Recently, we reported that the novel mitochondrial RNA editing factor SLO2 is essential for mitochondrial electron transport, and vital for plant growth through regulation of carbon and energy metabolism. Here, we show that mutation in SLO2 causes hypersensitivity to ABA and insensitivity to ethylene, suggesting a link with stress responses. Indeed, slo2 mutants are hypersensitive to salt and osmotic stress during the germination stage, while adult plants show increased drought and salt tolerance. Moreover, slo2 mutants are more susceptible to Botrytis cinerea infection. An increased expression of nuclear-encoded stress-responsive genes, as well as mitochondrial-encoded NAD genes of complex I and genes of the alternative respiratory pathway, was observed in slo2 mutants, further enhanced by ABA treatment. In addition, H2O2 accumulation and altered amino acid levels were recorded in slo2 mutants. We conclude that SLO2 is required for plant sensitivity to ABA, ethylene, biotic, and abiotic stress. Although two stress-related RNA editing factors were reported very recently, this study demonstrates a unique role of SLO2, and further supports a link between mitochondrial RNA editing events and stress response.

Mutations in Alternative Carbon Utilization Pathways in Candida albicans Attenuate Virulence and Confer Pleiotropic Phenotypes▿

PubMed Central

Ramírez, Melissa A.; Lorenz, Michael C.

2007-01-01

The interaction between Candida albicans and cells of the innate immune system is a key determinant of disease progression. Transcriptional profiling has revealed that C. albicans has a complex response to phagocytosis, much of which is similar to carbon starvation. This suggests that nutrient limitation is a significant stress in vivo, and we have shown that glyoxylate cycle mutants are less virulent in mice. To examine whether other aspects of carbon metabolism are important in vivo during an infection, we have constructed strains lacking FOX2 and FBP1, which encode key components of fatty acid β-oxidation and gluconeogenesis, respectively. As expected, fox2Δ mutants failed to utilize several fatty acids as carbon sources. Surprisingly, however, these mutants also failed to grow in the presence of several other carbon sources, whose assimilation is independent of β-oxidation, including ethanol and citric acid. Mutants lacking the glyoxylate enzyme ICL1 also had more severe carbon utilization phenotypes than were expected. These results suggest that the regulation of alternative carbon metabolism in C. albicans is significantly different from that in other fungi. In vivo, fox2Δ mutants show a moderate but significant reduction in virulence in a mouse model of disseminated candidiasis, while disruption of the glyoxylate cycle or gluconeogenesis confers a severe attenuation in this model. These data indicate that C. albicans often encounters carbon-poor conditions during growth in the host and that the ability to efficiently utilize multiple nonfermentable carbon sources is a virulence determinant. Consistent with this in vivo requirement, C. albicans uniquely regulates carbon metabolism in a more integrated manner than in Saccharomyces cerevisiae, such that defects in one part of the machinery have wider impacts than expected. These aspects of alternative carbon metabolism may then be useful as targets for therapeutic intervention. PMID:17158734

Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius

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

Lee, Brady D.; Apel, William A.; DeVeaux, Linda C.

Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in chemostats, followed by attempted induction of CCR with glucose or arabinose. A. acidocaldarius grew while simultaneouslymore » metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating CCR did not control carbon metabolism. Microarrays showed down-regulation of genes during growth on one sugar compared to two. Regulation occurred primarily in genes: 1) encoding regulators, 2) encoding enzymes for cell synthesis, and 3) encoding sugar transporters.« less

Identification of Bicarbonate as a Trigger and Genes Involved with Extracellular DNA Export in Mycobacterial Biofilms.

PubMed

Rose, Sasha J; Bermudez, Luiz E

2016-12-06

Extracellular DNA (eDNA) is an integral biofilm matrix component of numerous pathogens, including nontuberculous mycobacteria (NTM). Cell lysis is the source of eDNA in certain bacteria, but the source of eDNA remains unidentified for NTM, as well as for other eDNA-containing bacterial species. In this study, conditions affecting eDNA export were examined, and genes involved with the eDNA export mechanism were identified. After a method for monitoring eDNA in real time in undisturbed biofilms was established, different conditions affecting eDNA were investigated. Bicarbonate positively influenced eDNA export in a pH-independent manner in Mycobacterium avium, M. abscessus, and M. chelonae The surface-exposed proteome of M. avium in eDNA-containing biofilms revealed abundant carbonic anhydrases. Chemical inhibition of carbonic anhydrases with ethoxzolamide significantly reduced eDNA export. An unbiased transposon mutant library screen for eDNA export in M. avium identified many severely eDNA-attenuated mutants, including one not expressing a unique FtsK/SpoIIIE-like DNA-transporting pore, two with inactivation of carbonic anhydrases, and nine with inactivation of genes belonging to a unique genomic region, as well as numerous mutants involved in metabolism and energy production. Complementation of nine mutants that included the FtsK/SpoIIIE and carbonic anhydrase significantly restored eDNA export. Interestingly, several attenuated eDNA mutants have mutations in genes encoding proteins that were found with the surface proteomics, and many more mutations are localized in operons potentially encoding surface proteins. Collectively, our data strengthen the evidence of eDNA export being an active mechanism that is activated by the bacterium responding to bicarbonate. Many bacteria contain extracellular DNA (eDNA) in their biofilm matrix, as it has various biological and physical functions. We recently reported that nontuberculous mycobacteria (NTM) can contain significant quantities of eDNA in their biofilms. In some bacteria, eDNA is derived from dead cells, but that does not appear to be the case for all eDNA-containing organisms, including NTM. In this study, we found that eDNA export in NTM is conditionally dependent on the molecules to which the bacteria are exposed and that bicarbonate positively influences eDNA export. We also identified genes and proteins important for eDNA export, which begins to piece together a description of a mechanism for eDNA. Better understanding of eDNA export can give new targets for the development of antivirulence drugs, which are attractive because resistance to classical antibiotics is currently a significant problem. Copyright © 2016 Rose and Bermudez.

The Saccharomyces cerevisiae enolase-related regions encode proteins that are active enolases.

PubMed

Kornblatt, M J; Richard Albert, J; Mattie, S; Zakaib, J; Dayanandan, S; Hanic-Joyce, P J; Joyce, P B M

2013-02-01

In addition to two genes (ENO1 and ENO2) known to code for enolase (EC4.2.1.11), the Saccharomyces cerevisiae genome contains three enolase-related regions (ERR1, ERR2 and ERR3) which could potentially encode proteins with enolase function. Here, we show that products of these genes (Err2p and Err3p) have secondary and quaternary structures similar to those of yeast enolase (Eno1p). In addition, Err2p and Err3p can convert 2-phosphoglycerate to phosphoenolpyruvate, with kinetic parameters similar to those of Eno1p, suggesting that these proteins could function as enolases in vivo. To address this possibility, we overexpressed the ERR2 and ERR3 genes individually in a double-null yeast strain lacking ENO1 and ENO2, and showed that either ERR2 or ERR3 could complement the growth defect in this strain when cells are grown in medium with glucose as the carbon source. Taken together, these data suggest that the ERR genes in Saccharomyces cerevisiae encode a protein that could function in glycolysis as enolase. The presence of these enolase-related regions in Saccharomyces cerevisiae and their absence in other related yeasts suggests that these genes may play some unique role in Saccharomyces cerevisiae. Further experiments will be required to determine whether these functions are related to glycolysis or other cellular processes. Copyright © 2012 John Wiley & Sons, Ltd.

Review of Random Phase Encoding in Volume Holographic Storage

PubMed Central

Su, Wei-Chia; Sun, Ching-Cherng

2012-01-01

Random phase encoding is a unique technique for volume hologram which can be applied to various applications such as holographic multiplexing storage, image encryption, and optical sensing. In this review article, we first review and discuss diffraction selectivity of random phase encoding in volume holograms, which is the most important parameter related to multiplexing capacity of volume holographic storage. We then review an image encryption system based on random phase encoding. The alignment of phase key for decryption of the encoded image stored in holographic memory is analyzed and discussed. In the latter part of the review, an all-optical sensing system implemented by random phase encoding and holographic interconnection is presented.

Molecular characterization and analysis of the acrB gene of Aspergillus nidulans: a gene identified by genetic interaction as a component of the regulatory network that includes the CreB deubiquitination enzyme.

PubMed Central

Boase, Natasha A; Lockington, Robin A; Adams, Julian R J; Rodbourn, Louise; Kelly, Joan M

2003-01-01

Mutations in the acrB gene, which were originally selected through their resistance to acriflavine, also result in reduced growth on a range of sole carbon sources, including fructose, cellobiose, raffinose, and starch, and reduced utilization of omega-amino acids, including GABA and beta-alanine, as sole carbon and nitrogen sources. The acrB2 mutation suppresses the phenotypic effects of mutations in the creB gene that encodes a regulatory deubiquitinating enzyme, and in the creC gene that encodes a WD40-repeat-containing protein. Thus AcrB interacts with a regulatory network controlling carbon source utilization that involves ubiquitination and deubiquitination. The acrB gene was cloned and physically analyzed, and it encodes a novel protein that contains three putative transmembrane domains and a coiled-coil region. AcrB may play a role in the ubiquitination aspect of this regulatory network. PMID:12750323

Synthesis and antibacterial activity of novel 15-membered macrolide derivatives: 4''-carbamate, 11,12-cyclic carbonate-4''-carbamate and 11,4''-di-O-arylcarbamoyl analogs of azithromycin.

PubMed

Ma, Shutao; Ma, Ruixin; Liu, Zhaopeng; Ma, Chenchen; Shen, Xuecui

2009-10-01

4''-Carbamate, 11,12-cyclic carbonate-4''-carbamate and 11,4''-di-O-arylcarbamoyl analogs of azithromycin were designed, synthesized and evaluated. The 4''-carbamate analogs retained excellent activity against erythromycin-susceptible Staphylococcus pneumoniae and showed improved activity against erythromycin-resistant Staphylococcus pneumoniae. Compared with 4''-carbamate analogs, 11,12-cyclic carbonate-4''-carbamate analogs exhibited improved activity against erythromycin-resistant Staphylococcus pneumoniae encoded by the mef gene or the erm and mef genes, and 11,4''-di-O-arylalkylcarbamoyl analogs showed greatly improved activity (0.25-0.5 microg/mL) against erythromycin-resistant Staphylococcus pneumoniae encoded by the erm gene. Among them, the novel series of 11,4''-di-O-arylalkylcarbamoyl analogs 7a-k exhibited potent and balanced activity against susceptible and resistant bacteria. In particular, compounds 7f and 7k were the most effective against susceptible bacteria and resistant bacteria encoded by the erm gene or the mef gene.

Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis.

PubMed

Mehdizadeh Gohari, Iman; Kropinski, Andrew M; Weese, Scott J; Parreira, Valeria R; Whitehead, Ashley E; Boerlin, Patrick; Prescott, John F

2016-01-01

The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly associated with canine and foal necrotizing enteritis should improve our understanding of the role of type A Clostridium perfringens associated disease in these animals. The current study presents the complete genome sequence of two netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively. Genome sequencing was done using Single Molecule, Real-Time (SMRT) technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include five circular plasmids. Plasmid annotation revealed that three plasmids were shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin genes, netF, netE and netG, were located in unique pathogenicity loci on tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825 protein-coding genes whereas the chromosome of JFP838 contains 3,014 protein-encoding genes. Comparison of these two chromosomes with three available reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81 (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these divergent genomic regions in both chromosomes are phage- and plasmid-related segments. Sixteen of these unique chromosomal regions (~69 kb) were shared between the two isolates. Five of these shared regions formed a mosaic of plasmid-integrated segments, suggesting that these elements were acquired early in a clonal lineage of netF-positive C. perfringens strains. These results provide significant insight into the basis of canine and foal necrotizing enteritis and are the first to demonstrate that netF resides on a large and unique plasmid-encoded locus.

The molecular genetics of Usher syndrome.

PubMed

Ahmed, Z M; Riazuddin, S; Riazuddin, S; Wilcox, E R

2003-06-01

Association of sensorineural deafness and progressive retinitis pigmentosa with and without a vestibular abnormality is the hallmark of Usher syndrome and involves at least 12 loci among three different clinical subtypes. Genes identified for the more commonly inherited loci are USH2A (encoding usherin), MYO7A (encoding myosin VIIa), CDH23 (encoding cadherin 23), PCDH15 (encoding protocadherin 15), USH1C (encoding harmonin), USH3A (encoding clarin 1), and USH1G (encoding SANS). Transcripts from all these genes are found in many tissues/cell types other than the inner ear and retina, but all are uniquely critical for retinal and cochlear cell function. Many of these protein products have been demonstrated to have direct interactions with each other and perform an essential role in stereocilia homeostasis.

A Unique Chromosomal Rearrangement in the Cryptococcus neoformans var. grubii Type Strain Enhances Key Phenotypes Associated with Virulence

PubMed Central

Morrow, Carl A.; Lee, I. Russel; Chow, Eve W. L.; Ormerod, Kate L.; Goldinger, Anita; Byrnes, Edmond J.; Nielsen, Kirsten; Heitman, Joseph; Schirra, Horst Joachim; Fraser, James A.

2012-01-01

ABSTRACT The accumulation of genomic structural variation between closely related populations over time can lead to reproductive isolation and speciation. The fungal pathogen Cryptococcus is thought to have recently diversified, forming a species complex containing members with distinct morphologies, distributions, and pathologies of infection. We have investigated structural changes in genomic architecture such as inversions and translocations that distinguish the most pathogenic variety, Cryptococcus neoformans var. grubii, from the less clinically prevalent Cryptococcus neoformans var. neoformans and Cryptococcus gattii. Synteny analysis between the genomes of the three Cryptococcus species/varieties (strains H99, JEC21, and R265) reveals that C. neoformans var. grubii possesses surprisingly few unique genomic rearrangements. All but one are relatively small and are shared by all molecular subtypes of C. neoformans var. grubii. In contrast, the large translocation peculiar to the C. neoformans var. grubii type strain is found in all tested subcultures from multiple laboratories, suggesting that it has possessed this rearrangement since its isolation from a human clinical sample. Furthermore, we find that the translocation directly disrupts two genes. The first of these encodes a novel protein involved in metabolism of glucose at human body temperature and affects intracellular levels of trehalose. The second encodes a homeodomain-containing transcription factor that modulates melanin production. Both mutations would be predicted to increase pathogenicity; however, when recreated in an alternate genetic background, these mutations do not affect virulence in animal models. The type strain of C. neoformans var. grubii in which the majority of molecular studies have been performed is therefore atypical for carbon metabolism and key virulence attributes. PMID:22375073

Intensity-invariant coding in the auditory system.

PubMed

Barbour, Dennis L

2011-11-01

The auditory system faithfully represents sufficient details from sound sources such that downstream cognitive processes are capable of acting upon this information effectively even in the face of signal uncertainty, degradation or interference. This robust sound source representation leads to an invariance in perception vital for animals to interact effectively with their environment. Due to unique nonlinearities in the cochlea, sound representations early in the auditory system exhibit a large amount of variability as a function of stimulus intensity. In other words, changes in stimulus intensity, such as for sound sources at differing distances, create a unique challenge for the auditory system to encode sounds invariantly across the intensity dimension. This challenge and some strategies available to sensory systems to eliminate intensity as an encoding variable are discussed, with a special emphasis upon sound encoding. Copyright © 2011 Elsevier Ltd. All rights reserved.

Unusual Genomic Traits Suggest Methylocystis bryophila S285 to Be Well Adapted for Life in Peatlands

PubMed Central

Han, Dongfei; Dedysh, Svetlana N

2018-01-01

Abstract The genus Methylocystis belongs to the class Alphaproteobacteria, the family Methylocystaceae, and encompasses aerobic methanotrophic bacteria with the serine pathway of carbon assimilation. All Methylocystis species are able to fix dinitrogen and several members of this genus are also capable of using acetate or ethanol in the absence of methane, which explains their wide distribution in various habitats. One additional trait that enables their survival in the environment is possession of two methane-oxidizing isozymes, the conventional particulate methane monooxygenase (pMMO) with low-affinity to substrate (pMMO1) and the high-affinity enzyme (pMMO2). Here, we report the finished genome sequence of Methylocystis bryophila S285, a pMMO2-possessing methanotroph from a Sphagnum-dominated wetland, and compare it to the genome of Methylocystis sp. strain SC2, which is the first methanotroph with confirmed high-affinity methane oxidation potential. The complete genome of Methylocystis bryophila S285 consists of a 4.53 Mb chromosome and one plasmid, 175 kb in size. The genome encodes two types of particulate MMO (pMMO1 and pMMO2), soluble MMO and, in addition, contains a pxmABC-like gene cluster similar to that present in some gammaproteobacterial methanotrophs. The full set of genes related to the serine pathway, the tricarboxylic acid cycle as well as the ethylmalonyl-CoA pathway is present. In contrast to most described methanotrophs including Methylocystis sp. strain SC2, two different types of nitrogenases, that is, molybdenum–iron and vanadium–iron types, are encoded in the genome of strain S285. This unique combination of genome-based traits makes Methylocystis bryophila well adapted to the fluctuation of carbon and nitrogen sources in wetlands. PMID:29390143

An inorganic carbon transport system responsible for acclimation specific to air levels of CO2 in Chlamydomonas reinhardtii.

PubMed

Wang, Yingjun; Spalding, Martin H

2006-06-27

Many photosynthetic microorganisms acclimate to CO(2) limited environments by induction and operation of CO(2)-concentrating mechanisms (CCMs). Despite their central role in CCM function, inorganic carbon (Ci) transport systems never have been identified in eukaryotic photosynthetic organisms. In the green alga Chlamydomonas reinhardtii, a mutant, pmp1, was described in 1983 with deficiencies in Ci transport, and a Pmp1 protein-associated Ci uptake system has been proposed to be responsible for Ci uptake in low CO(2) (air level)-acclimated cells. However, even though pmp1 represents the only clear genetic link to Ci transport in microalgae and is one of only a very few mutants directly affecting the CCM itself, the identity of Pmp1 has remained unknown. Physiological analyses indicate that C. reinhardtii possesses multiple Ci transport systems responsible for acclimation to different levels of limiting CO(2) and that the Pmp1-associated transport system is required specifically for low (air level) CO(2) acclimation. In the current study, we identified and characterized a pmp1 allelic mutant, air dier 1 (ad1) that, like pmp1, cannot grow in low CO(2) (350 ppm) but can grow either in high CO(2) (5% CO(2)) or in very low CO(2) (<200 ppm). Molecular analyses revealed that the Ad1/Pmp1 protein is encoded by LciB, a gene previously identified as a CO(2)-responsive gene. LciB and three related genes in C. reinhardtii compose a unique gene family that encode four closely related, apparently soluble plastid proteins with no clearly identifiable conserved motifs.

Enzymological evidence for the function of a plastid-located pyruvate carboxylase in the Haptophyte alga Emiliania huxleyi: a novel pathway for the production of C4 compounds.

PubMed

Tsuji, Yoshinori; Suzuki, Iwane; Shiraiwa, Yoshihiro

2012-06-01

Pyruvate carboxylase (PYC) catalyzes the β-carboxylation of pyruvate to yield oxaloacetate (OAA). We previously isolated a cDNA encoding a putative PYC (EhPYC1) from the haptophyte alga Emiliania huxleyi and then proposed that EhPYC1 contributes to active anaplerotic β-carboxylation during photosynthesis although PYC activity was not detected in the cell extracts. Involvement of PYC in photosynthetic carbon metabolism is unique, since PYC generally functions in non-photosynthetic organisms. In the present study, we demonstrate that EhPYC1 is highly sensitive to endogenous proteases and therefore is easily degraded in cell extracts. By avoiding proteolytic degradation, PYC activity can be detected in the cell extracts of E. huxleyi. The activity of a recombinant His-tagged EhPYC1 expressed in Streptomyces lividans was inhibited by l-malate in a mixed non-competitive manner. Immunofluorescence labeling showed that EhPYC1 is located in the plastid. This result agrees with the prediction that a bipartite plastid-targeting signal is present that functions to deliver proteins into the four-membrane plastid of haptophyte algae. This is the first finding of a plastid-located PYC. These results indicate that E. huxleyi possesses a unique pathway to produce OAA catalyzed by PYC, and the pathway may provide carbon skeletons for amino acid biosynthesis in the plastid. A database search indicates that PYC genes are widespread in green algae, diatoms and brown algae, suggesting the crucial role of PYC in various aquatic phototrophs.

Requirement of carbon dioxide for initial growth of facultative methylotroph, Acidomonas methanolica MB58.

PubMed

Mitsui, Ryoji; Katayama, Hiroko; Tanaka, Mitsuo

2015-07-01

The facultative methylotrophic bacterium Acidomonas methanolica MB58 can utilize C1 compounds via the ribulose monophosphate pathway. A large gene cluster comprising three components related to C1 metabolism was found in the genome. From upstream, the first was an mxa cluster encoding proteins for oxidation of methanol to formaldehyde; the second was the rmp cluster encoding enzymes for formaldehyde fixation; and the third was the cbb gene cluster encoding proteins for carbon dioxide (CO2) fixation. Examination of CO2 requirements for growth of A. methanolica MB58 cells demonstrated that it did not grow on any carbon source under CO2-free conditions. Measurement of ribulose-1,5-bisphosphate carboxylase activity and RT-PCR analysis demonstrated enzymatic activity was detected in A. methanolica MB58 at growth phase, regardless of carbon sources. However, methanol dehydrogenase and 3-hexlose-6-phosphate synthase expression was regulated by methanol or formaldehyde; it were detected during growth and apparently differed from ribulose-1,5-bisphosphate carboxylase expression. These results suggested that A. methanolica MB58 may be initially dependent on autotrophic growth and that carbon assimilation was subsequently coupled with the ribulose monophosphate pathway at early- to mid-log phases during methylotrophic growth. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease.

PubMed

Karmi, Ola; Marjault, Henri-Baptiste; Pesce, Luca; Carloni, Paolo; Onuchic, Jose' N; Jennings, Patricia A; Mittler, Ron; Nechushtai, Rachel

2018-02-12

NEET proteins comprise a new class of [2Fe-2S] cluster proteins. In human, three genes encode for NEET proteins: cisd1 encodes mitoNEET (mNT), cisd2 encodes the Nutrient-deprivation autophagy factor-1 (NAF-1) and cisd3 encodes MiNT (Miner2). These recently discovered proteins play key roles in many processes related to normal metabolism and disease. Indeed, NEET proteins are involved in iron, Fe-S, and reactive oxygen homeostasis in cells and play an important role in regulating apoptosis and autophagy. mNT and NAF-1 are homodimeric and reside on the outer mitochondrial membrane. NAF-1 also resides in the membranes of the ER associated mitochondrial membranes (MAM) and the ER. MiNT is a monomer with distinct asymmetry in the molecular surfaces surrounding the clusters. Unlike its paralogs mNT and NAF-1, it resides within the mitochondria. NAF-1 and mNT share similar backbone folds to the plant homodimeric NEET protein (At-NEET), while MiNT's backbone fold resembles a bacterial MiNT protein. Despite the variation of amino acid composition among these proteins, all NEET proteins retained their unique CDGSH domain harboring their unique 3Cys:1His [2Fe-2S] cluster coordination through evolution. The coordinating exposed His was shown to convey the lability to the NEET proteins' [2Fe-2S] clusters. In this minireview, we discuss the NEET fold and its structural elements. Special attention is given to the unique lability of the NEETs' [2Fe-2S] cluster and the implication of the latter to the NEET proteins' cellular and systemic function in health and disease.

Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

PubMed Central

Ulas, Thomas; Riemer, S. Alexander; Zaparty, Melanie; Siebers, Bettina; Schomburg, Dietmar

2012-01-01

We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2–4 (optimum 3.5) and a temperature of 75–80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism. PMID:22952675

Physiological and Molecular Biological Characterization of Intracellular Carbonic Anhydrase from the Marine Diatom Phaeodactylum tricornutum1

PubMed Central

Satoh, Dan; Hiraoka, Yasutaka; Colman, Brian; Matsuda, Yusuke

2001-01-01

A single intracellular carbonic anhydrase (CA) was detected in air-grown and, at reduced levels, in high CO2-grown cells of the marine diatom Phaeodactylum tricornutum (UTEX 642). No external CA activity was detected irrespective of growth CO2 conditions. Ethoxyzolamide (0.4 mm), a CA-specific inhibitor, severely inhibited high-affinity photosynthesis at low concentrations of dissolved inorganic carbon, whereas 2 mm acetazolamide had little effect on the affinity for dissolved inorganic carbon, suggesting that internal CA is crucial for the operation of a carbon concentrating mechanism in P. tricornutum. Internal CA was purified 36.7-fold of that of cell homogenates by ammonium sulfate precipitation, and two-step column chromatography on diethylaminoethyl-sephacel and p-aminomethylbenzene sulfone amide agarose. The purified CA was shown, by SDS-PAGE, to comprise an electrophoretically single polypeptide of 28 kD under both reduced and nonreduced conditions. The entire sequence of the cDNA of this CA was obtained by the rapid amplification of cDNA ends method and indicated that the cDNA encodes 282 amino acids. Comparison of this putative precursor sequence with the N-terminal amino acid sequence of the purified CA indicated that it included a possible signal sequence of up to 46 amino acids at the N terminus. The mature CA was found to consist of 236 amino acids and the sequence was homologous to β-type CAs. Even though the zinc-ligand amino acid residues were shown to be completely conserved, the amino acid residues that may constitute a CO2-binding site appeared to be unique among the β-CAs so far reported. PMID:11500545

48 CFR 252.211-7003 - Item unique identification and valuation.

Code of Federal Regulations, 2014 CFR

2014-10-01

... reader or interrogator, used to retrieve data encoded on machine-readable media. Concatenated unique item... identifier. Item means a single hardware article or a single unit formed by a grouping of subassemblies... manufactured under identical conditions. Machine-readable means an automatic identification technology media...

Gene encoding γ-carbonic anhydrase is cotranscribed with argC and induced in response to stationary phase and high CO2 in Azospirillum brasilense Sp7

PubMed Central

2010-01-01

Background Carbonic anhydrase (CA) is a ubiquitous enzyme catalyzing the reversible hydration of CO2 to bicarbonate, a reaction underlying diverse biochemical and physiological processes. Gamma class carbonic anhydrases (γ-CAs) are widespread in prokaryotes but their physiological roles remain elusive. At present, only γ-CA of Methanosarcina thermophila (Cam) has been shown to have CA activity. Genome analysis of a rhizobacterium Azospirillum brasilense, revealed occurrence of ORFs encoding one β-CA and two γ-CAs. Results One of the putative γ-CA encoding genes of A. brasilense was cloned and overexpressed in E. coli. Electrometric assays for CA activity of the whole cell extracts overexpressing recombinant GCA1 did not show CO2 hydration activity. Reverse transcription-PCR analysis indicated that gca1 in A. brasilense is co-transcribed with its upstream gene annotated as argC, which encodes a putative N-acetyl-γ-glutamate-phosphate reductase. 5'-RACE also demonstrated that there was no transcription start site between argC and gca1, and the transcription start site located upstream of argC transcribed both the genes (argC-gca1). Using transcriptional fusions of argC-gca1 upstream region with promoterless lacZ, we further demonstrated that gca1 upstream region did not have any promoter and its transcription occurred from a promoter located in the argC upstream region. The transcription of argC-gca1 operon was upregulated in stationary phase and at elevated CO2 atmosphere. Conclusions This study shows lack of CO2 hydration activity in a recombinant protein expressed from a gene predicted to encode a γ-carbonic anhydrase in A. brasilense although it cross reacts with anti-Cam antibody raised against a well characterized γ-CA. The organization and regulation of this gene along with the putative argC gene suggests its involvement in arginine biosynthetic pathway instead of the predicted CO2 hydration. PMID:20598158

Gene encoding gamma-carbonic anhydrase is cotranscribed with argC and induced in response to stationary phase and high CO2 in Azospirillum brasilense Sp7.

PubMed

Kaur, Simarjot; Mishra, Mukti N; Tripathi, Anil K

2010-07-04

Carbonic anhydrase (CA) is a ubiquitous enzyme catalyzing the reversible hydration of CO2 to bicarbonate, a reaction underlying diverse biochemical and physiological processes. Gamma class carbonic anhydrases (gamma-CAs) are widespread in prokaryotes but their physiological roles remain elusive. At present, only gamma-CA of Methanosarcina thermophila (Cam) has been shown to have CA activity. Genome analysis of a rhizobacterium Azospirillum brasilense, revealed occurrence of ORFs encoding one beta-CA and two gamma-CAs. One of the putative gamma-CA encoding genes of A. brasilense was cloned and overexpressed in E. coli. Electrometric assays for CA activity of the whole cell extracts overexpressing recombinant GCA1 did not show CO2 hydration activity. Reverse transcription-PCR analysis indicated that gca1 in A. brasilense is co-transcribed with its upstream gene annotated as argC, which encodes a putative N-acetyl-gamma-glutamate-phosphate reductase. 5'-RACE also demonstrated that there was no transcription start site between argC and gca1, and the transcription start site located upstream of argC transcribed both the genes (argC-gca1). Using transcriptional fusions of argC-gca1 upstream region with promoterless lacZ, we further demonstrated that gca1 upstream region did not have any promoter and its transcription occurred from a promoter located in the argC upstream region. The transcription of argC-gca1 operon was upregulated in stationary phase and at elevated CO2 atmosphere. This study shows lack of CO2 hydration activity in a recombinant protein expressed from a gene predicted to encode a gamma-carbonic anhydrase in A. brasilense although it cross reacts with anti-Cam antibody raised against a well characterized gamma-CA. The organization and regulation of this gene along with the putative argC gene suggests its involvement in arginine biosynthetic pathway instead of the predicted CO2 hydration.

nuID: a universal naming scheme of oligonucleotides for Illumina, Affymetrix, and other microarrays

PubMed Central

Du, Pan; Kibbe, Warren A; Lin, Simon M

2007-01-01

Background Oligonucleotide probes that are sequence identical may have different identifiers between manufacturers and even between different versions of the same company's microarray; and sometimes the same identifier is reused and represents a completely different oligonucleotide, resulting in ambiguity and potentially mis-identification of the genes hybridizing to that probe. Results We have devised a unique, non-degenerate encoding scheme that can be used as a universal representation to identify an oligonucleotide across manufacturers. We have named the encoded representation 'nuID', for nucleotide universal identifier. Inspired by the fact that the raw sequence of the oligonucleotide is the true definition of identity for a probe, the encoding algorithm uniquely and non-degenerately transforms the sequence itself into a compact identifier (a lossless compression). In addition, we added a redundancy check (checksum) to validate the integrity of the identifier. These two steps, encoding plus checksum, result in an nuID, which is a unique, non-degenerate, permanent, robust and efficient representation of the probe sequence. For commercial applications that require the sequence identity to be confidential, we have an encryption schema for nuID. We demonstrate the utility of nuIDs for the annotation of Illumina microarrays, and we believe it has universal applicability as a source-independent naming convention for oligomers. Reviewers This article was reviewed by Itai Yanai, Rong Chen (nominated by Mark Gerstein), and Gregory Schuler (nominated by David Lipman). PMID:17540033

Highly stable beta-class carbonic anhydrases useful in carbon capture systems

DOEpatents

Alvizo, Oscar; Benoit, Mike; Novick, Scott

2013-04-16

The present disclosure relates to .beta.-class carbonic anhydrase polypeptides having improved properties including increased thermostability and/or stability in the presence of amine compounds, ammonia, or carbonate ion. The present disclosure also provides formulations and uses of the polypeptides for accelerating the absorption of carbon dioxide from a gas stream into a solution as well as for the release of the absorbed carbon dioxide for further treatment and/or sequestering. Also provided are polynucleotides encoding the carbonic anhydrase polypeptides and host cells capable of expressing them.

Highly stable beta-class carbonic anhydrases useful in carbon capture systems

DOEpatents

Alvizo, Oscar; Benoit, Michael R; Novick, Scott J

2013-08-20

The present disclosure relates to .beta.-class carbonic anhydrase polypeptides having improved properties including increased thermostability and/or stability in the presence of amine compounds, ammonia, or carbonate ion. The present disclosure also provides formulations and uses of the polypeptides for accelerating the absorption of carbon dioxide from a gas stream into a solution as well as for the release of the absorbed carbon dioxide for further treatment and/or sequestering. Also provided are polynucleotides encoding the carbonic anhydrase polypeptides and host cells capable of expressing them.

An Introduction to Heredity: Part 1

ERIC Educational Resources Information Center

Powell, Britnie; Malone, Molly; Drits-Esser, Dina; Stark, Louisa A.

2018-01-01

The mechanics by which unique individuals are built from the instructions encoded in DNA is too advanced for elementary-age children. However, students can easily understand that organisms have observable traits and that each individual has a unique combination of traits, ideas that are included in the "Next Generation Science Standards"…

Memory as discrimination: a challenge to the encoding-retrieval match principle.

PubMed

Poirier, Marie; Nairne, James S; Morin, Caroline; Zimmermann, Friederike G S; Koutmeridou, Kyriaki; Fowler, James

2012-01-01

Four experiments contrasted the predictions of a general encoding-retrieval match hypothesis with those of a view claiming that the distinctiveness of the cue-target relationship is the causal factor in retrieval. In Experiments 1, 2, and 4 participants learned the relationships between 4 targets and trios of cues; in Experiment 3 there were 3 targets, each associated with a pair of cues. A learning phase was followed by a cued-recognition task where the correct target had to be identified based on 1 or more of the cues. The main performance measurement was response time. Learning was designed to lead to high accuracy so effects could be attributed to retrieval efficiency rather than to variations in encoding. The nature of the cues and targets was varied across experiments. The critical factor was whether each cue was uniquely associated with the to-be-recalled target. All experiments orthogonally manipulated (a) how discriminative-or uniquely associated with a target-each cue was and (b) the degree of overlap between the cues present during learning and those present at retrieval. The novel finding reported here is that increasing the encoding-retrieval match can hinder performance if the increase simultaneously reduces how well cues predict a target-that is, a cue's diagnostic value. Encoding-retrieval match was not the factor that determined the effectiveness of retrieval. Our findings suggest that increasing the encoding-retrieval match can lead to no change, an increase, or a decrease in retrieval performance.

Plasmid Characterization and Chromosome Analysis of Two netF+ Clostridium perfringens Isolates Associated with Foal and Canine Necrotizing Enteritis

PubMed Central

Mehdizadeh Gohari, Iman; Kropinski, Andrew M.; Weese, Scott J.; Parreira, Valeria R.; Whitehead, Ashley E.; Boerlin, Patrick; Prescott, John F.

2016-01-01

The recent discovery of a novel beta-pore-forming toxin, NetF, which is strongly associated with canine and foal necrotizing enteritis should improve our understanding of the role of type A Clostridium perfringens associated disease in these animals. The current study presents the complete genome sequence of two netF-positive strains, JFP55 and JFP838, which were recovered from cases of foal necrotizing enteritis and canine hemorrhagic gastroenteritis, respectively. Genome sequencing was done using Single Molecule, Real-Time (SMRT) technology-PacBio and Illumina Hiseq2000. The JFP55 and JFP838 genomes include a single 3.34 Mb and 3.53 Mb chromosome, respectively, and both genomes include five circular plasmids. Plasmid annotation revealed that three plasmids were shared by the two newly sequenced genomes, including a NetF/NetE toxins-encoding tcp-conjugative plasmid, a CPE/CPB2 toxins-encoding tcp-conjugative plasmid and a putative bacteriocin-encoding plasmid. The putative beta-pore-forming toxin genes, netF, netE and netG, were located in unique pathogenicity loci on tcp-conjugative plasmids. The C. perfringens JFP55 chromosome carries 2,825 protein-coding genes whereas the chromosome of JFP838 contains 3,014 protein-encoding genes. Comparison of these two chromosomes with three available reference C. perfringens chromosome sequences identified 48 (~247 kb) and 81 (~430 kb) regions unique to JFP55 and JFP838, respectively. Some of these divergent genomic regions in both chromosomes are phage- and plasmid-related segments. Sixteen of these unique chromosomal regions (~69 kb) were shared between the two isolates. Five of these shared regions formed a mosaic of plasmid-integrated segments, suggesting that these elements were acquired early in a clonal lineage of netF-positive C. perfringens strains. These results provide significant insight into the basis of canine and foal necrotizing enteritis and are the first to demonstrate that netF resides on a large and unique plasmid-encoded locus. PMID:26859667

All-benzene carbon nanocages: size-selective synthesis, photophysical properties, and crystal structure.

PubMed

Matsui, Katsuma; Segawa, Yasutomo; Itami, Kenichiro

2014-11-19

The design and synthesis of a series of carbon nanocages consisting solely of benzene rings are described. Carbon nanocages are appealing molecules not only because they represent junction unit structures of branched carbon nanotubes, but also because of their potential utilities as unique optoelectronic π-conjugated materials and guest-encapsulating hosts. Three sizes of strained, conjugated [n.n.n]carbon nanocages (1, n = 4; 2, n = 5; 3, n = 6) were synthesized with perfect size-selectivity. Cyclohexane-containing units and 1,3,5-trisubstituted benzene-containing units were assembled to yield the minimally strained bicyclic precursors, which were successfully converted into the corresponding carbon nanocages via acid-mediated aromatization. X-ray crystallography of 1 confirmed the cage-shaped structure with an approximately spherical void inside the cage molecule. The present studies revealed the unique properties of carbon nanocages, including strain energies, size-dependent absorption and fluorescence, as well as unique size-dependency for the electronic features of 1-3.

Accumulation of slightly deleterious mutations in the mitochondrial genome: a hallmark of animal domestication.

PubMed

Hughes, Austin L

2013-02-15

The hypothesis that domestication leads to a relaxation of purifying selection on mitochondrial (mt) genomes was tested by comparative analysis of mt genes from dog, pig, chicken, and silkworm. The three vertebrate species showed mt genome phylogenies in which domestic and wild isolates were intermingled, whereas the domestic silkworm (Bombyx mori) formed a distinct cluster nested within its closest wild relative (Bombyx mandarina). In spite of these differences in phylogenetic pattern, significantly greater proportions of nonsynonymous SNPs than of synonymous SNPs were unique to the domestic populations of all four species. Likewise, in all four species, significantly greater proportions of RNA-encoding SNPs than of synonymous SNPs were unique to the domestic populations. Thus, domestic populations were characterized by an excess of unique polymorphisms in two categories generally subject to purifying selection: nonsynonymous sites and RNA-encoding sites. Many of these unique polymorphisms thus seem likely to be slightly deleterious; the latter hypothesis was supported by the generally lower gene diversities of polymorphisms unique to domestic populations in comparison to those of polymorphisms shared by domestic and wild populations. Copyright © 2012 Elsevier B.V. All rights reserved.

Plasticity and Kinky Chemistry of Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Srivastava, Deepak; Dzegilenko, Fedor

2000-01-01

Since their discovery in 1991, carbon nanotubes have been the subject of intense research interest based on early predictions of their unique mechanical, electronic, and chemical properties. Materials with the predicted unique properties of carbon nanotubes are of great interest for use in future generations of aerospace vehicles. For their structural properties, carbon nanotubes could be used as reinforcing fibers in ultralight multifunctional composites. For their electronic properties, carbon nanotubes offer the potential of very high-speed, low-power computing elements, high-density data storage, and unique sensors. In a continuing effort to model and predict the properties of carbon nanotubes, Ames accomplished three significant results during FY99. First, accurate values of the nanomechanics and plasticity of carbon nanotubes based on quantum molecular dynamics simulations were computed. Second, the concept of mechanical deformation catalyzed-kinky-chemistry as a means to control local chemistry of nanotubes was discovered. Third, the ease of nano-indentation of silicon surfaces with carbon nanotubes was established. The elastic response and plastic failure mechanisms of single-wall nanotubes were investigated by means of quantum molecular dynamics simulations.

Autolytic hydrolases affect sexual and asexual development of Aspergillus nidulans.

PubMed

Emri, Tamás; Vékony, Viktória; Gila, Barnabás; Nagy, Flóra; Forgács, Katalin; Pócsi, István

2018-03-30

Radial growth, asexual sporulation, and cleistothecia formation as well as extracellular chitinase and proteinase formation of Aspergillus nidulans were monitored in surface cultures in order to study the physiological role of extracellular hydrolase production in carbon-stressed cultures. We set up carbon-stressed and carbon-overfed experimental conditions by varying the starting glucose concentration within the range of 2.5 and 40 g/L. Glucose starvation induced radial growth and hydrolase production and enhanced the maturation of cleistothecia; meanwhile, glucose-rich conditions enhanced mycelial biomass, conidia, and cleistothecia production. Double deletion of chiB and engA (encoding an extracellular endochitinase and a β-1,3-endoglucanase, respectively) decreased conidia production under carbon-stressed conditions, suggesting that these autolytic hydrolases can support conidia formation by releasing nutrients from the cell wall polysaccharides of dead hyphae. Double deletion of prtA and pepJ (both genes encode extracellular proteases) reduced the number of cleistothecia even under carbon-rich conditions except in the presence of casamino acids, which supports the view that sexual development and amino acid metabolism are tightly connected to each other in this fungus.

A novel shape-based coding-decoding technique for an industrial visual inspection system.

PubMed

Mukherjee, Anirban; Chaudhuri, Subhasis; Dutta, Pranab K; Sen, Siddhartha; Patra, Amit

2004-01-01

This paper describes a unique single camera-based dimension storage method for image-based measurement. The system has been designed and implemented in one of the integrated steel plants of India. The purpose of the system is to encode the frontal cross-sectional area of an ingot. The encoded data will be stored in a database to facilitate the future manufacturing diagnostic process. The compression efficiency and reconstruction error of the lossy encoding technique have been reported and found to be quite encouraging.

Genome Sequence of the Obligate Gammaproteobacterial Methanotroph Methylomicrobium album strain BG8

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

Kits, K. Dimitri; Kalyuzhnaya, Marina G.; Klotz, Martin G

2013-01-01

The complete genome sequence of Methylomicrobium album BG8, a methane-oxidizing gammaproteobacterium isolated from freshwater, is reported. Aside from conserved inventory for growth on single-carbon compounds, M. album BG8 encodes a range of inventory for additional carbon and nitrogen transformations, but no genes for growth on multi-carbon substrates or for N-fixation.

Hollow Mesoporous Carbon Microparticles and Micromotors with Single Holes Templated by Colloidal Silica-Assisted Gas Bubbles.

PubMed

Huang, Xiaoxi; Zhang, Tao; Asefa, Tewodros

2017-07-01

A simple, new synthetic method that produces hollow, mesoporous carbon microparticles, each with a single hole on its surface, is reported. The synthesis involves unique templates, which are composed of gaseous bubbles and colloidal silica, and poly(furfuryl alcohol) as a carbon precursor. The conditions that give these morphologically unique carbon microparticles are investigated, and the mechanisms that result in their unique structures are proposed. Notably, the amount of colloidal silica and the type of polymer are found to hugely dictate whether or not the synthesis results in hollow asymmetrical microparticles, each with a single hole. The potential application of the particles as self-propelled micromotors is demonstrated. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Molecular Basis for Bifidobacterial Enrichment in the Infant Gastrointestinal Tract123

PubMed Central

Garrido, Daniel; Barile, Daniela; Mills, David A.

2012-01-01

Bifidobacteria are commonly used as probiotics in dairy foods. Select bifidobacterial species are also early colonizers of the breast-fed infant colon; however, the mechanism for this enrichment is unclear. We previously showed that Bifidobacterium longum subsp. infantis is a prototypical bifidobacterial species that can readily utilize human milk oligosaccharides as the sole carbon source. MS-based glycoprofiling has revealed that numerous B. infantis strains preferentially consume small mass oligosaccharides, abundant in human milks. Genome sequencing revealed that B. infantis possesses a bias toward genes required to use mammalian-derived carbohydrates. Many of these genomic features encode enzymes that are active on milk oligosaccharides including a novel 40-kb region dedicated to oligosaccharide utilization. Biochemical and molecular characterization of the encoded glycosidases and transport proteins has further resolved the mechanism by which B. infantis selectively imports and catabolizes milk oligosaccharides. Expression studies indicate that many of these key functions are only induced during growth on milk oligosaccharides and not expressed during growth on other prebiotics. Analysis of numerous B. infantis isolates has confirmed that these genomic features are common among the B. infantis subspecies and likely constitute a competitive colonization strategy used by these unique bifidobacteria. By detailed characterization of the molecular mechanisms responsible, these studies provide a conceptual framework for bifidobacterial persistence and host interaction in the infant gastrointestinal tract mediated in part through consumption of human milk oligosaccharides. PMID:22585920

The evolution of mollusc shells.

PubMed

McDougall, Carmel; Degnan, Bernard M

2018-05-01

Molluscan shells are externally fabricated by specialized epithelial cells on the dorsal mantle. Although a conserved set of regulatory genes appears to underlie specification of mantle progenitor cells, the genes that contribute to the formation of the mature shell are incredibly diverse. Recent comparative analyses of mantle transcriptomes and shell proteomes of gastropods and bivalves are consistent with shell diversity being underpinned by a rapidly evolving mantle secretome (suite of genes expressed in the mantle that encode secreted proteins) that is the product of (a) high rates of gene co-option into and loss from the mantle gene regulatory network, and (b) the rapid evolution of coding sequences, particular those encoding repetitive low complexity domains. Outside a few conserved genes, such as carbonic anhydrase, a so-called "biomineralization toolkit" has yet to be discovered. Despite this, a common suite of protein domains, which are often associated with the extracellular matrix and immunity, appear to have been independently and often uniquely co-opted into the mantle secretomes of different species. The evolvability of the mantle secretome provides a molecular explanation for the evolution and diversity of molluscan shells. These genomic processes are likely to underlie the evolution of other animal biominerals, including coral and echinoderm skeletons. This article is categorized under: Comparative Development and Evolution > Regulation of Organ Diversity Comparative Development and Evolution > Evolutionary Novelties. © 2018 Wiley Periodicals, Inc.

Mutational analysis of the major soybean UreF paralogue involved in urease activation

USDA-ARS?s Scientific Manuscript database

In soybean, mutation at Eu2 or Eu3 eliminates the urease activities of both the embryo-specific and the tissue-ubiquitous (assimilatory) isozymes, encoded by Eu1 and Eu4, respectively. Eu3 encodes UreG, a GTP’ase necessary for proper emplacement of Ni and carbon dioxide in the urease active site. ...

Arxula adeninivorans (Blastobotrys adeninivorans) — A Dimorphic Yeast of Great Biotechnological Potential

NASA Astrophysics Data System (ADS)

Böer, Erik; Steinborn, Gerhard; Florschütz, Kristina; Körner, Martina; Gellissen, Gerd; Kunze, Gotthard

The dimorphic ascomycetous yeast Arxula adeninivorans exhibits some unusual properties. Being a thermo- and halotolerant species it is able to assimilate and ferment many compounds as sole carbon and/or nitrogen source. It utilises n-alkanes and is capable of degrading starch. Due to these unusual biochemical properties A. adeninivorans can be exploited as a gene donor for the production of enzymes with attractive biotechnological characteristics. Examples of A. adeninivorans-derived genes that are overexpressed include the ALIP1 gene encoding a secretory lipase, the AINV encoding invertase, the AXDH encoding xylitol dehydrogenase and the APHY encoding a secretory phosphatase with phytase activity.

Degradation of Benzene by Pseudomonas veronii 1YdBTEX2 and 1YB2 Is Catalyzed by Enzymes Encoded in Distinct Catabolism Gene Clusters.

PubMed

de Lima-Morales, Daiana; Chaves-Moreno, Diego; Wos-Oxley, Melissa L; Jáuregui, Ruy; Vilchez-Vargas, Ramiro; Pieper, Dietmar H

2016-01-01

Pseudomonas veronii 1YdBTEX2, a benzene and toluene degrader, and Pseudomonas veronii 1YB2, a benzene degrader, have previously been shown to be key players in a benzene-contaminated site. These strains harbor unique catabolic pathways for the degradation of benzene comprising a gene cluster encoding an isopropylbenzene dioxygenase where genes encoding downstream enzymes were interrupted by stop codons. Extradiol dioxygenases were recruited from gene clusters comprising genes encoding a 2-hydroxymuconic semialdehyde dehydrogenase necessary for benzene degradation but typically absent from isopropylbenzene dioxygenase-encoding gene clusters. The benzene dihydrodiol dehydrogenase-encoding gene was not clustered with any other aromatic degradation genes, and the encoded protein was only distantly related to dehydrogenases of aromatic degradation pathways. The involvement of the different gene clusters in the degradation pathways was suggested by real-time quantitative reverse transcription PCR. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The genome sequence of Dyella jiangningensis FCAV SCS01 from a lignocellulose-decomposing microbial consortium metagenome reveals potential for biotechnological applications.

PubMed

Desiderato, Joana G; Alvarenga, Danillo O; Constancio, Milena T L; Alves, Lucia M C; Varani, Alessandro M

2018-05-14

Cellulose and its associated polymers are structural components of the plant cell wall, constituting one of the major sources of carbon and energy in nature. The carbon cycle is dependent on cellulose- and lignin-decomposing microbial communities and their enzymatic systems acting as consortia. These microbial consortia are under constant exploration for their potential biotechnological use. Herein, we describe the characterization of the genome of Dyella jiangningensis FCAV SCS01, recovered from the metagenome of a lignocellulose-degrading microbial consortium, which was isolated from a sugarcane crop soil under mechanical harvesting and covered by decomposing straw. The 4.7 Mbp genome encodes 4,194 proteins, including 36 glycoside hydrolases (GH), supporting the hypothesis that this bacterium may contribute to lignocellulose decomposition. Comparative analysis among fully sequenced Dyella species indicate that the genome synteny is not conserved, and that D. jiangningensis FCAV SCS01 carries 372 unique genes, including an alpha-glucosidase and maltodextrin glucosidase coding genes, and other potential biomass degradation related genes. Additional genomic features, such as prophage-like, genomic islands and putative new biosynthetic clusters were also uncovered. Overall, D. jiangningensis FCAV SCS01 represents the first South American Dyella genome sequenced and shows an exclusive feature among its genus, related to biomass degradation.

SNTP propellant management system

NASA Technical Reports Server (NTRS)

Tippetts, Tom

1993-01-01

Viewgraphs on the following are presented: (1) space nuclear thermal propulsion (SNTP) propellant management system; (2) SNTP cycle selection; (3) NTP system components unique design constraints; (4) bleed cycle unique design requirement for turbopump; (5) bleed cycle turbopump; (6) SNTP carbon-carbon turbine wheel; and (7) turbine development program.

In utero exposure to cigarette chemicals induces sex-specific disruption of one-carbon metabolism and DNA methylation in the human fetal liver.

PubMed

Drake, Amanda J; O'Shaughnessy, Peter J; Bhattacharya, Siladitya; Monteiro, Ana; Kerrigan, David; Goetz, Sven; Raab, Andrea; Rhind, Stewart M; Sinclair, Kevin D; Meharg, Andrew A; Feldmann, Jörg; Fowler, Paul A

2015-01-29

Maternal smoking is one of the most important modifiable risk factors for low birthweight, which is strongly associated with increased cardiometabolic disease risk in adulthood. Maternal smoking reduces the levels of the methyl donor vitamin B12 and is associated with altered DNA methylation at birth. Altered DNA methylation may be an important mechanism underlying increased disease susceptibility; however, the extent to which this can be induced in the developing fetus is unknown. In this retrospective study, we measured concentrations of cobalt, vitamin B12, and mRNA transcripts encoding key enzymes in the 1-carbon cycle in 55 fetal human livers obtained from 11 to 21 weeks of gestation elective terminations and matched for gestation and maternal smoking. DNA methylation was measured at critical regions known to be susceptible to the in utero environment. Homocysteine concentrations were analyzed in plasma from 60 fetuses. In addition to identifying baseline sex differences, we found that maternal smoking was associated with sex-specific alterations of fetal liver vitamin B12, plasma homocysteine and expression of enzymes in the 1-carbon cycle in fetal liver. In the majority of the measured parameters which showed a sex difference, maternal smoking reduced the magnitude of that difference. Maternal smoking also altered DNA methylation at the imprinted gene IGF2 and the glucocorticoid receptor (GR/NR3C1). Our unique data strengthen studies linking in utero exposures to altered DNA methylation by showing, for the first time, that such changes are present in fetal life and in a key metabolic target tissue, human fetal liver. Furthermore, these data propose a novel mechanism by which such changes are induced, namely through alterations in methyl donor availability and changes in 1-carbon metabolism.

Scanning mirror for infrared sensors

NASA Technical Reports Server (NTRS)

Anderson, R. H.; Bernstein, S. B.

1972-01-01

A high resolution, long life angle-encoded scanning mirror, built for application in an infrared attitude sensor, is described. The mirror uses a Moire' fringe type optical encoder and unique torsion bar suspension together with a magnetic drive to meet stringent operational and environmental requirements at a minimum weight and with minimum power consumption. Details of the specifications, design, and construction are presented with an analysis of the mirror suspension that allows accurate prediction of performance. The emphasis is on mechanical design considerations, and brief discussions are included on the encoder and magnetic drive to provide a complete view of the mirror system and its capabilities.

Genetically Engineered Cyanobacteria

NASA Technical Reports Server (NTRS)

Zhou, Ruanbao (Inventor); Gibbons, William (Inventor)

2015-01-01

The disclosed embodiments provide cyanobacteria spp. that have been genetically engineered to have increased production of carbon-based products of interest. These genetically engineered hosts efficiently convert carbon dioxide and light into carbon-based products of interest such as long chained hydrocarbons. Several constructs containing polynucleotides encoding enzymes active in the metabolic pathways of cyanobacteria are disclosed. In many instances, the cyanobacteria strains have been further genetically modified to optimize production of the carbon-based products of interest. The optimization includes both up-regulation and down-regulation of particular genes.

Isolation and characterization of two cDNA clones encoding for glutamate dehydrogenase in Nicotiana plumbaginifolia.

PubMed

Ficarelli, A; Tassi, F; Restivo, F M

1999-03-01

We have isolated two full length cDNA clones encoding Nicotiana plumbaginifolia NADH-glutamate dehydrogenase. Both clones share amino acid boxes of homology corresponding to conserved GDH catalytic domains and putative mitochondrial targeting sequence. One clone shows a putative EF-hand loop. The level of the two transcripts is affected differently by carbon source.

Aligned Carbon Nanotube to Enhance Through Thickness Thermal Conductivity in Adhesive Joints (Preprint)

DTIC Science & Technology

2006-12-01

aligned CNT films were prepared by pyrolyzing iron (II) phthalocyanine under Ar/H2 at 900°C as described in details elsewhere16. The average diameter...zone. Keywords: thermal conductivity, carbon nanotubes The unique properties of carbon nanotubes ( CNTs ) have generated interest amongst many...structure and high aspect ratio. These 2 unique properties make CNTs the material of choice for numerous applications like sensors5, actuators6, energy

The life of plant mitochondrial complex I.

PubMed

Braun, Hans-Peter; Binder, Stefan; Brennicke, Axel; Eubel, Holger; Fernie, Alisdair R; Finkemeier, Iris; Klodmann, Jennifer; König, Ann-Christine; Kühn, Kristina; Meyer, Etienne; Obata, Toshihiro; Schwarzländer, Markus; Takenaka, Mizuki; Zehrmann, Anja

2014-11-01

The mitochondrial NADH dehydrogenase complex (complex I) of the respiratory chain has several remarkable features in plants: (i) particularly many of its subunits are encoded by the mitochondrial genome, (ii) its mitochondrial transcripts undergo extensive maturation processes (e.g. RNA editing, trans-splicing), (iii) its assembly follows unique routes, (iv) it includes an additional functional domain which contains carbonic anhydrases and (v) it is, indirectly, involved in photosynthesis. Comprising about 50 distinct protein subunits, complex I of plants is very large. However, an even larger number of proteins are required to synthesize these subunits and assemble the enzyme complex. This review aims to follow the complete "life cycle" of plant complex I from various molecular perspectives. We provide arguments that complex I represents an ideal model system for studying the interplay of respiration and photosynthesis, the cooperation of mitochondria and the nucleus during organelle biogenesis and the evolution of the mitochondrial oxidative phosphorylation system. Copyright © 2014 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

Reprogramming One-Carbon Metabolic Pathways To Decouple l-Serine Catabolism from Cell Growth in Corynebacterium glutamicum.

PubMed

Zhang, Yun; Shang, Xiuling; Lai, Shujuan; Zhang, Yu; Hu, Qitiao; Chai, Xin; Wang, Bo; Liu, Shuwen; Wen, Tingyi

2018-02-16

l-Serine, the principal one-carbon source for DNA biosynthesis, is difficult for microorganisms to accumulate due to the coupling of l-serine catabolism and microbial growth. Here, we reprogrammed the one-carbon unit metabolic pathways in Corynebacterium glutamicum to decouple l-serine catabolism from cell growth. In silico model-based simulation showed a negative influence on glyA-encoding serine hydroxymethyltransferase flux with l-serine productivity. Attenuation of glyA transcription resulted in increased l-serine accumulation, and a decrease in purine pools, poor growth and longer cell shapes. The gcvTHP-encoded glycine cleavage (Gcv) system from Escherichia coli was introduced into C. glutamicum, allowing glycine-derived 13 CH 2 to be assimilated into intracellular purine synthesis, which resulted in an increased amount of one-carbon units. Gcv introduction not only restored cell viability and morphology but also increased l-serine accumulation. Moreover, comparative proteomic analysis indicated that abundance changes of the enzymes involved in one-carbon unit cycles might be responsible for maintaining one-carbon unit homeostasis. Reprogramming of the one-carbon metabolic pathways allowed cells to reach a comparable growth rate to accumulate 13.21 g/L l-serine by fed-batch fermentation in minimal medium. This novel strategy provides new insights into the regulation of cellular properties and essential metabolite accumulation by introducing an extrinsic pathway.

The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger

PubMed Central

van Munster, Jolanda M.; Daly, Paul; Delmas, Stéphane; Pullan, Steven T.; Blythe, Martin J.; Malla, Sunir; Kokolski, Matthew; Noltorp, Emelie C.M.; Wennberg, Kristin; Fetherston, Richard; Beniston, Richard; Yu, Xiaolan; Dupree, Paul; Archer, David B.

2014-01-01

Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that the transcriptional response after 6 h of exposure to wheat straw was very different from the response at 24 h of exposure to the same substrate. For example, less than half of the genes encoding carbohydrate active enzymes that were induced after 24 h of exposure to wheat straw, were also induced after 6 h exposure. Importantly, over a third of the genes induced after 6 h of exposure to wheat straw were also induced during 6 h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. We show, using proteomics, that carbon-starved cultures indeed release CAZymes with predicted activity on plant polysaccharides. Analysis of the enzymatic activity and the reaction products, indicates that these proteins are enzymes that can degrade various plant polysaccharides to generate both known, as well as potentially new, inducers of CAZymes. PMID:24792495

The role of carbon starvation in the induction of enzymes that degrade plant-derived carbohydrates in Aspergillus niger.

PubMed

van Munster, Jolanda M; Daly, Paul; Delmas, Stéphane; Pullan, Steven T; Blythe, Martin J; Malla, Sunir; Kokolski, Matthew; Noltorp, Emelie C M; Wennberg, Kristin; Fetherston, Richard; Beniston, Richard; Yu, Xiaolan; Dupree, Paul; Archer, David B

2014-11-01

Fungi are an important source of enzymes for saccharification of plant polysaccharides and production of biofuels. Understanding of the regulation and induction of expression of genes encoding these enzymes is still incomplete. To explore the induction mechanism, we analysed the response of the industrially important fungus Aspergillus niger to wheat straw, with a focus on events occurring shortly after exposure to the substrate. RNA sequencing showed that the transcriptional response after 6h of exposure to wheat straw was very different from the response at 24h of exposure to the same substrate. For example, less than half of the genes encoding carbohydrate active enzymes that were induced after 24h of exposure to wheat straw, were also induced after 6h exposure. Importantly, over a third of the genes induced after 6h of exposure to wheat straw were also induced during 6h of carbon starvation, indicating that carbon starvation is probably an important factor in the early response to wheat straw. The up-regulation of the expression of a high number of genes encoding CAZymes that are active on plant-derived carbohydrates during early carbon starvation suggests that these enzymes could be involved in a scouting role during starvation, releasing inducing sugars from complex plant polysaccharides. We show, using proteomics, that carbon-starved cultures indeed release CAZymes with predicted activity on plant polysaccharides. Analysis of the enzymatic activity and the reaction products, indicates that these proteins are enzymes that can degrade various plant polysaccharides to generate both known, as well as potentially new, inducers of CAZymes. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

The Use of Amino Sugars by Bacillus subtilis: Presence of a Unique Operon for the Catabolism of Glucosamine

PubMed Central

Gaugué, Isabelle; Oberto, Jacques; Putzer, Harald; Plumbridge, Jacqueline

2013-01-01

B. subtilis grows more rapidly using the amino sugar glucosamine as carbon source, than with N-acetylglucosamine. Genes for the transport and metabolism of N-acetylglucosamine (nagP and nagAB) are found in all the sequenced Bacilli (except Anoxybacillus flavithermus). In B. subtilis there is an additional operon (gamAP) encoding second copies of genes for the transport and catabolism of glucosamine. We have developed a method to make multiple deletion mutations in B. subtilis employing an excisable spectinomycin resistance cassette. Using this method we have analysed the contribution of the different genes of the nag and gam operons for their role in utilization of glucosamine and N-acetylglucosamine. Faster growth on glucosamine is due to the presence of the gamAP operon, which is strongly induced by glucosamine. Although the gamA and nagB genes encode isozymes of GlcN6P deaminase, catabolism of N-acetylglucosamine relies mostly upon the gamA gene product. The genes for use of N-acetylglucosamine, nagAB and nagP, are repressed by YvoA (NagR), a GntR family regulator, whose gene is part of the nagAB yvoA(nagR) operon. The gamAP operon is repressed by YbgA, another GntR family repressor, whose gene is expressed divergently from gamAP. The nagAB yvoA synton is found throughout the Bacilli and most firmicutes. On the other hand the ybgA-gamAP synton, which includes the ybgB gene for a small protein of unknown provenance, is only found in B. subtilis (and a few very close relatives). The origin of ybgBA-gamAP grouping is unknown but synteny analysis suggests lateral transfer from an unidentified donor. The presence of gamAP has enabled B. subtilis to efficiently use glucosamine as carbon source. PMID:23667565

Single-cell sequencing of Thiomargarita reveals genomic flexibility for adaptation to dynamic redox conditions

DOE PAGES

Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja; ...

2016-06-21

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiornargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of amore » chain-forming " Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. " Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that " Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO 2 fixation pathway. Surprisingly, " Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na +-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae " Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In conclusion, the genome of " Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.« less

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

Winkel, Matthias; Salman-Carvalho, Verena; Woyke, Tanja

Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known free-living bacteria with cell sizes of up to 750 μm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiornargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of amore » chain-forming " Candidatus Thiomargarita nelsonii Thio36", and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. " Ca. T. nelsonii Thio36" is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that " Ca. T. nelsonii Thio36" can function as a chemolithoautotroph. Carbon can be fixed via the Calvin-Benson-Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO 2 fixation pathway. Surprisingly, " Ca. T. nelsonii Thio36" also encodes key genes of the C2-cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a Na +-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae " Ca. T. nelsonii Thio36" encodes many genes similar to those of (filamentous) cyanobacteria. In conclusion, the genome of " Ca. T. nelsonii Thio36" provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.« less

Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius

DOE PAGES

Lee, Brady D.; Apel, William A.; DeVeaux, Linda C.; ...

2017-08-03

Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in this paper in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grewmore » while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Finally, microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.« less

Concurrent metabolism of pentose and hexose sugars by the polyextremophile Alicyclobacillus acidocaldarius

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

Lee, Brady D.; Apel, William A.; DeVeaux, Linda C.

Alicyclobacillus acidocaldarius is a thermoacidophilic bacterium capable of growth on sugars from plant biomass. Carbon catabolite repression (CCR) allows bacteria to focus cellular resources on a sugar that provides efficient growth, but also allows sequential, rather than simultaneous use when more than one sugar is present. The A. acidocaldarius genome encodes all components of CCR, but transporters encoded are multifacilitator superfamily and ATP-binding cassette-type transporters, uncommon for CCR. Therefore, global transcriptome analysis of A. acidocaldarius grown on xylose or fructose was performed in this paper in chemostats, followed by attempted induction of CCR with glucose or arabinose. Alicyclobacillus acidocaldarius grewmore » while simultaneously metabolizing xylose and glucose, xylose and arabinose, and fructose and glucose, indicating that CCR did not control carbon metabolism. Finally, microarrays showed down-regulation of genes during growth on one sugar compared to two, and occurred primarily in genes encoding: (1) regulators; (2) enzymes for cell wall synthesis; and (3) sugar transporters.« less

Encoding, Consolidation, and Retrieval of Contextual Memory: Differential Involvement of Dorsal CA3 and CA1 Hippocampal Subregions

ERIC Educational Resources Information Center

Daumas, Stephanie; Halley, Helene; Frances, Bernard; Lassalle, Jean-Michel

2005-01-01

Studies on human and animals shed light on the unique hippocampus contributions to relational memory. However, the particular role of each hippocampal subregion in memory processing is still not clear. Hippocampal computational models and theories have emphasized a unique function in memory for each hippocampal subregion, with the CA3 area acting…

Two Pathways to Stimulus Encoding in Category Learning?

PubMed Central

Davis, Tyler; Love, Bradley C.; Maddox, W. Todd

2008-01-01

Category learning theorists tacitly assume that stimuli are encoded by a single pathway. Motivated by theories of object recognition, we evaluate a dual-pathway account of stimulus encoding. The part-based pathway establishes mappings between sensory input and symbols that encode discrete stimulus features, whereas the image-based pathway applies holistic templates to sensory input. Our experiments use rule-plus-exception structures in which one exception item in each category violates a salient regularity and must be distinguished from other items. In Experiment 1, we find that discrete representations are crucial for recognition of exceptions following brief training. Experiments 2 and 3 involve multi-session training regimens designed to encourage either part or image-based encoding. We find that both pathways are able to support exception encoding, but have unique characteristics. We speculate that one advantage of the part-based pathway is the ability to generalize across domains, whereas the image-based pathway provides faster and more effortless recognition. PMID:19460948

Methanol Expression Regulator 1 (Mxr1p) Is Essential for the Utilization of Amino Acids as the Sole Source of Carbon by the Methylotrophic Yeast, Pichia pastoris.

PubMed

Sahu, Umakant; Rangarajan, Pundi N

2016-09-23

Unlike Saccharomyces cerevisiae, the methylotrophic yeast Pichia pastoris can assimilate amino acids as the sole source of carbon and nitrogen. It can grow in media containing yeast extract and peptone (YP), yeast nitrogen base (YNB) + glutamate (YNB + Glu), or YNB + aspartate (YNB + Asp). Methanol expression regulator 1 (Mxr1p), a zinc finger transcription factor, is essential for growth in these media. Mxr1p regulates the expression of several genes involved in the utilization of amino acids as the sole source of carbon and nitrogen. These include the following: (i) GDH2 encoding NAD-dependent glutamate dehydrogenase; (ii) AAT1 and AAT2 encoding mitochondrial and cytosolic aspartate aminotransferases, respectively; (iii) MDH1 and MDH2 encoding mitochondrial and cytosolic malate dehydrogenases, respectively; and (iv) GLN1 encoding glutamine synthetase. Synthesis of all these enzymes is regulated by Mxr1p at the level of transcription except GDH2, whose synthesis is regulated at the level of translation. Mxr1p activates the transcription of AAT1, AAT2, and GLN1 in cells cultured in YP as well as in YNB + Glu media, whereas transcription of MDH1 and MDH2 is activated in cells cultured in YNB + Glu but not in YP. A truncated Mxr1p composed of 400 N-terminal amino acids activates transcription of target genes in cells cultured in YP but not in YNB + Glu. Mxr1p binds to Mxr1p response elements present in the promoters of AAT2, MDH2, and GLN1 We conclude that Mxr1p is essential for utilization of amino acids as the sole source of carbon and nitrogen, and it is a global regulator of multiple metabolic pathways in P. pastoris. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Mineralogy of Tagish Lake, a Unique Type 2 Carbonaceous Chondrite

NASA Technical Reports Server (NTRS)

Gounelle, M.; Zolensky, M. E.; Tonui, E.; Mikouchi, T.

2001-01-01

We have identified in Tagish Lake an abondant carbonate-poor lithology and a less common carbonate-rich lithology. Tagish Lake shows similarities and differences with CMs and CI1s. It is a unique carbonaceous chondrite recording specific aqueous alteration conditions. Additional information is contained in the original extended abstract.

A novel approach of an absolute coding pattern based on Hamiltonian graph

NASA Astrophysics Data System (ADS)

Wang, Ya'nan; Wang, Huawei; Hao, Fusheng; Liu, Liqiang

2017-02-01

In this paper, a novel approach of an optical type absolute rotary encoder coding pattern is presented. The concept is based on the principle of the absolute encoder to find out a unique sequence that ensures an unambiguous shaft position of any angular. We design a single-ring and a n-by-2 matrix absolute encoder coding pattern by using the variations of Hamiltonian graph principle. 12 encoding bits is used in the single-ring by a linear array CCD to achieve an 1080-position cycle encoding. Besides, a 2-by-2 matrix is used as an unit in the 2-track disk to achieve a 16-bits encoding pattern by using an area array CCD sensor (as a sample). Finally, a higher resolution can be gained by an electronic subdivision of the signals. Compared with the conventional gray or binary code pattern (for a 2n resolution), this new pattern has a higher resolution (2n*n) with less coding tracks, which means the new pattern can lead to a smaller encoder, which is essential in the industrial production.

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling

PubMed Central

2013-01-01

Background Sediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic contaminants, and impact drinking water quality. Recent 16S rRNA gene profiling indicates that members of the bacterial phylum Chloroflexi are common in sediment. Only the role of the class Dehalococcoidia, which degrade halogenated solvents, is well understood. Genomic sampling is available for only six of the approximate 30 Chloroflexi classes, so little is known about the phylogenetic distribution of reductive dehalogenation or about the broader metabolic characteristics of Chloroflexi in sediment. Results We used metagenomics to directly evaluate the metabolic potential and diversity of Chloroflexi in aquifer sediments. We sampled genomic sequence from 86 Chloroflexi representing 15 distinct lineages, including members of eight classes previously characterized only by 16S rRNA sequences. Unlike in the Dehalococcoidia, genes for organohalide respiration are rare within the Chloroflexi genomes sampled here. Near-complete genomes were reconstructed for three Chloroflexi. One, a member of an unsequenced lineage in the Anaerolinea, is an aerobe with the potential for respiring diverse carbon compounds. The others represent two genomically unsampled classes sibling to the Dehalococcoidia, and are anaerobes likely involved in sugar and plant-derived-compound degradation to acetate. Both fix CO2 via the Wood-Ljungdahl pathway, a pathway not previously documented in Chloroflexi. The genomes each encode unique traits apparently acquired from Archaea, including mechanisms of motility and ATP synthesis. Conclusions Chloroflexi in the aquifer sediments are abundant and highly diverse. Genomic analyses provide new evolutionary boundaries for obligate organohalide respiration. We expand the potential roles of Chloroflexi in sediment carbon cycling beyond organohalide respiration to include respiration of sugars, fermentation, CO2 fixation, and acetogenesis with ATP formation by substrate-level phosphorylation. PMID:24450983

A Unique 3D Nitrogen-Doped Carbon Composite as High-Performance Oxygen Reduction Catalyst

PubMed Central

Karunagaran, Ramesh; Tung, Tran Thanh; Tran, Diana; Coghlan, Campbell; Doonan, Christian

2017-01-01

The synthesis and properties of an oxygen reduction catalyst based on a unique 3-dimensional (3D) nitrogen doped (N-doped) carbon composite are described. The composite material is synthesised via a two-step hydrothermal and pyrolysis method using bio-source low-cost materials of galactose and melamine. Firstly, the use of iron salts and galactose to hydrothermally produceiron oxide (Fe2O3) magnetic nanoparticle clusters embedded carbon spheres. Secondly, magnetic nanoparticles diffused out of the carbon sphere when pyrolysed in the presence of melamine as nitrogen precursor. Interestingly, many of these nanoparticles, as catalyst-grown carbon nanotubes (CNTs), resulted in the formation of N-doped CNTs and N-doped carbon spheres under the decomposition of carbon and a nitrogen environment. The composite material consists of integrated N-doped carbon microspheres and CNTs show high ORR activity through a predominantly four-electron pathway. PMID:28792432

Authentication of gold nanoparticle encoded pharmaceutical tablets using polarimetric signatures.

PubMed

Carnicer, Artur; Arteaga, Oriol; Suñé-Negre, Josep M; Javidi, Bahram

2016-10-01

The counterfeiting of pharmaceutical products represents concerns for both industry and the safety of the general public. Falsification produces losses to companies and poses health risks for patients. In order to detect fake pharmaceutical tablets, we propose producing film-coated tablets with gold nanoparticle encoding. These coated tablets contain unique polarimetric signatures. We present experiments to show that ellipsometric optical techniques, in combination with machine learning algorithms, can be used to distinguish genuine and fake samples. To the best of our knowledge, this is the first report using gold nanoparticles encoded with optical polarimetric classifiers to prevent the counterfeiting of pharmaceutical products.

