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Sample records for prokaryotic gene finder

  1. Efficient decoding algorithms for generalized hidden Markov model gene finders

    PubMed Central

    Majoros, William H; Pertea, Mihaela; Delcher, Arthur L; Salzberg, Steven L

    2005-01-01

    Background The Generalized Hidden Markov Model (GHMM) has proven a useful framework for the task of computational gene prediction in eukaryotic genomes, due to its flexibility and probabilistic underpinnings. As the focus of the gene finding community shifts toward the use of homology information to improve prediction accuracy, extensions to the basic GHMM model are being explored as possible ways to integrate this homology information into the prediction process. Particularly prominent among these extensions are those techniques which call for the simultaneous prediction of genes in two or more genomes at once, thereby increasing significantly the computational cost of prediction and highlighting the importance of speed and memory efficiency in the implementation of the underlying GHMM algorithms. Unfortunately, the task of implementing an efficient GHMM-based gene finder is already a nontrivial one, and it can be expected that this task will only grow more onerous as our models increase in complexity. Results As a first step toward addressing the implementation challenges of these next-generation systems, we describe in detail two software architectures for GHMM-based gene finders, one comprising the common array-based approach, and the other a highly optimized algorithm which requires significantly less memory while achieving virtually identical speed. We then show how both of these architectures can be accelerated by a factor of two by optimizing their content sensors. We finish with a brief illustration of the impact these optimizations have had on the feasibility of our new homology-based gene finder, TWAIN. Conclusions In describing a number of optimizations for GHMM-based gene finders and making available two complete open-source software systems embodying these methods, it is our hope that others will be more enabled to explore promising extensions to the GHMM framework, thereby improving the state-of-the-art in gene prediction techniques. PMID:15667658

  2. Next-Generation Annotation of Prokaryotic Genomes with EuGene-P: Application to Sinorhizobium meliloti 2011

    PubMed Central

    Sallet, Erika; Roux, Brice; Sauviac, Laurent; Jardinaud, Marie-Franc¸oise; Carrère, Sébastien; Faraut, Thomas; de Carvalho-Niebel, Fernanda; Gouzy, Jérôme; Gamas, Pascal; Capela, Delphine; Bruand, Claude; Schiex, Thomas

    2013-01-01

    The availability of next-generation sequences of transcripts from prokaryotic organisms offers the opportunity to design a new generation of automated genome annotation tools not yet available for prokaryotes. In this work, we designed EuGene-P, the first integrative prokaryotic gene finder tool which combines a variety of high-throughput data, including oriented RNA-Seq data, directly into the prediction process. This enables the automated prediction of coding sequences (CDSs), untranslated regions, transcription start sites (TSSs) and non-coding RNA (ncRNA, sense and antisense) genes. EuGene-P was used to comprehensively and accurately annotate the genome of the nitrogen-fixing bacterium Sinorhizobium meliloti strain 2011, leading to the prediction of 6308 CDSs as well as 1876 ncRNAs. Among them, 1280 appeared as antisense to a CDS, which supports recent findings that antisense transcription activity is widespread in bacteria. Moreover, 4077 TSSs upstream of protein-coding or non-coding genes were precisely mapped providing valuable data for the study of promoter regions. By looking for RpoE2-binding sites upstream of annotated TSSs, we were able to extend the S. meliloti RpoE2 regulon by ∼3-fold. Altogether, these observations demonstrate the power of EuGene-P to produce a reliable and high-resolution automatic annotation of prokaryotic genomes. PMID:23599422

  3. Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes.

    PubMed

    Ku, Chuan; Nelson-Sathi, Shijulal; Roettger, Mayo; Garg, Sriram; Hazkani-Covo, Einat; Martin, William F

    2015-08-18

    Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners--the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)--and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic--and plant and algal--lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller's ratchet--the origin of eukaryotic recombination, or sex--might have required surprisingly little evolutionary innovation.

  4. Endosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes

    PubMed Central

    Ku, Chuan; Nelson-Sathi, Shijulal; Roettger, Mayo; Garg, Sriram; Hazkani-Covo, Einat; Martin, William F.

    2015-01-01

    Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners—the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)—and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic—and plant and algal—lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller’s ratchet—the origin of eukaryotic recombination, or sex—might have required surprisingly little evolutionary innovation. PMID:25733873

  5. Detection of Prokaryotic Genes in the Amphimedon queenslandica Genome

    PubMed Central

    Conaco, Cecilia; Tsoulfas, Pantelis; Sakarya, Onur; Dolan, Amanda; Werren, John; Kosik, Kenneth S.

    2016-01-01

    Horizontal gene transfer (HGT) is common between prokaryotes and phagotrophic eukaryotes. In metazoans, the scale and significance of HGT remains largely unexplored but is usually linked to a close association with parasites and endosymbionts. Marine sponges (Porifera), which host many microorganisms in their tissues and lack an isolated germ line, are potential carriers of genes transferred from prokaryotes. In this study, we identified a number of potential horizontally transferred genes within the genome of the sponge, Amphimedon queenslandica. We further identified homologs of some of these genes in other sponges. The transferred genes, most of which possess catalytic activity for carbohydrate or protein metabolism, have assimilated host genome characteristics and are actively expressed. The diversity of functions contributed by the horizontally transferred genes is likely an important factor in the adaptation and evolution of A. queenslandica. These findings highlight the potential importance of HGT on the success of sponges in diverse ecological niches. PMID:26959231

  6. Sequence determinants of prokaryotic gene expression level under heat stress.

    PubMed

    Xiong, Heng; Yang, Yi; Hu, Xiao-Pan; He, Yi-Ming; Ma, Bin-Guang

    2014-11-01

    Prokaryotic gene expression is environment-dependent and temperature plays an important role in shaping the gene expression profile. Revealing the regulation mechanisms of gene expression pertaining to temperature has attracted tremendous efforts in recent years particularly owning to the yielding of transcriptome and proteome data by high-throughput techniques. However, most of the previous works concentrated on the characterization of the gene expression profile of individual organism and little effort has been made to disclose the commonality among organisms, especially for the gene sequence features. In this report, we collected the transcriptome and proteome data measured under heat stress condition from recently published literature and studied the sequence determinants for the expression level of heat-responsive genes on multiple layers. Our results showed that there indeed exist commonness and consistent patterns of the sequence features among organisms for the differentially expressed genes under heat stress condition. Some features are attributed to the requirement of thermostability while some are dominated by gene function. The revealed sequence determinants of bacterial gene expression level under heat stress complement the knowledge about the regulation factors of prokaryotic gene expression responding to the change of environmental conditions. Furthermore, comparisons to thermophilic adaption have been performed to reveal the similarity and dissimilarity of the sequence determinants for the response to heat stress and for the adaption to high habitat temperature, which elucidates the complex landscape of gene expression related to the same physical factor of temperature.

  7. Gene analogue finder: a GRID solution for finding functionally analogous gene products

    PubMed Central

    Tulipano, Angelica; Donvito, Giacinto; Licciulli, Flavio; Maggi, Giorgio; Gisel, Andreas

    2007-01-01

    Background To date more than 2,1 million gene products from more than 100000 different species have been described specifying their function, the processes they are involved in and their cellular localization using a very well defined and structured vocabulary, the gene ontology (GO). Such vast, well defined knowledge opens the possibility of compare gene products at the level of functionality, finding gene products which have a similar function or are involved in similar biological processes without relying on the conventional sequence similarity approach. Comparisons within such a large space of knowledge are highly data and computing intensive. For this reason this project was based upon the use of the computational GRID, a technology offering large computing and storage resources. Results We have developed a tool, GENe AnaloGue FINdEr (ENGINE) that parallelizes the search process and distributes the calculation and data over the computational GRID, splitting the process into many sub-processes and joining the calculation and the data on the same machine and therefore completing the whole search in about 3 days instead of occupying one single machine for more than 5 CPU years. The results of the functional comparison contain potential functional analogues for more than 79000 gene products from the most important species. 46% of the analyzed gene products are well enough described for such an analysis to individuate functional analogues, such as well-known members of the same gene family, or gene products with similar functions which would never have been associated by standard methods. Conclusion ENGINE has produced a list of potential functionally analogous relations between gene products within and between species using, in place of the sequence, the gene description of the GO, thus demonstrating the potential of the GO. However, the current limiting factor is the quality of the associations of many gene products from non-model organisms that often have

  8. Comparative analysis of essential genes in prokaryotic genomic islands

    PubMed Central

    Zhang, Xi; Peng, Chong; Zhang, Ge; Gao, Feng

    2015-01-01

    Essential genes are thought to encode proteins that carry out the basic functions to sustain a cellular life, and genomic islands (GIs) usually contain clusters of horizontally transferred genes. It has been assumed that essential genes are not likely to be located in GIs, but systematical analysis of essential genes in GIs has not been explored before. Here, we have analyzed the essential genes in 28 prokaryotes by statistical method and reached a conclusion that essential genes in GIs are significantly fewer than those outside GIs. The function of 362 essential genes found in GIs has been explored further by BLAST against the Virulence Factor Database (VFDB) and the phage/prophage sequence database of PHAge Search Tool (PHAST). Consequently, 64 and 60 eligible essential genes are found to share the sequence similarity with the virulence factors and phage/prophages-related genes, respectively. Meanwhile, we find several toxin-related proteins and repressors encoded by these essential genes in GIs. The comparative analysis of essential genes in genomic islands will not only shed new light on the development of the prediction algorithm of essential genes, but also give a clue to detect the functionality of essential genes in genomic islands. PMID:26223387

  9. Gene set analyses for interpreting microarray experiments on prokaryotic organisms

    PubMed Central

    Tintle, Nathan L; Best, Aaron A; DeJongh, Matthew; Van Bruggen, Dirk; Heffron, Fred; Porwollik, Steffen; Taylor, Ronald C

    2008-01-01

    Background Despite the widespread usage of DNA microarrays, questions remain about how best to interpret the wealth of gene-by-gene transcriptional levels that they measure. Recently, methods have been proposed which use biologically defined sets of genes in interpretation, instead of examining results gene-by-gene. Despite a serious limitation, a method based on Fisher's exact test remains one of the few plausible options for gene set analysis when an experiment has few replicates, as is typically the case for prokaryotes. Results We extend five methods of gene set analysis from use on experiments with multiple replicates, for use on experiments with few replicates. We then use simulated and real data to compare these methods with each other and with the Fisher's exact test (FET) method. As a result of the simulation we find that a method named MAXMEAN-NR, maintains the nominal rate of false positive findings (type I error rate) while offering good statistical power and robustness to a variety of gene set distributions for set sizes of at least 10. Other methods (ABSSUM-NR or SUM-NR) are shown to be powerful for set sizes less than 10. Analysis of three sets of experimental data shows similar results. Furthermore, the MAXMEAN-NR method is shown to be able to detect biologically relevant sets as significant, when other methods (including FET) cannot. We also find that the popular GSEA-NR method performs poorly when compared to MAXMEAN-NR. Conclusion MAXMEAN-NR is a method of gene set analysis for experiments with few replicates, as is common for prokaryotes. Results of simulation and real data analysis suggest that the MAXMEAN-NR method offers increased robustness and biological relevance of findings as compared to FET and other methods, while maintaining the nominal type I error rate. PMID:18986519

  10. GenePRIMP: A GENE PRediction IMprovement Pipeline for Prokaryotic genomes

    SciTech Connect

    Pati, Amrita; Ivanova, Natalia N.; Mikhailova, Natalia; Ovchinnikova, Galina; Hooper, Sean D.; Lykidis, Athanasios; Kyrpides, Nikos C.

    2010-04-01

    We present 'gene prediction improvement pipeline' (GenePRIMP; http://geneprimp.jgi-psf.org/), a computational process that performs evidence-based evaluation of gene models in prokaryotic genomes and reports anomalies including inconsistent start sites, missed genes and split genes. We found that manual curation of gene models using the anomaly reports generated by GenePRIMP improved their quality, and demonstrate the applicability of GenePRIMP in improving finishing quality and comparing different genome-sequencing and annotation technologies.

  11. ThioFinder: a web-based tool for the identification of thiopeptide gene clusters in DNA sequences.

    PubMed

    Li, Jing; Qu, Xudong; He, Xinyi; Duan, Lian; Wu, Guojun; Bi, Dexi; Deng, Zixin; Liu, Wen; Ou, Hong-Yu

    2012-01-01

    Thiopeptides are a growing class of sulfur-rich, highly modified heterocyclic peptides that are mainly active against Gram-positive bacteria including various drug-resistant pathogens. Recent studies also reveal that many thiopeptides inhibit the proliferation of human cancer cells, further expanding their application potentials for clinical use. Thiopeptide biosynthesis shares a common paradigm, featuring a ribosomally synthesized precursor peptide and conserved posttranslational modifications, to afford a characteristic core system, but differs in tailoring to furnish individual members. Identification of new thiopeptide gene clusters, by taking advantage of increasing information of DNA sequences from bacteria, may facilitate new thiopeptide discovery and enrichment of the unique biosynthetic elements to produce novel drug leads by applying the principle of combinatorial biosynthesis. In this study, we have developed a web-based tool ThioFinder to rapidly identify thiopeptide biosynthetic gene cluster from DNA sequence using a profile Hidden Markov Model approach. Fifty-four new putative thiopeptide biosynthetic gene clusters were found in the sequenced bacterial genomes of previously unknown producing microorganisms. ThioFinder is fully supported by an open-access database ThioBase, which contains the sufficient information of the 99 known thiopeptides regarding the chemical structure, biological activity, producing organism, and biosynthetic gene (cluster) along with the associated genome if available. The ThioFinder website offers researchers a unique resource and great flexibility for sequence analysis of thiopeptide biosynthetic gene clusters. ThioFinder is freely available at http://db-mml.sjtu.edu.cn/ThioFinder/.

  12. Path Finder

    SciTech Connect

    Rigdon, J. Brian; Smith, Marcus Daniel; Mulder, Samuel A

    2014-01-07

    PathFinder is a graph search program, traversing a directed cyclic graph to find pathways between labeled nodes. Searches for paths through ordered sequences of labels are termed signatures. Determining the presence of signatures within one or more graphs is the primary function of Path Finder. Path Finder can work in either batch mode or interactively with an analyst. Results are limited to Path Finder whether or not a given signature is present in the graph(s).

  13. ColoFinder: a prognostic 9-gene signature improves prognosis for 871 stage II and III colorectal cancer patients

    PubMed Central

    He, Jianmin

    2016-01-01

    Colorectal cancer (CRC) is a heterogeneous disease with a high mortality rate and is still lacking an effective treatment. Our goal is to develop a robust prognosis model for predicting the prognosis in CRC patients. In this study, 871 stage II and III CRC samples were collected from six gene expression profilings. ColoFinder was developed using a 9-gene signature based Random Survival Forest (RSF) prognosis model. The 9-gene signature recurrence score was derived with a 5-fold cross validation to test the association with relapse-free survival, and the value of AUC was gained with 0.87 in GSE39582(95% CI [0.83–0.91]). The low-risk group had a significantly better relapse-free survival (HR, 14.8; 95% CI [8.17–26.8]; P < 0.001) than the high-risk group. We also found that the 9-gene signature recurrence score contributed more information about recurrence than standard clinical and pathological variables in univariate and multivariate Cox analyses when applied to GSE17536(p = 0.03 and p = 0.01 respectively). Furthermore, ColoFinder improved the predictive ability and better stratified the risk subgroups when applied to CRC gene expression datasets GSE14333, GSE17537, GSE12945and GSE24551. In summary, ColoFinder significantly improves the risk assessment in stage II and III CRC patients. The 9-gene prognostic classifier informs patient prognosis and treatment response. PMID:26989635

  14. GeneTack database: genes with frameshifts in prokaryotic genomes and eukaryotic mRNA sequences.

    PubMed

    Antonov, Ivan; Baranov, Pavel; Borodovsky, Mark

    2013-01-01

    Database annotations of prokaryotic genomes and eukaryotic mRNA sequences pay relatively low attention to frame transitions that disrupt protein-coding genes. Frame transitions (frameshifts) could be caused by sequencing errors or indel mutations inside protein-coding regions. Other observed frameshifts are related to recoding events (that evolved to control expression of some genes). Earlier, we have developed an algorithm and software program GeneTack for ab initio frameshift finding in intronless genes. Here, we describe a database (freely available at http://topaz.gatech.edu/GeneTack/db.html) containing genes with frameshifts (fs-genes) predicted by GeneTack. The database includes 206 991 fs-genes from 1106 complete prokaryotic genomes and 45 295 frameshifts predicted in mRNA sequences from 100 eukaryotic genomes. The whole set of fs-genes was grouped into clusters based on sequence similarity between fs-proteins (conceptually translated fs-genes), conservation of the frameshift position and frameshift direction (-1, +1). The fs-genes can be retrieved by similarity search to a given query sequence via a web interface, by fs-gene cluster browsing, etc. Clusters of fs-genes are characterized with respect to their likely origin, such as pseudogenization, phase variation, etc. The largest clusters contain fs-genes with programed frameshifts (related to recoding events).

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

    PubMed Central

    Thybert, David; Avner, Stéphane; Lucchetti-Miganeh, Céline; Chéron, Angélique; Barloy-Hubler, Frédérique

    2008-01-01

    Background Oxidative stress is a common stress encountered by living organisms and is due to an imbalance between intracellular reactive oxygen and nitrogen species (ROS, RNS) and cellular antioxidant defence. To defend themselves against ROS/RNS, bacteria possess a subsystem of detoxification enzymes, which are classified with regard to their substrates. To identify such enzymes in prokaryotic genomes, different approaches based on similarity, enzyme profiles or patterns exist. Unfortunately, several problems persist in the annotation, classification and naming of these enzymes due mainly to some erroneous entries in databases, mistake propagation, absence of updating and disparity in function description. Description In order to improve the current annotation of oxidative stress subsystems, an innovative platform named OxyGene has been developed. It integrates an original database called OxyDB, holding thoroughly tested anchor-based signatures associated to subfamilies of oxidative stress enzymes, and a new anchor-driven annotator, for ab initio detection of ROS/RNS response genes. All complete Bacterial and Archaeal genomes have been re-annotated, and the results stored in the OxyGene repository can be interrogated via a Graphical User Interface. Conclusion OxyGene enables the exploration and comparative analysis of enzymes belonging to 37 detoxification subclasses in 664 microbial genomes. It proposes a new classification that improves both the ontology and the annotation of the detoxification subsystems in prokaryotic whole genomes, while discovering new ORFs and attributing precise function to hypothetical annotated proteins. OxyGene is freely available at: PMID:19117520

  16. Prokaryotic origins for the mitochondrial alternative oxidase and plastid terminal oxidase nuclear genes.

    PubMed

    Finnegan, Patrick M; Umbach, Ann L; Wilce, Jackie A

    2003-12-18

    The mitochondrial alternative oxidase is a diiron carboxylate quinol oxidase (Dox) found in plants and some fungi and protists, but not animals. The plastid terminal oxidase is distantly related to alternative oxidase and is most likely also a Dox protein. Database searches revealed that the alpha-proteobacterium Novosphingobium aromaticivorans and the cyanobacteria Nostoc sp. PCC7120, Synechococcus sp. WH8102 and Prochlorococcus marinus subsp. pastoris CCMP1378 each possess a Dox homolog. Each prokaryotic protein conforms to the current structural models of the Dox active site and phylogenetic analyses suggest that the eukaryotic Dox genes arose from an ancestral prokaryotic gene.

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

    PubMed

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

    2015-11-23

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

  18. Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences.

    PubMed

    Wagner, Andreas; de la Chaux, Nicole

    2008-11-01

    Horizontal gene transfer in prokaryotes is rampant on short and intermediate evolutionary time scales. It poses a fundamental problem to our ability to reconstruct the evolutionary tree of life. Is it also frequent over long evolutionary distances? To address this question, we analyzed the evolution of 2,091 insertion sequences from all 20 major families in 438 completely sequenced prokaryotic genomes. Specifically, we mapped insertion sequence occurrence on a 16S rDNA tree of the genomes we analyzed, and we also constructed phylogenetic trees of the insertion sequence transposase coding sequences. We found only 30 cases of likely horizontal transfer among distantly related prokaryotic clades. Most of these horizontal transfer events are ancient. Only seven events are recent. Almost all of these transfer events occur between pairs of human pathogens or commensals. If true also for other, non-mobile DNA, the rarity of distant horizontal transfer increases the odds of reliable phylogenetic inference from sequence data.

  19. Long-range cooperativity between gene regulatory sequences in a prokaryote.

    PubMed

    Dandanell, G; Valentin-Hansen, P; Larsen, J E; Hammer, K

    Regulation of transcription initiation by proteins binding at DNA sequences some distance from the promoter region itself seems to be a general phenomenon in both eukaryotes and prokaryotes. Proteins bound to an enhancer site in eukaryotes can turn on a distant gene, whereas efficient repression of some prokaryotic genes such as the gal, ara and deo operons of Escherichia coli, requires the presence of two operator sites, separated by 110, 200 and 600 base pairs (bp) respectively. In the deo operon, which encodes nucleoside catabolizing enzymes, we have shown that efficient and cooperative repression can be obtained when the distance between the two sites ranges from 224 to 997 bp. Here, we report that transcription initiation can be regulated from an operator site placed 1 to 5 kilobases (kb) downstream of the deoP2 promoter (and downstream of the transcribed gene), and present the first experimental data for prokaryotic regulation at distances greater than 1 kb. Our results support the model of DNA loop formation as a common regulatory mechanism explaining both some prokaryotic regulation and the action of eukaryotic enhancers.

  20. Fault finder

    DOEpatents

    Bunch, Richard H.

    1986-01-01

    A fault finder for locating faults along a high voltage electrical transmission line. Real time monitoring of background noise and improved filtering of input signals is used to identify the occurrence of a fault. A fault is detected at both a master and remote unit spaced along the line. A master clock synchronizes operation of a similar clock at the remote unit. Both units include modulator and demodulator circuits for transmission of clock signals and data. All data is received at the master unit for processing to determine an accurate fault distance calculation.

  1. Gene set analyses for interpreting microarray experiments on prokaryotic organisms.

    SciTech Connect

    Tintle, Nathan; Best, Aaron; Dejongh, Matthew; VanBruggen, Dirk; Heffron, Fred; Porwollik, Steffen; Taylor, Ronald C.

    2008-11-05

    Background: Recent advances in microarray technology have brought with them the need for enhanced methods of biologically interpreting gene expression data. Recently, methods like Gene Set Enrichment Analysis (GSEA) and variants of Fisher’s exact test have been proposed which utilize a priori biological information. Typically, these methods are demonstrated with a priori biological information from the Gene Ontology. Results: Alternative gene set definitions are presented based on gene sets inferred from the SEED: open-source software environment for comparative genome annotation and analysis of microbial organisms. Many of these gene sets are then shown to provide consistent expression across a series of experiments involving Salmonella Typhimurium. Implementation of the gene sets in an analysis of microarray data is then presented for the Salmonella Typhimurium data. Conclusions: SEED inferred gene sets can be naturally defined based on subsystems in the SEED. The consistent expression values of these SEED inferred gene sets suggest their utility for statistical analyses of gene expression data based on a priori biological information

  2. Prokaryotic Gene Clusters: A Rich Toolbox for Synthetic Biology

    PubMed Central

    Fischbach, Michael; Voigt, Christopher A.

    2014-01-01

    Bacteria construct elaborate nanostructures, obtain nutrients and energy from diverse sources, synthesize complex molecules, and implement signal processing to react to their environment. These complex phenotypes require the coordinated action of multiple genes, which are often encoded in a contiguous region of the genome, referred to as a gene cluster. Gene clusters sometimes contain all of the genes necessary and sufficient for a particular function. As an evolutionary mechanism, gene clusters facilitate the horizontal transfer of the complete function between species. Here, we review recent work on a number of clusters whose functions are relevant to biotechnology. Engineering these clusters has been hindered by their regulatory complexity, the need to balance the expression of many genes, and a lack of tools to design and manipulate DNA at this scale. Advances in synthetic biology will enable the large-scale bottom-up engineering of the clusters to optimize their functions, wake up cryptic clusters, or to transfer them between organisms. Understanding and manipulating gene clusters will move towards an era of genome engineering, where multiple functions can be “mixed-and-matched” to create a designer organism. PMID:21154668

  3. Census of solo LuxR genes in prokaryotic genomes

    PubMed Central

    Hudaiberdiev, Sanjarbek; Choudhary, Kumari S.; Vera Alvarez, Roberto; Gelencsér, Zsolt; Ligeti, Balázs; Lamba, Doriano; Pongor, Sándor

    2015-01-01

    luxR genes encode transcriptional regulators that control acyl homoserine lactone-based quorum sensing (AHL QS) in Gram negative bacteria. On the bacterial chromosome, luxR genes are usually found next or near to a luxI gene encoding the AHL signal synthase. Recently, a number of luxR genes were described that have no luxI genes in their vicinity on the chromosome. These so-called solo luxR genes may either respond to internal AHL signals produced by a non-adjacent luxI in the chromosome, or can respond to exogenous signals. Here we present a survey of solo luxR genes found in complete and draft bacterial genomes in the NCBI databases using HMMs. We found that 2698 of the 3550 luxR genes found are solos, which is an unexpectedly high number even if some of the hits may be false positives. We also found that solo LuxR sequences form distinct clusters that are different from the clusters of LuxR sequences that are part of the known luxR-luxI topological arrangements. We also found a number of cases that we termed twin luxR topologies, in which two adjacent luxR genes were in tandem or divergent orientation. Many of the luxR solo clusters were devoid of the sequence motifs characteristic of AHL binding LuxR proteins so there is room to speculate that the solos may be involved in sensing hitherto unknown signals. It was noted that only some of the LuxR clades are rich in conserved cysteine residues. Molecular modeling suggests that some of the cysteines may be involved in disulfide formation, which makes us speculate that some LuxR proteins, including some of the solos may be involved in redox regulation. PMID:25815274

  4. Methods for identifying an essential gene in a prokaryotic microorganism

    DOEpatents

    Shizuya, Hiroaki

    2006-01-31

    Methods are provided for the rapid identification of essential or conditionally essential DNA segments in any species of haploid cell (one copy chromosome per cell) that is capable of being transformed by artificial means and is capable of undergoing DNA recombination. This system offers an enhanced means of identifying essential function genes in diploid pathogens, such as gram-negative and gram-positive bacteria.

  5. [Establishment of prokaryotic expression and optimization ox expression conditions of Eleutherococcus senticosus P450 gene].

    PubMed

    Wu, Peng; Xiu, Le-shan; Li, Fei-fei; Xing, Zhao-bin

    2015-04-01

    According to the sequence of P450 cDNA of Eleutherococcus senticosus, specific primers were designed. Frokaryotic ex pression vector pET30a-P450 was constructed and the prokaryotic expression conditions were optimized. Results showed that the BL21 after being transformed with the recombinant expression vector accumulated the high amount of recombinant protein. SDS-PAGE analysis showed that the recombinant protein was about 53 kDa. The recombinant accumulated the highest amount of recombinant protein af ter IPTG (1 mmol x L(-1)) at 27-37 degrees C for 24 h. Consequently P450 gene of E. senticosus could be expressed successfully by prokaryotic expression vector pET30a-P450. Induction temperature, IPTG concentration, medium type and amount of induction time could all influence the expression of target protein, but the impact strength was different.

  6. Prokaryotic ancestry and gene fusion of a dual localized peroxiredoxin in malaria parasites

    PubMed Central

    Djuika, Carine F.; Huerta-Cepas, Jaime; Przyborski, Jude M.; Deil, Sophia; Sanchez, Cecilia P.; Doerks, Tobias; Bork, Peer; Lanzer, Michael; Deponte, Marcel

    2015-01-01

    Horizontal gene transfer has emerged as a crucial driving force for the evolution of eukaryotes. This also includes Plasmodium falciparum and related economically and clinically relevant apicomplexan parasites, whose rather small genomes have been shaped not only by natural selection in different host populations but also by horizontal gene transfer following endosymbiosis. However, there is rather little reliable data on horizontal gene transfer between animal hosts or bacteria and apicomplexan parasites. Here we show that apicomplexan homologues of peroxiredoxin 5 (Prx5) have a prokaryotic ancestry and therefore represent a special subclass of Prx5 isoforms in eukaryotes. Using two different immunobiochemical approaches, we found that the P. falciparum Prx5 homologue is dually localized to the parasite plastid and cytosol. This dual localization is reflected by a modular Plasmodium-specific gene architecture consisting of two exons. Despite the plastid localization, our phylogenetic analyses contradict an acquisition by secondary endosymbiosis and support a gene fusion event following a horizontal prokaryote-to-eukaryote gene transfer in early apicomplexans. The results provide unexpected insights into the evolution of apicomplexan parasites as well as the molecular evolution of peroxiredoxins, an important family of ubiquitous, usually highly concentrated thiol-dependent hydroperoxidases that exert functions as detoxifying enzymes, redox sensors and chaperones. PMID:28357258

  7. Comparative Genomics Reveals New Candidate Genes Involved in Selenium Metabolism in Prokaryotes

    PubMed Central

    Lin, Jie; Peng, Ting; Jiang, Liang; Ni, Jia-Zuan; Liu, Qiong; Chen, Luonan; Zhang, Yan

    2015-01-01

    Selenium (Se) is an important micronutrient that mainly occurs in proteins in the form of selenocysteine and in tRNAs in the form of selenouridine. In the past 20 years, several genes involved in Se utilization have been characterized in both prokaryotes and eukaryotes. However, Se homeostasis and the associated regulatory network are not fully understood. In this study, we conducted comparative genomics and phylogenetic analyses to examine the occurrence of all known Se utilization traits in prokaryotes. Our results revealed a highly mosaic pattern of species that use Se (in different forms) in spite that most organisms do not use this element. Further investigation of genomic context of known Se-related genes in different organisms suggested novel candidate genes that may participate in Se metabolism in bacteria and/or archaea. Among them, a membrane protein, YedE, which contains ten transmembrane domains and shows distant similarity to a sulfur transporter, is exclusively found in Se-utilizing organisms, suggesting that it may be involved in Se transport. A LysR-like transcription factor subfamily might be important for the regulation of Sec biosynthesis and/or other Se-related genes. In addition, a small protein family DUF3343 is widespread in Se-utilizing organisms, which probably serves as an important chaperone for Se trafficking within the cells. Finally, we proposed a simple model of Se homeostasis based on our findings. Our study reveals new candidate genes involved in Se metabolism in prokaryotes and should be useful for a further understanding of the complex metabolism and the roles of Se in biology. PMID:25638258

  8. Gene coexpression as Hebbian learning in prokaryotic genomes.

    PubMed

    Vey, Gregory

    2013-12-01

    Biological interaction networks represent a powerful tool for characterizing intracellular functional relationships, such as transcriptional regulation and protein interactions. Although artificial neural networks are routinely employed for a broad range of applications across computational biology, their underlying connectionist basis has not been extensively applied to modeling biological interaction networks. In particular, the Hopfield network offers nonlinear dynamics that represent the minimization of a system energy function through temporally distinct rewiring events. Here, a scaled energy minimization model is presented to test the feasibility of deriving a composite biological interaction network from multiple constituent data sets using the Hebbian learning principle. The performance of the scaled energy minimization model is compared against the standard Hopfield model using simulated data. Several networks are also derived from real data, compared to one another, and then combined to produce an aggregate network. The utility and limitations of the proposed model are discussed, along with possible implications for a genomic learning analogy where the fundamental Hebbian postulate is rendered into its genomic equivalent: Genes that function together junction together.

  9. Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts.

    PubMed

    Neves, Mariana; Damaschun, Alexander; Mah, Nancy; Lekschas, Fritz; Seltmann, Stefanie; Stachelscheid, Harald; Fontaine, Jean-Fred; Kurtz, Andreas; Leser, Ulf

    2013-01-01

    Biomedical literature curation is the process of automatically and/or manually deriving knowledge from scientific publications and recording it into specialized databases for structured delivery to users. It is a slow, error-prone, complex, costly and, yet, highly important task. Previous experiences have proven that text mining can assist in its many phases, especially, in triage of relevant documents and extraction of named entities and biological events. Here, we present the curation pipeline of the CellFinder database, a repository of cell research, which includes data derived from literature curation and microarrays to identify cell types, cell lines, organs and so forth, and especially patterns in gene expression. The curation pipeline is based on freely available tools in all text mining steps, as well as the manual validation of extracted data. Preliminary results are presented for a data set of 2376 full texts from which >4500 gene expression events in cell or anatomical part have been extracted. Validation of half of this data resulted in a precision of ~50% of the extracted data, which indicates that we are on the right track with our pipeline for the proposed task. However, evaluation of the methods shows that there is still room for improvement in the named-entity recognition and that a larger and more robust corpus is needed to achieve a better performance for event extraction. Database URL: http://www.cellfinder.org/

  10. Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts

    PubMed Central

    Neves, Mariana; Damaschun, Alexander; Mah, Nancy; Lekschas, Fritz; Seltmann, Stefanie; Stachelscheid, Harald; Fontaine, Jean-Fred; Kurtz, Andreas; Leser, Ulf

    2013-01-01

    Biomedical literature curation is the process of automatically and/or manually deriving knowledge from scientific publications and recording it into specialized databases for structured delivery to users. It is a slow, error-prone, complex, costly and, yet, highly important task. Previous experiences have proven that text mining can assist in its many phases, especially, in triage of relevant documents and extraction of named entities and biological events. Here, we present the curation pipeline of the CellFinder database, a repository of cell research, which includes data derived from literature curation and microarrays to identify cell types, cell lines, organs and so forth, and especially patterns in gene expression. The curation pipeline is based on freely available tools in all text mining steps, as well as the manual validation of extracted data. Preliminary results are presented for a data set of 2376 full texts from which >4500 gene expression events in cell or anatomical part have been extracted. Validation of half of this data resulted in a precision of ∼50% of the extracted data, which indicates that we are on the right track with our pipeline for the proposed task. However, evaluation of the methods shows that there is still room for improvement in the named-entity recognition and that a larger and more robust corpus is needed to achieve a better performance for event extraction. Database URL: http://www.cellfinder.org/ PMID:23599415

  11. Selective pressure against horizontally acquired prokaryotic genes as a driving force of plastid evolution

    PubMed Central

    Llorente, Briardo; de Souza, Flavio S. J.; Soto, Gabriela; Meyer, Cristian; Alonso, Guillermo D.; Flawiá, Mirtha M.; Bravo-Almonacid, Fernando; Ayub, Nicolás D.; Rodríguez-Concepción, Manuel

    2016-01-01

    The plastid organelle comprises a high proportion of nucleus-encoded proteins that were acquired from different prokaryotic donors via independent horizontal gene transfers following its primary endosymbiotic origin. What forces drove the targeting of these alien proteins to the plastid remains an unresolved evolutionary question. To better understand this process we screened for suitable candidate proteins to recapitulate their prokaryote-to-eukaryote transition. Here we identify the ancient horizontal transfer of a bacterial polyphenol oxidase (PPO) gene to the nuclear genome of an early land plant ancestor and infer the possible mechanism behind the plastidial localization of the encoded enzyme. Arabidopsis plants expressing PPO versions either lacking or harbouring a plastid-targeting signal allowed examining fitness consequences associated with its subcellular localization. Markedly, a deleterious effect on plant growth was highly correlated with PPO activity only when producing the non-targeted enzyme, suggesting that selection favoured the fixation of plastid-targeted protein versions. Our results reveal a possible evolutionary mechanism of how selection against heterologous genes encoding cytosolic proteins contributed in incrementing plastid proteome complexity from non-endosymbiotic gene sources, a process that may also impact mitochondrial evolution. PMID:26750147

  12. Selective pressure against horizontally acquired prokaryotic genes as a driving force of plastid evolution.

    PubMed

    Llorente, Briardo; de Souza, Flavio S J; Soto, Gabriela; Meyer, Cristian; Alonso, Guillermo D; Flawiá, Mirtha M; Bravo-Almonacid, Fernando; Ayub, Nicolás D; Rodríguez-Concepción, Manuel

    2016-01-11

    The plastid organelle comprises a high proportion of nucleus-encoded proteins that were acquired from different prokaryotic donors via independent horizontal gene transfers following its primary endosymbiotic origin. What forces drove the targeting of these alien proteins to the plastid remains an unresolved evolutionary question. To better understand this process we screened for suitable candidate proteins to recapitulate their prokaryote-to-eukaryote transition. Here we identify the ancient horizontal transfer of a bacterial polyphenol oxidase (PPO) gene to the nuclear genome of an early land plant ancestor and infer the possible mechanism behind the plastidial localization of the encoded enzyme. Arabidopsis plants expressing PPO versions either lacking or harbouring a plastid-targeting signal allowed examining fitness consequences associated with its subcellular localization. Markedly, a deleterious effect on plant growth was highly correlated with PPO activity only when producing the non-targeted enzyme, suggesting that selection favoured the fixation of plastid-targeted protein versions. Our results reveal a possible evolutionary mechanism of how selection against heterologous genes encoding cytosolic proteins contributed in incrementing plastid proteome complexity from non-endosymbiotic gene sources, a process that may also impact mitochondrial evolution.

  13. Selective pressure against horizontally acquired prokaryotic genes as a driving force of plastid evolution

    NASA Astrophysics Data System (ADS)

    Llorente, Briardo; de Souza, Flavio S. J.; Soto, Gabriela; Meyer, Cristian; Alonso, Guillermo D.; Flawiá, Mirtha M.; Bravo-Almonacid, Fernando; Ayub, Nicolás D.; Rodríguez-Concepción, Manuel

    2016-01-01

    The plastid organelle comprises a high proportion of nucleus-encoded proteins that were acquired from different prokaryotic donors via independent horizontal gene transfers following its primary endosymbiotic origin. What forces drove the targeting of these alien proteins to the plastid remains an unresolved evolutionary question. To better understand this process we screened for suitable candidate proteins to recapitulate their prokaryote-to-eukaryote transition. Here we identify the ancient horizontal transfer of a bacterial polyphenol oxidase (PPO) gene to the nuclear genome of an early land plant ancestor and infer the possible mechanism behind the plastidial localization of the encoded enzyme. Arabidopsis plants expressing PPO versions either lacking or harbouring a plastid-targeting signal allowed examining fitness consequences associated with its subcellular localization. Markedly, a deleterious effect on plant growth was highly correlated with PPO activity only when producing the non-targeted enzyme, suggesting that selection favoured the fixation of plastid-targeted protein versions. Our results reveal a possible evolutionary mechanism of how selection against heterologous genes encoding cytosolic proteins contributed in incrementing plastid proteome complexity from non-endosymbiotic gene sources, a process that may also impact mitochondrial evolution.

  14. Prokaryotic suppression subtractive hybridization PCR cDNA subtraction, a targeted method to identify differentially expressed genes.

    PubMed

    De Long, Susan K; Kinney, Kerry A; Kirisits, Mary Jo

    2008-01-01

    Molecular biology tools can be used to monitor and optimize biological treatment systems, but the application of nucleic acid-based tools has been hindered by the lack of available sequences for environmentally relevant biodegradation genes. The objective of our work was to extend an existing molecular method for eukaryotes to prokaryotes, allowing us to rapidly identify differentially expressed genes for subsequent sequencing. Suppression subtractive hybridization (SSH) PCR cDNA subtraction is a technique that can be used to identify genes that are expressed under specific conditions (e.g., growth on a given pollutant). While excellent methods for eukaryotic SSH PCR cDNA subtraction are available, to our knowledge, no methods previously existed for prokaryotes. This work describes our methodology for prokaryotic SSH PCR cDNA subtraction, which we validated using a model system: Pseudomonas putida mt-2 degrading toluene. cDNA from P. putida mt-2 grown on toluene (model pollutant) or acetate (control substrate) was subjected to our prokaryotic SSH PCR cDNA subtraction protocol to generate subtraction clone libraries. Over 90% of the sequenced clones contained gene fragments encoding toluene-related enzymes, and 20 distinct toluene-related genes from three key operons were sequenced. Based on these results, prokaryotic SSH PCR cDNA subtraction shows promise as a targeted method for gene identification.

  15. Skin Condition Finder

    MedlinePlus

    ... SKIN CONDITIONS HEALTH TOPICS FOR PROFESSIONALS Rash and Skin Condition Finder 1 Select Age Group Infant Child ... Toe Toe Webspace Toe Nail CLOSE About the Skin Condition Finder Have a health question or concern? ...

  16. Sequence analysis and prokaryotic expression of Giardia lamblia α-18 giardin gene.

    PubMed

    Wu, Sheng; Yu, Xingang; Abdullahi, Auwalu Yusuf; Hu, Wei; Pan, Weida; Shi, Xianli; Tan, Liping; Song, Meiran; Li, Guoqing

    2016-03-01

    To study the genetic variation and prokaryotic expression of α18 giardin gene of Giardia lamblia zoonotic assemblage A and host-specific assemblage F, the α18 genes were amplified from G. lamblia assemblages A and F by PCR and sequenced. The PCR product was cloned into the prokaryotic expression vector pET-28a(+) and the positive recombinant plasmid was transformed into Escherichia coli Rosetta (DE3) strain for the expression. The expressed α18 giardin fusion protein was validated by SDS-PAGE and Western blot analysis, and purified by Ni-Agarose resin. The putative sequence of α18 giardin amino acid was analyzed by bioinformatics software. Results showed that the α18 giardin gene was 861 bp in length, encoding 286 amino acids; it was 100% homologous between human-derived and dog-derived G. lamblia assemblage A, but it was 86.8% homologous with G. lamblia assemblage F (cat-derived). Giardin α18 was about 36 kDa in molecular weight, with good reactivity. Prediction based on in silico analyses: it had hydrophobicity, without signal peptide and transmembrane domain, and contained 11 alpha regions, 13 beta sheets, 1 beta turn and 7 random coils in secondary structure. The above information would lay the foundation for research about the subcellular localization and biological function of α18 giardin in G. lamblia.

  17. EUGENE'HOM: A generic similarity-based gene finder using multiple homologous sequences.

    PubMed

    Foissac, Sylvain; Bardou, Philippe; Moisan, Annick; Cros, Marie-Josée; Schiex, Thomas

    2003-07-01

    EUGENE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. EUGENE'HOM is able to take into account multiple homologous sequences from more or less closely related organisms. It integrates the results of TBLASTX analysis, splice site and start codon prediction and a robust coding/non-coding probabilistic model which allows EUGENE'HOM to handle sequences from a variety of organisms. The current target of EUGENE'HOM is plant sequences. The EUGENE'HOM web site is available at http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl.

  18. EUGÈNE'HOM: a generic similarity-based gene finder using multiple homologous sequences

    PubMed Central

    Foissac, Sylvain; Bardou, Philippe; Moisan, Annick; Cros, Marie-Josée; Schiex, Thomas

    2003-01-01

    EUGÈNE'HOM is a gene prediction software for eukaryotic organisms based on comparative analysis. EUGÈNE'HOM is able to take into account multiple homologous sequences from more or less closely related organisms. It integrates the results of TBLASTX analysis, splice site and start codon prediction and a robust coding/non-coding probabilistic model which allows EUGÈNE'HOM to handle sequences from a variety of organisms. The current target of EUGÈNE'HOM is plant sequences. The EUGÈNE'HOM web site is available at http://genopole.toulouse.inra.fr/bioinfo/eugene/EuGeneHom/cgi-bin/EuGeneHom.pl. PMID:12824408

  19. Functional specialization of cellulose synthase genes of prokaryotic origin in chordate larvaceans.

    PubMed

    Sagane, Yoshimasa; Zech, Karin; Bouquet, Jean-Marie; Schmid, Martina; Bal, Ugur; Thompson, Eric M

    2010-05-01

    Extracellular matrices play important, but poorly investigated, roles in morphogenesis. Extracellular cellulose is central to regulation of pattern formation in plants, but among metazoans only tunicates are capable of cellulose biosynthesis. Cellulose synthase (CesA) gene products are present in filter-feeding structures of all tunicates and also regulate metamorphosis in the ascidian Ciona. Ciona CesA is proposed to have been acquired by lateral gene transfer from a prokaryote. We identified two CesA genes in the sister-class larvacean Oikopleura dioica. Each has a mosaic structure of a glycoslyltransferase 2 domain upstream of a glycosyl hydrolase family 6 cellulase-like domain, a signature thus far unique to tunicates. Spatial-temporal expression analysis revealed that Od-CesA1 produces long cellulose fibrils along the larval tail, whereas Od-CesA2 is responsible for the cellulose scaffold of the post-metamorphic filter-feeding house. Knockdown of Od-CesA1 inhibited cellulose production in the extracellular matrix of the larval tail. Notochord cells either failed to align or were misaligned, the tail did not elongate properly and tailbud embryos also exhibited a failure to hatch. Knockdown of Od-CesA2 did not elicit any of these phenotypes and instead caused a mild delay in pre-house formation. Phylogenetic analyses including Od-CesAs indicate that a single lateral gene transfer event from a prokaryote at the base of the lineage conferred biosynthetic capacity in all tunicates. Ascidians possess one CesA gene, whereas duplicated larvacean genes have evolved distinct temporal and functional specializations. Extracellular cellulose microfibrils produced by the pre-metamorphic Od-CesA1 duplicate have a role in notochord and tail morphogenesis.

  20. Prokaryotic Expression of α-13 Giardin Gene and Its Intracellular Localization in Giardia lamblia.

    PubMed

    Yu, Xingang; Abdullahi, Auwalu Yusuf; Wu, Sheng; Pan, Weida; Shi, Xianli; Hu, Wei; Tan, Liping; Li, Kangxin; Wang, Zhen; Li, Guoqing

    2017-01-01

    To study prokaryotic expression and subcellular localization of α-13 giardin in Giardia lamblia trophozoites, α-13 giardin gene was amplified and cloned into prokaryotic expression vector pET-28a(+). The positive recombinant plasmid was transformed into E. coli BL21(DE3) for expression by using IPTG and autoinduction expression system (ZYM-5052). The target protein was validated by SDS-PAGE and Western blotting and purified by Ni-NTA Resin. Rabbits were immunized with purified fusion proteins for preparation of polyclonal antibody; then the intracellular location of α-13 giardin was determined by fluorescence immunoassay. The results showed that the length of α-13 giardin gene was 1038 bp, encoding a polypeptide of 345 amino acids. The expressed product was a fusion protein with about 40 kDa largely present in soluble form. The target protein accounted for 21.0% of total proteins after being induced with IPTG, while it accounted for 28.8% with ZYM-5052. The anti-α13-giardin polyclonal antibody possessed good antigenic specificity as well as excellent binding activity with recombinant α-13 giardin. Immunofluorescence assays revealed that α-13 giardin was localized in the cytoplasm of G. lamblia trophozoite, suggesting that it is a cytoplasm-associated protein. The present study may lay a foundation for further functional research on α-13 giardin of G. lamblia.

  1. Prokaryotic Expression of α-13 Giardin Gene and Its Intracellular Localization in Giardia lamblia

    PubMed Central

    Yu, Xingang; Pan, Weida; Shi, Xianli; Hu, Wei; Tan, Liping; Li, Kangxin; Wang, Zhen

    2017-01-01

    To study prokaryotic expression and subcellular localization of α-13 giardin in Giardia lamblia trophozoites, α-13 giardin gene was amplified and cloned into prokaryotic expression vector pET-28a(+). The positive recombinant plasmid was transformed into E. coli BL21(DE3) for expression by using IPTG and autoinduction expression system (ZYM-5052). The target protein was validated by SDS-PAGE and Western blotting and purified by Ni-NTA Resin. Rabbits were immunized with purified fusion proteins for preparation of polyclonal antibody; then the intracellular location of α-13 giardin was determined by fluorescence immunoassay. The results showed that the length of α-13 giardin gene was 1038 bp, encoding a polypeptide of 345 amino acids. The expressed product was a fusion protein with about 40 kDa largely present in soluble form. The target protein accounted for 21.0% of total proteins after being induced with IPTG, while it accounted for 28.8% with ZYM-5052. The anti-α13-giardin polyclonal antibody possessed good antigenic specificity as well as excellent binding activity with recombinant α-13 giardin. Immunofluorescence assays revealed that α-13 giardin was localized in the cytoplasm of G. lamblia trophozoite, suggesting that it is a cytoplasm-associated protein. The present study may lay a foundation for further functional research on α-13 giardin of G. lamblia. PMID:28286754

  2. Systematic Search for Evidence of Interdomain Horizontal Gene Transfer from Prokaryotes to Oomycete Lineages

    PubMed Central

    McCarthy, Charley G. P.

    2016-01-01

    ABSTRACT While most commonly associated with prokaryotes, horizontal gene transfer (HGT) can also have a significant influence on the evolution of microscopic eukaryotes. Systematic analysis of HGT in the genomes of the oomycetes, filamentous eukaryotic microorganisms in the Stramenopiles-Alveolates-Rhizaria (SAR) supergroup, has to date focused mainly on intradomain transfer events between oomycetes and fungi. Using systematic whole-genome analysis followed by phylogenetic reconstruction, we have investigated the extent of interdomain HGT between bacteria and plant-pathogenic oomycetes. We report five putative instances of HGT from bacteria into the oomycetes. Two transfers were found in Phytophthora species, including one unique to the cucurbit pathogen Phytophthora capsici. Two were found in Pythium species only, and the final transfer event was present in Phytopythium and Pythium species, the first reported bacterium-inherited genes in these genera. Our putative transfers included one protein that appears to be a member of the Pythium secretome, metabolic proteins, and enzymes that could potentially break down xenobiotics within the cell. Our findings complement both previous reports of bacterial genes in oomycete and SAR genomes and the growing body of evidence suggesting that interdomain transfer from prokaryotes into eukaryotes occurs more frequently than previously thought. IMPORTANCE Horizontal gene transfer (HGT) is the nonvertical inheritance of genetic material by transfer between different species. HGT is an important evolutionary mechanism for prokaryotes and in some cases is responsible for the spread of antibiotic resistance from resistant to benign species. Genome analysis has shown that examples of HGT are not as frequent in eukaryotes, but when they do occur they may have important evolutionary consequences. For example, the acquisition of fungal genes by an ancestral Phytophthora (plant destroyer) species is responsible for the large repertoire

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

    SciTech Connect

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

    2009-07-23

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

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

    PubMed Central

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

    2009-01-01

    The database of Alignable Tight Genomic Clusters (ATGCs) consists of closely related genomes of archaea and bacteria, and is a resource for research into prokaryotic microevolution. Construction of a data set with appropriate characteristics is a major hurdle for this type of studies. With the current rate of genome sequencing, it is difficult to follow the progress of the field and to determine which of the available genome sets meet the requirements of a given research project, in particular, with respect to the minimum and maximum levels of similarity between the included genomes. Additionally, extraction of specific content, such as genomic alignments or families of orthologs, from a selected set of genomes is a complicated and time-consuming process. The database addresses these problems by providing an intuitive and efficient web interface to browse precomputed ATGCs, select appropriate ones and access ATGC-derived data such as multiple alignments of orthologous proteins, matrices of pairwise intergenomic distances based on genome-wide analysis of synonymous and nonsynonymous substitution rates and others. The ATGC database will be regularly updated following new releases of the NCBI RefSeq. The database is hosted by the Genomics Division at Lawrence Berkeley National laboratory and is publicly available at http://atgc.lbl.gov PMID:18845571

  5. The Identification of Novel Diagnostic Marker Genes for the Detection of Beer Spoiling Pediococcus damnosus Strains Using the BlAst Diagnostic Gene findEr

    PubMed Central

    Schmid, Jonas; Zehe, Anja; Vogel, Rudi F.

    2016-01-01

    As the number of bacterial genomes increases dramatically, the demand for easy to use tools with transparent functionality and comprehensible output for applied comparative genomics grows as well. We present BlAst Diagnostic Gene findEr (BADGE), a tool for the rapid prediction of diagnostic marker genes (DMGs) for the differentiation of bacterial groups (e.g. pathogenic / nonpathogenic). DMG identification settings can be modified easily and installing and running BADGE does not require specific bioinformatics skills. During the BADGE run the user is informed step by step about the DMG finding process, thus making it easy to evaluate the impact of chosen settings and options. On the basis of an example with relevance for beer brewing, being one of the oldest biotechnological processes known, we show a straightforward procedure, from phenotyping, genome sequencing, assembly and annotation, up to a discriminant marker gene PCR assay, making comparative genomics a means to an end. The value and the functionality of BADGE were thoroughly examined, resulting in the successful identification and validation of an outstanding novel DMG (fabZ) for the discrimination of harmless and harmful contaminations of Pediococcus damnosus, which can be applied for spoilage risk determination in breweries. Concomitantly, we present and compare five complete P. damnosus genomes sequenced in this study, finding that the ability to produce the unwanted, spoilage associated off-flavor diacetyl is a plasmid encoded trait in this important beer spoiling species. PMID:27028007

  6. Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression

    NASA Astrophysics Data System (ADS)

    Roussel, Marc R.; Zhu, Rui

    2006-12-01

    The quantitative modeling of gene transcription and translation requires a treatment of two key features: stochastic fluctuations due to the limited copy numbers of key molecules (genes, RNA polymerases, ribosomes), and delayed output due to the time required for biopolymer synthesis. Recently proposed algorithms allow for efficient simulations of such systems. However, it is critical to know whether the results of delay stochastic simulations agree with those from more detailed models of the transcription and translation processes. We present a generalization of previous delay stochastic simulation algorithms which allows both for multiple delays and for distributions of delay times. We show that delay stochastic simulations closely approximate simulations of a detailed transcription model except when two-body effects (e.g. collisions between polymerases on a template strand) are important. Finally, we study a delay stochastic model of prokaryotic transcription and translation which reproduces observations from a recent experimental study in which a single gene was expressed under the control of a repressed lac promoter in E. coli cells. This demonstrates our ability to quantitatively model gene expression using these new methods.

  7. Ranking Gene Ontology terms for predicting non-classical secretory proteins in eukaryotes and prokaryotes.

    PubMed

    Huang, Wen-Lin

    2012-11-07

    Protein secretion is an important biological process for both eukaryotes and prokaryotes. Several sequence-based methods mainly rely on utilizing various types of complementary features to design accurate classifiers for predicting non-classical secretory proteins. Gene Ontology (GO) terms are increasing informative in predicting protein functions. However, the number of used GO terms is often very large. For example, there are 60,020 GO terms used in the prediction method Euk-mPLoc 2.0 for subcellular localization. This study proposes a novel approach to identify a small set of m top-ranked GO terms served as the only type of input features to design a support vector machine (SVM) based method Sec-GO to predict non-classical secretory proteins in both eukaryotes and prokaryotes. To evaluate the Sec-GO method, two existing methods and their used datasets are adopted for performance comparisons. The Sec-GO method using m=436 GO terms yields an independent test accuracy of 96.7% on mammalian proteins, much better than the existing method SPRED (82.2%) which uses frequencies of tri-peptides and short peptides, secondary structure, and physicochemical properties as input features of a random forest classifier. Furthermore, when applying to Gram-positive bacterial proteins, the Sec-GO with m=158 GO terms has a test accuracy of 94.5%, superior to NClassG+ (90.0%) which uses SVM with several feature types, comprising amino acid composition, di-peptides, physicochemical properties and the position specific weighting matrix. Analysis of the distribution of secretory proteins in a GO database indicates the percentage of the non-classical secretory proteins annotated by GO is larger than that of classical secretory proteins in both eukaryotes and prokaryotes. Of the m top-ranked GO features, the top-four GO terms are all annotated by such subcellular locations as GO:0005576 (Extracellular region). Additionally, the method Sec-GO is easily implemented and its web tool of

  8. Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains

    SciTech Connect

    Lan, Yemin; Rosen, Gail; Hershberg, Ruth

    2016-05-03

    The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels. In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that the percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage. In conclusion, our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.

  9. Marker genes that are less conserved in their sequences are useful for predicting genome-wide similarity levels between closely related prokaryotic strains

    DOE PAGES

    Lan, Yemin; Rosen, Gail; Hershberg, Ruth

    2016-05-03

    The 16s rRNA gene is so far the most widely used marker for taxonomical classification and separation of prokaryotes. Since it is universally conserved among prokaryotes, it is possible to use this gene to classify a broad range of prokaryotic organisms. At the same time, it has often been noted that the 16s rRNA gene is too conserved to separate between prokaryotes at finer taxonomic levels. In this paper, we examine how well levels of similarity of 16s rRNA and 73 additional universal or nearly universal marker genes correlate with genome-wide levels of gene sequence similarity. We demonstrate that themore » percent identity of 16s rRNA predicts genome-wide levels of similarity very well for distantly related prokaryotes, but not for closely related ones. In closely related prokaryotes, we find that there are many other marker genes for which levels of similarity are much more predictive of genome-wide levels of gene sequence similarity. Finally, we show that the identities of the markers that are most useful for predicting genome-wide levels of similarity within closely related prokaryotic lineages vary greatly between lineages. However, the most useful markers are always those that are least conserved in their sequences within each lineage. In conclusion, our results show that by choosing markers that are less conserved in their sequences within a lineage of interest, it is possible to better predict genome-wide gene sequence similarity between closely related prokaryotes than is possible using the 16s rRNA gene. We point readers towards a database we have created (POGO-DB) that can be used to easily establish which markers show lowest levels of sequence conservation within different prokaryotic lineages.« less

  10. Terpenoid biosynthesis in prokaryotes.

    PubMed

    Boronat, Albert; Rodríguez-Concepción, Manuel

    2015-01-01

    Prokaryotic organisms (archaea and eubacteria) are found in all habitats where life exists on our planet. This would not be possible without the astounding biochemical plasticity developed by such organisms. Part of the metabolic diversity of prokaryotes was transferred to eukaryotic cells when endosymbiotic prokaryotes became mitochondria and plastids but also in a large number of horizontal gene transfer episodes. A group of metabolites produced by all free-living organisms is terpenoids (also known as isoprenoids). In prokaryotes, terpenoids play an indispensable role in cell-wall and membrane biosynthesis (bactoprenol, hopanoids), electron transport (ubiquinone, menaquinone), or conversion of light into chemical energy (chlorophylls, bacteriochlorophylls, rhodopsins, carotenoids), among other processes. But despite their remarkable structural and functional diversity, they all derive from the same metabolic precursors. Here we describe the metabolic pathways producing these universal terpenoid units and provide a complete picture of the main terpenoid compounds found in prokaryotic organisms.

  11. Molecular cloning and prokaryotic expression of vp5 gene of grass carp reovirus strain GCRV096.

    PubMed

    Jian, Ji-chang; Wang, Ya; Yan, Xiu-ying; Ding, Yu; Wu, Zao-he; Lu, Yi-shan

    2013-12-01

    VP5 is an outer capsid protein of grass carp reovirus (GCRV). It is predicted to involve in helping GCRV enter the host cells. In this study, the full-length vp5 gene (accession number in GenBank: JN206664.1) was cloned from GCRV strain GCRV096, which was isolated from diseased grass carp (Ctenopharyngodon idella) in southern China by RT-PCR technique using the primers designed from the known vp5 gene sequences of other strains of GCRV published in GenBank. The ORF sequence of vp5 is composed of 1,947 nucleotides encoding a 648-residues protein with a calculated molecular mass of 68.6 kDa and an estimated isoelectric point of 6.1. Sequence analysis results showed that VP5 might serve as a penetration protein and play an important role in GCRV penetration into the host cells. A full length of vp5 gene was subcloned into the prokaryotic expression vector pET-28a (+) and the recombinant plasmid (pET/GCRV-VP5) was then transduced into Escherichia coli BL21 (DE3) cells to express VP5 in vitro. SDS-PAGE and western blotting analysis indicated that the protein expressed successfully. Results also showed that the fusion protein expressed in the form of inclusion body, and it expressed in the highest level when induced with 0.2-mM IPTG at 28 °C for 4 h. These results are important for the future study on the molecular structure, function, and immunogenicity of GCRV capsid protein.

  12. Changes in 16s RNA Gene Microbial Community Profiling by Concentration of Prokaryotic DNA.

    PubMed

    Glassing, Angela; Dowd, Scot E; Galandiuk, Susan; Davis, Brian; Jorden, Jeffrey R; Chiodini, Rodrick J

    2015-12-01

    Microbial metagenomics are hindered in clinical tissue samples as a result of the large relative amount of human DNA in relation to microbial DNA acting as competitive inhibitors of downstream applications. We evaluated the LOOXSTER® Enrichment Kit to separate eukaryotic and prokaryotic DNA in submucosal intestinal tissue samples having a low microbial biomass and to determine the effects of enrichment on 16s rRNA microbiota sequencing. The enrichment kit reduced the amount of human DNA in the samples 40-70% resulting in a 3.5-fold increase in the number of 16s bacterial gene sequences detected on the Illumina MiSeq platform. This increase was accompanied by the detection of 41 additional bacterial genera and 94 tentative species. The additional bacterial taxa detected accounted for as much as 25% of the total bacterial population that significantly altered the relative prevalence and composition of the intestinal microbiota. The ability to reduce the competitive inhibition created by human DNA and the concentration of bacterial DNA may allow metagenomics to be performed on complex tissues containing a low bacterial biomass.

  13. [Cloning and prokaryotic expression of major ampullate spidroin gene of spider].

    PubMed

    Pan, Hong-Chun; Song, Da-Xiang; Zhou, Kai-Ya; Zhu, Guo-Ping

    2007-05-01

    RT-PCR was conducted with one degenerate primer designed according to repetitive regions' amino acid sequence of major ampullate spidroin (MaSp) in spiders and adaptor primer in the SMART cDNA Library Construction Kit. By cloning and sequencing of amplified products, one cDNA clone (GenBank Accession No. AY365017) of Argiope amoena MaSp gene was obtained. The deduced amino acid sequence can be distinctly divided into two regions: (1) Repetitive region that consists of an alternating alanine-rich and glycine-rich domain in which many prolines are present; and (2) C-terminal non-repetitive region. The region coding for 272 amino acids of MaSp gene was subcloned into prokaryotic expression vector pET28b(+) and an about 26kD recombinant protein was expressed at high levels in Escherichia coli BL21 (DE3) after induction of IPTG. After being purified with metal-affinity chromatography on Ni(2+) -IDA-Sepharose columns as well as gel filtration chromatography, the recombinant protein was confirmed to be predicted MaSp by means of amino acid composition analysis and N-terminal amino acid sequence analysis. The solubility behavior of recombinant MaSp with C-terminal non-repetitive region in the present study is similar to that of recombinant dragline silk proteins without C-terminal non-repetitive region expressed by bacteria and yeast in the other studies. The result shows that absence or presence of C-terminal non-repetitive region is not a crucial factor affecting the solubility of the recombinant MaSp.

  14. Detection of single-copy functional genes in prokaryotic cells by two-pass TSA-FISH with polynucleotide probes.

    PubMed

    Kawakami, Shuji; Hasegawa, Takuya; Imachi, Hiroyuki; Yamaguchi, Takashi; Harada, Hideki; Ohashi, Akiyoshi; Kubota, Kengo

    2012-02-01

    In situ detection of functional genes with single-cell resolution is currently of interest to microbiologists. Here, we developed a two-pass tyramide signal amplification (TSA)-fluorescence in situ hybridization (FISH) protocol with PCR-derived polynucleotide probes for the detection of single-copy genes in prokaryotic cells. The mcrA gene and the apsA gene in methanogens and sulfate-reducing bacteria, respectively, were targeted. The protocol showed bright fluorescence with a good signal-to-noise ratio and achieved a high efficiency of detection (>98%). The discrimination threshold was approximately 82-89% sequence identity. Microorganisms possessing the mcrA or apsA gene in anaerobic sludge samples were successfully detected by two-pass TSA-FISH with polynucleotide probes. The developed protocol is useful for identifying single microbial cells based on functional gene sequences.

  15. FrameD: A flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences.

    PubMed

    Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

    2003-07-01

    We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms.

  16. FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences

    PubMed Central

    Schiex, Thomas; Gouzy, Jérôme; Moisan, Annick; de Oliveira, Yannick

    2003-01-01

    We describe FrameD, a program that predicts coding regions in prokaryotic and matured eukaryotic sequences. Initially targeted at gene prediction in bacterial GC rich genomes, the gene model used in FrameD also allows to predict genes in the presence of frameshifts and partially undetermined sequences which makes it also very suitable for gene prediction and frameshift correction in unfinished sequences such as EST and EST cluster sequences. Like recent eukaryotic gene prediction programs, FrameD also includes the ability to take into account protein similarity information both in its prediction and its graphical output. Its performances are evaluated on different bacterial genomes. The web site (http://genopole.toulouse.inra.fr/bioinfo/FrameD/FD) allows direct prediction, sequence correction and translation and the ability to learn new models for new organisms. PMID:12824407

  17. A close relationship between primary nucleotides sequence structure and the composition of functional genes in the genome of prokaryotes.

    PubMed

    Garcia, Juan A L; Fernández-Guerra, Antoni; Casamayor, Emilio O

    2011-12-01

    Comparative genomics is an essential tool to unravel how genomes change over evolutionary time and to gain clues on the links between functional genomics and evolution. In prokaryotes, the large, good quality, genome sequences available in public databases and the recently developed large-scale computational methods, offer an unprecedent view on the ecology and evolution of microorganisms through comparative genomics. In this work, we examined the links among genome structure (i.e., the sequential distribution of nucleotides itself by detrended fluctuation analysis, DFA) and genomic diversity (i.e., gene functionality by Clusters of Orthologous Genes, COGs) in 828 full sequenced prokaryotic genomes from 548 different bacteria and archaea species. DFA scaling exponent α indicated persistent long-range correlations (fractality) in each genome analyzed. Higher resolution power was found when considering the sequential succession of purine (AG) vs. pyrimidine (CT) bases than either keto (GT) to amino (AC) forms or strongly (GC) vs. weakly (AT) bonded nucleotides. Interestingly, the phyla Aquificae, Fusobacteria, Dictyoglomi, Nitrospirae, and Thermotogae were closer to archaea than to their bacterial counterparts. A strong significant correlation was found between scaling exponent α and COGs distribution, and we consistently observed that the larger α the more heterogeneous was the gene distribution within each functional category, suggesting a close relationship between primary nucleotides sequence structure and functional genes composition.

  18. Construction and expression of prokaryotic expression vectors fused with genes of Magnaporthe oryzae effector proteins and mCherry.

