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Sample records for bacterial insecticide sequence

  1. Value of a newly sequenced bacterial genome

    DEFF Research Database (Denmark)

    Barbosa, Eudes; Aburjaile, Flavia F; Ramos, Rommel Tj;

    2014-01-01

    Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also...... heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting...... in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome...

  2. Value of a newly sequenced bacterial genome.

    Science.gov (United States)

    Barbosa, Eudes Gv; Aburjaile, Flavia F; Ramos, Rommel Tj; Carneiro, Adriana R; Le Loir, Yves; Baumbach, Jan; Miyoshi, Anderson; Silva, Artur; Azevedo, Vasco

    2014-05-26

    Next-generation sequencing (NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft (partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information. PMID:24921006

  3. Value of a newly sequenced bacterial genome

    Institute of Scientific and Technical Information of China (English)

    Eudes; GV; Barbosa; Flavia; F; Aburjaile; Rommel; TJ; Ramos; Adriana; R; Carneiro; Yves; Le; Loir; Jan; Baumbach; Anderson; Miyoshi; Artur; Silva; Vasco; Azevedo

    2014-01-01

    Next-generation sequencing(NGS) technologies have made high-throughput sequencing available to medium- and small-size laboratories, culminating in a tidal wave of genomic information. The quantity of sequenced bacterial genomes has not only brought excitement to the field of genomics but also heightened expectations that NGS would boost antibacterial discovery and vaccine development. Although many possible drug and vaccine targets have been discovered, the success rate of genome-based analysis has remained below expectations. Furthermore, NGS has had consequences for genome quality, resulting in an exponential increase in draft(partial data) genome deposits in public databases. If no further interests are expressed for a particular bacterial genome, it is more likely that the sequencing of its genome will be limited to a draft stage, and the painstaking tasks of completing the sequencing of its genome and annotation will not be undertaken. It is important to know what is lost when we settle for a draft genome and to determine the "scientific value" of a newly sequenced genome. This review addresses the expected impact of newly sequenced genomes on antibacterial discovery and vaccinology. Also, it discusses the factors that could be leading to the increase in the number of draft deposits and the consequent loss of relevant biological information.

  4. Bacterial population succession and adaptation affected by insecticide application and soil spraying history

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    Hideomi eItoh

    2014-08-01

    Full Text Available Although microbial communities have varying degrees of exposure to environmental stresses such as chemical pollution, little is known on how these communities respond to environmental disturbances and how past disturbance history affects these community-level responses. To comprehensively understand the effect of organophosphorus insecticide application on microbiota in soils with or without insecticide-spraying history, we investigated the microbial succession in response to the addition of fenitrothion (O,O-dimethyl O-(3-methyl-p-nitrophenyl phosphorothioate, abbreviated as MEP by culture-dependent experiments and deep sequencing of 16S rRNA genes. Despite similar microbial composition at the initial stage, microbial response to MEP application was remarkably different between soils with and without MEP-spraying history. MEP-degrading microbes more rapidly increased in the soils with MEP-spraying history, suggesting that MEP-degrading bacteria might already exist at a certain level and could quickly respond to MEP re-treatment in the soil. Culture-dependent and -independent evaluations revealed that MEP-degrading Burkholderia bacteria are predominant in soils after MEP application, limited members of which might play a pivotal role in MEP-degradation in soils. Notably, deep sequencing also revealed that some methylotrophs dramatically increased after MEP application, strongly suggesting that these bacteria play a role in the consumption and removal of methanol, a harmful derivative from MEP-degradation, for better growth of MEP-degrading bacteria. This comprehensive study demonstrated the succession and adaptation processes of microbial communities under MEP application, which were critically affected by past experience of insecticide-spraying.

  5. Insights from 20 years of bacterial genome sequencing

    DEFF Research Database (Denmark)

    Land, Miriam; Hauser, Loren; Jun, Se-Ran;

    2015-01-01

    genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in......Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the...... genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative...

  6. DNA sequencing reveals the midgut microbiota of diamondback moth, Plutella xylostella (L. and a possible relationship with insecticide resistance.

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    Xiaofeng Xia

    Full Text Available BACKGROUND: Insect midgut microbiota is important in host nutrition, development and immune response. Recent studies indicate possible links between insect gut microbiota and resistance to biological and chemical toxins. Studies of this phenomenon and symbionts in general have been hampered by difficulties in culture-based approach. In the present study, DNA sequencing was used to examine the midgut microbiota of diamondback moth (DBM, Plutella xylostella (L., a destructive pest that attacks cruciferous crops worldwide. Its ability to develop resistance to many types of synthetic insecticide and even Bacillus thuringiensis toxins makes it an important species to study. METHODOLOGY/PRINCIPAL FINDINGS: Bacteria of the DBM larval midgut in a susceptible and two insecticide (chlorpyrifos and fipronil resistant lines were examined by Illumina sequencing sampled from an insect generation that was not exposed to insecticide. This revealed that more than 97% of the bacteria were from three orders: Enterobacteriales, Vibrionales and Lactobacillales. Both insecticide-resistant lines had more Lactobacillales and the much scarcer taxa Pseudomonadales and Xanthomonadales with fewer Enterobacteriales compared with the susceptible strain. Consistent with this, a second study observed an increase in the proportion of Lactobacillales in the midgut of DBM individuals from a generation treated with insecticides. CONCLUSIONS/SIGNIFICANCE: This is the first report of high-throughput DNA sequencing of the entire microbiota of DBM. It reveals differences related to inter- and intra-generational exposure to insecticides. Differences in the midgut microbiota among susceptible and insecticide-resistant lines are independent of insecticide exposure in the sampled generations. While this is consistent with the hypothesis that Lactobacillales or other scarcer taxa play a role in conferring DBM insecticide resistance, further studies are necessary to rule out other

  7. Deep sequencing of New World screw-worm transcripts to discover genes involved in insecticide resistance

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    Azeredo-Espin Ana Maria L

    2010-12-01

    Full Text Available Abstract Background The New World screw-worm (NWS, Cochliomyia hominivorax, is one of the most important myiasis-causing flies, causing severe losses to the livestock industry. In its current geographical distribution, this species has been controlled by the application of insecticides, mainly organophosphate (OP compounds, but a number of lineages have been identified that are resistant to such chemicals. Despite its economic importance, only limited genetic information is available for the NWS. Here, as a part of an effort to characterize the C. hominivorax genome and identify putative genes involved in insecticide resistance, we sampled its transcriptome by deep sequencing of polyadenylated transcripts using the 454 sequencing technology. Results Deep sequencing on the 454 platform of three normalized libraries (larval, adult male and adult female generated a total of 548,940 reads. Eighteen candidate genes coding for three metabolic detoxification enzyme families, cytochrome P450 monooxygenases, glutathione S-transferases and carboxyl/cholinesterases were selected and gene expression levels were measured using quantitative real-time polymerase chain reaction (qRT-PCR. Of the investigated candidates, only one gene was expressed differently between control and resistant larvae with, at least, a 10-fold down-regulation in the resistant larvae. The presence of mutations in the acetylcholinesterase (target site and carboxylesterase E3 genes was investigated and all of the resistant flies presented E3 mutations previously associated with insecticide resistance. Conclusions Here, we provided the largest database of NWS expressed sequence tags that is an important resource, not only for further studies on the molecular basis of the OP resistance in NWS fly, but also for functional and comparative studies among Calliphoridae flies. Among our candidates, only one gene was found differentially expressed in resistant individuals, and its role on

  8. Bacterial epidemiology and biology - lessons from genome sequencing.

    OpenAIRE

    Parkhill, J.; Wren, BW

    2011-01-01

    : ABSTRACT: Next-generation sequencing has ushered in a new era of microbial genomics, enabling the detailed historical and geographical tracing of bacteria. This is helping to shape our understanding of bacterial evolution.

  9. Insights from twenty years of bacterial genome sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Land, Miriam L [ORNL; Hauser, Loren John [ORNL; Jun, Se Ran [ORNL; Nookaew, Intawat [ORNL; Leuze, Michael Rex [ORNL; Ahn, Tae-Hyuk [ORNL; Karpinets, Tatiana V [ORNL; Lund, Ole [Technical University of Denmark; Kora, Guruprasad H [ORNL; Wassenaar, Trudy [Molecular Microbiology & Genomics Consultants, Zotzenheim, Germany; Poudel, Suresh [ORNL; Ussery, David W [ORNL

    2015-01-01

    Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome

  10. Draft Genome Sequence of Insecticidal Streptomyces sp. Strain PCS3-D2, Isolated from Mangrove Soil in Philippines

    OpenAIRE

    Bayot-Custodio, Aileen N.; Alcantara, Edwin P.; Zulaybar, Teofila O.

    2014-01-01

    A draft genome sequence of a Streptomyces sp. isolated from mangrove soil in Cebu, Philippines, is described here. This isolate produced compounds with contact insecticidal activity against important corn pests. The genome contains 7,479,793 bp (in 27 scaffolds), 6,297 predicted genes, and 29 secondary metabolite biosynthetic gene clusters.

  11. Sequence Analysis of Insecticide Action and Detoxification-Related Genes in the Insect Pest Natural Enemy Pardosa pseudoannulata.

    Science.gov (United States)

    Meng, Xiangkun; Zhang, Yixi; Bao, Haibo; Liu, Zewen

    2015-01-01

    The pond wolf spider Pardosa pseudoannulata, an important natural predatory enemy of rice planthoppers, is found widely distributed in paddy fields. However, data on the genes involved in insecticide action, detoxification, and response are very limited for P. pseudoannulata, which inhibits the development and appropriate use of selective insecticides to control insect pests on rice. We used transcriptome construction from adult spider cephalothoraxes to analyze and manually identify genes enconding metabolic enzymes and target receptors related to insecticide action and detoxification, including 90 cytochrome P450s, 14 glutathione S-transferases (GSTs), 17 acetylcholinesterases (AChEs), 17 nicotinic acetylcholine receptors (nAChRs), and 17 gamma-aminobutyric acid (GABA) receptors, as well as 12 glutamate-gated chloride channel (GluCl) unigenes. Sequence alignment and phylogenetic analysis revealed the different subclassifications of P450s and GSTs, some important sequence diversities in nAChRs and GABA receptors, polymorphism in AChEs, and high similarities in GluCls. For P450s in P. pseudoannulata, the number of unigenes belonging to the CYP2 clade was much higher than that in CYP3 and CYP4 clades. The results differed from insects in which most P450 genes were in CYP3 and CYP4 clades. For GSTs, most unigenes belonged to the delta and sigma classes, and no epsilon GST class gene was found, which differed from the findings for insects and acarina. Our results will be useful for studies on insecticide action, selectivity, and detoxification in the spider and other related animals, and the sequence differences in target genes between the spider and insects will provide important information for the design of selective insecticides. PMID:25923714

  12. Sequence Analysis of Insecticide Action and Detoxification-Related Genes in the Insect Pest Natural Enemy Pardosa pseudoannulata.

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    Xiangkun Meng

    Full Text Available The pond wolf spider Pardosa pseudoannulata, an important natural predatory enemy of rice planthoppers, is found widely distributed in paddy fields. However, data on the genes involved in insecticide action, detoxification, and response are very limited for P. pseudoannulata, which inhibits the development and appropriate use of selective insecticides to control insect pests on rice. We used transcriptome construction from adult spider cephalothoraxes to analyze and manually identify genes enconding metabolic enzymes and target receptors related to insecticide action and detoxification, including 90 cytochrome P450s, 14 glutathione S-transferases (GSTs, 17 acetylcholinesterases (AChEs, 17 nicotinic acetylcholine receptors (nAChRs, and 17 gamma-aminobutyric acid (GABA receptors, as well as 12 glutamate-gated chloride channel (GluCl unigenes. Sequence alignment and phylogenetic analysis revealed the different subclassifications of P450s and GSTs, some important sequence diversities in nAChRs and GABA receptors, polymorphism in AChEs, and high similarities in GluCls. For P450s in P. pseudoannulata, the number of unigenes belonging to the CYP2 clade was much higher than that in CYP3 and CYP4 clades. The results differed from insects in which most P450 genes were in CYP3 and CYP4 clades. For GSTs, most unigenes belonged to the delta and sigma classes, and no epsilon GST class gene was found, which differed from the findings for insects and acarina. Our results will be useful for studies on insecticide action, selectivity, and detoxification in the spider and other related animals, and the sequence differences in target genes between the spider and insects will provide important information for the design of selective insecticides.

  13. Minimum taxonomic criteria for bacterial genome sequence depositions and announcements.

    Science.gov (United States)

    Bull, Matthew J; Marchesi, Julian R; Vandamme, Peter; Plummer, Sue; Mahenthiralingam, Eshwar

    2012-04-01

    Multiple bioinformatic methods are available to analyse the information encoded within the complete genome sequence of a bacterium and accurately assign its species status or nearest phylogenetic neighbour. However, it is clear that even now in what is the third decade of bacterial genomics, taxonomically incorrect genome sequence depositions are still being made. We outline a simple scheme of bioinformatic analysis and a set of minimum criteria that should be applied to all bacterial genomic data to ensure that they are accurately assigned to the species or genus level prior to database deposition. To illustrate the utility of the bioinformatic workflow, we analysed the recently deposited genome sequence of Lactobacillus acidophilus 30SC and demonstrated that this DNA was in fact derived from a strain of Lactobacillus amylovorus. Using these methods researchers can ensure that the taxonomic accuracy of genome sequence depositions is maintained within the ever increasing nucleic acid datasets. PMID:22366464

  14. Pyrosequencing the Bemisia tabaci transcriptome reveals a highly diverse bacterial community and a robust system for insecticide resistance.

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    Wen Xie

    Full Text Available BACKGROUND: Bemisia tabaci (Gennadius is a phloem-feeding insect poised to become one of the major insect pests in open field and greenhouse production systems throughout the world. The high level of resistance to insecticides is a main factor that hinders continued use of insecticides for suppression of B. tabaci. Despite its prevalence, little is known about B. tabaci at the genome level. To fill this gap, an invasive B. tabaci B biotype was subjected to pyrosequencing-based transcriptome analysis to identify genes and gene networks putatively involved in various physiological and toxicological processes. METHODOLOGY AND PRINCIPAL FINDINGS: Using Roche 454 pyrosequencing, 857,205 reads containing approximately 340 megabases were obtained from the B. tabaci transcriptome. De novo assembly generated 178,669 unigenes including 30,980 from insects, 17,881 from bacteria, and 129,808 from the nohit. A total of 50,835 (28.45% unigenes showed similarity to the non-redundant database in GenBank with a cut-off E-value of 10-5. Among them, 40,611 unigenes were assigned to one or more GO terms and 6,917 unigenes were assigned to 288 known pathways. De novo metatranscriptome analysis revealed highly diverse bacterial symbionts in B. tabaci, and demonstrated the host-symbiont cooperation in amino acid production. In-depth transcriptome analysis indentified putative molecular markers, and genes potentially involved in insecticide resistance and nutrient digestion. The utility of this transcriptome was validated by a thiamethoxam resistance study, in which annotated cytochrome P450 genes were significantly overexpressed in the resistant B. tabaci in comparison to its susceptible counterparts. CONCLUSIONS: This transcriptome/metatranscriptome analysis sheds light on the molecular understanding of symbiosis and insecticide resistance in an agriculturally important phloem-feeding insect pest, and lays the foundation for future functional genomics research of the

  15. A Markovian analysis of bacterial genome sequence constraints

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    Aaron D. Skewes

    2013-08-01

    Full Text Available The arrangement of nucleotides within a bacterial chromosome is influenced by numerous factors. The degeneracy of the third codon within each reading frame allows some flexibility of nucleotide selection; however, the third nucleotide in the triplet of each codon is at least partly determined by the preceding two. This is most evident in organisms with a strong G + C bias, as the degenerate codon must contribute disproportionately to maintaining that bias. Therefore, a correlation exists between the first two nucleotides and the third in all open reading frames. If the arrangement of nucleotides in a bacterial chromosome is represented as a Markov process, we would expect that the correlation would be completely captured by a second-order Markov model and an increase in the order of the model (e.g., third-, fourth-…order would not capture any additional uncertainty in the process. In this manuscript, we present the results of a comprehensive study of the Markov property that exists in the DNA sequences of 906 bacterial chromosomes. All of the 906 bacterial chromosomes studied exhibit a statistically significant Markov property that extends beyond second-order, and therefore cannot be fully explained by codon usage. An unrooted tree containing all 906 bacterial chromosomes based on their transition probability matrices of third-order shares ∼25% similarity to a tree based on sequence homologies of 16S rRNA sequences. This congruence to the 16S rRNA tree is greater than for trees based on lower-order models (e.g., second-order, and higher-order models result in diminishing improvements in congruence. A nucleotide correlation most likely exists within every bacterial chromosome that extends past three nucleotides. This correlation places significant limits on the number of nucleotide sequences that can represent probable bacterial chromosomes. Transition matrix usage is largely conserved by taxa, indicating that this property is likely

  16. Discovery of the butenyl-spinosyn insecticides: novel macrolides from the new bacterial strain Saccharopolyspora pogona.

    Science.gov (United States)

    Lewer, Paul; Hahn, Donald R; Karr, Laura L; Duebelbeis, Dennis O; Gilbert, Jeffrey R; Crouse, Gary D; Worden, Thomas; Sparks, Thomas C; Edwards, Pat McKamey Rex; Graupner, Paul R

    2009-06-15

    A new bacterium, Saccharopolyspora pogona (NRRL30141) was discovered which produced a series of very potent insecticidal compounds structurally related to the 'classical' (i.e., C-21-ethyl) spinosyns. A series of fermentations gave sufficient extract to allow the isolation and characterization of a total of 31 new metabolites. The majority of these compounds contained a but-1-enyl group at C-21 of the macrolide in place of the ethyl group in the 'classical' spinosyn series, corresponding to an additional acetate group incorporated during their biosynthesis. Additionally a variety of other new functionality was seen including hydroxylations, several novel forosamine sugar replacements, and a novel 14-membered macrolide ring analog. PMID:19324553

  17. Dynamics of Sequence -Discrete Bacterial Populations Inferred Using Metagenomes

    Energy Technology Data Exchange (ETDEWEB)

    Stevens, Sarah; Bendall, Matthew; Kang, Dongwan; Froula, Jeff; Egan, Rob; Chan, Leong-Keat; Tringe, Susannah; McMahon, Katherine; Malmstrom, Rex

    2014-03-14

    From a multi-year metagenomic time series of two dissimilar Wisconsin lakes we have assembled dozens of genomes using a novel approach that bins contigs into distinct genome based on sequence composition, e.g. kmer frequencies, and contig coverage patterns at various times points. Next, we investigated how these genomes, which represent sequence-discrete bacterial populations, evolved over time and used the time series to discover the population dynamics. For example, we explored changes in single nucleotide polymorphism (SNP) frequencies as well as patterns of gene gain and loss in multiple populations. Interestingly, SNP diversity was purged at nearly every genome position in some populations during the course of this study, suggesting these populations may have experienced genome-wide selective sweeps. This represents the first direct, time-resolved observations of periodic selection in natural populations, a key process predicted by the ecotype model of bacterial diversification.

  18. The Chaotic Structure of Bacterial Virulence Protein Sequences

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    Sevdanur Genc

    2015-01-01

    Full Text Available Bacterial virulence proteins, which have been class ified on structure of virulence, causes several diseases. For instance, Adhesins play an important role in th e host cells. They are inserted DNA sequences for a variety of virulence properties. Several important methods conducted for the prediction of bacterial virulence proteins for finding new drugs or vaccines. In this study, we propose a method for feature sele ction about classification of bacterial virulence protein. The features are constituted dir ectly from the amino acid sequence of a given protein. Amino acids form proteins, which are criti cal to life, and have many important functions in living cells. They occurring with diff erent physicochemical properties by a vector of 20 numerical values, and collected in AAIndex datab ases of known 544 indices. For all that, this approach have two steps. Firstly , the amino acid sequence of a given protein analysed with Lyapunov Exponents that they have a chaotic structure in accordance wi th the chaos theory. After that, if the results show chara cterization over the complete distribution in the phase space from the point of deterministic sys tem, it means related protein will show a chaotic structure. Empirical results revealed that generated feature v ectors give the best performance with chaotic structure of physicochemical features of amino acid s with Adhesins and non-Adhesins data sets.

  19. Toward Complete Bacterial Genome Sequencing Through the Combined Use of Multiple Next-Generation Sequencing Platforms.

    Science.gov (United States)

    Jeong, Haeyoung; Lee, Dae-Hee; Ryu, Choong-Min; Park, Seung-Hwan

    2016-01-01

    PacBio's long-read sequencing technologies can be successfully used for a complete bacterial genome assembly using recently developed non-hybrid assemblers in the absence of secondgeneration, high-quality short reads. However, standardized procedures that take into account multiple pre-existing second-generation sequencing platforms are scarce. In addition to Illumina HiSeq and Ion Torrent PGM-based genome sequencing results derived from previous studies, we generated further sequencing data, including from the PacBio RS II platform, and applied various bioinformatics tools to obtain complete genome assemblies for five bacterial strains. Our approach revealed that the hierarchical genome assembly process (HGAP) non-hybrid assembler resulted in nearly complete assemblies at a moderate coverage of ~75x, but that different versions produced non-compatible results requiring post processing. The other two platforms further improved the PacBio assembly through scaffolding and a final error correction. PMID:26464377

  20. Compiling Multicopy Single-Stranded DNA Sequences from Bacterial Genome Sequences

    OpenAIRE

    Yoo, Wonseok; Lim, Dongbin; Kim, Sangsoo

    2016-01-01

    A retron is a bacterial retroelement that encodes an RNA gene and a reverse transcriptase (RT). The former, once transcribed, works as a template primer for reverse transcription by the latter. The resulting DNA is covalently linked to the upstream part of the RNA; this chimera is called multicopy single-stranded DNA (msDNA), which is extrachromosomal DNA found in many bacterial species. Based on the conserved features in the eight known msDNA sequences, we developed a detection method and ap...

  1. De novo sequencing-based transcriptome and digital gene expression analysis reveals insecticide resistance-relevant genes in Propylaea japonica (Thunberg (Coleoptea: Coccinellidae.

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    Liang-De Tang

    Full Text Available The ladybird Propylaea japonica (Thunberg is one of most important natural enemies of aphids in China. This species is threatened by the extensive use of insecticides but genomics-based information on the molecular mechanisms underlying insecticide resistance is limited. Hence, we analyzed the transcriptome and expression profile data of P. japonica in order to gain a deeper understanding of insecticide resistance in ladybirds. We performed de novo assembly of a transcriptome using Illumina's Solexa sequencing technology and short reads. A total of 27,243,552 reads were generated. These were assembled into 81,458 contigs and 33,647 unigenes (6,862 clusters and 26,785 singletons. Of the unigenes, 23,965 (71.22% have putative homologues in the non-redundant (nr protein database from NCBI, using BLASTX, with a cut-off E-value of 10(-5. We examined COG, GO and KEGG annotations to better understand the functions of these unigenes. Digital gene expression (DGE libraries showed differences in gene expression profiles between two insecticide resistant strains. When compared with an insecticide susceptible profile, a total of 4,692 genes were significantly up- or down- regulated in a moderately resistant strain. Among these genes, 125 putative insecticide resistance genes were identified. To confirm the DGE results, 16 selected genes were validated using quantitative real time PCR (qRT-PCR. This study is the first to report genetic information on P. japonica and has greatly enriched the sequence data for ladybirds. The large number of gene sequences produced from the transcriptome and DGE sequencing will greatly improve our understanding of this important insect, at the molecular level, and could contribute to the in-depth research into insecticide resistance mechanisms.

  2. Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

    OpenAIRE

    Momchilo Vuyisich; Ayesha Arefin; Karen Davenport; Shihai Feng; Cheryl Gleasner; Kim McMurry; Beverly Parson-Quintana; Jennifer Price; Matthew Scholz; Patrick Chain

    2014-01-01

    Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the util...

  3. Interactive effects of a bacterial parasite and the insecticide carbaryl to life-history and physiology of two Daphnia magna clones differing in carbaryl sensitivity

    International Nuclear Information System (INIS)

    Highlights: ► Interactive effects between a bacterial parasite and an insecticide in Daphnia magna. ► Two D. magna clones differing strongly in their sensitivity to the insecticide. ► Effects studied on various life-history and physiological endpoints. ► Genetic differences in strength and direction of interaction effects. -- Abstract: Natural and chemical stressors occur simultaneously in the aquatic environment. Their combined effects on biota are usually difficult to predict from their individual effects due to interactions between the different stressors. Several recent studies have suggested that synergistic effects of multiple stressors on organisms may be more common at high compared to low overall levels of stress. In this study, we used a three-way full factorial design to investigate whether interactive effects between a natural stressor, the bacterial parasite Pasteuria ramosa, and a chemical stressor, the insecticide carbaryl, were different between two genetically distinct clones of Daphnia magna that strongly differ in their sensitivity to carbaryl. Interactive effects on various life-history and physiological endpoints were assessed as significant deviations from the reference Independent Action (IA) model, which was implemented by testing the significance of the two-way carbaryl × parasite interaction term in two-way ANOVA's on log-transformed observational data for each clone separately. Interactive effects (and thus significant deviations from IA) were detected in both the carbaryl-sensitive clone (on survival, early reproduction and growth) and in the non-sensitive clone (on growth, electron transport activity and prophenoloxidase activity). No interactions were found for maturation rate, filtration rate, and energy reserve fractions (carbohydrate, protein, lipid). Furthermore, only antagonistic interactions were detected in the non-sensitive clone, while only synergistic interactions were observed in the carbaryl sensitive clone. Our

  4. Interactive effects of a bacterial parasite and the insecticide carbaryl to life-history and physiology of two Daphnia magna clones differing in carbaryl sensitivity

    Energy Technology Data Exchange (ETDEWEB)

    De Coninck, Dieter I.M., E-mail: Dieter.DeConinck@UGent.be [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, J. Plateaustraat 22, B-9000 Ghent (Belgium); De Schamphelaere, Karel A.C. [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, J. Plateaustraat 22, B-9000 Ghent (Belgium); Jansen, Mieke; De Meester, Luc [Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Ch. Deberiotstraat 32, B-3000 Leuven (Belgium); Janssen, Colin R. [Laboratory of Environmental Toxicology and Aquatic Ecology, Ghent University, J. Plateaustraat 22, B-9000 Ghent (Belgium)

    2013-04-15

    Highlights: ► Interactive effects between a bacterial parasite and an insecticide in Daphnia magna. ► Two D. magna clones differing strongly in their sensitivity to the insecticide. ► Effects studied on various life-history and physiological endpoints. ► Genetic differences in strength and direction of interaction effects. -- Abstract: Natural and chemical stressors occur simultaneously in the aquatic environment. Their combined effects on biota are usually difficult to predict from their individual effects due to interactions between the different stressors. Several recent studies have suggested that synergistic effects of multiple stressors on organisms may be more common at high compared to low overall levels of stress. In this study, we used a three-way full factorial design to investigate whether interactive effects between a natural stressor, the bacterial parasite Pasteuria ramosa, and a chemical stressor, the insecticide carbaryl, were different between two genetically distinct clones of Daphnia magna that strongly differ in their sensitivity to carbaryl. Interactive effects on various life-history and physiological endpoints were assessed as significant deviations from the reference Independent Action (IA) model, which was implemented by testing the significance of the two-way carbaryl × parasite interaction term in two-way ANOVA's on log-transformed observational data for each clone separately. Interactive effects (and thus significant deviations from IA) were detected in both the carbaryl-sensitive clone (on survival, early reproduction and growth) and in the non-sensitive clone (on growth, electron transport activity and prophenoloxidase activity). No interactions were found for maturation rate, filtration rate, and energy reserve fractions (carbohydrate, protein, lipid). Furthermore, only antagonistic interactions were detected in the non-sensitive clone, while only synergistic interactions were observed in the carbaryl sensitive clone

  5. Evolutionary changes in gene expression, coding sequence and copy-number at the Cyp6g1 locus contribute to resistance to multiple insecticides in Drosophila.

    Directory of Open Access Journals (Sweden)

    Thomas W R Harrop

    Full Text Available Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However, it is not known whether the ability of the CYP6G1 enzyme to provide resistance to multiple insecticides evolved recently in D. melanogaster or if this function is present in all Drosophila species. Here we show that duplication of the Cyp6g1 gene occurred at least four times during the evolution of different Drosophila species, and the ability of CYP6G1 to confer resistance to multiple insecticides exists in D. melanogaster and D. simulans but not in Drosophila willistoni or Drosophila virilis. In D. virilis, which has multiple copies of Cyp6g1, one copy confers resistance to DDT and another to nitenpyram, suggesting that the divergence of protein sequence between copies subsequent to the duplication affected the activity of the enzyme. All orthologs tested conferred resistance to one or more insecticides, suggesting that CYP6G1 had the capacity to provide resistance to anthropogenic chemicals before they existed. Finally, we show that expression of Cyp6g1 in the Malpighian tubules, which contributes to DDT resistance in D. melanogaster, is specific to the D. melanogaster-D. simulans lineage. Our results suggest that a combination of gene duplication, regulatory changes and protein coding changes has taken place at the Cyp6g1 locus during evolution and this locus may play a role in providing resistance to different environmental toxins in different Drosophila species.

  6. A Bacterial Analysis Platform: An Integrated System for Analysing Bacterial Whole Genome Sequencing Data for Clinical Diagnostics and Surveillance

    DEFF Research Database (Denmark)

    Thomsen, Martin Christen Frølund; Ahrenfeldt, Johanne; Bellod Cisneros, Jose Luis;

    2016-01-01

    and antimicrobial resistance genes. A short printable report for each sample will be provided and an Excel spreadsheet containing all the metadata and a summary of the results for all submitted samples can be downloaded. The pipeline was benchmarked using datasets previously used to test the...... web-based tools we developed a single pipeline for batch uploading of whole genome sequencing data from multiple bacterial isolates. The pipeline will automatically identify the bacterial species and, if applicable, assemble the genome, identify the multilocus sequence type, plasmids, virulence genes...... platform was developed and made publicly available, providing easy-to-use automated analysis of bacterial whole genome sequencing data. The platform may be of immediate relevance as a guide for investigators using whole genome sequencing for clinical diagnostics and surveillance. The platform is freely...

  7. Beginner’s guide to comparative bacterial genome analysis using next-generation sequence data

    OpenAIRE

    Edwards, David J.; Holt, Kathryn E.

    2013-01-01

    High throughput sequencing is now fast and cheap enough to be considered part of the toolbox for investigating bacteria, and there are thousands of bacterial genome sequences available for comparison in the public domain. Bacterial genome analysis is increasingly being performed by diverse groups in research, clinical and public health labs alike, who are interested in a wide array of topics related to bacterial genetics and evolution. Examples include outbreak analysis and the study of patho...