Toward a rigorous network of protein-protein interactions of the model sulfate reducer Desulfovibrio vulgaris Hildenborough

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

Chhabra, S.R.; Joachimiak, M.P.; Petzold, C.J.

Protein–protein interactions offer an insight into cellular processes beyond what may be obtained by the quantitative functional genomics tools of proteomics and transcriptomics. The aforementioned tools have been extensively applied to study E. coli and other aerobes and more recently to study the stress response behavior of Desulfovibrio 5 vulgaris Hildenborough, a model anaerobe and sulfate reducer. In this paper we present the first attempt to identify protein-protein interactions in an obligate anaerobic bacterium. We used suicide vector-assisted chromosomal modification of 12 open reading frames encoded by this sulfate reducer to append an eight amino acid affinity tag to themore » carboxy-terminus of the chosen proteins. Three biological replicates of the 10 ‘pulled-down’ proteins were separated and analyzed using liquid chromatography-mass spectrometry. Replicate agreement ranged between 35% and 69%. An interaction network among 12 bait and 90 prey proteins was reconstructed based on 134 bait-prey interactions computationally identified to be of high confidence. We discuss the biological significance of several unique metabolic features of D. vulgaris revealed by this protein-protein interaction data 15 and protein modifications that were observed. These include the distinct role of the putative carbon monoxide-induced hydrogenase, unique electron transfer routes associated with different oxidoreductases, and the possible role of methylation in regulating sulfate reduction.« less

Feed in summer, rest in winter: microbial carbon utilization in forest topsoil.

PubMed

Žifčáková, Lucia; Větrovský, Tomáš; Lombard, Vincent; Henrissat, Bernard; Howe, Adina; Baldrian, Petr

2017-09-18

Evergreen coniferous forests contain high stocks of organic matter. Significant carbon transformations occur in litter and soil of these ecosystems, making them important for the global carbon cycle. Due to seasonal allocation of photosynthates to roots, carbon availability changes seasonally in the topsoil. The aim of this paper was to describe the seasonal differences in C source utilization and the involvement of various members of soil microbiome in this process. Here, we show that microorganisms in topsoil encode a diverse set of carbohydrate-active enzymes, including glycoside hydrolases and auxiliary enzymes. While the transcription of genes encoding enzymes degrading reserve compounds, such as starch or trehalose, was high in soil in winter, summer was characterized by high transcription of ligninolytic and cellulolytic enzymes produced mainly by fungi. Fungi strongly dominated the transcription in litter and an equal contribution of bacteria and fungi was found in soil. The turnover of fungal biomass appeared to be faster in summer than in winter, due to high activity of enzymes targeting its degradation, indicating fast growth in both litter and soil. In each enzyme family, hundreds to thousands of genes were typically transcribed simultaneously. Seasonal differences in the transcription of glycoside hydrolases and auxiliary enzyme genes are more pronounced in soil than in litter. Our results suggest that mainly fungi are involved in decomposition of recalcitrant biopolymers in summer, while bacteria replace them in this role in winter. Transcripts of genes encoding enzymes targeting plant biomass biopolymers, reserve compounds and fungal cell walls were especially abundant in the coniferous forest topsoil.

Transcriptional Profiling of Caulobacter crescentus during Growth on Complex and Minimal Media

PubMed Central

Hottes, Alison K.; Meewan, Maliwan; Yang, Desiree; Arana, Naomi; Romero, Pedro; McAdams, Harley H.; Stephens, Craig

2004-01-01

Microarray analysis was used to examine gene expression in the freshwater oligotrophic bacterium Caulobacter crescentus during growth on three standard laboratory media, including peptone-yeast extract medium (PYE) and minimal salts medium with glucose or xylose as the carbon source. Nearly 400 genes (approximately 10% of the genome) varied significantly in expression between at least two of these media. The differentially expressed genes included many encoding transport systems, most notably diverse TonB-dependent outer membrane channels of unknown substrate specificity. Amino acid degradation pathways constituted the largest class of genes induced in PYE. In contrast, many of the genes upregulated in minimal media encoded enzymes for synthesis of amino acids, including incorporation of ammonia and sulfate into glutamate and cysteine. Glucose availability induced expression of genes encoding enzymes of the Entner-Doudoroff pathway, which was demonstrated here through mutational analysis to be essential in C. crescentus for growth on glucose. Xylose induced expression of genes encoding several hydrolytic exoenzymes as well as an operon that may encode a novel pathway for xylose catabolism. A conserved DNA motif upstream of many xylose-induced genes was identified and shown to confer xylose-specific expression. Xylose is an abundant component of xylan in plant cell walls, and the microarray data suggest that in addition to serving as a carbon source for growth of C. crescentus, this pentose may be interpreted as a signal to produce enzymes associated with plant polymer degradation. PMID:14973021

Satellite remote sensing data can be used to model marine microbial metabolite turnover

PubMed Central

Larsen, Peter E; Scott, Nicole; Post, Anton F; Field, Dawn; Knight, Rob; Hamada, Yuki; Gilbert, Jack A

2015-01-01

Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes' predicted relative abundance was highly correlated (Pearson Correlation 0.72, P-value <10−6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ∼3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology. PMID:25072414

Satellite remote sensing data can be used to model marine microbial metabolite turnover

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

Larsen, Peter E.; Scott, Nicole; Post, Anton F.

Sampling ecosystems, even at a local scale, at the temporal and spatial resolution necessary to capture natural variability in microbial communities are prohibitively expensive. We extrapolated marine surface microbial community structure and metabolic potential from 72 16S rRNA amplicon and 8 metagenomic observations using remotely sensed environmental parameters to create a system-scale model of marine microbial metabolism for 5904 grid cells (49 km2) in the Western English Chanel, across 3 years of weekly averages. Thirteen environmental variables predicted the relative abundance of 24 bacterial Orders and 1715 unique enzyme-encoding genes that encode turnover of 2893 metabolites. The genes’ predicted relativemore » abundance was highly correlated (Pearson Correlation 0.72, P-value <10-6) with their observed relative abundance in sequenced metagenomes. Predictions of the relative turnover (synthesis or consumption) of CO2 were significantly correlated with observed surface CO2 fugacity. The spatial and temporal variation in the predicted relative abundances of genes coding for cyanase, carbon monoxide and malate dehydrogenase were investigated along with the predicted inter-annual variation in relative consumption or production of ~3000 metabolites forming six significant temporal clusters. These spatiotemporal distributions could possibly be explained by the co-occurrence of anaerobic and aerobic metabolisms associated with localized plankton blooms or sediment resuspension, which facilitate the presence of anaerobic micro-niches. This predictive model provides a general framework for focusing future sampling and experimental design to relate biogeochemical turnover to microbial ecology.« less

Targeting malaria parasite proteins to the erythrocyte.

PubMed

Templeton, Thomas J; Deitsch, Kirk W

2005-09-01

The intraerythrocytic stages of the protozoan parasite Plasmodium falciparum reside within a parasitophorous vacuole (PV) and set up unique "extraparasite, intraerythrocyte" protein-trafficking pathways that target parasite-encoded proteins to the erythrocyte cytoplasm and cell surface. Two recent articles report the identification of trafficking motifs that regulate the transport of parasite-encoded proteins across the PV. These articles greatly aid the annotation of the parasite "secretome" catalog of proteins that are targeted to the erythrocyte cytoplasm or cell membrane.

Functionalized carbon nanotubes for potential medicinal applications.

PubMed

Zhang, Yi; Bai, Yuhong; Yan, Bing

2010-06-01

Functionalized carbon nanotubes display unique properties that enable a variety of medicinal applications, including the diagnosis and treatment of cancer, infectious diseases and central nervous system disorders, and applications in tissue engineering. These potential applications are particularly encouraged by their ability to penetrate biological membranes and relatively low toxicity. High aspect ratio, unique optical property and the likeness as small molecule make carbon nanotubes an unusual allotrope of element carbon. After functionalization, carbon nanotubes display potentials for a variety of medicinal applications, including the diagnosis and treatment of cancer, infectious diseases and central nervous system disorders, and applications in tissue engineering. These potential applications are particularly encouraged by their ability to penetrate biological membranes and relatively low toxicity. (c) 2010 Elsevier Ltd. All rights reserved.

Ab initio structure determination of n-diamond.

PubMed

Li, Da; Tian, Fubo; Chu, Binhua; Duan, Defang; Sha, Xiaojing; Lv, Yunzhou; Zhang, Huadi; Lu, Nan; Liu, Bingbing; Cui, Tian

2015-08-24

A systematic computational study on the crystal structure of n-diamond has been performed using first-principle methods. A novel carbon allotrope with hexagonal symmetry R32 space group has been predicted. We name it as HR-carbon. HR-carbon composed of lonsdaleite layers and unique C3 isosceles triangle rings, is stable over graphite phase above 14.2 GPa. The simulated x-ray diffraction pattern, Raman, and energy-loss near-edge spectrum can match the experimental results very well, indicating that HR-carbon is a likely candidate structure for n-diamond. HR-carbon has an incompressible atomic arrangement because of unique C3 isosceles triangle rings. The hardness and bulk modulus of HR-carbon are calculated to be 80 GPa and 427 GPa, respectively, which are comparable to those of diamond. C3 isosceles triangle rings are very important for the stability and hardness of HR-carbon.

The organization of the fuc regulon specifying L-fucose dissimilation in Escherichia coli K12 as determined by gene cloning.

PubMed

Chen, Y M; Zhu, Y; Lin, E C

1987-12-01

In Escherichia coli the six known genes specifying the utilization of L-fucose as carbon and energy source cluster at 60.2 min and constitute a regulon. These genes include fucP (encoding L-fucose permease), fucI (encoding L-fucose isomerase), fucK (encoding L-fuculose kinase), fucA (encoding L-fuculose 1-phosphate aldolase), fucO (encoding L-1,2-propanediol oxidoreductase), and fucR (encoding the regulatory protein). In this study the fuc genes were cloned and their positions on the chromosome were established by restriction endonuclease and complementation analyses. Clockwise, the gene order is: fucO-fucA-fucP-fucI-fucK-fucR. The operons comprising the structural genes and the direction of transcription were determined by complementation analysis and Southern blot hybridization. The fucPIK and fucA operons are transcribed clockwise. The fucO operon is transcribed counterclockwise. The fucR gene product activates the three structural operons in trans.

Plasmid-dependent methylotrophy in thermotolerant Bacillus methanolicus.

PubMed

Brautaset, Trygve; Jakobsen M, Øyvind M; Flickinger, Michael C; Valla, Svein; Ellingsen, Trond E

2004-03-01

Bacillus methanolicus can efficiently utilize methanol as a sole carbon source and has an optimum growth temperature of 50 degrees C. With the exception of mannitol, no sugars have been reported to support rapid growth of this organism, which is classified as a restrictive methylotroph. Here we describe the DNA sequence and characterization of a 19,167-bp circular plasmid, designated pBM19, isolated from B. methanolicus MGA3. Sequence analysis of pBM19 demonstrated the presence of the methanol dehydrogenase gene, mdh, which is crucial for methanol consumption in this bacterium. In addition, five genes (pfk, encoding phosphofructokinase; rpe, encoding ribulose-5-phosphate 3-epimerase; tkt, encoding transketolase; glpX, encoding fructose-1,6-bisphosphatase; and fba, encoding fructose-1,6-bisphosphate aldolase) with deduced roles in methanol assimilation via the ribulose monophosphate pathway are encoded by pBM19. A shuttle vector, pTB1.9, harboring the pBM19 minimal replicon (repB and ori) was constructed and used to transform MGA3. Analysis of the resulting recombinant strain demonstrated that it was cured of pBM19 and was not able to grow on methanol. A pTB1.9 derivative harboring the complete mdh gene could not restore growth on methanol when it was introduced into the pBM19-cured strain, suggesting that additional pBM19 genes are required for consumption of this carbon source. Screening of 13 thermotolerant B. methanolicus wild-type strains showed that they all harbor plasmids similar to pBM19, and this is the first report describing plasmid-linked methylotrophy in any microorganism. Our findings should have an effect on future genetic manipulations of this organism, and they contribute to a new understanding of the biology of methylotrophs.

Plasmid-Dependent Methylotrophy in Thermotolerant Bacillus methanolicus

PubMed Central

Brautaset, Trygve; Jakobsen, Øyvind M.; Flickinger, Michael C.; Valla, Svein; Ellingsen, Trond E.

2004-01-01

Bacillus methanolicus can efficiently utilize methanol as a sole carbon source and has an optimum growth temperature of 50°C. With the exception of mannitol, no sugars have been reported to support rapid growth of this organism, which is classified as a restrictive methylotroph. Here we describe the DNA sequence and characterization of a 19,167-bp circular plasmid, designated pBM19, isolated from B. methanolicus MGA3. Sequence analysis of pBM19 demonstrated the presence of the methanol dehydrogenase gene, mdh, which is crucial for methanol consumption in this bacterium. In addition, five genes (pfk, encoding phosphofructokinase; rpe, encoding ribulose-5-phosphate 3-epimerase; tkt, encoding transketolase; glpX, encoding fructose-1,6-bisphosphatase; and fba, encoding fructose-1,6-bisphosphate aldolase) with deduced roles in methanol assimilation via the ribulose monophosphate pathway are encoded by pBM19. A shuttle vector, pTB1.9, harboring the pBM19 minimal replicon (repB and ori) was constructed and used to transform MGA3. Analysis of the resulting recombinant strain demonstrated that it was cured of pBM19 and was not able to grow on methanol. A pTB1.9 derivative harboring the complete mdh gene could not restore growth on methanol when it was introduced into the pBM19-cured strain, suggesting that additional pBM19 genes are required for consumption of this carbon source. Screening of 13 thermotolerant B. methanolicus wild-type strains showed that they all harbor plasmids similar to pBM19, and this is the first report describing plasmid-linked methylotrophy in any microorganism. Our findings should have an effect on future genetic manipulations of this organism, and they contribute to a new understanding of the biology of methylotrophs. PMID:14973041

A Putative Gene Cluster from a Lyngbya wollei Bloom that Encodes Paralytic Shellfish Toxin Biosynthesis

PubMed Central

Mihali, Troco K.; Carmichael, Wayne W.; Neilan, Brett A.

2011-01-01

Saxitoxin and its analogs cause the paralytic shellfish-poisoning syndrome, adversely affecting human health and coastal shellfish industries worldwide. Here we report the isolation, sequencing, annotation, and predicted pathway of the saxitoxin biosynthetic gene cluster in the cyanobacterium Lyngbya wollei. The gene cluster spans 36 kb and encodes enzymes for the biosynthesis and export of the toxins. The Lyngbya wollei saxitoxin gene cluster differs from previously identified saxitoxin clusters as it contains genes that are unique to this cluster, whereby the carbamoyltransferase is truncated and replaced by an acyltransferase, explaining the unique toxin profile presented by Lyngbya wollei. These findings will enable the creation of toxin probes, for water monitoring purposes, as well as proof-of-concept for the combinatorial biosynthesis of these natural occurring alkaloids for the production of novel, biologically active compounds. PMID:21347365

Imaging episodic memory: implications for cognitive theories and phenomena.

PubMed

Nyberg, L

1999-01-01

Functional neuroimaging studies are beginning to identify neuroanatomical correlates of various cognitive functions. This paper presents results relevant to several theories and phenomena of episodic memory, including component processes of episodic retrieval, encoding specificity, inhibition, item versus source memory, encoding-retrieval overlap, and the picture-superiority effect. Overall, by revealing specific activation patterns, the results provide support for existing theoretical views and they add some unique information which may be important to consider in future attempts to develop cognitive theories of episodic memory.

Slow-Theta-to-Gamma Phase–Amplitude Coupling in Human Hippocampus Supports the Formation of New Episodic Memories

PubMed Central

Lega, Bradley; Burke, John; Jacobs, Joshua; Kahana, Michael J.

2016-01-01

Phase–amplitude coupling (PAC) has been proposed as a neural mechanism for coordinating information processing across brain regions. Here we sought to characterize PAC in the human hippocampus, and in temporal and frontal cortices, during the formation of new episodic memories. Intracranial recordings taken as 56 neurosurgical patients studied and recalled lists of words revealed significant hippocampal PAC, with slow-theta activity (2.5–5 Hz) modulating gamma band activity (34–130 Hz). Furthermore, a significant number of hippocampal electrodes exhibited greater PAC during successful than unsuccessful encoding, with the gamma activity at these sites coupled to the trough of the slow-theta oscillation. These same conditions facilitate LTP in animal models, providing a possible mechanism of action for this effect in human memory. Uniquely in the hippocampus, phase preference during item encoding exhibited a biphasic pattern. Overall, our findings help translate between the patterns identified during basic memory tasks in animals and those present during complex human memory encoding. We discuss the unique properties of human hippocampal PAC and how our findings relate to influential theories of information processing based on theta–gamma interactions. PMID:25316340

Carbon-based layer-by-layer nanostructures: from films to hollow capsules

NASA Astrophysics Data System (ADS)

Hong, Jinkee; Han, Jung Yeon; Yoon, Hyunsik; Joo, Piljae; Lee, Taemin; Seo, Eunyong; Char, Kookheon; Kim, Byeong-Su

2011-11-01

Over the past years, the layer-by-layer (LbL) assembly has been widely developed as one of the most powerful techniques to prepare multifunctional films with desired functions, structures and morphologies because of its versatility in the process steps in both material and substrate choices. Among various functional nanoscale objects, carbon-based nanomaterials, such as carbon nanotubes and graphene sheets, are promising candidates for emerging science and technology with their unique physical, chemical, and mechanical properties. In particular, carbon-based functional multilayer coatings based on the LbL assembly are currently being actively pursued as conducting electrodes, batteries, solar cells, supercapacitors, fuel cells and sensor applications. In this article, we give an overview on the use of carbon materials in nanostructured films and capsules prepared by the LbL assembly with the aim of unraveling the unique features and their applications of carbon multilayers prepared by the LbL assembly.

L-rhamnose induction of Aspergillus nidulans α-L-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake.

PubMed

Tamayo-Ramos, Juan A; Flipphi, Michel; Pardo, Ester; Manzanares, Paloma; Orejas, Margarita

2012-02-21

Little is known about the structure and regulation of fungal α-L-rhamnosidase genes despite increasing interest in the biotechnological potential of the enzymes that they encode. Whilst the paradigmatic filamentous fungus Aspergillus nidulans growing on L-rhamnose produces an α-L-rhamnosidase suitable for oenological applications, at least eight genes encoding putative α-L-rhamnosidases have been found in its genome. In the current work we have identified the gene (rhaE) encoding the former activity, and characterization of its expression has revealed a novel regulatory mechanism. A shared pattern of expression has also been observed for a second α-L-rhamnosidase gene, (AN10277/rhaA). Amino acid sequence data for the oenological α-L-rhamnosidase were determined using MALDI-TOF mass spectrometry and correspond to the amino acid sequence deduced from AN7151 (rhaE). The cDNA of rhaE was expressed in Saccharomyces cerevisiae and yielded pNP-rhamnohydrolase activity. Phylogenetic analysis has revealed this eukaryotic α-L-rhamnosidase to be the first such enzyme found to be more closely related to bacterial rhamnosidases than other α-L-rhamnosidases of fungal origin. Northern analyses of diverse A. nidulans strains cultivated under different growth conditions indicate that rhaA and rhaE are induced by L-rhamnose and repressed by D-glucose as well as other carbon sources, some of which are considered to be non-repressive growth substrates. Interestingly, the transcriptional repression is independent of the wide domain carbon catabolite repressor CreA. Gene induction and glucose repression of these rha genes correlate with the uptake, or lack of it, of the inducing carbon source L-rhamnose, suggesting a prominent role for inducer exclusion in repression. The A. nidulans rhaE gene encodes an α-L-rhamnosidase phylogenetically distant to those described in filamentous fungi, and its expression is regulated by a novel CreA-independent mechanism. The identification of rhaE and the characterization of its regulation will facilitate the design of strategies to overproduce the encoded enzyme - or homologs from other fungi - for industrial applications. Moreover, A. nidulans α-L-rhamnosidase encoding genes could serve as prototypes for fungal genes coding for plant cell wall degrading enzymes regulated by a novel mechanism of CCR.

L-Rhamnose induction of Aspergillus nidulans α-L-rhamnosidase genes is glucose repressed via a CreA-independent mechanism acting at the level of inducer uptake

PubMed Central

2012-01-01

Background Little is known about the structure and regulation of fungal α-L-rhamnosidase genes despite increasing interest in the biotechnological potential of the enzymes that they encode. Whilst the paradigmatic filamentous fungus Aspergillus nidulans growing on L-rhamnose produces an α-L-rhamnosidase suitable for oenological applications, at least eight genes encoding putative α-L-rhamnosidases have been found in its genome. In the current work we have identified the gene (rhaE) encoding the former activity, and characterization of its expression has revealed a novel regulatory mechanism. A shared pattern of expression has also been observed for a second α-L-rhamnosidase gene, (AN10277/rhaA). Results Amino acid sequence data for the oenological α-L-rhamnosidase were determined using MALDI-TOF mass spectrometry and correspond to the amino acid sequence deduced from AN7151 (rhaE). The cDNA of rhaE was expressed in Saccharomyces cerevisiae and yielded pNP-rhamnohydrolase activity. Phylogenetic analysis has revealed this eukaryotic α-L-rhamnosidase to be the first such enzyme found to be more closely related to bacterial rhamnosidases than other α-L-rhamnosidases of fungal origin. Northern analyses of diverse A. nidulans strains cultivated under different growth conditions indicate that rhaA and rhaE are induced by L-rhamnose and repressed by D-glucose as well as other carbon sources, some of which are considered to be non-repressive growth substrates. Interestingly, the transcriptional repression is independent of the wide domain carbon catabolite repressor CreA. Gene induction and glucose repression of these rha genes correlate with the uptake, or lack of it, of the inducing carbon source L-rhamnose, suggesting a prominent role for inducer exclusion in repression. Conclusions The A. nidulans rhaE gene encodes an α-L-rhamnosidase phylogenetically distant to those described in filamentous fungi, and its expression is regulated by a novel CreA-independent mechanism. The identification of rhaE and the characterization of its regulation will facilitate the design of strategies to overproduce the encoded enzyme - or homologs from other fungi - for industrial applications. Moreover, A. nidulans α-L-rhamnosidase encoding genes could serve as prototypes for fungal genes coding for plant cell wall degrading enzymes regulated by a novel mechanism of CCR. PMID:22353731

Characterization of the aes gene of Escherichia coli encoding an enzyme with esterase activity.

PubMed Central

Peist, R; Koch, A; Bolek, P; Sewitz, S; Kolbus, T; Boos, W

1997-01-01

malQ mutants of Escherichia coli lacking amylomaltase cannot grow on maltose. They express the maltose system constitutively and are sensitive to maltose when grown on another carbon source. In an attempt to isolate a multicopy suppressor that would result in growth on maltose, we transformed a malQ mutant with a gene bank of E. coli DNA which had been digested with Sau3a and cloned in pBR322. We screened the transformants on MacConkey maltose plates. A colony was isolated that appeared to be resistant to maltose and was pink on these plates, but it was still unable to grow on minimal medium with maltose as the carbon source. The plasmid was isolated, and the gene causing this phenotype was characterized. The deduced amino acid sequence of the encoded protein shows homology to that of lipases and esterases. We termed the gene aes, for acetyl esterase. Extracts of cells harboring plasmid-encoded aes under its own promoter exhibit a fivefold higher capacity to hydrolyze p-nitrophenyl acetate than do extracts of cells of plasmid-free strains. Similarly, strains harboring plasmid-encoded aes are able to grow on triacetyl glycerol (triacetin) whereas the plasmid-free strains are not. The expression of plasmid-encoded aes resulted in strong repression of the maltose transport genes in malT+ strains (10-fold reduction), but not in a malT(Con) strain which is independent of the inducer. Also, overproduction of MalT counteracted the Aes-dependent repression, indicating a direct interaction between MalT and Aes. PMID:9401025

The LysR-type transcription factor PacR is a global regulator of photosynthetic carbon assimilation in Anabaena.

PubMed

Picossi, Silvia; Flores, Enrique; Herrero, Antonia

2015-09-01

Cyanobacteria perform water-splitting photosynthesis and are important primary producers impacting the carbon and nitrogen cycles at global scale. They fix CO2 through ribulose-bisphosphate carboxylase/oxygenase (RuBisCo) and have evolved a distinct CO2 concentrating mechanism (CCM) that builds high CO2 concentrations in the vicinity of RuBisCo favouring its carboxylase activity. Filamentous cyanobacteria such as Anabaena fix CO2 in photosynthetic vegetative cells, which donate photosynthate to heterocysts that rely on a heterotrophic metabolism to fix N2 . CCM elements are induced in response to inorganic carbon limitation, a cue that exposes the photosynthetic apparatus to photodamage by over-reduction. An Anabaena mutant lacking the LysR-type transcription factor All3953 grew poorly and dies under high light. The rbcL operon encoding RuBisCo was induced upon carbon limitation in the wild type but not in the mutant. ChIP-Seq analysis was used to globally identify All3953 targets under carbon limitation. Targets include, besides rbcL, genes encoding CCM elements, photorespiratory pathway- photosystem- and electron transport-related components, and factors, including flavodiiron proteins, with a demonstrated or putative function in photoprotection. Quantitative reverse transcription polymerase chain reaction analysis of selected All3953 targets showed regulation in the wild type but not in the mutant. All3953 (PacR) is a global regulator of carbon assimilation in an oxygenic photoautotroph. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Investigation of the medical applications of the unique biocarbons developed by NASA. [compatibility of percutaneous prosthetic carbon devices

NASA Technical Reports Server (NTRS)

Mooney, V.

1973-01-01

The biocompatibility of percutaneous endoskeletal fixation devices made from carbon compounds, and their applications are considered. The clinical application of these carbons to solve human problems is demonstrated and the nature of myoelectric simulation by carbon implants is studied.

Are soil carbon models transferable across distinct regions or scales in Florida?

USDA-ARS?s Scientific Manuscript database

Some Florida soils have great capacity to accumulate carbon due to unique geographical and topographical conditions (high net primary productivity, precipitation, high water table, and flat topography). Soil carbon models have been used to quantify the carbon pools usually at a specific scale or in ...

76 FR 67200 - Prospective Grant of Exclusive License: Electron Paramagnetic Resonance Devices and Systems for...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-31

... that is a unique combination of: (1) multi-gradient Single Point Imaging involving global phase...-encoding gradients. The combination approach of single point imaging with the spin-echo signal detection...

Comparative Metagenomics of Freshwater Microbial Communities

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

Hemme, Chris; Deng, Ye; Tu, Qichao

2010-05-17

Previous analyses of a microbial metagenome from uranium and nitric-acid contaminated groundwater (FW106) showed significant environmental effects resulting from the rapid introduction of multiple contaminants. Effects include a massive loss of species and strain biodiversity, accumulation of toxin resistant genes in the metagenome and lateral transfer of toxin resistance genes between community members. To better understand these results in an ecological context, a second metagenome from a pristine groundwater system located along the same geological strike was sequenced and analyzed (FW301). It is hypothesized that FW301 approximates the ancestral FW106 community based on phylogenetic profiles and common geological parameters; however,more » even if is not the case, the datasets still permit comparisons between healthy and stressed groundwater ecosystems. Complex carbohydrate metabolism has been almost entirely lost in the stressed ecosystem. In contrast, the pristine system encodes a wide diversity of complex carbohydrate metabolism systems, suggesting that carbon turnover is very rapid and less leaky in the healthy groundwater system. FW301 encodes many (~;;160+) carbon monoxide dehydrogenase genes while FW106 encodes none. This result suggests that the community is frequently exposed to oxygen from aerated rainwater percolating into the subsurface, with a resulting high rate of carbon metabolism and CO production. When oxygen levels fall, the CO then serves as a major carbon source for the community. FW301 appears to be capable of CO2 fixation via the reductive carboxylase (reverse TCA) cycle and possibly acetogenesis, activities; these activities are lacking in the heterotrophic FW106 system which relies exclusively on respiration of nitrate and/or oxygen for energy production. FW301 encodes a complete set of B12 biosynthesis pathway at high abundance suggesting the use of sodium gradients for energy production in the healthy groundwater community. Overall comparative analysis suggests that the introduction of contaminants is accompanied by a decrease in biodiversity, loss of nutrient cycling, less metabolic diversity, increased respiration and dominance by r-strategists. These results are consistent with trends predicted for stressed ecosystems.« less

Nasalization by Nasalis larvatus: Larger noses audiovisually advertise conspecifics in proboscis monkeys.

PubMed

Koda, Hiroki; Murai, Tadahiro; Tuuga, Augustine; Goossens, Benoit; Nathan, Senthilvel K S S; Stark, Danica J; Ramirez, Diana A R; Sha, John C M; Osman, Ismon; Sipangkui, Rosa; Seino, Satoru; Matsuda, Ikki

2018-02-01

Male proboscis monkeys have uniquely enlarged noses that are prominent adornments, which may have evolved through their sexually competitive harem group social system. Nevertheless, the ecological roles of the signals encoded by enlarged noses remain unclear. We found significant correlations among nose, body, and testis sizes and a clear link between nose size and number of harem females. Therefore, there is evidence supporting both male-male competition and female choice as causal factors in the evolution of enlarged male noses. We also observed that nasal enlargement systematically modifies the resonance properties of male vocalizations, which probably encode male quality. Our results indicate that the audiovisual contributions of enlarged male noses serve as advertisements to females in their mate selection. This is the first primate research to evaluate the evolutionary processes involved in linking morphology, acoustics, and socioecology with unique masculine characteristics.

Nasalization by Nasalis larvatus: Larger noses audiovisually advertise conspecifics in proboscis monkeys

PubMed Central

Koda, Hiroki; Murai, Tadahiro; Tuuga, Augustine; Goossens, Benoit; Nathan, Senthilvel K.S.S.; Stark, Danica J.; Ramirez, Diana A. R.; Sha, John C. M.; Osman, Ismon; Sipangkui, Rosa; Seino, Satoru; Matsuda, Ikki

2018-01-01

Male proboscis monkeys have uniquely enlarged noses that are prominent adornments, which may have evolved through their sexually competitive harem group social system. Nevertheless, the ecological roles of the signals encoded by enlarged noses remain unclear. We found significant correlations among nose, body, and testis sizes and a clear link between nose size and number of harem females. Therefore, there is evidence supporting both male-male competition and female choice as causal factors in the evolution of enlarged male noses. We also observed that nasal enlargement systematically modifies the resonance properties of male vocalizations, which probably encode male quality. Our results indicate that the audiovisual contributions of enlarged male noses serve as advertisements to females in their mate selection. This is the first primate research to evaluate the evolutionary processes involved in linking morphology, acoustics, and socioecology with unique masculine characteristics. PMID:29507881

Virocell Metabolism: Metabolic Innovations During Host-Virus Interactions in the Ocean.

PubMed

Rosenwasser, Shilo; Ziv, Carmit; Creveld, Shiri Graff van; Vardi, Assaf

2016-10-01

Marine viruses are considered to be major ecological, evolutionary, and biogeochemical drivers of the marine environment, responsible for nutrient recycling and determining species composition. Viruses can re-shape their host's metabolic network during infection, generating the virocell-a unique metabolic state that supports their specific requirement. Here we discuss the concept of 'virocell metabolism' and its formation by rewiring of host-encoded metabolic networks, or by introducing virus-encoded auxiliary metabolic genes which provide the virocell with novel metabolic capabilities. The ecological role of marine viruses is commonly assessed by their relative abundance and phylogenetic diversity, lacking the ability to assess the dynamics of active viral infection. The new ability to define a unique metabolic state of the virocell will expand the current virion-centric approaches in order to quantify the impact of marine viruses on microbial food webs. Copyright © 2016. Published by Elsevier Ltd.

The neural basis of episodic memory: evidence from functional neuroimaging.

PubMed Central

Rugg, Michael D; Otten, Leun J; Henson, Richard N A

2002-01-01

We review some of our recent research using functional neuroimaging to investigate neural activity supporting the encoding and retrieval of episodic memories, that is, memories for unique events. Findings from studies of encoding indicate that, at the cortical level, the regions responsible for the effective encoding of a stimulus event as an episodic memory include some of the regions that are also engaged to process the event 'online'. Thus, it appears that there is no single cortical site or circuit responsible for episodic encoding. The results of retrieval studies indicate that successful recollection of episodic information is associated with activation of lateral parietal cortex, along with more variable patterns of activity in dorsolateral and anterior prefrontal cortex. Whereas parietal regions may play a part in the representation of retrieved information, prefrontal areas appear to support processes that act on the products of retrieval to align behaviour with the demands of the retrieval task. PMID:12217177

Multicolor quantum dot-encoded microspheres for the fluoroimmunoassays of chicken newcastle disease and goat pox virus.

PubMed

Yuan, Pingfan; Ma, Qiang; Meng, Rizeng; Wang, Chao; Dou, Wenchao; Wang, Guannan; Su, Xingguang

2009-05-01

Semiconductor nanocrystals (or quantum dots, QDs) have the potential to overcome some of the limitations encountered by traditional fluorophores in fluorescence labeling applications. The unique spectroscopic properties of QDs make them hold immense promise as versatile labels for biological applications. In this work, we employ the layer-by-layer (LbL) method for the construction of bio-functional multicolor QD-encoded microspheres. Polystyrene microspheres with diameter of 3 microm were used as templates for the deposition of different sized CdTe QDs/polyelectrolyte multilayers. Two different antigens, Chicken newcastle disease (CND) antigen and goat pox virus (GPV) antigen, were conjugated to two kinds of biofunctional multicolor microspheres with different optical encoding. The multicolor microspheres can capture corresponding antibodies labeled with QDs, QDs-CND antibody and QDs-GPV antibody in the fluoroimmunoassays. The microspheres can be distinguished from each other based on their optical encoding.

The Nostoc punctiforme Genome

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

John C. Meeks

2001-12-31

Nostoc punctiforme is a filamentous cyanobacterium with extensive phenotypic characteristics and a relatively large genome, approaching 10 Mb. The phenotypic characteristics include a photoautotrophic, diazotrophic mode of growth, but N. punctiforme is also facultatively heterotrophic; its vegetative cells have multiple development alternatives, including terminal differentiation into nitrogen-fixing heterocysts and transient differentiation into spore-like akinetes or motile filaments called hormogonia; and N. punctiforme has broad symbiotic competence with fungi and terrestrial plants, including bryophytes, gymnosperms and an angiosperm. The shotgun-sequencing phase of the N. punctiforme strain ATCC 29133 genome has been completed by the Joint Genome Institute. Annotation of an 8.9more » Mb database yielded 7432 open reading frames, 45% of which encode proteins with known or probable known function and 29% of which are unique to N. punctiforme. Comparative analysis of the sequence indicates a genome that is highly plastic and in a state of flux, with numerous insertion sequences and multilocus repeats, as well as genes encoding transposases and DNA modification enzymes. The sequence also reveals the presence of genes encoding putative proteins that collectively define almost all characteristics of cyanobacteria as a group. N. punctiforme has an extensive potential to sense and respond to environmental signals as reflected by the presence of more than 400 genes encoding sensor protein kinases, response regulators and other transcriptional factors. The signal transduction systems and any of the large number of unique genes may play essential roles in the cell differentiation and symbiotic interaction properties of N. punctiforme.« less

Proteomic and Mutant Analysis of the CO 2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena

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

Mangiapia, Mary; Brown, Terry-René W.; Chaput, Dale

Many autotrophic microorganisms are likely to adapt to scarcity in dissolved inorganic carbon (DIC; CO 2+ HCO 3 -+ CO 3 2-) with CO 2 concentrating mechanisms (CCM) that actively transport DIC across the cell membrane to facilitate carbon fixation. Surprisingly, DIC transport has been well studied among cyanobacteria and microalgae only. The deep-sea vent gammaproteobacterial chemolithoautotrophThiomicrospira crunogenahas a low-DIC inducible CCM, though the mechanism for uptake is unclear, as homologs to cyanobacterial transporters are absent. To identify the components of this CCM, proteomes ofT. crunogenacultivated under low- and high-DIC conditions were compared. Fourteen proteins, including those comprising carboxysomes, weremore » at least 4-fold more abundant under low-DIC conditions. One of these proteins was encoded byTcr_0854; strains carrying mutated copies of this gene, as well as the adjacent Tcr_0853, required elevated DIC for growth. Strains carrying mutated copies of Tcr_0853 and Tcr_0854 overexpressed carboxysomes and had diminished ability to accumulate intracellular DIC. Based on reverse transcription (RT)-PCR, Tcr_0853 and Tcr_0854 were cotranscribed and upregulated under low-DIC conditions. The Tcr_0853 -encoded protein was predicted to have 13 transmembrane helices. Given the mutant phenotypes described above, Tcr_0853 and Tcr_0854 may encode a two-subunit DIC transporter that belongs to a previously undescribed transporter family, though it is widespread among autotrophs from multiple phyla.DIC uptake and fixation by autotrophs are the primary input of inorganic carbon into the biosphere. The mechanism for dissolved inorganic carbon uptake has been characterized only for cyanobacteria despite the importance of DIC uptake by autotrophic microorganisms from many phyla among theBacteriaandArchaea. In this work, proteins necessary for dissolved inorganic carbon utilization in the deep-sea vent chemolithoautotrophT. crunogenawere identified, and two of these may be able to form a novel transporter. Homologs of these proteins are present in 14 phyla inBacteriaand also in one phylum ofArchaea, theEuryarchaeota. Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon uptake and fixation well beyond the genusThiomicrospira.« less

Proteomic and Mutant Analysis of the CO 2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena

DOE PAGES

Mangiapia, Mary; Brown, Terry-René W.; Chaput, Dale; ...

2017-01-23

Many autotrophic microorganisms are likely to adapt to scarcity in dissolved inorganic carbon (DIC; CO 2+ HCO 3 -+ CO 3 2-) with CO 2 concentrating mechanisms (CCM) that actively transport DIC across the cell membrane to facilitate carbon fixation. Surprisingly, DIC transport has been well studied among cyanobacteria and microalgae only. The deep-sea vent gammaproteobacterial chemolithoautotrophThiomicrospira crunogenahas a low-DIC inducible CCM, though the mechanism for uptake is unclear, as homologs to cyanobacterial transporters are absent. To identify the components of this CCM, proteomes ofT. crunogenacultivated under low- and high-DIC conditions were compared. Fourteen proteins, including those comprising carboxysomes, weremore » at least 4-fold more abundant under low-DIC conditions. One of these proteins was encoded byTcr_0854; strains carrying mutated copies of this gene, as well as the adjacent Tcr_0853, required elevated DIC for growth. Strains carrying mutated copies of Tcr_0853 and Tcr_0854 overexpressed carboxysomes and had diminished ability to accumulate intracellular DIC. Based on reverse transcription (RT)-PCR, Tcr_0853 and Tcr_0854 were cotranscribed and upregulated under low-DIC conditions. The Tcr_0853 -encoded protein was predicted to have 13 transmembrane helices. Given the mutant phenotypes described above, Tcr_0853 and Tcr_0854 may encode a two-subunit DIC transporter that belongs to a previously undescribed transporter family, though it is widespread among autotrophs from multiple phyla.DIC uptake and fixation by autotrophs are the primary input of inorganic carbon into the biosphere. The mechanism for dissolved inorganic carbon uptake has been characterized only for cyanobacteria despite the importance of DIC uptake by autotrophic microorganisms from many phyla among theBacteriaandArchaea. In this work, proteins necessary for dissolved inorganic carbon utilization in the deep-sea vent chemolithoautotrophT. crunogenawere identified, and two of these may be able to form a novel transporter. Homologs of these proteins are present in 14 phyla inBacteriaand also in one phylum ofArchaea, theEuryarchaeota. Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon uptake and fixation well beyond the genusThiomicrospira.« less

Proteomic and Mutant Analysis of the CO2 Concentrating Mechanism of Hydrothermal Vent Chemolithoautotroph Thiomicrospira crunogena

PubMed Central

Mangiapia, Mary; Brown, Terry-René W.; Chaput, Dale; Haller, Edward; Harmer, Tara L.; Hashemy, Zahra; Keeley, Ryan; Leonard, Juliana; Mancera, Paola; Nicholson, David; Stevens, Stanley; Wanjugi, Pauline; Zabinski, Tania; Pan, Chongle

2017-01-01

ABSTRACT Many autotrophic microorganisms are likely to adapt to scarcity in dissolved inorganic carbon (DIC; CO2 + HCO3− + CO32−) with CO2 concentrating mechanisms (CCM) that actively transport DIC across the cell membrane to facilitate carbon fixation. Surprisingly, DIC transport has been well studied among cyanobacteria and microalgae only. The deep-sea vent gammaproteobacterial chemolithoautotroph Thiomicrospira crunogena has a low-DIC inducible CCM, though the mechanism for uptake is unclear, as homologs to cyanobacterial transporters are absent. To identify the components of this CCM, proteomes of T. crunogena cultivated under low- and high-DIC conditions were compared. Fourteen proteins, including those comprising carboxysomes, were at least 4-fold more abundant under low-DIC conditions. One of these proteins was encoded by Tcr_0854; strains carrying mutated copies of this gene, as well as the adjacent Tcr_0853, required elevated DIC for growth. Strains carrying mutated copies of Tcr_0853 and Tcr_0854 overexpressed carboxysomes and had diminished ability to accumulate intracellular DIC. Based on reverse transcription (RT)-PCR, Tcr_0853 and Tcr_0854 were cotranscribed and upregulated under low-DIC conditions. The Tcr_0853-encoded protein was predicted to have 13 transmembrane helices. Given the mutant phenotypes described above, Tcr_0853 and Tcr_0854 may encode a two-subunit DIC transporter that belongs to a previously undescribed transporter family, though it is widespread among autotrophs from multiple phyla. IMPORTANCE DIC uptake and fixation by autotrophs are the primary input of inorganic carbon into the biosphere. The mechanism for dissolved inorganic carbon uptake has been characterized only for cyanobacteria despite the importance of DIC uptake by autotrophic microorganisms from many phyla among the Bacteria and Archaea. In this work, proteins necessary for dissolved inorganic carbon utilization in the deep-sea vent chemolithoautotroph T. crunogena were identified, and two of these may be able to form a novel transporter. Homologs of these proteins are present in 14 phyla in Bacteria and also in one phylum of Archaea, the Euryarchaeota. Many organisms carrying these homologs are autotrophs, suggesting a role in facilitating dissolved inorganic carbon uptake and fixation well beyond the genus Thiomicrospira. PMID:28115547

Novel materials for electrochemical power sources—introduction of PUREBLACK ® Carbons

NASA Astrophysics Data System (ADS)

Barsukov, Igor V.; Gallego, Maritza A.; Doninger, Joseph E.

Graphitization heat treatment of a precursor carbon black was seen to effectively produce a wide variety of forms of partially graphitized nano-sized carbonaceous materials with a set of unique properties, some of which are reported in this paper in comparison with those properties of the precursor carbon material. These novel materials were given the name of PUREBLACK ® Carbons. Among some of the unique properties are: higher conductivity than that of acetylene type carbon blacks due to PUREBLACK ® Carbon's particles having more graphitic structure; very low to zero volatile content (external oxygen, sulfur, etc., groups, which are often believed to be the cause of initiation of self-discharge reactions in batteries); very low equilibrium moisture pickup (20 ppm level), which makes it particularly attractive in lithium metal or lithium-ion based electrochemical systems; high purity. Electrochemical testing of the newly proposed PUREBLACK ® Carbons in several battery systems offers significant promise that it presents a viable solution to the needs of industry.

Synthesis, properties and biomedical applications of carbon-based quantum dots: An updated review.

PubMed

Namdari, Pooria; Negahdari, Babak; Eatemadi, Ali

2017-03-01

Carbon-based quantum dots (CQDs) are a newly developed class of carbon nano-materials that have attracted much interest and attention as promising competitors to already available semiconductor quantum dots owing to their un-comparable and unique properties. In addition, controllability of CQDs unique physiochemical properties is as a result of their surface passivation and functionalization. This is an update article (between 2013 and 2016) on the recent progress, characteristics and synthesis methods of CQDs and different advantages in varieties of applications. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Autolytic enzymes are responsible for increased melanization of carbon stressed Aspergillus nidulans cultures.

PubMed

Szilágyi, Melinda; Anton, Fruzsina; Pócsi, István; Emri, Tamás

2018-05-01

Melanization of carbon stressed Aspergillus nidulans cultures were studied. Melanin production showed strong positive correlation with the activity of the secreted chitinase and ß-1,3-glucanase. Deletion of either chiB encoding an autolytic endochitinase or engA encoding an autolytic ß-1,3-endoglucanase, or both, almost completely prevented melanization of carbon stressed cultures. In contrast, addition of Trichoderma lyticase to cultures induced melanin production. Synthetic melanin could efficiently inhibit the purified ChiB chitinase activity. It could also efficiently decrease the intensity of hyphal fragmentation and pellet disorganization in Trichoderma lyticase treated cultures. Glyphosate, an inhibitor of L-3,4-dihydroxyphenylalanine-type melanin synthesis, could prevent melanization of carbon-starved cultures and enhanced pellet disorganization, while pyroquilon, a 1,8-dihydroxynaphthalene-type melanin synthesis inhibitor, enhanced melanization, and prevented pellet disorganization. We concluded that cell wall stress induced by autolytic cell wall hydrolases was responsible for melanization of carbon-starved cultures. The produced melanin can shield the living cells but may not inhibit the degradation and reutilization of cell wall materials of dead hyphae. Controlling the activity of autolytic hydrolase production can be an efficient approach to prevent unwanted melanization in the fermentation industry, while applying melanin synthesis inhibitors can decrease the resistance of pathogenic fungi against the chitinases produced by the host organism. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Incomplete Wood–Ljungdahl pathway facilitates one-carbon metabolism in organohalide-respiring Dehalococcoides mccartyi

PubMed Central

Zhuang, Wei-Qin; Yi, Shan; Bill, Markus; Brisson, Vanessa L.; Feng, Xueyang; Men, Yujie; Conrad, Mark E.; Tang, Yinjie J.; Alvarez-Cohen, Lisa

2014-01-01

The acetyl-CoA “Wood–Ljungdahl” pathway couples the folate-mediated one-carbon (C1) metabolism to either CO2 reduction or acetate oxidation via acetyl-CoA. This pathway is distributed in diverse anaerobes and is used for both energy conservation and assimilation of C1 compounds. Genome annotations for all sequenced strains of Dehalococcoides mccartyi, an important bacterium involved in the bioremediation of chlorinated solvents, reveal homologous genes encoding an incomplete Wood–Ljungdahl pathway. Because this pathway lacks key enzymes for both C1 metabolism and CO2 reduction, its cellular functions remain elusive. Here we used D. mccartyi strain 195 as a model organism to investigate the metabolic function of this pathway and its impacts on the growth of strain 195. Surprisingly, this pathway cleaves acetyl-CoA to donate a methyl group for production of methyl-tetrahydrofolate (CH3-THF) for methionine biosynthesis, representing an unconventional strategy for generating CH3-THF in organisms without methylene-tetrahydrofolate reductase. Carbon monoxide (CO) was found to accumulate as an obligate by-product from the acetyl-CoA cleavage because of the lack of a CO dehydrogenase in strain 195. CO accumulation inhibits the sustainable growth and dechlorination of strain 195 maintained in pure cultures, but can be prevented by CO-metabolizing anaerobes that coexist with D. mccartyi, resulting in an unusual syntrophic association. We also found that this pathway incorporates exogenous formate to support serine biosynthesis. This study of the incomplete Wood–Ljungdahl pathway in D. mccartyi indicates a unique bacterial C1 metabolism that is critical for D. mccartyi growth and interactions in dechlorinating communities and may play a role in other anaerobic communities. PMID:24733917

The genome sequence of E. coli W (ATCC 9637): comparative genome analysis and an improved genome-scale reconstruction of E. coli

PubMed Central

2011-01-01

Background Escherichia coli is a model prokaryote, an important pathogen, and a key organism for industrial biotechnology. E. coli W (ATCC 9637), one of four strains designated as safe for laboratory purposes, has not been sequenced. E. coli W is a fast-growing strain and is the only safe strain that can utilize sucrose as a carbon source. Lifecycle analysis has demonstrated that sucrose from sugarcane is a preferred carbon source for industrial bioprocesses. Results We have sequenced and annotated the genome of E. coli W. The chromosome is 4,900,968 bp and encodes 4,764 ORFs. Two plasmids, pRK1 (102,536 bp) and pRK2 (5,360 bp), are also present. W has unique features relative to other sequenced laboratory strains (K-12, B and Crooks): it has a larger genome and belongs to phylogroup B1 rather than A. W also grows on a much broader range of carbon sources than does K-12. A genome-scale reconstruction was developed and validated in order to interrogate metabolic properties. Conclusions The genome of W is more similar to commensal and pathogenic B1 strains than phylogroup A strains, and therefore has greater utility for comparative analyses with these strains. W should therefore be the strain of choice, or 'type strain' for group B1 comparative analyses. The genome annotation and tools created here are expected to allow further utilization and development of E. coli W as an industrial organism for sucrose-based bioprocesses. Refinements in our E. coli metabolic reconstruction allow it to more accurately define E. coli metabolism relative to previous models. PMID:21208457

Lactobacillus casei Ferments the N-Acetylglucosamine Moiety of Fucosyl-α-1,3-N-Acetylglucosamine and Excretes l-Fucose

PubMed Central

Rodríguez-Díaz, Jesús; Rubio-del-Campo, Antonio

2012-01-01

We have previously characterized from Lactobacillus casei BL23 three α-l-fucosidases, AlfA, AlfB, and AlfC, which hydrolyze in vitro natural fucosyl-oligosaccharides. In this work, we have shown that L. casei is able to grow in the presence of fucosyl-α-1,3-N-acetylglucosamine (Fuc-α-1,3-GlcNAc) as a carbon source. Interestingly, L. casei excretes the l-fucose moiety during growth on Fuc-α-1,3-GlcNAc, indicating that only the N-acetylglucosamine moiety is being metabolized. Analysis of the genomic sequence of L. casei BL23 shows that downstream from alfB, which encodes the α-l-fucosidase AlfB, a gene, alfR, that encodes a transcriptional regulator is present. Divergently from alfB, three genes, alfEFG, that encode proteins with homology to the enzyme IIAB (EIIAB), EIIC, and EIID components of a mannose-class phosphoenolpyruvate:sugar phosphotransferase system (PTS) are present. Inactivation of either alfB or alfF abolishes the growth of L. casei on Fuc-α-1,3-GlcNAc. This proves that AlfB is involved in Fuc-α-1,3-GlcNAc metabolism and that the transporter encoded by alfEFG participates in the uptake of this disaccharide. A mutation in the PTS general component enzyme I does not eliminate the utilization of Fuc-α-1,3-GlcNAc, suggesting that the transport via the PTS encoded by alfEFG is not coupled to phosphorylation of the disaccharide. Transcriptional analysis with alfR and ccpA mutants shows that the two gene clusters alfBR and alfEFG are regulated by substrate-specific induction mediated by the inactivation of the transcriptional repressor AlfR and by carbon catabolite repression mediated by the catabolite control protein A (CcpA). This work reports for the first time the characterization of the physiological role of an α-l-fucosidase in lactic acid bacteria and the utilization of Fuc-α-1,3-GlcNAc as a carbon source for bacteria. PMID:22544237

Functional analysis of environmental DNA-derived type II polyketide synthases reveals structurally diverse secondary metabolites.

PubMed

Feng, Zhiyang; Kallifidas, Dimitris; Brady, Sean F

2011-08-02

A single gram of soil is predicted to contain thousands of unique bacterial species. The majority of these species remain recalcitrant to standard culture methods, prohibiting their use as sources of unique bioactive small molecules. The cloning and analysis of DNA extracted directly from environmental samples (environmental DNA, eDNA) provides a means of exploring the biosynthetic capacity of natural bacterial populations. Environmental DNA libraries contain large reservoirs of bacterial genetic diversity from which new secondary metabolite gene clusters can be systematically recovered and studied. The identification and heterologous expression of type II polyketide synthase-containing eDNA clones is reported here. Functional analysis of three soil DNA-derived polyketide synthase systems in Streptomyces albus revealed diverse metabolites belonging to well-known, rare, and previously uncharacterized structural families. The first of these systems is predicted to encode the production of the known antibiotic landomycin E. The second was found to encode the production of a metabolite with a previously uncharacterized pentacyclic ring system. The third was found to encode the production of unique KB-3346-5 derivatives, which show activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis. These results, together with those of other small-molecule-directed metagenomic studies, suggest that culture-independent approaches are capable of accessing biosynthetic diversity that has not yet been extensively explored using culture-based methods. The large-scale functional screening of eDNA clones should be a productive strategy for generating structurally previously uncharacterized chemical entities for use in future drug development efforts.

Diversity of viral photosystem-I psaA genes

PubMed Central

Hevroni, Gur; Enav, Hagay; Rohwer, Forest; Béjà, Oded

2015-01-01

Marine photosynthesis is one of the major contributors to the global carbon cycle and the world's oxygen supply. This process is largely driven by cyanobacteria, namely Synechococcus and Prochlorococcus. Genes encoding photosystem-II (PSII) reaction center proteins are found in many cyanophage genomes, and are expressed during the infection of their hosts. On the basis of metagenomics, cyanophage photosystem-I (PSI) gene cassettes were recently discovered with two gene arrangements psaJF→C→A→B→K→E→D and psaD→C→A→B. It was suggested that the horizontal transfer of PSII and PSI genes is increasing phage fitness. To better understand their diversity, we designed degenerate primers to cover a wide diversity of organisms, and using PCR we targeted the psaC→A arrangement, which is unique to cyanophages cassettes. We examined viral concentrates from four islands in the Pacific Ocean and found samples containing the psaC→A arrangement. Analyses of the amplified viral psaA gene revealed six subgroups varying in their level of similarity and %G+C content, suggesting that the diversity of cyanophage PSI genes is greater than originally thought. PMID:25535938

Phototrophy and starvation-based induction of autophagy upon removal of Gcn5-catalyzed acetylation of Atg7 in Magnaporthe oryzae.

PubMed

Zhang, Shulin; Liang, Meiling; Naqvi, Naweed I; Lin, Chaoxiang; Qian, Wanqiang; Zhang, Lian-Hui; Deng, Yi Zhen

2017-08-03

Magnaporthe oryzae, the ascomycete fungus that causes rice blast disease, initiates conidiation in response to light when grown on Prune-Agar medium containing both carbon and nitrogen sources. Macroautophagy/autophagy was shown to be essential for M. oryzae conidiation and induced specifically upon exposure to light but is undetectable in the dark. Therefore, it is inferred that autophagy is naturally induced by light, rather than by starvation during M. oryzae conidiation. However, the signaling pathway(s) involved in such phototropic induction of autophagy remains unknown. We identified an M. oryzae ortholog of GCN5 (MGG_03677), encoding a histone acetyltransferase (HAT) that negatively regulates light- and nitrogen-starvation-induced autophagy, by acetylating the autophagy protein Atg7. Furthermore, we unveiled novel regulatory mechanisms on Gcn5 at both transcriptional and post-translational levels, governing its function associated with the unique phototropic response of autophagy in this pathogenic fungus. Thus, our study depicts a signaling network and regulatory mechanism underlying the autophagy induction by important environmental clues such as light and nutrients.

Reusable glucose sensing using carbon nanotube-based self-assembly

NASA Astrophysics Data System (ADS)

Bhattacharyya, Tamoghna; Samaddar, Sarbani; Dasgupta, Anjan Kr.

2013-09-01

Lipid functionalized single walled carbon nanotube-based self assembly forms a super-micellar structure. This assemblage has been exploited to trap glucose oxidase in a molecular cargo for glucose sensing. The advantage of such a molecular trap is that all components of this unique structure (both the trapping shell and the entrapped enzyme) are reusable and rechargeable. The unique feature of this sensing method lies in the solid state functionalization of single walled carbon nanotubes that facilitates liquid state immobilization of the enzyme. The method can be used for soft-immobilization (a new paradigm in enzyme immobilization) of enzymes with better thermostability that is imparted by the strong hydrophobic environment provided through encapsulation by the nanotubes.Lipid functionalized single walled carbon nanotube-based self assembly forms a super-micellar structure. This assemblage has been exploited to trap glucose oxidase in a molecular cargo for glucose sensing. The advantage of such a molecular trap is that all components of this unique structure (both the trapping shell and the entrapped enzyme) are reusable and rechargeable. The unique feature of this sensing method lies in the solid state functionalization of single walled carbon nanotubes that facilitates liquid state immobilization of the enzyme. The method can be used for soft-immobilization (a new paradigm in enzyme immobilization) of enzymes with better thermostability that is imparted by the strong hydrophobic environment provided through encapsulation by the nanotubes. Electronic supplementary information (ESI) available. See DOI: 10.1039/c3nr02609d

Complementary DNA sequences encoding the multimammate rat MHC class II DQ alpha and beta chains and cross-species sequence comparison in rodents.

PubMed

de Bellocq, J Goüy; Leirs, H

2009-09-01

Sequences of the complete open reading frame (ORF) for rodents major histocompatibility complex (MHC) class II genes are rare. Multimammate rat (Mastomys natalensis) complementary DNA (cDNA) encoding the alpha and beta chains of MHC class II DQ gene was cloned from a rapid amplifications of cDNA Emds (RACE) cDNA library. The ORFs consist of 801 and 771 bp encoding 266 and 256 amino acid residues for DQB and DQA, respectively. The genomic structure of Mana-DQ genes is globally analogous to that described for other rodents except for the insertion of a serine residue in the signal peptide of Mana-DQB, which is unique among known rodents.

CARBON NANOTUBES IN MICROWAVE ENVIRONMENT-IGNITION AND RECONSTRUCTION

EPA Science Inventory

The unusual property of single-walled carbon nanotubes (SWNT), multi-wall (MWNT) nanotubes and Buckminsterfullerene (C-60) is observed upon exposure to microwave-assisted ignition. Carbon nanotubes known for a range of mechanical and electronic properties because of their unique...

A Genomic View of the Sea Urchin Nervous System

PubMed Central

Burke, RD; Angerer, LM; Elphick, MR; Humphrey, GW; Yaguchi, S; Kiyama, T; Liang, S; Mu, X; Agca, C; Klein, WH; Brandhorst, BP; Rowe, M; Wilson, K; Churcher, AM; Taylor, JS; Chen, N; Murray, G; Wang, D; Mellott, D; Olinski, R; Hallböök, F; Thorndyke, MC

2007-01-01

The sequencing of the Strongylocentrotus purpuratus genome provides a unique opportunity to investigate the function and evolution of neural genes. The neurobiology of sea urchins is of particular interest because they have a close phylogenetic relationship with chordates, yet a distinctive pentaradiate body plan and unusual neural organization. Orthologues of transcription factors that regulate neurogenesis in other animals have been identified and several are expressed in neurogenic domains before gastrulation indicating that they may operate near the top of a conserved neural gene regulatory network. A family of genes encoding voltage-gated ion channels is present but, surprisingly, genes encoding gap junction proteins (connexins and pannexins) appear to be absent. Genes required for synapse formation and function have been identified and genes for synthesis and transport of neurotransmitters are present. There is a large family of G-protein-coupled receptors, including 874 rhodopsin-type receptors, 28 metabotropic glutamate-like receptors and a remarkably expanded group of 161 secretin receptor-like proteins. Absence of cannabinoid, lysophospholipid and melanocortin receptors indicates that this group may be unique to chordates. There are at least 37 putative G-protein coupled peptide receptors and precursors for several neuropeptides and peptide hormones have been identified, including SALMFamides, NGFFFamide, a vasotocin-like peptide, glycoprotein hormones, and insulin/insulin-like growth factors. Identification of a neurotrophin-like gene and Trk receptor in sea urchin indicates that this neural signaling system is not unique to chordates. Several hundred chemoreceptor genes have been predicted using several approaches, a number similar to that for other animals. Intriguingly, genes encoding homologues of rhodopsin, Pax6 and several other key mammalian retinal transcription factors are expressed in tube feet, suggesting tube feet function as photosensory organs. Analysis of the sea urchin genome presents a unique perspective on the evolutionary history of deuterostome nervous systems and reveals new approaches to investigate the development and neurobiology of sea urchins. PMID:16965768

Nucleic acids encoding plant glutamine phenylpyruvate transaminase (GPT) and uses thereof

DOEpatents

Unkefer, Pat J.; Anderson, Penelope S.; Knight, Thomas J.

2016-03-29

Glutamine phenylpyruvate transaminase (GPT) proteins, nucleic acid molecules encoding GPT proteins, and uses thereof are disclosed. Provided herein are various GPT proteins and GPT gene coding sequences isolated from a number of plant species. As disclosed herein, GPT proteins share remarkable structural similarity within plant species, and are active in catalyzing the synthesis of 2-hydroxy-5-oxoproline (2-oxoglutaramate), a powerful signal metabolite which regulates the function of a large number of genes involved in the photosynthesis apparatus, carbon fixation and nitrogen metabolism.

Functional Neuroimaging of Self-Referential Encoding with Age

PubMed Central

Gutchess, Angela H.; Kensinger, Elizabeth A.; Schacter, Daniel L.

2009-01-01

Aging impacts memory formation and the engagement of frontal and medial temporal regions. However, much of the research to date has focused on the encoding of neutral verbal and visual information. The present fMRI study investigated age differences in a social encoding task while participants made judgments about the self or another person. Although previous studies identified an intact self-reference effect with age, subserved by robust engagement of medial prefrontal cortex (mPFC) by both young and older adults, we identified a number of age differences. In regions including superior mPFC, inferior prefrontal cortex, and anterior and posterior cingulate cortex, young and older adults exhibited reversals in the pattern of activity for self and other conditions. Whereas young primarily evidenced subsequent forgetting effects in the self-reference condition, older adults demonstrated subsequent memory effects in the other-reference condition. These results indicate fundamental differences across the age groups in the engagement of elaborative encoding processes. We suggest that older adults may encode information about the self in a more normative manner, whereas young adults focus on encoding the unique aspects of the self and distinguishing the self from others. PMID:19765600

New insights into the reduction systems of plastidial thioredoxins point out the unique properties of thioredoxin z from Arabidopsis.

PubMed

Bohrer, Anne-Sophie; Massot, Vincent; Innocenti, Gilles; Reichheld, Jean-Philippe; Issakidis-Bourguet, Emmanuelle; Vanacker, Hélène

2012-11-01

In plants, thioredoxins (TRX) constitute a large protein disulphide oxidoreductase family comprising 10 plastidial members in Arabidopsis thaliana and subdivided in five types. The f- and m-types regulate enzymes involved mainly in carbon metabolism whereas the x, y, and z types have an antioxidant function. The reduction of TRXm and f in chloroplasts is performed in the light by ferredoxin:thioredoxin reductase (FTR) that uses photosynthetically reduced ferredoxin (Fd) as a reductant. The reduction system of Arabidopsis TRXx, y, and z has never been demonstrated. Recently, a gene encoding an atypical plastidial NADPH-dependent TRX reductase (NTRC) was found. In the present study, gene expression analysis revealed that both reductases are expressed in all organs of Arabidopsis and could potentially serve as electron donors to plastidial TRX. This ability was tested in vitro either with purified NTRC in presence of NADPH or with a light-driven reconstituted system comprising thylakoids and purified Fd and FTR. The results demonstrate that FTR reduces the x and y TRX isoforms but not the recently identified TRXz. Moreover, the results show that NTRC cannot be an efficient alternative reducing system, neither for TRXz nor for the other plastidial TRX. The data reveal that TRXf, m, x, and y, known as redox regulators in the chloroplast, have also the ability to reduce TRXz in vitro. Overall, the present study points out the unique properties of TRXz among plastidial TRX.

Nosiheptide Biosynthesis Featuring a Unique Indole Side Ring Formation on the Characteristic Thiopeptide Framework

PubMed Central

Yu, Yi; Duan, Lian; Zhang, Qi; Liao, Rijing; Ding, Ying; Pan, Haixue; Wendt-Pienkowski, Evelyn; Tang, Gongli; Shen, Ben; Liu, Wen

2009-01-01

Nosiheptide (NOS), belonging to the e series of thiopeptide antibiotics that exhibit potent activity against various bacterial pathogens, bears a unique indole side ring system and regiospecific hydroxyl groups on the characteristic macrocyclic core. Here, cloning, sequencing and characterization of the nos gene cluster from Streptomyces actuosus ATCC 25421 as a model for this series of thiopeptides has unveiled new insights into their biosynthesis. Bioinformatics-based sequence analysis and in vivo investigation into the gene functions show that NOS biosynthesis shares a common strategy with recently characterized b or c series thiopeptides for forming the characteristic macrocyclic core, which features a ribosomally synthesized precursor peptide with conserved posttranslational modifications. However, it apparently proceeds via a different route for tailoring the thiopeptide framework, allowing the final product to exhibit the distinct structural characteristics of e series thiopeptides, such as the indole side ring system. Chemical complementation supports the notion that the S-adenosylmethionine (AdoMet)-dependent protein NosL may play a central role in converting Trp to the key 3-methylindole moiety by an unusual carbon side chain rearrangement, most likely via a radical-initiated mechanism. Characterization of the indole side ring-opened analog of NOS from the nosN mutant strain is consistent with the proposed methyltransferase activity of its encoded protein, shedding light into the timing of the individual steps for indole side ring biosynthesis. These results also suggest the feasibility of engineering novel thiopeptides for drug discovery by manipulating the NOS biosynthetic machinery. PMID:19678698

Parameterizing A Surface Water Model for Multiwalled Carbon Nanotubes

EPA Science Inventory

The unique electronic, mechanical, and structural properties of carbon nanotubes (CNTs) has lead to increasing production of these versatile materials; currently, the use of carbon-based nanomaterials in consumer products is second only to that of nano-scale silver. Although ther...

Beyond carbon budgets

NASA Astrophysics Data System (ADS)

Peters, Glen P.

2018-06-01

The remaining carbon budget consistent with limiting warming to 1.5 °C allows 20 more years of current emissions according to one study, but is already exhausted according to another. Both are defensible. We need to move on from a unique carbon budget, and face the nuances.

Quantitative Analysis of Carbon Flow into Photosynthetic Products Functioning as Carbon Storage in the Marine Coccolithophore, Emiliania huxleyi.

PubMed

Tsuji, Yoshinori; Yamazaki, Masatoshi; Suzuki, Iwane; Shiraiwa, Yoshihiro

2015-08-01

The bloom-forming coccolithophore Emiliania huxleyi (Haptophyta) is a dominant marine phytoplankton, cells of which are covered with calcareous plates (coccoliths). E. huxleyi produces unique lipids of C37-C40 long-chain ketones (alkenones) with two to four trans-unsaturated bonds, β-glucan (but not α-glucan) and acid polysaccharide (AP) associated with the morphogenesis of CaCO3 crystals in coccoliths. Despite such unique features, there is no detailed information on the patterns of carbon allocation into these compounds. Therefore, we performed quantitative estimation of carbon flow into various macromolecular products by conducting (14)C-radiotracer experiments using NaH(14)CO3 as a substrate. Photosynthetic (14)C incorporation into low molecular-mass compounds (LMC), extracellular AP, alkenones, and total lipids except alkenones was estimated to be 35, 13, 17, and 25 % of total (14)C fixation in logarithmic growth phase cells and 33, 19, 18, and 18 % in stationary growth phase cells, respectively. However, less than 1 % of (14)C was incorporated into β-glucan in both cells. (14)C-mannitol occupied ca. 5 % of total fixed (14)C as the most dominant LMC product. Levels of all (14)C compounds decreased in the dark. Therefore, alkenones and LMC (including mannitol), but not β-glucan, function in carbon/energy storage in E. huxleyi, irrespective of the growth phase. Compared with other algae, the low carbon flux into β-glucan is a unique feature of carbon metabolism in E. huxelyi.

Metabolic engineering of Pseudomonas putida for the utilization of parathion as a carbon and energy source.

PubMed

Walker, Andy W; Keasling, Jay D

2002-06-30

Pseudomonas putida KT2442 was engineered to use the organophosphate pesticide parathion, a compound similar to other organophosphate pesticides and chemical warfare agents, as a source of carbon and energy. The initial step in the engineered degradation pathway was parathion hydrolysis by organophosphate hydrolase (OPH) to p-nitrophenol (PNP) and diethyl thiophosphate, compounds that cannot be metabolized by P. putida KT2442. The gene encoding the native OPH (opd), with and without the secretory leader sequence, was cloned into broad-host-range plasmids under the control of tac and taclac promoters. Expression of opd from the tac promoter resulted in high OPH activity, whereas expression from the taclac promoter resulted in low activity. A plasmid-harboring operons encoding enzymes for p-nitrophenol transformation to beta-ketoadipate was transformed into P. putida allowing the organism to use 0.5 mM PNP as a carbon and energy source. Transformation of P. putida with the plasmids harboring opd and the PNP operons allowed the organism to utilize 0.8 mM parathion as a source of carbon and energy. Degradation studies showed that parathion formed a separate dense, non-aqueous phase liquid phase but was still bioavailable. Copyright 2002 Wiley Periodicals, Inc.

Physiology and Genetics of Biogenic Methane-Production from Acetate

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

Sowers, Kevin R

Biomass conversion catalyzed by methanogenic consortia is a widely available, renewable resource for both energy production and waste treatment. The efficiency of this process is directly dependent upon the interaction of three metabolically distinct groups of microorganisms; the fermentative and acetogenic Bacteria and the methanogenic Archaea. One of the rate limiting steps in the degradation of soluble organic matter is the dismutation of acetate, a predominant intermediate in the process, which accounts for 70 % or more of the methane produced by the methanogens. Acetate utilization is controlled by regulation of expression of carbon monoxide dehydrogensase (COdh), which catalyzes themore » dismutation of acetate. However, physiological and molecular factors that control differential substrate utilization have not been identified in these Archaea. Our laboratory has identified sequence elements near the promoter of the gene (cdh) encoding for COdh and we have confirmed that these sequences have a role in the in vivo expression of cdh. The current proposal focuses on identifying the regulatory components that interact with DNA and RNA elements, and identifying the mechanisms used to control cdh expression. We will determine whether expression is controlled at the level of transcription or if it is mediated by coordinate interaction of transcription initiation with other processes such as transcription elongation rate and differential mRNA stability. Utilizing recently sequenced methanosarcinal genomes and a DNA microarray currently under development genes that encode regulatory proteins and transcription factors will be identified and function confirmed by gene disruption and subsequent screening on different substrates. Functional interactions will be determined in vivo by assaying the effects of gene dosage and site-directed mutagenesis of the regulatory gene on the expression of a cdh::lacZ operon fusion. Results of this study will reveal whether this critical catabolic pathway is controlled by mechanisms similar to those employed by the Bacteria and Eukarya, or by a regulatory paradigm that is unique to the Archaea. The mechanism(s) revealed by this investigation will provide insight into the regulatory strategies employed by the aceticlastic methanogenic Archaea to efficiently direct carbon and electron flow in anaerobic consortia during fermentative processes.« less

The Effects of Emotional Visual Context on the Encoding and Retrieval of Body Odor Information.

PubMed

Parma, Valentina; Macedo, Stephanie; Rocha, Marta; Alho, Laura; Ferreira, Jacqueline; Soares, Sandra C

2018-04-01

Conditions during information encoding and retrieval are known to influence the sensory material stored and its recapitulation. However, little is known about such processes in olfaction. Here, we capitalized on the uniqueness of body odors (BOs) which, similar to fingerprints, allow for the identification of a specific person, by associating their presentation to a negative or a neutral emotional context. One hundred twenty-five receivers (68 F) were exposed to a male BO while watching either criminal or neutral videos (encoding phase) and were subsequently asked to recognize the target BO within either a congruent or an incongruent visual context (retrieval phase). The results showed that criminal videos were rated as more vivid, unpleasant, and arousing than neutral videos both at encoding and retrieval. Moreover, in terms of BO ratings, we found that odor intensity and arousal allow to distinguish the target from the foils when congruent criminal information is presented at encoding and retrieval. Finally, the accuracy performance was not significantly different from chance level for either condition. These findings provide insights on how olfactory memories are processed in emotional situations.

Parameterizing water quality analysis and simulation program (WASP) for carbon-based nanomaterials

EPA Science Inventory

Carbon nanotubes (CNT) and graphenes are among the most popular carbon-based nanomaterials due to their unique electronic, mechanic and structural properties. Exposure modeling of these nanomaterials in the aquatic environment is necessary to predict the fate of these materials. ...

Low-dimensional carbon and MXene-based electrochemical capacitor electrodes.

PubMed

Yoon, Yeoheung; Lee, Keunsik; Lee, Hyoyoung

2016-04-29

Due to their unique structure and outstanding intrinsic physical properties such as extraordinarily high electrical conductivity, large surface area, and various chemical functionalities, low-dimension-based materials exhibit great potential for application in electrochemical capacitors (ECs). The electrical properties of electrochemical capacitors are determined by the electrode materials. Because energy charge storage is a surface process, the surface properties of the electrode materials greatly influence the electrochemical performance of the cell. Recently, graphene, a single layer of sp(2)-bonded carbon atoms arrayed into two-dimensional carbon nanomaterial, has attracted wide interest as an electrode material for electrochemical capacitor applications due to its unique properties, including a high electrical conductivity and large surface area. Several low-dimensional materials with large surface areas and high conductivity such as onion-like carbons (OLCs), carbide-derived carbons (CDCs), carbon nanotubes (CNTs), graphene, metal hydroxide, transition metal dichalcogenides (TMDs), and most recently MXene, have been developed for electrochemical capacitors. Therefore, it is useful to understand the current issues of low-dimensional materials and their device applications.