    PubMed

    Yang, Y Q; Wang, H; Liang, M L; Yan, J L; Liu, L; Li, C Y; Yang, J

    2015-09-09

    The aim of the current study was to investigate the prokaryotic expression of the Magnaporthe oryzae effector genes BAS1 and BAS4 fused to the fluorescent protein mCherry. Based on previous polymorphic analysis of BAS1 and BAS4 in rice blast strains using PCR, blast strains containing the PCR products of BAS1 and BAS4 were selected for liquid culture for total RNA extraction. For PCR analysis, cDNA was selected as a template to amplify the coding region of BAS1 and BAS4, the plasmid pXY201 was selected as template to amplify the mCherry sequence, and the three sequences were cloned into pMD®19-T vectors. Positive recombinant plasmids were digested using two restriction enzymes and the cleaved fragments of BAS1 and mCherry and BAS4 and mCherry were ligated to pGEX-4T-1 vectors and expression was induced using IPTG. The PCR results showed that the sequence sizes of BAS1, BAS4, and mCherry were 348, 309, and 711 bp, respectively, and these were cloned into pMD®19-T vectors. After digestion and gel purification, the fragments of BAS1 and mCherry, BAS4 and mCherry were ligated into pGEX-4T-1 vectors and expressed in Escherichia coli BL21 competent cells. The expressed proteins were approximately 60 kDa, corresponding to their theoretical size. Prokaryotic expression products of BAS1 and BAS4 fused to mCherry were presented in this study, providing a base for constructing prokaryotic expression vectors of pathogen effector genes fused to mCherry, which will contribute to further study of the subcellular localization, function, and protein interactions of these effectors.

  19. Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).

    PubMed

    Kosuge, Takehide; Abe, Takashi; Okido, Toshihisa; Tanaka, Naoto; Hirahata, Masaki; Maruyama, Yutaka; Mashima, Jun; Tomiki, Aki; Kurokawa, Motoyoshi; Himeno, Ryutaro; Fukuchi, Satoshi; Miyazaki, Satoru; Gojobori, Takashi; Tateno, Yoshio; Sugawara, Hideaki

    2006-12-31

    A large number of complete microorganism genomes has been sequenced and submitted to the public database and then incorporated into our complete genome database, Genome Information Broker (GIB, http://gib.genes.nig.ac.jp/). However, when comparative genomics is carried out, researchers must be aware that there are protein-coding genes not confirmed by homology or motif search and that reliable protein-coding genes are missing. Therefore, we developed a protocol (Gene Trek in Prokaryote Space, GTPS) for finding possible protein-coding genes in bacterial genomes. GTPS assigns a degree of reliability to predicted protein-coding genes. We first systematically applied the protocol to the complete genomes of all 123 bacterial species and strains that were publicly available as of July 2003, and then to those of 183 species and strains available as of September 2004. We found a number of incorrect genes and several new ones in the genome data in question. We also found a way to estimate the total number of orthologous genes in the bacterial world.

  20. Recent events dominate interdomain lateral gene transfers between prokaryotes and eukaryotes and, with the exception of endosymbiotic gene transfers, few ancient transfer events persist

    PubMed Central

    Katz, Laura A.

    2015-01-01

    While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals include searching for LGTs that unite major eukaryotic clades, and describing the relative contributions of LGT and EGT across the eukaryotic tree of life. Given the difficulties in interpreting single gene trees that aim to capture the approximately 1.8 billion years of eukaryotic evolution, we focus on presence–absence data to identify interdomain transfer events. Specifically, we identify 1138 genes found only in prokaryotes and representatives of three or fewer major clades of eukaryotes (e.g. Amoebozoa, Archaeplastida, Excavata, Opisthokonta, SAR and orphan lineages). The majority of these genes have phylogenetic patterns that are consistent with recent interdomain LGTs and, with the notable exception of EGTs involving photosynthetic eukaryotes, we detect few ancient interdomain LGTs. These analyses suggest that LGTs have probably occurred throughout the history of eukaryotes, but that ancient events are not maintained unless they are associated with endosymbiotic gene transfer among photosynthetic lineages. PMID:26323756

  1. AHF: AMIGA'S HALO FINDER

    SciTech Connect

    Knollmann, Steffen R.; Knebe, Alexander

    2009-06-15

    Cosmological simulations are the key tool for investigating the different processes involved in the formation of the universe from small initial density perturbations to galaxies and clusters of galaxies observed today. The identification and analysis of bound objects, halos, is one of the most important steps in drawing useful physical information from simulations. In the advent of larger and larger simulations, a reliable and parallel halo finder, able to cope with the ever-increasing data files, is a must. In this work we present the freely available MPI parallel halo finder AHF. We provide a description of the algorithm and the strategy followed to handle large simulation data. We also describe the parameters a user may choose in order to influence the process of halo finding, as well as pointing out which parameters are crucial to ensure untainted results from the parallel approach. Furthermore, we demonstrate the ability of AHF to scale to high-resolution simulations.

  2. Evolution of small prokaryotic genomes.

    PubMed

    Martínez-Cano, David J; Reyes-Prieto, Mariana; Martínez-Romero, Esperanza; Partida-Martínez, Laila P; Latorre, Amparo; Moya, Andrés; Delaye, Luis

    2014-01-01

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

  3. Evolution of small prokaryotic genomes

    PubMed Central

    Martínez-Cano, David J.; Reyes-Prieto, Mariana; Martínez-Romero, Esperanza; Partida-Martínez, Laila P.; Latorre, Amparo; Moya, Andrés; Delaye, Luis

    2015-01-01

    As revealed by genome sequencing, the biology of prokaryotes with reduced genomes is strikingly diverse. These include free-living prokaryotes with ∼800 genes as well as endosymbiotic bacteria with as few as ∼140 genes. Comparative genomics is revealing the evolutionary mechanisms that led to these small genomes. In the case of free-living prokaryotes, natural selection directly favored genome reduction, while in the case of endosymbiotic prokaryotes neutral processes played a more prominent role. However, new experimental data suggest that selective processes may be at operation as well for endosymbiotic prokaryotes at least during the first stages of genome reduction. Endosymbiotic prokaryotes have evolved diverse strategies for living with reduced gene sets inside a host-defined medium. These include utilization of host-encoded functions (some of them coded by genes acquired by gene transfer from the endosymbiont and/or other bacteria); metabolic complementation between co-symbionts; and forming consortiums with other bacteria within the host. Recent genome sequencing projects of intracellular mutualistic bacteria showed that previously believed universal evolutionary trends like reduced G+C content and conservation of genome synteny are not always present in highly reduced genomes. Finally, the simplified molecular machinery of some of these organisms with small genomes may be used to aid in the design of artificial minimal cells. Here we review recent genomic discoveries of the biology of prokaryotes endowed with small gene sets and discuss the evolutionary mechanisms that have been proposed to explain their peculiar nature. PMID:25610432

  4. Ecology of prokaryotic viruses.

    PubMed

    Weinbauer, Markus G

    2004-05-01

    The finding that total viral abundance is higher than total prokaryotic abundance and that a significant fraction of the prokaryotic community is infected with phages in aquatic systems has stimulated research on the ecology of prokaryotic viruses and their role in ecosystems. This review treats the ecology of prokaryotic viruses ('phages') in marine, freshwater and soil systems from a 'virus point of view'. The abundance of viruses varies strongly in different environments and is related to bacterial abundance or activity suggesting that the majority of the viruses found in the environment are typically phages. Data on phage diversity are sparse but indicate that phages are extremely diverse in natural systems. Lytic phages are predators of prokaryotes, whereas lysogenic and chronic infections represent a parasitic interaction. Some forms of lysogeny might be described best as mutualism. The little existing ecological data on phage populations indicate a large variety of environmental niches and survival strategies. The host cell is the main resource for phages and the resource quality, i.e., the metabolic state of the host cell, is a critical factor in all steps of the phage life cycle. Virus-induced mortality of prokaryotes varies strongly on a temporal and spatial scale and shows that phages can be important predators of bacterioplankton. This mortality and the release of cell lysis products into the environment can strongly influence microbial food web processes and biogeochemical cycles. Phages can also affect host diversity, e.g., by 'killing the winner' and keeping in check competitively dominant species or populations. Moreover, they mediate gene transfer between prokaryotes, but this remains largely unknown in the environment. Genomics or proteomics are providing us now with powerful tools in phage ecology, but final testing will have to be performed in the environment.

  5. CellFinder: a cell data repository.

    PubMed

    Stachelscheid, Harald; Seltmann, Stefanie; Lekschas, Fritz; Fontaine, Jean-Fred; Mah, Nancy; Neves, Mariana; Andrade-Navarro, Miguel A; Leser, Ulf; Kurtz, Andreas

    2014-01-01

    CellFinder (http://www.cellfinder.org) is a comprehensive one-stop resource for molecular data characterizing mammalian cells in different tissues and in different development stages. It is built from carefully selected data sets stemming from other curated databases and the biomedical literature. To date, CellFinder describes 3394 cell types and 50 951 cell lines. The database currently contains 3055 microscopic and anatomical images, 205 whole-genome expression profiles of 194 cell/tissue types from RNA-seq and microarrays and 553 905 protein expressions for 535 cells/tissues. Text mining of a corpus of >2000 publications followed by manual curation confirmed expression information on ∼900 proteins and genes. CellFinder's data model is capable to seamlessly represent entities from single cells to the organ level, to incorporate mappings between homologous entities in different species and to describe processes of cell development and differentiation. Its ontological backbone currently consists of 204 741 ontology terms incorporated from 10 different ontologies unified under the novel CELDA ontology. CellFinder's web portal allows searching, browsing and comparing the stored data, interactive construction of developmental trees and navigating the partonomic hierarchy of cells and tissues through a unique body browser designed for life scientists and clinicians.

  6. Promoters responsive to DNA bending: a common theme in prokaryotic gene expression.

    PubMed Central

    Pérez-Martín, J; Rojo, F; de Lorenzo, V

    1994-01-01

    The early notion of DNA as a passive target for regulatory proteins has given way to the realization that higher-order DNA structures and DNA-protein complexes are at the basis of many molecular processes, including control of promoter activity. Protein binding may direct the bending of an otherwise linear DNA, exacerbate the angle of an intrinsic bend, or assist the directional flexibility of certain sequences within prokaryotic promoters. The important, sometimes essential role of intrinsic or protein-induced DNA bending in transcriptional regulation has become evident in virtually every system examined. As discussed throughout this article, not every function of DNA bends is understood, but their presence has been detected in a wide variety of bacterial promoters subjected to positive or negative control. Nonlinear DNA structures facilitate and even determine proximal and distal DNA-protein and protein-protein contacts involved in the various steps leading to transcription initiation. PMID:8078436

  7. Analysis of the multi-copied genes and the impact of the redundant protein coding sequences on gene annotation in prokaryotic genomes.

    PubMed

    Yu, Jia-Feng; Chen, Qing-Li; Ren, Jing; Yang, Yan-Ling; Wang, Ji-Hua; Sun, Xiao

    2015-07-07

    The important roles of duplicated genes in evolutional process have been recognized in bacteria, archaebacteria and eukaryotes, while there is very little study on the multi-copied protein coding genes that share sequence identity of 100%. In this paper, the multi-copied protein coding genes in a number of prokaryotic genomes are comprehensively analyzed firstly. The results show that 0-15.93% of the protein coding genes in each genome are multi-copied genes and 0-16.49% of the protein coding genes in each genome are highly similar with the sequence identity ≥ 80%. Function and COG (Clusters of Orthologous Groups of proteins) analysis shows that 64.64% of multi-copied genes concentrate on the function of transposase and 86.28% of the COG assigned multi-copied genes concentrate on the COG code of 'L'. Furthermore, the impact of redundant protein coding sequences on the gene prediction results is studied. The results show that the problem of protein coding sequence redundancies cannot be ignored and the consistency of the gene annotation results before and after excluding the redundant sequences is negatively related with the sequences redundancy degree of the protein coding sequences in the training set.

  8. [Prokaryotic expression of vp3 gene of Muscovy duck parvovirus, and its antiserum preparation for detection of virus multiplication].

    PubMed

    Huang, Yu; Zhu, Yumin; Dong, Shijuan; Yu, Ruisong; Zhang, Yuanshu; Li, Zhen

    2015-01-01

    New epidemic broke out in recent year which was suspected to be caused by variant Muscovy duck parvovirus (MDPV). For this reason, new MDPV detection methods are needed for the new virus strains. In this study, a pair of primers were designed according to the full-length genome of MDPV strain SAAS-SHNH, which were identified in 2012, and were used to amplify the vp3 gene of MDPV by polymerase chain reaction. After being sequenced, the vp3 gene was subcloned into the prokaryotic expression vector PET28a. The recombinant plasmid was transformed into E. coli BL21 and induced with IPTG. SDS-PAGE and Western blotting analysis showed the MDPV vp3 gene was successfully expressed. After being purified by Ni2+ affinity chromatography system, the recombinant protein was used as antigen to immunize rabbits to obtain antiserum. Western blotting analysis showed that the acquired antiserum could react specifically with VP3 protein of J3D6 strain and MDPV vaccine strain. The antiserum could also be used for detection of cultured MDPV from primary duck embryo fibroblasts by immune fluorescence assay (IFA). It could be concluded that the VP3 protein and its antibody prepared in the research could be used for detection of VP3 antiserum and antigen respectively.

  9. Functional genes (dsr) approach reveals similar sulphidogenic prokaryotes diversity but different structure in saline waters from corroding high temperature petroleum reservoirs.

    PubMed

    Guan, Jing; Zhang, Bing-Liang; Mbadinga, Serge Maurice; Liu, Jin-Feng; Gu, Ji-Dong; Mu, Bo-Zhong

    2014-02-01

    Oil reservoirs and production facilities are generally contaminated with H2S resulting from the activity of sulphidogenic prokaryotes (SRP). Sulphidogenesis plays a major role in reservoir souring and microbial influenced corrosion in oil production systems. In the present study, sulphidogenic microbial diversity and composition in saline production fluids retrieved from three blocks of corroding high temperature (79 ~ 95 °C) oil reservoirs with high sulfate concentrations were investigated by phylogenetic analyses of gene fragments of the dissimilatory sulfite reductase (dsr). Analysis of dsr gene fragments revealed the presence of several clusters of sulphidogenic prokaryotes that cover the orders Desulfovibrionales (Desulfovibrio, Desulfomicrobium thermophilum), Desulfobacterales (Desulfobacterium, Desulfosarcina, Desulfococcus, Desulfotignum, Desulfobotulus, Desulfobulbus), Syntrophobacterales (Desulfacinum, Thermodesulforhabdus, Desulforhabdus), Clostridiales (Desulfotomaculum) and Archaeoglobales (Archaeoglobus); among which sequences affiliated to members of Desulfomicrobium, Desulfotomaculum and Desulfovibrio appeared to be the most encountered genera within the three blocks. Collectively, phylogenetic and non-metric multidimensional scaling analyses indicated similar but structurally different sulphidogenic prokaryotes communities within the waters retrieved from the three Blocks. This study show the diversity and composition of sulphidogenic prokaryotes that may play a role in the souring mediated corrosion of the oilfield and also provides a fundamental basis for further investigation to control oil reservoir souring and corrosion of pipelines and topside installations.

  10. Beta-lactam antibiotic biosynthetic genes have been conserved in clusters in prokaryotes and eukaryotes.

    PubMed Central

    Smith, D J; Burnham, M K; Bull, J H; Hodgson, J E; Ward, J M; Browne, P; Brown, J; Barton, B; Earl, A J; Turner, G

    1990-01-01

    A cosmid clone containing closely linked beta-lactam antibiotic biosynthetic genes was isolated from a gene library of Flavobacterium sp. SC 12,154. The location within the cluster of the DNA thought to contain the gene for delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS), the first step in the beta-lactam antibiotic biosynthetic pathway, was identified by a novel method. This DNA facilitated the isolation, by cross-hybridization, of the corresponding DNA from Streptomyces clavuligerus ATCC 27064, Penicillium chrysogenum Oli13 and Aspergillus nidulans R153. Evidence was obtained which confirmed that the cross-hybridizing sequences contained the ACVS gene. In each case the ACVS gene was found to be closely linked to other beta-lactam biosynthetic genes and constituted part of a gene cluster. Images Fig. 1. Fig. 2. Fig. 4. Fig. 5. Fig. 6. Fig. 7. PMID:2107074

  11. A statistical framework for improving genomic annotations of prokaryotic essential genes.

    PubMed

    Deng, Jingyuan; Su, Shengchang; Lin, Xiaodong; Hassett, Daniel J; Lu, Long Jason

    2013-01-01

    Large-scale systematic analysis of gene essentiality is an important step closer toward unraveling the complex relationship between genotypes and phenotypes. Such analysis cannot be accomplished without unbiased and accurate annotations of essential genes. In current genomic databases, most of the essential gene annotations are derived from whole-genome transposon mutagenesis (TM), the most frequently used experimental approach for determining essential genes in microorganisms under defined conditions. However, there are substantial systematic biases associated with TM experiments. In this study, we developed a novel Poisson model-based statistical framework to simulate the TM insertion process and subsequently correct the experimental biases. We first quantitatively assessed the effects of major factors that potentially influence the accuracy of TM and subsequently incorporated relevant factors into the framework. Through iteratively optimizing parameters, we inferred the actual insertion events occurred and described each gene's essentiality on probability measure. Evaluated by the definite mapping of essential gene profile in Escherichia coli, our model significantly improved the accuracy of original TM datasets, resulting in more accurate annotations of essential genes. Our method also showed encouraging results in improving subsaturation level TM datasets. To test our model's broad applicability to other bacteria, we applied it to Pseudomonas aeruginosa PAO1 and Francisella tularensis novicida TM datasets. We validated our predictions by literature as well as allelic exchange experiments in PAO1. Our model was correct on six of the seven tested genes. Remarkably, among all three cases that our predictions contradicted the TM assignments, experimental validations supported our predictions. In summary, our method will be a promising tool in improving genomic annotations of essential genes and enabling large-scale explorations of gene essentiality. Our

  12. Ranking of Prokaryotic Genomes Based on Maximization of Sortedness of Gene Lengths.

    PubMed

    Bolshoy, A; Salih, B; Cohen, I; Tatarinova, T

    How variations of gene lengths (some genes become longer than their predecessors, while other genes become shorter and the sizes of these factions are randomly different from organism to organism) depend on organismal evolution and adaptation is still an open question. We propose to rank the genomes according to lengths of their genes, and then find association between the genome rank and variousproperties, such as growth temperature, nucleotide composition, and pathogenicity. This approach reveals evolutionary driving factors. The main purpose of this study is to test effectiveness and robustness of several ranking methods. The selected method of evaluation is measuring of overall sortedness of the data. We have demonstrated that all considered methods give consistent results and Bubble Sort and Simulated Annealing achieve the highest sortedness. Also, Bubble Sort is considerably faster than the Simulated Annealing method.

  13. Ranking of Prokaryotic Genomes Based on Maximization of Sortedness of Gene Lengths

    PubMed Central

    Bolshoy, A; Salih, B; Cohen, I; Tatarinova, T

    2014-01-01

    How variations of gene lengths (some genes become longer than their predecessors, while other genes become shorter and the sizes of these factions are randomly different from organism to organism) depend on organismal evolution and adaptation is still an open question. We propose to rank the genomes according to lengths of their genes, and then find association between the genome rank and variousproperties, such as growth temperature, nucleotide composition, and pathogenicity. This approach reveals evolutionary driving factors. The main purpose of this study is to test effectiveness and robustness of several ranking methods. The selected method of evaluation is measuring of overall sortedness of the data. We have demonstrated that all considered methods give consistent results and Bubble Sort and Simulated Annealing achieve the highest sortedness. Also, Bubble Sort is considerably faster than the Simulated Annealing method. PMID:26146586

  14. Evolutionary rewiring: a modified prokaryotic gene-regulatory pathway in chloroplasts

    PubMed Central

    Puthiyaveetil, Sujith; Ibrahim, Iskander M.; Allen, John F.

    2013-01-01

    Photosynthetic electron transport regulates chloroplast gene transcription through the action of a bacterial-type sensor kinase known as chloroplast sensor kinase (CSK). CSK represses photosystem I (PS I) gene transcription in PS I light and thus initiates photosystem stoichiometry adjustment. In cyanobacteria and in non-green algae, CSK homologues co-exist with their response regulator partners in canonical bacterial two-component systems. In green algae and plants, however, no response regulator partner of CSK is found. Yeast two-hybrid analysis has revealed interaction of CSK with sigma factor 1 (SIG1) of chloroplast RNA polymerase. Here we present further evidence for the interaction between CSK and SIG1. We also show that CSK interacts with quinone. Arabidopsis SIG1 becomes phosphorylated in PS I light, which then specifically represses transcription of PS I genes. In view of the identical signalling properties of CSK and SIG1 and of their interactions, we suggest that CSK is a SIG1 kinase. We propose that the selective repression of PS I genes arises from the operation of a gene-regulatory phosphoswitch in SIG1. The CSK-SIG1 system represents a novel, rewired chloroplast-signalling pathway created by evolutionary tinkering. This regulatory system supports a proposal for the selection pressure behind the evolutionary stasis of chloroplast genes. PMID:23754813

  15. Evolutionary rewiring: a modified prokaryotic gene-regulatory pathway in chloroplasts.

    PubMed

    Puthiyaveetil, Sujith; Ibrahim, Iskander M; Allen, John F

    2013-07-19

    Photosynthetic electron transport regulates chloroplast gene transcription through the action of a bacterial-type sensor kinase known as chloroplast sensor kinase (CSK). CSK represses photosystem I (PS I) gene transcription in PS I light and thus initiates photosystem stoichiometry adjustment. In cyanobacteria and in non-green algae, CSK homologues co-exist with their response regulator partners in canonical bacterial two-component systems. In green algae and plants, however, no response regulator partner of CSK is found. Yeast two-hybrid analysis has revealed interaction of CSK with sigma factor 1 (SIG1) of chloroplast RNA polymerase. Here we present further evidence for the interaction between CSK and SIG1. We also show that CSK interacts with quinone. Arabidopsis SIG1 becomes phosphorylated in PS I light, which then specifically represses transcription of PS I genes. In view of the identical signalling properties of CSK and SIG1 and of their interactions, we suggest that CSK is a SIG1 kinase. We propose that the selective repression of PS I genes arises from the operation of a gene-regulatory phosphoswitch in SIG1. The CSK-SIG1 system represents a novel, rewired chloroplast-signalling pathway created by evolutionary tinkering. This regulatory system supports a proposal for the selection pressure behind the evolutionary stasis of chloroplast genes.

  16. [Cloning, prokaryotic expression, and functional identification of a sesquiterpene synthase gene (AsSS4) from Aquilaria sinensis].

    PubMed

    Liang, Liang; Guo, Qing-Mei; Zhang, Zheng; Xu, Yan-Hong; Han, Xiao-Min; Liu, Juan

    2014-12-01

    A sesquiterpene synthase (AsSS4) full-length open reading frame (ORF) cDNA was cloned from wounded stems of Aquilaria sinensis by RT-PCR method. The result showed that the ORF of AsSS4 was 1,698 bp encoding 565 amino acids. Prokaryotic expression vector pET28a-AsSS4 was constructed and transformed into E. coli BL21 (DE3) pLysS. Recombinant AsSS4 protein was obtained after induction by IPTG and SDS-PAGE analysis with a MW of 64 kD. Enzymatic reactions using farnesyl pyrophosphate showed that recombinant AsSS4 protein purified by Ni-agarose gel yielded five sesquiterpene compounds, cyclohexane, 1-ethenyl-1-methyl-2, 4-bis(1-methylethenyl)-, β-elemene, α-guaiene, α-caryophyllene and δ-guaiene. This paper reported the first cloning and functional characterization of AsSS4 gene from A. sinensis, which will establish a foundation for future studies on the molecular mechanisms of wound-induce agarwood formation in A. sinensis

  17. Unsuspected Diversity of Arsenite-Oxidizing Bacteria as Revealed by Widespread Distribution of the aoxB Gene in Prokaryotes ▿ †

    PubMed Central

    Heinrich-Salmeron, Audrey; Cordi, Audrey; Brochier-Armanet, Céline; Halter, David; Pagnout, Christophe; Abbaszadeh-fard, Elham; Montaut, Didier; Seby, Fabienne; Bertin, Philippe N.; Bauda, Pascale; Arsène-Ploetze, Florence

    2011-01-01

    In this study, new strains were isolated from an environment with elevated arsenic levels, Sainte-Marie-aux-Mines (France), and the diversity of aoxB genes encoding the arsenite oxidase large subunit was investigated. The distribution of bacterial aoxB genes is wider than what was previously thought. AoxB subfamilies characterized by specific signatures were identified. An exhaustive analysis of AoxB sequences from this study and from public databases shows that horizontal gene transfer has likely played a role in the spreading of aoxB in prokaryotic communities. PMID:21571879

  18. Gene cloning and prokaryotic expression of recombinant flagellin A from Vibrio parahaemolyticus

    NASA Astrophysics Data System (ADS)

    Yuan, Ye; Wang, Xiuli; Guo, Sheping; Liu, Yang; Ge, Hui; Qiu, Xuemei

    2010-11-01

    The Gram-negative Vibrio parahaemolyticus is a common pathogen in humans and marine animals. Bacteria flagellins play an important role during infection and induction of the host immune response. Thus, flagellin proteins are an ideal target for vaccines. We amplified the complete flagellin subunit gene ( flaA) from V. parahaemolyticus ATCC 17802. We then cloned and expressed the gene into Escherichia coli BL21 (DE3) cells. The gene coded for a protein that was 62.78 kDa. We purified and characterized the protein using Ni-NTA affinity chromatography and Anti-His antibody Western blotting, respectively. Our results provide a basis for further studies into the utility of the FlaA protein as a vaccine candidate against infection by Vibrio parahaemolyticus. In addition, the purified FlaA protein can be used for further functional and structural studies.

  19. Gene cloning and prokaryotic expression of recombinant outer membrane protein from Vibrio parahaemolyticus

    NASA Astrophysics Data System (ADS)

    Yuan, Ye; Wang, Xiuli; Guo, Sheping; Qiu, Xuemei

    2011-06-01

    Gram-negative Vibrio parahaemolyticus is a common pathogen in humans and marine animals. The outer membrane protein of bacteria plays an important role in the infection and pathogenicity to the host. Thus, the outer membrane proteins are an ideal target for vaccines. We amplified a complete outer membrane protein gene (ompW) from V. parahaemolyticus ATCC 17802. We then cloned and expressed the gene into Escherichia coli BL21 (DE3) cells. The gene coded for a protein that was 42.78 kDa. We purified the protein using Ni-NTA affinity chromatography and Anti-His antibody Western blotting, respectively. Our results provide a basis for future application of the OmpW protein as a vaccine candidate against infection by V. parahaemolyticus. In addition, the purified OmpW protein can be used for further functional and structural studies.

  20. Insights into secondary metabolism from a global analysis of prokaryotic biosynthetic gene clusters

    PubMed Central

    Cimermancic, Peter; Medema, Marnix H.; Claesen, Jan; Kurita, Kenji; Wieland Brown, Laura C.; Mavrommatis, Konstantinos; Pati, Amrita; Godfrey, Paul A.; Koehrsen, Michael; Clardy, Jon; Birren, Bruce W.; Takano, Eriko; Sali, Andrej; Linington, Roger G.; Fischbach, Michael A.

    2014-01-01

    Summary Although biosynthetic gene clusters (BGCs) have been discovered for hundreds of bacterial metabolites, our knowledge of their diversity remains limited. Here, we used a novel algorithm to systematically identify BGCs in the extensive extant microbial sequencing data. Network analysis of the predicted BGCs revealed large gene cluster families, the vast majority uncharacterized. We experimentally characterized the most prominent family, consisting of two subfamilies of hundreds of BGCs distributed throughout the Proteobacteria; their products are aryl polyenes, lipids with an aryl head group conjugated to a polyene tail. We identified a distant relationship to a third subfamily of aryl polyene BGCs, and together the three subfamilies represent the largest known family of biosynthetic gene clusters, with more than 1,000 members. Although these clusters are widely divergent in sequence, their small molecule products are remarkably conserved, indicating for the first time the important roles these compounds play in Gram-negative cell biology. PMID:25036635

  1. [Cloning, prokaryotic expression and characterization of lysine decarboxylase gene from Huperzia serrata].

    PubMed

    Di, Ci; Li, Jing; Tang, Yuntao; Peng, Qingzhong

    2014-08-01

    Huperzine A is a promising drug to treat Alzheimer's disease (AD). To date, its biosynthetic pathway is still unknown. Lysine decarboxylase (LDC) has been proposed to catalyze the first-step of the biosynthesis of huperzine A. To identify and characterize LDCs from Huperzia serrata, we isolated two LDC fragments (LDC1 and LDC2) from leaves of H. serrata by RT-PCR and then cloned them into pMD 19-T vector. Sequence analysis showed that LDC1 and LDC2 genes shared 95.3% identity and encoded the protein of 212 and 202 amino acid residues respectively. Thus, we ligated LDC genes into pET-32a(+) to obtain recombinant expressing vectors pET-32a(+)/LDC1 and pET-32a(+)/LDC2 respectively. We further introduced two expression vectors into Escherichia coli BL21(DE3) and cultured positive colonies of E. coli in liquid LB medium. After inducing for 4 hours with 260 μg/mL IPTG at 30 degrees C, soluble recombinant Trx-LDC1 and Trx-LDC2 were obtained and isolated for purification using a Ni-NTA affinity chromatography. We incubated purified recombinant proteins with L-lysine in the enzyme reaction buffer at 37 degrees C and then derived the reaction products using dansyl chloride. It was found that both Trx-LDC1 and Trx-LDC2 had decarboxylase activity, could convert L-lysine into cadaverine by way of thin layer chromatography assay. Further, bioinformatics analysis indicated that deduced LDC1 and LDC2 had different physicochemical properties, but similar secondary and three-dimensional structures.

  2. Unveiling DNA structural features of promoters associated with various types of TSSs in prokaryotic transcriptomes and their role in gene expression

    PubMed Central

    Kumar, Aditya

    2017-01-01

    Abstract Next-generation sequencing studies have revealed that a variety of transcripts are present in the prokaryotic transcriptome and a significant fraction of them are functional, being involved in various regulatory activities apart from coding for proteins. Identification of promoters associated with different transcripts is necessary for characterization of the transcriptome. Promoter regions have been shown to have unique structural features as compared with their flanking region, in organisms covering all domains of life. Here we report an in silico analysis of DNA sequence dependent structural properties like stability, bendability and curvature in the promoter region of six different prokaryotic transcriptomes. Using these structural features, we predicted promoters associated with different categories of transcripts (mRNA, internal, antisense and non-coding), which constitute the transcriptome. Promoter annotation using structural features is fairly accurate and reliable with about 50% of the primary promoters being characterized by all three structural properties while at least one property identifies 95%. We also studied the relative differences of these structural features in terms of gene expression and found that the features, viz. lower stability, lesser bendability and higher curvature are more prominent in the promoter regions which are associated with high gene expression as compared with low expression genes. Hence, promoters, which are associated with higher gene expression, get annotated well using DNA structural features as compared with those, which are linked to lower gene expression. PMID:27803028

  3. Comparative Genomic Analysis Reveals a Diverse Repertoire of Genes Involved in Prokaryote-Eukaryote Interactions within the Pseudovibrio Genus

    PubMed Central

    Romano, Stefano; Fernàndez-Guerra, Antonio; Reen, F. Jerry; Glöckner, Frank O.; Crowley, Susan P.; O'Sullivan, Orla; Cotter, Paul D.; Adams, Claire; Dobson, Alan D. W.; O'Gara, Fergal

    2016-01-01

    Strains of the Pseudovibrio genus have been detected worldwide, mainly as part of bacterial communities associated with marine invertebrates, particularly sponges. This recurrent association has been considered as an indication of a symbiotic relationship between these microbes and their host. Until recently, the availability of only two genomes, belonging to closely related strains, has limited the knowledge on the genomic and physiological features of the genus to a single phylogenetic lineage. Here we present 10 newly sequenced genomes of Pseudovibrio strains isolated from marine sponges from the west coast of Ireland, and including the other two publicly available genomes we performed an extensive comparative genomic analysis. Homogeneity was apparent in terms of both the orthologous genes and the metabolic features shared amongst the 12 strains. At the genomic level, a key physiological difference observed amongst the isolates was the presence only in strain P. axinellae AD2 of genes encoding proteins involved in assimilatory nitrate reduction, which was then proved experimentally. We then focused on studying those systems known to be involved in the interactions with eukaryotic and prokaryotic cells. This analysis revealed that the genus harbors a large diversity of toxin-like proteins, secretion systems and their potential effectors. Their distribution in the genus was not always consistent with the phylogenetic relationship of the strains. Finally, our analyses identified new genomic islands encoding potential toxin-immunity systems, previously unknown in the genus. Our analyses shed new light on the Pseudovibrio genus, indicating a large diversity of both metabolic features and systems for interacting with the host. The diversity in both distribution and abundance of these systems amongst the strains underlines how metabolically and phylogenetically similar bacteria may use different strategies to interact with the host and find a niche within its

  4. Optimal Jet Finder

    NASA Astrophysics Data System (ADS)

    Grigoriev, D. Yu.; Jankowski, E.; Tkachov, F. V.

    2003-09-01

    We describe a FORTRAN 77 implementation of the optimal jet definition for identification of jets in hadronic final states of particle collisions. We discuss details of the implementation, explain interface subroutines and provide a usage example. The source code is available from http://www.inr.ac.ru/~ftkachov/projects/jets/. Program summaryTitle of program: Optimal Jet Finder (OJF_014) Catalogue identifier: ADSB Program Summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSB Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: Any computer with the FORTRAN 77 compiler Tested with: g77/Linux on Intel, Alpha and Sparc; Sun f77/Solaris (thwgs.cern.ch); xlf/AIX (rsplus.cern.ch); MS Fortran PowerStation 4.0/Win98 Programming language used: FORTRAN 77 Memory required: ˜1 MB (or more, depending on the settings) Number of bytes in distributed program, including examples and test data: 251 463 Distribution format: tar gzip file Keywords: Hadronic jets, jet finding algorithms Nature of physical problem: Analysis of hadronic final states in high energy particle collision experiments often involves identification of hadronic jets. A large number of hadrons detected in the calorimeter is reduced to a few jets by means of a jet finding algorithm. The jets are used in further analysis which would be difficult or impossible when applied directly to the hadrons. Grigoriev et al. [ hep-ph/0301185] provide a brief introduction to the subject of jet finding algorithms and a general review of the physics of jets can be found in [Rep. Prog. Phys. 36 (1993) 1067]. Method of solution: The software we provide is an implementation of the so-called optimal jet definition ( OJD). The theory of OJD was developed by Tkachov [Phys. Rev. Lett. 73 (1994) 2405; 74 (1995) 2618; Int. J. Mod. Phys. A 12 (1997) 5411; 17 (2002) 2783]. The desired jet configuration is obtained as the one that minimizes Ω R, a certain function of the input particles and jet

  5. Design and experimental application of a novel non-degenerate universal primer set that amplifies prokaryotic 16S rRNA genes with a low possibility to amplify eukaryotic rRNA genes.

    PubMed

    Mori, Hiroshi; Maruyama, Fumito; Kato, Hiromi; Toyoda, Atsushi; Dozono, Ayumi; Ohtsubo, Yoshiyuki; Nagata, Yuji; Fujiyama, Asao; Tsuda, Masataka; Kurokawa, Ken

    2014-01-01

    The deep sequencing of 16S rRNA genes amplified by universal primers has revolutionized our understanding of microbial communities by allowing the characterization of the diversity of the uncultured majority. However, some universal primers also amplify eukaryotic rRNA genes, leading to a decrease in the efficiency of sequencing of prokaryotic 16S rRNA genes with possible mischaracterization of the diversity in the microbial community. In this study, we compared 16S rRNA gene sequences from genome-sequenced strains and identified candidates for non-degenerate universal primers that could be used for the amplification of prokaryotic 16S rRNA genes. The 50 identified candidates were investigated to calculate their coverage for prokaryotic and eukaryotic rRNA genes, including those from uncultured taxa and eukaryotic organelles, and a novel universal primer set, 342F-806R, covering many prokaryotic, but not eukaryotic, rRNA genes was identified. This primer set was validated by the amplification of 16S rRNA genes from a soil metagenomic sample and subsequent pyrosequencing using the Roche 454 platform. The same sample was also used for pyrosequencing of the amplicons by employing a commonly used primer set, 338F-533R, and for shotgun metagenomic sequencing using the Illumina platform. Our comparison of the taxonomic compositions inferred by the three sequencing experiments indicated that the non-degenerate 342F-806R primer set can characterize the taxonomic composition of the microbial community without substantial bias, and is highly expected to be applicable to the analysis of a wide variety of microbial communities.

  6. Molecular analysis of the distribution and phylogeny of dissimilatory adenosine-5'-phosphosulfate reductase-encoding genes (aprBA) among sulfur-oxidizing prokaryotes.

    PubMed

    Meyer, Birte; Kuever, Jan

    2007-10-01

    Dissimilatory adenosine-5'-phosphosulfate (APS) reductase (AprBA) is a key enzyme of the dissimilatory sulfate-reduction pathway. Homologues have been found in photo- and chemotrophic sulfur-oxidizing prokaryotes (SOP), in which they are postulated to operate in the reverse direction, oxidizing sulfite to APS. Newly developed PCR assays allowed the amplification of 92-93 % (2.1-2.3 kb) of the APS reductase locus aprBA. PCR-based screening of 116 taxonomically divergent SOP reference strains revealed a distribution of aprBA restricted to photo- and chemotrophs with strict anaerobic or at least facultative anaerobic lifestyles, including Chlorobiaceae, Chromatiaceae, Thiobacillus, Thiothrix and invertebrate symbionts. In the AprBA-based tree, the SOP diverge into two distantly related phylogenetic lineages, Apr lineages I and II, with the proteins of lineage II (Chlorobiaceae and others) in closer affiliation to the enzymes of the sulfate-reducing prokaryotes (SRP). This clustering is discordant with the dissimilatory sulfite reductase (DsrAB) phylogeny and indicates putative lateral aprBA gene transfer from SRP to the respective SOB lineages. In support of lateral gene transfer (LGT), several beta- and gammaproteobacterial species harbour both aprBA homologues, the DsrAB-congruent 'authentic' and the SRP-related, LGT-derived gene loci, while some relatives possess exclusively the SRP-related apr genes as a possible result of resident gene displacement by the xenologue. The two-gene state might be an intermediate in the replacement of the resident essential gene. Collected genome data demonstrate the correlation between the AprBA tree topology and the composition/arrangement of the apr gene loci (occurrence of qmoABC or aprM genes) from SRP and SOP of lineages I and II. The putative functional role of the SRP-related APS reductases in photo- and chemotrophic SOP is discussed.

  7. PROKARYOTIC EXPRESSION AND BIOACTIVITY EVALUATION OF THE CHIMERIC GENE DERIVED FROM THE GROUP 1 ALLERGENS OF DUST MITES.

    PubMed

    Zhan, Xiaodong; Li, Chaopin; Guo, Wei; Jiang, Yuxin

    2015-12-01

    Antecedentes: se reconstituyó con éxito el gen del grupo 1 alérgenos de los ácaros del polvo, y obtuvo un conjunto de genes barajadas. Con el fin de verificar la predicción en el gen quimérico, hemos clonado tentativamente R8 en el vector que se expresó prokaryoticly, purificó y se evaluó por sus actividades-bio. Métodos: el producto expresado se detectó por SDS-PAGE y la proteína diana se purificó. La proteína purificada R8 se detectó por ELISA. Setenta y cinco ratones BALB/ c se dividieron en 5 grupos, a saber: PBS, rDer f1, rDer p1, R8 y el grupo de asma. Los ratones fueron tratados con alérgenos de ácaros del polvo a los 0, 7, 14 días mediante inyección intraperitoneal y inhaladas desafío como aerosol en día 21 durante 7 días. La inmunoterapia específica para el alérgeno se realizó utilizando rDer f1, rDer p1 y alérgenos R8, respectivamente. El nivel de IFN e IL-4 en BALF se detectó por ELISA. Resultados: el gen quimérico R8 se expresó con una banda de aproximadamente Mr 35000. En comparación con los grupos de rDer f 1 y rDer p 1 [(80,44 ± 15,50) y (90,79 ± 10,38) μg/ml, respectivamente], la capacidad de unión a IgE de la proteína R8 (37,03 ± 12,46) μg/ml fue estadísticamente inferior (P.

  8. Environmental distribution of prokaryotic taxa

    PubMed Central

    2010-01-01

    Background The increasing availability of gene sequences of prokaryotic species in samples extracted from all kind of locations allows addressing the study of the influence of environmental patterns in prokaryotic biodiversity. We present a comprehensive study to address the potential existence of environmental preferences of prokaryotic taxa and the commonness of the specialist and generalist strategies. We also assessed the most significant environmental factors shaping the environmental distribution of taxa. Results We used 16S rDNA sequences from 3,502 sampling experiments in natural and artificial sources. These sequences were taxonomically assigned, and the corresponding samples were also classified into a hierarchical classification of environments. We used several statistical methods to analyze the environmental distribution of taxa. Our results indicate that environmental specificity is not very common at the higher taxonomic levels (phylum to family), but emerges at lower taxonomic levels (genus and species). The most selective environmental characteristics are those of animal tissues and thermal locations. Salinity is another very important factor for constraining prokaryotic diversity. On the other hand, soil and freshwater habitats are the less restrictive environments, harboring the largest number of prokaryotic taxa. All information on taxa, samples and environments is provided at the envDB online database, http://metagenomics.uv.es/envDB. Conclusions This is, as far as we know, the most comprehensive assessment of the distribution and diversity of prokaryotic taxa and their associations with different environments. Our data indicate that we are still far from characterizing prokaryotic diversity in any environment, except, perhaps, for human tissues such as the oral cavity and the vagina. PMID:20307274

  9. Shift in prokaryotic diversity in Arctic sediment along a continuum Glacier -River - Fjord using massive 16S rRNA gene tag sequencing

    NASA Astrophysics Data System (ADS)

    Laghdass, M.; Deloffre, J.; Lafite, R.; Hänni, C.; Gillet, B.; Cecillon, S.; Simonet, P.; Petit, F.

    2012-04-01

    In Arctic environment, one of indirect consequences of the global climate warming is the significant amplification of the amount of inland water during the spring thaw resulting from the snow cover and permafrost melting. These freshwater transfers to the coast cause sedimentary transfers. The Arctic fjords that represent deep glacial valleys of the sea are particularly vulnerable systems. Although the previous studies have highlighted potentially the high bacterial diversity in Arctic environment by the pyrosequencing, a new-generation sequencing and high throughput method, does not escape the same bias as the one of classical molecular biology techniques involved at different stages of the analysis. In this context, our objective was to characterize the prokaryotic diversity associated to the sediment transfer along a gradient from the head of the glacier to mud patch sediment in the Goule river streaming in Kongsfjorden (Svalbard) during an active thaw. The prokaryotic diversity in sediment was characterized by combining a massive of 16S rRNA gene tag sequencing with a specific and original approach in order to overcome the bias associated to the sampling and extraction. The sediment was extracted by three different methods. One method was done in duplicate. Negative controls performed at extraction and PCR stages were also sequenced. The phylogenetic analysis of the environmental samples below phylum level revealed significantly changes in the diversity and the function of the prokaryotic community along the gradient. The subglacial Goule river sediment is characterized by bacteria with specific functions methylotroph bacteria, aerobic chemoautolithotrophic bacteria (Alphaproteobacteria with Methylobacteriaceae) whereas the mouth of the river Goule and the freshwater part of the Goule River was dominated by sulphate-reducing-bacteria, anaerobic chemooorganotroph (Deltaprotobacteria with the Desulfobulbaceae and Desulfuromonadaceae) and by

  10. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes.

    PubMed

    Kim, Mincheol; Oh, Hyun-Seok; Park, Sang-Cheol; Chun, Jongsik

    2014-02-01

    Among available genome relatedness indices, average nucleotide identity (ANI) is one of the most robust measurements of genomic relatedness between strains, and has great potential in the taxonomy of bacteria and archaea as a substitute for the labour-intensive DNA-DNA hybridization (DDH) technique. An ANI threshold range (95-96%) for species demarcation had previously been suggested based on comparative investigation between DDH and ANI values, albeit with rather limited datasets. Furthermore, its generality was not tested on all lineages of prokaryotes. Here, we investigated the overall distribution of ANI values generated by pairwise comparison of 6787 genomes of prokaryotes belonging to 22 phyla to see whether the suggested range can be applied to all species. There was an apparent distinction in the overall ANI distribution between intra- and interspecies relationships at around 95-96% ANI. We went on to determine which level of 16S rRNA gene sequence similarity corresponds to the currently accepted ANI threshold for species demarcation using over one million comparisons. A twofold cross-validation statistical test revealed that 98.65% 16S rRNA gene sequence similarity can be used as the threshold for differentiating two species, which is consistent with previous suggestions (98.2-99.0%) derived from comparative studies between DDH and 16S rRNA gene sequence similarity. Our findings should be useful in accelerating the use of genomic sequence data in the taxonomy of bacteria and archaea.

  11. CellFinder: a cell data repository

    PubMed Central

    Stachelscheid, Harald; Seltmann, Stefanie; Lekschas, Fritz; Fontaine, Jean-Fred; Mah, Nancy; Neves, Mariana; Andrade-Navarro, Miguel A.; Leser, Ulf; Kurtz, Andreas

    2014-01-01

    CellFinder (http://www.cellfinder.org) is a comprehensive one-stop resource for molecular data characterizing mammalian cells in different tissues and in different development stages. It is built from carefully selected data sets stemming from other curated databases and the biomedical literature. To date, CellFinder describes 3394 cell types and 50 951 cell lines. The database currently contains 3055 microscopic and anatomical images, 205 whole-genome expression profiles of 194 cell/tissue types from RNA-seq and microarrays and 553 905 protein expressions for 535 cells/tissues. Text mining of a corpus of >2000 publications followed by manual curation confirmed expression information on ∼900 proteins and genes. CellFinder’s data model is capable to seamlessly represent entities from single cells to the organ level, to incorporate mappings between homologous entities in different species and to describe processes of cell development and differentiation. Its ontological backbone currently consists of 204 741 ontology terms incorporated from 10 different ontologies unified under the novel CELDA ontology. CellFinder’s web portal allows searching, browsing and comparing the stored data, interactive construction of developmental trees and navigating the partonomic hierarchy of cells and tissues through a unique body browser designed for life scientists and clinicians. PMID:24304896

  12. The presence of a copper/zinc superoxide dismutase in the bacterium Photobacterium leiognathi: a likely case of gene transfer from eukaryotes to prokaryotes.

    PubMed

    Bannister, J V; Parker, M W

    1985-01-01

    The free-living bacterium Photobacterium leiognathi is also known to be a symbiont of ponyfish. The presence of a copper/zinc superoxide dismutase in P. leiognathi has been considered to be a case of gene transfer from eukaryotes to prokaryotes because this form of superoxide dismutase is normally present only in higher eukaryotic species. However, the amino acid sequence of the enzyme from the bacterium exhibited low identities (25-30%) with the same enzyme from eukaryotes. When amino acid mutations are taken into consideration, the weighted sequence similarity increases significantly; furthermore, the bacterial enzyme has the same active site residues and similar predicted secondary structure as the eukaryotic enzymes. The possibility of convergence is ruled out and the case of divergence is considered unlikely because of the observed phylogenetic distribution of the enzyme. This indicates that the presence of the copper/zinc superoxide dismutase in P. leiognathi can indeed be considered a case of gene transfer from eukaryotic species to prokaryotic species.

  13. X-ray beam finder

    DOEpatents

    Gilbert, H.W.

    1983-06-16

    An X-ray beam finder for locating a focal spot of an X-ray tube includes a mass of X-ray opaque material having first and second axially-aligned, parallel-opposed faces connected by a plurality of substantially identical parallel holes perpendicular to the faces and a film holder for holding X-ray sensitive film tightly against one face while the other face is placed in contact with the window of an X-ray head.

  14. Evidence for Lateral Transfer of Genes Encoding Ferredoxins, Nitroreductases, NADH Oxidase, and Alcohol Dehydrogenase 3 from Anaerobic Prokaryotes to Giardia lamblia and Entamoeba histolytica

    PubMed Central

    Nixon, Julie E. J.; Wang, Amy; Field, Jessica; Morrison, Hilary G.; McArthur, Andrew G.; Sogin, Mitchell L.; Loftus, Brendan J.; Samuelson, John

    2002-01-01

    Giardia lamblia and Entamoeba histolytica are amitochondriate, microaerophilic protists which use fermentation enzymes like those of bacteria to survive anaerobic conditions within the intestinal lumen. Genes encoding fermentation enzymes and related electron transport peptides (e.g., ferredoxins) in giardia organisms and amebae are hypothesized to be derived from either an ancient anaerobic eukaryote (amitochondriate fossil hypothesis), a mitochondrial endosymbiont (hydrogen hypothesis), or anaerobic bacteria (lateral transfer hypothesis). The goals here were to complete the molecular characterization of giardial and amebic fermentation enzymes and to determine the origins of the genes encoding them, when possible. A putative giardia [2Fe-2S]ferredoxin which had a hypothetical organelle-targeting sequence at its N terminus showed similarity to mitochondrial ferredoxins and the hydrogenosomal ferredoxin of Trichomonas vaginalis (another luminal protist). However, phylogenetic trees were star shaped, with weak bootstrap support, so we were unable to confirm or rule out the endosymbiotic origin of the giardia [2Fe-2S]ferredoxin gene. Putative giardial and amebic 6-kDa ferredoxins, ferredoxin-nitroreductase fusion proteins, and oxygen-insensitive nitroreductases each tentatively supported the lateral transfer hypothesis. Although there were not enough sequences to perform meaningful phylogenetic analyses, the unique common occurrence of these peptides and enzymes in giardia organisms, amebae, and the few anaerobic prokaryotes suggests the possibility of lateral transfer. In contrast, there was more robust phylogenetic evidence for the lateral transfer of G. lamblia genes encoding an NADH oxidase from a gram-positive coccus and a microbial group 3 alcohol dehydrogenase from thermoanaerobic prokaryotes. In further support of lateral transfer, the G. lamblia NADH oxidase and adh3 genes appeared to have an evolutionary history distinct from those of E. histolytica. PMID

  15. Impacts of human activities on distribution of sulfate-reducing prokaryotes and antibiotic resistance genes in marine coastal sediments of Hong Kong.

    PubMed

    Guo, Feng; Li, Bing; Yang, Ying; Deng, Yu; Qiu, Jian-Wen; Li, Xiangdong; Leung, Kenneth My; Zhang, Tong

    2016-09-01

    Sulfate-reducing prokaryotes (SRPs) and antibiotic resistance genes (ARGs) in sediments could be biomarkers for evaluating the environmental impacts of human activities, although factors governing their distribution are not clear yet. By using metagenomic approach, this study investigated the distributions of SRPs and ARGs in marine sediments collected from 12 different coastal locations of Hong Kong, which exhibited different pollution levels and were classified into two groups based on sediment parameters. Our results showed that relative abundances of major SRP genera to total prokaryotes were consistently lower in the more seriously polluted sediments (P-value < 0.05 in 13 of 20 genera), indicating that the relative abundance of SRPs is a negatively correlated biomarker for evaluating human impacts. Moreover, a unimodel distribution pattern for SRPs along with the pollution gradient was observed. Although total ARGs were enriched in sediments from the polluted sites, distribution of single major ARG types could be explained neither by individual sediment parameters nor by corresponding concentration of antibiotics. It supports the hypothesis that the persistence of ARGs in sediments may not need the selection of antibiotics. In summary, our study provided important hints of the niche differentiation of SRPs and behavior of ARGs in marine coastal sediment.

  16. STAR cluster-finder ASIC

    SciTech Connect

    Botlo, M.; LeVine, M.J.; Scheetz, R.A.

    1997-12-31

    The STAR experiment reads out a TPC and an SVT (silicon vertex tracker), both of which require in-line pedestal subtraction, compression of ADC values from 10-bit to 8-bit, and location of time sequences representing responses to charged-particle tracks. The STAR cluster finder ASIC responds to all of these needs. Pedestal subtraction and compression are performed using lookup tables in attached RAM. We describe its design and implementation, as well as testing methodology and results of tests performed on foundry prototypes.

  17. NCBI prokaryotic genome annotation pipeline.

    PubMed

    Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat; Chetvernin, Vyacheslav; Nawrocki, Eric P; Zaslavsky, Leonid; Lomsadze, Alexandre; Pruitt, Kim D; Borodovsky, Mark; Ostell, James

    2016-08-19

    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/.

  18. Microarray and Functional Gene Analyses of Sulfate-Reducing Prokaryotes in Low-Sulfate, Acidic Fens Reveal Cooccurrence of Recognized Genera and Novel Lineages

    PubMed Central

    Loy, Alexander; Küsel, Kirsten; Lehner, Angelika; Drake, Harold L.; Wagner, Michael

    2004-01-01

    Low-sulfate, acidic (approximately pH 4) fens in the Lehstenbach catchment in the Fichtelgebirge mountains in Germany are unusual habitats for sulfate-reducing prokaryotes (SRPs) that have been postulated to facilitate the retention of sulfur and protons in these ecosystems. Despite the low in situ availability of sulfate (concentration in the soil solution, 20 to 200 μM) and the acidic conditions (soil and soil solution pHs, approximately 4 and 5, respectively), the upper peat layers of the soils from two fens (Schlöppnerbrunnen I and II) of this catchment displayed significant sulfate-reducing capacities. 16S rRNA gene-based oligonucleotide microarray analyses revealed stable diversity patterns for recognized SRPs in the upper 30 cm of both fens. Members of the family “Syntrophobacteraceae” were detected in both fens, while signals specific for the genus Desulfomonile were observed only in soils from Schlöppnerbrunnen I. These results were confirmed and extended by comparative analyses of environmentally retrieved 16S rRNA and dissimilatory (bi)sulfite reductase (dsrAB) gene sequences; dsrAB sequences from Desulfobacca-like SRPs, which were not identified by microarray analysis, were obtained from both fens. Hypotheses concerning the ecophysiological role of these three SRP groups in the fens were formulated based on the known physiological properties of their cultured relatives. In addition to these recognized SRP lineages, six novel dsrAB types that were phylogenetically unrelated to all known SRPs were detected in the fens. These dsrAB sequences had no features indicative of pseudogenes and likely represent novel, deeply branching, sulfate- or sulfite-reducing prokaryotes that are specialized colonists of low-sulfate habitats. PMID:15574893

  19. [Progress in proteogenomics of prokaryotes].

    PubMed

    Zhang, Chengpu; Xu, Ping; Zhu, Yunping

    2014-07-01

    With the rapid development of genome sequencing technologies, a large amount of prokaryote genomes have been sequenced in recent years. To further investigate the models and functions of genomes, the algorithms for genome annotations based on the sequence and homology features have been widely implemented to newly sequenced genomes. However, gene annotations only using the genomic information are prone to errors, such as the incorrect N-terminals and pseudogenes. It is even harder to provide reasonable annotating results in the case of the poor genome sequencing results. The transcriptomics based on the technologies such as microarray and RNA-seq and the proteomics based on the MS/MS have been used widely to identify the gene products with high throughput and high sensitivity, providing the powerful tools for the verification and correction of annotated genome. Compared with transcriptomics, proteomics can generate the protein list for the expressed genes in the samples or cells without any confusion of the non-coding RNA, leading the proteogenomics an important basis for the genome annotations in prokaryotes. In this paper, we first described the traditional genome annotation algorithms and pointed out the shortcomings. Then we summarized the advantages of proteomics in the genome annotations and reviewed the progress of proteogenomics in prokaryotes. Finally we discussed the challenges and strategies in the data analyses and potential solutions for the developments of proteogenomics.

  20. Cyclic AMP in prokaryotes.

    PubMed Central

    Botsford, J L; Harman, J G

    1992-01-01

    Cyclic AMP (cAMP) is found in a variety of prokaryotes including both eubacteria and archaebacteria. cAMP plays a role in regulating gene expression, not only for the classic inducible catabolic operons, but also for other categories. In the enteric coliforms, the effects of cAMP on gene expression are mediated through its interaction with and allosteric modification of a cAMP-binding protein (CRP). The CRP-cAMP complex subsequently binds specific DNA sequences and either activates or inhibits transcription depending upon the positioning of the complex relative to the promoter. Enteric coliforms have provided a model to explore the mechanisms involved in controlling adenylate cyclase activity, in regulating adenylate cyclase synthesis, and in performing detailed examinations of CRP-cAMP complex-regulated gene expression. This review summarizes recent work focused on elucidating the molecular mechanisms of CRP-cAMP complex-mediated processes. For other bacteria, less detail is known. cAMP has been implicated in regulating antibiotic production, phototrophic growth, and pathogenesis. A role for cAMP has been suggested in nitrogen fixation. Often the only data that support cAMP involvement in these processes includes cAMP measurement, detection of the enzymes involved in cAMP metabolism, or observed effects of high concentrations of the nucleotide on cell growth. PMID:1315922

  1. The Precarious Prokaryotic Chromosome

    PubMed Central

    2014-01-01

    Evolutionary selection for optimal genome preservation, replication, and expression should yield similar chromosome organizations in any type of cells. And yet, the chromosome organization is surprisingly different between eukaryotes and prokaryotes. The nuclear versus cytoplasmic accommodation of genetic material accounts for the distinct eukaryotic and prokaryotic modes of genome evolution, but it falls short of explaining the differences in the chromosome organization. I propose that the two distinct ways to organize chromosomes are driven by the differences between the global-consecutive chromosome cycle of eukaryotes and the local-concurrent chromosome cycle of prokaryotes. Specifically, progressive chromosome segregation in prokaryotes demands a single duplicon per chromosome, while other “precarious” features of the prokaryotic chromosomes can be viewed as compensations for this severe restriction. PMID:24633873

  2. Application of CRISPRi for prokaryotic metabolic engineering involving multiple genes, a case study: Controllable P(3HB-co-4HB) biosynthesis.

    PubMed

    Lv, Li; Ren, Yi-Lin; Chen, Jin-Chun; Wu, Qiong; Chen, Guo-Qiang

    2015-05-01

    Clustered regularly interspaced short palindromic repeats interference (CRISPRi) is used to edit eukaryotic genomes. Here, we show that CRISPRi can also be used for fine-tuning prokaryotic gene expression while simultaneously regulating multiple essential gene expression with less labor and time consumption. As a case study, CRISPRi was used to control polyhydroxyalkanoate (PHA) biosynthesis pathway flux and to adjust PHA composition. A pathway was constructed in Escherichia coli for the production of poly(3-hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] from glucose. The native gene sad encoding E. coli succinate semi-aldehyde dehydrogenase was expressed under the control of CRISPRi using five specially designed single guide RNAs (sgRNAs) for regulating carbon flux to 4-hydroxybutyrate (4HB) biosynthesis. The system allowed formation of P(3HB-co-4HB) consisting of 1-9mol% 4HB. Additionally, succinate, generated by succinyl-coA synthetase and succinate dehydrogenase (respectively encoded by genes sucC, sucD and sdhA, sdhB) was channeled preferentially to the 4HB precursor by using selected sgRNAs such as sucC2, sucD2, sdhB2 and sdhA1 via CRISPRi. The resulting 4HB content in P(3HB-co-4HB) was found to range from 1.4 to 18.4mol% depending on the expression levels of down-regulated genes. The results show that CRISPRi is a feasible method to simultaneously manipulate multiple genes in E. coli.

  3. Digital laser range finder emulator

    NASA Astrophysics Data System (ADS)

    McDowell, Vaughn P.; Holland, Orgal T.; Wilkerson, Christina G.

    1993-05-01

    A digital laser range finder emulator receives N-bits of range-to-target data in a parallel format and generates N-bits of serial data representative of the range-to-target data and an external synchronization pulse whose presence is indicative of valid serial data. First and second clock pulses are generated such that the second clock pulse is delayed with respect to the first clock pulse. Control logic, responsive to the first clock pulse, generates validity logic while control logic, responsive to the second clock pulse, generates transmit logic. The parallel format range-to-target data is converted into the serial data in response to the first clock pulse. The serial data is then output in response to the transmit logic. A gate, responsive to the second clock pulse and the validity logic, generates the synchronization pulse when the second clock pulse and validity logic occupy a common logic state.

  4. An in silico analysis of T-box regulated genes and T-box evolution in prokaryotes, with emphasis on prediction of substrate specificity of transporters

    PubMed Central

    Wels, Michiel; Kormelink, Tom Groot; Kleerebezem, Michiel; Siezen, Roland J; Francke, Christof

    2008-01-01

    Background T-box anti-termination is an elegant and sensitive mechanism by which many bacteria maintain constant levels of amino acid-charged tRNAs. The amino acid specificity of the regulatory element is related to a so-called specifier codon and can in principle be used to guide the functional annotation of the genes controlled via the T-box anti-termination mechanism. Results Hidden Markov Models were defined to search the T-box regulatory element and were applied to all completed prokaryotic genomes. The vast majority of the genes found downstream of the retrieved elements encoded functionalities related to transport and synthesis of amino acids and the charging of tRNA. This is completely in line with findings reported in literature and with the proposed biological role of the regulatory element. For several species, the functional annotation of a large number of genes encoding proteins involved in amino acid transport could be improved significantly on basis of the amino acid specificity of the identified T-boxes. In addition, these annotations could be extrapolated to a larger number of orthologous systems in other species. Analysis of T-box distribution confirmed that the element is restricted predominantly to species of the phylum Firmicutes. Furthermore, it appeared that the distribution was highly species specific and that in the case of amino acid transport some boxes seemed to "pop-up" only recently. Conclusion We have demonstrated that the identification of the molecular specificity of a regulatory element can be of great help in solving notoriously difficult annotation issues, e.g. by defining the substrate specificity of genes encoding amino acid transporters on basis of the amino acid specificity of the regulatory T-box. Furthermore, our analysis of the species-dependency of the occurrence of specific T-boxes indicated that these regulatory elements propagate in a semi-independent way from the genes that they control. PMID:18625071

  5. Evolutionary assembly patterns of prokaryotic genomes

    PubMed Central

    Press, Maximilian O.; Queitsch, Christine; Borenstein, Elhanan

    2016-01-01

    Evolutionary innovation must occur in the context of some genomic background, which limits available evolutionary paths. For example, protein evolution by sequence substitution is constrained by epistasis between residues. In prokaryotes, evolutionary innovation frequently happens by macrogenomic events such as horizontal gene transfer (HGT). Previous work has suggested that HGT can be influenced by ancestral genomic content, yet the extent of such gene-level constraints has not yet been systematically characterized. Here, we evaluated the evolutionary impact of such constraints in prokaryotes, using probabilistic ancestral reconstructions from 634 extant prokaryotic genomes and a novel framework for detecting evolutionary constraints on HGT events. We identified 8228 directional dependencies between genes and demonstrated that many such dependencies reflect known functional relationships, including for example, evolutionary dependencies of the photosynthetic enzyme RuBisCO. Modeling all dependencies as a network, we adapted an approach from graph theory to establish chronological precedence in the acquisition of different genomic functions. Specifically, we demonstrated that specific functions tend to be gained sequentially, suggesting that evolution in prokaryotes is governed by functional assembly patterns. Finally, we showed that these dependencies are universal rather than clade-specific and are often sufficient for predicting whether or not a given ancestral genome will acquire specific genes. Combined, our results indicate that evolutionary innovation via HGT is profoundly constrained by epistasis and historical contingency, similar to the evolution of proteins and phenotypic characters, and suggest that the emergence of specific metabolic and pathological phenotypes in prokaryotes can be predictable from current genomes. PMID:27197212

  6. Bioinformatics of prokaryotic RNAs

    PubMed Central

    Backofen, Rolf; Amman, Fabian; Costa, Fabrizio; Findeiß, Sven; Richter, Andreas S; Stadler, Peter F

    2014-01-01

    The genome of most prokaryotes gives rise to surprisingly complex transcriptomes, comprising not only protein-coding mRNAs, often organized as operons, but also harbors dozens or even hundreds of highly structured small regulatory RNAs and unexpectedly large levels of anti-sense transcripts. Comprehensive surveys of prokaryotic transcriptomes and the need to characterize also their non-coding components is heavily dependent on computational methods and workflows, many of which have been developed or at least adapted specifically for the use with bacterial and archaeal data. This review provides an overview on the state-of-the-art of RNA bioinformatics focusing on applications to prokaryotes. PMID:24755880

  7. Bioinformatics of prokaryotic RNAs.

    PubMed

    Backofen, Rolf; Amman, Fabian; Costa, Fabrizio; Findeiß, Sven; Richter, Andreas S; Stadler, Peter F

    2014-01-01

    The genome of most prokaryotes gives rise to surprisingly complex transcriptomes, comprising not only protein-coding mRNAs, often organized as operons, but also harbors dozens or even hundreds of highly structured small regulatory RNAs and unexpectedly large levels of anti-sense transcripts. Comprehensive surveys of prokaryotic transcriptomes and the need to characterize also their non-coding components is heavily dependent on computational methods and workflows, many of which have been developed or at least adapted specifically for the use with bacterial and archaeal data. This review provides an overview on the state-of-the-art of RNA bioinformatics focusing on applications to prokaryotes.

  8. AMA Physician Select: Online Doctor Finder

    MedlinePlus

    ... Membership | JAMA Network | AMA Store DoctorFinder This online physician Locator helps you find a perfect match for ... with basic professional information on virtually every licensed physician in the United States. This includes more than ...

  9. The Epigenomic Landscape of Prokaryotes.

    PubMed

    Blow, Matthew J; Clark, Tyson A; Daum, Chris G; Deutschbauer, Adam M; Fomenkov, Alexey; Fries, Roxanne; Froula, Jeff; Kang, Dongwan D; Malmstrom, Rex R; Morgan, Richard D; Posfai, Janos; Singh, Kanwar; Visel, Axel; Wetmore, Kelly; Zhao, Zhiying; Rubin, Edward M; Korlach, Jonas; Pennacchio, Len A; Roberts, Richard J

    2016-02-01

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

  10. The Epigenomic Landscape of Prokaryotes

    PubMed Central

    Blow, Matthew J.; Clark, Tyson A.; Daum, Chris G.; Deutschbauer, Adam M.; Fomenkov, Alexey; Fries, Roxanne; Froula, Jeff; Kang, Dongwan D.; Malmstrom, Rex R.; Morgan, Richard D.; Posfai, Janos; Singh, Kanwar; Visel, Axel; Wetmore, Kelly; Zhao, Zhiying; Rubin, Edward M.; Korlach, Jonas; Pennacchio, Len A.; Roberts, Richard J.