  8. Sequencing of Bacterial Genomes: Principles and Insights into Pathogenesis and Development of Antibiotics

    Directory of Open Access Journals (Sweden)

    Eric S. Donkor

    2013-10-01

    Full Text Available The impact of bacterial diseases on public health has become enormous, and is partly due to the increasing trend of antibiotic resistance displayed by bacterial pathogens. Sequencing of bacterial genomes has significantly improved our understanding about the biology of many bacterial pathogens as well as identification of novel antibiotic targets. Since the advent of genome sequencing two decades ago, about 1,800 bacterial genomes have been fully sequenced and these include important aetiological agents such as Streptococcus pneumoniae, Mycobacterium tuberculosis, Escherichia coli O157:H7, Vibrio cholerae, Clostridium difficile and Staphylococcus aureus. Very recently, there has been an explosion of bacterial genome data and is due to the development of next generation sequencing technologies, which are evolving so rapidly. Indeed, the field of microbial genomics is advancing at a very fast rate and it is difficult for researchers to be abreast with the new developments. This highlights the need for regular updates in microbial genomics through comprehensive reviews. This review paper seeks to provide an update on bacterial genome sequencing generally, and to analyze insights gained from sequencing in two areas, including bacterial pathogenesis and the development of antibiotics.

  9. First report of bacterial community from a Bat Guano using Illumina next-generation sequencing

    Directory of Open Access Journals (Sweden)

    Surajit De Mandal

    2015-06-01

    Full Text Available V4 hypervariable region of 16S rDNA was analyzed for identifying the bacterial communities present in Bat Guano from the unexplored cave — Pnahkyndeng, Meghalaya, Northeast India. Metagenome comprised of 585,434 raw Illumina sequences with a 59.59% G+C content. A total of 416,490 preprocessed reads were clustered into 1282 OTUs (operational taxonomical units comprising of 18 bacterial phyla. The taxonomic profile showed that the guano bacterial community is dominated by Chloroflexi, Actinobacteria and Crenarchaeota which account for 70.73% of all sequence reads and 43.83% of all OTUs. Metagenome sequence data are available at NCBI under the accession no. SRP051094. This study is the first to characterize Bat Guano bacterial community using next-generation sequencing approach.

  10. Draft Genome Sequences of Six Novel Bacterial Isolates from Chicken Ceca

    Science.gov (United States)

    Duggett, Nicholas A.; Kay, Gemma L.; Sergeant, Martin J.; Bedford, Michael; Constantinidou, Chrystala I.; Penn, Charles W.; Millard, Andrew D.

    2016-01-01

    The chicken is the most common domesticated animal and the most abundant bird in the world. However, the chicken gut is home to many previously uncharacterized bacterial taxa. Here, we report draft genome sequences from six bacterial isolates from chicken ceca, all of which fall outside any named species. PMID:27231374

  11. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    OpenAIRE

    Seung Hak Yang; Joung Soo Lim; Modabber Ahmed Khan; Bong Soo Kim; Dong Yoon Choi; Eun Young Lee; Hee Kwon Ahn

    2015-01-01

    The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses) and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gen...

  12. Identification of Bacterial Small RNAs by RNA Sequencing

    DEFF Research Database (Denmark)

    Gómez Lozano, María; Marvig, Rasmus Lykke; Molin, Søren;

    2014-01-01

    Small regulatory RNAs (sRNAs) in bacteria are known to modulate gene expression and control a variety of processes including metabolic reactions, stress responses, and pathogenesis in response to environmental signals. A method to identify bacterial sRNAs on a genome-wide scale based on RNA seque...

  13. MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island.

    Science.gov (United States)

    Ashton, Philip M; Nair, Satheesh; Dallman, Tim; Rubino, Salvatore; Rabsch, Wolfgang; Mwaigwisya, Solomon; Wain, John; O'Grady, Justin

    2015-03-01

    Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes. The MinION nanopore sequencer can produce long sequencing reads on a device similar in size to a USB memory stick. Here we apply a MinION sequencer to resolve the structure and chromosomal insertion site of a composite antibiotic resistance island in Salmonella Typhi Haplotype 58. Nanopore sequencing data from a single 18-h run was used to create a scaffold for an assembly generated from short-read Illumina data. Our results demonstrate the potential of the MinION device in clinical laboratories to fully characterize the epidemic spread of bacterial pathogens. PMID:25485618

  14. Determining and comparing protein function in Bacterial genome sequences

    DEFF Research Database (Denmark)

    Vesth, Tammi Camilla

    predictions were made in about 60% of the cases. This project has highlighted the difficulties and challenges in functional annotation and computational analysis of sequence data. It has provided possible solutions for creating reproducible pipelines for comparative genomics as well as constructed a number of......In November 2013, there was around 21.000 different prokaryotic genomes sequenced and publicly available, and the number is growing daily with another 20.000 or more genomes expected to be sequenced and deposited by the end of 2014. An important part of the analysis of this data is the functional...... known functions. This thesis describes the development of new tools for comparative functional annotation and a system for comparative genomics in general. As novel sequenced genomes are becoming more readily available, there is a need for standard analysis tools. The system CMG-biotools is presented...

  15. Genomic and Global Approaches to Unravelling How Hypermutable Sequences Influence Bacterial Pathogenesis

    Directory of Open Access Journals (Sweden)

    Fadil A. Bidmos

    2014-02-01

    Full Text Available Rapid adaptation to fluctuations in the host milieu contributes to the host persistence and virulence of bacterial pathogens. Adaptation is frequently mediated by hypermutable sequences in bacterial pathogens. Early bacterial genomic studies identified the multiplicity and virulence-associated functions of these hypermutable sequences. Thus, simple sequence repeat tracts (SSRs and site-specific recombination were found to control capsular type, lipopolysaccharide structure, pilin diversity and the expression of outer membrane proteins. We review how the population diversity inherent in the SSR-mediated mechanism of localised hypermutation is being unlocked by the investigation of whole genome sequences of disease isolates, analysis of clinical samples and use of model systems. A contrast is presented between the problematical nature of analysing simple sequence repeats in next generation sequencing data and in simpler, pragmatic PCR-based approaches. Specific examples are presented of the potential relevance of this localized hypermutation to meningococcal pathogenesis. This leads us to speculate on the future prospects for unravelling how hypermutable mechanisms may contribute to the transmission, spread and persistence of bacterial pathogens.

  16. CISA: contig integrator for sequence assembly of bacterial genomes.

    Directory of Open Access Journals (Sweden)

    Shin-Hung Lin

    Full Text Available A plethora of algorithmic assemblers have been proposed for the de novo assembly of genomes, however, no individual assembler guarantees the optimal assembly for diverse species. Optimizing various parameters in an assembler is often performed in order to generate the most optimal assembly. However, few efforts have been pursued to take advantage of multiple assemblies to yield an assembly of high accuracy. In this study, we employ various state-of-the-art assemblers to generate different sets of contigs for bacterial genomes. A tool, named CISA, has been developed to integrate the assemblies into a hybrid set of contigs, resulting in assemblies of superior contiguity and accuracy, compared with the assemblies generated by the state-of-the-art assemblers and the hybrid assemblies merged by existing tools. This tool is implemented in Python and requires MUMmer and BLAST+ to be installed on the local machine. The source code of CISA and examples of its use are available at http://sb.nhri.org.tw/CISA/.

  17. Optical mapping as a routine tool for bacterial genome sequence finishing

    Directory of Open Access Journals (Sweden)

    Gaudriault Sophie

    2007-09-01

    Full Text Available Abstract Background In sequencing the genomes of two Xenorhabdus species, we encountered a large number of sequence repeats and assembly anomalies that stalled finishing efforts. This included a stretch of about 12 Kb that is over 99.9% identical between the plasmid and chromosome of X. nematophila. Results Whole genome restriction maps of the sequenced strains were produced through optical mapping technology. These maps allowed rapid resolution of sequence assembly problems, permitted closing of the genome, and allowed correction of a large inversion in a genome assembly that we had considered finished. Conclusion Our experience suggests that routine use of optical mapping in bacterial genome sequence finishing is warranted. When combined with data produced through 454 sequencing, an optical map can rapidly and inexpensively generate an ordered and oriented set of contigs to produce a nearly complete genome sequence assembly.

  18. Sequence of retrovirus provirus resembles that of bacterial transposable elements

    Science.gov (United States)

    Shimotohno, Kunitada; Mizutani, Satoshi; Temin, Howard M.

    1980-06-01

    The nucleotide sequences of the terminal regions of an infectious integrated retrovirus cloned in the modified λ phage cloning vector Charon 4A have been elucidated. There is a 569-base pair direct repeat at both ends of the viral DNA. The cell-virus junctions at each end consist of a 5-base pair direct repeat of cell DNA next to a 3-base pair inverted repeat of viral DNA. This structure resembles that of a transposable element and is consistent with the protovirus hypothesis that retroviruses evolved from the cell genome.

  19. High-throughput nucleotide sequence analysis of diverse bacterial communities in leachates of decomposing pig carcasses

    Directory of Open Access Journals (Sweden)

    Seung Hak Yang

    2015-09-01

    Full Text Available The leachate generated by the decomposition of animal carcass has been implicated as an environmental contaminant surrounding the burial site. High-throughput nucleotide sequencing was conducted to investigate the bacterial communities in leachates from the decomposition of pig carcasses. We acquired 51,230 reads from six different samples (1, 2, 3, 4, 6 and 14 week-old carcasses and found that sequences representing the phylum Firmicutes predominated. The diversity of bacterial 16S rRNA gene sequences in the leachate was the highest at 6 weeks, in contrast to those at 2 and 14 weeks. The relative abundance of Firmicutes was reduced, while the proportion of Bacteroidetes and Proteobacteria increased from 3–6 weeks. The representation of phyla was restored after 14 weeks. However, the community structures between the samples taken at 1–2 and 14 weeks differed at the bacterial classification level. The trend in pH was similar to the changes seen in bacterial communities, indicating that the pH of the leachate could be related to the shift in the microbial community. The results indicate that the composition of bacterial communities in leachates of decomposing pig carcasses shifted continuously during the study period and might be influenced by the burial site.

  20. Bacterial populations on brewery filling hall surfaces as revealed by next-generation sequencing.

    Science.gov (United States)

    Priha, Outi; Raulio, Mari; Maukonen, Johanna; Vehviläinen, Anna-Kaisa; Storgårds, Erna

    2016-01-01

    Due to the presence of moisture and nutrients, brewery filling line surfaces are susceptible to unwanted microbial attachment. Knowledge of the attaching microbes will aid in designing hygienic control of the process. In this study the bacterial diversity present on brewery filling line surfaces was revealed by next generation sequencing. The two filling lines studied maintained their characteristic bacterial community throughout three sampling times (13-163 days). On the glass bottle line, γ-proteobacteria dominated (35-82% of all OTUs), whereas on the canning line α-, β- and γ-proteobacteria and actinobacteria were most common. The most frequently detected genera were Acinetobacter, Propinobacterium and Pseudomonas. The halophilic genus Halomonas was commonly detected, which might be due to its tolerance to alkaline foam cleaners. This study has revealed a detailed overall picture of the bacterial groups present on filling line surfaces. Further effort should be given to determine the efficacy of washing procedures on different bacterial groups. PMID:27064426

  1. Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

    Science.gov (United States)

    Vuyisich, Momchilo; Arefin, Ayesha; Davenport, Karen; Feng, Shihai; Gleasner, Cheryl; McMurry, Kim; Parson-Quintana, Beverly; Price, Jennifer; Scholz, Matthew; Chain, Patrick

    2014-01-01

    Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used. PMID:25478564

  2. Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

    Directory of Open Access Journals (Sweden)

    Momchilo Vuyisich

    2014-01-01

    Full Text Available Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 μg. There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp., which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used.

  3. Multiple gene sequence analysis using genes of the bacterial DNA repair pathway

    Directory of Open Access Journals (Sweden)

    Miguel Rotelok Neto

    2015-06-01

    Full Text Available The ability to recognize and repair abnormal DNA structures is common to all forms of life. Physiological studies and genomic sequencing of a variety of bacterial species have identified an incredible diversity of DNA repair pathways. Despite the amount of available genes in public database, the usual method to place genomes in a taxonomic context is based mainly on the 16S rRNA or housekeeping genes. Thus, the relationships among genomes remain poorly understood. In this work, an approach of multiple gene sequence analysis based on genes of DNA repair pathway was used to compare bacterial genomes. Housekeeping and DNA repair genes were searched in 872 completely sequenced bacterial genomes. Seven DNA repair and housekeeping genes from distinct metabolic pathways were selected, aligned, edited and concatenated head-to-tail to form a super-gene. Results showed that the multiple gene sequence analysis using DNA repair genes had better resolution at class level than the housekeeping genes. As housekeeping genes, the DNA repair genes were advantageous to separate bacterial groups at low taxonomic levels and also sensitive to genes derived from horizontal transfer.

  4. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.

    Science.gov (United States)

    Croucher, Nicholas J; Page, Andrew J; Connor, Thomas R; Delaney, Aidan J; Keane, Jacqueline A; Bentley, Stephen D; Parkhill, Julian; Harris, Simon R

    2015-02-18

    The emergence of new sequencing technologies has facilitated the use of bacterial whole genome alignments for evolutionary studies and outbreak analyses. These datasets, of increasing size, often include examples of multiple different mechanisms of horizontal sequence transfer resulting in substantial alterations to prokaryotic chromosomes. The impact of these processes demands rapid and flexible approaches able to account for recombination when reconstructing isolates' recent diversification. Gubbins is an iterative algorithm that uses spatial scanning statistics to identify loci containing elevated densities of base substitutions suggestive of horizontal sequence transfer while concurrently constructing a maximum likelihood phylogeny based on the putative point mutations outside these regions of high sequence diversity. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistically parameterized models of bacterial evolution, and achieves convergence in only a few hours on alignments of hundreds of bacterial genome sequences. Gubbins is appropriate for reconstructing the recent evolutionary history of a variety of haploid genotype alignments, as it makes no assumptions about the underlying mechanism of recombination. The software is freely available for download at github.com/sanger-pathogens/Gubbins, implemented in Python and C and supported on Linux and Mac OS X. PMID:25414349

  5. Multiplex sequencing of bacterial artificial chromosomes for assembling complex plant genomes.

    Science.gov (United States)

    Beier, Sebastian; Himmelbach, Axel; Schmutzer, Thomas; Felder, Marius; Taudien, Stefan; Mayer, Klaus F X; Platzer, Matthias; Stein, Nils; Scholz, Uwe; Mascher, Martin

    2016-07-01

    Hierarchical shotgun sequencing remains the method of choice for assembling high-quality reference sequences of complex plant genomes. The efficient exploitation of current high-throughput technologies and powerful computational facilities for large-insert clone sequencing necessitates the sequencing and assembly of a large number of clones in parallel. We developed a multiplexed pipeline for shotgun sequencing and assembling individual bacterial artificial chromosomes (BACs) using the Illumina sequencing platform. We illustrate our approach by sequencing 668 barley BACs (Hordeum vulgare L.) in a single Illumina HiSeq 2000 lane. Using a newly designed parallelized computational pipeline, we obtained sequence assemblies of individual BACs that consist, on average, of eight sequence scaffolds and represent >98% of the genomic inserts. Our BAC assemblies are clearly superior to a whole-genome shotgun assembly regarding contiguity, completeness and the representation of the gene space. Our methods may be employed to rapidly obtain high-quality assemblies of a large number of clones to assemble map-based reference sequences of plant and animal species with complex genomes by sequencing along a minimum tiling path. PMID:26801048

  6. Evolutionary Changes in Gene Expression, Coding Sequence and Copy-Number at the Cyp6g1 Locus Contribute to Resistance to Multiple Insecticides in Drosophila

    OpenAIRE

    Harrop, Thomas W. R.; Tamar Sztal; Christopher Lumb; Good, Robert T.; Daborn, Phillip J.; Philip Batterham; Henry Chung

    2014-01-01

    Widespread use of insecticides has led to insecticide resistance in many populations of insects. In some populations, resistance has evolved to multiple pesticides. In Drosophila melanogaster, resistance to multiple classes of insecticide is due to the overexpression of a single cytochrome P450 gene, Cyp6g1. Overexpression of Cyp6g1 appears to have evolved in parallel in Drosophila simulans, a sibling species of D. melanogaster, where it is also associated with insecticide resistance. However...

  7. Characterization of bacterial communities in sediments receiving various wastewater effluents with high-throughput sequencing analysis.

    Science.gov (United States)

    Lu, Xiao-Ming; Lu, Peng-Zhen

    2014-04-01

    454 Pyrosequencing was applied to examine bacterial communities in sediment samples collected from a river receiving effluent discharge from rural domestic sewage (RDS) and various factories, including a tannery (TNS), clothing plant (CTS), and button factory (BTS), respectively. For each sample, 4,510 effective sequences were selected and utilized to do the bacterial diversity and abundance analysis, respectively. In total, 1,288, 2,036, 1,800, and 2,150 operational taxonomic units were obtained at 3% distance cutoff in TNS, CTS, BTS, and RDS, respectively. Bacterial phylotype richness in RDS was higher than the other samples, and TNS had the least richness. The most predominant class in the TNS, CTS, and BTS samples is Betaproteobacteria. Cyanobacteria (no_rank) is the most predominant one in the RDS sample. Circa 31% sequences in TNS were affiliated with the Rhodocyclales order. In the four samples, Aeromonas, Arcobacter, Clostridium, Legionella, Leptospira, Mycobacterium, Pseudomonas, and Treponema genera containing pathogenic bacteria were detected. Characterization of bacterial communities in sediments from various downstream branches indicated that distinct wastewater effluents have similar potential to reduce the natural variability in river ecosystems and contribute to the river biotic homogenization. PMID:24477925

  8. Generalized Gap Model for Bacterial Artificial Chromosome Clone Fingerprint Mapping and Shotgun Sequencing

    OpenAIRE

    Wendl, Michael C; Robert H Waterston

    2002-01-01

    We develop an extension to the Lander-Waterman theory for characterizing gaps in bacterial artificial chromosome fingerprint mapping and shotgun sequencing projects. It supports a larger set of descriptive statistics and is applicable to a wider range of project parameters. We show that previous assertions regarding inconsistency of the Lander-Waterman theory at higher coverages are incorrect and that another well-known but ostensibly different model is in fact the same. The apparent paradox ...

  9. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    OpenAIRE

    Glass John I; Yooseph Shibu; Foecking Mark F; Röske Kerstin; Calcutt Michael J; Wise Kim S

    2010-01-01

    Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT). Expanding genome sequence datab...

  10. Multiple gene sequence analysis using genes of the bacterial DNA repair pathway

    OpenAIRE

    Miguel Rotelok Neto; Carolina Weigert Galvão; Leonardo Magalhães Cruz; Dieval Guizelini; Leilane Caline Silva; Jarem Raul Garcia; Rafael Mazer Etto

    2015-01-01

    The ability to recognize and repair abnormal DNA structures is common to all forms of life. Physiological studies and genomic sequencing of a variety of bacterial species have identified an incredible diversity of DNA repair pathways. Despite the amount of available genes in public database, the usual method to place genomes in a taxonomic context is based mainly on the 16S rRNA or housekeeping genes. Thus, the relationships among genomes remain poorly understood. In this work, an approach of...

  11. Insights into the emergent bacterial pathogen Cronobacter spp., generated by multilocus sequence typing and analysis

    Directory of Open Access Journals (Sweden)

    StephenForsythe

    2012-11-01

    Full Text Available Cronobacter spp. (previously known as Enterobacter sakazakii is a bacterial pathogen affecting all age groups, with particularly severe clinical complications in neonates and infants. One recognised route of infection being the consumption of contaminated infant formula. As a recently recognised bacterial pathogen of considerable importance and regulatory control, appropriate detection and identification schemes are required. The application of multilocus sequence typing (MLST and analysis (MLSA of the seven alleles atpD, fusA, glnS, gltB, gyrB, infB and ppsA (concatenated length 3036 base pairs has led to considerable advances in our understanding of the genus. This approach is supported by both the reliability of DNA sequencing over subjective phenotyping and the establishment of a MLST database which has open access and is also curated; http://www.pubMLST.org/cronobacter. MLST has been used to describe the diversity of the newly recognised genus, instrumental in the formal recognition of new Cronobacter species (C. universalis and C. condimenti and revealed the high clonality of strains and the association of clonal complex 4 with neonatal meningitis cases. Clearly the MLST approach has considerable benefits over the use of non-DNA sequence based methods of analysis for newly emergent bacterial pathogens. The application of MLST and MLSA has dramatically enabled us to better understand this opportunistic bacterium which can cause irreparable damage to a newborn baby’s brain, and has contributed to improved control measures to protect neonatal health.

  12. A Comparison between Transcriptome Sequencing and 16S Metagenomics for Detection of Bacterial Pathogens in Wildlife.

    Directory of Open Access Journals (Sweden)

    Maria Razzauti

    Full Text Available Rodents are major reservoirs of pathogens responsible for numerous zoonotic diseases in humans and livestock. Assessing their microbial diversity at both the individual and population level is crucial for monitoring endemic infections and revealing microbial association patterns within reservoirs. Recently, NGS approaches have been employed to characterize microbial communities of different ecosystems. Yet, their relative efficacy has not been assessed. Here, we compared two NGS approaches, RNA-Sequencing (RNA-Seq and 16S-metagenomics, assessing their ability to survey neglected zoonotic bacteria in rodent populations.We first extracted nucleic acids from the spleens of 190 voles collected in France. RNA extracts were pooled, randomly retro-transcribed, then RNA-Seq was performed using HiSeq. Assembled bacterial sequences were assigned to the closest taxon registered in GenBank. DNA extracts were analyzed via a 16S-metagenomics approach using two sequencers: the 454 GS-FLX and the MiSeq. The V4 region of the gene coding for 16S rRNA was amplified for each sample using barcoded universal primers. Amplicons were multiplexed and processed on the distinct sequencers. The resulting datasets were de-multiplexed, and each read was processed through a pipeline to be taxonomically classified using the Ribosomal Database Project. Altogether, 45 pathogenic bacterial genera were detected. The bacteria identified by RNA-Seq were comparable to those detected by 16S-metagenomics approach processed with MiSeq (16S-MiSeq. In contrast, 21 of these pathogens went unnoticed when the 16S-metagenomics approach was processed via 454-pyrosequencing (16S-454. In addition, the 16S-metagenomics approaches revealed a high level of coinfection in bank voles.We concluded that RNA-Seq and 16S-MiSeq are equally sensitive in detecting bacteria. Although only the 16S-MiSeq method enabled identification of bacteria in each individual reservoir, with subsequent derivation of

  13. BG7: a new approach for bacterial genome annotation designed for next generation sequencing data.

    Directory of Open Access Journals (Sweden)

    Pablo Pareja-Tobes

    Full Text Available BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version - which is developed in Java, takes advantage of Amazon Web Services (AWS cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future.

  14. BG7: a new approach for bacterial genome annotation designed for next generation sequencing data.

    Science.gov (United States)

    Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Pareja, Eduardo; Tobes, Raquel

    2012-01-01

    BG7 is a new system for de novo bacterial, archaeal and viral genome annotation based on a new approach specifically designed for annotating genomes sequenced with next generation sequencing technologies. The system is versatile and able to annotate genes even in the step of preliminary assembly of the genome. It is especially efficient detecting unexpected genes horizontally acquired from bacterial or archaeal distant genomes, phages, plasmids, and mobile elements. From the initial phases of the gene annotation process, BG7 exploits the massive availability of annotated protein sequences in databases. BG7 predicts ORFs and infers their function based on protein similarity with a wide set of reference proteins, integrating ORF prediction and functional annotation phases in just one step. BG7 is especially tolerant to sequencing errors in start and stop codons, to frameshifts, and to assembly or scaffolding errors. The system is also tolerant to the high level of gene fragmentation which is frequently found in not fully assembled genomes. BG7 current version - which is developed in Java, takes advantage of Amazon Web Services (AWS) cloud computing features, but it can also be run locally in any operating system. BG7 is a fast, automated and scalable system that can cope with the challenge of analyzing the huge amount of genomes that are being sequenced with NGS technologies. Its capabilities and efficiency were demonstrated in the 2011 EHEC Germany outbreak in which BG7 was used to get the first annotations right the next day after the first entero-hemorrhagic E. coli genome sequences were made publicly available. The suitability of BG7 for genome annotation has been proved for Illumina, 454, Ion Torrent, and PacBio sequencing technologies. Besides, thanks to its plasticity, our system could be very easily adapted to work with new technologies in the future. PMID:23185310

  15. Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization.

    Science.gov (United States)

    Anahtar, Melis N; Bowman, Brittany A; Kwon, Douglas S

    2016-01-01

    There is a growing appreciation for the role of microbial communities as critical modulators of human health and disease. High throughput sequencing technologies have allowed for the rapid and efficient characterization of bacterial communities using 16S rRNA gene sequencing from a variety of sources. Although readily available tools for 16S rRNA sequence analysis have standardized computational workflows, sample processing for DNA extraction remains a continued source of variability across studies. Here we describe an efficient, robust, and cost effective method for extracting nucleic acid from swabs. We also delineate downstream methods for 16S rRNA gene sequencing, including generation of sequencing libraries, data quality control, and sequence analysis. The workflow can accommodate multiple samples types, including stool and swabs collected from a variety of anatomical locations and host species. Additionally, recovered DNA and RNA can be separated and used for other applications, including whole genome sequencing or RNA-seq. The method described allows for a common processing approach for multiple sample types and accommodates downstream analysis of genomic, metagenomic and transcriptional information. PMID:27168460

  16. Bacterial Genomic Data Analysis in the Next-Generation Sequencing Era.

    Science.gov (United States)

    Orsini, Massimiliano; Cuccuru, Gianmauro; Uva, Paolo; Fotia, Giorgio

    2016-01-01

    Bacterial genome sequencing is now an affordable choice for many laboratories for applications in research, diagnostic, and clinical microbiology. Nowadays, an overabundance of tools is available for genomic data analysis. However, tools differ for algorithms, languages, hardware requirements, and user interface, and combining them as it is necessary for sequence data interpretation often requires (bio)informatics skills which can be difficult to find in many laboratories. In addition, multiple data sources, as well as exceedingly large dataset sizes, and increasingly computational complexity further challenge the accessibility, reproducibility, and transparency of the entire process. In this chapter we will cover the main bioinformatics steps required for a complete bacterial genome analysis using next-generation sequencing data, from the raw sequence data to assembled and annotated genomes. All the tools described are available in the Orione framework ( http://orione.crs4.it ), which uniquely combines in a transparent way the most used open source bioinformatics tools for microbiology, allowing microbiologist without any specific hardware or informatics skill to conduct data-intensive computational analyses from quality control to microbial gene annotation. PMID:27115645

  17. Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582

    OpenAIRE

    Michael Florea; Benjamin Reeve; James Abbott; Freemont, Paul S.; Tom Ellis

    2016-01-01

    Bacterial cellulose is a strong, highly pure form of cellulose that is used in a range of applications in industry, consumer goods and medicine. Gluconacetobacter hansenii ATCC 53582 is one of the highest reported bacterial cellulose producing strains and has been used as a model organism in numerous studies of bacterial cellulose production and studies aiming to increased cellulose productivity. Here we present a high-quality draft genome sequence for G. hansenii ATCC 53582 and find that in ...

  18. LLNL Genomic Assessment: Viral and Bacterial Sequencing Needs for TMTI, Task 1.4.2 Report

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T; Borucki, M; Lam, M; Lenhoff, R; Vitalis, E

    2010-01-26

    Good progress has been made on both bacterial and viral sequencing by the TMTI centers. While access to appropriate samples is a limiting factor to throughput, excellent progress has been made with respect to getting agreements in place with key sources of relevant materials. Sharing of sequenced genomes funded by TMTI has been extremely limited to date. The April 2010 exercise should force a resolution to this, but additional managerial pressures may be needed to ensure that rapid sharing of TMTI-funded sequencing occurs, regardless of collaborator constraints concerning ultimate publication(s). Policies to permit TMTI-internal rapid sharing of sequenced genomes should be written into all TMTI agreements with collaborators now being negotiated. TMTI needs to establish a Web-based system for tracking samples destined for sequencing. This includes metadata on sample origins and contributor, information on sample shipment/receipt, prioritization by TMTI, assignment to one or more sequencing centers (including possible TMTI-sponsored sequencing at a contributor site), and status history of the sample sequencing effort. While this system could be a component of the AFRL system, it is not part of any current development effort. Policy and standardized procedures are needed to ensure appropriate verification of all TMTI samples prior to the investment in sequencing. PCR, arrays, and classical biochemical tests are examples of potential verification methods. Verification is needed to detect miss-labeled, degraded, mixed or contaminated samples. Regular QC exercises are needed to ensure that the TMTI-funded centers are meeting all standards for producing quality genomic sequence data.

  19. Assembled sequence contigs by SOAPdenova and Volvet algorithms from metagenomic short reads of a new bacterial isolate of gut origin

    Science.gov (United States)

    Assembled sequence contigs by SOAPdenova and Volvet algorithms from metagenomic short reads of a new bacterial isolate of gut origin. This study included 2 submissions with a total of 9.8 million bp of assembled contigs....

  20. Solving the problem of comparing whole bacterial genomes across different sequencing platforms.

    Directory of Open Access Journals (Sweden)

    Rolf S Kaas

    Full Text Available Whole genome sequencing (WGS shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent. We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools.

  1. Solving the problem of comparing whole bacterial genomes across different sequencing platforms.

    Science.gov (United States)

    Kaas, Rolf S; Leekitcharoenphon, Pimlapas; Aarestrup, Frank M; Lund, Ole

    2014-01-01

    Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites and inferring phylogenies in WGS data across multiple platforms. The methods were evaluated on three bacterial data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a validation of all informative sites that are included in the analysis. The procedures are available as web tools. PMID:25110940

  2. A peptide identification-free, genome sequence-independent shotgun proteomics workflow for strain-level bacterial differentiation

    OpenAIRE

    Wenguang Shao; Min Zhang; Henry Lam; Lau, Stanley C K

    2015-01-01

    Shotgun proteomics is an emerging tool for bacterial identification and differentiation. However, the identification of the mass spectra of peptides to genome-derived peptide sequences remains a key issue that limits the use of shotgun proteomics to bacteria with genome sequences available. In this proof-of-concept study, we report a novel bacterial fingerprinting method that enjoys the resolving power and accuracy of mass spectrometry without the burden of peptide identification (i.e. genome...