High-flux water desalination with interfacial salt sieving effect in nanoporous carbon composite membranes

NASA Astrophysics Data System (ADS)

Chen, Wei; Chen, Shuyu; Liang, Tengfei; Zhang, Qiang; Fan, Zhongli; Yin, Hang; Huang, Kuo-Wei; Zhang, Xixiang; Lai, Zhiping; Sheng, Ping

2018-04-01

Freshwater flux and energy consumption are two important benchmarks for the membrane desalination process. Here, we show that nanoporous carbon composite membranes, which comprise a layer of porous carbon fibre structures grown on a porous ceramic substrate, can exhibit 100% desalination and a freshwater flux that is 3-20 times higher than existing polymeric membranes. Thermal accounting experiments demonstrated that the carbon composite membrane saved over 80% of the latent heat consumption. Theoretical calculations combined with molecular dynamics simulations revealed the unique microscopic process occurring in the membrane. When the salt solution is stopped at the openings to the nanoscale porous channels and forms a meniscus, the vapour can rapidly transport across the nanoscale gap to condense on the permeate side. This process is driven by the chemical potential gradient and aided by the unique smoothness of the carbon surface. The high thermal conductivity of the carbon composite membrane ensures that most of the latent heat is recovered.

Multiplexed SNP genotyping using the Qbead™ system: a quantum dot-encoded microsphere-based assay

PubMed Central

Xu, Hongxia; Sha, Michael Y.; Wong, Edith Y.; Uphoff, Janet; Xu, Yanzhang; Treadway, Joseph A.; Truong, Anh; O’Brien, Eamonn; Asquith, Steven; Stubbins, Michael; Spurr, Nigel K.; Lai, Eric H.; Mahoney, Walt

2003-01-01

We have developed a new method using the Qbead™ system for high-throughput genotyping of single nucleotide polymorphisms (SNPs). The Qbead system employs fluorescent Qdot™ semiconductor nanocrystals, also known as quantum dots, to encode microspheres that subsequently can be used as a platform for multiplexed assays. By combining mixtures of quantum dots with distinct emission wavelengths and intensities, unique spectral ‘barcodes’ are created that enable the high levels of multiplexing required for complex genetic analyses. Here, we applied the Qbead system to SNP genotyping by encoding microspheres conjugated to allele-specific oligonucleotides. After hybridization of oligonucleotides to amplicons produced by multiplexed PCR of genomic DNA, individual microspheres are analyzed by flow cytometry and each SNP is distinguished by its unique spectral barcode. Using 10 model SNPs, we validated the Qbead system as an accurate and reliable technique for multiplexed SNP genotyping. By modifying the types of probes conjugated to microspheres, the Qbead system can easily be adapted to other assay chemistries for SNP genotyping as well as to other applications such as analysis of gene expression and protein–protein interactions. With its capability for high-throughput automation, the Qbead system has the potential to be a robust and cost-effective platform for a number of applications. PMID:12682378

Phenotypic and genomic survey on organic acid utilization profile of Pseudomonas mendocina strain S5.2, a vineyard soil isolate.

PubMed

Chong, Teik Min; Chen, Jian-Woon; See-Too, Wah-Seng; Yu, Choo-Yee; Ang, Geik-Yong; Lim, Yan Lue; Yin, Wai-Fong; Grandclément, Catherine; Faure, Denis; Dessaux, Yves; Chan, Kok-Gan

2017-12-01

Root exudates are chemical compounds that are released from living plant roots and provide significant energy, carbon, nitrogen and phosphorus sources for microbes inhabiting the rhizosphere. The exudates shape the microflora associated with the plant, as well as influences the plant health and productivity. Therefore, a better understanding of the trophic link that is established between the plant and the associated bacteria is necessary. In this study, a comprehensive survey on the utilization of grapevine and rootstock related organic acids were conducted on a vineyard soil isolate which is Pseudomonas mendocina strain S5.2. Phenotype microarray analysis has demonstrated that this strain can utilize several organic acids including lactic acid, succinic acid, malic acid, citric acid and fumaric acid as sole growth substrates. Complete genome analysis using single molecule real-time technology revealed that the genome consists of a 5,120,146 bp circular chromosome and a 252,328 bp megaplasmid. A series of genetic determinants associated with the carbon utilization signature of the strain were subsequently identified in the chromosome. Of note, the coexistence of genes encoding several iron-sulfur cluster independent isoenzymes in the genome indicated the importance of these enzymes in the events of iron deficiency. Synteny and comparative analysis have also unraveled the unique features of D-lactate dehydrogenase of strain S5.2 in the study. Collective information of this work has provided insights on the metabolic role of this strain in vineyard soil rhizosphere.

Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices.

PubMed

Dehmer, Matthias; Emmert-Streib, Frank; Shi, Yongtang; Stefu, Monica; Tripathi, Shailesh

2015-01-01

In this paper, we study the discrimination power of graph measures that are based on graph-theoretical matrices. The paper generalizes the work of [M. Dehmer, M. Moosbrugger. Y. Shi, Encoding structural information uniquely with polynomial-based descriptors by employing the Randić matrix, Applied Mathematics and Computation, 268(2015), 164-168]. We demonstrate that by using the new functional matrix approach, exhaustively generated graphs can be discriminated more uniquely than shown in the mentioned previous work.

Discrimination Power of Polynomial-Based Descriptors for Graphs by Using Functional Matrices

PubMed Central

Dehmer, Matthias; Emmert-Streib, Frank; Shi, Yongtang; Stefu, Monica; Tripathi, Shailesh

2015-01-01

In this paper, we study the discrimination power of graph measures that are based on graph-theoretical matrices. The paper generalizes the work of [M. Dehmer, M. Moosbrugger. Y. Shi, Encoding structural information uniquely with polynomial-based descriptors by employing the Randić matrix, Applied Mathematics and Computation, 268(2015), 164–168]. We demonstrate that by using the new functional matrix approach, exhaustively generated graphs can be discriminated more uniquely than shown in the mentioned previous work. PMID:26479495

Carbohydrate utilization and metabolism is highly differentiated in Agaricus bisporus

PubMed Central

2013-01-01

Background Agaricus bisporus is commercially grown on compost, in which the available carbon sources consist mainly of plant-derived polysaccharides that are built out of various different constituent monosaccharides. The major constituent monosaccharides of these polysaccharides are glucose, xylose, and arabinose, while smaller amounts of galactose, glucuronic acid, rhamnose and mannose are also present. Results In this study, genes encoding putative enzymes from carbon metabolism were identified and their expression was studied in different growth stages of A. bisporus. We correlated the expression of genes encoding plant and fungal polysaccharide modifying enzymes identified in the A. bisporus genome to the soluble carbohydrates and the composition of mycelium grown compost, casing layer and fruiting bodies. Conclusions The compost grown vegetative mycelium of A. bisporus consumes a wide variety of monosaccharides. However, in fruiting bodies only hexose catabolism occurs, and no accumulation of other sugars was observed. This suggests that only hexoses or their conversion products are transported from the vegetative mycelium to the fruiting body, while the other sugars likely provide energy for growth and maintenance of the vegetative mycelium. Clear correlations were found between expression of the genes and composition of carbohydrates. Genes encoding plant cell wall polysaccharide degrading enzymes were mainly expressed in compost-grown mycelium, and largely absent in fruiting bodies. In contrast, genes encoding fungal cell wall polysaccharide modifying enzymes were expressed in both fruiting bodies and vegetative mycelium, but different gene sets were expressed in these samples. PMID:24074284

The influence of strategic encoding on false memory in patients with mild cognitive impairment and Alzheimer's disease dementia.

PubMed

Tat, Michelle J; Soonsawat, Anothai; Nagle, Corinne B; Deason, Rebecca G; O'Connor, Maureen K; Budson, Andrew E

2016-11-01

Patients with Alzheimer's disease (AD) dementia exhibit high rates of memory distortions in addition to their impairments in episodic memory. Several investigations have demonstrated that when healthy individuals (young and old) engaged in an encoding strategy that emphasized the uniqueness of study items (an item-specific encoding strategy), they were able to improve their discrimination between old items and unstudied critical lure items in a false memory task. In the present study we examined if patients with AD could also improve their memory discrimination when engaging in an item-specific encoding strategy. Healthy older adult controls, patients with mild cognitive impairment (MCI) due to AD, and patients with mild AD dementia were asked to study lists of categorized words. In the Item-Specific condition, participants were asked to provide a unique detail or personal experience with each study item. In the Relational condition, they were asked to determine how each item in the list was related to the others. To assess the influence of both strategies, recall and recognition memory tests were administered. Overall, both patient groups exhibited poorer memory in both recall and recognition tests compared to controls. In terms of recognition, healthy older controls and patients with MCI due to AD exhibited improved memory discrimination in the Item-Specific condition compared to the Relational condition, whereas patients with AD dementia did not. We speculate that patients with MCI due to AD use intact frontal networks to effectively engage in this strategy. Published by Elsevier Inc.

The influence of strategic encoding on false memory in patients with mild cognitive impairment and Alzheimer’s disease dementia

PubMed Central

Tat, Michelle J.; Soonsawat, Anothai; Nagle, Corinne B.; Deason, Rebecca G.; O’Connor, Maureen K.; Budson, Andrew E.

2018-01-01

Patients with Alzheimer’s disease (AD) dementia exhibit high rates of memory distortions in addition to their impairments in episodic memory. Several investigations have demonstrated that when healthy individuals (young and old) engaged in an encoding strategy that emphasized the uniqueness of study items (an item-specific encoding strategy), they were able to improve their discrimination between old items and unstudied critical lure items in a false memory task. In the present study we examined if patients with AD could also improve their memory discrimination when engaging in an item-specific encoding strategy. Healthy older adult controls, patients with mild cognitive impairment (MCI) due to AD, and patients with mild AD dementia were asked to study lists of categorized words. In the Item-Specific condition, participants were asked to provide a unique detail or personal experience with each study item. In the Relational condition, they were asked to determine how each item in the list was related to the others. To assess the influence of both strategies, recall and recognition memory tests were administered. Overall, both patient groups exhibited poorer memory in both recall and recognition tests compared to controls. In terms of recognition, healthy older controls and patients with MCI due to AD exhibited improved memory discrimination in the Item-Specific condition compared to the Relational condition, whereas patients with AD dementia did not. We speculate that patients with MCI due to AD use intact frontal networks to effectively engage in this strategy. PMID:27643951

Marek's disease virus protein kinase gene identified within the short unique region of the viral genome is not essential for viral replication in cell culture and vaccine-induced immunity in chickens.

PubMed

Sakaguchi, M; Urakawa, T; Hirayama, Y; Miki, N; Yamamoto, M; Zhu, G S; Hirai, K

1993-07-01

The open reading frame (ORF) of 1206 bp within the short unique region (Us) of Marek's disease virus type 1 (MDV1) shows significant homology with the herpes simplex virus type 1 US3 gene encoding protein kinase (PK). The lacZ gene of Escherichia coli was inserted within the ORF, designated MDV1-US3, of MDV1 K544 strain DNA by homologous recombination. The plaque-purified recombinant MDV1 stably expressed the beta-galactosidase encoded by the inserted lacZ gene in infected cells and replicated well as the parental K544 strain. Antibodies against both MDV1 antigen and beta-galactosidase were detected in the sera of chickens immunized with recombinant MDV1. Chickens vaccinated with the recombinant MDV1 were protected from challenge with virulent MDV1. The MDV1 US3 gene expressed by a baculovirus vector encoded a 44-kDa protein. Mouse antisera against the 44-kDa protein reacted with two proteins of 44 and 45 kDa in extracts of cells infected with MDV1 but not with MDV types 2 or 3. The PK activity was detected in immune complexes of the anti-44-kDa sera with extracts of cells infected with MDV1 but not with the recombinant MDV1. Thus, PK encoded from the MDV1-US3 is not essential for virus replication in cell culture and vaccine-induced immunity.

Carbon-carbon cylinder block

NASA Technical Reports Server (NTRS)

Ransone, Philip O. (Inventor)

1995-01-01

A lightweight cylinder block composed of carbon-carbon is disclosed. The use of carbon-carbon over conventional materials, such as cast iron or aluminum, reduces the weight of the cylinder block and improves thermal efficiency of the internal combustion reciprocating engine. Due to the negligible coefficient of thermal expansion and unique strength at elevated temperatures of carbon-carbon, the piston-to-cylinder wall clearance can be small, especially when the carbon-carbon cylinder block is used in conjunction with a carbon-carbon piston. Use of the carbon-carbon cylinder has the effect of reducing the weight of other reciprocating engine components allowing the piston to run at higher speeds and improving specific engine performance.

Lignin peroxidase gene family of Phanerochaete chrysosporium : complex regulation by carbon and nitrogen limitation and identification of a second dimorphic chromosome

Treesearch

Philip Stewart; Philip Kersten; Amber J. Vanden Wymelenberg; Jill A. Gaskell; Daniel Cullen

1992-01-01

Lignin peroxidases (LiP) of Phanerochaete chrysosporium are encoded by a family of six closely related genes. Five LiP genes have been localized to the same dimorphic chromosome. In this investigation, relative transcript levels of the LiP genes were determined. Transcripts of the LiPA, LiPB, and 0282 genes were at similar levels in both carbon-and nitrogen-limited...

Xylan utilization in human gut commensal bacteria is orchestrated by unique modular organization of polysaccharide-degrading enzymes.

PubMed

Zhang, Meiling; Chekan, Jonathan R; Dodd, Dylan; Hong, Pei-Ying; Radlinski, Lauren; Revindran, Vanessa; Nair, Satish K; Mackie, Roderick I; Cann, Isaac

2014-09-02

Enzymes that degrade dietary and host-derived glycans represent the most abundant functional activities encoded by genes unique to the human gut microbiome. However, the biochemical activities of a vast majority of the glycan-degrading enzymes are poorly understood. Here, we use transcriptome sequencing to understand the diversity of genes expressed by the human gut bacteria Bacteroides intestinalis and Bacteroides ovatus grown in monoculture with the abundant dietary polysaccharide xylan. The most highly induced carbohydrate active genes encode a unique glycoside hydrolase (GH) family 10 endoxylanase (BiXyn10A or BACINT_04215 and BACOVA_04390) that is highly conserved in the Bacteroidetes xylan utilization system. The BiXyn10A modular architecture consists of a GH10 catalytic module disrupted by a 250 amino acid sequence of unknown function. Biochemical analysis of BiXyn10A demonstrated that such insertion sequences encode a new family of carbohydrate-binding modules (CBMs) that binds to xylose-configured oligosaccharide/polysaccharide ligands, the substrate of the BiXyn10A enzymatic activity. The crystal structures of CBM1 from BiXyn10A (1.8 Å), a cocomplex of BiXyn10A CBM1 with xylohexaose (1.14 Å), and the CBM from its homolog in the Prevotella bryantii B14 Xyn10C (1.68 Å) reveal an unanticipated mode for ligand binding. A minimal enzyme mix, composed of the gene products of four of the most highly up-regulated genes during growth on wheat arabinoxylan, depolymerizes the polysaccharide into its component sugars. The combined biochemical and biophysical studies presented here provide a framework for understanding fiber metabolism by an important group within the commensal bacterial population known to influence human health.

Baseline and projected future carbon storage and carbon fluxes in ecosystems of Hawai‘i

Treesearch

P.C. Selmants; C.P. Giardina; J.D. Jacobi; Zhiliang  Zhu

2017-01-01

Hawaii is unique among the United States because of its tropical climate, geographic isolation, high rates of species endemism and discontinuous land mass. The year-round warm, wet climate on the windward sides of islands and the high fertility of relatively young volcanically derived soils are ideal conditions for carbon input, storage and carbon sequestration in...

Gas and aerosol carbon in California: comparison of measurements and model predictions in Pasadena and Bakersfield.

EPA Science Inventory

Co-located measurements of fine particulate matter (PM2.5) organic carbon (OC), elemental carbon, radiocarbon (14C), speciated volatile organic compounds (VOCs),and OH radicals during the CalNex field campaign provide a unique opportunity to evaluate the Community Multiscale Air ...

Influence of acid functionalization on the cardio-pulmonary toxicity of carbon nanotubes and carbon black in mice

EPA Science Inventory

Engineered carbon nanotubes are being developed for a wide range of industrial and medical applications. Because of their unique properties, nanotubes can impose potentially toxic effects, particularly if they have been modified to express functionally reactive chemical groups o...

Unconscious relational inference recruits the hippocampus.

PubMed

Reber, Thomas P; Luechinger, Roger; Boesiger, Peter; Henke, Katharina

2012-05-02

Relational inference denotes the capacity to encode, flexibly retrieve, and integrate multiple memories to combine past experiences to update knowledge and improve decision-making in new situations. Although relational inference is thought to depend on the hippocampus and consciousness, we now show in young, healthy men that it may occur outside consciousness but still recruits the hippocampus. In temporally distinct and unique subliminal episodes, we presented word pairs that either overlapped ("winter-red", "red-computer") or not. Effects of unconscious relational inference emerged in reaction times recorded during unconscious encoding and in the outcome of decisions made 1 min later at test, when participants judged the semantic relatedness of two supraliminal words. These words were either episodically related through a common word ("winter-computer" related through "red") or unrelated. Hippocampal activity increased during the unconscious encoding of overlapping versus nonoverlapping word pairs and during the unconscious retrieval of episodically related versus unrelated words. Furthermore, hippocampal activity during unconscious encoding predicted the outcome of decisions made at test. Hence, unconscious inference may influence decision-making in new situations.

Horizontal gene transfer of chromosomal Type II toxin-antitoxin systems of Escherichia coli.

PubMed

Ramisetty, Bhaskar Chandra Mohan; Santhosh, Ramachandran Sarojini

2016-02-01

Type II toxin-antitoxin systems (TAs) are small autoregulated bicistronic operons that encode a toxin protein with the potential to inhibit metabolic processes and an antitoxin protein to neutralize the toxin. Most of the bacterial genomes encode multiple TAs. However, the diversity and accumulation of TAs on bacterial genomes and its physiological implications are highly debated. Here we provide evidence that Escherichia coli chromosomal TAs (encoding RNase toxins) are 'acquired' DNA likely originated from heterologous DNA and are the smallest known autoregulated operons with the potential for horizontal propagation. Sequence analyses revealed that integration of TAs into the bacterial genome is unique and contributes to variations in the coding and/or regulatory regions of flanking host genome sequences. Plasmids and genomes encoding identical TAs of natural isolates are mutually exclusive. Chromosomal TAs might play significant roles in the evolution and ecology of bacteria by contributing to host genome variation and by moderation of plasmid maintenance. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Multi-voxel patterns of visual category representation during episodic encoding are predictive of subsequent memory

PubMed Central

Kuhl, Brice A.; Rissman, Jesse; Wagner, Anthony D.

2012-01-01

Successful encoding of episodic memories is thought to depend on contributions from prefrontal and temporal lobe structures. Neural processes that contribute to successful encoding have been extensively explored through univariate analyses of neuroimaging data that compare mean activity levels elicited during the encoding of events that are subsequently remembered vs. those subsequently forgotten. Here, we applied pattern classification to fMRI data to assess the degree to which distributed patterns of activity within prefrontal and temporal lobe structures elicited during the encoding of word-image pairs were diagnostic of the visual category (Face or Scene) of the encoded image. We then assessed whether representation of category information was predictive of subsequent memory. Classification analyses indicated that temporal lobe structures contained information robustly diagnostic of visual category. Information in prefrontal cortex was less diagnostic of visual category, but was nonetheless associated with highly reliable classifier-based evidence for category representation. Critically, trials associated with greater classifier-based estimates of category representation in temporal and prefrontal regions were associated with a higher probability of subsequent remembering. Finally, consideration of trial-by-trial variance in classifier-based measures of category representation revealed positive correlations between prefrontal and temporal lobe representations, with the strength of these correlations varying as a function of the category of image being encoded. Together, these results indicate that multi-voxel representations of encoded information can provide unique insights into how visual experiences are transformed into episodic memories. PMID:21925190

Neural activity in the hippocampus and perirhinal cortex during encoding is associated with the durability of episodic memory.

PubMed

Carr, Valerie A; Viskontas, Indre V; Engel, Stephen A; Knowlton, Barbara J

2010-11-01

Studies examining medial temporal lobe (MTL) involvement in memory formation typically assess memory performance after a single, short delay. Thus, the relationship between MTL encoding activity and memory durability over time remains poorly characterized. To explore this relationship, we scanned participants using high-resolution functional imaging of the MTL as they encoded object pairs; using the remember/know paradigm, we then assessed memory performance for studied items both 10 min and 1 week later. Encoding trials were classified as either subsequently recollected across both delays, transiently recollected (i.e., recollected at 10 min but not after 1 week), consistently familiar, or consistently forgotten. Activity in perirhinal cortex (PRC) and a hippocampal subfield comprising the dentate gyrus and CA fields 2 and 3 reflected successful encoding only when items were recollected consistently across both delays. Furthermore, in PRC, encoding activity for items that later were consistently recollected was significantly greater than that for transiently recollected and consistently familiar items. Parahippocampal cortex, in contrast, showed a subsequent memory effect during encoding of items that were recollected after 10 min, regardless of whether they also were recollected after 1 week. These data suggest that MTL subfields contribute uniquely to the formation of memories that endure over time, and highlight a role for PRC in supporting subsequent durable episodic recollection.

Associative Encoding and Retrieval Are Predicted by Functional Connectivity in Distinct Hippocampal Area CA1 Pathways

PubMed Central

Duncan, Katherine; Tompary, Alexa

2014-01-01

Determining how the hippocampus supports the unique demands of memory encoding and retrieval is fundamental for understanding the biological basis of episodic memory. One possibility proposed by theoretical models is that the distinct computational demands of encoding and retrieval are accommodated by shifts in the functional interaction between the hippocampal CA1 subregion and its input structures. However, empirical tests of this hypothesis are lacking. To test this in humans, we used high-resolution fMRI to measure functional connectivity between hippocampal area CA1 and regions of the medial temporal lobe and midbrain during extended blocks of associative encoding and retrieval tasks. We found evidence for a double dissociation between the pathways supporting successful encoding and retrieval. Specifically, during the associative encoding task, but not the retrieval task, functional connectivity only between area CA1 and the ventral tegmental area predicted associative long-term memory. In contrast, connectivity between area CA1 and DG/CA3 was greater, on average, during the retrieval task compared with the encoding task, and, importantly, the strength of this connectivity significantly correlated with retrieval success. Together, these findings serve as an important first step toward understanding how the demands of fundamental memory processes may be met by changes in the relative strength of connectivity within hippocampal pathways. PMID:25143600

A unique research partnership investigating the fundamental principles of subsurface carbon dioxide behaviour and carbonate reservoirs

NASA Astrophysics Data System (ADS)

Macdonald, I.; Blunt, M. J.; Maitland, G. C.

2017-12-01

Carbonate reservoirs hold the majority of CO2 sequestration potential, however, they are also more complicated than sandstone reservoirs in terms of heterogeneity and potential reactivity impact on operations. There are both significant carbonate reservoir CO2 sinks and CO2 point sources around Qatar making carbon capture and storage a potential decarbonisation pathway. The Qatar Carbonates and Carbon Storage Research Centre (QCCSRC) was formed in 2009 to address the gaps in our current knowledge of both local carbonate reservoir platforms and how CO2 would behave post sequestration. Our work spans 35 graduated PhD students, 10 still studying, 29 post-doctoral researchers, 18 faculty members all aided by 5 support staff and more than 100 MSc and summer students from 30 different countries, the centre has published over 150 papers in over 40 different journals. Our research is based within the Department of Chemical Engineering and the Department of Earth Science and Engineering. Our team annually attends over 20 conferences world-wide to disseminate our findings and activity engage in outreach events (UNFCCC, science festivals, social media, science bars, school visits, etc.). QCCSRC is a research framework agreement over 10 years and valued at $70 million between Qatar Petroleum, Shell, the Qatar Science and Technology Park and Imperial College London bringing together each organisation's unique capabilities. This novel quadruple helix management structure is responsible for the largest single industrially funded research programme conducted at Imperial College London. Our research has focused on data to create and/or improve predictive models for CO2 storage in carbonate reservoirs. Our three broad thematic areas include: Rocks : Rock-fluid interactions : Fluid-fluid interactions and are supported by 5 laboratories. Overall this unique programme is an example of how to approach grand challenges in the energy-carbon dilemma through long-term and multidisciplinary cooperative research.

Expression of Marek's disease virus oncoprotein Meq during infection in the natural host

USDA-ARS?s Scientific Manuscript database

Marek's disease virus (MDV, Gallid herpesvirus 2) causes a lymphoproliferative disease known as Marek's disease (MD), which is unique among alphaherpesviruses as the viral genome encodes an oncoprotein, Meq. Previous studies, using cultured fibroblasts and MDV-transformed lymphoblastoid cell lines, ...

48 CFR 252.211-7003 - Item identification and valuation.

Code of Federal Regulations, 2013 CFR

2013-10-01

..., used to retrieve data encoded on machine-readable media. Concatenated unique item identifier means— (1... (or controlling) authority for the enterprise identifier. Item means a single hardware article or a...-readable means an automatic identification technology media, such as bar codes, contact memory buttons...

48 CFR 252.211-7003 - Item identification and valuation.

Code of Federal Regulations, 2011 CFR

2011-10-01

..., used to retrieve data encoded on machine-readable media. Concatenated unique item identifier means— (1... (or controlling) authority for the enterprise identifier. Item means a single hardware article or a...-readable means an automatic identification technology media, such as bar codes, contact memory buttons...

48 CFR 252.211-7003 - Item identification and valuation.

Code of Federal Regulations, 2012 CFR

2012-10-01

..., used to retrieve data encoded on machine-readable media. Concatenated unique item identifier means— (1... (or controlling) authority for the enterprise identifier. Item means a single hardware article or a...-readable means an automatic identification technology media, such as bar codes, contact memory buttons...

Mutation in LEMD3 (Man1) Associated with Osteopoikilosis and Late-Onset Generalized Morphea: A New Buschke-Ollendorf Syndrome Variant

PubMed Central

Korman, Benjamin; Wei, Jun; Laumann, Anne; Ferguson, Polly; Varga, John

2016-01-01

Introduction. Buschke-Ollendorf syndrome (BOS) is an uncommon syndrome characterized by osteopoikilosis and other bone abnormalities, accompanied by skin lesions, most frequently connective tissue nevi. BOS is caused by mutations in the LEMD3 gene, which encodes the inner nuclear membrane protein Man1. We describe a unique case of osteopoikilosis associated with late-onset localized scleroderma and familial LEMD3 mutations. Case Report. A 72-year-old woman presented with adult-onset diffuse morphea and bullous skin lesions. Evaluation revealed multiple hyperostotic lesions (osteopoikilosis) suggestive of BOS. DNA sequencing identified a previously undescribed nonsense mutation (Trp621X) in the LEMD3 gene encoding Man1. Two additional family members were found to have osteopoikilosis and carry the same LEMD3 mutation. Conclusions and Relevance. We report a unique familial LEMD3 mutation in an individual with osteopoikilosis and late-onset morphea. We propose that this constellation represents a novel syndromic variant of BOS. PMID:27382493

Wearable Spiral Passive Electromagnetic Sensor (SPES) glove for sign language recognition of alphabet letters and numbers: a preliminary study

NASA Astrophysics Data System (ADS)

Iervolino, Onorio; Meo, Michele

2017-04-01

Sign language is a method of communication for deaf-mute people with articulated gestures and postures of hands and fingers to represent alphabet letters or complete words. Recognizing gestures is a difficult task, due to intrapersonal and interpersonal variations in performing them. This paper investigates the use of Spiral Passive Electromagnetic Sensor (SPES) as a motion recognition tool. An instrumented glove integrated with wearable multi-SPES sensors was developed to encode data and provide a unique response for each hand gesture. The device can be used for recognition of gestures; motion control and well-defined gesture sets such as sign languages. Each specific gesture was associated to a unique sensor response. The gloves encode data regarding the gesture directly in the frequency spectrum response of the SPES. The absence of chip or complex electronic circuit make the gloves light and comfortable to wear. Results showed encouraging data to use SPES in wearable applications.

Analysis of strain-specific genes in glutamic acid-producing Corynebacterium glutamicum ssp. lactofermentum AJ 1511.

PubMed

Nishio, Yousuke; Koseki, Chie; Tonouchi, Naoto; Matsui, Kazuhiko; Sugimoto, Shinichi; Usuda, Yoshihiro

2017-07-11

Strains of the bacterium, Corynebacterium glutamicum, are widely used for the industrial production of L-glutamic acid and various other substances. C. glutamicum ssp. lactofermentum AJ 1511, formerly classified as Brevibacterium lactofermentum, and the closely related C. glutamicum ATCC 13032 have been used as industrial strains for more than 50 years. We determined the whole genome sequence of C. glutamicum AJ 1511 and performed genome-wide comparative analysis with C. glutamicum ATCC 13032 to determine strain-specific genetic differences. This analysis revealed that the genomes of the two industrial strains are highly similar despite the phenotypic differences between the two strains. Both strains harbored unique genes but gene transpositions or inversions were not observed. The largest unique region, a 220-kb AT-rich region located between 1.78 and 2.00 Mb position in C. glutamicum ATCC 13032 genome, was missing in the genome of C. glutamicum AJ 1511. The next two largest unique regions were present in C. glutamicum AJ 1511. The first region (413-484 kb position) contains several predicted transport proteins, enzymes involved in sugar metabolism, and transposases. The second region (1.47-1.50 Mb position) encodes restriction modification systems. A gene predicted to encode NADH-dependent glutamate dehydrogenase, which is involved in L-glutamate biosynthesis, is present in C. glutamicum AJ 1511. Strain-specific genes identified in this study are likely to govern phenotypes unique to each strain.

A Naturally Encoded Dipeptide Handle for Bioorthogonal Chan-Lam Coupling.

PubMed

Ohata, Jun; Zeng, Yimeng; Segatori, Laura; Ball, Zachary T

2018-04-03

Manipulation of biomacromolecules is ideally achieved through unique and bioorthogonal chemical reactions of genetically encoded, naturally occurring functional groups. The toolkit of methods for site-specific conjugation is limited by selectivity concerns and a dearth of naturally occurring functional groups with orthogonal reactivity. We report that pyroglutamate amide N-H bonds exhibit bioorthogonal copper-catalyzed Chan-Lam coupling at pyroglutamate-histidine dipeptide sequences. The pyroglutamate residue is readily incorporated into proteins of interest by natural enzymatic pathways, allowing specific bioconjugation at a minimalist dipeptide tag. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Memorization and recall of very long lists accounted for within the Long-Term Working Memory framework.

PubMed

Hu, Yi; Ericsson, K Anders

2012-06-01

In a recent paper, Hu, Ericsson, Yang, and Lu (2009) found that an ability to memorize very long lists of digits is not mediated by the same mechanisms as exceptional memory for rapidly presented lists, which has been the traditional focus of laboratory research. Chao Lu is the holder of the Guinness World Record for reciting the most decimal positions of pi, yet he lacks an exceptional memory span for digits. In the first part of this paper we analyzed the reliability and structure of his reported encodings for lists of 300 digits and his application of the story mnemonic. Next, his study and recall times for lists of digits were analyzed to test hypotheses about his detailed encoding processes, and cued-recall performance was used to assess the structure of his encodings. Three experiments were then designed to interfere with the uniqueness of Chao Lu's story encodings, and evidence was found for his remarkable ability to adapt his encoding processes to reduce the interference. Finally, we show how his skills for encoding and recalling long lists can be accounted for within the theoretical framework of Ericsson and Kintsch's (1995) Long-Term Working Memory. Copyright © 2012 Elsevier Inc. All rights reserved.

Carbon with hierarchical pores from carbonized metal-organic frameworks for lithium sulphur batteries.

PubMed

Xi, Kai; Cao, Shuai; Peng, Xiaoyu; Ducati, Caterina; Kumar, R Vasant; Cheetham, Anthony K

2013-03-18

This paper presents a novel method and rationale for utilizing carbonized MOFs for sulphur loading to fabricate cathode structures for lithium-sulphur batteries. Unique carbon materials with differing hierarchical pore structures were synthesized from four types of zinc-containing metal-organic frameworks (MOFs). It is found that cathode materials made from MOFs-derived carbons with higher mesopore (2-50 nm) volumes exhibit increased initial discharge capacities, whereas carbons with higher micropore (<2 nm) volumes lead to cathode materials with better cycle stability.

Role of penA polymorphisms for penicillin susceptibility in Neisseria lactamica and Neisseria meningitidis.

PubMed

Karch, André; Vogel, Ulrich; Claus, Heike

2015-10-01

In meningococci, reduced penicillin susceptibility is associated with five specific mutations in the transpeptidase region of penicillin binding protein 2 (PBP2). We showed that the same set of mutations was present in 64 of 123 Neisseria lactamica strains obtained from a carriage study (MIC range: 0.125-2.0mg/L). The PBP2 encoding penA alleles in these strains were genetically similar to those found in intermediate resistant meningococci suggesting frequent interspecies genetic exchange. Fifty-six N. lactamica isolates with mostly lower penicillin MICs (range: 0.064-0.38mg/L) exhibited only three of the five mutations. The corresponding penA alleles were unique to N. lactamica and formed a distinct genetic clade. PenA alleles with no mutations on the other hand were unique to meningococci. Under penicillin selective pressure, genetic transformation of N. lactamica penA alleles in meningococci was only possible for alleles encoding five mutations, but not for those encoding three mutations; the transfer resulted in MICs comparable to those of meningococci harboring penA alleles that encoded PBP2 with five mutations, but considerably lower than those of the corresponding N. lactamica donor strains. Due to a transformation barrier the complete N. lactamica penA could not be transformed into N. meningitidis. In summary, penicillin MICs in N. lactamica were associated with the number of mutations in the transpeptidase region of PBP2. Evidence for interspecific genetic transfer was only observed for penA alleles associated with higher MICs, suggesting that alleles encoding only three mutations in the transpeptidase region are biologically not effective in N. meningitidis. Factors other than PBP2 seem to be responsible for the high levels of penicillin resistance in N. lactamica. A reduction of penicillin susceptibility in N. meningitidis by horizontal gene transfer from N. lactamica is unlikely to happen. Copyright © 2015 Elsevier GmbH. All rights reserved.

Method for Making a Carbon-Carbon Cylinder Block

NASA Technical Reports Server (NTRS)

Ransone, Phillip O. (Inventor)

1997-01-01

A method for making a lightweight cylinder block composed of carbon-carbon is disclosed. The use of carbon-carbon over conventional materials. such as cast iron or aluminum, reduces the weight of the cylinder block and improves thermal efficiency of the internal combustion reciprocating engine. Due to the negligible coefficient of thermal expansion and unique strength at elevated temperatures of carbon-carbon, the piston-to-cylinder wall clearance can be small, especially when the carbon-carbon cylinder block is used in conjunction with a carbon-carbon piston. Use of the carbon-carbon cylinder block has the effect of reducing the weight of other reciprocating engine components allowing the piston to run at higher speeds and improving specific engine performance.

New Perspectives on Acetate and One-Carbon Metabolism in the Methanoarchaea

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

Ferry, James

Carbonic anhydrases catalyze the reversible hydration of carbon dioxide to bicarbonate. Although widespread in prokaryotes of the domains Bacteria and Archaea, few have been investigated and the physiological functions are largely unknown. Carbonic anhydrases are of biotechnological interest for carbon dioxide capture and sequestration at point sources. Prokaryotes encode three independently evolved classes. The alpha-class is restricted to a few pathogens and the other two are uniformly distributed in phylogenetically and physiologically diverse species. Although wide-spread in prokaryotes, only three gamma-class enzymes have been biochemically characterized and the physiological functions have not been investigated. The gamma-class is prominent in anaerobicmore » acetate-utilizing methane-producing species of the genus Methanosarcina that encode three subclasses. Enzymes from two of the subclasses, Cam and CamH from Methanosarcina thermophila, have been characterized and found to utilize iron in the active site which is the first example of an iron-containing carbonic anhydrase. No representative of the third subclass has been isolated, although this subclass constitutes the great majority of the β-class. This grant application proposed to characterize gamma-class carbonic anhydrases from diverse anaerobic prokaryotes from the domains Bacteria and Archaea to broaden the understanding of this enzyme. In particular, the three subclasses present the genetically tractable acetate-utilizing methanogen Methanosarcina acetivorans will be investigated to extend studies of acetate and one-carbon metabolism in this species. A genetic approach will be taken to ascertain the physiological functions. It is also proposed to delve deeper into the mechanism of Cam from M. thermophila, the archetype of the gamma-class, via a high resolution neutron structure and kinetic analysis of site-specific amino acid replacement variants. In the course of the investigation, goals were added to take advantage of discoveries on enzymes responding to oxidative stress.« less

Involvement of EupR, a response regulator of the NarL/FixJ family, in the control of the uptake of the compatible solutes ectoines by the halophilic bacterium Chromohalobacter salexigens.

PubMed

Rodríguez-Moya, Javier; Argandoña, Montserrat; Reina-Bueno, Mercedes; Nieto, Joaquín J; Iglesias-Guerra, Fernando; Jebbar, Mohamed; Vargas, Carmen

2010-10-13

Osmosensing and associated signal transduction pathways have not yet been described in obligately halophilic bacteria. Chromohalobacter salexigens is a halophilic bacterium with a broad range of salt tolerance. In response to osmotic stress, it synthesizes and accumulates large amounts of the compatible solutes ectoine and hydroxyectoine. In a previous work, we showed that ectoines can be also accumulated upon transport from the external medium, and that they can be used as carbon sources at optimal, but not at low salinity. This was related to an insufficient ectoine(s) transport under these conditions. A C. salexigens Tn1732-induced mutant (CHR95) showed a delayed growth with glucose at low and optimal salinities, could not grow at high salinity, and was able to use ectoines as carbon sources at low salinity. CHR95 was affected in the transport and/or metabolism of glucose, and showed a deregulated ectoine uptake at any salinity, but it was not affected in ectoine metabolism. Transposon insertion in CHR95 caused deletion of three genes, Csal0865-Csal0867: acs, encoding an acetyl-CoA synthase, mntR, encoding a transcriptional regulator of the DtxR/MntR family, and eupR, encoding a putative two-component response regulator with a LuxR_C-like DNA-binding helix-turn-helix domain. A single mntR mutant was sensitive to manganese, suggesting that mntR encodes a manganese-dependent transcriptional regulator. Deletion of eupR led to salt-sensitivity and enabled the mutant strain to use ectoines as carbon source at low salinity. Domain analysis included EupR as a member of the NarL/FixJ family of two component response regulators. Finally, the protein encoded by Csal869, located three genes downstream of eupR was suggested to be the cognate histidine kinase of EupR. This protein was predicted to be a hybrid histidine kinase with one transmembrane and one cytoplasmic sensor domain. This work represents the first example of the involvement of a two-component response regulator in the osmoadaptation of a true halophilic bacterium. Our results pave the way to the elucidation of the signal transduction pathway involved in the control of ectoine transport in C. salexigens.

Surface display of a massively variable lipoprotein by a Legionella diversity-generating retroelement.

PubMed

Arambula, Diego; Wong, Wenge; Medhekar, Bob A; Guo, Huatao; Gingery, Mari; Czornyj, Elizabeth; Liu, Minghsun; Dey, Sanghamitra; Ghosh, Partho; Miller, Jeff F

2013-05-14

Diversity-generating retroelements (DGRs) are a unique family of retroelements that confer selective advantages to their hosts by facilitating localized DNA sequence evolution through a specialized error-prone reverse transcription process. We characterized a DGR in Legionella pneumophila, an opportunistic human pathogen that causes Legionnaires disease. The L. pneumophila DGR is found within a horizontally acquired genomic island, and it can theoretically generate 10(26) unique nucleotide sequences in its target gene, legionella determinent target A (ldtA), creating a repertoire of 10(19) distinct proteins. Expression of the L. pneumophila DGR resulted in transfer of DNA sequence information from a template repeat to a variable repeat (VR) accompanied by adenine-specific mutagenesis of progeny VRs at the 3'end of ldtA. ldtA encodes a twin-arginine translocated lipoprotein that is anchored in the outer leaflet of the outer membrane, with its C-terminal variable region surface exposed. Related DGRs were identified in L. pneumophila clinical isolates that encode unique target proteins with homologous VRs, demonstrating the adaptability of DGR components. This work characterizes a DGR that diversifies a bacterial protein and confirms the hypothesis that DGR-mediated mutagenic homing occurs through a conserved mechanism. Comparative bioinformatics predicts that surface display of massively variable proteins is a defining feature of a subset of bacterial DGRs.

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

PubMed Central

Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinIzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

2013-01-01

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP–encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. PMID:23357949

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

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

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species,more » while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.« less

Gene Discovery and Expression Profiling in the Toxin-Producing Marine Diatom, Pseudo-nitzschia Multiseries (Hasle) Hasle

DTIC Science & Technology

2004-09-01

carboxylase/oxygenase ( rubisco ) is a another principal carbon fixation enzyme, which is alleged to represent the most abundant enzyme on earth...known to have plastid-encoded rubisco , which would account for why this gene was not identified in the P. multiseries library (Hwang and Tabita, 1989...thought to have evolved in certain plants as an adaptation to the competition of oxygen with carbon dioxide for ribulose- 15-bisphosphate ( rubisco ), a

Switching between nitrogen and glucose limitation: Unraveling transcriptional dynamics in Escherichia coli.

PubMed

Löffler, Michael; Simen, Joana Danica; Müller, Jan; Jäger, Günter; Laghrami, Salaheddine; Schäferhoff, Karin; Freund, Andreas; Takors, Ralf

2017-09-20

Transcriptional control under nitrogen and carbon-limitation conditions have been well analyzed for Escherichia coli. However, the transcriptional dynamics that underlie the shift in regulatory programs from nitrogen to carbon limitation is not well studied. In the present study, cells were cultivated at steady state under nitrogen (ammonia)-limited conditions then shifted to carbon (glucose) limitation to monitor changes in transcriptional dynamics. Nitrogen limitation was found to be dominated by sigma 54 (RpoN) and sigma 38 (RpoS), whereas the "housekeeping" sigma factor 70 (RpoD) and sigma 38 regulate cellular status under glucose limitation. During the transition, nitrogen-mediated control was rapidly redeemed and mRNAs that encode active uptake systems, such as ptsG and manXYZ, were quickly amplified. Next, genes encoding facilitators such as lamB were overexpressed, followed by high affinity uptake systems such as mglABC and non-specific porins such as ompF. These regulatory programs are complex and require well-equilibrated and superior control. At the metabolome level, 2-oxoglutarate is the likely component that links carbon- and nitrogen-mediated regulation by interacting with major regulatory elements. In the case of dual glucose and ammonia limitation, sigma 24 (RpoE) appears to play a key role in orchestrating these complex regulatory networks. Copyright © 2017 Elsevier B.V. All rights reserved.

The Antisense RNA As1_flv4 in the Cyanobacterium Synechocystis sp. PCC 6803 Prevents Premature Expression of the flv4-2 Operon upon Shift in Inorganic Carbon Supply*

PubMed Central

Eisenhut, Marion; Georg, Jens; Klähn, Stephan; Sakurai, Isamu; Mustila, Henna; Zhang, Pengpeng; Hess, Wolfgang R.; Aro, Eva-Mari

2012-01-01

The functional relevance of natural cis-antisense transcripts is mostly unknown. Here we have characterized the association of three antisense RNAs and one intergenically encoded noncoding RNA with an operon that plays a crucial role in photoprotection of photosystem II under low carbon conditions in the cyanobacterium Synechocystis sp. PCC 6803. Cyanobacteria show strong gene expression dynamics in response to a shift of cells from high carbon to low levels of inorganic carbon (Ci), but the regulatory mechanisms are poorly understood. Among the most up-regulated genes in Synechocystis are flv4, sll0218, and flv2, which are organized in the flv4-2 operon. The flavodiiron proteins encoded by this operon open up an alternative electron transfer route, likely starting from the QB site in photosystem II, under photooxidative stress conditions. Our expression analysis of cells shifted from high carbon to low carbon demonstrated an inversely correlated transcript accumulation of the flv4-2 operon mRNA and one antisense RNA to flv4, designated as As1_flv4. Overexpression of As1_flv4 led to a decrease in flv4-2 mRNA. The promoter activity of as1_flv4 was transiently stimulated by Ci limitation and negatively regulated by the AbrB-like transcription regulator Sll0822, whereas the flv4-2 operon was positively regulated by the transcription factor NdhR. The results indicate that the tightly regulated antisense RNA As1_flv4 establishes a transient threshold for flv4-2 expression in the early phase after a change in Ci conditions. Thus, it prevents unfavorable synthesis of the proteins from the flv4-2 operon. PMID:22854963

Quantitative trait loci associated with anthracnose resistance in sorghum

USDA-ARS?s Scientific Manuscript database

With an aim to develop a durable resistance to the fungal disease anthracnose, two unique genetic sources of resistance were selected to create genetic mapping populations to identify regions of the sorghum genome that encode anthracnose resistance. A series of quantitative trait loci were identifi...

A Signal Detection Theory Analysis of Behavioral Pattern Separation Paradigms

ERIC Educational Resources Information Center

Loiotile, Rita E.; Courtney, Susan M.

2015-01-01

Behavioral pattern separation (BPS) paradigms ask participants to discriminate previously encoded (old) stimuli from highly similar (lure) and categorically distinct (novel) stimuli. The lure-old discrimination, thought to uniquely reflect pattern separation in the hippocampal formation, is typically pitted against the traditional novel-old…

48 CFR 252.211-7003 - Item identification and valuation.

Code of Federal Regulations, 2010 CFR

2010-10-01

..., used to retrieve data encoded on machine-readable media. Concatenated unique item identifier means— (1... Defense Logistics Information System (DLIS) Commercial and Government Entity (CAGE) Code). Issuing agency... identifier. Item means a single hardware article or a single unit formed by a grouping of subassemblies...

Contextual Variability in Free Recall

ERIC Educational Resources Information Center

Lohnas, Lynn J.; Polyn, Sean M.; Kahana, Michael J.

2011-01-01

According to contextual-variability theory, experiences encoded at different times tend to be associated with different contextual states. The gradual evolution of context implies that spaced items will be associated with more distinct contextual states, and thus have more unique retrieval cues, than items presented in proximity. Ross and Landauer…

Patterned functional carbon fibers from polyethylene.

PubMed

Hunt, Marcus A; Saito, Tomonori; Brown, Rebecca H; Kumbhar, Amar S; Naskar, Amit K

2012-05-08

Carbon fibers having unique morphologies, from hollow circular to gear-shaped, are produced from a novel melt-processable precursor and method. The resulting carbon fiber exhibits microstructural and topological properties that are dependent on processing conditions, rendering them highly amenable to myriad applications. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Toxicity of Military Unique Compounds in Aquatic Organisms: An Annotated Bibliography (Studies Published Through 1996)

DTIC Science & Technology

1998-04-01

containing zinc, cadmium , arsenic, lead, aluminum, carbon tetrachloride, perchloroethylene, hexachloroethane, hexachlorobenzene, and hydrochloric...Siphonaptera/Solvent Dyes/Toxicity/Trout/Water/Zinc/SmokeMunitions/Propellants/Water Pollution/ Cadmium /Lead(Metal)/Carbon Tetrachloride/Aquatic Biology...combustion products that are a complex mixture containing zinc, cadmium , arsenic, lead, aluminum, carbon tetrachloride, perchloroethylene

Carbon nanomaterials for advanced energy conversion and storage.

PubMed

Dai, Liming; Chang, Dong Wook; Baek, Jong-Beom; Lu, Wen

2012-04-23

It is estimated that the world will need to double its energy supply by 2050. Nanotechnology has opened up new frontiers in materials science and engineering to meet this challenge by creating new materials, particularly carbon nanomaterials, for efficient energy conversion and storage. Comparing to conventional energy materials, carbon nanomaterials possess unique size-/surface-dependent (e.g., morphological, electrical, optical, and mechanical) properties useful for enhancing the energy-conversion and storage performances. During the past 25 years or so, therefore, considerable efforts have been made to utilize the unique properties of carbon nanomaterials, including fullerenes, carbon nanotubes, and graphene, as energy materials, and tremendous progress has been achieved in developing high-performance energy conversion (e.g., solar cells and fuel cells) and storage (e.g., supercapacitors and batteries) devices. This article reviews progress in the research and development of carbon nanomaterials during the past twenty years or so for advanced energy conversion and storage, along with some discussions on challenges and perspectives in this exciting field. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Facilely prepared, N, O-codoped nanosheet derived from pre-functionalized polymer as supercapacitor electrodes

NASA Astrophysics Data System (ADS)

Wang, Jun; Yang, Ting; Zeng, Zheling; Deng, Shuguang

2018-04-01

Nitrogen and oxygen codoped carbon nanosheets derived from pre-functionalized polymer were prepared using a facile direct pyrolysis method. The carbon microstructures are tunable with micro- and mesopore size distribution and a large specific surface area (1628.9-2146.1 m2 g-1). Furthermore, a significant morphology change, from carbon granules to carbon nanosheets, occurred at an annealing temperature of 1273 K. The unique carbon sheet morphology guaranteed a good specific capacitance of 246.4 F g-1 at 0.5 A g-1 in 1 M H2SO4 aqueous solution and an excellent rate capability with a retention of 87.9% at 5 A g-1 as coin cell. The outstanding capacitance attributes to the combination of pseudocapacitance due to the N,O dual-doping and unique nanosheet morphology. Moreover, its outstanding cycling performance with 95% retention over 10,000 cycles at 10 A g-1 and an acceptable energy density of 8.6 Wh kg-1 at 0.2 A g-1 make the N,O-codoped carbon nanosheet potent and promising electrode material for high performance supercapacitors.

Fish as major carbonate mud producers and missing components of the tropical carbonate factory

USGS Publications Warehouse

Perry, C.T.; Salter, M.A.; Harborne, A.R.; Crowley, S.F.; Jelks, H.L.; Wilson, R.W.

2011-01-01

Carbonate mud is a major constituent of recent marine carbonate sediments and of ancient limestones, which contain unique records of changes in ocean chemistry and climate shifts in the geological past. However, the origin of carbonate mud is controversial and often problematic to resolve. Here we show that tropical marine fish produce and excrete various forms of precipitated (nonskeletal) calcium carbonate from their guts ("low" and "high" Mg-calcite and aragonite), but that very fine-grained (mostly <2 ??m) high Mg-calcite crystallites (i.e., >4 mole % MgCO3) are their dominant excretory product. Crystallites from fish are morphologically diverse and species-specific, but all are unique relative to previously known biogenic and abiotic sources of carbonate within open marine systems. Using site specific fish biomass and carbonate excretion rate data we estimate that fish produce ???6.1 ?? 106 kg CaCO3/year across the Bahamian archipelago, all as mud-grade (the <63 ??m fraction) carbonate and thus as a potential sediment constituent. Estimated contributions from fish to total carbonate mud production average ???14% overall, and exceed 70% in specific habitats. Critically, we also document the widespread presence of these distinctive fish-derived carbonates in the finest sediment fractions from all habitat types in the Bahamas, demonstrating that these carbonates have direct relevance to contemporary carbonate sediment budgets. Fish thus represent a hitherto unrecognized but significant source of fine-grained carbonate sediment, the discovery of which has direct application to the conceptual ideas of how marine carbonate factories function both today and in the past.

Fish as major carbonate mud producers and missing components of the tropical carbonate factory

USGS Publications Warehouse

Perry, Chris T.; Salter, Michael A.; Harborne, Alastair R.; Crowley, Stephen F.; Jelks, Howard L.; Wilson, Rod W.

2011-01-01

Carbonate mud is a major constituent of recent marine carbonate sediments and of ancient limestones, which contain unique records of changes in ocean chemistry and climate shifts in the geological past. However, the origin of carbonate mud is controversial and often problematic to resolve. Here we show that tropical marine fish produce and excrete various forms of precipitated (nonskeletal) calcium carbonate from their guts ("low" and "high" Mg-calcite and aragonite), but that very fine-grained (mostly 4 mole % MgCO3) are their dominant excretory product. Crystallites from fish are morphologically diverse and species-specific, but all are unique relative to previously known biogenic and abiotic sources of carbonate within open marine systems. Using site specific fish biomass and carbonate excretion rate data we estimate that fish produce ~6.1 x 106 kg CaCO3/year across the Bahamian archipelago, all as mud-grade (the <63 μm fraction) carbonate and thus as a potential sediment constituent. Estimated contributions from fish to total carbonate mud production average ~14% overall, and exceed 70% in specific habitats. Critically, we also document the widespread presence of these distinctive fish-derived carbonates in the finest sediment fractions from all habitat types in the Bahamas, demonstrating that these carbonates have direct relevance to contemporary carbonate sediment budgets. Fish thus represent a hitherto unrecognized but significant source of fine-grained carbonate sediment, the discovery of which has direct application to the conceptual ideas of how marine carbonate factories function both today and in the past.

Observing the operational significance of discord consumption

NASA Astrophysics Data System (ADS)

Gu, Mile; Chrzanowski, Helen M.; Assad, Syed M.; Symul, Thomas; Modi, Kavan; Ralph, Timothy C.; Vedral, Vlatko; Lam, Ping Koy

2012-09-01

Coherent interactions that generate negligible entanglement can still exhibit unique quantum behaviour. This observation has motivated a search beyond entanglement for a complete description of all quantum correlations. Quantum discord is a promising candidate. Here, we demonstrate that under certain measurement constraints, discord between bipartite systems can be consumed to encode information that can only be accessed by coherent quantum interactions. The inability to access this information by any other means allows us to use discord to directly quantify this `quantum advantage'. We experimentally encode information within the discordant correlations of two separable Gaussian states. The amount of extra information recovered by coherent interaction is quantified and directly linked with the discord consumed during encoding. No entanglement exists at any point of this experiment. Thus we introduce and demonstrate an operational method to use discord as a physical resource.

Pattern recognition of electronic bit-sequences using a semiconductor mode-locked laser and spatial light modulators

NASA Astrophysics Data System (ADS)

Bhooplapur, Sharad; Akbulut, Mehmetkan; Quinlan, Franklyn; Delfyett, Peter J.

2010-04-01

A novel scheme for recognition of electronic bit-sequences is demonstrated. Two electronic bit-sequences that are to be compared are each mapped to a unique code from a set of Walsh-Hadamard codes. The codes are then encoded in parallel on the spectral phase of the frequency comb lines from a frequency-stabilized mode-locked semiconductor laser. Phase encoding is achieved by using two independent spatial light modulators based on liquid crystal arrays. Encoded pulses are compared using interferometric pulse detection and differential balanced photodetection. Orthogonal codes eight bits long are compared, and matched codes are successfully distinguished from mismatched codes with very low error rates, of around 10-18. This technique has potential for high-speed, high accuracy recognition of bit-sequences, with applications in keyword searches and internet protocol packet routing.

Synthesis of monolithic graphene – graphite integrated electronics

PubMed Central

Park, Jang-Ung; Nam, SungWoo; Lee, Mi-Sun; Lieber, Charles M.

2013-01-01

Encoding electronic functionality into nanoscale elements during chemical synthesis has been extensively explored over the past decade as the key to developing integrated nanosystems1 with functions defined by synthesis2-6. Graphene7-12 has been recently explored as a two-dimensional nanoscale material, and has demonstrated simple device functions based on conventional top-down fabrication13-20. However, the synthetic approach to encoding electronic functionality and thus enabling an entire integrated graphene electronics in a chemical synthesis had not previously been demonstrated. Here we report an unconventional approach for the synthesis of monolithically-integrated electronic devices based on graphene and graphite. Spatial patterning of heterogeneous catalyst metals permits the selective growth of graphene and graphite, with controlled number of graphene layers. Graphene transistor arrays with graphitic electrodes and interconnects were formed from synthesis. These functional, all-carbon structures were transferrable onto a variety of substrates. The integrated transistor arrays were used to demonstrate real-time, multiplexed chemical sensing, and more significantly, multiple carbon layers of the graphene-graphite device components were vertically assembled to form a three-dimensional flexible structure which served as a top-gate transistor array. These results represent a substantial progress towards encoding electronic functionality via chemical synthesis and suggest future promise for one-step integration of graphene-graphite based electronics. PMID:22101813

Synthesis of monolithic graphene-graphite integrated electronics.

PubMed

Park, Jang-Ung; Nam, SungWoo; Lee, Mi-Sun; Lieber, Charles M

2011-11-20

Encoding electronic functionality into nanoscale elements during chemical synthesis has been extensively explored over the past decade as the key to developing integrated nanosystems with functions defined by synthesis. Graphene has been recently explored as a two-dimensional nanoscale material, and has demonstrated simple device functions based on conventional top-down fabrication. However, the synthetic approach to encoding electronic functionality and thus enabling an entire integrated graphene electronics in a chemical synthesis had not previously been demonstrated. Here we report an unconventional approach for the synthesis of monolithically integrated electronic devices based on graphene and graphite. Spatial patterning of heterogeneous metal catalysts permits the selective growth of graphene and graphite, with a controlled number of graphene layers. Graphene transistor arrays with graphitic electrodes and interconnects were formed from the synthesis. These functional, all-carbon structures were transferable onto a variety of substrates. The integrated transistor arrays were used to demonstrate real-time, multiplexed chemical sensing and more significantly, multiple carbon layers of the graphene-graphite device components were vertically assembled to form a three-dimensional flexible structure which served as a top-gate transistor array. These results represent substantial progress towards encoding electronic functionality through chemical synthesis and suggest the future promise of one-step integration of graphene-graphite based electronics.

Multiple Hfq-Crc target sites are required to impose catabolite repression on (methyl)phenol metabolism in Pseudomonas putida CF600.

PubMed

Wirebrand, Lisa; Madhushani, Anjana W K; Irie, Yasuhiko; Shingler, Victoria

2018-01-01

The dmp-system encoded on the IncP-2 pVI150 plasmid of Pseudomonas putida CF600 confers the ability to assimilate (methyl)phenols. Regulation of the dmp-genes is subject to sophisticated control, which includes global regulatory input to subvert expression of the pathway in the presence of preferred carbon sources. Previously we have shown that in P. putida, translational inhibition exerted by the carbon repression control protein Crc operates hand-in-hand with the RNA chaperon protein Hfq to reduce translation of the DmpR regulator of the Dmp-pathway. Here, we show that Crc and Hfq co-target four additional sites to form riboprotein complexes within the proximity of the translational initiation sites of genes encoding the first two steps of the Dmp-pathway to mediate two-layered control in the face of selection of preferred substrates. Furthermore, we present evidence that Crc plays a hitherto unsuspected role in maintaining the pVI150 plasmid within a bacterial population, which has implications for (methyl)phenol degradation and a wide variety of other physiological processes encoded by the IncP-2 group of Pseudomonas-specific mega-plasmids. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Identity and mechanisms of alkane-oxidizing metalloenzymes from deep-sea hydrothermal vents

PubMed Central

Bertrand, Erin M.; Keddis, Ramaydalis; Groves, John T.; Vetriani, Costantino; Austin, Rachel Narehood

2013-01-01

Six aerobic alkanotrophs (organism that can metabolize alkanes as their sole carbon source) isolated from deep-sea hydrothermal vents were characterized using the radical clock substrate norcarane to determine the metalloenzyme and reaction mechanism used to oxidize alkanes. The organisms studied were Alcanivorax sp. strains EPR7 and MAR14, Marinobacter sp. strain EPR21, Nocardioides sp. strains EPR26w, EPR28w, and Parvibaculum hydrocarbonoclasticum strain EPR92. Each organism was able to grow on n-alkanes as the sole carbon source and therefore must express genes encoding an alkane-oxidizing enzyme. Results from the oxidation of the radical-clock diagnostic substrate norcarane demonstrated that five of the six organisms (EPR7, MAR14, EPR21, EPR26w, and EPR28w) used an alkane hydroxylase functionally similar to AlkB to catalyze the oxidation of medium-chain alkanes, while the sixth organism (EPR92) used an alkane-oxidizing cytochrome P450 (CYP)-like protein to catalyze the oxidation. DNA sequencing indicated that EPR7 and EPR21 possess genes encoding AlkB proteins, while sequencing results from EPR92 confirmed the presence of a gene encoding CYP-like alkane hydroxylase, consistent with the results from the norcarane experiments. PMID:23825470

A Review of Carbon Nanomaterials' Synthesis via the Chemical Vapor Deposition (CVD) Method.

PubMed

Manawi, Yehia M; Samara, Ayman; Al-Ansari, Tareq; Atieh, Muataz A

2018-05-17

Carbon nanomaterials have been extensively used in many applications owing to their unique thermal, electrical and mechanical properties. One of the prime challenges is the production of these nanomaterials on a large scale. This review paper summarizes the synthesis of various carbon nanomaterials via the chemical vapor deposition (CVD) method. These carbon nanomaterials include fullerenes, carbon nanotubes (CNTs), carbon nanofibers (CNFs), graphene, carbide-derived carbon (CDC), carbon nano-onion (CNO) and MXenes. Furthermore, current challenges in the synthesis and application of these nanomaterials are highlighted with suggested areas for future research.

A Review of Carbon Nanomaterials’ Synthesis via the Chemical Vapor Deposition (CVD) Method

PubMed Central

Manawi, Yehia M.; Samara, Ayman; Al-Ansari, Tareq; Atieh, Muataz A.

2018-01-01

Carbon nanomaterials have been extensively used in many applications owing to their unique thermal, electrical and mechanical properties. One of the prime challenges is the production of these nanomaterials on a large scale. This review paper summarizes the synthesis of various carbon nanomaterials via the chemical vapor deposition (CVD) method. These carbon nanomaterials include fullerenes, carbon nanotubes (CNTs), carbon nanofibers (CNFs), graphene, carbide-derived carbon (CDC), carbon nano-onion (CNO) and MXenes. Furthermore, current challenges in the synthesis and application of these nanomaterials are highlighted with suggested areas for future research. PMID:29772760

Type 3 Fimbriae Encoded on Plasmids Are Expressed from a Unique Promoter without Affecting Host Motility, Facilitating an Exceptional Phenotype That Enhances Conjugal Plasmid Transfer

PubMed Central

Madsen, Jonas Stenløkke; Riber, Leise; Kot, Witold; Basfeld, Alrun; Burmølle, Mette; Hansen, Lars Hestbjerg; Sørensen, Søren Johannes

2016-01-01

Horizontal gene transfer (HGT), the transmission of genetic material to a recipient that is not the progeny of the donor, is fundamental in bacterial evolution. HGT is often mediated by mobile genetic elements such as conjugative plasmids, which may be in conflict with the chromosomal elements of the genome because they are independent replicons that may petition their own evolutionary strategy. Here we study differences between type 3 fimbriae encoded on wild type plasmids and in chromosomes. Using known and newly characterized plasmids we show that the expression of type 3 fimbriae encoded on plasmids is systematically different, as MrkH, a c-di-GMP dependent transcriptional activator is not needed for strong expression of the fimbriae. MrkH is required for expression of type 3 fimbriae of the Klebsiella pneumoniae chromosome, wherefrom the fimbriae operon (mrkABCDF) of plasmids is believed to have originated. We find that mrkABCDFs of plasmids are highly expressed via a unique promoter that differs from the original Klebsiella promoter resulting in fundamental behavioral consequences. Plasmid associated mrkABCDFs did not influence the swimming behavior of the host, that hereby acquired an exceptional phenotype being able to both actively swim (planktonic behavior) and express biofilm associated fimbriae (sessile behavior). We show that this exceptional phenotype enhances the conjugal transfer of the plasmid. PMID:27627107

A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus.

PubMed

Doddapaneni, Harshavardhan; Subramanian, Venkataramanan; Fu, Bolei; Cullen, Dan

2013-06-01

The oxidative enzymatic machinery for degradation of organic substrates in Agaricus bisporus (Ab) is at the core of the carbon recycling mechanisms in this fungus. To date, 156 genes have been tentatively identified as part of this oxidative enzymatic machinery, which includes 26 peroxidase encoding genes, nine copper radical oxidase [including three putative glyoxal oxidase-encoding genes (GLXs)], 12 laccases sensu stricto and 109 cytochrome P450 monooxygenases. Comparative analyses of these enzymes in Ab with those of the white-rot fungus, Phanerochaete chrysosporium, the brown-rot fungus, Postia placenta, the coprophilic litter fungus, Coprinopsis cinerea and the ectomychorizal fungus, Laccaria bicolor, revealed enzyme diversity consistent with adaptation to substrates rich in humic substances and partially degraded plant material. For instance, relative to wood decay fungi, Ab cytochrome P450 genes were less numerous (109 gene models), distributed among distinctive families, and lacked extensive duplication and clustering. Viewed together with P450 transcript accumulation patterns in three tested growth conditions, these observations were consistent with the unique Ab lifestyle. Based on tandem gene arrangements, a certain degree of gene duplication seems to have occurred in this fungus in the copper radical oxidase (CRO) and the laccase gene families. In Ab, high transcript levels and regulation of the heme-thiolate peroxidases, two manganese peroxidases and the three GLX-like genes are likely in response to complex natural substrates, including lignocellulose and its derivatives, thereby suggesting an important role in lignin degradation. On the other hand, the expression patterns of the related CROs suggest a developmental role in this fungus. Based on these observations, a brief comparative genomic overview of the Ab oxidative enzyme machinery is presented. Copyright © 2013 Elsevier Inc. All rights reserved.

Sequence analysis of the phs operon in Salmonella typhimurium and the contribution of thiosulfate reduction to anaerobic energy metabolism.

PubMed Central

Heinzinger, N K; Fujimoto, S Y; Clark, M A; Moreno, M S; Barrett, E L

1995-01-01

The phs chromosomal locus of Salmonella typhimurium is essential for the dissimilatory anaerobic reduction of thiosulfate to hydrogen sulfide. Sequence analysis of the phs region revealed a functional operon with three open reading frames, designated phsA, phsB, and phsC, which encode peptides of 82.7, 21.3, and 28.5 kDa, respectively. The predicted products of phsA and phsB exhibited significant homology with the catalytic and electron transfer subunits of several other anaerobic molybdoprotein oxidoreductases, including Escherichia coli dimethyl sulfoxide reductase, nitrate reductase, and formate dehydrogenase. Simultaneous comparison of PhsA to seven homologous molybdoproteins revealed numerous similarities among all eight throughout the entire frame, hence, significant amino acid conservation among molybdoprotein oxidoreductases. Comparison of PhsB to six other homologous sequences revealed four highly conserved iron-sulfur clusters. The predicted phsC product was highly hydrophobic and similar in size to the hydrophobic subunits of the molybdoprotein oxidoreductases containing subunits homologous to phsA and phsB. Thus, phsABC appears to encode thiosulfate reductase. Single-copy phs-lac translational fusions required both anaerobiosis and thiosulfate for full expression, whereas multicopy phs-lac translational fusions responded to either thiosulfate or anaerobiosis, suggesting that oxygen and thiosulfate control of phs involves negative regulation. A possible role for thiosulfate reduction in anaerobic respiration was examined. Thiosulfate did not significantly augment the final densities of anaerobic cultures grown on any of the 18 carbon sources tested. on the other hand, washed stationary-phase cells depleted of ATP were shown to synthesize small amounts of ATP on the addition of the formate and thiosulfate, suggesting that the thiosulfate reduction plays a unique role in anaerobic energy conservation by S typhimurium. PMID:7751291

Identification of tertiary butyl alcohol (TBA)-utilizing organisms in BioGAC reactors using 13C-DNA stable isotope probing.

PubMed

Aslett, Denise; Haas, Joseph; Hyman, Michael

2011-09-01

Biodegradation of the gasoline oxygenates methyl tertiary-butyl ether (MTBE) and ethyl tertiary-butyl ether (ETBE) can cause tertiary butyl alcohol (TBA) to accumulate in gasoline-impacted environments. One remediation option for TBA-contaminated groundwater involves oxygenated granulated activated carbon (GAC) reactors that have been self-inoculated by indigenous TBA-degrading microorganisms in ground water extracted from contaminated aquifers. Identification of these organisms is important for understanding the range of TBA-metabolizing organisms in nature and for determining whether self-inoculation of similar reactors is likely to occur at other sites. In this study (13)C-DNA-stable isotope probing (SIP) was used to identify TBA-utilizing organisms in samples of self-inoculated BioGAC reactors operated at sites in New York and California. Based on 16S rRNA nucleotide sequences, all TBA-utilizing organisms identified were members of the Burkholderiales order of the β-proteobacteria. Organisms similar to Cupriavidus and Methylibium were observed in both reactor samples while organisms similar to Polaromonas and Rhodoferax were unique to the reactor sample from New York. Organisms similar to Hydrogenophaga and Paucibacter strains were only detected in the reactor sample from California. We also analyzed our samples for the presence of several genes previously implicated in TBA oxidation by pure cultures of bacteria. Genes Mpe_B0532, B0541, B0555, and B0561 were all detected in (13)C-metagenomic DNA from both reactors and deduced amino acid sequences suggested these genes all encode highly conserved enzymes. One gene (Mpe_B0555) encodes a putative phthalate dioxygenase-like enzyme that may be particularly appropriate for determining the potential for TBA oxidation in contaminated environmental samples.

The detection and phylogenetic analysis of the alkane 1-monooxygenase gene of members of the genus Rhodococcus.

PubMed

Táncsics, András; Benedek, Tibor; Szoboszlay, Sándor; Veres, Péter G; Farkas, Milán; Máthé, István; Márialigeti, Károly; Kukolya, József; Lányi, Szabolcs; Kriszt, Balázs

2015-02-01

Naturally occurring and anthropogenic petroleum hydrocarbons are potential carbon sources for many bacteria. The AlkB-related alkane hydroxylases, which are integral membrane non-heme iron enzymes, play a key role in the microbial degradation of many of these hydrocarbons. Several members of the genus Rhodococcus are well-known alkane degraders and are known to harbor multiple alkB genes encoding for different alkane 1-monooxygenases. In the present study, 48 Rhodococcus strains, representing 35 species of the genus, were investigated to find out whether there was a dominant type of alkB gene widespread among species of the genus that could be used as a phylogenetic marker. Phylogenetic analysis of rhodococcal alkB gene sequences indicated that a certain type of alkB gene was present in almost every member of the genus Rhodococcus. These alkB genes were common in a unique nucleotide sequence stretch absent from other types of rhodococcal alkB genes that encoded a conserved amino acid motif: WLG(I/V/L)D(G/D)GL. The sequence identity of the targeted alkB gene in Rhodococcus ranged from 78.5 to 99.2% and showed higher nucleotide sequence variation at the inter-species level compared to the 16S rRNA gene (93.9-99.8%). The results indicated that the alkB gene type investigated might be applicable for: (i) differentiating closely related Rhodococcus species, (ii) properly assigning environmental isolates to existing Rhodococcus species, and finally (iii) assessing whether a new Rhodococcus isolate represents a novel species of the genus. Copyright © 2014 Elsevier GmbH. All rights reserved.

Evaluating standard terminologies for encoding allergy information.

PubMed

Goss, Foster R; Zhou, Li; Plasek, Joseph M; Broverman, Carol; Robinson, George; Middleton, Blackford; Rocha, Roberto A

2013-01-01

Allergy documentation and exchange are vital to ensuring patient safety. This study aims to analyze and compare various existing standard terminologies for representing allergy information. Five terminologies were identified, including the Systemized Nomenclature of Medical Clinical Terms (SNOMED CT), National Drug File-Reference Terminology (NDF-RT), Medication Dictionary for Regulatory Activities (MedDRA), Unique Ingredient Identifier (UNII), and RxNorm. A qualitative analysis was conducted to compare desirable characteristics of each terminology, including content coverage, concept orientation, formal definitions, multiple granularities, vocabulary structure, subset capability, and maintainability. A quantitative analysis was also performed to compare the content coverage of each terminology for (1) common food, drug, and environmental allergens and (2) descriptive concepts for common drug allergies, adverse reactions (AR), and no known allergies. Our qualitative results show that SNOMED CT fulfilled the greatest number of desirable characteristics, followed by NDF-RT, RxNorm, UNII, and MedDRA. Our quantitative results demonstrate that RxNorm had the highest concept coverage for representing drug allergens, followed by UNII, SNOMED CT, NDF-RT, and MedDRA. For food and environmental allergens, UNII demonstrated the highest concept coverage, followed by SNOMED CT. For representing descriptive allergy concepts and adverse reactions, SNOMED CT and NDF-RT showed the highest coverage. Only SNOMED CT was capable of representing unique concepts for encoding no known allergies. The proper terminology for encoding a patient's allergy is complex, as multiple elements need to be captured to form a fully structured clinical finding. Our results suggest that while gaps still exist, a combination of SNOMED CT and RxNorm can satisfy most criteria for encoding common allergies and provide sufficient content coverage.

Virulence factors encoded by Legionella longbeachae identified on the basis of the genome sequence analysis of clinical isolate D-4968.