    2016-01-01

    DNA methylation acts in concert with restriction enzymes to protect the integrity of prokaryotic genomes. Studies in a limited number of organisms suggest that methylation also contributes to prokaryotic genome regulation, but the prevalence and properties of such non-restriction-associated methylation systems remain poorly understood. Here, we used single molecule, real-time sequencing to map DNA modifications including m6A, m4C, and m5C across the genomes of 230 diverse bacterial and archaeal species. We observed DNA methylation in nearly all (93%) organisms examined, and identified a total of 834 distinct reproducibly methylated motifs. This data enabled annotation of the DNA binding specificities of 620 DNA Methyltransferases (MTases), doubling known specificities for previously hard to study Type I, IIG and III MTases, and revealing their extraordinary diversity. Strikingly, 48% of organisms harbor active Type II MTases with no apparent cognate restriction enzyme. These active ‘orphan’ MTases are present in diverse bacterial and archaeal phyla and show motif specificities and methylation patterns consistent with functions in gene regulation and DNA replication. Our results reveal the pervasive presence of DNA methylation throughout the prokaryotic kingdoms, as well as the diversity of sequence specificities and potential functions of DNA methylation systems. PMID:26870957

  11. Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms

    PubMed Central

    Tamames, Javier; Sánchez, Pablo D.; Nikel, Pablo I.; Pedrós-Alió, Carlos

    2016-01-01

    Two complementary forces shape microbial genomes: vertical inheritance of genes by phylogenetic descent, and acquisition of new genes related to adaptation to particular habitats and lifestyles. Quantification of the relative importance of each driving force proved difficult. We determined the contribution of each factor, and identified particular genes or biochemical/cellular processes linked to environmental preferences (i.e., propensity of a taxon to live in particular habitats). Three types of data were confronted: (i) complete genomes, which provide gene content of different taxa; (ii) phylogenetic information, via alignment of 16S rRNA sequences, which allowed determination of the distance between taxa, and (iii) distribution of species in environments via 16S rRNA sampling experiments, reflecting environmental preferences of different taxa. The combination of these three datasets made it possible to describe and quantify the relationships among them. We found that, although phylogenetic descent was responsible for shaping most genomes, a discernible part of the latter was correlated to environmental adaptations. Particular families of genes were identified as environmental markers, as supported by direct studies such as metagenomic sequencing. These genes are likely important for adaptation of bacteria to particular conditions or habitats, such as carbohydrate or glycan metabolism genes being linked to host-associated environments. PMID:27065987

  12. Terrestrial Planet Finder: science overview

    NASA Technical Reports Server (NTRS)

    Unwin, Stephen C.; Beichman, C. A.

    2004-01-01

    The Terrestrial Planet Finder (TPF) seeks to revolutionize our understanding of humanity's place in the universe - by searching for Earth-like planets using reflected light, or thermal emission in the mid-infrared. Direct detection implies that TPF must separate planet light from glare of the nearby star, a technical challenge which has only in recent years been recognized as surmountable. TPF will obtain a low-resolution spectra of each planets it detects, providing some of its basic physical characteristics and its main atmospheric constituents, thereby allowing us to assess the likelihood that habitable conditions exist there. NASA has decided the scientific importance of this research is so high that TPF will be pursued as two complementary space observatories: a visible-light coronagraph and a mid-infrared formation flying interferometer. The combination of spectra from both wavebands is much more valuable than either taken separately, and it will allow a much fuller understanding of the wide diversity of planetary atmospheres that may be expected to exist. Measurements across a broad wavelength range will yield not only physical properties such as size and albedo, but will also serve as the foundations of a reliable and robust assessment of habitability and the presence of life.

  13. Cloning, sequencing and overexpression of the gene for prokaryotic factor EF-P involved in peptide bond synthesis.

    PubMed Central

    Aoki, H; Adams, S L; Chung, D G; Yaguchi, M; Chuang, S E; Ganoza, M C

    1991-01-01

    A soluble protein EF-P (elongation factor P) from Escherichia coli has been purified and shown to stimulate efficient translation and peptide-bond synthesis on native or reconstituted 70S ribosomes in vitro. Based on the partial amino acid sequence of EF-P, 18- and 24-nucleotide DNA probes were synthesized and used to screen lambda phage clones from the Kohara Gene Bank. The entire EF-P gene was detected on lambda clone #650 which contains sequences from the 94 minute region of the E.coli genome. Two DNA fragments, 3.0 and 0.78 kilobases in length encompassing the gene, were isolated and cloned into pUC18 and pUC19. Partially purified extracts from cells transformed with these plasmids overrepresented a protein which co-migrates with EF-P upon SDS polyacrylamide gel electrophoresis, and also exhibited increased EF-P mediated peptide-bond synthetic activity. Based on DNA sequence analysis of this gene, the EF-P protein consists of 187 amino acids with a calculated molecular weight of 20,447. The sequence and chromosomal location of EF-P establishes it as a unique gene product. Images PMID:1956781

  14. Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification.

    PubMed

    McDonald, Tami R; Dietrich, Fred S; Lutzoni, François

    2012-01-01

    The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to

  15. Multiple Horizontal Gene Transfers of Ammonium Transporters/Ammonia Permeases from Prokaryotes to Eukaryotes: Toward a New Functional and Evolutionary Classification

    PubMed Central

    McDonald, Tami R.; Dietrich, Fred S.; Lutzoni, François

    2012-01-01

    The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to

  16. IC-Finder: inferring robustly the hierarchical organization of chromatin folding.

    PubMed

    Haddad, Noelle; Vaillant, Cédric; Jost, Daniel

    2017-01-26

    The spatial organization of the genome plays a crucial role in the regulation of gene expression. Recent experimental techniques like Hi-C have emphasized the segmentation of genomes into interaction compartments that constitute conserved functional domains participating in the maintenance of a proper cell identity. Here, we propose a novel method, IC-Finder, to identify interaction compartments (IC) from experimental Hi-C maps. IC-Finder is based on a hierarchical clustering approach that we adapted to account for the polymeric nature of chromatin. Based on a benchmark of realistic in silico Hi-C maps, we show that IC-Finder is one of the best methods in terms of reliability and is the most efficient numerically. IC-Finder proposes two original options: a probabilistic description of the inferred compartments and the possibility to explore the various hierarchies of chromatin organization. Applying the method to experimental data in fly and human, we show how the predicted segmentation may depend on the normalization scheme and how 3D compartmentalization is tightly associated with epigenomic information. IC-Finder provides a robust and generic 'all-in-one' tool to uncover the general principles of 3D chromatin folding and their influence on gene regulation. The software is available at http://membres-timc.imag.fr/Daniel.Jost/DJ-TIMC/Software.html.

  17. LinkFinder: An expert system that constructs phylogenic trees

    NASA Technical Reports Server (NTRS)

    Inglehart, James; Nelson, Peter C.

    1991-01-01

    An expert system has been developed using the C Language Integrated Production System (CLIPS) that automates the process of constructing DNA sequence based phylogenies (trees or lineages) that indicate evolutionary relationships. LinkFinder takes as input homologous DNA sequences from distinct individual organisms. It measures variations between the sequences, selects appropriate proportionality constants, and estimates the time that has passed since each pair of organisms diverged from a common ancestor. It then designs and outputs a phylogenic map summarizing these results. LinkFinder can find genetic relationships between different species, and between individuals of the same species, including humans. It was designed to take advantage of the vast amount of sequence data being produced by the Genome Project, and should be of value to evolution theorists who wish to utilize this data, but who have no formal training in molecular genetics. Evolutionary theory holds that distinct organisms carrying a common gene inherited that gene from a common ancestor. Homologous genes vary from individual to individual and species to species, and the amount of variation is now believed to be directly proportional to the time that has passed since divergence from a common ancestor. The proportionality constant must be determined experimentally; it varies considerably with the types of organisms and DNA molecules under study. Given an appropriate constant, and the variation between two DNA sequences, a simple linear equation gives the divergence time.

  18. Exhaustive Search for Over-represented DNA Sequence Motifs with CisFinder

    PubMed Central

    Sharov, Alexei A.; Ko, Minoru S.H.

    2009-01-01

    We present CisFinder software, which generates a comprehensive list of motifs enriched in a set of DNA sequences and describes them with position frequency matrices (PFMs). A new algorithm was designed to estimate PFMs directly from counts of n-mer words with and without gaps; then PFMs are extended over gaps and flanking regions and clustered to generate non-redundant sets of motifs. The algorithm successfully identified binding motifs for 12 transcription factors (TFs) in embryonic stem cells based on published chromatin immunoprecipitation sequencing data. Furthermore, CisFinder successfully identified alternative binding motifs of TFs (e.g. POU5F1, ESRRB, and CTCF) and motifs for known and unknown co-factors of genes associated with the pluripotent state of ES cells. CisFinder also showed robust performance in the identification of motifs that were only slightly enriched in a set of DNA sequences. PMID:19740934

  19. Western Michigan University Libraries' "Electronic Journal Finder"

    ERIC Educational Resources Information Center

    Gedeon, Randle; Boston, George

    2005-01-01

    This article describes the development of the "Electronic Journal Finder," a TDNet installation for the University Libraries of Western Michigan University. Topics covered include: rationale for subscription project timeline, content, product customization, set-up, maintenance issues, reporting functions, directing URL links, searching…

  20. The universally conserved prokaryotic GTPases.

    PubMed

    Verstraeten, Natalie; Fauvart, Maarten; Versées, Wim; Michiels, Jan

    2011-09-01

    Members of the large superclass of P-loop GTPases share a core domain with a conserved three-dimensional structure. In eukaryotes, these proteins are implicated in various crucial cellular processes, including translation, membrane trafficking, cell cycle progression, and membrane signaling. As targets of mutation and toxins, GTPases are involved in the pathogenesis of cancer and infectious diseases. In prokaryotes also, it is hard to overestimate the importance of GTPases in cell physiology. Numerous papers have shed new light on the role of bacterial GTPases in cell cycle regulation, ribosome assembly, the stress response, and other cellular processes. Moreover, bacterial GTPases have been identified as high-potential drug targets. A key paper published over 2 decades ago stated that, "It may never again be possible to capture [GTPases] in a family portrait" (H. R. Bourne, D. A. Sanders, and F. McCormick, Nature 348:125-132, 1990) and indeed, the last 20 years have seen a tremendous increase in publications on the subject. Sequence analysis identified 13 bacterial GTPases that are conserved in at least 75% of all bacterial species. We here provide an overview of these 13 protein subfamilies, covering their cellular functions as well as cellular localization and expression levels, three-dimensional structures, biochemical properties, and gene organization. Conserved roles in eukaryotic homologs will be discussed as well. A comprehensive overview summarizing current knowledge on prokaryotic GTPases will aid in further elucidating the function of these important proteins.

  1. Interaction of the atypical prokaryotic transcription activator FlhD2C2 with early promoters of the flagellar gene hierarchy.

    PubMed

    Claret, Laurent; Hughes, Colin

    2002-08-09

    The transcriptional activator FlhD2C2 is the master regulator of bacterial flagellum biogenesis and swarming migration, activating the "early" class II promoters of the large flagellar gene hierarchy. Using primer extensions, band-shift assays, and enzymatic and chemical footprinting, we describe the binding of the FlhD2C2 heterotetramer to the promoter regions of four class II flagella operons, fliAZ, flhBA and the divergent flgAMN and flgBCD(EFGHIJ). Each of the promoter regions was bound by a single heterotetramer, i.e. the flgAMN and flgBCD operons are characterised by a single FlhD2C2 binding site. Binding affinity differed, and correlated with previously reported promoter strength and order of activation. Methylation protection and interference, and depurination and depyrimidation interference provided a detailed map of critical bases within a common 46-59bp DNaseI footprint overlapping the promoter -35 sequences. These data and compilation of the 12 known class II promoter sequences of Escherichia coli, Proteus mirabilis and Salmonella typhimurium allowed determination of a FlhD2C2 binding site with pseudo symmetry, comprising two 17-18bp inverted repeats, each a consensus FlhD2C2 box, separated by a 10-11bp spacer. DNaseI hypersensitivity indicated that binding may cause a conformational change in the promoter regions. Only the FlhC subunit can bind DNA independently, but the specificity and stability of the interaction is strengthened by FlhD. Here, photo-crosslinking established that both FlhC and the stabilising FlhD contact the DNA within the FlhD2C2 tetramer. Our data suggest that specificity of recognition and stability of the FlhD2C2/DNA complex require protein-protein interaction and interaction of both FlhC and FlhD subunits with DNA. These characteristics of the FlhD and FlhC subunits in the FlhD2C2/DNA complex are strikingly atypical of prokaryotic regulators.

  2. Wheelchair assisted with laser range finder

    NASA Astrophysics Data System (ADS)

    Kang, Cheol U.; Wang, Hongbo; Ishimatsu, Takakazu; Ochiai, Tsumoru

    1995-12-01

    The paper presents a wheel chair system with the capability of self-localization and obstacle avoidance. Firstly, the approaches of landmark recognition and the self-localization of the wheel chair are described. Then, the principal of the obstacle avoidance using a laser range finder is described. Subsequently, the total system of the wheel chair is introduced. Finally, a navigation experiment is given. Experimental results indicate the effectiveness of our system.

  3. The design of ultrasonic range finder

    NASA Astrophysics Data System (ADS)

    Na, Yongyi

    2017-03-01

    Electronic rangefinder measurement scope in 0.10˜5.00 m, 1 cm measurement precision, measurement with no direct contact with the object to be tested, able to display measurement results clear and stable. Because ultrasonic directivity is strong, energy consumption is slow, in the medium transmission distance is farther, so ultrasonic often used for distance measurement, such as range finder and level measurement instrument can be done by ultrasound.

  4. New aspects of RNA processing in prokaryotes.

    PubMed

    Evguenieva-Hackenberg, Elena; Klug, Gabriele

    2011-10-01

    The pivotal role of posttranscriptional gene regulation is strongly underlined by genome-wide analyses showing strikingly low correlation between mRNA and protein levels in bacterial and archaeal cells. The stability of an mRNA and its availability for translation contribute to posttranscriptional gene regulation, and are determined by the following factors: i) the cell-specific set of ribonucleases and related proteins, ii) regulatory RNAs, and iii) the sequence and structural features of the RNA molecule itself. High-resolution analyses of whole prokaryotic transcriptomes allow comprehensive mapping of processed transcripts, detection of essentially all expressed regulatory RNAs, and monitoring of the global impact of ribonucleases and other processing factors. This opens new perspectives for the understanding of the molecular mechanisms responsible for mRNA decay in prokaryotes.

  5. Cell biology of prokaryotic organelles.

    PubMed

    Murat, Dorothee; Byrne, Meghan; Komeili, Arash

    2010-10-01

    Mounting evidence in recent years has challenged the dogma that prokaryotes are simple and undefined cells devoid of an organized subcellular architecture. In fact, proteins once thought to be the purely eukaryotic inventions, including relatives of actin and tubulin control prokaryotic cell shape, DNA segregation, and cytokinesis. Similarly, compartmentalization, commonly noted as a distinguishing feature of eukaryotic cells, is also prevalent in the prokaryotic world in the form of protein-bounded and lipid-bounded organelles. In this article we highlight some of these prokaryotic organelles and discuss the current knowledge on their ultrastructure and the molecular mechanisms of their biogenesis and maintenance.

  6. Thiol biochemistry of prokaryotes

    NASA Technical Reports Server (NTRS)

    Fahey, Robert C.

    1986-01-01

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

  7. Do prokaryotes contain microtubules?

    PubMed Central

    Bermudes, D; Hinkle, G; Margulis, L

    1994-01-01

    In eukaryotic cells, microtubules are 24-nm-diameter tubular structures composed of a class of conserved proteins called tubulin. They are involved in numerous cell functions including ciliary motility, nerve cell elongation, pigment migration, centrosome formation, and chromosome movement. Although cytoplasmic tubules and fibers have been observed in bacteria, some with diameters similar to those of eukaryotes, no homologies to eukaryotic microtubules have been established. Certain groups of bacteria including azotobacters, cyanobacteria, enteric bacteria, and spirochetes have been frequently observed to possess microtubule-like structures, and others, including archaebacteria, have been shown to be sensitive to drugs that inhibit the polymerization of microtubules. Although little biochemical or molecular biological information is available, the differences observed among these prokaryotic structures suggest that their composition generally differs among themselves as well as from that of eukaryotes. We review the distribution of cytoplasmic tubules in prokaryotes, even though, in all cases, their functions remain unknown. At least some tend to occur in cells that are large, elongate, and motile, suggesting that they may be involved in cytoskeletal functions, intracellular motility, or transport activities comparable to those performed by eukaryotic microtubules. In Escherichia coli, the FtsZ protein is associated with the formation of a ring in the division zone between the newly forming offspring cells. Like tubulin, FtsZ is a GTPase and shares with tubulin a 7-amino-acid motif, making it a promising candidate in which to seek the origin of tubulins. Images PMID:7968920

  8. Do prokaryotes contain microtubules?

    NASA Technical Reports Server (NTRS)

    Bermudes, D.; Hinkle, G.; Margulis, L.

    1994-01-01

    In eukaryotic cells, microtubules are 24-nm-diameter tubular structures composed of a class of conserved proteins called tubulin. They are involved in numerous cell functions including ciliary motility, nerve cell elongation, pigment migration, centrosome formation, and chromosome movement. Although cytoplasmic tubules and fibers have been observed in bacteria, some with diameters similar to those of eukaryotes, no homologies to eukaryotic microtubules have been established. Certain groups of bacteria including azotobacters, cyanobacteria, enteric bacteria, and spirochetes have been frequently observed to possess microtubule-like structures, and others, including archaebacteria, have been shown to be sensitive to drugs that inhibit the polymerization of microtubules. Although little biochemical or molecular biological information is available, the differences observed among these prokaryotic structures suggest that their composition generally differs among themselves as well as from that of eukaryotes. We review the distribution of cytoplasmic tubules in prokaryotes, even though, in all cases, their functions remain unknown. At least some tend to occur in cells that are large, elongate, and motile, suggesting that they may be involved in cytoskeletal functions, intracellular motility, or transport activities comparable to those performed by eukaryotic microtubules. In Escherichia coli, the FtsZ protein is associated with the formation of a ring in the division zone between the newly forming offspring cells. Like tubulin, FtsZ is a GTPase and shares with tubulin a 7-amino-acid motif, making it a promising candidate in which to seek the origin of tubulins.

  9. Desiccation tolerance of prokaryotes.

    PubMed Central

    Potts, M

    1994-01-01

    The removal of cell-bound water through air drying and the addition of water to air-dried cells are forces that have played a pivotal role in the evolution of the prokaryotes. In bacterial cells that have been subjected to air drying, the evaporation of free cytoplasmic water (Vf) can be instantaneous, and an equilibrium between cell-bound water (Vb) and the environmental water (vapor) potential (psi wv) may be achieved rapidly. In the air-dried state some bacteria survive only for seconds whereas others can tolerate desiccation for thousands, perhaps millions, of years. The desiccated (anhydrobiotic) cell is characterized by its singular lack of water--with contents as low as 0.02 g of H2O g (dry weight)-1. At these levels the monolayer coverage by water of macromolecules, including DNA and proteins, is disturbed. As a consequence the mechanisms that confer desiccation tolerance upon air-dried bacteria are markedly different from those, such as the mechanism of preferential exclusion of compatible solutes, that preserve the integrity of salt-, osmotically, and freeze-thaw-stressed cells. Desiccation tolerance reflects a complex array of interactions at the structural, physiological, and molecular levels. Many of the mechanisms remain cryptic, but it is clear that they involve interactions, such as those between proteins and co-solvents, that derive from the unique properties of the water molecule. A water replacement hypothesis accounts for how the nonreducing disaccharides trehalose and sucrose preserve the integrity of membranes and proteins. Nevertheless, we have virtually no insight into the state of the cytoplasm of an air-dried cell. There is no evidence for any obvious adaptations of proteins that can counter the effects of air drying or for the occurrence of any proteins that provide a direct and a tangible contribution to cell stability. Among the prokaryotes that can exist as anhydrobiotic cells, the cyanobacteria have a marked capacity to do so. One

  10. Target & Propagation Models for the FINDER Radar

    NASA Technical Reports Server (NTRS)

    Cable, Vaughn; Lux, James; Haque, Salmon

    2013-01-01

    Finding persons still alive in piles of rubble following an earthquake, a severe storm, or other disaster is a difficult problem. JPL is currently developing a victim detection radar called FINDER (Finding Individuals in Emergency and Response). The subject of this paper is directed toward development of propagation & target models needed for simulation & testing of such a system. These models are both physical (real rubble piles) and numerical. Early results from the numerical modeling phase show spatial and temporal spreading characteristics when signals are passed through a randomly mixed rubble pile.

  11. The STAR cluster-finder ASIC

    SciTech Connect

    Botlo, M.; LeVine, M.J.; Scheetz, R.A.; Schulz, M.W.; Short, P.; Woods, J.; Crosetto, D.

    1997-12-01

    STAR is a large TPC-based experiment at RHIC, the relativistic heavy ion collider at Brookhaven National Laboratory. The STAR experiment reads out a TPC and an SVT (silicon vertex tracker), both of which require in-line pedestal subtraction, compression of ADC values from 10-bit to 8-bit, and location of time sequences representing responses to charged-particle tracks. The STAR cluster finder ASIC responds to all of these needs. Pedestal subtraction and compression are performed using lookup tables in attached RAM. The authors describe its design and implementation, as well as testing methodology and results of tests performed on foundry prototypes.

  12. Rockstar: Phase-space halo finder

    NASA Astrophysics Data System (ADS)

    Behroozi, Peter; Wechsler, Risa; Wu, Hao-Yi

    2012-10-01

    Rockstar (Robust Overdensity Calculation using K-Space Topologically Adaptive Refinement) identifies dark matter halos, substructure, and tidal features. The approach is based on adaptive hierarchical refinement of friends-of-friends groups in six phase-space dimensions and one time dimension, which allows for robust (grid-independent, shape-independent, and noise-resilient) tracking of substructure. Our method is massively parallel (up to 10^5 CPUs) and runs on the largest current simulations (>10^10 particles) with high efficiency (10 CPU hours and 60 gigabytes of memory required per billion particles analyzed). Rockstar offers significant improvement in substructure recovery as compared to several other halo finders.

  13. Comparison of Potential ASKAP HI Survey Source Finders

    NASA Astrophysics Data System (ADS)

    Popping, A.; Jurek, R.; Westmeier, T.; Serra, P.; Flöer, L.; Meyer, M.; Koribalski, B.

    2012-02-01

    The large size of the ASKAP HI surveys DINGO and WALLABY necessitates automated 3D source finding. A performance difference of a few percent corresponds to a significant number of galaxies being detected or undetected. As such, the performance of the automated source finding is of paramount importance to both of these surveys. We have analysed the performance of various source finders to determine which will allow us to meet our survey goals during the DINGO and WALLABY design studies. Here we present a comparison of the performance of five different methods of automated source finding. These source finders are duchamp, gamma-finder, a CNHI finder, a 2d-1d wavelet reconstruction finder and a sigma clipping method (s+c finder). Each source finder was applied to the same three-dimensional data cubes containing (a) point sources with a Gaussian velocity profile and (b) spatially extended model-galaxies with inclinations and rotation profiles. We focus on the completeness and reliability of each algorithm when comparing the performance of the different source finders.

  14. 2. VIEW SOUTHWEST, prime search radar tower, height finder radar ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    2. VIEW SOUTHWEST, prime search radar tower, height finder radar towards, height finder radar towers, and radar tower (unknown function) - Fort Custer Military Reservation, P-67 Radar Station, .25 mile north of Dickman Road, east of Clark Road, Battle Creek, Calhoun County, MI

  15. 47 CFR 80.289 - Requirements for radio direction finder.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 47 Telecommunication 5 2014-10-01 2014-10-01 false Requirements for radio direction finder. 80.289 Section 80.289 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO... Requirements for radio direction finder. (a) The radio direction finding apparatus must: (1) Be capable...

  16. 47 CFR 80.289 - Requirements for radio direction finder.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 5 2012-10-01 2012-10-01 false Requirements for radio direction finder. 80.289 Section 80.289 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO... Requirements for radio direction finder. (a) The radio direction finding apparatus must: (1) Be capable...

  17. 47 CFR 80.289 - Requirements for radio direction finder.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 5 2010-10-01 2010-10-01 false Requirements for radio direction finder. 80.289 Section 80.289 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO... Requirements for radio direction finder. (a) The radio direction finding apparatus must: (1) Be capable...

  18. 47 CFR 80.289 - Requirements for radio direction finder.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 5 2013-10-01 2013-10-01 false Requirements for radio direction finder. 80.289 Section 80.289 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO... Requirements for radio direction finder. (a) The radio direction finding apparatus must: (1) Be capable...

  19. 47 CFR 80.289 - Requirements for radio direction finder.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 5 2011-10-01 2011-10-01 false Requirements for radio direction finder. 80.289 Section 80.289 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED) SAFETY AND SPECIAL RADIO... Requirements for radio direction finder. (a) The radio direction finding apparatus must: (1) Be capable...

  20. Humanitarian Mine Finder Experiment for Humanitarian Demining (HD)

    DTIC Science & Technology

    2009-06-01

    surface and buried Airborne techniques offer safety and speed over traditional HD th d UHF Band 2-D SAR L-band 2 D SAR me o s underground ...Backup Slides 20 Mine Finder Phase 1 •Design Mine Finder Rader •Determine which frequency bands (VHF, UHF, L, S, C, X, K) will provide greatest

  1. Coevolution of the Organization and Structure of Prokaryotic Genomes.

    PubMed

    Touchon, Marie; Rocha, Eduardo P C

    2016-01-04

    The cytoplasm of prokaryotes contains many molecular machines interacting directly with the chromosome. These vital interactions depend on the chromosome structure, as a molecule, and on the genome organization, as a unit of genetic information. Strong selection for the organization of the genetic elements implicated in these interactions drives replicon ploidy, gene distribution, operon conservation, and the formation of replication-associated traits. The genomes of prokaryotes are also very plastic with high rates of horizontal gene transfer and gene loss. The evolutionary conflicts between plasticity and organization lead to the formation of regions with high genetic diversity whose impact on chromosome structure is poorly understood. Prokaryotic genomes are remarkable documents of natural history because they carry the imprint of all of these selective and mutational forces. Their study allows a better understanding of molecular mechanisms, their impact on microbial evolution, and how they can be tinkered in synthetic biology.

  2. Horizontal transfer and evolution of prokaryote transposable elements in eukaryotes.

    PubMed

    Gilbert, Clément; Cordaux, Richard

    2013-01-01

    Horizontal transfer (HT) of transposable elements (TEs) plays a key role in prokaryotic evolution, and mounting evidence suggests that it has also had an important impact on eukaryotic evolution. Although many prokaryote-to-prokaryote and eukaryote-to-eukaryote HTs of TEs have been characterized, only few cases have been reported between prokaryotes and eukaryotes. Here, we carried out a comprehensive search for all major groups of prokaryotic insertion sequences (ISs) in 430 eukaryote genomes. We uncovered a total of 80 sequences, all deriving from the IS607 family, integrated in the genomes of 14 eukaryote species belonging to four distinct phyla (Amoebozoa, Ascomycetes, Basidiomycetes, and Stramenopiles). Given that eukaryote IS607-like sequences are most closely related to cyanobacterial IS607 and that their phylogeny is incongruent with that of their hosts, we conclude that the presence of IS607-like sequences in eukaryotic genomes is the result of several HT events. Selection analyses further suggest that our ability to detect these prokaryote TEs today in eukaryotes is because HT of these sequences occurred recently and/or some IS607 elements were domesticated after HT, giving rise to new eukaryote genes. Supporting the recent age of some of these HTs, we uncovered intact full-length, potentially active IS607 copies in the amoeba Acanthamoeba castellani. Overall, our study shows that prokaryote-to-eukaryote HT of TEs occurred at relatively low frequency during recent eukaryote evolution and it sets IS607 as the most widespread TE (being present in prokaryotes, eukaryotes, and viruses).

  3. Translational Selection Is Ubiquitous in Prokaryotes

    PubMed Central

    Supek, Fran; Škunca, Nives; Repar, Jelena; Vlahoviček, Kristian; Šmuc, Tomislav

    2010-01-01

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

  4. Multilocus sequence analysis (MLSA) in prokaryotic taxonomy.

    PubMed

    Glaeser, Stefanie P; Kämpfer, Peter

    2015-06-01

    To obtain a higher resolution of the phylogenetic relationships of species within a genus or genera within a family, multilocus sequence analysis (MLSA) is currently a widely used method. In MLSA studies, partial sequences of genes coding for proteins with conserved functions ('housekeeping genes') are used to generate phylogenetic trees and subsequently deduce phylogenies. However, MLSA is not only suggested as a phylogenetic tool to support and clarify the resolution of bacterial species with a higher resolution, as in 16S rRNA gene-based studies, but has also been discussed as a replacement for DNA-DNA hybridization (DDH) in species delineation. Nevertheless, despite the fact that MLSA has become an accepted and widely used method in prokaryotic taxonomy, no common generally accepted recommendations have been devised to date for either the whole area of microbial taxonomy or for taxa-specific applications of individual MLSA schemes. The different ways MLSA is performed can vary greatly for the selection of genes, their number, and the calculation method used when comparing the sequences obtained. Here, we provide an overview of the historical development of MLSA and critically review its current application in prokaryotic taxonomy by highlighting the advantages and disadvantages of the method's numerous variations. This provides a perspective for its future use in forthcoming genome-based genotypic taxonomic analyses.

  5. Terrestrial Planet Finder: Technology Development Plans

    NASA Technical Reports Server (NTRS)

    Lindensmith, Chris

    2004-01-01

    One of humanity's oldest questions is whether life exists elsewhere in the universe. The Terrestrial Planet Finder (TPF) mission will survey stars in our stellar neighborhood to search for planets and perform spectroscopic measurements to identify potential biomarkers in their atmospheres. In response to the recently published President's Plan for Space Exploration, TPF has plans to launch a visible-light coronagraph in 2014, and a separated-spacecraft infrared interferometer in 2016. Substantial funding has been committed to the development of the key technologies that are required to meet these goals for launch in the next decade. Efforts underway through industry and university contracts and at JPL include a number of system and subsystem testbeds, as well as components and numerical modeling capabilities. The science, technology, and design efforts are closely coupled to ensure that requirements and capabilities will be consistent and meet the science goals.

  6. Statechart Analysis with Symbolic PathFinder

    NASA Technical Reports Server (NTRS)

    Pasareanu, Corina S.

    2012-01-01

    We report here on our on-going work that addresses the automated analysis and test case generation for software systems modeled using multiple Statechart formalisms. The work is motivated by large programs such as NASA Exploration, that involve multiple systems that interact via safety-critical protocols and are designed with different Statechart variants. To verify these safety-critical systems, we have developed Polyglot, a framework for modeling and analysis of model-based software written using different Statechart formalisms. Polyglot uses a common intermediate representation with customizable Statechart semantics and leverages the analysis and test generation capabilities of the Symbolic PathFinder tool. Polyglot is used as follows: First, the structure of the Statechart model (expressed in Matlab Stateflow or Rational Rhapsody) is translated into a common intermediate representation (IR). The IR is then translated into Java code that represents the structure of the model. The semantics are provided as "pluggable" modules.

  7. Haloes gone MAD: The Halo-Finder Comparison Project

    NASA Astrophysics Data System (ADS)

    Knebe, Alexander; Knollmann, Steffen R.; Muldrew, Stuart I.; Pearce, Frazer R.; Aragon-Calvo, Miguel Angel; Ascasibar, Yago; Behroozi, Peter S.; Ceverino, Daniel; Colombi, Stephane; Diemand, Juerg; Dolag, Klaus; Falck, Bridget L.; Fasel, Patricia; Gardner, Jeff; Gottlöber, Stefan; Hsu, Chung-Hsing; Iannuzzi, Francesca; Klypin, Anatoly; Lukić, Zarija; Maciejewski, Michal; McBride, Cameron; Neyrinck, Mark C.; Planelles, Susana; Potter, Doug; Quilis, Vicent; Rasera, Yann; Read, Justin I.; Ricker, Paul M.; Roy, Fabrice; Springel, Volker; Stadel, Joachim; Stinson, Greg; Sutter, P. M.; Turchaninov, Victor; Tweed, Dylan; Yepes, Gustavo; Zemp, Marcel

    2011-08-01

    We present a detailed comparison of fundamental dark matter halo properties retrieved by a substantial number of different halo finders. These codes span a wide range of techniques including friends-of-friends, spherical-overdensity and phase-space-based algorithms. We further introduce a robust (and publicly available) suite of test scenarios that allow halo finder developers to compare the performance of their codes against those presented here. This set includes mock haloes containing various levels and distributions of substructure at a range of resolutions as well as a cosmological simulation of the large-scale structure of the universe. All the halo-finding codes tested could successfully recover the spatial location of our mock haloes. They further returned lists of particles (potentially) belonging to the object that led to coinciding values for the maximum of the circular velocity profile and the radius where it is reached. All the finders based in configuration space struggled to recover substructure that was located close to the centre of the host halo, and the radial dependence of the mass recovered varies from finder to finder. Those finders based in phase space could resolve central substructure although they found difficulties in accurately recovering its properties. Through a resolution study we found that most of the finders could not reliably recover substructure containing fewer than 30-40 particles. However, also here the phase-space finders excelled by resolving substructure down to 10-20 particles. By comparing the halo finders using a high-resolution cosmological volume, we found that they agree remarkably well on fundamental properties of astrophysical significance (e.g. mass, position, velocity and peak of the rotation curve). We further suggest to utilize the peak of the rotation curve, vmax, as a proxy for mass, given the arbitrariness in defining a proper halo edge. Airport code for Madrid, Spain

  8. 3. VIEW NORTHWEST, height finder radar towers, and radar tower ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. VIEW NORTHWEST, height finder radar towers, and radar tower (unknown function) - Fort Custer Military Reservation, P-67 Radar Station, .25 mile north of Dickman Road, east of Clark Road, Battle Creek, Calhoun County, MI

  9. 1. VIEW NORTHWEST, operations building, height finder radar tower, and ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1. VIEW NORTHWEST, operations building, height finder radar tower, and radar tower (unknown function) - Fort Custer Military Reservation, P-67 Radar Station, .25 mile north of Dickman Road, east of Clark Road, Battle Creek, Calhoun County, MI

  10. Terrestrial Planet Finder coronagraph status and enabling technologies

    NASA Technical Reports Server (NTRS)

    Ford, Virginia G.; Lisman, Douglas; Shaklan, Stuart B.; Ho, Timothy Y.; Kissil, Andrew; Kwack, Eug-Yun; Lowman, Andrew

    2004-01-01

    The goal of the Terrestrial Planet Finder Project Mission is to find life-bearing planets around nearby stars. Two types of instruments are competing for flight in 2015: a visible coronagraph and an infrared interferometer.

  11. Introduction to Searching with SciFinder Scholar

    NASA Astrophysics Data System (ADS)

    Ridley, Damon D.

    2001-04-01

    With SciFinder Scholar now one of the preferred access routes to information in the sciences, many college information retrieval courses that dealt with online networks need to be redesigned. Although one of the basic assumptions within the design of SciFinder Scholar is that staff and students may retrieve valuable answers with little training, nevertheless, with a little instruction improved search results may be obtained. We present here our basic teaching program for senior undergraduate and postgraduate classes.

  12. Micro-Laser Range Finder Development: Using the Monolithic Approach

    DTIC Science & Technology

    1999-02-01

    Approved for public release; distribution is unlimited. Micro- Laser Range Finder Development: Using the Monolithic Approach February 1999 John... Nettleton , Dallas Barr, Brad Schilling & Jonathan Lei US ARMY CECOM RDEC NVESD Fort Belvoir, VA Samuel M. Goldwasser Engineering Consultant Bala-Cynwyd, PA...ABSTRACT Laser range finders are a vital component of high precision targeting engagements. The precise and accurate range-to-target information is

  13. A novel method to transform prokaryotic cells using shock waves

    NASA Astrophysics Data System (ADS)

    Nataraja, K. N.; Udayakumar, M.; Jagadeesh, G.

    The transgenic approach that is being used to study gene function or to improve the efficiency of crop plants/organisms involves transformation of a wide range of cells, tissues, and organisms with nucleic acid. In this study we report a new micro- shock assisted prokaryotic cell transformation technique. An underwater electric discharge based shock wave generator (25 kV; 150 m A; high voltage capacitor) has been designed and fabricated to carry out the prokaryotic cell transformation experiments. Test tubes with bacterial cell suspension with appropriate plasmid DNA, immersed in water are exposed to shock wave loading (typical overpressure 130 bar). The transformation efficiency of samples of the prokaryotic cells exposed to shock waves is very high compared to conventional methods.

  14. Capturing prokaryotic dark matter genomes.

    PubMed

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

    2015-12-01

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

  15. The automated planet finder at Lick Observatory

    NASA Astrophysics Data System (ADS)

    Radovan, Matt V.; Lanclos, Kyle; Holden, Bradford P.; Kibrick, Robert I.; Allen, S. L.; Deich, William T. S.; Rivera, Eugenio; Burt, Jennifer; Fulton, Benjamin; Butler, Paul; Vogt, Steven S.

    2014-07-01

    By July 2014, the Automated Planet Finder (APF) at Lick Observatory on Mount Hamilton will have completed its first year of operation. This facility combines a modern 2.4m computer-controlled telescope with a flexible development environment that enables efficient use of the Levy Spectrometer for high cadence observations. The Levy provides both sub-meter per second radial velocity precision and high efficiency, with a peak total system throughput of 24%. The modern telescope combined with efficient spectrometer routinely yields over 100 observations of 40 stars in a single night, each of which has velocity errors of 0.7 to 1.4 meters per second, all with typical seeing of < 1 arc second full-width-half-maximum (FWHM). The whole observing process is automated using a common application programming interface (API) for inter-process communication which allows scripting to be done in a variety of languages (Python, Tcl, bash, csh, etc.) The flexibility and ease-of-use of the common API allowed the science teams to be directly involved in the automation of the observing process, ensuring that the facility met their requirements. Since November 2013, the APF has been routinely conducting autonomous observations without human intervention.

  16. Sensitivity of the terrestrial planet finder

    NASA Technical Reports Server (NTRS)

    Beichman, Charles

    1998-01-01

    A key long-term goal of NASA's Origins program is the detection and characterization of habitable planets orbiting stars within the solar neighborhood. A cold, space-borne interferometer operating in the mid-infrared with a approx. 75 m baseline can null the light of a parent star and detect the million-times fainter radiation from an Earth-like planet located in the "habitable zone" around stars as far as 15 pc away. Such an interferometer, designated the Terrestrial Planet Finder (TPF) by NASA, could even detect atmospheric signatures of species such as CO2, O3, and H2O indicative of either the possibility or presence of primitive life. This talk highlights some of the sensitivity issues affecting the detectability of terrestrial planets. Sensitivity calculations show that a system consisting of 2 m apertures operating at 5 AU or 4 m apertures operating at 1 AU can detect terrestrial planets in reasonable integration times for levels of exo-zodiacal emission up to 10 times that seen in our solar system (hereafter denoted as 10xSS). Additionally, simulations show that confusion noise from structures in the exo-zodiacal cloud should not impede planet detection until the exo-zodiacal emission reaches the 10xSS level.

  17. Energetics and genetics across the prokaryote-eukaryote divide

    PubMed Central

    2011-01-01

    Background All complex life on Earth is eukaryotic. All eukaryotic cells share a common ancestor that arose just once in four billion years of evolution. Prokaryotes show no tendency to evolve greater morphological complexity, despite their metabolic virtuosity. Here I argue that the eukaryotic cell originated in a unique prokaryotic endosymbiosis, a singular event that transformed the selection pressures acting on both host and endosymbiont. Results The reductive evolution and specialisation of endosymbionts to mitochondria resulted in an extreme genomic asymmetry, in which the residual mitochondrial genomes enabled the expansion of bioenergetic membranes over several orders of magnitude, overcoming the energetic constraints on prokaryotic genome size, and permitting the host cell genome to expand (in principle) over 200,000-fold. This energetic transformation was permissive, not prescriptive; I suggest that the actual increase in early eukaryotic genome size was driven by a heavy early bombardment of genes and introns from the endosymbiont to the host cell, producing a high mutation rate. Unlike prokaryotes, with lower mutation rates and heavy selection pressure to lose genes, early eukaryotes without genome-size limitations could mask mutations by cell fusion and genome duplication, as in allopolyploidy, giving rise to a proto-sexual cell cycle. The side effect was that a large number of shared eukaryotic basal traits accumulated in the same population, a sexual eukaryotic common ancestor, radically different to any known prokaryote. Conclusions The combination of massive bioenergetic expansion, release from genome-size constraints, and high mutation rate favoured a protosexual cell cycle and the accumulation of eukaryotic traits. These factors explain the unique origin of eukaryotes, the absence of true evolutionary intermediates, and the evolution of sex in eukaryotes but not prokaryotes. Reviewers This article was reviewed by: Eugene Koonin, William Martin

  18. Characterization of C1-Metabolizing Prokaryotic Communities in Methane Seep Habitats at the Kuroshima Knoll, Southern Ryukyu Arc, by Analyzing pmoA, mmoX, mxaF, mcrA, and 16S rRNA Genes

    PubMed Central

    Inagaki, Fumio; Tsunogai, Urumu; Suzuki, Masae; Kosaka, Ayako; Machiyama, Hideaki; Takai, Ken; Nunoura, Takuro; Nealson, Kenneth H.; Horikoshi, Koki

    2004-01-01

    Samples from three submerged sites (MC, a core obtained in the methane seep area; MR, a reference core obtained at a distance from the methane seep; and HC, a gas-bubbling carbonate sample) at the Kuroshima Knoll in the southern Ryuku arc were analyzed to gain insight into the organisms present and the processes involved in this oxic-anoxic methane seep environment. 16S rRNA gene analyses by quantitative real-time PCR and clone library sequencing revealed that the MC core sediments contained abundant archaea (∼34% of the total prokaryotes), including both mesophilic methanogens related to the genus Methanolobus and ANME-2 members of the Methanosarcinales, as well as members of the δ-Proteobacteria, suggesting that both anaerobic methane oxidation and methanogenesis occurred at this site. In addition, several functional genes connected with methane metabolism were analyzed by quantitative competitive-PCR, including the genes encoding particulate methane monooxygenase (pmoA), soluble methane monooxygenase (mmoX), methanol dehydrogenese (mxaF), and methyl coenzyme M reductase (mcrA). In the MC core sediments, the most abundant gene was mcrA (2.5 × 106 copies/g [wet weight]), while the pmoA gene of the type I methanotrophs (5.9 × 106 copies/g [wet weight]) was most abundant at the surface of the MC core. These results indicate that there is a very complex environment in which methane production, anaerobic methane oxidation, and aerobic methane oxidation all occur in close proximity. The HC carbonate site was rich in γ-Proteobacteria and had a high copy number of mxaF (7.1 × 106 copies/g [wet weight]) and a much lower copy number of the pmoA gene (3.2 × 102 copies/g [wet weight]). The mmoX gene was never detected. In contrast, the reference core contained familiar sequences of marine sedimentary archaeal and bacterial groups but not groups specific to C1 metabolism. Geochemical characterization of the amounts and isotopic composition of pore water methane and

  19. Detecting uber-operons in prokaryotic genomes.

    PubMed

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

    2006-01-01

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

  20. Precursor Science for the Terrestrial Planet Finder

    NASA Technical Reports Server (NTRS)

    Lawson, P. R. (Editor); Unwin, S. C. (Editor); Beichman, C. A. (Editor)

    2004-01-01

    This document outlines a path for the development of the field of extrasolar planet research, with a particular emphasis on the goals of the Terrestrial Planet Finder (TPF). Over the past decade, a new field of research has developed, the study of extrasolar planetary systems, driven by the discovery of massive planets around nearby stars. The planet count now stands at over 130. Are there Earth-like planets around nearby stars? Might any of those planets be conducive to the formation and maintenance of life? These arc the questions that TPF seeks to answer. TPF will be implemented as a suite of two space observatories, a 6-m class optical coronagraph, to be launched around 20 14, and a formation flying mid-infrared interferometer, to be launched sometime prior to 2020. These facilities will survey up to 165 or more nearby stars and detect planets like Earth should they be present in the 'habitable zone' around each star. With observations over a broad wavelength range, TPF will provide a robust determination of the atmospheric composition of planets to assess habitability and the presence of life. At this early stage of TPF's development, precursor observational and theoretical programs are essential to help define the mission, to aid our understanding of the planets that TPF could discover, and to characterize the stars that TPF will eventually study. This document is necessarily broad in scope because the significance of individual discoveries is greatly enhanced when viewed in thc context of the field as a whole. This document has the ambitious goal of taking us from our limited knowledge today, in 2004, to the era of TPF observations in the middle of the next decade. We must use the intervening years wisely. This document will be reviewed annually and updated as needed. The most recent edition is available online at http://tpf.jpl.nasa.gov/ or by email request to lawson@hucy.jpl.nasa.gov

  1. Optimization of Planet Finder Observing Strategy

    NASA Astrophysics Data System (ADS)

    Sinukoff, E.

    2014-03-01

    We evaluate radial velocity observing strategies to be considered for future planethunting surveys with the Automated Planet Finder, a new 2.4-m telescope at Lick Observatory. Observing strategies can be optimized to mitigate stellar noise, which can mask and imitate the weak Doppler signals of low-mass planets. We estimate and compare sensitivities of 5 different observing strategies to planets around G2-M2 dwarfs, constructing RV noise models for each stellar spectral type, accounting for acoustic, granulation, and magnetic activity modes. The strategies differ in exposure time, nightly and monthly cadence, and number of years. Synthetic RV time-series are produced by injecting a planet signal onto the stellar noise, sampled according to each observing strategy. For each star and each observing strategy, thousands of planet injection recovery trials are conducted to determine the detection efficiency as a function of orbital period, minimum mass, and eccentricity. We find that 4-year observing strategies of 10 nights per month are sensitive to planets ~25-40% lower in mass than the corresponding 1 year strategies of 30 nights per month. Three 5-minute exposures spaced evenly throughout each night provide a 10% gain in sensitivity over the corresponding single 15-minute exposure strategies. All strategies are sensitive to planets of lowest mass around the modeled K7 dwarf. This study indicates that APF surveys adopting the 4-year strategies should detect Earth-mass planets on < 10-day orbits around quiet late-K dwarfs as well as > 1.6 Earth-mass planets in their habitable zones.

  2. Real-Time PCR Quantification and Diversity Analysis of the Functional Genes aprA and dsrA of Sulfate-Reducing Prokaryotes in Marine Sediments of the Peru Continental Margin and the Black Sea.

    PubMed

    Blazejak, Anna; Schippers, Axel

    2011-01-01

    Sulfate-reducing prokaryotes (SRP) are ubiquitous and quantitatively important members in many ecosystems, especially in marine sediments. However their abundance and diversity in subsurface marine sediments is poorly understood. In this study, the abundance and diversity of the functional genes for the enzymes adenosine 5'-phosphosulfate reductase (aprA) and dissimilatory sulfite reductase (dsrA) of SRP in marine sediments of the Peru continental margin and the Black Sea were analyzed, including samples from the deep biosphere (ODP site 1227). For aprA quantification a Q-PCR assay was designed and evaluated. Depth profiles of the aprA and dsrA copy numbers were almost equal for all sites. Gene copy numbers decreased concomitantly with depth from around 10(8)/g sediment close to the sediment surface to less than 10(5)/g sediment at 5 mbsf. The 16S rRNA gene copy numbers of total bacteria were much higher than those of the functional genes at all sediment depths and used to calculate the proportion of SRP to the total Bacteria. The aprA and dsrA copy numbers comprised in average 0.5-1% of the 16S rRNA gene copy numbers of total bacteria in the sediments up to a depth of ca. 40 mbsf. In the zone without detectable sulfate in the pore water from about 40-121 mbsf (Peru margin ODP site 1227), only dsrA (but not aprA) was detected with copy numbers of less than 10(4)/g sediment, comprising ca. 14% of the 16S rRNA gene copy numbers of total bacteria. In this zone, sulfate might be provided for SRP by anaerobic sulfide oxidation. Clone libraries of aprA showed that all isolated sequences originate from SRP showing a close relationship to aprA of characterized species or form a new cluster with only distant relation to aprA of isolated SRP. For dsrA a high diversity was detected, even up to 121 m sediment depth in the deep biosphere.

  3. Tracking of Humans and Robots Using Laser Range Finders

    NASA Astrophysics Data System (ADS)

    Bršcic, Drazen; Sasaki, Takeshi; Hashimoto, Hideki

    There exist various applications where tracking of humans or robots in an area is needed. An example of such applications are Intelligent Spaces, where humans and robots share a common space and their positions are tracked by a system of sensors in the space. In this paper a system for tracking both humans and robots that utilizes laser range finders as sensing devices is described. The details of the extraction of objects from the laser scan, data association and estimation are given, and results of tracking humans and robots are described. Calibration of the distributed laser range finders, which is important for the operation of the tracking system is also described, both in a manual and automated variant and experimental results are given. Finally, the inclusion of a laser range finder onboard the mobile robot in the tracking process is described and accompanied with experimental results. The distributed fusion of static and onboard sensors is also discussed.

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2014-01-27

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

  6. ASM Conference on Prokaryotic Development

    SciTech Connect

    Kaplan, H. B.

    2005-07-13

    Support was provided by DOE for the 2nd ASM Conference on Prokaryotic Development. The final conference program and abstracts book is attached. The conference presentations are organized around topics that are central to the current research areas in prokaryotic development. The program starts with topics that involve relatively simple models systems and ends with systems that are more complex. The topics are: i) the cell cycle, ii) the cytoskeleton, iii) morphogenesis, iv) developmental transcription, v) signaling, vi) multicellularity, and vii) developmental diversity and symbiosis. The best-studied prokaryotic development model systems will be highlighted at the conference through research presentations by leaders in the field. Many of these systems are also model systems of relevance to the DOE mission including carbon sequestration (Bradyrizobium, Synechococcus), energy production (Anabaena, Rhodobacter) and bioremediation (Caulobacter, Mesorhizobium). In addition, many of the highlighted organisms have important practical applications; the actinomycetes and myxobacteria produce antimicrobials that are of commercial interest. It is certain that the cutting-edge science presented at the conference will be applicable to the large group of bacteria relevant to the DOE mission.

  7. FilFinder: Filamentary structure in molecular clouds

    NASA Astrophysics Data System (ADS)

    Koch, Eric W.; Rosolowsky, Erik W.

    2016-08-01

    FilFinder extracts and analyzes filamentary structure in molecular clouds. In particular, it is capable of uniformly extracting structure over a large dynamical range in intensity. It returns the main filament properties: local amplitude and background, width, length, orientation and curvature. FilFinder offers additional tools to, for example, create a filament-only image based on the properties of the radial fits. The resulting mask and skeletons may be saved in FITS format, and property tables may be saved as a CSV, FITS or LaTeX table.

  8. Validation of the Applied Biosystems RapidFinder Shiga Toxin-Producing E. coli (STEC) Detection Workflow.

    PubMed

    Cloke, Jonathan; Matheny, Sharon; Swimley, Michelle; Tebbs, Robert; Burrell, Angelia; Flannery, Jonathan; Bastin, Benjamin; Bird, Patrick; Benzinger, M Joseph; Crowley, Erin; Agin, James; Goins, David; Salfinger, Yvonne; Brodsky, Michael; Fernandez, Maria Cristina

    2016-11-01

    The Applied Biosystems™ RapidFinder™ STEC Detection Workflow (Thermo Fisher Scientific) is a complete protocol for the rapid qualitative detection of Escherichia coli (E. coli) O157:H7 and the "Big 6" non-O157 Shiga-like toxin-producing E. coli (STEC) serotypes (defined as serogroups: O26, O45, O103, O111, O121, and O145). The RapidFinder STEC Detection Workflow makes use of either the automated preparation of PCR-ready DNA using the Applied Biosystems PrepSEQ™ Nucleic Acid Extraction Kit in conjunction with the Applied Biosystems MagMAX™ Express 96-well magnetic particle processor or the Applied Biosystems PrepSEQ Rapid Spin kit for manual preparation of PCR-ready DNA. Two separate assays comprise the RapidFinder STEC Detection Workflow, the Applied Biosystems RapidFinder STEC Screening Assay and the Applied Biosystems RapidFinder STEC Confirmation Assay. The RapidFinder STEC Screening Assay includes primers and probes to detect the presence of stx1 (Shiga toxin 1), stx2 (Shiga toxin 2), eae (intimin), and E. coli O157 gene targets. The RapidFinder STEC Confirmation Assay includes primers and probes for the "Big 6" non-O157 STEC and E. coli O157:H7. The use of these two assays in tandem allows a user to detect accurately the presence of the "Big 6" STECs and E. coli O157:H7. The performance of the RapidFinder STEC Detection Workflow was evaluated in a method comparison study, in inclusivity and exclusivity studies, and in a robustness evaluation. The assays were compared to the U.S. Department of Agriculture (USDA), Food Safety and Inspection Service (FSIS) Microbiology Laboratory Guidebook (MLG) 5.09: Detection, Isolation and Identification of Escherichia coli O157:H7 from Meat Products and Carcass and Environmental Sponges for raw ground beef (73% lean) and USDA/FSIS-MLG 5B.05: Detection, Isolation and Identification of Escherichia coli non-O157:H7 from Meat Products and Carcass and Environmental Sponges for raw beef trim. No statistically significant

  9. Codon Preference Optimization Increases Prokaryotic Cystatin C Expression

    PubMed Central

    Wang, Qing; Mei, Cui; Zhen, Honghua; Zhu, Jess

    2012-01-01

    Gene expression is closely related to optimal vector-host system pairing in many prokaryotes. Redesign of the human cystatin C (cysC) gene using the preferred codons of the prokaryotic system may significantly increase cysC expression in Escherichia coli (E. coli). Specifically, cysC expression may be increased by removing unstable sequences and optimizing GC content. According to E. coli expression system codon preferences, the gene sequence was optimized while the amino acid sequence was maintained. The codon-optimized cysC (co-cysC) and wild-type cysC (wt-cysC) were expressed by cloning the genes into a pET-30a plasmid, thus transforming the recombinant plasmid into E. coli BL21. Before and after the optimization process, the prokaryotic expression vector and host bacteria were examined for protein expression and biological activation of CysC. The recombinant proteins in the lysate of the transformed bacteria were purified using Ni2+-NTA resin. Recombinant protein expression increased from 10% to 46% based on total protein expression after codon optimization. Recombinant CysC purity was above 95%. The significant increase in cysC expression in E. coli expression produced by codon optimization techniques may be applicable to commercial production systems. PMID:23093857

  10. "Anticipated" nucleosome positioning pattern in prokaryotes.

    PubMed

    Rapoport, Alexandra E; Trifonov, Edward N

    2011-11-15

    Linguistic (word count) analysis of prokaryotic genome sequences, by Shannon N-gram extension, reveals that the dominant hidden motifs in A+T rich genomes are T(A)(T)A and G(A)(T)C with uncertain number of repeating A and T. Since prokaryotic sequences are largely protein-coding, the motifs would correspond to amphipathic alpha-helices with alternating lysine and phenylalanine as preferential polar and non-polar residues. The motifs are also known in eukaryotes, as nucleosome positioning patterns. Their existence in prokaryotes as well may serve for binding of histone-like proteins to DNA. In this case the above patterns in prokaryotes may be considered as "anticipated" nucleosome positioning patterns which, quite likely, existed in prokaryotic genomes before the evolutionary separation between eukaryotes and prokaryotes.

  11. Assembly complexity of prokaryotic genomes using short reads

    PubMed Central

    2010-01-01

    Background De Bruijn graphs are a theoretical framework underlying several modern genome assembly programs, especially those that deal with very short reads. We describe an application of de Bruijn graphs to analyze the global repeat structure of prokaryotic genomes. Results We provide the first survey of the repeat structure of a large number of genomes. The analysis gives an upper-bound on the performance of genome assemblers for de novo reconstruction of genomes across a wide range of read lengths. Further, we demonstrate that the majority of genes in prokaryotic genomes can be reconstructed uniquely using very short reads even if the genomes themselves cannot. The non-reconstructible genes are overwhelmingly related to mobile elements (transposons, IS elements, and prophages). Conclusions Our results improve upon previous studies on the feasibility of assembly with short reads and provide a comprehensive benchmark against which to compare the performance of the short-read assemblers currently being developed. PMID:20064276

  12. The Terrestrial Planet Finder coronagraph dynamics error budget

    NASA Technical Reports Server (NTRS)

    Shaklan, Stuart B.; Marchen, Luis; Green, Joseph J.; Lay, Oliver P.

    2005-01-01

    The Terrestrial Planet Finder Coronagraph (TPF-C) demands extreme wave front control and stability to achieve its goal of detecting earth-like planets around nearby stars. We describe the performance models and error budget used to evaluate image plane contrast and derive engineering requirements for this challenging optical system.

  13. 5. VIEW EAST, height finder radar towers, radar tower (unknown ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. VIEW EAST, height finder radar towers, radar tower (unknown function), prime search radar tower, operations building, and central heating plant - Fort Custer Military Reservation, P-67 Radar Station, .25 mile north of Dickman Road, east of Clark Road, Battle Creek, Calhoun County, MI

  14. Comparison of several coronagraphic approaches to the Terrestrial Planet Finder

    NASA Astrophysics Data System (ADS)

    Ridgway, Stephen T.; Burrows, Christopher J.; Friedman, Edward J.; Gezari, Daniel Y.; Harwit, Martin O.; Kaplan, Michael H.; Kaylor, Larry; Lyon, Richard G.; Melnick, Gary J.; Nisenson, Peter; Peterson, Lee D.; Spergel, David N.; Woodruff, Robert A.

    2003-10-01

    Planetological and technical issues have led to a renewed interest in visible coronographic concepts for a Terrestrial Planet Finder mission. This has stimulated rapid development of new, generalized coronagraphic techniques, including exotic apodizations and nulling schemes. Hitherto, it has been difficult to compare different concepts, owing to the complex interaction between details of the concepts and instrument and mission parameters and optimization.

  15. FACTOR FINDER CD-ROM | Science Inventory | US EPA

    EPA Pesticide Factsheets

    The Factor Finder CD-ROM is a user-friendly, searchable tool used to locate exposure factors and sociodemographic data for user-defined populations. Factor Finder improves the exposure assessors and risk assessors (etc.) ability to efficiently locate exposure-related information for a population of concern. Users can either enter keywords into a user-defined search box or use pull-down menus to help pinpoint specific information. The pull-down menu features general categories such as chemicals of concern, contaminated media, geographic region, exposure pathways and routes, age, food categories, and activities to name just a few. Numerous subcategories are available for selection from the pull down menu as well. Factor Finder searches both documents to retrieve the specified data and displays the information on the user's personal computer (PC) screen. Factor Finder is used by exposure assessors, risk assessors, and other concerned communities to locate exposure-related data contained within the Exposure Factors Handbook (EFH) and Sociodemographic Data Used in Identifying Potentially Highly Exposed Populations (HEP). The EFH and the HEP are companion guidance documents produced by the National Center for Environmental Assessment (NCEA) within EPA's Office of Research and Development. The Exposure Factors Handbook (EFH) summarizes data on exposure factors (values that describe human behaviors and characteristics that affect exposure to environmental cont

  16. NASA's Terrestrial Planet Finder: The Search for (Habitable) Planets

    NASA Technical Reports Server (NTRS)

    Beichman, C.

    1999-01-01

    One of the primary goals of NASA's Origins program is the search for habitable planets. I will describe how the Terrestrial Planet Finder (TPF) will revolutionize our understanding of the origin and evolution of planetary systems, and possibly even find signs of life beyond the Earth.

  17. NASA's terrestial planet finder: the search for (habitable) planets

    NASA Technical Reports Server (NTRS)

    Beichman, C. A.

    2000-01-01

    One of the primary goals of NASA's Origins program is the search for hospitable planets. I will describe how the Terrestrial Planet Finder (TPF) will revolutionize our understanding of the origin and evolution of planetary systems, and possibly even find signs of life beyond Earth.

  18. 12 CFR 7.1002 - National bank acting as finder.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... OPERATIONS Bank Powers § 7.1002 National bank acting as finder. (a) General. It is part of the business of... and terms to potential markets for these products and services; (2) Communicating to the seller an... sellers, and conducting market research to identify potential new customers for retailers; (5)...

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

    PubMed

    Salazar, Guillem; Cornejo-Castillo, Francisco M; Benítez-Barrios, Verónica; Fraile-Nuez, Eugenio; Álvarez-Salgado, X Antón; Duarte, Carlos M; Gasol, Josep M; Acinas, Silvia G

    2016-03-01

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

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

    PubMed Central

    Salazar, Guillem; Cornejo-Castillo, Francisco M; Benítez-Barrios, Verónica; Fraile-Nuez, Eugenio; Álvarez-Salgado, X Antón; Duarte, Carlos M; Gasol, Josep M; Acinas, Silvia G

    2016-01-01

    The deep-sea is the largest biome of the biosphere, and contains more than half of the whole ocean's microbes. Uncovering their general patterns of diversity and community structure at a global scale remains a great challenge, as only fragmentary information of deep-sea microbial diversity exists based on regional-scale studies. Here we report the first globally comprehensive survey of the prokaryotic communities inhabiting the bathypelagic ocean using high-throughput sequencing of the 16S rRNA gene. This work identifies the dominant prokaryotes in the pelagic deep ocean and reveals that 50% of the operational taxonomic units (OTUs) belong to previously unknown prokaryotic taxa, most of which are rare and appear in just a few samples. We show that whereas the local richness of communities is comparable to that observed in previous regional studies, the global pool of prokaryotic taxa detected is modest (~3600 OTUs), as a high proportion of OTUs are shared among samples. The water masses appear to act as clear drivers of the geographical distribution of both particle-attached and free-living prokaryotes. In addition, we show that the deep-oceanic basins in which the bathypelagic realm is divided contain different particle-attached (but not free-living) microbial communities. The combination of the aging of the water masses and a lack of complete dispersal are identified as the main drivers for this biogeographical pattern. All together, we identify the potential of the deep ocean as a reservoir of still unknown biological diversity with a higher degree of spatial complexity than hitherto considered. PMID:26251871

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

    PubMed Central

    Tatarinova, Tatiana; Dien Bard, Jennifer; Cohen, Irit

    2015-01-01

    Proteins of the same functional family (for example, kinases) may have significantly different lengths. It is an open question whether such variation in length is random or it appears as a response to some unknown evolutionary driving factors. The main purpose of this paper is to demonstrate existence of factors affecting prokaryotic gene lengths. We believe that the ranking of genomes according to lengths of their genes, followed by the calculation of coefficients of association between genome rank and genome property, is a reasonable approach in revealing such evolutionary driving factors. As we demonstrated earlier, our chosen approach, Bubble-sort, combines stability, accuracy, and computational efficiency as compared to other ranking methods. Application of Bubble Sort to the set of 1390 prokaryotic genomes confirmed that genes of Archaeal species are generally shorter than Bacterial ones. We observed that gene lengths are affected by various factors: within each domain, different phyla have preferences for short or long genes; thermophiles tend to have shorter genes than the soil-dwellers; halophiles tend to have longer genes. We also found that species with overrepresentation of cytosines and guanines in the third position of the codon (GC3 content) tend to have longer genes than species with low GC3 content. PMID:26114113

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

    PubMed

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

    2015-01-01

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

  3. The evolution of ecological tolerance in prokaryotes

    NASA Technical Reports Server (NTRS)

    Knoll, A. H.; Bauld, J.

    1989-01-01

    The ecological ranges of Archaeobacteria and Eubacteria are constrained by a requirement for liquid water and the physico-chemical stability limits of biomolecules, but within this broad envelope, prokaryotes have evolved adaptations that permit them to tolerate a remarkable spectrum of habitats. Laboratory experiments indicate that prokaryotes can adapt rapidly to novel environmental conditions, yet geological studies suggest early diversification and long-term stasis within the prokaryotic kingdoms. These apparently contradictory perspectives can be reconciled by understanding that, in general, rates and patterns of prokaryotic evolution reflect the developmental history of the Earth's surface environments. Our understanding of modern microbial ecology provides a lens through which our accumulating knowledge of physiology, molecular phylogeny and the Earth's history can be integrated and focussed on the phenomenon of prokaryotic evolution.

  4. Curved track segment finding using Tiny Triplet Finder (TTF)

    SciTech Connect

    Wu, Jin-Yuan; Wang, M.; Gottschalk, E.; Shi, Z.; /Fermilab

    2006-11-01

    We describe the applications of a track segment recognition scheme called the Tiny Triplet Finder (TTF) that involves the grouping of three hits satisfying a constraint forming of a track segment. The TTF was originally developed solving straight track segment finding problem, however, it is also suitable in many curved track segment finding problems. The examples discussed in this document are among popular detector layouts in high-energy/nuclear physics experiments. Although it is not practical to find a universal recipe for arbitrary detector layouts, the method of the TTF application is illustrated via the discussion of the examples. Generally speaking, whenever the data item to be found in a pattern recognition problem contains two free parameters, and if the constraint connecting the measurements and the two free parameters has an approximate shift invariant property, the Tiny Triplet Finder can be used.

  5. Detectability of active triangulation range finder: a solar irradiance approach.

    PubMed

    Liu, Huizhe; Gao, Jason; Bui, Viet Phuong; Liu, Zhengtong; Lee, Kenneth Eng Kian; Peh, Li-Shiuan; Png, Ching Eng

    2016-06-27

    Active triangulation range finders are widely used in a variety of applications such as robotics and assistive technologies. The power of the laser source should be carefully selected in order to satisfy detectability and still remain eye-safe. In this paper, we present a systematic approach to assess the detectability of an active triangulation range finder in an outdoor environment. For the first time, we accurately quantify the background noise of a laser system due to solar irradiance by coupling the Perez all-weather sky model and ray tracing techniques. The model is validated with measurements with a modeling error of less than 14.0%. Being highly generic and sufficiently flexible, the proposed model serves as a guide to define a laser system for any geographical location and microclimate.

  6. The CMS Level-1 Trigger Barrel Track Finder

    NASA Astrophysics Data System (ADS)

    Ero, J.; Evangelou, I.; Flouris, G.; Foudas, C.; Guiducci, L.; Loukas, N.; Manthos, N.; Papadopoulos, I.; Paradas, E.; Sotiropoulos, S.; Sphicas, P.; Triossi, A.; Wulz, C.

    2016-03-01

    The design and performance of the upgraded CMS Level-1 Trigger Barrel Muon Track Finder (BMTF) is presented. Monte Carlo simulation data as well as cosmic ray data from a CMS muon detector slice test have been used to study in detail the performance of the new track finder. The design architecture is based on twelve MP7 cards each of which uses a Xilinx Virtex-7 FPGA and can receive and transmit data at 10 Gbps from 72 input and 72 output fibers. According to the CMS Trigger Upgrade TDR the BMTF receives trigger primitive data which are computed using both RPC and DT data and transmits data from a number of muon candidates to the upgraded Global Muon Trigger. Results from detailed studies of comparisons between the BMTF algorithm results and the results of a C++ emulator are also presented. The new BMTF will be commissioned for data taking in 2016.

  7. Terrestrial Planet Finder Interferometer: 2007-2008 Progress and Plans

    NASA Technical Reports Server (NTRS)

    Lawson, P. R.; Lay, O. P.; Martin, S. R.; Peters, R. D.; Gappinger, R. O.; Ksendzov, A.; Scharf, D. P.; Booth, A. J.; Beichman, C. A.; Serabyn, E.; Johnston, K. J.; Danchi, W. C.