  3. Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing

    Directory of Open Access Journals (Sweden)

    Wolcott Benjamin M

    2008-03-01

    Full Text Available Abstract Background Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. These bacterial populations cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. The use of 3 separate16S-based molecular amplifications followed by pyrosequencing, shotgun Sanger sequencing, and denaturing gradient gel electrophoresis were utilized to survey the major populations of bacteria that occur in the pathogenic biofilms of three types of chronic wound types: diabetic foot ulcers (D, venous leg ulcers (V, and pressure ulcers (P. Results There are specific major populations of bacteria that were evident in the biofilms of all chronic wound types, including Staphylococcus, Pseudomonas, Peptoniphilus, Enterobacter, Stenotrophomonas, Finegoldia, and Serratia spp. Each of the wound types reveals marked differences in bacterial populations, such as pressure ulcers in which 62% of the populations were identified as obligate anaerobes. There were also populations of bacteria that were identified but not recognized as wound pathogens, such as Abiotrophia para-adiacens and Rhodopseudomonas spp. Results of molecular analyses were also compared to those obtained using traditional culture-based diagnostics. Only in one wound type did culture methods correctly identify the primary bacterial population indicating the need for improved diagnostic methods. Conclusion If clinicians can gain a better understanding of the wound's microbiota, it will give them a greater understanding of the wound's ecology and will allow them to better manage healing of the wound improving the prognosis of patients. This research highlights the necessity to begin evaluating, studying, and treating chronic wound pathogenic biofilms as multi-species entities in

  4. LLNL Genomic Assessment: Viral and Bacterial Sequencing Needs for TMTI, Tier 1 Report

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T; Borucki, M; Lenhoff, R; Vitalis, E

    2009-09-29

    identify key virulence or host range genes. This approach will provide information that can be used by structural biologists to help develop therapeutics and vaccines. We have pointed out such high priority strains of which we are aware, and note that if any such isolates should be discovered, they will rise to the top priority. We anticipate difficulty locating samples with unusual resistance phenotypes, in particular. Sequencing strategies for isolates in queue 1 should aim for as complete finishing status as possible, since high-quality initial annotation (gene-calling) will be necessary for the follow-on protein structure analyses contributing to countermeasure development. Queue 2 for sequencing determination will be more dynamic than queue 1, and samples will be added to it as they become available to the TMTI program. 2. Selection of isolates that will provide broader information about diversity and phylogenetics and aid in specific detection as well as forensics. This approach focuses on sequencing of isolates that will provide better resolution of variants that are (or were) circulating in nature. The finishing strategy for queue 2 does not require complete closing with annotation. This queue is more static, as there is considerable phylogenetic data, and in this report we have sought to reveal gaps and make suggestions to fill them given existing sequence data and strain information. In this report we identify current sequencing gaps in both priority queue categories. Note that this is most applicable to the bacterial pathogens, as most viruses are by default in queue 1. The Phase I focus of this project is on viral hemorrhagic fever viruses and Category A bacterial agents as defined to us by TMTI. We have carried out individual analyses on each species of interest, and these are included as chapters in this report. Viruses and bacteria are biologically very distinct from each other and require different methods of analysis and criteria for sequencing

  5. LLNL Genomic Assessment: Viral and Bacterial Sequencing Needs for TMTI, Tier 1 Report

    Energy Technology Data Exchange (ETDEWEB)

    Slezak, T; Borucki, M; Lenhoff, R; Vitalis, E

    2009-09-29

    identify key virulence or host range genes. This approach will provide information that can be used by structural biologists to help develop therapeutics and vaccines. We have pointed out such high priority strains of which we are aware, and note that if any such isolates should be discovered, they will rise to the top priority. We anticipate difficulty locating samples with unusual resistance phenotypes, in particular. Sequencing strategies for isolates in queue 1 should aim for as complete finishing status as possible, since high-quality initial annotation (gene-calling) will be necessary for the follow-on protein structure analyses contributing to countermeasure development. Queue 2 for sequencing determination will be more dynamic than queue 1, and samples will be added to it as they become available to the TMTI program. 2. Selection of isolates that will provide broader information about diversity and phylogenetics and aid in specific detection as well as forensics. This approach focuses on sequencing of isolates that will provide better resolution of variants that are (or were) circulating in nature. The finishing strategy for queue 2 does not require complete closing with annotation. This queue is more static, as there is considerable phylogenetic data, and in this report we have sought to reveal gaps and make suggestions to fill them given existing sequence data and strain information. In this report we identify current sequencing gaps in both priority queue categories. Note that this is most applicable to the bacterial pathogens, as most viruses are by default in queue 1. The Phase I focus of this project is on viral hemorrhagic fever viruses and Category A bacterial agents as defined to us by TMTI. We have carried out individual analyses on each species of interest, and these are included as chapters in this report. Viruses and bacteria are biologically very distinct from each other and require different methods of analysis and criteria for sequencing

  6. AgdbNet – antigen sequence database software for bacterial typing

    Directory of Open Access Journals (Sweden)

    Maiden Martin CJ

    2006-06-01

    Full Text Available Abstract Background Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. Results Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. Conclusion The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated.

  7. Genomic Epidemiology: Whole-Genome-Sequencing-Powered Surveillance and Outbreak Investigation of Foodborne Bacterial Pathogens.

    Science.gov (United States)

    Deng, Xiangyu; den Bakker, Henk C; Hendriksen, Rene S

    2016-01-01

    As we are approaching the twentieth anniversary of PulseNet, a network of public health and regulatory laboratories that has changed the landscape of foodborne illness surveillance through molecular subtyping, public health microbiology is undergoing another transformation brought about by so-called next-generation sequencing (NGS) technologies that have made whole-genome sequencing (WGS) of foodborne bacterial pathogens a realistic and superior alternative to traditional subtyping methods. Routine, real-time, and widespread application of WGS in food safety and public health is on the horizon. Technological, operational, and policy challenges are still present and being addressed by an international and multidisciplinary community of researchers, public health practitioners, and other stakeholders. PMID:26772415

  8. Complete Genome Sequence of Lactobacillus rhamnosus Strain BPL5 (CECT 8800), a Probiotic for Treatment of Bacterial Vaginosis.

    Science.gov (United States)

    Chenoll, Empar; Codoñer, Francisco M; Martinez-Blanch, Juan F; Ramón, Daniel; Genovés, Salvador; Menabrito, Marco

    2016-01-01

    ITALIC! Lactobacillus rhamnosusBPL5 (CECT 8800), is a probiotic strain suitable for the treatment of bacterial vaginosis. Here, we report its complete genome sequence deciphered by PacBio single-molecule real-time (SMRT) technology. Analysis of the sequence may provide insight into its functional activity. PMID:27103719

  9. Complete Genome Sequence of Lactobacillus rhamnosus Strain BPL5 (CECT 8800), a Probiotic for Treatment of Bacterial Vaginosis

    Science.gov (United States)

    Codoñer, Francisco M.; Martinez-Blanch, Juan F.; Ramón, Daniel; Menabrito, Marco

    2016-01-01

    Lactobacillus rhamnosus BPL5 (CECT 8800), is a probiotic strain suitable for the treatment of bacterial vaginosis. Here, we report its complete genome sequence deciphered by PacBio single-molecule real-time (SMRT) technology. Analysis of the sequence may provide insight into its functional activity. PMID:27103719

  10. A versatile palindromic amphipathic repeat coding sequence horizontally distributed among diverse bacterial and eucaryotic microbes

    Directory of Open Access Journals (Sweden)

    Glass John I

    2010-07-01

    Full Text Available Abstract Background Intragenic tandem repeats occur throughout all domains of life and impart functional and structural variability to diverse translation products. Repeat proteins confer distinctive surface phenotypes to many unicellular organisms, including those with minimal genomes such as the wall-less bacterial monoderms, Mollicutes. One such repeat pattern in this clade is distributed in a manner suggesting its exchange by horizontal gene transfer (HGT. Expanding genome sequence databases reveal the pattern in a widening range of bacteria, and recently among eucaryotic microbes. We examined the genomic flux and consequences of the motif by determining its distribution, predicted structural features and association with membrane-targeted proteins. Results Using a refined hidden Markov model, we document a 25-residue protein sequence motif tandemly arrayed in variable-number repeats in ORFs lacking assigned functions. It appears sporadically in unicellular microbes from disparate bacterial and eucaryotic clades, representing diverse lifestyles and ecological niches that include host parasitic, marine and extreme environments. Tracts of the repeats predict a malleable configuration of recurring domains, with conserved hydrophobic residues forming an amphipathic secondary structure in which hydrophilic residues endow extensive sequence variation. Many ORFs with these domains also have membrane-targeting sequences that predict assorted topologies; others may comprise reservoirs of sequence variants. We demonstrate expressed variants among surface lipoproteins that distinguish closely related animal pathogens belonging to a subgroup of the Mollicutes. DNA sequences encoding the tandem domains display dyad symmetry. Moreover, in some taxa the domains occur in ORFs selectively associated with mobile elements. These features, a punctate phylogenetic distribution, and different patterns of dispersal in genomes of related taxa, suggest that the

  11. Viral Bacterial Artificial Chromosomes: Generation, Mutagenesis, and Removal of Mini-F Sequences

    Directory of Open Access Journals (Sweden)

    B. Karsten Tischer

    2012-01-01

    Full Text Available Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process.

  12. Identification of pets and raccoons as sources of bacterial contamination of urban storm sewers using a sequence-based bacterial source tracking method.

    Science.gov (United States)

    Ram, Jeffrey L; Thompson, Brooke; Turner, Carrie; Nechvatal, Jordan M; Sheehan, Harry; Bobrin, Janis

    2007-08-01

    In urbanized areas, contaminated storm sewers can feed high bacterial levels into free-flowing streams and rivers. Although illicit connections sometimes cause contamination, urban wildlife and free-roaming domesticated or feral pets may be another source. After eliminating illicit connections as sources of high levels of Escherichia coli in two storm sewers tributary to the Huron River in southeast Michigan, the roles of urban wildlife, pets, humans, and birds were investigated using a sequence-based bacterial source tracking technology. After enumeration, E. coli were isolated from water samples collected during spring to fall, 2005. Sequences in the gene beta-glucuronidase of each isolate were compared to sequences of reference strains from humans, raccoons, pets (cats and dogs), and birds. The highest percentage source for six of ten events was pets (ANOVA, p=0.005). Among isolates attributed to pets, strains from cats occurred more frequently on seven of nine events in which pets had a non-zero probability. High raccoon percentages (up to 60%) occurred in late summer and fall, and varied significantly more than in the spring (F-test), possibly reflecting urban raccoon den-site mobility. The sequence-based bacterial source tracking method suggests that feces from pets and raccoons are important contributors to urban storm sewers. PMID:17540431

  13. ESTIMATING BACTERIAL DIVERSITY IN SCIRTOTHRIPS DORSALIS (THYSANOPTERA: THRIPIDAE) VIA NEXT GENERATION SEQUENCING

    Science.gov (United States)

    Dickey, Aaron M.; Trease, Andrew J.; Jara-Cavieres, Antonella; Kumar, Vivek; Christenson, Matthew K.; Potluri, Lakshmi-Prasad; Morgan, J. Kent; Shatters, Robert G.; Mckenzie, Cindy L.; Davis, Paul H.; Osborne, Lance S.

    2014-01-01

    The last 2 decades have produced a better understanding of insect-microbial associations and yielded some important opportunities for insect control. However, most of our knowledge comes from model systems. Thrips (Thysanoptera: Thripidae) have been understudied despite their global importance as invasive species, plant pests and disease vectors. Using a culture and primer independent next-generation sequencing and metagenomics pipeline, we surveyed the bacteria of the globally important pest, Scirtothrips dorsalis Hood. The most abundant bacterial phyla identified were Actinobacteria and Proteobacteria and the most abundant genera were Propionibacterium, Stenotrophomonas, and Pseudomonas. A total of 189 genera of bacteria were identified. The absence of any vertically transferred symbiont taxa commonly found in insects is consistent with other studies suggesting that thrips primarilly acquire resident microbes from their environment. This does not preclude a possible beneficial/intimate association between S. dorsalis and the dominant taxa identified and future work should determine the nature of these associations. PMID:25382863

  14. Characterization of oral bacterial diversity of irradiated patients by high-throughput sequencing

    Institute of Scientific and Technical Information of China (English)

    Yue-Jian Hu; Qian Wang; Yun-Tao Jiang; Rui Ma; Wen-Wei Xia; Zi-Sheng Tang; Zheng Liu; Jing-Ping Liang; Zheng-Wei Huang

    2013-01-01

    The objective of this study was to investigate the compositional profiles and microbial shifts of oral microbiota during head-and-neck radiotherapy. Bioinformatic analysis based on 16S rRNA gene pyrosequencing was performed to assess the diversity and variation of oral microbiota of irradiated patients. Eight patients with head and neck cancers were involved in this study. For each patient, supragingival plaque samples were collected at seven time points before and during radiotherapy. A total of 147232 qualified sequences were obtained through pyrosequencing and bioinformatic analysis, representing 3460 species level operational taxonomic units (OTUs) and 140 genus level taxa. Temporal variations were observed across different time points and supported by cluster analysis based on weighted UniFrac metrics, Moreover, the low evenness of oral microbial communities in relative abundance was revealed by Lorenz curves. This study contributed to a better understanding of the detailed characterization of oral bacterial diversity of irradiated patients.

  15. Optimization of Mutation Pressure in Relation to Properties of Protein-Coding Sequences in Bacterial Genomes.

    Directory of Open Access Journals (Sweden)

    Paweł Błażej

    Full Text Available Most mutations are deleterious and require energetically costly repairs. Therefore, it seems that any minimization of mutation rate is beneficial. On the other hand, mutations generate genetic diversity indispensable for evolution and adaptation of organisms to changing environmental conditions. Thus, it is expected that a spontaneous mutational pressure should be an optimal compromise between these two extremes. In order to study the optimization of the pressure, we compared mutational transition probability matrices from bacterial genomes with artificial matrices fulfilling the same general features as the real ones, e.g., the stationary distribution and the speed of convergence to the stationarity. The artificial matrices were optimized on real protein-coding sequences based on Evolutionary Strategies approach to minimize or maximize the probability of non-synonymous substitutions and costs of amino acid replacements depending on their physicochemical properties. The results show that the empirical matrices have a tendency to minimize the effects of mutations rather than maximize their costs on the amino acid level. They were also similar to the optimized artificial matrices in the nucleotide substitution pattern, especially the high transitions/transversions ratio. We observed no substantial differences between the effects of mutational matrices on protein-coding sequences in genomes under study in respect of differently replicated DNA strands, mutational cost types and properties of the referenced artificial matrices. The findings indicate that the empirical mutational matrices are rather adapted to minimize mutational costs in the studied organisms in comparison to other matrices with similar mathematical constraints.

  16. Salivary bacterial fingerprints of established oral disease revealed by the Human Oral Microbe Identification using Next Generation Sequencing (HOMINGS) technique

    DEFF Research Database (Denmark)

    Belstrøm, Daniel; Paster, Bruce J; Fiehn, Nils-Erik; Jensen, Allan Bardow; Holmstrup, Palle

    2016-01-01

    Identification using Next Generation Sequencing) for comparison of the salivary microbiota in patients with periodontitis, patients with dental caries, and orally healthy individuals. The hypothesis was that this method could add on to the existing knowledge on salivary bacterial profiles in oral health and...... HOMINGS analysis showed that different salivary bacterial profiles were associated with oral health and disease. Future large-scale prospective studies are needed to evaluate if saliva-based screening for disease-associated oral bacterial profiles may be used for identification of patients at risk of...... caries (mean 221, range 165-353) as compared to orally healthy individuals (mean 174, range 120-260) (p=0.04 and p=0.04). Nine probe targets were identified with a different relative abundance between groups (p<0.05). CONCLUSIONS: Cross-sectional comparison of salivary bacterial profiles by means of...

  17. Draft Genome Sequence of Clostridium straminisolvens Strain JCM 21531T, Isolated from a Cellulose-Degrading Bacterial Community

    OpenAIRE

    Yuki, Masahiro; Oshima, Kenshiro; Suda, Wataru; Sakamoto, Mitsuo; Kitamura, Keiko; Iida, Toshiya; Hattori, Masahira; Ohkuma, Moriya

    2014-01-01

    Here, we report the draft genome sequence of a fibrolytic bacterium, Clostridium straminisolvens JCM 21531T, isolated from a cellulose-degrading bacterial community. The genome information of this strain will be useful for studies on the degradation enzymes and functional interactions with other members in the community.

  18. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

    NARCIS (Netherlands)

    Medema, M.H.; Blin, K.; Cimermancic, P.; Jager, de V.C.L.; Zakrzewski, P.; Fischbach, M.A.; Weber, T.; Takano, E.; Breitling, R.

    2011-01-01

    Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide var

  19. antiSMASH: rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences.

    NARCIS (Netherlands)

    Medema, M.H.; Blin, K.; Cimermancic, P.; Jager, V.C.L. de; Zakrzewski, P.; Fischbach, M.A.; Weber, T.; Takano, E.; Breitling, R.

    2011-01-01

    Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide var

  20. antiSMASH : rapid identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genome sequences

    NARCIS (Netherlands)

    Medema, Marnix H.; Blin, Kai; Cimermancic, Peter; de Jager, Victor; Zakrzewski, Piotr; Fischbach, Michael A.; Weber, Tilmann; Takano, Eriko; Breitling, Rainer

    2011-01-01

    Bacterial and fungal secondary metabolism is a rich source of novel bioactive compounds with potential pharmaceutical applications as antibiotics, anti-tumor drugs or cholesterol-lowering drugs. To find new drug candidates, microbiologists are increasingly relying on sequencing genomes of a wide var

  1. Complete Genome Sequence of Japanese Erwinia Strain Ejp617, a Bacterial Shoot Blight Pathogen of Pear ▿

    OpenAIRE

    Park, Duck Hwan; Thapa, Shree Prasad; Choi, Beom-Soon; Kim, Won-Sik; Hur, Jang Hyun; Cho, Jun Mo; Lim, Jong-Sung; Choi, Ik-Young; Lim, Chun Keun

    2010-01-01

    The Japanese Erwinia strain Ejp617 is a plant pathogen that causes bacterial shoot blight of pear in Japan. Here, we report the complete genome sequence of strain Ejp617 isolated from Nashi pears in Japan to provide further valuable insight among related Erwinia species.

  2. Complete Genome Sequence of Gluconacetobacter hansenii Strain NQ5 (ATCC 53582), an Efficient Producer of Bacterial Cellulose.

    Science.gov (United States)

    Pfeffer, Sarah; Mehta, Kalpa; Brown, R Malcolm

    2016-01-01

    This study reports the release of the complete nucleotide sequence of Gluconacetobacter hansenii strain NQ5 (ATCC 53582). This strain was isolated by R. Malcolm Brown, Jr. in a sugar mill in North Queensland, Australia, and is an efficient producer of bacterial cellulose. The elucidation of the genome will contribute to the study of the molecular mechanisms necessary for cellulose biosynthesis. PMID:27516505

  3. Soil Parameters Drive the Structure, Diversity and Metabolic Potentials of the Bacterial Communities Across Temperate Beech Forest Soil Sequences.

    Science.gov (United States)

    Jeanbille, M; Buée, M; Bach, C; Cébron, A; Frey-Klett, P; Turpault, M P; Uroz, S

    2016-02-01

    Soil and climatic conditions as well as land cover and land management have been shown to strongly impact the structure and diversity of the soil bacterial communities. Here, we addressed under a same land cover the potential effect of the edaphic parameters on the soil bacterial communities, excluding potential confounding factors as climate. To do this, we characterized two natural soil sequences occurring in the Montiers experimental site. Spatially distant soil samples were collected below Fagus sylvatica tree stands to assess the effect of soil sequences on the edaphic parameters, as well as the structure and diversity of the bacterial communities. Soil analyses revealed that the two soil sequences were characterized by higher pH and calcium and magnesium contents in the lower plots. Metabolic assays based on Biolog Ecoplates highlighted higher intensity and richness in usable carbon substrates in the lower plots than in the middle and upper plots, although no significant differences occurred in the abundance of bacterial and fungal communities along the soil sequences as assessed using quantitative PCR. Pyrosequencing analysis of 16S ribosomal RNA (rRNA) gene amplicons revealed that Proteobacteria, Acidobacteria and Bacteroidetes were the most abundantly represented phyla. Acidobacteria, Proteobacteria and Chlamydiae were significantly enriched in the most acidic and nutrient-poor soils compared to the Bacteroidetes, which were significantly enriched in the soils presenting the higher pH and nutrient contents. Interestingly, aluminium, nitrogen, calcium, nutrient availability and pH appeared to be the best predictors of the bacterial community structures along the soil sequences. PMID:26370112

  4. Profile of bacterial communities in South African mine-water samples using Illumina next-generation sequencing platform.

    Science.gov (United States)

    Keshri, Jitendra; Mankazana, Boitumelo B J; Momba, Maggy N B

    2015-04-01

    Mine water is an example of an extreme environment that contains a large number of diverse and specific bacteria. It is imperative to gain an understanding of these bacterial communities in order to develop effective strategies for the bioremediation of polluted aquatic systems. In this study, the high-throughput sequencing approach was used to characterize the bacterial communities in two different mine waters of South Africa: vanadium and gold mine water. Over 2629 operational taxonomic units (OTUs) were recovered from 15,802 reads of the 16S ribosomal RNA (rRNA) gene. They represented 8 phyla, 43 orders, 84 families and 105 genera. Proteobacteria and unclassified bacterial sequences were the most dominant. Apart from these, Firmicutes, Bacteroidetes, Actinobacteria, Candidate phylum OD1, Cyanobacteria, Verrucomicrobia and Deinococcus-Thermus were the recovered phyla, although their relative abundance differed between both the mine-water samples. Yet, diversity indices suggested that the bacterial communities inhabiting the vanadium mine water were more diverse than those in gold mine water. Interestingly, substantial percentages of the reads from either sample (58 % in vanadium and 17 % in gold mine water) could not be assigned to any phylum and remained unclassified, suggesting hitherto unidentified populations, and vast untapped microbial diversity. Overall, the results of this study exhibited bacterial community structures with high diversity in mine water, which can be explored further for their role in bioremediation and environmental management. PMID:25416590

  5. Analysis of the cystic fibrosis lung microbiota via serial Illumina sequencing of bacterial 16S rRNA hypervariable regions.

    Directory of Open Access Journals (Sweden)

    Heather Maughan

    Full Text Available The characterization of bacterial communities using DNA sequencing has revolutionized our ability to study microbes in nature and discover the ways in which microbial communities affect ecosystem functioning and human health. Here we describe Serial Illumina Sequencing (SI-Seq: a method for deep sequencing of the bacterial 16S rRNA gene using next-generation sequencing technology. SI-Seq serially sequences portions of the V5, V6 and V7 hypervariable regions from barcoded 16S rRNA amplicons using an Illumina short-read genome analyzer. SI-Seq obtains taxonomic resolution similar to 454 pyrosequencing for a fraction of the cost, and can produce hundreds of thousands of reads per sample even with very high multiplexing. We validated SI-Seq using single species and mock community controls, and via a comparison to cystic fibrosis lung microbiota sequenced using 454 FLX Titanium. Our control runs show that SI-Seq has a dynamic range of at least five orders of magnitude, can classify >96% of sequences to the genus level, and performs just as well as 454 and paired-end Illumina methods in estimation of standard microbial ecology diversity measurements. We illustrate the utility of SI-Seq in a pilot sample of central airway secretion samples from cystic fibrosis patients.

  6. Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns

    Directory of Open Access Journals (Sweden)

    Tümmler Burkhard

    2004-07-01

    Full Text Available Abstract Background Oligonucleotide frequencies were shown to be conserved signatures for bacterial genomes, however, the underlying constraints have yet not been resolved in detail. In this paper we analyzed oligonucleotide usage (OU biases in a comprehensive collection of 155 completely sequenced bacterial chromosomes, 316 plasmids and 104 phages. Results Two global features were analyzed: pattern skew (PS and variance of OU deviations normalized by mononucleotide content of the sequence (OUV. OUV reflects the strength of OU biases and taxonomic signals. PS denotes asymmetry of OU in direct and reverse DNA strands. A trend towards minimal PS was observed for almost all complete sequences of bacterial chromosomes and plasmids, however, PS was substantially higher in separate genomic loci and several types of plasmids and phages characterized by long stretches of non-coding DNA and/or asymmetric gene distribution on the two DNA strands. Five of the 155 bacterial chromosomes have anomalously high PS, of which the chromosomes of Xylella fastidiosa 9a5c and Prochlorococcus marinus MIT9313 exhibit extreme PS values suggesting an intermediate unstable state of these two genomes. Conclusions Strand symmetry as indicated by minimal PS is a universally conserved feature of complete bacterial genomes that results from the matching mutual compensation of local OU biases on both replichors while OUV is more a taxon specific feature. Local events such as inversions or the incorporation of genome islands are balanced by global changes in genome organization to minimize PS that may represent one of the leading evolutionary forces driving bacterial genome diversification.

  7. A low dose of an organophosphate insecticide causes dysbiosis and sex-dependent responses in the intestinal microbiota of the Japanese quail (Coturnix japonica)

    Science.gov (United States)

    Moreno-Moyano, Laura T.; Wilkinson, Ngare; Prasai, Tanka; Brown, Philip H.; Moore, Robert J.; Stanley, Dragana

    2016-01-01

    Organophosphate insecticides have been directly or indirectly implicated in avian populations declining worldwide. Birds in agricultural environments are commonly exposed to these insecticides, mainly through ingestion of invertebrates after insecticide application. Despite insecticide exposure in birds occurring mostly by ingestion, the impact of organophosphates on the avian digestive system has been poorly researched. In this work we used the Japanese quail (Coturnix japonica) as an avian model to study short-term microbial community responses to a single dose of trichlorfon at low concentration in three sample origins of the gastrointestinal tract (GIT): caecum, large intestine and faeces. Using next-generation sequencing of 16S rRNA gene amplicons as bacterial markers, the study showed that ingestion of insecticide caused significant changes in the GIT microbiome. Specifically, microbiota composition and diversity differed between treated and untreated quail. Insecticide-associated responses in the caecum showed differences between sexes which did not occur with the other sample types. In caecal microbiota, only treated females showed significant shifts in a number of genera within the Lachnospiraceae and the Enterobacteriaceae families. The major responses in the large intestine were a significant reduction in the genus Lactobacillus and increases in abundance of a number of Proteobacteria genera. All microbial shifts in faeces occurred in phylotypes that were represented at low relative abundances. In general, changes in microbiota possibly resulted from contrasting responses towards the insecticide, either positive (e.g., biodegrading bacteria) or negative (e.g., insecticide-susceptible bacteria). This study demonstrates the significant impact that organophosphate insecticides have on the avian gut microbiota; showing that a single small dose of trichlorfon caused dysbiosis in the GIT of the Japanese quail. Further research is necessary to understand the

  8. Bacterial diversity assessment of pristine mangrove microbial community from Dhulibhashani, Sundarbans using 16S rRNA gene tag sequencing.

    Science.gov (United States)

    Basak, Pijush; Pramanik, Arnab; Sengupta, Sohan; Nag, Sudip; Bhattacharyya, Anish; Roy, Debojyoti; Pattanayak, Rudradip; Ghosh, Abhrajyoti; Chattopadhyay, Dhrubajyoti; Bhattacharyya, Maitree

    2016-03-01

    The global knowledge of microbial diversity and function in Sundarbans ecosystem is still scarce, despite global advancement in understanding the microbial diversity. In the present study, we have analyzed the diversity and distribution of bacteria in the tropical mangrove sediments of Sundarbans using 16S rRNA gene amplicon sequencing. Metagenome is comprised of 1,53,926 sequences with 108.8 Mbp data and with 55 ± 2% G + C content. Metagenome sequence data are available at NCBI under the Bioproject database with accession no. PRJNA245459. Bacterial community metagenome sequences were analyzed by MG-RAST software representing the presence of 56,547 species belonging to 44 different phyla. The taxonomic analysis revealed the dominance of phyla Proteobacteria within our dataset. Further taxonomic analysis revealed abundance of Bacteroidetes, Acidobactreia, Firmicutes, Actinobacteria, Nitrospirae, Cyanobacteria, Planctomycetes and Fusobacteria group as the predominant bacterial assemblages in this largely pristine mangrove habitat. The distribution of different community datasets obtained from four sediment samples originated from one sampling station at two different depths providing better understanding of the sediment bacterial diversity and its relationship to the ecosystem dynamics of this pristine mangrove sediment of Dhulibhashani in, Sundarbans. PMID:26981367

  9. Rapid 16S rRNA next-generation sequencing of polymicrobial clinical samples for diagnosis of complex bacterial infections.

    Directory of Open Access Journals (Sweden)

    Stephen J Salipante

    Full Text Available Classifying individual bacterial species comprising complex, polymicrobial patient specimens remains a challenge for culture-based and molecular microbiology techniques in common clinical use. We therefore adapted practices from metagenomics research to rapidly catalog the bacterial composition of clinical specimens directly from patients, without need for prior culture. We have combined a semiconductor deep sequencing protocol that produces reads spanning 16S ribosomal RNA gene variable regions 1 and 2 (∼360 bp with a de-noising pipeline that significantly improves the fraction of error-free sequences. The resulting sequences can be used to perform accurate genus- or species-level taxonomic assignment. We explore the microbial composition of challenging, heterogeneous clinical specimens by deep sequencing, culture-based strain typing, and Sanger sequencing of bulk PCR product. We report that deep sequencing can catalog bacterial species in mixed specimens from which usable data cannot be obtained by conventional clinical methods. Deep sequencing a collection of sputum samples from cystic fibrosis (CF patients reveals well-described CF pathogens in specimens where they were not detected by standard clinical culture methods, especially for low-prevalence or fastidious bacteria. We also found that sputa submitted for CF diagnostic workup can be divided into a limited number of groups based on the phylogenetic composition of the airway microbiota, suggesting that metagenomic profiling may prove useful as a clinical diagnostic strategy in the future. The described method is sufficiently rapid (theoretically compatible with same-day turnaround times and inexpensive for routine clinical use.

  10. Genome sequence and plasmid transformation of the model high-yield bacterial cellulose producer Gluconacetobacter hansenii ATCC 53582

    Science.gov (United States)

    Florea, Michael; Reeve, Benjamin; Abbott, James; Freemont, Paul S.; Ellis, Tom

    2016-03-01

    Bacterial cellulose is a strong, highly pure form of cellulose that is used in a range of applications in industry, consumer goods and medicine. Gluconacetobacter hansenii ATCC 53582 is one of the highest reported bacterial cellulose producing strains and has been used as a model organism in numerous studies of bacterial cellulose production and studies aiming to increased cellulose productivity. Here we present a high-quality draft genome sequence for G. hansenii ATCC 53582 and find that in addition to the previously described cellulose synthase operon, ATCC 53582 contains two additional cellulose synthase operons and several previously undescribed genes associated with cellulose production. In parallel, we also develop optimized protocols and identify plasmid backbones suitable for transformation of ATCC 53582, albeit with low efficiencies. Together, these results provide important information for further studies into cellulose synthesis and for future studies aiming to genetically engineer G. hansenii ATCC 53582 for increased cellulose productivity.

  11. Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing

    OpenAIRE

    Wolcott Benjamin M; Rhoads Daniel D; Secor Patrick R; Sun Yan; Dowd Scot E; James Garth A; Wolcott Randall D

    2008-01-01

    Abstract Background Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species. These bacterial populations cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the bacterial populations that occur within different types of chronic wound biofilms. The use of 3 separate16S-based molecular amplifications followed by pyrosequencing, shotgun Sanger ...

  12. Potential use of bacterial community succession for estimating post-mortem interval as revealed by high-throughput sequencing.