PubMed

Kozak, Natalia A; Buss, Meghan; Lucas, Claressa E; Frace, Michael; Govil, Dhwani; Travis, Tatiana; Olsen-Rasmussen, Melissa; Benson, Robert F; Fields, Barry S

2010-02-01

Legionella longbeachae causes most cases of legionellosis in Australia and may be underreported worldwide due to the lack of L. longbeachae-specific diagnostic tests. L. longbeachae displays distinctive differences in intracellular trafficking, caspase 1 activation, and infection in mouse models compared to Legionella pneumophila, yet these two species have indistinguishable clinical presentations in humans. Unlike other legionellae, which inhabit freshwater systems, L. longbeachae is found predominantly in moist soil. In this study, we sequenced and annotated the genome of an L. longbeachae clinical isolate from Oregon, isolate D-4968, and compared it to the previously published genomes of L. pneumophila. The results revealed that the D-4968 genome is larger than the L. pneumophila genome and has a gene order that is different from that of the L. pneumophila genome. Genes encoding structural components of type II, type IV Lvh, and type IV Icm/Dot secretion systems are conserved. In contrast, only 42/140 homologs of genes encoding L. pneumophila Icm/Dot substrates have been found in the D-4968 genome. L. longbeachae encodes numerous proteins with eukaryotic motifs and eukaryote-like proteins unique to this species, including 16 ankyrin repeat-containing proteins and a novel U-box protein. We predict that these proteins are secreted by the L. longbeachae Icm/Dot secretion system. In contrast to the L. pneumophila genome, the L. longbeachae D-4968 genome does not contain flagellar biosynthesis genes, yet it contains a chemotaxis operon. The lack of a flagellum explains the failure of L. longbeachae to activate caspase 1 and trigger pyroptosis in murine macrophages. These unique features of L. longbeachae may reflect adaptation of this species to life in soil.

Evaluating standard terminologies for encoding allergy information

PubMed Central

Goss, Foster R; Zhou, Li; Plasek, Joseph M; Broverman, Carol; Robinson, George; Middleton, Blackford; Rocha, Roberto A

2013-01-01

Objective Allergy documentation and exchange are vital to ensuring patient safety. This study aims to analyze and compare various existing standard terminologies for representing allergy information. Methods Five terminologies were identified, including the Systemized Nomenclature of Medical Clinical Terms (SNOMED CT), National Drug File–Reference Terminology (NDF-RT), Medication Dictionary for Regulatory Activities (MedDRA), Unique Ingredient Identifier (UNII), and RxNorm. A qualitative analysis was conducted to compare desirable characteristics of each terminology, including content coverage, concept orientation, formal definitions, multiple granularities, vocabulary structure, subset capability, and maintainability. A quantitative analysis was also performed to compare the content coverage of each terminology for (1) common food, drug, and environmental allergens and (2) descriptive concepts for common drug allergies, adverse reactions (AR), and no known allergies. Results Our qualitative results show that SNOMED CT fulfilled the greatest number of desirable characteristics, followed by NDF-RT, RxNorm, UNII, and MedDRA. Our quantitative results demonstrate that RxNorm had the highest concept coverage for representing drug allergens, followed by UNII, SNOMED CT, NDF-RT, and MedDRA. For food and environmental allergens, UNII demonstrated the highest concept coverage, followed by SNOMED CT. For representing descriptive allergy concepts and adverse reactions, SNOMED CT and NDF-RT showed the highest coverage. Only SNOMED CT was capable of representing unique concepts for encoding no known allergies. Conclusions The proper terminology for encoding a patient's allergy is complex, as multiple elements need to be captured to form a fully structured clinical finding. Our results suggest that while gaps still exist, a combination of SNOMED CT and RxNorm can satisfy most criteria for encoding common allergies and provide sufficient content coverage. PMID:23396542

Novel plasmids and resistance phenotypes in Yersinia pestis: unique plasmid inventory of strain Java 9 mediates high levels of arsenic resistance.

PubMed

Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L

2012-01-01

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium.

Novel Plasmids and Resistance Phenotypes in Yersinia pestis: Unique Plasmid Inventory of Strain Java 9 Mediates High Levels of Arsenic Resistance

PubMed Central

Eppinger, Mark; Radnedge, Lyndsay; Andersen, Gary; Vietri, Nicholas; Severson, Grant; Mou, Sherry; Ravel, Jacques; Worsham, Patricia L.

2012-01-01

Growing evidence suggests that the plasmid repertoire of Yersinia pestis is not restricted to the three classical virulence plasmids. The Java 9 strain of Y. pestis is a biovar Orientalis isolate obtained from a rat in Indonesia. Although it lacks the Y. pestis-specific plasmid pMT, which encodes the F1 capsule, it retains virulence in mouse and non-human primate animal models. While comparing diverse Y. pestis strains using subtractive hybridization, we identified sequences in Java 9 that were homologous to a Y. enterocolitica strain carrying the transposon Tn2502, which is known to encode arsenic resistance. Here we demonstrate that Java 9 exhibits high levels of arsenic and arsenite resistance mediated by a novel promiscuous class II transposon, named Tn2503. Arsenic resistance was self-transmissible from Java 9 to other Y. pestis strains via conjugation. Genomic analysis of the atypical plasmid inventory of Java 9 identified pCD and pPCP plasmids of atypical size and two previously uncharacterized cryptic plasmids. Unlike the Tn2502-mediated arsenic resistance encoded on the Y. enterocolitica virulence plasmid; the resistance loci in Java 9 are found on all four indigenous plasmids, including the two novel cryptic plasmids. This unique mobilome introduces more than 105 genes into the species gene pool. The majority of these are encoded by the two entirely novel self-transmissible plasmids, which show partial homology and synteny to other enterics. In contrast to the reductive evolution in Y. pestis, this study underlines the major impact of a dynamic mobilome and lateral acquisition in the genome evolution of the plague bacterium. PMID:22479347

Photonic Sorting of Aligned, Crystalline Carbon Nanotube Textiles.

PubMed

Bulmer, John S; Gspann, Thurid S; Orozco, Francisco; Sparkes, Martin; Koerner, Hilmar; Di Bernardo, A; Niemiec, Arkadiusz; Robinson, J W A; Koziol, Krzysztof K; Elliott, James A; O'Neill, William

2017-10-11

Floating catalyst chemical vapor deposition uniquely generates aligned carbon nanotube (CNT) textiles with individual CNT lengths magnitudes longer than competing processes, though hindered by impurities and intrinsic/extrinsic defects. We present a photonic-based post-process, particularly suited for these textiles, that selectively removes defective CNTs and other carbons not forming a threshold thermal pathway. In this method, a large diameter laser beam rasters across the surface of a partly aligned CNT textile in air, suspended from its ends. This results in brilliant, localized oxidation, where remaining material is an optically transparent film comprised of few-walled CNTs with profound and unique improvement in microstructure alignment and crystallinity. Raman spectroscopy shows substantial D peak suppression while preserving radial breathing modes. This increases the undoped, specific electrical conductivity at least an order of magnitude to beyond that of single-crystal graphite. Cryogenic conductivity measurements indicate intrinsic transport enhancement, opposed to simply removing nonconductive carbons/residual catalyst.

Hierarchically structured activated carbon for ultracapacitors

NASA Astrophysics Data System (ADS)

Kim, Mok-Hwa; Kim, Kwang-Bum; Park, Sun-Min; Roh, Kwang Chul

2016-02-01

To resolve the pore-associated bottleneck problem observed in the electrode materials used for ultracapacitors, which inhibits the transport of the electrolyte ions, we designed hierarchically structured activated carbon (HAC) by synthesizing a mesoporous silica template/carbon composite and chemically activating it to simultaneously remove the silica template and increase the pore volume. The resulting HAC had a well-designed, unique porous structure, which allowed for large interfaces for efficient electric double-layer formation. Given the unique characteristics of the HAC, we believe that the developed synthesis strategy provides important insights into the design and fabrication of hierarchical carbon nanostructures. The HAC, which had a specific surface area of 1,957 m2 g-1, exhibited an extremely high specific capacitance of 157 F g-1 (95 F cc-1), as well as a high rate capability. This indicated that it had superior energy storage capability and was thus suitable for use in advanced ultracapacitors.

An Interdisciplinary Module on Regulating Carbon Emissions to Mitigate Climate Change

NASA Astrophysics Data System (ADS)

Penny, S.; Sethi, G.; Smyth, R.; Leibensperger, E. M.; Gervich, C.; Batur, P.

2016-12-01

The dynamics of the unfolding carbon regulatory process presents a unique and timely opportunity to teach students about the grand challenge brought by climate change and the importance of systems thinking and interdisciplinary problem solving. In this poster, we summarize our recently developed 4-week activity-based class module "Regulating Carbon Emissions to Mitigate Climate Change," which we have developed as part of the InTeGrate ("Interdisciplinary Teaching about Earth for a Sustainable Future") program. These materials are suitable for introductory non-majors, environmental sciences majors, and political science majors, and we have formally piloted in each of these settings. This module is truly interdisciplinary and spans topics such as the Supreme Court ruling in Massachusetts v. EPA, costs and benefits of carbon abatement, and climate sensitivity. We discuss the unique challenges (and rewards!) that we experienced teaching materials entirely outside one's expertise.

Squid inks-derived nanocarbons with unique ;shell@pearls; structure for high performance supercapacitors

NASA Astrophysics Data System (ADS)

Cheng, Fengli; Liu, Wei; Zhang, Yuan; Wang, Huanlei; Liu, Shuang; Hao, Enchao; Zhao, Shuping; Yang, Hongzhan

2017-06-01

Porous carbons derived from biomass are one current hotspot in exploring advanced electrode materials for supercapacitors. In this work, based on nanoparticles from squid inks, an N-doping porous carbons with a unique "shell@pearls" structure has been fabricated through a direct carbonization/activation procedure. Remarkably, a fantastic structural evolution from core-shell, yolk-shell to the porous matrix embedded with small spheres (like pears in shell) has been observed. The as-obtained products exhibit a hierarchical porosity comprised of micro-, meso- and macropores, as well with a large surface area (1957 m2 g-1) and N-doping (2.09%). As the electrode materials for supercapacitors, the "shell@pearls"bio-carbons show the very high capacitance of 329 F g-1 at 0.5 A g-1 and 265 F g-1 at 30 A g-1 and also a superior retention of 99.5% after 10000 cycles at 5 A g-1.

A cytosolic carbonic anhydrase molecular switch occurs in the gills of metamorphic sea lamprey

USGS Publications Warehouse

Ferreira-Martins, D.; McCormick, Stephen; Campos, A.; Lopes-Marques, M.; Osorio, H.; Coimbra, J.; Castro, L.F.C.; Wilson, Jonthan M

2016-01-01

Carbonic anhydrase plays a key role in CO2 transport, acid-base and ion regulation and metabolic processes in vertebrates. While several carbonic anhydrase isoforms have been identified in numerous vertebrate species, basal lineages such as the cyclostomes have remained largely unexamined. Here we investigate the repertoire of cytoplasmic carbonic anhydrases in the sea lamprey (Petromyzon marinus), that has a complex life history marked by a dramatic metamorphosis from a benthic filter-feeding ammocoete larvae into a parasitic juvenile which migrates from freshwater to seawater. We have identified a novel carbonic anhydrase gene (ca19) beyond the single carbonic anhydrase gene (ca18) that was known previously. Phylogenetic analysis and synteny studies suggest that both carbonic anhydrase genes form one or two independent gene lineages and are most likely duplicates retained uniquely in cyclostomes. Quantitative PCR of ca19 and ca18 and protein expression in gill across metamorphosis show that the ca19 levels are highest in ammocoetes and decrease during metamorphosis while ca18 shows the opposite pattern with the highest levels in post-metamorphic juveniles. We propose that a unique molecular switch occurs during lamprey metamorphosis resulting in distinct gill carbonic anhydrases reflecting the contrasting life modes and habitats of these life-history stages.

Electrocatalytic interface based on novel carbon nanomaterials for advanced electrochemical sensors

DOE PAGES

Zhou, Ming; Guo, Shaojun

2015-07-17

The rapid development of nanoscience and nanotechnology provides new opportunities for the sustainable progress of nanoscale catalysts (i.e., nanocatalysts). The introduction of nanocatalysts into electronic devices implants their novel functions into electronic sensing systems, resulting in the testing of many advanced electrochemical sensors and the fabrication of some highly sensitive, selective, and stable sensing platforms. In this Review, we will summarize recent significant progress on exploring advanced carbon nanomaterials (such as carbon nanotubes, graphene, highly ordered mesoporous carbons, and electron cyclotron resonance sputtered nanocarbon film) as nanoscale electrocatalysts (i.e., nanoelectrocatalysts) for constructing the catalytic nanointerfaces of electronic devices to achievemore » high-sensitivity and high-selectivity electrochemical sensors. Furthermore, different mechanisms for the extraordinary and unique electrocatalytic activities of these carbon nanomaterials will be also highlighted, compared and discussed. An outlook on the future trends and developments in this area will be provided at the end. Notably, to elaborate the nature of carbon nanomaterial, we will mainly focus on the electrocatalysis of single kind of carbon materials rather than their hybrid composite materials. As a result, we expect that advanced carbon nanomaterials with unique electrocatalytic activities will continue to attract increasing research interest and lead to new opportunities in various fields of research.« less

Electrocatalytic interface based on novel carbon nanomaterials for advanced electrochemical sensors

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

Zhou, Ming; Guo, Shaojun

The rapid development of nanoscience and nanotechnology provides new opportunities for the sustainable progress of nanoscale catalysts (i.e., nanocatalysts). The introduction of nanocatalysts into electronic devices implants their novel functions into electronic sensing systems, resulting in the testing of many advanced electrochemical sensors and the fabrication of some highly sensitive, selective, and stable sensing platforms. In this Review, we will summarize recent significant progress on exploring advanced carbon nanomaterials (such as carbon nanotubes, graphene, highly ordered mesoporous carbons, and electron cyclotron resonance sputtered nanocarbon film) as nanoscale electrocatalysts (i.e., nanoelectrocatalysts) for constructing the catalytic nanointerfaces of electronic devices to achievemore » high-sensitivity and high-selectivity electrochemical sensors. Furthermore, different mechanisms for the extraordinary and unique electrocatalytic activities of these carbon nanomaterials will be also highlighted, compared and discussed. An outlook on the future trends and developments in this area will be provided at the end. Notably, to elaborate the nature of carbon nanomaterial, we will mainly focus on the electrocatalysis of single kind of carbon materials rather than their hybrid composite materials. As a result, we expect that advanced carbon nanomaterials with unique electrocatalytic activities will continue to attract increasing research interest and lead to new opportunities in various fields of research.« less

Revolting Developments in Our Understanding of the Organization of the Eukaryotic Genome.

ERIC Educational Resources Information Center

Krider, Hallie M.

1984-01-01

Various typs of DNA are discussed. Areas considered include highly repetitive and satellite sequences, genes encoding, ribosomal RNA, histone protein genes, and dispersed repeated genes that jump. Regulated genetic misbehavior, structure and use of unique genes, and higher order complexities of chromosomes are also discussed. (JN)

Positional Velar Fronting: An Updated Articulatory Account

ERIC Educational Resources Information Center

Byun, Tara McAllister

2012-01-01

This study develops the hypothesis that the child-specific phenomenon of positional velar fronting can be modeled as the product of phonologically encoded articulatory limitations unique to immature speakers. Children have difficulty executing discrete tongue movements, preferring to move the tongue and jaw as a single unit. This predisposes the…

Primary structural variation in anaplasma marginale Msp2 efficiently generates immune escape variants

USDA-ARS?s Scientific Manuscript database

Antigenic variation allows microbial pathogens to evade immune clearance and establish persistent infection. Anaplasma marginale utilizes gene conversion of a repertoire of silent msp2 alleles into a single active expression site to encode unique Msp2 variants. As the genomic complement of msp2 alle...

HNCA-TOCSY-CANH experiments with alternate 13C-12C labeling: a set of 3D experiment with unique supra-sequential information for mainchain resonance assignment

PubMed Central

Takeuchi, Koh; Gal, Maayan; Takahashi, Hideo; Shimada, Ichio

2011-01-01

Described here is a set of three-dimensional (3D) NMR experiments that rely on CACA-TOCSY magnetization transfer via the weak 3JCαCα coupling. These pulse sequences, which resemble recently described 13C detected CACA-TOCSY (Takeuchi et al. 2010) experiments, are recorded in 1H2O, and use 1H excitation and detection. These experiments require alternate 13C-12C labeling together with perdeuteration, which allows utilizing the small 3JCαCα scalar coupling that is otherwise masked by the stronger 1JCC couplings in uniformly 13C labeled samples. These new experiments provide a unique assignment ladder-mark that yields bidirectional supra-sequential information and can readily straddle proline residues. Unlike the conventional HNCA experiment, which contains only sequential information to the 13Cα of the preceding residue, the 3D hnCA-TOCSY-caNH experiment can yield sequential correlations to alpha carbons in positions i−1, i + 1 and i−2. Furthermore, the 3D hNca-TOCSY-caNH and Hnca-TOC-SY-caNH experiments, which share the same magnetization pathway but use a different chemical shift encoding, directly couple the 15N-1H spin pair of residue i to adjacent amide protons and nitrogens at positions i−2, i−1, i + 1 and i + 2, respectively. These new experimental features make protein backbone assignments more robust by reducing the degeneracy problem associated with the conventional 3D NMR experiments. PMID:21110064

Monolithic graphene transistor biointerface.

PubMed

Nam, SungWoo; Lee, Mi-Sun; Park, Jang-Ung

2012-01-01

We report monolithic integration of graphene and graphite for all-carbon integrated bioelectronics. First, we demonstrate that the electrical properties of graphene and graphite can be modulated by controlling the number of graphene layers, and such capabilities allow graphene to be used as active channels and graphite as metallic interconnects for all-carbon bioelectronics. Furthermore, we show that monolithic graphene-graphite devices exhibit mechanical flexibility and robustness while their electrical responses are not perturbed by mechanical deformation, demonstrating their unique electromechanical properties. Chemical sensing capability of all-carbon integrated bioelectronics is manifested in real-time, complementary pH detection. These unique capabilities of our monolithic graphene-graphite bioelectronics could be exploited in chemical and biological detection and conformal interface with biological systems in the future.

A superhard sp3 microporous carbon with direct bandgap

NASA Astrophysics Data System (ADS)

Pan, Yilong; Xie, Chenlong; Xiong, Mei; Ma, Mengdong; Liu, Lingyu; Li, Zihe; Zhang, Shuangshuang; Gao, Guoying; Zhao, Zhisheng; Tian, Yongjun; Xu, Bo; He, Julong

2017-12-01

Carbon allotropes with distinct sp, sp2, and sp3 hybridization possess various different properties. Here, a novel all-sp3 hybridized tetragonal carbon, namely the P carbon, was predicted by the evolutionary particle swarm structural search. It demonstrated a low density among all-sp3 carbons, due to the corresponding distinctive microporous structure. P carbon is thermodynamically stable than the known C60 and could be formed through the single-walled carbon nanotubes (SWCNTs) compression. P carbon is a direct bandgap semiconductor displaying a strong and superhard nature. The unique combination of electrical and mechanical properties constitutes P carbon a potential superhard material for semiconductor industrial fields.

Confabulation in healthy aging is related to poor encoding and retrieval of over-learned information.

PubMed

Attali, Eve; Dalla Barba, Gianfranco

2013-01-01

Normal aging is characterized by deficits that cross multiple cognitive domains including episodic memory and attention. Compared to young adults (YA), older adults (OA) not only show reduction in true memories, but also an increase in false memories. In this study we aim to elucidate how the production of confabulation is influenced by encoding and retrieval processes. We hypothesized that in OA, compared to YA, over-learned information interferes with the recall of specific, unique past episodes and this interference should be more prominent when a concurrent task perturbs the encoding of the episodes to be recalled. We tested this hypothesis using an experimental paradigm in which a group of OA and a group of YA had to recall three different types of story: a previously unknown story, a well-known fairy tale (Snow White), and a modified well-known fairy tale (Little Red Riding Hood is not eaten by the wolf), in three different experimental conditions: (1) free encoding and free retrieval; (2) Divided attention (DA) at encoding and free retrieval; and (3) free encoding and DA at retrieval. Results showed that OA produced significantly more confabulations than YA, particularly, in the recall of the modified fairy tale. Moreover, DA at encoding markedly increased the number of confabulations, whereas DA at retrieval had no effect on confabulation. Our findings reveal the implications of two phenomena in the production of confabulation in normal aging: the effect of poor encoding and the interference of strongly represented, over-learned information in episodic memory recall.

Fueling Future with Algal Genomics

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

Grigoriev, Igor

Algae constitute a major component of fundamental eukaryotic diversity, play profound roles in the carbon cycle, and are prominent candidates for biofuel production. The US Department of Energy Joint Genome Institute (JGI) is leading the world in algal genome sequencing (http://jgi.doe.gov/Algae) and contributes of the algal genome projects worldwide (GOLD database, 2012). The sequenced algal genomes offer catalogs of genes, networks, and pathways. The sequenced first of its kind genomes of a haptophyte E.huxleyii, chlorarachniophyte B.natans, and cryptophyte G.theta fill the gaps in the eukaryotic tree of life and carry unique genes and pathways as well as molecular fossils ofmore » secondary endosymbiosis. Natural adaptation to conditions critical for industrial production is encoded in algal genomes, for example, growth of A.anophagefferens at very high cell densities during the harmful algae blooms or a global distribution across diverse environments of E.huxleyii, able to live on sparse nutrients due to its expanded pan-genome. Communications and signaling pathways can be derived from simple symbiotic systems like lichens or complex marine algae metagenomes. Collectively these datasets derived from algal genomics contribute to building a comprehensive parts list essential for algal biofuel development.« less

Robert Curl, Jr. and the Discovery of Fullerenes

Science.gov Websites

produced thousands of variations of the buckyball, including carbon sheets one atom thick and microscopic equilibrium in the carbon vapor that allowed the group to identify a unique, 60-atom configuration of carbon Interview with Robert F. Curl, Jr., nobelprize.org (video) Interview with Robert Curl (video) Buckyballs

Climate seasonality limits leaf carbon assimilation and wood productivity in tropical forests

Treesearch

Fabien H. Wagner; Bruno Herault; Damien Bonal; Clement Stahl; Liana O. Anderson; Timothy R. Baker; Gabriel Sebastian Becker; Hans Beeckman; Danilo Boanerges Souza; Paulo Cesar Botosso; David M. J. S. Bowman; Achim Brauning; Benjamin Brede; Foster Irving Brown; Jesus Julio Camarero; Plinio Barbosa Camargo; Fernanda C. G. Cardoso; Fabricio Alvim Carvalho; Wendeson Castro; Rubens Koloski Chagas; Jerome Chave; Emmanuel N. Chidumayo; Deborah A. Clark; Flavia Regina Capellotto Costa; Camille Couralet; Paulo Henrique da Silva Mauricio; Helmut Dalitz; Vinicius Resende de Castro; Jacanan Eloisa de Freitas Milani; Edilson Consuelo de Oliveira; Luciano de Souza Arruda; Jean-Louis Devineau; David M. Drew; Oliver Dunisch; Giselda Durigan; Elisha Elifuraha; Marcio Fedele; Ligia Ferreira Fedele; Afonso Figueiredo Filho; Cesar Augusto Guimaraes Finger; Augusto Cesar Franco; Joao Lima Freitas Junior; Franklin Galvao; Aster Gebrekirstos; Robert Gliniars; Paulo Mauricio Lima de Alencastro Graca; Anthony D. Griffiths; James Grogan; Kaiyu Guan; Jurgen Homeier; Maria Raquel Kanieski; Lip Khoon Kho; Jennifer Koenig; Sintia Valerio Kohler; Julia Krepkowski; Jose Pires Lemos-Filho; Diana Lieberman; Milton Eugene Lieberman; Claudio Sergio Lisi; Tomaz Longhi Santos; Jose Luis Lopez Ayala; Eduardo Eijji Maeda; Yadvinder Malhi; Vivian R. B. Maria; Marcia C. M. Marques; Renato Marques; Hector Maza Chamba; Lawrence Mbwambo; Karina Liana Lisboa Melgaco; Hooz Angela Mendivelso; Brett P. Murphy; Joseph O' Brien; Steven F. Oberbauer; Naoki Okada; Raphael Pelissier; Lynda D. Prior; Fidel Alejandro Roig; Michael Ross; Davi Rodrigo Rossatto; Vivien Rossi; Lucy Rowland; Ervan Rutishauser; Hellen Santana; Mark Schulze; Diogo Selhorst; Williamar Rodrigues Silva; Marcos Silveira; Susanne Spannl; Michael D. Swaine; Jose Julio Toledo; Marcos Miranda Toledo; Marisol Toledo; Takeshi Toma; Mario Tomazello Filho; Juan Ignacio Valdez Hernandez; Jan Verbesselt; Simone Aparecida Vieira; Gregoire Vincent; Carolina Volkmer de Castilho; Franziska Volland; Martin Worbes; Magda Lea Bolzan Zanon; Luiz E. O. C. Aragao

2016-01-01

The seasonal climate drivers of the carbon cycle in tropical forests remain poorly known, although these forests account for more carbon assimilation and storage than any other terrestrial ecosystem. Based on a unique combination of seasonal pan-tropical data sets from 89 experimental sites (68 include aboveground wood productivity measurements and 35 litter...

Estimates of forest canopy height and aboveground biomass using ICESat.

Treesearch

Michael A. Lefsky; David J. Harding; Michael Keller; Warren B. Cohen; Claudia C. Carabajal; Fernando Del Bom Espirito-Santo; Maria O. Hunter; Raimundo de Oliveira Jr.

2005-01-01

Exchange of carbon between forests and the atmosphere is a vital component of the global carbon cycle. Satellite laser altimetry has a unique capability for estimating forest canopy height, which has a direct and increasingly well understood relationship to aboveground carbon storage. While the Geoscience Laser Altimeter System (GLAS) onboard the Ice, Cloud and land...

Two pectin lyase genes, pnl-1 and pnl-2, from Colletotrichum gloeosporioides f. sp. malvae differ in a cellulose-binding domain and in their expression during infection of Malva pusilla.

PubMed

Wei, Yangdou; Shih, Jenny; Li, Jieran; Goodwin, Paul H

2002-07-01

Two pectin lyase genes, designated pnl-1 and pnl-2, were cloned from Colletotrichum gloeosporioides f. sp. malvae, a pathogen of round-leaved mallow (Malva pusilla). pnl-1 was isolated using cDNA from infected plant material; pnl-2 was isolated using cDNA from 3-day-old mycelia grown in mallow-cell-wall extract (MCWE) broth. pnl-1 is the first pectinase gene described thus far to encode a cellulose-binding domain (CBD), which is common in cellulases and xylanases, whereas pnl-2 encodes a pectin lyase that lacks a CBD. In pure culture, pnl-1 expression could be detected when purified pectin or glucose was the sole carbon source, but not when MCWE was the sole carbon source. The lack of pnl-1 expression appeared to be due to gene repression by some unknown factor(s) in the cell-wall extract. In contrast, expression of pnl-2 was detected in cultures when MCWE, but not when purified pectin or glucose, was the sole carbon source. In infected tissue, detection of pnl-1 expression by Northern-blot hybridization and by RT-PCR began with the onset of the necrotrophic phase of infection. Expression ofpnl-2 was not detectable by Northern-blot hybridization, but was observed byRT-PCR in both the biotrophic and necrotrophic phases of infection. The differences between pnl-1 and pnl-2 (i.e. pnl-1 encoding a CBD and differences in the expression patterns of both genes) may be related to the requirements of C. gloeosporioides f. sp. malvae to be able to grow in host tissue under the different conditions present during the biotrophic and necrotrophic phases of infection.

Biodegradation of the Organic Disulfide 4,4′-Dithiodibutyric Acid by Rhodococcus spp.

PubMed Central

Khairy, Heba; Wübbeler, Jan Hendrik

2015-01-01

Four Rhodococcus spp. exhibited the ability to use 4,4′-dithiodibutyric acid (DTDB) as a sole carbon source for growth. The most important step for the production of a novel polythioester (PTE) using DTDB as a precursor substrate is the initial cleavage of DTDB. Thus, identification of the enzyme responsible for this step was mandatory. Because Rhodococcus erythropolis strain MI2 serves as a model organism for elucidation of the biodegradation of DTDB, it was used to identify the genes encoding the enzymes involved in DTDB utilization. To identify these genes, transposon mutagenesis of R. erythropolis MI2 was carried out using transposon pTNR-TA. Among 3,261 mutants screened, 8 showed no growth with DTDB as the sole carbon source. In five mutants, the insertion locus was mapped either within a gene coding for a polysaccharide deacetyltransferase, a putative ATPase, or an acetyl coenzyme A transferase, 1 bp upstream of a gene coding for a putative methylase, or 176 bp downstream of a gene coding for a putative kinase. In another mutant, the insertion was localized between genes encoding a putative transcriptional regulator of the TetR family (noxR) and an NADH:flavin oxidoreductase (nox). Moreover, in two other mutants, the insertion loci were mapped within a gene encoding a hypothetical protein in the vicinity of noxR and nox. The interruption mutant generated, R. erythropolis MI2 noxΩtsr, was unable to grow with DTDB as the sole carbon source. Subsequently, nox was overexpressed and purified, and its activity with DTDB was measured. The specific enzyme activity of Nox amounted to 1.2 ± 0.15 U/mg. Therefore, we propose that Nox is responsible for the initial cleavage of DTDB into 2 molecules of 4-mercaptobutyric acid (4MB). PMID:26407888

Improved annotation through genome-scale metabolic modeling of Aspergillus oryzae

PubMed Central

Vongsangnak, Wanwipa; Olsen, Peter; Hansen, Kim; Krogsgaard, Steen; Nielsen, Jens

2008-01-01

Background Since ancient times the filamentous fungus Aspergillus oryzae has been used in the fermentation industry for the production of fermented sauces and the production of industrial enzymes. Recently, the genome sequence of A. oryzae with 12,074 annotated genes was released but the number of hypothetical proteins accounted for more than 50% of the annotated genes. Considering the industrial importance of this fungus, it is therefore valuable to improve the annotation and further integrate genomic information with biochemical and physiological information available for this microorganism and other related fungi. Here we proposed the gene prediction by construction of an A. oryzae Expressed Sequence Tag (EST) library, sequencing and assembly. We enhanced the function assignment by our developed annotation strategy. The resulting better annotation was used to reconstruct the metabolic network leading to a genome scale metabolic model of A. oryzae. Results Our assembled EST sequences we identified 1,046 newly predicted genes in the A. oryzae genome. Furthermore, it was possible to assign putative protein functions to 398 of the newly predicted genes. Noteworthy, our annotation strategy resulted in assignment of new putative functions to 1,469 hypothetical proteins already present in the A. oryzae genome database. Using the substantially improved annotated genome we reconstructed the metabolic network of A. oryzae. This network contains 729 enzymes, 1,314 enzyme-encoding genes, 1,073 metabolites and 1,846 (1,053 unique) biochemical reactions. The metabolic reactions are compartmentalized into the cytosol, the mitochondria, the peroxisome and the extracellular space. Transport steps between the compartments and the extracellular space represent 281 reactions, of which 161 are unique. The metabolic model was validated and shown to correctly describe the phenotypic behavior of A. oryzae grown on different carbon sources. Conclusion A much enhanced annotation of the A. oryzae genome was performed and a genome-scale metabolic model of A. oryzae was reconstructed. The model accurately predicted the growth and biomass yield on different carbon sources. The model serves as an important resource for gaining further insight into our understanding of A. oryzae physiology. PMID:18500999

Efficacy of Distortion Correction on Diffusion Imaging: Comparison of FSL Eddy and Eddy_Correct Using 30 and 60 Directions Diffusion Encoding

PubMed Central

Yamada, Haruyasu; Abe, Osamu; Shizukuishi, Takashi; Kikuta, Junko; Shinozaki, Takahiro; Dezawa, Ko; Nagano, Akira; Matsuda, Masayuki; Haradome, Hiroki; Imamura, Yoshiki

2014-01-01

Diffusion imaging is a unique noninvasive tool to detect brain white matter trajectory and integrity in vivo. However, this technique suffers from spatial distortion and signal pileup or dropout originating from local susceptibility gradients and eddy currents. Although there are several methods to mitigate these problems, most techniques can be applicable either to susceptibility or eddy-current induced distortion alone with a few exceptions. The present study compared the correction efficiency of FSL tools, “eddy_correct” and the combination of “eddy” and “topup” in terms of diffusion-derived fractional anisotropy (FA). The brain diffusion images were acquired from 10 healthy subjects using 30 and 60 directions encoding schemes based on the electrostatic repulsive forces. For the 30 directions encoding, 2 sets of diffusion images were acquired with the same parameters, except for the phase-encode blips which had opposing polarities along the anteroposterior direction. For the 60 directions encoding, non–diffusion-weighted and diffusion-weighted images were obtained with forward phase-encoding blips and non–diffusion-weighted images with the same parameter, except for the phase-encode blips, which had opposing polarities. FA images without and with distortion correction were compared in a voxel-wise manner with tract-based spatial statistics. We showed that images corrected with eddy and topup possessed higher FA values than images uncorrected and corrected with eddy_correct with trilinear (FSL default setting) or spline interpolation in most white matter skeletons, using both encoding schemes. Furthermore, the 60 directions encoding scheme was superior as measured by increased FA values to the 30 directions encoding scheme, despite comparable acquisition time. This study supports the combination of eddy and topup as a superior correction tool in diffusion imaging rather than the eddy_correct tool, especially with trilinear interpolation, using 60 directions encoding scheme. PMID:25405472

Efficacy of distortion correction on diffusion imaging: comparison of FSL eddy and eddy_correct using 30 and 60 directions diffusion encoding.

PubMed

Yamada, Haruyasu; Abe, Osamu; Shizukuishi, Takashi; Kikuta, Junko; Shinozaki, Takahiro; Dezawa, Ko; Nagano, Akira; Matsuda, Masayuki; Haradome, Hiroki; Imamura, Yoshiki

2014-01-01

Diffusion imaging is a unique noninvasive tool to detect brain white matter trajectory and integrity in vivo. However, this technique suffers from spatial distortion and signal pileup or dropout originating from local susceptibility gradients and eddy currents. Although there are several methods to mitigate these problems, most techniques can be applicable either to susceptibility or eddy-current induced distortion alone with a few exceptions. The present study compared the correction efficiency of FSL tools, "eddy_correct" and the combination of "eddy" and "topup" in terms of diffusion-derived fractional anisotropy (FA). The brain diffusion images were acquired from 10 healthy subjects using 30 and 60 directions encoding schemes based on the electrostatic repulsive forces. For the 30 directions encoding, 2 sets of diffusion images were acquired with the same parameters, except for the phase-encode blips which had opposing polarities along the anteroposterior direction. For the 60 directions encoding, non-diffusion-weighted and diffusion-weighted images were obtained with forward phase-encoding blips and non-diffusion-weighted images with the same parameter, except for the phase-encode blips, which had opposing polarities. FA images without and with distortion correction were compared in a voxel-wise manner with tract-based spatial statistics. We showed that images corrected with eddy and topup possessed higher FA values than images uncorrected and corrected with eddy_correct with trilinear (FSL default setting) or spline interpolation in most white matter skeletons, using both encoding schemes. Furthermore, the 60 directions encoding scheme was superior as measured by increased FA values to the 30 directions encoding scheme, despite comparable acquisition time. This study supports the combination of eddy and topup as a superior correction tool in diffusion imaging rather than the eddy_correct tool, especially with trilinear interpolation, using 60 directions encoding scheme.

A Carbon Dioxide Limitation-Inducible Protein, ColA, Supports the Growth of Synechococcus sp. PCC 7002.

PubMed

Shimakawa, Ginga; Watanabe, Satoru; Miyake, Chikahiro

2017-12-15

A limitation in carbon dioxide (CO₂), which occurs as a result of natural environmental variation, suppresses photosynthesis and has the potential to cause photo-oxidative damage to photosynthetic cells. Oxygenic phototrophs have strategies to alleviate photo-oxidative damage to allow life in present atmospheric CO₂ conditions. However, the mechanisms for CO₂ limitation acclimation are diverse among the various oxygenic phototrophs, and many mechanisms remain to be discovered. In this study, we found that the gene encoding a CO₂ limitation-inducible protein, ColA, is required for the cyanobacterium Synechococcus sp. PCC 7002 (S. 7002) to acclimate to limited CO₂ conditions. An S. 7002 mutant deficient in ColA (Δ colA ) showed lower chlorophyll content, based on the amount of nitrogen, than that in S. 7002 wild-type (WT) under ambient air but not high CO₂ conditions. Both thermoluminescence and protein carbonylation detected in the ambient air grown cells indicated that the lack of ColA promotes oxidative stress in S. 7002. Alterations in the photosynthetic O₂ evolution rate and relative electron transport rate in the short-term response, within an hour, to CO₂ limitation were the same between the WT and Δ colA . Conversely, these photosynthetic parameters were mostly lower in the long-term response of a few days in Δ colA than in the WT. These data suggest that ColA is required to sustain photosynthetic activity for living under ambient air in S. 7002. The unique phylogeny of ColA revealed diverse strategies to acclimate to CO₂ limitation among cyanobacteria.

X-ray and EPR Characterization of the Auxiliary Fe-S Clusters in the Radical SAM Enzyme PqqE.

PubMed

Barr, Ian; Stich, Troy A; Gizzi, Anthony S; Grove, Tyler L; Bonanno, Jeffrey B; Latham, John A; Chung, Tyler; Wilmot, Carrie M; Britt, R David; Almo, Steven C; Klinman, Judith P

2018-02-27

The Radical SAM (RS) enzyme PqqE catalyzes the first step in the biosynthesis of the bacterial cofactor pyrroloquinoline quinone, forming a new carbon-carbon bond between two side chains within the ribosomally synthesized peptide substrate PqqA. In addition to the active site RS 4Fe-4S cluster, PqqE is predicted to have two auxiliary Fe-S clusters, like the other members of the SPASM domain family. Here we identify these sites and examine their structure using a combination of X-ray crystallography and Mössbauer and electron paramagnetic resonance (EPR) spectroscopies. X-ray crystallography allows us to identify the ligands to each of the two auxiliary clusters at the C-terminal region of the protein. The auxiliary cluster nearest the RS site (AuxI) is in the form of a 2Fe-2S cluster ligated by four cysteines, an Fe-S center not seen previously in other SPASM domain proteins; this assignment is further supported by Mössbauer and EPR spectroscopies. The second, more remote cluster (AuxII) is a 4Fe-4S center that is ligated by three cysteine residues and one aspartate residue. In addition, we examined the roles these ligands play in catalysis by the RS and AuxII clusters using site-directed mutagenesis coupled with EPR spectroscopy. Lastly, we discuss the possible functional consequences that these unique AuxI and AuxII clusters may have in catalysis for PqqE and how these may extend to additional RS enzymes catalyzing the post-translational modification of ribosomally encoded peptides.

Converting Carbon Dioxide to Butyrate with an Engineered Strain of Clostridium ljungdahlii

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

Ueki, T; Nevin, KP; Woodard, TL

2014-08-26

Microbial conversion of carbon dioxide to organic commodities via syngas metabolism or microbial electrosynthesis is an attractive option for production of renewable biocommodities. The recent development of an initial genetic toolbox for the acetogen Clostridium ljungdahlii has suggested that C. ljungdahlii may be an effective chassis for such conversions. This possibility was evaluated by engineering a strain to produce butyrate, a valuable commodity that is not a natural product of C. ljungdahlii metabolism. Heterologous genes required for butyrate production from acetyl-coenzyme A (CoA) were identified and introduced initially on plasmids and in subsequent strain designs integrated into the C. ljungdahliimore » chromosome. Iterative strain designs involved increasing translation of a key enzyme by modifying a ribosome binding site, inactivating the gene encoding the first step in the conversion of acetyl-CoA to acetate, disrupting the gene which encodes the primary bifunctional aldehyde/alcohol dehydrogenase for ethanol production, and interrupting the gene for a CoA transferase that potentially represented an alternative route for the production of acetate. These modifications yielded a strain in which ca. 50 or 70% of the carbon and electron flow was diverted to the production of butyrate with H-2 or CO as the electron donor, respectively. These results demonstrate the possibility of producing high-value commodities from carbon dioxide with C. ljungdahlii as the catalyst. IMPORTANCE The development of a microbial chassis for efficient conversion of carbon dioxide directly to desired organic products would greatly advance the environmentally sustainable production of biofuels and other commodities. Clostridium ljungdahlii is an effective catalyst for microbial electrosynthesis, a technology in which electricity generated with renewable technologies, such as solar or wind, powers the conversion of carbon dioxide and water to organic products. Other electron donors for C. ljungdahlii include carbon monoxide, which can be derived from industrial waste gases or the conversion of recalcitrant biomass to syngas, as well as hydrogen, another syngas component. The finding that carbon and electron flow in C. ljungdahlii can be diverted from the production of acetate to butyrate synthesis is an important step toward the goal of renewable commodity production from carbon dioxide with this organism.« less

Fish as major carbonate mud producers and missing components of the tropical carbonate factory

PubMed Central

Perry, Chris T.; Salter, Michael A.; Harborne, Alastair R.; Crowley, Stephen F.; Jelks, Howard L.; Wilson, Rod W.

2011-01-01

Carbonate mud is a major constituent of recent marine carbonate sediments and of ancient limestones, which contain unique records of changes in ocean chemistry and climate shifts in the geological past. However, the origin of carbonate mud is controversial and often problematic to resolve. Here we show that tropical marine fish produce and excrete various forms of precipitated (nonskeletal) calcium carbonate from their guts (“low” and “high” Mg-calcite and aragonite), but that very fine-grained (mostly < 2 μm) high Mg-calcite crystallites (i.e., MgCO3) are their dominant excretory product. Crystallites from fish are morphologically diverse and species-specific, but all are unique relative to previously known biogenic and abiotic sources of carbonate within open marine systems. Using site specific fish biomass and carbonate excretion rate data we estimate that fish produce ∼6.1 × 106 kg CaCO3/year across the Bahamian archipelago, all as mud-grade (the < 63 μm fraction) carbonate and thus as a potential sediment constituent. Estimated contributions from fish to total carbonate mud production average ∼14% overall, and exceed 70% in specific habitats. Critically, we also document the widespread presence of these distinctive fish-derived carbonates in the finest sediment fractions from all habitat types in the Bahamas, demonstrating that these carbonates have direct relevance to contemporary carbonate sediment budgets. Fish thus represent a hitherto unrecognized but significant source of fine-grained carbonate sediment, the discovery of which has direct application to the conceptual ideas of how marine carbonate factories function both today and in the past. PMID:21368155

Cloning and characterization of a cDNA encoding a novel extracellular peroxidase from Trametes versicolor.

PubMed

Collins, P J; O'Brien, M M; Dobson, A D

1999-03-01

The white rot basidiomycete Trametes versicolor secretes a large number of peroxidases which are believed to be involved in the degradation of polymeric lignin. These peroxidases have been classified previously as lignin peroxidases or manganese peroxidases (MnP). We have isolated a novel extracellular peroxidase-encoding cDNA sequence from T. versicolor CU1, the transcript levels of which are repressed by low concentrations of Mn2+ and induced by nitrogen and carbon but not induced in response to a range of stresses which have been reported to induce MnP expression.

Cloning and Characterization of a cDNA Encoding a Novel Extracellular Peroxidase from Trametes versicolor

PubMed Central

Collins, Patrick J.; O’Brien, Margaret M.; Dobson, Alan D. W.

1999-01-01

The white rot basidiomycete Trametes versicolor secretes a large number of peroxidases which are believed to be involved in the degradation of polymeric lignin. These peroxidases have been classified previously as lignin peroxidases or manganese peroxidases (MnP). We have isolated a novel extracellular peroxidase-encoding cDNA sequence from T. versicolor CU1, the transcript levels of which are repressed by low concentrations of Mn2+ and induced by nitrogen and carbon but not induced in response to a range of stresses which have been reported to induce MnP expression. PMID:10049906

Benefits and Costs of Context Reinstatement in Episodic Memory: An ERP Study.

PubMed

Bramão, Inês; Johansson, Mikael

2017-01-01

This study investigated context-dependent episodic memory retrieval. An influential idea in the memory literature is that performance benefits when the retrieval context overlaps with the original encoding context. However, such memory facilitation may not be driven by the encoding-retrieval overlap per se but by the presence of diagnostic features in the reinstated context that discriminate the target episode from competing episodes. To test this prediction, the encoding-retrieval overlap and the diagnostic value of the context were manipulated in a novel associative recognition memory task. Participants were asked to memorize word pairs presented together with diagnostic (unique) and nondiagnostic (shared) background scenes. At test, participants recognized the word pairs in the presence and absence of the previously encoded contexts. Behavioral data show facilitated memory performance in the presence of the original context but, importantly, only when the context was diagnostic of the target episode. The electrophysiological data reveal an early anterior ERP encoding-retrieval overlap effect that tracks the cost associated with having nondiagnostic contexts present at retrieval, that is, shared by multiple previous episodes, and a later posterior encoding-retrieval overlap effect that reflects facilitated access to the target episode during retrieval in diagnostic contexts. Taken together, our results underscore the importance of the diagnostic value of the context and suggest that context-dependent episodic memory effects are multiple determined.

MxaY regulates the lanthanide-mediated methanol dehydrogenase switch in Methylomicrobium buryatense

DOE PAGES

Chu, Frances; Beck, David A. C.; Lidstrom, Mary E.

2016-09-07

Many methylotrophs, microorganisms that consume carbon compounds lacking carbon–carbon bonds, use two different systems to oxidize methanol for energy production and biomass accumulation. The MxaFI methanol dehydrogenase (MDH) contains calcium in its active site, while the XoxF enzyme contains a lanthanide in its active site. The genes encoding the MDH enzymes are differentially regulated by the presence of lanthanides. In this study, we found that the histidine kinase MxaY controls the lanthanide-mediated switch in Methylomicrobium buryatense 5GB1C. MxaY controls the transcription of genes encoding MxaFI and XoxF at least partially by controlling the transcript levels of the orphan response regulatormore » MxaB. We identify a constitutively active version of MxaY, and identify the mutated residue that may be involved in lanthanide sensing. Finally, we find evidence to suggest that tight control of active MDH production is required for wild-type growth rates.« less

Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n-Butanol Production in Escherichia coli.

PubMed

Heo, Min-Ji; Jung, Hwi-Min; Um, Jaeyong; Lee, Sang-Woo; Oh, Min-Kyu

2017-02-17

Genome editing using CRISPR/Cas9 was successfully demonstrated in Esherichia coli to effectively produce n-butanol in a defined medium under microaerobic condition. The butanol synthetic pathway genes including those encoding oxygen-tolerant alcohol dehydrogenase were overexpressed in metabolically engineered E. coli, resulting in 0.82 g/L butanol production. To increase butanol production, carbon flux from acetyl-CoA to citric acid cycle should be redirected to acetoacetyl-CoA. For this purpose, the 5'-untranslated region sequence of gltA encoding citrate synthase was designed using an expression prediction program, UTR designer, and modified using the CRISPR/Cas9 genome editing method to reduce its expression level. E. coli strains with decreased citrate synthase expression produced more butanol and the citrate synthase activity was correlated with butanol production. These results demonstrate that redistributing carbon flux using genome editing is an efficient engineering tool for metabolite overproduction.

Function and Regulation of the Formate Dehydrogenase Genes of the Methanogenic Archaeon Methanococcus maripaludis

PubMed Central

Wood, Gwendolyn E.; Haydock, Andrew K.; Leigh, John A.

2003-01-01

Methanococcus maripaludis is a mesophilic species of Archaea capable of producing methane from two substrates: hydrogen plus carbon dioxide and formate. To study the latter, we identified the formate dehydrogenase genes of M. maripaludis and found that the genome contains two gene clusters important for formate utilization. Phylogenetic analysis suggested that the two formate dehydrogenase gene sets arose from duplication events within the methanococcal lineage. The first gene cluster encodes homologs of formate dehydrogenase α (FdhA) and β (FdhB) subunits and a putative formate transporter (FdhC) as well as a carbonic anhydrase analog. The second gene cluster encodes only FdhA and FdhB homologs. Mutants lacking either fdhA gene exhibited a partial growth defect on formate, whereas a double mutant was completely unable to grow on formate as a sole methanogenic substrate. Investigation of fdh gene expression revealed that transcription of both gene clusters is controlled by the presence of H2 and not by the presence of formate. PMID:12670979

A unique memory process modulated by emotion underpins successful odor recognition and episodic retrieval in humans

PubMed Central

Saive, Anne-Lise; Royet, Jean-Pierre; Ravel, Nadine; Thévenet, Marc; Garcia, Samuel; Plailly, Jane

2014-01-01

We behaviorally explore the link between olfaction, emotion and memory by testing the hypothesis that the emotion carried by odors facilitates the memory of specific unique events. To investigate this idea, we used a novel behavioral approach inspired by a paradigm developed by our team to study episodic memory in a controlled and as ecological as possible way in humans. The participants freely explored three unique and rich laboratory episodes; each episode consisted of three unfamiliar odors (What) positioned at three specific locations (Where) within a visual context (Which context). During the retrieval test, which occurred 24–72 h after the encoding, odors were used to trigger the retrieval of the complex episodes. The participants were proficient in recognizing the target odors among distractors and retrieving the visuospatial context in which they were encountered. The episodic nature of the task generated high and stable memory performances, which were accompanied by faster responses and slower and deeper breathing. Successful odor recognition and episodic memory were not related to differences in odor investigation at encoding. However, memory performances were influenced by the emotional content of the odors, regardless of odor valence, with both pleasant and unpleasant odors generating higher recognition and episodic retrieval than neutral odors. Finally, the present study also suggested that when the binding between the odors and the spatio-contextual features of the episode was successful, the odor recognition and the episodic retrieval collapsed into a unique memory process that began as soon as the participants smelled the odors. PMID:24936176

Genetically encoded sensors for monitoring the transport and concentration of nitrogen-containing and phosphorus-containing molecules in plants.

PubMed

Okumoto, Sakiko; Versaw, Wayne

2017-10-01

Nitrogen and phosphorus are macronutrients indispensable for plant growth. The acquisition and reallocation of both elements require a multitude of dedicated transporters that specifically recognize inorganic and organic forms of nitrogen and phosphorous. Although many transporters have been discovered through elegant screening processes and sequence homology, many remain uncharacterized for their functions in planta. Genetically encoded sensors for nitrogen and phosphorous molecules offer a unique opportunity for studying transport mechanisms that were previously inaccessible. In the past few years, sensors for some of the key nitrogen molecules became available, and many improvements have been made for existing sensors for phosphorus molecules. Methodologies for detailed in vivo analysis also improved. We summarize the recent improvements in genetically encoded sensors for nitrogen and phosphorus molecules, and the discoveries made by using such sensors. Copyright © 2017. Published by Elsevier Ltd.

A novel chlorophyll a/b binding (Cab) protein gene from petunia which encodes the lower molecular weight Cab precursor protein.

PubMed

Stayton, M M; Black, M; Bedbrook, J; Dunsmuir, P

1986-12-22

The 16 petunia Cab genes which have been characterized are all closely related at the nucleotide sequence level and they encode Cab precursor polypeptides which are similar in sequence and length. Here we describe a novel petunia Cab gene which encodes a unique Cab precursor protein. This protein is a member of the smallest class of Cab precursor proteins for which no gene has previously been assigned in petunia or any other species. The features of this Cab precursor protein are that it is shorter by 2-3 amino acids than the formerly characterized Cab precursors, its transit peptide sequence is unrelated, and the mature polypeptide is significantly diverged at the functionally important N terminus from other petunia Cab proteins. Gene structure also discriminates this gene which is the only intron containing Cab gene in petunia genomic DNA.

Get the gist? The effects of processing depth on false recognition in short-term and long-term memory.

PubMed

Flegal, Kristin E; Reuter-Lorenz, Patricia A

2014-07-01

Gist-based processing has been proposed to account for robust false memories in the converging-associates task. The deep-encoding processes known to enhance verbatim memory also strengthen gist memory and increase distortions of long-term memory (LTM). Recent research has demonstrated that compelling false memory illusions are relatively delay-invariant, also occurring under canonical short-term memory (STM) conditions. To investigate the contributions of gist to false memory at short and long delays, processing depth was manipulated as participants encoded lists of four semantically related words and were probed immediately, following a filled 3- to 4-s retention interval, or approximately 20 min later, in a surprise recognition test. In two experiments, the encoding manipulation dissociated STM and LTM on the frequency, but not the phenomenology, of false memory. Deep encoding at STM increases false recognition rates at LTM, but confidence ratings and remember/know judgments are similar across delays and do not differ as a function of processing depth. These results suggest that some shared and some unique processes underlie false memory illusions at short and long delays.

Inventory of high-abundance mRNAs in skeletal muscle of normal men.

PubMed

Welle, S; Bhatt, K; Thornton, C A

1999-05-01

G42875rial analysis of gene expression (SAGE) method was used to generate a catalog of 53,875 short (14 base) expressed sequence tags from polyadenylated RNA obtained from vastus lateralis muscle of healthy young men. Over 12,000 unique tags were detected. The frequency of occurrence of each tag reflects the relative abundance of the corresponding mRNA. The mRNA species that were detected 10 or more times, each comprising >/=0.02% of the mRNA population, accounted for 64% of the mRNA mass but <10% of the total number of mRNA species detected. Almost all of the abundant tags matched mRNA or EST sequences cataloged in GenBank. Mitochondrial transcripts accounted for approximately 20% of the polyadenylated RNA. Transcripts encoding proteins of the myofibrils were the most abundant nuclear-encoded mRNAs. Transcripts encoding ribosomal proteins, and those encoding proteins involved in energy metabolism, also were very abundant. The database can be used as a reference for investigations of alterations in gene expression associated with conditions that influence muscle function, such as muscular dystrophies, aging, and exercise.

The great billion-year war between ribosome- and capsid-encoding organisms (cells and viruses) as the major source of evolutionary novelties.

PubMed

Forterre, Patrick; Prangishvili, David

2009-10-01

Our conceptions on the origin, nature, and role of viruses have been shaken recently by several independent lines of research. There are many reasons to believe now that viruses are more ancient than modern cells and have always been more abundant and diverse than their cellular targets. Viruses can be defined as capsid-encoding organisms that transform their "host" cell into a viral factory. If capsid-encoding organisms (viruses) and ribosome-encoding organisms (cells) are the major types of living entities on our planet, it seems logical to conclude that their conflict has been a major engine of biological evolution (in the framework of natural selection). In particular, many novelties first selected in the viral world might have been transferred to cells as a consequence of the continuous flow of viral genes into cellular genomes. We discuss recent observations and hypotheses suggesting that viruses have played a major role at different stages of biological evolution, such as the RNA to DNA transition, the origin of the eukaryotic nucleus, or, alternatively, the origin of unique features in multicellular macrobes.

In vivo detection of SERS-encoded plasmonic nanostars in human skin grafts and live animal models.

PubMed

Register, Janna K; Fales, Andrew M; Wang, Hsin-Neng; Norton, Stephen J; Cho, Eugenia H; Boico, Alina; Pradhan, Sulolit; Kim, Jason; Schroeder, Thies; Wisniewski, Natalie A; Klitzman, Bruce; Vo-Dinh, Tuan

2015-11-01

Surface-enhanced Raman scattering (SERS)-active plasmonic nanomaterials have become a promising agent for molecular imaging and multiplex detection. Among the wide variety of plasmonics-active nanoparticles, gold nanostars offer unique plasmon properties that efficiently induce strong SERS signals. Furthermore, nanostars, with their small core size and multiple long thin branches, exhibit high absorption cross sections that are tunable in the near-infrared region of the tissue optical window, rendering them efficient for in vivo spectroscopic detection. This study investigated the use of SERS-encoded gold nanostars for in vivo detection. Ex vivo measurements were performed using human skin grafts to investigate the detection of SERS-encoded nanostars through tissue. We also integrated gold nanostars into a biocompatible scaffold to aid in performing in vivo spectroscopic analyses. In this study, for the first time, we demonstrate in vivo SERS detection of gold nanostars using small animal (rat) as well as large animal (pig) models. The results of this study establish the usefulness and potential of SERS-encoded gold nanostars for future use in long-term in vivo analyte sensing.

Characterization of a cDNA encoding a protein involved in formation of the skeleton during development of the sea urchin Lytechinus pictus.

PubMed

Livingston, B T; Shaw, R; Bailey, A; Wilt, F

1991-12-01

In order to investigate the role of proteins in the formation of mineralized tissues during development, we have isolated a cDNA that encodes a protein that is a component of the organic matrix of the skeletal spicule of the sea urchin, Lytechinus pictus. The expression of the RNA encoding this protein is regulated over development and is localized to the descendents of the micromere lineage. Comparison of the sequence of this cDNA to homologous cDNAs from other species of urchin reveal that the protein is basic and contains three conserved structural motifs: a signal peptide, a proline-rich region, and an unusual region composed of a series of direct repeats. Studies on the protein encoded by this cDNA confirm the predicted reading frame deduced from the nucleotide sequence and show that the protein is secreted and not glycosylated. Comparison of the amino acid sequence to databases reveal that the repeat domain is similar to proteins that form a unique beta-spiral supersecondary structure.

ACID FUNCTIONALIZED SINGLE-WALLED CARBON NANOTUBES ENHANCE CARDIAC ISCHEMIC/REPERFUSIOIN INJURY

EPA Science Inventory

Engineered carbon nanotubes are being intensively developed for wide applications. Because of their unique light properties, nanotubes can impose some potentially toxic effects, particularly if they have been modified to express functionally reactive chemical groups on their sur...

Materials Science: Nanotube composites

NASA Astrophysics Data System (ADS)

Ajayan, Pulickel M.; Tour, James M.

2007-06-01

A carbon revolution has occurred - carbon atoms can be coaxed into several topologies to make materials with unique properties. Nanotubes are the vanguard of this innovation, and are on the cusp of commercial exploitation as the multifunctional components of the next generation of composite materials.

Partially unzipped carbon nanotubes as a superior catalyst support for PEM fuel cells.

PubMed

Long, Donghui; Li, Wei; Qiao, Wenming; Miyawaki, Jin; Yoon, Seong-Ho; Mochida, Isao; Ling, Licheng

2011-09-07

Partially unzipped carbon nanotubes prepared by strong oxidation and thermal expansion of carbon nanotubes were explored as an advanced catalyst support for PEM fuel cells. The unique hybrid structure of 1D nanotube and 2D double-side graphene resulted in an outstanding electrocatalytic performance. This journal is © The Royal Society of Chemistry 2011

Nanoporous Carbons: Looking Beyond Their Perception as Adsorbents, Catalyst Supports and Supercapacitors.

PubMed

Bandosz, Teresa J

2016-02-01

The discovery of carbon nanoforms, and especially graphene, has opened up new directions of science and technology. Many applications are based on the unique properties of graphene, such as its high electrical and thermal conductivity, strength, flexibility, photoactivity and transparency. Inspired by the emerging graphene science, we directed our efforts to the exploration of new applications of nanoporous (microporous) carbons. Their matrix is built of distorted graphene layers, between which pores with sizes ranging from a fraction of a nanometer to hundreds of nanometers exist. This is a very unique feature of nanoporous carbons resulting in their developed surface areas. Moreover, there are vast possibilities to modify the surface chemistry of carbons and thus their surface properties. Even though the traditional applications of porous carbons focus mainly on adsorption and separation, we decided to explore them as photocatalysts, oxygen reduction catalysts and sensors. Related to their visible-light activity, their possible application in solar energy harvesting is also indicated. This Personal Account presents our paths leading to the exploration of these directions, describing the results collected and difficulties encountered, along with the challenges remaining to be addressed. © 2015 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Identification of potential hydrophobic properties of carbon layer from the coffee bean waste

NASA Astrophysics Data System (ADS)

Fitria, D.; Baroroh, L. A. Al; Destyorini, F.; Widayatno, W. B.; Amal, M. I.; Wismogroho, A. S.

2018-03-01

The significant increase of waste due to vast development of human civilization and industrialization has plunged humanity into various environmental issues. Nowadays, the concern on waste handling and conversion into more valuable material has become one of hot research topics. Biomass waste has great abundance with various types that can be utilized for many applications such as landfill, recycled-material, adsorbent, separation, catalysis, and so on. In this study, coffee bean waste (CBW) was used as a source to produce hydrophobic layer. The CBW was converted into amorphous carbon using simple carbonization method at 500 °C, dispersed in acetic acid and then mixed with polyvinyl alcohol (PVA) at low temperature heating. In order to investigate effects of composition on hydrophobicity properties, ratio of carbon and PVA was varied. In addition, acetic acid was used to evaluate effect of dispersant on hydrophobic properties. SEM analysis reveals unique morphology of carbon layer. The measurement of contact angle demonstrates that this unique morphology possesses comparable hydrophobicity with that of some well-known materials. Fourier transform infrared spectroscopy (FTIR) analysis confirms the effect of PVA bonding and carbon layer on its hydrophobicity.

A novel omega3-fatty acid desaturase involved in the biosynthesis of eicosapentaenoic acid.

PubMed Central

Pereira, Suzette L; Huang, Yung-Sheng; Bobik, Emil G; Kinney, Anthony J; Stecca, Kevin L; Packer, Jeremy C L; Mukerji, Pradip

2004-01-01

Long-chain n-3 PUFAs (polyunsaturated fatty acids) such as EPA (eicosapentaenoic acid; 20:5 n-3) have important therapeutic and nutritional benefits in humans. In plants, cyanobacteria and nematodes, omega3-desaturases catalyse the formation of these n-3 fatty acids from n-6 fatty acid precursors. Here we describe the isolation and characterization of a gene ( sdd17 ) derived from an EPA-rich fungus, Saprolegnia diclina, that encodes a novel omega3-desaturase. This gene was isolated by PCR amplification of an S. diclina cDNA library using oligonucleotide primers corresponding to conserved regions of known omega3-desaturases. Expression of this gene in Saccharomyces cerevisiae, in the presence of various fatty acid substrates, revealed that the recombinant protein could exclusively desaturate 20-carbon n-6 fatty acid substrates with a distinct preference for ARA (arachidonic acid; 20:4 n-6), converting it into EPA. This activity differs from that of the known omega3-desaturases from any organism. Plant and cyanobacterial omega3-desaturases exclusively desaturate 18-carbon n-6 PUFAs, and a Caenorhabditis elegans omega3-desaturase preferentially desaturated 18-carbon PUFAs over 20-carbon substrates, and could not convert ARA into EPA when expressed in yeast. The sdd17 -encoded desaturase was also functional in transgenic somatic soya bean embryos, resulting in the production of EPA from exogenously supplied ARA, thus demonstrating its potential for use in the production of EPA in transgenic oilseed crops. PMID:14651475

Blowing Carbon Nanotubes to Carbon Nanobulbs

NASA Astrophysics Data System (ADS)

Su, D. S.; Zhu, Z. P.; Lu, Y.; Schlögl, R.; Weinberg, G.; Liu, Z. Y.

2004-09-01

We report the blowing of multi-walled carbon nanotubes into carbon nanobulbs. This is realized in a unique tube growth environment generated by explosive decomposition of picric acid mixed with nickel formate. The carbon spherical bulbs are characterized by large dimensions (up to 900 nm), thin walls (around 10 nm), and fully hollow cores. The walls are in graphitic structure of sp2 hybridized carbons. Bulb-tube assemblies are found as intermediate derivatives of blowing. A joint action of the filled high-pressure gases and the structural defects in the carbon nanotubes is responsible to the formation of the carbon nanobulbs. Our finding may indicate the possibility to engineer the carbon nanotubes to the designed nanostructures.

N-doped yolk-shell hollow carbon sphere wrapped with graphene as sulfur host for high-performance lithium-sulfur batteries

NASA Astrophysics Data System (ADS)

Zhang, Yongzheng; Sun, Kai; Liang, Zhan; Wang, Yanli; Ling, Licheng

2018-01-01

N-doped yolk-shell hollow carbon sphere wrapped with reduced graphene oxide (rGO/N-YSHCS) is designed and fabricated as sulfur host for lithium-sulfur batteries. The shuttle effect of polysulfides can be suppressed effectively by the porous yolk-shell structure, graphene layer and N-doping. A good conductivity network is provided for electron transportation through the graphene layer coupled with the unique yolk-shell carbon matrix. Such unique structure offers the synthesized rGO/N-YSHCS/S electrode with a high reversible capacity (800 mAh g-1 at 0.2 C after 100 cycles) and good high-rate capability (636 mAh g-1 at 1 C and 540 mAh g-1 at 2 C).

Is Chemically Synthesized Graphene ‘Really’ a Unique Substrate for SERS and Fluorescence Quenching?

NASA Astrophysics Data System (ADS)

Sil, Sanchita; Kuhar, Nikki; Acharya, Somnath; Umapathy, Siva

2013-11-01

We demonstrate observation of Raman signals of different analytes adsorbed on carbonaceous materials, such as, chemically reduced graphene, graphene oxide (GO), multi-walled carbon nanotube (MWCNT), graphite and activated carbon. The analytes selected for the study were Rhodamine 6G (R6G) (in resonant conditions), Rhodamine B (RB), Nile blue (NBA), Crystal Violet (CV) and acetaminophen (paracetamol). All the analytes except paracetamol absorb and fluoresce in the visible region. In this article we provide experimental evidence of the fact that observation of Raman signals of analytes on such carbonaceous materials are more due to resonance effect, suppression of fluorescence and efficient adsorption and that this property in not unique to graphene or nanotubes but prevalent for various type of carbon materials.

Cancer in the crosshairs: targeting cancer metabolism with hyperpolarized carbon-13 MRI technology.

PubMed

von Morze, Cornelius; Merritt, Matthew E

2018-06-05

Magnetic resonance (MR)-based hyperpolarized (HP) 13 C metabolic imaging is under active pursuit as a new clinical diagnostic method for cancer detection, grading, and monitoring of therapeutic response. Following the tremendous success of metabolic imaging by positron emission tomography, which already plays major roles in clinical oncology, the added value of HP 13 C MRI is emerging. Aberrant glycolysis and central carbon metabolism is a hallmark of many forms of cancer. The chemical transformations associated with these pathways produce metabolites ranging in general from three to six carbons, and are dependent on the redox state and energy charge of the tissue. The significant changes in chemistry associated with flux through these pathways imply that HP imaging can take advantage of the underlying chemical shift information encoded into an MR experiment to produce images of the injected substrate as well as its metabolites. However, imaging of HP metabolites poses unique constraints on pulse sequence design related to detection of X-nuclei, decay of the HP magnetization due to T 1 , and the consumption of HP signal by the inspection pulses. Advancements in the field continue to depend critically on customization of MRI systems and pulse sequences for optimized detection of HP 13 C signals, focused largely on extracting the maximum amount of information during the short lifetime of the HP magnetization. From a clinical perspective, the success of HP 13 C MRI of cancer will largely depend upon the utility of HP pyruvate for the detection of lactate pools associated with the Warburg effect, though several other agents are also under investigation, with novel agents continually being formulated. In this review, the salient aspects of HP 13 C imaging will be highlighted, with an emphasis on both technological challenges and the biochemical aspects of HP experimental design. Copyright © 2018 John Wiley & Sons, Ltd.

Deep Levels of Processing Elicit a Distinctiveness Heuristic: Evidence from the Criterial Recollection Task

ERIC Educational Resources Information Center

Gallo, David A.; Meadow, Nathaniel G.; Johnson, Elizabeth L.; Foster, Katherine T.

2008-01-01

Thinking about the meaning of studied words (deep processing) enhances memory on typical recognition tests, relative to focusing on perceptual features (shallow processing). One explanation for this levels-of-processing effect is that deep processing leads to the encoding of more distinctive representations (i.e., more unique semantic or…

Primary structure of the Aequorea victoria green-fluorescent protein.

PubMed

Prasher, D C; Eckenrode, V K; Ward, W W; Prendergast, F G; Cormier, M J

1992-02-15

Many cnidarians utilize green-fluorescent proteins (GFPs) as energy-transfer acceptors in bioluminescence. GFPs fluoresce in vivo upon receiving energy from either a luciferase-oxyluciferin excited-state complex or a Ca(2+)-activated phosphoprotein. These highly fluorescent proteins are unique due to the chemical nature of their chromophore, which is comprised of modified amino acid (aa) residues within the polypeptide. This report describes the cloning and sequencing of both cDNA and genomic clones of GFP from the cnidarian, Aequorea victoria. The gfp10 cDNA encodes a 238-aa-residue polypeptide with a calculated Mr of 26,888. Comparison of A. victoria GFP genomic clones shows three different restriction enzyme patterns which suggests that at least three different genes are present in the A. victoria population at Friday Harbor, Washington. The gfp gene encoded by the lambda GFP2 genomic clone is comprised of at least three exons spread over 2.6 kb. The nucleotide sequences of the cDNA and the gene will aid in the elucidation of structure-function relationships in this unique class of proteins.

The Unique Biosynthetic Route from Lupinus β-Conglutin Gene to Blad

PubMed Central

Monteiro, Sara; Freitas, Regina; Rajasekhar, Baru T.; Teixeira, Artur R.; Ferreira, Ricardo B.

2010-01-01

Background During seed germination, β-conglutin undergoes a major cycle of limited proteolysis in which many of its constituent subunits are processed into a 20 kDa polypeptide termed blad. Blad is the main component of a glycooligomer, accumulating exclusively in the cotyledons of Lupinus species, between days 4 and 12 after the onset of germination. Principal Findings The sequence of the gene encoding β-conglutin precursor (1791 nucleotides) is reported. This gene, which shares 44 to 57% similarity and 20 to 37% identity with other vicilin-like protein genes, includes several features in common with these globulins, but also specific hallmarks. Most notable is the presence of an ubiquitin interacting motif (UIM), which possibly links the unique catabolic route of β-conglutin to the ubiquitin/proteasome proteolytic pathway. Significance Blad forms through a unique route from and is a stable intermediary product of its precursor, β-conglutin, the major Lupinus seed storage protein. It is composed of 173 amino acid residues, is encoded by an intron-containing, internal fragment of the gene that codes for β-conglutin precursor (nucleotides 394 to 913) and exhibits an isoelectric point of 9.6 and a molecular mass of 20,404.85 Da. Consistent with its role as a storage protein, blad contains an extremely high proportion of the nitrogen-rich amino acids. PMID:20066045

A novel mycovirus from Aspergillus fumigatus contains four unique dsRNAs as its genome and is infectious as dsRNA

PubMed Central

Kanhayuwa, Lakkhana; Kotta-Loizou, Ioly; Özkan, Selin; Gunning, A. Patrick; Coutts, Robert H. A.

2015-01-01

We report the discovery and characterization of a double-stranded RNA (dsRNA) mycovirus isolated from the human pathogenic fungus Aspergillus fumigatus, Aspergillus fumigatus tetramycovirus-1 (AfuTmV-1), which reveals several unique features not found previously in positive-strand RNA viruses, including the fact that it represents the first dsRNA (to our knowledge) that is not only infectious as a purified entity but also as a naked dsRNA. The AfuTmV-1 genome consists of four capped dsRNAs, the largest of which encodes an RNA-dependent RNA polymerase (RdRP) containing a unique GDNQ motif normally characteristic of negative-strand RNA viruses. The third largest dsRNA encodes an S-adenosyl methionine–dependent methyltransferase capping enzyme and the smallest dsRNA a P-A-S–rich protein that apparently coats but does not encapsidate the viral genome as visualized by atomic force microscopy. A combination of a capping enzyme with a picorna-like RdRP in the AfuTmV-1 genome is a striking case of chimerism and the first example (to our knowledge) of such a phenomenon. AfuTmV-1 appears to be intermediate between dsRNA and positive-strand ssRNA viruses, as well as between encapsidated and capsidless RNA viruses. PMID:26139522

The FBPase Encoding Gene glpX Is Required for Gluconeogenesis, Bacterial Proliferation and Division In Vivo of Mycobacterium marinum

PubMed Central

Lyu, Liangdong; Wang, Chuan; Li, Yang; Gao, Qian; Yang, Chen

2016-01-01

Lipids have been identified as important carbon sources for Mycobacterium tuberculosis (Mtb) to utilize in vivo. Thus gluconeogenesis bears a key role for Mtb to survive and replicate in host. A rate-limiting enzyme of gluconeogenesis, fructose 1, 6-bisphosphatase (FBPase) is encoded by the gene glpX. The functions of glpX were studied in M. marinum, a closely related species to Mtb. The glpX deletion strain (ΔglpX) displayed altered gluconeogenesis, attenuated virulence, and altered bacterial proliferation. Metabolic profiles indicate an accumulation of the FBPase substrate, fructose 1, 6-bisphosphate (FBP) and altered gluconeogenic flux when ΔglpX is cultivated in a gluconeogenic carbon substrate, acetate. In both macrophages and zebrafish, the proliferation of ΔglpX was halted, resulting in dramatically attenuated virulence. Intracellular ΔglpX exhibited an elongated morphology, which was also observed when ΔglpX was grown in a gluconeogenic carbon source. This elongated morphology is also supported by the observation of unseparated multi-nucleoid cell, indicating that a complete mycobacterial division in vivo is correlated with intact gluconeogenesis. Together, our results indicate that glpX has essential functions in gluconeogenesis, and plays an indispensable role in bacterial proliferation in vivo and virulence of M. marinum. PMID:27233038

The FBPase Encoding Gene glpX Is Required for Gluconeogenesis, Bacterial Proliferation and Division In Vivo of Mycobacterium marinum.