    2008-01-01

    This paper provides an overview of technology development for the Terrestrial Planet Finder Interferometer (TPF-I). TPF-I is a mid-infrared space interferometer being designed with the capability of detecting Earth-like planets in the habitable zones around nearby stars. The overall technology roadmap is presented and progress with each of the testbeds is summarized. The current interferometer architecture, design trades, and the viability of possible reduced-scope mission concepts are also presented.

  8. Adaptive Nulling for the Terrestrial Planet Finder Interferometer

    NASA Technical Reports Server (NTRS)

    Peters, Robert D.; Lay, Oliver P.; Jeganathan, Muthu; Hirai, Akiko

    2006-01-01

    A description of adaptive nulling for Terrestrial Planet Finder Interferometer (TPFI) is presented. The topics include: 1) Nulling in TPF-I; 2) Why Do Adaptive Nulling; 3) Parallel High-Order Compensator Design; 4) Phase and Amplitude Control; 5) Development Activates; 6) Requirements; 7) Simplified Experimental Setup; 8) Intensity Correction; and 9) Intensity Dispersion Stability. A short summary is also given on adaptive nulling for the TPFI.

  9. Location Of A Vehicle With A Laser Range Finder

    NASA Astrophysics Data System (ADS)

    Zhao, C. J.; Monchaud, S.; Marce, L.; Julliere, M.

    1984-02-01

    Absolute location of a mobile robot is necessary to improve the autonomy of vehicle built for hostile environments. We are developing a scanning laser range finder based on triangulation to get range data about the edges of a cylindrical polyhedral world. From the matching between the measurements and data computed from a model of the a priori known environment, the position of the robot is deduced accurately.

  10. Terrestrial Planet Finder Interferometer: Architecture, Mission Design, and Technology Development

    NASA Technical Reports Server (NTRS)

    Henry, Curt

    2004-01-01

    This slide presentation represents an overview progress report about the system design and technology development of two interferometer concepts studied for the Terrestrial Planet Finder (TPF) project. The two concepts are a structurally-connected interferometer (SCI) intended to fulfill minimum TPF science goals and a formation-flying interferometer (FFI) intended to fulfill full science goals. Described are major trades, analyses, and technology experiments completed. Near term plans are also described. This paper covers progress since August 2003

  11. Fusion of a Variable Baseline System and a Range Finder

    PubMed Central

    Hernández-Aceituno, Javier; Acosta, Leopoldo; Arnay, Rafael

    2012-01-01

    One of the greatest difficulties in stereo vision is the appearance of ambiguities when matching similar points from different images. In this article we analyze the effectiveness of using a fusion of multiple baselines and a range finder from a theoretical point of view, focusing on the results of using both prismatic and rotational articulations for baseline generation, and offer a practical case to prove its efficiency on an autonomous vehicle. PMID:22368469

  12. Utilization of SciFinder Scholar at an Undergraduate Institution

    NASA Astrophysics Data System (ADS)

    O'Reilly, Stacy A.; Wilson, Anne M.; Howes, Barbara

    2002-04-01

    The use of tools to search chemical information databases continues to be important to science educators. The ability to perform online searches of Chemical Abstracts Service can have a significant impact on teaching and research. The implementation of SciFinder Scholar at Butler University has resulted in significant changes in teaching, student-based research, and faculty development in the Chemistry Department. Details of these changes in courses, student research projects and proposals, and the professional growth of the faculty are discussed.

  13. The Voronoi Tessellation Cluster Finder in 2 1 Dimensions

    SciTech Connect

    Soares-Santos, Marcelle; de Carvalho, Reinaldo R.; Annis, James; Gal, Roy R.; La Barbera, Francesco; Lopes, Paulo A.A.; Wechsler, Risa H.; Busha, Michael T.; Gerke, Brian F.; /SLAC /KIPAC, Menlo Park

    2011-06-23

    We present a detailed description of the Voronoi Tessellation (VT) cluster finder algorithm in 2+1 dimensions, which improves on past implementations of this technique. The need for cluster finder algorithms able to produce reliable cluster catalogs up to redshift 1 or beyond and down to 10{sup 13.5} solar masses is paramount especially in light of upcoming surveys aiming at cosmological constraints from galaxy cluster number counts. We build the VT in photometric redshift shells and use the two-point correlation function of the galaxies in the field to both determine the density threshold for detection of cluster candidates and to establish their significance. This allows us to detect clusters in a self-consistent way without any assumptions about their astrophysical properties. We apply the VT to mock catalogs which extend to redshift 1.4 reproducing the ?CDM cosmology and the clustering properties observed in the Sloan Digital Sky Survey data. An objective estimate of the cluster selection function in terms of the completeness and purity as a function of mass and redshift is as important as having a reliable cluster finder. We measure these quantities by matching the VT cluster catalog with the mock truth table. We show that the VT can produce a cluster catalog with completeness and purity >80% for the redshift range up to {approx}1 and mass range down to {approx}10{sup 13.5} solar masses.

  14. The Voronoi Tessellation cluster finder in 2+1 dimensions

    SciTech Connect

    Soares-Santos, Marcelle; de Carvalho, Reinaldo R.; Annis, James; Gal, Roy R.; La Barbera, Francesco; Lopes, Paulo A.A.; Wechsler, Risa H.; Busha, Michael T.; Gerke, Brian F.; /SLAC /KIPAC, Menlo Park

    2010-11-01

    We present a detailed description of the Voronoi Tessellation (VT) cluster finder algorithm in 2+1 dimensions, which improves on past implementations of this technique. The need for cluster finder algorithms able to produce reliable cluster catalogs up to redshift 1 or beyond and down to 10{sup 13.5} solar masses is paramount especially in light of upcoming surveys aiming at cosmological constraints from galaxy cluster number counts. We build the VT in photometric redshift shells and use the two-point correlation function of the galaxies in the field to both determine the density threshold for detection of cluster candidates and to establish their significance. This allows us to detect clusters in a self-consistent way without any assumptions about their astrophysical properties. We apply the VT to mock catalogs which extend to redshift 1.4 reproducing the {Lambda}CDM cosmology and the clustering properties observed in the Sloan Digital Sky Survey data. An objective estimate of the cluster selection function in terms of the completeness and purity as a function of mass and redshift is as important as having a reliable cluster finder. We measure these quantities by matching the VT cluster catalog with the mock truth table. We show that the VT can produce a cluster catalog with completeness and purity >80% for the redshift range up to {approx}1 and mass range down to {approx}10{sup 13.5} solar masses.

  15. Stygofauna enhance prokaryotic transport in groundwater ecosystems

    PubMed Central

    Smith, Renee J.; Paterson, James S.; Launer, Elise; Tobe, Shanan S.; Morello, Eliesa; Leijs, Remko; Marri, Shashikanth; Mitchell, James G.

    2016-01-01

    More than 97% of the world’s freshwater reserves are found in aquifers, making groundwater one of the most important resources on the planet. Prokaryotic communities in groundwater underpin the turnover of energy and matter while also maintaining groundwater purity. Thus, knowledge of microbial transport in the subsurface is crucial for maintaining groundwater health. Here, we describe for the first time the importance of stygofauna as vectors for prokaryotes. The “hitch-hiking” prokaryotes associated with stygofauna may be up to 5 orders of magnitude higher in abundance and transported up to 34× faster than bulk groundwater flow. We also demonstrate that prokaryotic diversity associated with stygofauna may be higher than that of the surrounding groundwater. Stygofauna are a newly recognized prokaryotic niche in groundwater ecosystems that have the potential to transport remediating, water purifying and pathogenic prokaryotes. Therefore, stygofauna may influence ecosystem dynamics and health at a microbial level, and at a larger scale could be a new source of prokaryotic diversity in groundwater ecosystems. PMID:27597322

  16. The Evolution of Epigenetics: From Prokaryotes to Humans and Its Biological Consequences

    PubMed Central

    Willbanks, Amber; Leary, Meghan; Greenshields, Molly; Tyminski, Camila; Heerboth, Sarah; Lapinska, Karolina; Haskins, Kathryn; Sarkar, Sibaji

    2016-01-01

    The evolution process includes genetic alterations that started with prokaryotes and now continues in humans. A distinct difference between prokaryotic chromosomes and eukaryotic chromosomes involves histones. As evolution progressed, genetic alterations accumulated and a mechanism for gene selection developed. It was as if nature was experimenting to optimally utilize the gene pool without changing individual gene sequences. This mechanism is called epigenetics, as it is above the genome. Curiously, the mechanism of epigenetic regulation in prokaryotes is strikingly different from that in eukaryotes, mainly higher eukaryotes, like mammals. In fact, epigenetics plays a significant role in the conserved process of embryogenesis and human development. Malfunction of epigenetic regulation results in many types of undesirable effects, including cardiovascular disease, metabolic disorders, autoimmune diseases, and cancer. This review provides a comparative analysis and new insights into these aspects. PMID:27512339

  17. Prokaryotic Community Diversity Along an Increasing Salt Gradient in a Soda Ash Concentration Pond.

    PubMed

    Simachew, Addis; Lanzén, Anders; Gessesse, Amare; Øvreås, Lise

    2016-02-01

    The effect of salinity on prokaryotic community diversity in Abijata-Shalla Soda Ash Concentration Pond system was investigated by using high-throughput 16S rRNA gene 454 pyrosequencing. Surface water and brine samples from five sites spanning a salinity range of 3.4 % (Lake Abijata) to 32 % (SP230F, crystallizer pond) were analyzed. Overall, 33 prokaryotic phyla were detected, and the dominant prokaryotic phyla accounted for more than 95 % of the reads consisting of Planctomycetes, Bacteroidetes, candidate division TM7, Deinococcus-Thermus, Firmicutes, Actinobacteria, Proteobacteria, and Euryarchaeota. Diversity indices indicated that operational taxonomic unit (OTU) richness decreases drastically with increasing salinity in the pond system. A total of 471 OTUs were found at 3.4 % salinity whereas 49 OTUs were detected in pond SP211 (25 % salinity), and only 19 OTUs in the crystallization pond at 32 % salinity (SP230F). Along the salinity gradient, archaeal community gradually replaced bacterial community. Thus, archaeal community accounted for 0.4 % in Lake Abijata while 99.0 % in pond SP230F. This study demonstrates that salinity appears to be the key environmental parameter in structuring the prokaryotic communities of haloalkaline environments. Further, it confirmed that the prokaryotic diversity in Lake Abijata is high and it harbors taxa with low or no phylogenetic similarities to existing prokaryotic taxa and thus represents novel microorganisms.

  18. A Novel Prokaryotic Promoter Identified in the Genome of Some Monopartite Begomoviruses

    PubMed Central

    Wang, Wei-Chen; Hsu, Yau-Heiu; Lin, Na-Sheng; Wu, Chia-Ying; Lai, Yi-Chin; Hu, Chung-Chi

    2013-01-01

    Geminiviruses are known to exhibit both prokaryotic and eukaryotic features in their genomes, with the ability to express their genes and even replicate in bacterial cells. We have demonstrated previously the existence of unit-length single-stranded circular DNAs of Ageratum yellow vein virus (AYVV, a species in the genus Begomovirus, family Geminiviridae) in Escherichia coli cells, which prompted our search for unknown prokaryotic functions in the begomovirus genomes. By using a promoter trapping strategy, we identified a novel prokaryotic promoter, designated AV3 promoter, in nts 762-831 of the AYVV genome. Activity assays revealed that the AV3 promoter is strong, unidirectional, and constitutive, with an endogenous downstream ribosome binding site and a translatable short open reading frame of eight amino acids. Sequence analyses suggested that the AV3 promoter might be a remnant of prokaryotic ancestors that could be related to certain promoters of bacteria from marine or freshwater environments. The discovery of the prokaryotic AV3 promoter provided further evidence for the prokaryotic origin in the evolutionary history of geminiviruses. PMID:23936138

  19. Prokaryote diversity and viral production in deep-sea sediments and seamounts

    NASA Astrophysics Data System (ADS)

    Danovaro, Roberto; Corinaldesi, Cinzia; Luna, Gian Marco; Magagnini, Mirko; Manini, Elena; Pusceddu, Antonio

    2009-05-01

    Despite the fact that marine prokaryotes and viruses have been increasingly investigated over the last decade, knowledge on prokaryote diversity and viral production in bathyal sediments is limited. We investigated microbial variables in the deep-sea sediments around two seamounts at 3000-m depth in the Tyrrhenian Sea and sediments located at the same depth, but not affected by the presence of the seamounts. We hypothesized that seamounts altered significantly prokaryotes-viruses interactions in surrounding deep-sea sediments. Sediments surrounding seamounts were characterised by prokaryotic abundances significantly higher than those observed in non-seamount sediments. Benthic viral production was about double in sediments close to seamounts than in non-seamount sediments, where virus turnover was up to 3 times lower. Total Bacteria, as assessed by CARD-FISH, dominated prokaryotic community structure, whereas Archaea accounted on average for approximately 10%. The fraction of Crenarchaeota was always higher than Euryarchaeota. Bacterial diversity, estimated using ARISA, was high, with up to 127 different microbial operational taxonomic units (OTUs) in a single sample. Archaeal richness (determined using T-RFLP of the 16S rRNA gene) ranged from 12 to 20 OTUs, while Archaeal evenness was comprised between 0.529±0.018 and 0.623±0.08. Results represent a pointer for future investigations dealing with the interactions between viruses and prokaryotes in deep-sea sediments.

  20. Birth, death, and diversification of mobile promoters in prokaryotes.

    PubMed

    van Passel, Mark W J; Nijveen, Harm; Wahl, Lindi M

    2014-05-01

    A previous study of prokaryotic genomes identified large reservoirs of putative mobile promoters (PMPs), that is, homologous promoter sequences associated with nonhomologous coding sequences. Here we extend this data set to identify the full complement of mobile promoters in sequenced prokaryotic genomes. The expanded search identifies nearly 40,000 PMP sequences, 90% of which occur in noncoding regions of the genome. To gain further insight from this data set, we develop a birth-death-diversification model for mobile genetic elements subject to sequence diversification; applying the model to PMPs we are able to quantify the relative importance of duplication, loss, horizontal gene transfer (HGT), and diversification to the maintenance of the PMP reservoir. The model predicts low rates of HGT relative to the duplication and loss of PMP copies, rapid dynamics of PMP families, and a pool of PMPs that exist as a single copy in a genome at any given time, despite their mobility. We report evidence of these "singletons" at high frequencies in prokaryotic genomes. We also demonstrate that including selection, either for or against PMPs, was not necessary to describe the observed data.

  1. Distribution of glucan-branching enzymes among prokaryotes.

    PubMed

    Suzuki, Eiji; Suzuki, Ryuichiro

    2016-07-01

    Glucan-branching enzyme plays an essential role in the formation of branched polysaccharides, glycogen, and amylopectin. Only one type of branching enzyme, belonging to glycoside hydrolase family 13 (GH13), is found in eukaryotes, while two types of branching enzymes (GH13 and GH57) occur in prokaryotes (Bacteria and Archaea). Both of these types are the members of protein families containing the diverse specificities of amylolytic glycoside hydrolases. Although similarities are found in the catalytic mechanism between the two types of branching enzyme, they are highly distinct from each other in terms of amino acid sequence and tertiary structure. Branching enzymes are found in 29 out of 30 bacterial phyla and 1 out of 5 archaeal phyla, often along with glycogen synthase, suggesting the existence of α-glucan production and storage in a wide range of prokaryotes. Enormous variability is observed as to which type and how many copies of branching enzyme are present depending on the phylum and, in some cases, even among species of the same genus. Such a variation may have occurred through lateral transfer, duplication, and/or differential loss of genes coding for branching enzyme during the evolution of prokaryotes.

  2. The "Giant Virus Finder" discovers an abundance of giant viruses in the Antarctic dry valleys.

    PubMed

    Kerepesi, Csaba; Grolmusz, Vince

    2017-02-28

    Mimivirus was identified in 2003 from a biofilm of an industrial water-cooling tower in England. Later, numerous new giant viruses were found in oceans and freshwater habitats, some of them having 2,500 genes. We have demonstrated their likely presence in four soil samples taken from the Kutch Desert (Gujarat, India). Here we describe a bioinformatics work-flow, called the "Giant Virus Finder" that is capable of discovering the likely presence of the genomes of giant viruses in metagenomic shotgun-sequenced datasets. The new workflow is applied to numerous hot and cold desert soil samples as well as some tundra- and forest soils. We show that most of these samples contain giant viruses, especially in the Antarctic dry valleys. The results imply that giant viruses could be frequent not only in aqueous habitats, but in a wide spectrum of soils on our planet.

  3. Test technology on divergence angle of laser range finder based on CCD imaging fusion

    NASA Astrophysics Data System (ADS)

    Shi, Sheng-bing; Chen, Zhen-xing; Lv, Yao

    2016-09-01

    Laser range finder has been equipped with all kinds of weapons, such as tank, ship, plane and so on, is important component of fire control system. Divergence angle is important performance and incarnation of horizontal resolving power for laser range finder, is necessary appraised test item in appraisal test. In this paper, based on high accuracy test on divergence angle of laser range finder, divergence angle test system is designed based on CCD imaging, divergence angle of laser range finder is acquired through fusion technology for different attenuation imaging, problem that CCD characteristic influences divergence angle test is solved.

  4. ProOpDB: Prokaryotic Operon DataBase.

    PubMed

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

    2012-01-01

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

  5. [GTPases of prokaryotic translational apparatus].

    PubMed

    Hauryliuk, V V

    2006-01-01

    Four protein factors, belonging to the GTPase superfamily, participate in bacterial biosynthesis: IF2, EF-G, EF-Tu and RF3. The exact role and mechanism of action of these proteins was of particular interest over the last several decades. Recent advances in structural methods of ribosomal research, especially application of cryoelectron microscopy, provided powerful experimental tools for the investigation of ribosomal dynamics during translation. Simultaneously, progress in the biochemical investigation of translation allowed us to link structural rearrangements occurring in the ribosome to functional changes in the ribosome-bound translational GTPases--GDP/GTP exchange, GTPase activation and its conformational changes. Accumulated data have lead to formulation of current models of mechanisms of translation. More and more facts testify in favor of the idea that the ribosome plays a prominent role both in the nucleotide exchange and in GTPase activation, thus playing the role both of GAP and GEF for RF3, IF2 and EF-G. In our work we attempted to systematize the most important experimental findings and models for mechanisms of GTPases function and regulation in prokaryotic translation.

  6. Evolution of photosynthetic prokaryotes: a maximum-likelihood mapping approach.

    PubMed Central

    Raymond, Jason; Zhaxybayeva, Olga; Gogarten, J Peter; Blankenship, Robert E

    2003-01-01

    Reconstructing the early evolution of photosynthesis has been guided in part by the geological record, but the complexity and great antiquity of these early events require molecular genetic techniques as the primary tools of inference. Recent genome sequencing efforts have made whole genome data available from representatives of each of the five phyla of bacteria with photosynthetic members, allowing extensive phylogenetic comparisons of these organisms. Here, we have undertaken whole genome comparisons using maximum likelihood to compare 527 unique sets of orthologous genes from all five photosynthetic phyla. Substantiating recent whole genome analyses of other prokaryotes, our results indicate that horizontal gene transfer (HGT) has played a significant part in the evolution of these organisms, resulting in genomes with mosaic evolutionary histories. A small plurality phylogenetic signal was observed, which may be a core of remnant genes not subject to HGT, or may result from a propensity for gene exchange between two or more of the photosynthetic organisms compared. PMID:12594930

  7. StarFinder: A code for stellar field analysis

    NASA Astrophysics Data System (ADS)

    Diolaiti, Emiliano; Bendinelli, Orazio; Bonaccini, Domenico; Close, Laird M.; Currie, Doug G.; Parmeggiani, Gianluigi

    2000-11-01

    StarFinder is an IDL code for the deep analysis of stellar fields, designed for Adaptive Optics well-sampled images with high and low Strehl ratio. The Point Spread Function is extracted directly from the frame, to take into account the actual structure of the instrumental response and the atmospheric effects. The code is written in IDL language and organized in the form of a self-contained widget-based application, provided with a series of tools for data visualization and analysis. A description of the method and some applications to Adaptive Optics data are presented.

  8. Terrestrial Planet Finder Interferometer Technology Status and Plans

    NASA Technical Reports Server (NTRS)

    Lawson, Perter R.; Ahmed, A.; Gappinger, R. O.; Ksendzov, A.; Lay, O. P.; Martin, S. R.; Peters, R. D.; Scharf, D. P.; Wallace, J. K.; Ware, B.

    2006-01-01

    A viewgraph presentation on the technology status and plans for Terrestrial Planet Finder Interferometer is shown. The topics include: 1) The Navigator Program; 2) TPF-I Project Overview; 3) Project Organization; 4) Technology Plan for TPF-I; 5) TPF-I Testbeds; 6) Nulling Error Budget; 7) Nulling Testbeds; 8) Nulling Requirements; 9) Achromatic Nulling Testbed; 10) Single Mode Spatial Filter Technology; 11) Adaptive Nuller Testbed; 12) TPF-I: Planet Detection Testbed (PDT); 13) Planet Detection Testbed Phase Modulation Experiment; and 14) Formation Control Testbed.

  9. Status of the Terrestrial Planet Finder Interferometer (TPF-I)

    NASA Technical Reports Server (NTRS)

    Beichman, Charles; Lawson, Peter; Lay, Oliver; Ahmed, Asif; Unwin, Steve; Johnston, K.

    2006-01-01

    The interferometric version of the Terrestrial Planet Finder (TPF-I) has the potential to find and characterize earth-sized planets in the habitable zones of over 250 nearby stars and to search for life using biomarkers in the atmospheres of any planets found. The scientific case for such a mission continues to be strengthened by on-going progress in the detection of planets via indirect means. This paper summarizes the status of TPF-I, illustrative scientific requirements for the mission, and its enabling technologies.

  10. Terrestrial Planet Finder Interferometer: Architecture, Mission Design and Technology Development

    NASA Technical Reports Server (NTRS)

    Henry, Curt; Lay, Oliver; Aung, MiMi; Gunter, Steven M.; Dubovitsky, Serge; Blackwood, Gary

    2004-01-01

    This overview paper is a progress report about the system design and technology development of two interferometer concepts studied for the Terrestrial Planet Finder (TPF) project. The two concepts are a structurally-connected interferometer (SCI) intended to fulfill minimum TPF science goals and a formation-flying interferometer (FFI) intended to fulfill full science goals. Described are major trades, analyses, and technology experiments completed. Near term plans are also described. This paper covers progress since August 2003 and serves as an update to a paper presented at that month's SPIE conference, 'Techniques and Instrumentation for Detection of Exoplanets.

  11. Metrology system for the Terrestrial Planet Finder Coronagraph

    NASA Technical Reports Server (NTRS)

    Shaklin, Stuart; Marchen, Luis; Zhao, Feng; Peters, Robert D.; Ho, Tim; Holmes, Buck

    2004-01-01

    The Terrestrial Planet Finder (TPF) employs an aggressive coronagraph designed to obtain better than 1e-10 contrast inside the third Airy ring. Minute changes in low-order aberration content scatter significant light at this position. One implication is the requirement to control low-order aberrations induced by motion of the secondary mirror relative to the primary mirror; sub-nanometer relative positional stability is required. We propose a 6-beam laser truss to monitor the relative positions of the two mirrors. The truss is based on laser metrology developed for the Space Interferometry Mission.

  12. Key software architecture decisions for the automated planet finder

    NASA Astrophysics Data System (ADS)

    Lanclos, Kyle; Deich, William T. S.; Holden, Bradford P.; Allen, S. L.

    2016-08-01

    The Automated Planet Finder (APF) at Lick Observatory on Mount Hamilton is a modern 2.4 meter computer controlled telescope. At one Nasmyth focus is the Levy Spectrometer, at present the sole instrument used with the APF. The primary research mission of the APF and the Levy Spectrometer is high-precision Doppler spectroscopy. Observing at the APF is unattended; custom software written by diverse authors in diverse languages manage all aspects of a night's observing. This paper will cover some of the key software architecture decisions made in the development of autonomous observing at the APF. The relevance to future projects of these decisions will be emphasized throughout.

  13. Strategies for chemical reaction searching in SciFinder

    PubMed

    Ridley

    2000-09-01

    The bibliographic, chemical structure, and chemical reaction databases produced by Chemical Abstracts Service allow a number of possibilities for chemical reaction searching. While these same databases may be searched through the STN network, many end-users find the intuitive software interface SciFinder simpler, but there still are issues to address. Searching may be performed through keywords, chemical structures, or chemical reactions, and the answers may vary with respect to precision and comprehension. Often combinations of search options may be needed to best solve the problem. Retrosynthetic analyses are easily performed in the chemical reaction database and can give unique insights into synthetic alternatives.

  14. Introduction to Structure Searching with SciFinder Scholar

    NASA Astrophysics Data System (ADS)

    Ridley, Damon D.

    2001-04-01

    CAS Registry Numbers provide a key to searching for chemical substances in CAS databases, and the challenge is to obtain the Registry Numbers for all the substances required. When the substances can be represented by structures, then one option is to find the Registry Numbers through structure searches. With SciFinder Scholar, the process of drawing and searching structures is intuitive; however, there are underlying issues and opportunities that need some explanation in courses on chemical information retrieval.We describe here our introductory course, which addresses the major ones.

  15. Prokaryotic and eukaryotic unicellular chronomics

    PubMed Central

    Halberg, F.; Cornélissen, G.; Faraone, P.; Poeggeler, B.; Hardeland, R.; Katinas, G.; Schwartzkopff, O.; Otsuka, K.; Bakken, E. E.

    2008-01-01

    An impeccable time series, published in 1930, consisting of hourly observations on colony advance in a fluid culture of E. coli, was analyzed by a periodogram and power spectrum in 1961. While the original senior author had emphasized specifically periodicity with no estimate of period length, he welcomed further analyses. After consulting his technician, he knew of no environmental periodicity related to human schedules other than an hourly photography. A periodogram analysis in 1961 showed a 20.75-h period. It was emphasized that “… the circadian period disclosed is not of exactly 24-h length.” Confirmations notwithstanding, a committee ruled out microbial circadian rhythms based on grounds that could have led to a different conclusion, namely first, the inability of some committee members to see (presumably by eyeballing) the rhythms in their own data, and second, what hardly follows, that there were “too many analyses” in the published papers. Our point in dealing with microbes and humans is that analyses are indispensable for quantification and for discovering a biologically novel spectrum of cyclicities, matching physical ones. The scope of circadian organization estimated in 1961 has become broader, including about 7-day, about half-yearly, about-yearly and ex-yearly and decadal periodisms, among others. Microbial circadians have become a field of their own with eyeballing, yet time-microscopy can quantify characteristics with their uncertainties and can assess broad chronomes (time structures) with features beyond circadians. As yet only suggestive differences between eukaryotes and prokaryotes further broaden the perspective and may lead to life’s sites of origin and to new temporal aspects of life’ s development as a chronomic tree by eventual rhythm dating in ontogeny and phylogeny. PMID:16275493

  16. Dynamic evolution of translation initiation mechanisms in prokaryotes

    PubMed Central

    Nakagawa, So; Niimura, Yoshihito; Miura, Kin-ichiro; Gojobori, Takashi

    2010-01-01

    It is generally believed that prokaryotic translation is initiated by the interaction between the Shine-Dalgarno (SD) sequence in the 5′ UTR of an mRNA and the anti-SD sequence in the 3′ end of a 16S ribosomal RNA. However, there are two exceptional mechanisms, which do not require the SD sequence for translation initiation: one is mediated by a ribosomal protein S1 (RPS1) and the other used leaderless mRNA that lacks its 5′ UTR. To understand the evolutionary changes of the mechanisms of translation initiation, we examined how universal the SD sequence is as an effective initiator for translation among prokaryotes. We identified the SD sequence from 277 species (249 eubacteria and 28 archaebacteria). We also devised an SD index that is a proportion of SD-containing genes in which the differences of GC contents are taken into account. We found that the SD indices varied among prokaryotic species, but were similar within each phylum. Although the anti-SD sequence is conserved among species, loss of the SD sequence seems to have occurred multiple times, independently, in different phyla. For those phyla, RPS1-mediated or leaderless mRNA-used mechanisms of translation initiation are considered to be working to a greater extent. Moreover, we also found that some species, such as Cyanobacteria, may acquire new mechanisms of translation initiation. Our findings indicate that, although translation initiation is indispensable for all protein-coding genes in the genome of every species, its mechanisms have dynamically changed during evolution. PMID:20308567

  17. Knickpoint finder: A software tool that improves neotectonic analysis

    NASA Astrophysics Data System (ADS)

    Queiroz, G. L.; Salamuni, E.; Nascimento, E. R.

    2015-03-01

    This work presents a new software tool for morphometric analysis of drainage networks based on the methods of Hack (1973) and Etchebehere et al. (2004). This tool is applicable to studies of morphotectonics and neotectonics. The software used a digital elevation model (DEM) to identify the relief breakpoints along drainage profiles (knickpoints). The program was coded in Python for use on the ArcGIS platform and is called Knickpoint Finder. A study area was selected to test and evaluate the software's ability to analyze and identify neotectonic morphostructures based on the morphology of the terrain. For an assessment of its validity, we chose an area of the James River basin, which covers most of the Piedmont area of Virginia (USA), which is an area of constant intraplate seismicity and non-orogenic active tectonics and exhibits a relatively homogeneous geodesic surface currently being altered by the seismogenic features of the region. After using the tool in the chosen area, we found that the knickpoint locations are associated with the geologic structures, epicenters of recent earthquakes, and drainages with rectilinear anomalies. The regional analysis demanded the use of a spatial representation of the data after processing using Knickpoint Finder. The results were satisfactory in terms of the correlation of dense areas of knickpoints with active lineaments and the rapidity of the identification of deformed areas. Therefore, this software tool may be considered useful in neotectonic analyses of large areas and may be applied to any area where there is DEM coverage.

  18. Laser Range and Bearing Finder for Autonomous Missions

    NASA Technical Reports Server (NTRS)

    Granade, Stephen R.

    2004-01-01

    NASA has recently re-confirmed their interest in autonomous systems as an enabling technology for future missions. In order for autonomous missions to be possible, highly-capable relative sensor systems are needed to determine an object's distance, direction, and orientation. This is true whether the mission is autonomous in-space assembly, rendezvous and docking, or rover surface navigation. Advanced Optical Systems, Inc. has developed a wide-angle laser range and bearing finder (RBF) for autonomous space missions. The laser RBF has a number of features that make it well-suited for autonomous missions. It has an operating range of 10 m to 5 km, with a 5 deg field of view. Its wide field of view removes the need for scanning systems such as gimbals, eliminating moving parts and making the sensor simpler and space qualification easier. Its range accuracy is 1% or better. It is designed to operate either as a stand-alone sensor or in tandem with a sensor that returns range, bearing, and orientation at close ranges, such as NASA's Advanced Video Guidance Sensor. We have assembled the initial prototype and are currently testing it. We will discuss the laser RBF's design and specifications. Keywords: laser range and bearing finder, autonomous rendezvous and docking, space sensors, on-orbit sensors, advanced video guidance sensor

  19. Supramolecular organization in prokaryotic respiratory systems.

    PubMed

    Magalon, Axel; Arias-Cartin, Rodrigo; Walburger, Anne

    2012-01-01

    Prokaryotes are characterized by an extreme flexibility of their respiratory systems allowing them to cope with various extreme environments. To date, supramolecular organization of respiratory systems appears as a conserved evolutionary feature as supercomplexes have been isolated in bacteria, archaea, and eukaryotes. Most of the yet identified supercomplexes in prokaryotes are involved in aerobic respiration and share similarities with those reported in mitochondria. Supercomplexes likely reflect a snapshot of the cellular respiration in a given cell population. While the exact nature of the determinants for supramolecular organization in prokaryotes is not understood, lipids, proteins, and subcellular localization can be seen as key players. Owing to the well-reported supramolecular organization of the mitochondrial respiratory chain in eukaryotes, several hypotheses have been formulated to explain the consequences of such arrangement and can be tested in the context of prokaryotes. Considering the inherent metabolic flexibility of a number of prokaryotes, cellular distribution and composition of the supramolecular assemblies should be studied in regards to environmental signals. This would pave the way to new concepts in cellular respiration.

  20. The repertoire of ICE in prokaryotes underscores the unity, diversity, and ubiquity of conjugation.

    PubMed

    Guglielmini, Julien; Quintais, Leonor; Garcillán-Barcia, Maria Pilar; de la Cruz, Fernando; Rocha, Eduardo P C

    2011-08-01

    Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ICE) in prokaryotes remained unknown. We defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. We found 682 putative conjugative systems among all major phylogenetic clades and showed that ICEs are the most abundant conjugative elements in prokaryotes. Nearly half of the genomes contain a type IV secretion system (T4SS), with larger genomes encoding more conjugative systems. Surprisingly, almost half of the chromosomal T4SS lack co-localized relaxases and, consequently, might be devoted to protein transport instead of conjugation. This class of elements is preponderant among small genomes, is less commonly associated with integrases, and is rarer in plasmids. ICEs and conjugative plasmids in proteobacteria have different preferences for each type of T4SS, but all types exist in both chromosomes and plasmids. Mobilizable elements outnumber self-conjugative elements in both ICEs and plasmids, which suggests an extensive use of T4SS in trans. Our evolutionary analysis indicates that switch of plasmids to and from ICEs were frequent and that extant elements began to differentiate only relatively recently. According to the present results, ICEs are the most abundant conjugative elements in practically all prokaryotic clades and might be far more frequently domesticated into non-conjugative protein transport systems than previously thought. While conjugative plasmids and ICEs have different means of genomic stabilization, their mechanisms of mobility by conjugation show strikingly conserved patterns, arguing for a unitary view of conjugation in shaping the genomes of prokaryotes by

  1. The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation

    PubMed Central

    Guglielmini, Julien; Quintais, Leonor; Garcillán-Barcia, Maria Pilar; de la Cruz, Fernando; Rocha, Eduardo P. C.

    2011-01-01

    Horizontal gene transfer shapes the genomes of prokaryotes by allowing rapid acquisition of novel adaptive functions. Conjugation allows the broadest range and the highest gene transfer input per transfer event. While conjugative plasmids have been studied for decades, the number and diversity of integrative conjugative elements (ICE) in prokaryotes remained unknown. We defined a large set of protein profiles of the conjugation machinery to scan over 1,000 genomes of prokaryotes. We found 682 putative conjugative systems among all major phylogenetic clades and showed that ICEs are the most abundant conjugative elements in prokaryotes. Nearly half of the genomes contain a type IV secretion system (T4SS), with larger genomes encoding more conjugative systems. Surprisingly, almost half of the chromosomal T4SS lack co-localized relaxases and, consequently, might be devoted to protein transport instead of conjugation. This class of elements is preponderant among small genomes, is less commonly associated with integrases, and is rarer in plasmids. ICEs and conjugative plasmids in proteobacteria have different preferences for each type of T4SS, but all types exist in both chromosomes and plasmids. Mobilizable elements outnumber self-conjugative elements in both ICEs and plasmids, which suggests an extensive use of T4SS in trans. Our evolutionary analysis indicates that switch of plasmids to and from ICEs were frequent and that extant elements began to differentiate only relatively recently. According to the present results, ICEs are the most abundant conjugative elements in practically all prokaryotic clades and might be far more frequently domesticated into non-conjugative protein transport systems than previously thought. While conjugative plasmids and ICEs have different means of genomic stabilization, their mechanisms of mobility by conjugation show strikingly conserved patterns, arguing for a unitary view of conjugation in shaping the genomes of prokaryotes by

  2. Regional variations in the diversity and predicted metabolic potential of benthic prokaryotes in coastal northern Zhejiang, East China Sea

    PubMed Central

    Wang, Kai; Ye, Xiansen; Zhang, Huajun; Chen, Heping; Zhang, Demin; Liu, Lian

    2016-01-01

    Knowledge about the drivers of benthic prokaryotic diversity and metabolic potential in interconnected coastal sediments at regional scales is limited. We collected surface sediments across six zones covering ~200 km in coastal northern Zhejiang, East China Sea and combined 16 S rRNA gene sequencing, community-level metabolic prediction, and sediment physicochemical measurements to investigate variations in prokaryotic diversity and metabolic gene composition with geographic distance and under local environmental conditions. Geographic distance was the most influential factor in prokaryotic β-diversity compared with major environmental drivers, including temperature, sediment texture, acid-volatile sulfide, and water depth, but a large unexplained variation in community composition suggested the potential effects of unmeasured abiotic/biotic factors and stochastic processes. Moreover, prokaryotic assemblages showed a biogeographic provincialism across the zones. The predicted metabolic gene composition similarly shifted as taxonomic composition did. Acid-volatile sulfide was strongly correlated with variation in metabolic gene composition. The enrichments in the relative abundance of sulfate-reducing bacteria and genes relevant with dissimilatory sulfate reduction were observed and predicted, respectively, in the Yushan area. These results provide insights into the relative importance of geographic distance and environmental condition in driving benthic prokaryotic diversity in coastal areas and predict specific biogeochemically-relevant genes for future studies. PMID:27917954

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

    PubMed Central

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

    2016-01-01

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

  4. Assessment of diversity indices for the characterization of the soil prokaryotic community by metagenomic analysis

    NASA Astrophysics Data System (ADS)

    Chernov, T. I.; Tkhakakhova, A. K.; Kutovaya, O. V.

    2015-04-01

    The diversity indices used in ecology for assessing the metagenomes of soil prokaryotic communities at different phylogenetic levels were compared. The following indices were considered: the number of detected taxa and the Shannon, Menhinick, Margalef, Simpson, Chao1, and ACE indices. The diversity analysis of the prokaryotic communities in the upper horizons of a typical chernozem (Haplic Chernozem (Pachic)), a dark chestnut soil (Haplic Kastanozem (Chromic)), and an extremely arid desert soil (Endosalic Calcisol (Yermic)) was based on the analysis of 16S rRNA genes. The Menhinick, Margalef, Chao1, and ACE indices gave similar results for the classification of the communities according to their diversity levels; the Simpson index gave good results only for the high-level taxa (phyla); the best results were obtained with the Shannon index. In general, all the indices used showed a decrease in the diversity of the soil prokaryotes in the following sequence: chernozem > dark chestnut soil > extremely arid desert soil.

  5. Evidence for an early prokaryotic endosymbiosis.

    PubMed

    Lake, James A

    2009-08-20

    Endosymbioses have dramatically altered eukaryotic life, but are thought to have negligibly affected prokaryotic evolution. Here, by analysing the flows of protein families, I present evidence that the double-membrane, gram-negative prokaryotes were formed as the result of a symbiosis between an ancient actinobacterium and an ancient clostridium. The resulting taxon has been extraordinarily successful, and has profoundly altered the evolution of life by providing endosymbionts necessary for the emergence of eukaryotes and by generating Earth's oxygen atmosphere. Their double-membrane architecture and the observed genome flows into them suggest a common evolutionary mechanism for their origin: an endosymbiosis between a clostridium and actinobacterium.

  6. Phase-space structures - II. Hierarchical Structure Finder

    NASA Astrophysics Data System (ADS)

    Maciejewski, M.; Colombi, S.; Springel, V.; Alard, C.; Bouchet, F. R.

    2009-07-01

    A new multidimensional Hierarchical Structure Finder (HSF) to study the phase-space structure of dark matter in N-body cosmological simulations is presented. The algorithm depends mainly on two parameters, which control the level of connectivity of the detected structures and their significance compared to Poisson noise. By working in six-dimensional phase space, where contrasts are much more pronounced than in three-dimensional (3D) position space, our HSF algorithm is capable of detecting subhaloes including their tidal tails, and can recognize other phase-space structures such as pure streams and candidate caustics. If an additional unbinding criterion is added, the algorithm can be used as a self-consistent halo and subhalo finder. As a test, we apply it to a large halo of the Millennium Simulation, where 19 per cent of the halo mass is found to belong to bound substructures, which is more than what is detected with conventional 3D substructure finders, and an additional 23-36 per cent of the total mass belongs to unbound HSF structures. The distribution of identified phase-space density peaks is clearly bimodal: high peaks are dominated by the bound structures and show a small spread in their height distribution; low peaks belong mostly to tidal streams, as expected. However, the projected (3D) density distribution of the structures shows that some of the streams can have comparable density to the bound structures in position space. In order to better understand what HSF provides, we examine the time evolution of structures, based on the merger tree history. Given the resolution limit of the Millennium Simulation, bound structures typically make only up to six orbits inside the main halo. The number of orbits scales approximately linearly with the redshift corresponding to the moment of merging of the structures with the halo. At fixed redshift, the larger the initial mass of the structure which enters the main halo, the faster it loses mass. The difference in

  7. GAPP: A Proteogenomic Software for Genome Annotation and Global Profiling of Post-translational Modifications in Prokaryotes.

    PubMed

    Zhang, Jia; Yang, Ming-Kun; Zeng, Honghui; Ge, Feng

    2016-11-01

    Although the number of sequenced prokaryotic genomes is growing rapidly, experimentally verified annotation of prokaryotic genome remains patchy and challenging. To facilitate genome annotation efforts for prokaryotes, we developed an open source software called GAPP for genome annotation and global profiling of post-translational modifications (PTMs) in prokaryotes. With a single command, it provides a standard workflow to validate and refine predicted genetic models and discover diverse PTM events. We demonstrated the utility of GAPP using proteomic data from Helicobacter pylori, one of the major human pathogens that is responsible for many gastric diseases. Our results confirmed 84.9% of the existing predicted H. pylori proteins, identified 20 novel protein coding genes, and corrected four existing gene models with regard to translation initiation sites. In particular, GAPP revealed a large repertoire of PTMs using the same proteomic data and provided a rich resource that can be used to examine the functions of reversible modifications in this human pathogen. This software is a powerful tool for genome annotation and global discovery of PTMs and is applicable to any sequenced prokaryotic organism; we expect that it will become an integral part of ongoing genome annotation efforts for prokaryotes. GAPP is freely available at https://sourceforge.net/projects/gappproteogenomic/.

  8. Prokaryotic orthologues of mitochondrial alternative oxidase and plastid terminal oxidase.

    PubMed

    McDonald, Allison E; Amirsadeghi, Sasan; Vanlerberghe, Greg C

    2003-12-01

    The mitochondrial alternative oxidase (AOX) and the plastid terminal oxidase (PTOX) are two similar members of the membrane-bound diiron carboxylate group of proteins. AOX is a ubiquinol oxidase present in all higher plants, as well as some algae, fungi, and protists. It may serve to dampen reactive oxygen species generation by the respiratory electron transport chain. PTOX is a plastoquinol oxidase in plants and some algae. It is required in carotenoid biosynthesis and may represent the elusive oxidase in chlororespiration. Recently, prokaryotic orthologues of both AOX and PTOX proteins have appeared in sequence databases. These include PTOX orthologues present in four different cyanobacteria as well as an AOX orthologue in an alpha-proteobacterium. We used PCR, RT-PCR and northern analyses to confirm the presence and expression of the PTOX gene in Anabaena variabilis PCC 7120. An extensive phylogeny of newly found prokaryotic and eukaryotic AOX and PTOX proteins supports the idea that AOX and PTOX represent two distinct groups of proteins that diverged prior to the endosymbiotic events that gave rise to the eukaryotic organelles. Using multiple sequence alignment, we identified residues conserved in all AOX and PTOX proteins. We also provide a scheme to readily distinguish PTOX from AOX proteins based upon differences in amino acid sequence in motifs around the conserved iron-binding residues. Given the presence of PTOX in cyanobacteria, we suggest that this acronym now stand for plastoquinol terminal oxidase. Our results have implications for the photosynthetic and respiratory metabolism of these prokaryotes, as well as for the origin and evolution of eukaryotic AOX and PTOX proteins.

  9. Variation in global codon usage bias among prokaryotic organisms is associated with their lifestyles

    PubMed Central

    2011-01-01

    Background It is widely acknowledged that synonymous codons are used unevenly among genes in a genome. In organisms under translational selection, genes encoding highly expressed proteins are enriched with specific codons. This phenomenon, termed codon usage bias, is common to many organisms and has been recognized as influencing cellular fitness. This suggests that the global extent of codon usage bias of an organism might be associated with its phenotypic traits. Results To test this hypothesis we used a simple measure for assessing the extent of codon bias of an organism, and applied it to hundreds of sequenced prokaryotes. Our analysis revealed a large variability in this measure: there are organisms showing very high degrees of codon usage bias and organisms exhibiting almost no differential use of synonymous codons among different genes. Remarkably, we found that the extent of codon usage bias corresponds to the lifestyle of the organism. Especially, organisms able to live in a wide range of habitats exhibit high extents of codon usage bias, consistent with their need to adapt efficiently to different environments. Pathogenic prokaryotes also demonstrate higher extents of codon usage bias than non-pathogenic prokaryotes, in accord with the multiple environments that many pathogens occupy. Our results show that the previously observed correlation between growth rate and metabolic variability is attributed to their individual associations with codon usage bias. Conclusions Our results suggest that the extent of codon usage bias of an organism plays a role in the adaptation of prokaryotes to their environments. PMID:22032172

  10. Echo tracker/range finder for radars and sonars

    NASA Technical Reports Server (NTRS)

    Constantinides, N. J. (Inventor)

    1982-01-01

    An echo tracker/range finder or altimeter is described. The pulse repetition frequency (PFR) of a predetermined plurality of transmitted pulses is adjusted so that echo pulses received from a reflecting object are positioned between transmitted pulses and divided their interpulse time interval into two time intervals having a predetermined ratio with respect to each other. The invention described provides a means whereby the arrival time of a plurality of echo pulses is defined as the time at which a composite echo pulse formed of a sum of the individual echo pulses has the highest amplitude. The invention is applicable to radar systems, sonar systems, or any other kind of system in which pulses are transmitted and echoes received therefrom.

  11. Design for a source-agile automatic direction finder (ADF)

    NASA Astrophysics Data System (ADS)

    Myler, Harley

    2015-05-01

    The design is intended for aircraft although any vehicle or even a man-mobile system could use the concept. An automatically reconfigurable antenna using MEMS RF switches is driven to seek signals consistent with the current location of the system. The antenna feeds a Software Defined Radio (SDR) that scans for signals and when a signal is found, it is identified and then the azimuth to the signal is used, along with a signal strength parameter, to confirm the location of the system. This is an extension of the now obsolete Automatic Direction Finder (ADF) aircraft navigation tool that used AM broadcast non-directional beacons (NDB), many of which are still in service. The current system can access any radio signal within the limits of the reconfigurable antenna and the SDR.

  12. High Contrast Imaging Testbed for the Terrestrial Planet Finder Coronagraph

    NASA Technical Reports Server (NTRS)

    Lowmman, Andrew E.; Trauger, John T.; Gordon, Brian; Green, Joseph J.; Moody, Dwight; Niessner, Albert F.; Shi, Fang

    2004-01-01

    The Terrestrial Planet Finder (TPF) mission is planning to launch a visible coronagraphic space telescope in 2014. To achieve TPF science goals, the coronagraph must have extreme levels of wavefront correction (less than 1 Angstrom rms over controllable spatial frequencies) and stability to get the necessary suppression of diffracted starlight (approximately l0(exp -10)) contrast at an angular separation approximately 4 (lamda)/D). TPF Coronagraph's primary platform for experimentation is the High Contrast Imaging Testbed, which will provide laboratory validation of key technologies as well as demonstration of a flight-traceable approach to implementation. Precision wavefront control in the testbed is provided by a high actuator density deformable mirror. Diffracted light control is achieved through use of occulting or apodizing masks and stops. Contrast measurements will establish the technical feasibility of TPF requirements, while model and error budget validation will demonstrate implementation viability. This paper describes the current testbed design, development approach, and recent experimental results.

  13. Terrestrial Planet Finder: Coda to 10 Years of Technology Development

    NASA Technical Reports Server (NTRS)

    Lawson, Peter R.

    2009-01-01

    The Terrestrial Planet Finder (TPF) was proposed as a mission concept to the 2000 Decadal Survey, and received a very high ranking amongst the major initiatives that were then reviewed. As proposed, it was a formation flying array of four 3-m class mid-infrared telescopes, linked together as an interferometer. Its science goal was to survey 150 nearby stars for the presence of Earth-like planets, to detect signs of life or habitability, and to enable revolutionary advances in high angular resolution astrophysics. The Decadal Survey Committee recommended that $200M be invested to advance TPF technology development in the Decade of 2000-2010. This paper presents the results of NASA's investment.

  14. Electromagnetic formation flight for the Terrestrial Planet Finder

    NASA Astrophysics Data System (ADS)

    Kwon, Daniel W.; Miller, David W.

    2005-08-01

    Current techniques for actuating spacecraft in formation flying systems such as NASA's Terrestrial Planet Finder (TPF) use propellant-based systems. While maintaining relative orientation, propellant can become a critical consumable which can limit the mission lifetime. Additionally, propellant can cause optimal contamination, plume impingement, thermal emission, and vibration excitation. A novel technique called Electromagnetic Formation Flight (EMFF) can be used to eliminate propellant-based systems to control the relative degrees of freedom for TPF. The EMFF system consists of electromagnets in concert with reaction wheels and is used to replace the consumables. Solar energy, a renewable resource provides power for EMFF. This paper investigates the design for TPF using EMFF. The results show that EMFF is a viable option for TPF and compares favorably in terms of mass to propellant-based systems.

  15. Terrestrial Planet Finder Interferometer Science Working Group Report

    NASA Technical Reports Server (NTRS)

    Lawson, Peter R. (Editor); Lay, Oliver P. (Editor); Johnston, Kenneth J. (Editor); Beichman, Charles A. (Editor)

    2007-01-01

    Over the past two years, the focus of the project for the interferometric version of the Terrestrial Planet Finder(TPF-I) has been on the development of the scientific rational for the mission, the assessment of TPF-I architectures, the laboratory demonstration of key technologies, and the development of a detailed technology roadmap. The Science Working Group (SWG), in conjunction with European colleagues working on the European Space Agency's (ESA's) Darwin project, has reaffirmed the goals of TPF-I as part of a broad vision for the detection and characterization of Earth-like planets orbiting nearby stars and for the search for life on those planets. The SWG also helped to assess the performance of different interferometric configurations for TPF-I/Darwin. Building on earlier SWG reports, this document restates the scientific case for TPF-I, assesses suitable target stars and relevant wavelengths for observation, discusses dramatic new capabilities for general astrophysical observations, and summarizes how Spitzer has improved our knowledge of the incidence of zodiacal emission on the search for planets. This document discusses in some detail on laboratory advances in interferometric nulling and formation flying. Laboratory experiments have now achieved stable narrow- and broad-band nulling the levels of 10-6 and 2.0x10-5, respectively. A testbed has demonstrated formation flying using two realistic spacecraft mockups. With a suitably funded program of technology development, as summarized herein and described in more detail in the Technology Plan for the Terrestrial Planet Finder Interferometer (2005), the National Aeronautics and Space Administration (NASA) and ESA would be able to start within the coming decade a full-scale TPF-I/Darwin mission capable of finding Earths orbiting more than 150 nearby stars, or a scaled back interferometer capable of studying more than 30 stars. Finding evidence for life on just one of those planets would revolutionize our

  16. Laser Range and Bearing Finder with No Moving Parts

    NASA Technical Reports Server (NTRS)

    Bryan, Thomas C.; Howard, Richard T.; Book, Michael L.

    2007-01-01

    A proposed laser-based instrument would quickly measure the approximate distance and approximate direction to the closest target within its field of view. The instrument would not contain any moving parts and its mode of operation would not entail scanning over of its field of view. Typically, the instrument would be used to locate a target at a distance on the order of meters to kilometers. The instrument would be best suited for use in an uncluttered setting in which the target is the only or, at worst, the closest object in the vicinity; for example, it could be used aboard an aircraft to detect and track another aircraft flying nearby. The proposed instrument would include a conventional time-of-flight or echo-phase-shift laser range finder, but unlike most other range finders, this one would not generate a narrow cylindrical laser beam; instead, it would generate a conical laser beam spanning the field of view. The instrument would also include a quadrant detector, optics to focus the light returning from the target onto the quadrant detector, and circuitry to synchronize the acquisition of the quadrant-detector output with the arrival of laser light returning from the nearest target. A quadrant detector constantly gathers information from the entire field of view, without scanning; its output is a direct measure of the position of the target-return light spot on the focal plane and is thus a measure of the direction to the target. The instrument should be able to operate at a repetition rate high enough to enable it to track a rapidly moving target. Of course, a target that is not sufficiently reflective could not be located by this instrument. Preferably, retroreflectors should be attached to the target to make it sufficiently reflective.

  17. Eukaryotic versus prokaryotic marine picoplankton ecology.

    PubMed

    Massana, Ramon; Logares, Ramiro

    2013-05-01

    Marine microorganisms contribute markedly to global biomass and ecosystem function. They include a diverse collection of organisms differing in cell size and in evolutionary history. In particular, microbes within the picoplankton are similar in size but belong to two drastically different cellular plans, the prokaryotes and the eukaryotes. Compared with larger organisms, prokaryotes and picoeukaryotes share ecological features, such as high specific activity, large and constant abundances, and high dispersal potential. Still, there are some aspects where their different cell organization influences their ecological performance. First, prokaryotes have a huge metabolic versatility and are involved in all biogeochemical cycles, whereas picoeukaryotes are metabolically less flexible but can exploit diverse predatory life strategies due to their phagocytic capacity. Second, sexual reproduction is absent in prokaryotes but may be present in picoeukaryotes, thus determining different evolutionary diversification dynamics and making species limits clearer in picoeukaryotes. Finally, it is plausible that picoeukaryotes are less flexible to enter a reversible state of low metabolic activity, thus picoeukaryote assemblages may have fewer rare species and may be less resilient to environmental change. In summary, lumping together pico-sized microbes may be convenient for some ecological studies, but it is also important to keep in mind their differences.

  18. In vivo analysis of polyadenylation in prokaryotes.

    PubMed

    Mohanty, Bijoy K; Kushner, Sidney R

    2014-01-01

    Polyadenylation at the 3' ends of mRNAs, tRNAs, rRNAs, and sRNAs plays important roles in RNA metabolism in both prokaryotes and eukaryotes. However, the nature of poly(A) tails in prokaryotes is distinct compared to their eukaryotic counterparts. Specifically, depending on the organism, eukaryotic poly(A) tails average between 50 and >200 nt and can easily be isolated by several techniques involving oligo(dT)-dependent cDNA amplification. In contrast, the bulk of the poly(A) tails present on prokaryotic transcripts is relatively short (<10 nt) and is difficult to characterize using similar techniques. This chapter describes methods that can circumvent these problems. For example, we discuss how to isolate total RNA and characterize its overall polyadenylation status employing a poly(A) sizing assay. Furthermore, we describe a technique involving RNase H treatment of total RNA followed by northern analysis in order to distinguish length of poly(A) tails on various types of transcripts. Finally, we outline a useful procedure to clone the poly(A) tails of specific transcripts using 5'-3' end-ligated RNA, which is independent of oligo(dT)-dependent cDNA amplification. These approaches are particularly helpful in analyzing transcripts with either short or long poly(A) tails both in prokaryotes and eukaryotes.

  19. Microcompartments and Protein Machines in Prokaryotes

    PubMed Central

    Saier, Milton H.

    2013-01-01

    The prokaryotic cell was once thought of as a “bag of enzymes” with little or no intracellular compartmentalization. In this view, most reactions essential for life occurred as a consequence of random molecular collisions involving substrates, cofactors and cytoplasmic enzymes. Our current conception of a prokaryote is far from this view. We now consider a bacterium or an archaeon as a highly structured, non-random collection of functional membrane-embedded and proteinaceous molecular machines, each of which serves a specialized function. In this article we shall present an overview of such microcompartments including (i) the bacterial cytoskeleton and the apparati allowing DNA segregation during cells division, (ii) energy transduction apparati involving light-driven proton pumping and ion gradient-driven ATP synthesis, (iii) prokaryotic motility and taxis machines that mediate cell movements in response to gradients of chemicals and physical forces, (iv) machines of protein folding, secretion and degradation, (v) metabolasomes carrying out specific chemical reactions, (vi) 24 hour clocks allowing bacteria to coordinate their metabolic activities with the daily solar cycle and (vii) proteinaceous membrane compartmentalized structures such as sulfur granules and gas vacuoles. Membrane-bounded prokaryotic organelles were considered in a recent JMMB written symposium concerned with membraneous compartmentalization in bacteria [Saier and Bogdanov, 2013]. By contrast, in this symposium, we focus on proteinaceous microcompartments. These two symposia, taken together, provide the interested reader with an objective view of the remarkable complexity of what was once thought of as a simple non-compartmentalized cell. PMID:23920489

  20. Prokaryotic arsenate reductase enhances arsenate resistance in Mammalian cells.

    PubMed

    Wu, Dan; Tao, Xuanyu; Wu, Gaofeng; Li, Xiangkai; Liu, Pu

    2014-01-01

    Arsenic is a well-known heavy metal toxicant in the environment. Bioremediation of heavy metals has been proposed as a low-cost and eco-friendly method. This article described some of recent patents on transgenic plants with enhanced heavy metal resistance. Further, to test whether genetic modification of mammalian cells could render higher arsenic resistance, a prokaryotic arsenic reductase gene arsC was transfected into human liver cancer cell HepG2. In the stably transfected cells, the expression level of arsC gene was determined by quantitative real-time PCR. Results showed that arsC was expressed in HepG2 cells and the expression was upregulated by 3 folds upon arsenate induction. To further test whether arsC has function in HepG2 cells, the viability of HepG2-pCI-ArsC cells exposed to arsenite or arsenate was compared to that of HepG2-pCI cells without arsC gene. The results indicated that arsC increased the viability of HepG2 cells by 25% in arsenate, but not in arsenite. And the test of reducing ability of stably transfected cells revealed that the concentration of accumulated trivalent arsenic increased by 25% in HepG2-pCI-ArsC cells. To determine the intracellular localization of ArsC, a fusion vector with fluorescent marker pEGFP-N1-ArsC was constructed and transfected into.HepG2. Laser confocal microscopy showed that EGFP-ArsC fusion protein was distributed throughout the cells. Taken together, these results demonstrated that prokaryotic arsenic resistant gene arsC integrated successfully into HepG2 genome and enhanced arsenate resistance of HepG2, which brought new insights of arsenic detoxification in mammalian cells.

  1. The Gas Vacuole - an Early Organelle of Prokaryote Motility

    NASA Astrophysics Data System (ADS)

    Staley, James T.

    1980-06-01

    Several lines of evidence suggest that the gas vesicle may have been an early organelle of prokaryote motility. First, it is found in bacteria that are thought to be representatives of primitive groups. Second, it is a simple structure, and the structure alone imparts the function of motility. Thirdly, it is widely distributed amongst prokaryotes, having been found in the purple and green sulfur photosynthetic bacteria, cyanobacteria, methanogenic bacteria, obligate and facultative anaerobic heterotrophic bacteria, as well as aerobic heterotrophic bacteria that divide by budding and binary transverse fission. Recent evidence suggests that in some bacteria the genes for gas vesicle synthesis occur on plasmids. Thus, the wide distribution of this characteristic could be due to recent evolution and rapid dispersal, though early evolution is not precluded. Though the gas vesicle structure itself appears to be highly conserved among the various groups of bacteria, it seems doubtful that the regulatory mechanism to control its synthesis could be the same for the diverse gas vacuolate bacterial groups.

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

    PubMed Central

    Koonin, Eugene V.; Wolf, Yuri I.

    2008-01-01

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

  3. Redox proteins in mammalian cell death: an evolutionarily conserved function in mitochondria and prokaryotes.

    PubMed

    Punj, Vasu; Chakrabarty, A M

    2003-04-01

    Mammalian cell mitochondria are believed to have prokaryotic ancestry. Mitochondria are not only the powerhouse of energy generation within the eukaryotic cell but they also play a major role in inducing apoptotic cell death through release of redox proteins such as cytochrome c and the apoptosis-inducing factor (AIF), a flavoprotein with NADH oxidase activity. Recent evidence indicates that some present day prokaryotes release redox proteins that induce apoptosis in mammalian cells through stabilization of the tumour suppressor protein p53. p53 interacts with mitochondria either directly or through activation of the genes for pro-apoptotic proteins such as Bax or NOXA or genes that encode redox enzymes responsible for the production of reactive oxygen species (ROS). The analogy between the ancient ancestors of present day bacteria, the mitochondria, and the present day bacteria with regard to their ability to release redox proteins for triggering mammalian cell death is an interesting example of functional conservation during the hundreds of millions of years of evolution. It is possible that the ancestors of the present day prokaryotes released redox proteins to kill the ancestors of the eukaryotes. During evolution of the mitochondria from prokaryotes as obligate endosymbionts, the mitochondria maintained the same functions to programme their own host cell death.

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

    PubMed Central

    Wuichet, Kristin; Søgaard-Andersen, Lotte

    2015-01-01

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

  5. Source tracking of prokaryotic communities in fermented grain of Chinese strong-flavor liquor.

    PubMed

    Wang, Xueshan; Du, Hai; Xu, Yan

    2017-03-06

    The fermentation process of Chinese strong-flavor liquor involves numerous microbes originating from Daqu and pit mud. Daqu is the starter of fermentation, and pit mud acts as another source of inoculum of microbes in the liquor-making process. However, the contribution of microbes in pit mud and Daqu to fermented grain, and the sources of microbes in fermented grain are still waiting to be defined clearly. In this study, prokaryotic communities in fermented grain, pit mud and Daqu were identified via next generation sequencing of the V4 region of 16S rRNA gene. Principal-coordinate analysis indicated that Daqu had stronger influence on the prokaryotic communities in fermented grain at the prophase of fermentation, but pit mud influenced the fermented grain continuously during the whole fermentation process. Totally, 299 genera were detected in all fermented grain, pit mud and Daqu samples. Among them, 204 genera were detected in 3days' fermented grain. Ten genera (Lactobacillus, Leuconostoc, Staphylococcus, Gluconobacter, Acetobacter, Petrimonas, Clostridium, Ruminococcus, Methanobacterium and Methanobrevibacter) were dominant, and accounted for 84.31%-87.13% relative abundance of the total prokaryotic community in fermented grain. Venn analysis indicated Daqu was the main source of strict aerobes and facultative aerobes, which took up over 74% of prokaryotic communities in fermented grain. Conversely, pit mud was the sustained-release source of anaerobes, which accounted for over 14% of prokaryotic communities in fermented grain. In addition, part of anaerobes originated from both Daqu and pit mud. This study could help track the source of prokaryotic communities in fermented grain, and improve the quality and controllability in liquor production.

  6. Evolution and diversity of the Ras superfamily of small GTPases in prokaryotes.

    PubMed

    Wuichet, Kristin; Søgaard-Andersen, Lotte

    2014-12-04

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

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

    PubMed

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

    2014-10-01

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

  8. 77 FR 47911 - Notice of a Change in Direction Finder Availability in Alaska

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-10

    .... Newer technologies such as Global Positioning System (GPS) and Automatic Dependent Surveillance... From the Federal Register Online via the Government Publishing Office DEPARTMENT OF TRANSPORTATION Federal Aviation Administration Notice of a Change in Direction Finder Availability in Alaska...

  9. Progress in four-beam nulling: results from the Terrestrial Planet Finder Planet Detection Testbed

    NASA Technical Reports Server (NTRS)

    Martin, Stefan

    2006-01-01

    The Terrestrial Planet Finder Interferometer (TPF-I) is a large space telescope consisting of four 4 meter diameter telescopes flying in formation in space together with a fifth beam combiner spacecraft.

  10. Progress in four-beam nulling: results from the Terrestrial Planet Finder planet detection testbed

    NASA Technical Reports Server (NTRS)

    Martin, Stefan

    2006-01-01

    The Terrestrial Planet Finder Interferometer (TPF-I) is a large space telescope consisting of four 4 meter diameter telescopes flying in formation in space together with a fifth beam combiner spacecraft.

  11. Technology Plan for the Terrestrial Planet Finder Interferometer

    NASA Technical Reports Server (NTRS)

    Lawson, Peter R. (Editor); Dooley, Jennifer A. (Editor)

    2005-01-01

    The technology plan for the Terrestrial Planet Finder Interferometer (TPF-I) describes the breadth of technology development currently envisaged to enable TPF-I to search for habitable worlds around nearby stars. TPF-I is currently in Pre-Phase A (the Advanced Study Phase) of its development. For planning purposes, it is expected to enter into Phase A in 2010 and be launched sometime before 2020. TPF-I is being developed concurrently with the Terrestrial Planet Finder Coronagraph (TPF-C), whose launch is anticipated in 201 6. The missions are being designed with the capability to detect Earth-like planets should they exist in the habitable zones of Sun-like (F,G, and K) stars out to a distance of about 60 light-years. Each mission will have the starlight-suppression and spectroscopic capability to enable the characterization of extrasolar planetary atmospheres, identifying biomarkers and signs of life. TPF-C is designed as a visible-light coronagraph; TPF-I is designed as a mid-infrared formation-flying interferometer. The two missions, working together, promise to yield unambiguous detections and characterizations of Earth-like planets. The challenges of planet detections with mid-infrared formation-flying interferometry are described within this technology plan. The approach to developing the technology is described through roadmaps that lead from our current state of the art through the different phases of mission development to launch. Technology metrics and milestones are given to measure progress. The emphasis of the plan is development and acquisition of technology during pre-Phase A to establish feasibility of the mission to enter Phase A sometime around 2010. Plans beyond 2010 are outlined. The plan contains descriptions of the development of new component technology as well as testbeds that demonstrate the viability of new techniques and technology required for the mission. Starlight-suppression (nulling) and formation-flying technology are highlighted

  12. Prokaryotic DNA ligases unwind superhelical DNA.

    PubMed

    Ivanchenko, M; van Holde, K; Zlatanova, J

    1996-09-13

    We have studied the effect on DNA topology of binding of prokaryotic DNA ligases (T4 and E. coli) to superhelical or nicked circular DNA. Performing topoisomerase I-mediated relaxation in the presence of increasing amounts of T4 ligase led to a shift in the topoisomer distribution to increasingly more negative values. This result suggested that T4 ligase unwound the DNA and was further substantiated by ligation of nicked circular molecules by E. coli DNA ligase in the presence of increasing amounts of T4 ligase. Such an experiment was possible since the two DNA ligases require different cofactors for enzymatic activity. Performing a similar experiment with reverse partners, using E. coli DNA ligase as ligand, and T4 ligase as sealing agent, we observed that the E. coli enzyme also unwound the DNA. Thus, prokaryotic DNA ligases can be added to an ever-growing list of DNA-binding proteins that unwind the DNA upon binding.