    Science.gov (United States)

    Guo, Juanjuan; Fu, Xiaoliang; Liao, Huidan; Hu, Zhenyu; Long, Lingling; Yan, Weitao; Ding, Yanjun; Zha, Lagabaiyila; Guo, Yadong; Yan, Jie; Chang, Yunfeng; Cai, Jifeng

    2016-01-01

    Decomposition is a complex process involving the interaction of both biotic and abiotic factors. Microbes play a critical role in the process of carrion decomposition. In this study, we analysed bacterial communities from live rats and rat remains decomposed under natural conditions, or excluding sarcosaphagous insect interference, in China using Illumina MiSeq sequencing of 16S rRNA gene amplicons. A total of 1,394,842 high-quality sequences and 1,938 singleton operational taxonomic units were obtained. Bacterial communities showed notable variation in relative abundance and became more similar to each other across body sites during the decomposition process. As decomposition progressed, Proteobacteria (mostly Gammaproteobacteria) became the predominant phylum in both the buccal cavity and rectum, while Firmicutes and Bacteroidetes in the mouth and rectum, respectively, gradually decreased. In particular, the arrival and oviposition of sarcosaphagous insects had no obvious influence on bacterial taxa composition, but accelerated the loss of biomass. In contrast to the rectum, the microbial community structure in the buccal cavity of live rats differed considerably from that of rats immediately after death. Although this research indicates that bacterial communities can be used as a "microbial clock" for the estimation of post-mortem interval, further work is required to better understand this concept. PMID:27052375

  13. Phyllosphere Bacterial Community of Floating Macrophytes in Paddy Soil Environments as Revealed by Illumina High-Throughput Sequencing

    OpenAIRE

    Xie, Wan-Ying; Su, Jian-Qiang; Zhu, Yong-Guan

    2014-01-01

    The phyllosphere of floating macrophytes in paddy soil ecosystems, a unique habitat, may support large microbial communities but remains largely unknown. We took Wolffia australiana as a representative floating plant and investigated its phyllosphere bacterial community and the underlying driving forces of community modulation in paddy soil ecosystems using Illumina HiSeq 2000 platform-based 16S rRNA gene sequence analysis. The results showed that the phyllosphere of W. australiana harbored c...

  14. Complete Genome Sequence of Cell Culture-Attenuated Guinea Pig Cytomegalovirus Cloned as an Infectious Bacterial Artificial Chromosome

    OpenAIRE

    Yang, Dongmei; Alam, Zohaib; Cui, Xiaohong; Chen, Michael; Sherrod, Carly J.; McVoy, Michael A.; Schleiss, Mark R.; Dittmer, Dirk P

    2014-01-01

    The complete genome sequence of attenuated guinea pig cytomegalovirus cloned as bacterial artificial chromosome N13R10 was determined. Comparison to pathogenic salivary gland-derived virus revealed 13 differences, 1 of which disrupted overlapping open reading frames encoding GP129 and GP130. Attenuation of N13R10 may arise from an inability to express GP129 and/or GP130.

  15. Sub-chronic exposure to the insecticide dimethoate induces a proinflammatory status and enhances the neuroinflammatory response to bacterial lypopolysaccharide in the hippocampus and striatum of male mice

    International Nuclear Information System (INIS)

    Dimethoate is an organophosphorus insecticide extensively used in horticulture. Previous studies have shown that the administration of dimethoate to male rats, at a very low dose and during a sub-chronic period, increases the oxidation of lipids and proteins, reduces the levels of antioxidants and impairs mitochondrial function in various brain regions. In this study, we have assessed in C57Bl/6 adult male mice, whether sub-chronic (5 weeks) intoxication with a low dose of dimethoate (1.4 mg/kg) affects the expression of inflammatory molecules and the reactivity of microglia in the hippocampus and striatum under basal conditions and after an immune challenge caused by the systemic administration of lipopolysaccharide. Dimethoate increased mRNA levels of tumor necrosis factor α (TNFα) and interleukin (IL) 6 in the hippocampus, and increased the proportion of Iba1 immunoreactive cells with reactive phenotype in dentate gyrus and striatum. Lipopolysaccharide caused a significant increase in the mRNA levels of IL1β, TNFα, IL6 and interferon-γ-inducible protein 10, and a significant increase in the proportion of microglia with reactive phenotype in the hippocampus and the striatum. Some of the effects of lipopolysaccharide (proportion of Iba1 immunoreactive cells with reactive phenotype and IL6 mRNA levels) were amplified in the animals treated with dimethoate, but only in the striatum. These findings indicate that a sub-chronic period of administration of a low dose of dimethoate, comparable to the levels of the pesticide present as residues in food, causes a proinflammatory status in the brain and enhances the neuroinflammatory response to the lipopolysaccharide challenge with regional specificity. - Highlights: • The dose of pesticide used was comparable to the levels of residues found in food. • Dimethoate administration increased cytokine expression and microglia reactivity. • Hippocampus and striatum were differentially affected by the treatment.

  16. Sub-chronic exposure to the insecticide dimethoate induces a proinflammatory status and enhances the neuroinflammatory response to bacterial lypopolysaccharide in the hippocampus and striatum of male mice

    Energy Technology Data Exchange (ETDEWEB)

    Astiz, Mariana, E-mail: marianaastiz@gmail.com; Diz-Chaves, Yolanda, E-mail: ydiz@cajal.csic.es; Garcia-Segura, Luis M., E-mail: lmgs@cajal.csic.es

    2013-10-15

    Dimethoate is an organophosphorus insecticide extensively used in horticulture. Previous studies have shown that the administration of dimethoate to male rats, at a very low dose and during a sub-chronic period, increases the oxidation of lipids and proteins, reduces the levels of antioxidants and impairs mitochondrial function in various brain regions. In this study, we have assessed in C57Bl/6 adult male mice, whether sub-chronic (5 weeks) intoxication with a low dose of dimethoate (1.4 mg/kg) affects the expression of inflammatory molecules and the reactivity of microglia in the hippocampus and striatum under basal conditions and after an immune challenge caused by the systemic administration of lipopolysaccharide. Dimethoate increased mRNA levels of tumor necrosis factor α (TNFα) and interleukin (IL) 6 in the hippocampus, and increased the proportion of Iba1 immunoreactive cells with reactive phenotype in dentate gyrus and striatum. Lipopolysaccharide caused a significant increase in the mRNA levels of IL1β, TNFα, IL6 and interferon-γ-inducible protein 10, and a significant increase in the proportion of microglia with reactive phenotype in the hippocampus and the striatum. Some of the effects of lipopolysaccharide (proportion of Iba1 immunoreactive cells with reactive phenotype and IL6 mRNA levels) were amplified in the animals treated with dimethoate, but only in the striatum. These findings indicate that a sub-chronic period of administration of a low dose of dimethoate, comparable to the levels of the pesticide present as residues in food, causes a proinflammatory status in the brain and enhances the neuroinflammatory response to the lipopolysaccharide challenge with regional specificity. - Highlights: • The dose of pesticide used was comparable to the levels of residues found in food. • Dimethoate administration increased cytokine expression and microglia reactivity. • Hippocampus and striatum were differentially affected by the treatment.

  17. Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

    Directory of Open Access Journals (Sweden)

    Barriuso Jorge

    2011-12-01

    Full Text Available Abstract Background Next generation sequencing (NGS enables a more comprehensive analysis of bacterial diversity from complex environmental samples. NGS data can be analysed using a variety of workflows. We test several simple and complex workflows, including frequently used as well as recently published tools, and report on their respective accuracy and efficiency under various conditions covering different sequence lengths, number of sequences and real world experimental data from rhizobacterial populations of glyphosate-tolerant maize treated or untreated with two different herbicides representative of differential diversity studies. Results Alignment and distance calculations affect OTU estimations, and multiple sequence alignment exerts a major impact on the computational time needed. Generally speaking, most of the analyses produced consistent results that may be used to assess differential diversity changes, however, dataset characteristics dictate which workflow should be preferred in each case. Conclusions When estimating bacterial diversity, ESPRIT as well as the web-based workflow, RDP pyrosequencing pipeline, produced good results in all circumstances, however, its computational requirements can make method-combination workflows more attractive, depending on sequence variability, number and length.

  18. Repetitive genome elements in a European corn borer, Ostrinia nubilalis, bacterial artificial chromosome library were indicated by bacterial artificial chromosome end sequencing and development of sequence tag site markers: implications for lepidopteran genomic research.

    Science.gov (United States)

    Coates, Brad S; Sumerford, Douglas V; Hellmich, Richard L; Lewis, Leslie C

    2009-01-01

    The European corn borer, Ostrinia nubilalis, is a serious pest of food, fiber, and biofuel crops in Europe, North America, and Asia and a model system for insect olfaction and speciation. A bacterial artificial chromosome library constructed for O. nubilalis contains 36 864 clones with an estimated average insert size of >or=120 kb and genome coverage of 8.8-fold. Screening OnB1 clones comprising approximately 2.76 genome equivalents determined the physical position of 24 sequence tag site markers, including markers linked to ecologically important and Bacillus thuringiensis toxin resistance traits. OnB1 bacterial artificial chromosome end sequence reads (GenBank dbGSS accessions ET217010 to ET217273) showed homology to annotated genes or expressed sequence tags and identified repetitive genome elements, O. nubilalis miniature subterminal inverted repeat transposable elements (OnMITE01 and OnMITE02), and ezi-like long interspersed nuclear elements. Mobility of OnMITE01 was demonstrated by the presence or absence in O. nubilalis of introns at two different loci. A (GTCT)n tetranucleotide repeat at the 5' ends of OnMITE01 and OnMITE02 are evidence for transposon-mediated movement of lepidopteran microsatellite loci. The number of repetitive elements in lepidopteran genomes will affect genome assembly and marker development. Single-locus sequence tag site markers described here have downstream application for integration within linkage maps and comparative genomic studies. PMID:19132072

  19. Insecticide solvents: interference with insecticidal action.

    Science.gov (United States)

    Brattsten, L B; Wilkinson, C F

    1977-06-10

    Several commercial solvent mixtures commonly used as insecticide carriers in spray formulations increase by more than threefold the microsomal N-demethylation of p-chloro N-methylaniline in midgut preparations of southern army-worm (Spodoptera eridania) larvae exposed orally to the test solvents. Under laboratory conditions, the same solvent mixtures exhibit a protective action against the in vivo toxicity of the insecticide carbaryl to the larvae. The data are discussed with respect to possible solvent-insecticide interactions occurring under field conditions and, more broadly, to potential toxicological hazards of these solvents to humans. PMID:860135

  20. Fourier and spectral envelope analysis of medically important bacterial and fungal sequences

    OpenAIRE

    Chang, C.; Chan, KKH; Chan, FHY

    2004-01-01

    In this paper, we introduce the Fourier and spectral envelope analysis methods to analyze some biomolecular sequences, particularly medically important bacteria and fungi DNA sequences, to get their interesting frequency properties. Fourier analysis includes mapping character strings into numerical sequences, calculating spectra of DNA sequences and setting and solving optimization problem in order to construct a powerful predictor of exons along the long DNA sequences. The spectral envelope ...

  1. Determination of selected pesticides in water samples adjacent to agricultural fields and removal of organophosphorus insecticide chlorpyrifos using soil bacterial isolates

    Science.gov (United States)

    Hossain, M. S.; Chowdhury, M. Alamgir Zaman; Pramanik, Md. Kamruzzaman; Rahman, M. A.; Fakhruddin, A. N. M.; Alam, M. Khorshed

    2015-06-01

    The use of pesticide for crops leads to serious environmental pollution, therefore, it is essential to monitor and develop approaches to remove pesticide from contaminated environment. In this study, water samples were collected to monitor pesticide residues, and degradation of chlorpyrifos was also performed using soil bacteria. Identification of pesticide residues and determination of their levels were performed by high-performance liquid chromatography with photodiode array detector. Among 12 samples, 10 samples were found contaminated with pesticides. Chlorpyrifos was detected in four tested samples and concentrations ranged from 3.27 to 9.31 μg/l whereas fenitrothion ranging from (Below Detection Limit, pesticide residues in water, to protect the aquatic environment. Chlorpyrifos degrading bacterial isolates can be used to clean up environmental samples contaminated with the organophosphate pesticides.

  2. Co-transcriptomic Analysis by RNA Sequencing to Simultaneously Measure Regulated Gene Expression in Host and Bacterial Pathogen

    KAUST Repository

    Ravasi, Timothy

    2016-01-24

    Intramacrophage pathogens subvert antimicrobial defence pathways using various mechanisms, including the targeting of host TLR-mediated transcriptional responses. Conversely, TLR-inducible host defence mechanisms subject intramacrophage pathogens to stress, thus altering pathogen gene expression programs. Important biological insights can thus be gained through the analysis of gene expression changes in both the host and the pathogen during an infection. Traditionally, research methods have involved the use of qPCR, microarrays and/or RNA sequencing to identify transcriptional changes in either the host or the pathogen. Here we describe the application of RNA sequencing using samples obtained from in vitro infection assays to simultaneously quantify both host and bacterial pathogen gene expression changes, as well as general approaches that can be undertaken to interpret the RNA sequencing data that is generated. These methods can be used to provide insights into host TLR-regulated transcriptional responses to microbial challenge, as well as pathogen subversion mechanisms against such responses.

  3. Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

    Directory of Open Access Journals (Sweden)

    Hwang Jennifer

    2010-07-01

    Full Text Available Abstract Intense interest centers on the role of the human gut microbiome in health and disease, but optimal methods for analysis are still under development. Here we present a study of methods for surveying bacterial communities in human feces using 454/Roche pyrosequencing of 16S rRNA gene tags. We analyzed fecal samples from 10 individuals and compared methods for storage, DNA purification and sequence acquisition. To assess reproducibility, we compared samples one cm apart on a single stool specimen for each individual. To analyze storage methods, we compared 1 immediate freezing at -80°C, 2 storage on ice for 24 or 3 48 hours. For DNA purification methods, we tested three commercial kits and bead beating in hot phenol. Variations due to the different methodologies were compared to variation among individuals using two approaches--one based on presence-absence information for bacterial taxa (unweighted UniFrac and the other taking into account their relative abundance (weighted UniFrac. In the unweighted analysis relatively little variation was associated with the different analytical procedures, and variation between individuals predominated. In the weighted analysis considerable variation was associated with the purification methods. Particularly notable was improved recovery of Firmicutes sequences using the hot phenol method. We also carried out surveys of the effects of different 454 sequencing methods (FLX versus Titanium and amplification of different 16S rRNA variable gene segments. Based on our findings we present recommendations for protocols to collect, process and sequence bacterial 16S rDNA from fecal samples--some major points are 1 if feasible, bead-beating in hot phenol or use of the PSP kit improves recovery; 2 storage methods can be adjusted based on experimental convenience; 3 unweighted (presence-absence comparisons are less affected by lysis method.

  4. Diversity and dynamics of dominant and rare bacterial taxa in replicate sequencing batch reactors operated under different solids retention time

    KAUST Repository

    Bagchi, Samik

    2014-10-19

    In this study, 16S rRNA gene pyrosequencing was applied in order to provide a better insight on the diversity and dynamics of total, dominant, and rare bacterial taxa in replicate lab-scale sequencing batch reactors (SBRs) operated at different solids retention time (SRT). Rank-abundance curves showed few dominant operational taxonomic units (OTUs) and a long tail of rare OTUs in all reactors. Results revealed that there was no detectable effect of SRT (2 vs. 10 days) on Shannon diversity index and OTU richness of both dominant and rare taxa. Nonmetric multidimensional scaling analysis showed that the total, dominant, and rare bacterial taxa were highly dynamic during the entire period of stable reactor performance. Also, the rare taxa were more dynamic than the dominant taxa despite expected low invasion rates because of the use of sterile synthetic media.

  5. Whole genome sequencing of bacteria in cystic fibrosis as a model for bacterial genome adaptation and evolution.

    Science.gov (United States)

    Sharma, Poonam; Gupta, Sushim Kumar; Rolain, Jean-Marc

    2014-03-01

    Cystic fibrosis (CF) airways harbor a wide variety of new and/or emerging multidrug resistant bacteria which impose a heavy burden on patients. These bacteria live in close proximity with one another, which increases the frequency of lateral gene transfer. The exchange and movement of mobile genetic elements and genomic islands facilitate the spread of genes between genetically diverse bacteria, which seem to be advantageous to the bacterium as it allows adaptation to the new niches of the CF lungs. Niche adaptation is one of the major evolutionary forces shaping bacterial genome composition and in CF the chronic strains adapt and become less virulent. The purpose of this review is to shed light on CF bacterial genome alterations. Next-generation sequencing technology is an exciting tool that may help us to decipher the genome architecture and the evolution of bacteria colonizing CF lungs. PMID:24502835

  6. Ultradeep 16S rRNA sequencing analysis of geographically similar but diverse unexplored marine samples reveal varied bacterial community composition.

    Directory of Open Access Journals (Sweden)

    Chairmandurai Aravindraja

    Full Text Available BACKGROUND: Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. METHODS AND PRINCIPAL FINDINGS: In the present study, 16S rRNA deep sequencing analysis targeting V3 region was performed using Illumina bar coded sequencing. A total of 22.44 million paired end reads were obtained from the metagenomic DNA of Marine sediment, Rhizosphere sediment, Seawater and the epibacterial DNA of Seaweed and Seagrass. Diversity index analysis revealed that Marine sediment has the highest bacterial diversity and the least bacterial diversity was observed in Rhizosphere sediment. Proteobacteria, Actinobacteria and Bacteroidetes were the dominant taxa present in all the marine samples. Nearly 62-71% of rare species were identified in all the samples and most of these rare species were unique to a particular sample. Further taxonomic assignment at the phylum and genus level revealed that the bacterial community compositions differ among the samples. CONCLUSION: This is the first report that supports the fact that, bacterial community composition is specific for specific samples irrespective of its similar geographical location. Existence of specific bacterial community for each sample may drive overall difference in bacterial structural composition of each sample. Further studies like whole metagenomic sequencing will throw more insights to the key stone players and its interconnecting metabolic pathways. In addition, this is one of the very few reports that depicts the unexplored bacterial diversity of marine samples (Marine sediment, Rhizosphere sediment, Seawater and the host associated

  7. Larvicidal efficacy of Catharanthus roseus Linn. (Family:Apocynaceae) leaf extract and bacterial insecticideBacillus thuringiensis againstAnopheles stephensi Liston

    Institute of Scientific and Technical Information of China (English)

    Chellasamy Panneerselvam; Kadarkarai Murugan; Kalimuthu Kovendan; Palanisamy Mahesh Kumar; Sekar Ponarulselvam; Duraisamy Amerasan; Jayapal Subramaniam; Jiang-Shiou Hwang

    2013-01-01

    Objective:To explore the larvicidal activity ofCatharanthus roseus(C. roseus) leaf extract and Bacillus thuringiensis(B. thuringiensis) against the malarial vectorAnopheles stephensi(An. stephensi), when being used alone or together.Methods:The larvicidal activity was assayed at various concentrations under the laboratory and field conditions.TheLC50 andLC90 values of theC. roseus leaf extract were determined by probit analysis.Results:The plant extract showed larvicidal effects after24 h of exposure;however, the highest larval mortality was found in the petroleum ether extract ofC. roseus against the first to fourth instars larvae withLC50=3.34,4.48, 5.90 and8.17 g/L, respectively;B. thuringiensis against the first to fourth instars larvae with LC50=1.72,1.93,2.17 and2.42 g/L, respectively; and the combined treatment withLC50=2.18,2.41, 2.76 and3.22 g/L, respectively.No mortality was observed in the control.Conclusions:The petroleum ether extract ofC. roseus extract andB. thuringiensis have potential to be used as ideal eco-friendly agents for the control ofAn. stephensi in vector control programs.The combined treatment with this plant crude extract and bacterial toxin has better larvicidal efficacy against An. stephensi.

  8. High-Throughput Sequencing Analysis of the Endophytic Bacterial Diversity and Dynamics in Roots of the Halophyte Salicornia europaea.

    Science.gov (United States)

    Zhao, Shuai; Zhou, Na; Zhao, Zheng-Yong; Zhang, Ke; Tian, Chang-Yan

    2016-05-01

    Endophytic bacterial communities of halophyte Salicornia europaea roots were analyzed by 16S rRNA gene pyrosequencing. A total of 20,151 partial 16S rRNA gene sequences were obtained. These sequences revealed huge amounts of operational taxonomic units (OTUs), that is, 747-1405 OTUs in a root sample, at 3 % cut-off level. Root endophytes mainly comprised four phyla, among which Proteobacteria was the most represented, followed by Bacteroidetes, Actinobacteria, and Firmicutes. Gammaproteobacteria was the most abundant class of Proteobacteria, followed by Betaproteobacteria and Alphaproteobacteria. Genera Pantoea, Halomonas, Azomonas, Serpens, and Pseudomonas were shared by all growth periods. A marked difference in endophytic bacterial communities was evident in roots from different host life-history stages. Gammaproteobacteria increased during the five periods, while Betaproteobacteria decreased. The richest endophytic bacteria diversity was detected in the seedling stage. Endophytic bacteria diversity was reduced during the flowering stage and fruiting stage. The five libraries contained 2321 different OTUs with 41 OTUs in common. As a whole, this study first surveys communities of endophytic bacteria by tracing crucial stages in the process of halophyte growth using high-throughput sequencing methods. PMID:26787546

  9. In Silico Structure and Sequence Analysis of Bacterial Porins and Specific Diffusion Channels for Hydrophilic Molecules: Conservation, Multimericity and Multifunctionality

    Science.gov (United States)

    Vollan, Hilde S.; Tannæs, Tone; Vriend, Gert; Bukholm, Geir

    2016-01-01

    Diffusion channels are involved in the selective uptake of nutrients and form the largest outer membrane protein (OMP) family in Gram-negative bacteria. Differences in pore size and amino acid composition contribute to the specificity. Structure-based multiple sequence alignments shed light on the structure-function relations for all eight subclasses. Entropy-variability analysis results are correlated to known structural and functional aspects, such as structural integrity, multimericity, specificity and biological niche adaptation. The high mutation rate in their surface-exposed loops is likely an important mechanism for host immune system evasion. Multiple sequence alignments for each subclass revealed conserved residue positions that are involved in substrate recognition and specificity. An analysis of monomeric protein channels revealed particular sequence patterns of amino acids that were observed in other classes at multimeric interfaces. This adds to the emerging evidence that all members of the family exist in a multimeric state. Our findings are important for understanding the role of members of this family in a wide range of bacterial processes, including bacterial food uptake, survival and adaptation mechanisms. PMID:27110766

  10. Bacterial communities in semen from men of infertile couples: metagenomic sequencing reveals relationships of seminal microbiota to semen quality.

    Directory of Open Access Journals (Sweden)

    Shun-Long Weng

    Full Text Available Some previous studies have identified bacteria in semen as being a potential factor in male infertility. However, only few types of bacteria were taken into consideration while using PCR-based or culturing methods. Here we present an analysis approach using next-generation sequencing technology and bioinformatics analysis to investigate the associations between bacterial communities and semen quality. Ninety-six semen samples collected were examined for bacterial communities, measuring seven clinical criteria for semen quality (semen volume, sperm concentration, motility, Kruger's strict morphology, antisperm antibody (IgA, Atypical, and leukocytes. Computer-assisted semen analysis (CASA was also performed. Results showed that the most abundant genera among all samples were Lactobacillus (19.9%, Pseudomonas (9.85%, Prevotella (8.51% and Gardnerella (4.21%. The proportion of Lactobacillus and Gardnerella was significantly higher in the normal samples, while that of Prevotella was significantly higher in the low quality samples. Unsupervised clustering analysis demonstrated that the seminal bacterial communities were clustered into three main groups: Lactobacillus, Pseudomonas, and Prevotella predominant group. Remarkably, most normal samples (80.6% were clustered in Lactobacillus predominant group. The analysis results showed seminal bacteria community types were highly associated with semen health. Lactobacillus might not only be a potential probiotic for semen quality maintenance, but also might be helpful in countering the negative influence of Prevotella and Pseudomonas. In this study, we investigated whole seminal bacterial communities and provided the most comprehensive analysis of the association between bacterial community and semen quality. The study significantly contributes to the current understanding of the etiology of male fertility.

  11. Survey of bacterial diversity in chronic wounds using Pyrosequencing, DGGE, and full ribosome shotgun sequencing.

    Science.gov (United States)

    Background: Chronic wound pathogenic biofilms are host-pathogen environments that colonize and exist as a cohabitation of many bacterial species that cooperate to promote their own survival and the chronic nature of the infection. Few studies have performed extensive surveys of the different populat...

  12. Visual analysis of next-generation sequencing data to detect overlapping genes in bacterial genomes

    OpenAIRE

    Simon, Svenja; Oelke, Daniela; Landstorfer, Richard; Neuhaus, Klaus; Keim, Daniel

    2011-01-01

    Next generation sequencing (NGS) technologies are about to revolutionize biological research. Being able to sequence large amounts of DNA or, indirectly, RNA sequences in a short time period opens numerous new possibilities. However, analyzing the large amounts of data generated in NGS is a serious challenge, which requires novel data analysis and visualization methods to allow the biological experimenter to understand the results. In this paper, we describe a novel system to deal with the fl...

  13. Construction of an Americn mink Bacterial Artificial Chromosome (BAC) library and sequencing candidate genes important for the fur industry

    DEFF Research Database (Denmark)

    Anistoroaei, Razvan Marian; Hallers, Boudewijn ten; Nefedov, Michael;

    2011-01-01

    consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs), representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library......BACKGROUND: Bacterial artificial chromosome (BAC) libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects. RESULTS: Here, we...... report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (Neovison vison). The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each...

  14. Genome Sequence of the Banana Pathogen Dickeya zeae Strain MS1, Which Causes Bacterial Soft Rot

    OpenAIRE

    Zhang, Jing-Xin; Lin, Bi-Run; Shen, Hui-Fang; Pu, Xiao-Ming

    2013-01-01

    We report a draft genome sequence of Dickeya zeae strain MS1, which is the causative agent of banana soft rot in China, and we show several of its specific properties compared with those of other D. zeae strains. Genome sequencing provides a tool for understanding the genomic determination of the pathogenicity and phylogeny placement of this pathogen.

  15. PathogenFinder - Distinguishing Friend from Foe Using Bacterial Whole Genome Sequence Data

    DEFF Research Database (Denmark)

    Cosentino, Salvatore; Larsen, Mette Voldby; Aarestrup, Frank Møller;

    2013-01-01

    Although the majority of bacteria are harmless or even beneficial to their host, others are highly virulent and can cause serious diseases, and even death. Due to the constantly decreasing cost of high-throughput sequencing there are now many completely sequenced genomes available from both human...

  16. Midgut bacteria required for Bacillus thuringiensis insecticidal activity

    OpenAIRE

    Broderick, Nichole A.; Raffa, Kenneth F.; Handelsman, Jo

    2006-01-01

    Bacillus thuringiensis is the most widely applied biological insecticide and is used to manage insects that affect forestry and agriculture and transmit human and animal pathogens. This ubiquitous spore-forming bacterium kills insect larvae largely through the action of insecticidal crystal proteins and is commonly deployed as a direct bacterial spray. Moreover, plants engineered with the cry genes encoding the B. thuringiensis crystal proteins are the most widely cultivated transgenic crops....

  17. Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees.

    Science.gov (United States)

    Sabree, Zakee L; Hansen, Allison K; Moran, Nancy A

    2012-01-01

    Starting in 2003, numerous studies using culture-independent methodologies to characterize the gut microbiota of honey bees have retrieved a consistent and distinctive set of eight bacterial species, based on near identity of the 16S rRNA gene sequences. A recent study [Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton ILG (2012) Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS ONE 7(3): e32962], using pyrosequencing of the V1-V2 hypervariable region of the 16S rRNA gene, reported finding entirely novel bacterial species in honey bee guts, and used taxonomic assignments from these reads to predict metabolic activities based on known metabolisms of cultivable species. To better understand this discrepancy, we analyzed the Mattila et al. pyrotag dataset. In contrast to the conclusions of Mattila et al., we found that the large majority of pyrotag sequences belonged to clusters for which representative sequences were identical to sequences from previously identified core species of the bee microbiota. On average, they represent 95% of the bacteria in each worker bee in the Mattila et al. dataset, a slightly lower value than that found in other studies. Some colonies contain small proportions of other bacteria, mostly species of Enterobacteriaceae. Reanalysis of the Mattila et al. dataset also did not support a relationship between abundances of Bifidobacterium and of putative pathogens or a significant difference in gut communities between colonies from queens that were singly or multiply mated. Additionally, consistent with previous studies, the dataset supports the occurrence of considerable strain variation within core species, even within single colonies. The roles of these bacteria within bees, or the implications of the strain variation, are not yet clear. PMID:22829932

  18. Independent studies using deep sequencing resolve the same set of core bacterial species dominating gut communities of honey bees.

    Directory of Open Access Journals (Sweden)

    Zakee L Sabree

    Full Text Available Starting in 2003, numerous studies using culture-independent methodologies to characterize the gut microbiota of honey bees have retrieved a consistent and distinctive set of eight bacterial species, based on near identity of the 16S rRNA gene sequences. A recent study [Mattila HR, Rios D, Walker-Sperling VE, Roeselers G, Newton ILG (2012 Characterization of the active microbiotas associated with honey bees reveals healthier and broader communities when colonies are genetically diverse. PLoS ONE 7(3: e32962], using pyrosequencing of the V1-V2 hypervariable region of the 16S rRNA gene, reported finding entirely novel bacterial species in honey bee guts, and used taxonomic assignments from these reads to predict metabolic activities based on known metabolisms of cultivable species. To better understand this discrepancy, we analyzed the Mattila et al. pyrotag dataset. In contrast to the conclusions of Mattila et al., we found that the large majority of pyrotag sequences belonged to clusters for which representative sequences were identical to sequences from previously identified core species of the bee microbiota. On average, they represent 95% of the bacteria in each worker bee in the Mattila et al. dataset, a slightly lower value than that found in other studies. Some colonies contain small proportions of other bacteria, mostly species of Enterobacteriaceae. Reanalysis of the Mattila et al. dataset also did not support a relationship between abundances of Bifidobacterium and of putative pathogens or a significant difference in gut communities between colonies from queens that were singly or multiply mated. Additionally, consistent with previous studies, the dataset supports the occurrence of considerable strain variation within core species, even within single colonies. The roles of these bacteria within bees, or the implications of the strain variation, are not yet clear.

  19. Phylogenetic analysis of bacterial and archaeal arsC gene sequences suggests an ancient, common origin for arsenate reductase

    Directory of Open Access Journals (Sweden)

    Dugas Sandra L

    2003-07-01

    Full Text Available Abstract Background The ars gene system provides arsenic resistance for a variety of microorganisms and can be chromosomal or plasmid-borne. The arsC gene, which codes for an arsenate reductase is essential for arsenate resistance and transforms arsenate into arsenite, which is extruded from the cell. A survey of GenBank shows that arsC appears to be phylogenetically widespread both in organisms with known arsenic resistance and those organisms that have been sequenced as part of whole genome projects. Results Phylogenetic analysis of aligned arsC sequences shows broad similarities to the established 16S rRNA phylogeny, with separation of bacterial, archaeal, and subsequently eukaryotic arsC genes. However, inconsistencies between arsC and 16S rRNA are apparent for some taxa. Cyanobacteria and some of the γ-Proteobacteria appear to possess arsC genes that are similar to those of Low GC Gram-positive Bacteria, and other isolated taxa possess arsC genes that would not be expected based on known evolutionary relationships. There is no clear separation of plasmid-borne and chromosomal arsC genes, although a number of the Enterobacteriales (γ-Proteobacteria possess similar plasmid-encoded arsC sequences. Conclusion The overall phylogeny of the arsenate reductases suggests a single, early origin of the arsC gene and subsequent sequence divergence to give the distinct arsC classes that exist today. Discrepancies between 16S rRNA and arsC phylogenies support the role of horizontal gene transfer (HGT in the evolution of arsenate reductases, with a number of instances of HGT early in bacterial arsC evolution. Plasmid-borne arsC genes are not monophyletic suggesting multiple cases of chromosomal-plasmid exchange and subsequent HGT. Overall, arsC phylogeny is complex and is likely the result of a number of evolutionary mechanisms.