PubMed

Tong, Jingfeng; Meng, Lu; Wang, Xinwei; Liu, Lixia; Lyu, Liangdong; Wang, Chuan; Li, Yang; Gao, Qian; Yang, Chen; Niu, Chen

2016-01-01

Lipids have been identified as important carbon sources for Mycobacterium tuberculosis (Mtb) to utilize in vivo. Thus gluconeogenesis bears a key role for Mtb to survive and replicate in host. A rate-limiting enzyme of gluconeogenesis, fructose 1, 6-bisphosphatase (FBPase) is encoded by the gene glpX. The functions of glpX were studied in M. marinum, a closely related species to Mtb. The glpX deletion strain (ΔglpX) displayed altered gluconeogenesis, attenuated virulence, and altered bacterial proliferation. Metabolic profiles indicate an accumulation of the FBPase substrate, fructose 1, 6-bisphosphate (FBP) and altered gluconeogenic flux when ΔglpX is cultivated in a gluconeogenic carbon substrate, acetate. In both macrophages and zebrafish, the proliferation of ΔglpX was halted, resulting in dramatically attenuated virulence. Intracellular ΔglpX exhibited an elongated morphology, which was also observed when ΔglpX was grown in a gluconeogenic carbon source. This elongated morphology is also supported by the observation of unseparated multi-nucleoid cell, indicating that a complete mycobacterial division in vivo is correlated with intact gluconeogenesis. Together, our results indicate that glpX has essential functions in gluconeogenesis, and plays an indispensable role in bacterial proliferation in vivo and virulence of M. marinum.

High resolution stable isotope and carbonate variability during the early Oligocene climate transition: Walvis Ridge (ODP Site 1263)

USGS Publications Warehouse

2007-01-01

resolution reconstruction of the Eocene/Oligocene from the Atlantic basin to date, and provide us with a unique opportunity to investigate the fine-scale interplay of glaciation and the global carbon cycle.

Metabolomic Analysis of Liver Cells Exposed to Carbon Nanotubes and Graphene Oxide

EPA Science Inventory

Carbon nanotubes (CNTs) and other graphenic nanomaterials are being used extensively in industrial, consumer, and mechanical applications based in part on their unique structural, optical and electronic properties. Due to the widespread use of these nanoparticles (NPs), human and...

Glucose-Induced Trophic Shift in an Endosymbiont Dinoflagellate with Physiological and Molecular Consequences1[OPEN

PubMed Central

Jinkerson, Robert E.; Clowez, Sophie; Onishi, Masayuki; Cleves, Phillip A.; Pringle, John R.

2018-01-01

Interactions between the dinoflagellate endosymbiont Symbiodinium and its cnidarian hosts (e.g. corals, sea anemones) are the foundation of coral-reef ecosystems. Carbon flow between the partners is a hallmark of this mutualism, but the mechanisms governing this flow and its impact on symbiosis remain poorly understood. We showed previously that although Symbiodinium strain SSB01 can grow photoautotrophically, it can grow mixotrophically or heterotrophically when supplied with Glc, a metabolite normally transferred from the alga to its host. Here we show that Glc supplementation of SSB01 cultures causes a loss of pigmentation and photosynthetic activity, disorganization of thylakoid membranes, accumulation of lipid bodies, and alterations of cell-surface morphology. We used global transcriptome analyses to determine if these physiological changes were correlated with changes in gene expression. Glc-supplemented cells exhibited a marked reduction in levels of plastid transcripts encoding photosynthetic proteins, although most nuclear-encoded transcripts (including those for proteins involved in lipid synthesis and formation of the extracellular matrix) exhibited little change in their abundances. However, the altered carbon metabolism in Glc-supplemented cells was correlated with modest alterations (approximately 2x) in the levels of some nuclear-encoded transcripts for sugar transporters. Finally, Glc-bleached SSB01 cells appeared unable to efficiently populate anemone larvae. Together, these results suggest links between energy metabolism and cellular physiology, morphology, and symbiotic interactions. However, the results also show that in contrast to many other organisms, Symbiodinium can undergo dramatic physiological changes that are not reflected by major changes in the abundances of nuclear-encoded transcripts and thus presumably reflect posttranscriptional regulatory processes. PMID:29217594

Error control techniques for satellite and space communications

NASA Technical Reports Server (NTRS)

Costello, Daniel J., Jr.

1994-01-01

The unequal error protection capabilities of convolutional and trellis codes are studied. In certain environments, a discrepancy in the amount of error protection placed on different information bits is desirable. Examples of environments which have data of varying importance are a number of speech coding algorithms, packet switched networks, multi-user systems, embedded coding systems, and high definition television. Encoders which provide more than one level of error protection to information bits are called unequal error protection (UEP) codes. In this work, the effective free distance vector, d, is defined as an alternative to the free distance as a primary performance parameter for UEP convolutional and trellis encoders. For a given (n, k), convolutional encoder, G, the effective free distance vector is defined as the k-dimensional vector d = (d(sub 0), d(sub 1), ..., d(sub k-1)), where d(sub j), the j(exp th) effective free distance, is the lowest Hamming weight among all code sequences that are generated by input sequences with at least one '1' in the j(exp th) position. It is shown that, although the free distance for a code is unique to the code and independent of the encoder realization, the effective distance vector is dependent on the encoder realization.

The impact of port emissions and marine biogenics on the single-particle chemistry of marine aerosol measured on board the R/V Atlantis during the CalNEX 2010 field campaign

NASA Astrophysics Data System (ADS)

Gaston, C. J.; Quinn, P.; Bates, T. S.; Prather, K. A.

2010-12-01

Marine environments are characterized by low particle concentrations and, as such, are sensitive to changes in particle number concentration and chemistry induced by biogenic and anthropogenic influences. Measurements of both gas phase and particle phase emissions on board the R/V Atlantis during the CalNEX 2010 field campaign provided an opportunity to examine the impact of anthropogenic and marine biogenic emissions on particle chemistry along the California coast. Real-time, single-particle measurements made using an aerosol time-of-flight mass spectrometer (ATOFMS) revealed the single-particle mixing state of the sampled marine aerosols. Submicron particles (0.2-1.0 um) containing organic carbon, elemental carbon mixed with organic carbon, and unique V-containing particles previously detected in port regions were prevalent throughout the Southern California coast; most of these particles were also associated with sulfate. Measurements made in the deep water channel near Sacramento, CA revealed dramatically different particle chemistry that was characterized by organic carbon and amines. Particles measured further away from the continent toward the open ocean were influenced by marine biological activity due to a phytoplankton bloom that was occurring off the California coast. During this sampling period, unique ocean-derived particles containing internal mixtures of Mg and organic carbon were detected in addition to unique particles containing elemental S ions, which were only detected at night. An aerosol generator used to bubble seawater in order to characterize primary emissions from the ocean confirmed that the Mg-organic carbon and S-containing particles were indeed emitted from the ocean. These measurements reveal the strong impact of both port emissions as well as marine biogenic emissions on aerosol chemistry along the California coast.

Carbon-dependent control of electron transfer and central carbon pathway genes for methane biosynthesis in the Archaean, Methanosarcina acetivorans strain C2A

PubMed Central

2010-01-01

Background The archaeon, Methanosarcina acetivorans strain C2A forms methane, a potent greenhouse gas, from a variety of one-carbon substrates and acetate. Whereas the biochemical pathways leading to methane formation are well understood, little is known about the expression of the many of the genes that encode proteins needed for carbon flow, electron transfer and/or energy conservation. Quantitative transcript analysis was performed on twenty gene clusters encompassing over one hundred genes in M. acetivorans that encode enzymes/proteins with known or potential roles in substrate conversion to methane. Results The expression of many seemingly "redundant" genes/gene clusters establish substrate dependent control of approximately seventy genes for methane production by the pathways for methanol and acetate utilization. These include genes for soluble-type and membrane-type heterodisulfide reductases (hdr), hydrogenases including genes for a vht-type F420 non-reducing hydrogenase, molybdenum-type (fmd) as well as tungsten-type (fwd) formylmethanofuran dehydrogenases, genes for rnf and mrp-type electron transfer complexes, for acetate uptake, plus multiple genes for aha- and atp-type ATP synthesis complexes. Analysis of promoters for seven gene clusters reveal UTR leaders of 51-137 nucleotides in length, raising the possibility of both transcriptional and translational levels of control. Conclusions The above findings establish the differential and coordinated expression of two major gene families in M. acetivorans in response to carbon/energy supply. Furthermore, the quantitative mRNA measurements demonstrate the dynamic range for modulating transcript abundance. Since many of these gene clusters in M. acetivorans are also present in other Methanosarcina species including M. mazei, and in M. barkeri, these findings provide a basis for predicting related control in these environmentally significant methanogens. PMID:20178638

The Phosphatidylinositol 3,5-Bisphosphate (PI(3,5)P2)-dependent Tup1 Conversion (PIPTC) Regulates Metabolic Reprogramming from Glycolysis to Gluconeogenesis*

PubMed Central

Han, Bong-Kwan; Emr, Scott D.

2013-01-01

Glucose/carbon metabolism is a fundamental cellular process in living cells. In response to varying environments, eukaryotic cells reprogram their glucose/carbon metabolism between aerobic or anaerobic glycolysis, oxidative phosphorylation, and/or gluconeogenesis. The distinct type of glucose/carbon metabolism that a cell carries out has significant effects on the cell's proliferation and differentiation. However, it is poorly understood how the reprogramming of glucose/carbon metabolism is regulated. Here, we report a novel endosomal PI(3,5)P2 lipid-dependent regulatory mechanism that is required for metabolic reprogramming from glycolysis to gluconeogenesis in Saccharomyces cerevisiae. Certain gluconeogenesis genes, such as FBP1 (encoding fructose-1,6-bisphosphatase 1) and ICL1 (encoding isocitrate lyase 1) are under control of the Mig1 repressor and Cyc8-Tup1 corepressor complex. We previously identified the PI(3,5)P2-dependent Tup1 conversion (PIPTC), a mechanism to convert Cyc8-Tup1 corepressor to Cti6-Cyc8-Tup1 coactivator. We demonstrate that the PIPTC plays a critical role for transcriptional activation of FBP1 and ICL1. Furthermore, without the PIPTC, the Cat8 and Sip4 transcriptional activators cannot be efficiently recruited to the promoters of FBP1 and ICL1, suggesting a key role for the PIPTC in remodulating the chromatin architecture at the promoters. Our findings expand our understanding of the regulatory mechanisms for metabolic reprogramming in eukaryotes to include key regulation steps outside the nucleus. Given that Tup1 and the metabolic enzymes that control PI(3,5)P2 are highly conserved among eukaryotes, our findings may provide important insights toward understanding glucose/carbon metabolic reprogramming in other eukaryotes, including humans. PMID:23733183

The phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2)-dependent Tup1 conversion (PIPTC) regulates metabolic reprogramming from glycolysis to gluconeogenesis.

PubMed

Han, Bong-Kwan; Emr, Scott D

2013-07-12

Glucose/carbon metabolism is a fundamental cellular process in living cells. In response to varying environments, eukaryotic cells reprogram their glucose/carbon metabolism between aerobic or anaerobic glycolysis, oxidative phosphorylation, and/or gluconeogenesis. The distinct type of glucose/carbon metabolism that a cell carries out has significant effects on the cell's proliferation and differentiation. However, it is poorly understood how the reprogramming of glucose/carbon metabolism is regulated. Here, we report a novel endosomal PI(3,5)P2 lipid-dependent regulatory mechanism that is required for metabolic reprogramming from glycolysis to gluconeogenesis in Saccharomyces cerevisiae. Certain gluconeogenesis genes, such as FBP1 (encoding fructose-1,6-bisphosphatase 1) and ICL1 (encoding isocitrate lyase 1) are under control of the Mig1 repressor and Cyc8-Tup1 corepressor complex. We previously identified the PI(3,5)P2-dependent Tup1 conversion (PIPTC), a mechanism to convert Cyc8-Tup1 corepressor to Cti6-Cyc8-Tup1 coactivator. We demonstrate that the PIPTC plays a critical role for transcriptional activation of FBP1 and ICL1. Furthermore, without the PIPTC, the Cat8 and Sip4 transcriptional activators cannot be efficiently recruited to the promoters of FBP1 and ICL1, suggesting a key role for the PIPTC in remodulating the chromatin architecture at the promoters. Our findings expand our understanding of the regulatory mechanisms for metabolic reprogramming in eukaryotes to include key regulation steps outside the nucleus. Given that Tup1 and the metabolic enzymes that control PI(3,5)P2 are highly conserved among eukaryotes, our findings may provide important insights toward understanding glucose/carbon metabolic reprogramming in other eukaryotes, including humans.

Karst Lands: The dissolution of carbonate rock produces unique landscapes and poses significant hydrological and environmental concerns

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

White, W.B.; Culver, D.C.; Herman, J.S.

1995-09-01

Karst lands are produced by the action of water on soluble rocks, a process among the most dynamic of all erosive forces that counterbalance the uplifting forces of tectonics. The dissolution of carbonate rock, primarily limestone and dolomite, produces unique landscapes and poses significant hydrological and environmental concerns. The major topic areas discussed in this article include the following: processes that form karst; karst drainage basins; discharge from karst aquifers; caves as paleoclimatic recorders; caves as ecosystems; water issues in karst regions; and sinkholes, soil piping and subsidence. 20 refs., 9 figs.

Sequences of two related multiple antibiotic resistance virulence plasmids sharing a unique IS26-related molecular signature isolated from different Escherichia coli pathotypes from different hosts.

PubMed

Venturini, Carola; Hassan, Karl A; Roy Chowdhury, Piklu; Paulsen, Ian T; Walker, Mark J; Djordjevic, Steven P

2013-01-01

Enterohemorrhagic Escherichia coli (EHEC) and atypical enteropathogenic E. coli (aEPEC) are important zoonotic pathogens that increasingly are becoming resistant to multiple antibiotics. Here we describe two plasmids, pO26-CRL125 (125 kb) from a human O26:H- EHEC, and pO111-CRL115 (115kb) from a bovine O111 aEPEC, that impart resistance to ampicillin, kanamycin, neomycin, streptomycin, sulfathiazole, trimethoprim and tetracycline and both contain atypical class 1 integrons with an identical IS26-mediated deletion in their 3´-conserved segment. Complete sequence analysis showed that pO26-CRL125 and pO111-CRL115 are essentially identical except for a 9.7 kb fragment, present in the backbone of pO26-CRL125 but absent in pO111-CRL115, and several indels. The 9.7 kb fragment encodes IncI-associated genes involved in plasmid stability during conjugation, a putative transposase gene and three imperfect repeats. Contiguous sequence identical to regions within these pO26-CRL125 imperfect repeats was identified in pO111-CRL115 precisely where the 9.7 kb fragment is missing, suggesting it may be mobile. Sequences shared between the plasmids include a complete IncZ replicon, a unique toxin/antitoxin system, IncI stability and maintenance genes, a novel putative serine protease autotransporter, and an IncI1 transfer system including a unique shufflon. Both plasmids carry a derivate Tn21 transposon with an atypical class 1 integron comprising a dfrA5 gene cassette encoding resistance to trimethoprim, and 24 bp of the 3´-conserved segment followed by Tn6026, which encodes resistance to ampicillin, kanymycin, neomycin, streptomycin and sulfathiazole. The Tn21-derivative transposon is linked to a truncated Tn1721, encoding resistance to tetracycline, via a region containing the IncP-1α oriV. Absence of the 5 bp direct repeats flanking Tn3-family transposons, indicates that homologous recombination events played a key role in the formation of this complex antibiotic resistance gene locus. Comparative sequence analysis of these closely related plasmids reveals aspects of plasmid evolution in pathogenic E. coli from different hosts.

Biomarker analysis of liver cells exposed to surfactant-wrapped and oxidized multi-walled carbon nanotubes (MWCNTs)

EPA Science Inventory

Carbon nanotubes (CNTs) have great potential in industrial, consumer, and mechanical applications, based partly on their unique structural, optical and electronic properties. CNTs are commonly oxidized or treated with surfactants to facilitate aqueous solution processing, and the...

Bioenergy production systems and biochar application in forests: potential for renewable energy, soil enhancement, and carbon sequestration

Treesearch

Kristin McElligott; Debbie Dumroese; Mark Coleman

2011-01-01

Bioenergy production from forest biomass offers a unique solution to reduce wildfire hazard fuel while producing a useful source of renewable energy. However, biomass removals raise concerns about reducing soil carbon and altering forest site productivity. Biochar additions have been suggested as a way to mitigate soil carbon loss and cycle nutrients back into forestry...

Nanoporous hard data: optical encoding of information within nanoporous anodic alumina photonic crystals

NASA Astrophysics Data System (ADS)

Santos, Abel; Law, Cheryl Suwen; Pereira, Taj; Losic, Dusan

2016-04-01

Herein, we present a method for storing binary data within the spectral signature of nanoporous anodic alumina photonic crystals. A rationally designed multi-sinusoidal anodisation approach makes it possible to engineer the photonic stop band of nanoporous anodic alumina with precision. As a result, the transmission spectrum of these photonic nanostructures can be engineered to feature well-resolved and selectively positioned characteristic peaks across the UV-visible spectrum. Using this property, we implement an 8-bit binary code and assess the versatility and capability of this system by a series of experiments aiming to encode different information within the nanoporous anodic alumina photonic crystals. The obtained results reveal that the proposed nanosized platform is robust, chemically stable, versatile and has a set of unique properties for data storage, opening new opportunities for developing advanced nanophotonic tools for a wide range of applications, including sensing, photonic tagging, self-reporting drug releasing systems and secure encoding of information.Herein, we present a method for storing binary data within the spectral signature of nanoporous anodic alumina photonic crystals. A rationally designed multi-sinusoidal anodisation approach makes it possible to engineer the photonic stop band of nanoporous anodic alumina with precision. As a result, the transmission spectrum of these photonic nanostructures can be engineered to feature well-resolved and selectively positioned characteristic peaks across the UV-visible spectrum. Using this property, we implement an 8-bit binary code and assess the versatility and capability of this system by a series of experiments aiming to encode different information within the nanoporous anodic alumina photonic crystals. The obtained results reveal that the proposed nanosized platform is robust, chemically stable, versatile and has a set of unique properties for data storage, opening new opportunities for developing advanced nanophotonic tools for a wide range of applications, including sensing, photonic tagging, self-reporting drug releasing systems and secure encoding of information. Electronic supplementary information (ESI) available: Further details about anodisation profiles, SEM cross-section images, digital pictures, transmission spectra, photonic barcodes and ASCII codes of the different NAA photonic crystals fabricated and analysed in our study. See DOI: 10.1039/c6nr01068g

Formation of Foam-like Microstructural Carbon Material by Carbonization of Porous Coordination Polymers through a Ligand-Assisted Foaming Process.

PubMed

Kongpatpanich, Kanokwan; Horike, Satoshi; Fujiwara, Yu-Ichi; Ogiwara, Naoki; Nishihara, Hirotomo; Kitagawa, Susumu

2015-09-14

Porous carbon material with a foam-like microstructure has been synthesized by direct carbonization of porous coordination polymer (PCP). In situ generation of foaming agents by chemical reactions of ligands in PCP during carbonization provides a simple way to create lightweight carbon material with a foam-like microstructure. Among several substituents investigated, the nitro group has been shown to be the key to obtain the unique foam-like microstructure, which is due to the fast kinetics of gas evolution during carbonization. Foam-like microstructural carbon materials showed higher pore volume and specific capacitance compared to a microporous carbon. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recent applications of carbon nanomaterials in fluorescence biosensing and bioimaging.

PubMed

Wen, Jia; Xu, Yongqian; Li, Hongjuan; Lu, Aiping; Sun, Shiguo

2015-07-21

Carbon-based nanomaterials as important agents for biological applications have emerged in the past few years due to their unique optical, electronic, mechanical, and chemical properties. Many of these applications rely on successful surface modifications. This review article comprises two main parts. In the first part, we briefly review the properties and surface modifications of several classes of carbon nanomaterials, mainly carbon nanotubes (CNTs), graphene and its derivatives, carbon dots (CDs) and graphene quantum dots (GQDs), as well as some other forms of carbon-based nanomaterials such as fullerene, carbon nanohorns (CNHs) and carbon nanoonions (CNOs). In the second part, we focus on the biological applications of these carbon nanomaterials, in particular their applications for fluorescence biosensing as well as bioimaging.

Enhanced practical photosynthetic CO2 mitigation

DOEpatents

Bayless, David J.; Vis-Chiasson, Morgan L.; Kremer, Gregory G.

2003-12-23

This process is unique in photosynthetic carbon sequestration. An on-site biological sequestration system directly decreases the concentration of carbon-containing compounds in the emissions of fossil generation units. In this process, photosynthetic microbes are attached to a growth surface arranged in a containment chamber that is lit by solar photons. A harvesting system ensures maximum organism growth and rate of CO.sub.2 uptake. Soluble carbon and nitrogen concentrations delivered to the cyanobacteria are enhanced, further increasing growth rate and carbon utilization.

An approach to instrument qualified visual range

NASA Astrophysics Data System (ADS)

Courtade, Benoît; Bonnet, Jordan; Woodruff, Chris; Larson, Josiah; Giles, Andrew; Sonde, Nikhil; Moore, C. J.; Schimon, David; Harris, David Money; Pond, Duane; Way, Scott

2008-04-01

This paper describes a system that calculates aircraft visual range with instrumentation alone. A unique message is encoded using modified binary phase shift keying and continuously flashed at high speed by ALSF-II runway approach lights. The message is sampled at 400 frames per second by an aircraft borne high-speed camera. The encoding is designed to avoid visible flicker and minimize frame rate. Instrument qualified visual range is identified as the largest distance at which the aircraft system can acquire and verify the correct, runway-specific signal. Scaled testing indicates that if the system were implemented on one full ALSF-II fixture, instrument qualified range could be established at 5 miles in clear weather conditions.

Versatile protein recognition by the encoded display of multiple chemical elements on a constant macrocyclic scaffold

NASA Astrophysics Data System (ADS)

Li, Yizhou; De Luca, Roberto; Cazzamalli, Samuele; Pretto, Francesca; Bajic, Davor; Scheuermann, Jörg; Neri, Dario

2018-03-01

In nature, specific antibodies can be generated as a result of an adaptive selection and expansion of lymphocytes with suitable protein binding properties. We attempted to mimic antibody-antigen recognition by displaying multiple chemical diversity elements on a defined macrocyclic scaffold. Encoding of the displayed combinations was achieved using distinctive DNA tags, resulting in a library size of 35,393,112. Specific binders could be isolated against a variety of proteins, including carbonic anhydrase IX, horseradish peroxidase, tankyrase 1, human serum albumin, alpha-1 acid glycoprotein, calmodulin, prostate-specific antigen and tumour necrosis factor. Similar to antibodies, the encoded display of multiple chemical elements on a constant scaffold enabled practical applications, such as fluorescence microscopy procedures or the selective in vivo delivery of payloads to tumours. Furthermore, the versatile structure of the scaffold facilitated the generation of protein-specific chemical probes, as illustrated by photo-crosslinking.

Identification of a novel fatty acid elongase with a wide substrate specificity from arachidonic acid-producing fungus Mortierella alpina 1S-4.

PubMed

Sakuradani, Eiji; Nojiri, Masutoshi; Suzuki, Haruna; Shimizu, Sakayu

2009-09-01

The isolation and characterization of a gene (MALCE1) that encodes a fatty acid elongase from arachidonic acid-producing fungus Mortierella alpina 1S-4 are described. MALCE1 was confirmed to encode a fatty acid elongase by its expression in yeast Saccharomyces cerevisiae, resulting in the accumulation of 18-, 19-, and 20-carbon monounsaturated fatty acids and eicosanoic acid. Furthermore, the MALCE1 yeast transformant efficiently elongated exogenous 9-hexadecenoic acid, 9,12-octadecadienoic acid, and 9,12,15-octadecatrienoic acid. The MALCE1 gene-silenced strain obtained from M. alpina 1S-4 exhibited a low content of octadecanoic acid and a high content of hexadecanoic acid, compared with those in the wild strain. The enzyme encoded by MALCE1 was demonstrated to be involved in the conversion of hexadecanoic acid to octadecanoic acid, its main role in M. alpina 1S-4.

Dioxygen in Polyoxometalate Mediated Reactions.

PubMed

Weinstock, Ira A; Schreiber, Roy E; Neumann, Ronny

2018-03-14

In this review article, we consider the use of molecular oxygen in reactions mediated by polyoxometalates. Polyoxometalates are anionic metal oxide clusters of a variety of structures that are soluble in liquid phases and therefore amenable to homogeneous catalytic transformations. Often, they are active for electron transfer oxidations of a myriad of substrates and upon reduction can be reoxidized by molecular oxygen. For example, the phosphovanadomolybdate, H 5 PV 2 Mo 10 O 40 , can oxidize Pd(0) thereby enabling aerobic reactions catalyzed by Pd and H 5 PV 2 Mo 10 O 40 . In a similar vein, polyoxometalates can stabilize metal nanoparticles, leading to additional transformations. Furthermore, electron transfer oxidation of other substrates such as halides and sulfur-containing compounds is possible. More uniquely, H 5 PV 2 Mo 10 O 40 and its analogues can mediate electron transfer-oxygen transfer reactions where oxygen atoms are transferred from the polyoxometalate to the substrate. This unique property has enabled correspondingly unique transformations involving carbon-carbon, carbon-hydrogen, and carbon-metal bond activation. The pathway for the reoxidation of vanadomolybdates with O 2 appears to be an inner-sphere reaction, but the oxidation of one-electron reduced polyoxotungstates has been shown through intensive research to be an outer-sphere reaction. Beyond electron transfer and electron transfer-oxygen transfer aerobic transformations, there a few examples of apparent dioxygenase activity where both oxygen atoms are donated to a substrate.

Genes of the N-Methylglutamate Pathway Are Essential for Growth of Methylobacterium extorquens DM4 with Monomethylamine

PubMed Central

Gruffaz, Christelle; Muller, Emilie E. L.; Louhichi-Jelail, Yousra; Nelli, Yella R.; Guichard, Gilles

2014-01-01

Monomethylamine (MMA, CH3NH2) can be used as a carbon and nitrogen source by many methylotrophic bacteria. Methylobacterium extorquens DM4 lacks the MMA dehydrogenase encoded by mau genes, which in M. extorquens AM1 is essential for growth on MMA. Identification and characterization of minitransposon mutants with an MMA-dependent phenotype showed that strain DM4 grows with MMA as the sole source of carbon, energy, and nitrogen by the N-methylglutamate (NMG) pathway. Independent mutations were found in a chromosomal region containing the genes gmaS, mgsABC, and mgdABCD for the three enzymes of the pathway, γ-glutamylmethylamide (GMA) synthetase, NMG synthase, and NMG dehydrogenase, respectively. Reverse transcription-PCR confirmed the operonic structure of the two divergent gene clusters mgsABC-gmaS and mgdABCD and their induction during growth with MMA. The genes mgdABCD and mgsABC were found to be essential for utilization of MMA as a carbon and nitrogen source. The gene gmaS was essential for MMA utilization as a carbon source, but residual growth of mutant DM4gmaS growing with succinate and MMA as a nitrogen source was observed. Plasmid copies of gmaS and the gmaS homolog METDI4690, which encodes a protein 39% identical to GMA synthetase, fully restored the ability of mutants DM4gmaS and DM4gmaSΔmetdi4690 to use MMA as a carbon and nitrogen source. Similarly, chemically synthesized GMA, the product of GMA synthetase, could be used as a nitrogen source for growth in the wild-type strain, as well as in DM4gmaS and DM4gmaSΔmetdi4690 mutants. The NADH:ubiquinone oxidoreductase respiratory complex component NuoG was also found to be essential for growth with MMA as a carbon source. PMID:24682302

Calpain-Mediated positional information directs cell wall orientation to sustain plant stem cell activity, growth and development

USDA-ARS?s Scientific Manuscript database

Eukaryotic development and stem cell control depend on the integration of cell positional sensing with cell cycle control and cell wall positioning, yet few factors that directly link these events are known. The DEFECTIVE KERNEL1 (DEK1) gene encoding the unique plant calpain protein is fundamental f...

The wheat Sr50 gene reveals rich diversity at a cereal disease resistance locus

USDA-ARS?s Scientific Manuscript database

We identify the wheat stem rust resistance gene Sr50 by physical mapping, mutation and complementation as homologous to barley Mla encoding a Coiled-Coil-Nucleotide-Binding-Leucine-Rich Repeat (CC-NB-LRR) protein. We show that Sr50 confers a unique resistance specificity, different from Sr31 and oth...

Rf8-mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L

USDA-ARS?s Scientific Manuscript database

Cytoplasmic male sterility (CMS) is a maternally inherited inability to produce functional pollen. In T-cytoplasm maize, CMS results from the action of the URF13 mitochondrial pore-forming protein, encoded by the unique T-urf13 mitochondrial gene. Full or partial restoration of fertility to T-cyto...

Deletion of the SACPD-C locus alters the symbiotic relationship between Bradyrhizobium japonicum USDA110 and soybean, resulting in elicitation of plant defense response and nodulation defects

USDA-ARS?s Scientific Manuscript database

Legumes form symbiotic association with soil-dwelling bacteria collectively called rhizobia. This association results in the formation of nodules, unique plant-derived organs, within which the rhizobia are housed. Rhizobia encoded-nitrogenase facilitates the conversation of atmospheric nitrogen int...

78 FR 76067 - Defense Federal Acquisition Regulation Supplement: Item Unique Identifier Update (DFARS Case 2011...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-16

... with the Air Transport Association Common Support Data Dictionary; and (ii) The encoded data elements... 211.274-2(a)(2) and (3) are revised to consolidate requirements. The definition of ``data matrix... Registry'' is added at 252.211-7003(c)(2). The phrase ``ECC200 data matrix specification'' is added at 252...

The photosensitivity of carbon quantum dots/CuAlO2 films composites.

PubMed

Pan, Jiaqi; Sheng, Yingzhuo; Zhang, Jingxiang; Wei, Jumeng; Huang, Peng; Zhang, Xin; Feng, Boxue

2015-07-31

Carbon quantum dots/CuAlO2 films were prepared by a simple route through which CuAlO2 films prepared by sol-gel on crystal quartz substrates were composited with carbon quantum dots on their surface. The characterization results indicated that CuAlO2 films were well combined with carbon quantum dots. The photoconductivity of carbon quantum dots/CuAlO2 films was investigated under illumination and darkness switching, and was demonstrated to be significantly enhanced compared with CuAlO2 films. Through analysis, this enhancement of photoconductivity was attributed to the carbon quantum dots with unique up-converted photoluminescence behavior.

The photosensitivity of carbon quantum dots/CuAlO2 films composites

NASA Astrophysics Data System (ADS)

Pan, Jiaqi; Sheng, Yingzhuo; Zhang, Jingxiang; Wei, Jumeng; Huang, Peng; Zhang, Xin; Feng, Boxue

2015-07-01

Carbon quantum dots/CuAlO2 films were prepared by a simple route through which CuAlO2 films prepared by sol-gel on crystal quartz substrates were composited with carbon quantum dots on their surface. The characterization results indicated that CuAlO2 films were well combined with carbon quantum dots. The photoconductivity of carbon quantum dots/CuAlO2 films was investigated under illumination and darkness switching, and was demonstrated to be significantly enhanced compared with CuAlO2 films. Through analysis, this enhancement of photoconductivity was attributed to the carbon quantum dots with unique up-converted photoluminescence behavior.

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion

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

Martinez, Diego; Challacombe, Jean; Morgenstern, Ingo

2009-02-04

Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in media containing cellulose as sole carbon source, transcripts corresponding tomore » many hemicellulases and to a single putative β-1-4 endoglucanase were expressed at high levels relative to glucose grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also upregulated under cellulolytic culture conditions were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H2O2. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H2O2 react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. In particular, comparisons between P. placenta and the closely related white-rot fungus, Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which efficient depolymerization of lignin was lost.« less

Genome, transcriptome, and secretome analysis of wood decay fungus postia placenta supports unique mechanisms of lignocellulose conversion

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

Martinez, Diego; Challacombe, Jean F; Misra, Monica

2008-01-01

Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding tomore » many hemicellulases and to a single putative {beta}-1-4 endoglucanase were expressed at high levels relative to glucose grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC{center_dot}MSIMS). Also upregulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H202. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H202 react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons to the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost.« less

Genome, transcriptome, and secretome analysis of wood decay fungus Postia placenta supports unique mechanisms of lignocellulose conversion

PubMed Central

Martinez, Diego; Challacombe, Jean; Morgenstern, Ingo; Hibbett, David; Schmoll, Monika; Kubicek, Christian P.; Ferreira, Patricia; Ruiz-Duenas, Francisco J.; Martinez, Angel T.; Kersten, Phil; Hammel, Kenneth E.; Vanden Wymelenberg, Amber; Gaskell, Jill; Lindquist, Erika; Sabat, Grzegorz; Splinter BonDurant, Sandra; Larrondo, Luis F.; Canessa, Paulo; Vicuna, Rafael; Yadav, Jagjit; Doddapaneni, Harshavardhan; Subramanian, Venkataramanan; Pisabarro, Antonio G.; Lavín, José L.; Oguiza, José A.; Master, Emma; Henrissat, Bernard; Coutinho, Pedro M.; Harris, Paul; Magnuson, Jon Karl; Baker, Scott E.; Bruno, Kenneth; Kenealy, William; Hoegger, Patrik J.; Kües, Ursula; Ramaiya, Preethi; Lucas, Susan; Salamov, Asaf; Shapiro, Harris; Tu, Hank; Chee, Christine L.; Misra, Monica; Xie, Gary; Teter, Sarah; Yaver, Debbie; James, Tim; Mokrejs, Martin; Pospisek, Martin; Grigoriev, Igor V.; Brettin, Thomas; Rokhsar, Dan; Berka, Randy; Cullen, Dan

2009-01-01

Brown-rot fungi such as Postia placenta are common inhabitants of forest ecosystems and are also largely responsible for the destructive decay of wooden structures. Rapid depolymerization of cellulose is a distinguishing feature of brown-rot, but the biochemical mechanisms and underlying genetics are poorly understood. Systematic examination of the P. placenta genome, transcriptome, and secretome revealed unique extracellular enzyme systems, including an unusual repertoire of extracellular glycoside hydrolases. Genes encoding exocellobiohydrolases and cellulose-binding domains, typical of cellulolytic microbes, are absent in this efficient cellulose-degrading fungus. When P. placenta was grown in medium containing cellulose as sole carbon source, transcripts corresponding to many hemicellulases and to a single putative β-1–4 endoglucanase were expressed at high levels relative to glucose-grown cultures. These transcript profiles were confirmed by direct identification of peptides by liquid chromatography-tandem mass spectrometry (LC-MS/MS). Also up-regulated during growth on cellulose medium were putative iron reductases, quinone reductase, and structurally divergent oxidases potentially involved in extracellular generation of Fe(II) and H2O2. These observations are consistent with a biodegradative role for Fenton chemistry in which Fe(II) and H2O2 react to form hydroxyl radicals, highly reactive oxidants capable of depolymerizing cellulose. The P. placenta genome resources provide unparalleled opportunities for investigating such unusual mechanisms of cellulose conversion. More broadly, the genome offers insight into the diversification of lignocellulose degrading mechanisms in fungi. Comparisons with the closely related white-rot fungus Phanerochaete chrysosporium support an evolutionary shift from white-rot to brown-rot during which the capacity for efficient depolymerization of lignin was lost. PMID:19193860

Polymeric carbon nitride nanomesh as an efficient and durable metal-free catalyst for oxidative desulfurization.

PubMed

Shen, Lijuan; Lei, Ganchang; Fang, Yuanxing; Cao, Yanning; Wang, Xinchen; Jiang, Lilong

2018-03-06

We report the first use of polymeric carbon nitride (CN) for the catalytic selective oxidation of H 2 S. The as-prepared CN with unique ultrathin "nanomeshes" structure exhibits excellent H 2 S conversion and high S selectivity. In particular, the CN nanomesh also displays better durability in the desulfurization reaction than traditional catalysts, such as carbon- and iron-based materials.

Electrochemical device for syngas and liquid fuels production

DOEpatents

Braun, Robert J.; Becker, William L.; Penev, Michael

2017-04-25

The invention relates to methods for creating high value liquid fuels such as gasoline, diesel, jet and alcohols using carbon dioxide and water as the starting raw materials and a system for using the same. These methods combine a novel solid oxide electrolytic cell (SOEC) for the efficient and clean conversion of carbon dioxide and water to hydrogen and carbon monoxide, uniquely integrated with a gas-to-liquid fuels producing method.

Novel polyelectrolyte complex based carbon nanotube composite architectures

NASA Astrophysics Data System (ADS)

Razdan, Sandeep

This study focuses on creating novel architectures of carbon nanotubes using polyelectrolytes. Polyelectrolytes are unique polymers possessing resident charges on the macromolecular chains. This property, along with their biocompatibility (true for most polymers used in this study) makes them ideal candidates for a variety of applications such as membranes, drug delivery systems, scaffold materials etc. Carbon nanotubes are also unique one-dimensional nanoscale materials that possess excellent electrical, mechanical and thermal properties owing to their small size, high aspect ratio, graphitic structure and strength arising from purely covalent bonds in the molecular structure. The present study tries to investigate the synthesis processes and material properties of carbon nanotube composites comprising of polyelectrolyte complexes. Carbon nanotubes are dispersed in a polyelectrolyte and are induced into taking part in a complexation process with two oppositely charged polyelectrolytes. The resulting stoichiometric precipitate is then drawn into fiber form and dried as such. The material properties of the carbon nanotube fibers were characterized and related to synthesis parameters and material interactions. Also, an effort was made to understand and predict fiber morphology resulting from the complexation and drawing process. The study helps to delineate the synthesis and properties of the said polyelectrolyte complex-carbon nanotube architectures and highlights useful properties, such as electrical conductivity and mechanical strength, which could make these structures promising candidates for a variety of applications.

Nacre-Templated Synthesis of Highly Dispersible Carbon Nanomeshes for Layered Membranes with High-Flux Filtration and Sensing Properties.

PubMed

Kong, Meng; Li, Mingjie; Shang, Ruoxu; Wu, Jingyu; Yan, Peisong; Xu, Dongmei; Li, Chaoxu

2018-01-24

Marine shells not only represent a rapidly accumulating type of fishery wastes but also offer a unique sort of hybrid nanomaterials produced greenly and massively in nature. The elaborate "brick and mortar" structures of nacre enabled the synthesis of carbon nanomeshes with <1 nm thickness, hierarchical porosity, and high specific surface area through pyrolysis, in which two-dimensional (2D) organic layers served as the carbonaceous precursor and aragonite platelets as the hard template. Mineral bridges within 2D organic layers templated the formation of mesh pores of 20-70 nm. In contrast to other hydrophobic carbon nanomaterials, these carbon nanomeshes showed super dispersibility in diverse solvents and thus processability for membranes through filtration, patterning, spray-coating, and ink-writing. The carbon membranes with layered structures were capable of serving not only for high-flux filtration and continuous flow absorption but also for electrochemical and strain sensing with high sensitivity. Thus, utilization of marine shells, on one hand, relieves the environmental concern of shellfish waste, on the other hand, offers a facile, green, low-cost, and massive approach to synthesize unique carbon nanomeshes alternative to graphene nanomeshes and applicable in environmental adsorption, filtration, wearable sensors, and flexible microelectronics.

Upscaling Our Approach to Peatland Carbon Sequestration: Remote Sensing as a Tool for Carbon Flux Estimation.

NASA Astrophysics Data System (ADS)

Lees, K.; Khomik, M.; Clark, J. M.; Quaife, T. L.; Artz, R.

2017-12-01

Peatlands are an important part of the Earth's carbon cycle, comprising approximately a third of the global terrestrial carbon store. However, peatlands are sensitive to climatic change and human mismanagement, and many are now degraded and acting as carbon sources. Restoration work is being undertaken at many sites around the world, but monitoring the success of these schemes can be difficult and costly using traditional methods. A landscape-scale alternative is to use satellite data in order to assess the condition of peatlands and estimate carbon fluxes. This work focuses on study sites in Northern Scotland, where parts of the largest blanket bog in Europe are being restored from forest plantations. A combination of laboratory and fieldwork has been used to assess the Net Ecosystem Exchange (NEE), Gross Primary Productivity (GPP) and respiration of peatland sites in different conditions, and the climatic vulnerability of key peat-forming Sphagnum species. The results from these studies have been compared with spectral data in order to evaluate the extent to which remote sensing can function as a source of information for peatland health and carbon flux models. This work considers particularly the effects of scale in calculating peatland carbon flux. Flux data includes chamber and eddy covariance measurements of carbon dioxide, and radiometric observations include both handheld spectroradiometer results and satellite images. Results suggest that despite the small-scale heterogeneity and unique ecosystem factors in blanket bogs, remote sensing can be a useful tool in monitoring peatland health and carbon sequestration. In particular, this study gives unique insights into the relationships between peatland vegetation, carbon flux and spectral reflectance.

Bacillus subtilis IolQ (DegA) is a transcriptional repressor of iolX encoding NAD+-dependent scyllo-inositol dehydrogenase.

PubMed

Kang, Dong-Min; Michon, Christophe; Morinaga, Tetsuro; Tanaka, Kosei; Takenaka, Shinji; Ishikawa, Shu; Yoshida, Ken-Ichi

2017-07-11

Bacillus subtilis is able to utilize at least three inositol stereoisomers as carbon sources, myo-, scyllo-, and D-chiro-inositol (MI, SI, and DCI, respectively). NAD + -dependent SI dehydrogenase responsible for SI catabolism is encoded by iolX. Even in the absence of functional iolX, the presence of SI or MI in the growth medium was found to induce the transcription of iolX through an unknown mechanism. Immediately upstream of iolX, there is an operon that encodes two genes, yisR and iolQ (formerly known as degA), each of which could encode a transcriptional regulator. Here we performed an inactivation analysis of yisR and iolQ and found that iolQ encodes a repressor of the iolX transcription. The coding sequence of iolQ was expressed in Escherichia coli and the gene product was purified as a His-tagged fusion protein, which bound to two sites within the iolX promoter region in vitro. IolQ is a transcriptional repressor of iolX. Genetic evidences allowed us to speculate that SI and MI might possibly be the intracellular inducers, however they failed to antagonize DNA binding of IolQ in in vitro experiments.

Soil drying effects on the carbon isotope composition of soil respiration

EPA Science Inventory

Stable isotopes are used widely as a tool for determining sources of carbon (C) fluxes in ecosystem C studies. Environmental factors that change over time, such as moisture, can create dynamic changes in the isotopic composition of C assimilated by plants, and offers a unique opp...

THE EFFECTS OF FUNCTIONALIZED AND NON-FUNCTIONALIZED CARBON NANOTUBES ON ROOT ELONGATION OF SELECTED CROP SPECIES

EPA Science Inventory

Single-walled carbon nanotubes (SWNT) have many potential beneficial uses with additional applications constantly being investigated. However, these unique properties create a potential cause for concern of toxicity, not only in humans and animals, but also in plants. Root elong...

Silk-regulated hierarchical hollow magnetite/carbon nanocomposite spheroids for lithium-ion battery anodes.

PubMed

Sheng, Weiqin; Zhu, Guobin; Kaplan, David L; Cao, Chuanbao; Zhu, Hesun; Lu, Qiang

2015-03-20

Hierarchical olive-like structured carbon-Fe3O4 nanocomposite particles composed of a hollow interior and a carbon coated surface are prepared by a facile, silk protein-assisted hydrothermal method. Silk nanofibers as templates and carbon precursors first regulate the formation of hollow Fe2O3 microspheres and then they are converted into carbon by a reduction process into Fe3O4. This process significantly simplifies the fabrication and carbon coating processes to form complex hollow structures. When tested as anode materials for lithium-ion batteries, these hollow carbon-coated particles exhibit high capacity (900 mAh g(-1)), excellent cycle stability (180 cycles) and rate performance due to their unique hierarchical hollow structure and carbon coating.

Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus

PubMed Central

Rineau, F; Shah, F; Smits, M M; Persson, P; Johansson, T; Carleer, R; Troein, C; Tunlid, A

2013-01-01

The majority of nitrogen in forest soils is found in organic matter–protein complexes. Ectomycorrhizal fungi (EMF) are thought to have a key role in decomposing and mobilizing nitrogen from such complexes. However, little is known about the mechanisms governing these processes, how they are regulated by the carbon in the host plant and the availability of more easily available forms of nitrogen sources. Here we used spectroscopic analyses and transcriptome profiling to examine how the presence or absence of glucose and/or ammonium regulates decomposition of litter material and nitrogen mobilization by the ectomycorrhizal fungus Paxillus involutus. We found that the assimilation of nitrogen and the decomposition of the litter material are triggered by the addition of glucose. Glucose addition also resulted in upregulation of the expression of genes encoding enzymes involved in oxidative degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism. In contrast, the addition of ammonium to organic matter had relatively minor effects on the expression of transcripts and the decomposition of litter material, occurring only when glucose was present. On the basis of spectroscopic analyses, three major types of chemical modifications of the litter material were observed, each correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggest that the expression of the decomposition and nitrogen assimilation processes of EMF can be tightly regulated by the host carbon supply and that the availability of inorganic nitrogen as such has limited effects on saprotrophic activities. PMID:23788332

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH

PubMed Central

Twing, Katrina I.; Brazelton, William J.; Kubo, Michael D. Y.; Hyer, Alex J.; Cardace, Dawn; Hoehler, Tori M.; McCollom, Tom M.; Schrenk, Matthew O.

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H2 and CH4) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments. PMID:28298908

Serpentinization-Influenced Groundwater Harbors Extremely Low Diversity Microbial Communities Adapted to High pH.

PubMed

Twing, Katrina I; Brazelton, William J; Kubo, Michael D Y; Hyer, Alex J; Cardace, Dawn; Hoehler, Tori M; McCollom, Tom M; Schrenk, Matthew O

2017-01-01

Serpentinization is a widespread geochemical process associated with aqueous alteration of ultramafic rocks that produces abundant reductants (H 2 and CH 4 ) for life to exploit, but also potentially challenging conditions, including high pH, limited availability of terminal electron acceptors, and low concentrations of inorganic carbon. As a consequence, past studies of serpentinites have reported low cellular abundances and limited microbial diversity. Establishment of the Coast Range Ophiolite Microbial Observatory (California, U.S.A.) allowed a comparison of microbial communities and physicochemical parameters directly within serpentinization-influenced subsurface aquifers. Samples collected from seven wells were subjected to a range of analyses, including solute and gas chemistry, microbial diversity by 16S rRNA gene sequencing, and metabolic potential by shotgun metagenomics, in an attempt to elucidate what factors drive microbial activities in serpentinite habitats. This study describes the first comprehensive interdisciplinary analysis of microbial communities in hyperalkaline groundwater directly accessed by boreholes into serpentinite rocks. Several environmental factors, including pH, methane, and carbon monoxide, were strongly associated with the predominant subsurface microbial communities. A single operational taxonomic unit (OTU) of Betaproteobacteria and a few OTUs of Clostridia were the almost exclusive inhabitants of fluids exhibiting the most serpentinized character. Metagenomes from these extreme samples contained abundant sequences encoding proteins associated with hydrogen metabolism, carbon monoxide oxidation, carbon fixation, and acetogenesis. Metabolic pathways encoded by Clostridia and Betaproteobacteria, in particular, are likely to play important roles in the ecosystems of serpentinizing groundwater. These data provide a basis for further biogeochemical studies of key processes in serpentinite subsurface environments.

Carbon dioxide conversion over carbon-based nanocatalysts.

PubMed

Khavarian, Mehrnoush; Chai, Siang-Piao; Mohamed, Abdul Rahman

2013-07-01

The utilization of carbon dioxide for the production of valuable chemicals via catalysts is one of the efficient ways to mitigate the greenhouse gases in the atmosphere. It is known that the carbon dioxide conversion and product yields are still low even if the reaction is operated at high pressure and temperature. The carbon dioxide utilization and conversion provides many challenges in exploring new concepts and opportunities for development of unique catalysts for the purpose of activating the carbon dioxide molecules. In this paper, the role of carbon-based nanocatalysts in the hydrogenation of carbon dioxide and direct synthesis of dimethyl carbonate from carbon dioxide and methanol are reviewed. The current catalytic results obtained with different carbon-based nanocatalysts systems are presented and how these materials contribute to the carbon dioxide conversion is explained. In addition, different strategies and preparation methods of nanometallic catalysts on various carbon supports are described to optimize the dispersion of metal nanoparticles and catalytic activity.

Active listening impairs visual perception and selectivity: an ERP study of auditory dual-task costs on visual attention.

PubMed

Gherri, Elena; Eimer, Martin

2011-04-01

The ability to drive safely is disrupted by cell phone conversations, and this has been attributed to a diversion of attention from the visual environment. We employed behavioral and ERP measures to study whether the attentive processing of spoken messages is, in itself, sufficient to produce visual-attentional deficits. Participants searched for visual targets defined by a unique feature (Experiment 1) or feature conjunction (Experiment 2), and simultaneously listened to narrated text passages that had to be recalled later (encoding condition), or heard backward-played speech sounds that could be ignored (control condition). Responses to targets were slower in the encoding condition, and ERPs revealed that the visual processing of search arrays and the attentional selection of target stimuli were less efficient in the encoding relative to the control condition. Results demonstrate that the attentional processing of visual information is impaired when concurrent spoken messages are encoded and maintained, in line with cross-modal links in selective attention, but inconsistent with the view that attentional resources are modality-specific. The distraction of visual attention by active listening could contribute to the adverse effects of cell phone use on driving performance.

Staying Cool when Things Get Hot: Emotion Regulation Modulates Neural Mechanisms of Memory Encoding

PubMed Central

Hayes, Jasmeet Pannu; Morey, Rajendra A.; Petty, Christopher M.; Seth, Srishti; Smoski, Moria J.; McCarthy, Gregory; LaBar, Kevin S.

2010-01-01

During times of emotional stress, individuals often engage in emotion regulation to reduce the experiential and physiological impact of negative emotions. Interestingly, emotion regulation strategies also influence memory encoding of the event. Cognitive reappraisal is associated with enhanced memory while expressive suppression is associated with impaired explicit memory of the emotional event. However, the mechanism by which these emotion regulation strategies affect memory is unclear. We used event-related fMRI to investigate the neural mechanisms that give rise to memory formation during emotion regulation. Twenty-five participants viewed negative pictures while alternately engaging in cognitive reappraisal, expressive suppression, or passive viewing. As part of the subsequent memory design, participants returned to the laboratory two weeks later for a surprise memory test. Behavioral results showed a reduction in negative affect and a retention advantage for reappraised stimuli relative to the other conditions. Imaging results showed that successful encoding during reappraisal was uniquely associated with greater co-activation of the left inferior frontal gyrus, amygdala, and hippocampus, suggesting a possible role for elaborative encoding of negative memories. This study provides neurobehavioral evidence that engaging in cognitive reappraisal is advantageous to both affective and mnemonic processes. PMID:21212840

Cellular dynamical mechanisms for encoding the time and place of events along spatiotemporal trajectories in episodic memory.

PubMed

Hasselmo, Michael E; Giocomo, Lisa M; Brandon, Mark P; Yoshida, Motoharu

2010-12-31

Understanding the mechanisms of episodic memory requires linking behavioral data and lesion effects to data on the dynamics of cellular membrane potentials and population interactions within brain regions. Linking behavior to specific membrane channels and neurochemicals has implications for therapeutic applications. Lesions of the hippocampus, entorhinal cortex and subcortical nuclei impair episodic memory function in humans and animals, and unit recording data from these regions in behaving animals indicate episodic memory processes. Intracellular recording in these regions demonstrates specific cellular properties including resonance, membrane potential oscillations and bistable persistent spiking that could underlie the encoding and retrieval of episodic trajectories. A model presented here shows how intrinsic dynamical properties of neurons could mediate the encoding of episodic memories as complex spatiotemporal trajectories. The dynamics of neurons allow encoding and retrieval of unique episodic trajectories in multiple continuous dimensions including temporal intervals, personal location, the spatial coordinates and sensory features of perceived objects and generated actions, and associations between these elements. The model also addresses how cellular dynamics could underlie unit firing data suggesting mechanisms for coding continuous dimensions of space, time, sensation and action. Copyright © 2010 Elsevier B.V. All rights reserved.

Cellular dynamical mechanisms for encoding the time and place of events along spatiotemporal trajectories in episodic memory

PubMed Central

Hasselmo, Michael E.; Giocomo, Lisa M.; Yoshida, Motoharu

2010-01-01

Understanding the mechanisms of episodic memory requires linking behavioural data and lesion effects to data on the dynamics of cellular membrane potentials and population interactions within these brain regions. Linking behavior to specific membrane channels and neurochemicals has implications for therapeutic applications. Lesions of the hippocampus, entorhinal cortex and subcortical nuclei impair episodic memory function in humans and animals, and unit recording data from these regions in behaving animals indicate episodic memory processes. Intracellular recording in these regions demonstrates specific cellular properties including resonance, membrane potential oscillations and bistable persistent spiking that could underlie the encoding and retrieval of episodic trajectories. A model presented here shows how intrinsic dynamical properties of neurons could mediate the encoding of episodic memories as complex spatiotemporal trajectories. The dynamics of neurons allow encoding and retrieval of unique episodic trajectories in multiple continuous dimensions including temporal intervals, personal location, the spatial coordinates and sensory features of perceived objects and generated actions, and associations between these elements. The model also addresses how cellular dynamics could underlie unit firing data suggesting mechanisms for coding continuous dimensions of space, time, sensation and action. PMID:20018213

Self-referential processing is distinct from semantic elaboration: evidence from long-term memory effects in a patient with amnesia and semantic impairments.

PubMed

Sui, Jie; Humphreys, Glyn W

2013-11-01

We report data demonstrating that self-referential encoding facilitates memory performance in the absence of effects of semantic elaboration in a severely amnesic patient also suffering semantic problems. In Part 1, the patient, GA, was trained to associate items with the self or a familiar other during the encoding phase of a memory task (self-ownership decisions in Experiment 1 and self-evaluation decisions in Experiment 2). Tests of memory showed a consistent self-reference advantage, relative to a condition where the reference was another person in both experiments. The pattern of the self-reference advantage was similar to that in healthy controls. In Part 2 we demonstrate that GA showed minimal effects of semantic elaboration on memory for items he semantically classified, compared with items subject to physical size decisions; in contrast, healthy controls demonstrated enhanced memory performance after semantic relative to physical encoding. The results indicate that self-referential encoding, not semantic elaboration, improves memory in amnesia. Self-referential processing may provide a unique scaffold to help improve learning in amnesic cases. Copyright © 2013 Elsevier Ltd. All rights reserved.

Synthesis of TiC Nanoparticles Anchored on Hollow Carbon Nanospheres for Enhanced Polysulfide Adsorption in Li-S Batteries.

PubMed

Cao, Bokai; Chen, Yong; Li, De; Yin, Lihong; Mo, Yan

2016-12-08

A novel spatial confinement strategy based on a carbon/TiO 2 /carbon sandwich structure is proposed to synthesize TiC nanoparticles anchored on hollow carbon nanospheres (TiC@C) through a carbothermal reduction reaction. During the synthesis process, two carbon layers not only serve as reductant to convert TiO 2 into TiC nanoparticles, but also create a spatial confinement to suppress the aggregation of TiO 2 , resulting in the formation of well-dispersed TiC nanoparticles. This unique TiC@C structure shows an outstanding long-term cycling stability at high rates owing to the strong physical and chemical adsorption of lithium polysulfides (i.e., a high capacity of 732.6 mA h g -1 at 1600 mA g -1 ) and it retains a capacity of 443.2 mA h g -1 after 1000 cycles, corresponding to a decay rate of only 0.0395 % per cycle. Therefore, this unique TiC@C composite could be considered as an important candidate for the cathode material in Li-S batteries. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

An integrative approach to energy, carbon, and redox metabolism in the cyanobacterium Synechocystis sp. PCC 6803

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

Overbeek, Ross; Fonstein, Veronika; Osterman, Andrei

2005-02-15

The team of the Fellowship for Interpretation of Genomes (FIG) under the leadership of Ross Overbeek, began working on this Project in November 2003. During the previous year, the Project was performed at Integrated Genomics Inc. A transition from the industrial environment to the public domain prompted us to adjust some aspects of the Project. Notwithstanding the challenges, we believe that these adjustments had a strong positive impact on our deliverables. Most importantly, the work of the research team led by R. Overbeek resulted in the deployment of a new open source genomic platform, the SEED (Specific Aim 1). Thismore » platform provided a foundation for the development of CyanoSEED a specialized portal to comparative analysis and metabolic reconstruction of all available cyanobacterial genomes (Specific Aim 3). The SEED represents a new generation of software for genome analysis. Briefly, it is a portable and extendable system, containing one of the largest and permanently growing collections of complete and partial genomes. The complete system with annotations and tools is freely available via browsing or via installation on a user's Mac or Linux computer. One of the important unique features of the SEED is the support of metabolic reconstruction and comparative genome analysis via encoding and projection of functional subsystems. During the project period, the FIG research team has validated the new software by developing a significant number of core subsystems, covering many aspects of central metabolism (Specific Aim 2), as well as metabolic areas specific for cyanobacteria and other photoautotrophic organisms (Specific Aim 3). In addition to providing a proof of technology and a starting point for further community-based efforts, these subsystems represent a valuable asset. An extensive coverage of central metabolism provides the bulk of information required for metabolic modeling in Synechocystis sp.PCC 6803. Detailed analysis of several subsystems covering energy, carbon, and redox metabolism in the Synechocystis sp. PCC 6803 and other cyanobacteria has been performed (Specific Aim 4). The main objectives for this year (adjusted to reflect a new, public domain, setting of the Project research team) were: Aim 1. To develop, test, and deploy a new open source system, the SEED, for integrating community-based annotation, and comparative analysis of all publicly available microbial genomes. Develop a comprehensive genomic database by integrating within SEED all publicly available complete and nearly complete genome sequences with special emphasis on genomes of cyanobacteria, phototrophic eukaryotes, and anoxygenic phototrophic bacteria--invaluable for comparative genomic studies of energy and carbon metabolism in Synechocystis sp. PCC 6803. Aim 2. To develop the SEED's biological content in the form of a collection of encoded Subsystems largely covering the conserved cellular machinery in prokaryotes (and central metabolic machinery in eukaryotes). Aim 3. To develop, utilizing core SEED technology, the CyanoSEED--a specialized WEB portal for community-based annotation, and comparative analysis of all publicly available cyanobacterial genomes. Encode the set of additional subsystems representing key metabolic transformations in cyanobacteria and other photoautotrophs. We envisioned this resource as complementary to other public access databases for comparative genomic analysis currently available to the cyanobacterial research community. Aim 4. Perform in-depth analysis of several subsystems covering energy, carbon, and redox metabolism in the Synechocystis sp. PCC 6803 and all other cyanobacteria with available genome sequences. Reveal inconsistencies and gaps in the current knowledge of these subsystems. Use functional and genome context analysis tools in CyanoSEED to predict, whenever possible, candidate genes for inferred functional roles. To disseminate freely these conjectures and predictions by publishing them on CyanoSEED (http://cyanoseed.thefig.info/) and the Subsystems Forum (http://brucella.uchicago.edu/SubsystemForum/) in order to facilitate experimental analysis by our collaborator on this Project and by other experimentalists working in various field of cyanobacterial physiology and biotechnology.« less

Molecular Characterization of a Novel Bovine Viral Diarrhea Virus Isolate SD-15

PubMed Central

Zhu, Lisai; Lu, Haibing; Cao, Yufeng; Gai, Xiaochun; Guo, Changming; Liu, Yajing; Liu, Jiaxu; Wang, Xinping

2016-01-01

As one of the major pathogens, bovine viral diarrhea virus caused a significant economic loss to the livestock industry worldwide. Although BVDV infections have increasingly been reported in China in recent years, the molecular aspects of those BVDV strains were barely characterized. In this study, we reported the identification and characterization of a novel BVDV isolate designated as SD-15 from cattle, which is associated with an outbreak characterized by severe hemorrhagic and mucous diarrhea with high morbidity and mortality in Shandong, China. SD-15 was revealed to be a noncytopathic BVDV, and has a complete genomic sequence of 12,285 nucleotides that contains a large open reading frame encoding 3900 amino acids. Alignment analysis showed that SD-15 has 93.8% nucleotide sequence identity with BVDV ZM-95 isolate, a previous BVDV strain isolated from pigs manifesting clinical signs and lesions resembling to classical swine fever. Phylogenetic analysis clustered SD-15 to a BVDV-1m subgenotype. Analysis of the deduced amino acid sequence of glycoproteins revealed that E2 has several highly conserved and variable regions within BVDV-1 genotypes. An additional N-glycosylation site (240NTT) was revealed exclusively in SD-15-encoded E2 in addition to four potential glycosylation sites (Asn-X-Ser/Thr) shared by all BVDV-1 genotypes. Furthermore, unique amino acid and linear epitope mutations were revealed in SD-15-encoded Erns glycoprotein compared with known BVDV-1 genotype. In conclusion, we have isolated a noncytopathic BVDV-1m strain that is associated with a disease characterized by high morbidity and mortality, revealed the complete genome sequence of the first BVDV-1m virus originated from cattle, and found a unique glycosylation site in E2 and a linear epitope mutation in Erns encoded by SD-15 strain. Those results will broaden the current understanding of BVDV infection and lay a basis for future investigation on SD-15-related pathogenesis. PMID:27764206

Urban warming reduces aboveground carbon storage.

PubMed

Meineke, Emily; Youngsteadt, Elsa; Dunn, Robert R; Frank, Steven D

2016-10-12

A substantial amount of global carbon is stored in mature trees. However, no experiments to date test how warming affects mature tree carbon storage. Using a unique, citywide, factorial experiment, we investigated how warming and insect herbivory affected physiological function and carbon sequestration (carbon stored per year) of mature trees. Urban warming increased herbivorous arthropod abundance on trees, but these herbivores had negligible effects on tree carbon sequestration. Instead, urban warming was associated with an estimated 12% loss of carbon sequestration, in part because photosynthesis was reduced at hotter sites. Ecosystem service assessments that do not consider urban conditions may overestimate urban tree carbon storage. Because urban and global warming are becoming more intense, our results suggest that urban trees will sequester even less carbon in the future. © 2016 The Author(s).

Complete genome sequence of "Thiodictyon syntrophicum" sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.

PubMed

Luedin, Samuel M; Pothier, Joël F; Danza, Francesco; Storelli, Nicola; Frigaard, Niels-Ulrik; Wittwer, Matthias; Tonolla, Mauro

2018-01-01

" Thiodictyon syntrophicum" sp. nov. strain Cad16 T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria . The type strain Cad16 T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16 T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16 T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232 T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16 T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno.

Draft genome sequence of Janthinobacterium lividum strain MTR reveals its mechanism of capnophilic behavior.

PubMed

Valdes, Natalia; Soto, Paola; Cottet, Luis; Alarcon, Paula; Gonzalez, Alex; Castillo, Antonio; Corsini, Gino; Tello, Mario

2015-01-01

Janthinobacterium lividum is a Gram-negative bacterium able to produce violacein, a pigment with antimicrobial and antitumor properties. Janthinobacterium lividum colonizes the skin of some amphibians and confers protection against fungal pathogens. The mechanisms underlying this association are not well understood. In order to identify the advantages for the bacterium to colonize amphibian skin we sequenced Janthinobacterium lividum strain MTR, a strain isolated from Cajón del Maipo, Chile. The strain has capnophilic behavior, with growth favored by high concentrations (5 %) of carbon dioxide. Its genome is 6,535,606 bp in size, with 5,362 coding sequences and a G + C content of 62.37 %. The presence of genes encoding for products that participate in the carbon fixation pathways (dark CAM pathways), and the entire set of genes encoding for the enzymes of the glyoxylate cycle may explain the capnophilic behavior and allow us to propose that the CO2 secreted by the skin of amphibians is the signal molecule that guides colonization by Janthinobacterium lividum.

Abundance and diversity of CO2-fixing bacteria in grassland soils close to natural carbon dioxide springs.

PubMed

Videmsek, Urska; Hagn, Alexandra; Suhadolc, Marjetka; Radl, Viviane; Knicker, Heike; Schloter, Michael; Vodnik, Dominik

2009-07-01

Gaseous conditions at natural CO2 springs (mofettes) affect many processes in these unique ecosystems. While the response of plants to extreme and fluctuating CO2 concentrations ([CO2]) is relatively well documented, little is known on microbial life in mofette soil. Therefore, it was the aim of this study to investigate the abundance and diversity of CO2-fixing bacteria in grassland soils in different distances to a natural carbon dioxide spring. Samples of the same soil type were collected from the Stavesinci mofette, a natural CO2 spring which is known for very pure CO2 emissions, at different distances from the CO2 releasing vents, at locations that clearly differed in soil CO2 efflux (from 12.5 to over 200 micromol CO2 m(-2) s(-1) yearly average). Bulk and rhizospheric soil samples were included into analyses. The microbial response was followed by a molecular analysis of cbbL genes, encoding for the large subunit of RubisCO, a carboxylase which is of crucial importance for C assimilation in chemolitoautotrophic microbes. In all samples analyzed, the "red-like" type of cbbL genes could be detected. In contrast, the "green-like" type of cbbL could not be measured by the applied technique. Surprisingly, a reduction of "red-like" cbbL genes copies was observed in bulk soil and rhizosphere samples from the sites with the highest CO2 concentrations. Furthermore, the diversity pattern of "red-like" cbbL genes changed depending on the CO(2) regime. This indicates that only a part of the autotrophic CO2-fixing microbes could adapt to the very high CO2 concentrations and adverse life conditions that are governed by mofette gaseous regime.

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity.

PubMed

Tang, Kai; Zhang, Yao; Lin, Dan; Han, Yu; Chen, Chen-Tung A; Wang, Deli; Lin, Yu-Shih; Sun, Jia; Zheng, Qiang; Jiao, Nianzhi

2018-01-01

Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile genetic potential to adapt to the unique environmental conditions.

A Carbon Dioxide Limitation-Inducible Protein, ColA, Supports the Growth of Synechococcus sp. PCC 7002

PubMed Central

Shimakawa, Ginga; Watanabe, Satoru; Miyake, Chikahiro

2017-01-01

A limitation in carbon dioxide (CO2), which occurs as a result of natural environmental variation, suppresses photosynthesis and has the potential to cause photo-oxidative damage to photosynthetic cells. Oxygenic phototrophs have strategies to alleviate photo-oxidative damage to allow life in present atmospheric CO2 conditions. However, the mechanisms for CO2 limitation acclimation are diverse among the various oxygenic phototrophs, and many mechanisms remain to be discovered. In this study, we found that the gene encoding a CO2 limitation-inducible protein, ColA, is required for the cyanobacterium Synechococcus sp. PCC 7002 (S. 7002) to acclimate to limited CO2 conditions. An S. 7002 mutant deficient in ColA (ΔcolA) showed lower chlorophyll content, based on the amount of nitrogen, than that in S. 7002 wild-type (WT) under ambient air but not high CO2 conditions. Both thermoluminescence and protein carbonylation detected in the ambient air grown cells indicated that the lack of ColA promotes oxidative stress in S. 7002. Alterations in the photosynthetic O2 evolution rate and relative electron transport rate in the short-term response, within an hour, to CO2 limitation were the same between the WT and ΔcolA. Conversely, these photosynthetic parameters were mostly lower in the long-term response of a few days in ΔcolA than in the WT. These data suggest that ColA is required to sustain photosynthetic activity for living under ambient air in S. 7002. The unique phylogeny of ColA revealed diverse strategies to acclimate to CO2 limitation among cyanobacteria. PMID:29244744

The glyoxylate shunt is essential for CO2-requiring oligotrophic growth of Rhodococcus erythropolis N9T-4.

PubMed

Yano, Takanori; Yoshida, Nobuyuki; Yu, Fujio; Wakamatsu, Miki; Takagi, Hiroshi

2015-07-01

Rhodococcus erythropolis N9T-4 shows extremely oligotrophic growth requiring atmospheric CO2 and forms its colonies on an inorganic basal medium (BM) without any additional carbon source. Screening of a random mutation library constructed by a unique genome deletion method that we established indicated that the aceA, aceB, and pckG genes encoding isocitrate lyase, malate synthase, and phosphoenolpyruvate carboxykinase, respectively, were requisite for survival on BM plates. The aceA- and aceB deletion mutants and the pckG deletion mutant grew well on BM plates containing L-malate and D-glucose, respectively, suggesting that the glyoxylate (GO) shunt and gluconeogenesis are essential for the oligotrophic growth of N9T-4. Interestingly, most of the enzyme activities in the TCA cycle were observed in the cell-free extract of N9T-4, with perhaps the most important exception being α-ketoglutarate dehydrogenase (KGDH) activity. Instead of the KGDH activity, we detected a remarkable level of α-ketoglutarate decarboxylase (KGD) activity, which is the activity exhibited by the E1 component of the KGDH complex in Mycobacterium tuberculosis. The recombinant KGD of N9T-4 catalyzed the decarboxylation of α-ketoglutarate to form succinic semialdehyde (SSA) in a time-dependent manner. Since N9T-4 also showed a detectable SSA dehydrogenase activity, we concluded that N9T-4 possesses a variant TCA cycle, which uses SSA rather than succinyl-CoA. These results suggest that oligotrophic N9T-4 cells utilize the GO shunt to avoid the loss of carbons as CO2 and to conserve CoA units in the TCA cycle.

Cultivation-Independent and Cultivation-Dependent Analysis of Microbes in the Shallow-Sea Hydrothermal System Off Kueishantao Island, Taiwan: Unmasking Heterotrophic Bacterial Diversity and Functional Capacity

PubMed Central

Tang, Kai; Zhang, Yao; Lin, Dan; Han, Yu; Chen, Chen-Tung A.; Wang, Deli; Lin, Yu-Shih; Sun, Jia; Zheng, Qiang; Jiao, Nianzhi

2018-01-01

Shallow-sea hydrothermal systems experience continuous fluctuations of physicochemical conditions due to seawater influx which generates variable habitats, affecting the phylogenetic composition and metabolic potential of microbial communities. Until recently, studies of submarine hydrothermal communities have focused primarily on chemolithoautotrophic organisms, however, there have been limited studies on heterotrophic bacteria. Here, fluorescence in situ hybridization, high throughput 16S rRNA gene amplicon sequencing, and functional metagenomes were used to assess microbial communities from the shallow-sea hydrothermal system off Kueishantao Island, Taiwan. The results showed that the shallow-sea hydrothermal system harbored not only autotrophic bacteria but abundant heterotrophic bacteria. The potential for marker genes sulfur oxidation and carbon fixation were detected in the metagenome datasets, suggesting a role for sulfur and carbon cycling in the shallow-sea hydrothermal system. Furthermore, the presence of diverse genes that encode transporters, glycoside hydrolases, and peptidase indicates the genetic potential for heterotrophic utilization of organic substrates. A total of 408 cultivable heterotrophic bacteria were isolated, in which the taxonomic families typically associated with oligotrophy, copiotrophy, and phototrophy were frequently found. The cultivation-independent and -dependent analyses performed herein show that Alphaproteobacteria and Gammaproteobacteria represent the dominant heterotrophs in the investigated shallow-sea hydrothermal system. Genomic and physiological characterization of a novel strain P5 obtained in this study, belonging to the genus Rhodovulum within Alphaproteobacteria, provides an example of heterotrophic bacteria with major functional capacity presented in the metagenome datasets. Collectively, in addition to autotrophic bacteria, the shallow-sea hydrothermal system also harbors many heterotrophic bacteria with versatile genetic potential to adapt to the unique environmental conditions. PMID:29527196

The first does the work, but the third time's the charm: the effects of massed repetition on episodic encoding of multimodal face-name associations.

PubMed

Mangels, Jennifer A; Manzi, Alberto; Summerfield, Christopher

2010-03-01

In social interactions, it is often necessary to rapidly encode the association between visually presented faces and auditorily presented names. The present study used event-related potentials to examine the neural correlates of associative encoding for multimodal face-name pairs. We assessed study-phase processes leading to high-confidence recognition of correct pairs (and consistent rejection of recombined foils) as compared to lower-confidence recognition of correct pairs (with inconsistent rejection of recombined foils) and recognition failures (misses). Both high- and low-confidence retrieval of face-name pairs were associated with study-phase activity suggestive of item-specific processing of the face (posterior inferior temporal negativity) and name (fronto-central negativity). However, only those pairs later retrieved with high confidence recruited a sustained centro-parietal positivity that an ancillary localizer task suggested may index an association-unique process. Additionally, we examined how these processes were influenced by massed repetition, a mnemonic strategy commonly employed in everyday situations to improve face-name memory. Differences in subsequent memory effects across repetitions suggested that associative encoding was strongest at the initial presentation, and thus, that the initial presentation has the greatest impact on memory formation. Yet, exploratory analyses suggested that the third presentation may have benefited later memory by providing an opportunity for extended processing of the name. Thus, although encoding of the initial presentation was critical for establishing a strong association, the extent to which processing was sustained across subsequent immediate (massed) presentations may provide additional encoding support that serves to differentiate face-name pairs from similar (recombined) pairs by providing additional encoding opportunities for the less dominant stimulus dimension (i.e., name).