  13. Prokaryotes Versus Eukaryotes: Who is Hosting Whom?

    PubMed

    Tellez, Guillermo

    2014-01-01

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

  14. Microcompartments and protein machines in prokaryotes.

    PubMed

    Saier, Milton H

    2013-01-01

    The prokaryotic cell was once thought of as a 'bag of enzymes' with little or no intracellular compartmentalization. In this view, most reactions essential for life occurred as a consequence of random molecular collisions involving substrates, cofactors and cytoplasmic enzymes. Our current conception of a prokaryote is far from this view. We now consider a bacterium or an archaeon as a highly structured, nonrandom collection of functional membrane-embedded and proteinaceous molecular machines, each of which serves a specialized function. In this article we shall present an overview of such microcompartments including (1) the bacterial cytoskeleton and the apparati allowing DNA segregation during cell division; (2) energy transduction apparati involving light-driven proton pumping and ion gradient-driven ATP synthesis; (3) prokaryotic motility and taxis machines that mediate cell movements in response to gradients of chemicals and physical forces; (4) machines of protein folding, secretion and degradation; (5) metabolosomes carrying out specific chemical reactions; (6) 24-hour clocks allowing bacteria to coordinate their metabolic activities with the daily solar cycle, and (7) proteinaceous membrane compartmentalized structures such as sulfur granules and gas vacuoles. Membrane-bound prokaryotic organelles were considered in a recent Journal of Molecular Microbiology and Biotechnology written symposium concerned with membranous compartmentalization in bacteria [J Mol Microbiol Biotechnol 2013;23:1-192]. By contrast, in this symposium, we focus on proteinaceous microcompartments. These two symposia, taken together, provide the interested reader with an objective view of the remarkable complexity of what was once thought of as a simple noncompartmentalized cell.

  15. Prokaryotes Versus Eukaryotes: Who is Hosting Whom?

    PubMed Central

    Tellez, Guillermo

    2014-01-01

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

  16. A quest for indigenous truffle helper prokaryotes.

    PubMed

    Gryndler, Milan; Soukupová, Lucie; Hršelová, Hana; Gryndlerová, Hana; Borovička, Jan; Streiblová, Eva; Jansa, Jan

    2013-06-01

    Tuber aestivum is the most common European truffle with significant commercial exploitation. Its production originates from natural habitats and from artificially inoculated host tree plantations. Formation of Tuber ectomycorrhizae in host seedling roots is often inefficient. One possible reason is the lack of indigenous associative microbes. Here we aimed at metagenetic characterization and cultivation of indigenous prokaryotes associated with T. aestivum in a field transect cutting through the fungus colony margin. Several operational taxonomic units (OTUs) showed close association with the T. aestivum in the ectomycorrhizae and in the soil, but there was no overlap between the associative prokaryotes in the two different habitats. Among those positively associated with the ectomycorrhizae, we identified several bacterial genera belonging to Pseudonocardineae. Extensive isolation efforts yielded many cultures of ectomycorrhizae-associative bacteria belonging to Rhizobiales and Streptomycineae, but none belonging to the Pseudonocardineae. The specific unculturable Tuber-associated prokaryotes are likely to play important roles in the biology of these ectomycorrhizal fungi, including modulation of competition with other symbiotic and saprotrophic microbes, facilitation of root penetration and/or accessing mineral nutrients in the soil. However, the ultimate proof of this hypothesis will require isolation of the microbes for metabolic studies, using novel cultivation approaches.

  17. Dynamic optimization identifies optimal programmes for pathway regulation in prokaryotes.

    PubMed

    Bartl, Martin; Kötzing, Martin; Schuster, Stefan; Li, Pu; Kaleta, Christoph

    2013-01-01

    To survive in fluctuating environmental conditions, microorganisms must be able to quickly react to environmental challenges by upregulating the expression of genes encoding metabolic pathways. Here we show that protein abundance and protein synthesis capacity are key factors that determine the optimal strategy for the activation of a metabolic pathway. If protein abundance relative to protein synthesis capacity increases, the strategies shift from the simultaneous activation of all enzymes to the sequential activation of groups of enzymes and finally to a sequential activation of individual enzymes along the pathway. In the case of pathways with large differences in protein abundance, even more complex pathway activation strategies with a delayed activation of low abundance enzymes and an accelerated activation of high abundance enzymes are optimal. We confirm the existence of these pathway activation strategies as well as their dependence on our proposed constraints for a large number of metabolic pathways in several hundred prokaryotes.

  18. Metabolic Compensation and Circadian Resilience in Prokaryotic Cyanobacteria

    PubMed Central

    Johnson, Carl Hirschie; Egli, Martin

    2014-01-01

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

  19. Planet Detection Algorithms for the Terrestrial Planet Finder-C

    NASA Astrophysics Data System (ADS)

    Kasdin, N. J.; Braems, I.

    2005-12-01

    Critical to mission planning for the terrestrial planet finder coronagraph (TPF-C) is the ability to estimate integration times for planet detection. This detection is complicated by the presence of background noise due to local and exo-zodiacal dust, by residual speckle due optical errors, and by the dependence of the PSF shape on the specific coronagraph. In this paper we examine in detail the use of PSF fitting (matched filtering) for planet detection, derive probabilistic bounds for the signal-to-noise ratio by balancing missed detection and false alarm rates, and demonstrate that this is close to the optimal linear detection technique. We then compare to a Bayesian detection approach and show that for very low background the Bayesian method offers integration time improvements, but rapidly approaches the PSF fitting result for reasonable levels of background noise. We confirm via monte-carlo simulations. This work was supported under a grant from the Jet Propulsion Laboratory and by a fellowship from the Institut National de Recherche en Informatique et Automatique (INRIA).

  20. 4D Cellular Automaton Track Finder in the CBM Experiment

    NASA Astrophysics Data System (ADS)

    Akishina, Valentina; Kisel, Ivan

    2016-11-01

    The CBM experiment (FAIR/GSI, Darmstadt, Germany) will focus on the measurement of rare probes at interaction rates up to 10MHz with data flow of up to 1 TB/s. It requires a novel read-out and data-acquisition concept with self-triggered electronics and free-streaming data. In this case resolving different collisions is a non-trivial task and event building must be performed in software online. That requires full online event reconstruction and selection not only in space, but also in time, so-called 4D event building and selection. This is a task of the First-Level Event Selection (FLES). The FLES reconstruction and selection package consists of several modules: track finding, track fitting, short-lived particles finding, event building and event selection. The Cellular Automaton (CA) track finder algorithm was adapted towards time-based reconstruction. In this article, we describe in detail the modification done to the algorithm, as well as the performance of the developed time-based CA approach.

  1. Automated scheduler improvements and generalizations for the Automated Planet Finder

    NASA Astrophysics Data System (ADS)

    Holden, Bradford P.; Burt, Jennifer A.; Deich, William T. S.

    2016-07-01

    The Automated Planet Finder (APF) was originally designed as a single purpose facility to search for exoplanets. The APF, however, has become a general use observatory that is used by astronomers the world over. We describe the improvements to our software for operations that both optimize finding planets with known periods and supporting a much broader community of astronomers with a variety of interests and requirements. These include a variety of observing modes beyond the originally envisioned fixed target lists, such as time dependent priorities to meet the needs of rapid varying targets, and improved tools for simulating observing cadence for the planet hunting teams. We discuss the underlying software for the APF, illustrating why its simplicity of use allows users to write software that focuses on scientific productivity. Because of this simplicity, we can then develop scheduling software, which is easily integrated into the APF operations suite. We test these new scheduling modes using a nightly simulator which uses historical weather and seeing data. After discussing this new simulation tool, we measure how well the methods work after a 36 month simulated campaign to follow-up transiting targets. We find that the data yield of each of the tested schemes is similar. Therefore, we can focus on the best potential scientific return with little concern about the impact on the number or duration of observations.

  2. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution

    PubMed Central

    Bhandari, Vaibhav; Naushad, Hafiz S.; Gupta, Radhey S.

    2012-01-01

    The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies. PMID

  3. Protein based molecular markers provide reliable means to understand prokaryotic phylogeny and support Darwinian mode of evolution.

    PubMed

    Bhandari, Vaibhav; Naushad, Hafiz S; Gupta, Radhey S

    2012-01-01

    The analyses of genome sequences have led to the proposal that lateral gene transfers (LGTs) among prokaryotes are so widespread that they disguise the interrelationships among these organisms. This has led to questioning of whether the Darwinian model of evolution is applicable to prokaryotic organisms. In this review, we discuss the usefulness of taxon-specific molecular markers such as conserved signature indels (CSIs) and conserved signature proteins (CSPs) for understanding the evolutionary relationships among prokaryotes and to assess the influence of LGTs on prokaryotic evolution. The analyses of genomic sequences have identified large numbers of CSIs and CSPs that are unique properties of different groups of prokaryotes ranging from phylum to genus levels. The species distribution patterns of these molecular signatures strongly support a tree-like vertical inheritance of the genes containing these molecular signatures that is consistent with phylogenetic trees. Recent detailed studies in this regard on the Thermotogae and Archaea, which are reviewed here, have identified large numbers of CSIs and CSPs that are specific for the species from these two taxa and a number of their major clades. The genetic changes responsible for these CSIs (and CSPs) initially likely occurred in the common ancestors of these taxa and then vertically transferred to various descendants. Although some CSIs and CSPs in unrelated groups of prokaryotes were identified, their small numbers and random occurrence has no apparent influence on the consistent tree-like branching pattern emerging from other markers. These results provide evidence that although LGT is an important evolutionary force, it does not mask the tree-like branching pattern of prokaryotes or understanding of their evolutionary relationships. The identified CSIs and CSPs also provide novel and highly specific means for identification of different groups of microbes and for taxonomical and biochemical studies.

  4. Development of a prokaryotic universal primer for simultaneous analysis of Bacteria and Archaea using next-generation sequencing.

    PubMed

    Takahashi, Shunsuke; Tomita, Junko; Nishioka, Kaori; Hisada, Takayoshi; Nishijima, Miyuki

    2014-01-01

    For the analysis of microbial community structure based on 16S rDNA sequence diversity, sensitive and robust PCR amplification of 16S rDNA is a critical step. To obtain accurate microbial composition data, PCR amplification must be free of bias; however, amplifying all 16S rDNA species with equal efficiency from a sample containing a large variety of microorganisms remains challenging. Here, we designed a universal primer based on the V3-V4 hypervariable region of prokaryotic 16S rDNA for the simultaneous detection of Bacteria and Archaea in fecal samples from crossbred pigs (Landrace × Large white × Duroc) using an Illumina MiSeq next-generation sequencer. In-silico analysis showed that the newly designed universal prokaryotic primers matched approximately 98.0% of Bacteria and 94.6% of Archaea rRNA gene sequences in the Ribosomal Database Project database. For each sequencing reaction performed with the prokaryotic universal primer, an average of 69,330 (± 20,482) reads were obtained, of which archaeal rRNA genes comprised approximately 1.2% to 3.2% of all prokaryotic reads. In addition, the detection frequency of Bacteria belonging to the phylum Verrucomicrobia, including members of the classes Verrucomicrobiae and Opitutae, was higher in the NGS analysis using the prokaryotic universal primer than that performed with the bacterial universal primer. Importantly, this new prokaryotic universal primer set had markedly lower bias than that of most previously designed universal primers. Our findings demonstrate that the prokaryotic universal primer set designed in the present study will permit the simultaneous detection of Bacteria and Archaea, and will therefore allow for a more comprehensive understanding of microbial community structures in environmental samples.

  5. Prokaryotic transport in electrohydrodynamic structures

    NASA Astrophysics Data System (ADS)

    Paulitsch-Fuchs, A. H.; Fuchs, E. C.; Wexler, A. D.; Freund, F. T.; Rothschild, L. J.; Cherukupally, A.; Euverink, G. J. W.

    2012-04-01

    When a high-voltage direct-current is applied to two beakers filled with water, a horizontal electrohydrodynamic (EHD) bridge forms between the two beakers. In this work we study the transport and behavior of bacterial cells added to an EHD bridge set-up. Organisms were added to one or to both beakers, and the transport of the cells through the bridge was monitored using optical and microbiological techniques. It is shown that Escherichia coli top10 (Invitrogen, Carlsbad, CA, USA) and bioluminescent E. coli YMC10 with a plasmid (pJE202) containing Vibrio fischeri genes can survive the exposure to an EHD liquid bridge set-up and the cells are drawn toward the anode due to their negative surface charge. Dielectrophoresis and hydrostatic forces are likely to be the cause for their transport in the opposite direction which was observed as well, but to a much lesser extent. Most E. coli YMC10 bacteria which passed the EHD bridge exhibited increased luminescent activity after 24 h. This can be explained by two likely mechanisms: nutrient limitation in the heavier inoculated vials and a ‘survival of the strongest’ mechanism.

  6. Short-Sequence DNA Repeats in Prokaryotic Genomes

    PubMed Central

    van Belkum, Alex; Scherer, Stewart; van Alphen, Loek; Verbrugh, Henri

    1998-01-01

    Short-sequence DNA repeat (SSR) loci can be identified in all eukaryotic and many prokaryotic genomes. These loci harbor short or long stretches of repeated nucleotide sequence motifs. DNA sequence motifs in a single locus can be identical and/or heterogeneous. SSRs are encountered in many different branches of the prokaryote kingdom. They are found in genes encoding products as diverse as microbial surface components recognizing adhesive matrix molecules and specific bacterial virulence factors such as lipopolysaccharide-modifying enzymes or adhesins. SSRs enable genetic and consequently phenotypic flexibility. SSRs function at various levels of gene expression regulation. Variations in the number of repeat units per locus or changes in the nature of the individual repeat sequences may result from recombination processes or polymerase inadequacy such as slipped-strand mispairing (SSM), either alone or in combination with DNA repair deficiencies. These rather complex phenomena can occur with relative ease, with SSM approaching a frequency of 10−4 per bacterial cell division and allowing high-frequency genetic switching. Bacteria use this random strategy to adapt their genetic repertoire in response to selective environmental pressure. SSR-mediated variation has important implications for bacterial pathogenesis and evolutionary fitness. Molecular analysis of changes in SSRs allows epidemiological studies on the spread of pathogenic bacteria. The occurrence, evolution and function of SSRs, and the molecular methods used to analyze them are discussed in the context of responsiveness to environmental factors, bacterial pathogenicity, epidemiology, and the availability of full-genome sequences for increasing numbers of microorganisms, especially those that are medically relevant. PMID:9618442

  7. The Evolution and Functional Role of Flavin-based Prokaryotic Photoreceptors.

    PubMed

    Losi, Aba; Mandalari, Carmen; Gärtner, Wolfgang

    2015-01-01

    Flavin-based photoreceptor proteins of the LOV (light, oxygen and voltage) superfamily are ubiquitous and appear to be essential blue-light sensing systems not only in plants, algae and fungi, but also in prokaryotes, where they are represented in more than 10% of known species. Despite their broad occurrence, only in few cases LOV proteins have been correlated with important phenomena such as bacterial infectivity, selective growth patterns or/and stress responses; nevertheless these few known roles are helping us understand the multiple ways by which prokaryotes can exploit these soluble blue-light photoreceptors. Given the large number of sequences now deposited in databases, it becomes meaningful to define a signature for bona fide LOV domains, a procedure that facilitates identification of proteins with new properties and phylogenetic analysis. The latter clearly evidences that a class of LOV proteins from alpha-proteobacteria is the closest prokaryotic relative of eukaryotic LOV domains, whereas cyanobacterial sequences cluster with the archaeal and the other bacterial LOV domains. Distance trees built for LOV domains suggest complex evolutionary patterns, possibly involving multiple horizontal gene transfer events. Based on available data, the in vivo relevance and evolution of prokaryotic LOV is discussed.

  8. Evolution of prokaryotic two-component systems: insights from comparative genomics.

    PubMed

    Whitworth, David E; Cock, Peter J A

    2009-09-01

    Two-component systems (TCSs) are diverse and abundant signal transduction pathways found predominantly in prokaryotes. This review focuses on insights into TCS evolution made possible by the sequencing of whole prokaryotic genomes. Typical TCSs comprise an autophosphorylating protein (a histidine kinase), which transfers a phosphoryl group onto an effector protein (a response regulator), thus modulating its activity. Histidine kinases and response regulators are usually found encoded as pairs of adjacent genes within a genome, with multiple examples in most prokaryotes. Recent studies have shed light on major themes of TCS evolution, including gene duplication, gene gain/loss, gene fusion/fission, domain gain/loss, domain shuffling and the emergence of complexity. Coupled with an understanding of the structural and biophysical properties of many TCS proteins, it has become increasingly possible to draw inferences regarding the functional consequences of such evolutionary changes. In turn, this increase in understanding has the potential to enhance both our ability to rationally engineer TCSs, and also allow us to more powerfully correlate TCS evolution with behavioural phenotypes and ecological niche occupancy.

  9. Alternative oxidase and plastoquinol terminal oxidase in marine prokaryotes of the Sargasso Sea.

    PubMed

    McDonald, Allison E; Vanlerberghe, Greg C

    2005-04-11

    Alternative oxidase (AOX) represents a non-energy conserving branch in mitochondrial electron transport while plastoquinol terminal oxidase (PTOX) represents a potential branch in photosynthetic electron transport. Using a metagenomics dataset, we have uncovered numerous and diverse AOX and PTOX genes from the Sargasso Sea. Sequence similarity, synteny and phylogenetic analyses indicate that the large majority of these genes are from prokaryotes. AOX appears to be widely distributed among marine Eubacteria while PTOX is widespread among strains of cyanobacteria closely related to the high-light adapted Prochlorococcus marinus MED4, as well as Synechococcus. The wide distribution of AOX and PTOX in marine prokaryotes may have important implications for productivity in the world's oceans.

  10. Influence of age of aggregates and prokaryotic abundance on glucose and leucine uptake by heterotrophic marine prokaryotes.

    PubMed

    Azúa, Iñigo; Unanue, Marian; Ayo, Begoña; Artolozaga, Itxaso; Iriberri, Juan

    2007-03-01

    The kinetics of glucose and leucine uptake in attached and free-living prokaryotes in two types of microcosms with different nutrient qualities were compared. Microcosm type M1, derived from unaltered seawater, and microcosm type M2, from phytoplankton cultures, clearly expressed different kinetic parameters (Vmax/cell and K' m). In aggregates with low cell densities (M1 microcosm), the attached prokaryotes benefited from attachment as reflected in the higher potential uptake rates, while in aggregates with high cell densities (M2 microcosm) differences in the potential uptake rates of attached and free-living prokaryotes were not evident. The aging process and the chemical changes in aggregates of M2 microcosms were followed for 15-20 days. The results showed that as the aggregates aged and prokaryotic abundance increased, attached prokaryotes decreased their potential uptake rate and their K' m for substrate. This suggests an adaptive response by attached prokaryotes when aggregates undergo quantitative and qualitative impoverishment.

  11. Modern Concepts for a Terrestrial Planet Finder Space Telescope

    NASA Astrophysics Data System (ADS)

    Kasting, James

    2012-01-01

    Astronomers have now found over 500 exoplanets from radial velocity measurements and another 1200 or more "planet candidates” using the transit method from Kepler. Some of these planets are small enough to be rocky, like Earth, and orbit within the liquid water habitable zone of their parent star. We know next to nothing about conditions on these planets, though, because we have not yet developed the tools needed to study them. Even JWST, if it flies, will likely be unable to characterize the atmosphere of an Earth-analogue exoplanet. What we need for this task is a direct imaging mission that combines a large optical/near-IR telescope with a device that can block out the light from the star and retain the light from a nearby exoplanet. Both internal coronagraphs and external occulters (starshades) are being studied for this purpose. In principle, a thermal-IR telescope operating as an interferometer could accomplish the same task, but this would require formation flying of multiple cooled telescopes and is thought to be a more expensive option. The size of the optical telescope that would be needed to find and characterize an Earth depends on the frequency of Earth-like planet, Earth, and the brightness of the average exozodiacal background. The first parameter will hopefully be determined by Kepler, and the second may be measured by the Large Binary Telescope Interferometer, LBTI. Once this information is in hand, and if sufficient money can be found--currently, a big `if'--there should be little reason to hold back on designing and launching such a Terrestrial Planet Finder telescope.

  12. Enceladus Life Finder: Search for Life in a Habitable Moon.

    NASA Astrophysics Data System (ADS)

    Lunine, J. I.; Waite, J. H., Jr.; Spilker, L. J.; Postberg, F.; Cable, M. L.; Srama, R.; Clark, K.; Lee, S. W.

    2015-12-01

    A thousand times smaller in mass than Ganymede, Enceladus was known from Voyager data to be extremely bright and a dearth of craters on some parts of its surface suggested geologic activity. Cassini discovered the presence and composition of a plume erupting from the south polar terrain of Enceladus, approximately 100 narrow, distinct "geysers" or "jets" that feed it, and anomalous thermal signatures along fractures from which the geysers erupt. Cassini discovered organic and nitrogen-bearing molecules in the plume vapor, and detected salts in the plume icy grains, arguing strongly for ocean water being in contact with a rocky core. As much as Cassini has done, it cannot tell us whether the ocean of Enceladus hosts an active biota today. Enceladus Life Finder (ELF) is a Discovery-class solar-powered Saturn orbiter designed to fly multiple times through the plume of Enceladus. It carries two state-of-the-art mass spectrometers designed to analyze the gas and grains in the plume. The goals of the mission are derived directly from the most recent decadal survey: first, to determine primordial sources of organics and sites of organic synthesis today, second, to determine if there are modern habitats in the solar system beyond Earth where the conditions for life exist today and third, if life exists there now. ELF conducts three tests for life. The first test looks for a non-abiotic distribution of amino acids, the second determines whether the carbon number distribution in fatty acids or isoprenoids is biased toward a particular rule, and the third measures carbon and hydrogen isotopic ratios, together with the abundance of methane relative to other alkanes, to assess whether the values fall in the range for biological processes. The ELF mission spacecraft conducts ten science plume fly-throughs; the baseline science is completed in the first five plume passages.

  13. Eye safe short range standoff aerosol cloud finder.

    SciTech Connect

    Bambha, Ray P.; Schroder, Kevin L.; Reichardt, Thomas A.

    2005-02-01

    Because many solid objects, both stationary and mobile, will be present in an indoor environment, the design of an indoor aerosol cloud finding lidar (light detection and ranging) instrument presents a number of challenges. The cloud finder must be able to discriminate between these solid objects and aerosol clouds as small as 1-meter in depth in order to probe suspect clouds. While a near IR ({approx}1.5-{micro}m) laser is desirable for eye-safety, aerosol scattering cross sections are significantly lower in the near-IR than at visible or W wavelengths. The receiver must deal with a large dynamic range since the backscatter from solid object will be orders of magnitude larger than for aerosol clouds. Fast electronics with significant noise contributions will be required to obtain the necessary temporal resolution. We have developed a laboratory instrument to detect aerosol clouds in the presence of solid objects. In parallel, we have developed a lidar performance model for performing trade studies. Careful attention was paid to component details so that results obtained in this study could be applied towards the development of a practical instrument. The amplitude and temporal shape of the signal return are analyzed for discrimination of aerosol clouds in an indoor environment. We have assessed the feasibility and performance of candidate approaches for a fieldable instrument. With the near-IR PMT and a 1.5-{micro}m laser source providing 20-{micro}J pulses, we estimate a bio-aerosol detection limit of 3000 particles/l.

  14. The Integrated Cluster Finder for the ARCHES project

    NASA Astrophysics Data System (ADS)

    Mints, Alexey; Schwope, Axel; Rosen, Simon; Pineau, François-Xavier; Carrera, Francisco

    2017-01-01

    Context. Clusters of galaxies are important for cosmology and astrophysics. They may be discovered through either the summed optical/IR radiation originating from their member galaxies or via X-ray emission originating from the hot intracluster medium. X-ray samples are not affected by projection effects but a redshift determination typically needs optical and infrared follow-up to then infer X-ray temperatures and luminosities. Aims: We want to confirm serendipitously discovered X-ray emitting cluster candidates and measure their cosmological redshift through the analysis and exploration of multi-wavelength photometric catalogues. Methods: We developed a tool, the Integrated Cluster Finder (ICF), to search for clusters by determining overdensities of potential member galaxies in optical and infrared catalogues. Based on a spectroscopic meta-catalogue we calibrated colour-redshift relations that combine optical (SDSS) and IR data (UKIDSS, WISE). The tool is used to quantify the overdensity of galaxies against the background via a modified redMaPPer technique and to quantify the confidence of a cluster detection. Results: Cluster finding results are compared to reference catalogues found in the literature. The results agree to within 95-98%. The tool is used to confirm 488 out of 830 cluster candidates drawn from 3XMMe in the footprint of the SDSS and CFHT catalogues. Conclusions: The ICF is a flexible and highly efficient tool to search for galaxy clusters in multiple catalogues and is freely available to the community. It may be used to identify the cluster content in future X-ray catalogues from XMM-Newton and eventually from eROSITA.

  15. The Automated Planet Finder's automation & first two years of science

    NASA Astrophysics Data System (ADS)

    Burt, Jennifer; Laughlin, Greg; Vogt, Steven S.; Holden, Bradford

    2016-01-01

    The Automated Planet Finder (APF) is the newest facility at Lick Observatory, comprised of a 2.4m telescope coupled with the high-resolution Levy echelle spectrograph. Purpose built for exoplanet detection and characterization, 80% of the telescope's observing time is dedicated to these science goals. The APF has demonstrated 1 m/s radial velocity precision on bright, RV standard stars and performs with the same speed-on-sky as Keck/HIRES when observing M-dwarfs.The telesope is fully automated for RV operations, using a dynamic scheduler that makes informed decisions on which targets to observe based on scientific interest, desired cadence, required precision levels and current observing conditions, all on a minute-to-minute basis. This ensures that time is not wasted chasing non-optimal targets on nights with poor conditions and enables rapid changes to the overall science observing strategy.The APF has contributed to the detection of four planetary systems in its first two years of scientific operations. Our most recent detection is that of a 6-planet system around the bright (V=5.5), nearby (d=6.5pc), K3V star HD 219134. The planets in this system have masses ranging from 3.5 to108 MEarth, with orbital periods from 3 to 2247 days. An independent detection of the inner 4 planets in this system by the HARPS-N team has shown that the 3d planet transits the star, making this system ideal for follow-up observations.I will discuss the design and implementation of the APF's dynamic scheduler, the telescope's planet detections to date, overall performance results of the telescope and our future observing strategy.

  16. Toward a standard in structural genome annotation for prokaryotes

    DOE PAGES

    Tripp, H. James; Sutton, Granger; White, Owen; ...

    2015-07-25

    In an effort to identify the best practice for finding genes in prokaryotic genomes and propose it as a standard for automated annotation pipelines, we collected 1,004,576 peptides from various publicly available resources, and these were used as a basis to evaluate various gene-calling methods. The peptides came from 45 bacterial replicons with an average GC content from 31 % to 74 %, biased toward higher GC content genomes. Automated, manual, and semi-manual methods were used to tally errors in three widely used gene calling methods, as evidenced by peptides mapped outside the boundaries of called genes. We found thatmore » the consensus set of identical genes predicted by the three methods constitutes only about 70 % of the genes predicted by each individual method (with start and stop required to coincide). Peptide data was useful for evaluating some of the differences between gene callers, but not reliable enough to make the results conclusive, due to limitations inherent in any proteogenomic study. A single, unambiguous, unanimous best practice did not emerge from this analysis, since the available proteomics data were not adequate to provide an objective measurement of differences in the accuracy between these methods. However, as a result of this study, software, reference data, and procedures have been better matched among participants, representing a step toward a much-needed standard. In the absence of sufficient amount of experimental data to achieve a universal standard, our recommendation is that any of these methods can be used by the community, as long as a single method is employed across all datasets to be compared.« less

  17. Toward a standard in structural genome annotation for prokaryotes

    SciTech Connect

    Tripp, H. James; Sutton, Granger; White, Owen; Wortman, Jennifer; Pati, Amrita; Mikhailova, Natalia; Ovchinnikova, Galina; Payne, Samuel H.; Kyrpides, Nikos C.; Ivanova, Natalia

    2015-07-25

    In an effort to identify the best practice for finding genes in prokaryotic genomes and propose it as a standard for automated annotation pipelines, we collected 1,004,576 peptides from various publicly available resources, and these were used as a basis to evaluate various gene-calling methods. The peptides came from 45 bacterial replicons with an average GC content from 31 % to 74 %, biased toward higher GC content genomes. Automated, manual, and semi-manual methods were used to tally errors in three widely used gene calling methods, as evidenced by peptides mapped outside the boundaries of called genes. We found that the consensus set of identical genes predicted by the three methods constitutes only about 70 % of the genes predicted by each individual method (with start and stop required to coincide). Peptide data was useful for evaluating some of the differences between gene callers, but not reliable enough to make the results conclusive, due to limitations inherent in any proteogenomic study. A single, unambiguous, unanimous best practice did not emerge from this analysis, since the available proteomics data were not adequate to provide an objective measurement of differences in the accuracy between these methods. However, as a result of this study, software, reference data, and procedures have been better matched among participants, representing a step toward a much-needed standard. In the absence of sufficient amount of experimental data to achieve a universal standard, our recommendation is that any of these methods can be used by the community, as long as a single method is employed across all datasets to be compared.

  18. A Novel Method for Accurate Operon Predictions in All SequencedProkaryotes

    SciTech Connect

    Price, Morgan N.; Huang, Katherine H.; Alm, Eric J.; Arkin, Adam P.

    2004-12-01

    We combine comparative genomic measures and the distance separating adjacent genes to predict operons in 124 completely sequenced prokaryotic genomes. Our method automatically tailors itself to each genome using sequence information alone, and thus can be applied to any prokaryote. For Escherichia coli K12 and Bacillus subtilis, our method is 85 and 83% accurate, respectively, which is similar to the accuracy of methods that use the same features but are trained on experimentally characterized transcripts. In Halobacterium NRC-1 and in Helicobacterpylori, our method correctly infers that genes in operons are separated by shorter distances than they are in E.coli, and its predictions using distance alone are more accurate than distance-only predictions trained on a database of E.coli transcripts. We use microarray data from sixphylogenetically diverse prokaryotes to show that combining intergenic distance with comparative genomic measures further improves accuracy and that our method is broadly effective. Finally, we survey operon structure across 124 genomes, and find several surprises: H.pylori has many operons, contrary to previous reports; Bacillus anthracis has an unusual number of pseudogenes within conserved operons; and Synechocystis PCC6803 has many operons even though it has unusually wide spacings between conserved adjacent genes.

  19. De Novo Identification of Regulatory Regions in Intergenic Spaces of Prokaryotic Genomes

    SciTech Connect

    Chain, P; Garcia, E; Mcloughlin, K; Ovcharenko, I

    2007-02-20

    This project was begun to implement, test, and experimentally validate the results of a novel algorithm for genome-wide identification of candidate transcription-factor binding sites in prokaryotes. Most techniques used to identify regulatory regions rely on conservation between different genomes or have a predetermined sequence motif(s) to perform a genome-wide search. Therefore, such techniques cannot be used with new genome sequences, where information regarding such motifs has not yet been discovered. This project aimed to apply a de novo search algorithm to identify candidate binding-site motifs in intergenic regions of prokaryotic organisms, initially testing the available genomes of the Yersinia genus. We retrofitted existing nucleotide pattern-matching algorithms, analyzed the candidate sites identified by these algorithms as well as their target genes to screen for meaningful patterns. Using properly annotated prokaryotic genomes, this project aimed to develop a set of procedures to identify candidate intergenic sites important for gene regulation. We planned to demonstrate this in Yersinia pestis, a model biodefense, Category A Select Agent pathogen, and then follow up with experimental evidence that these regions are indeed involved in regulation. The ability to quickly characterize transcription-factor binding sites will help lead to a better understanding of how known virulence pathways are modulated in biodefense-related organisms, and will help our understanding and exploration of regulons--gene regulatory networks--and novel pathways for metabolic processes in environmental microbes.

  20. Simple sequence repeats in prokaryotic genomes

    PubMed Central

    Mrázek, Jan; Guo, Xiangxue; Shah, Apurva

    2007-01-01

    Simple sequence repeats (SSRs) in DNA sequences are composed of tandem iterations of short oligonucleotides and may have functional and/or structural properties that distinguish them from general DNA sequences. They are variable in length because of slip-strand mutations and may also affect local structure of the DNA molecule or the encoded proteins. Long SSRs (LSSRs) are common in eukaryotes but rare in most prokaryotes. In pathogens, SSRs can enhance antigenic variance of the pathogen population in a strategy that counteracts the host immune response. We analyze representations of SSRs in >300 prokaryotic genomes and report significant differences among different prokaryotes as well as among different types of SSRs. LSSRs composed of short oligonucleotides (1–4 bp length, designated LSSR1–4) are often found in host-adapted pathogens with reduced genomes that are not known to readily survive in a natural environment outside the host. In contrast, LSSRs composed of longer oligonucleotides (5–11 bp length, designated LSSR5–11) are found mostly in nonpathogens and opportunistic pathogens with large genomes. Comparisons among SSRs of different lengths suggest that LSSR1–4 are likely maintained by selection. This is consistent with the established role of some LSSR1–4 in enhancing antigenic variance. By contrast, abundance of LSSR5–11 in some genomes may reflect the SSRs' general tendency to expand rather than their specific role in the organisms' physiology. Differences among genomes in terms of SSR representations and their possible interpretations are discussed. PMID:17485665

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2015-01-01

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

  3. CRISPR-Cas immunity in prokaryotes.

    PubMed

    Marraffini, Luciano A

    2015-10-01

    Prokaryotic organisms are threatened by a large array of viruses and have developed numerous defence strategies. Among these, only clustered, regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity against foreign elements. Upon viral injection, a small sequence of the viral genome, known as a spacer, is integrated into the CRISPR locus to immunize the host cell. Spacers are transcribed into small RNA guides that direct the cleavage of the viral DNA by Cas nucleases. Immunization through spacer acquisition enables a unique form of evolution whereby a population not only rapidly acquires resistance to its predators but also passes this resistance mechanism vertically to its progeny.

  4. Emerging spatial patterns in Antarctic prokaryotes

    PubMed Central

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

    2015-01-01

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

  5. Diversity of aquatic prokaryotic communities in the Cuatro Cienegas basin.

    PubMed

    Escalante, Ana E; Eguiarte, Luis E; Espinosa-Asuar, Laura; Forney, Larry J; Noguez, Ana M; Souza Saldivar, Valeria

    2008-07-01

    The Cuatro Cienegas basin (Coahuila, México) is a composite of different water systems in the middle of the desert with unusually high levels of endemism and diversity in different taxa. Although the diversity of macrobiota has been well described, little is known about the diversity and distribution of microorganisms in the oligotrophic ponds. Here we describe the extent and distribution of diversity found in aquatic prokaryotic communities by analysis of terminal restriction fragment length polymorphisms (T-RFLP) of 16S rRNA genes and phylogenetic analysis of cloned genes. Twelve locations within the basin were sampled. Among all the samples, we found a total of 117 operational taxonomic units (OTUs) using T-RFLPs, which ranged in any single sample from four to 49. OTU richness and Shannon diversity indices for different sites varied, but none were particularly high. 16S rRNA gene sequence data showed 68 different phylotypes among 198 clones. The most abundant phylotypes were Gamma- and Betaproteobacteria, and extreme halophiles. The differences among sites were significant; 45 TRFs were found only once, and 37% of the total diversity was represented by differences between sites, suggesting high beta-diversity. Further studies are needed to test whether this is a direct consequence of environmental heterogeneity in the basin.

  6. Prokaryote-derived protein inhibitors of peptidases: a sketchy occurrence and mostly unknown function

    PubMed Central

    Kantyka, Tomasz; Rawlings, Neil D.; Potempa, Jan

    2010-01-01

    In metazoan organisms protein inhibitors of peptidases are important factors essential for regulation of proteolytic activity. In vertebrates genes encoding peptidase inhibitors constitute up to 1% of genes reflecting a need for tight and specific control of proteolysis especially in extracellular body fluids. In stark contrast unicellular organisms, both prokaryotic and eukaryotic consistently contain only few, if any, genes coding for putative peptidase inhibitors. This may seem perplexing in the light of the fact that these organisms produce large numbers of proteases of different catalytic classes with the genes constituting up to 6% of the total gene count with the average being about 3%. Apparently, however, a unicellular life-style is fully compatible with other mechanisms of regulation of proteolysis and does not require protein inhibitors to control their intracellular and extracellular proteolytic activity. So in prokaryotes occurrence of genes encoding different types of peptidase inhibitors is infrequent and often scattered among phylogenetically distinct orders or even phyla of microbiota. Genes encoding proteins homologous to alpha-2-macroglobulin (family I39), serine carboxypeptidase Y inhibitor (family I51), alpha-1-peptidase inhibitor (family I4) and ecotin (family I11) are the most frequently represented in Bacteria. Although several of these gene products were shown to possess inhibitory activity, with an exception of ecotin and staphostatins, the biological function of microbial inhibitors is unclear. In this review we present distribution of protein inhibitors from different families among prokaryotes, describe their mode of action and hypothesize on their role in microbial physiology and interactions with hosts and environment. PMID:20558234

  7. Temporal and depth-related differences in prokaryotic communities in abyssal sediments associated with particulate organic carbon flux

    NASA Astrophysics Data System (ADS)

    Moeseneder, M. M.; Smith, K. L.; Ruhl, H. A.; Jones, D. O. B.; Witte, U.; Prosser, J. I.

    2012-12-01

    Particulate organic carbon (POC) flux is hypothesized to be the most important parameter influencing activity and biomass of prokaryotic and faunal communities in the abyssal seafloor, but there is little evidence of POC-related changes in community composition of prokaryotes. This hypothesis was tested by 16S rRNA-gene-based analysis of prokaryotic DNA and RNA extracted from abyssal seafloor sediments during periods of low and high POC flux. Fingerprint analysis of prokaryotic communities indicated that approximately 50% of the phylotypes were identical at each sediment horizon, regardless of the temporal variations in POC flux. However, phylotypes were also detected that represented a relatively dynamic component of these communities and were probably strongly influenced by the prevalent POC flux regime. These patterns were also detected in deeper sediment horizons. DNA- and RNA-based community profiles differed, although both approaches had similar community dynamics. Crenarchaeota showed the strongest shift in community composition in response to availability of labile POC, indicating that POC flux may have a more pronounced impact on crenarchaeal communities than on bacterial communities. The high number of phylotypes common to each sample time suggests that both standing stock and active prokaryotic communities are stable.

  8. Prokaryotic silicon utilizing microorganisms in the biosphere

    NASA Astrophysics Data System (ADS)

    Gupta, D.; Das, S.

    2012-12-01

    Although a little study has been done to determine the silicon utilizing prokaryotes, our previous experiments indicated that almost all Gram-positive bacteria are silicon utilizing; one of them, Streptococci survived exposure on the lunar surface for a long period in experiment done by others. Our initial experiments with these Gram positive microorganisms showed that there were limited growths of these microorganisms on carbon free silicate medium probably with the help of some carry over carbon and nitrogen during cultivation procedures. However, increase in growth rate after repeated subcultures could not be explained at present. The main groups of prokaryotes which were found silicon utilizing microorganisms were Mycobacterium, Bacillus, Nocardia, Streptomyces, Staphylococcus, Streptococcus, Lactobacillus, and Clostridium. In a another previous study by us when silicon level was studied in such grown up cells on carbon "free" silicate medium by electron prove microanalyser, it was found that silicon in cells grown on carbon "free" silicate medium was much higher (24.9%) than those grown on conventional carbon based medium (0.84%). However, these initial findings are encouraging for our future application of this group of organisms on extraterrestrial surfaces for artificial micro-ecosystem formation. It was found that when electropositive elements are less in extraterrestrial situation, then polymerization of silicon-oxygen profusion may occur easily, particularly in carbon and nitrogen paucity in the rocky worlds of the Universe.

  9. LISA and LISA PathFinder, the endeavour to detect low frequency GWs

    NASA Astrophysics Data System (ADS)

    Araújo, H.; Boatella, C.; Chmeissani, M.; Conchillo, A.; García-Berro, E.; Grimani, C.; Hajdas, W.; Lobo, A.; Martínez, Ll; Nofrarias, M.; Ortega, J. A.; Puigdengoles, C.; Ramos-Castro, J.; Sanjuán, J.; Wass, P.; Xirgu, X.

    2007-05-01

    This is a review about LISA and its technology demonstrator, LISAPathFinder. We first describe the conceptual problems which need to be overcome in order to set up a working interferometric detector of low frequency Gravitational Waves (GW), then summarise the solutions to them as currently conceived by the LISA mission team. This will show that some of these solutions require new technological abilities which are still under development, and which need proper test before being fully implemented. LISAPathFinder (LPF) is the the testbed for such technologies. The final part of the paper will address the ideas and concepts behind the PathFinder as well as their impact on LISA.

  10. CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization

    PubMed Central

    Zhu, Houxiang; Misel, Lauren; Graham, Mitchell; Robinson, Michael L.; Liang, Chun

    2016-01-01

    The CRISPR system holds much promise for successful genome engineering, but therapeutic, industrial, and research applications will place high demand on improving the specificity and efficiency of this tool. CT-Finder (http://bioinfolab.miamioh.edu/ct-finder) is a web service to help users design guide RNAs (gRNAs) optimized for specificity. CT-Finder accommodates the original single-gRNA Cas9 system and two specificity-enhancing paired-gRNA systems: Cas9 D10A nickases (Cas9n) and dimeric RNA-guided FokI nucleases (RFNs). Optimal target candidates can be chosen based on the minimization of predicted off-target effects. Graphical visualization of on-target and off-target sites in the genome is provided for target validation. Major model organisms are covered by this web service. PMID:27210050

  11. Recent Improvements to the Finite-Fault Rupture Detector Algorithm: FinDer II

    NASA Astrophysics Data System (ADS)

    Smith, D.; Boese, M.; Heaton, T. H.

    2015-12-01

    Constraining the finite-fault rupture extent and azimuth is crucial for accurately estimating ground-motion in large earthquakes. Detecting and modeling finite-fault ruptures in real-time is thus essential to both earthquake early warning (EEW) and rapid emergency response. Following extensive real-time and offline testing, the finite-fault rupture detector algorithm, FinDer (Böse et al., 2012 & 2015), was successfully integrated into the California-wide ShakeAlert EEW demonstration system. Since April 2015, FinDer has been scanning real-time waveform data from approximately 420 strong-motion stations in California for peak ground acceleration (PGA) patterns indicative of earthquakes. FinDer analyzes strong-motion data by comparing spatial images of observed PGA with theoretical templates modeled from empirical ground-motion prediction equations (GMPEs). If the correlation between the observed and theoretical PGA is sufficiently high, a report is sent to ShakeAlert including the estimated centroid position, length, and strike, and their uncertainties, of an ongoing fault rupture. Rupture estimates are continuously updated as new data arrives. As part of a joint effort between USGS Menlo Park, ETH Zurich, and Caltech, we have rewritten FinDer in C++ to obtain a faster and more flexible implementation. One new feature of FinDer II is that multiple contour lines of high-frequency PGA are computed and correlated with templates, allowing the detection of both large earthquakes and much smaller (~ M3.5) events shortly after their nucleation. Unlike previous EEW algorithms, FinDer II thus provides a modeling approach for both small-magnitude point-source and larger-magnitude finite-fault ruptures with consistent error estimates for the entire event magnitude range.

  12. GTAG- and CGTC-tagged palindromic DNA repeats in prokaryotes

    PubMed Central

    2013-01-01

    Background REPs (Repetitive Extragenic Palindromes) are small (20–40 bp) palindromic repeats found in high copies in some prokaryotic genomes, hypothesized to play a role in DNA supercoiling, transcription termination, mRNA stabilization. Results We have monitored a large number of REP elements in prokaryotic genomes, and found that most can be sorted into two large DNA super-families, as they feature at one end unpaired motifs fitting either the GTAG or the CGTC consensus. Tagged REPs have been identified in >80 species in 8 different phyla. GTAG and CGTC repeats reside predominantly in microorganisms of the gamma and alpha division of Proteobacteria, respectively. However, the identification of members of both super- families in deeper branching phyla such Cyanobacteria and Planctomycetes supports the notion that REPs are old components of the bacterial chromosome. On the basis of sequence content and overall structure, GTAG and CGTC repeats have been assigned to 24 and 4 families, respectively. Of these, some are species-specific, others reside in multiple species, and several organisms contain different REP types. In many families, most units are close to each other in opposite orientation, and may potentially fold into larger secondary structures. In different REP-rich genomes the repeats are predominantly located between unidirectionally and convergently transcribed ORFs. REPs are predominantly located downstream from coding regions, and many are plausibly transcribed and function as RNA elements. REPs located inside genes have been identified in several species. Many lie within replication and global genome repair genes. It has been hypothesized that GTAG REPs are miniature transposons mobilized by specific transposases known as RAYTs (REP associated tyrosine transposases). RAYT genes are flanked either by GTAG repeats or by long terminal inverted repeats (TIRs) unrelated to GTAG repeats. Moderately abundant families of TIRs have been identified in

  13. Applications of the Integrated High-Performance CMOS Image Sensor to Range Finders - from Optical Triangulation to the Automotive Field.

    PubMed

    Wu, Jih-Huah; Pen, Cheng-Chung; Jiang, Joe-Air

    2008-03-13

    With their significant features, the applications of complementary metal-oxidesemiconductor (CMOS) image sensors covers a very extensive range, from industrialautomation to traffic applications such as aiming systems, blind guidance, active/passiverange finders, etc. In this paper CMOS image sensor-based active and passive rangefinders are presented. The measurement scheme of the proposed active/passive rangefinders is based on a simple triangulation method. The designed range finders chieflyconsist of a CMOS image sensor and some light sources such as lasers or LEDs. Theimplementation cost of our range finders is quite low. Image processing software to adjustthe exposure time (ET) of the CMOS image sensor to enhance the performance oftriangulation-based range finders was also developed. An extensive series of experimentswere conducted to evaluate the performance of the designed range finders. From theexperimental results, the distance measurement resolutions achieved by the active rangefinder and the passive range finder can be better than 0.6% and 0.25% within themeasurement ranges of 1 to 8 m and 5 to 45 m, respectively. Feasibility tests onapplications of the developed CMOS image sensor-based range finders to the automotivefield were also conducted. The experimental results demonstrated that our range finders arewell-suited for distance measurements in this field.

  14. GLS-Finder: An Automated Data-Mining System for Fast Profiling Glucosinolates and its Application in Brassica Vegetables

    Technology Transfer Automated Retrieval System (TEKTRAN)

    A rapid computer-aided program for profiling glucosinolates, “GLS-Finder", was developed. GLS-Finder is a Matlab script based expert system that is capable for qualitative and semi-quantitative analysis of glucosinolates in samples using data generated by ultra-high performance liquid chromatograph...

  15. Unique criterion to estimate the performances of some laser diode range finders

    NASA Astrophysics Data System (ADS)

    Journet, Bernard A.; Bazin, Gaelle; Durieu, Cecile

    2001-09-01

    The purpose of this paper is to present a general method to estimate the intrinsic performances of some laser range finders based on flight time measurement. Classically this flight time can be measured directly, or after a conversion into a phase shift, or into a beat frequency. We prose here a criterion based on signal processing notions, as matched filtering to get the best detection, and ambiguity function to estimate the quality of the detection. The concept of characteristic length is introduced and applied to the different kind of laser range finders, which suggest a new possibility for flight time measurement.

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

    PubMed Central

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

    2016-01-01

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

  17. Intracellular minerals and metal deposits in prokaryotes.

    PubMed

    Edwards, K J; Bazylinski, D A

    2008-06-01

    Thanks to the work of Terrance J. Beveridge and other pioneers in the field of metal-microbe interactions, prokaryotes are well known to sequester metals and other ions intracellularly in various forms. These forms range from poorly ordered deposits of metals to well-ordered mineral crystals. Studies on well-ordered crystalline structures have generally focused on intracellular organelles produced by magnetotactic bacteria that are ubiquitous in terrestrial and marine environments that precipitate Fe(3)O(4) or Fe(3)S(4), Fe-bearing minerals that have magnetic properties and are enclosed in intracellular membranes. In contrast, studies on less-well ordered minerals have focused on Fe-, As-, Mn-, Au-, Se- and Cd-precipitates that occur intracellularly. The biological and environmental function of these particles remains a matter of debate.

  18. Evolution of thiol protective systems in prokaryotes

    NASA Technical Reports Server (NTRS)

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

    1986-01-01

    Biological thiols are essential elements in most aspects of cell function but undergo rapid oxidation to disulfides in the presence of oxygen. The evolution of systems to protect against such oxygen toxicity was essential to the emergence of aerobic life. The protection system used by eukaryotes is based upon glutathione (GSH) and GSH-dependent enzymes but many bacteria lack GSH and apparently use other mechanisms. The objective of this research is to elaborate the thiol protective mechanisms employed by prokaryotes of widely divergent evolutionary origin and to understand why GSH became the central thiol employed in essentially all higher organisms. Thiol-selective fluorescent labeling and HPLC analysis has been used to determine key monothiol components.

  19. Macromolecule diffusion and confinement in prokaryotic cells.

    PubMed

    Mika, Jacek T; Poolman, Bert

    2011-02-01

    We review recent observations on the mobility of macromolecules and their spatial organization in live bacterial cells. We outline the major fluorescence microscopy-based methods to determine the mobility and thus the diffusion coefficients (D) of molecules, which is not trivial in small cells. The extremely high macromolecule crowding of prokaryotes is used to rationalize the reported lower diffusion coefficients as compared to eukaryotes, and we speculate on the nature of the barriers for diffusion observed for proteins (and mRNAs) in vivo. Building on in vitro experiments and modeling studies, we evaluate the size dependence of diffusion coefficients for macromolecules in vivo, in case of both water-soluble and integral membrane proteins. We comment on the possibilities of anomalous diffusion and provide examples where the macromolecule mobility may be limiting biological processes.

  20. International code of nomenclature of prokaryotes

    DOE PAGES

    Garrity, George M.; Parker, Charles T.; Tindall, Brian J.

    2015-11-20

    Here, this volume contains the edition of the International Code of Nomenclature of Prokaryotes that was presented in draft form and available for comment at the Plenary Session of the Fourteenth International Congress of Bacteriology and Applied Microbiology (BAM), Montréal, 2014, together with updated lists of conserved and rejected bacterial names and of Opinions issued by the Judicial Commission. As in the past it brings together those changes accepted, published and documented by the ICSP and the Judicial Commission since the last revision was published. Several new appendices have been added to this edition. Appendix 11 addresses the appropriate applicationmore » of the Candidatus concept, Appendix 12 contains the history of the van Niel Prize, and Appendix 13 contains the summaries of Congresses.« less

  1. International code of nomenclature of prokaryotes

    SciTech Connect

    Garrity, George M.; Parker, Charles T.; Tindall, Brian J.

    2015-11-20

    Here, this volume contains the edition of the International Code of Nomenclature of Prokaryotes that was presented in draft form and available for comment at the Plenary Session of the Fourteenth International Congress of Bacteriology and Applied Microbiology (BAM), Montréal, 2014, together with updated lists of conserved and rejected bacterial names and of Opinions issued by the Judicial Commission. As in the past it brings together those changes accepted, published and documented by the ICSP and the Judicial Commission since the last revision was published. Several new appendices have been added to this edition. Appendix 11 addresses the appropriate application of the Candidatus concept, Appendix 12 contains the history of the van Niel Prize, and Appendix 13 contains the summaries of Congresses.

  2. Optimal Jet Finder (v1.0 C++)

    NASA Astrophysics Data System (ADS)

    Chumakov, S.; Jankowski, E.; Tkachov, F. V.

    2006-10-01

    We describe a C++ implementation of the Optimal Jet Definition for identification of jets in hadronic final states of particle collisions. We explain interface subroutines and provide a usage example. The source code is available from http://www.inr.ac.ru/~ftkachov/projects/jets/. Program summaryTitle of program: Optimal Jet Finder (v1.0 C++) Catalogue identifier: ADSB_v2_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADSB_v2_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer: any computer with a standard C++ compiler Tested with:GNU gcc 3.4.2, Linux Fedora Core 3, Intel i686; Forte Developer 7 C++ 5.4, SunOS 5.9, UltraSPARC III+; Microsoft Visual C++ Toolkit 2003 (compiler 13.10.3077, linker 7.10.30777, option /EHsc), Windows XP, Intel i686. Programming language used: C++ Memory required:˜1 MB (or more, depending on the settings) No. of lines in distributed program, including test data, etc.: 3047 No. of bytes in distributed program, including test data, etc.: 17 884 Distribution format: tar.gz Nature of physical problem: Analysis of hadronic final states in high energy particle collision experiments often involves identification of hadronic jets. A large number of hadrons detected in the calorimeter is reduced to a few jets by means of a jet finding algorithm. The jets are used in further analysis which would be difficult or impossible when applied directly to the hadrons. Grigoriev et al. [D.Yu. Grigoriev, E. Jankowski, F.V. Tkachov, Phys. Rev. Lett. 91 (2003) 061801] provide brief introduction to the subject of jet finding algorithms and a general review of the physics of jets can be found in [R. Barlow, Rep. Prog. Phys. 36 (1993) 1067]. Method of solution: The software we provide is an implementation of the so-called Optimal Jet Definition (OJD). The theory of OJD was developed in [F.V. Tkachov, Phys. Rev. Lett. 73 (1994) 2405; Erratum, Phys. Rev. Lett. 74 (1995) 2618; F.V. Tkachov, Int. J. Modern Phys

  3. Test of the principle of operation of a wideband magnetic direction finder for lightning return strokes

    NASA Technical Reports Server (NTRS)

    Herrman, B. D.; Uman, M. A.; Brantley, R. D.; Krider, E. P.

    1976-01-01

    The principle of operation of a wideband crossed-loop magnetic-field direction finder is studied by comparing the bearing determined from the NS and EW magnetic fields at various times up to 155 microsec after return stroke initiation with the TV-determined lightning channel base direction. For 40 lightning strokes in the 3 to 12 km range, the difference between the bearings found from magnetic fields sampled at times between 1 and 10 microsec and the TV channel-base data has a standard deviation of 3-4 deg. Included in this standard deviation is a 2-3 deg measurement error. For fields sampled at progressively later times, both the mean and the standard deviation of the difference between the direction-finder bearing and the TV bearing increase. Near 150 microsec, means are about 35 deg and standard deviations about 60 deg. The physical reasons for the late-time inaccuracies in the wideband direction finder and the occurrence of these effects in narrow-band VLF direction finders are considered.

  4. Modeling and Implementation of Multi-Position Non-Continuous Rotation Gyroscope North Finder.

    PubMed

    Luo, Jun; Wang, Zhiqian; Shen, Chengwu; Kuijper, Arjan; Wen, Zhuoman; Liu, Shaojin

    2016-09-20

    Even when the Global Positioning System (GPS) signal is blocked, a rate gyroscope (gyro) north finder is capable of providing the required azimuth reference information to a certain extent. In order to measure the azimuth between the observer and the north direction very accurately, we propose a multi-position non-continuous rotation gyro north finding scheme. Our new generalized mathematical model analyzes the elements that affect the azimuth measurement precision and can thus provide high precision azimuth reference information. Based on the gyro's principle of detecting a projection of the earth rotation rate on its sensitive axis and the proposed north finding scheme, we are able to deduct an accurate mathematical model of the gyro outputs against azimuth with the gyro and shaft misalignments. Combining the gyro outputs model and the theory of propagation of uncertainty, some approaches to optimize north finding are provided, including reducing the gyro bias error, constraining the gyro random error, increasing the number of rotation points, improving rotation angle measurement precision, decreasing the gyro and the shaft misalignment angles. According them, a north finder setup is built and the azimuth uncertainty of 18" is obtained. This paper provides systematic theory for analyzing the details of the gyro north finder scheme from simulation to implementation. The proposed theory can guide both applied researchers in academia and advanced practitioners in industry for designing high precision robust north finder based on different types of rate gyroscopes.

  5. 75 FR 25864 - Submission for OMB Review; Comment Request; Lost People Finder System

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-05-10

    ... information (e.g., the Google Person Finder system that was deployed during the 2010 earthquakes in Haiti.... Using the 2010 earthquake in Haiti as a model, we estimate that some 500 emergency responders might use... earthquake (which contained information on 55,000 people as of April 2010, most of whom were missing...

  6. Subtle.Nets.Finder: finely tuned interaction networks in DNA/RNA/protein complexes.

    PubMed

    Kantardjiev, Alexander A

    2017-03-01

    Graphical Abstract Subtle.Nets.Finder is a workflow of algorithms for identification of subtly interacting groups in DNA/RNA/protein complexes. It is founded on detailed and sophisticated evaluation of the self-consistency in the cooperative network of residue interactions via a combination of advanced calculations (fast multipole method and statistical mechanics) supplemented with graph-theoretical procedures.

  7. Modeling and Implementation of Multi-Position Non-Continuous Rotation Gyroscope North Finder

    PubMed Central

    Luo, Jun; Wang, Zhiqian; Shen, Chengwu; Kuijper, Arjan; Wen, Zhuoman; Liu, Shaojin

    2016-01-01

    Even when the Global Positioning System (GPS) signal is blocked, a rate gyroscope (gyro) north finder is capable of providing the required azimuth reference information to a certain extent. In order to measure the azimuth between the observer and the north direction very accurately, we propose a multi-position non-continuous rotation gyro north finding scheme. Our new generalized mathematical model analyzes the elements that affect the azimuth measurement precision and can thus provide high precision azimuth reference information. Based on the gyro’s principle of detecting a projection of the earth rotation rate on its sensitive axis and the proposed north finding scheme, we are able to deduct an accurate mathematical model of the gyro outputs against azimuth with the gyro and shaft misalignments. Combining the gyro outputs model and the theory of propagation of uncertainty, some approaches to optimize north finding are provided, including reducing the gyro bias error, constraining the gyro random error, increasing the number of rotation points, improving rotation angle measurement precision, decreasing the gyro and the shaft misalignment angles. According them, a north finder setup is built and the azimuth uncertainty of 18” is obtained. This paper provides systematic theory for analyzing the details of the gyro north finder scheme from simulation to implementation. The proposed theory can guide both applied researchers in academia and advanced practitioners in industry for designing high precision robust north finder based on different types of rate gyroscopes. PMID:27657067

  8. Development of the Terrestrial Planet Finder Coronagraph membrane V-grooves

    NASA Technical Reports Server (NTRS)

    Fang, Houfei; Ho, Timothy; Chen, Gun-Shing; Quijano, Ubaldo

    2004-01-01

    The Terrestrial Planet Finder mission will study all aaspecs of planets outside our solar system: from their formation and development in disks of dust and gas around newly forming stars to the presence of those planets orbiting the nearest stars; from the numbers at various sizes and places to their suitability as an abode for life.

  9. General Astrophysics and Comparative Planetology with the Terrestrial Planet Finder Missions

    NASA Technical Reports Server (NTRS)

    Kuchner, Marc J. (Editor)

    2005-01-01

    This document discusses the potential of the Terrestrial Planet Finder (TPF) for general astrophysics beyond its base mission, focusing on science obtainable with no or minimal modifications to the mission design, but also exploring possible modifications of TPF with high scientific merit and no impact on the basic search for extrasolar Earth analogs.

  10. The Relationship between Kolb's Learning Styles and StrengthsFinder's Talent Themes

    ERIC Educational Resources Information Center

    Caldwell, Adonna B.

    2009-01-01

    The purpose of this study was to investigate if there were relationships between college students' talent themes as defined by the Clifton StrengthsFinder(TM) Instrument and their learning style as defined by Kolb Learning Styles Inventory. Logistical regression methodology was utilized to assess the relationship between learning styles and talent…

  11. Precise pulsed time-of-flight laser range finder for industrial distance measurements

    NASA Astrophysics Data System (ADS)

    Kilpelä, Ari; Pennala, Riku; Kostamovaara, Juha

    2001-04-01

    A pulsed time-of-flight laser range finder with a 1 GHz avalanche photo diode (APD) receiver and a laser pulser with ˜35 ps pulse width has been developed and tested. The receiver channel is constructed using a silicon ASIC chip and a commercially available silicon APD placed on a hybrid ceramic susbstrate. The laser pulser utilizes a single heterostructure laser operating in Q-switching mode. It is shown that the single-shot precision of the complete laser range finder is ˜2.1 mm (σ value) at best. The nonaccuracy in the distance range of 0.5-34.5 m was ˜±2 mm excluding errors caused by the statistical variations and long-term instability. The single-shot precision is clearly better than the single-shot precision of the earlier laser range finders with ˜100-200 MHz bandwidths. Also, two types of optics, coaxial and paraxial, were tested. The linearity of the coaxial optics was better, especially with a long (4 m) receiver fiber. Some possible applications of the laser range finder utilizing ps level pulses are, for example, fast three-dimensional vision in industrial environments and structure analysis of materials.

  12. Teenage Pregnancy: An Intensive and Critical Problem in Search of a Solution. Student Fact Finder Leaflet.

    ERIC Educational Resources Information Center

    Glover-Smith, Alma

    This document presents materials from a course designed to teach adolescents about teenage pregnancy and parenting. The materials are organized into nine modules, each of which contains instructions on how to use the module; a pre- and post-test on the information presented in the module; a fact finder leaflet of information; and relevant…

  13. Microlithography and resist technology information at your fingertips via SciFinder

    NASA Astrophysics Data System (ADS)

    Konuk, Rengin; Macko, John R.; Staggenborg, Lisa

    1997-07-01

    Finding and retrieving the information you need about microlithography and resist technology in a timely fashion can make or break your competitive edge in today's business environment. Chemical Abstracts Service (CAS) provides the most complete and comprehensive database of the chemical literature in the CAplus, REGISTRY, and CASREACT files including 13 million document references, 15 million substance records and over 1.2 million reactions. This includes comprehensive coverage of positive and negative resist formulations and processing, photoacid generation, silylation, single and multilayer resist systems, photomasks, dry and wet etching, photolithography, electron-beam, ion-beam and x-ray lithography technologies and process control, optical tools, exposure systems, radiation sources and steppers. Journal articles, conference proceedings and patents related to microlithography and resist technology are analyzed and indexed by scientific information analysts with strong technical background in these areas. The full CAS database, which is updated weekly with new information, is now available at your desktop, via a convenient, user-friendly tool called 'SciFinder.' Author, subject and chemical substance searching is simplified by SciFinder's smart search features. Chemical substances can be searched by chemical structure, chemical name, CAS registry number or molecular formula. Drawing chemical structures in SciFinder is easy and does not require compliance with CA conventions. Built-in intelligence of SciFinder enables users to retrieve substances with multiple components, tautomeric forms and salts.

  14. The ammonia oxidizing and denitrifying prokaryotes associated with sponges from different sea areas.

    PubMed

    Han, Minqi; Li, Zhiyong; Zhang, Fengli

    2013-08-01

    Marine sponges have been suggested to play an important role in the marine nitrogen cycling. However, the role of sponge microbes in the nitrogen transformation remains limited, especially on the bacterial ammonia oxidization and denitrification. Hence, in the present study, using functional genes (amoA, nirS, nirK, and nxrA) involved in ammonia oxidization and denitrification and 16S rRNA genes for specific bacterial groups as markers, phylogenetically diverse prokaryotes including bacteria and archaea, which may be involved in the ammonia oxidization and denitrification processes in sponges, were revealed in seven sponge species. Ammonia oxidizers were found in all species, whereas three sponges (Placospongia sp., Acanthella sp., and Pericharax heteroraphis) harbor only ammonia-oxidizing bacteria (AOB), two sponges (Spirastrellidae diplastrella and Mycale fibrexilis) host only ammonia-oxidizing archaea (AOA), while the remaining two sponges (Haliclona sp. and Lamellomorpha sp.) harbor both AOB and AOA. S. diplastrella and Lamellomorpha sp. also harbor denitrifying bacteria. Nitrite reductase gene nirK was detected only in Lamellomorpha sp. with higher phylogenetic diversity than nirS gene observed only in S. diplastrella. The detected functional genes related to the ammonia oxidization and nitrite reduction in deep-sea and shallow-water sponges highlighted the potential ecological roles of prokaryotes in sponge-related nitrogen transformation.

  15. Lead Finder docking and virtual screening evaluation with Astex and DUD test sets

    NASA Astrophysics Data System (ADS)

    Novikov, Fedor N.; Stroylov, Viktor S.; Zeifman, Alexey A.; Stroganov, Oleg V.; Kulkov, Val; Chilov, Ghermes G.

    2012-06-01

    Lead Finder is a molecular docking software. Sampling uses an original implementation of the genetic algorithm that involves a number of additional optimization procedures. Lead Finder's scoring functions employ a set of semi-empiric molecular mechanics functionals that have been parameterized independently for docking, binding energy predictions and rank-ordering for virtual screening. Sampling and scoring both utilize a staged approach, moving from fast but less accurate algorithm versions to computationally more intensive but more accurate versions. Lead Finder includes tools for the preparation of full atom protein and ligand models. In this exercise, Lead Finder achieved 72.9% docking success rate on the Astex test set when the original author-prepared full atom models were used, and 74.1% success rate when the structures were prepared by Lead Finder. The major cause of docking failures were scoring errors resulting from the use of imperfect solvation models. In many cases, docking errors could be corrected by the proper protonation and the use of correct cyclic conformations of ligands. In virtual screening experiments on the DUD test set the early enrichment factor of several tens was achieved on average. However, the area under the ROC curve ("AUC ROC") ranged from 0.70 to 0.74 depending on the screening protocol used, and the separation from the null model was not perfect—0.12-0.15 units of AUC ROC. We assume that effective virtual screening in the whole range of enrichment curve and not just at the early enrichment stages requires more accurate solvation modeling and accounting for the protein backbone flexibility.

  16. Identification and functional characterization of Siberian wild rye (Elymus sibiricus L.) small heat shock protein 16.9 gene (EsHsp16.9) conferring diverse stress tolerance in prokaryotic cells.

    PubMed

    Lee, Sang-Hoon; Lee, Ki-Won; Lee, Dong-Gi; Son, Daeyoung; Park, Su Jung; Kim, Ki-Yong; Park, Hyung Soo; Cha, Joon-Yung

    2015-04-01

    Small heat shock proteins (Hsps) protect against stress-inducible denaturation of substrates. Our objectives were to clone and examine the mRNA expression of the Hsp16.9 gene from Siberian wild rye grown under diverse stress treatments. We characterized EsHsp16.9 from Elymus sibiricus L. EsHsp16.9 has a 456-bp open reading frame that encodes a 151-amino acid protein with a conserved α-crystallin domain. Northern blot analysis showed that EsHsp16.9 transcripts were enhanced by heat, drought, arsenate, methyl viologen, and H2O2 treatment. In addition, recombinant EsHsp16.9 protein acts as a molecular chaperone to prevent the denaturation of malate dehydrogenase. Growth of cells overexpressing EsHsp16.9 was up to 200% more rapid in the presence of NaCl, arsenate, and polyethylene glycol than that of cells harboring an empty vector. These data suggest that EsHsp16.9 acts as a molecular chaperone that enhances stress tolerance in living organisms.