  20. Construction of an American mink Bacterial Artificial Chromosome (BAC library and sequencing candidate genes important for the fur industry

    Directory of Open Access Journals (Sweden)

    Christensen Knud

    2011-07-01

    Full Text Available Abstract Background Bacterial artificial chromosome (BAC libraries continue to be invaluable tools for the genomic analysis of complex organisms. Complemented by the newly and fast growing deep sequencing technologies, they provide an excellent source of information in genomics projects. Results Here, we report the construction and characterization of the CHORI-231 BAC library constructed from a Danish-farmed, male American mink (Neovison vison. The library contains approximately 165,888 clones with an average insert size of 170 kb, representing approximately 10-fold coverage. High-density filters, each consisting of 18,432 clones spotted in duplicate, have been produced for hybridization screening and are publicly available. Overgo probes derived from expressed sequence tags (ESTs, representing 21 candidate genes for traits important for the mink industry, were used to screen the BAC library. These included candidate genes for coat coloring, hair growth and length, coarseness, and some receptors potentially involved in viral diseases in mink. The extensive screening yielded positive results for 19 of these genes. Thirty-five clones corresponding to 19 genes were sequenced using 454 Roche, and large contigs (184 kb in average were assembled. Knowing the complete sequences of these candidate genes will enable confirmation of the association with a phenotype and the finding of causative mutations for the targeted phenotypes. Additionally, 1577 BAC clones were end sequenced; 2505 BAC end sequences (80% of BACs were obtained. An excess of 2 Mb has been analyzed, thus giving a snapshot of the mink genome. Conclusions The availability of the CHORI-321 American mink BAC library will aid in identification of genes and genomic regions of interest. We have demonstrated how the library can be used to identify specific genes of interest, develop genetic markers, and for BAC end sequencing and deep sequencing of selected clones. To our knowledge, this is the

  1. Research Techniques Made Simple: Bacterial 16S Ribosomal RNA Gene Sequencing in Cutaneous Research.

    Science.gov (United States)

    Jo, Jay-Hyun; Kennedy, Elizabeth A; Kong, Heidi H

    2016-03-01

    Skin serves as a protective barrier and also harbors numerous microorganisms collectively comprising the skin microbiome. As a result of recent advances in sequencing (next-generation sequencing), our understanding of microbial communities on skin has advanced substantially. In particular, the 16S ribosomal RNA gene sequencing technique has played an important role in efforts to identify the global communities of bacteria in healthy individuals and patients with various disorders in multiple topographical regions over the skin surface. Here, we describe basic principles, study design, and a workflow of 16S ribosomal RNA gene sequencing methodology, primarily for investigators who are not familiar with this approach. This article will also discuss some applications and challenges of 16S ribosomal RNA sequencing as well as directions for future development. PMID:26902128

  2. Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing

    OpenAIRE

    Chao, Yuanqing; Mao, Yanping; Wang, Zhiping,; Tong ZHANG

    2015-01-01

    The development of biofilms in drinking water (DW) systems may cause various problems to water quality. To investigate the community structure of biofilms on different pipe materials and the global/specific metabolic functions of DW biofilms, PCR-based 454 pyrosequencing data for 16S rRNA genes and Illumina metagenomic data were generated and analysed. Considerable differences in bacterial diversity and taxonomic structure were identified between biofilms formed on stainless steel and biofilm...

  3. Uncultured bacterial diversity in a seawater recirculating aquaculture system revealed by 16S rRNA gene amplicon sequencing.

    Science.gov (United States)

    Lee, Da-Eun; Lee, Jinhwan; Kim, Young-Mog; Myeong, Jeong-In; Kim, Kyoung-Ho

    2016-04-01

    Bacterial diversity in a seawater recirculating aquaculture system (RAS) was investigated using 16S rRNA amplicon sequencing to understand the roles of bacterial communities in the system. The RAS was operated at nine different combinations of temperature (15°C, 20°C, and 25°C) and salinity (20‰, 25‰, and 32.5‰). Samples were collected from five or six RAS tanks (biofilters) for each condition. Fifty samples were analyzed. Proteobacteria and Bacteroidetes were most common (sum of both phyla: 67.2% to 99.4%) and were inversely proportional to each other. Bacteria that were present at an average of ≥ 1% included Actinobacteria (2.9%) Planctomycetes (2.0%), Nitrospirae (1.5%), and Acidobacteria (1.0%); they were preferentially present in packed bed biofilters, mesh biofilters, and maturation biofilters. The three biofilters showed higher diversity than other RAS tanks (aerated biofilters, floating bed biofilters, and fish tanks) from phylum to operational taxonomic unit (OTU) level. Samples were clustered into several groups based on the bacterial communities. Major taxonomic groups related to family Rhodobacteraceae and Flavobacteriaceae were distributed widely in the samples. Several taxonomic groups like [Saprospiraceae], Cytophagaceae, Octadecabacter, and Marivita showed a cluster-oriented distribution. Phaeobacter and Sediminicola-related reads were detected frequently and abundantly at low temperature. Nitrifying bacteria were detected frequently and abundantly in the three biofilters. Phylogenetic analysis of the nitrifying bacteria showed several similar OTUs were observed widely through the biofilters. The diverse bacterial communities and the minor taxonomic groups, except for Proteobacteria and Bacteroidetes, seemed to play important roles and seemed necessary for nitrifying activity in the RAS, especially in packed bed biofilters, mesh biofilters, and maturation biofilters. PMID:27033205

  4. Evaluation of bacterial contamination in raw milk, ultra-high temperature milk and infant formula using single molecule, real-time sequencing technology.

    Science.gov (United States)

    Hou, Qiangchuan; Xu, Haiyan; Zheng, Yi; Xi, Xiaoxia; Kwok, Lai-Yu; Sun, Zhihong; Zhang, Heping; Zhang, Wenyi

    2015-12-01

    The Pacific Biosciences (Menlo Park, CA) single molecule, real-time sequencing technology (SMRT) was reported to have some advantages in analyzing the bacterial profile of environmental samples. In this study, the presence of bacterial contaminants in raw milk, UHT milk, and infant formula was determined by SMRT sequencing of the full length 16S rRNA gene. The bacterial profiles obtained at different taxonomic levels revealed clear differences in bacterial community structure across the 16 analyzed dairy samples. No indicative pathogenic bacteria were found in any of these tested samples. However, some of the detected bacterial species (e.g., Bacillus cereus, Enterococcus casseliflavus, and Enterococcus gallinarum) might potentially relate with product quality defects and bacterial antibiotic gene transfer. Although only a limited number of dairy samples were analyzed here, our data have demonstrated for the first time the feasibility of using the SMRT sequencing platform in detecting bacterial contamination. Our paper also provides interesting reference information for future development of new precautionary strategies for controlling the dairy safety in large-scale industrialized production lines. PMID:26476945

  5. Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms

    DEFF Research Database (Denmark)

    Kaas, Rolf Sommer; Leekitcharoenphon, Pimlapas; Aarestrup, Frank Møller;

    2014-01-01

    Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one...... data sets and sequenced on three different platforms (Illumina, 454, Ion Torrent). We show that the methods are able to overcome the systematic biases caused by the sequencers and infer the expected phylogenies. It is concluded that the cause of the success of these new procedures is due to a...

  6. Analysis of bacterial communities and bacterial pathogens in a biogas plant by the combination of ethidium monoazide, PCR and Ion Torrent sequencing

    DEFF Research Database (Denmark)

    Luo, Gang; Angelidaki, Irini

    2014-01-01

    The present study investigated the changes of bacterial community composition including bacterial pathogens along a biogas plant, i.e. from the influent, to the biogas reactor and to the post-digester. The effects of post-digestion temperature and time on the changes of bacterial community...... had a significant effect on the changes of bacterial community composition. The changes of bacterial community composition were also reflected in the changes of relative abundance of bacterial pathogens. The richness and relative abundance of bacterial pathogens were reduced after anaerobic digestion...... in the biogas reactor. It was found in batch experiments that bacterial pathogens showed the highest relative abundance and richness after 30days' post-digestion. Streptococcus bovis was found in all the samples. Our results showed that special attention should be paid to the post-digestion since the...

  7. Tracing the Spread of Clostridium difficile Ribotype 027 in Germany Based on Bacterial Genome Sequences.

    Directory of Open Access Journals (Sweden)

    Matthias Steglich

    Full Text Available We applied whole-genome sequencing to reconstruct the spatial and temporal dynamics underpinning the expansion of Clostridium difficile ribotype 027 in Germany. Based on re-sequencing of genomes from 57 clinical C. difficile isolates, which had been collected from hospitalized patients at 36 locations throughout Germany between 1990 and 2012, we demonstrate that C. difficile genomes have accumulated sequence variation sufficiently fast to document the pathogen's spread at a regional scale. We detected both previously described lineages of fluoroquinolone-resistant C. difficile ribotype 027, FQR1 and FQR2. Using Bayesian phylogeographic analyses, we show that fluoroquinolone-resistant C. difficile 027 was imported into Germany at least four times, that it had been widely disseminated across multiple federal states even before the first outbreak was noted in 2007, and that it has continued to spread since.

  8. Genome dynamics of short oligonucleotides: the example of bacterial DNA uptake enhancing sequences.

    Directory of Open Access Journals (Sweden)

    Mohammed Bakkali

    Full Text Available Among the many bacteria naturally competent for transformation by DNA uptake-a phenomenon with significant clinical and financial implications- Pasteurellaceae and Neisseriaceae species preferentially take up DNA containing specific short sequences. The genomic overrepresentation of these DNA uptake enhancing sequences (DUES causes preferential uptake of conspecific DNA, but the function(s behind this overrepresentation and its evolution are still a matter for discovery. Here I analyze DUES genome dynamics and evolution and test the validity of the results to other selectively constrained oligonucleotides. I use statistical methods and computer simulations to examine DUESs accumulation in Haemophilus influenzae and Neisseria gonorrhoeae genomes. I analyze DUESs sequence and nucleotide frequencies, as well as those of all their mismatched forms, and prove the dependence of DUESs genomic overrepresentation on their preferential uptake by quantifying and correlating both characteristics. I then argue that mutation, uptake bias, and weak selection against DUESs in less constrained parts of the genome combined are sufficient enough to cause DUESs accumulation in susceptible parts of the genome with no need for other DUES function. The distribution of overrepresentation values across sequences with different mismatch loads compared to the DUES suggests a gradual yet not linear molecular drive of DNA sequences depending on their similarity to the DUES. Other genomically overrepresented sequences, both pro- and eukaryotic, show similar distribution of frequencies suggesting that the molecular drive reported above applies to other frequent oligonucleotides. Rare oligonucleotides, however, seem to be gradually drawn to genomic underrepresentation, thus, suggesting a molecular drag. To my knowledge this work provides the first clear evidence of the gradual evolution of selectively constrained oligonucleotides, including repeated, palindromic and protein

  9. Analysis of Comparative Sequence and Genomic Data to Verify Phylogenetic Relationship and Explore a New Subfamily of Bacterial Lipases.

    Directory of Open Access Journals (Sweden)

    Malihe Masomian

    Full Text Available Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca(2+-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65 °C and retained ≥ 97% activity after incubation at 50 °C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents.

  10. Analysis of Comparative Sequence and Genomic Data to Verify Phylogenetic Relationship and Explore a New Subfamily of Bacterial Lipases.

    Science.gov (United States)

    Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd; Salleh, Abu Bakar; Basri, Mahiran

    2016-01-01

    Thermostable and organic solvent-tolerant enzymes have significant potential in a wide range of synthetic reactions in industry due to their inherent stability at high temperatures and their ability to endure harsh organic solvents. In this study, a novel gene encoding a true lipase was isolated by construction of a genomic DNA library of thermophilic Aneurinibacillus thermoaerophilus strain HZ into Escherichia coli plasmid vector. Sequence analysis revealed that HZ lipase had 62% identity to putative lipase from Bacillus pseudomycoides. The closely characterized lipases to the HZ lipase gene are from thermostable Bacillus and Geobacillus lipases belonging to the subfamily I.5 with ≤ 57% identity. The amino acid sequence analysis of HZ lipase determined a conserved pentapeptide containing the active serine, GHSMG and a Ca(2+)-binding motif, GCYGSD in the enzyme. Protein structure modeling showed that HZ lipase consisted of an α/β hydrolase fold and a lid domain. Protein sequence alignment, conserved regions analysis, clustal distance matrix and amino acid composition illustrated differences between HZ lipase and other thermostable lipases. Phylogenetic analysis revealed that this lipase represented a new subfamily of family I of bacterial true lipases, classified as family I.9. The HZ lipase was expressed under promoter Plac using IPTG and was characterized. The recombinant enzyme showed optimal activity at 65 °C and retained ≥ 97% activity after incubation at 50 °C for 1h. The HZ lipase was stable in various polar and non-polar organic solvents. PMID:26934700

  11. First Complete Genome Sequence of Tenacibaculum dicentrarchi, an Emerging Bacterial Pathogen of Salmonids

    OpenAIRE

    Grothusen, Horst; Castillo, Alejandro; Henríquez, Patricio; Navas, Esteban; Bohle, Harry; Araya, Carolina; Bustamante, Fernando; Bustos, Patricio; Mancilla, Marcos

    2016-01-01

    Tenacibaculum-like bacilli have recently been isolated from diseased sea-reared Atlantic salmon in outbreaks that took place in the XI region (Región de Aysén) of Chile. Molecular typing identified the bacterium as Tenacibaculum dicentrarchi. Here, we report the complete genome sequence of the AY7486TD isolate recovered during those outbreaks.

  12. First Complete Genome Sequence of Tenacibaculum dicentrarchi, an Emerging Bacterial Pathogen of Salmonids.

    Science.gov (United States)

    Grothusen, Horst; Castillo, Alejandro; Henríquez, Patricio; Navas, Esteban; Bohle, Harry; Araya, Carolina; Bustamante, Fernando; Bustos, Patricio; Mancilla, Marcos

    2016-01-01

    Tenacibaculum-like bacilli have recently been isolated from diseased sea-reared Atlantic salmon in outbreaks that took place in the XI region (Región de Aysén) of Chile. Molecular typing identified the bacterium as Tenacibaculum dicentrarchi. Here, we report the complete genome sequence of the AY7486TD isolate recovered during those outbreaks. PMID:26893432

  13. RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions

    NARCIS (Netherlands)

    Wiedenheft, Blake; van Duijn, Esther; Bultema, Jelle; Waghmare, Sakharam; Zhou, Kaihong; Barendregt, Arjan; Westphal, Wiebke; Heck, Albert; Boekema, Egbert; Dickman, Mark; Doudna, Jennifer A.

    2011-01-01

    Prokaryotes have evolved multiple versions of an RNA-guided adaptive immune system that targets foreign nucleic acids. In each case, transcripts derived from clustered regularly interspaced short palindromic repeats (CRISPRs) are thought to selectively target invading phage and plasmids in a sequenc

  14. Draft Genome Sequence of Nocardia jinanensis, an Opportunistic Bacterial Pathogen That Causes Cellulitis

    Science.gov (United States)

    Chakrabortti, Alolika; Li, Jinming

    2016-01-01

    The draft genome sequence of Nocardia jinanensis, an opportunistic pathogen that can cause skin infections, reveals genes that may contribute to the lifestyle and pathogenicity of N. jinanensis. The genome also reveals the biosynthetic capacity of N. jinanensis in producing mycolic acids, siderophores, and other polyketide and nonribosomal peptide-derived secondary metabolites. PMID:27445366

  15. Draft genome sequence of Erwinia tracheiphila, an economically important bacterial pathogen of cucurbits

    Science.gov (United States)

    Erwinia tracheiphila is one of the most economically important pathogen of cucumbers, melons, squashes, pumpkins, and gourds, in the Northeastern and Midwestern United States, yet the molecular pathology remains uninvestigated. Here we report the first draft genome sequence of an E. tracheiphila str...

  16. Insecticides and Biological Control

    Science.gov (United States)

    Furness, G. O.

    1972-01-01

    Use of insecticides has been questioned due to their harmful effects on edible items. Biological control of insects along with other effective practices for checking spread of parasites on crops are discussed. (PS)

  17. Proteases as Insecticidal Agents

    OpenAIRE

    Harrison, Robert L.; Bonning, Bryony C.

    2010-01-01

    Proteases from a variety of sources (viruses, bacteria, fungi, plants, and insects) have toxicity towards insects. Some of these insecticidal proteases evolved as venom components, herbivore resistance factors, or microbial pathogenicity factors, while other proteases play roles in insect development or digestion, but exert an insecticidal effect when over-expressed from genetically engineered plants or microbial pathogens. Many of these proteases are cysteine proteases, although insect-toxic...

  18. More about Insecticides

    OpenAIRE

    E.K. Hartwig

    1980-01-01

    An insecticide is a chemical used to kill insects. Insect control can also include other materials such as repellents, oils, antifeedants and attractants. Ideally, an insecticide would effectively control any target insect exposed to it and would be harmless to man and his domestic animals. It would also be readily available in necessary quantitie s , s table chemically, noninflammable, easily prepared and applied, noncorrosive, non-staining, and would have no undesirable odour.

  19. More about Insecticides

    Directory of Open Access Journals (Sweden)

    E.K. Hartwig

    1980-09-01

    Full Text Available An insecticide is a chemical used to kill insects. Insect control can also include other materials such as repellents, oils, antifeedants and attractants. Ideally, an insecticide would effectively control any target insect exposed to it and would be harmless to man and his domestic animals. It would also be readily available in necessary quantitie s , s table chemically, noninflammable, easily prepared and applied, noncorrosive, non-staining, and would have no undesirable odour.

  20. Bayesian prediction of bacterial growth temperature range based on genome sequences

    DEFF Research Database (Denmark)

    Jensen, Dan Børge; Vesth, Tammi Camilla; Hallin, Peter Fischer;

    2012-01-01

    genomic sequence, would thus allow for an efficient and targeted search for production organisms, reducing the need for culturing experiments. Results: This study found a total of 40 protein families useful for distinction between three thermophilicity classes (thermophiles, mesophiles and psychrophiles......). The predictive performance of these protein families were compared to those of 87 basic sequence features (relative use of amino acids and codons, genomic and 16S rDNA AT content and genome size). When using naive Bayesian inference, it was possible to correctly predict the optimal temperature range...... with a Matthews correlation coefficient of up to 0.68. The best predictive performance was always achieved by including protein families as well as structural features, compared to either of these alone. A dedicated computer program was created to perform these predictions. Conclusions: This study...

  1. Solving the Problem of Comparing Whole Bacterial Genomes across Different Sequencing Platforms

    OpenAIRE

    Kaas, Rolf Sommer; Leekitcharoenphon, Pimlapas; Aarestrup, Frank Møller; Lund, Ole

    2014-01-01

    Whole genome sequencing (WGS) shows great potential for real-time monitoring and identification of infectious disease outbreaks. However, rapid and reliable comparison of data generated in multiple laboratories and using multiple technologies is essential. So far studies have focused on using one technology because each technology has a systematic bias making integration of data generated from different platforms difficult. We developed two different procedures for identifying variable sites ...

  2. Genome sequencing and systems biology analysis of a lipase-producing bacterial strain.

    Science.gov (United States)

    Li, N; Li, D D; Zhang, Y Z; Yuan, Y Z; Geng, H; Xiong, L; Liu, D L

    2016-01-01

    Lipase-producing bacteria are naturally-occurring, industrially-relevant microorganisms that produce lipases, which can be used to synthesize biodiesel from waste oils. The efficiency of lipase expression varies between various microbial strains. Therefore, strains that can produce lipases with high efficiency must be screened, and the conditions of lipase metabolism and optimization of the production process in a given environment must be thoroughly studied. A high efficiency lipase-producing strain was isolated from the sediments of Jinsha River, identified by 16S rRNA sequence analysis as Serratia marcescens, and designated as HS-L5. A schematic diagram of the genome sequence was constructed by high-throughput genome sequencing. A series of genes related to lipid degradation were identified by functional gene annotation through sequence homology analysis. A genome-scale metabolic model of HS-ML5 was constructed using systems biology techniques. The model consisted of 1722 genes and 1567 metabolic reactions. The topological graph of the genome-scale metabolic model was compared to that of conventional metabolic pathways using a visualization software and KEGG database. The basic components and boundaries of the tributyrin degradation subnetwork were determined, and its flux balance analyzed using Matlab and COBRA Toolbox to simulate the effects of different conditions on the catalytic efficiency of lipases produced by HS-ML5. We proved that the catalytic activity of microbial lipases was closely related to the carbon metabolic pathway. As production and catalytic efficiency of lipases varied greatly with the environment, the catalytic efficiency and environmental adaptability of microbial lipases can be improved by proper control of the production conditions. PMID:27050954

  3. Rates and mechanisms of bacterial mutagenesis from maximum-depth sequencing.

    Science.gov (United States)

    Jee, Justin; Rasouly, Aviram; Shamovsky, Ilya; Akivis, Yonatan; Steinman, Susan R; Mishra, Bud; Nudler, Evgeny

    2016-06-30

    In 1943, Luria and Delbrück used a phage-resistance assay to establish spontaneous mutation as a driving force of microbial diversity. Mutation rates are still studied using such assays, but these can only be used to examine the small minority of mutations conferring survival in a particular condition. Newer approaches, such as long-term evolution followed by whole-genome sequencing, may be skewed by mutational ‘hot’ or ‘cold’ spots. Both approaches are affected by numerous caveats. Here we devise a method, maximum-depth sequencing (MDS), to detect extremely rare variants in a population of cells through error-corrected, high-throughput sequencing. We directly measure locus-specific mutation rates in Escherichia coli and show that they vary across the genome by at least an order of magnitude. Our data suggest that certain types of nucleotide misincorporation occur 10(4)-fold more frequently than the basal rate of mutations, but are repaired in vivo. Our data also suggest specific mechanisms of antibiotic-induced mutagenesis, including downregulation of mismatch repair via oxidative stress, transcription–replication conflicts, and, in the case of fluoroquinolones, direct damage to DNA. PMID:27338792

  4. Diversity and functions of bacterial community in drinking water biofilms revealed by high-throughput sequencing

    Science.gov (United States)

    Chao, Yuanqing; Mao, Yanping; Wang, Zhiping; Zhang, Tong

    2015-06-01

    The development of biofilms in drinking water (DW) systems may cause various problems to water quality. To investigate the community structure of biofilms on different pipe materials and the global/specific metabolic functions of DW biofilms, PCR-based 454 pyrosequencing data for 16S rRNA genes and Illumina metagenomic data were generated and analysed. Considerable differences in bacterial diversity and taxonomic structure were identified between biofilms formed on stainless steel and biofilms formed on plastics, indicating that the metallic materials facilitate the formation of higher diversity biofilms. Moreover, variations in several dominant genera were observed during biofilm formation. Based on PCA analysis, the global functions in the DW biofilms were similar to other DW metagenomes. Beyond the global functions, the occurrences and abundances of specific protective genes involved in the glutathione metabolism, the SoxRS system, the OxyR system, RpoS regulated genes, and the production/degradation of extracellular polymeric substances were also evaluated. A near-complete and low-contamination draft genome was constructed from the metagenome of the DW biofilm, based on the coverage and tetranucleotide frequencies, and identified as a Bradyrhizobiaceae-like bacterium according to a phylogenetic analysis. Our findings provide new insight into DW biofilms, especially in terms of their metabolic functions.

  5. Structure of the Bacterial Cytoskeleton Protein Bactofilin by NMR Chemical Shifts and Sequence Variation.

    Science.gov (United States)

    Kassem, Maher M; Wang, Yong; Boomsma, Wouter; Lindorff-Larsen, Kresten

    2016-06-01

    Bactofilins constitute a recently discovered class of bacterial proteins that form cytoskeletal filaments. They share a highly conserved domain (DUF583) of which the structure remains unknown, in part due to the large size and noncrystalline nature of the filaments. Here, we describe the atomic structure of a bactofilin domain from Caulobacter crescentus. To determine the structure, we developed an approach that combines a biophysical model for proteins with recently obtained solid-state NMR spectroscopy data and amino acid contacts predicted from a detailed analysis of the evolutionary history of bactofilins. Our structure reveals a triangular β-helical (solenoid) conformation with conserved residues forming the tightly packed core and polar residues lining the surface. The repetitive structure explains the presence of internal repeats as well as strongly conserved positions, and is reminiscent of other fibrillar proteins. Our work provides a structural basis for future studies of bactofilin biology and for designing molecules that target them, as well as a starting point for determining the organization of the entire bactofilin filament. Finally, our approach presents new avenues for determining structures that are difficult to obtain by traditional means. PMID:27276252

  6. Bioaugmentation of a sequencing batch reactor with Pseudomonas putida ONBA-17, and its impact on reactor bacterial communities

    International Nuclear Information System (INIS)

    This study demonstrates the feasibility of using Pseudomonasputida ONBA-17 to bioaugment a sequencing batch reactor (SBR) treating o-nitrobenzaldehyde (ONBA) synthetic wastewater. To monitor its survival, the strain was chromosomally marked with gfp gene. After a transient adaptation, almost 100% degradation of ONBA was obtained within 8 days as compared with 23.47% of the non-inoculated control. The bioaugmented reactor has a better chemical oxygen demand (COD) removal performance (96.28%) than that (79.26%) of the control. The bioaugmentation not only enhanced the removal capability of target compound, but shortened system start-up time. After the increase in ONBA load, performance fluctuation of two reactors was observed, and the final treating effects of them were comparable. What is more, denaturing gradient gel electrophoresis (DGGE) analysis of 16S rRNA genes via a combination of pattern comparison and sequence phylogenetic analysis was performed to uncover changes in sludge microbial communities. Only the members of alpha, beta and gamma subdivisions of Proteobacteria were identified. To isolate ONBA-degrading relevant microorganisms, spread plate was used and four bacterial strains were obtained. Subsequent systematic studies on these bacteria characterized their traits which to some extent explained why such bacteria could be kept in the system. This study will help future research in better understanding of the bioreactor bioaugmentation.

  7. DNA Sequencing Diagnosis of Off-Season Spirochetemia with Low Bacterial Density in Borrelia burgdorferi and Borrelia miyamotoi Infections

    Directory of Open Access Journals (Sweden)

    Sin Hang Lee

    2014-06-01

    Full Text Available A highly conserved 357-bp segment of the 16S ribosomal RNA gene (16S rDNA of Borrelia burgdorferi sensu lato and the correspondent 358-bp segment of the Borrelia miyamotoi gene were amplified by a single pair of nested polymerase chain reaction (PCR primers for detection, and the amplicons were used as the templates for direct Sanger DNA sequencing. Reliable molecular diagnosis of these borreliae was confirmed by sequence alignment analysis of the hypervariable regions of the PCR amplicon, using the Basic Local Alignment Search Tool (BLAST provided by the GenBank. This methodology can detect and confirm B. burgdorferi and B. miyamotoi in blood samples of patients with off-season spirochetemia of low bacterial density. We found four B. miyamotoi infections among 14 patients with spirochetemia, including one patient co-infected by both B. miyamotoi and B. burgdorferi in a winter month when human exposure to tick bites is very limited in the Northeast of the U.S.A. We conclude that sensitive and reliable tests for these two Borrelia species should be implemented in the microbiology laboratory of hospitals located in the disease-endemic areas, for timely diagnosis and appropriate treatment of the patients at an early stage of the infection to prevent potential tissue damages.

  8. Draft Genome Sequence of Paracoccus sp. MKU1, a New Bacterial Strain Isolated from an Industrial Effluent with Potential for Bioremediation

    Science.gov (United States)

    Nisha, Kamaldeen Nasrin; Sridhar, Jayavel; Varalakshmi, Perumal; Ashokkumar, Balasubramaniem

    2016-01-01

    Paracoccus sp. MKU1, a novel dimethylformamide degrading bacterial strain was originally isolated from an industrial effluent, Tirupur region, Tamil Nadu, India. Here, we report the draft genome sequence of Paracoccus sp. MKU1, which could provide the genetic insights on its evolution and application of this versatile bacterium for effective degradation of xenobiotics and thus in bioremediation.

  9. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, Jiemin [National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190 (China); University of Chinese Academy of Sciences, Beijing 100049 (China); Zhou, Xuemei; Li, Yuguang [101 Institute, Ministry of Civil Affairs, Beijing 100070 (China); Xing, Jianmin, E-mail: jmxing@ipe.ac.cn [National Key Laboratory of Biochemical Engineering, Institute of Process Engineering, Chinese Academy of Sciences, P.O. Box 353, Beijing 100190 (China)

    2015-09-15

    Highlights: • Bacterial communities of haloalkaliphilic bioreactors were investigated. • MiSeq was first used in analysis of communities of haloalkaliphilic bioreactors. • Electron donors had significant effect on bacterial communities. - Abstract: Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities.