Limits on carbon sequestration in arid blue carbon ecosystems.

PubMed

Schile, Lisa M; Kauffman, J Boone; Crooks, Stephen; Fourqurean, James W; Glavan, Jane; Megonigal, J Patrick

2017-04-01

Coastal ecosystems produce and sequester significant amounts of carbon ("blue carbon"), which has been well documented in humid and semi-humid regions of temperate and tropical climates but less so in arid regions where mangroves, marshes, and seagrasses exist near the limit of their tolerance for extreme temperature and salinity. To better understand these unique systems, we measured whole-ecosystem carbon stocks in 58 sites across the United Arab Emirates (UAE) in natural and planted mangroves, salt marshes, seagrass beds, microbial mats, and coastal sabkha (inter- and supratidal unvegetated salt flats). Natural mangroves held significantly more carbon in above- and belowground biomass than other vegetated ecosystems. Planted mangrove carbon stocks increased with age, but there were large differences for sites of similar age. Soil carbon varied widely across sites (2-367 Mg C/ha), with ecosystem averages that ranged from 49 to 156 Mg C/ha. For the first time, microbial mats were documented to contain soil carbon pools comparable to vascular plant-dominated ecosystems, and could arguably be recognized as a unique blue carbon ecosystem. Total ecosystem carbon stocks ranged widely from 2 to 515 Mg C/ha (seagrass bed and mangrove, respectively). Seagrass beds had the lowest carbon stock per unit area, but the largest stock per total area due to their large spatial coverage. Compared to similar ecosystems globally, mangroves and marshes in the UAE have lower plant and soil carbon stocks; however, the difference in soil stocks is far larger than with plant stocks. This incongruent difference between stocks is likely due to poor carbon preservation under conditions of weakly reduced soils (200-350 mV), coarse-grained sediments, and active shoreline migration. This work represents the first attempt to produce a country-wide coastal ecosystem carbon accounting using a uniform sampling protocol, and was motivated by specific policy goals identified by the Abu Dhabi Global Environmental Data Initiative. These carbon stock data supported two objectives: to quantify carbon stocks and infer sequestration capacity in arid blue carbon ecosystems, and to explore the potential to incorporate blue carbon science into national reporting and planning documents. © 2016 by the Ecological Society of America.

Lafora disease offers a unique window into neuronal glycogen metabolism.

PubMed

Gentry, Matthew S; Guinovart, Joan J; Minassian, Berge A; Roach, Peter J; Serratosa, Jose M

2018-05-11

Lafora disease (LD) is a fatal, autosomal recessive, glycogen-storage disorder that manifests as severe epilepsy. LD results from mutations in the gene encoding either the glycogen phosphatase laforin or the E3 ubiquitin ligase malin. Individuals with LD develop cytoplasmic, aberrant glycogen inclusions in nearly all tissues that more closely resemble plant starch than human glycogen. This Minireview discusses the unique window into glycogen metabolism that LD research offers. It also highlights recent discoveries, including that glycogen contains covalently bound phosphate and that neurons synthesize glycogen and express both glycogen synthase and glycogen phosphorylase. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

A coded tracking telemetry system

USGS Publications Warehouse

Howey, P.W.; Seegar, W.S.; Fuller, M.R.; Titus, K.; Amlaner, Charles J.

1989-01-01

We describe the general characteristics of an automated radio telemetry system designed to operate for prolonged periods on a single frequency. Each transmitter sends a unique coded signal to a receiving system that encodes and records only the appropriater, pre-programmed codes. A record of the time of each reception is stored on diskettes in a micro-computer. This system enables continuous monitoring of infrequent signals (e.g. one per minute or one per hour), thus extending operation life or allowing size reduction of the transmitter, compared to conventional wildlife telemetry. Furthermore, when using unique codes transmitted on a single frequency, biologists can monitor many individuals without exceeding the radio frequency allocations for wildlife.

Brain Activity During the Encoding, Retention, and Retrieval of Stimulus Representations

PubMed Central

de Zubicaray, Greig I.; McMahon, Katie; Wilson, Stephen J.; Muthiah, Santhi

2001-01-01

Studies of delayed nonmatching-to-sample (DNMS) performance following lesions of the monkey cortex have revealed a critical circuit of brain regions involved in forming memories and retaining and retrieving stimulus representations. Using event-related functional magnetic resonance imaging (fMRI), we measured brain activity in 10 healthy human participants during performance of a trial-unique visual DNMS task using novel barcode stimuli. The event-related design enabled the identification of activity during the different phases of the task (encoding, retention, and retrieval). Several brain regions identified by monkey studies as being important for successful DNMS performance showed selective activity during the different phases, including the mediodorsal thalamic nucleus (encoding), ventrolateral prefrontal cortex (retention), and perirhinal cortex (retrieval). Regions showing sustained activity within trials included the ventromedial and dorsal prefrontal cortices and occipital cortex. The present study shows the utility of investigating performance on tasks derived from animal models to assist in the identification of brain regions involved in human recognition memory. PMID:11584070

Place field assembly distribution encodes preferred locations

PubMed Central

Mamad, Omar; Stumpp, Lars; McNamara, Harold M.; Ramakrishnan, Charu; Deisseroth, Karl; Reilly, Richard B.

2017-01-01

The hippocampus is the main locus of episodic memory formation and the neurons there encode the spatial map of the environment. Hippocampal place cells represent location, but their role in the learning of preferential location remains unclear. The hippocampus may encode locations independently from the stimuli and events that are associated with these locations. We have discovered a unique population code for the experience-dependent value of the context. The degree of reward-driven navigation preference highly correlates with the spatial distribution of the place fields recorded in the CA1 region of the hippocampus. We show place field clustering towards rewarded locations. Optogenetic manipulation of the ventral tegmental area demonstrates that the experience-dependent place field assembly distribution is directed by tegmental dopaminergic activity. The ability of the place cells to remap parallels the acquisition of reward context. Our findings present key evidence that the hippocampal neurons are not merely mapping the static environment but also store the concurrent context reward value, enabling episodic memory for past experience to support future adaptive behavior. PMID:28898248

Red fluorescent genetically encoded indicator for intracellular hydrogen peroxide

NASA Astrophysics Data System (ADS)

Ermakova, Yulia G.; Bilan, Dmitry S.; Matlashov, Mikhail E.; Mishina, Natalia M.; Markvicheva, Ksenia N.; Subach, Oksana M.; Subach, Fedor V.; Bogeski, Ivan; Hoth, Markus; Enikolopov, Grigori; Belousov, Vsevolod V.

2014-10-01

Reactive oxygen species (ROS) are conserved regulators of numerous cellular functions, and overproduction of ROS is a hallmark of various pathological processes. Genetically encoded fluorescent probes are unique tools to study ROS production in living systems of different scale and complexity. However, the currently available recombinant redox sensors have green emission, which overlaps with the spectra of many other probes. Expanding the spectral range of recombinant in vivo ROS probes would enable multiparametric in vivo ROS detection. Here we present the first genetically encoded red fluorescent sensor for hydrogen peroxide detection, HyPerRed. The performance of this sensor is similar to its green analogues. We demonstrate the utility of the sensor by tracing low concentrations of H2O2 produced in the cytoplasm of cultured cells upon growth factor stimulation. Moreover, using HyPerRed we detect local and transient H2O2 production in the mitochondrial matrix upon inhibition of the endoplasmic reticulum Ca2+ uptake.

Nanoporous hard data: optical encoding of information within nanoporous anodic alumina photonic crystals.

PubMed

Santos, Abel; Law, Cheryl Suwen; Pereira, Taj; Losic, Dusan

2016-04-21

Herein, we present a method for storing binary data within the spectral signature of nanoporous anodic alumina photonic crystals. A rationally designed multi-sinusoidal anodisation approach makes it possible to engineer the photonic stop band of nanoporous anodic alumina with precision. As a result, the transmission spectrum of these photonic nanostructures can be engineered to feature well-resolved and selectively positioned characteristic peaks across the UV-visible spectrum. Using this property, we implement an 8-bit binary code and assess the versatility and capability of this system by a series of experiments aiming to encode different information within the nanoporous anodic alumina photonic crystals. The obtained results reveal that the proposed nanosized platform is robust, chemically stable, versatile and has a set of unique properties for data storage, opening new opportunities for developing advanced nanophotonic tools for a wide range of applications, including sensing, photonic tagging, self-reporting drug releasing systems and secure encoding of information.

Distinct roles of visual, parietal, and frontal motor cortices in memory-guided sensorimotor decisions.

PubMed

Goard, Michael J; Pho, Gerald N; Woodson, Jonathan; Sur, Mriganka

2016-08-04

Mapping specific sensory features to future motor actions is a crucial capability of mammalian nervous systems. We investigated the role of visual (V1), posterior parietal (PPC), and frontal motor (fMC) cortices for sensorimotor mapping in mice during performance of a memory-guided visual discrimination task. Large-scale calcium imaging revealed that V1, PPC, and fMC neurons exhibited heterogeneous responses spanning all task epochs (stimulus, delay, response). Population analyses demonstrated unique encoding of stimulus identity and behavioral choice information across regions, with V1 encoding stimulus, fMC encoding choice even early in the trial, and PPC multiplexing the two variables. Optogenetic inhibition during behavior revealed that all regions were necessary during the stimulus epoch, but only fMC was required during the delay and response epochs. Stimulus identity can thus be rapidly transformed into behavioral choice, requiring V1, PPC, and fMC during the transformation period, but only fMC for maintaining the choice in memory prior to execution.

Cloning, expression and biochemical characterization of a β-carbonic anhydrase from the soil bacterium Enterobacter sp. B13.

PubMed

Eminoğlu, Ayşenur; Vullo, Daniela; Aşık, Aycan; Çolak, Dilşat Nigar; Supuran, Claudiu T; Çanakçı, Sabriye; Osman Beldüz, Ali

2016-12-01

A recombinant carbonic anhydrase (CA, EC 4.2.1.1) from the soil-dwelling bacterium Enterobacter sp. B13 was cloned and purified by Co(2+) affinity chromatography. Bioinformatic analysis showed that the new enzyme (denominated here B13-CA) belongs to the β-class CAs and to possess 95% homology with the ortholog enzyme from Escherichia coli encoded by the can gene, whereas its sequence homology with the other such enzyme from E. coli (encoded by the cynT gene) was of 33%. B13-CA was characterized kinetically as a catalyst for carbon dioxide hydration to bicarbonate and protons. The enzyme shows a significant catalytic activity, with the following kinetic parameters at 20 °C and pH of 8.3: kcat of 4.8 × 10(5) s(-1) and kcat/Km of 5.6 × 10(7) M(-1) × s(-1). This activity was potently inhibited by acetazolamide which showed a KI of 78.9 nM. Although only this compound was investigated for the moment as B13-CA inhibitor, further studies may reveal new classes of inhibitors/activators of this enzyme which may show biomedical or environmental applications, considering the posssible role of this enzyme in CaCO3 biomineralization processes.

SiCO-doped carbon fibers with unique dual superhydrophilicity/superoleophilicity and ductile and capacitance properties.

PubMed

Lu, Ping; Huang, Qing; Mukherjee, Amiya; Hsieh, You-Lo

2010-12-01

Silicon oxycarbide (SiCO) glass-doped carbon fibers with an average diameter of 163 nm were successfully synthesized by electrospinning polymer mixtures of preceramic precursor polyureasilazane (PUS) and carbon precursor polyacrylonitrile (PAN) into fibers then converting to ceramic/carbon hybrid via cross-linking, stabilization, and pyrolysis at temperatures up to 1000 °C. The transformation of PUS/PAN polymer precursors to SiCO/carbon structures was confirmed by EDS and FTIR. Both carbon and SiCO/carbon fibers were amorphous and slightly oxidized. Doping with SiCO enhanced the thermal stability of carbon fibers and acquired new ductile behavior in the SiCO/carbon fibers with significantly improved flexibility and breaking elongation. Furthermore, the SiCO/carbon fibers exhibited dual superhydrophilicity and superoleophilicity with water and decane absorbing capacities of 873 and 608%, respectively. The cyclic voltammetry also showed that SiCO/carbon composite fibers possess better capacitor properties than carbon fibers.

Fullerenes: An extraterrestrial carbon carrier phase for noble gases

PubMed Central

Becker, Luann; Poreda, Robert J.; Bunch, Ted E.

2000-01-01

In this work, we report on the discovery of naturally occurring fullerenes (C60 to C400) in the Allende and Murchison meteorites and some sediment samples from the 65 million-year-old Cretaceous/Tertiary boundary layer (KTB). Unlike the other pure forms of carbon (diamond and graphite), fullerenes are extractable in an organic solvent (e.g., toluene or 1,2,4-trichlorobenzene). The recognition of this unique property led to the detection and isolation of the higher fullerenes in the Kratschmer/Huffmann arc evaporated graphite soot and in the carbon material in the meteorite and impact deposits. By further exploiting the unique ability of the fullerene cage structure to encapsulate and retain noble gases, we have determined that both the Allende and Murchison fullerenes and the KTB fullerenes contain trapped noble gases with ratios that can only be described as extraterrestrial in origin. PMID:10725367

Origin of the Allyl Group in FK506 Biosynthesis*

PubMed Central

Goranovič, Dušan; Kosec, Gregor; Mrak, Peter; Fujs, Štefan; Horvat, Jaka; Kuščer, Enej; Kopitar, Gregor; Petković, Hrvoje

2010-01-01

FK506 (tacrolimus) is a secondary metabolite with a potent immunosuppressive activity, currently registered for use as immunosuppressant after organ transplantation. FK506 and FK520 are biogenetically related natural products that are synthesized by combined polyketide synthase/nonribosomal peptide synthetase systems. The entire gene cluster for biosynthesis of FK520 from Streptomyces hygroscopicus var. ascomyceticus has been cloned and sequenced. On the other hand, the FK506 gene cluster from Streptomyces sp. MA6548 (ATCC55098) was sequenced only partially, and it was reasonable to expect that additional genes would be required for the provision of substrate supply. Here we report the identification of a previously unknown region of the FK506 gene cluster from Streptomyces tsukubaensis NRRL 18488 containing genes encoding the provision of unusual building blocks for FK506 biosynthesis as well as a regulatory gene. Among others, we identified a group of genes encoding biosynthesis of the extender unit that forms the allyl group at carbon 21 of FK506. Interestingly, we have identified a small independent diketide synthase system involved in the biosynthesis of the allyl group. Inactivation of one of these genes, encoding an unusual ketosynthase domain, resulted in an FK506 nonproducing strain, and the production was restored when a synthetic analog of the allylmalonyl-CoA extender unit was added to the cultivation medium. Based on our results, we propose a biosynthetic pathway for the provision of an unusual five-carbon extender unit, which is carried out by a novel diketide synthase complex. PMID:20194504

Interactions between hemiparasitic plants and their hosts

PubMed Central

Plavcová, Lenka; Cameron, Duncan D

2010-01-01

Hemiparasitic plants display a unique strategy of resource acquisition combining parasitism of other species and own photosynthetic activity. Despite the active photoassimilation and green habit, they acquire substantial amount of carbon from their hosts. The organic carbon transfer has a crucial influence on the nature of the interaction between hemiparasites and their hosts which can oscillate between parasitism and competition for light. In this minireview, we summarize methodical approaches and results of various studies dealing with carbon budget of hemiparasites and the ecological implications of carbon heterotrophy in hemiparasites. PMID:20729638

Formation of polycyclic lactones through a ruthenium-catalyzed ring-closing metathesis/hetero-Pauson-Khand reaction sequence.

PubMed

Finnegan, David F; Snapper, Marc L

2011-05-20

Processes that form multiple carbon-carbon bonds in one operation can generate molecular complexity quickly and therefore be used to shorten syntheses of desirable molecules. We selected the hetero-Pauson-Khand (HPK) cycloaddition and ring-closing metathesis (RCM) as two unique carbon-carbon bond-forming reactions that could be united in a tandem ruthenium-catalyzed process. In doing so, complex polycyclic products can be obtained in one reaction vessel from acyclic precursors using a single ruthenium additive that can catalyze sequentially two mechanistically distinct transformations.

Biodegradation of the organic disulfide 4,4'-dithiodibutyric acid by Rhodococcus spp.

PubMed

Khairy, Heba; Wübbeler, Jan Hendrik; Steinbüchel, Alexander

2015-12-01

Four Rhodococcus spp. exhibited the ability to use 4,4'-dithiodibutyric acid (DTDB) as a sole carbon source for growth. The most important step for the production of a novel polythioester (PTE) using DTDB as a precursor substrate is the initial cleavage of DTDB. Thus, identification of the enzyme responsible for this step was mandatory. Because Rhodococcus erythropolis strain MI2 serves as a model organism for elucidation of the biodegradation of DTDB, it was used to identify the genes encoding the enzymes involved in DTDB utilization. To identify these genes, transposon mutagenesis of R. erythropolis MI2 was carried out using transposon pTNR-TA. Among 3,261 mutants screened, 8 showed no growth with DTDB as the sole carbon source. In five mutants, the insertion locus was mapped either within a gene coding for a polysaccharide deacetyltransferase, a putative ATPase, or an acetyl coenzyme A transferase, 1 bp upstream of a gene coding for a putative methylase, or 176 bp downstream of a gene coding for a putative kinase. In another mutant, the insertion was localized between genes encoding a putative transcriptional regulator of the TetR family (noxR) and an NADH:flavin oxidoreductase (nox). Moreover, in two other mutants, the insertion loci were mapped within a gene encoding a hypothetical protein in the vicinity of noxR and nox. The interruption mutant generated, R. erythropolis MI2 noxΩtsr, was unable to grow with DTDB as the sole carbon source. Subsequently, nox was overexpressed and purified, and its activity with DTDB was measured. The specific enzyme activity of Nox amounted to 1.2 ± 0.15 U/mg. Therefore, we propose that Nox is responsible for the initial cleavage of DTDB into 2 molecules of 4-mercaptobutyric acid (4MB). Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae

PubMed Central

Salusjärvi, Laura; Kankainen, Matti; Soliymani, Rabah; Pitkänen, Juha-Pekka; Penttilä, Merja; Ruohonen, Laura

2008-01-01

Background Considerable interest in the bioconversion of lignocellulosic biomass into ethanol has led to metabolic engineering of Saccharomyces cerevisiae for fermentation of xylose. In the present study, the transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with those of glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at the genome-wide level how signalling and carbon catabolite repression differ in cells grown on either glucose or xylose. The more detailed knowledge whether xylose is sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is rather recognised as a non-fermentable carbon source is important for further engineering this yeast for more efficient anaerobic fermentation of xylose. Results Genes encoding respiratory proteins, proteins of the tricarboxylic acid and glyoxylate cycles, and gluconeogenesis were only partially repressed by xylose, similar to the genes encoding their transcriptional regulators HAP4, CAT8 and SIP1-2 and 4. Several genes that are repressed via the Snf1p/Mig1p-pathway during growth on glucose had higher expression in the cells grown on xylose than in the glucose repressed cells but lower than in the glucose derepressed cells. The observed expression profiles of the transcription repressor RGT1 and its target genes HXT2-3, encoding hexose transporters suggested that extracellular xylose was sensed by the glucose sensors Rgt2p and Snf3p. Proteome analyses revealed distinct patterns in phosphorylation of hexokinase 2, glucokinase and enolase isoenzymes in the xylose- and glucose-grown cells. Conclusion The results indicate that the metabolism of yeast growing on xylose corresponds neither to that of fully glucose repressed cells nor that of derepressed cells. This may be one of the major reasons for the suboptimal fermentation of xylose by recombinant S. cerevisiae strains. Phosphorylation of different isoforms of glycolytic enzymes suggests that regulation of glycolysis also occurred at a post-translational level, supporting prior findings. PMID:18533012

Systems metabolic engineering of Corynebacterium glutamicum for the production of the carbon-5 platform chemicals 5-aminovalerate and glutarate.

PubMed

Rohles, Christina Maria; Gießelmann, Gideon; Kohlstedt, Michael; Wittmann, Christoph; Becker, Judith

2016-09-13

The steadily growing world population and our ever luxurious life style, along with the simultaneously decreasing fossil resources has confronted modern society with the issue and need of finding renewable routes to accommodate for our demands. Shifting the production pipeline from raw oil to biomass requires efficient processes for numerous platform chemicals being produced with high yield, high titer and high productivity. In the present work, we established a de novo bio-based production process for the two carbon-5 platform chemicals 5-aminovalerate and glutarate on basis of the lysine-hyperproducing strain Corynebacterium glutamicum LYS-12. Upon heterologous implementation of the Pseudomonas putida genes davA, encoding 5-aminovaleramidase and davB, encoding lysine monooxygenase, 5-aminovalerate production was established. Related to the presence of endogenous genes coding for 5-aminovalerate transaminase (gabT) and glutarate semialdehyde dehydrogenase, 5-aminovalerate was partially converted to glutarate. Moreover, residual L-lysine was secreted as by-product. The issue of by-product formation was then addressed by deletion of the lysE gene, encoding the L-lysine exporter. Additionally, a putative gabT gene was deleted to enhance 5-aminovalerate production. To fully exploit the performance of the optimized strain, fed-batch fermentation was carried out producing 28 g L(-1) 5-aminovalerate with a maximal space-time yield of 0.9 g L(-1) h(-1). The present study describes the construction of a recombinant microbial cell factory for the production of carbon-5 platform chemicals. Beyond a basic proof-of-concept, we were able to specifically increase the production flux of 5-aminovalerate thereby generating a strain with excellent production performance. Additional improvement can be expected by removal of remaining by-product formation and bottlenecks, associated to the terminal pathway, to generate a strain being applicable as centerpiece for a bio-based production of 5-aminovalerate.

NaKnowBaseTM: The EPA Nanomaterials Research ...

EPA Pesticide Factsheets

The ability to predict the environmental and health implications of engineered nanomaterials is an important research priority due to the exponential rate at which nanotechnology is being incorporated into consumer, industrial and biomedical applications. To address this need and develop predictive capability, we have created the NaKnowbaseTM, which provides a platform for the curation and dissemination of EPA nanomaterials data to support functional assay development, hazard risk models and informatic analyses. To date, we have combined relevant physicochemical parameters from other organizations (e.g., OECD, NIST), with those requested for nanomaterial data submitted to EPA under the Toxic Substances Control Act (TSCA). Physiochemical characterization data were collated from >400 unique nanomaterials including metals, metal oxides, carbon-based and hybrid materials evaluated or synthesized by EPA researchers. We constructed parameter requirements and table structures for encoding research metadata, including experimental factors and measured response variables. As a proof of concept, we illustrate how SQL-based queries facilitate a range of interrogations including, for example, relationships between nanoparticle characteristics and environmental or toxicological endpoints. The views expressed in this poster are those of the authors and may not reflect U.S. EPA policy. The purpose of this submission for clearance is an abstract for submission to a scientific

The making of a photosynthetic animal

PubMed Central

Rumpho, Mary E.; Pelletreau, Karen N.; Moustafa, Ahmed; Bhattacharya, Debashish

2011-01-01

Symbiotic animals containing green photobionts challenge the common perception that only plants are capable of capturing the sun's rays and converting them into biological energy through photoautotrophic CO2 fixation (photosynthesis). ‘Solar-powered’ sacoglossan molluscs, or sea slugs, have taken this type of symbiotic association one step further by solely harboring the photosynthetic organelle, the plastid (=chloroplast). One such sea slug, Elysia chlorotica, lives as a ‘plant’ when provided with only light and air as a result of acquiring plastids during feeding on its algal prey Vaucheria litorea. The captured plastids (kleptoplasts) are retained intracellularly in cells lining the digestive diverticula of the sea slug, a phenomenon sometimes referred to as kleptoplasty. Photosynthesis by the plastids provides E. chlorotica with energy and fixed carbon for its entire lifespan of ∼10 months. The plastids are not transmitted vertically (i.e. are absent in eggs) and do not undergo division in the sea slug. However, de novo protein synthesis continues, including plastid- and nuclear-encoded plastid-targeted proteins, despite the apparent absence of algal nuclei. Here we discuss current data and provide hypotheses to explain how long-term photosynthetic activity is maintained by the kleptoplasts. This fascinating ‘green animal’ provides a unique model to study the evolution of photosynthesis in a multicellular heterotrophic organism. PMID:21177950

Carbon source-dependent expansion of the genetic code in bacteria

PubMed Central

Prat, Laure; Heinemann, Ilka U.; Aerni, Hans R.; Rinehart, Jesse; O’Donoghue, Patrick; Söll, Dieter

2012-01-01

Despite the fact that the genetic code is known to vary between organisms in rare cases, it is believed that in the lifetime of a single cell the code is stable. We found Acetohalobium arabaticum cells grown on pyruvate genetically encode 20 amino acids, but in the presence of trimethylamine (TMA), A. arabaticum dynamically expands its genetic code to 21 amino acids including pyrrolysine (Pyl). A. arabaticum is the only known organism that modulates the size of its genetic code in response to its environment and energy source. The gene cassette pylTSBCD, required to biosynthesize and genetically encode UAG codons as Pyl, is present in the genomes of 24 anaerobic archaea and bacteria. Unlike archaeal Pyl-decoding organisms that constitutively encode Pyl, we observed that A. arabaticum controls Pyl encoding by down-regulating transcription of the entire Pyl operon under growth conditions lacking TMA, to the point where no detectable Pyl-tRNAPyl is made in vivo. Pyl-decoding archaea adapted to an expanded genetic code by minimizing TAG codon frequency to typically ∼5% of ORFs, whereas Pyl-decoding bacteria (∼20% of ORFs contain in-frame TAGs) regulate Pyl-tRNAPyl formation and translation of UAG by transcriptional deactivation of genes in the Pyl operon. We further demonstrate that Pyl encoding occurs in a bacterium that naturally encodes the Pyl operon, and identified Pyl residues by mass spectrometry in A. arabaticum proteins including two methylamine methyltransferases. PMID:23185002

Is Neocortical-Hippocampal Connectivity a Better Predictor of Subsequent Recollection than Local Increases in Hippocampal Activity? New Insights on the Role of Priming

ERIC Educational Resources Information Center

Gagnepain, Pierre; Henson, Richard; Chetelat, Gael; Desgranges, Beatrice; Lebreton, Karine; Eustache, Francis

2011-01-01

During memory encoding, increased hippocampal activity--thought to reflect the binding of different types of information into unique episodes--has been shown to correlate with subsequent recollection of those episodes. Repetition priming--thought to induce more efficient perceptual processing of stimuli--is normally associated with decreased…

What Should Be the Unique Application of Teaching in Departments of Speech Communication Located in Urban Environments?

ERIC Educational Resources Information Center

Galvin, Kathleen M.

This paper focuses on certain approaches which an urban speech department can use as it contributes to the preparation of urban school teachers to communicate effectively with their students. The contents include: "Verbal and Nonverbal Codes," which discusses the teacher as an encoder of verbal messages and emphasizes that teachers must learn to…

Deletion of Marek’s disease virus large subunit of ribonucleotide reductase (RR) impairs virus growth in vitro and in vivo

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus (MDV), a highly cell-associated lymphotropic alphaherpesvirus, is the causative agent of a neoplastic disease in domestic chickens, called Marek’s disease (MD). In the unique long region of the MDV genome, open reading frames UL39 and UL40 encode the large and small subunits o...

Sleep: Helicon Cells Charge the Circuit.

PubMed

Yurgel, Maria E; Keene, Alex C

2018-04-02

A new study in the fruit fly, Drosophila melanogaster, has identified a neural circuitry that connects regions that control sleep with those that encode sleep pressure. These novel cells, termed helicon cells for their unique morphology, are modulated by sleep control centers and integrate sensory information, providing a novel mechanism for gating of sleep. Copyright © 2018 Elsevier Ltd. All rights reserved.

Brain Region-Specific Activity Patterns after Recent or Remote Memory Retrieval of Auditory Conditioned Fear

ERIC Educational Resources Information Center

Kwon, Jeong-Tae; Jhang, Jinho; Kim, Hyung-Su; Lee, Sujin; Han, Jin-Hee

2012-01-01

Memory is thought to be sparsely encoded throughout multiple brain regions forming unique memory trace. Although evidence has established that the amygdala is a key brain site for memory storage and retrieval of auditory conditioned fear memory, it remains elusive whether the auditory brain regions may be involved in fear memory storage or…

Episodic-like memory in the rat.

PubMed

Babb, Stephanie J; Crystal, Jonathon D

2006-07-11

A fundamental question in comparative cognition is whether animals remember unique, personal past experiences. It has long been argued that memories for specific events (referred to as episodic memory) are unique to humans. Recently, considerable evidence has accumulated to show that food-storing birds possess critical behavioral elements of episodic memory, referred to as episodic-like memory in acknowledgment of the fact that behavioral criteria do not assess subjective experiences. Here we show that rats have a detailed representation of remembered events and meet behavioral criteria for episodic-like memory. We provided rats with access to locations baited with distinctive (e.g., grape and raspberry) or nondistinctive (regular chow) flavors. Locations with a distinctive flavor replenished after a long but not a short delay, and locations with the nondistinctive flavor never replenished. One distinctive flavor was devalued after encoding its location by prefeeding that flavor (satiation) or by pairing it with lithium chloride (acquired taste aversion), while the other distinctive flavor was not devalued. The rats selectively decreased revisits to the devalued distinctive flavor but not to the nondevalued distinctive flavor. The present studies demonstrate that rats selectively encode the content of episodic-like memories.

The Complete Plastome Sequence of an Antarctic Bryophyte Sanionia uncinata (Hedw.) Loeske

PubMed Central

Park, Mira; Park, Hyun; Lee, Hyoungseok; Lee, Byeong-ha

2018-01-01

Organellar genomes of bryophytes are poorly represented with chloroplast genomes of only four mosses, four liverworts and two hornworts having been sequenced and annotated. Moreover, while Antarctic vegetation is dominated by the bryophytes, there are few reports on the plastid genomes for the Antarctic bryophytes. Sanionia uncinata (Hedw.) Loeske is one of the most dominant moss species in the maritime Antarctic. It has been researched as an important marker for ecological studies and as an extremophile plant for studies on stress tolerance. Here, we report the complete plastome sequence of S. uncinata, which can be exploited in comparative studies to identify the lineage-specific divergence across different species. The complete plastome of S. uncinata is 124,374 bp in length with a typical quadripartite structure of 114 unique genes including 82 unique protein-coding genes, 37 tRNA genes and four rRNA genes. However, two genes encoding the α subunit of RNA polymerase (rpoA) and encoding the cytochrome b6/f complex subunit VIII (petN) were absent. We could identify nuclear genes homologous to those genes, which suggests that rpoA and petN might have been relocated from the chloroplast genome to the nuclear genome. PMID:29494552

A Recessive Contiguous Gene Deletion of Chromosome 2p16 Associated with Cystinuria and a Mitochondrial Disease

PubMed Central

Parvari, Ruti; Brodyansky, Irena; Elpeleg, Orly; Moses, Shimon; Landau, Daniel; Hershkovitz, Eli

2001-01-01

Deletions ranging from 100 Kb to 1 Mb—too small to be detected under the microscope—may still involve dozens of genes, thus causing microdeletion syndromes. The vast majority of these syndromes are caused by haploinsufficiency of one or several genes and are transmitted as dominant traits. We identified seven patients originating from an extended family and presenting with a unique syndrome, inherited in a recessive mode, consisting of cystinuria, neonatal seizures, hypotonia, severe somatic and developmental delay, facial dysmorphism, and lactic acidemia. Reduced activity of all the respiratory chain enzymatic complexes that are encoded in the mitochondria was found in muscle biopsy specimens of the patients examined. The molecular basis of this disorder is a homozygous deletion of 179,311 bp on chromosome 2p16, which includes the type I cystinuria gene (SLC3A1), the protein phosphatase 2Cβ gene (PP2Cβ), an unidentified gene (KIAA0436), and several expressed sequence tags. The extent of the deletion suggests that this unique syndrome is related to the complete absence of these genes’ products, one of which may be essential for the synthesis of mitochondrial encoded proteins. PMID:11524703

A recessive contiguous gene deletion of chromosome 2p16 associated with cystinuria and a mitochondrial disease.

PubMed

Parvari, R; Brodyansky, I; Elpeleg, O; Moses, S; Landau, D; Hershkovitz, E

2001-10-01

Deletions ranging from 100 Kb to 1 Mb--too small to be detected under the microscope--may still involve dozens of genes, thus causing microdeletion syndromes. The vast majority of these syndromes are caused by haploinsufficiency of one or several genes and are transmitted as dominant traits. We identified seven patients originating from an extended family and presenting with a unique syndrome, inherited in a recessive mode, consisting of cystinuria, neonatal seizures, hypotonia, severe somatic and developmental delay, facial dysmorphism, and lactic acidemia. Reduced activity of all the respiratory chain enzymatic complexes that are encoded in the mitochondria was found in muscle biopsy specimens of the patients examined. The molecular basis of this disorder is a homozygous deletion of 179,311 bp on chromosome 2p16, which includes the type I cystinuria gene (SLC3A1), the protein phosphatase 2Cbeta gene (PP2Cbeta), an unidentified gene (KIAA0436), and several expressed sequence tags. The extent of the deletion suggests that this unique syndrome is related to the complete absence of these genes' products, one of which may be essential for the synthesis of mitochondrial encoded proteins.

Hippocampal maturity promotes memory distinctiveness in childhood and adolescence

PubMed Central

Keresztes, Attila; Bender, Andrew R.; Bodammer, Nils C.; Shing, Yee Lee

2017-01-01

Adaptive learning systems need to meet two complementary and partially conflicting goals: detecting regularities in the world versus remembering specific events. The hippocampus (HC) keeps a fine balance between computations that extract commonalities of incoming information (i.e., pattern completion) and computations that enable encoding of highly similar events into unique representations (i.e., pattern separation). Histological evidence from young rhesus monkeys suggests that HC development is characterized by the differential development of intrahippocampal subfields and associated networks. However, due to challenges in the in vivo investigation of such developmental organization, the ontogenetic timing of HC subfield maturation remains controversial. Delineating its course is important, as it directly influences the fine balance between pattern separation and pattern completion operations and, thus, developmental changes in learning and memory. Here, we relate in vivo, high-resolution structural magnetic resonance imaging data of HC subfields to behavioral memory performance in children aged 6–14 y and in young adults. We identify a multivariate profile of age-related differences in intrahippocampal structures and show that HC maturity as captured by this pattern is associated with age differences in the differential encoding of unique memory representations. PMID:28784801

Various plus unique: Viral protein U as a plurifunctional protein for HIV-1 replication.

PubMed

Soper, Andrew; Juarez-Fernandez, Guillermo; Aso, Hirofumi; Moriwaki, Miyu; Yamada, Eri; Nakano, Yusuke; Koyanagi, Yoshio; Sato, Kei

2017-04-01

Human immunodeficiency virus type 1 (HIV-1), the causative agent of acquired immunodeficiency syndrome, encodes four accessory genes, one of which is viral protein U (Vpu). Recently, the study of Vpu has been of great interest. For instance, various cellular proteins are degraded (e.g. CD4) and down-modulated (e.g. tetherin) by Vpu. Vpu also antagonizes the function of tetherin and inhibits NF-κB. Moreover, Vpu is a viroporin forming ion channels and may represent a promising target for anti-HIV-1 drugs. In this review, we summarize the domains/residues that are responsible for Vpu's functions, describe the current understanding of the role of Vpu in HIV-1-infected cells, and review the effect of Vpu on HIV-1 in replication and pathogenesis. Future investigations that simultaneously assess a combination of Vpu functions are required to clearly delineate the most important functions for viral replication. Impact statement Viral protein U (Vpu) is a unique protein encoded by human immunodeficiency virus type 1 (HIV-1) and related lentiviruses, playing multiple roles in viral replication and pathogenesis. In this review, we briefly summarize the most up-to-date knowledge of HIV-1 Vpu.

Spatial and temporal regulation of the forisome gene for1 in the phloem during plant development.

PubMed

Noll, Gundula A; Fontanellaz, Maria E; Rüping, Boris; Ashoub, Ahmed; van Bel, Aart J E; Fischer, Rainer; Knoblauch, Michael; Prüfer, Dirk

2007-10-01

Forisomes are protein aggregates found uniquely in the sieve elements of Fabaceaen plants. Upon wounding they undergo a reversible, calcium-dependent conformational switch which enables them to act as cellular stopcocks. Forisomes begin to form in young sieve elements at an early stage of metaphloem differentiation. Genes encoding forisome components could therefore be useful as markers of early sieve element development. Here we present a comprehensive analysis of the developmental expression profile of for1, which encodes such a forisome component. The for1 gene is highly conserved among Fabaceaen species and appears to be unique to this phylogenetic lineage since no orthologous genes have been found in other plants, including Arabidopsis and rice. Even so, transgenic tobacco plants expressing reporter genes under the control of the for1 promoter display reporter activity exclusively in immature sieve elements. This suggests that the regulation of sieve element development is highly conserved even in plants where mature forisomes have not been detected. The promoter system could therefore provide a powerful tool for the detailed analysis of differentiation in metaphloem sieve elements in an unexpectedly broad range of plant species.

Carbon Nanofibrous Materials from Electrospinning: Preparation and Energy Applications

NASA Astrophysics Data System (ADS)

Aboagye, Alex

Carbon nanofibers with diameters that fall into submicron and nanometer range have attracted growing attention in recent years due to their superior chemical, electrical, and mechanical properties in combination with their unique one-dimensional nanostructures. Unlike catalytic synthesis, electrospinning polyacrylonitrile (PAN) followed by stabilization and carbonization has become a straightforward and convenient route to make continuous carbon nanofibers. The overall objective of this research was the design and production fiber based carbon nanomaterials, investigation of their structures and use in functional applications. Specifically, these carbon nanofibrous materials were employed as electrode material for energy storage and conversion devices such as dye sensitized solar cells and supercapacitors Morphology and structure of the carbon nanofibrous materials were investigated and their performance in corresponding applications were evaluated.

Graphene in the Sky and Beyond

NASA Technical Reports Server (NTRS)

Siochi, Emilie J.

2014-01-01

With the premium placed on strong, lightweight structures, carbon materials have a long history of use in aerospace applications. Graphitized carbon and carbon/carbon composites are used in thermal protection systems and heat shields, carbon fiber composites in aircraft, and more recently, carbon nanotubes have been used on spacecraft. As the newest member of this family of materials, graphene also has a number of interesting properties that intersect with unique aerospace requirements. Despite its many attractive properties, graphene-based structures and systems, like any other material used in aerospace, must clear a number of hurdles before it will be accepted for use in flight structures. Carbon fiber, for example, underwent a development period of several decades between initial discovery and large-scale application in commercial aircraft.

Tuning Organic Carbon Dioxide Absorbents for Carbonation and Decarbonation

PubMed Central

Rajamanickam, Ramachandran; Kim, Hyungsoo; Park, Ji-Woong

2015-01-01

The reaction of carbon dioxide with a mixture of a superbase and alcohol affords a superbase alkylcarbonate salt via a process that can be reversed at elevated temperatures. To utilize the unique chemistry of superbases for carbon capture technology, it is essential to facilitate carbonation and decarbonation at desired temperatures in an easily controllable manner. Here, we demonstrate that the thermal stabilities of the alkylcarbonate salts of superbases in organic solutions can be tuned by adjusting the compositions of hydroxylic solvent and polar aprotic solvent mixtures, thereby enabling the best possible performances to be obtained from the various carbon dioxide capture agents based on these materials. The findings provides valuable insights into the design and optimization of organic carbon dioxide absorbents. PMID:26033537

Improved α-Amylase Production by Dephosphorylation Mutation of CreD, an Arrestin-Like Protein Required for Glucose-Induced Endocytosis of Maltose Permease and Carbon Catabolite Derepression in Aspergillus oryzae

PubMed Central

Tanaka, Mizuki; Hiramoto, Tetsuya; Tada, Hinako; Shintani, Takahiro

2017-01-01

ABSTRACT Aspergillus oryzae produces copious amount of amylolytic enzymes, and MalP, a major maltose permease, is required for the expression of amylase-encoding genes. The expression of these genes is strongly repressed by carbon catabolite repression (CCR) in the presence of glucose. MalP is transported from the plasma membrane to the vacuole by endocytosis, which requires the homolog of E6-AP carboxyl terminus ubiquitin ligase HulA, an ortholog of yeast Rsp5. In yeast, arrestin-like proteins mediate endocytosis as adaptors of Rsp5 and transporters. In the present study, we examined the involvement of CreD, an arrestin-like protein, in glucose-induced MalP endocytosis and CCR of amylase-encoding genes. Deletion of creD inhibited the glucose-induced endocytosis of MalP, and CreD showed physical interaction with HulA. Phosphorylation of CreD was detected by Western blotting, and two serine residues were determined as the putative phosphorylation sites. However, the phosphorylation state of the serine residues did not regulate MalP endocytosis and its interaction with HulA. Although α-amylase production was significantly repressed by creD deletion, both phosphorylation and dephosphorylation mimics of CreD had a negligible effect on α-amylase activity. Interestingly, dephosphorylation of CreD was required for CCR relief of amylase genes that was triggered by disruption of the deubiquitinating enzyme-encoding gene creB. The α-amylase activity of the creB mutant was 1.6-fold higher than that of the wild type, and the dephosphorylation mimic of CreD further improved the α-amylase activity by 2.6-fold. These results indicate that a combination of the dephosphorylation mutation of CreD and creB disruption increased the production of amylolytic enzymes in A. oryzae. IMPORTANCE In eukaryotes, glucose induces carbon catabolite repression (CCR) and proteolytic degradation of plasma membrane transporters via endocytosis. Glucose-induced endocytosis of transporters is mediated by their ubiquitination, and arrestin-like proteins act as adaptors of transporters and ubiquitin ligases. In this study, we showed that CreD, an arrestin-like protein, is involved in glucose-induced endocytosis of maltose permease and carbon catabolite derepression of amylase gene expression in Aspergillus oryzae. Dephosphorylation of CreD was required for CCR relief triggered by the disruption of creB, which encodes a deubiquitinating enzyme; a combination of the phosphorylation-defective mutation of CreD and creB disruption dramatically improved α-amylase production. This study shows the dual function of an arrestin-like protein and provides a novel approach for improving the production of amylolytic enzymes in A. oryzae. PMID:28455339

Improved α-Amylase Production by Dephosphorylation Mutation of CreD, an Arrestin-Like Protein Required for Glucose-Induced Endocytosis of Maltose Permease and Carbon Catabolite Derepression in Aspergillus oryzae.

PubMed

Tanaka, Mizuki; Hiramoto, Tetsuya; Tada, Hinako; Shintani, Takahiro; Gomi, Katsuya

2017-07-01

Aspergillus oryzae produces copious amount of amylolytic enzymes, and MalP, a major maltose permease, is required for the expression of amylase-encoding genes. The expression of these genes is strongly repressed by carbon catabolite repression (CCR) in the presence of glucose. MalP is transported from the plasma membrane to the vacuole by endocytosis, which requires the homolog of E6-AP carboxyl terminus ubiquitin ligase HulA, an ortholog of yeast Rsp5. In yeast, arrestin-like proteins mediate endocytosis as adaptors of Rsp5 and transporters. In the present study, we examined the involvement of CreD, an arrestin-like protein, in glucose-induced MalP endocytosis and CCR of amylase-encoding genes. Deletion of creD inhibited the glucose-induced endocytosis of MalP, and CreD showed physical interaction with HulA. Phosphorylation of CreD was detected by Western blotting, and two serine residues were determined as the putative phosphorylation sites. However, the phosphorylation state of the serine residues did not regulate MalP endocytosis and its interaction with HulA. Although α-amylase production was significantly repressed by creD deletion, both phosphorylation and dephosphorylation mimics of CreD had a negligible effect on α-amylase activity. Interestingly, dephosphorylation of CreD was required for CCR relief of amylase genes that was triggered by disruption of the deubiquitinating enzyme-encoding gene creB The α-amylase activity of the creB mutant was 1.6-fold higher than that of the wild type, and the dephosphorylation mimic of CreD further improved the α-amylase activity by 2.6-fold. These results indicate that a combination of the dephosphorylation mutation of CreD and creB disruption increased the production of amylolytic enzymes in A. oryzae IMPORTANCE In eukaryotes, glucose induces carbon catabolite repression (CCR) and proteolytic degradation of plasma membrane transporters via endocytosis. Glucose-induced endocytosis of transporters is mediated by their ubiquitination, and arrestin-like proteins act as adaptors of transporters and ubiquitin ligases. In this study, we showed that CreD, an arrestin-like protein, is involved in glucose-induced endocytosis of maltose permease and carbon catabolite derepression of amylase gene expression in Aspergillus oryzae Dephosphorylation of CreD was required for CCR relief triggered by the disruption of creB , which encodes a deubiquitinating enzyme; a combination of the phosphorylation-defective mutation of CreD and creB disruption dramatically improved α-amylase production. This study shows the dual function of an arrestin-like protein and provides a novel approach for improving the production of amylolytic enzymes in A. oryzae . Copyright © 2017 American Society for Microbiology.

Land-use and hydroperiod affect kettle hole sediment carbon and nitrogen biogeochemistry

Treesearch

Kai Nils Nitzsche; Thomas Kalettka; Katrin Premke; Gunnar Lischeid; Arthur Gessler; Zachary Eric Kayler

2017-01-01

Kettle holes are glaciofluvially created depressional wetlands that collect organic matter (OM) and nutrients from their surrounding catchment. Kettle holes mostly undergo pronounced wet-dry cycles. Fluctuations in water table, land-use, andmanagement can affect sediment biogeochemical transformations and perhaps threaten the carbon stocks of these unique ecosystems....

CONSIDERATIONS FOR A REGULATORY FRAMEWORK FOR LARGE-SCALE GEOLOGIC SEQUESTRATION OF CARBON DIOXIDE: A NORTH AMERICAN PERSPECTIVE

EPA Science Inventory

Large scale geologic sequestration (GS) of carbon dioxide poses a novel set of challenges for regulators. This paper focuses on the unique needs of large scale GS projects in light of the existing regulatory regimes in the United States and Canada and identifies several differen...

Nanostructured core-shell electrode materials for electrochemical capacitors

NASA Astrophysics Data System (ADS)

Jiang, Long-bo; Yuan, Xing-zhong; Liang, Jie; Zhang, Jin; Wang, Hou; Zeng, Guang-ming

2016-11-01

Core-shell nanostructure represents a unique system for applications in electrochemical energy storage devices. Owing to the unique characteristics featuring high power delivery and long-term cycling stability, electrochemical capacitors (ECs) have emerged as one of the most attractive electrochemical storage systems since they can complement or even replace batteries in the energy storage field, especially when high power delivery or uptake is needed. This review aims to summarize recent progress on core-shell nanostructures for advanced supercapacitor applications in view of their hierarchical architecture which not only create the desired hierarchical porous channels, but also possess higher electrical conductivity and better structural mechanical stability. The core-shell nanostructures include carbon/carbon, carbon/metal oxide, carbon/conducting polymer, metal oxide/metal oxide, metal oxide/conducting polymer, conducting polymer/conducting polymer, and even more complex ternary core-shell nanoparticles. The preparation strategies, electrochemical performances, and structural stabilities of core-shell materials for ECs are summarized. The relationship between core-shell nanostructure and electrochemical performance is discussed in detail. In addition, the challenges and new trends in core-shell nanomaterials development have also been proposed.

Flexible supercapacitors with high areal capacitance based on hierarchical carbon tubular nanostructures

NASA Astrophysics Data System (ADS)

Zhang, Haitao; Su, Hai; Zhang, Lei; Zhang, Binbin; Chun, Fengjun; Chu, Xiang; He, Weidong; Yang, Weiqing

2016-11-01

Hierarchical structure design can greatly enhance the unique properties of primary material(s) but suffers from complicated preparation process and difficult self-assembly of materials with different dimensionalities. Here we report on the growth of single carbon tubular nanostructures with hierarchical structure (hCTNs) through a simple method based on direct conversion of carbon dioxide. Resorting to in-situ transformation and self-assembly of carbon micro/nano-structures, the obtained hCTNs are blood-like multichannel hierarchy composed of one large channel across the hCTNs and plenty of small branches connected to each other. Due to the unique pore structure and high surface area, these hCTN-based flexible supercapacitors possess the highest areal capacitance of ∼320 mF cm-2, as well as good rate-capability and excellent cycling stability (95% retention after 2500 cycles). It was established that this method can control the morphology, size, and density of hCTNs and effectively construct hCTNs well anchored to the various substrates. Our work unambiguously demonstrated the potential of hCTNs for large flexible supercapacitors and integrated energy management electronics.

Facile synthesis of 3D silicon/carbon nanotube capsule composites as anodes for high-performance lithium-ion batteries

NASA Astrophysics Data System (ADS)

Yue, Xinyang; Sun, Wang; Zhang, Jing; Wang, Fang; Sun, Kening

2016-10-01

Carbon nanotubes have attracted widespread attention as ideal materials for Lithium-ion batteries (LIBs) due to their excellent conductivity, mechanical flexibility, chemical stability and extremely large surface area. Here, three-dimensional (3D) silicon/carbon nanotube capsule composites (Si/CNCs) are firstly prepared via water-in-oil (W/O) emulsion technique with more than 75 wt% loading amount of silicon. CNCs with unique hollow sphere structure act as a 3D interconnected conductive network skeleton, and the cross-linked carbon nanotubes (CNTs) of CNCs can effectively enhance the strength, flexibility and conductivity of the electrode. This Si/CNCs can not only alleviate the volume expansion, but also effectively improve the electrochemical performance of the LIBs. Such Si/CNCs electrode with the unique structure achieves a high initial discharge specific capacity of 2950 mAh g-1 and retains 1226 mAh g-1 after 100 cycles at 0.5 A g-1, as well as outstanding rate performance of 547 mAh g-1 at 10 A g-1.

The integration of laser communication and ranging

NASA Astrophysics Data System (ADS)

Xu, Mengmeng; Sun, Jianfeng; Zhou, Yu; Zhang, Bo; Zhang, Guo; Li, Guangyuan; He, Hongyu; Lao, Chenzhe

2017-08-01

The method to realize the integration of laser communication and ranging is proposed in this paper. In the transmitter of two places, the ranging codes with uniqueness, good autocorrelation and cross-correlation properties are embed in the communication data and the encoded with the communication data to realize serial communication. And then the encoded data are modulated and send to each other, which can realize high speed two one-way laser communication. At the receiver, we can get the received ranging code after the demodulation, decoding and clock recovery. The received ranging codes and the local ranging codes do the autocorrelation to get a roughly range, while the phase difference between the local clock and the recovery clock to achieve the precision of the distance.

Genome complexity in the coelacanth is reflected in its adaptive immune system

USGS Publications Warehouse

Saha, Nil Ratan; Ota, Tatsuya; Litman, Gary W.; Hansen, John; Parra, Zuly; Hsu, Ellen; Buonocore, Francesco; Canapa, Adriana; Cheng, Jan-Fang; Amemiya, Chris T.

2014-01-01

We have analyzed the available genome and transcriptome resources from the coelacanth in order to characterize genes involved in adaptive immunity. Two highly distinctive IgW-encoding loci have been identified that exhibit a unique genomic organization, including a multiplicity of tandemly repeated constant region exons. The overall organization of the IgW loci precludes typical heavy chain class switching. A locus encoding IgM could not be identified either computationally or by using several different experimental strategies. Four distinct sets of genes encoding Ig light chains were identified. This includes a variant sigma-type Ig light chain previously identified only in cartilaginous fishes and which is now provisionally denoted sigma-2. Genes encoding α/β and γ/δ T-cell receptors, and CD3, CD4, and CD8 co-receptors also were characterized. Ig heavy chain variable region genes and TCR components are interspersed within the TCR α/δ locus; this organization previously was reported only in tetrapods and raises questions regarding evolution and functional cooption of genes encoding variable regions. The composition, organization and syntenic conservation of the major histocompatibility complex locus have been characterized. We also identified large numbers of genes encoding cytokines and their receptors, and other genes associated with adaptive immunity. In terms of sequence identity and organization, the adaptive immune genes of the coelacanth more closely resemble orthologous genes in tetrapods than those in teleost fishes, consistent with current phylogenomic interpretations. Overall, the work reported described herein highlights the complexity inherent in the coelacanth genome and provides a rich catalog of immune genes for future investigations.

CA1 subfield contributions to memory integration and inference

PubMed Central

Schlichting, Margaret L.; Zeithamova, Dagmar; Preston, Alison R.

2014-01-01

The ability to combine information acquired at different times to make novel inferences is a powerful function of episodic memory. One perspective suggests that by retrieving related knowledge during new experiences, existing memories can be linked to the new, overlapping information as it is encoded. The resulting memory traces would thus incorporate content across event boundaries, representing important relationships among items encountered during separate experiences. While prior work suggests that the hippocampus is involved in linking memories experienced at different times, the involvement of specific subfields in this process remains unknown. Using both univariate and multivariate analyses of high-resolution functional magnetic resonance imaging (fMRI) data, we localized this specialized encoding mechanism to human CA1. Specifically, right CA1 responses during encoding of events that overlapped with prior experience predicted subsequent success on a test requiring inferences about the relationships among events. Furthermore, we employed neural pattern similarity analysis to show that patterns of activation evoked during overlapping event encoding were later reinstated in CA1 during successful inference. The reinstatement of CA1 patterns during inference was specific to those trials that were performed quickly and accurately, consistent with the notion that linking memories during learning facilitates novel judgments. These analyses provide converging evidence that CA1 plays a unique role in encoding overlapping events and highlight the dynamic interactions between hippocampal-mediated encoding and retrieval processes. More broadly, our data reflect the adaptive nature of episodic memories, in which representations are derived across events in anticipation of future judgments. PMID:24888442

Ecophysiology of Freshwater Verrucomicrobia Inferred from Metagenome-Assembled Genomes

PubMed Central

He, Shaomei; Stevens, Sarah L. R.; Chan, Leong-Keat; Bertilsson, Stefan; Glavina del Rio, Tijana; Tringe, Susannah G.; Malmstrom, Rex R.

2017-01-01

ABSTRACT Microbes are critical in carbon and nutrient cycling in freshwater ecosystems. Members of the Verrucomicrobia are ubiquitous in such systems, and yet their roles and ecophysiology are not well understood. In this study, we recovered 19 Verrucomicrobia draft genomes by sequencing 184 time-series metagenomes from a eutrophic lake and a humic bog that differ in carbon source and nutrient availabilities. These genomes span four of the seven previously defined Verrucomicrobia subdivisions and greatly expand knowledge of the genomic diversity of freshwater Verrucomicrobia. Genome analysis revealed their potential role as (poly)saccharide degraders in freshwater, uncovered interesting genomic features for this lifestyle, and suggested their adaptation to nutrient availabilities in their environments. Verrucomicrobia populations differ significantly between the two lakes in glycoside hydrolase gene abundance and functional profiles, reflecting the autochthonous and terrestrially derived allochthonous carbon sources of the two ecosystems, respectively. Interestingly, a number of genomes recovered from the bog contained gene clusters that potentially encode a novel porin-multiheme cytochrome c complex and might be involved in extracellular electron transfer in the anoxic humus-rich environment. Notably, most epilimnion genomes have large numbers of so-called “Planctomycete-specific” cytochrome c-encoding genes, which exhibited distribution patterns nearly opposite to those seen with glycoside hydrolase genes, probably associated with the different levels of environmental oxygen availability and carbohydrate complexity between lakes/layers. Overall, the recovered genomes represent a major step toward understanding the role, ecophysiology, and distribution of Verrucomicrobia in freshwater. IMPORTANCE Freshwater Verrucomicrobia spp. are cosmopolitan in lakes and rivers, and yet their roles and ecophysiology are not well understood, as cultured freshwater Verrucomicrobia spp. are restricted to one subdivision of this phylum. Here, we greatly expanded the known genomic diversity of this freshwater lineage by recovering 19 Verrucomicrobia draft genomes from 184 metagenomes collected from a eutrophic lake and a humic bog across multiple years. Most of these genomes represent the first freshwater representatives of several Verrucomicrobia subdivisions. Genomic analysis revealed Verrucomicrobia to be potential (poly)saccharide degraders and suggested their adaptation to carbon sources of different origins in the two contrasting ecosystems. We identified putative extracellular electron transfer genes and so-called “Planctomycete-specific” cytochrome c-encoding genes and identified their distinct distribution patterns between the lakes/layers. Overall, our analysis greatly advances the understanding of the function, ecophysiology, and distribution of freshwater Verrucomicrobia, while highlighting their potential role in freshwater carbon cycling. PMID:28959738

The transformation of inorganic sulfur compounds and the assimilation of organic and inorganic carbon by the sulfur disproportionating bacterium Desulfocapsa sulfoexigens.

PubMed

Frederiksen, Trine-Maria; Finster, Kai

2004-02-01

The physiology of the sulfur disproportionator Desulfocapsa sulfoexigens was investigated in batch cultures and in a pH-regulated continuously flushed fermentor system. It was shown that a sulphide scavanger in the form of ferric iron was not obligatory and that the control of pH allowed production of more biomass than was possible in carbonate buffered but unregulated batch cultures. Small amounts of sulphite were produced during disproportionation of elemental sulfur and thiosulphate. In addition, it was shown that in the presence of hydrogen, a respiratory type of process is favored before the disproportionation of sulphite, thiosulphate and elemental sulfur. Sulphate reduction was not observed. D. sulfoexigens assimilated inorganic carbon even in the presence of organic carbon sources. Inorganic carbon assimilation was probably catalyzed by the reverse CO-dehydrogenase pathway, which was supported by the constitutive expression of the gene encoding CO-dehydrogenase in cultures grown in the presence of acetate and by the high carbon fractionation values that are indicative of this pathway.

Functionalized Natural Carbon-Supported Nanoparticles as Excellent Catalysts for Hydrocarbon Production.

PubMed

Sun, Jian; Guo, Lisheng; Ma, Qingxiang; Gao, Xinhua; Yamane, Noriyuki; Xu, Hengyong; Tsubaki, Noritatsu

2017-02-01

We report a one-pot and eco-friendly synthesis of carbon-supported cobalt nanoparticles, achieved by carbonization of waste biomass (rice bran) with a cobalt source. The functionalized biomass provides carbon microspheres as excellent catalyst support, forming a unique interface between hydrophobic and hydrophilic groups. The latter, involving hydroxyl and amino groups, can catch much more active cobalt nanoparticles on surface for Fischer-Tropsch synthesis than chemical carbon. The loading amount of cobalt on the final catalyst is much higher than that prepared with a chemical carbon source, such as glucose. The proposed concept of using a functionalized natural carbon source shows great potential compared with conventional carbon sources, and will be meaningful for other fields concerning carbon support, such as heterogeneous catalysis or electrochemical fields. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

One Carbon Metabolism in Pregnancy: Impact on Maternal, Fetal and Neonatal Health

PubMed Central

Kalhan, Satish C

2016-01-01

One carbon metabolism or methyl transfer, a crucial component of metabolism in all cells and tissues, supports the critical function of synthesis of purines, thymidylate and methylation via multiple methyl transferases driven by the ubiquitous methyl donor s-adenosylmethionine. Serine is the primary methyl donor to the one carbon pool. Intracellular folates and methionine metabolism are the critical components of one carbon transfer. Methionine metabolism requires vitamin B12, B6 as cofactors and is modulated by endocrine signals and is responsive to nutrient intake. Perturbations in one carbon transfer can have profound effects on cell proliferation, growth and function. Epidemiological studies in humans and experimental model have established a strong relationship between impaired fetal growth and the immediate and long term consequences to the health of the offspring. It is speculated that during development, maternal environmental and nutrient influences by their effects on one carbon transfer can impact the health of the mother, impair growth and reprogram metabolism of the fetus, and cause long term morbidity in the offspring. The potential for such effects is underscored by the unique responses in methionine metabolism in the human mother during pregnancy, the absence of transsulfuration activity in the fetus, ontogeny of methionine metabolism in the placenta and the unique metabolism of serine and glycine in the fetus. Dietary protein restriction in animals and marginal protein intake in humans causes characteristic changes in one carbon metabolism. The impact of perturbations in one carbon metabolism on the health of the mother during pregnancy, on fetal growth and the neonate are discussed and their possible mechanism explored. PMID:27267668

Synthesis of Hierarchically Porous Sandwich-Like Carbon Materials for High-Performance Supercapacitors.

PubMed

Li, Yiju; Chen, Chaoji; Gao, Tingting; Zhang, Dongming; Huang, Xiaomei; Pan, Yue; Ye, Ke; Cheng, Kui; Cao, Dianxue; Wang, Guiling

2016-11-14

For the first time, hierarchically porous carbon materials with a sandwich-like structure are synthesized through a facile and efficient tri-template approach. The hierarchically porous microstructures consist of abundant macropores and numerous micropores embedded into the crosslinked mesoporous walls. As a result, the obtained carbon material with a unique sandwich-like structure has a relatively high specific surface (1235 m 2  g -1 ), large pore volume (1.30 cm 3  g -1 ), and appropriate pore size distribution. These merits lead to a comparably high specific capacitance of 274.8 F g -1 at 0.2 A g -1 and satisfying rate performance (87.7 % retention from 1 to 20 A g -1 ). More importantly, the symmetric supercapacitor with two identical as-prepared carbon samples shows a superior energy density of 18.47 Wh kg -1 at a power density of 179.9 W kg -1 . The asymmetric supercapacitor based on as-obtained carbon sample and its composite with manganese dioxide (MnO 2 ) can reach up to an energy density of 25.93 Wh kg -1 at a power density of 199.9 W kg -1 . Therefore, these unique carbon material open a promising prospect for future development and utilization in the field of energy storage. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improved characterization of the botanical origin of sugar by carbon-13 SNIF-NMR applied to ethanol.

PubMed

Thomas, Freddy; Randet, Celia; Gilbert, Alexis; Silvestre, Virginie; Jamin, Eric; Akoka, Serge; Remaud, Gerald; Segebarth, Nicolas; Guillou, Claude

2010-11-24

Until now, no analytical method, not even isotopic ones, had been able to differentiate between sugars coming from C4-metabolism plants (cane, maize, etc.) and some crassulacean acid metabolism plants (e.g., pineapple, agave) because in both cases the isotope distributions of the overall carbon-13/carbon-12 and site-specific deuterium/hydrogen isotope ratios are very similar. Following recent advances in the field of quantitative isotopic carbon-13 NMR measurements, a procedure for the analysis of the positional carbon-13/carbon-12 isotope ratios of ethanol derived from the sugars of pineapples and agave using the site-specific natural isotopic fractionation-nuclear magnetic resonance (SNIF-NMR) method is presented. It is shown that reproducible results can be obtained when appropriate analytical conditions are used. When applied to pineapple juice, this new method demonstrates a unique ability to detect cane and maize sugar, which are major potential adulterants, with a detection limit in the order of 15% of the total sugars, which provides an efficient mean of controlling the authenticity of juices made from this specific fruit. When applied to tequila products, this new method demonstrates a unique ability to unambiguously differentiate authentic 100% agave tequila, as well as misto tequila (made from at least 51% agave), from products made from a larger proportion of cane or maize sugar and therefore not complying with the legal definition of tequila.

Molecular characterization of the Hansenula polymorpha FLD1 gene encoding formaldehyde dehydrogenase.

Treesearch

Richard J. Baerends; Grietje J. Sulter; Thomas W. Jeffries; James M. Cregg; Marten Veenhuis

2002-01-01

Glutathione-dependent formaldehyde dehydrogenase (FLD) is a key enzyme required for the catabolism of methanol as a carbon source and certain primary amines, such as methylamine as nitrogen sources in methylotrophic yeasts. Here we describe the molecular characterization of the FLD1 gene from the yeast Hansenula polymorpha. Unlike the recently described Pichia pastoris...

Isolation and functional expression of human COQ2, a gene encoding a polyprenyl transferase involved in the synthesis of CoQ.

PubMed

Forsgren, Margareta; Attersand, Anneli; Lake, Staffan; Grünler, Jacob; Swiezewska, Ewa; Dallner, Gustav; Climent, Isabel

2004-09-01

The COQ2 gene in Saccharomyces cerevisiae encodes a Coq2 (p-hydroxybenzoate:polyprenyl transferase), which is required in the biosynthetic pathway of CoQ (ubiquinone). This enzyme catalyses the prenylation of p-hydroxybenzoate with an all-trans polyprenyl group. We have isolated cDNA which we believe encodes the human homologue of COQ2 from a human muscle and liver cDNA library. The clone contained an open reading frame of length 1263 bp, which encodes a polypeptide that has sequence homology with the Coq2 homologues in yeast, bacteria and mammals. The human COQ2 gene, when expressed in yeast Coq2 null mutant cells, rescued the growth of this yeast strain in the absence of a non-fermentable carbon source and restored CoQ biosynthesis. However, the rate of CoQ biosynthesis in the rescued cells was lower when compared with that in cells rescued with the yeast COQ2 gene. CoQ formed when cells were incubated with labelled decaprenyl pyrophosphate and nonaprenyl pyrophosphate, showing that the human enzyme is active and that it participates in the biosynthesis of CoQ.

Systematic review: the effects of carbonated beverages on gastro-oesophageal reflux disease.

PubMed

Johnson, T; Gerson, L; Hershcovici, T; Stave, C; Fass, R

2010-03-01

Carbonated beverages have unique properties that may potentially exacerbate gastro-oesophageal reflux disease (GERD), such as high acidity and carbonation. Cessation of carbonated beverage consumption is commonly recommended as part of lifestyle modifications for patients with GERD. To evaluate the relationship of carbonated beverages with oesophageal pH, oesophageal motility, oesophageal damage, GERD symptoms and GERD complications. A systematic review. Carbonated beverage consumption results in a very short decline in intra-oesophageal pH. In addition, carbonated beverages may lead to a transient reduction in lower oesophageal sphincter basal pressure. There is no evidence that carbonated beverages directly cause oesophageal damage. Carbonated beverages have not been consistently shown to cause GERD-related symptoms. Furthermore, there is no evidence that these popular drinks lead to GERD complications or oesophageal cancer. Based on the currently available literature, it appears that there is no direct evidence that carbonated beverages promote or exacerbate GERD.

Shifting locus of carbonate sedimentation and the trajectory of Paleozoic pCO2

NASA Astrophysics Data System (ADS)

Husson, J. M.; Peters, S. E.

2016-12-01

The burial of calcium carbonate is a determinant of planetary habitability, dictated by CO2 input to the surface environment and rates of chemical weathering. An important source of CO2 is the metamorphism of carbon-bearing sediments, which is responsive to the locus of sedimentation. For example, deep sea sediments are prone to recycling as sea floor is consumed at convergent margins; by contrast, sediments deposited on continental crust can be stable for billions of years.The predominant feature in the empirical sedimentary rock record, as measured by Macrostrat (https://macrostrat.org) and global geological syntheses, is a step-wise increase in continental sedimentation at the Neoproterozoic-Paleozoic transition. Although early Paleozoic carbonate volumes are sufficient to account for a CO2 flux 5x greater than present, Proterozoic continental burial fluxes were likely below the modern estimate. This observation implies that most carbonate sedimentation in the Proterozoic took place on the deep sea floor. The establishment of persistent, widespread continental flooding during the Paleozoic shifted the locus of carbonate sedimentation to continental interiors. A major implication of this shift is that CO2 flux declined during the Paleozoic as carbonate-laden Precambrian seafloor was metamorphosed and recycled. This prediction is consistent with independent proxy records and our model for Phanerozoic carbonate burial. An important corollary is that as carbonate-rich Precambrian seafloor was progressively destroyed, the carbonate content of deep sea sediments decreased concordantly because Paleozoic continents effectively captured global alkalinity fluxes. This process culminated near the Permian/Triassic, with metamorphic CO2 flux at a Phanerozoic minimum and the global ocean uniquely unbuffered against acidification. Such a condition could enhance the environmental effects of transient CO2 injections. Because the mid-Mesozoic appearance of pelagic calcifiers and Cenozoic fall in continental flooding reestablished a deep sea carbonate sink, the Paleozoic was a unique time in Earth history when the continents were the only major, quantitatively important locus of carbonate burial.

A mutant crp allele that differentially activates the operons of the fuc regulon in Escherichia coli.

PubMed

Zhu, Y; Lin, E C

1988-05-01

L-Fucose is used by Escherichia coli through an inducible pathway mediated by a fucP-encoded permease, a fucI-encoded isomerase, a fucK-encoded kinase, and a fucA-encoded aldolase. The adolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Anaerobically, lactaldehyde is converted by a fucO-encoded oxidoreductase to L-1,2-propanediol, which is excreted. The fuc genes belong to a regulon comprising four linked operons: fucO, fucA, fucPIK, and fucR. The positive regulator encoded by fucR responds to fuculose 1-phosphate as the effector. Mutants serially selected for aerobic growth on propanediol became constitutive in fucO and fucA [fucO(Con) fucA(Con)], but noninducible in fucPIK [fucPIK(Non)]. An external suppressor mutation that restored growth on fucose caused constitutive expression of fucPIK. Results from this study indicate that this suppressor mutation occurred in crp, which encodes the cyclic AMP-binding (or receptor) protein. When the suppressor allele (crp-201) was transduced into wild-type strains, the recipient became fucose negative and fucose sensitive (with glycerol as the carbon and energy source) because of impaired expression of fucA. The fucPIK operon became hyperinducible. The growth rate on maltose was significantly reduced, but growth on L-rhamnose, D-galactose, L-arabinose, glycerol, or glycerol 3-phosphate was close to normal. Lysogenization of fuc+ crp-201 cells by a lambda bacteriophage bearing crp+ restored normal growth ability on fucose. In contrast, lysogenization of [fucO(Con)fucA(Con)fucPIK(Non)crp-201] cells by the same phage retarded their growth on fucose.

A mutant crp allele that differentially activates the operons of the fuc regulon in Escherichia coli.

PubMed Central

Zhu, Y; Lin, E C

1988-01-01

L-Fucose is used by Escherichia coli through an inducible pathway mediated by a fucP-encoded permease, a fucI-encoded isomerase, a fucK-encoded kinase, and a fucA-encoded aldolase. The adolase catalyzes the formation of dihydroxyacetone phosphate and L-lactaldehyde. Anaerobically, lactaldehyde is converted by a fucO-encoded oxidoreductase to L-1,2-propanediol, which is excreted. The fuc genes belong to a regulon comprising four linked operons: fucO, fucA, fucPIK, and fucR. The positive regulator encoded by fucR responds to fuculose 1-phosphate as the effector. Mutants serially selected for aerobic growth on propanediol became constitutive in fucO and fucA [fucO(Con) fucA(Con)], but noninducible in fucPIK [fucPIK(Non)]. An external suppressor mutation that restored growth on fucose caused constitutive expression of fucPIK. Results from this study indicate that this suppressor mutation occurred in crp, which encodes the cyclic AMP-binding (or receptor) protein. When the suppressor allele (crp-201) was transduced into wild-type strains, the recipient became fucose negative and fucose sensitive (with glycerol as the carbon and energy source) because of impaired expression of fucA. The fucPIK operon became hyperinducible. The growth rate on maltose was significantly reduced, but growth on L-rhamnose, D-galactose, L-arabinose, glycerol, or glycerol 3-phosphate was close to normal. Lysogenization of fuc+ crp-201 cells by a lambda bacteriophage bearing crp+ restored normal growth ability on fucose. In contrast, lysogenization of [fucO(Con)fucA(Con)fucPIK(Non)crp-201] cells by the same phage retarded their growth on fucose. PMID:2834341

Scale-up of Carbon/Carbon Bipolar Plates

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

David P. Haack

2009-04-08

This project was focused upon developing a unique material technology for use in PEM fuel cell bipolar plates. The carbon/carbon composite material developed in this program is uniquely suited for use in fuel cell systems, as it is lightweight, highly conductive and corrosion resistant. The project further focused upon developing the manufacturing methodology to cost-effectively produce this material for use in commercial fuel cell systems. United Technology Fuel Cells Corp., a leading fuel cell developer was a subcontractor to the project was interested in the performance and low-cost potential of the material. The accomplishments of the program included the developmentmore » and testing of a low-cost, fully molded, net-shape carbon-carbon bipolar plate. The process to cost-effectively manufacture these carbon-carbon bipolar plates was focused on extensively in this program. Key areas for cost-reduction that received attention in this program was net-shape molding of the detailed flow structures according to end-user design. Correlations between feature detail and process parameters were formed so that mold tooling could be accurately designed to meet a variety of flow field dimensions. A cost model was developed that predicted the cost of manufacture for the product in near-term volumes and long-term volumes (10+ million units per year). Because the roduct uses lowcost raw materials in quantities that are less than competitive tech, it was found that the cost of the product in high volume can be less than with other plate echnologies, and can meet the DOE goal of $4/kW for transportation applications. The excellent performance of the all-carbon plate in net shape was verified in fuel cell testing. Performance equivalent to much higher cost, fully machined graphite plates was found.« less

Heterologous production of an energy-conserving carbon monoxide dehydrogenase complex in the hyperthermophile Pyrococcus furiosus

DOE PAGES

Schut, Gerrit J.; Lipscomb, Gina L.; Nguyen, Diep M. N.; ...