  17. Single prokaryotic cell isolation and total transcript amplification protocol for transcriptomic analysis.

    PubMed

    Kang, Yun; McMillan, Ian; Norris, Michael H; Hoang, Tung T

    2015-07-01

    Until recently, transcriptome analyses of single cells have been confined to eukaryotes. The information obtained from single-cell transcripts can provide detailed insight into spatiotemporal gene expression, and it could be even more valuable if expanded to prokaryotic cells. Transcriptome analysis of single prokaryotic cells is a recently developed and powerful tool. Here we describe a procedure that allows amplification of the total transcript of a single prokaryotic cell for in-depth analysis. This is performed by using a laser-capture microdissection instrument for single-cell isolation, followed by reverse transcription via Moloney murine leukemia virus, degradation of chromosomal DNA with McrBC and DpnI restriction enzymes, single-stranded cDNA (ss-cDNA) ligation using T4 polynucleotide kinase and CircLigase, and polymerization of ss-cDNA to double-stranded cDNA (ds-cDNA) by Φ29 polymerase. This procedure takes ∼5 d, and sufficient amounts of ds-cDNA can be obtained from single-cell RNA template for further microarray analysis.

  18. Evidence of the activity of dissimilatory sulfate-reducing prokaryotes in nonsulfidogenic tropical mobile muds.

    PubMed

    Madrid, Vanessa M; Aller, Robert C; Aller, Josephine Y; Chistoserdov, Andrei Y

    2006-08-01

    In spite of the nonsulfidic conditions and abundant reactive iron(III) commonly found in mobile tropical deltaic muds, genes encoding dissimilatory sulfite reductase (dsr) were successfully amplified from the upper approximately 1 m of coastal deposits sampled along French Guiana and in the Gulf of Papua. The dsr sequences retrieved were highly diverse, were generally represented in both study regions and fell into six large phylogenetic groupings: Deltaproteobacteria, Thermodesulfovibrio groups, Firmicutes and three groups without known cultured representatives. The spatial and temporal distribution of dsr sequences strongly supports the contention that the sulfate-reducing prokaryote communities in mobile mud environments are cosmopolitan and stable over a period of years. The decrease in the (35)SO(4) (2-) tracer demonstrates that, despite abundant reactive sedimentary iron(III) ( approximately 350-400 mumol g(-1)), the sulfate-reducing prokaryotes present are active, with the highest levels of sulfide being generated in the upper zones of the cores (0-30 cm). Both the time course of the (35)S-sulfide tracer activity and the lack of reduced sulfur in sediments demonstrate virtually complete anaerobic loss of solid phase sulfides. We propose a pathway of organic matter oxidation involving at least 5-25% of the remineralized carbon, wherein sulfide produced by sulfate-reducing prokaryotes is cyclically oxidized biotically or abiotically by metal oxides.

  19. Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

    PubMed Central

    2009-01-01

    Background The cystatin superfamily comprises cysteine protease inhibitors that play key regulatory roles in protein degradation processes. Although they have been the subject of many studies, little is known about their genesis, evolution and functional diversification. Our aim has been to obtain a comprehensive insight into their origin, distribution, diversity, evolution and classification in Eukaryota, Bacteria and Archaea. Results We have identified in silico the full complement of the cystatin superfamily in more than 2100 prokaryotic and eukaryotic genomes. The analysis of numerous eukaryotic genomes has provided strong evidence for the emergence of this superfamily in the ancestor of eukaryotes. The progenitor of this superfamily was most probably intracellular and lacked a signal peptide and disulfide bridges, much like the extant Giardia cystatin. A primordial gene duplication produced two ancestral eukaryotic lineages, cystatins and stefins. While stefins remain encoded by a single or a small number of genes throughout the eukaryotes, the cystatins have undergone a more complex and dynamic evolution through numerous gene and domain duplications. In the cystatin superfamily we discovered twenty vertebrate-specific and three angiosperm-specific orthologous families, indicating that functional diversification has occurred only in multicellular eukaryotes. In vertebrate orthologous families, the prevailing trends were loss of the ancestral inhibitory activity and acquisition of novel functions in innate immunity. Bacterial cystatins and stefins may be emergency inhibitors that enable survival of bacteria in the host, defending them from the host's proteolytic activity. Conclusion This study challenges the current view on the classification, origin and evolution of the cystatin superfamily and provides valuable insights into their functional diversification. The findings of this comprehensive study provide guides for future structural and evolutionary studies

  20. Genomes of Stigonematalean cyanobacteria (subsection V) and the evolution of oxygenic photosynthesis from prokaryotes to plastids.

    PubMed

    Dagan, Tal; Roettger, Mayo; Stucken, Karina; Landan, Giddy; Koch, Robin; Major, Peter; Gould, Sven B; Goremykin, Vadim V; Rippka, Rosmarie; Tandeau de Marsac, Nicole; Gugger, Muriel; Lockhart, Peter J; Allen, John F; Brune, Iris; Maus, Irena; Pühler, Alfred; Martin, William F

    2013-01-01

    Cyanobacteria forged two major evolutionary transitions with the invention of oxygenic photosynthesis and the bestowal of photosynthetic lifestyle upon eukaryotes through endosymbiosis. Information germane to understanding those transitions is imprinted in cyanobacterial genomes, but deciphering it is complicated by lateral gene transfer (LGT). Here, we report genome sequences for the morphologically most complex true-branching cyanobacteria, and for Scytonema hofmanni PCC 7110, which with 12,356 proteins is the most gene-rich prokaryote currently known. We investigated components of cyanobacterial evolution that have been vertically inherited, horizontally transferred, and donated to eukaryotes at plastid origin. The vertical component indicates a freshwater origin for water-splitting photosynthesis. Networks of the horizontal component reveal that 60% of cyanobacterial gene families have been affected by LGT. Plant nuclear genes acquired from cyanobacteria define a lower bound frequency of 611 multigene families that, in turn, specify diazotrophic cyanobacterial lineages as having a gene collection most similar to that possessed by the plastid ancestor.

  1. Biogeography of sulfate-reducing prokaryotes in river floodplains.

    PubMed

    Miletto, Marzia; Loy, Alexander; Antheunisse, A Martijn; Loeb, Roos; Bodelier, Paul L E; Laanbroek, Hendrikus J

    2008-06-01

    In this study, a large-scale field survey was conducted to describe the biogeography of sulfate-reducing prokaryotes (SRPs) in river floodplains. Fingerprints obtained with three methods, i.e. 16S rRNA gene-based oligonucleotide microarray, dsrB-based denaturing gradient gel electrophoresis (DGGE) and polar lipid-derived fatty acid (PLFA) analyses, were used as a proxy to describe the SRPs community diversity. Each set of profiles was subjected to a combined multivariate/correlation analysis in order to compare SRP community profiles and to highlight the environmental variables influencing the SRPs distribution along environmental gradients. Floodplain soils harbored distinct SRP communities displaying biogeographic patterns. Nearly all profiles from the tidal sites consistently separated from the nontidal sites, independently from the screening method and the multivariate statistics used. The distribution of the microarray/DGGE/PLFA-based fingerprints in the principal component plots could be correlated to eight soil variables, i.e. soil organic matter, total nitrogen, total phosphorous and total potassium, and extractable ammonium, nitrate, phosphate and sulfate, as well as seven pore water variables, i.e. phosphate, sulfate, sulfide, chloride, sodium, potassium and magnesium ions. Indication of a salinity- and plant nutrient-dependent distribution of SRPs related to Desulfosarcina, Desulfomonile and Desulfobacter was suggested by microarray, DGGE and PLFA analyses.

  2. Linking environmental prokaryotic viruses and their host through CRISPRs.

    PubMed

    Sanguino, Laura; Franqueville, Laure; Vogel, Timothy M; Larose, Catherine

    2015-05-01

    The ecological pressure that viruses place on microbial communities is not only based on predation, but also on gene transfer. In order to determine the potential impact of viruses and transduction, we need a better understanding of the dynamics of interactions between viruses and their hosts in the environment. Data on environmental viruses are scarce, and methods for tracking their interactions with prokaryotes are needed. Clustered regularly interspaced short palindromic repeats (CRISPRs), which contain viral sequences in bacterial genomes, might help document the history of virus-host interactions in the environment. In this study, a bioinformatics network linking viruses and their hosts using CRISPR sequences obtained from metagenomic data was developed and applied to metagenomes from Arctic glacial ice and soil. The application of our network approach showed that putative interactions were more commonly detected in the ice samples than the soil which would be consistent with the ice viral-bacterial interactions being more dynamic than those in soil. Further analysis of the viral sequences in the CRISPRs indicated that Ralstonia phages might be agents of transduction in the Arctic glacial ice.

  3. Ribosomal oxygenases are structurally conserved from prokaryotes to humans.

    PubMed

    Chowdhury, Rasheduzzaman; Sekirnik, Rok; Brissett, Nigel C; Krojer, Tobias; Ho, Chia-Hua; Ng, Stanley S; Clifton, Ian J; Ge, Wei; Kershaw, Nadia J; Fox, Gavin C; Muniz, Joao R C; Vollmar, Melanie; Phillips, Claire; Pilka, Ewa S; Kavanagh, Kathryn L; von Delft, Frank; Oppermann, Udo; McDonough, Michael A; Doherty, Aidan J; Schofield, Christopher J

    2014-06-19

    2-Oxoglutarate (2OG)-dependent oxygenases have important roles in the regulation of gene expression via demethylation of N-methylated chromatin components and in the hydroxylation of transcription factors and splicing factor proteins. Recently, 2OG-dependent oxygenases that catalyse hydroxylation of transfer RNA and ribosomal proteins have been shown to be important in translation relating to cellular growth, TH17-cell differentiation and translational accuracy. The finding that ribosomal oxygenases (ROXs) occur in organisms ranging from prokaryotes to humans raises questions as to their structural and evolutionary relationships. In Escherichia coli, YcfD catalyses arginine hydroxylation in the ribosomal protein L16; in humans, MYC-induced nuclear antigen (MINA53; also known as MINA) and nucleolar protein 66 (NO66) catalyse histidine hydroxylation in the ribosomal proteins RPL27A and RPL8, respectively. The functional assignments of ROXs open therapeutic possibilities via either ROX inhibition or targeting of differentially modified ribosomes. Despite differences in the residue and protein selectivities of prokaryotic and eukaryotic ROXs, comparison of the crystal structures of E. coli YcfD and Rhodothermus marinus YcfD with those of human MINA53 and NO66 reveals highly conserved folds and novel dimerization modes defining a new structural subfamily of 2OG-dependent oxygenases. ROX structures with and without their substrates support their functional assignments as hydroxylases but not demethylases, and reveal how the subfamily has evolved to catalyse the hydroxylation of different residue side chains of ribosomal proteins. Comparison of ROX crystal structures with those of other JmjC-domain-containing hydroxylases, including the hypoxia-inducible factor asparaginyl hydroxylase FIH and histone N(ε)-methyl lysine demethylases, identifies branch points in 2OG-dependent oxygenase evolution and distinguishes between JmjC-containing hydroxylases and demethylases

  4. Applications of the Integrated High-Performance CMOS Image Sensor to Range Finders — from Optical Triangulation to the Automotive Field

    PubMed Central

    Wu, Jih-Huah; Pen, Cheng-Chung; Jiang, Joe-Air

    2008-01-01

    With their significant features, the applications of complementary metal-oxide semiconductor (CMOS) image sensors covers a very extensive range, from industrial automation to traffic applications such as aiming systems, blind guidance, active/passive range finders, etc. In this paper CMOS image sensor-based active and passive range finders are presented. The measurement scheme of the proposed active/passive range finders is based on a simple triangulation method. The designed range finders chiefly consist of a CMOS image sensor and some light sources such as lasers or LEDs. The implementation cost of our range finders is quite low. Image processing software to adjust the exposure time (ET) of the CMOS image sensor to enhance the performance of triangulation-based range finders was also developed. An extensive series of experiments were conducted to evaluate the performance of the designed range finders. From the experimental results, the distance measurement resolutions achieved by the active range finder and the passive range finder can be better than 0.6% and 0.25% within the measurement ranges of 1 to 8 m and 5 to 45 m, respectively. Feasibility tests on applications of the developed CMOS image sensor-based range finders to the automotive field were also conducted. The experimental results demonstrated that our range finders are well-suited for distance measurements in this field. PMID:27879789

  5. Evolution of prokaryote and eukaryote lines inferred from sequence evidence

    NASA Technical Reports Server (NTRS)

    Hunt, L. T.; George, D. G.; Yeh, L.-S.; Dayhoff, M. O.

    1984-01-01

    This paper describes the evolution of prokaryotes and early eukaryotes, including their symbiotic relationships, as inferred from phylogenetic trees of bacterial ferredoxin, 5S ribosomal RNA, ribulose-1,5-biphosphate carboxylase large chain, and mitochondrial cytochrome oxidase polypeptide II.

  6. Directed shotgun proteomics guided by saturated RNA-seq identifies a complete expressed prokaryotic proteome

    PubMed Central

    Omasits, Ulrich; Quebatte, Maxime; Stekhoven, Daniel J.; Fortes, Claudia; Roschitzki, Bernd; Robinson, Mark D.; Dehio, Christoph; Ahrens, Christian H.

    2013-01-01

    Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ∼90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor. PMID:23878158

  7. Directed Shotgun Proteomics Guided by Saturated RNA-seq Identifies a Complete Expressed Prokaryotic Proteome

    SciTech Connect

    Omasits, U.; Quebatte, Maxime; Stekhoven, Daniel J.; Fortes, Claudia; Roschitzki, Bernd; Robinson, Mark D.; Dehio, Christoph; Ahrens, Christian H.

    2013-11-01

    Prokaryotes, due to their moderate complexity, are particularly amenable to the comprehensive identification of the protein repertoire expressed under different conditions. We applied a generic strategy to identify a complete expressed prokaryotic proteome, which is based on the analysis of RNA and proteins extracted from matched samples. Saturated transcriptome profiling by RNA-seq provided an endpoint estimate of the protein-coding genes expressed under two conditions which mimic the interaction of Bartonella henselae with its mammalian host. Directed shotgun proteomics experiments were carried out on four subcellular fractions. By specifically targeting proteins which are short, basic, low abundant, and membrane localized, we could eliminate their initial underrepresentation compared to the estimated endpoint. A total of 1250 proteins were identified with an estimated false discovery rate below 1%. This represents 85% of all distinct annotated proteins and ~90% of the expressed protein-coding genes. Genes that were detected at the transcript but not protein level, were found to be highly enriched in several genomic islands. Furthermore, genes that lacked an ortholog and a functional annotation were not detected at the protein level; these may represent examples of overprediction in genome annotations. A dramatic membrane proteome reorganization was observed, including differential regulation of autotransporters, adhesins, and hemin binding proteins. Particularly noteworthy was the complete membrane proteome coverage, which included expression of all members of the VirB/D4 type IV secretion system, a key virulence factor.

  8. Functional characterization of recombinant bromelain of Ananas comosus expressed in a prokaryotic system.

    PubMed

    George, Susan; Bhasker, Salini; Madhav, Harish; Nair, Archana; Chinnamma, Mohankumar

    2014-02-01

    Bromelain (BRM) is a defense protein present in the fruit and stem of pineapple (Ananas comosus) and it is grouped as a cysteine protease enzyme with diversified medicinal uses. Based on its therapeutic applications, bromelain has got sufficient attention in pharmaceutical industries. In the present study, the full coding gene of bromelain in pineapple stem (1,093 bp) was amplified by RT-PCR. The PCR product was cloned, sequenced, and characterized. The sequence analysis of the gene revealed the single nucleotide polymorphism and its phylogenetic relatedness. The peptide sequence deduced from the gene showed the amino acid variations, physicochemical properties and secondary and tertiary structural features of the protein. The full BRM gene was transformed to prokaryotic vector pET32b and expressed in Escherichia coli BL21 DE3pLysS host cells successfully. The identity of the recombinant bromelain (rBRM) protein was confirmed by Western blot analysis using anti-BRM-rabbit IgG antibody. The activity of recombinant bromelain compared with purified native bromelain was determined by protease assay. The inhibitory effect of rBRM compared with native BRM in the growth of Gram-positive and Gram-negative strains of Streptococcus agalactiae and Escherichia coli O111 was evident from the antibacterial sensitivity test. To the best of our knowledge, this is the first report showing the bactericidal property of rBRM expressed in a prokaryotic system.

  9. Prokaryote diversity and taxonomy: current status and future challenges.

    PubMed Central

    Oren, Aharon

    2004-01-01

    The prokaryotes are by far the most abundant organisms inhabiting planet Earth. They are also by far the most diverse, both metabolically and phylogenetically; they encompass the Bacteria and the Archaea, two out of the three major divisions of living organisms. The current prokaryote species classification is based on a combination of genomic and phenotypic properties. The recommended cut-off value of 70% DNA-DNA similarity to delineate species signifies an extremely broad species definition for the prokaryotes compared with the higher eukaryotes. The number of validly named species of prokaryotes is currently slightly more than 6200. However, on the basis of small-subunit rDNA characterization of whole communities and other approaches, the more exact number of species present can be inferred to be at least two orders of magnitude larger. Classic culturing methods based on colony formation on agar are generally unsatisfactory for the recovery of bacteria from the environment. Many of the most abundant prokaryotes in nature have not yet been brought into culture. Some of these may thrive by means of as yet unknown modes of energy generation. Several novel methods have recently enabled the isolation of some interesting organisms of environmental significance. A better coverage of the prokaryote diversity on Earth depends on such innovative approaches, combined with appropriate funding. PMID:15253349

  10. Eukaryotic and Prokaryotic Cytoskeletons: Structure and Mechanics

    NASA Astrophysics Data System (ADS)

    Gopinathan, Ajay

    2013-03-01

    The eukaryotic cytoskeleton is an assembly of filamentous proteins and a host of associated proteins that collectively serve functional needs ranging from spatial organization and transport to the production and transmission of forces. These systems can exhibit a wide variety of non-equilibrium, self-assembled phases depending on context and function. While much recent progress has been made in understanding the self-organization, rheology and nonlinear mechanical properties of such active systems, in this talk, we will concentrate on some emerging aspects of cytoskeletal physics that are promising. One such aspect is the influence of cytoskeletal network topology and its dynamics on both active and passive intracellular transport. Another aspect we will highlight is the interplay between chirality of filaments, their elasticity and their interactions with the membrane that can lead to novel conformational states with functional implications. Finally we will consider homologs of cytoskeletal proteins in bacteria, which are involved in templating cell growth, segregating genetic material and force production, which we will discuss with particular reference to contractile forces during cell division. These prokaryotic structures function in remarkably similar yet fascinatingly different ways from their eukaryotic counterparts and can enrich our understanding of cytoskeletal functioning as a whole.

  11. The aspartate aminotransferase family in conifers: biochemical analysis of a prokaryotic-type enzyme from maritime pine.

    PubMed

    de la Torre, Fernando; Suárez, María Fernanda; Santis, Laura de; Cánovas, Francisco M

    2007-09-01

    Plant aspartate aminotransferase (AAT, EC 2.6.1.1) plays a key role in primary nitrogen assimilation, the transfer of reducing equivalents and the interchanges of carbon and nitrogen pools between subcellular compartments. We investigated the AAT family in conifers using maritime pine as the experimental model. Genes for cytosolic, mitochondrial and two plastidic isoenzymes (eukaryotic- and prokaryotic-types) were identified and their deduced amino acid sequences compared. The primary structure of the eukaryotic-type enzymes is quite well conserved, whereas the prokaryotic-type AAT is highly divergent (15% of identity). These molecular data were confirmed by the absence of immunological cross-reactivity between the two types of native AATs. The mature prokaryotic-type polypeptide was overexpressed in Escherichia coli, and the native enzyme was purified to apparent homogeneity and its molecular properties determined. The fully active recombinant holoenzyme showed highest catalytic activity at 50-60 degrees C and was moderately thermostable, retaining about 50% of its activity after incubation at 70 degrees C for 5-10 min. The presence of pyridoxal 5'-phosphate significantly increased the thermostability of the enzyme. These molecular characteristics were exploited to develop a rapid protocol for the purification of this prokaryotic-type enzyme from pine cotyledons. The results will be useful for studying aspartate and amino acid metabolism in trees.

  12. Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata).

    PubMed

    Kormas, Konstantinos A; Meziti, Alexandra; Mente, Eleni; Frentzos, Athanasios

    2014-10-01

    We compared the gut prokaryotic communities in wild, organically-, and conventionally reared sea bream (Sparus aurata) individuals. Gut microbial communities were identified using tag pyrosequencing of the 16S rRNA genes. There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. Most of the Bacteria belonged to the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The number of bacterial operational taxonomic units (OTUs) was reduced from the wild to the conventionally reared fish, implying a response of the gut microorganisms to the supplied food and possibly alterations in food assimilation. The dominant bacterial OTU in all examined fish was closely related to the genus Diaphorobacter. This is the first time that a member of the β-Proteobacteria, which dominate in freshwaters, are so important in a marine fish gut. In total the majority of the few Archaea OTUs found, were related to methane metabolism. The inferred physiological roles of the dominant prokaryotes are related to the metabolism of carbohydrates and nitrogenous compounds. This study showed the responsive feature of the sea bream gut prokaryotic communities to their diets and also the differences of the conventional in comparison to the organic and wild sea bream gut microbiota.

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

    PubMed

    Al-Attar, Sinan; Westra, Edze R; van der Oost, John; Brouns, Stan J J

    2011-04-01

    Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences (repeats), interspaced by highly variable sequences referred to as spacers. The spacers originate from either phages or plasmids and comprise the prokaryotes' 'immunological memory'. CRISPR-associated (cas) genes encode conserved proteins that together with CRISPRs make-up the CRISPR/Cas system, responsible for defending the prokaryotic cell against invaders. CRISPR-mediated resistance has been proposed to involve three stages: (i) CRISPR-Adaptation, the invader DNA is encountered by the CRISPR/Cas machinery and an invader-derived short DNA fragment is incorporated in the CRISPR array. (ii) CRISPR-Expression, the CRISPR array is transcribed and the transcript is processed by Cas proteins. (iii) CRISPR-Interference, the invaders' nucleic acid is recognized by complementarity to the crRNA and neutralized. An application of the CRISPR/Cas system is the immunization of industry-relevant prokaryotes (or eukaryotes) against mobile-genetic invasion. In addition, the high variability of the CRISPR spacer content can be exploited for phylogenetic and evolutionary studies. Despite impressive progress during the last couple of years, the elucidation of several fundamental details will be a major challenge in future research.

  14. Dietary differences are reflected on the gut prokaryotic community structure of wild and commercially reared sea bream (Sparus aurata)

    PubMed Central

    Kormas, Konstantinos A; Meziti, Alexandra; Mente, Eleni; Frentzos, Athanasios

    2014-01-01

    We compared the gut prokaryotic communities in wild, organically-, and conventionally reared sea bream (Sparus aurata) individuals. Gut microbial communities were identified using tag pyrosequencing of the 16S rRNA genes. There were distinct prokaryotic communities in the three different fish nutritional treatments, with the bacteria dominating over the Archaea. Most of the Bacteria belonged to the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. The number of bacterial operational taxonomic units (OTUs) was reduced from the wild to the conventionally reared fish, implying a response of the gut microorganisms to the supplied food and possibly alterations in food assimilation. The dominant bacterial OTU in all examined fish was closely related to the genus Diaphorobacter. This is the first time that a member of the β-Proteobacteria, which dominate in freshwaters, are so important in a marine fish gut. In total the majority of the few Archaea OTUs found, were related to methane metabolism. The inferred physiological roles of the dominant prokaryotes are related to the metabolism of carbohydrates and nitrogenous compounds. This study showed the responsive feature of the sea bream gut prokaryotic communities to their diets and also the differences of the conventional in comparison to the organic and wild sea bream gut microbiota. PMID:25066034

  15. [Biosynthesis of geosmin and 2-methylisoborneol in the prokaryotes--a review].

    PubMed

    Zhang, Ting; Li, Deliang; Li, Jie

    2012-02-04

    The occurrence of off-flavor problems caused by prokaryotes cyanobacteria and actinomycetes is a worldwide water and food quality issue. Based on literatures on two earthy-muddy-smelling metabolites, (i. e., geosmin and 2-methylisoborneol (2-MIB)), we reviewed their chemical characteristics, biosynthetic pathways, genes and enzymes that are involved in biosynthesis. Then we discussed current research questions related to off-flavor and future directions. Finally, we addressed the significance of probable key regulatory mechanism for the production and release of geosmin and 2-MIB, which could provide more scientific strategies to better control off-flavors outbreaks in drinking and aquaculture water.

  16. A New Genomic Evolutionary Model for Rearrangements, Duplications, and Losses That Applies across Eukaryotes and Prokaryotes

    NASA Astrophysics Data System (ADS)

    Lin, Yu; Moret, Bernard M. E.

    Background: Genomic rearrangements have been studied since the beginnings of modern genetics and models for such rearrangements have been the subject of many papers over the last 10 years. However, none of the extant models can predict the evolution of genomic organization into circular unichromosomal genomes (as in most prokaryotes) and linear multichromosomal genomes (as in most eukaryotes). Very few of these models support gene duplications and losses - yet these events may be more common in evolutionary history than rearrangements and themselves cause apparent rearrangements.

  17. On the acceleration of the N-FINDER algorithm for hyperspectral endmembers extraction

    NASA Astrophysics Data System (ADS)

    Guerra, Raul; López, Sebastian; Callicó, Gustavo M.; Lopez, Jose F.; Sarmiento, Roberto

    2014-05-01

    This paper presents a new method in order to perform the endmembers extraction with the same accuracy in the results that the well known Winter's N-Finder algorithm but with less computational effort. In particular, our proposal makes use of the Orthogonal Subspace Projection algorithm, OSP, as well as the information provided by the dimensionality reduction step that takes place prior to the endmembers extraction itself. The results obtained using the proposed methodology demonstrate that more than half of the computing time is saved with negligible variations in the quality of the endmembers extracted, compared with the results obtained with the Winter's N-Finder algorithm. Moreover, this is achieved with independence of the amount of noise and/or the number of endmembers of the hyperspectral image under processing.

  18. Searching the Web for Influenza Vaccines: HealthMap Vaccine Finder

    PubMed Central

    Huston, Jane E.; Mekaru, Sumiko R.; Kluberg, Sheryl; Brownstein, John S.

    2015-01-01

    Objectives The goal of the HealthMap Vaccine Finder is to provide a free, comprehensive, online service where users can search for locations that offer immunizations. In this article, we describe the data and systems underlying the HealthMap Vaccine Finder (HVF) and summarize the project’s first year of operations. Methods We collected data on vaccination services from a variety of providers for 2012–2013. Data are used to populate an online, public, searchable map. Results In its first year, HVF collected information from 1256 providers representing 46 381 locations. The public Web site received 625 124 visits during the 2012–2013 influenza vaccination season. Conclusions HVF is a unique tool that connects the public to vaccine providers in their communities. During the 2012–2013 influenza season, HVF experienced significant usage and was able to respond to user feedback with new features. PMID:25880945

  19. Evolutionary constraints of phosphorylation in eukaryotes, prokaryotes, and mitochondria.

    PubMed

    Gnad, Florian; Forner, Francesca; Zielinska, Dorota F; Birney, Ewan; Gunawardena, Jeremy; Mann, Matthias

    2010-12-01

    High accuracy mass spectrometry has proven to be a powerful technology for the large scale identification of serine/threonine/tyrosine phosphorylation in the living cell. However, despite many described phosphoproteomes, there has been no comparative study of the extent of phosphorylation and its evolutionary conservation in all domains of life. Here we analyze the results of phosphoproteomics studies performed with the same technology in a diverse set of organisms. For the most ancient organisms, the prokaryotes, only a few hundred proteins have been found to be phosphorylated. Applying the same technology to eukaryotic species resulted in the detection of thousands of phosphorylation events. Evolutionary analysis shows that prokaryotic phosphoproteins are preferentially conserved in all living organisms, whereas-site specific phosphorylation is not. Eukaryotic phosphosites are generally more conserved than their non-phosphorylated counterparts (with similar structural constraints) throughout the eukaryotic domain. Yeast and Caenorhabditis elegans are two exceptions, indicating that the majority of phosphorylation events evolved after the divergence of higher eukaryotes from yeast and reflecting the unusually large number of nematode-specific kinases. Mitochondria present an interesting intermediate link between the prokaryotic and eukaryotic domains. Applying the same technology to this organelle yielded 174 phosphorylation sites mapped to 74 proteins. Thus, the mitochondrial phosphoproteome is similarly sparse as the prokaryotic phosphoproteomes. As expected from the endosymbiotic theory, phosphorylated as well as non-phosphorylated mitochondrial proteins are significantly conserved in prokaryotes. However, mitochondrial phosphorylation sites are not conserved throughout prokaryotes, consistent with the notion that serine/threonine phosphorylation in prokaryotes occurred relatively recently in evolution. Thus, the phosphoproteome reflects major events in the

  20. The copper metallome in prokaryotic cells.

    PubMed

    Rensing, Christopher; McDevitt, Sylvia Franke

    2013-01-01

    As a trace element copper has an important role in cellular function like many other transition metals. Its ability to undergo redox changes [Cu(I) ↔ Cu(II)] makes copper an ideal cofactor in enzymes catalyzing electron transfers. However, this redox change makes copper dangerous for a cell since it is able to be involved in Fenton-like reactions creating reactive oxygen species (ROS). Cu(I) also is a strong soft metal and can attack and destroy iron-sulfur clusters thereby releasing iron which can in turn cause oxidative stress. Therefore, copper homeostasis has to be highly balanced to ensure proper cellular function while avoiding cell damage.Throughout evolution bacteria and archaea have developed a highly regulated balance in copper metabolism. While for many prokaryotes copper uptake seems to be unspecific, others have developed highly sophisticated uptake mechanisms to ensure the availability of sufficient amounts of copper. Within the cytoplasm copper is sequestered by various proteins and molecules, including specific copper chaperones, to prevent cellular damage. Copper-containing proteins are usually located in the cytoplasmic membrane with the catalytic domain facing the periplasm, in the periplasm of Gram-negative bacteria, or they are secreted, limiting the necessity of copper to accumulate in the cytoplasm. To prevent cellular damage due to excess copper, bacteria and archaea have developed various copper detoxification strategies. In this chapter we attempt to give an overview of the mechanisms employed by bacteria and archaea to handle copper and the importance of the metal for cellular function as well as in the global nutrient cycle.

  1. Captain Cook, the Terrestrial Planet Finder and the search for extraterrestrial intelligence

    NASA Technical Reports Server (NTRS)

    Beichman, C.

    2002-01-01

    A recently completed NASA study has concluded that a Terrestrial Planet Finder could be launched within a decade to detect terrestrial planets around nearby stars. Such a mission, complemented by projects (Kepler and Eddington) that will provide statistical information on the frequency of Earth-sized planets in the habitable zone, will determine key terms in the Drake equation that describes the number of intelligent civilizations in the Universe.

  2. Providing a USSD location based clinic finder in South Africa: did it work?

    PubMed

    Parsons, Annie Neo; Timler, Dagmar

    2014-01-01

    A new mHealth service, Clinic Finder, was designed to provide a location-based service for any cellphone user in South Africa dialing a dedicated USSD string to find the nearest public primary health care facility. The service was funded by a European Union grant to Cell-Life to support the National Department of Health. Clinic Finder's aims were to provide a reliable and accurate service, and to assess both the most effective means of advertising the service as well as interest in the service. Users dialing the USSD string are asked to agree to geo-location (Vodacom and MTN users) or asked to enter their province, town and street (virtual network users and those choosing not to geo-locate). The service provider, AAT, sends the data to Cell-Life where an SMS with details of the nearest public primary health care facility is sent to the user by Cell-Life's open-source Communicate platform. The service was advertised on 3 days in 2014 using two different means: a newspaper ad on 20 May 2014 and Please Call Me ads on 30 July 2014 and 14 August 2014. 28.2% of unique users on 20 May 2014, 10.5% of unique users on 30 July 2014 and 92.8% of unique users on 14 August 2014 who agreed to geo-location successfully received SMSs. However, only 4.2%, 0.5%, and 2.4% of unique users responding to each advertisement who did not geo-locate then received an SMS. A small survey of users following the 20 May 2014 newspaper ad found overall interest in the idea of Clinic Finder, though unsuccessful users were more likely to dislike the service. The overall experience of using location based services and USSD for Clinic Finder suggests a need in the field of mHealth for wider availability of data on service usability and effectiveness.

  3. Examination of Prokaryotic Multipartite Genome Evolution through Experimental Genome Reduction

    PubMed Central

    diCenzo, George C.; MacLean, Allyson M.; Milunovic, Branislava; Golding, G. Brian; Finan, Turlough M.

    2014-01-01

    Many bacteria carry two or more chromosome-like replicons. This occurs in pathogens such as Vibrio cholerea and Brucella abortis as well as in many N2-fixing plant symbionts including all isolates of the alfalfa root-nodule bacteria Sinorhizobium meliloti. Understanding the evolution and role of this multipartite genome organization will provide significant insight into these important organisms; yet this knowledge remains incomplete, in part, because technical challenges of large-scale genome manipulations have limited experimental analyses. The distinct evolutionary histories and characteristics of the three replicons that constitute the S. meliloti genome (the chromosome (3.65 Mb), pSymA megaplasmid (1.35 Mb), and pSymB chromid (1.68 Mb)) makes this a good model to examine this topic. We transferred essential genes from pSymB into the chromosome, and constructed strains that lack pSymB as well as both pSymA and pSymB. This is the largest reduction (45.4%, 3.04 megabases, 2866 genes) of a prokaryotic genome to date and the first removal of an essential chromid. Strikingly, strains lacking pSymA and pSymB (ΔpSymAB) lost the ability to utilize 55 of 74 carbon sources and various sources of nitrogen, phosphorous and sulfur, yet the ΔpSymAB strain grew well in minimal salts media and in sterile soil. This suggests that the core chromosome is sufficient for growth in a bulk soil environment and that the pSymA and pSymB replicons carry genes with more specialized functions such as growth in the rhizosphere and interaction with the plant. These experimental data support a generalized evolutionary model, in which non-chromosomal replicons primarily carry genes with more specialized functions. These large secondary replicons increase the organism's niche range, which offsets their metabolic burden on the cell (e.g. pSymA). Subsequent co-evolution with the chromosome then leads to the formation of a chromid through the acquisition of functions core to all niches (e.g. p

  4. Accurate time delay technology in simulated test for high precision laser range finder

    NASA Astrophysics Data System (ADS)

    Chen, Zhibin; Xiao, Wenjian; Wang, Weiming; Xue, Mingxi

    2015-10-01

    With the continuous development of technology, the ranging accuracy of pulsed laser range finder (LRF) is higher and higher, so the maintenance demand of LRF is also rising. According to the dominant ideology of "time analog spatial distance" in simulated test for pulsed range finder, the key of distance simulation precision lies in the adjustable time delay. By analyzing and comparing the advantages and disadvantages of fiber and circuit delay, a method was proposed to improve the accuracy of the circuit delay without increasing the count frequency of the circuit. A high precision controllable delay circuit was designed by combining the internal delay circuit and external delay circuit which could compensate the delay error in real time. And then the circuit delay accuracy could be increased. The accuracy of the novel circuit delay methods proposed in this paper was actually measured by a high sampling rate oscilloscope actual measurement. The measurement result shows that the accuracy of the distance simulated by the circuit delay is increased from +/- 0.75m up to +/- 0.15m. The accuracy of the simulated distance is greatly improved in simulated test for high precision pulsed range finder.

  5. PPInterFinder--a mining tool for extracting causal relations on human proteins from literature.

    PubMed

    Raja, Kalpana; Subramani, Suresh; Natarajan, Jeyakumar

    2013-01-01

    One of the most common and challenging problem in biomedical text mining is to mine protein-protein interactions (PPIs) from MEDLINE abstracts and full-text research articles because PPIs play a major role in understanding the various biological processes and the impact of proteins in diseases. We implemented, PPInterFinder--a web-based text mining tool to extract human PPIs from biomedical literature. PPInterFinder uses relation keyword co-occurrences with protein names to extract information on PPIs from MEDLINE abstracts and consists of three phases. First, it identifies the relation keyword using a parser with Tregex and a relation keyword dictionary. Next, it automatically identifies the candidate PPI pairs with a set of rules related to PPI recognition. Finally, it extracts the relations by matching the sentence with a set of 11 specific patterns based on the syntactic nature of PPI pair. We find that PPInterFinder is capable of predicting PPIs with the accuracy of 66.05% on AIMED corpus and outperforms most of the existing systems. DATABASE URL: http://www.biomining-bu.in/ppinterfinder/

  6. A comparison of efficiency of manual and automatic fibres search with the Maxcan fibre finder.

    PubMed

    Monard Sermier, F; Massonnet, G; Buzzini, P; Fortini, A; Gason, F; De Wael, K; Rovas, P

    2006-07-13

    The aim of this work was to study the efficiency of automatic fibre searching with the Maxcan fibre finder (Cox Analytical Systems, Sweden) in comparison to manual searching. The influence of some parameters (color, thickness, background noise) on the results of a fibre search was considered. Eighteen experimental tapes with different target fibres and different background noises were prepared in the laboratory. Searching of fibres was performed manually and with the Maxcan fibre finder by different operators from four European laboratories. Two laboratories have the Maxcan fibre finder system and the two instruments were used and compared in this study. The results show that searching with the Maxcan is generally as efficient as manual searching, except for very pale or very dark fibres. Note that the tapes used for these experiments were prepared in laboratory, and are not completely representative of the tape that could be obtained in real cases. To generalize the results obtained, further research on real case samples would be necessary.

  7. LipidFinder: A computational workflow for discovery of lipids identifies eicosanoid-phosphoinositides in platelets

    PubMed Central

    O’Connor, Anne; Brasher, Christopher J.; Slatter, David A.; Meckelmann, Sven W.; Hawksworth, Jade I.; Allen, Stuart M.; O’Donnell, Valerie B.

    2017-01-01

    Accurate and high-quality curation of lipidomic datasets generated from plasma, cells, or tissues is becoming essential for cell biology investigations and biomarker discovery for personalized medicine. However, a major challenge lies in removing artifacts otherwise mistakenly interpreted as real lipids from large mass spectrometry files (>60 K features), while retaining genuine ions in the dataset. This requires powerful informatics tools; however, available workflows have not been tailored specifically for lipidomics, particularly discovery research. We designed LipidFinder, an open-source Python workflow. An algorithm is included that optimizes analysis based on users’ own data, and outputs are screened against online databases and categorized into LIPID MAPS classes. LipidFinder outperformed three widely used metabolomics packages using data from human platelets. We show a family of three 12-hydroxyeicosatetraenoic acid phosphoinositides (16:0/, 18:1/, 18:0/12-HETE-PI) generated by thrombin-activated platelets, indicating crosstalk between eicosanoid and phosphoinositide pathways in human cells. The software is available on GitHub (https://github.com/cjbrasher/LipidFinder), with full userguides.

  8. PubFinder: a tool for improving retrieval rate of relevant PubMed abstracts.

    PubMed

    Goetz, Thomas; von der Lieth, Claus-Wilhelm

    2005-07-01

    Since it is becoming increasingly laborious to manually extract useful information embedded in the ever-growing volumes of literature, automated intelligent text analysis tools are becoming more and more essential to assist in this task. PubFinder (www.glycosciences.de/tools/PubFinder) is a publicly available web tool designed to improve the retrieval rate of scientific abstracts relevant for a specific scientific topic. Only the selection of a representative set of abstracts is required, which are central for a scientific topic. No special knowledge concerning the query-syntax is necessary. Based on the selected abstracts, a list of discriminating words is automatically calculated, which is subsequently used for scoring all defined PubMed abstracts for their probability of belonging to the defined scientific topic. This results in a hit-list of references in the descending order of their likelihood score. The algorithms and procedures implemented in PubFinder facilitate the perpetual task for every scientist of staying up-to-date with current publications dealing with a specific subject in biomedicine.

  9. Prokaryotic Genomes from Microbes Online Database

    DOE Data Explorer

    Alm, Eric J.; Huang, Katherine H.; Price, Morgan N.; Koche, Richard P.; Keller, Keith; Dubchak, Inna L.; Arkin, Adam P.

    To describe the potential functions of genes, MicrobesOnline includes protein family analyses (from InterPro and COG), metabolic maps (from KEGG), links to research papers (from UniProt and PubMed), and operon predictions for every genome. To examine each gene's evolutionary history, MicrobesOnline includes precomputed phylogenetic trees for all the gene families. It displays gene trees with genomic context or it compares the gene tree to the species tree. The tools provided with MicrobesOnline allow users to: compute customized motifs, sequence alignments, and phylogenetic trees change expression patterns in metabolic maps annotate genes in various ways. A browse tree tool and a genome browser are available, along with specialized search capabilities. (Specialized Interface)

  10. Prokaryotic Argonautes - variations on the RNA interference theme

    PubMed Central

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

    2014-01-01

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

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

    PubMed

    Satoh, Soichirou; Mimuro, Mamoru; Tanaka, Ayumi

    2013-01-01

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

  12. Structure-function insights into prokaryotic and eukaryotic translation initiation.

    PubMed

    Myasnikov, Alexander G; Simonetti, Angelita; Marzi, Stefano; Klaholz, Bruno P

    2009-06-01

    Translation initiation is the rate-limiting and most complexly regulated step of protein synthesis in prokaryotes and eukaryotes. In the last few years, cryo-electron microscopy has provided several novel insights into the universal process of translation initiation. Structures of prokaryotic 30S and 70S ribosomal initiation complexes with initiator transfer RNA (tRNA), messenger RNA (mRNA), and initiation factors have recently revealed the mechanism of initiator tRNA recruitment to the assembling ribosomal machinery, involving molecular rearrangements of the ribosome and associated factors. First three-dimensional pictures of the particularly complex eukaryotic translation initiation machinery have been obtained, revealing how initiation factors tune the ribosome for recruiting the mRNA. A comparison of the available prokaryotic and eukaryotic structures shows that--besides significant differences--some key ribosomal features are universally conserved.

  13. Predation between prokaryotes and the origin of eukaryotes.

    PubMed

    Davidov, Yaacov; Jurkevitch, Edouard

    2009-07-01

    Accumulating data suggest that the eukaryotic cell originated from a merger of two prokaryotes, an archaeal host and a bacterial endosymbiont. However, since prokaryotes are unable to perform phagocytosis, the means by which the endosymbiont entered its host is an enigma. We suggest that a predatory or parasitic interaction between prokaryotes provides a reasonable explanation for this conundrum. According to the model presented here, the host in this interaction was an anaerobic archaeon with a periplasm-like space. The predator was a small (facultative) aerobic alpha-proteobacterium, which penetrated and replicated within the host periplasm, and later became the mitochondria. Plausible conditions under which this interaction took place and circumstances that may have led to the contemporary complex eukaryotic cell are discussed.

  14. ARC: automated resource classifier for agglomerative functional classification of prokaryotic proteins using annotation texts.

    PubMed

    Gnanamani, Muthiah; Kumar, Naveen; Ramachandran, Srinivasan

    2007-08-01

    Functional classification of proteins is central to comparative genomics. The need for algorithms tuned to enable integrative interpretation of analytical data is felt globally. The availability of a general,automated software with built-in flexibility will significantly aid this activity. We have prepared ARC (Automated Resource Classifier), which is an open source software meeting the user requirements of flexibility. The default classification scheme based on keyword match is agglomerative and directs entries into any of the 7 basic non-overlapping functional classes: Cell wall, Cell membrane and Transporters (C), Cell division (D), Information (I), Translocation (L), Metabolism (M), Stress(R), Signal and communication (S) and 2 ancillary classes: Others (O) and Hypothetical (H). The keyword library of ARC was built serially by first drawing keywords from Bacillus subtilis and Escherichia coli K12. In subsequent steps,this library was further enriched by collecting terms from archaeal representative Archaeoglobus fulgidus, Gene Ontology, and Gene Symbols. ARC is 94.04% successful on 6,75,663 annotated proteins from 348 prokaryotes. Three examples are provided to illuminate the current perspectives on mycobacterial physiology and costs of proteins in 333 prokaryotes. ARC is available at http://arc.igib.res.in.

  15. Isoprenoid-Based Biofuels: Homologous Expression and Heterologous Expression in Prokaryotes

    PubMed Central

    Phulara, Suresh Chandra; Chaturvedi, Preeti

    2016-01-01

    Enthusiasm for mining advanced biofuels from microbial hosts has increased remarkably in recent years. Isoprenoids are one of the highly diverse groups of secondary metabolites and are foreseen as an alternative to petroleum-based fuels. Most of the prokaryotes synthesize their isoprenoid backbone via the deoxyxylulose-5-phosphate pathway from glyceraldehyde-3-phosphate and pyruvate, whereas eukaryotes synthesize isoprenoids via the mevalonate pathway from acetyl coenzyme A (acetyl-CoA). Microorganisms do not accumulate isoprenoids in large quantities naturally, which restricts their application for fuel purposes. Various metabolic engineering efforts have been utilized to overcome the limitations associated with their natural and nonnatural production. The introduction of heterologous pathways/genes and overexpression of endogenous/homologous genes have shown a remarkable increase in isoprenoid yield and substrate utilization in microbial hosts. Such modifications in the hosts' genomes have enabled researchers to develop commercially competent microbial strains for isoprenoid-based biofuel production utilizing a vast array of substrates. The present minireview briefly discusses the recent advancement in metabolic engineering efforts in prokaryotic hosts for the production of isoprenoid-based biofuels, with an emphasis on endogenous, homologous, and heterologous expression strategies. PMID:27422837

  16. Using high-throughput sequencing to assess the impacts of treated and untreated wastewater discharge on prokaryotic communities in an urban river.

    PubMed

    Bai, Yaohui; Qi, Weixiao; Liang, Jinsong; Qu, Jiuhui

    2014-02-01

    In many megacities wastewater is an important source of surface water, particularly during drought periods. While changes in surface water chemistry associated with effluent inflow have generally been well-studied, few data have been collected on the effects to prokaryotic communities. The objective of this study was to explore the impacts of treated and untreated wastewater discharges on prokaryotic community in an urban river. High-throughput sequencing was conducted for analyzing the prokaryotic community composition and function in river water, treated wastewater and untreated wastewater. Results revealed that the prokaryotic community compositions in the upstream river reach were dominated by treated wastewater discharge. In the middle- and downstream river reaches, untreated effluent volumes are higher, thus affecting the structure of the prokaryotic community, promoting a rise in Cyanobacteria and Thaumarchaeota. Function annotation revealed a number of genes associated with xenobiotic metabolism and human diseases were observed in river and wastewater samples, suggesting wastewater discharge to river may pose a risk to human health. Quantitative real-time PCR results revealed that the treated and untreated wastewater discharges also affected the abundance of ammonia oxidation bacteria (AOB) and ammonia oxidation archaea (AOA) in river.

  17. Factors important for women who breastfeed in public: a content analysis of review data from FeedFinder

    PubMed Central

    Simpson, Emma; Garbett, Andrew; Comber, Rob; Balaam, Madeline

    2016-01-01

    Objective To examine how the breastfeeding experience is represented by users of FeedFinder (a mobile phone application for finding, reviewing and sharing places to breastfeed in public). Design Content analysis using FeedFinder database. Setting FeedFinder, UK, September 2013–June 2015. Methods Reviews obtained through FeedFinder over a period of 21 months were systematically coded using a conventional content analysis approach, average review scores were calculated for the rating criteria in FeedFinder (comfort, hygiene, privacy, baby facilities) and review texts were analysed for sentiment. We used data from Foursquare to describe the type of venues visited and cross-referenced the location of venues with the Indices of Multiple Deprivation. Results A total of 1757 reviews were analysed. Of all the reviews obtained, 80% of those were classified as positive, 15.4% were classified as neutral and 4.3% were classified as negative. Important factors that were discussed by women include facilities, service, level of privacy available and qualities of a venue. The majority of venues were classified as cafes (26.4%), shops (24.4%) and pubs (13.4%). Data on IMD were available for 1229 venues mapped within FeedFinder, 23% were located within the most deprived quintile and 16% were located in the least deprived quintile. Conclusions Women create content that is positive and informative when describing their breastfeeding experience in public. Public health bodies and business owners have the potential to use the data from FeedFinder to impact on service provision. Further work is needed to explore the demographic differences that may help to tailor public health interventions aimed at increasing breastfeeding rates in the UK. PMID:27797996

  18. Laser scanning methods and a phase comparison, modulated laser range finder for terrain sensing on a Mars roving vehicle. M.S. Thesis

    NASA Technical Reports Server (NTRS)

    Herb, G. T.

    1973-01-01

    Two areas of a laser range finder for a Mars roving vehicle are investigated: (1) laser scanning systems, and (2) range finder methods and implementation. Several ways of rapidly scanning a laser are studied. Two digital deflectors and a matrix of laser diodes, are found to be acceptable. A complete range finder scanning system of high accuracy is proposed. The problem of incident laser spot distortion on the terrain is discussed. The instrumentation for a phase comparison, modulated laser range finder is developed and sections of it are tested.

  19. Identification and functional analysis of a prokaryotic-type aspartate aminotransferase: implications for plant amino acid metabolism.

    PubMed

    de la Torre, Fernando; De Santis, Laura; Suárez, María Fernanda; Crespillo, Remedios; Cánovas, Francisco M

    2006-05-01

    In this paper, we report the identification of genes from pine (PpAAT), Arabidopsis (AtAAT) and rice (OsAAT) encoding a novel class of aspartate aminotransferase (AAT, EC 2.6.1.1) in plants. The enzyme is unrelated to other eukaryotic AATs from plants and animals but similar to bacterial enzymes. Phylogenetic analysis indicates that this prokaryotic-type AAT is closely related to cyanobacterial enzymes, suggesting it might have an endosymbiotic origin. Interestingly, most of the essential residues involved in the interaction with the substrate and the attachment of pyridoxal phosphate cofactor in the active site of the enzyme were conserved in the deduced polypeptide. The polypeptide is processed in planta to a mature subunit of 45 kDa that is immunologically distinct from the cytosolic, mitochondrial and chloroplastic isoforms of AAT previously characterized in plants. Functional expression of PpAAT sequences in Escherichia coli showed that the processed precursor is assembled into a catalytically active homodimeric holoenzyme that is strictly specific for aspartate. These atypical genes are predominantly expressed in green tissues of pine, Arabidopsis and rice, suggesting a key role of this AAT in nitrogen metabolism associated with photosynthetic activity. Moreover, immunological analyses revealed that the plant prokaryotic-type AAT is a nuclear-encoded chloroplast protein. This implies that two plastidic AAT co-exist in plants: a eukaryotic type previously characterized and the prokaryotic type described here. The respective roles of these two enzymes in plant amino acid metabolism are discussed.

  20. The mRNA of human cytoplasmic arginyl-tRNA synthetase recruits prokaryotic ribosomes independently.

    PubMed

    Yang, Fang; Ji, Quan-Quan; Ruan, Liang-Liang; Ye, Qing; Wang, En-Duo

    2014-07-25

    There are two isoforms of cytoplasmic arginyl-tRNA synthetase (hcArgRS) in human cells. The long form is a component of the multiple aminoacyl-tRNA synthetase complex, and the other is an N-terminal truncated form (NhcArgRS), free in the cytoplasm. It has been shown that the two forms of ArgRS arise from alternative translational initiation in a single mRNA. The short form is produced from the initiation at a downstream, in-frame AUG start codon. Interestingly, our data suggest that the alternative translational initiation of hcArgRS mRNA also takes place in Escherichia coli transformants. When the gene encoding full-length hcArgRS was overexpressed in E. coli, two forms of hcArgRS were observed. The N-terminal sequencing experiment identified that the short form was identical to the NhcArgRS in human cytoplasm. By constructing a bicistronic system, our data support that the mRNA encoding the N-terminal extension of hcArgRS has the capacity of independently recruiting E. coli ribosomes. Furthermore, two critical elements for recruiting prokaryotic ribosomes were identified, the “AGGA” core of the Shine-Dalgarno sequence and the “A-rich” sequence located just proximal to the alternative in-frame initiation site. Although the mechanisms of prokaryotic and eukaryotic translational initiation are distinct, they share some common features. The ability of the hcArgRS mRNA to recruit the prokaryotic ribosome may provide clues for shedding light on the mechanism of alternative translational initiation of hcArgRS mRNA in eukaryotic cells.

  1. Prokaryote community dynamics in anaerobic co-digestion of swine manure, rice straw and industrial clay residuals.

    PubMed

    Jiménez, Janet; Theuerl, Susanne; Bergmann, Ingo; Klocke, Michael; Guerra, Gilda; Romero-Romero, Osvaldo

    The aim of this study was to analyze the effect of the addition of rice straw and clay residuals on the prokaryote methane-producing community structure in a semi-continuously stirred tank reactor fed with swine manure. Molecular techniques, including terminal restriction fragment length polymorphism and a comparative nucleotide sequence analyses of the prokaryotic 16S rRNA genes, were performed. The results showed a positive effect of clay addition on methane yield during the co-digestion of swine manure and rice straw. At the digestion of swine manure, the bacterial phylum Firmicutes and the archaeal family Methanosarcinaceae, particularly Methanosarcina species, were predominant. During the co-digestion of swine manure and rice straw the microbial community changed, and with the addition of clay residual, the phylum Bacteroidetes predominated. The new nutritional conditions resulted in a shift in the archaeal family Methanosarcinaceae community as acetoclastic Methanosaeta species became dominant.

  2. PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces

    PubMed Central

    Saladin, Adrien; Rey, Julien; Thévenet, Pierre; Zacharias, Martin; Moroy, Gautier; Tufféry, Pierre

    2014-01-01

    Peptide–protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide–protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein surface, and we have found, as the result of a benchmark over 41 complexes, that the best poses overlap to some extent the experimental patch of interaction for close to 90% complexes. In addition, PEP-SiteFinder also returns a propensity index we have found informative about the confidence of the prediction. The PEP-SiteFinder web server is available at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder. PMID:24803671

  3. PEP-SiteFinder: a tool for the blind identification of peptide binding sites on protein surfaces.

    PubMed

    Saladin, Adrien; Rey, Julien; Thévenet, Pierre; Zacharias, Martin; Moroy, Gautier; Tufféry, Pierre

    2014-07-01

    Peptide-protein interactions are important to many processes of life, particularly for signal transmission or regulatory mechanisms. When no information is known about the interaction between a protein and a peptide, it is of interest to propose candidate sites of interaction at the protein surface, to assist the design of biological experiments to probe the interaction, or to serve as a starting point for more focused in silico approaches. PEP-SiteFinder is a tool that will, given the structure of a protein and the sequence of a peptide, identify protein residues predicted to be at peptide-protein interface. PEP-SiteFinder relies on the 3D de novo generation of peptide conformations given its sequence. These conformations then undergo a fast blind rigid docking on the complete protein surface, and we have found, as the result of a benchmark over 41 complexes, that the best poses overlap to some extent the experimental patch of interaction for close to 90% complexes. In addition, PEP-SiteFinder also returns a propensity index we have found informative about the confidence of the prediction. The PEP-SiteFinder web server is available at http://bioserv.rpbs.univ-paris-diderot.fr/PEP-SiteFinder.

  4. Reference Gene Validation for RT-qPCR, a Note on Different Available Software Packages

    PubMed Central

    De Spiegelaere, Ward; Dern-Wieloch, Jutta; Weigel, Roswitha; Schumacher, Valérie; Schorle, Hubert; Nettersheim, Daniel; Bergmann, Martin; Brehm, Ralph; Kliesch, Sabine; Vandekerckhove, Linos; Fink, Cornelia

    2015-01-01

    Background An appropriate normalization strategy is crucial for data analysis from real time reverse transcription polymerase chain reactions (RT-qPCR). It is widely supported to identify and validate stable reference genes, since no single biological gene is stably expressed between cell types or within cells under different conditions. Different algorithms exist to validate optimal reference genes for normalization. Applying human cells, we here compare the three main methods to the online available RefFinder tool that integrates these algorithms along with R-based software packages which include the NormFinder and GeNorm algorithms. Results 14 candidate reference genes were assessed by RT-qPCR in two sample sets, i.e. a set of samples of human testicular tissue containing carcinoma in situ (CIS), and a set of samples from the human adult Sertoli cell line (FS1) either cultured alone or in co-culture with the seminoma like cell line (TCam-2) or with equine bone marrow derived mesenchymal stem cells (eBM-MSC). Expression stabilities of the reference genes were evaluated using geNorm, NormFinder, and BestKeeper. Similar results were obtained by the three approaches for the most and least stably expressed genes. The R-based packages NormqPCR, SLqPCR and the NormFinder for R script gave identical gene rankings. Interestingly, different outputs were obtained between the original software packages and the RefFinder tool, which is based on raw Cq values for input. When the raw data were reanalysed assuming 100% efficiency for all genes, then the outputs of the original software packages were similar to the RefFinder software, indicating that RefFinder outputs may be biased because PCR efficiencies are not taken into account. Conclusions This report shows that assay efficiency is an important parameter for reference gene validation. New software tools that incorporate these algorithms should be carefully validated prior to use. PMID:25825906

  5. Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes.

    PubMed

    Kumar, Manjeet; Balaji, Petety V

    2011-05-01

    Glycosylation of proteins in prokaryotes has been known for the last few decades. Glycan structures and/or the glycosylation pathways have been experimentally characterized in only a small number of prokaryotes. Even this has become possible only during the last decade or so, primarily due to technological and methodological developments. Glycosylated proteins are diverse in their function and localization. Glycosylation has been shown to be associated with a wide range of biological phenomena. Characterization of the various types of glycans and the glycosylation machinery is critical to understand such processes. Such studies can help in the identification of novel targets for designing drugs, diagnostics, and engineering of therapeutic proteins. In view of this, the experimentally characterized pgl system of Campylobacter jejuni, responsible for N-linked glycosylation, has been used in this study to identify glycosylation loci in 865 prokaryotes whose genomes have been completely sequenced. Results from the present study show that only a small number of organisms have homologs for all the pgl enzymes and a few others have homologs for none of the pgl enzymes. Most of the organisms have homologs for only a subset of the pgl enzymes. There is no specific pattern for the presence or absence of pgl homologs vis-à-vis the 16S rRNA sequence-based phylogenetic tree. This may be due to differences in the glycan structures, high sequence divergence, horizontal gene transfer or non-orthologous gene displacement. Overall, the presence of homologs for pgl enzymes in a large number of organisms irrespective of their habitat, pathogenicity, energy generation mechanism, etc., hints towards the ubiquity of N-linked glycosylation in prokaryotes.

  6. TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases

    PubMed Central

    Riadi, Gonzalo; Medina-Moenne, Cristobal; Holmes, David S.

    2012-01-01

    Transposases (Tnps) are enzymes that participate in the movement of insertion sequences (ISs) within and between genomes. Genes that encode Tnps are amongst the most abundant and widely distributed genes in nature. However, they are difficult to predict bioinformatically and given the increasing availability of prokaryotic genomes and metagenomes, it is incumbent to develop rapid, high quality automatic annotation of ISs. This need prompted us to develop a web service, termed TnpPred for Tnp discovery. It provides better sensitivity and specificity for Tnp predictions than given by currently available programs as determined by ROC analysis. TnpPred should be useful for improving genome annotation. The TnpPred web service is freely available for noncommercial use. PMID:23251097

  7. A galinstan expansion femtosyringe for microinjection of eukaryotic organelles and prokaryotes.

    PubMed

    Knoblauch, M; Hibberd, J M; Gray, J C; van Bel, A J

    1999-09-01

    A galinstan expansion femtosyringe enables femtoliter to attoliter samples to be introduced into prokaryotes and subcellular compartments of eukaryotes. The method uses heat-induced expansion of galinstan (a liquid metal alloy of gallium, indium, and tin) within a glass syringe to expel samples through a tip diameter of about 0.1 microm. The narrow tip inflicts less damage than conventional capillaries, and the heat-induced expansion of the galinstan allows fine control over the rate of injection. We demonstrate injection of Lucifer Yellow and Lucifer Yellow-dextran conjugates into cyanobacteria, and into nuclei and chloroplasts of higher organisms. Injection of a plasmid containing the bla gene into the cyanobacterium Phormidium laminosum resulted in transformed ampicillin-resistant cultures. Green fluorescent protein was expressed in attached leaves of tobacco and Vicia faba following injection of DNA containing its gene into individual chloroplasts.

  8. Jamming prokaryotic cell-to-cell communications in a model biofilm.

    PubMed

    Timp, Winston; Mirsaidov, Utkur; Matsudaira, Paul; Timp, Gregory

    2009-04-07

    We report on the physical parameters governing prokaryotic cell-to-cell signaling in a model biofilm. The model biofilm is comprised of bacteria that are genetically engineered to transmit and receive quorum-sensing (QS) signals. The model is formed using arrays of time-shared, holographic optical traps in conjunction with microfluidics to precisely position bacteria, and then encapsulated within a hydrogel that mimics the extracellular matrix. Using fluorescent protein reporters functionally linked to QS genes, we assay the intercellular signaling. We find that there isn't a single cell density for which QS-regulated genes are induced or repressed. On the contrary, cell-to-cell signaling is largely governed by diffusion, and is acutely sensitive to mass-transfer to the surroundings and the cell location. These observations are consistent with the view that QS-signals act simply as a probe measuring mixing, flow, or diffusion in the microenvironment of the cell.

  9. A neural network gravitational arc finder based on the Mediatrix filamentation method

    NASA Astrophysics Data System (ADS)

    Bom, C. R.; Makler, M.; Albuquerque, M. P.; Brandt, C. H.

    2017-01-01

    Context. Automated arc detection methods are needed to scan the ongoing and next-generation wide-field imaging surveys, which are expected to contain thousands of strong lensing systems. Arc finders are also required for a quantitative comparison between predictions and observations of arc abundance. Several algorithms have been proposed to this end, but machine learning methods have remained as a relatively unexplored step in the arc finding process. Aims: In this work we introduce a new arc finder based on pattern recognition, which uses a set of morphological measurements that are derived from the Mediatrix filamentation method as entries to an artificial neural network (ANN). We show a full example of the application of the arc finder, first training and validating the ANN on simulated arcs and then applying the code on four Hubble Space Telescope (HST) images of strong lensing systems. Methods: The simulated arcs use simple prescriptions for the lens and the source, while mimicking HST observational conditions. We also consider a sample of objects from HST images with no arcs in the training of the ANN classification. We use the training and validation process to determine a suitable set of ANN configurations, including the combination of inputs from the Mediatrix method, so as to maximize the completeness while keeping the false positives low. Results: In the simulations the method was able to achieve a completeness of about 90% with respect to the arcs that are input into the ANN after a preselection. However, this completeness drops to 70% on the HST images. The false detections are on the order of 3% of the objects detected in these images. Conclusions: The combination of Mediatrix measurements with an ANN is a promising tool for the pattern-recognition phase of arc finding. More realistic simulations and a larger set of real systems are needed for a better training and assessment of the efficiency of the method.

  10. Parallel HOP: A Scalable Halo Finder for Massive Cosmological Data Sets

    NASA Astrophysics Data System (ADS)

    Skory, Stephen; Turk, Matthew J.; Norman, Michael L.; Coil, Alison L.

    2010-11-01

    Modern N-body cosmological simulations contain billions (109) of dark matter particles. These simulations require hundreds to thousands of gigabytes of memory and employ hundreds to tens of thousands of processing cores on many compute nodes. In order to study the distribution of dark matter in a cosmological simulation, the dark matter halos must be identified using a halo finder, which establishes the halo membership of every particle in the simulation. The resources required for halo finding are similar to the requirements for the simulation itself. In particular, simulations have become too extensive to use commonly employed halo finders, such that the computational requirements to identify halos must now be spread across multiple nodes and cores. Here, we present a scalable-parallel halo finding method called Parallel HOP for large-scale cosmological simulation data. Based on the halo finder HOP, it utilizes message passing interface and domain decomposition to distribute the halo finding workload across multiple compute nodes, enabling analysis of much larger data sets than is possible with the strictly serial or previous parallel implementations of HOP. We provide a reference implementation of this method as a part of the toolkit "yt", an analysis toolkit for adaptive mesh refinement data that include complementary analysis modules. Additionally, we discuss a suite of benchmarks that demonstrate that this method scales well up to several hundred tasks and data sets in excess of 20003 particles. The Parallel HOP method and our implementation can be readily applied to any kind of N-body simulation data and is therefore widely applicable.

  11. The prokaryotic FAD synthetase family: a potential drug target.

    PubMed

    Serrano, Ana; Ferreira, Patricia; Martínez-Júlvez, Marta; Medina, Milagros

    2013-01-01

    Disruption of cellular production of the flavin cofactors, flavin adenine mononucleotide (FMN) and flavin adenine dinucleotide(FAD) will prevent the assembly of a large number of flavoproteins and flavoenzymes involved in key metabolic processes in all types of organisms. The enzymes responsible for FMN and FAD production in prokaryotes and eukaryotes exhibit various structural characteristics to catalyze the same chemistry, a fact that converts the prokaryotic FAD synthetase (FADS) in a potential drug target for the development of inhibitors endowed with anti-pathogenic activity. The first step before searching for selective inhibitors of FADS is to understand the structural and functional mechanisms for the riboflavin kinase and FMN adenylyltransferase activities of the prokaryotic enzyme, and particularly to identify their differential functional characteristics with regard to the enzymes performing similar functions in other organisms, particularly humans. In this paper, an overview of the current knowledge of the structure-function relationships in prokaryotic FADS has been presented, as well as of the state of the art in the use of these enzymes as drug targets.

  12. Calcium binding proteins and calcium signaling in prokaryotes.

    PubMed

    Domínguez, Delfina C; Guragain, Manita; Patrauchan, Marianna

    2015-03-01

    With the continued increase of genomic information and computational analyses during the recent years, the number of newly discovered calcium binding proteins (CaBPs) in prokaryotic organisms has increased dramatically. These proteins contain sequences that closely resemble a variety of eukaryotic calcium (Ca(2+)) binding motifs including the canonical and pseudo EF-hand motifs, Ca(2+)-binding β-roll, Greek key motif and a novel putative Ca(2+)-binding domain, called the Big domain. Prokaryotic CaBPs have been implicated in diverse cellular activities such as division, development, motility, homeostasis, stress response, secretion, transport, signaling and host-pathogen interactions. However, the majority of these proteins are hypothetical, and only few of them have been studied functionally. The finding of many diverse CaBPs in prokaryotic genomes opens an exciting area of research to explore and define the role of Ca(2+) in organisms other than eukaryotes. This review presents the most recent developments in the field of CaBPs and novel advancements in the role of Ca(2+) in prokaryotes.

  13. Terrestrial Planet Finder Coronagraph 2005: Overview of Technology Development and System Design Studies

    NASA Technical Reports Server (NTRS)

    Ford, Virginia G.