  10. Bacterial communities in haloalkaliphilic sulfate-reducing bioreactors under different electron donors revealed by 16S rRNA MiSeq sequencing

    International Nuclear Information System (INIS)

    Highlights: • Bacterial communities of haloalkaliphilic bioreactors were investigated. • MiSeq was first used in analysis of communities of haloalkaliphilic bioreactors. • Electron donors had significant effect on bacterial communities. - Abstract: Biological technology used to treat flue gas is useful to replace conventional treatment, but there is sulfide inhibition. However, no sulfide toxicity effect was observed in haloalkaliphilic bioreactors. The performance of the ethanol-fed bioreactor was better than that of lactate-, glucose-, and formate-fed bioreactor, respectively. To support this result strongly, Illumina MiSeq paired-end sequencing of 16S rRNA gene was applied to investigate the bacterial communities. A total of 389,971 effective sequences were obtained and all of them were assigned to 10,220 operational taxonomic units (OTUs) at a 97% similarity. Bacterial communities in the glucose-fed bioreactor showed the greatest richness and evenness. The highest relative abundance of sulfate-reducing bacteria (SRB) was found in the ethanol-fed bioreactor, which can explain why the performance of the ethanol-fed bioreactor was the best. Different types of SRB, sulfur-oxidizing bacteria, and sulfur-reducing bacteria were detected, indicating that sulfur may be cycled among these microorganisms. Because high-throughput 16S rRNA gene paired-end sequencing has improved resolution of bacterial community analysis, many rare microorganisms were detected, such as Halanaerobium, Halothiobacillus, Desulfonatronum, Syntrophobacter, and Fusibacter. 16S rRNA gene sequencing of these bacteria would provide more functional and phylogenetic information about the bacterial communities

  11. Construction of a recombinant bacterial plasmid containing DNA sequences for a mouse embryonic globin chain.

    Science.gov (United States)

    Fantoni, A; Bozzoni, I; Ullu, E; Farace, M G

    1979-01-01

    Messenger RNAs for mouse embryonic globins were purified from yolk sac derived eyrthroid cells in mouse fetuses. Double stranded DNAs complementary to these messengers were synthesized and blunt end ligated to a EcoRI digested and DNA polymerase I repaired pBR322 plasmid. Of the ampicillin resistant transformants, one contained a plasmid with globin-specific cDNA. The inserted sequence is about 350 base pairs long. It contains one restriction site for EcoRI and one restriction site for HinfI about 170 and 80 base pairs from one end. The insert is not cleaved by HindIII, HindII, BamHI, PstI, SalI, AvaI, TaqI, HpaII, BglI. A mixture of purified messengers coding for alpha chains and for x, y and z embryonic chains was incubated with the recombinant plasmid and the hybridized messenger was translated in a mRNA depleted reticulocyte lysate protein synthesizing system. The product of translation was identified as a z chain by carboxymethylcellulose cromatography. The recombinant plasmid is named "pBR322-egz" after embryonic globin z. Images PMID:493112

  12. Construction of a recombinant bacterial plasmid containing DNA sequences for a mouse embryonic globin chain.

    Science.gov (United States)

    Fantoni, A; Bozzoni, I; Ullu, E; Farace, M G

    1979-08-10

    Messenger RNAs for mouse embryonic globins were purified from yolk sac derived eyrthroid cells in mouse fetuses. Double stranded DNAs complementary to these messengers were synthesized and blunt end ligated to a EcoRI digested and DNA polymerase I repaired pBR322 plasmid. Of the ampicillin resistant transformants, one contained a plasmid with globin-specific cDNA. The inserted sequence is about 350 base pairs long. It contains one restriction site for EcoRI and one restriction site for HinfI about 170 and 80 base pairs from one end. The insert is not cleaved by HindIII, HindII, BamHI, PstI, SalI, AvaI, TaqI, HpaII, BglI. A mixture of purified messengers coding for alpha chains and for x, y and z embryonic chains was incubated with the recombinant plasmid and the hybridized messenger was translated in a mRNA depleted reticulocyte lysate protein synthesizing system. The product of translation was identified as a z chain by carboxymethylcellulose cromatography. The recombinant plasmid is named "pBR322-egz" after embryonic globin z. PMID:493112

  13. Insecticide Resistance in Fleas.

    Science.gov (United States)

    Rust, Michael K

    2016-01-01

    Fleas are the major ectoparasite of cats, dogs, and rodents worldwide and potential vectors of animal diseases. In the past two decades the majority of new control treatments have been either topically applied or orally administered to the host. Most reports concerning the development of insecticide resistance deal with the cat flea, Ctenocephalides felis felis. Historically, insecticide resistance has developed to many of the insecticides used to control fleas in the environment including carbamates, organophosphates, and pyrethroids. Product failures have been reported with some of the new topical treatments, but actual resistance has not yet been demonstrated. Failures have often been attributed to operational factors such as failure to adequately treat the pet and follow label directions. With the addition of so many new chemistries additional monitoring of flea populations is needed. PMID:26999217

  14. A short history of insecticides

    OpenAIRE

    Oberemok Volodymyr Volodymyrovych; Laikova Kateryna Volodymyrivna; Gninenko Yuri Ivanovich; Zaitsev Aleksei Sergeevich; Nyadar Palmah Mutah; Adeyemi Tajudeen Adesoji

    2015-01-01

    This review contains a brief history of the use of insecticides. The peculiarities, main advantages, and disadvantages of some modern insecticides are described. The names of the discoverers of some of the most popular insecticide preparations on the world market, are listed. The tendencies to find new insecticides to control the quantity of phytophagous insects are discussed. Special attention is paid to the perspective of creating preparations based on nucleic acids, in particular DNA insec...

  15. Botanical Insecticides in Plant Protection

    OpenAIRE

    Martina Grdiša; Kristina Gršić

    2013-01-01

    Botanical insecticides are natural compounds with insecticidal properties and their use in crop protection is as old as agricultural practice. Although they have been in use for over one hundred years, the advent of synthetic insecticides has unfortunately displaced their use today. Due to fast action, low cost, easy application and efficiency against a wide range of harmful species, synthetic insecticides have become an important part of pest management in modern agricultural systems...

  16. Resistance to Insecticides in Insects

    OpenAIRE

    ÇAKIR, Şükran; Şengül YAMANEL

    2005-01-01

    In recent years, the frequent usage of insecticides in struggle aganist insects, has caused development of resistance to those chemicals in insects. The increase in dosage of insecticide used due to development of resistance in insects, causes important problems in terms of environment and human health. This study includes topics such as insecticides which are used frequently in insect struggle, insecticide resistant types, genetic changes posing resistance, enzymes of resistance and resistan...

  17. Exploring the sources of bacterial spoilers in beefsteaks by culture-independent high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Francesca De Filippis

    Full Text Available Microbial growth on meat to unacceptable levels contributes significantly to change meat structure, color and flavor and to cause meat spoilage. The types of microorganisms initially present in meat depend on several factors and multiple sources of contamination can be identified. The aims of this study were to evaluate the microbial diversity in beefsteaks before and after aerobic storage at 4°C and to investigate the sources of microbial contamination by examining the microbiota of carcasses wherefrom the steaks originated and of the processing environment where the beef was handled. Carcass, environmental (processing plant and meat samples were analyzed by culture-independent high-throughput sequencing of 16S rRNA gene amplicons. The microbiota of carcass swabs was very complex, including more than 600 operational taxonomic units (OTUs belonging to 15 different phyla. A significant association was found between beef microbiota and specific beef cuts (P<0.01 indicating that different cuts of the same carcass can influence the microbial contamination of beef. Despite the initially high complexity of the carcass microbiota, the steaks after aerobic storage at 4°C showed a dramatic decrease in microbial complexity. Pseudomonas sp. and Brochothrix thermosphacta were the main contaminants, and Acinetobacter, Psychrobacter and Enterobacteriaceae were also found. Comparing the relative abundance of OTUs in the different samples it was shown that abundant OTUs in beefsteaks after storage occurred in the corresponding carcass. However, the abundance of these same OTUs clearly increased in environmental samples taken in the processing plant suggesting that spoilage-associated microbial species originate from carcasses, they are carried to the processing environment where the meat is handled and there they become a resident microbiota. Such microbiota is then further spread on meat when it is handled and it represents the starting microbial association

  18. Investigation of bacterial and archaeal communities: novel protocols using modern sequencing by Illumina MiSeq and traditional DGGE-cloning.

    Science.gov (United States)

    Kraková, Lucia; Šoltys, Katarína; Budiš, Jaroslav; Grivalský, Tomáš; Ďuriš, František; Pangallo, Domenico; Szemes, Tomáš

    2016-09-01

    Different protocols based on Illumina high-throughput DNA sequencing and denaturing gradient gel electrophoresis (DGGE)-cloning were developed and applied for investigating hot spring related samples. The study was focused on three target genes: archaeal and bacterial 16S rRNA and mcrA of methanogenic microflora. Shorter read lengths of the currently most popular technology of sequencing by Illumina do not allow analysis of the complete 16S rRNA region, or of longer gene fragments, as was the case of Sanger sequencing. Here, we demonstrate that there is no need for special indexed or tailed primer sets dedicated to short variable regions of 16S rRNA since the presented approach allows the analysis of complete bacterial 16S rRNA amplicons (V1-V9) and longer archaeal 16S rRNA and mcrA sequences. Sample augmented with transposon is represented by a set of approximately 300 bp long fragments that can be easily sequenced by Illumina MiSeq. Furthermore, a low proportion of chimeric sequences was observed. DGGE-cloning based strategies were performed combining semi-nested PCR, DGGE and clone library construction. Comparing both investigation methods, a certain degree of complementarity was observed confirming that the DGGE-cloning approach is not obsolete. Novel protocols were created for several types of laboratories, utilizing the traditional DGGE technique or using the most modern Illumina sequencing. PMID:27338271

  19. Insecticidal crystal proteins of Bacillus thuringiensis.

    OpenAIRE

    Höfte, H; Whiteley, H. R.

    1989-01-01

    A classification for crystal protein genes of Bacillus thuringiensis is presented. Criteria used are the insecticidal spectra and the amino acid sequences of the encoded proteins. Fourteen genes are distinguished, encoding proteins active against either Lepidoptera (cryI), Lepidoptera and Diptera (cryII), Coleoptera (cryIII), or Diptera (cryIV). One gene, cytA, encodes a general cytolytic protein and shows no structural similarities with the other genes. Toxicity studies with single purified ...

  20. The Genomic Sequence of the Oral Pathobiont Strain NI1060 Reveals Unique Strategies for Bacterial Competition and Pathogenicity.

    Directory of Open Access Journals (Sweden)

    Youssef Darzi

    Full Text Available Strain NI1060 is an oral bacterium responsible for periodontitis in a murine ligature-induced disease model. To better understand its pathogenicity, we have determined the complete sequence of its 2,553,982 bp genome. Although closely related to Pasteurella pneumotropica, a pneumonia-associated rodent commensal based on its 16S rRNA, the NI1060 genomic content suggests that they are different species thriving on different energy sources via alternative metabolic pathways. Genomic and phylogenetic analyses showed that strain NI1060 is distinct from the genera currently described in the family Pasteurellaceae, and is likely to represent a novel species. In addition, we found putative virulence genes involved in lipooligosaccharide synthesis, adhesins and bacteriotoxic proteins. These genes are potentially important for host adaption and for the induction of dysbiosis through bacterial competition and pathogenicity. Importantly, strain NI1060 strongly stimulates Nod1, an innate immune receptor, but is defective in two peptidoglycan recycling genes due to a frameshift mutation. The in-depth analysis of its genome thus provides critical insights for the development of NI1060 as a prime model system for infectious disease.

  1. ISOLATION AND CHARACTERIZATION OF HALOPHILIC BACTERIAL STRAINS FROM SALINE WATERS OF KHEWRA SALT MINES ON THE BASIS OF 16S rRNA GENE SEQUENCE

    Directory of Open Access Journals (Sweden)

    Muhammad Kaleem Sarwar

    2014-02-01

    Full Text Available Halophiles are salt loving microbes optimally growing at high concentrations of salt. Khewra salt mines of Pakistan provide extreme saline conditions where enormous halophilic microbial biota thrives. The present study aimed at isolation and molecular identification of bacterial strains from saline waters of Khewra salt mines. Using halophilic media, nine halophilic bacterial strains from saline water bodies were cultured and studied under optimized growth conditions (NaCl, pH and temperature. Bacterial growth at different NaCl concentrations was measured at 600nm wavelength, showing optimal growth at 1.5M NaCl. 769bp size 16S rRNA gene was amplified for molecular identification of bacterial strains. The amplified genes of the strains FA2.2 and FA3.3 were sequenced and their homology with other bacterial strains was analyzed. The results showed FA2.2 shared maximum homology with Bacillus anthracis strain while FA3.3 showed close resemblance with Staphylococcus saprophyticus subsp. bovis. Isolated halophilic bacterial strains possess potential for various biotechnological applications. They could be manipulated for synthesizing transgenic crops tolerating high salinity boosting the agricultural yield. Moreover extremozymes of these bacteria holds great industrial importance.

  2. A unique DNA repair and recombination gene (recN) sequence for identification and intraspecific molecular typing of bacterial wilt pathogen Ralstonia solanacearum and its comparative analysis with ribosomal DNA sequences

    Indian Academy of Sciences (India)

    Aundy Kumar; Thekkan Puthiyaveedu Prameela; Rajamma Suseelabhai

    2013-06-01

    Ribosomal gene sequences are a popular choice for identification of bacterial species and, often, for making phylogenetic interpretations. Although very popular, the sequences of 16S rDNA and 16-23S intergenic sequences often fail to differentiate closely related species of bacteria. The availability of complete genome sequences of bacteria, in the recent years, has accelerated the search for new genome targets for phylogenetic interpretations. The recently published full genome data of nine strains of R. solanacearum, which causes bacterial wilt of crop plants, has provided enormous genomic choices for phylogenetic analysis in this globally important plant pathogen. We have compared a gene candidate recN, which codes for DNA repair and recombination function, with 16S rDNA/16-23S intergenic ribosomal gene sequences for identification and intraspecific phylogenetic interpretations in R. solanacearum. recN gene sequence analysis of R. solanacearum revealed subgroups within phylotypes (or newly proposed species within plant pathogenic genus, Ralstonia), indicating its usefulness for intraspecific genotyping. The taxonomic discriminatory power of recN gene sequence was found to be superior to ribosomal DNA sequences. In all, the recN-sequence-based phylogenetic tree generated with the Bayesian model depicted 21 haplotypes against 15 and 13 haplotypes obtained with 16S rDNA and 16-23S rDNA intergenic sequences, respectively. Besides this, we have observed high percentage of polymorphic sites (S 23.04%), high rate of mutations (Eta 276) and high codon bias index (CBI 0.60), which makes the recN an ideal gene candidate for intraspecific molecular typing of this important plant pathogen.

  3. Multilocus Sequence Analysis of the Marine Bacterial Genus Tenacibaculum Suggests Parallel Evolution of Fish Pathogenicity and Endemic Colonization of Aquaculture Systems

    OpenAIRE

    Habib, Christophe; Houel, Armel; Lunazzi, Aurélie; Bernardet, Jean-François; Olsen, Anne Berit; Nilsen, Hanne; Toranzo, Alicia E.; Castro, Nuria; Nicolas, Pierre; Duchaud, Eric

    2014-01-01

    The genus Tenacibaculum, a member of the family Flavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogen Tenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicat...

  4. Bacterial Lifestyle in a Deep-sea Hydrothermal Vent Chimney Revealed by the Genome Sequence of the Thermophilic Bacterium Deferribacter desulfuricans SSM1

    OpenAIRE

    Takaki, Yoshihiro; Shimamura, Shigeru; Nakagawa, Satoshi; Fukuhara, Yasuo; Horikawa, Hiroshi; Ankai, Akiho; Harada, Takeshi; Hosoyama, Akira; Oguchi, Akio; Fukui, Shigehiro; Fujita, Nobuyuki; Takami, Hideto; Takai, Ken

    2010-01-01

    The complete genome sequence of the thermophilic sulphur-reducing bacterium, Deferribacter desulfuricans SMM1, isolated from a hydrothermal vent chimney has been determined. The genome comprises a single circular chromosome of 2 234 389 bp and a megaplasmid of 308 544 bp. Many genes encoded in the genome are most similar to the genes of sulphur- or sulphate-reducing bacterial species within Deltaproteobacteria. The reconstructed central metabolisms showed a heterotrophic lifestyle primarily d...

  5. Effect of Introns and AT-Rich Sequences on Expression of the Bacterial Hygromycin B Resistance Gene in the Basidiomycete Schizophyllum commune

    OpenAIRE

    Scholtmeijer, K.; Wosten, H.A.B.; Springer, J.; Wessels, J.G.H.

    2001-01-01

    Previously, it was shown that introns are required for efficient mRNA accumulation in Schizophyllum commune and that the presence of AT-rich sequences in the coding region of genes can result in truncation of transcripts in this homobasidiomycete. Here we show that intron-dependent mRNA accumulation and truncation of transcripts are two independent events that both affect expression of the bacterial hygromycin B resistance gene in S. commune.

  6. Diatomaceous Earths - Natural Insecticides

    OpenAIRE

    Zlatko Korunić

    2013-01-01

    The regulatory issues for diatomaceous earth (DE) cover three fields: consumer safety, worker safety, and proof of efficacy against pests. For consumer safety, regulatory issues are similar to those for other additives, and a principal benefit of DEs is their removal by normal processing methods. For worker safety, regulatory issues are similar to those for other dusts, such as lime. The proof of potential insecticide values of DE may be assessed by using t...

  7. Botanical Insecticides in Plant Protection

    Directory of Open Access Journals (Sweden)

    Martina Grdiša

    2013-06-01

    Full Text Available Botanical insecticides are natural compounds with insecticidal properties and their use in crop protection is as old as agricultural practice. Although they have been in use for over one hundred years, the advent of synthetic insecticides has unfortunately displaced their use today. Due to fast action, low cost, easy application and efficiency against a wide range of harmful species, synthetic insecticides have become an important part of pest management in modern agricultural systems. However, after decades of use, their negative side effects, such as toxicity to humans and animals, environmental contamination, and toxicity to non-target insects have become apparent and interest in less hazardous alternatives of pest control is therefore being renewed. Plant species with known insecticidal actions are being promoted and research is being conducted to find new sources of botanical insecticides. The most important botanical insecticide is pyrethrin, a secondary metabolite of Dalmatian pyrethrum, neem, followed by insecticides based on the essential oils, rotenone, quassia, ryania and sabadilla. They have various chemical properties and modes of action. However, some general characteristics include fast degradation in sunlight, air and moisture, and selectivity to non-target insects. Unfortunately, neither of these insecticides is widely used as a pest control agent but is recognized by organic crop producers in industrialized countries.

  8. Formyltetrahydrofolate Synthetase Sequences from Salt Marsh Plant Roots Reveal a Diversity of Acetogenic Bacteria and Other Bacterial Functional Groups

    OpenAIRE

    Leaphart, A. B.; Friez, M. J.; Lovell, C R

    2003-01-01

    Sixty-two partial formyltetrahydrofolate synthetase (FTHFS) structural gene sequences were recovered from roots of salt marsh plants, including Spartina alterniflora, Salicornia virginica, and Juncus roemerianus. Only S. alterniflora roots yielded sequences grouping with FTHFS sequences from known acetogens. Most other FTHFS or FTHFS-like sequences grouped with those from sulfate-reducing bacteria. Several sequences that grouped with Sphingomonas paucimobilis ligH were also recovered.

  9. Complete genome sequence of the extremely acidophilic methanotroph isolate V4, Methylacidiphilum infernorum, a representative of the bacterial phylum Verrucomicrobia

    Directory of Open Access Journals (Sweden)

    Stott Matthew B

    2008-07-01

    Full Text Available Abstract Background The phylum Verrucomicrobia is a widespread but poorly characterized bacterial clade. Although cultivation-independent approaches detect representatives of this phylum in a wide range of environments, including soils, seawater, hot springs and human gastrointestinal tract, only few have been isolated in pure culture. We have recently reported cultivation and initial characterization of an extremely acidophilic methanotrophic member of the Verrucomicrobia, strain V4, isolated from the Hell's Gate geothermal area in New Zealand. Similar organisms were independently isolated from geothermal systems in Italy and Russia. Results We report the complete genome sequence of strain V4, the first one from a representative of the Verrucomicrobia. Isolate V4, initially named "Methylokorus infernorum" (and recently renamed Methylacidiphilum infernorum is an autotrophic bacterium with a streamlined genome of ~2.3 Mbp that encodes simple signal transduction pathways and has a limited potential for regulation of gene expression. Central metabolism of M. infernorum was reconstructed almost completely and revealed highly interconnected pathways of autotrophic central metabolism and modifications of C1-utilization pathways compared to other known methylotrophs. The M. infernorum genome does not encode tubulin, which was previously discovered in bacteria of the genus Prosthecobacter, or close homologs of any other signature eukaryotic proteins. Phylogenetic analysis of ribosomal proteins and RNA polymerase subunits unequivocally supports grouping Planctomycetes, Verrucomicrobia and Chlamydiae into a single clade, the PVC superphylum, despite dramatically different gene content in members of these three groups. Comparative-genomic analysis suggests that evolution of the M. infernorum lineage involved extensive horizontal gene exchange with a variety of bacteria. The genome of M. infernorum shows apparent adaptations for existence under extremely

  10. Common sequence motifs coding for higher-plant and prokaryotic O-acetylserine (thiol)-lyases: bacterial origin of a chloroplast transit peptide?

    Science.gov (United States)

    Rolland, N; Job, D; Douce, R

    1993-08-01

    A comparison of the amino acid sequence of O-acetylserine (thiol)-lyase (EC 4.2.99.8) from Escherichia coli and the isoforms of this enzyme found in the cytosolic and chloroplastic compartments of spinach (Spinacia oleracea) leaf cells allows the essential lysine residue involved in the binding of the pyridoxal 5'-phosphate cofactor to be identified. The results of further sequence comparison of cDNAs coding for these proteins are discussed in the frame of the endosymbiotic theory of chloroplast evolution. The results are compatible with a mechanism in which the chloroplast enzyme originated from the cytosolic enzyme and both plant genes originated from a common prokaryotic ancestor. The comparison also suggests that the 5'-non-coding sequence of the bacterial gene was transferred to the plant cell nucleus and that it has been used to create the N-terminal portions of both plant enzymes, and possibly the transit peptide of the chloroplast enzyme. PMID:7916619

  11. Use of 16S rRNA sequencing and quantitative PCR to correlate venous leg ulcer bacterial bioburden dynamics with wound expansion, antibiotic therapy, and healing.

    Science.gov (United States)

    Sprockett, Daniel D; Ammons, Christine G; Tuttle, Marie S

    2015-09-01

    Clinical diagnosis of infection in chronic wounds is currently limited to subjective clinical signs and culture-based methods that underestimate the complexity of wound microbial bioburden as revealed by DNA-based microbial identification methods. Here, we use 16S rRNA next generation sequencing and quantitative polymerase chain reaction to characterize weekly changes in bacterial load, community structure, and diversity associated with a chronic venous leg ulcer over the 15-week course of treatment and healing. Our DNA-based methods and detailed sampling scheme reveal that the bacterial bioburden of the wound is unexpectedly dynamic, including changes in the bacterial load and community structure that correlate with wound expansion, antibiotic therapy, and healing. We demonstrate that these multidimensional changes in bacterial bioburden can be summarized using swabs taken prior to debridement, and therefore, can be more easily collected serially than debridement or biopsy samples. Overall, this case illustrates the importance of detailed clinical indicators and longitudinal sampling to determine the pathogenic significance of chronic wound microbial dynamics and guide best use of antimicrobials for improvement of healing outcomes. PMID:25902876

  12. Responses of bacterial and archaeal communities to nitrate stimulation after oil pollution in mangrove sediment revealed by Illumina sequencing.

    Science.gov (United States)

    Wang, Lei; Huang, Xu; Zheng, Tian-Ling

    2016-08-15

    This study aimed to investigate microbial responses to nitrate stimulation in oiled mangrove mesocosm. Both supplementary oil and nitrate changed the water and sediment chemical properties contributing to the shift of microbial communities. Denitrifying genes nirS and nirK were increased several times by the interaction of oil spiking and nitrate addition. Bacterial chao1 was reduced by oil spiking and further by nitrate stimulation, whereas archaeal chao1 was only inhibited by oil pollution on early time. Sampling depth explained most of variation and significantly impacted bacterial and archaeal communities, while oil pollution only significantly impacted bacterial communities (pexplaining less variation, nitrate addition coupled with oil spiking enhanced the growth of hydrocarbon degraders in mangrove. The findings demonstrate the impacts of environmental factors and their interactions in shaping microbial communities during nitrate stimulation. Our study suggests introducing genera Desulfotignum and Marinobacter into oiled mangrove for bioaugmentation. PMID:27262497

  13. Renibacterium salmoninarum, the causative agent of bacterial kidney disease in salmonid fish, detected by nested reverse transcription-PCR of 16S rRNA sequences.

    Science.gov (United States)

    Magnússon, H B; Fridjónsson, O H; Andrésson, O S; Benediktsdóttir, E; Gudmundsdóttir, S; Andrésdóttir, V

    1994-12-01

    An assay based on reverse transcription and nested PCR amplification of hypervariable regions within the 16S rRNA sequence was used to specifically detect Renibacterium salmoninarum, the slowly growing causative agent of bacterial kidney disease in salmonid fish. This assay detected 1 to 10 bacteria per sample and took 1 to 2 days to perform. The assay was used to detect R. salmoninarum in ovarian fluid obtained from naturally infected fish. The assay was unreliable when it was used to examine kidney tissue. PMID:7529017

  14. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

    Directory of Open Access Journals (Sweden)

    Mu Peng

    2015-09-01

    Full Text Available Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future.

  15. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes.

    Science.gov (United States)

    Peng, Mu; Zi, Xiaoxue; Wang, Qiuyu

    2015-10-01

    Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Planctomycetes and Proteobacteria were the dominant phyla among all the soil samples. The heatmap plot depicted the relative percentage of each bacterial family within each sample and clustered five samples into two groups. For the samples, bacteria in the soils varied at different periods of oil exposure. The oil pollution exerted strong selective pressure to propagate many potentially petroleum degrading bacteria. Redundancy analysis (RDA) indicated that organic matter was the highest determinant factor for explaining the variations in community compositions. This suggests that compared to clean soils, oil-polluted soils support more diverse bacterial communities and soil bacterial community shifts were mainly controlled by organic matter and exposure time. These results provide some useful information for bioremediation of petroleum contaminated soil in the future. PMID:26404329

  16. Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers.

    Science.gov (United States)

    Myer, Phillip R; Kim, MinSeok; Freetly, Harvey C; Smith, Timothy P L

    2016-08-01

    Next generation sequencing technologies have vastly changed the approach of sequencing of the 16S rRNA gene for studies in microbial ecology. Three distinct technologies are available for large-scale 16S sequencing. All three are subject to biases introduced by sequencing error rates, amplification primer selection, and read length, which can affect the apparent microbial community. In this study, we compared short read 16S rRNA variable regions, V1-V3, with that of near-full length 16S regions, V1-V8, using highly diverse steer rumen microbial communities, in order to examine the impact of technology selection on phylogenetic profiles. Short paired-end reads from the Illumina MiSeq platform were used to generate V1-V3 sequence, while long "circular consensus" reads from the Pacific Biosciences RSII instrument were used to generate V1-V8 data. The two platforms revealed similar microbial operational taxonomic units (OTUs), as well as similar species richness, Good's coverage, and Shannon diversity metrics. However, the V1-V8 amplified ruminal community resulted in significant increases in several orders of taxa, such as phyla Proteobacteria and Verrucomicrobia (P niche-specific database to use in analyzing data from shorter read technologies when budgetary constraints preclude use of near-full length 16S sequencing. PMID:27282101

  17. Next Generation Sequencing of Classical Swine Fever Virus and Border Disease virus cloned in Bacterial Artificial Chromosomes

    DEFF Research Database (Denmark)

    Fahnøe, Ulrik; Höper, Dirk; Beer, martin;

    2012-01-01

    be rescued only from some of our BAC constructs whereas others are not replication competent. To further analyze this discrepancy we have completely sequenced selected pestivirus BAC DNAs using a 454 Genome Sequencer FLX to evaluate the number/kind of deviations in the cloned genome sequences. In addition......, we have sequenced the full genome cDNA fragments used for the BACs by the same approach. This enables us to evaluate in more detail the nature of nucleotide changes in the pestivirus BACs that lead to lack of replicationcompetence and/or virus rescue. Additionally, detailed knowledge of the genomic...

  18. Botanical Insecticides in Plant Protection

    Directory of Open Access Journals (Sweden)

    Martina Grdiša

    2013-07-01

    Full Text Available Normal 0 21 false false false MicrosoftInternetExplorer4 Botanical insecticides are natural compounds with insecticidal properties and their use in crop protection is as old as agricultural practice. Although they have been in use for over one hundred years, the advent of synthetic insecticides has unfortunately displaced their use today. Due to fast action, low cost, easy application and efficiency against a wide range of harmful species, synthetic insecticides have become an important part of pest management in modern agricultural systems. However, after decades of use, their negative side effects, such as toxicity to humans and animals, environmental contamination, and toxicity to non-target insects have become apparent and interest in less hazardous alternatives of pest control is therefore being renewed. Plant species with known insecticidal actions are being promoted and research is being conducted to find new sources of botanical insecticides. The most important botanical insecticide is pyrethrin, a secondary metabolite of Dalmatian pyrethrum, neem, followed by insecticides based on the essential oils, rotenone, quassia, ryania and sabadilla. Th ey have various chemical properties and modes of action. However, some general characteristics include fast degradation in sunlight, air and moisture, and selectivity to non-target insects. Unfortunately, neither of these insecticides is widely used as a pest control agent but is recognized by organic crop producers in industrialized countries. /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Obična tablica"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;}

  19. Bacterial diversity in typical Italian salami at different ripening stages as revealed by high-throughput sequencing of 16S rRNA amplicons.

    Science.gov (United States)

    Połka, Justyna; Rebecchi, Annalisa; Pisacane, Vincenza; Morelli, Lorenzo; Puglisi, Edoardo

    2015-04-01

    The bacterial diversity involved in food fermentations is one of the most important factors shaping the final characteristics of traditional foods. Knowledge about this diversity can be greatly improved by the application of high-throughput sequencing technologies (HTS) coupled to the PCR amplification of the 16S rRNA subunit. Here we investigated the bacterial diversity in batches of Salame Piacentino PDO (Protected Designation of Origin), a dry fermented sausage that is typical of a regional area of Northern Italy. Salami samples from 6 different local factories were analysed at 0, 21, 49 and 63 days of ripening; raw meat at time 0 and casing samples at 21 days of ripening where also analysed, and the effect of starter addition was included in the experimental set-up. Culture-based microbiological analyses and PCR-DGGE were carried out in order to be compared with HTS results. A total of 722,196 high quality sequences were obtained after trimming, paired-reads assembly and quality screening of raw reads obtained by Illumina MiSeq sequencing of the two bacterial 16S hypervariable regions V3 and V4; manual curation of 16S database allowed a correct taxonomical classification at the species for 99.5% of these reads. Results confirmed the presence of main bacterial species involved in the fermentation of salami as assessed by PCR-DGGE, but with a greater extent of resolution and quantitative assessments that are not possible by the mere analyses of gel banding patterns. Thirty-two different Staphylococcus and 33 Lactobacillus species where identified in the salami from different producers, while the whole data set obtained accounted for 13 main families and 98 rare ones, 23 of which were present in at least 10% of the investigated samples, with casings being the major sources of the observed diversity. Multivariate analyses also showed that batches from 6 local producers tend to cluster altogether after 21 days of ripening, thus indicating that HTS has the potential

  20. Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters

    Science.gov (United States)

    Bao, Weichen; Mi, Zhihui; Xu, Haiyan; Zheng, Yi; Kwok, Lai Yu; Zhang, Heping; Zhang, Wenyi

    2016-01-01

    The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage. PMID:27340760

  1. Assessing quality of Medicago sativa silage by monitoring bacterial composition with single molecule, real-time sequencing technology and various physiological parameters.

    Science.gov (United States)

    Bao, Weichen; Mi, Zhihui; Xu, Haiyan; Zheng, Yi; Kwok, Lai Yu; Zhang, Heping; Zhang, Wenyi

    2016-01-01

    The present study applied the PacBio single molecule, real-time sequencing technology (SMRT) in evaluating the quality of silage production. Specifically, we produced four types of Medicago sativa silages by using four different lactic acid bacteria-based additives (AD-I, AD-II, AD-III and AD-IV). We monitored the changes in pH, organic acids (including butyric acid, the ratio of acetic acid/lactic acid, γ-aminobutyric acid, 4-hyroxy benzoic acid and phenyl lactic acid), mycotoxins, and bacterial microbiota during silage fermentation. Our results showed that the use of the additives was beneficial to the silage fermentation by enhancing a general pH and mycotoxin reduction, while increasing the organic acids content. By SMRT analysis of the microbial composition in eight silage samples, we found that the bacterial species number and relative abundances shifted apparently after fermentation. Such changes were specific to the LAB species in the additives. Particularly, Bacillus megaterium was the initial dominant species in the raw materials; and after the fermentation process, Pediococcus acidilactici and Lactobacillus plantarum became the most prevalent species, both of which were intrinsically present in the LAB additives. Our data have demonstrated that the SMRT sequencing platform is applicable in assessing the quality of silage. PMID:27340760

  2. Bacterial Community Diversity of Oil-Contaminated Soils Assessed by High Throughput Sequencing of 16S rRNA Genes

    OpenAIRE

    Mu Peng; Xiaoxue Zi; Qiuyu Wang

    2015-01-01

    Soil bacteria play a major role in ecological and biodegradable function processes in oil-contaminated soils. Here, we assessed the bacterial diversity and changes therein in oil-contaminated soils exposed to different periods of oil pollution using 454 pyrosequencing of 16S rRNA genes. No less than 24,953 valid reads and 6246 operational taxonomic units (OTUs) were obtained from all five studied samples. OTU richness was relatively higher in contaminated soils than clean samples. Acidobacte...