2016-01-29

In this study, carbon monoxide (CO) is an important intermediate in anaerobic carbon fixation pathways in acetogenesis and methanogenesis. In addition, some anaerobes can utilize CO as an energy source. In the hyperthermophilic archaeon Thermococcus onnurineus, which grows optimally at 80°C, CO oxidation and energy conservation is accomplished by a respiratory complex encoded by a 16-gene cluster containing a CO dehydrogenase, a membrane-bound [NiFe]-hydrogenase and a Na +/H + antiporter module. This complex oxidizes CO, evolves CO 2 and H 2, and generates a Na+ motive force that is used to conserve energy by a Na+-dependent ATP synthase. Herein wemore » used a bacterial artificial chromosome to insert the 13.2 kb gene cluster encoding the CO-oxidizing respiratory complex of T. onnurineus into the genome of the heterotrophic archaeon, Pyrococcus furiosus, which grows optimally at 100° C. P. furiosus is normally unable to utilize CO, however, the recombinant strain readily oxidized CO and generated H 2 at 80° C. Moreover, CO also served as an energy source and allowed the P. furiosus strain to grow with a limiting concentration of sugar or with peptides as the carbon source. Moreover, CO oxidation by P. furiosus was also coupled to the re-utilization, presumably for biosynthesis, of acetate generated by fermentation. The functional transfer of CO utilization between Thermococcus and Pyrococcus species demonstrated herein is representative of the horizontal gene transfer of an environmentally relevant metabolic capability. The transfer of CO utilizing, hydrogen-producing genetic modules also has applications for biohydrogen production and a CO-based industrial platform for various thermophilic organisms.« less

Sulfide oxidation, nitrate respiration, carbon acquisition, and electron transport pathways suggested by the draft genome of a single orange Guaymas Basin Beggiatoa (Cand. Maribeggiatoa) sp. filament.

PubMed

MacGregor, Barbara J; Biddle, Jennifer F; Harbort, Christopher; Matthysse, Ann G; Teske, Andreas

2013-09-01

A near-complete draft genome has been obtained for a single vacuolated orange Beggiatoa (Cand. Maribeggiatoa) filament from a Guaymas Basin seafloor microbial mat, the third relatively complete sequence for the Beggiatoaceae. Possible pathways for sulfide oxidation; nitrate respiration; inorganic carbon fixation by both Type II RuBisCO and the reductive tricarboxylic acid cycle; acetate and possibly formate uptake; and energy-generating electron transport via both oxidative phosphorylation and the Rnf complex are discussed here. A role in nitrite reduction is suggested for an abundant orange cytochrome produced by the Guaymas strain; this has a possible homolog in Beggiatoa (Cand. Isobeggiatoa) sp. PS, isolated from marine harbor sediment, but not Beggiatoa alba B18LD, isolated from a freshwater rice field ditch. Inferred phylogenies for the Calvin-Benson-Bassham (CBB) cycle and the reductive (rTCA) and oxidative (TCA) tricarboxylic acid cycles suggest that genes encoding succinate dehydrogenase and enzymes for carboxylation and/or decarboxylation steps (including RuBisCO) may have been introduced to (or exported from) one or more of the three genomes by horizontal transfer, sometimes by different routes. Sequences from the two marine strains are generally more similar to each other than to sequences from the freshwater strain, except in the case of RuBisCO: only the Guaymas strain encodes a Type II enzyme, which (where studied) discriminates less against oxygen than do Type I RuBisCOs. Genes subject to horizontal transfer may represent key steps for adaptation to factors such as oxygen and carbon dioxide concentration, organic carbon availability, and environmental variability. © 2013.

SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter.

PubMed

Landry, Zachary; Swan, Brandon K; Herndl, Gerhard J; Stepanauskas, Ramunas; Giovannoni, Stephen J

2017-04-18

Deep-ocean regions beyond the reach of sunlight contain an estimated 615 Pg of dissolved organic matter (DOM), much of which persists for thousands of years. It is thought that bacteria oxidize DOM until it is too dilute or refractory to support microbial activity. We analyzed five single-amplified genomes (SAGs) from the abundant SAR202 clade of dark-ocean bacterioplankton and found they encode multiple families of paralogous enzymes involved in carbon catabolism, including several families of oxidative enzymes that we hypothesize participate in the degradation of cyclic alkanes. The five partial genomes encoded 152 flavin mononucleotide/F420-dependent monooxygenases (FMNOs), many of which are predicted to be type II Baeyer-Villiger monooxygenases (BVMOs) that catalyze oxygen insertion into semilabile alicyclic alkanes. The large number of oxidative enzymes, as well as other families of enzymes that appear to play complementary roles in catabolic pathways, suggests that SAR202 might catalyze final steps in the biological oxidation of relatively recalcitrant organic compounds to refractory compounds that persist. IMPORTANCE Carbon in the ocean is massively sequestered in a complex mixture of biologically refractory molecules that accumulate as the chemical end member of biological oxidation and diagenetic change. However, few details are known about the biochemical machinery of carbon sequestration in the deep ocean. Reconstruction of the metabolism of a deep-ocean microbial clade, SAR202, led to postulation of new biochemical pathways that may be the penultimate stages of DOM oxidation to refractory forms that persist. These pathways are tied to a proliferation of oxidative enzymes. This research illuminates dark-ocean biochemistry that is broadly consequential for reconstructing the global carbon cycle. Copyright © 2017 Landry et al.

Regulation of autotrophic CO2 fixation in the archaeon Thermoproteus neutrophilus.

PubMed

Ramos-Vera, W Hugo; Labonté, Valérie; Weiss, Michael; Pauly, Julia; Fuchs, Georg

2010-10-01

Thermoproteus neutrophilus, a hyperthermophilic, chemolithoautotrophic, anaerobic crenarchaeon, uses a novel autotrophic CO(2) fixation pathway, the dicarboxylate/hydroxybutyrate cycle. The regulation of the central carbon metabolism was studied on the level of whole cells, enzyme activity, the proteome, transcription, and gene organization. The organism proved to be a facultative autotroph, which prefers organic acids as carbon sources that can easily feed into the metabolite pools of this cycle. Addition of the preferred carbon sources acetate, pyruvate, succinate, and 4-hydroxybutyrate to cultures resulted in stimulation of the growth rate and a diauxic growth response. The characteristic enzyme activities of the carbon fixation cycle, fumarate hydratase, fumarate reductase, succinyl coenzyme A (CoA) synthetase, and enzymes catalyzing the conversion of succinyl-CoA to crotonyl-CoA, were differentially downregulated in the presence of acetate and, to a lesser extent, in the presence of other organic substrates. This regulation pattern correlated well with the differential expression profile of the proteome as well as with the transcription of the encoding genes. The genes encoding phosphoenolpyruvate (PEP) carboxylase, fumarate reductase, and four enzymes catalyzing the conversion of succinyl-CoA to crotonyl-CoA are clustered. Two putative operons, one comprising succinyl-CoA reductase plus 4-hydroxybutyrate-CoA ligase genes and the other comprising 4-hydroxybutyryl-CoA dehydratase plus fumarate reductase genes, were divergently transcribed into leaderless mRNAs. The promoter regions were characterized and used for isolating DNA binding proteins. Besides an Alba protein, a 18-kDa protein characteristic for autotrophic Thermoproteales that bound specifically to the promoter region was identified. This system may be suitable for molecular analysis of the transcriptional regulation of autotrophy-related genes.

Distribution of anaerobic carbon monoxide dehydrogenase genes in deep subseafloor sediments.

PubMed

Hoshino, T; Inagaki, F

2017-05-01

Carbon monoxide (CO) is the simplest oxocarbon generated by the decomposition of organic compounds, and it is expected to be in marine sediments in substantial amounts. However, the availability of CO in the deep subseafloor sedimentary biosphere is largely unknown even though anaerobic oxidation of CO is a thermodynamically favourable reaction that possibly occurs with sulphate reduction, methanogenesis, acetogenesis and hydrogenesis. In this study, we surveyed for the first time the distribution of the CO dehydrogenase gene (cooS), which encodes the catalytic beta subunit of anaerobic CO dehydrogenase (CODH), in subseafloor sediment-core samples from the eastern flank of the Juan de Fuca Ridge, Mars-Ursa Basin, Kumano Basin, and off the Shimokita Peninsula, Japan, during Integrated Ocean Drilling Program (IODP) Expeditions 301, 308 and 315 and the D/V Chikyu shakedown cruise CK06-06, respectively. Our results show the occurrence of diverse cooS genes from the seafloor down to about 390 m below the seafloor, suggesting that microbial communities have metabolic functions to utilize CO in anoxic microbial ecosystems beneath the ocean floor, and that the microbial community potentially responsible for anaerobic CO oxidation differs in accordance with possible energy-yielding metabolic reactions in the deep subseafloor sedimentary biosphere. Little is known about the microbial community associated with carbon monoxide (CO) in the deep subseafloor. This study is the first survey of a functional gene encoding anaerobic carbon monoxide dehydrogenase (CODH). The widespread occurrence of previously undiscovered CO dehydrogenase genes (cooS) suggests that diverse micro-organisms are capable of anaerobic oxidation of CO in the deep subseafloor sedimentary biosphere. © 2017 The Society for Applied Microbiology.

Expression-based clustering of CAZyme-encoding genes of Aspergillus niger.

PubMed

Gruben, Birgit S; Mäkelä, Miia R; Kowalczyk, Joanna E; Zhou, Miaomiao; Benoit-Gelber, Isabelle; De Vries, Ronald P

2017-11-23

The Aspergillus niger genome contains a large repertoire of genes encoding carbohydrate active enzymes (CAZymes) that are targeted to plant polysaccharide degradation enabling A. niger to grow on a wide range of plant biomass substrates. Which genes need to be activated in certain environmental conditions depends on the composition of the available substrate. Previous studies have demonstrated the involvement of a number of transcriptional regulators in plant biomass degradation and have identified sets of target genes for each regulator. In this study, a broad transcriptional analysis was performed of the A. niger genes encoding (putative) plant polysaccharide degrading enzymes. Microarray data focusing on the initial response of A. niger to the presence of plant biomass related carbon sources were analyzed of a wild-type strain N402 that was grown on a large range of carbon sources and of the regulatory mutant strains ΔxlnR, ΔaraR, ΔamyR, ΔrhaR and ΔgalX that were grown on their specific inducing compounds. The cluster analysis of the expression data revealed several groups of co-regulated genes, which goes beyond the traditionally described co-regulated gene sets. Additional putative target genes of the selected regulators were identified, based on their expression profile. Notably, in several cases the expression profile puts questions on the function assignment of uncharacterized genes that was based on homology searches, highlighting the need for more extensive biochemical studies into the substrate specificity of enzymes encoded by these non-characterized genes. The data also revealed sets of genes that were upregulated in the regulatory mutants, suggesting interaction between the regulatory systems and a therefore even more complex overall regulatory network than has been reported so far. Expression profiling on a large number of substrates provides better insight in the complex regulatory systems that drive the conversion of plant biomass by fungi. In addition, the data provides additional evidence in favor of and against the similarity-based functions assigned to uncharacterized genes.

Co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis.

PubMed

Sasaki, Eita; Zhang, Xuan; Sun, He G; Lu, Mei-yeh Jade; Liu, Tsung-lin; Ou, Albert; Li, Jeng-yi; Chen, Yu-hsiang; Ealick, Steven E; Liu, Hung-wen

2014-06-19

Sulphur is an essential element for life and is ubiquitous in living systems. Yet how the sulphur atom is incorporated into many sulphur-containing secondary metabolites is poorly understood. For bond formation between carbon and sulphur in primary metabolites, the major ionic sulphur sources are the persulphide and thiocarboxylate groups on sulphur-carrier (donor) proteins. Each group is post-translationally generated through the action of a specific activating enzyme. In all reported bacterial cases, the gene encoding the enzyme that catalyses the carbon-sulphur bond formation reaction and that encoding the cognate sulphur-carrier protein exist in the same gene cluster. To study the production of the 2-thiosugar moiety in BE-7585A, an antibiotic from Amycolatopsis orientalis, we identified a putative 2-thioglucose synthase, BexX, whose protein sequence and mode of action seem similar to those of ThiG, the enzyme that catalyses thiazole formation in thiamine biosynthesis. However, no gene encoding a sulphur-carrier protein could be located in the BE-7585A cluster. Subsequent genome sequencing uncovered a few genes encoding sulphur-carrier proteins that are probably involved in the biosynthesis of primary metabolites but only one activating enzyme gene in the A. orientalis genome. Further experiments showed that this activating enzyme can adenylate each of these sulphur-carrier proteins and probably also catalyses the subsequent thiolation, through its rhodanese domain. A proper combination of these sulphur-delivery systems is effective for BexX-catalysed 2-thioglucose production. The ability of BexX to selectively distinguish sulphur-carrier proteins is given a structural basis using X-ray crystallography. This study is, to our knowledge, the first complete characterization of thiosugar formation in nature and also demonstrates the receptor promiscuity of the A. orientalis sulphur-delivery system. Our results also show that co-opting the sulphur-delivery machinery of primary metabolism for the biosynthesis of sulphur-containing natural products is probably a general strategy found in nature.

Carbon dioxide (CO2) laser treatment of cutaneous papillomas in a common snapping turtle, Chelydra serpentina.

PubMed

Raiti, Paul

2008-06-01

Carbon dioxide (CO2) laser was used to treat multiple cutaneous papillomas on an adult female common snapping turtle, Chelydra serpentina serpentina. A combination of excisional and ablative techniques provided excellent intraoperative visibility and postoperative results due to the laser's unique ability to incise and vaporize soft tissue.

Carbon sequestration and natural longleaf pine ecosystem

Treesearch

Ram Thapa; Dean Gjerstad; John Kush; Bruce Zutter

2010-01-01

The Southeastern United States was once dominated by a longleaf pine ecosystem which ranged from Virginia to Texas and covered approximately 22 to 36 million ha. The unique fire tolerant species provided the necessary habitat for numerous plant and animal species. Different seasons of prescribed fire have various results on the ecosystem and the carbon which is stored...

Modified secondary lithium metal batteries with the polyaniline-carbon nanotube composite buffer layer.

PubMed

Zhang, Ding; Yin, Yanli; Liu, Changhong; Fan, Shoushan

2015-01-07

A modified secondary lithium metal battery inserted with a polyaniline-carbon nanotube nanoporous composite buffer layer was fabricated. This unique and simple design of battery has the great potential to decrease the safety risk of the secondary Li metal battery in cycles of recharging processes and improve its cycle life in the future.

A systematic framework for Monte Carlo simulation of remote sensing errors map in carbon assessments

Treesearch

S. Healey; P. Patterson; S. Urbanski

2014-01-01

Remotely sensed observations can provide unique perspective on how management and natural disturbance affect carbon stocks in forests. However, integration of these observations into formal decision support will rely upon improved uncertainty accounting. Monte Carlo (MC) simulations offer a practical, empirical method of accounting for potential remote sensing errors...

Quantifying fire severity, carbon, and nitrogen emissions in Alaska's boreal forest

Treesearch

Leslie A. Boby; Edward A.G. Schuur; Michelle C. Mack; David Verbyla; Jill F. Johnstone

2010-01-01

The boreal region stores a large proportion of the world's terrestrial carbon (C) and is subject to high-intensity, stand-replacing wildfires that release C and nitrogen (N) stored in biomass and soils through combustion. While severity and extent of fires drives overall emissions, methods for accurately estimating fire severity are poorly tested in this unique...

The QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions

USDA-ARS?s Scientific Manuscript database

The allocation of carbon and nitrogen resources to the synthesis of plant proteins, carbohydrates, and lipids is complex and under the control of many genes; much remains to be understood about this process. QQS (Qua Quine Starch, At3g30720), an orphan gene unique to Arabidopsis thaliana, regulates...

Functional and Neuroanatomical Specificity of Episodic Memory Dysfunction in Schizophrenia: An fMRI study of the Relational and Item-Specific Encoding Task

PubMed Central

Ragland, J. Daniel; Ranganath, Charan; Harms, Michael P.; Barch, Deanna M.; Gold, James M.; Layher, Evan; Lesh, Tyler A.; MacDonald, Angus W.; Niendam, Tara A.; Phillips, Joshua; Silverstein, Steven M.; Yonelinas, Andrew P.; Carter, Cameron S.

2015-01-01

Importance Individuals with schizophrenia (SZ) can encode item-specific information to support familiarity-based recognition, but are disproportionately impaired encoding inter-item relationships (relational encoding) and recollecting information. The Relational and Item-Specific Encoding (RiSE) paradigm has been used to disentangle these encoding and retrieval processes, which may be dependent on specific medial temporal lobe (MTL) and prefrontal cortex (PFC) subregions. Functional imaging during RiSE task performance could help to specify dysfunctional neural circuits in SZ that can be targeted for interventions to improve memory and functioning in the illness. Objectives To use functional magnetic resonance imaging (fMRI) to test the hypothesis that SZ disproportionately affects MTL and PFC subregions during relational encoding and retrieval, relative to item-specific memory processes. Imaging results from healthy comparison subjects (HC) will also be used to establish neural construct validity for RiSE. Design, Setting, and Participants This multi-site, case-control, cross-sectional fMRI study was conducted at five CNTRACS sites. The final sample included 52 clinically stable outpatients with SZ, and 57 demographically matched HC. Main Outcomes and Measures Behavioral performance speed and accuracy (d’) on item recognition and associative recognition tasks. Voxelwise statistical parametric maps for a priori MTL and PFC regions of interest (ROI), testing activation differences between relational and item-specific memory during encoding and retrieval. Results Item recognition was disproportionately impaired in SZ patients relative to controls following relational encoding. The differential deficit was accompanied by reduced dorsolateral prefrontal cortex (DLPFC) activation during relational encoding in SZ, relative to HC. Retrieval success (hits > misses) was associated with hippocampal (HI) activation in HC during relational item recognition and associative recognition conditions, and HI activation was specifically reduced in SZ for recognition of relational but not item-specific information. Conclusions In this unique, multi-site fMRI study, HC results supported RiSE construct validity by revealing expected memory effects in PFC and MTL subregions during encoding and retrieval. Comparison of SZ and HC revealed disproportionate memory deficits in SZ for relational versus item-specific information, accompanied by regionally and functionally specific deficits in DLPFC and HI activation. PMID:26200928

Sea shell diversity and rapidly evolving secretomes: insights into the evolution of biomineralization.

PubMed

Kocot, Kevin M; Aguilera, Felipe; McDougall, Carmel; Jackson, Daniel J; Degnan, Bernard M

2016-01-01

An external skeleton is an essential part of the body plan of many animals and is thought to be one of the key factors that enabled the great expansion in animal diversity and disparity during the Cambrian explosion. Molluscs are considered ideal to study the evolution of biomineralization because of their diversity of highly complex, robust and patterned shells. The molluscan shell forms externally at the interface of animal and environment, and involves controlled deposition of calcium carbonate within a framework of macromolecules that are secreted from the dorsal mantle epithelium. Despite its deep conservation within Mollusca, the mantle is capable of producing an incredible diversity of shell patterns, and macro- and micro-architectures. Here we review recent developments within the field of molluscan biomineralization, focusing on the genes expressed in the mantle that encode secreted proteins. The so-called mantle secretome appears to regulate shell deposition and patterning and in some cases becomes part of the shell matrix. Recent transcriptomic and proteomic studies have revealed marked differences in the mantle secretomes of even closely-related molluscs; these typically exceed expected differences based on characteristics of the external shell. All mantle secretomes surveyed to date include novel genes encoding lineage-restricted proteins and unique combinations of co-opted ancient genes. A surprisingly large proportion of both ancient and novel secreted proteins containing simple repetitive motifs or domains that are often modular in construction. These repetitive low complexity domains (RLCDs) appear to further promote the evolvability of the mantle secretome, resulting in domain shuffling, expansion and loss. RLCD families further evolve via slippage and other mechanisms associated with repetitive sequences. As analogous types of secreted proteins are expressed in biomineralizing tissues in other animals, insights into the evolution of the genes underlying molluscan shell formation may be applied more broadly to understanding the evolution of metazoan biomineralization.

Transcriptional up-regulation of genes involved in photosynthesis of the Zn/Cd hyperaccumulator Sedum alfredii in response to zinc and cadmium.

PubMed

Tang, Lu; Yao, Aijun; Ming Yuan; Tang, Yetao; Liu, Jian; Liu, Xi; Qiu, Rongliang

2016-12-01

Zinc (Zn) and cadmium (Cd) are two closely related chemical elements with very different biological roles in photosynthesis. Zinc plays unique biochemical functions in photosynthesis. Previous studies suggested that in some Zn/Cd hyperaccumulators, many steps in photosynthesis may be Cd tolerant or even Cd stimulated. Using RNA-seq data, we found not only that Cd and Zn both up-regulated the CA1 gene, which encodes a β class carbonic anhydrase (CA) in chloroplasts, but that a large number of other Zn up-regulated genes in the photosynthetic pathway were also significantly up-regulated by Cd in leaves of the Zn/Cd hyperaccumulator Sedum alfredii. These genes also include chloroplast genes involved in transcription and translation (rps18 and rps14), electron transport and ATP synthesis (atpF and ccsA), Photosystem II (PSBI, PSBM, PSBK, PSBZ/YCF9, PSBO-1, PSBQ, LHCB1.1, LHCB1.4, LHCB2.1, LHCB4.3 and LHCB6) and Photosystem I (PSAE-1, PSAF, PSAH2, LHCA1 and LHCA4). Cadmium and Zn also up-regulated the VAR1 gene, which encodes the ATP-dependent zinc metalloprotease FTSH 5 (a member of the FtsH family), and the DAG gene, which influences chloroplast differentiation and plastid development, and the CP29 gene, which supports RNA processing in chloroplasts and has a potential role in signal-dependent co-regulation of chloroplast genes. Further morphological parameters (dry biomass, cross-sectional thickness, chloroplast size, chlorophyll content) and chlorophyll fluorescence parameters confirmed that leaf photosynthesis of S. alfredii responded to Cd much as it did to Zn, which will contribute to our understanding of the positive effects of Zn and Cd on growth of this plant. Copyright © 2016 Elsevier Ltd. All rights reserved.

Oil and Protein Accumulation in Developing Seeds Is Influenced by the Expression of a Cytosolic Pyrophosphatase in Arabidopsis[C][W][OA

PubMed Central

Meyer, Knut; Stecca, Kevin L.; Ewell-Hicks, Kim; Allen, Stephen M.; Everard, John D.

2012-01-01

This study describes a dominant low-seed-oil mutant (lo15571) of Arabidopsis (Arabidopsis thaliana) generated by enhancer tagging. Compositional analysis of developing siliques and mature seeds indicated reduced conversion of photoassimilates to oil. Immunoblot analysis revealed increased levels of At1g01050 protein in developing siliques of lo15571. At1g01050 encodes a soluble, cytosolic pyrophosphatase and is one of five closely related genes that share predicted cytosolic localization and at least 70% amino acid sequence identity. Expression of At1g01050 using a seed-preferred promoter recreated most features of the lo15571 seed phenotype, including low seed oil content and increased levels of transient starch and soluble sugars in developing siliques. Seed-preferred RNA interference-mediated silencing of At1g01050 and At3g53620, a second cytosolic pyrophosphatase gene that shows expression during seed filling, led to a heritable oil increase of 1% to 4%, mostly at the expense of seed storage protein. These results are consistent with a scenario in which the rate of mobilization of sucrose, for precursor supply of seed storage lipid biosynthesis by cytosolic glycolysis, is strongly influenced by the expression of endogenous pyrophosphatase enzymes. This emphasizes the central role of pyrophosphate-dependent reactions supporting cytosolic glycolysis during seed maturation when ATP supply is low, presumably due to hypoxic conditions. This route is the major route providing precursors for seed oil biosynthesis. ATP-dependent reactions at the entry point of glycolysis in the cytosol or plastid cannot fully compensate for the loss of oil content observed in transgenic events with increased expression of cytosolic pyrophosphatase enzyme in the cytosol. These findings shed new light on the dynamic properties of cytosolic pyrophosphate pools in developing seed and their influence on carbon partitioning during seed filling. Finally, our work uniquely demonstrates that genes encoding cytosolic pyrophosphatase enzymes provide novel targets to improve seed composition for plant biotechnology applications. PMID:22566496

Encoding Optoelectrical Sub-Components in an Al2O3 Nanowire for Rewritable High-Resolution Nanopatterning.

PubMed

Sun, Bo; Sun, Yong; Wang, Chengxin

2018-06-14

Nanoscale encoding denotes the creation of distinct electric and photonic properties within small, artificially defined regions by physical or chemical means. An encoded single nanostructure includes independent subcomponents as functional units that can also work as functional integrated nanosystems. These can be applied in high-resolution displays, detection systems, and even more complex devices. However, there is still no agreed-upon best platform satisfying all requirements. This paper demonstrates a competitive candidate based on defect engineering, that is, low energy focused e-beam-induced oxygen ion migration in a carbon-doped Al 2 O 3 nanowire. The electronic and photonic properties of these singular units are examined to be significantly modified. Their application in a nanoscale steganography strategy was also evaluated in detail. Complex patterns composed of points, lines, and planes were printed on a single nanowire using a focused e-beam and were subsequently erasable via a simple thermal process in air.

A mutation affecting carbon catabolite repression suppresses growth defects in pyruvate carboxylase mutants from Saccharomyces cerevisiae.

PubMed

Blázquez, M A; Gamo, F J; Gancedo, C

1995-12-18

Yeasts with disruptions in the genes PYC1 and PYC2 encoding the isoenzymes of pyruvate carboxylase cannot grow in a glucose-ammonium medium (Stucka et al. (1991) Mol. Gen. Genet. 229, 307-315). We have isolated a dominant mutation, BPC1-1, that allows growth in this medium of yeasts with interrupted PYC1 and PYC2 genes. The BPC1-1 mutation abolishes catabolite repression of a series of genes and allows expression of the enzymes of the glyoxylate cycle during growth in glucose. A functional glyoxylate cycle is necessary for suppression as a disruption of gene ICL1 encoding isocitrate lyase abolished the phenotypic effect of BPC1-1 on growth in glucose-ammonium. Concurrent expression from constitutive promoters of genes ICL1 and MLS1 (encoding malate synthase) also suppressed the growth phenotype of pyc1 pyc2 mutants. The mutation BPC1-1 is either allelic or closely linked to the mutation DGT1-1.

Cloning and characterization of the nagA gene that encodes beta-n-acetylglucosaminidase from Aspergillus nidulans and its expression in Aspergillus oryzae.

PubMed

Kim, Sunhwa; Matsuo, Ichiro; Ajisaka, Katsumi; Nakajima, Harushi; Kitamoto, Katsuhiko

2002-10-01

We isolated a beta-N-acetylglucosaminidase encoding gene and its cDNA from the filamentous fungus Aspergillus nidulans, and designated it nagA. The nagA gene contained no intron and encoded a polypeptide of 603 amino acids with a putative 19-amino acid signal sequence. The deduced amino acid sequence was very similar to the sequence of Candida albicans Hex1 and Trichoderma harzianum Nag1. Yeast cells containing the nagA cDNA under the control of the GAL1 promoter expressed beta-N-acetylglucosaminidase activity. The chromosomal nagA gene of A. nidulans was disrupted by replacement with the argB marker gene. The disruptant strains expressed low levels of beta-N-acetylglucosaminidase activity and showed poor growth on a medium containing chitobiose as a carbon source. Aspergillus oryzae strain carrying the nagA gene under the control of the improved glaA promoter produced large amounts of beta-N-acetylglucosaminidase in a wheat bran solid culture.

Molecular Biology of Archaebacteria

DTIC Science & Technology

1988-03-31

Biology of Archaebacteria i2 PERSONAL AUTHOR(S) Patrick P. Dennis 13a. TYPE OF REPORT 13b- TIME COVERED 114. DATE OF REPORT (Year, Month, Day) 15. PAGE...elucidate at the molecular level some of the features that make archaebacteria unique and distinguish them from eubacteria and eucaryotes. Three types...of genes, encoding rRNAs, ribosomal proteins and superoxide dismutase are phylogenetically conserved in all three kingdoms . The structure, organization

High sequence variations in the region containing genes encoding a cellular morphogenesis protein and the repressor of sexual development help to reveal origins of Aspergillus oryzae

USDA-ARS?s Scientific Manuscript database

Aspergillus oryzae and Aspergillus flavus are closely related fungal species. The A. flavus population that produces numerous small sclerotia (S strain) and aflatoxin has a unique 1.5 kb deletion in the norB-cypA region of the aflatoxin gene cluster (the S genotype). Phylogenetic studies have indica...

Smallpox Antiviral Drug

DTIC Science & Technology

2006-01-01

preparing a Continuation in Part ( CIP ) to add the new I7L cleavage assays recently developed by SIGA. Conclusions By using homology-based... developmental cycle . RNA viruses and retroviruses commonly undergo formative proteolysis in which large polyproteins are cleaved by viral encoded proteinases to...structural model of the vaccinia virus (VV) I7L proteinase was developed at Transtech Pharma. A unique chemical library of ~ 51,000 compounds was

Creating With Carbon

NASA Technical Reports Server (NTRS)

2003-01-01

A subsidiary of SI Diamond Technology, Inc., Applied Nanotech, of Austin, Texas, is creating a buzz among various technology firms and venture capital groups interested in the company s progressive research on carbon-related field emission devices, including carbon nanotubes, filaments of pure carbon less than one ten-thousandth the width of human hair. Since their discovery in 1991, carbon nanotubes have gained considerable attention due to their unique physical properties. For example, a single perfect carbon nanotube can range from 10 to 100 times stronger than steel, per unit weight. Recent studies also indicate that the nanotubes may be the best heat-conducting material in existence. These properties, combined with the ease of growing thin films or nanotubes by a variety of deposition techniques, make the carbon-based material one of the most desirable for cold field emission cathodes.

Carbon Nanomaterials in Biological Studies and Biomedicine.

PubMed

Teradal, Nagappa L; Jelinek, Raz

2017-09-01

The "carbon nano-world" has made over the past few decades huge contributions in diverse scientific disciplines and technological advances. While dramatic advances have been widely publicized in using carbon nanomaterials such as fullerenes, carbon nanotubes, and graphene in materials sciences, nano-electronics, and photonics, their contributions to biology and biomedicine have been noteworthy as well. This Review focuses on the use of carbon nanotubes (CNTs), graphene, and carbon quantum dots [encompassing graphene quantum dots (GQDs) and carbon dots (C-dots)] in biologically oriented materials and applications. Examples of these remarkable nanomaterials in bio-sensing, cell- and tissue-imaging, regenerative medicine, and other applications are presented and discussed, emphasizing the significance of their unique properties and their future potential. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Carbon Management In the Post-Cap-and-Trade Carbon Economy: An Economic Model for Limiting Climate Change by Managing Anthropogenic Carbon Flux

NASA Astrophysics Data System (ADS)

DeGroff, F. A.

2013-05-01

In this paper, we discuss an economic model for comprehensive carbon management that focuses on changes in carbon flux in the biosphere due to anthropogenic activity. The two unique features of the model include: 1. A shift in emphasis from primarily carbon emissions, toward changes in carbon flux, mainly carbon extraction, and 2. A carbon price vector (CPV) to express the value of changes in carbon flux, measured in changes in carbon sequestration, or carbon residence time. The key focus with the economic model is the degree to which carbon flux changes due to anthropogenic activity. The economic model has three steps: 1. The CPV metric is used to value all forms of carbon associated with any anthropogenic activity. In this paper, the CPV used is a logarithmic chronological scale to gauge expected carbon residence (or sequestration) time. In future economic models, the CPV may be expanded to include other factors to value carbon. 2. Whenever carbon changes form (and CPV) due to anthropogenic activity, a carbon toll is assessed as determined by the change in the CPV. The standard monetary unit for carbon tolls are carbon toll units, or CTUs. The CTUs multiplied by the quantity of carbon converted (QCC) provides the total carbon toll, or CT. For example, CT = (CTU /mole carbon) x (QCC moles carbon). 3. Whenever embodied carbon (EC) attributable to a good or service moves via trade to a jurisdiction with a different CPV metric, a carbon toll (CT) is assessed representing the CPV difference between the two jurisdictions. This economic model has three clear advantages. First, the carbon pricing and cost scheme use existing and generally accepted accounting methodologies to ensure the veracity and verifiability of carbon management efforts with minimal effort and expense using standard, existing auditing protocols. Implementing this economic model will not require any new, special, unique, or additional training, tools, or systems for any entity to achieve their minimum carbon target goals within their jurisdictional framework. Second, given the wide spectrum of carbon affinities across jurisdictions worldwide, the economic model recognizes and provides for flexible carbon pricing regimes, but does not undermine or penalize domestic carbon-consuming producers subject to imports from exporters in lower carbon pricing jurisdictions. Thus, the economic model avoids a key shortcoming of cap-and-trade carbon pricing, and eliminates any incentive to shift carbon consumption to jurisdictions with lower carbon tolls. Third, the economic model is a comprehensive, efficient, and effective strategy that allows for the implementation of a carbon pricing structure without the complete, explicit agreement of carbon consumers worldwide.

High Temperature Carbonized Grass as a High Performance Sodium Ion Battery Anode.

PubMed

Zhang, Fang; Yao, Yonggang; Wan, Jiayu; Henderson, Doug; Zhang, Xiaogang; Hu, Liangbing

2017-01-11

Hard carbon is currently considered the most promising anode candidate for room temperature sodium ion batteries because of its relatively high capacity, low cost, and good scalability. In this work, switchgrass as a biomass example was carbonized under an ultrahigh temperature, 2050 °C, induced by Joule heating to create hard carbon anodes for sodium ion batteries. Switchgrass derived carbon materials intrinsically inherit its three-dimensional porous hierarchical architecture, with an average interlayer spacing of 0.376 nm. The larger interlayer spacing than that of graphite allows for the significant Na ion storage performance. Compared to the sample carbonized under 1000 °C, switchgrass derived carbon at 2050 °C induced an improved initial Coulombic efficiency. Additionally, excellent rate capability and superior cycling performance are demonstrated for the switchgrass derived carbon due to the unique high temperature treatment.

A Critical Review of Glucose Biosensors Based on Carbon Nanomaterials: Carbon Nanotubes and Graphene

PubMed Central

Zhu, Zhigang; Garcia-Gancedo, Luis; Flewitt, Andrew J.; Xie, Huaqing; Moussy, Francis; Milne, William I.

2012-01-01

There has been an explosion of research into the physical and chemical properties of carbon-based nanomaterials, since the discovery of carbon nanotubes (CNTs) by Iijima in 1991. Carbon nanomaterials offer unique advantages in several areas, like high surface-volume ratio, high electrical conductivity, chemical stability and strong mechanical strength, and are thus frequently being incorporated into sensing elements. Carbon nanomaterial-based sensors generally have higher sensitivities and a lower detection limit than conventional ones. In this review, a brief history of glucose biosensors is firstly presented. The carbon nanotube and grapheme-based biosensors, are introduced in Sections 3 and 4, respectively, which cover synthesis methods, up-to-date sensing approaches and nonenzymatic hybrid sensors. Finally, we briefly outline the current status and future direction for carbon nanomaterials to be used in the sensing area. PMID:22778628

Carbon-Based Nanomaterials: Multi-Functional Materials for Biomedical Engineering

PubMed Central

Cha, Chaenyung; Shin, Su Ryon; Annabi, Nasim; Dokmeci, Mehmet R.; Khademhosseini, Ali

2013-01-01

Functional carbon-based nanomaterials (CBNs) have become important due to their unique combinations of chemical and physical properties (i.e., thermal and electrical conductivity, high mechanical strength, and optical properties), extensive research efforts are being made to utilize these materials for various industrial applications, such as high-strength materials and electronics. These advantageous properties of CBNs are also actively investigated in several areas of biomedical engineering. This Perspective highlights different types of carbon-based nanomaterials currently used in biomedical applications. PMID:23560817

Carbon-based nanomaterials: multifunctional materials for biomedical engineering.

PubMed

Cha, Chaenyung; Shin, Su Ryon; Annabi, Nasim; Dokmeci, Mehmet R; Khademhosseini, Ali

2013-04-23

Functional carbon-based nanomaterials (CBNs) have become important due to their unique combinations of chemical and physical properties (i.e., thermal and electrical conductivity, high mechanical strength, and optical properties), and extensive research efforts are being made to utilize these materials for various industrial applications, such as high-strength materials and electronics. These advantageous properties of CBNs are also actively investigated in several areas of biomedical engineering. This Perspective highlights different types of carbon-based nanomaterials currently used in biomedical applications.

Spine-like Nanostructured Carbon Interconnected by Graphene for High-performance Supercapacitors

NASA Astrophysics Data System (ADS)

Park, Sang-Hoon; Yoon, Seung-Beom; Kim, Hyun-Kyung; Han, Joong Tark; Park, Hae-Woong; Han, Joah; Yun, Seok-Min; Jeong, Han Gi; Roh, Kwang Chul; Kim, Kwang-Bum

2014-08-01

Recent studies on supercapacitors have focused on the development of hierarchical nanostructured carbons by combining two-dimensional graphene and other conductive sp2 carbons, which differ in dimensionality, to improve their electrochemical performance. Herein, we report a strategy for synthesizing a hierarchical graphene-based carbon material, which we shall refer to as spine-like nanostructured carbon, from a one-dimensional graphitic carbon nanofiber by controlling the local graphene/graphitic structure via an expanding process and a co-solvent exfoliation method. Spine-like nanostructured carbon has a unique hierarchical structure of partially exfoliated graphitic blocks interconnected by thin graphene sheets in the same manner as in the case of ligaments. Owing to the exposed graphene layers and interconnected sp2 carbon structure, this hierarchical nanostructured carbon possesses a large, electrochemically accessible surface area with high electrical conductivity and exhibits high electrochemical performance.

Spine-like nanostructured carbon interconnected by graphene for high-performance supercapacitors.

PubMed

Park, Sang-Hoon; Yoon, Seung-Beom; Kim, Hyun-Kyung; Han, Joong Tark; Park, Hae-Woong; Han, Joah; Yun, Seok-Min; Jeong, Han Gi; Roh, Kwang Chul; Kim, Kwang-Bum

2014-08-19

Recent studies on supercapacitors have focused on the development of hierarchical nanostructured carbons by combining two-dimensional graphene and other conductive sp(2) carbons, which differ in dimensionality, to improve their electrochemical performance. Herein, we report a strategy for synthesizing a hierarchical graphene-based carbon material, which we shall refer to as spine-like nanostructured carbon, from a one-dimensional graphitic carbon nanofiber by controlling the local graphene/graphitic structure via an expanding process and a co-solvent exfoliation method. Spine-like nanostructured carbon has a unique hierarchical structure of partially exfoliated graphitic blocks interconnected by thin graphene sheets in the same manner as in the case of ligaments. Owing to the exposed graphene layers and interconnected sp(2) carbon structure, this hierarchical nanostructured carbon possesses a large, electrochemically accessible surface area with high electrical conductivity and exhibits high electrochemical performance.

Spine-like Nanostructured Carbon Interconnected by Graphene for High-performance Supercapacitors

PubMed Central

Park, Sang-Hoon; Yoon, Seung-Beom; Kim, Hyun-Kyung; Han, Joong Tark; Park, Hae-Woong; Han, Joah; Yun, Seok-Min; Jeong, Han Gi; Roh, Kwang Chul; Kim, Kwang-Bum

2014-01-01

Recent studies on supercapacitors have focused on the development of hierarchical nanostructured carbons by combining two-dimensional graphene and other conductive sp2 carbons, which differ in dimensionality, to improve their electrochemical performance. Herein, we report a strategy for synthesizing a hierarchical graphene-based carbon material, which we shall refer to as spine-like nanostructured carbon, from a one-dimensional graphitic carbon nanofiber by controlling the local graphene/graphitic structure via an expanding process and a co-solvent exfoliation method. Spine-like nanostructured carbon has a unique hierarchical structure of partially exfoliated graphitic blocks interconnected by thin graphene sheets in the same manner as in the case of ligaments. Owing to the exposed graphene layers and interconnected sp2 carbon structure, this hierarchical nanostructured carbon possesses a large, electrochemically accessible surface area with high electrical conductivity and exhibits high electrochemical performance. PMID:25134517

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs.

PubMed

Fozo, Elizabeth M; Kawano, Mitsuoki; Fontaine, Fanette; Kaya, Yusuf; Mendieta, Kathy S; Jones, Kristi L; Ocampo, Alejandro; Rudd, Kenneth E; Storz, Gisela

2008-12-01

The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, although the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five-sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18- to 19-amino-acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by coexpression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell.

Repression of small toxic protein synthesis by the Sib and OhsC small RNAs

PubMed Central

Fozo, Elizabeth M.; Kawano, Mitsuoki; Fontaine, Fanette; Kaya, Yusuf; Mendieta, Kathy S.; Jones, Kristi L.; Ocampo, Alejandro; Rudd, Kenneth E.; Storz, Gisela

2008-01-01

Summary The sequences encoding the QUAD1 RNAs were initially identified as four repeats in Escherichia coli. These repeats, herein renamed SIB, are conserved in closely related bacteria, though the number of repeats varies. All five Sib RNAs in E. coli MG1655 are expressed, and no phenotype was observed for a five sib deletion strain. However, a phenotype reminiscent of plasmid addiction was observed for overexpression of the Sib RNAs, and further examination of the SIB repeat sequences revealed conserved open reading frames encoding highly hydrophobic 18–19 amino acid proteins (Ibs) opposite each sib gene. The Ibs proteins were found to be toxic when overexpressed and this toxicity could be prevented by co-expression of the corresponding Sib RNA. Two other RNAs encoded divergently in the yfhL-acpS intergenic region were similarly found to encode a small hydrophobic protein (ShoB) and an antisense RNA regulator (OhsC). Overexpression of both IbsC and ShoB led to immediate changes in membrane potential suggesting both proteins affect the cell envelope. Whole genome expression analysis showed that overexpression of IbsC and ShoB, as well as the small hydrophobic LdrD and TisB proteins, has both overlapping and unique consequences for the cell. PMID:18710431

Spiking, Bursting, and Population Dynamics in a Network of Growth Transform Neurons.

PubMed

Gangopadhyay, Ahana; Chakrabartty, Shantanu

2018-06-01

This paper investigates the dynamical properties of a network of neurons, each of which implements an asynchronous mapping based on polynomial growth transforms. In the first part of this paper, we present a geometric approach for visualizing the dynamics of the network where each of the neurons traverses a trajectory in a dual optimization space, whereas the network itself traverses a trajectory in an equivalent primal optimization space. We show that as the network learns to solve basic classification tasks, different choices of primal-dual mapping produce unique but interpretable neural dynamics like noise shaping, spiking, and bursting. While the proposed framework is general enough, in this paper, we demonstrate its use for designing support vector machines (SVMs) that exhibit noise-shaping properties similar to those of modulators, and for designing SVMs that learn to encode information using spikes and bursts. It is demonstrated that the emergent switching, spiking, and burst dynamics produced by each neuron encodes its respective margin of separation from a classification hyperplane whose parameters are encoded by the network population dynamics. We believe that the proposed growth transform neuron model and the underlying geometric framework could serve as an important tool to connect well-established machine learning algorithms like SVMs to neuromorphic principles like spiking, bursting, population encoding, and noise shaping.

Decoding the Formation of New Semantics: MVPA Investigation of Rapid Neocortical Plasticity during Associative Encoding through Fast Mapping.

PubMed

Atir-Sharon, Tali; Gilboa, Asaf; Hazan, Hananel; Koilis, Ester; Manevitz, Larry M

2015-01-01

Neocortical structures typically only support slow acquisition of declarative memory; however, learning through fast mapping may facilitate rapid learning-induced cortical plasticity and hippocampal-independent integration of novel associations into existing semantic networks. During fast mapping the meaning of new words and concepts is inferred, and durable novel associations are incidentally formed, a process thought to support early childhood's exuberant learning. The anterior temporal lobe, a cortical semantic memory hub, may critically support such learning. We investigated encoding of semantic associations through fast mapping using fMRI and multivoxel pattern analysis. Subsequent memory performance following fast mapping was more efficiently predicted using anterior temporal lobe than hippocampal voxels, while standard explicit encoding was best predicted by hippocampal activity. Searchlight algorithms revealed additional activity patterns that predicted successful fast mapping semantic learning located in lateral occipitotemporal and parietotemporal neocortex and ventrolateral prefrontal cortex. By contrast, successful explicit encoding could be classified by activity in medial and dorsolateral prefrontal and parahippocampal cortices. We propose that fast mapping promotes incidental rapid integration of new associations into existing neocortical semantic networks by activating related, nonoverlapping conceptual knowledge. In healthy adults, this is better captured by unique anterior and lateral temporal lobe activity patterns, while hippocampal involvement is less predictive of this kind of learning.

Two Crinivirus-specific proteins of Lettuce infectious yellows virus (LIYV), P26 and P9, are self-interacting.

PubMed

Stewart, Lucy R; Hwang, Min Sook; Falk, Bryce W

2009-11-01

Interactions of Lettuce infectious yellows virus (LIYV)-encoded proteins were tested by yeast-two-hybrid (Y2H) assays. LIYV-encoded P34, Hsp70h, P59, CP, CPm, and P26 were tested in all possible pairwise combinations. Interaction was detected only for the P26-P26 combination. P26 self-interaction domains were mapped using a series of N- and C-terminal truncations. Orthologous P26 proteins from the criniviruses Beet pseudoyellows virus (BPYV), Cucurbit yellow stunting disorder virus (CYSDV), and Lettuce chlorosis virus (LCV) were also tested, and each exhibited strong self-interaction but no interaction with orthologous proteins. Two small putative proteins encoded by LIYV RNA2, P5 and P9, were also tested for interactions with the six aforementioned LIYV proteins and each other. No interactions were detected for P5, but P9-P9 self-interaction was detected. P26- and P9-encoding genes are present in all described members of the genus Crinivirus, but are not present in other members of the family Closteroviridae. LIYV P26 has previously been demonstrated to induce a unique LIYV cytopathology, plasmalemma deposits (PLDs), but no role is yet known for P9.

Carbon nanopipettes and microtubes for electrochemical sensing and microfluidics

NASA Astrophysics Data System (ADS)

Mani, Radhika C.; Bhimarasetti, Gopinath; Lowe, Randall; Sunkara, Mahendra K.

2004-12-01

We present the synthesis of two novel morphologies for carbon tubular structures: Nanopipettes and Micropipes. The synthesis procedures for both these structures are both unique and different from each other and the conventional methods used for carbon nanotubes. Carbon nanopipettes, open at both ends, are made up of a central nanotube (~10-20 nm) surrounded by helical sheets of graphite. Thus nanopipettes have an outer conical structure, with a base size of about a micron, that narrows down to about 10-20 nm at the tip. Due to their unique morphology, the outer walls of the nanopipettes continuously expose edge planes of graphite, giving a very stable and reversible electrochemical response for detecting neurological compounds such as dopamine. The synthesis of carbon nanopipettes is based on high temperature nucleation and growth of carbon nanotubes under conditions of hydrogen etching during growth. Carbon micropipes, on the other hand, are tubular structures whose internal diameters range from a few nanometers to a few microns with a constant wall thickness of 10-20 nm. In addition to tuning the internal diameters, the conical angles of these structures could also be changed during synthesis. Due to their larger inner diameters and thin walls, both the straight and conical micro-tubular structures are suitable for microfluidic devices such as throttle valves, micro-reactors, and distribution channels. The synthesis of carbon micro-tubular structures is based on the wetting behavior of gallium with carbon during growth. The contact angle between gallium and the carbon wall determines the conical angle of the structure. By varying the contact angle, one can alter the conical angles from 400 to -150, and synthesize straight tubes using different N2/O2 dosing compositions. An 'n-step' dosing sequence at various stages of growth resulted in 'n-staged' morphologies for carbon micro-tubular structures such as funnels, tube-on-cone, Y-junctions and dumbbells.

Musicians change their tune: how hearing loss alters the neural code.

PubMed

Parbery-Clark, Alexandra; Anderson, Samira; Kraus, Nina

2013-08-01

Individuals with sensorineural hearing loss have difficulty understanding speech, especially in background noise. This deficit remains even when audibility is restored through amplification, suggesting that mechanisms beyond a reduction in peripheral sensitivity contribute to the perceptual difficulties associated with hearing loss. Given that normal-hearing musicians have enhanced auditory perceptual skills, including speech-in-noise perception, coupled with heightened subcortical responses to speech, we aimed to determine whether similar advantages could be observed in middle-aged adults with hearing loss. Results indicate that musicians with hearing loss, despite self-perceptions of average performance for understanding speech in noise, have a greater ability to hear in noise relative to nonmusicians. This is accompanied by more robust subcortical encoding of sound (e.g., stimulus-to-response correlations and response consistency) as well as more resilient neural responses to speech in the presence of background noise (e.g., neural timing). Musicians with hearing loss also demonstrate unique neural signatures of spectral encoding relative to nonmusicians: enhanced neural encoding of the speech-sound's fundamental frequency but not of its upper harmonics. This stands in contrast to previous outcomes in normal-hearing musicians, who have enhanced encoding of the harmonics but not the fundamental frequency. Taken together, our data suggest that although hearing loss modifies a musician's spectral encoding of speech, the musician advantage for perceiving speech in noise persists in a hearing-impaired population by adaptively strengthening underlying neural mechanisms for speech-in-noise perception. Copyright © 2013 Elsevier B.V. All rights reserved.

Fully refocused multi-shot spatiotemporally encoded MRI: robust imaging in the presence of metallic implants.

PubMed

Ben-Eliezer, Noam; Solomon, Eddy; Harel, Elad; Nevo, Nava; Frydman, Lucio

2012-12-01

An approach has been recently introduced for acquiring arbitrary 2D NMR spectra or images in a single scan, based on the use of frequency-swept RF pulses for the sequential excitation and acquisition of the spins response. This spatiotemporal-encoding (SPEN) approach enables a unique, voxel-by-voxel refocusing of all frequency shifts in the sample, for all instants throughout the data acquisition. The present study investigates the use of this full-refocusing aspect of SPEN-based imaging in the multi-shot MRI of objects, subject to sizable field inhomogeneities that complicate conventional imaging approaches. 2D MRI experiments were performed at 7 T on phantoms and on mice in vivo, focusing on imaging in proximity to metallic objects. Fully refocused SPEN-based spin echo imaging sequences were implemented, using both Cartesian and back-projection trajectories, and compared with k-space encoded spin echo imaging schemes collected on identical samples under equal bandwidths and acquisition timing conditions. In all cases assayed, the fully refocused spatiotemporally encoded experiments evidenced a ca. 50 % reduction in signal dephasing in the proximity of the metal, as compared to analogous results stemming from the k-space encoded spin echo counterparts. The results in this study suggest that SPEN-based acquisition schemes carry the potential to overcome strong field inhomogeneities, of the kind that currently preclude high-field, high-resolution tissue characterizations in the neighborhood of metallic implants.

Time-dependent effects of cortisol on the contextualization of emotional memories.

PubMed

van Ast, Vanessa A; Cornelisse, Sandra; Meeter, Martijn; Joëls, Marian; Kindt, Merel

2013-12-01

The inability to store fearful memories into their original encoding context is considered to be an important vulnerability factor for the development of anxiety disorders like posttraumatic stress disorder. Altered memory contextualization most likely involves effects of the stress hormone cortisol, acting via receptors located in the memory neurocircuitry. Cortisol via these receptors induces rapid nongenomic effects followed by slower genomic effects, which are thought to modulate cognitive function in opposite, complementary ways. Here, we targeted these time-dependent effects of cortisol during memory encoding and tested subsequent contextualization of emotional and neutral memories. In a double-blind, placebo-controlled design, 64 men were randomly assigned to one of three groups: 1) received 10 mg hydrocortisone 30 minutes (rapid cortisol effects) before a memory encoding task; 2) received 10 mg hydrocortisone 210 minutes (slow cortisol) before a memory encoding task; or 3) received placebo at both times. During encoding, participants were presented with neutral and emotional words in unique background pictures. Approximately 24 hours later, context dependency of their memories was assessed. Recognition data revealed that cortisol's rapid effects impair emotional memory contextualization, while cortisol's slow effects enhance it. Neutral memory contextualization remained unaltered by cortisol, irrespective of the timing of the drug. This study shows distinct time-dependent effects of cortisol on the contextualization of specifically emotional memories. The results suggest that rapid effects of cortisol may lead to impaired emotional memory contextualization, while slow effects of cortisol may confer protection against emotional memory generalization. © 2013 Society of Biological Psychiatry.

A SSVEP Stimuli Encoding Method Using Trinary Frequency-Shift Keying Encoded SSVEP (TFSK-SSVEP).

PubMed

Zhao, Xing; Zhao, Dechun; Wang, Xia; Hou, Xiaorong

2017-01-01

SSVEP is a kind of BCI technology with advantage of high information transfer rate. However, due to its nature, frequencies could be used as stimuli are scarce. To solve such problem, a stimuli encoding method which encodes SSVEP signal using Frequency Shift-Keying (FSK) method is developed. In this method, each stimulus is controlled by a FSK signal which contains three different frequencies that represent "Bit 0," "Bit 1" and "Bit 2" respectively. Different to common BFSK in digital communication, "Bit 0" and "Bit 1" composited the unique identifier of stimuli in binary bit stream form, while "Bit 2" indicates the ending of a stimuli encoding. EEG signal is acquired on channel Oz, O1, O2, Pz, P3, and P4, using ADS1299 at the sample rate of 250 SPS. Before original EEG signal is quadrature demodulated, it is detrended and then band-pass filtered using FFT-based FIR filtering to remove interference. Valid peak of the processed signal is acquired by calculating its derivative and converted into bit stream using window method. Theoretically, this coding method could implement at least 2 n -1 ( n is the length of bit command) stimulus while keeping the ITR the same. This method is suitable to implement stimuli on a monitor and where the frequency and phase could be used to code stimuli is limited as well as implementing portable BCI devices which is not capable of performing complex calculations.

Complete genome sequence of Nitrosospira multiformis, an ammonia-oxidizing bacterium from the soil environment

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

Norton, Jeanette M.; Klotz, Martin G; Stein, Lisa Y

2008-01-01

The complete genome of the ammonia-oxidizing bacterium, Nitrosospira multiformis (ATCC 25196T), consists of a circular chromosome and three small plasmids totaling 3,234,309 bp and encoding 2827 putative proteins. Of these, 2026 proteins have predicted functions and 801 are without conserved functional domains, yet 747 of these have similarity to other predicted proteins in databases. Gene homologs from Nitrosomonas europaea and N. eutropha were the best match for 42% of the predicted genes in N. multiformis. The genome contains three nearly identical copies of amo and hao gene clusters as large repeats. Distinguishing features compared to N. europaea include: the presencemore » of gene clusters encoding urease and hydrogenase, a RuBisCO-encoding operon of distinctive structure and phylogeny, and a relatively small complement of genes related to Fe acquisition. Systems for synthesis of a pyoverdine-like siderophore and for acyl-homoserine lactone were unique to N. multiformis among the sequenced AOB genomes. Gene clusters encoding proteins associated with outer membrane and cell envelope functions including transporters, porins, exopolysaccharide synthesis, capsule formation and protein sorting/export were abundant. Numerous sensory transduction and response regulator gene systems directed towards sensing of the extracellular environment are described. Gene clusters for glycogen, polyphosphate and cyanophycin storage and utilization were identified providing mechanisms for meeting energy requirements under substrate-limited conditions. The genome of N. multiformis encodes the core pathways for chemolithoautotrophy along with adaptations for surface growth and survival in soil environments.« less

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle.

PubMed

Kirkness, Ewen F; Haas, Brian J; Sun, Weilin; Braig, Henk R; Perotti, M Alejandra; Clark, John M; Lee, Si Hyeock; Robertson, Hugh M; Kennedy, Ryan C; Elhaik, Eran; Gerlach, Daniel; Kriventseva, Evgenia V; Elsik, Christine G; Graur, Dan; Hill, Catherine A; Veenstra, Jan A; Walenz, Brian; Tubío, José Manuel C; Ribeiro, José M C; Rozas, Julio; Johnston, J Spencer; Reese, Justin T; Popadic, Aleksandar; Tojo, Marta; Raoult, Didier; Reed, David L; Tomoyasu, Yoshinori; Kraus, Emily; Krause, Emily; Mittapalli, Omprakash; Margam, Venu M; Li, Hong-Mei; Meyer, Jason M; Johnson, Reed M; Romero-Severson, Jeanne; Vanzee, Janice Pagel; Alvarez-Ponce, David; Vieira, Filipe G; Aguadé, Montserrat; Guirao-Rico, Sara; Anzola, Juan M; Yoon, Kyong S; Strycharz, Joseph P; Unger, Maria F; Christley, Scott; Lobo, Neil F; Seufferheld, Manfredo J; Wang, Naikuan; Dasch, Gregory A; Struchiner, Claudio J; Madey, Greg; Hannick, Linda I; Bidwell, Shelby; Joardar, Vinita; Caler, Elisabet; Shao, Renfu; Barker, Stephen C; Cameron, Stephen; Bruggner, Robert V; Regier, Allison; Johnson, Justin; Viswanathan, Lakshmi; Utterback, Terry R; Sutton, Granger G; Lawson, Daniel; Waterhouse, Robert M; Venter, J Craig; Strausberg, Robert L; Berenbaum, May R; Collins, Frank H; Zdobnov, Evgeny M; Pittendrigh, Barry R

2010-07-06

As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens.

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

PubMed Central

Kirkness, Ewen F.; Haas, Brian J.; Sun, Weilin; Braig, Henk R.; Perotti, M. Alejandra; Clark, John M.; Lee, Si Hyeock; Robertson, Hugh M.; Kennedy, Ryan C.; Elhaik, Eran; Gerlach, Daniel; Kriventseva, Evgenia V.; Elsik, Christine G.; Graur, Dan; Hill, Catherine A.; Veenstra, Jan A.; Walenz, Brian; Tubío, José Manuel C.; Ribeiro, José M. C.; Rozas, Julio; Johnston, J. Spencer; Reese, Justin T.; Popadic, Aleksandar; Tojo, Marta; Raoult, Didier; Reed, David L.; Tomoyasu, Yoshinori; Kraus, Emily; Mittapalli, Omprakash; Margam, Venu M.; Li, Hong-Mei; Meyer, Jason M.; Johnson, Reed M.; Romero-Severson, Jeanne; VanZee, Janice Pagel; Alvarez-Ponce, David; Vieira, Filipe G.; Aguadé, Montserrat; Guirao-Rico, Sara; Anzola, Juan M.; Yoon, Kyong S.; Strycharz, Joseph P.; Unger, Maria F.; Christley, Scott; Lobo, Neil F.; Seufferheld, Manfredo J.; Wang, NaiKuan; Dasch, Gregory A.; Struchiner, Claudio J.; Madey, Greg; Hannick, Linda I.; Bidwell, Shelby; Joardar, Vinita; Caler, Elisabet; Shao, Renfu; Barker, Stephen C.; Cameron, Stephen; Bruggner, Robert V.; Regier, Allison; Johnson, Justin; Viswanathan, Lakshmi; Utterback, Terry R.; Sutton, Granger G.; Lawson, Daniel; Waterhouse, Robert M.; Venter, J. Craig; Strausberg, Robert L.; Collins, Frank H.; Zdobnov, Evgeny M.; Pittendrigh, Barry R.

2010-01-01

As an obligatory parasite of humans, the body louse (Pediculus humanus humanus) is an important vector for human diseases, including epidemic typhus, relapsing fever, and trench fever. Here, we present genome sequences of the body louse and its primary bacterial endosymbiont Candidatus Riesia pediculicola. The body louse has the smallest known insect genome, spanning 108 Mb. Despite its status as an obligate parasite, it retains a remarkably complete basal insect repertoire of 10,773 protein-coding genes and 57 microRNAs. Representing hemimetabolous insects, the genome of the body louse thus provides a reference for studies of holometabolous insects. Compared with other insect genomes, the body louse genome contains significantly fewer genes associated with environmental sensing and response, including odorant and gustatory receptors and detoxifying enzymes. The unique architecture of the 18 minicircular mitochondrial chromosomes of the body louse may be linked to the loss of the gene encoding the mitochondrial single-stranded DNA binding protein. The genome of the obligatory louse endosymbiont Candidatus Riesia pediculicola encodes less than 600 genes on a short, linear chromosome and a circular plasmid. The plasmid harbors a unique arrangement of genes required for the synthesis of pantothenate, an essential vitamin deficient in the louse diet. The human body louse, its primary endosymbiont, and the bacterial pathogens that it vectors all possess genomes reduced in size compared with their free-living close relatives. Thus, the body louse genome project offers unique information and tools to use in advancing understanding of coevolution among vectors, symbionts, and pathogens. PMID:20566863

Nitrogen Loss from Pristine Carbonate-Rock Aquifers of the Hainich Critical Zone Exploratory (Germany) Is Primarily Driven by Chemolithoautotrophic Anammox Processes

PubMed Central

Kumar, Swatantar; Herrmann, Martina; Thamdrup, Bo; Schwab, Valérie F.; Geesink, Patricia; Trumbore, Susan E.; Totsche, Kai-Uwe; Küsel, Kirsten

2017-01-01

Despite the high relevance of anaerobic ammonium oxidation (anammox) for nitrogen loss from marine systems, its relative importance compared to denitrification has less been studied in freshwater ecosystems, and our knowledge is especially scarce for groundwater. Surprisingly, phospholipid fatty acids (PLFA)-based studies identified zones with potentially active anammox bacteria within two superimposed pristine limestone aquifer assemblages of the Hainich Critical Zone Exploratory (CZE; Germany). We found anammox to contribute an estimated 83% to total nitrogen loss in suboxic groundwaters of these aquifer assemblages at rates of 3.5–4.7 nmol L−1 d−1, presumably favored over denitrification by low organic carbon availability. Transcript abundances of hzsA genes encoding hydrazine synthase exceeded nirS and nirK transcript abundances encoding denitrifier nitrite reductase by up to two orders of magnitude, providing further support of a predominance of anammox. Anammox bacteria, dominated by groups closely related to Cand. Brocadia fulgida, constituted up to 10.6% of the groundwater microbial community and were ubiquitously present across the two aquifer assemblages with indication of active anammox bacteria even in the presence of 103 μmol L−1 oxygen. Co-occurrence of hzsA and amoA gene transcripts encoding ammonia mono-oxygenase suggested coupling between aerobic and anaerobic ammonium oxidation under suboxic conditions. These results clearly demonstrate the relevance of anammox as a key process driving nitrogen loss from oligotrophic groundwater environments, which might further be enhanced through coupling with incomplete nitrification. PMID:29067012

Engineering high-level production of fatty alcohols by Saccharomyces cerevisiae from lignocellulosic feedstocks.

PubMed

d'Espaux, Leo; Ghosh, Amit; Runguphan, Weerawat; Wehrs, Maren; Xu, Feng; Konzock, Oliver; Dev, Ishaan; Nhan, Melissa; Gin, Jennifer; Reider Apel, Amanda; Petzold, Christopher J; Singh, Seema; Simmons, Blake A; Mukhopadhyay, Aindrila; García Martín, Héctor; Keasling, Jay D

2017-07-01

Fatty alcohols in the C12-C18 range are used in personal care products, lubricants, and potentially biofuels. These compounds can be produced from the fatty acid pathway by a fatty acid reductase (FAR), yet yields from the preferred industrial host Saccharomyces cerevisiae remain under 2% of the theoretical maximum from glucose. Here we improved titer and yield of fatty alcohols using an approach involving quantitative analysis of protein levels and metabolic flux, engineering enzyme level and localization, pull-push-block engineering of carbon flux, and cofactor balancing. We compared four heterologous FARs, finding highest activity and endoplasmic reticulum localization from a Mus musculus FAR. After screening an additional twenty-one single-gene edits, we identified increasing FAR expression; deleting competing reactions encoded by DGA1, HFD1, and ADH6; overexpressing a mutant acetyl-CoA carboxylase; limiting NADPH and carbon usage by the glutamate dehydrogenase encoded by GDH1; and overexpressing the Δ9-desaturase encoded by OLE1 as successful strategies to improve titer. Our final strain produced 1.2g/L fatty alcohols in shake flasks, and 6.0g/L in fed-batch fermentation, corresponding to ~ 20% of the maximum theoretical yield from glucose, the highest titers and yields reported to date in S. cerevisiae. We further demonstrate high-level production from lignocellulosic feedstocks derived from ionic-liquid treated switchgrass and sorghum, reaching 0.7g/L in shake flasks. Altogether, our work represents progress towards efficient and renewable microbial production of fatty acid-derived products. Published by Elsevier Inc.

How chemical information processing interferes with face processing: a magnetoencephalographic study.

PubMed

Walla, Peter; Mayer, Dagmar; Deecke, Lüder; Lang, Wilfried

2005-01-01

Magnetic field changes related to face encoding were recorded in 20 healthy young participants. Faces had to be deeply encoded under four kinds of simultaneous nasal chemical stimulation. Neutral room air, phenyl ethyl alcohol (PEA, rose flavor), carbon dioxide (CO2, pain), and hydrogen sulfide (H2S, rotten eggs flavor) were used as chemical stimuli. PEA and H2S represented odor stimuli, whereas CO2 was used for trigeminal stimulation (pain sensation). After the encoding of faces, the respective recognition performances were tested focusing on recognition effects related to specific chemical stimulation during encoding. The number of correctly recognized faces (hits) varied between chemical conditions. PEA stimulation during face encoding significantly increased the number of hits compared to the control condition. H2S also led to an increased mean number of hits, whereas simultaneous CO2 administration during face encoding resulted in a reduction. Analysis of the physiological data revealed two latency regions of interest. Compared to the control condition, both olfactory stimulus conditions resulted in reduced activity components peaking at about 260 ms after stimulus onset, whereas CO2 produced a strongly pronounced enhanced activity component peaking at about 700 ms after stimulus onset. Both olfactory conditions elicited only weak enhanced activities at about 700 ms, and CO2 did not show any difference activity at 260 ms after stimulus onset compared to the control condition. It is concluded that the early activity differences represent subconscious olfactory information processing leading to enhanced memory performances irrespective of the hedonic value, at least if they are only subconsciously processed. The later activity is suggested to reflect conscious CO2 perception negatively affecting face encoding and therefore leading to reduced subsequent face recognition. We interpret that conscious processing of nasal chemical stimulation competes with deep face encoding with respect to cortical resources, whereas subconscious processing of nasal chemical stimulation does not.

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions.

PubMed

Szabó, Attila; Korponai, Kristóf; Kerepesi, Csaba; Somogyi, Boglárka; Vörös, Lajos; Bartha, Dániel; Márialigeti, Károly; Felföldi, Tamás

2017-05-01

Soda pans of the Pannonian steppe are unique environments regarding their physical and chemical characteristics: shallowness, high turbidity, intermittent character, alkaline pH, polyhumic organic carbon concentration, hypertrophic condition, moderately high salinity, sodium and carbonate ion dominance. The pans are highly productive environments with picophytoplankton predominance. Little is known about the planktonic bacterial communities inhabiting these aquatic habitats; therefore, amplicon sequencing and shotgun metagenomics were applied to reveal their composition and functional properties. Results showed a taxonomically complex bacterial community which was distinct from other soda lakes regarding its composition, e.g. the dominance of class Alphaproteobacteria was observed within phylum Proteobacteria. The shotgun metagenomic analysis revealed several functional gene components related to the harsh and at the same time hypertrophic environmental conditions, e.g. proteins involved in stress response, transport and hydrolase systems targeting phytoplankton-derived organic matter. This is the first detailed report on the indigenous planktonic bacterial communities coping with the multiple extreme conditions present in the unique soda pans of the Pannonian steppe.

Photoautotrophic Polyhydroxybutyrate Granule Formation Is Regulated by Cyanobacterial Phasin PhaP in Synechocystis sp. Strain PCC 6803

PubMed Central

Hauf, Waldemar; Watzer, Björn; Roos, Nora; Klotz, Alexander

2015-01-01

Cyanobacteria are photoautotrophic microorganisms which fix atmospheric carbon dioxide via the Calvin-Benson cycle to produce carbon backbones for primary metabolism. Fixed carbon can also be stored as intracellular glycogen, and in some cyanobacterial species like Synechocystis sp. strain PCC 6803, polyhydroxybutyrate (PHB) accumulates when major nutrients like phosphorus or nitrogen are absent. So far only three enzymes which participate in PHB metabolism have been identified in this organism, namely, PhaA, PhaB, and the heterodimeric PHB synthase PhaEC. In this work, we describe the cyanobacterial PHA surface-coating protein (phasin), which we term PhaP, encoded by ssl2501. Translational fusion of Ssl2501 with enhanced green fluorescent protein (eGFP) showed a clear colocalization to PHB granules. A deletion of ssl2501 reduced the number of PHB granules per cell, whereas the mean PHB granule size increased as expected for a typical phasin. Although deletion of ssl2501 had almost no effect on the amount of PHB, the biosynthetic activity of PHB synthase was negatively affected. Secondary-structure prediction and circular dichroism (CD) spectroscopy of PhaP revealed that the protein consists of two α-helices, both of them associating with PHB granules. Purified PhaP forms oligomeric structures in solution, and both α-helices of PhaP contribute to oligomerization. Together, these results support the idea that Ssl2501 encodes a cyanobacterial phasin, PhaP, which regulates the surface-to-volume ratio of PHB granules. PMID:25911471

Metabolic potential and in situ activity of marine Marinimicrobia bacteria in an anoxic water column.

PubMed

Bertagnolli, Anthony D; Padilla, Cory C; Glass, Jennifer B; Thamdrup, Bo; Stewart, Frank J

2017-11-01

Marinimicrobia bacteria are widespread in subeuphotic areas of the oceans and particularly abundant in oxygen minimum zones (OMZs). Information on Marinimicrobia metabolism is sparse, making the biogeochemical influence of this group challenging to predict. Here, metagenome-assembled genomes representing Marinimicrobia subgroups PN262000N21 and ARCTIC96B-7 were retrieved to near completion (97% and 94%) from OMZ metagenomes, with contamination (14.1%) observed only in ARCTIC96B-7. Genes for aerobic carbon monoxide (CO) oxidation, polysulfide metabolism and hydrogen utilization were identified only in PN262000N21, while genes for partial denitrification occurred in both genomes. Transcripts mapping to these genomes increased from <0.3% of total mRNA from the oxic zone to a max of 22% under anoxia. ARCTIC96B-7 transcript representation decreased an order of magnitude from non-sulfidic to sulfidic depths. In contrast, PN262000N21 representation was relatively constant throughout the OMZ, although transcripts encoding sulfur-utilizing proteins, including sulfur transferases, were enriched at sulfidic depths. PN262000N21 transcripts encoding a protein with fibronectin domains similar to those in cellulosome-producing bacteria were also abundant, suggesting a potential for high molecular weight carbon cycling. These data provide omic-level descriptions of metabolic potential and activity in OMZ-associated Marinimicrobia, suggesting differentiation between subgroups with roles in carbon and dissimilatory inorganic nitrogen and sulfur cycling. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Unique case of fatal carbon monoxide poisoning in the absence of a combustible fossil fuel.

PubMed

Morgan, D R; Poon, P; Titley, J; Jagger, S F; Rutty, G N

2001-09-01

A 37-year-old man died as a result of exposure to carbon monoxide within an apartment. An investigation of the apartment showed no gas appliances or gas supply to the apartment and no evidence of any combustion event to any part of the apartment or roof space. Inhalation of dichloromethane was excluded. Heating to the apartment was found to be via an electrical storage heater, the examination of which revealed that the cast-iron core and insulating material showed evidence of heat damage with significant areas devoid of carbon. This electric storage heater is hypothesized to be the source of carbon for the fatal production of carbon monoxide within the apartment.

Evolution and Distribution of Teleost myomiRNAs: Functionally Diversified myomiRs in Teleosts.

PubMed

Siddique, Bhuiyan Sharmin; Kinoshita, Shigeharu; Wongkarangkana, Chaninya; Asakawa, Shuichi; Watabe, Shugo

2016-06-01

Myosin heavy chain (MYH) genes belong to a multigene family, and the regulated expression of each member determines the physiological and contractile muscle properties. Among these, MYH6, MYH7, and MYH14 occupy unique positions in the mammalian MYH gene family because of their specific expression in slow/cardiac muscles and the existence of intronic micro(mi) RNAs. MYH6, MYH7, and MYH14 encode miR-208a, miR-208b, and miR-499, respectively. These MYH encoded miRNAs are designated as myomiRs because of their muscle-specific expression and functions. In mammals, myomiRs and host MYHs form a transcription network involved in muscle fiber-type specification; thus, genomic positions and expression patterns of them are well conserved. However, our previous studies revealed divergent distribution and expression of MYH14/miR-499 among teleosts, suggesting the unique evolution of myomiRs and host MYHs in teleosts. Here, we examined distribution and expression of myomiRs and host MYHs in various teleost species. The major cardiac MYH isoforms in teleosts are an intronless gene, atrial myosin heavy chain (amhc), and ventricular myosin heavy chain (vmhc) gene that encodes an intronic miRNA, miR-736. Phylogenetic analysis revealed that vmhc/miR-736 is a teleost-specific myomiR that differed from tetrapoda MYH6/MYH7/miR-208s. Teleost genomes also contain species-specific orthologs in addition to vmhc and amhc, indicating complex gene duplication and gene loss events during teleost evolution. In medaka and torafugu, miR-499 was highly expressed in slow/cardiac muscles whereas the expression of miR-736 was quite low and not muscle specific. These results suggest functional diversification of myomiRs in teleost with the diversification of host MYHs.