    2005-01-01

    Technology research, design trades, and modeling and analysis guide the definition of a Terrestrial Planet Finder Coronagraph Mission that will search for and characterize earth-like planets around near-by stars. Operating in visible wavebands, this mission will use coronagraphy techniques to suppress starlight to enable capturing and imaging the reflected light from a planet orbiting in the habitable zone of its parent star. The light will be spectrally characterized to determine the presence of life-indicating chemistry in the planet atmosphere.

  14. SciFinder Scholar 2006: an empirical analysis of research topic query processing.

    PubMed

    Wagner, A Ben

    2006-01-01

    Topical search queries in SciFinder Scholar are processed through an extensive set of natural language processing algorithms that greatly enhance the relevance and comprehensiveness of the search results. Little detailed documentation on these algorithms has been published. However, a careful examination of the highlighted hit terms coupled with a comparison of results from small variations in query language reveal much additional, useful information about these algorithms. An understanding of how these algorithms work can lead to better search results and explain many unexpected results, including differing hit counts for singular versus plural query words and phrases.

  15. Tumor malignancy is engaged to prokaryotic homolog toolbox.

    PubMed

    Fernandes, Janaina; Guedes, Patrícia G; Lage, Celso Luiz S; Rodrigues, Juliany Cola F; Lage, Claudia de Alencar S

    2012-04-01

    Cancer cells display high proliferation rates and survival provided by high glycolysis, chemoresistance and radioresistance, metabolic features that appear to be activated with malignancy, and seemed to have arisen as early in evolution as in unicellular/prokaryotic organisms. Based on these assumptions, we hypothesize that aggressive phenotypes found in malignant cells may be related to acquired unicellular behavior, launched within a tumor when viral and prokaryotic homologs are overexpressed performing likely robust functions. The ensemble of these expressed viral and prokaryotic close homologs in the proteome of a tumor tissue gives them advantage over normal cells. To assess the hypothesis validity, sequences of human proteins involved in apoptosis, energetic metabolism, cell mobility and adhesion, chemo- and radio-resistance were aligned to homologs present in other life forms, excluding all eukaryotes, using PSI-BLAST, with further corroboration from data available in the literature. The analysis revealed that selected sequences of proteins involved in apoptosis and tumor suppression (as p53 and pRB) scored non-significant (E-value>0.001) with prokaryotic homologs; on the other hand, human proteins involved in cellular chemo- and radio-resistance scored highly significant with prokaryotic and viral homologs (as catalase, E-value=zero). We inferred that such upregulated and/or functionally activated proteins in aggressive malignant cells represent a toolbox of modern human homologs evolved from a similar key set that have granted survival of ancient prokaryotes against extremely harsh environments. According to what has been discussed along this analysis, high mutation rates usually hit hotspots in important conserved protein domains, allowing uncontrolled expansion of more resistant, death-evading malignant clones. That is the case of point mutations in key viral proteins affording viruses escape to chemotherapy, and human homologs of such retroviral

  16. Rapid quantification and taxonomic classification of environmentalDNA from both prokaryotic and eukaryotic origins using a microarray

    SciTech Connect

    DeSantis, Todd Z.; Stone, Carol E.; Murray, Sonya R.; Moberg,Jordan P.; Andersen, Gary L.

    2005-02-22

    A microarray has been designed using 62,358 probes matched to both prokaryotic and eukaryotic small-subunit ribosomal RNA genes. The array categorized environmental DNA to specific phylogenetic clusters in under 9 h. To a background of DNA generated from natural outdoor aerosols, known quantities of rRNA gene copies from distinct organisms were added producing corresponding hybridization intensity scores that correlated well with their concentrations (r=0.917). Reproducible differences in microbial community composition were observed by altering the genomic DNA extraction method. Notably, gentle extractions produced peak intensities for Mycoplasmatales and Burkholderiales, whereas a vigorous disruption produced peak intensities for Vibrionales,Clostridiales, and Bacillales.

  17. The Frequency of Internal Shine-Dalgarno-like Motifs in Prokaryotes.

    PubMed

    Diwan, Gaurav D; Agashe, Deepa

    2016-06-14

    In prokaryotes, translation initiation typically depends on complementary binding between a G-rich Shine-Dalgarno (SD) motif in the 5' untranslated region of mRNAs, and the 3' tail of the 16S ribosomal RNA (the anti-SD sequence). In some cases, internal SD-like motifs in the coding region generate "programmed" ribosomal pauses that are beneficial for protein folding or accurate targeting. On the other hand, such pauses can also reduce protein production, generating purifying selection against internal SD-like motifs. This selection should be stronger in GC-rich genomes that are more likely to harbor the G-rich SD motif. However, the nature and consequences of selection acting on internal SD-like motifs within genomes and across species remains unclear. We analyzed the frequency of SD-like hexamers in the coding regions of 284 prokaryotes (277 with known anti-SD sequences and 7 without a typical SD mechanism). After accounting for GC content, we found that internal SD-like hexamers are avoided in 230 species, including three without a typical SD mechanism. The degree of avoidance was higher in GC-rich genomes, mesophiles, and N-terminal regions of genes. In contrast, 54 species either showed no signature of avoidance or were enriched in internal SD-like motifs. C-terminal gene regions were relatively enriched in SD-like hexamers, particularly for genes in operons or those followed closely by downstream genes. Together, our results suggest that the frequency of internal SD-like hexamers is governed by multiple factors including GC content and genome organization, and further empirical work is necessary to understand the evolution and functional roles of these motifs.

  18. Keeping the Wolves at Bay: Antitoxins of Prokaryotic Type II Toxin-Antitoxin Systems

    PubMed Central

    Chan, Wai Ting; Espinosa, Manuel; Yeo, Chew Chieng

    2016-01-01

    In their initial stages of discovery, prokaryotic toxin-antitoxin (TA) systems were confined to bacterial plasmids where they function to mediate the maintenance and stability of usually low- to medium-copy number plasmids through the post-segregational killing of any plasmid-free daughter cells that developed. Their eventual discovery as nearly ubiquitous and repetitive elements in bacterial chromosomes led to a wealth of knowledge and scientific debate as to their diversity and functionality in the prokaryotic lifestyle. Currently categorized into six different types designated types I–VI, type II TA systems are the best characterized. These generally comprised of two genes encoding a proteic toxin and its corresponding proteic antitoxin, respectively. Under normal growth conditions, the stable toxin is prevented from exerting its lethal effect through tight binding with the less stable antitoxin partner, forming a non-lethal TA protein complex. Besides binding with its cognate toxin, the antitoxin also plays a role in regulating the expression of the type II TA operon by binding to the operator site, thereby repressing transcription from the TA promoter. In most cases, full repression is observed in the presence of the TA complex as binding of the toxin enhances the DNA binding capability of the antitoxin. TA systems have been implicated in a gamut of prokaryotic cellular functions such as being mediators of programmed cell death as well as persistence or dormancy, biofilm formation, as defensive weapons against bacteriophage infections and as virulence factors in pathogenic bacteria. It is thus apparent that these antitoxins, as DNA-binding proteins, play an essential role in modulating the prokaryotic lifestyle whilst at the same time preventing the lethal action of the toxins under normal growth conditions, i.e., keeping the proverbial wolves at bay. In this review, we will cover the diversity and characteristics of various type II TA antitoxins. We shall

  19. Validation of reference genes for RT-qPCR analysis in Herbaspirillum seropedicae.

    PubMed

    Pessoa, Daniella Duarte Villarinho; Vidal, Marcia Soares; Baldani, José Ivo; Simoes-Araujo, Jean Luiz

    2016-08-01

    The RT-qPCR technique needs a validated set of reference genes for ensuring the consistency of the results from the gene expression. Expression stabilities for 9 genes from Herbaspirillum seropedicae, strain HRC54, grown with different carbon sources were calculated using geNorm and NormFinder, and the gene rpoA showed the best stability values.

  20. PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses.

    PubMed

    Lanfear, Robert; Frandsen, Paul B; Wright, April M; Senfeld, Tereza; Calcott, Brett

    2017-03-01

    PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many new methods and features. These include the ability to analyze morphological datasets, new methods to analyze genome-scale datasets, new output formats to facilitate interoperability with downstream software, and many new models of molecular evolution. PartitionFinder 2 is freely available under an open source license and works on Windows, OSX, and Linux operating systems. It can be downloaded from www.robertlanfear.com/partitionfinder. The source code is available at https://github.com/brettc/partitionfinder.

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

    PubMed Central

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

    2013-01-01

    Despite the recent and significant increase in the study of aquatic microbial communities, little is known about the microbial diversity of complex ecosystems such as running waters. This study investigated the biodiversity of biofilm communities formed in a river with 454 Sequencing™. This river has the particularity of integrating both organic and microbiological pollution, as receiver of agricultural pollution in its upstream catchment area and urban pollution through discharges of the wastewater treatment plant of the town of Billom. Different regions of the small subunit (SSU) ribosomal RNA gene were targeted using nine pairs of primers, either universal or specific for bacteria, eukarya, or archaea. Our aim was to characterize the widest range of rDNA sequences using different sets of polymerase chain reaction (PCR) primers. A first look at reads abundance revealed that a large majority (47–48%) were rare sequences (<5 copies). Prokaryotic phyla represented the species richness, and eukaryotic phyla accounted for a small part. Among the prokaryotic phyla, Proteobacteria (beta and alpha) predominated, followed by Bacteroidetes together with a large number of nonaffiliated bacterial sequences. Bacillariophyta plastids were abundant. The remaining bacterial phyla, Verrucomicrobia and Cyanobacteria, made up the rest of the bulk biodiversity. The most abundant eukaryotic phyla were annelid worms, followed by Diatoms, and Chlorophytes. These latter phyla attest to the abundance of plastids and the importance of photosynthetic activity for the biofilm. These findings highlight the existence and plasticity of multiple trophic levels within these complex biological systems. PMID:23520129

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

    PubMed

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

    2013-06-01

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

  3. SigMol: repertoire of quorum sensing signaling molecules in prokaryotes.

    PubMed

    Rajput, Akanksha; Kaur, Karambir; Kumar, Manoj

    2016-01-04

    Quorum sensing is a widespread phenomenon in prokaryotes that helps them to communicate among themselves and with eukaryotes. It is driven through quorum sensing signaling molecules (QSSMs) in a density dependent manner that assists in numerous biological functions like biofilm formation, virulence factors secretion, swarming motility, bioluminescence, etc. Despite immense implications, dedicated resources of QSSMs are lacking. Therefore, we have developed SigMol (http://bioinfo.imtech.res.in/manojk/sigmol), a specialized repository of these molecules in prokaryotes. SigMol harbors information on QSSMs pertaining to different quorum sensing signaling systems namely acylated homoserine lactones (AHLs), diketopiperazines (DKPs), 4-hydroxy-2-alkylquinolines (HAQs), diffusible signal factors (DSFs), autoinducer-2 (AI-2) and others. Database contains 1382: entries of 182: unique signaling molecules from 215: organisms. It encompasses biological as well as chemical aspects of signaling molecules. Biological information includes genes, preliminary bioassays, identification assays and applications, while chemical detail comprises of IUPAC name, SMILES and structure. We have provided user-friendly browsing and searching facilities for easy data retrieval and comparison. We have gleaned information of diverse QSSMs reported in literature at a single platform 'SigMol'. This comprehensive resource will assist the scientific community in understanding intraspecies, interspecies or interkingdom networking and further help to unfold different facets of quorum sensing and related therapeutics.

  4. Prokaryotic complex of newly formed soils on nepheline-containing industrial waste

    NASA Astrophysics Data System (ADS)

    Evdokimova, G. A.; Kalmykova, V. V.

    2010-06-01

    The characteristics are given of the prokaryotic complex participating in the processes of the primary soil formation on nepheline-containing waste and depending on the time of the waste disposal and degree of reclamation. The total population density of the bacteria determined with the method of fluorescent microscopy in “pure” sand ranged within 0.34—0.60 billion CFU/g soil; in the reclaimed sand under different vegatation communities, from 2.6 to 7.2 billion CFU/g soil. Gram-positive bacteria dominate in the prokaryotic complex of the nepheline sands, whereas the Grarrmegative ones dominate in the zonal soils. The bacteria predominating in the nepheline sands were classified on the basis of the comparative analysis of the nucleotide sequences in the 16S rRNA genes within the Actinobacteria class (Arthrobacter boritolerans, A. ramosus, Rhodococcusfascians, Micrococcus luteus, and Streptomyces spp.). The evolution of the microbial community in the nepheline sands in the course of their reclamation and in the course of their overgrowing by plants proceeds in way toward the microbial communities of the zonal soils on moraine deposits.

  5. An epitope tagged mammalian/prokaryotic expression vector with positive selection of cloned inserts.

    PubMed

    Schneider, S; Georgiev, O; Buchert, M; Adams, M T; Moelling, K; Hovens, C M

    1997-09-15

    A dual eukaryotic/prokaryotic expression vector has been developed which combines the features of positive selection for cloned inserts along with the production of an epitope-tagged cDNA insert by transient transfection in mammalian cells as well as high level induced expression in E. coli cells harbouring T7 RNA polymerase. This vector, pZilch, has two MCSs flanking a mutant E. coli phenylalanyl-tRNA synthetase gene, pheS, which when expressed in combination with the phenylalanine analog p-CI-Phe, results in termination of host cell protein synthesis. Cloning of inserts using unique sites in the flanking MCS regions results in loss of the pZilch pheS allele and hence permits growth of colonies harbouring recombinants on p-Cl-Phe plates. Additional features of the vector include an optimal Kozak consensus sequence for high level eukaryotic cell expression and an efficient prokaryotic translation initiation site in frame and downstream from the eukaryotic initiation site. Recombinant proteins can be produced with an N-terminal FLAG epitope which can be removed via a specific protease cleavage site. Flanking T7 and SP6 RNA polymerase promoter sites permit in vitro transcription and translation of cloned inserts. A derivative of the vector has also been constructed enabling nuclear accumulation of the tagged proteins via an SV40 nuclear localisation signal upstream of the 5' MCS.

  6. Evolution and Distribution of C7-Cyclitol Synthases in Prokaryotes and Eukaryotes.

    PubMed

    Osborn, Andrew R; Kean, Kelsey M; Alseud, Khaled M; Almabruk, Khaled H; Asamizu, Shumpei; Lee, Janet A; Karplus, P Andrew; Mahmud, Taifo

    2017-02-17

    2-Epi-5-epi-valiolone synthase (EEVS), a C7-sugar phosphate cyclase (SPC) homologous to 3-dehydroquinate synthase (DHQS), was discovered during studies of the biosynthesis of the C7N-aminocyclitol family of natural products. EEVS was originally thought to be present only in certain actinomycetes, but analyses of genome sequences showed that it is broadly distributed in both prokaryotes and eukaryotes, including vertebrates. Another SPC, desmethyl-4-deoxygadusol synthase (DDGS), was later discovered as being involved in the biosynthesis of mycosporine-like amino acid sunscreen compounds. Current database annotations are quite unreliable, with many EEVSs reported as DHQS, and most DDGSs reported as EEVS, DHQS, or simply hypothetical proteins. Here, we identify sequence features useful for distinguishing these enzymes, report a crystal structure of a representative DDGS showing the high similarity of the EEVS and DDGS enzymes, identify notable active site differences, and demonstrate the importance of two of these active site residues for catalysis by point mutations. Further, we functionally characterized two representatives of a distinct clade equidistant from known EEVS and known DDGS groups and show them to be authentic EEVSs. Moreover, we document and discuss the distribution of genes that encode EEVS and DDGS in various prokaryotes and eukaryotes, including pathogenic bacteria, plant symbionts, nitrogen-fixing bacteria, myxobacteria, cyanobacteria, fungi, stramenopiles, and animals, suggesting their broad potential biological roles in nature.

  7. Identification of SmtB/ArsR cis elements and proteins in archaea using the Prokaryotic InterGenic Exploration Database (PIGED)

    PubMed Central

    Bose, Michael; Slick, David; Sarto, Mickey J.; Roberts, David; Roberts, Jacqueline; Barber, Robert D.

    2006-01-01

    Microbial genome sequencing projects have revealed an apparently wide distribution of SmtB/ArsR metal-responsive transcriptional regulators among prokaryotes. Using a position-dependent weight matrix approach, prokaryotic genome sequences were screened for SmtB/ArsR DNA binding sites using data derived from intergenic sequences upstream of orthologous genes encoding these regulators. Sixty SmtB/ArsR operators linked to metal detoxification genes, including nine among various archaeal species, are predicted among 230 annotated and draft prokaryotic genome sequences. Independent multiple sequence alignments of putative operator sites and corresponding winged helix-turn-helix motifs define sequence signatures for the DNA binding activity of this SmtB/ArsR subfamily. Prediction of an archaeal SmtB/ArsR based upon these signature sequences is confirmed using purified Methanosarcina acetivorans C2A protein and electrophoretic mobility shift assays. Tools used in this study have been incorporated into a web application, the Prokaryotic InterGenic Exploration Database (PIGED; http://bioinformatics.uwp.edu/~PIGED/home.htm), facilitating comparable studies. Use of this tool and establishment of orthology based on DNA binding signatures holds promise for deciphering potential cellular roles of various archaeal winged helix-turn-helix transcriptional regulators. PMID:16877320

  8. Viral Regulation of Prokaryotic Carbon Metabolism in a Hypereutrophic Freshwater Reservoir Ecosystem (Villerest, France)

    PubMed Central

    Pradeep Ram, Angia Sriram; Colombet, Jonathan; Perriere, Fanny; Thouvenot, Antoine; Sime-Ngando, Télesphore

    2016-01-01

    The current consensus concerning the viral regulation of prokaryotic carbon metabolism is less well-studied, compared to substrate availability. We explored the seasonal and vertical distribution of viruses and its relative influence on prokaryotic carbon metabolism in a hypereutrophic reservoir, Lake Villerest (France). Flow cytometry and transmission electron microscopy (TEM) analyses to determine viral abundance (VA; range = 6.1–63.5 × 107 ml-1) and viral infection rates of prokaryotes (range = 5.3–32%) respectively suggested that both the parameters varied more significantly with depths than with seasons. Prokaryotic growth efficiency (PGE, considered as a proxy of prokaryotic carbon metabolism) calculated from prokaryotic production and respiration measurements (PGE = prokaryotic production/[prokaryotic production + prokaryotic respiration] × 100) varied from 14 to 80% across seasons and depths. Viruses through selective lyses had antagonistic impacts on PGE by regulating key prokaryotic metabolic processes (i.e., production and respiration). Higher viral lysis accompanied by higher respiration rates and lower PGE in the summer (mean = 22.9 ± 10.3%) than other seasons (mean = 59.1 ± 18.6%), led to significant loss of carbon through bacterial-viral loop and shifted the reservoir system to net heterotrophy. Our data therefore suggests that the putative adverse impact of viruses on the growth efficiency of the prokaryotic community can have strong implications on nutrient flux patterns and on the overall ecosystem metabolism in anthropogenic dominated aquatic systems such as Lake Villerest. PMID:26903963

  9. Surging Seas Risk Finder: A Tool for Local-Scale Flood Risk Assessments in Coastal Cities

    NASA Astrophysics Data System (ADS)

    Kulp, S. A.; Strauss, B.

    2015-12-01

    Local decision makers in coastal cities require accurate, accessible, and thorough assessments of flood exposure risk within their individual municipality, in their efforts to mitigate against damage due to future sea level rise. To fill this need, we have developed Climate Central's Surging Seas Risk Finder, an interactive data toolkit which presents our sea level rise and storm surge analysis for every coastal town, city, county, and state within the USA. Using this tool, policy makers can easily zoom in on their local place of interest to receive a detailed flood risk assessment, which synthesizes a wide range of features including total population, socially vulnerable population, housing, property value, road miles, power plants, schools, hospitals, and many other critical facilities. Risk Finder can also be used to identify specific points of interest in danger of exposure at different flood levels. Additionally, this tool provides localized storm surge probabilities and sea level rise projections at tidal gauges along the coast, so that users can quickly understand the risk of flooding in their area over the coming decades.

  10. Life Finder Detectors: An Overview of Detector Technologies for Detecting Life on Other Worlds

    NASA Astrophysics Data System (ADS)

    Rauscher, Bernard J.; Domagal-Goldman, Shawn; Greenhouse, Matthew A.; Hsieh, Wen-Ting; McElwain, Michael W.; Moseley, Samuel H.; Noroozian, Omid; Norton, Tim; Kutyrev, Alexander; Rinehart, Stephen; stock, Joseph

    2015-01-01

    Future large space telescopes will seek evidence for life on other worlds by searching for spectroscopic biosignatures. Atmospheric biosignature gases include oxygen, ozone, water vapor, and methane. Non-biological gases, including carbon monoxide and carbon dioxide, are important for discriminating false positives. All of these gases imprint spectroscopic features in the UV through mid-IR that are potentially detectable using future space based coronagraphs or star shades for starlight suppression.Direct spectroscopic biosignature detection requires sensors capable of robustly measuring photon arrival rates on the order of 10 per resolution element per hour. Photon counting is required for some wavefront sensing and control approaches to achieve the requisite high contrast ratios. We review life finder detector technologies that either exist today, or are under development, that have the potential to meet these challenging requirements. We specifically highlight areas where more work or development is needed.Life finder detectors will be invaluable for a wide variety of other major science programs. Because of its cross cutting nature; UV, optical, and infrared (UVOIR) detector development features prominently in the 2010 National Research Council Decadal Survey, 'New Worlds, New Horizons in Astronomy and Astrophysics', and the NASA Cosmic Origins Program Technology Roadmap.

  11. Relevance and feasibility of Diagnostics Subsystems in LISA PathFinder and LISA

    NASA Astrophysics Data System (ADS)

    Lobo, Alberto; Grimani, Catia; Canizares, Priscilla; Chmeissani, Mokhtar; Diaz-Aguilo, Marc; Conchillo, Aleix; Gesa, Lluis; Lloro, Ivan; Mateos, Ignacio; Nofrarias, Miquel; Ramos-Castro, Juan; Sanjuan, Josep; Sopuerta, Carlos

    LISA PathFinder will fly equipped with a Diagnostics Subsystem which includes: 1) a Radi-ation Monitor, providing almost real time charged particle counting and spectral resolution, 2) a thermal diagnostics set with high sensitivity temperature sensors and precision heaters, and 3) four fluxgate vector magnetometers plus a pair of induction coils. The role of this in-strumentation in LISA PathFinder is to provide the necessary tools to evaluate the effect of charging, temperature and magnetic fluctuations on the interferometer readout. The use of this is to understand how the mentioned fluctuations in the LTP (LISA Technology Package) can be modelled, then use the measured data to quantify their contribution to the overall LTP noise. In this presentation we will review the LPF Diagnostics System, recently delivered for LTP and spacecraft integration. We will also make some considerations on the meaning of the diagnostics for the future LISA, and propose lines of action to meet the more severe requirements which LISA will impose on environmental conditions.

  12. Monoblock laser for a low-cost, eyesafe, microlaser range finder.

    PubMed

    Nettleton, J E; Schilling, B W; Barr, D N; Lei, J S

    2000-05-20

    A small, lightweight, low-cost prototype laser has been developed for use in a microlaser range finder (muLRF). The laser design is based on a flash-lamp-pumped, Nd:YAG laser with a Cr(4+) passive Q switch. The design incorporates a monolithic potassium titanyl arsenide (KTA) optical parametric oscillator (OPO) in an intracavity configuration, producing output at 1.54 mum. Precisely cut, properly coated crystals make up the laser resonator, reducing the number of components and enabling laser oscillation with the simplest of alignment fixtures. The 1.54-mum laser cavity consists of only four rectangular-shaped crystals: a Nd:YAG laser rod, a Nd:YAG endcap, a Cr(4+) Q switch, and a KTA OPO. Along with a ceramic laser pallet and a flash lamp, these six components make up a prototype monoblock (essentially a one-piece) laser transmitter. Several of these simple prototypes have been built and tested, giving a nominal output of >3.0 mJ at 1.54 mum with a 27-ns pulse width. The transmitter was incorporated into a breadboard laser range finder, and successful ranging operations were performed to targets at ranges in excess of 3 km.

  13. Fat Finders

    ERIC Educational Resources Information Center

    Christie-Blick, Kottie

    2006-01-01

    Every day the media bombards the nation with concern over childhood obesity. More American children than ever before are developing health problems related to their eating habits and lack of exercise. The classroom is the perfect place to deal with this national crisis by speaking directly to the children. If children could become more aware of…

  14. Genome Data from DOOR: a Database for prOkaryotic OpeRons

    DOE Data Explorer

    DOOR (Database of prOkaryotic OpeRons) is an operon database developed by Computational Systems Biology Lab (CSBL) at University of Georgia. Although the operons in the database are based on prediction, there are some unique features. These are: • A algorithm is consistently best at all aspects including sensitivity and specificity for both true positives and true negatives, and the overall accuracy reaches 90 percent. The prediction algorithm is based on this paper: P. Dam, V. Olman, K. Harris, Z. Su, Y. Xu., Operon prediction using both genome-specific and general genomic information, Nucleic Acids Res., 35(1):288-98, 2007 • DOOR provides one of the largest data sets of operon information available to the public. DOOR provides operons for 675 prokaryotic genomes. Although most of operons in DOOR are not verified by experiments, the creators are also trying to provide some limited literature information, which is extracted from ODB. They emphasize that if the users are looking for strictly experimentally verified operons, they should look into DBTBS and RegulonDB first. • Operons which include RNA genes, which are rarely seen in other operon databases especially for predicted operon databases • Defined the similarity scores between operons, which is based on weighted maximum matching between operons. Similar operon groups can be used to predict accurate orthologous genes,and their upstream regions can be used to find the consensus binding motifs. • Integration of two motif finding programs in the database: MEME and CUBIC. DOOR provides an Organism View for browsing, a gene search tool, an operon search tool, and the operon prediction interface.[Text taken and edited from http://csbl1.bmb.uga.edu/OperonDB/tutorial.php

  15. Nonmagnetotactic multicellular prokaryotes from low-saline, nonmarine aquatic environments and their unusual negative phototactic behavior.

    PubMed

    Lefèvre, Christopher T; Abreu, Fernanda; Lins, Ulysses; Bazylinski, Dennis A

    2010-05-01

    Magnetotactic multicellular prokaryotes (MMPs) are unique magnetotactic bacteria of the Deltaproteobacteria class and the first found to biomineralize the magnetic mineral greigite (Fe(3)S(4)). Thus far they have been reported only from marine habitats. We questioned whether MMPs exist in low-saline, nonmarine environments. MMPs were observed in samples from shallow springs in the Great Boiling Springs geothermal field and Pyramid Lake, both located in northwestern Nevada. The temperature at all sites was ambient, and salinities ranged from 5 to 11 ppt. These MMPs were not magnetotactic and did not contain magnetosomes (called nMMPs here). nMMPs ranged from 7 to 11 microm in diameter, were composed of about 40 to 60 Gram-negative cells, and were motile by numerous flagella that covered each cell on one side, characteristics similar to those of MMPs. 16S rRNA gene sequences of nMMPs show that they form a separate phylogenetic branch within the MMP group in the Deltaproteobacteria class, probably representing a single species. nMMPs exhibited a negative phototactic behavior to white light and to wavelengths of < or =480 nm (blue). We devised a "light racetrack" to exploit this behavior, which was used to photoconcentrate nMMPs for specific purposes (e.g., DNA extraction) even though their numbers were low in the sample. Our results show that the unique morphology of the MMP is not restricted to marine and magnetotactic prokaryotes. Discovery of nonmagnetotactic forms of the MMP might support the hypothesis that acquisition of the magnetosome genes involves horizontal gene transfer. To our knowledge, this is the first report of phototaxis in bacteria of the Deltaproteobacteria class.

  16. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments

    PubMed Central

    Jeanbille, Mathilde; Gury, Jérôme; Duran, Robert; Tronczynski, Jacek; Ghiglione, Jean-François; Agogué, Hélène; Saïd, Olfa Ben; Taïb, Najwa; Debroas, Didier; Garnier, Cédric; Auguet, Jean-Christophe

    2016-01-01

    Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales. PMID:27594854

  17. A novel mechanism for direct real-time polymerase chain reaction that does not require DNA isolation from prokaryotic cells.

    PubMed

    Soejima, Takashi; Xiao, Jin-Zhong; Abe, Fumiaki

    2016-06-23

    Typically, polymerase chain reaction (PCR) is performed after DNA isolation. Real-time PCR (qPCR), also known as direct qPCR in mammalian cells with weak membranes, is a common technique using crude samples subjected to preliminary boiling to elute DNA. However, applying this methodology to prokaryotic cells, which have solid cell walls, in contrast to mammalian cells which immediately burst in water, can result in poor detection. We successfully achieved PCR elongation with the addition of 1.3 cfu of Cronobacter muytjensii to a newly developed direct qPCR master mix without performing any crude DNA extraction (detection limit of 1.6 × 10(0) cfu/ml for the test sample compared with a detection limit of 1.6 × 10(3) cfu/ml primarily for crude (boiling) or classical DNA isolation). We revealed that the chromosomal DNA retained in prokaryotic cells can function as a PCR template, similarly to the mechanism in in situ PCR. Elucidating this reaction mechanism may contribute to the development of an innovative master mix for direct qPCR to detect genes in a single bacterium with solid cell walls and might lead to numerous novel findings in prokaryotic genomics research.

  18. Chronic Polyaromatic Hydrocarbon (PAH) Contamination Is a Marginal Driver for Community Diversity and Prokaryotic Predicted Functioning in Coastal Sediments.

    PubMed

    Jeanbille, Mathilde; Gury, Jérôme; Duran, Robert; Tronczynski, Jacek; Ghiglione, Jean-François; Agogué, Hélène; Saïd, Olfa Ben; Taïb, Najwa; Debroas, Didier; Garnier, Cédric; Auguet, Jean-Christophe

    2016-01-01

    Benthic microorganisms are key players in the recycling of organic matter and recalcitrant compounds such as polyaromatic hydrocarbons (PAHs) in coastal sediments. Despite their ecological importance, the response of microbial communities to chronic PAH pollution, one of the major threats to coastal ecosystems, has received very little attention. In one of the largest surveys performed so far on coastal sediments, the diversity and composition of microbial communities inhabiting both chronically contaminated and non-contaminated coastal sediments were investigated using high-throughput sequencing on the 18S and 16S rRNA genes. Prokaryotic alpha-diversity showed significant association with salinity, temperature, and organic carbon content. The effect of particle size distribution was strong on eukaryotic diversity. Similarly to alpha-diversity, beta-diversity patterns were strongly influenced by the environmental filter, while PAHs had no influence on the prokaryotic community structure and a weak impact on the eukaryotic community structure at the continental scale. However, at the regional scale, PAHs became the main driver shaping the structure of bacterial and eukaryotic communities. These patterns were not found for PICRUSt predicted prokaryotic functions, thus indicating some degree of functional redundancy. Eukaryotes presented a greater potential for their use as PAH contamination biomarkers, owing to their stronger response at both regional and continental scales.

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

    NASA Astrophysics Data System (ADS)

    Kyle, J. E.; Ferris, G.

    2009-05-01

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

  20. A Prokaryotic Twist on Argonaute Function

    PubMed Central

    Willkomm, Sarah; Zander, Adrian; Gust, Alexander; Grohmann, Dina

    2015-01-01

    Argonaute proteins can be found in all three domains of life. In eukaryotic organisms, Argonaute is, as the functional core of the RNA-silencing machinery, critically involved in the regulation of gene expression. Despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic Argonaute proteins, the biological function of bacterial and archaeal Argonautes has remained elusive. This review discusses new findings in the field that shed light on the structure and function of Argonaute. We especially focus on archaeal Argonautes when discussing the details of the structural and dynamic features in Argonaute that promote substrate recognition and cleavage, thereby revealing differences and similarities in Argonaute biology. PMID:25692904

  1. Functional Advantages Conferred by Extracellular Prokaryotic Membrane Vesicles

    PubMed Central

    Manning, Andrew J.; Kuehn, Meta J.

    2015-01-01

    The absence of subcellular organelles is a characteristic typically used to distinguish prokaryotic from eukaryotic cells. But recent discoveries do not support this dogma. Over the past 50 years, researchers have begun to appreciate and characterize Gram-negative bacterial outer membrane derived vesicles and Gram-positive and archaeal membrane vesicles. These extracellular, membrane-bound organelles can perform a variety of functions, including binding and delivery of DNA, transport of virulence factors, protection of the cell from outer membrane targeting antimicrobials, and ridding the cell of toxic envelope proteins. Here we review the contributions of these extracellular organelles to prokaryotic physiology and compare these with the contributions of the bacterial interior membrane bound organelles responsible for harvesting light energy and for generating magnetic crystals of heavy metals. Understanding the roles of these multifunctional extracellular vesicle organelles as microbial tools will help us to better realize the diverse interactions that occur in our polymicrobial world. PMID:23615201

  2. Membranes, energetics, and evolution across the prokaryote-eukaryote divide

    PubMed Central

    Lynch, Michael; Marinov, Georgi K

    2017-01-01

    The evolution of the eukaryotic cell marked a profound moment in Earth’s history, with most of the visible biota coming to rely on intracellular membrane-bound organelles. It has been suggested that this evolutionary transition was critically dependent on the movement of ATP synthesis from the cell surface to mitochondrial membranes and the resultant boost to the energetic capacity of eukaryotic cells. However, contrary to this hypothesis, numerous lines of evidence suggest that eukaryotes are no more bioenergetically efficient than prokaryotes. Thus, although the origin of the mitochondrion was a key event in evolutionary history, there is no reason to think membrane bioenergetics played a direct, causal role in the transition from prokaryotes to eukaryotes and the subsequent explosive diversification of cellular and organismal complexity. DOI: http://dx.doi.org/10.7554/eLife.20437.001 PMID:28300533

  3. Functional advantages conferred by extracellular prokaryotic membrane vesicles.

    PubMed

    Manning, Andrew J; Kuehn, Meta J

    2013-01-01

    The absence of subcellular organelles is a characteristic typically used to distinguish prokaryotic from eukaryotic cells. But recent discoveries do not support this dogma. Over the past 50 years, researchers have begun to appreciate and characterize Gram-negative bacterial outer membrane-derived vesicles and Gram-positive and archaeal membrane vesicles. These extracellular, membrane-bound organelles can perform a variety of functions, including binding and delivery of DNA, transport of virulence factors, protection of the cell from outer membrane targeting antimicrobials and ridding the cell of toxic envelope proteins. Here, we review the contributions of these extracellular organelles to prokaryotic physiology and compare these with the contributions of the bacterial interior membrane-bound organelles responsible for harvesting light energy and for generating magnetic crystals of heavy metals. Understanding the roles of these multifunctional extracellular vesicle organelles as microbial tools will help us to better realize the diverse interactions that occur in our polymicrobial world.

  4. Classification of prokaryotic genetic replicators: between selfishness and altruism

    PubMed Central

    Jalasvuori, Matti; Koonin, Eugene V.

    2015-01-01

    Prokaryotes harbor a variety of genetic replicators, including plasmids, viruses, and chromosomes, each having differing effects on the phenotype of the hosting cell. Here, we propose a classification for replicators of bacteria and archaea on the basis of their horizontal-transfer potential and the type of relationships (mutualistic, symbiotic, commensal, or parasitic) that they have with the host cell vehicle. Horizontal movement of replicators can be either active or passive, reflecting whether or not the replicator encodes the means to mediate its own transfer from one cell to another. Some replicators also have an infectious extracellular state, thus separating viruses from other mobile elements. From the perspective of the cell vehicle, the different types of replicators form a continuum from genuinely mutualistic to completely parasitic replicators. This classification provides a general framework for dissecting prokaryotic systems into evolutionarily meaningful components. PMID:25703428

  5. Cytoplasmic sulfur trafficking in sulfur-oxidizing prokaryotes.

    PubMed

    Dahl, Christiane

    2015-04-01

    Persulfide groups are chemically versatile and participate in a wide array of biochemical pathways. Although it is well documented that persulfurated proteins supply a number of important and elaborate biosynthetic pathways with sulfane sulfur, it is far less acknowledged that the enzymatic generation of persulfidic sulfur, the successive transfer of sulfur as a persulfide between multiple proteins, and the oxidation of sulfane sulfur in protein-bound form are also essential steps during dissimilatory sulfur oxidation in bacteria and archaea. Here, the currently available information on sulfur trafficking in sulfur oxidizing prokaryotes is reviewed, and the idea is discussed that sulfur is always presented to cytoplasmic oxidizing enzymes in a protein-bound form, thus preventing the occurrence of free sulfide inside of the prokaryotic cell. Thus, sulfur trafficking emerges as a central element in sulfur-oxidizing pathways, and TusA homologous proteins appear to be central and common elements in these processes.

  6. Pyrophosphate-Fueled Na+ and H+ Transport in Prokaryotes

    PubMed Central

    Malinen, Anssi M.; Luoto, Heidi H.

    2013-01-01

    SUMMARY In its early history, life appeared to depend on pyrophosphate rather than ATP as the source of energy. Ancient membrane pyrophosphatases that couple pyrophosphate hydrolysis to active H+ transport across biological membranes (H+-pyrophosphatases) have long been known in prokaryotes, plants, and protists. Recent studies have identified two evolutionarily related and widespread prokaryotic relics that can pump Na+ (Na+-pyrophosphatase) or both Na+ and H+ (Na+,H+-pyrophosphatase). Both these transporters require Na+ for pyrophosphate hydrolysis and are further activated by K+. The determination of the three-dimensional structures of H+- and Na+-pyrophosphatases has been another recent breakthrough in the studies of these cation pumps. Structural and functional studies have highlighted the major determinants of the cation specificities of membrane pyrophosphatases and their potential use in constructing transgenic stress-resistant organisms. PMID:23699258

  7. Prokaryotic biodiversity and activity in the deep subseafloor biosphere.

    PubMed

    Fry, John C; Parkes, R John; Cragg, Barry A; Weightman, Andrew J; Webster, Gordon

    2008-11-01

    The deep subseafloor biosphere supports a diverse population of prokaryotes belonging to the Bacteria and Archaea. Most of the taxonomic groups identified by molecular methods contain mainly uncultured phylotypes. Despite this several cultured strains have been isolated from this habitat, but they probably do not represent the majority of the population. Evidence is starting to suggest that some of the activities measured, such as sulphate reduction and methanogenesis, reflected in geochemical profiles, are carried out by a small subset of the community detected by molecular methods. It is further possible that heterotrophy may be the most important mode of metabolism in subsurface sediments and heterotrophic microorganisms could dominate the uncultured prokaryotic population. Although, heterotrophy is limited by the increasing recalcitrance of organic matter with depth, this may be counteracted by thermal activation of buried organic matter providing additional substrates at depth.

  8. Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

    DOE PAGES

    Martí-Arbona, Ricardo; Mu, Fangping; Nowak-Lovato, Kristy L.; ...

    2014-12-18

    The clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity. A software tool that identifies the genes encoded within a defined genomic neighborhood for the subject TR and its homologs was developed. The output lists of genes in the genetic neighborhoods, their annotated functions, the reactants/products, and identifies the metabolic pathway in which the encoded-proteins function. When a set of TRs of known function was analyzed, we observedmore » that their homologs frequently had conserved genomic neighborhoods that co-located the metabolically related genes regulated by the subject TR. We postulate that TR effectors are metabolites in the identified pathways; indeed the known effectors were present. We analyzed Bxe_B3018 from Burkholderia xenovorans, a TR of unknown function and predicted that this TR was related to the glycine, threonine and serine degradation. We tested the binding of metabolites in these pathways and for those that bound, their ability to modulate TR binding to its specific DNA operator sequence. Using rtPCR, we confirmed that methylglyoxal was an effector of Bxe_3018.« less

  9. Automated genomic context analysis and experimental validation platform for discovery of prokaryote transcriptional regulator functions

    SciTech Connect

    Martí-Arbona, Ricardo; Mu, Fangping; Nowak-Lovato, Kristy L.; Wren, Melinda S.; Unkefer, Clifford J.; Unkefer, Pat J.

    2014-12-18

    The clustering of genes in a pathway and the co-location of functionally related genes is widely recognized in prokaryotes. We used these characteristics to predict the metabolic involvement for a Transcriptional Regulator (TR) of unknown function, identified and confirmed its biological activity. A software tool that identifies the genes encoded within a defined genomic neighborhood for the subject TR and its homologs was developed. The output lists of genes in the genetic neighborhoods, their annotated functions, the reactants/products, and identifies the metabolic pathway in which the encoded-proteins function. When a set of TRs of known function was analyzed, we observed that their homologs frequently had conserved genomic neighborhoods that co-located the metabolically related genes regulated by the subject TR. We postulate that TR effectors are metabolites in the identified pathways; indeed the known effectors were present. We analyzed Bxe_B3018 from Burkholderia xenovorans, a TR of unknown function and predicted that this TR was related to the glycine, threonine and serine degradation. We tested the binding of metabolites in these pathways and for those that bound, their ability to modulate TR binding to its specific DNA operator sequence. Using rtPCR, we confirmed that methylglyoxal was an effector of Bxe_3018.

  10. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.

    PubMed

    Martin, William; Russell, Michael J

    2003-01-29

    prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes.

  11. On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells.

    PubMed Central

    Martin, William; Russell, Michael J

    2003-01-01

    prokaryotic lineages from inorganic confines occurred independently, facilitated by the independent origins of membrane-lipid biosynthesis: isoprenoid ether membranes in the archaebacterial and fatty acid ester membranes in the eubacterial lineage. The eukaryotes, all of which are ancestrally heterotrophs and possess eubacterial lipids, are suggested to have arisen ca. 2 Gyr ago through symbiosis involving an autotrophic archaebacterial host and a heterotrophic eubacterial symbiont, the common ancestor of mitochondria and hydrogenosomes. The attributes shared by all prokaryotes are viewed as inheritances from their confined universal ancestor. The attributes that distinguish eubacteria and archaebacteria, yet are uniform within the groups, are viewed as relics of their phase of differentiation after divergence from the non-free-living universal ancestor and before the origin of the free-living chemoautotrophic lifestyle. The attributes shared by eukaryotes with eubacteria and archaebacteria, respectively, are viewed as inheritances via symbiosis. The attributes unique to eukaryotes are viewed as inventions specific to their lineage. The origin of the eukaryotic endomembrane system and nuclear membrane are suggested to be the fortuitous result of the expression of genes for eubacterial membrane lipid synthesis by an archaebacterial genetic apparatus in a compartment that was not fully prepared to accommodate such compounds, resulting in vesicles of eubacterial lipids that accumulated in the cytosol around their site of synthesis. Under these premises, the most ancient divide in the living world is that between eubacteria and archaebacteria, yet the steepest evolutionary grade is that between prokaryotes and eukaryotes. PMID:12594918

  12. A comprehensive repertoire of prokaryotic species identified in human beings.

    PubMed

    Hugon, Perrine; Dufour, Jean-Charles; Colson, Philippe; Fournier, Pierre-Edouard; Sallah, Kankoe; Raoult, Didier

    2015-10-01

    The compilation of the complete prokaryotic repertoire associated with human beings as commensals or pathogens is a major goal for the scientific and medical community. The use of bacterial culture techniques remains a crucial step to describe new prokaryotic species. The large number of officially acknowledged bacterial species described since 1980 and the recent increase in the number of recognised pathogenic species have highlighted the absence of an exhaustive compilation of species isolated in human beings. By means of a thorough investigation of several large culture databases and a search of the scientific literature, we built an online database containing all human-associated prokaryotic species described, whether or not they had been validated and have standing in nomenclature. We list 2172 species that have been isolated in human beings. They were classified in 12 different phyla, mostly in the Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes phyla. Our online database is useful for both clinicians and microbiologists and forms part of the Human Microbiome Project, which aims to characterise the whole human microbiota and help improve our understanding of the human predisposition and susceptibility to infectious agents.

  13. Distributions of Virus-Like Particles and Prokaryotes within Microenvironments

    PubMed Central

    Dann, Lisa M.; Paterson, James S.; Newton, Kelly; Oliver, Rod; Mitchell, James G.

    2016-01-01

    Microbial interactions are important for ecosystem function, but occur at the microscale and so are difficult to observe. Previous studies in marine systems have shown significant shifts in microbial community abundance and composition over scales of micrometres to centimetres. This study investigates the microscale abundance distributions of virus-like particles (VLPs) and prokaryotes in the lower reaches of a river to determine the extent to which microscale microbial patchiness exists in freshwater systems. Here we report local hotspots surrounded by gradients that reach a maximum 80 and 107 fold change in abundance over 0.9 cm for prokaryotic and VLP subpopulations. Changes in prokaryotic and VLP hotspots were tightly coupled. There were no gradients at tens of centimetres across the boundary layers, which is consistent with strong mixing and turbulence-driven aggregation found in river systems. Quantification of the patchiness shows a marked asymmetry with patches 10 times greater than background common, but depletions being rare or absent in most samples. This consistent asymmetry suggests that coldspots depleted by grazing and lysis are rapidly mixed to background concentrations, while the prevalence of hotspots indicates persistence against disruption. The hotspot to coldspot relative abundance may be useful for understanding microbial river dynamics. The patchiness indicates that the mean- field approach of bulk phase sampling misses the microbially relevant community variation and may underestimate the concentrations of these important microbial groups. PMID:26785114

  14. Predatory prokaryotes: predation and primary consumption evolved in bacteria

    NASA Technical Reports Server (NTRS)

    Guerrero, R.; Pedros-Alio, C.; Esteve, I.; Mas, J.; Chase, D.; Margulis, L.

    1986-01-01

    Two kinds of predatory bacteria have been observed and characterized by light and electron microscopy in samples from freshwater sulfurous lakes in northeastern Spain. The first bacterium, named Vampirococcus, is Gram-negative and ovoidal (0.6 micrometer wide). An anaerobic epibiont, it adheres to the surface of phototrophic bacteria (Chromatium spp.) by specific attachment structures and, as it grows and divides by fission, destroys its prey. An important in situ predatory role can be inferred for Vampirococcus from direct counts in natural samples. The second bacterium, named Daptobacter, is a Gram-negative, facultatively anaerobic straight rod (0.5 x 1.5 micrometers) with a single polar flagellum, which collides, penetrates, and grows inside the cytoplasm of its prey (several genera of Chromatiaceae). Considering also the well-known case of Bdellovibrio, a Gram-negative, aerobic curved rod that penetrates and divides in the periplasmic space of many chemotrophic Gram-negative bacteria, there are three types of predatory prokaryotes presently known (epibiotic, cytoplasmic, and periplasmic). Thus, we conclude that antagonistic relationships such as primary consumption, predation, and scavenging had already evolved in microbial ecosystems prior to the appearance of eukaryotes. Furthermore, because they represent methods by which prokaryotes can penetrate other prokaryotes in the absence of phagocytosis, these associations can be considered preadaptation for the origin of intracellular organelles.

  15. Genomic and functional adaptation in surface ocean planktonic prokaryotes.

    PubMed

    Yooseph, Shibu; Nealson, Kenneth H; Rusch, Douglas B; McCrow, John P; Dupont, Christopher L; Kim, Maria; Johnson, Justin; Montgomery, Robert; Ferriera, Steve; Beeson, Karen; Williamson, Shannon J; Tovchigrechko, Andrey; Allen, Andrew E; Zeigler, Lisa A; Sutton, Granger; Eisenstadt, Eric; Rogers, Yu-Hui; Friedman, Robert; Frazier, Marvin; Venter, J Craig

    2010-11-04

    The understanding of marine microbial ecology and metabolism has been hampered by the paucity of sequenced reference genomes. To this end, we report the sequencing of 137 diverse marine isolates collected from around the world. We analysed these sequences, along with previously published marine prokaryotic genomes, in the context of marine metagenomic data, to gain insights into the ecology of the surface ocean prokaryotic picoplankton (0.1-3.0 μm size range). The results suggest that the sequenced genomes define two microbial groups: one composed of only a few taxa that are nearly always abundant in picoplanktonic communities, and the other consisting of many microbial taxa that are rarely abundant. The genomic content of the second group suggests that these microbes are capable of slow growth and survival in energy-limited environments, and rapid growth in energy-rich environments. By contrast, the abundant and cosmopolitan picoplanktonic prokaryotes for which there is genomic representation have smaller genomes, are probably capable of only slow growth and seem to be relatively unable to sense or rapidly acclimate to energy-rich conditions. Their genomic features also lead us to propose that one method used to avoid predation by viruses and/or bacterivores is by means of slow growth and the maintenance of low biomass.

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

    PubMed

    Souza, Wanderley de

    2012-05-01

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

  17. The Prokaryote-Eukaryote Dichotomy: Meanings and Mythology

    PubMed Central

    Sapp, Jan

    2005-01-01

    Drawing on documents both published and archival, this paper explains how the prokaryote-eukaryote dichotomy of the 1960s was constructed, the purposes it served, and what it implied in terms of classification and phylogeny. In doing so, I first show how the concept was attributed to Edouard Chatton and the context in which he introduced the terms. Following, I examine the context in which the terms were reintroduced into biology in 1962 by Roger Stanier and C. B. van Niel. I study the discourse over the subsequent decade to understand how the organizational dichotomy took on the form of a natural classification as the kingdom Monera or superkingdom Procaryotae. Stanier and van Niel admitted that, in regard to constructing a natural classification of bacteria, structural characteristics were no more useful than physiological properties. They repeatedly denied that bacterial phylogenetics was possible. I thus examine the great historical irony that the “prokaryote,” in both its organizational and phylogenetic senses, was defined (negatively) on the basis of structure. Finally, we see how phylogenetic research based on 16S rRNA led by Carl Woese and his collaborators confronted the prokaryote concept while moving microbiology to the center of evolutionary biology. PMID:15944457

  18. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    SciTech Connect

    McNair, Katelyn; Edwards, Robert A.

    2015-06-16

    As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping error rates low, as well as offering unique data visualization options.

  19. GenomePeek—an online tool for prokaryotic genome and metagenome analysis

    DOE PAGES

    McNair, Katelyn; Edwards, Robert A.

    2015-06-16

    As increases in prokaryotic sequencing take place, a method to quickly and accurately analyze this data is needed. Previous tools are mainly designed for metagenomic analysis and have limitations; such as long runtimes and significant false positive error rates. The online tool GenomePeek (edwards.sdsu.edu/GenomePeek) was developed to analyze both single genome and metagenome sequencing files, quickly and with low error rates. GenomePeek uses a sequence assembly approach where reads to a set of conserved genes are extracted, assembled and then aligned against the highly specific reference database. GenomePeek was found to be faster than traditional approaches while still keeping errormore » rates low, as well as offering unique data visualization options.« less

  20. Prokaryotic genome regulation: A revolutionary paradigm

    PubMed Central

    ISHIHAMA, Akira

    2012-01-01

    After determination of the whole genome sequence, the research frontier of bacterial molecular genetics has shifted to reveal the genome regulation under stressful conditions in nature. The gene selectivity of RNA polymerase is modulated after interaction with two groups of regulatory proteins, 7 sigma factors and 300 transcription factors. For identification of regulation targets of transcription factors in Escherichia coli, we have developed Genomic SELEX system and subjected to screening the binding sites of these factors on the genome. The number of regulation targets by a single transcription factor was more than those hitherto recognized, ranging up to hundreds of promoters. The number of transcription factors involved in regulation of a single promoter also increased to as many as 30 regulators. The multi-target transcription factors and the multi-factor promoters were assembled into complex networks of transcription regulation. The most complex network was identified in the regulation cascades of transcription of two master regulators for planktonic growth and biofilm formation. PMID:23138451

  1. Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation

    PubMed Central

    Grazziotin, Ana Laura; Koonin, Eugene V.; Kristensen, David M.

    2017-01-01

    Viruses are the most abundant and diverse biological entities on earth, and while most of this diversity remains completely unexplored, advances in genome sequencing have provided unprecedented glimpses into the virosphere. The Prokaryotic Virus Orthologous Groups (pVOGs, formerly called Phage Orthologous Groups, POGs) resource has aided in this task over the past decade by using automated methods to keep pace with the rapid increase in genomic data. The uses of pVOGs include functional annotation of viral proteins, identification of genes and viruses in uncharacterized DNA samples, phylogenetic analysis, large-scale comparative genomics projects, and more. The pVOGs database represents a comprehensive set of orthologous gene families shared across multiple complete genomes of viruses that infect bacterial or archaeal hosts (viruses of eukaryotes will be added at a future date). The pVOGs are constructed within the Clusters of Orthologous Groups (COGs) framework that is widely used for orthology identification in prokaryotes. Since the previous release of the POGs, the size has tripled to nearly 3000 genomes and 300 000 proteins, and the number of conserved orthologous groups doubled to 9518. User-friendly webpages are available, including multiple sequence alignments and HMM profiles for each VOG. These changes provide major improvements to the pVOGs database, at a time of rapid advances in virus genomics. The pVOGs database is hosted jointly at the University of Iowa at http://dmk-brain.ecn.uiowa.edu/pVOGs and the NCBI at ftp://ftp.ncbi.nlm.nih.gov/pub/kristensen/pVOGs/home.html. PMID:27789703

  2. Wastewater Effluent Impacts Ammonia-Oxidizing Prokaryotes of the Grand River, Canada

    PubMed Central

    Sonthiphand, Puntipar; Cejudo, Eduardo; Schiff, Sherry L.

    2013-01-01

    The Grand River (Ontario, Canada) is impacted by wastewater treatment plants (WWTPs) that release ammonia (NH3 and NH4+) into the river. In-river microbial communities help transform this ammonia into more oxidized compounds (e.g., NO3− or N2), although the spatial distribution and relative abundance of freshwater autotrophic ammonia-oxidizing prokaryotes (AOP) are not well characterized. This study investigated freshwater N cycling within the Grand River, focusing on sediment and water columns, both inside and outside a WWTP effluent plume. The diversity, relative abundance, and nitrification activity of AOP were investigated by denaturing gradient gel electrophoresis (DGGE), quantitative real-time PCR (qPCR), and reverse transcriptase qPCR (RT-qPCR), targeting both 16S rRNA and functional genes, together with activity assays. The analysis of bacterial 16S rRNA gene fingerprints showed that the WWTP effluent strongly affected autochthonous bacterial patterns in the water column but not those associated with sediment nucleic acids. Molecular and activity data demonstrated that ammonia-oxidizing archaea (AOA) were numerically and metabolically dominant in samples taken from outside the WWTP plume, whereas ammonia-oxidizing bacteria (AOB) dominated numerically within the WWTP effluent plume. Potential nitrification rate measurements supported the dominance of AOB activity in downstream sediment. Anaerobic ammonia-oxidizing (anammox) bacteria were detected primarily in sediment nucleic acids. In-river AOA patterns were completely distinct from effluent AOA patterns. This study demonstrates the importance of combined molecular and activity-based studies for disentangling molecular signatures of wastewater effluent from autochthonous prokaryotic communities. PMID:24056472

  3. Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment.

    PubMed

    Gittel, Antje; Sørensen, Ketil Bernt; Skovhus, Torben Lund; Ingvorsen, Kjeld; Schramm, Andreas

    2009-11-01

    Sulfate-reducing prokaryotes (SRP) cause severe problems like microbial corrosion and reservoir souring in seawater-injected oil production systems. One strategy to control SRP activity is the addition of nitrate to the injection water. Production waters from two adjacent, hot (80 degrees C) oil reservoirs, one with and one without nitrate treatment, were compared for prokaryotic community structure and activity of SRP. Bacterial and archaeal 16S rRNA gene analyses revealed higher prokaryotic abundance but lower diversity for the nitrate-treated field. The 16S rRNA gene clone libraries from both fields were dominated by sequences affiliated with Firmicutes (Bacteria) and Thermococcales (Archaea). Potential heterotrophic nitrate reducers (Deferribacterales) were exclusively found at the nitrate-treated field, possibly stimulated by nitrate addition. Quantitative PCR of dsrAB genes revealed that archaeal SRP (Archaeoglobus) dominated the SRP communities, but with lower relative abundance at the nitrate-treated site. Bacterial SRP were found in only low abundance at both sites and were nearly exclusively affiliated with thermophilic genera (Desulfacinum and Desulfotomaculum). Despite the high abundance of archaeal SRP, no archaeal SRP activity was detected in [(35)S]sulfate incubations at 80 degrees C. Sulfate reduction was found at 60 degrees C in samples from the untreated field and accompanied by the growth of thermophilic bacterial SRP in batch cultures. Samples from the nitrate-treated field generally lacked SRP activity. These results indicate that (i) Archaeoglobus can be a major player in hot oil reservoirs, and (ii) nitrate may act in souring control-not only by inhibiting SRP, but also by changing the overall community structure, including the stimulation of competitive nitrate reducers.

  4. Identification of prokaryotic homologues indicates an endosymbiotic origin for the alternative oxidases of mitochondria (AOX) and chloroplasts (PTOX).

    PubMed

    Atteia, Ariane; van Lis, Robert; van Hellemond, Jaap J; Tielens, Aloysius G M; Martin, William; Henze, Katrin

    2004-04-14

    The alternative oxidase is a ubiquinol oxidase that has been found to date in the mitochondrial respiratory chain of plants, some fungi and protists. Because of its sparse distribution among eukaryotic lineages and because of its diversity in regulatory mechanisms, the origin of AOX has been a mystery, particularly since no prokaryotic homologues have previously been identified. Here we report the identification of a gene encoding a clear homologue of the mitochondrial alternative oxidase in an alpha-proteobacterium, and the identification of three cyanobacterial genes that encode clear homologues of the plastid-specific alternative oxidase of plants and algae. These findings suggest that the eukaryotic nuclear genes for the alternative oxidases of mitochondria and chloroplasts were acquired via endosymbiotic gene transfer from the eubacterial ancestors of these two organelles, respectively.

  5. Thiol-based redox switches in prokaryotes

    PubMed Central

    Hillion, Melanie; Antelmann, Haike

    2015-01-01

    Summary Bacteria encounter reactive oxygen species (ROS) as consequence of the aerobic life or as oxidative burst of activated neutrophils during infections. In addition, bacteria are exposed to other redox-active compounds including hypochloric acid (HOCl) and reactive electrophilic species (RES), such as quinones and aldehydes. These reactive species often target the thiol groups of cysteines in proteins and lead to thiol-disulfide switches in redox-sensing regulators to activate specific detoxification pathways and to restore the redox balance. Here, we review bacterial thiol-based redox sensors that specifically sense ROS, RES and HOCl via thiol-based mechanisms and regulate gene transcription in Gram-positive model bacteria and in human pathogens, such as Staphylococcus aureus and Mycobacterium tuberculosis. We also pay particular attention to emerging widely conserved HOCl-specific redox regulators that have been recently characterized in Escherichia coli. Different mechanisms are used to sense and respond to ROS, RES and HOCl by 1-Cys-type and 2-Cys-type thiol-based redox sensors that include versatile thiol-disulfide switches (OxyR, OhrR, HypR, YodB, NemR, RclR, Spx, RsrA/RshA) or alternative Cys-phosphorylations (SarZ, MgrA, SarA), thiol-S-alkylation (QsrR), His-oxidation (PerR) and methionine oxidation (HypT). In pathogenic bacteria, these redox-sensing regulators are often important virulence regulators and required for adapation to the host immune defense. PMID:25720121

  6. Thiol-based redox switches in prokaryotes.

    PubMed

    Hillion, Melanie; Antelmann, Haike

    2015-05-01

    Bacteria encounter reactive oxygen species (ROS) as a consequence of the aerobic life or as an oxidative burst of activated neutrophils during infections. In addition, bacteria are exposed to other redox-active compounds, including hypochloric acid (HOCl) and reactive electrophilic species (RES) such as quinones and aldehydes. These reactive species often target the thiol groups of cysteines in proteins and lead to thiol-disulfide switches in redox-sensing regulators to activate specific detoxification pathways and to restore the redox balance. Here, we review bacterial thiol-based redox sensors that specifically sense ROS, RES and HOCl via thiol-based mechanisms and regulate gene transcription in Gram-positive model bacteria and in human pathogens, such as Staphylococcus aureus and Mycobacterium tuberculosis. We also pay particular attention to emerging widely conserved HOCl-specific redox regulators that have been recently characterized in Escherichia coli. Different mechanisms are used to sense and respond to ROS, RES and HOCl by 1-Cys-type and 2-Cys-type thiol-based redox sensors that include versatile thiol-disulfide switches (OxyR, OhrR, HypR, YodB, NemR, RclR, Spx, RsrA/RshA) or alternative Cys phosphorylations (SarZ, MgrA, SarA), thiol-S-alkylation (QsrR), His-oxidation (PerR) and methionine oxidation (HypT). In pathogenic bacteria, these redox-sensing regulators are often important virulence regulators and required for adapation to the host immune defense.

  7. An innovative concept for the AsteroidFinder/SSB focal plane assembly

    NASA Astrophysics Data System (ADS)

    Schindler, Karsten; Tschentscher, Matthias; Koncz, Alexander; Solbrig, Michael; Michaelis, Harald

    2012-06-01

    This paper gives a summary on the system concept and design of the focal plane assembly of AsteroidFinder/SSB, a small satellite mission which is currently under development at the German Aerospace Center (DLR). An athermal design concept has been developed in accordance to the requirements of the instrument and spacecraft. Key aspects leading to this approach have been a trade-off study of the mechanical telescope interface, the definition of electrical and thermal interfaces and a material selection which minimizes thermally induced stresses. As a novelty, the structure will be manufactured from a machinable AlN-BN composite ceramic. To enable rapid design iterations and development, an integrated modeling approach has been used to conduct a thermo-mechanical analysis of the proposed concept in order to proof its feasibility. The steady-state temperature distribution for various load cases and the resulting stress and strain within the assembly have both been computed using a finite element simulation.

  8. Fragment Finder: a web-based software to identify similar three-dimensional structural motif

    PubMed Central

    Ananthalakshmi, P.; Kumar, Ch. Kiran; Jeyasimhan, M.; Sumathi, K.; Sekar, K.

    2005-01-01

    FF (Fragment Finder) is a web-based interactive search engine developed to retrieve the user-desired similar 3D structural fragments from the selected subset of 25 or 90% non-homologous protein chains. The search is based on the comparison of the main chain backbone conformational angles (φ and ϕ). Additionally, the queried motifs can be superimposed to find out how similar the structural fragments are, so that the information can be effectively used in molecular modeling. The engine has facilities to view the resultant superposed or individual 3D structure(s) on the client machine. The proposed web server is made freely accessible at the following URL: or . PMID:15980587

  9. Milli-Hertz Gravitational Waves: LISA and LISA PathFinder

    NASA Astrophysics Data System (ADS)

    Araújo, H.; Cañizares, P.; Chmeissani, M.; Conchillo, A.; Díaz-Aguiló, M.; García-Berro, E.; Gesa, L.; Gibert, F.; Grimani, C.; Hajdas, W.; Hollington, D.; Lloro, I.; Lobo, A.; Mateos, I.; Nofrarias, M.; Puigdengoles, C.; Ramos-Castro, J.; Sanjuán, J.; Sopuerta, Cf; Wass, P.

    2011-09-01

    Ground based GW detectors are limited at their lower frequency band (1-10 Hz) by settlement gravity gradients and seismic noise, and their sensitivity peaks at around 100 Hz. Sources in this band are mostly short duration signals, and their rates uncertain. Going down to milli-Hertz frequencies significantly increases the number and types of available sources. LISA was planned with the idea to explore a likely richer region of the GW spectrum, beyond that accessible to ground detectors; the latter are however expected to produce the first GW observations. In this paper I will present the main LISA concepts; in particular, emphasis will be placed on LISAPathFinder, the ESA precursor of LISA, in which our research group in Barcelona is heavily involved.

  10. Simulation-Based Verification of Autonomous Controllers via Livingstone PathFinder

    NASA Technical Reports Server (NTRS)

    Lindsey, A. E.; Pecheur, Charles

    2004-01-01

    AI software is often used as a means for providing greater autonomy to automated systems, capable of coping with harsh and unpredictable environments. Due in part to the enormous space of possible situations that they aim to addrs, autonomous systems pose a serious challenge to traditional test-based verification approaches. Efficient verification approaches need to be perfected before these systems can reliably control critical applications. This publication describes Livingstone PathFinder (LPF), a verification tool for autonomous control software. LPF applies state space exploration algorithms to an instrumented testbed, consisting of the controller embedded in a simulated operating environment. Although LPF has focused on NASA s Livingstone model-based diagnosis system applications, the architecture is modular and adaptable to other systems. This article presents different facets of LPF and experimental results from applying the software to a Livingstone model of the main propulsion feed subsystem for a prototype space vehicle.

  11. Implementation of the data acquisition system for the Overlap Muon Track Finder in the CMS experiment

    NASA Astrophysics Data System (ADS)

    Zabołotny, W. M.; Bluj, M.; Buńkowski, K.; Byszuk, A. P.; Dobosz, J.; Doroba, K.; Drabik, P.; Górski, M.; Kalinowski, A.; Kierzkowski, K. Z.; Konecki, M.; Okliński, W.; Olszewski, M.; Poźniak, K.; Zawistowski, K.

    2017-01-01

    The Overlap Muon Track Finder (OMTF) is the new system developed during the upgrade of the CMS experiment which includes the upgrade of its Level-1 trigger. It uses the novelty approach to finding muon candidates based on data received from three types of detectors: RPC, DT, and CSC . The upgrade of the trigger system requires also upgrade of the associated Data Acquisition (DAQ) system. The OMTF DAQ transmits the data from the connected detectors that were the basis for the Level-1 trigger decision. To increase its diagnostic potential, it may also transmit the data from a few bunch crossings (BXes) preceding or following the BX, in which the L1 trigger was generated. The paper describes the technical concepts and solutions used in the OMTF DAQ system. The system is still under development. However, it successfully passed the first tests.

  12. Low virus to prokaryote ratios in the cold: benthic viruses and prokaryotes in a subpolar marine ecosystem (Hornsund, Svalbard).

    PubMed

    Wróbel, Borys; Filippini, Manuela; Piwowarczyk, Joanna; Kedra, Monika; Kuliński, Karol; Middelboe, Mathias

    2013-03-01

    The density and spatial distribution of benthic viruses and prokaryotes in relation to biotic and abiotic factors were investigated in sediment cores collected in Hornsund, a permanently cold fjord on the West coast of Svalbard, Norway. The cores were obtained from the mouth of the fjord to the central basin, along a longitudinal transect. The results of our analyses showed lower densities of viruses (0.2 x 10(8) to 5.4 x 10(8) virus-like particles/g) and lower virus-to-prokaryote ratios (0.2-0.6, with the exception of the uppermost layer in the central basin, where the ratio was about 1.2) at the study site than generally found in the temperate areas, despite the relatively high organic matter content in subpolar sediments. Variations in benthic viral and prokaryote abundances along gradients of particle sedimentation rates, phytopigment concentrations, and macrobenthic species composition together suggested the influence of particle sedimentation and macrobenthic bioturbation on the abundance and spatial distribution ofprokaryotes and viruses in cold habitats.