  3. Eukaryotic gene invasion by a bacterial mobile insertion sequence element IS2 during cloning into a plasmid vector.

    Science.gov (United States)

    Senejani, Alireza G; Sweasy, Joann B

    2010-01-01

    Escherichia coli (E. coli) are commonly used as hosts for DNA cloning and sequencing. Upon transformation of E. coli with recombined vector carrying a gene of interest, the bacteria multiply the gene of interest while maintaining the integrity of its content. During the subcloning of a mouse genomic fragment into a plasmid vector, we noticed that the size of the insert increased significantly upon replication in E. coli. The sequence of the insert was determined and found to contain a novel DNA sequence within the mouse genomic insert. A BLAST search of GenBank revealed the novel sequence to be that of the Insertion Sequence 2 (IS2) element from E. coli that was likely inserted during replication in that organism. Importantly, a detailed search of GenBank shows that the IS2 is present within many eukaryotic nucleotide sequences, and in many cases, has been annotated as being part of the protein. The results of this study suggest that one must perform additional careful analysis of the sequence results using BLAST comparisons, and further verification of gene annotation before submission into the GenBank. PMID:20678256

  4. Eukaryotic gene invasion by a bacterial mobile insertion sequence element IS2 during cloning into a plasmid vector

    Directory of Open Access Journals (Sweden)

    Senejani Alireza G

    2010-05-01

    Full Text Available Abstract Escherichia coli (E. coli are commonly used as hosts for DNA cloning and sequencing. Upon transformation of E. coli with recombined vector carrying a gene of interest, the bacteria multiply the gene of interest while maintaining the integrity of its content. During the subcloning of a mouse genomic fragment into a plasmid vector, we noticed that the size of the insert increased significantly upon replication in E. coli. The sequence of the insert was determined and found to contain a novel DNA sequence within the mouse genomic insert. A BLAST search of GenBank revealed the novel sequence to be that of the Insertion Sequence 2 (IS2 element from E. coli that was likely inserted during replication in that organism. Importantly, a detailed search of GenBank shows that the IS2 is present within many eukaryotic nucleotide sequences, and in many cases, has been annotated as being part of the protein. The results of this study suggest that one must perform additional careful analysis of the sequence results using BLAST comparisons, and further verification of gene annotation before submission into the GenBank.

  5. A renaissance for botanical insecticides?

    Science.gov (United States)

    Isman, Murray B

    2015-12-01

    Botanical insecticides continue to be a subject of keen interest among the international research community, reflected in the steady growth in scientific publications devoted to the subject. Until very recently though, the translation of that theory to practice, i.e. the commercialisation and adoption of new botanical insecticides in the marketplace, has seriously lagged behind. Strict regulatory regimes, long the bane of small pesticide producers, are beginning to relax some of the data requirements for 'low-risk' pesticide products, facilitating movement of more botanicals into the commercial arena. In this paper I discuss some of the jurisdictions where botanicals are increasingly finding favour, some of the newer botanical insecticides in the plant and animal health arsenal and some of the specific sectors where botanicals are most likely to compete effectively with other types of insecticidal product. PMID:26251334

  6. Insecticide resistence of bumblebee species

    Czech Academy of Sciences Publication Activity Database

    Zarevúcka, Marie

    Rijeka: InTech, 2013 - (Chamy, R.; Rosenkranz, F.), s. 207-228 ISBN 978-953-51-1154-2 R&D Projects: GA ČR GA203/09/1446; GA TA ČR TA01020969 Institutional support: RVO:61388963 Keywords : bumblebee * insecticide Subject RIV: CC - Organic Chemistry http://www.intechopen.com/books/biodegradation-life-of-science/insecticide-resistence-of-bumblebee-species

  7. DNA Sequencing Diagnosis of Off-Season Spirochetemia with Low Bacterial Density in Borrelia burgdorferi and Borrelia miyamotoi Infections

    OpenAIRE

    Sin Hang Lee; Vigliotti, Jessica S.; Vigliotti, Veronica S; William Jones; Moorcroft, Thomas A.; Katherine Lantsman

    2014-01-01

    A highly conserved 357-bp segment of the 16S ribosomal RNA gene (16S rDNA) of Borrelia burgdorferi sensu lato and the correspondent 358-bp segment of the Borrelia miyamotoi gene were amplified by a single pair of nested polymerase chain reaction (PCR) primers for detection, and the amplicons were used as the templates for direct Sanger DNA sequencing. Reliable molecular diagnosis of these borreliae was confirmed by sequence alignment analysis of the hypervariable regions of the PCR amplicon,...

  8. Molecular characterization and genetic diversity of insecticidal crystal protein genes in native Bacillus thuringiensis isolates.

    Science.gov (United States)

    Mahadeva Swamy, H M; Asokan, R; Mahmood, Riaz; Nagesha, S N

    2013-04-01

    The Western Ghats of Karnataka natural ecosystem are among the most diverse and is one of the eight hottest hotspots of biological diversity in the world, that runs along the western part of India through four states including Karnataka. Bacillus thuringiensis (Bt) strains were isolated from soils of Western Ghats of Karnataka and characterized by molecular and analytical methods as a result of which 28 new Bt-like isolates were identified. Bt strains were isolated from soil samples using sodium acetate selection method. The morphology of crystals was studied using light and phase contrast microscopy. Isolates were further characterized for insecticidal cry gene by PCR, composition of toxins in bacterial crystals by SDS-PAGE cloning, sequencing and evaluation of toxicity was done. As a result 28 new Bt-like isolates were identified. Majority of the isolates showed the presence of a 55 kDa protein bands on SDS-PAGE while the rest showed 130, 73, 34, and 25 kDa bands. PCR analysis revealed predominance of Coleopteran-active cry genes in these isolates. The variations in the nucleotide sequences, crystal morphology, and mass of crystal protein(s) purified from the Bt isolates revealed genetic and molecular diversity. Three strains containing Coleopteran-active cry genes showed higher activity against larvae Myllocerus undecimpustulatus undatus Marshall (Coleoptera: Curculionidae) than B. thuringiensis subsp. Morrisoni. Results indicated that Bt isolates could be utilized for bioinsecticide production, aiming to reduce the use of chemical insecticide which could be useful to use in integrated pest management to control agriculturally important pests for sustainable crop production. PMID:23207696

  9. Identification of genes involved in pyrethroid-, propoxur-, and dichlorvos- insecticides resistance in the mosquitoes, Culex pipiens complex (Diptera: Culicidae).

    Science.gov (United States)

    Li, Chun-xiao; Guo, Xiao-xia; Zhang, Ying-mei; Dong, Yan-de; Xing, Dan; Yan, Ting; Wang, Gang; Zhang, Heng-duan; Zhao, Tong-yan

    2016-05-01

    Culex pipiens pallens and Cx. p. quinquefasciatus are important vectors of many diseases, such as West Nile fever and lymphatic filariasis. The widespread use of insecticides to control these disease vectors and other insect pests has led to insecticide resistance becoming common in these species. In this study, high throughout Illumina sequencing was used to identify hundreds of Cx. p. pallens and Cx. p. quinquefasciatus genes that were differentially expressed in response to insecticide exposure. The identification of these genes is a vital first step for more detailed investigation of the molecular mechanisms involved in insecticide resistance in Culex mosquitoes. PMID:26802491

  10. Identification of a novel calcium binding motif based on the detection of sequence insertions in the animal peroxidase domain of bacterial proteins.

    Directory of Open Access Journals (Sweden)

    Saray Santamaría-Hernando

    Full Text Available Proteins of the animal heme peroxidase (ANP superfamily differ greatly in size since they have either one or two catalytic domains that match profile PS50292. The orf PP_2561 of Pseudomonas putida KT2440 that we have called PepA encodes a two-domain ANP. The alignment of these domains with those of PepA homologues revealed a variable number of insertions with the consensus G-x-D-G-x-x-[GN]-[TN]-x-D-D. This motif has also been detected in the structure of pseudopilin (pdb 3G20, where it was found to be involved in Ca(2+ coordination although a sequence analysis did not reveal the presence of any known calcium binding motifs in this protein. Isothermal titration calorimetry revealed that a peptide containing this consensus motif bound specifically calcium ions with affinities ranging between 33-79 µM depending on the pH. Microcalorimetric titrations of the purified N-terminal ANP-like domain of PepA revealed Ca(2+ binding with a K(D of 12 µM and stoichiometry of 1.25 calcium ions per protein monomer. This domain exhibited peroxidase activity after its reconstitution with heme. These data led to the definition of a novel calcium binding motif that we have termed PERCAL and which was abundantly present in animal peroxidase-like domains of bacterial proteins. Bacterial heme peroxidases thus possess two different types of calcium binding motifs, namely PERCAL and the related hemolysin type calcium binding motif, with the latter being located outside the catalytic domains and in their C-terminal end. A phylogenetic tree of ANP-like catalytic domains of bacterial proteins with PERCAL motifs, including single domain peroxidases, was divided into two major clusters, representing domains with and without PERCAL motif containing insertions. We have verified that the recently reported classification of bacterial heme peroxidases in two families (cd09819 and cd09821 is unrelated to these insertions. Sequences matching PERCAL were detected in all kingdoms of

  11. Diatomaceous Earths - Natural Insecticides

    Directory of Open Access Journals (Sweden)

    Zlatko Korunić

    2013-01-01

    Full Text Available The regulatory issues for diatomaceous earth (DE cover three fields: consumer safety,worker safety, and proof of efficacy against pests. For consumer safety, regulatory issuesare similar to those for other additives, and a principal benefit of DEs is their removal bynormal processing methods. For worker safety, regulatory issues are similar to those forother dusts, such as lime. The proof of potential insecticide values of DE may be assessedby using the analysis of physical and chemical properties of DE and its effect on grainproperties and the proof of efficacy may be regulated by bioassay of standard design.Integrated pest management (IPM, a knowledge-based system, is rapidly providing aframework to reduce dependence on synthetic chemical pesticides. The main principleof post-harvest IPM is to prevent problems rather than to react to them. The specificcurative measures using synthetic pesticides should be applied only when infestationoccurs. DE and enhanced diatomaceous earth (EDE formulations hold significant promiseto increase the effectiveness and broaden the adoption of IPM strategies, thereby reducingthe need for synthetic pesticides. By incorporating DE in an effective IPM program,grain is protected against infestation, loss caused by insects is prevented and grain qualityis maintained until the grain is processed. Cases study data on the use of DE for commodityand structural treatment show that DE is already a practical alternative to syntheticpesticides in some applications.

  12. Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon.

    Science.gov (United States)

    Feinauer, Christoph; Szurmant, Hendrik; Weigt, Martin; Pagnani, Andrea

    2016-01-01

    Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on the Direct-Coupling Analysis of the co-evolution between inter-protein residue pairs. We use ribosomal and trp operon proteins as test cases: For the small resp. large ribosomal subunit our approach predicts protein-interaction partners at a true-positive rate of 70% resp. 90% within the first 10 predictions, with areas of 0.69 resp. 0.81 under the ROC curves for all predictions. In the trp operon, it assigns the two largest interaction scores to the only two interactions experimentally known. On the level of residue interactions we show that for both the small and the large ribosomal subunit our approach predicts interacting residues in the system with a true positive rate of 60% and 85% in the first 20 predictions. We use artificial data to show that the performance of our approach depends crucially on the size of the joint multiple sequence alignments and analyze how many sequences would be necessary for a perfect prediction if the sequences were sampled from the same model that we use for prediction. Given the performance of our approach on the test data we speculate that it can be used to detect new interactions, especially in the light of the rapid growth of available sequence data. PMID:26882169

  13. Inter-Protein Sequence Co-Evolution Predicts Known Physical Interactions in Bacterial Ribosomes and the Trp Operon.

    Directory of Open Access Journals (Sweden)

    Christoph Feinauer

    Full Text Available Interaction between proteins is a fundamental mechanism that underlies virtually all biological processes. Many important interactions are conserved across a large variety of species. The need to maintain interaction leads to a high degree of co-evolution between residues in the interface between partner proteins. The inference of protein-protein interaction networks from the rapidly growing sequence databases is one of the most formidable tasks in systems biology today. We propose here a novel approach based on the Direct-Coupling Analysis of the co-evolution between inter-protein residue pairs. We use ribosomal and trp operon proteins as test cases: For the small resp. large ribosomal subunit our approach predicts protein-interaction partners at a true-positive rate of 70% resp. 90% within the first 10 predictions, with areas of 0.69 resp. 0.81 under the ROC curves for all predictions. In the trp operon, it assigns the two largest interaction scores to the only two interactions experimentally known. On the level of residue interactions we show that for both the small and the large ribosomal subunit our approach predicts interacting residues in the system with a true positive rate of 60% and 85% in the first 20 predictions. We use artificial data to show that the performance of our approach depends crucially on the size of the joint multiple sequence alignments and analyze how many sequences would be necessary for a perfect prediction if the sequences were sampled from the same model that we use for prediction. Given the performance of our approach on the test data we speculate that it can be used to detect new interactions, especially in the light of the rapid growth of available sequence data.

  14. Abundance and diversity of bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants revealed by high-throughput sequencing.

    Directory of Open Access Journals (Sweden)

    Zhu Wang

    Full Text Available Biological nitrification/denitrification is frequently used to remove nitrogen from tannery wastewater containing high concentrations of ammonia. However, information is limited about the bacterial nitrifiers and denitrifiers and their functional genes in tannery wastewater treatment plants (WWTPs due to the low-throughput of the previously used methods. In this study, 454 pyrosequencing and Illumina high-throughput sequencing, combined with molecular methods, were used to comprehensively characterize structures and functions of nitrification and denitrification bacterial communities in aerobic and anaerobic sludge of two full-scale tannery WWTPs. Pyrosequencing of 16S rRNA genes showed that Proteobacteria and Synergistetes dominated in the aerobic and anaerobic sludge, respectively. Ammonia-oxidizing bacteria (AOB amoA gene cloning revealed that Nitrosomonas europaea dominated the ammonia-oxidizing community in the WWTPs. Metagenomic analysis showed that the denitrifiers mainly included the genera of Thauera, Paracoccus, Hyphomicrobium, Comamonas and Azoarcus, which may greatly contribute to the nitrogen removal in the two WWTPs. It is interesting that AOB and ammonia-oxidizing archaea had low abundance although both WWTPs demonstrated high ammonium removal efficiency. Good correlation between the qPCR and metagenomic analysis is observed for the quantification of functional genes amoA, nirK, nirS and nosZ, indicating that the metagenomic approach may be a promising method used to comprehensively investigate the abundance of functional genes of nitrifiers and denitrifiers in the environment.

  15. Synthesis of insecticidal sucrose esters

    Institute of Scientific and Technical Information of China (English)

    Song Zi-juan; Li Shu-jun; Chen Xi; Liu Li-mei; Song Zhan-qian

    2006-01-01

    Some synthetic sucrose esters (SE) are a relatively new class of insecticidal compounds produced by reacting sugars with fatty acids, which are safe for the environment. Especially, sucrose esters composed of C6-C12 fatty acids have desirable insecticidal properties against many soft-bodied arthropod pests. In our study, sucrose octanoate which has the highest activity against a range of arthropod species was synthesized by a trans-esterification method and proved its insecticidal property. Under the condition of a homogeneous liquid, sucrose octanoate was prepared by reacting ethyl octanoate with sucrose at reduced pressure; the yield was 79.11%. Sucrose octanoate synthesized was identified and its property analyzed by IR, TLC and spectrophotometric analysis. It was shown that the ratio of monoester to polyester in sucrose octanoate was 1.48:1. The insecticidal activity of the synthetic sucrose octanoate was evaluated at a concentration of 4 and 8 mg·mL-1. The mortality of first-instar larvae ofLymantria dispar from its contact toxicity was 72.5% after 36 hours, the revision insect reduced rate of Aphis glycines reached above 80% at 4 and 8 mg·mL-1 after being treated for 5 days. Since the SE products are nontoxic to humans and higher animals, fully biodegradable and hydrolyzed to readily metabolizable sucrose and fatty acid, they are not harmful to crops and appear to be good insecticide candidates.

  16. Integration of sequence-similarity and functional association information can overcome intrinsic problems in orthology mapping across bacterial genomes

    OpenAIRE

    Li, Guojun; Ma, Qin; Mao, Xizeng; Yin, Yanbin; Zhu, Xiaoran; Xu, Ying

    2011-01-01

    Existing methods for orthologous gene mapping suffer from two general problems: (i) they are computationally too slow and their results are difficult to interpret for automated large-scale applications when based on phylogenetic analyses; or (ii) they are too prone to making mistakes in dealing with complex situations involving horizontal gene transfers and gene fusion due to the lack of a sound basis when based on sequence similarity information. We present a novel algorithm, Global Optimiza...

  17. Repellency of selected biorational insecticides to potato psyllid, Bactericera cockerelli (Hemiptera: Psyllidae)

    Science.gov (United States)

    Bactericera cockerelli has recently become a major concern because of its direct feeding and vectoring of bacterial diseases in many solanaceous crops. The repellency of four biorational insecticides, MOI-201 (a Chinese medicine plant extract), Requiem (a plant extract of Chenopodium ambrosioides), ...

  18. The selectivity of DNA insecticides

    OpenAIRE

    Oberemok V.; Nyadar P.

    2014-01-01

    Single-stranded LdMNPV iap3 gene fragments on tobacco hornworm and black cutworm, and a significant effect of single-stranded TnSNPV iap3 gene fragments on the viability of cabbage looper and their harmlessness on black cutworm was found. DNA insecticides based on LdMNPV iap3 and TnSNPV iap3 gene fragments are selective in action. Our findings emphasize the importance of appropriate concentrations of DNA insecticides used to control phyllophagous insects. This article has b...

  19. Bacterial lifestyle in a deep-sea hydrothermal vent chimney revealed by the genome sequence of the thermophilic bacterium Deferribacter desulfuricans SSM1.

    Science.gov (United States)

    Takaki, Yoshihiro; Shimamura, Shigeru; Nakagawa, Satoshi; Fukuhara, Yasuo; Horikawa, Hiroshi; Ankai, Akiho; Harada, Takeshi; Hosoyama, Akira; Oguchi, Akio; Fukui, Shigehiro; Fujita, Nobuyuki; Takami, Hideto; Takai, Ken

    2010-06-01

    The complete genome sequence of the thermophilic sulphur-reducing bacterium, Deferribacter desulfuricans SMM1, isolated from a hydrothermal vent chimney has been determined. The genome comprises a single circular chromosome of 2,234,389 bp and a megaplasmid of 308,544 bp. Many genes encoded in the genome are most similar to the genes of sulphur- or sulphate-reducing bacterial species within Deltaproteobacteria. The reconstructed central metabolisms showed a heterotrophic lifestyle primarily driven by C1 to C3 organics, e.g. formate, acetate, and pyruvate, and also suggested that the inability of autotrophy via a reductive tricarboxylic acid cycle may be due to the lack of ATP-dependent citrate lyase. In addition, the genome encodes numerous genes for chemoreceptors, chemotaxis-like systems, and signal transduction machineries. These signalling networks may be linked to this bacterium's versatile energy metabolisms and may provide ecophysiological advantages for D. desulfuricans SSM1 thriving in the physically and chemically fluctuating environments near hydrothermal vents. This is the first genome sequence from the phylum Deferribacteres. PMID:20189949

  20. A novel shortcut nitrogen removal process using an algal-bacterial consortium in a photo-sequencing batch reactor (PSBR).

    Science.gov (United States)

    Wang, Meng; Yang, Han; Ergas, Sarina J; van der Steen, Peter

    2015-12-15

    Removal of nitrogen from anaerobically digested swine manure centrate was investigated in a photo-sequencing batch reactor (PSBR) with alternating light and dark periods. Microalgal photosynthesis was shown to provide enough oxygen for complete nitritation during the light period. With addition of an organic carbon source during the dark period, the reactor removed over 90% total nitrogen (TN) without aeration other than by mixing. Overall, 80% of the TN removal was through nitritation/denitritation and the rest was due to biomass uptake. The high concentrations of ammonia and nitrite and low dissolved oxygen concentration in the PSBR effectively inhibited nitrite oxidizing bacteria, resulting in stable nitritation. The hybrid microalgal photosynthesis and shortcut nitrogen removal process has the potential to substantially reduce aeration requirements for treatment of anaerobic digestion side streams. The PSBR also produced well settling biomass with sludge volume index of 62 ± 16 mL mg(-1). PMID:26378730

  1. Proficiency testing for bacterial whole genome sequencing: an end-user survey of current capabilities, requirements and priorities

    DEFF Research Database (Denmark)

    Moran-Gilad, Jacob; Sintchenko, Vitali; Karlsmose Pedersen, Susanne;

    2015-01-01

    costs. The priority pathogens reported by respondents reflected the key drivers for NGS use (high burden disease and 'high profile' pathogens). The performance of and participation in PT was perceived as important by most respondents. The wide range of sequencing and bioinformatics practices reported by...... end-users highlights the importance of standardisation and harmonisation of NGS in public health and underpins the use of PT as a means to assuring quality. The findings of this survey will guide the design of the GMI PT program in relation to the spectrum of pathogens included, testing frequency and...... volume as well as technical requirements. The PT program for external quality assurance will evolve and inform the introduction of NGS into clinical and public health microbiology practice in the post-genomic era....

  2. Proficiency Testing for Bacterial Whole Genome Sequencing: An End-User Survey of Current Capabilities, Requirements and Priorities

    DEFF Research Database (Denmark)

    Moran-Gilad, Jacob; Sintchenko, Vitali; Karlsmose Pedersen, Susanne;

    2015-01-01

    range of costs. The priority pathogens reported by respondents reflected the key drivers for NGS use (high burden disease and ‘high profile’ pathogens). The performance of and participation in PT was perceived as important by most respondents. The wide range of sequencing and bioinformatics practices...... reported by end-users highlights the importance of standardisation and harmonisation of NGS in public health and underpins the use of PT as a means to assuring quality. The findings of this survey will guide the design of the GMI PT program in relation to the spectrum of pathogens included, testing...... frequency and volume as well as technical requirements. The PT program for external quality assurance will evolve and inform the introduction of NGS into clinical and public health microbiology practice in the post-genomic era....

  3. Evaluating the efficacy of the new Ion PGM Hi-Q Sequencing Kit applied to bacterial genomes.

    Science.gov (United States)

    Pereira, Felipe L; Soares, Siomar C; Dorella, Fernanda A; Leal, Carlos A G; Figueiredo, Henrique C P

    2016-05-01

    Benchtop NGS platforms are constantly evolving to follow new advances in genomics. Thus, the manufacturers are making improvements, such as the recent Ion PGM Hi-Q chemistry. We evaluate the efficacy of this new Hi-Q approach by comparing it with the former Ion PGM kit and the Illumina MiSEQ Nextera 3rd version. The Hi-Q chemistry showed improvement on mapping reads, with 49 errors for 10kbp mapped; in contrast, the former kit had 89 errors. Additionally, there was a reduction of 80% in erroneous variant detection with the Torrent Variant Caller. Also, an enhancement was observed in de novo assembly with a more confident result in whole-genome MLST, with up to 96% of the alleles assembled correctly for both tested microbial genomes. All of these advantages result in a final genome sequence closer to the performance with MiSEQ and will contribute to turn comparative genomic analysis a reliable task. PMID:27033417

  4. Chimeric FimH adhesin of type 1 fimbriae: a bacterial surface display system for heterologous sequences

    DEFF Research Database (Denmark)

    Pallesen, L; Poulsen, LK; Christiansen, Gunna; Klemm, P

    1995-01-01

    The FimH adhesin of type 1 fimbriae has been tested as a display system for heterologous protein segments on the surface of Escherichia coli. This was carried out by introduction of restriction site handles (BglII sites) in two different positions in the fimH gene, followed by in-frame insertion of...... heterologous DNA segments encoding two reporter sequences. In the selected positions such insertions did not significantly alter the function of the FimH protein with regard to surface location and adhesive ability. The system seemed to be quite flexible, since chimeric versions of the FimH adhesin containing...... feasibility study point to the possibility of using the FimH adhesin as a general surface display system for sizeable protein segments....

  5. Bacterial gastroenteritis

    Science.gov (United States)

    Infectious diarrhea - bacterial gastroenteritis; Acute gastroenteritis; Gastroenteritis - bacterial ... Bacterial gastroenteritis can affect 1 person or a group of people who all ate the same food. It is ...

  6. Survey of culture, goldengate assay, universal biosensor assay, and 16S rRNA Gene sequencing as alternative methods of bacterial pathogen detection.

    Science.gov (United States)

    Lindsay, Brianna; Pop, Mihai; Antonio, Martin; Walker, Alan W; Mai, Volker; Ahmed, Dilruba; Oundo, Joseph; Tamboura, Boubou; Panchalingam, Sandra; Levine, Myron M; Kotloff, Karen; Li, Shan; Magder, Laurence S; Paulson, Joseph N; Liu, Bo; Ikumapayi, Usman; Ebruke, Chinelo; Dione, Michel; Adeyemi, Mitchell; Rance, Richard; Stares, Mark D; Ukhanova, Maria; Barnes, Bret; Lewis, Ian; Ahmed, Firoz; Alam, Meer Taifur; Amin, Ruhul; Siddiqui, Sabbir; Ochieng, John B; Ouma, Emmanuel; Juma, Jane; Mailu, Eunice; Omore, Richard; O'Reilly, Ciara E; Hannis, James; Manalili, Sheri; Deleon, Jonna; Yasuda, Irene; Blyn, Lawrence; Ranken, Raymond; Li, Feng; Housley, Roberta; Ecker, David J; Hossain, M Anowar; Breiman, Robert F; Morris, J Glenn; McDaniel, Timothy K; Parkhill, Julian; Saha, Debasish; Sampath, Rangarajan; Stine, O Colin; Nataro, James P

    2013-10-01

    Cultivation-based assays combined with PCR or enzyme-linked immunosorbent assay (ELISA)-based methods for finding virulence factors are standard methods for detecting bacterial pathogens in stools; however, with emerging molecular technologies, new methods have become available. The aim of this study was to compare four distinct detection technologies for the identification of pathogens in stools from children under 5 years of age in The Gambia, Mali, Kenya, and Bangladesh. The children were identified, using currently accepted clinical protocols, as either controls or cases with moderate to severe diarrhea. A total of 3,610 stool samples were tested by established clinical culture techniques: 3,179 DNA samples by the Universal Biosensor assay (Ibis Biosciences, Inc.), 1,466 DNA samples by the GoldenGate assay (Illumina), and 1,006 DNA samples by sequencing of 16S rRNA genes. Each method detected different proportions of samples testing positive for each of seven enteric pathogens, enteroaggregative Escherichia coli (EAEC), enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), Shigella spp., Campylobacter jejuni, Salmonella enterica, and Aeromonas spp. The comparisons among detection methods included the frequency of positive stool samples and kappa values for making pairwise comparisons. Overall, the standard culture methods detected Shigella spp., EPEC, ETEC, and EAEC in smaller proportions of the samples than either of the methods based on detection of the virulence genes from DNA in whole stools. The GoldenGate method revealed the greatest agreement with the other methods. The agreement among methods was higher in cases than in controls. The new molecular technologies have a high potential for highly sensitive identification of bacterial diarrheal pathogens. PMID:23884998

  7. Effect of cypermethrin insecticide on the microbial community in cucumber phyllosphere

    Institute of Scientific and Technical Information of China (English)

    ZHANG Baoguo; ZHANG Hongxun; JIN Bo; TANG Ling; YANG Jianzhou; LI Baoju; ZHUANG Guoqiang; BAI Zhihui

    2008-01-01

    Cucumber (Cucumis sativus) is one of the most widely used vegetable in the world, and different pesticides have been extensively used for controlling the insects and disease pathogens of this plant. However, little is known about how the pesticides affect the microbial community in cucumber phyllosphere. This study was the first attempt to assess the impact of pyrethroid insecticide cyperemethrin on the microbial communities of cucumber phyllosphere using biochemical and genetic approaches. Phospholipid fatty acid (PLFA) assay indicated that cyperemethrin insecticide treatment led to a significant increase in both total and bacterial biomass and a decrease in fungal biomass and the ratio of Gram-positive (GP) bacteria to Gram-negative (GN) bacteria within the cucumber phyllosphere. Principal-component analyses (PCA) suggested that the number of unsaturated and cyclopropane PLFAs (16:1ω9t,18:1ω7, cy17:0, cy19:0) increased with the insecticide treatment, whereas the saturated PLFA i16:0, i17:0 decreased. The increase of GN bacteria implied that the cypermethrin insecticide might be a nutrient for the growth of these phyllosphere microbes. Terminal restriction fragment length polymorphism (T-RFLP) reinforced the PLFA results. A significant change of bacterial community structure was observed in the separate dendrogram cluster between control and treated samples with the cucumber phyllosphere following cypermethrin insecticide treatment. Moreover, the increased terminal restriction fragments (T-RFs) (58, 62, 89, 99, 119, 195, 239,311,340, and 473 bp) indicated that some bacteria might play a significant role in the insecticide degradation within the cucumber phylosphere, whereas the disappeared T-RFs (44, 51, 96, 223, 306, and 338 bp) implied that some other bacteria might potentially serve as microbial indicator of cyperemethrin insecticide exposure.

  8. Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing.