Plant Proteins Are Smaller Because They Are Encoded by Fewer Exons than Animal Proteins.

PubMed

Ramírez-Sánchez, Obed; Pérez-Rodríguez, Paulino; Delaye, Luis; Tiessen, Axel

2016-12-01

Protein size is an important biochemical feature since longer proteins can harbor more domains and therefore can display more biological functionalities than shorter proteins. We found remarkable differences in protein length, exon structure, and domain count among different phylogenetic lineages. While eukaryotic proteins have an average size of 472 amino acid residues (aa), average protein sizes in plant genomes are smaller than those of animals and fungi. Proteins unique to plants are ∼81aa shorter than plant proteins conserved among other eukaryotic lineages. The smaller average size of plant proteins could neither be explained by endosymbiosis nor subcellular compartmentation nor exon size, but rather due to exon number. Metazoan proteins are encoded on average by ∼10 exons of small size [∼176 nucleotides (nt)]. Streptophyta have on average only ∼5.7 exons of medium size (∼230nt). Multicellular species code for large proteins by increasing the exon number, while most unicellular organisms employ rather larger exons (>400nt). Among subcellular compartments, membrane proteins are the largest (∼520aa), whereas the smallest proteins correspond to the gene ontology group of ribosome (∼240aa). Plant genes are encoded by half the number of exons and also contain fewer domains than animal proteins on average. Interestingly, endosymbiotic proteins that migrated to the plant nucleus became larger than their cyanobacterial orthologs. We thus conclude that plants have proteins larger than bacteria but smaller than animals or fungi. Compared to the average of eukaryotic species, plants have ∼34% more but ∼20% smaller proteins. This suggests that photosynthetic organisms are unique and deserve therefore special attention with regard to the evolutionary forces acting on their genomes and proteomes. Copyright © 2016 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

Deubiquitinase function of arterivirus papain-like protease 2 suppresses the innate immune response in infected host cells.

PubMed

van Kasteren, Puck B; Bailey-Elkin, Ben A; James, Terrence W; Ninaber, Dennis K; Beugeling, Corrine; Khajehpour, Mazdak; Snijder, Eric J; Mark, Brian L; Kikkert, Marjolein

2013-02-26

Protein ubiquitination regulates important innate immune responses. The discovery of viruses encoding deubiquitinating enzymes (DUBs) suggests they remove ubiquitin to evade ubiquitin-dependent antiviral responses; however, this has never been conclusively demonstrated in virus-infected cells. Arteriviruses are economically important positive-stranded RNA viruses that encode an ovarian tumor (OTU) domain DUB known as papain-like protease 2 (PLP2). This enzyme is essential for arterivirus replication by cleaving a site within the viral replicase polyproteins and also removes ubiquitin from cellular proteins. To dissect this dual specificity, which relies on a single catalytic site, we determined the crystal structure of equine arteritis virus PLP2 in complex with ubiquitin (1.45 Å). PLP2 binds ubiquitin using a zinc finger that is uniquely integrated into an exceptionally compact OTU-domain fold that represents a new subclass of zinc-dependent OTU DUBs. Notably, the ubiquitin-binding surface is distant from the catalytic site, which allowed us to mutate this surface to significantly reduce DUB activity without affecting polyprotein cleavage. Viruses harboring such mutations exhibited WT replication kinetics, confirming that PLP2-mediated polyprotein cleavage was intact, but the loss of DUB activity strikingly enhanced innate immune signaling. Compared with WT virus infection, IFN-β mRNA levels in equine cells infected with PLP2 mutants were increased by nearly an order of magnitude. Our findings not only establish PLP2 DUB activity as a critical factor in arteriviral innate immune evasion, but the selective inactivation of DUB activity also opens unique possibilities for developing improved live attenuated vaccines against arteriviruses and other viruses encoding similar dual-specificity proteases.

Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis

DOE PAGES

Christopherson, Melissa R.; Dawson, John A.; Stevenson, David M.; ...

2014-12-04

Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable by its bovine host. Moreover, it is one of the few organisms that ferments cellulose to form ethanol at mesophilic temperatures in vitro. The mechanism of cellulose degradation by R. albus 7 is not well-defined and is thought to involve pilin-like proteins, unique carbohydrate-binding domains, a glycocalyx, and cellulosomes. We used a combination of comparativemore » genomics, fermentation analyses, and transcriptomics to further clarify the cellulolytic and fermentative potential of R. albus 7. A comparison of the R. albus 7 genome sequence against the genome sequences of related bacteria that either encode or do not encode cellulosomes revealed that R. albus 7 does not encode for most canonical cellulosomal components. Fermentation analysis of R. albus 7 revealed the ability to produce ethanol and acetate on a wide range of fibrous substrates in vitro. Global transcriptomic analysis of R. albus 7 grown at identical dilution rates on cellulose and cellobiose in a chemostat showed that this bacterium, when growing on cellulose, utilizes a carbohydrate-degrading strategy that involves increased transcription of the rare carbohydrate-binding module (CBM) family 37 domain and the tryptophan biosynthetic operon. Our data suggest that R. albus 7 does not use canonical cellulosomal components to degrade cellulose, but rather up-regulates the expression of CBM37-containing enzymes and tryptophan biosynthesis. This study contributes to a revised model of carbohydrate degradation by this key member of the rumen ecosystem.« less

A comparative genomic analysis of the oxidative enzymes potentially involved in lignin degradation by Agaricus bisporus

Treesearch

Harshavardhan Doddapaneni; Venkataramanan Subramanian; Bolei Fu; Dan Cullen

2013-01-01

The oxidative enzymatic machinery for degradation of organic substrates in Agaricus bisporus (Ab) is at the core of the carbon recycling mechanisms in this fungus. To date, 156 genes have been tentatively identified as part of this oxidative enzymatic machinery, which includes 26 peroxidase encoding genes, nine copper radical oxidase [including three...

Ensemble codes involving hippocampal neurons are at risk during delayed performance tests.

PubMed

Hampson, R E; Deadwyler, S A

1996-11-26

Multielectrode recording techniques were used to record ensemble activity from 10 to 16 simultaneously active CA1 and CA3 neurons in the rat hippocampus during performance of a spatial delayed-nonmatch-to-sample task. Extracted sources of variance were used to assess the nature of two different types of errors that accounted for 30% of total trials. The two types of errors included ensemble "miscodes" of sample phase information and errors associated with delay-dependent corruption or disappearance of sample information at the time of the nonmatch response. Statistical assessment of trial sequences and associated "strength" of hippocampal ensemble codes revealed that miscoded error trials always followed delay-dependent error trials in which encoding was "weak," indicating that the two types of errors were "linked." It was determined that the occurrence of weakly encoded, delay-dependent error trials initiated an ensemble encoding "strategy" that increased the chances of being correct on the next trial and avoided the occurrence of further delay-dependent errors. Unexpectedly, the strategy involved "strongly" encoding response position information from the prior (delay-dependent) error trial and carrying it forward to the sample phase of the next trial. This produced a miscode type error on trials in which the "carried over" information obliterated encoding of the sample phase response on the next trial. Application of this strategy, irrespective of outcome, was sufficient to reorient the animal to the proper between trial sequence of response contingencies (nonmatch-to-sample) and boost performance to 73% correct on subsequent trials. The capacity for ensemble analyses of strength of information encoding combined with statistical assessment of trial sequences therefore provided unique insight into the "dynamic" nature of the role hippocampus plays in delay type memory tasks.

The effect of scene context on episodic object recognition: parahippocampal cortex mediates memory encoding and retrieval success.

PubMed

Hayes, Scott M; Nadel, Lynn; Ryan, Lee

2007-01-01

Previous research has investigated intentional retrieval of contextual information and contextual influences on object identification and word recognition, yet few studies have investigated context effects in episodic memory for objects. To address this issue, unique objects embedded in a visually rich scene or on a white background were presented to participants. At test, objects were presented either in the original scene or on a white background. A series of behavioral studies with young adults demonstrated a context shift decrement (CSD)-decreased recognition performance when context is changed between encoding and retrieval. The CSD was not attenuated by encoding or retrieval manipulations, suggesting that binding of object and context may be automatic. A final experiment explored the neural correlates of the CSD, using functional Magnetic Resonance Imaging. Parahippocampal cortex (PHC) activation (right greater than left) during incidental encoding was associated with subsequent memory of objects in the context shift condition. Greater activity in right PHC was also observed during successful recognition of objects previously presented in a scene. Finally, a subset of regions activated during scene encoding, such as bilateral PHC, was reactivated when the object was presented on a white background at retrieval. Although participants were not required to intentionally retrieve contextual information, the results suggest that PHC may reinstate visual context to mediate successful episodic memory retrieval. The CSD is attributed to automatic and obligatory binding of object and context. The results suggest that PHC is important not only for processing of scene information, but also plays a role in successful episodic memory encoding and retrieval. These findings are consistent with the view that spatial information is stored in the hippocampal complex, one of the central tenets of Multiple Trace Theory. (c) 2007 Wiley-Liss, Inc.

Modulation of Oscillatory Power and Connectivity in the Human Posterior Cingulate Cortex Supports the Encoding and Retrieval of Episodic Memories.

PubMed

Lega, Bradley; Germi, James; Rugg, Michael

2017-08-01

Existing data from noninvasive studies have led researchers to posit that the posterior cingulate cortex (PCC) supports mnemonic processes: It exhibits degeneration in memory disorders, and fMRI investigations have demonstrated memory-related activation principally during the retrieval of memory items. Despite these data, the role of the PCC in episodic memory has received only limited treatment using the spatial and temporal precision of intracranial EEG, with previous analyses focused on item retrieval. Using data gathered from 21 human participants who underwent stereo-EEG for seizure localization, we characterized oscillatory patterns in the PCC during the encoding and retrieval of episodic memories. We identified a subsequent memory effect during item encoding characterized by increased gamma band oscillatory power and a low-frequency power desynchronization. Fourteen participants had stereotactic electrodes located simultaneously in the hippocampus and PCC, and with these unique data, we describe connectivity changes between these structures that predict successful item encoding and that precede item retrieval. Oscillatory power during retrieval matched the pattern we observed during encoding, with low-frequency (below 15 Hz) desynchronization and a gamma band (especially high gamma, 70-180 Hz) power increase. Encoding is characterized by synchrony between the hippocampus and PCC, centered at 3 Hz, consistent with other observations of properties of this oscillation akin to those for rodent theta activity. We discuss our findings in light of existing theories of episodic memory processing, including the information via desynchronization hypothesis and retrieved context theory, and examine how our data fit with existing theories for the functional role of the PCC. These include a postulated role for the PCC in modulating internally directed attention and for representing or integrating contextual information for memory items.

Diversity Analysis of Dairy and Nondairy Lactococcus lactis Isolates, Using a Novel Multilocus Sequence Analysis Scheme and (GTG)5-PCR Fingerprinting▿

PubMed Central

Rademaker, Jan L. W.; Herbet, Hélène; Starrenburg, Marjo J. C.; Naser, Sabri M.; Gevers, Dirk; Kelly, William J.; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E. T.

2007-01-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)5-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene. PMID:17890345

Diversity analysis of dairy and nondairy Lactococcus lactis isolates, using a novel multilocus sequence analysis scheme and (GTG)5-PCR fingerprinting.

PubMed

Rademaker, Jan L W; Herbet, Hélène; Starrenburg, Marjo J C; Naser, Sabri M; Gevers, Dirk; Kelly, William J; Hugenholtz, Jeroen; Swings, Jean; van Hylckama Vlieg, Johan E T

2007-11-01

The diversity of a collection of 102 lactococcus isolates including 91 Lactococcus lactis isolates of dairy and nondairy origin was explored using partial small subunit rRNA gene sequence analysis and limited phenotypic analyses. A subset of 89 strains of L. lactis subsp. cremoris and L. lactis subsp. lactis isolates was further analyzed by (GTG)(5)-PCR fingerprinting and a novel multilocus sequence analysis (MLSA) scheme. Two major genomic lineages within L. lactis were found. The L. lactis subsp. cremoris type-strain-like genotype lineage included both L. lactis subsp. cremoris and L. lactis subsp. lactis isolates. The other major lineage, with a L. lactis subsp. lactis type-strain-like genotype, comprised L. lactis subsp. lactis isolates only. A novel third genomic lineage represented two L. lactis subsp. lactis isolates of nondairy origin. The genomic lineages deviate from the subspecific classification of L. lactis that is based on a few phenotypic traits only. MLSA of six partial genes (atpA, encoding ATP synthase alpha subunit; pheS, encoding phenylalanine tRNA synthetase; rpoA, encoding RNA polymerase alpha chain; bcaT, encoding branched chain amino acid aminotransferase; pepN, encoding aminopeptidase N; and pepX, encoding X-prolyl dipeptidyl peptidase) revealed 363 polymorphic sites (total length, 1,970 bases) among 89 L. lactis subsp. cremoris and L. lactis subsp. lactis isolates with unique sequence types for most isolates. This allowed high-resolution cluster analysis in which dairy isolates form subclusters of limited diversity within the genomic lineages. The pheS DNA sequence analysis yielded two genetic groups dissimilar to the other genotyping analysis-based lineages, indicating a disparate acquisition route for this gene.

A mutagenesis study of a catalytic antibody

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

Jackson, D.Y.; Prudent, J.R.; Baldwin, E.P.

1991-01-01

The authors have generated seven site-specific mutations in the genes encoding the variable region of the heavy chain domain (V{sub H}) of the phosphocholine-binding antibody S107.S107 is a member of a family of well-characterized highly homologous antibodies that bind phosphorylcholine mono- and diesters. Two of these antibodies, MOPC-167 and T15, have previously been shown to catalyze the hydrolysis of 4-nitrophenyl N-trimethylammonioethyl carbonate. Two conserved heavy-chain residues, Tyr-33 and Arg-52, were postulated to be involved in binding and hydrolysis of 4-nitrophenylcholine carbonate esters. To more precisely define the catalytic roles of these residues, three Arg-52 mutants (R52K, R52Q, R52C) and fourmore » Tyr-33 mutants (Y33H, Y33F, Y33E, Y33D) of antibody S107 were generated. The genes encoding the V{sub H} binding domain of S107 were inserted into plasmid pUC-fl, and in vitro mutagenesis was performed. These results not only demonstrate the importance of electrostatic interactions in catalysis by antibody S107 but also show that catalytic side chains can be introduced into antibodies to enhance their catalytic efficiency.« less

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

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

Fredrickson, Jim K.; Balkwill, David L.; Romine, Margaret F.

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteriamore » cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.« less

Ecology, physiology, and phylogeny of deep subsurface Sphingomonas sp.

PubMed

Fredrickson, J K; Balkwill, D L; Romine, M F; Shi, T

1999-10-01

Several new species of the genus Sphingomonas including S. aromaticivorans, S. stygia, and S. subterranea that have the capacity for degrading a broad range of aromatic compounds including toluene, naphthalene, xylenes, p-cresol, fluorene, biphenyl, and dibenzothiophene, were isolated from deeply-buried (>200 m) sediments of the US Atlantic coastal plain (ACP). In S. aromaticivorans F199, many of the genes involved in the catabolism of these aromatic compounds are encoded on a 184-kb conjugative plasmid; some of the genes involved in aromatic catabolism are plasmid-encoded in the other strains as well. Members of the genus Sphingomonas were common among aerobic heterotrophic bacteria cultured from ACP sediments and have been detected in deep subsurface environments elsewhere. The major source of organic carbon for heterotrophic metabolism in ACP deep aquifers is lignite that originated from plant material buried with the sediments. We speculate that the ability of the subsurface Sphingomonas strains to degrade a wide array of aromatic compounds represents an adaptation for utilization of sedimentary lignite. These and related subsurface Sphingomonas spp may play an important role in the transformation of sedimentary organic carbon in the aerobic and microaerobic regions of the deep aquifers of the ACP.

Development of the International Space Station (ISS) Fine Water Mist (FWM) Portable Fire Extinguisher

NASA Technical Reports Server (NTRS)

Rodriquez, Branelle; Graf, John; Carlile, Christie; Young, GIna

2012-01-01

The National Aeronautics and Space Administration (NASA) is developing a Fine Water Mist (FWM) Portable Fire Extinguisher (PFE) for use on the International Space Station (ISS). The ISS presently uses two different types of fire extinguishers: a water foam extinguisher in the Russian Segment, and a carbon dioxide extinguisher in the United States Orbital Segments, which include Columbus and Kibo pressurized elements. Currently, there are operational concerns with the emergency breathing equipment and the carbon dioxide extinguisher. The toxicity of the carbon dioxide requires the crew members to have an oxygen supply present during a fire event, therefore inherently creating an unsafe environment. The FWM PFE extinguishes a fire without creating a hazardous breathing environment for crew members. The following paper will discuss the unique functional and performance requirements that have been levied on the FWM PFE, identify unique microgravity design considerations for liquid and gas systems, as well as discuss the NASA ISS specific fire standards that were developed to establish an acceptable portable fire extinguisher s performance.

Safety management of an underground-based gravitational wave telescope: KAGRA

NASA Astrophysics Data System (ADS)

Ohishi, Naoko; Miyoki, Shinji; Uchiyama, Takashi; Miyakawa, Osamu; Ohashi, Masatake

2014-08-01

KAGRA is a unique gravitational wave telescope with its location underground and use of cryogenic mirrors. Safety management plays an important role for secure development and operation of such a unique and large facility. Based on relevant law in Japan, Labor Standard Act and Industrial Safety and Health Law, various countermeasures are mandated to avoid foreseeable accidents and diseases. In addition to the usual safety management of hazardous materials, such as cranes, organic solvents, lasers, there are specific safety issues in the tunnel. Prevention of collapse, flood, and fire accidents are the most critical issues for the underground facility. Ventilation is also important for prevention of air pollution by carbon monoxide, carbon dioxide, organic solvents and radon. Oxygen deficiency should also be prevented.

Nanodiamonds do not provide unique evidence for a Younger Dryas impact

PubMed Central

Tian, H.; Schryvers, D.; Claeys, Ph.

2011-01-01

Microstructural, δ13C isotope and C/N ratio investigations were conducted on excavated material from the black Younger Dryas boundary in Lommel, Belgium, aiming for a characterisation of the carbon content and structures. Cubic diamond nanoparticles are found in large numbers. The larger ones with diameters around or above 10 nm often exhibit single or multiple twins. The smaller ones around 5 nm in diameter are mostly defect-free. Also larger flake-like particles, around 100 nm in lateral dimension, with a cubic diamond structure are observed as well as large carbon onion structures. The combination of these characteristics does not yield unique evidence for an exogenic impact related to the investigated layer. PMID:21173270

Species and media effects on soil carbon dynamics in the landscape: opportunities for climate change mitigation from urban landscape plantings

USDA-ARS?s Scientific Manuscript database

Most scientists now agree that climate change is occurring as a direct result of human activities. Agricultural production has been shown to be a major emitter of greenhouse gas (GHG) emissions; however, horticulture production is unique in that it also has the potential to serve as a major carbon (...

Development of the International Space Station Fine Water Mist Portable Fire Extinguisher

NASA Technical Reports Server (NTRS)

Rodriquez, Branelle; Young, GIna

2013-01-01

The National Aeronautics and Space Administration (NASA) is developing a Fine Water Mist (FWM) Portable Fire Extinguisher (PFE) for use on the International Space Station (ISS). The ISS presently uses two different types of fire extinguishers: a water foam extinguisher in the Russian Segments, and a carbon dioxide extinguisher in the United States Orbital Segments, which include Columbus and Kibo pressurized elements. Currently, there are operational and compatibility concerns with the emergency breathing equipment and the carbon dioxide extinguisher. ISS emergency response breathing equipment does not filter carbon dioxide; therefore, crew members are required to have an oxygen supply present during a fire event since the carbon dioxide PFE creates an unsafe breathing environment. The ISS program recommended a nontoxic fire extinguisher to mitigate this operational risk. The FWM PFE can extinguish a fire without creating a hazardous breathing environment for crewmembers. This paper will discuss the unique functional and performance requirements that have been levied on the FWM PFE, identify unique microgravity design considerations for liquid and gas systems, and discuss the NASA ISS specific fire standards that were developed to establish an acceptable portable fire extinguisher s performance.

Bioinspired Single-Walled Carbon Nanotubes as a Spider Silk Structure for Ultrahigh Mechanical Property.

PubMed

Luo, Chengzhi; Li, Fangying; Li, Delong; Fu, Qiang; Pan, Chunxu

2016-11-16

Due to its unique hierarchical structure, natural spider silk features exceptional mechanical properties such as high tensile strength and great extensibility, making it one of the toughest materials. Herein, we design bioinspired spider silk single-walled carbon nanotubes (BISS-SWCNTs) that combine the hierarchical structure of spider silk and the high strength and conductivity of SWCNTs. To imitate the hierarchical structure, Fe nanoparticles are embedded on the surface of directly synthesized SWCNTs skeleton followed by coating an amorphous carbon layer. The carbon layer forms the spider silk-featured skin-core structure with SWCNTs, thus making the tube junction tougher. The embedded Fe nanoparticles act as glue spots for preventing interfacial slippages between the BISS-SWCNTs and the reinforced matrix. With only 2.1 wt % BISS-SWCNTs added, the tensile strength and Young's modulus of the BISS-SWCNTs/PMMA composites can be improved by 300%. More importantly, the BISS-SWCNTs also retain the high conductivity and transmittance of the pristine SWCNTs film. This unique bioinspired material will be of great importance in applications of multifunctional composite materials and has important implications for the future of biomimetic materials.

Biostratigraphic and chemostratigraphic correlation of Neoproterozoic sedimentary successions: upper Tindir Group, northwestern Canada, as a test case

NASA Technical Reports Server (NTRS)

Kaufman, A. J.; Knoll, A. H.; Awramik, S. M.

1992-01-01

Recent advances in Proterozoic micropaleontology and sedimentary isotope geochemistry suggest that improved interbasinal correlation of Neoproterozoic (1000-540 Ma) successions is possible. Because widely varying interpretations of its age have been suggested and no reliable radiometric dates or paleomagnetic data are available, the upper Tindir Group of northwestern Canada provides an opportunity to test this hypothesis. The age of these strata is of paleontological importance because silicified carbonates near the top of the group contain disc-shaped-scale microfossils that may provide insights into the early evolution of biomineralization. A reinterpretation of upper Tindir microfossil assemblages suggests a late Riphean age. Although diagenesis and contact metamorphism have altered the isotopic compositions of some carbonates, least altered samples indicate that delta 13C of contemporaneous seawater was at least +4.7%, typical of Neoproterozoic, but not Cambrian, carbonates. Strontium isotopic compositions of the least altered samples yield values of approximately 0.7065, which can be uniquely correlated with late Riphean seawater. Together, micropaleontology and the isotopic tracers of C and Sr constrain the upper Tindir carbonates and their unique fossils to be late Riphean, likely between 620 and 780 Ma.

Idiosyncratic Patterns of Representational Similarity in Prefrontal Cortex Predict Attentional Performance.

PubMed

Lee, Jeongmi; Geng, Joy J

2017-02-01

The efficiency of finding an object in a crowded environment depends largely on the similarity of nontargets to the search target. Models of attention theorize that the similarity is determined by representations stored within an "attentional template" held in working memory. However, the degree to which the contents of the attentional template are individually unique and where those idiosyncratic representations are encoded in the brain are unknown. We investigated this problem using representational similarity analysis of human fMRI data to measure the common and idiosyncratic representations of famous face morphs during an identity categorization task; data from the categorization task were then used to predict performance on a separate identity search task. We hypothesized that the idiosyncratic categorical representations of the continuous face morphs would predict their distractability when searching for each target identity. The results identified that patterns of activation in the lateral prefrontal cortex (LPFC) as well as in face-selective areas in the ventral temporal cortex were highly correlated with the patterns of behavioral categorization of face morphs and search performance that were common across subjects. However, the individually unique components of the categorization behavior were reliably decoded only in right LPFC. Moreover, the neural pattern in right LPFC successfully predicted idiosyncratic variability in search performance, such that reaction times were longer when distractors had a higher probability of being categorized as the target identity. These results suggest that the prefrontal cortex encodes individually unique components of categorical representations that are also present in attentional templates for target search. Everyone's perception of the world is uniquely shaped by personal experiences and preferences. Using functional MRI, we show that individual differences in the categorization of face morphs between two identities could be decoded from the prefrontal cortex and the ventral temporal cortex. Moreover, the individually unique representations in prefrontal cortex predicted idiosyncratic variability in attentional performance when looking for each identity in the "crowd" of another morphed face in a separate search task. Our results reveal that the representation of task-related information in prefrontal cortex is individually unique and preserved across categorization and search performance. This demonstrates the possibility of predicting individual behaviors across tasks with patterns of brain activity. Copyright © 2017 the authors 0270-6474/17/371257-12$15.00/0.

A Code Division Design Strategy for Multiplexing Fiber Bragg Grating Sensing Networks

PubMed Central

Varón, Margarita

2017-01-01

In this paper, an encoding strategy is used to design specialized fiber Bragg grating (FBG) sensors. The encoding of each sensor requires two binary codewords to define the amplitude and phase patterns of each sensor. The combined pattern (amplitude and phase) makes each sensor unique and therefore two or more sensors can be identified under spectral overlapping. In this way, we add another dimension to the multiplexing of FBG sensors, obtaining an increase factor ‘n’ to enhance the number of sensors that the system can handle. A proof-of-concept scenario with three sensors was performed, including the manufacturing of the encoded sensors. Furthermore, an interrogation setup to detect the sensors central wavelength was proposed and its working principle was theoretically developed. Results show that total identification of the central wavelength is performed under spectral overlapping between the manufactured sensors, achieving a three-time improvement of the system capacity. Finally, the error due to overlapping between the sensors was assessed obtaining approximately 3 pm, which makes the approach suitable for use in real measurement systems. PMID:29104231

Identification of the Gene Encoding Isoprimeverose-producing Oligoxyloglucan Hydrolase in Aspergillus oryzae*

PubMed Central

Matsuzawa, Tomohiko; Mitsuishi, Yasushi; Kameyama, Akihiko

2016-01-01

Aspergillus oryzae produces a unique β-glucosidase, isoprimeverose-producing oligoxyloglucan hydrolase (IPase), that recognizes and releases isoprimeverose (α-d-xylopyranose-(1→6)-d-glucopyranose) units from the non-reducing ends of oligoxyloglucans. A gene encoding A. oryzae IPase, termed ipeA, was identified and expressed in Pichia pastoris. With the exception of cellobiose, IpeA hydrolyzes a variety of oligoxyloglucans and is a member of the glycoside hydrolase family 3. Xylopyranosyl branching at the non-reducing ends was vital for IPase activity, and galactosylation at a α-1,6-linked xylopyranosyl side chain completely abolished IpeA activity. Hepta-oligoxyloglucan saccharide (Xyl3Glc4) substrate was preferred over tri- (Xyl1Glc2) and tetra- (Xyl2Glc2) oligoxyloglucan saccharides substrates. IpeA transferred isoprimeverose units to other saccharides, indicating transglycosylation activity. The ipeA gene was expressed in xylose and xyloglucan media and was strongly induced in the presence of xyloglucan endo-xyloglucanase-hydrolyzed products. This is the first study to report the identification of a gene encoding IPase in eukaryotes. PMID:26755723

The Genome of the Obligately Intracellular Bacterium Ehrlichia canis Reveals Themes of Complex Membrane Structure and Immune Evasion Strategies

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

Mavromatis, K; Doyle, C Kuyler; Lykidis, A

2006-01-01

Ehrlichia canis, a small obligately intracellular, tick-transmitted, gram-negative, {alpha}-proteobacterium, is the primary etiologic agent of globally distributed canine monocytic ehrlichiosis. Complete genome sequencing revealed that the E. canis genome consists of a single circular chromosome of 1,315,030 bp predicted to encode 925 proteins, 40 stable RNA species, 17 putative pseudogenes, and a substantial proportion of noncoding sequence (27%). Interesting genome features include a large set of proteins with transmembrane helices and/or signal sequences and a unique serine-threonine bias associated with the potential for O glycosylation that was prominent in proteins associated with pathogen-host interactions. Furthermore, two paralogous protein families associatedmore » with immune evasion were identified, one of which contains poly(G-C) tracts, suggesting that they may play a role in phase variation and facilitation of persistent infections. Genes associated with pathogen-host interactions were identified, including a small group encoding proteins (n = 12) with tandem repeats and another group encoding proteins with eukaryote-like ankyrin domains (n = 7).« less

Measuring sickle cell morphology in flow using spectrally encoded flow cytometry (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kviatkovsky, Inna; Zeidan, Adel; Yeheskely-Hayon, Daniella; Dann, Eldad J.; Yelin, Dvir

2017-02-01

During a sickle cell crisis in sickle cell anemia patients, deoxygenated red blood cells may change their mechanical properties and block small blood vessels, causing pain, local tissue damage and even organ failure. Measuring these cellular structural and morphological changes is important for understanding the factors contributing to vessel blockage and developing an effective treatment. In this work, we use spectrally encoded flow cytometry for confocal, high-resolution imaging of flowing blood cells from sickle cell anemia patients. A wide variety of cell morphologies were observed by analyzing the interference patterns resulting from reflections from the front and back faces of the cells' membrane. Using numerical simulation for calculating the two-dimensional reflection pattern from the cells, we propose an analytical expression for the three-dimensional shape of a characteristic sickle cell and compare it to a previous from the literature. In vitro spectrally encoded flow cytometry offers new means for analyzing the morphology of sickle cells in stress-free environment, and could provide an effective tool for studying the unique physiological properties of these cells.

Item-specific processing reduces false memories.

PubMed

McCabe, David P; Presmanes, Alison G; Robertson, Chuck L; Smith, Anderson D

2004-12-01

We examined the effect of item-specific and relational encoding instructions on false recognition in two experiments in which the DRM paradigm was used (Deese, 1959; Roediger & McDermott, 1995). Type of encoding (item-specific or relational) was manipulated between subjects in Experiment 1 and within subjects in Experiment 2. Decision-based explanations (e.g., the distinctiveness heuristic) predict reductions in false recognition in between-subjects designs, but not in within-subjects designs, because they are conceptualized as global shifts in decision criteria. Memory-based explanations predict reductions in false recognition in both designs, resulting from enhanced recollection of item-specific details. False recognition was reduced following item-specific encoding instructions in both experiments, favoring a memory-based explanation. These results suggest that providing unique cues for the retrieval of individual studied items results in enhanced discrimination between those studied items and critical lures. Conversely, enhancing the similarity of studied items results in poor discrimination among items within a particular list theme. These results are discussed in terms of the item-specific/ relational framework (Hunt & McDaniel, 1993).

Synthesis and structure-activity relationship of the first nonpeptidergic inverse agonists for the human cytomegalovirus encoded chemokine receptor US28.

PubMed

Hulshof, Janneke W; Casarosa, Paola; Menge, Wiro M P B; Kuusisto, Leena M S; van der Goot, Henk; Smit, Martine J; de Esch, Iwan J P; Leurs, Rob

2005-10-06

US28 is a human cytomegalovirus (HCMV) encoded G-protein-coupled receptor that signals in a constitutively active manner. Recently, we identified 1 [5-(4-(4-chlorophenyl)-4-hydroxypiperidin-1-yl)-2,2-diphenylpentanenitrile] as the first reported nonpeptidergic inverse agonist for a viral-encoded chemokine receptor. Interestingly, this compound is able to partially inhibit the viral entry of HIV-1. In this study we describe the synthesis of 1 and several of its analogues and unique structure-activity relationships for this first class of small-molecule ligands for the chemokine receptor US28. Moreover, the compounds have been pharmacologically characterized as inverse agonists on US28. By modification of lead structure 1, it is shown that a 4-phenylpiperidine moiety is essential for affinity and activity. Other structural features of 1 are shown to be of less importance. These compounds define the first SAR of ligands on a viral GPCR (US28) and may therefore serve as important tools to investigate the significance of US28-mediated constitutive activity during viral infection.

Distinct roles of visual, parietal, and frontal motor cortices in memory-guided sensorimotor decisions

PubMed Central

Goard, Michael J; Pho, Gerald N; Woodson, Jonathan; Sur, Mriganka

2016-01-01

Mapping specific sensory features to future motor actions is a crucial capability of mammalian nervous systems. We investigated the role of visual (V1), posterior parietal (PPC), and frontal motor (fMC) cortices for sensorimotor mapping in mice during performance of a memory-guided visual discrimination task. Large-scale calcium imaging revealed that V1, PPC, and fMC neurons exhibited heterogeneous responses spanning all task epochs (stimulus, delay, response). Population analyses demonstrated unique encoding of stimulus identity and behavioral choice information across regions, with V1 encoding stimulus, fMC encoding choice even early in the trial, and PPC multiplexing the two variables. Optogenetic inhibition during behavior revealed that all regions were necessary during the stimulus epoch, but only fMC was required during the delay and response epochs. Stimulus identity can thus be rapidly transformed into behavioral choice, requiring V1, PPC, and fMC during the transformation period, but only fMC for maintaining the choice in memory prior to execution. DOI: http://dx.doi.org/10.7554/eLife.13764.001 PMID:27490481

Methylotrophic Methylobacterium Bacteria Nodulate and Fix Nitrogen in Symbiosis with Legumes

PubMed Central

Sy, Abdoulaye; Giraud, Eric; Jourand, Philippe; Garcia, Nelly; Willems, Anne; de Lajudie, Philippe; Prin, Yves; Neyra, Marc; Gillis, Monique; Boivin-Masson, Catherine; Dreyfus, Bernard

2001-01-01

Rhizobia described so far belong to three distinct phylogenetic branches within the α-2 subclass of Proteobacteria. Here we report the discovery of a fourth rhizobial branch involving bacteria of the Methylobacterium genus. Rhizobia isolated from Crotalaria legumes were assigned to a new species, “Methylobacterium nodulans,” within the Methylobacterium genus on the basis of 16S ribosomal DNA analyses. We demonstrated that these rhizobia facultatively grow on methanol, which is a characteristic of Methylobacterium spp. but a unique feature among rhizobia. Genes encoding two key enzymes of methylotrophy and nodulation, the mxaF gene, encoding the α subunit of the methanol dehydrogenase, and the nodA gene, encoding an acyltransferase involved in Nod factor biosynthesis, were sequenced for the type strain, ORS2060. Plant tests and nodA amplification assays showed that “M. nodulans” is the only nodulating Methylobacterium sp. identified so far. Phylogenetic sequence analysis showed that “M. nodulans” NodA is closely related to Bradyrhizobium NodA, suggesting that this gene was acquired by horizontal gene transfer. PMID:11114919

Synthesis of carbon nanotubes over 3D cubical Co-KIT-6 and nickel decorated graphene by Hummer's method, its application as counter electrode in dye sensitive solar cell

NASA Astrophysics Data System (ADS)

Subramanian, Sunu; Pandurangan, Arumugam

2016-04-01

The challenges on carbon nanotubes and graphene are still the subject of many research works due to its unique properties. There are three main methods to synthesis carbon nanotubes in which chemical vapor deposition (CVD) method can use for large scale production. The principle of CVD is the decomposition of various hydrocarbons over transition metal supported catalyst. KIT-6 molecular sieve was used as a support to prepare cobalt catalyst for CVD method using metal impregnation method to produce cobalt loadings of 2, 4 and 6 wt%. The catalysts were characterized by XRD, FTIR &TEM. Carbon nanotubes (CNTs) synthesized on Co-KIT-6 was also characterized by XRD, TGA, SEM & Raman spectra. Graphene was synthesized by Hummers method, which is the most common method for preparing graphene oxide. Graphene oxide was prepared by oxidation of graphite using some oxidizing agents like sulphuric acid, sodium nitrate and potassium permanganate. This graphene oxide is further treated with hydrazine solution to convert it into chemically converted graphene and also decorated with nickel metal and characterized. Hummer's method is important for large scale production of graphene. Both Graphene and carbon nanotubes are used in different fields due to its unique properties. Both Graphene and carbon nanotubes are fabricated in counter electrode of Dye sensitized solar cells (DSSC). By cyclic voltammetry study, it confirms that both materials are good and efficient to replace platinum in the DSSC.

High performance carbon fibers from very high molecular weight polyacrylonitrile precursors

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

Morris, E. Ashley; Weisenberger, Matthew C.; Abdallah, Mohamed G.

In this study, carbon fibers are unique reinforcing agents for lightweight composite materials due to their outstanding mechanical properties and low density. Current technologies are capable of producing carbon fibers with 90-95% of the modulus of perfect graphite (~1025 GPa). However, these same carbon fibers possess less than 10% of the theoretical carbon fiber strength, estimated to be about 100 GPa.[1] Indeed, attempts to increase carbon fiber rigidity results in lower breaking strength. To develop advanced carbon fibers with both very high strength and modulus demands a new manufacturing methodology. Here, we report a method of manufacturing high strength, verymore » high modulus carbon fibers from a very high molecular weight (VHMW) polyacrylonitrile (PAN) precursor without the use of nanomaterial additives such as nucleating or structure-templating agents, as have been used by others.[2,3]« less

High performance carbon fibers from very high molecular weight polyacrylonitrile precursors

DOE PAGES

Morris, E. Ashley; Weisenberger, Matthew C.; Abdallah, Mohamed G.; ...

2016-02-02

In this study, carbon fibers are unique reinforcing agents for lightweight composite materials due to their outstanding mechanical properties and low density. Current technologies are capable of producing carbon fibers with 90-95% of the modulus of perfect graphite (~1025 GPa). However, these same carbon fibers possess less than 10% of the theoretical carbon fiber strength, estimated to be about 100 GPa.[1] Indeed, attempts to increase carbon fiber rigidity results in lower breaking strength. To develop advanced carbon fibers with both very high strength and modulus demands a new manufacturing methodology. Here, we report a method of manufacturing high strength, verymore » high modulus carbon fibers from a very high molecular weight (VHMW) polyacrylonitrile (PAN) precursor without the use of nanomaterial additives such as nucleating or structure-templating agents, as have been used by others.[2,3]« less

High-performance reactionless scan mechanism

NASA Technical Reports Server (NTRS)

Williams, Ellen I.; Summers, Richard T.; Ostaszewski, Miroslaw A.

1995-01-01

A high-performance reactionless scan mirror mechanism was developed for space applications to provide thermal images of the Earth. The design incorporates a unique mechanical means of providing reactionless operation that also minimizes weight, mechanical resonance operation to minimize power, combined use of a single optical encoder to sense coarse and fine angular position, and a new kinematic mount of the mirror. A flex pivot hardware failure and current project status are discussed.

Safety and efficacy of a backpassaged rMd5-delta-Meq vaccine virus in chickens

USDA-ARS?s Scientific Manuscript database

Marek’s disease virus EcoR1-Q fragment of the viral genome encodes meq (MDV EcoQ) gene. Meq is an unique oncogene, present only in serotype 1 MDV and is consistently expressed in all latent or tumor cells. The meq gene was deleted from the very virulent rMd5 genome and was designated as rMd5-delta-M...

Unexpected link between polyketide synthase and calcium carbonate biomineralization.

PubMed

Hojo, Motoki; Omi, Ai; Hamanaka, Gen; Shindo, Kazutoshi; Shimada, Atsuko; Kondo, Mariko; Narita, Takanori; Kiyomoto, Masato; Katsuyama, Yohei; Ohnishi, Yasuo; Irie, Naoki; Takeda, Hiroyuki

2015-01-01

Calcium carbonate biominerals participate in diverse physiological functions. Despite intensive studies, little is known about how mineralization is initiated in organisms. We analyzed the medaka spontaneous mutant, ha, defective in otolith (calcareous ear stone) formation. ha lacks a trigger for otolith mineralization, and the causative gene was found to encode polyketide synthase (pks), a multifunctional enzyme mainly found in bacteria, fungi, and plant. Subsequent experiments demonstrate that the products of medaka PKS, most likely polyketides or their derivatives, act as nucleation facilitators in otolith mineralization. The generality of this novel PKS function is supported by the essential role of echinoderm PKS in calcareous skeleton formation together with the presence of PKSs in a much wider range of animals from coral to vertebrates. The present study first links PKS to biomineralization and provides a genetic cue for biogeochemistry of carbon and calcium cycles.

Identification of proteins from Mycobacterium tuberculosis missing in attenuated Mycobacterium bovis BCG strains.

PubMed

Mattow, J; Jungblut, P R; Schaible, U E; Mollenkopf, H J; Lamer, S; Zimny-Arndt, U; Hagens, K; Müller, E C; Kaufmann, S H

2001-08-01

A proteome approach, combining high-resolution two-dimensional electrophoresis (2-DE) with mass spectrometry, was used to compare the cellular protein composition of two virulent strains of Mycobacterium tuberculosis with two attenuated strains of Mycobacterium bovis Bacillus Calmette-Guerin (BCG), in order to identify unique proteins of these strains. Emphasis was given to the identification of M. tuberculosis specific proteins, because we consider these proteins to represent putative virulence factors and interesting candidates for vaccination and diagnosis of tuberculosis. The genome of M. tuberculosis strain H37Rv comprises nearly 4000 predicted open reading frames. In contrast, the separation of proteins from whole mycobacterial cells by 2-DE resulted in silver-stained patterns comprising about 1800 distinct protein spots. Amongst these, 96 spots were exclusively detected either in the virulent (56 spots) or in the attenuated (40 spots) mycobacterial strains. Fifty-three of these spots were analyzed by mass spectrometry, of which 41 were identified, including 32 M. tuberculosis specific spots. Twelve M. tuberculosis specific spots were identified as proteins, encoded by genes previously reported to be deleted in M. bovis BCG. The remaining 20 spots unique for M. tuberculosis were identified as proteins encoded by genes that are not known to be missing in M. bovis BCG.

Robust extrema features for time-series data analysis.

PubMed

Vemulapalli, Pramod K; Monga, Vishal; Brennan, Sean N

2013-06-01

The extraction of robust features for comparing and analyzing time series is a fundamentally important problem. Research efforts in this area encompass dimensionality reduction using popular signal analysis tools such as the discrete Fourier and wavelet transforms, various distance metrics, and the extraction of interest points from time series. Recently, extrema features for analysis of time-series data have assumed increasing significance because of their natural robustness under a variety of practical distortions, their economy of representation, and their computational benefits. Invariably, the process of encoding extrema features is preceded by filtering of the time series with an intuitively motivated filter (e.g., for smoothing), and subsequent thresholding to identify robust extrema. We define the properties of robustness, uniqueness, and cardinality as a means to identify the design choices available in each step of the feature generation process. Unlike existing methods, which utilize filters "inspired" from either domain knowledge or intuition, we explicitly optimize the filter based on training time series to optimize robustness of the extracted extrema features. We demonstrate further that the underlying filter optimization problem reduces to an eigenvalue problem and has a tractable solution. An encoding technique that enhances control over cardinality and uniqueness is also presented. Experimental results obtained for the problem of time series subsequence matching establish the merits of the proposed algorithm.

Molecular Genetic Analysis of Orf Virus: A Poxvirus That Has Adapted to Skin

PubMed Central

Fleming, Stephen B.; Wise, Lyn M.; Mercer, Andrew A.

2015-01-01

Orf virus is the type species of the Parapoxvirus genus of the family Poxviridae. It induces acute pustular skin lesions in sheep and goats and is transmissible to humans. The genome is G+C rich, 138 kbp and encodes 132 genes. It shares many essential genes with vaccinia virus that are required for survival but encodes a number of unique factors that allow it to replicate in the highly specific immune environment of skin. Phylogenetic analysis suggests that both viral interleukin-10 and vascular endothelial growth factor genes have been “captured” from their host during the evolution of the parapoxviruses. Genes such as a chemokine binding protein and a protein that binds granulocyte-macrophage colony-stimulating factor and interleukin-2 appear to have evolved from a common poxvirus ancestral gene while three parapoxvirus nuclear factor (NF)-κB signalling pathway inhibitors have no homology to other known NF-κB inhibitors. A homologue of an anaphase-promoting complex subunit that is believed to manipulate the cell cycle and enhance viral DNA synthesis appears to be a specific adaptation for viral-replication in keratinocytes. The review focuses on the unique genes of orf virus, discusses their evolutionary origins and their role in allowing viral-replication in the skin epidermis. PMID:25807056

Transcriptional transitions in Alphonso mango (Mangifera indica L.) during fruit development and ripening explain its distinct aroma and shelf life characteristics.

PubMed

Deshpande, Ashish B; Anamika, Krishanpal; Jha, Vineet; Chidley, Hemangi G; Oak, Pranjali S; Kadoo, Narendra Y; Pujari, Keshav H; Giri, Ashok P; Gupta, Vidya S

2017-08-18

Alphonso is known as the "King of mangos" due to its unique flavor, attractive color, low fiber pulp and long shelf life. We analyzed the transcriptome of Alphonso mango through Illumina sequencing from seven stages of fruit development and ripening as well as flower. Total transcriptome data from these stages ranged between 65 and 143 Mb. Importantly, 20,755 unique transcripts were annotated and 4,611 were assigned enzyme commission numbers, which encoded 142 biological pathways. These included ethylene and flavor related secondary metabolite biosynthesis pathways, as well as those involved in metabolism of starch, sucrose, amino acids and fatty acids. Differential regulation (p-value ≤ 0.05) of thousands of transcripts was evident in various stages of fruit development and ripening. Novel transcripts for biosynthesis of mono-terpenes, sesqui-terpenes, di-terpenes, lactones and furanones involved in flavor formation were identified. Large number of transcripts encoding cell wall modifying enzymes was found to be steady in their expression, while few were differentially regulated through these stages. Novel 79 transcripts of inhibitors of cell wall modifying enzymes were simultaneously detected throughout Alphonso fruit development and ripening, suggesting controlled activity of these enzymes involved in fruit softening.

Candida glabrata's Genome Plasticity Confers a Unique Pattern of Expressed Cell Wall Proteins.

PubMed

López-Fuentes, Eunice; Gutiérrez-Escobedo, Guadalupe; Timmermans, Bea; Van Dijck, Patrick; De Las Peñas, Alejandro; Castaño, Irene

2018-06-05

Candida glabrata is the second most common cause of candidemia, and its ability to adhere to different host cell types, to microorganisms, and to medical devices are important virulence factors. Here, we consider three characteristics that confer extraordinary advantages to C. glabrata within the host. (1) C. glabrata has a large number of genes encoding for adhesins most of which are localized at subtelomeric regions. The number and sequence of these genes varies substantially depending on the strain, indicating that C. glabrata can tolerate high genomic plasticity; (2) The largest family of CWPs (cell wall proteins) is the EPA (epithelial adhesin) family of adhesins. Epa1 is the major adhesin and mediates adherence to epithelial, endothelial and immune cells. Several layers of regulation like subtelomeric silencing, cis- acting regulatory regions, activators, nutritional signaling, and stress conditions tightly regulate the expression of many adhesin-encoding genes in C. glabrata , while many others are not expressed. Importantly, there is a connection between acquired resistance to xenobiotics and increased adherence; (3) Other subfamilies of adhesins mediate adherence to Candida albicans , allowing C. glabrata to efficiently invade the oral epithelium and form robust biofilms. It is noteworthy that every C. glabrata strain analyzed presents a unique pattern of CWPs at the cell surface.

Metagenomic insights into the rumen microbial fibrolytic enzymes in Indian crossbred cattle fed finger millet straw.

PubMed

Jose, V Lyju; Appoothy, Thulasi; More, Ravi P; Arun, A Sha

2017-12-01

The rumen is a unique natural habitat, exhibiting an unparalleled genetic resource of fibrolytic enzymes of microbial origin that degrade plant polysaccharides. The objectives of this study were to identify the principal plant cell wall-degrading enzymes and the taxonomic profile of rumen microbial communities that are associated with it. The cattle rumen microflora and the carbohydrate-active enzymes were functionally classified through a whole metagenomic sequencing approach. Analysis of the assembled sequences by the Carbohydrate-active enzyme analysis Toolkit identified the candidate genes encoding fibrolytic enzymes belonging to different classes of glycoside hydrolases(11,010 contigs), glycosyltransferases (6366 contigs), carbohydrate esterases (4945 contigs), carbohydrate-binding modules (1975 contigs), polysaccharide lyases (480 contigs), and auxiliary activities (115 contigs). Phylogenetic analysis of CAZyme encoding contigs revealed that a significant proportion of CAZymes were contributed by bacteria belonging to genera Prevotella, Bacteroides, Fibrobacter, Clostridium, and Ruminococcus. The results indicated that the cattle rumen microbiome and the CAZymes are highly complex, structurally similar but compositionally distinct from other ruminants. The unique characteristics of rumen microbiota and the enzymes produced by resident microbes provide opportunities to improve the feed conversion efficiency in ruminants and serve as a reservoir of industrially important enzymes for cellulosic biofuel production.

Frequency-Modulated Continuous Flow Analysis Electrospray Ionization Mass Spectrometry (FM-CFA-ESI-MS) for Sample Multiplexing.

PubMed

Filla, Robert T; Schrell, Adrian M; Coulton, John B; Edwards, James L; Roper, Michael G

2018-02-20

A method for multiplexed sample analysis by mass spectrometry without the need for chemical tagging is presented. In this new method, each sample is pulsed at unique frequencies, mixed, and delivered to the mass spectrometer while maintaining a constant total flow rate. Reconstructed ion currents are then a time-dependent signal consisting of the sum of the ion currents from the various samples. Spectral deconvolution of each reconstructed ion current reveals the identity of each sample, encoded by its unique frequency, and its concentration encoded by the peak height in the frequency domain. This technique is different from other approaches that have been described, which have used modulation techniques to increase the signal-to-noise ratio of a single sample. As proof of concept of this new method, two samples containing up to 9 analytes were multiplexed. The linear dynamic range of the calibration curve was increased with extended acquisition times of the experiment and longer oscillation periods of the samples. Because of the combination of the samples, salt had little effect on the ability of this method to achieve relative quantitation. Continued development of this method is expected to allow for increased numbers of samples that can be multiplexed.

A novel cysteine desulfurase influencing organosulfur compounds in Lentinula edodes

PubMed Central

Liu, Ying; Lei, Xiao-Yu; Chen, Lian-Fu; Bian, Yin-Bing; Yang, Hong; Ibrahim, Salam A.; Huang, Wen

2015-01-01

Organosulfur compounds are the basis for the unique aroma of Lentinula edodes, and cysteine sulfoxide lyase (C-S lyase) is the key enzyme in this trait. The enzyme from Alliium sativum has been crystallized and well-characterized; however, there have been no reports of the characterization of fungi C-S lyase at the molecular level. We identified a L. edodes C-S lyase (Lecsl), cloned a gene of Csl encoded Lecsl and then combined modeling, simulations, and experiments to understand the molecular basis of the function of Lecsl. Our analysis revealed Lecsl to be a novel cysteine desulfurase and not a type of cysteine sulfoxide lyase. The pyridoxal-5-phosphate (PLP) molecule bonded tightly to Lecsl to form a Lecsl-PLP complex. Moreover, the Lecsl had one active center that served to bind two kinds of substrates, S-methyl-L-cysteine sulfoxide and L-cysteine, and had both cysteine sulfoxide lyase and cysteine desulfurase activity. We found that the amino acid residue Asn393 was essential for the catalytic activity of Lecsl and that the gene Csl encoded a novel cysteine desulfurase to influence organosulfur compounds in L. edodes. Our results provide a new insight into understanding the formation of the unique aroma of L. edodes. PMID:26054293

A novel cysteine desulfurase influencing organosulfur compounds in Lentinula edodes.

PubMed

Liu, Ying; Lei, Xiao-Yu; Chen, Lian-Fu; Bian, Yin-Bing; Yang, Hong; Ibrahim, Salam A; Huang, Wen

2015-06-09

Organosulfur compounds are the basis for the unique aroma of Lentinula edodes, and cysteine sulfoxide lyase (C-S lyase) is the key enzyme in this trait. The enzyme from Alliium sativum has been crystallized and well-characterized; however, there have been no reports of the characterization of fungi C-S lyase at the molecular level. We identified a L. edodes C-S lyase (Lecsl), cloned a gene of Csl encoded Lecsl and then combined modeling, simulations, and experiments to understand the molecular basis of the function of Lecsl. Our analysis revealed Lecsl to be a novel cysteine desulfurase and not a type of cysteine sulfoxide lyase. The pyridoxal-5-phosphate (PLP) molecule bonded tightly to Lecsl to form a Lecsl-PLP complex. Moreover, the Lecsl had one active center that served to bind two kinds of substrates, S-methyl-L-cysteine sulfoxide and L-cysteine, and had both cysteine sulfoxide lyase and cysteine desulfurase activity. We found that the amino acid residue Asn393 was essential for the catalytic activity of Lecsl and that the gene Csl encoded a novel cysteine desulfurase to influence organosulfur compounds in L. edodes. Our results provide a new insight into understanding the formation of the unique aroma of L. edodes.

The Crc protein inhibits the production of polyhydroxyalkanoates in Pseudomonas putida under balanced carbon/nitrogen growth conditions.

PubMed

La Rosa, Ruggero; de la Peña, Fernando; Prieto, María Axiliadora; Rojo, Fernando

2014-01-01

Pseudomonas putida synthesizes polyhydroxyalkanoates (PHAs) as storage compounds. PHA synthesis is more active when the carbon source is in excess and the nitrogen source is limiting, but can also occur at a lower rate under balanced carbon/nitrogen ratios. This work shows that PHA synthesis is controlled by the Crc global regulator, a protein that optimizes carbon metabolism by inhibiting the expression of genes involved in the use of non-preferred carbon sources. Crc acts post-transcriptionally. The mRNAs of target genes contain characteristic catabolite activity (CA) motifs near the ribosome binding site. Sequences resembling CA motifs can be predicted for the phaC1 gene, which codes for a PHA polymerase, and for phaI and phaF, which encode proteins associated to PHA granules. Our results show that Crc inhibits the translation of phaC1 mRNA, but not that of phaI or phaF, reducing the amount of PHA accumulated in the cell. Crc inhibited PHA synthesis during exponential growth in media containing a balanced carbon/nitrogen ratio. No inhibition was seen when the carbon/nitrogen ratio was imbalanced. This extends the role of Crc beyond that of controlling the hierarchical utilization of carbon sources and provides a link between PHA synthesis and the global regulatory networks controlling carbon flow. © 2013 Society for Applied Microbiology and John Wiley & Sons Ltd.

3D hybrid-porous carbon derived from carbonization of metal organic frameworks for high performance supercapacitors

NASA Astrophysics Data System (ADS)

Bao, Weizhai; Mondal, Anjon Kumar; Xu, Jing; Wang, Chengyin; Su, Dawei; Wang, Guoxiu

2016-09-01

We report a rational design and synthesis of 3D hybrid-porous carbon with a hierarchical pore architecture for high performance supercapacitors. It contains micropores (<2 nm diameter) and mesopores (2-4 nm), derived from carbonization of unique porous metal organic frameworks (MOFs). Owning to the synergistic effect of micropores and mesopores, the hybrid-porous carbon has exceptionally high ion-accessible surface area and low ion diffusion resistance, which is desired for supercapacitor applications. When applied as electrode materials in supercapacitors, 3D hybrid-porous carbon demonstrates a specific capacitance of 332 F g-1 at a constant charge/discharge current of 500 mA g-1. The supercapacitors can endure more than 10,000 cycles without degradation of capacitance.

Carbon-doped BN nanosheets for metal-free photoredox catalysis

PubMed Central

Huang, Caijin; Chen, Cheng; Zhang, Mingwen; Lin, Lihua; Ye, Xinxin; Lin, Sen; Antonietti, Markus; Wang, Xinchen

2015-01-01

The generation of sustainable and stable semiconductors for solar energy conversion by photoredox catalysis, for example, light-induced water splitting and carbon dioxide reduction, is a key challenge of modern materials chemistry. Here we present a simple synthesis of a ternary semiconductor, boron carbon nitride, and show that it can catalyse hydrogen or oxygen evolution from water as well as carbon dioxide reduction under visible light illumination. The ternary B–C–N alloy features a delocalized two-dimensional electron system with sp2 carbon incorporated in the h-BN lattice where the bandgap can be adjusted by the amount of incorporated carbon to produce unique functions. Such sustainable photocatalysts made of lightweight elements facilitate the innovative construction of photoredox cascades to utilize solar energy for chemical conversion. PMID:26159752

Improvement of L-phenylalanine production from glycerol by recombinant Escherichia coli strains: The role of extra copies of glpK, glpX, and tktA genes

PubMed Central

2014-01-01

Background For the production of L-phenylalanine (L-Phe), two molecules of phosphoenolpyruvate (PEP) and one molecule erythrose-4-phosphate (E4P) are necessary. PEP stems from glycolysis whereas E4P is formed in the pentose phosphate pathway (PPP). Glucose, commonly used for L-Phe production with recombinant E. coli, is taken up via the PEP-dependent phosphotransferase system which delivers glucose-6-phosphate (G6P). G6P enters either glycolysis or the PPP. In contrast, glycerol is phosphorylated by an ATP-dependent glycerol kinase (GlpK) thus saving one PEP. However, two gluconeogenic reactions (fructose-1,6-bisphosphate aldolase, fructose-1,6-bisphosphatase, FBPase) are necessary for growth and provision of E4P. Glycerol has become an important carbon source for biotechnology and reports on production of L-Phe from glycerol are available. However, the influence of FBPase and transketolase reactions on L-Phe production has not been reported. Results L-Phe productivity of parent strain FUS4/pF81 (plasmid-encoded genes for aroF, aroB, aroL, pheA) was compared on glucose and glycerol as C sources. On glucose, a maximal carbon recovery of 0.19 mM CPhe/CGlucose and a maximal space-time-yield (STY) of 0.13 g l−1 h−1 was found. With glycerol, the maximal carbon recovery was nearly the same (0.18 mM CPhe/CGlycerol), but the maximal STY was higher (0.21 g l−1 h−1). We raised the chromosomal gene copy number of the genes glpK (encoding glycerol kinase), tktA (encoding transketolase), and glpX (encoding fructose-1,6-bisphosphatase) individually. Overexpression of glpK (or its feedback-resistant variant, glpKG232D) had little effect on growth rate; L-Phe production was about 30% lower than in FUS4/pF81. Whereas the overexpression of either glpX or tktA had minor effects on productivity (0.20 mM CPhe/CGlycerol; 0.25 g l−1 h−1 and 0.21 mM CPhe/CGlycerol; 0.23 g l−1 h−1, respectively), the combination of extra genes of glpX and tktA together led to an increase in maximal STY of about 80% (0.37 g l−1 h−1) and a carbon recovery of 0.26 mM CPhe/CGlycerol. Conclusions Enhancing the gene copy numbers for glpX and tktA increased L-Phe productivity from glycerol without affecting growth rate. Engineering of glycerol metabolism towards L-Phe production in E. coli has to balance the pathways of gluconeogenesis, glycolysis, and PPP to improve the supply of the precursors, PEP and E4P. PMID:25012491

Improvement of L-phenylalanine production from glycerol by recombinant Escherichia coli strains: the role of extra copies of glpK, glpX, and tktA genes.

PubMed

Gottlieb, Katrin; Albermann, Christoph; Sprenger, Georg A

2014-07-11

For the production of L-phenylalanine (L-Phe), two molecules of phosphoenolpyruvate (PEP) and one molecule erythrose-4-phosphate (E4P) are necessary. PEP stems from glycolysis whereas E4P is formed in the pentose phosphate pathway (PPP). Glucose, commonly used for L-Phe production with recombinant E. coli, is taken up via the PEP-dependent phosphotransferase system which delivers glucose-6-phosphate (G6P). G6P enters either glycolysis or the PPP. In contrast, glycerol is phosphorylated by an ATP-dependent glycerol kinase (GlpK) thus saving one PEP. However, two gluconeogenic reactions (fructose-1,6-bisphosphate aldolase, fructose-1,6-bisphosphatase, FBPase) are necessary for growth and provision of E4P. Glycerol has become an important carbon source for biotechnology and reports on production of L-Phe from glycerol are available. However, the influence of FBPase and transketolase reactions on L-Phe production has not been reported. L-Phe productivity of parent strain FUS4/pF81 (plasmid-encoded genes for aroF, aroB, aroL, pheA) was compared on glucose and glycerol as C sources. On glucose, a maximal carbon recovery of 0.19 mM C(Phe)/C(Glucose) and a maximal space-time-yield (STY) of 0.13 g l(-1) h(-1) was found. With glycerol, the maximal carbon recovery was nearly the same (0.18 mM C(Phe)/C(Glycerol)), but the maximal STY was higher (0.21 g l(-1) h(-1)). We raised the chromosomal gene copy number of the genes glpK (encoding glycerol kinase), tktA (encoding transketolase), and glpX (encoding fructose-1,6-bisphosphatase) individually. Overexpression of glpK (or its feedback-resistant variant, glpK(G232D)) had little effect on growth rate; L-Phe production was about 30% lower than in FUS4/pF81. Whereas the overexpression of either glpX or tktA had minor effects on productivity (0.20 mM C(Phe)/C(Glycerol); 0.25 g l(-1) h(-1) and 0.21 mM C(Phe)/C(Glycerol); 0.23 g l(-1) h(-1), respectively), the combination of extra genes of glpX and tktA together led to an increase in maximal STY of about 80% (0.37 g l(-1) h(-1)) and a carbon recovery of 0.26 mM C(Phe)/C(Glycerol). Enhancing the gene copy numbers for glpX and tktA increased L-Phe productivity from glycerol without affecting growth rate. Engineering of glycerol metabolism towards L-Phe production in E. coli has to balance the pathways of gluconeogenesis, glycolysis, and PPP to improve the supply of the precursors, PEP and E4P.

Carbon-carbon piston development

NASA Technical Reports Server (NTRS)

Gorton, Mark P.

1994-01-01

A new piston concept, made of carbon-carbon refractory-composite material, has been developed that overcomes a number of the shortcomings of aluminum pistons. Carbon-carbon material, developed in the early 1960's, is lighter in weight than aluminum, has higher strength and stiffness than aluminum and maintains these properties at temperatures over 2500 F. In addition, carbon-carbon material has a low coefficient of thermal expansion and excellent resistance to thermal shock. An effort, called the Advanced Carbon-Carbon Piston Program was started in 1986 to develop and test carbon-carbon pistons for use in spark ignition engines. The carbon-carbon pistons were designed to be replacements for existing aluminum pistons, using standard piston pin assemblies and using standard rings. Carbon-carbon pistons can potentially enable engines to be more reliable, more efficient and have greater power output. By utilizing the unique characteristics of carbon-carbon material a piston can: (1) have greater resistance to structural damage caused by overheating, lean air-fuel mixture conditions and detonation; (2) be designed to be lighter than an aluminum piston thus, reducing the reciprocating mass of an engine, and (3) be operated in a higher combustion temperature environment without failure.

Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR

PubMed Central

Lagares, Antonio; Borella, Germán Ceizel; Linne, Uwe; Becker, Anke

2017-01-01

ABSTRACT Riboregulation has a major role in the fine-tuning of multiple bacterial processes. Among the RNA players, trans-encoded untranslated small RNAs (sRNAs) regulate complex metabolic networks by tuning expression from multiple target genes in response to numerous signals. In Sinorhizobium meliloti, over 400 sRNAs are expressed under different stimuli. The sRNA MmgR (standing for Makes more granules Regulator) has been of particular interest to us since its sequence and structure are highly conserved among the alphaproteobacteria and its expression is regulated by the amount and quality of the bacterium's available nitrogen source. In this work, we explored the biological role of MmgR in S. meliloti 2011 by characterizing the effect of a deletion of the internal conserved core of mmgR (mmgRΔ33–51). This mutation resulted in larger amounts of polyhydroxybutyrate (PHB) distributed into more intracellular granules than are found in the wild-type strain. This phenotype was expressed upon cessation of balanced growth owing to nitrogen depletion in the presence of surplus carbon (i.e., at a carbon/nitrogen molar ratio greater than 10). The normal PHB accumulation was complemented with a wild-type mmgR copy but not with unrelated sRNA genes. Furthermore, the expression of mmgR limited PHB accumulation in the wild type, regardless of the magnitude of the C surplus. Quantitative proteomic profiling and quantitative reverse transcription-PCR (qRT-PCR) revealed that the absence of MmgR results in a posttranscriptional overexpression of both PHB phasin proteins (PhaP1 and PhaP2). Together, our results indicate that the widely conserved alphaproteobacterial MmgR sRNA fine-tunes the regulation of PHB storage in S. meliloti. IMPORTANCE High-throughput RNA sequencing has recently uncovered an overwhelming number of trans-encoded small RNAs (sRNAs) in diverse prokaryotes. In the nitrogen-fixing alphaproteobacterial symbiont of alfalfa root nodules Sinorhizobium meliloti, only four out of hundreds of identified sRNA genes have been functionally characterized. Thus, uncovering the biological role of sRNAs currently represents a major issue and one that is particularly challenging because of the usually subtle quantitative regulation contributed by most characterized sRNAs. Here, we have characterized the function of the broadly conserved alphaproteobacterial sRNA gene mmgR in S. meliloti. Our results strongly suggest that mmgR encodes a negative regulator of the accumulation of polyhydroxybutyrate, the major carbon and reducing power storage polymer in S. meliloti cells growing under conditions of C/N overbalance. PMID:28167519

A novel frequency analysis method for assessing K(ir)2.1 and Na (v)1.5 currents.

PubMed

Rigby, J R; Poelzing, S

2012-04-01

Voltage clamping is an important tool for measuring individual currents from an electrically active cell. However, it is difficult to isolate individual currents without pharmacological or voltage inhibition. Herein, we present a technique that involves inserting a noise function into a standard voltage step protocol, which allows one to characterize the unique frequency response of an ion channel at different step potentials. Specifically, we compute the fast Fourier transform for a family of current traces at different step potentials for the inward rectifying potassium channel, K(ir)2.1, and the channel encoding the cardiac fast sodium current, Na(v)1.5. Each individual frequency magnitude, as a function of voltage step, is correlated to the peak current produced by each channel. The correlation coefficient vs. frequency relationship reveals that these two channels are associated with some unique frequencies with high absolute correlation. The individual IV relationship can then be recreated using only the unique frequencies with magnitudes of high absolute correlation. Thus, this study demonstrates that ion channels may exhibit unique frequency responses.

Electrospun carbon nanofibers surface-grafted with vapor-grown carbon nanotubes as hierarchical electrodes for supercapacitors

NASA Astrophysics Data System (ADS)

Zhou, Zhengping; Wu, Xiang-Fa; Fong, Hao

2012-01-01

This letter reports the fabrication and electrochemical properties of electrospun carbon nanofibers surface-grafted with vapor-grown carbon nanotubes (CNTs) as hierarchical electrodes for supercapacitors. The specific capacitance of the fabricated electrodes was measured up to 185 F/g at the low discharge current density of 625 mA/g; a decrease of 38% was detected at the high discharge current density of 2.5 A/g. The morphology and microstructure of the electrodes were examined by electron microscopy, and the unique connectivity of the hybrid nanomaterials was responsible for the high specific capacitance and low intrinsic contact electric resistance of the hierarchical electrodes.

Penetration of Solar Radiation into Solid Carbon Dioxide

NASA Astrophysics Data System (ADS)

Chinnery, H. E.; Hagermann, A.; Kaufmann, E.; Lewis, S. R.; Grady, M. M.

2017-09-01

Carbon dioxide ice exists naturally on the surface of Mars. This is a unique environment, with no Earth analogues, and so determining the properties of such a surface is important to further our understanding of the Martian environment. Laboratory experiments have determined the e-folding scale, or absorption scale length, for carbon dioxide slab ice, granular ice and snow. This is a universal measure of how transparent a material is to visible light, and so has implications for the radiative budget of carbon dioxide ice covered surfaces, as well as physical processes, such as the so-called spider formations in the cryptic region near the Martian south pole.

Gene Cluster Encoding Cholate Catabolism in Rhodococcus spp.

PubMed Central

Wilbrink, Maarten H.; Casabon, Israël; Stewart, Gordon R.; Liu, Jie; van der Geize, Robert; Eltis, Lindsay D.

2012-01-01

Bile acids are highly abundant steroids with important functions in vertebrate digestion. Their catabolism by bacteria is an important component of the carbon cycle, contributes to gut ecology, and has potential commercial applications. We found that Rhodococcus jostii RHA1 grows well on cholate, as well as on its conjugates, taurocholate and glycocholate. The transcriptome of RHA1 growing on cholate revealed 39 genes upregulated on cholate, occurring in a single gene cluster. Reverse transcriptase quantitative PCR confirmed that selected genes in the cluster were upregulated 10-fold on cholate versus on cholesterol. One of these genes, kshA3, encoding a putative 3-ketosteroid-9α-hydroxylase, was deleted and found essential for growth on cholate. Two coenzyme A (CoA) synthetases encoded in the cluster, CasG and CasI, were heterologously expressed. CasG was shown to transform cholate to cholyl-CoA, thus initiating side chain degradation. CasI was shown to form CoA derivatives of steroids with isopropanoyl side chains, likely occurring as degradation intermediates. Orthologous gene clusters were identified in all available Rhodococcus genomes, as well as that of Thermomonospora curvata. Moreover, Rhodococcus equi 103S, Rhodococcus ruber Chol-4 and Rhodococcus erythropolis SQ1 each grew on cholate. In contrast, several mycolic acid bacteria lacking the gene cluster were unable to grow on cholate. Our results demonstrate that the above-mentioned gene cluster encodes cholate catabolism and is distinct from a more widely occurring gene cluster encoding cholesterol catabolism. PMID:23024343

Methylotrophic Bacillus methanolicus Encodes Two Chromosomal and One Plasmid Born NAD+ Dependent Methanol Dehydrogenase Paralogs with Different Catalytic and Biochemical Properties

PubMed Central

Müller, Jonas E. N.; Kupper, Christiane E.; Schneider, Olha; Vorholt, Julia A.; Ellingsen, Trond E.; Brautaset, Trygve

2013-01-01

Bacillus methanolicus can utilize methanol as the sole carbon source for growth and it encodes an NAD+-dependent methanol dehydrogenase (Mdh), catalyzing the oxidation of methanol to formaldehyde. Recently, the genomes of the B. methanolicus strains MGA3 (ATCC53907) and PB1 (NCIMB13113) were sequenced and found to harbor three different putative Mdh encoding genes, each belonging to the type III Fe-NAD+-dependent alcohol dehydrogenases. In each strain, two of these genes are encoded on the chromosome and one on a plasmid; only one chromosomal act gene encoding the previously described activator protein ACT was found. The six Mdhs and the ACT proteins were produced recombinantly in Escherichia coli, purified, and characterized. All Mdhs required NAD+ as cosubstrate, were catalytically stimulated by ACT, exhibited a broad and different substrate specificity range and displayed both dehydrogenase and reductase activities. All Mdhs catalyzed the oxidation of methanol; however the catalytic activity for methanol was considerably lower than for most other alcohols tested, suggesting that these enzymes represent a novel class of alcohol dehydrogenases. The kinetic constants for the Mdhs were comparable when acting as pure enzymes, but together with ACT the differences were more pronounced. Quantitative PCR experiments revealed major differences with respect to transcriptional regulation of the paralogous genes. Taken together our data indicate that the repertoire of methanol oxidizing enzymes in thermotolerant bacilli is larger than expected with complex mechanisms involved in their regulation. PMID:23527128

Methylotrophic Bacillus methanolicus encodes two chromosomal and one plasmid born NAD+ dependent methanol dehydrogenase paralogs with different catalytic and biochemical properties.

PubMed

Krog, Anne; Heggeset, Tonje M B; Müller, Jonas E N; Kupper, Christiane E; Schneider, Olha; Vorholt, Julia A; Ellingsen, Trond E; Brautaset, Trygve

2013-01-01

Bacillus methanolicus can utilize methanol as the sole carbon source for growth and it encodes an NAD(+)-dependent methanol dehydrogenase (Mdh), catalyzing the oxidation of methanol to formaldehyde. Recently, the genomes of the B. methanolicus strains MGA3 (ATCC53907) and PB1 (NCIMB13113) were sequenced and found to harbor three different putative Mdh encoding genes, each belonging to the type III Fe-NAD(+)-dependent alcohol dehydrogenases. In each strain, two of these genes are encoded on the chromosome and one on a plasmid; only one chromosomal act gene encoding the previously described activator protein ACT was found. The six Mdhs and the ACT proteins were produced recombinantly in Escherichia coli, purified, and characterized. All Mdhs required NAD(+) as cosubstrate, were catalytically stimulated by ACT, exhibited a broad and different substrate specificity range and displayed both dehydrogenase and reductase activities. All Mdhs catalyzed the oxidation of methanol; however the catalytic activity for methanol was considerably lower than for most other alcohols tested, suggesting that these enzymes represent a novel class of alcohol dehydrogenases. The kinetic constants for the Mdhs were comparable when acting as pure enzymes, but together with ACT the differences were more pronounced. Quantitative PCR experiments revealed major differences with respect to transcriptional regulation of the paralogous genes. Taken together our data indicate that the repertoire of methanol oxidizing enzymes in thermotolerant bacilli is larger than expected with complex mechanisms involved in their regulation.