  13. Comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems and related mobile stress response systems in prokaryotes

    PubMed Central

    Makarova, Kira S; Wolf, Yuri I; Koonin, Eugene V

    2009-01-01

    Background The prokaryotic toxin-antitoxin systems (TAS, also referred to as TA loci) are widespread, mobile two-gene modules that can be viewed as selfish genetic elements because they evolved mechanisms to become addictive for replicons and cells in which they reside, but also possess "normal" cellular functions in various forms of stress response and management of prokaryotic population. Several distinct TAS of type 1, where the toxin is a protein and the antitoxin is an antisense RNA, and numerous, unrelated TAS of type 2, in which both the toxin and the antitoxin are proteins, have been experimentally characterized, and it is suspected that many more remain to be identified. Results We report a comprehensive comparative-genomic analysis of Type 2 toxin-antitoxin systems in prokaryotes. Using sensitive methods for distant sequence similarity search, genome context analysis and a new approach for the identification of mobile two-component systems, we identified numerous, previously unnoticed protein families that are homologous to toxins and antitoxins of known type 2 TAS. In addition, we predict 12 new families of toxins and 13 families of antitoxins, and also, predict a TAS or TAS-like activity for several gene modules that were not previously suspected to function in that capacity. In particular, we present indications that the two-gene module that encodes a minimal nucleotidyl transferase and the accompanying HEPN protein, and is extremely abundant in many archaea and bacteria, especially, thermophiles might comprise a novel TAS. We present a survey of previously known and newly predicted TAS in 750 complete genomes of archaea and bacteria, quantitatively demonstrate the exceptional mobility of the TAS, and explore the network of toxin-antitoxin pairings that combines plasticity with selectivity. Conclusion The defining properties of the TAS, namely, the typically small size of the toxin and antitoxin genes, fast evolution, and extensive horizontal mobility

  14. A Fast Apparent-Horizon Finder for 3-Dimensional Cartesian Grids in Numerical Relativity

    NASA Astrophysics Data System (ADS)

    Thornburg, Jonathan

    2003-10-01

    In 3 + 1 numerical simulations of dynamic black hole spacetimes, it's useful to be able to find the apparent horizon(s) (AH) in each slice of a time evolution. A number of AH finders are available, but they often take many minutes to run, so they're too slow to be practically usable at each time step. Here I present a new AH finder, AHFINDERDIRECT, which is very fast and accurate, typically taking only a few seconds to find an AH to ~ 10-5m accuracy on a GHz-class processor. I assume that an AH to be searched for is a Strahlkörper (``star-shaped region'') with respect to some local origin, and so parameterize the AH shape by r = h(angle) for some single-valued function h: S2 --> R+. The AH equation then becomes a nonlinear elliptic PDE in h on S2, whose coefficients are algebraic functions of gij, Kij, and the Cartesian-coordinate spatial derivatives of gij. I discretize S2 using 6 angular patches (one each in the neighborhood of the +/-x, +/-y, and +/-z axes) to avoid coordinate singularities, and finite difference the AH equation in the angular coordinates using 4th order finite differencing. I solve the resulting system of nonlinear algebraic equations (for h at the angular grid points) by Newton's method, using a ``symbolic differentiation'' technique to compute the Jacobian matrix. AHFINDERDIRECT is implemented as a thorn in the CACTUS computational toolkit, and will be made freely available starting in fall 2003.

  15. Feasibility of Virtual Research Visits in Fox Trial Finder

    PubMed Central

    Dorsey, E. Ray; Wagner, Joseph D.; Bull, Michael T.; Rizzieri, Ashley; Grischkan, Justin; Achey, Meredith A.; Sherer, Todd; Chowdhury, Sohini; Meunier, Claire; Cappelletti, Lily; Rocker, Charlotte; Richard, Irene H.; Schwarz, Heidi; Kang, Gail; Ahmad, Stacy H.; Biemiller, Rachel A.; Biglan, Kevin M.

    2015-01-01

    Abstract Background: Fox Trial Finder is an online registry for individuals with and without Parkinson disease (PD) interested in participating in PD research. However, distance or disability could prevent such individuals from participating in traditional, clinic-based research at major centers. Objective: Use videoconferencing to connect participants to specialists to: (1) demonstrate feasibility of virtual research visits within this population (2) collect phenotypic data of the participants, (3) validate self-reported diagnosis, and (4) gauge interest in virtual research visits. Methods: We solicited volunteers throughout the United States through Fox Trial Finder. Interested individuals with PD provided consent, were given web cameras if needed, completed baseline surveys, and downloaded videoconferencing software remotely. Participants had a test connection and assessment appointment which included the Montreal Cognitive Assessment (MoCA), then a virtual research visit with a neurologist who reviewed their history and assessed their PD using a modified Movement Disorders Society Unified Parkinson’s Disease Rating Scale. Neurologists assessed PD diagnosis and symptomatology. Physicians and participants were surveyed about their experience. Results: Of 204 individuals who consented, 166 (81% ) individuals from 39 states completed all visits. The mean age was 62 and mean disease duration was 8.0 years. Mean MoCA score was 26.5, and mean modified MDS-UPDRS motor score was 22.8 (out of a possible 124). Neurologists judged PD as the most likely diagnosis in 97% of cases. Overall satisfaction with the visits was 79% (satisfied or very satisfied) among neurologists and 93% among participants. Conclusions: Through virtual research visits, neurologists engaged, characterized, and validated self-reported diagnosis in individuals with PD over a broad geography. This model may facilitate future research participation. PMID:26406130

  16. Seekers, Finders, Settlers, and Stumblers: Identifying the Career Paths of Males in the Genetic Counseling Profession.

    PubMed

    Chen, Anthony; Veach, Pat McCarthy; Schoonveld, Cheri; Zierhut, Heather

    2017-03-14

    Genetic counseling is a female-dominated profession, with 96% of counselors self-identifying as female. Research suggests gender diversification benefits healthcare professionals and the populations they serve. Therefore, this study explored how men choose a genetic counseling career, associations between career satisfaction and their career entry dynamics and experience levels, and differences due to experience level in how they decide on this profession. Twenty-five novice, experienced, or seasoned male counselors and 8 male genetic counseling students participated in semi-structured phone interviews. Interpretive content and cross-case analyses of interview data were informed by Simpson's "Seekers, Finders, and Settlers" theory describing career entry dynamics of men in non-traditional (i.e., female-dominated) fields. Results revealed 13 interviewees were Seekers, who initially knew they wanted a career in genetic counseling, actively chose the profession, and were satisfied with their decision. Eleven were Settlers, who had tried different, traditional jobs, with limited satisfaction before actively finding and choosing genetic counseling. Two were Finders, who discovered genetic counseling while in the career decision making process and made a passive choice to pursue it as they had no feasible, satisfactory alternative. Seven men fit a new category, we termed "Stumblers," who were in another career and satisfied, but changed to genetic counseling after happening to hear about it. Prevalent themes pertaining to participants' experiences in the career include desire for a multidisciplinary career; lack of a priori knowledge of genetic counselor roles; late exposure to the profession; and varied perceptions of being in a non-traditional career. There were few differences due to experience level and career satisfaction was high across the sample. Results suggest earlier exposure to the career and availability of detailed descriptions of its multidisciplinary

  17. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts

    PubMed Central

    Oliveira, Pedro H.; Touchon, Marie; Rocha, Eduardo P.C.

    2014-01-01

    The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs. PMID:25120263

  18. Sequence motifs and prokaryotic expression of the reptilian paramyxovirus fusion protein

    USGS Publications Warehouse

    Franke, J.; Batts, W.N.; Ahne, W.; Kurath, G.; Winton, J.R.

    2006-01-01

    Fourteen reptilian paramyxovirus isolates were chosen to represent the known extent of genetic diversity among this novel group of viruses. Selected regions of the fusion (F) gene were sequenced, analyzed and compared. The F gene of all isolates contained conserved motifs homologous to those described for other members of the family Paramyxoviridae including: signal peptide, transmembrane domain, furin cleavage site, fusion peptide, N-linked glycosylation sites, and two heptad repeats, the second of which (HRB-LZ) had the characteristics of a leucine zipper. Selected regions of the fusion gene of isolate Gono-GER85 were inserted into a prokaryotic expression system to generate three recombinant protein fragments of various sizes. The longest recombinant protein was cleaved by furin into two fragments of predicted length. Western blot analysis with virus-neutralizing rabbit-antiserum against this isolate demonstrated that only the longest construct reacted with the antiserum. This construct was unique in containing 30 additional C-terminal amino acids that included most of the HRB-LZ. These results indicate that the F genes of reptilian paramyxoviruses contain highly conserved motifs typical of other members of the family and suggest that the HRB-LZ domain of the reptilian paramyxovirus F protein contains a linear antigenic epitope. ?? Springer-Verlag 2005.

  19. Linking host prokaryotic physiology to viral lifestyle dynamics in a temperate freshwater lake (Lake Pavin, France).

    PubMed

    Palesse, S; Colombet, J; Pradeep Ram, A S; Sime-Ngando, T

    2014-11-01

    In aquatic ecosystems, fluctuations in environmental conditions and prokaryotic host physiological states can strongly affect the dynamics of viral life strategies. The influence of prokaryote physiology and environmental factors on viral replication cycles (lytic and lysogeny) was investigated from April to September 2011 at three different strata (epi, meta, and hypolimnion) in the mixolimnion of deep volcanic temperate freshwater Lake Pavin (France). Overall, the euphotic region (epi and metalimnion) was more dynamic and showed significant variation in microbial standing stocks, prokaryotic physiological state, and viral life strategies compared to the aphotic hypolimnion which was stable within sampled months. The prokaryotic host physiology as inferred from the nucleic acid content of prokaryotic cells (high or low nucleic acid) was strongly regulated by the chlorophyll concentration. The predominance of the high nucleic acid (HNA) prokaryotes (cells) over low nucleic acid (LNA) prokaryotes (cells) in the spring (HNA/LNA = 1.2) and vice versa in the summer period (HNA/LNA = 0.4) suggest that the natural prokaryotic communities underwent major shifts in their physiological states during investigated time period. The increase in the percentage of inducible lysogenic prokaryotes in the summer period was associated with the switch in the dominance of LNA over HNA cells, which coincided with the periods of strong resource (nutrient) limitation. This supports the idea that lysogeny represents a maintenance strategy for viruses in unproductive or harsh nutrient/host conditions. A negative correlation of percentage of lysogenic prokaryotes with HNA cell abundance and chlorophyll suggest that lysogenic cycle is closely related to prokaryotic cells which are stressed or starved due to unavailability of resources for its growth and activity. Our results provide support to previous findings that changes in prokaryote physiology are critical for the promotion and

  20. Development of a RAD-Seq Based DNA Polymorphism Identification Software, AgroMarker Finder, and Its Application in Rice Marker-Assisted Breeding.

    PubMed

    Fan, Wei; Zong, Jie; Luo, Zhijing; Chen, Mingjiao; Zhao, Xiangxiang; Zhang, Dabing; Qi, Yiping; Yuan, Zheng

    2016-01-01

    Rapid and accurate genome-wide marker detection is essential to the marker-assisted breeding and functional genomics studies. In this work, we developed an integrated software, AgroMarker Finder (AMF: http://erp.novelbio.com/AMF), for providing graphical user interface (GUI) to facilitate the recently developed restriction-site associated DNA (RAD) sequencing data analysis in rice. By application of AMF, a total of 90,743 high-quality markers (82,878 SNPs and 7,865 InDels) were detected between rice varieties JP69 and Jiaoyuan5A. The density of the identified markers is 0.2 per Kb for SNP markers, and 0.02 per Kb for InDel markers. Sequencing validation revealed that the accuracy of genome-wide marker detection by AMF is 93%. In addition, a validated subset of 82 SNPs and 31 InDels were found to be closely linked to 117 important agronomic trait genes, providing a basis for subsequent marker-assisted selection (MAS) and variety identification. Furthermore, we selected 12 markers from 31 validated InDel markers to identify seed authenticity of variety Jiaoyuanyou69, and we also identified 10 markers closely linked to the fragrant gene BADH2 to minimize linkage drag for Wuxiang075 (BADH2 donor)/Jiachang1 recombinants selection. Therefore, this software provides an efficient approach for marker identification from RAD-seq data, and it would be a valuable tool for plant MAS and variety protection.

  1. Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes

    PubMed Central

    Bruto, Maxime; Prigent-Combaret, Claire; Luis, Patricia; Moënne-Loccoz, Yvan; Muller, Daniel

    2014-01-01

    Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes—as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude. PMID:24990676

  2. Frequent, independent transfers of a catabolic gene from bacteria to contrasted filamentous eukaryotes.

    PubMed

    Bruto, Maxime; Prigent-Combaret, Claire; Luis, Patricia; Moënne-Loccoz, Yvan; Muller, Daniel

    2014-08-22

    Even genetically distant prokaryotes can exchange genes between them, and these horizontal gene transfer events play a central role in adaptation and evolution. While this was long thought to be restricted to prokaryotes, certain eukaryotes have acquired genes of bacterial origin. However, gene acquisitions in eukaryotes are thought to be much less important in magnitude than in prokaryotes. Here, we describe the complex evolutionary history of a bacterial catabolic gene that has been transferred repeatedly from different bacterial phyla to stramenopiles and fungi. Indeed, phylogenomic analysis pointed to multiple acquisitions of the gene in these filamentous eukaryotes-as many as 15 different events for 65 microeukaryotes. Furthermore, once transferred, this gene acquired introns and was found expressed in mRNA databases for most recipients. Our results show that effective inter-domain transfers and subsequent adaptation of a prokaryotic gene in eukaryotic cells can happen at an unprecedented magnitude.

  3. Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic

    PubMed Central

    Baltar, Federico; Lundin, Daniel; Palovaara, Joakim; Lekunberri, Itziar; Reinthaler, Thomas; Herndl, Gerhard J.; Pinhassi, Jarone

    2016-01-01

    To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates—assumed to be related to autotrophic metabolisms—were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention. PMID:27818655

  4. Information Dynamics in Living Systems: Prokaryotes, Eukaryotes, and Cancer

    PubMed Central

    Frieden, B. Roy; Gatenby, Robert A.

    2011-01-01

    Background Living systems use information and energy to maintain stable entropy while far from thermodynamic equilibrium. The underlying first principles have not been established. Findings We propose that stable entropy in living systems, in the absence of thermodynamic equilibrium, requires an information extremum (maximum or minimum), which is invariant to first order perturbations. Proliferation and death represent key feedback mechanisms that promote stability even in a non-equilibrium state. A system moves to low or high information depending on its energy status, as the benefit of information in maintaining and increasing order is balanced against its energy cost. Prokaryotes, which lack specialized energy-producing organelles (mitochondria), are energy-limited and constrained to an information minimum. Acquisition of mitochondria is viewed as a critical evolutionary step that, by allowing eukaryotes to achieve a sufficiently high energy state, permitted a phase transition to an information maximum. This state, in contrast to the prokaryote minima, allowed evolution of complex, multicellular organisms. A special case is a malignant cell, which is modeled as a phase transition from a maximum to minimum information state. The minimum leads to a predicted power-law governing the in situ growth that is confirmed by studies measuring growth of small breast cancers. Conclusions We find living systems achieve a stable entropic state by maintaining an extreme level of information. The evolutionary divergence of prokaryotes and eukaryotes resulted from acquisition of specialized energy organelles that allowed transition from information minima to maxima, respectively. Carcinogenesis represents a reverse transition: of an information maximum to minimum. The progressive information loss is evident in accumulating mutations, disordered morphology, and functional decline characteristics of human cancers. The findings suggest energy restriction is a critical first step

  5. Biogenesis of actin-like bacterial cytoskeletal filaments destined for positioning prokaryotic magnetic organelles.

    PubMed

    Pradel, Nathalie; Santini, Claire-Lise; Bernadac, Alain; Fukumori, Yoshihiro; Wu, Long-Fei

    2006-11-14

    Magnetosomes comprise a magnetic nanocrystal surrounded by a lipid bilayer membrane. These unique prokaryotic organelles align inside magnetotactic bacterial cells and serve as an intracellular compass allowing the bacteria to navigate along the geomagnetic field in aquatic environments. Cryoelectron tomography of Magnetospirillum strains has revealed that the magnetosome chain is surrounded by a network of filaments that may be composed of MamK given that the filaments are absent in the mamK mutant cells. The process of the MamK filament assembly is unknown. Here we prove the authenticity of the MamK filaments and show that MamK exhibits linear distribution inside Magnetospirillum sp. cells even in the area without magnetosomes. The mamK gene alone is sufficient to direct the synthesis of straight filaments in Escherichia coli, and one extremity of the MamK filaments is located at the cellular pole. By using dual fluorescent labeling of MamK, we found that MamK nucleates at multiple sites and assembles into mosaic filaments. Time-lapse experiments reveal that the assembly of the MamK filaments is a highly dynamic and kinetically asymmetrical process. MamK bundles might initiate the formation of a new filament or associate to one preexistent filament. Our results demonstrate the mechanism of biogenesis of prokaryotic cytoskeletal filaments that are structurally and functionally distinct from the known MreB and ParM filaments. In addition to positioning magnetosomes, other hypothetical functions of the MamK filaments in magnetotaxis might include anchoring magnetosomes and being involved in magnetic reception.

  6. Why cannot a β-lactamase gene be detected using an efficient molecular diagnostic method?

    PubMed Central

    Park, Kwang Seung; Lee, Jung Hun; Park, Moonhee; Karim, Asad Mustafa; Lee, Sang Hee

    2016-01-01

    Objective: Fast detection of β-lactamase (bla) genes can minimize the spread of antibiotic resistance. Although several molecular diagnostic methods have been developed to detect limited bla gene types, these methods have significant limitations, such as their failure to detect almost all clinically available bla genes. We have evaluated a further refinement of our fast and accurate molecular method, developed to overcome these limitations, using clinical isolates. Methods: We have recently developed the efficient large-scale bla detection method (large-scaleblaFinder) that can detect bla gene types including almost all clinically available 1,352 bla genes with perfect specificity and sensitivity. Using this method, we have evaluated a further refinement of this method using clinical isolates provided by International Health Management Associates, Inc. (Schaumburg, Illinois, USA). Results were interpreted in a blinded manner by researchers who did not know any information on bla genes harbored by these isolates. Results: With only one exception, the large-scaleblaFinder detected all bla genes identified by the provider using microarray and multiplex PCR. In one of the Escherichia coli test isolates, a blaDHA-1 gene was detected using the multiplex PCR assay but it was not detected using the large-scaleblaFinder. Conclusion: The truncation of a blaDHA-1 gene is an important reason for an efficient molecular diagnostic method (large-scaleblaFinder) not to detect the bla gene. PMID:27882043

  7. The enigma of prokaryotic life in deep hypersaline anoxic basins.

    PubMed

    van der Wielen, Paul W J J; Bolhuis, Henk; Borin, Sara; Daffonchio, Daniele; Corselli, Cesare; Giuliano, Laura; D'Auria, Giuseppe; de Lange, Gert J; Huebner, Andreas; Varnavas, Sotirios P; Thomson, John; Tamburini, Christian; Marty, Danielle; McGenity, Terry J; Timmis, Kenneth N

    2005-01-07

    Deep hypersaline anoxic basins in the Mediterranean Sea are a legacy of dissolution of ancient subterranean salt deposits from the Miocene period. Our study revealed that these hypersaline basins are not biogeochemical dead ends, but support in situ sulfate reduction, methanogenesis, and heterotrophic activity. A wide diversity of prokaryotes was observed, including a new, abundant, deeply branching order within the Euryarchaeota. Furthermore, we demonstrated the presence of a unique, metabolically active microbial community in the Discovery basin, which is one of the most extreme terrestrial saline environments known, as it is almost saturated with MgCl2 (5 M).

  8. Oxygenase-catalyzed ribosome hydroxylation occurs in prokaryotes and humans.

    PubMed

    Ge, Wei; Wolf, Alexander; Feng, Tianshu; Ho, Chia-hua; Sekirnik, Rok; Zayer, Adam; Granatino, Nicolas; Cockman, Matthew E; Loenarz, Christoph; Loik, Nikita D; Hardy, Adam P; Claridge, Timothy D W; Hamed, Refaat B; Chowdhury, Rasheduzzaman; Gong, Lingzhi; Robinson, Carol V; Trudgian, David C; Jiang, Miao; Mackeen, Mukram M; McCullagh, James S; Gordiyenko, Yuliya; Thalhammer, Armin; Yamamoto, Atsushi; Yang, Ming; Liu-Yi, Phebee; Zhang, Zhihong; Schmidt-Zachmann, Marion; Kessler, Benedikt M; Ratcliffe, Peter J; Preston, Gail M; Coleman, Mathew L; Schofield, Christopher J

    2012-12-01

    The finding that oxygenase-catalyzed protein hydroxylation regulates animal transcription raises questions as to whether the translation machinery and prokaryotic proteins are analogously modified. Escherichia coli ycfD is a growth-regulating 2-oxoglutarate oxygenase catalyzing arginyl hydroxylation of the ribosomal protein Rpl16. Human ycfD homologs, Myc-induced nuclear antigen (MINA53) and NO66, are also linked to growth and catalyze histidyl hydroxylation of Rpl27a and Rpl8, respectively. This work reveals new therapeutic possibilities via oxygenase inhibition and by targeting modified over unmodified ribosomes.

  9. Cas6 is an endoribonuclease that generates guide RNAs for invader defense in prokaryotes

    SciTech Connect

    Carte, Jason; Wang, Ruiying; Li, Hong; Terns, Rebecca M.; Terns, Michael P.

    2010-11-09

    An RNA-based gene silencing pathway that protects bacteria and archaea from viruses and other genome invaders is hypothesized to arise from guide RNAs encoded by CRISPR loci and proteins encoded by the cas genes. CRISPR loci contain multiple short invader-derived sequences separated by short repeats. The presence of virus-specific sequences within CRISPR loci of prokaryotic genomes confers resistance against corresponding viruses. The CRISPR loci are transcribed as long RNAs that must be processed to smaller guide RNAs. Here we identified Pyrococcus furiosus Cas6 as a novel endoribonuclease that cleaves CRISPR RNAs within the repeat sequences to release individual invader targeting RNAs. Cas6 interacts with a specific sequence motif in the 5{prime} region of the CRISPR repeat element and cleaves at a defined site within the 3{prime} region of the repeat. The 1.8 angstrom crystal structure of the enzyme reveals two ferredoxin-like folds that are also found in other RNA-binding proteins. The predicted active site of the enzyme is similar to that of tRNA splicing endonucleases, and concordantly, Cas6 activity is metal-independent. cas6 is one of the most widely distributed CRISPR-associated genes. Our findings indicate that Cas6 functions in the generation of CRISPR-derived guide RNAs in numerous bacteria and archaea.

  10. A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments

    PubMed Central

    Bentkowski, Piotr; Van Oosterhout, Cock; Mock, Thomas

    2015-01-01

    Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt. PMID:26242601

  11. A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments.

    PubMed

    Bentkowski, Piotr; Van Oosterhout, Cock; Mock, Thomas

    2015-08-04

    Temporal variability in ecosystems significantly impacts species diversity and ecosystem productivity and therefore the evolution of organisms. Different levels of environmental perturbations such as seasonal fluctuations, natural disasters, and global change have different impacts on organisms and therefore their ability to acclimatize and adapt. Thus, to understand how organisms evolve under different perturbations is a key for predicting how environmental change will impact species diversity and ecosystem productivity. Here, we developed a computer simulation utilizing the individual-based model approach to investigate genome size evolution of a haploid, clonal and free-living prokaryotic population across different levels of environmental perturbations. Our results show that a greater variability of the environment resulted in genomes with a larger number of genes. Environmental perturbations were more effectively buffered by populations of individuals with relatively large genomes. Unpredictable changes of the environment led to a series of population bottlenecks followed by adaptive radiations. Our model shows that the evolution of genome size is indirectly driven by the temporal variability of the environment. This complements the effects of natural selection directly acting on genome optimization. Furthermore, species that have evolved in relatively stable environments may face the greatest risk of extinction under global change as genome streamlining genetically constrains their ability to acclimatize to the new environmental conditions, unless mechanisms of genetic diversification such as horizontal gene transfer will enrich their gene pool and therefore their potential to adapt.

  12. Gene Transfers Between Distantly Related Organisms

    NASA Technical Reports Server (NTRS)

    Doolittle, Russell F.

    2003-01-01

    With the completion of numerous microbial genome sequences, reports of individual gene transfers between distantly related prokaryotes have become commonplace. On the other hand, transfers between prokaryotes and eukaryotes still excite the imagination. Many of these claims may be premature, but some are certainly valid. In this chapter, the kinds of supporting data needed to propose transfers between distantly related organisms and cite some interesting examples are considered.

  13. Endosymbiotic origin and differential loss of eukaryotic genes.

    PubMed

    Ku, Chuan; Nelson-Sathi, Shijulal; Roettger, Mayo; Sousa, Filipa L; Lockhart, Peter J; Bryant, David; Hazkani-Covo, Einat; McInerney, James O; Landan, Giddy; Martin, William F

    2015-08-27

    Chloroplasts arose from cyanobacteria, mitochondria arose from proteobacteria. Both organelles have conserved their prokaryotic biochemistry, but their genomes are reduced, and most organelle proteins are encoded in the nucleus. Endosymbiotic theory posits that bacterial genes in eukaryotic genomes entered the eukaryotic lineage via organelle ancestors. It predicts episodic influx of prokaryotic genes into the eukaryotic lineage, with acquisition corresponding to endosymbiotic events. Eukaryotic genome sequences, however, increasingly implicate lateral gene transfer, both from prokaryotes to eukaryotes and among eukaryotes, as a source of gene content variation in eukaryotic genomes, which predicts continuous, lineage-specific acquisition of prokaryotic genes in divergent eukaryotic groups. Here we discriminate between these two alternatives by clustering and phylogenetic analysis of eukaryotic gene families having prokaryotic homologues. Our results indicate (1) that gene transfer from bacteria to eukaryotes is episodic, as revealed by gene distributions, and coincides with major evolutionary transitions at the origin of chloroplasts and mitochondria; (2) that gene inheritance in eukaryotes is vertical, as revealed by extensive topological comparison, sparse gene distributions stemming from differential loss; and (3) that continuous, lineage-specific lateral gene transfer, although it sometimes occurs, does not contribute to long-term gene content evolution in eukaryotic genomes.

  14. MinFinder: Locating all the local minima of a function

    NASA Astrophysics Data System (ADS)

    Tsoulos, Ioannis G.; Lagaris, Isaac E.

    2006-01-01

    A new stochastic clustering algorithm is introduced that aims to locate all the local minima of a multidimensional continuous and differentiable function inside a bounded domain. The accompanying software (MinFinder) is written in ANSI C++. However, the user may code his objective function either in C++, C or Fortran 77. We compare the performance of this new method to the performance of Multistart and Topographical Multilevel Single Linkage Clustering on a set of benchmark problems. Program summaryTitle of program:MinFinder Catalogue identifier:ADWU Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWU Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Computer for which the program is designed and others on which is has been tested:The tool is designed to be portable in all systems running the GNU C++ compiler Installation:University of Ioannina, Greece Programming language used:GNU-C++, GNU-C, GNU Fortran 77 Memory required to execute with typical data:200 KB No. of bits in a word:32 No. of processors used:1 Has the code been vectorized or parallelized?:no No. of lines in distributed program, including test data, etc.:5797 No. of bytes in distributed program, including test data, etc.:588 121 Distribution format:gzipped tar file Nature of the physical problem:A multitude of problems in science and engineering are often reduced to minimizing a function of many variables. There are instances that a local optimum does not correspond to the desired physical solution and hence the search for a better solution is required. Local optimization techniques can be trapped in any local minimum. Global optimization is then the appropriate tool. For example, solving a non-linear system of equations via optimization, employing a "least squares" type of objective, one may encounter many local minima that do not correspond to solutions, i.e. they are far from zero. Method of solution:Using a uniform pdf, points are sampled from the

  15. RNA helicases: diverse roles in prokaryotic response to abiotic stress.

    PubMed

    Owttrim, George W

    2013-01-01

    Similar to proteins, RNA molecules must fold into the correct conformation and associate with protein complexes in order to be functional within a cell. RNA helicases rearrange RNA secondary structure and RNA-protein interactions in an ATP-dependent reaction, performing crucial functions in all aspects of RNA metabolism. In prokaryotes, RNA helicase activity is associated with roles in housekeeping functions including RNA turnover, ribosome biogenesis, translation and small RNA metabolism. In addition, RNA helicase expression and/or activity are frequently altered during cellular response to abiotic stress, implying they perform defined roles during cellular adaptation to changes in the growth environment. Specifically, RNA helicases contribute to the formation of cold-adapted ribosomes and RNA degradosomes, implying a role in alleviation of RNA secondary structure stabilization at low temperature. A common emerging theme involves RNA helicases acting as scaffolds for protein-protein interaction and functioning as molecular clamps, holding RNA-protein complexes in specific conformations. This review highlights recent advances in DEAD-box RNA helicase association with cellular response to abiotic stress in prokaryotes.

  16. Membrane remodeling and organization: Elements common to prokaryotes and eukaryotes.

    PubMed

    Vega-Cabrera, Luz A; Pardo-López, Liliana

    2017-02-01

    Membrane remodeling processes in eukaryotes, such as those involved in endocytosis and intracellular trafficking, are mediated by a large number of structural, accessory and regulatory proteins. These processes occur in all cell types, enabling the exchange of signals and/or nutrients with the external medium and with neighboring cells; likewise, they are required for the intracellular trafficking of various cargo molecules between organelles, as well as the recycling of these structures. Recent studies have demonstrated that some elements of the molecular machinery involved in regulating and mediating endocytosis in eukaryotic cells are also present in some bacteria, where they participate in processes such as cell division, sporulation and signal transduction. However, the mechanism whereby this prokaryotic machinery carries out such functions has barely begun to be elucidated. This review summarizes recent information about the cytoskeletal and membrane-organizing proteins for which bacterial homologs have been identified; given their known functions, they may be considered to be part of an ancestral membrane organization system that first emerged in prokaryotes and which further evolved into the more complex regulatory networks operating in eukaryotes. © 2017 IUBMB Life, 69(2):55-62, 2017.

  17. Early evolution: prokaryotes, the new kids on the block.

    PubMed

    Poole, A; Jeffares, D; Penny, D

    1999-10-01

    Prokaryotes are generally assumed to be the oldest existing form of life on earth. This assumption, however, makes it difficult to understand certain aspects of the transition from earlier stages in the origin of life to more complex ones, and it does not account for many apparently ancient features in the eukaryotes. From a model of the RNA world, based on relic RNA species in modern organisms, one can infer that there was an absolute requirement for a high-accuracy RNA replicase even before proteins evolved. In addition, we argue here that the ribosome (together with the RNAs involved in its assembly) is so large that it must have had a prior function before protein synthesis. A model that connects and equates these two requirements (high-accuracy RNA replicase and prior function of the ribosome) can explain many steps in the origin of life while accounting for the observation that eukaryotes have retained more vestiges of the RNA world. The later derivation of prokaryote RNA metabolism and genome structure can be accounted for by the two complementary mechanisms of r-selection and thermoreduction.

  18. Environmental Pressure May Change the Composition Protein Disorder in Prokaryotes.

    PubMed

    Vicedo, Esmeralda; Schlessinger, Avner; Rost, Burkhard

    2015-01-01

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

  19. Meltwater export of prokaryotic cells from the Greenland ice sheet.

    PubMed

    Cameron, Karen A; Stibal, Marek; Hawkings, Jon R; Mikkelsen, Andreas B; Telling, Jon; Kohler, Tyler J; Gözdereliler, Erkin; Zarsky, Jakub D; Wadham, Jemma L; Jacobsen, Carsten S

    2017-02-01

    Microorganisms are flushed from the Greenland Ice Sheet (GrIS) where they may contribute towards the nutrient cycling and community compositions of downstream ecosystems. We investigate meltwater microbial assemblages as they exit the GrIS from a large outlet glacier, and as they enter a downstream river delta during the record melt year of 2012. Prokaryotic abundance, flux and community composition was studied, and factors affecting community structures were statistically considered. The mean concentration of cells exiting the ice sheet was 8.30 × 10(4) cells mL(-1) and we estimate that ∼1.02 × 10(21) cells were transported to the downstream fjord in 2012, equivalent to 30.95 Mg of carbon. Prokaryotic microbial assemblages were dominated by Proteobacteria, Bacteroidetes, and Actinobacteria. Cell concentrations and community compositions were stable throughout the sample period, and were statistically similar at both sample sites. Based on our observations, we argue that the subglacial environment is the primary source of the river-transported microbiota, and that cell export from the GrIS is dependent on discharge. We hypothesise that the release of subglacial microbiota to downstream ecosystems will increase as freshwater flux from the GrIS rises in a warming world.

  20. Is wheat mitochondrial 5S ribosomal RNA prokaryotic in nature?

    PubMed Central

    Gray, M W; Spencer, D F

    1981-01-01

    Küntzel et al. (1981) (Nucleic Acids Res. 9, 1451-1461) recently concluded that the sequence of wheat mitochondrial 5S rRNA is significantly more related to prokaryotic than to eukaryotic 5S rRNA sequences, and displays an especially high affinity to that of the thermophilic Gram-negative bacterium, Thermus aquaticus. However, the sequence on which this conclusion was based, although attributed to us, differs in several places from the one determined by us. We show here that the correct sequence (Spencer, D.F., Bonen, L. and Gray, M.W. (1981) Biochemistry, in press) does not support the conclusions of Küntzel et al. about potential secondary structure in wheat mitochondrial 5S rRNA and its phylogenetic significance. We further show that when the wheat mitochondrial 5S rRNA sequence is matched against published alignments for E. coli, T. aquaticus, and wheat cytosol 5S rRNAs, the mitochondrial sequence shows no greater homology to the T. aquaticus sequence than to the E. coli sequence, and only slightly more homology to these two sequences than to wheat cytosol 5S rRNA. This analysis confirms our original view (Biochemistry, in press) that wheat mitochondrial 5S rRNA is neither obviously prokaryotic nor eukaryotic in nature, but shows characteristics of both classes of 5S rRNA, as well as some unique features. PMID:7024917

  1. Structural and functional relationships between prokaryotic and eukaryotic DNA polymerases.

    PubMed Central

    Bernad, A; Zaballos, A; Salas, M; Blanco, L

    1987-01-01

    The Bacillus subtilis phage luminal diameter 29 DNA polymerase, involved in protein-primed viral DNA replication, was inhibited by phosphonoacetic acid (PAA), a known inhibitor of alpha-like DNA polymerases, by decreasing the rate of elongation. Three highly conserved regions of amino acid homology, found in several viral alpha-like DNA polymerases and in the luminal diameter 29 DNA polymerase, one of them proposed to be the PAA binding site, were also found in the T4 DNA polymerase. This prokaryotic enzyme was highly sensitive to the drugs aphidicolin and the nucleotide analogues butylanilino dATP (BuAdATP) and butylphenyl dGTP (BuPdGTP), known to be specific inhibitors of eukaryotic alpha-like DNA polymerases. Two potential DNA polymerases from the linear plasmid pGKL1 from yeast and the S1 mitochondrial DNA from maize have been identified, based on the fact that they contain the three conserved regions of amino acid homology. Comparison of DNA polymerases from prokaryotic and eukaryotic origin showed extensive amino acid homology in addition to highly conserved domains. These findings reflect evolutionary relationships between hypothetically unrelated DNA polymerases. Images Fig. 1. Fig. 2. Fig. 4. PMID:3127204

  2. MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation

    PubMed Central

    Liao, Yu-Chieh; Lin, Hsin-Hung; Sabharwal, Amarpreet; Haase, Elaine M.; Scannapieco, Frank A.

    2016-01-01

    MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease. PMID:25911337

  3. MyPro: A seamless pipeline for automated prokaryotic genome assembly and annotation.

    PubMed

    Liao, Yu-Chieh; Lin, Hsin-Hung; Sabharwal, Amarpreet; Haase, Elaine M; Scannapieco, Frank A

    2015-06-01

    MyPro is a software pipeline for high-quality prokaryotic genome assembly and annotation. It was validated on 18 oral streptococcal strains to produce submission-ready, annotated draft genomes. MyPro installed as a virtual machine and supported by updated databases will enable biologists to perform quality prokaryotic genome assembly and annotation with ease.

  4. Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems

    NASA Astrophysics Data System (ADS)

    Wang, Jun-Tao; Zheng, Yuan-Ming; Hu, Hang-Wei; Li, Jing; Zhang, Li-Mei; Chen, Bao-Dong; Chen, Wei-Ping; He, Ji-Zheng

    2016-01-01

    The belowground soil prokaryotic community plays a cardinal role in sustaining the stability and functions of forest ecosystems. Yet, the nature of how soil prokaryotic diversity co-varies with aboveground plant diversity along a latitudinal gradient remains elusive. By establishing three hundred 400-m2 quadrats from tropical rainforest to boreal forest in a large-scale parallel study on both belowground soil prokaryote and aboveground tree and herb communities, we found that soil prokaryotic diversity couples with the diversity of herbs rather than trees. The diversity of prokaryotes and herbs responds similarly to environmental factors along the latitudinal gradient. These findings revealed that herbs provide a good predictor of belowground biodiversity in forest ecosystems, and provide new perspective on the aboveground and belowground interactions in forest ecosystems.

  5. Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems.

    PubMed

    Wang, Jun-Tao; Zheng, Yuan-Ming; Hu, Hang-Wei; Li, Jing; Zhang, Li-Mei; Chen, Bao-Dong; Chen, Wei-Ping; He, Ji-Zheng

    2016-01-19

    The belowground soil prokaryotic community plays a cardinal role in sustaining the stability and functions of forest ecosystems. Yet, the nature of how soil prokaryotic diversity co-varies with aboveground plant diversity along a latitudinal gradient remains elusive. By establishing three hundred 400-m(2) quadrats from tropical rainforest to boreal forest in a large-scale parallel study on both belowground soil prokaryote and aboveground tree and herb communities, we found that soil prokaryotic diversity couples with the diversity of herbs rather than trees. The diversity of prokaryotes and herbs responds similarly to environmental factors along the latitudinal gradient. These findings revealed that herbs provide a good predictor of belowground biodiversity in forest ecosystems, and provide new perspective on the aboveground and belowground interactions in forest ecosystems.

  6. Coupling of soil prokaryotic diversity and plant diversity across latitudinal forest ecosystems

    PubMed Central

    Wang, Jun-Tao; Zheng, Yuan-Ming; Hu, Hang-Wei; Li, Jing; Zhang, Li-Mei; Chen, Bao-Dong; Chen, Wei-Ping; He, Ji-Zheng

    2016-01-01

    The belowground soil prokaryotic community plays a cardinal role in sustaining the stability and functions of forest ecosystems. Yet, the nature of how soil prokaryotic diversity co-varies with aboveground plant diversity along a latitudinal gradient remains elusive. By establishing three hundred 400-m2 quadrats from tropical rainforest to boreal forest in a large-scale parallel study on both belowground soil prokaryote and aboveground tree and herb communities, we found that soil prokaryotic diversity couples with the diversity of herbs rather than trees. The diversity of prokaryotes and herbs responds similarly to environmental factors along the latitudinal gradient. These findings revealed that herbs provide a good predictor of belowground biodiversity in forest ecosystems, and provide new perspective on the aboveground and belowground interactions in forest ecosystems. PMID:26781165

  7. Environmental use of a Laser Range Finder and the Advanced Visualization System

    NASA Astrophysics Data System (ADS)

    Thornton, E. N.; Bohn, S.; Baker, C. P.; Jones, D. R.; Strope, L. A.

    1993-05-01

    The United States Department of Energy (DOE) is facing a large task in characterizing and remediating the contents of hazardous waste inside storage tanks. The characterization process of these tanks is a key step to the remediation process. Due to the hazardous materials inside the waste tanks, all of the work must be done remotely utilizing robotic systems. The Laser Range Finder (LRF) is a single point sensor used to remotely collect range and intensity data. The LRF sensor data is used to reconstruct the tank surface environment based on multiple LRF scans. This reconstructed surface definition can be used by a robotic controller to perform obstacle avoidance with items in the tank. The Pacific Northwest Laboratory (PNL) has used Advanced Visualization System (AVS) to prototype the filtering, transformation, and reconstructing process. AVS software modules have been written to address LRF filtering on both the range and intensity images. A coordinate transformation module was constructed to convert the raw LRF data into a Cartesian coordinate reference frame. The results of filtering and transforms are integrated into a master map of the tank using an octree database. Master octrees are traversed and made into AVS geometry to visualize the tank interior. The graphical display of the tank interior can be used for robotic path planning and monitoring waste removal progress.

  8. Parallel 4-Dimensional Cellular Automaton Track Finder for the CBM Experiment

    NASA Astrophysics Data System (ADS)

    Akishina, Valentina; Kisel, Ivan

    2016-10-01

    The CBM experiment (FAIR/GSI, Darmstadt, Germany) will focus on the measurement of rare probes at interaction rates up to 10 MHz with data flow of up to 1 TB/s. It requires a novel read-out and data-acquisition concept with self-triggered electronics and free-streaming data. In this case resolving different collisions is not a trivial task and event building must be performed in software online. That requires full online event reconstruction and selection not only in space, but also in time, so-called 4D event building and selection. This is a task of the First-Level Event Selection (FLES). The FLES reconstruction and selection package consists of several modules: track finding, track fitting, short-lived particles finding, event building and event selection. The Cellular Automaton (CA) track finder algorithm was adapted towards time-slice-based reconstruction and included into the CBMROOT framework. In this article, we describe the modification done to the algorithm, as well as the performance of the developed time-based approach.

  9. Passive isolator design for jitter reduction in the Terrestrial Planet Finder Coronagraph

    NASA Technical Reports Server (NTRS)

    Blaurock, Carl; Liu, Kuo-Chia; Dewell, Larry; Alexander, James

    2005-01-01

    Terrestrial Planet Finder (TPF) is a mission to locate and study extrasolar Earth-like planets. The TPF Coronagraph (TPF-C), planned for launch in the latter half of the next decade, will use a coronagraphic mask and other optics to suppress the light of the nearby star in order to collect visible light from such planets. The required contrast ratio of 5e-11 can only be achieved by maintaining pointing accuracy to 4 milli-arcseconds, and limiting optics jitter to below 5 nm. Numerous mechanical disturbances act to induce jitter. This paper concentrates on passive isolation techniques to minimize the optical degradation introduced by disturbance sources. A passive isolation system, using compliant mounts placed at an energy bottleneck to reduce energy transmission above a certain frequency, is a low risk, flight proven design approach. However, the attenuation is limited, compared to an active system, so the feasibility of the design must be demonstrated by analysis. The paper presents the jitter analysis for the baseline TPF design, using a passive isolation system. The analysis model representing the dynamics of the spacecraft and telescope is described, with emphasis on passive isolator modeling. Pointing and deformation metrics, consistent with the TPF-C error budget, are derived. Jitter prediction methodology and results are presented. Then an analysis of the critical design parameters that drive the TPF-C jitter response is performed.

  10. FINDER, A system providing complex decision support for commercial transport replanning operations

    NASA Astrophysics Data System (ADS)

    Bittermann, Vincent; Deker, Guy; Sassus, Pierre; Mielnik, Jean-Christophe; Jud, Jean-Marie

    1994-03-01

    Decision-aid systems, likely to appear in future aircraft generations, could play a central role in the cockpit thanks to the broad spectrum of functionalities and decision support facilities they will offer to the crew. As part of such systems, the exploratory FINDER mock-up is a knowledge based system (KBS) designed to help crew members continually optimize their flight plan by suggesting solutions considering exhaustive information related to flight context, either on pilot request or upon external information occurrence. The successful evaluation by Air France pilots of that first mock-up dedicated to diversion procedure on pilot request has led to the current development of an enhanced system with nominal enroute operations and real-time capabilities. Nominal enroute operations concern the optimization with respect to an evolutive constraining of favoring environment (due to weather, traffic or regulated areas, and ETOPS constraints). This study paves the way for a future flight assistant system concept which is already under investigation and may take place in SEXTANT Avionique's future development steps.

  11. Recognition of flow in everyday life using sensor agent robot with laser range finder

    NASA Astrophysics Data System (ADS)

    Goshima, Misa; Mita, Akira

    2011-04-01

    In the present paper, we suggest an algorithm for a sensor agent robot with a laser range finder to recognize the flows of residents in the living spaces in order to achieve flow recognition in the living spaces, recognition of the number of people in spaces, and the classification of the flows. House reform is or will be demanded to prolong the lifetime of the home. Adaption for the individuals is needed for our aging society which is growing at a rapid pace. Home autonomous mobile robots will become popular in the future for aged people to assist them in various situations. Therefore we have to collect various type of information of human and living spaces. However, a penetration in personal privacy must be avoided. It is essential to recognize flows in everyday life in order to assist house reforms and aging societies in terms of adaption for the individuals. With background subtraction, extra noise removal, and the clustering based k-means method, we got an average accuracy of more than 90% from the behavior from 1 to 3 persons, and also confirmed the reliability of our system no matter the position of the sensor. Our system can take advantages from autonomous mobile robots and protect the personal privacy. It hints at a generalization of flow recognition methods in the living spaces.

  12. Out-of-the-ecliptic Trajectories to Reduce Zodiacal Dust Interference for Terrestrial Planet Finder

    NASA Astrophysics Data System (ADS)

    Arrell, R.; Gurfil, P.; Kasdin, J.; Seager, S.; Nissanke, S.

    2001-05-01

    Out-of-the-ecliptic trajectories that are beneficial to space observatories such as the Terrestrial Planet Finder and other potential mid-IR missions are introduced. These novel trajectories result in significantly reduced background noise from the zodiacal dust and therefore allow a reduction in the necessary size of the telescope collecting area. The reduced size of the mirrors allows for a considerable reduction in payload mass and manufacturing costs. Two types of optimal trajectories that are energetically feasible were derived using genetic algorithms. These are highly inclined non-Keplerian heliocentric orbits. We use the zodiacal dust model from the COBE data (Kelsall et al. 1998) to determine how well the orbits mitigate the zodi dust interference. The first optimal trajectory can use existing launch technology and yields a maximum decrease of 67% in the zodiacal cloud brightness. The zodi brightness for this trajectory is reduced by at least 50% for 60% of the mission lifetime. The second optimal trajectory requires planned improvement in launch technology but it renders a dramatic 97% maximum noise decrease. The zodi brightness is reduced by at least 70% for 82% of the mission lifetime for this trajectory. Heliocentric orbits at 5 AU have been discussed because the zodi dust concentration is extremely low there. Unfortunately such orbits are exceedingly impractical because of high cost, power source constraints (inability to use solar cells), and a long travel time before science return.

  13. Bore-Sight Calibration of Multiple Laser Range Finders for Kinematic 3D Laser Scanning Systems.

    PubMed

    Jung, Jaehoon; Kim, Jeonghyun; Yoon, Sanghyun; Kim, Sangmin; Cho, Hyoungsig; Kim, Changjae; Heo, Joon

    2015-05-04

    The Simultaneous Localization and Mapping (SLAM) technique has been used for autonomous navigation of mobile systems; now, its applications have been extended to 3D data acquisition of indoor environments. In order to reconstruct 3D scenes of indoor space, the kinematic 3D laser scanning system, developed herein, carries three laser range finders (LRFs): one is mounted horizontally for system-position correction and the other two are mounted vertically to collect 3D point-cloud data of the surrounding environment along the system's trajectory. However, the kinematic laser scanning results can be impaired by errors resulting from sensor misalignment. In the present study, the bore-sight calibration of multiple LRF sensors was performed using a specially designed double-deck calibration facility, which is composed of two half-circle-shaped aluminum frames. Moreover, in order to automatically achieve point-to-point correspondences between a scan point and the target center, a V-shaped target was designed as well. The bore-sight calibration parameters were estimated by a constrained least squares method, which iteratively minimizes the weighted sum of squares of residuals while constraining some highly-correlated parameters. The calibration performance was analyzed by means of a correlation matrix. After calibration, the visual inspection of mapped data and residual calculation confirmed the effectiveness of the proposed calibration approach.

  14. Using a laser range finder mounted on a MicroVision robot to estimate environmental parameters

    NASA Astrophysics Data System (ADS)

    Fehr, Duc; Papanikolopoulos, Nikos

    2009-05-01

    In this article we will present a new robot (MicroVision) that has been designed at the University of Minnesota (UMN), Center for Distributed Robotics. Its design reminds of the designs of previous robots built at the UMN such as the COTS Scouts or the eROSIs. It is composed of a body with two wheels and a tail just like the two aforementioned robots. However, the MicroVision has more powerful processing and sensing capabilities and we utilized these to compute areas in the surrounding environment by using a convex hull approach. We are trying to estimate the projected area of an object onto the ground. This is done by the computation of convex hulls that are based on the data received from the MicroVision's laser range finder. Although localization of the robot is an important feature in being able to compute these convex hulls, localization and mapping techniques are only used as a tool and are not an end in this work. The main idea of this work is to demonstrate the ability of the laser carrying MicroVision robot to move around an object in order to get a scan from each side. From these scans, the convex hull of the shape is deduced and its projected area onto the ground is estimated.

  15. ProGeRF: Proteome and Genome Repeat Finder Utilizing a Fast Parallel Hash Function

    PubMed Central

    Moraes, Walas Jhony Lopes; Rodrigues, Thiago de Souza; Bartholomeu, Daniella Castanheira

    2015-01-01

    Repetitive element sequences are adjacent, repeating patterns, also called motifs, and can be of different lengths; repetitions can involve their exact or approximate copies. They have been widely used as molecular markers in population biology. Given the sizes of sequenced genomes, various bioinformatics tools have been developed for the extraction of repetitive elements from DNA sequences. However, currently available tools do not provide options for identifying repetitive elements in the genome or proteome, displaying a user-friendly web interface, and performing-exhaustive searches. ProGeRF is a web site for extracting repetitive regions from genome and proteome sequences. It was designed to be efficient, fast, and accurate and primarily user-friendly web tool allowing many ways to view and analyse the results. ProGeRF (Proteome and Genome Repeat Finder) is freely available as a stand-alone program, from which the users can download the source code, and as a web tool. It was developed using the hash table approach to extract perfect and imperfect repetitive regions in a (multi)FASTA file, while allowing a linear time complexity. PMID:25811026

  16. The instrument control software package for the Habitable-Zone Planet Finder spectrometer

    NASA Astrophysics Data System (ADS)

    Bender, Chad F.; Robertson, Paul; Stefansson, Gudmundur Kari; Monson, Andrew; Anderson, Tyler; Halverson, Samuel; Hearty, Frederick; Levi, Eric; Mahadevan, Suvrath; Nelson, Matthew; Ramsey, Larry; Roy, Arpita; Schwab, Christian; Shetrone, Matthew; Terrien, Ryan

    2016-08-01

    We describe the Instrument Control Software (ICS) package that we have built for The Habitable-Zone Planet Finder (HPF) spectrometer. The ICS controls and monitors instrument subsystems, facilitates communication with the Hobby-Eberly Telescope facility, and provides user interfaces for observers and telescope operators. The backend is built around the asynchronous network software stack provided by the Python Twisted engine, and is linked to a suite of custom hardware communication protocols. This backend is accessed through Python-based command-line and PyQt graphical frontends. In this paper we describe several of the customized subsystem communication protocols that provide access to and help maintain the hardware systems that comprise HPF, and show how asynchronous communication benefits the numerous hardware components. We also discuss our Detector Control Subsystem, built as a set of custom Python wrappers around a C-library that provides native Linux access to the SIDECAR ASIC and Hawaii-2RG detector system used by HPF. HPF will be one of the first astronomical instruments on sky to utilize this native Linux capability through the SIDECAR Acquisition Module (SAM) electronics. The ICS we have created is very flexible, and we are adapting it for NEID, NASA's Extreme Precision Doppler Spectrometer for the WIYN telescope; we will describe this adaptation, and describe the potential for use in other astronomical instruments.

  17. Capabilities and performance of the Automated Planet Finder telescope with the implementation of a dynamic scheduler

    NASA Astrophysics Data System (ADS)

    Burt, Jennifer; Holden, Bradford; Hanson, Russell; Laughlin, Greg; Vogt, Steve; Butler, Paul; Keiser, Sandy; Deich, William

    2015-10-01

    We report initial performance results emerging from 600 h of observations with the Automated Planet Finder (APF) telescope and Levy spectrometer located at UCO/Lick Observatory. We have obtained multiple spectra of 80 G, K, and M-type stars, which comprise 4954 individual Doppler radial velocity (RV) measurements with a median internal uncertainty of 1.35 ms-1. We find a strong, expected correlation between the number of photons accumulated in the 5000 to 6200 Å iodine region of the spectrum and the resulting internal uncertainty estimates. Additionally, we find an offset between the population of G and K stars and the M stars within the dataset when comparing these parameters. As a consequence of their increased spectral line densities, M-type stars permit the same level of internal uncertainty with 2× fewer photons than G-type and K-type stars. When observing M stars, we show that the APF/Levy has essentially the same speed-on-sky as Keck/high resolution echelle spectrometer (HIRES) for precision RVs. In the interest of using the APF for long-duration RV surveys, we have designed and implemented a dynamic scheduling algorithm. We discuss the operation of the scheduler, which monitors ambient conditions and combines on-sky information with a database of survey targets to make intelligent, real-time targeting decisions.

  18. Lightning Radio Source Retrieval Using Advanced Lightning Direction Finder (ALDF) Networks

    NASA Technical Reports Server (NTRS)

    Koshak, William J.; Blakeslee, Richard J.; Bailey, J. C.

    1998-01-01

    A linear algebraic solution is provided for the problem of retrieving the location and time of occurrence of lightning ground strikes from an Advanced Lightning Direction Finder (ALDF) network. The ALDF network measures field strength, magnetic bearing and arrival time of lightning radio emissions. Solutions for the plane (i.e., no Earth curvature) are provided that implement all of tile measurements mentioned above. Tests of the retrieval method are provided using computer-simulated data sets. We also introduce a quadratic planar solution that is useful when only three arrival time measurements are available. The algebra of the quadratic root results are examined in detail to clarify what portions of the analysis region lead to fundamental ambiguities in source location. Complex root results are shown to be associated with the presence of measurement errors when the lightning source lies near an outer sensor baseline of the ALDF network. In the absence of measurement errors, quadratic root degeneracy (no source location ambiguity) is shown to exist exactly on the outer sensor baselines for arbitrary non-collinear network geometries. The accuracy of the quadratic planar method is tested with computer generated data sets. The results are generally better than those obtained from the three station linear planar method when bearing errors are about 2 deg. We also note some of the advantages and disadvantages of these methods over the nonlinear method of chi(sup 2) minimization employed by the National Lightning Detection Network (NLDN) and discussed in Cummins et al.(1993, 1995, 1998).

  19. The ROCKSTAR Phase-space Temporal Halo Finder and the Velocity Offsets of Cluster Cores

    NASA Astrophysics Data System (ADS)

    Behroozi, Peter S.; Wechsler, Risa H.; Wu, Hao-Yi

    2013-01-01

    We present a new algorithm for identifying dark matter halos, substructure, and tidal features. The approach is based on adaptive hierarchical refinement of friends-of-friends groups in six phase-space dimensions and one time dimension, which allows for robust (grid-independent, shape-independent, and noise-resilient) tracking of substructure; as such, it is named ROCKSTAR (Robust Overdensity Calculation using K-Space Topologically Adaptive Refinement). Our method is massively parallel (up to 105 CPUs) and runs on the largest current simulations (>1010 particles) with high efficiency (10 CPU hours and 60 gigabytes of memory required per billion particles analyzed). A previous paper has shown ROCKSTAR to have excellent recovery of halo properties; we expand on these comparisons with more tests and higher-resolution simulations. We show a significant improvement in substructure recovery compared to several other halo finders and discuss the theoretical and practical limits of simulations in this regard. Finally, we present results that demonstrate conclusively that dark matter halo cores are not at rest relative to the halo bulk or substructure average velocities and have coherent velocity offsets across a wide range of halo masses and redshifts. For massive clusters, these offsets can be up to 350 km s-1 at z = 0 and even higher at high redshifts. Our implementation is publicly available at http://code.google.com/p/rockstar.

  20. On-board SLAM for indoor UAV using a laser range finder

    NASA Astrophysics Data System (ADS)

    Alpen, M.; Willrodt, C.; Frick, K.; Horn, J.

    2010-04-01

    Here we present a real-time algorithm for on-board SLAM (simultaneous localization and mapping) of a quadrotor using a laser range finder. Based on successfully implemented techniques for ground robots, we developed an algorithm that merges a new scan into the global map without any iteration. This causes some inaccuracy of the global map which leads to an error propagation during the robot's mission. Therefore an optimization algorithm reducing this inaccuracy is essential. Within this optimization lines with the same orientation and an overlapping in one of the two possible coordinates of a 2D-plane are merged if their distance is below a certain threshold value. Due to reduction of the required computing power for SLAM calculation by using orthogonal SLAM a real time SLAM running on a microcontroller becomes possible. Because of the small weight and the low electric power consumption, this controller can be mounted on an industrial quadrotor. Therefore acting autonomously in an unknown indoor environment becomes possible. In this paper we also show the validation of the presented SLAM algorithm. The first step of validation is an offline implementation in Matlab and the second step is the online validation of our algorithm on the industrial quadrotor AR100B of the AirRobot Company.

  1. Integrated modeling of optical performance for the Terrestrial Planet Finder structurally connected interferometer

    NASA Astrophysics Data System (ADS)

    LoBosco, David M.; Blaurock, Carl; Chung, Soon-Jo; Miller, David W.

    2004-09-01

    The Terrestrial Planet Finder (TPF) mission, to be launched in 2014 as a part of NASA's Origins Program, will search for Earth-like planets orbiting other stars. One main concept under study is a structurally connected interferometer. Integrated modeling of all aspects of the flight system is necessary to ensure that the stringent dynamic stability requirements imposed by the mission are met. The MIT Space Systems Laboratory has developed a suite of analysis tools known as DOCS (Disturbances Optics Controls Structures) that provides a MATLAB environment for managing integrated models and performing analysis and design optimization. DOCS provides a framework for identifying critical subsystem design parameters and efficiently computing system performance as a function of subsystem design. Additionally, the gradients of the performance outputs with respect to design variables can be analytically computed and used for automated exploration and optimization of the design space. The TPF integrated model consists of a structural finite element model, optical performance model, reaction wheel isolation stage, and attitude/optical control systems. The integrated model is expandable and upgradeable due to the modularity of the state-space subsystem models. Optical performance under reaction wheel disturbances is computed, and the effects of changing design parameters are explored. The results identify redesign options that meet performance requirements with improved margins, reduced cost and minimized risk.

  2. Compact MEMS mirror based Q-switch module for pulse-on-demand laser range finders

    NASA Astrophysics Data System (ADS)

    Milanović, Veljko; Kasturi, Abhishek; Atwood, Bryan; Su, Yu; Limkrailassiri, Kevin; Nettleton, John E.; Goldberg, Lew; Cole, Brian J.; Hough, Nathaniel

    2015-02-01

    A highly compact and low power consuming Q-switch module was developed based on a fast single-axis MEMS mirror, for use in eye-safe battery-powered laser range finders The module's 1.6mm x 1.6mm mirror has <99% reflectance at 1535nm wavelength and can achieve mechanical angle slew rates of over 500 rad/sec when switching the Er/Yb:Glass lasing cavity from pumping to lasing state. The design targeted higher efficiency, smaller size, and lower cost than the traditional Electro-Optical Q-Switch. Because pulse-on-demand capability is required, resonant mirrors cannot be used to achieve the needed performance. Instead, a fast point-to-point analog single-axis tilt actuator was designed with a custom-coated high reflectance (HR) mirror to withstand the high intra-cavity laser fluence levels. The mirror is bonded on top of the MEMS actuator in final assembly. A compact MEMS controller was further implemented with the capability of autonomous on-demand operation based on user-provided digital trigger. The controller is designed to receive an external 3V power supply and a digital trigger and it consumes ~90mW during the short switching cycle and ~10mW in standby mode. Module prototypes were tested in a laser cavity and demonstrated high quality laser pulses with duration of ~20ns and energy of over 3mJ.

  3. Environmental use of a Laser Range Finder and the Advanced Visualization System

    SciTech Connect

    Thornton, E.N.; Bohn, S.; Baker, C.P.; Jones, D.R.; Strope, L.A.

    1993-05-01

    The United States Department of Energy (DOE) is facing a large task in characterizing and remediating the contents of hazardous waste inside storage tanks. The characterization process of these tanks is a key step to the remediation process. Due to the hazardous materials inside the waste tanks, all of the work must be done remotely utilizing robotic systems. The Laser Range Finder (LRF) is a single point sensor used to remotely collect range and intensity data. The LRF sensor data is used to reconstruct the tank surface environment based on multiple LRF scans. This reconstructed surface definition can be used by a robotic controller to perform obstacle avoidance with items in the tank. The Pacific Northwest Laboratory (PNL) has used Advanced Visualization System (AVS) to prototype the filtering, transformation and reconstructing process. AVS software modules have been written to address LRF filtering on both the range and intensity images. A coordinate transformation module was constructed to convert the raw LRF data into a Cartesian coordinate reference frame. The results of filtering and transforms are integrated into a master map of the tank using an octree database. Master octrees are traversed and made into AVS geometry to visualize the tank interior. The graphical display of the tank interior can be used for robotic path planning and monitoring waste removal progress.

  4. Exploration tools for drug discovery and beyond: applying SciFinder to interdisciplinary research.

    PubMed

    Haldeman, Margaret; Vieira, Barbara; Winer, Fred; Knutsen, Lars J S

    2005-06-01

    Chemists have long recognized the value of online databases for surveying the literature of their field. Chemical Abstracts Service (CAS) databases covering almost a century's worth of journal articles and patent documents are among the best known and widely used for searching information on compounds. Today's research presents a new challenge, however, as the boundaries of chemistry and biological sciences overlap increasingly. This trend is especially true in the drug discovery field where published findings relating to both chemical and biological entities and their interactions are examined. CAS has expanded its resources to meet the requirements of the new, interdisciplinary challenges faced by today's researchers. This is evident both in the content of CAS databases, which have been expanded to include more biology-related information, and in the technology of the search tools now available to researchers on their desktop. It is the integration of content and search-and-retrieval technology that enables new insights to be made in the vast body of accumulated information. CAS's SciFinder is a widely used research tool for this purpose.

  5. Bore-Sight Calibration of Multiple Laser Range Finders for Kinematic 3D Laser Scanning Systems

    PubMed Central

    Jung, Jaehoon; Kim, Jeonghyun; Yoon, Sanghyun; Kim, Sangmin; Cho, Hyoungsig; Kim, Changjae; Heo, Joon

    2015-01-01

    The Simultaneous Localization and Mapping (SLAM) technique has been used for autonomous navigation of mobile systems; now, its applications have been extended to 3D data acquisition of indoor environments. In order to reconstruct 3D scenes of indoor space, the kinematic 3D laser scanning system, developed herein, carries three laser range finders (LRFs): one is mounted horizontally for system-position correction and the other two are mounted vertically to collect 3D point-cloud data of the surrounding environment along the system’s trajectory. However, the kinematic laser scanning results can be impaired by errors resulting from sensor misalignment. In the present study, the bore-sight calibration of multiple LRF sensors was performed using a specially designed double-deck calibration facility, which is composed of two half-circle-shaped aluminum frames. Moreover, in order to automatically achieve point-to-point correspondences between a scan point and the target center, a V-shaped target was designed as well. The bore-sight calibration parameters were estimated by a constrained least squares method, which iteratively minimizes the weighted sum of squares of residuals while constraining some highly-correlated parameters. The calibration performance was analyzed by means of a correlation matrix. After calibration, the visual inspection of mapped data and residual calculation confirmed the effectiveness of the proposed calibration approach. PMID:25946627

  6. The role of prokaryotes in subsurface weathering of hydrothermal sediments: A combined geochemical and microbiological investigation

    NASA Astrophysics Data System (ADS)

    Severmann, Silke; Mills, Rachel A.; Palmer, Martin R.; Telling, Jon P.; Cragg, Barry; John Parkes, R.

    2006-04-01

    A detailed geochemical and microbiological study of a ˜2 m sediment core from the inactive Alvin mounds within the TAG hydrothermal field was conducted to examine, for the first time, the role of prokaryotes in subsurface weathering of hydrothermal sediments. Results show that there has been substantial post-depositional remobilisation of metal species and diagenetic overprinting of the original high-temperature hydrothermal minerals, and aspects have involved prokaryotic processes. Prokaryotic enumeration demonstrates the presence of a population smaller than the average for deep sea sediments, probably due to the low organic carbon content, but not inhibited by (and hence adapted to) the metal rich environment. There was a small but significant increase in population size associated with the active redox boundary in an upper metal sulphide layer (50-70 cm) around which active metal remobilisation was concentrated (Cu, Au, Cd, Ag, U, Zn and Zn). Hence, subsurface prokaryotes were potentially obtaining energy from metal metabolism in this near surface zone. Close association of numbers of culturable Mn and Fe reducing prokaryotes with subsurface Fe 2+ and Mn 2+ pore water profiles suggested active prokaryotic metal reduction at depth in core CD102/43 (to ˜175 cm). In addition, a prokaryotic mechanism, which is associated with bacterial sulphate reduction, is invoked to explain the U enrichment on pyrite surfaces and Zn and Pb remobilisation in the upper sediment. Although prokaryotic populations are present throughout this metalliferous sediment, thermodynamic calculations indicated that the inferred low pH of pore waters and the suboxic/anoxic conditions limits the potential energy available from Fe(II) oxidation, which may restrict prokaryotic chemolithotrophic biomass. This suggests that intense prokaryotic Fe oxidation and weathering of seafloor massive sulphide deposits may be restricted to the upper portion of the deposit that is influenced by near neutral

  7. The Role of Eukaryotic and Prokaryotic ABC Transporter Family in Failure of Chemotherapy

    PubMed Central

    El-Awady, Raafat; Saleh, Ekram; Hashim, Amna; Soliman, Nehal; Dallah, Alaa; Elrasheed, Azza; Elakraa, Ghada

    2017-01-01

    Over the years chemotherapy failure has been a vital research topic as researchers have been striving to discover reasons behind it. The extensive studies carried out on chemotherapeutic agents confirm that resistance to chemotherapy is a major reason for treatment failure. “Resistance to chemotherapy,” however, is a comprehensive phrase that refers to a variety of different mechanisms in which ATP-binding cassette (ABC) mediated efflux dominates. The ABC is one of the largest gene superfamily of transporters among both eukaryotes and prokaryotes; it represents a variety of genes that code for proteins, which perform countless functions, including drug efflux – a natural process that protects cells from foreign chemicals. Up to date, chemotherapy failure due to ABC drug efflux is an active research topic that continuously provides further evidence on multiple drug resistance (MDR), aiding scientists in tackling and overcoming this issue. This review focuses on drug resistance by ABC efflux transporters in human, viral, parasitic, fungal and bacte