    Science.gov (United States)

    Hong, Youwei; Liao, Dan; Hu, Anyi; Wang, Han; Chen, Jinsheng; Khan, Sardar; Su, Jianqiang; Li, Hu

    2015-10-01

    Root-associated microbial communities are very important for biogeochemical cycles in wetland ecosystems and help to elaborate the mechanisms of plant invasions. In the estuary of Jiulong River (China), Spartina alterniflora has widely invaded Kandelia obovata-dominated habitats, offering an opportunity to study the influence of root-associated bacteria. The community structures of endophytic and rhizosphere bacteria associated with selected plant species were investigated using the barcoded Illumina paired-end sequencing technique. The diversity indices of bacteria associated with the roots of S. alterniflora were higher than those of the transition stands and K. obovata monoculture. Using principal coordinate analysis with UniFrac metrics, the comparison of β-diversity showed that all samples could be significantly clustered into 3 major groups, according to the bacteria communities of origin. Four phyla, namely Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, were enriched in the rhizoplane of both salt marsh plants, while they shared higher abundances of Cyanobacteria and Proteobacteria among endophytic bacteria. Members of the phyla Spirochaetes and Chloroflexi were found among the endophytic bacteria of S. alterniflora and K. obovata, respectively. One of the interesting findings was that endophytes were more sensitive in response to plant invasion than were rhizosphere bacteria. With linear discriminate analysis, we found some predominant rhizoplane and endophytic bacteria, including Methylococcales, Pseudoalteromonadacea, Clostridium, Vibrio, and Desulfovibrio, which have the potential to affect the carbon, nitrogen, and sulfur cycles. Thus, the results provide clues to the isolation of functional bacteria and the effects of root-associated microbial groups on S. alterniflora invasions. PMID:26223001

  9. Ultradeep 16S rRNA Sequencing Analysis of Geographically Similar but Diverse Unexplored Marine Samples Reveal Varied Bacterial Community Composition

    OpenAIRE

    Chairmandurai Aravindraja; Dharmaprakash Viszwapriya; Shunmugiah Karutha Pandian

    2013-01-01

    BACKGROUND: Bacterial community composition in the marine environment differs from one geographical location to another. Reports that delineate the bacterial diversity of different marine samples from geographically similar location are limited. The present study aims to understand whether the bacterial community compositions from different marine samples harbour similar bacterial diversity since these are geographically related to each other. METHODS AND PRINCIPAL FINDINGS: In the present st...

  10. Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits

    Science.gov (United States)

    Eckshtain-Levi, Noam; Shkedy, Dafna; Gershovits, Michael; Da Silva, Gustavo M.; Tamir-Ariel, Dafna; Walcott, Ron; Pupko, Tal; Burdman, Saul

    2016-01-01

    Acidovorax citrulli is a seedborne bacterium that causes bacterial fruit blotch of cucurbit plants including watermelon and melon. A. citrulli strains can be divided into two major groups based on DNA fingerprint analyses and biochemical properties. Group I strains have been generally isolated from non-watermelon cucurbits, while group II strains are closely associated with watermelon. In the present study, we report the genome sequence of M6, a group I model A. citrulli strain, isolated from melon. We used comparative genome analysis to investigate differences between the genome of strain M6 and the genome of the group II model strain AAC00-1. The draft genome sequence of A. citrulli M6 harbors 139 contigs, with an overall approximate size of 4.85 Mb. The genome of M6 is ∼500 Kb shorter than that of strain AAC00-1. Comparative analysis revealed that this size difference is mainly explained by eight fragments, ranging from ∼35–120 Kb and distributed throughout the AAC00-1 genome, which are absent in the M6 genome. In agreement with this finding, while AAC00-1 was found to possess 532 open reading frames (ORFs) that are absent in strain M6, only 123 ORFs in M6 were absent in AAC00-1. Most of these M6 ORFs are hypothetical proteins and most of them were also detected in two group I strains that were recently sequenced, tw6 and pslb65. Further analyses by PCR assays and coverage analyses with other A. citrulli strains support the notion that some of these fragments or significant portions of them are discriminative between groups I and II strains of A. citrulli. Moreover, GC content, effective number of codon values and cluster of orthologs’ analyses indicate that these fragments were introduced into group II strains by horizontal gene transfer events. Our study reports the genome sequence of a model group I strain of A. citrulli, one of the most important pathogens of cucurbits. It also provides the first comprehensive comparison at the genomic level between

  11. Insights from the Genome Sequence of Acidovorax citrulli M6, a Group I Strain of the Causal Agent of Bacterial Fruit Blotch of Cucurbits.

    Science.gov (United States)

    Eckshtain-Levi, Noam; Shkedy, Dafna; Gershovits, Michael; Da Silva, Gustavo M; Tamir-Ariel, Dafna; Walcott, Ron; Pupko, Tal; Burdman, Saul

    2016-01-01

    Acidovorax citrulli is a seedborne bacterium that causes bacterial fruit blotch of cucurbit plants including watermelon and melon. A. citrulli strains can be divided into two major groups based on DNA fingerprint analyses and biochemical properties. Group I strains have been generally isolated from non-watermelon cucurbits, while group II strains are closely associated with watermelon. In the present study, we report the genome sequence of M6, a group I model A. citrulli strain, isolated from melon. We used comparative genome analysis to investigate differences between the genome of strain M6 and the genome of the group II model strain AAC00-1. The draft genome sequence of A. citrulli M6 harbors 139 contigs, with an overall approximate size of 4.85 Mb. The genome of M6 is ∼500 Kb shorter than that of strain AAC00-1. Comparative analysis revealed that this size difference is mainly explained by eight fragments, ranging from ∼35-120 Kb and distributed throughout the AAC00-1 genome, which are absent in the M6 genome. In agreement with this finding, while AAC00-1 was found to possess 532 open reading frames (ORFs) that are absent in strain M6, only 123 ORFs in M6 were absent in AAC00-1. Most of these M6 ORFs are hypothetical proteins and most of them were also detected in two group I strains that were recently sequenced, tw6 and pslb65. Further analyses by PCR assays and coverage analyses with other A. citrulli strains support the notion that some of these fragments or significant portions of them are discriminative between groups I and II strains of A. citrulli. Moreover, GC content, effective number of codon values and cluster of orthologs' analyses indicate that these fragments were introduced into group II strains by horizontal gene transfer events. Our study reports the genome sequence of a model group I strain of A. citrulli, one of the most important pathogens of cucurbits. It also provides the first comprehensive comparison at the genomic level between the

  12. Bacterial curli protein promotes the conversion of PAP248-286 into the amyloid SEVI: cross-seeding of dissimilar amyloid sequences

    Directory of Open Access Journals (Sweden)

    Kevin Hartman

    2013-02-01

    Full Text Available Fragments of prostatic acid phosphatase (PAP248-286 in human semen dramatically increase HIV infection efficiency by increasing virus adhesion to target cells. PAP248-286 only enhances HIV infection in the form of amyloid aggregates termed SEVI (Semen Enhancer of Viral Infection, however monomeric PAP248-286 aggregates very slowly in isolation. It has therefore been suggested that SEVI fiber formation in vivo may be promoted by exogenous factors. We show here that a bacterially-produced extracellular amyloid (curli or Csg acts as a catalytic agent for SEVI formation from PAP248-286 at low concentrations in vitro, producing fibers that retain the ability to enhance HIV (Human Immunodeficiency Virus infection. Kinetic analysis of the cross-seeding effect shows an unusual pattern. Cross-seeding PAP248-286 with curli only moderately affects the nucleation rate while significantly enhancing the growth of fibers from existing nuclei. This pattern is in contrast to most previous observations of cross-seeding, which show cross-seeding partially bypasses the nucleation step but has little effect on fiber elongation. Seeding other amyloidogenic proteins (IAPP (islet amyloid polypeptide and Aβ1−40 with curli showed varied results. Curli cross-seeding decreased the lag-time of IAPP amyloid formation but strongly inhibited IAPP elongation. Curli cross-seeding exerted a complicated concentration dependent effect on Aβ1−40 fibrillogenesis kinetics. Combined, these results suggest that the interaction of amyloidogenic proteins with preformed fibers of a different type can take a variety of forms and is not limited to epitaxial nucleation between proteins of similar sequence. The ability of curli fibers to interact with proteins of dissimilar sequences suggests cross-seeding may be a more general phenomenon than previously supposed.

  13. Carbon transformations in deep granitic groundwater by attached bacterial populations characterized with 16S-rRNA gene sequencing technique and scanning electron microscopy

    International Nuclear Information System (INIS)

    This report presents molecular characterization of attached bacterial populations growing in slowly flowing (1-3 mm s-1) artesian groundwater from deep crystalline bed-rock of the Stripa research mine, south central Sweden. The assimilation rate of CO2 and lactate, and the lactate respiration rates were also determined. The bacteria studied grew in anoxic, high pH, 9-10, and low redox artesian groundwater flowing up through tubings from two levels of a borehole designated V2, 812-820 m and 970-1240 m below ground. The major groups of bacteria were found. Signature bases placed them in the appropriate systematic groups. All belonged to the Proteobacterial groups beta and gamma. One group was found only at the 812-820 m level, where it constituted 63% of the sequenced clones, whereas the second group existed almost exclusively and constituted 85% of the sequenced clones at the 970-1240 m level. The third group was equally distributed between the levels. A few other bacteria were also found. None of the 16S-rRNA genes from the dominating bacteria resembled any of the other by more than 90% similarity, and none of them resembled anything in the database by more than 96%. Temperature did not seem to have any effect on species composition at the deeper level. SEM images showed rods appearing in microcolonies. The difference in population diversity between the two levels studied presumably reflect the different environments. The earlier proposed presence of sulphate reducing bacteria could no be confirmed

  14. Multilocus sequence analysis of the marine bacterial genus Tenacibaculum suggests parallel evolution of fish pathogenicity and endemic colonization of aquaculture systems.

    Science.gov (United States)

    Habib, Christophe; Houel, Armel; Lunazzi, Aurélie; Bernardet, Jean-François; Olsen, Anne Berit; Nilsen, Hanne; Toranzo, Alicia E; Castro, Nuria; Nicolas, Pierre; Duchaud, Eric

    2014-09-01

    The genus Tenacibaculum, a member of the family Flavobacteriaceae, is an abundant component of marine bacterial ecosystems that also hosts several fish pathogens, some of which are of serious concern for marine aquaculture. Here, we applied multilocus sequence analysis (MLSA) to 114 representatives of most known species in the genus and of the worldwide diversity of the major fish pathogen Tenacibaculum maritimum. Recombination hampers precise phylogenetic reconstruction, but the data indicate intertwined environmental and pathogenic lineages, which suggests that pathogenicity evolved independently in several species. At lower phylogenetic levels recombination is also important, and the species T. maritimum constitutes a cohesive group of isolates. Importantly, the data reveal no trace of long-distance dissemination that could be linked to international fish movements. Instead, the high number of distinct genotypes suggests an endemic distribution of strains. The MLSA scheme and the data described in this study will help in monitoring Tenacibaculum infections in marine aquaculture; we show, for instance, that isolates from tenacibaculosis outbreaks in Norwegian salmon farms are related to T. dicentrarchi, a recently described species. PMID:24973065

  15. Insecticide control of vector-borne diseases : when is insecticide resistance a problem ?

    OpenAIRE

    Rivero, Ana; Vézilier, Julien; Weill, Mylène; Read, Andrew F.; Gandon, Sylvain

    2010-01-01

    Many of the most dangerous human diseases are transmitted by insect vectors. After decades of repeated insecticide use, all of these vector species have demonstrated the capacity to evolve resistance to insecticides. Insecticide resistance is generally considered to undermine control of vector-transmitted diseases because it increases the number of vectors that survive the insecticide treatment. Disease control failure, however, need not follow from vector control failure. Here, we review evi...

  16. The risk of insecticides to pollinating insects

    OpenAIRE

    Connolly, Christopher N.

    2013-01-01

    A key new risk to our pollinators has been identified as exposure to neonicotinoid insecticides. These discoveries have refuelled the debate over whether or not the neonicotinoid insecticides should be banned and conflicting evidence is used in this battle. However, the issue is not black or white, but gray. It is not an issue of whether the neonicotinoids are toxic to insects or not. Clearly, all insecticides were designed and optimized for this attribute. The real question is, or at least s...

  17. Prenatal Insecticide Exposure and Children's Cognitive Development

    OpenAIRE

    Gaspar, Fraser William

    2014-01-01

    Although approximately 123 million people may be exposed to high levels of insecticides through the use of indoor residual spraying (IRS) for malaria control, very little data exists on exposure levels and risk to residents. In addition, certain populations may be more susceptible to the unintended health effects of insecticide exposure from IRS including the developing fetus. The aims of this dissertation were as follows: 1) build indoor transport and fate models to estimate insecticide expo...

  18. Analysis of bacterial DNA in synovial tissue of Tunisian patients with reactive and undifferentiated arthritis by broad-range PCR, cloning and sequencing

    OpenAIRE

    Siala, Mariam; Jaulhac, Benoit; Gdoura, Radhouane; Sibilia, Jean; Fourati, Hela; Younes, Mohamed; Baklouti, Sofien; Bargaoui, Naceur; Sellami, Slaheddine; Znazen, Abir; Barthel, Cathy; Collin, Elody; Hammami, Adnane; Sghir, Abdelghani

    2008-01-01

    Introduction Bacteria and/or their antigens have been implicated in the pathogenesis of reactive arthritis (ReA). Several studies have reported the presence of bacterial antigens and nucleic acids of bacteria other than those specified by diagnostic criteria for ReA in joint specimens from patients with ReA and various arthritides. The present study was conducted to detect any bacterial DNA and identify bacterial species that are present in the synovial tissue of Tunisian patients with reacti...

  19. Long-term exposure of bacterial and protozoan communities to TiO2 nanoparticles in an aerobic-sequencing batch reactor

    Science.gov (United States)

    Supha, Chitpisud; Boonto, Yuphada; Jindakaraked, Manee; Ananpattarachai, Jirapat; Kajitvichyanukul, Puangrat

    2015-06-01

    Titanium dioxide (TiO2) nanopowders at different concentrations (0-50 mg L-1) were injected into an aerobic-sequencing batch reactor (SBR) to investigate the effects of long-term exposure to nanoparticles on bacterial and protozoan communities. The detection of nanoparticles in the bioflocs was analyzed by scanning electron microscopy, transmission electron microscopy, and energy-dispersive x-ray spectroscopy. The SBR wastewater experiments were conducted under the influence of ultraviolet light with photocatalytic TiO2. The intrusion of TiO2 nanoparticles was found both on the surface and inside of the bioflocs. The change of microbial population in terms of mixed liquor-suspended solids and the sludge volume index was monitored. The TiO2 nanoparticles tentatively exerted an adverse effect on the microbial population, causing the reduction of microorganisms (both bacteria and protozoa) in the SBR. The respiration inhibition rate of the bacteria was increased, and the viability of the microbial population was reduced at the high concentration (50 mg L-1) of TiO2. The decreasing number of protozoa in the presence of TiO2 nanoparticles during 20 days of treatment with 0.5 and 1.0 mg L-1 TiO2 is clearly demonstrated. The measured chemical oxygen demand (COD) in the effluent tends to increase with a long-term operation. The increase of COD in the system suggests a decrease in the efficiency of the wastewater treatment plant. However, the SBR can effectively remove the TiO2 nanoparticles (up to 50 mg L-1) from the effluent.

  20. Using trap crops for control of Acalymma vittatum (Coleoptera: Chrysomelidae) reduces insecticide use in butternut squash.

    Science.gov (United States)

    Cavanagh, A; Hazzard, R; Adler, L S; Boucher, J

    2009-06-01

    Striped cucumber beetle, Acalymma vittatum F., is the primary insect pest of cucurbit crops in the northeastern United States. Adult beetles colonize squash crops from field borders, causing feeding damage at the seedling stage and transmitting bacterial wilt Erwinia tracheiphila Hauben et al. 1999. Conventional control methods rely on insecticide applications to the entire field, but surrounding main crops with a more attractive perimeter could reduce reliance on insecticides. A. cittatum shows a marked preference for Blue Hubbard squash (Cucurbita maxima Duchesne) over butternut squash (C. moschata Poir). Given this preference, Blue Hubbard squash has the potential to be an effective perimeter trap crop. We evaluated this system in commercial butternut fields in 2003 and 2004, comparing fields using perimeter trap cropping with Blue Hubbard to conventionally managed fields. In 2003, we used a foliar insecticide to control beetles in the trap crop borders, and in 2004, we compared systemic and foliar insecticide treatments for the trap crop borders. We found that using a trap crop system reduced or eliminated the need to spray the main crop area, reducing insecticide use by up to 94% compared with conventional control methods, with no increase in herbivory or beetle numbers. We surveyed the growers who participated in these experiments and found a high level of satisfaction with the effectiveness and simplicity of the system. These results suggest that this method of pest control is both effective and simple enough in its implementation to have high potential for adoption among growers. PMID:19610425

  1. Organophosphorus and carbamate insecticide poisoning.

    Science.gov (United States)

    Vale, Allister; Lotti, Marcello

    2015-01-01

    Both organophosphorus (OP) and carbamate insecticides inhibit acetylcholinesterase (AChE), which results in accumulation of acetylcholine (ACh) at autonomic and some central synapses and at autonomic postganglionic and neuromuscular junctions. As a consequence, ACh binds to, and stimulates, muscarinic and nicotinic receptors, thereby producing characteristic features. With OP insecticides (but not carbamates), "aging" may also occur by partial dealkylation of the serine group at the active site of AChE; recovery of AChE activity requires synthesis of new enzyme in the liver. Relapse after apparent resolution of cholinergic symptoms has been reported with OP insecticides and is termed the intermediate syndrome. This involves the onset of muscle paralysis affecting particularly upper-limb muscles, neck flexors, and cranial nerves some 24-96 hours after OP exposure and is often associated with the development of respiratory failure. OP-induced delayed neuropathy results from phosphorylation and subsequent aging of at least 70% of neuropathy target esterase. Cramping muscle pain in the lower limbs, distal numbness, and paresthesiae are followed by progressive weakness, depression of deep tendon reflexes in the lower limbs and, in severe cases, in the upper limbs. The therapeutic combination of oxime, atropine, and diazepam is well established experimentally in the treatment of OP pesticide poisoning. However, there has been controversy as to whether oximes improve morbidity and mortality in human poisoning. The explanation may be that the solvents in many formulations are primarily responsible for the high morbidity and mortality; oximes would not be expected to reduce toxicity in these circumstances. even if given in appropriate dose. PMID:26563788

  2. Insecticide Resistance Reducing Effectiveness of Malaria Control

    Centers for Disease Control (CDC) Podcasts

    2007-01-24

    Malaria prevention is increasingly insecticide based. Dr. John Gimnig, an entomologist with the Division of Parasitic Diseases, CDC, discusses evidence that mosquito resistance to insecticides, which is measured in the laboratory, could compromise malaria prevention in the field.  Created: 1/24/2007 by Emerging Infectious Diseases.   Date Released: 3/13/2007.

  3. Insecticide Recommendations for Arkansas. MP 144.

    Science.gov (United States)

    Jones, Bill F.; Barnes, Gordon

    This publication gives, in chart form, insecticides for use on animals, field crops, fruits, flowers, trees and shrubs, household pests, recreation areas, lawn and turf grass, pecans, stored grain, and vegetables. Included in the charts are the insecticides recommended for each insect, formulation to be used, amount, time to apply, and other…

  4. Insecticidal compounds from Kalanchoe daigremontiana x tubiflora.

    Science.gov (United States)

    Supratman, U; Fujita, T; Akiyama, K; Hayashi, H

    2001-09-01

    Methyl daigremonate, an insecticidal bufadienolide, was isolated from the leaves of Kalanchoe daigremontianaxtubiflora (Crassulaceae) along with four known bufadienolides. Its structure was established by spectroscopic analysis, and insecticidal activities were assessed against the third instar larvae of silkworm (Bombyx mori). The results suggest that the orthoester and alpha-pyrone moieties played an important role in the activity. PMID:11551556

  5. Poisoning by organophosphorus insecticides and sensory neuropathy

    OpenAIRE

    Moretto, A; M. Lotti

    1998-01-01

    OBJECTIVES—Poisoning by organophosphate insecticides causes cholinergic toxicity. Organophosphate induced delayed polyneuropathy (OPIDP) is a sensory-motor distal axonopathy which usually occurs after ingestion of large doses of certain organophosphate insecticides and has so far only been reported in patients with preceding cholinergic toxicity. Surprisingly, it was recently reported by other authors that an exclusively sensory neuropathy developed in eight patients afte...

  6. Natural factors as potential insecticides

    International Nuclear Information System (INIS)

    In order to reduce environmental pollution, it is of great interest to find alternative methods for controlling insect pests. With the progress made in the isolation and identification of peptides and endogenous toxins from insects, the question can be raised whether or not these natural factors are potentially useful as insecticides. The aim of the present study was to test certain toxins and myotropic peptides isolated from insects for their usefulness as insecticides. Over twenty neuropeptides isolated from different insect species have been isolated and identified in the laboratory. To date, tests have been carried out on the influence of four neuropeptides on the food intake of L1 larvae of Mamestra brassicae. Also, the crude haemolymph, as well as some of the purified fractions of the Colorado potato beetle, have been tested. At least one of the neuropeptides and some of the compounds present in the haemolymph and the purified fraction D have a negative influence on the development of L1 larvae of M. brassicae after oral intake. (author). 6 refs, 1 fig

  7. Calibrating bacterial evolution

    OpenAIRE

    Ochman, Howard; Elwyn, Susannah; Moran, Nancy A

    1999-01-01

    Attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. Despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal appl...

  8. Genome-wide Screening Reveals the Genetic Determinants of an Antibiotic Insecticide in Bacillus thuringiensis*

    OpenAIRE

    Liu, Xiao-Yan; Ruan, Li-Fang; Hu, Zhen-Fei; Peng, Dong-hai; Cao, Shi-Yun; Yu, Zi-Niu; Liu, Yao; Zheng, Jin-Shui; Sun, Ming

    2010-01-01

    Thuringiensin is a thermostable secondary metabolite in Bacillus thuringiensis and has insecticidal activity against a wide range of insects. Until now, the regulatory mechanisms and genetic determinants involved in thuringiensin production have remained unclear. Here, we successfully used heterologous expression-guided screening in an Escherichia coli–Bacillus thuringiensis shuttle bacterial artificial chromosome library, to clone the intact thuringiensin synthesis (thu) cluster. Then the th...

  9. Bacterial diversity analysis of Huanglongbing pathogen-infected citrus, using PhyloChip and 16S rRNA gene clone library sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Shankar Sagaram, U.; DeAngelis, K.M.; Trivedi, P.; Andersen, G.L.; Lu, S.-E.; Wang, N.

    2009-03-01

    The bacterial diversity associated with citrus leaf midribs was characterized 1 from citrus groves that contained the Huanglongbing (HLB) pathogen, which has yet to be cultivated in vitro. We employed a combination of high-density phylogenetic 16S rDNA microarray and 16S rDNA clone library sequencing to determine the microbial community composition of symptomatic and asymptomatic citrus midribs. Our results revealed that citrus leaf midribs can support a diversity of microbes. PhyloChip analysis indicated that 47 orders of bacteria from 15 phyla were present in the citrus leaf midribs while 20 orders from phyla were observed with the cloning and sequencing method. PhyloChip arrays indicated that nine taxa were significantly more abundant in symptomatic midribs compared to asymptomatic midribs. Candidatus Liberibacter asiaticus (Las) was detected at a very low level in asymptomatic plants, but was over 200 times more abundant in symptomatic plants. The PhyloChip analysis was further verified by sequencing 16S rDNA clone libraries, which indicated the dominance of Las in symptomatic leaves. These data implicate Las as the pathogen responsible for HLB disease. Citrus is the most important commercial fruit crop in Florida. In recent years, citrus Huanglongbing (HLB), also called citrus greening, has severely affected Florida's citrus production and hence has drawn an enormous amount of attention. HLB is one of the most devastating diseases of citrus (6,13), characterized by blotchy mottling with green islands on leaves, as well as stunting, fruit decline, and small, lopsided fruits with poor coloration. The disease tends to be associated with a phloem-limited fastidious {alpha}-proteobacterium given a provisional Candidatus status (Candidatus Liberobacter spp. later changed to Candidatus Liberibacter spp.) in nomenclature (18,25,34). Previous studies indicate that HLB infection causes disorder in the phloem and severely impairs the translocation of assimilates in

  10. Culturable bacterial microbiota of Plagiodera versicolora (L.) (Coleoptera: Chrysomelidae) and virulence of the isolated strains.

    Science.gov (United States)

    Demirci, Meryem; Sevim, Elif; Demir, İsmail; Sevim, Ali

    2013-05-01

    Plagiodera versicolora (Laicharting, 1781) (Coleoptera: Chrysomelidae) is an important forest pest which damages many trees such as willow, poplar, and hazelnut. In order to find new microbes that can be utilized as a possible microbial control agent against this pest, we investigated the culturable bacterial flora of it and tested the isolated bacteria against P. versicolora larvae and adults. We were able to isolate nine bacteria from larvae and adults. The isolates were characterized using a combination of morphological, biochemical, and physiological methods. Additionally, we sequenced the partial sequence of the 16S rRNA gene to verify conventional identification results. Based on characterization studies, the isolates were identified as Staphylococcus sp. Pv1, Rahnella sp. Pv2, Rahnella sp. Pv3, Rahnella sp. Pv4, Rahnella sp. Pv5, Pantoea agglomerans Pv6, Staphylococcus sp. Pv7, Micrococcus luteus Pv8, and Rahnella sp. Pv9. The highest insecticidal activity against larvae and adults was obtained from M. luteus Pv8 with 50 and 40 % mortalities within 10 days after treatment, respectively. Extracellular enzyme activity of the bacterial isolates such as amylase, proteinase, lipase, cellulose, and chitinase was also determined. Consequently, our results show that M. luteus Pv8 might be a good candidate as a possible microbial control agent against P. versicolora and were discussed with respect to biocontrol potential of the bacterial isolates. PMID:23054688

  11. Insertion sequences.

    OpenAIRE

    Mahillon, Jacques; Chandler, M.

    1998-01-01

    Insertion sequences (ISs) constitute an important component of most bacterial genomes. Over 500 individual ISs have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. The last 10 years have also seen some striking advances in our understanding of the transposition process itself. Not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryoti...

  12. An Indigenously Developed Insecticidal Aerosol

    Directory of Open Access Journals (Sweden)

    R. N. Varma

    1969-10-01

    Full Text Available A total of 6 "Test" insecticidal aerosols (TA-I to VI indigenously produced were tested during the years 1966-67 as suitable replacements for imported aerosols.TA-I produced deep yellow staining and a yellowish spray mist. Its capacity was only 120 ml fluid. TA-III types II and III containing modified aerosol formulation with "Esso solvent 3245" and mineral turpentine oil (Burmah Shelland Freon 12 11 (all indigenouswere comparable to he "SRA" in insecticidial efficacy. The container was also manufactured in the country and it compared well with the "SRA" in construction, resistance against rough usage and mechanical function. They were both finally approved for introduction in the services as replacement for imported aerosols. TA-IV performed well in inscticidial assessment, but the aerosols formulation. TA-V and VI were similar to TA-III types II and III respectively.

  13. Bacterial diversity assessment in soil of an active Brazilian copper mine using high-throughput sequencing of 16S rDNA amplicons.

    Science.gov (United States)

    Rodrigues, Viviane D; Torres, Tatiana T; Ottoboni, Laura M M

    2014-11-01

    Mining activities pose severe environmental risks worldwide, generating extreme pH conditions and high concentrations of heavy metals, which can have major impacts on the survival of organisms. In this work, pyrosequencing of the V3 region of the 16S rDNA was used to analyze the bacterial communities in soil samples from a Brazilian copper mine. For the analysis, soil samples were collected from the slopes (geotechnical structures) and the surrounding drainage of the Sossego mine (comprising the Sossego and Sequeirinho deposits). The results revealed complex bacterial diversity, and there was no influence of deposit geographic location on the composition of the communities. However, the environment type played an important role in bacterial community divergence; the composition and frequency of OTUs in the slope samples were different from those of the surrounding drainage samples, and Acidobacteria, Chloroflexi, Firmicutes, and Gammaproteobacteria were responsible for the observed difference. Chemical analysis indicated that both types of sample presented a high metal content, while the amounts of organic matter and water were higher in the surrounding drainage samples. Non-metric multidimensional scaling (N-MDS) analysis identified organic matter and water as important distinguishing factors between the bacterial communities from the two types of mine environment. Although habitat-specific OTUs were found in both environments, they were more abundant in the surrounding drainage samples (around 50 %), and contributed to the higher bacterial diversity found in this habitat. The slope samples were dominated by a smaller number of phyla, especially Firmicutes. The bacterial communities from the slope and surrounding drainage samples were different in structure and composition, and the organic matter and water present in these environments contributed to the observed differences. PMID:25129578

  14. Draft Genome Sequence of Pseudomonas stutzeri ODKF13, Isolated from Farmland Soil in Alvin, Texas

    OpenAIRE

    Iyer, Rupa; Damania, Ashish

    2016-01-01

    Pseudomonas stutzeri ODKF13 is a bacterial microorganism isolated from farmland soil in Alvin, Texas. This strain is notable for its naphthalene degradation and nitrogen fixation pathways and for its characterization as an organophosphate degrader of phosphotriester and phosphorothioate insecticides.

  15. Inhibition of aflatoxin production by selected insecticides.

    OpenAIRE

    Draughon, F A; Ayres, J. C.

    1981-01-01

    The insecticide naled completed inhibition production of aflatoxins B1, B2, G1, and G2 by and growth of Aspergillus parasiticus at a 100-ppm (100 microgram/ml) concentration. The insecticides dichlorvos, Landrin, pyrethrum, Sevin, malathion, and Diazinon significantly (P = 0.05) inhibited production of aflatoxins at a 100-ppm concentration. However, at a concentration of 10 ppm, significant inhibition in production of aflatoxins was found only with naled, dichlorvos, Sevin, Landrin, and pyret...

  16. Management of Insecticide Resistance: Adana Model

    OpenAIRE

    Alptekin, Davut

    2015-01-01

    Many diseases in the world have been transmitted to humans by insects. Chemical substances that are used against pests or insect vectors in agricultural production and public health are called pesticide. Insecticides are chemical substances or a group of substances used to kill Insects which are classified within pesticides forming the class of Insecta including any biological stage of insects (larva, pupa, adult). Insecticides are classified according to their effective biological stage (adu...

  17. Insecticide Resistanca in Maleria Vector An. sacharovi

    OpenAIRE

    Üniversitesi, Çukurova; ABD, Tıp Fakültesi Tıbbi Biyoloji; Balcalı,; Adana-TÜRKİYE,

    2000-01-01

    Susceptibility tests have been successfully used for many years to determine insecticide resistance raised in pest and vector insects, including An. sacharovi,the primary human malaria vector in Turkey. As this method does not provide sufficient information about physiological resistance, an alternative method of enzyme tests based on biochemical and genetic evaluations has been developed. In this study, both methods were used for comparison. First of all, susceptibility to insecticides w...

  18. Insecticidal sugar baits for adult biting midges.

    Science.gov (United States)

    Snyder, D; Cernicchiaro, N; Allan, S A; Cohnstaedt, L W

    2016-06-01

    The mixing of an insecticide with sugar solution creates an oral toxin or insecticidal sugar bait (ISB) useful for reducing adult insect populations. The ability of ISBs to kill the biting midge Culicoides sonorensis Wirth and Jones (Diptera: Ceratopogonidae), a vector of bluetongue virus, epizootic hemorrhagic disease and vesicular stomatitis viruses, was tested. The commercial insecticide formulations (percentage active ingredient) tested included bifenthrin, cyfluthrin, deltamethrin, permethrin, dinotefuran, imidacloprid, thiamethoxam and spinosad. Mortality rates were determined for various concentrations of commercial formulations (0.01, 0.05, 0.1, 1, 2 and 3%) and observed at 1, 4, 10 and 24 h post-exposure to the ISB. In the first set of assays, laboratory-reared midges were fed sugar ad libitum and then exposed to insecticide-treated sugar solutions to measure mortality. The second assay assessed competitive feeding: midges were provided with a control sugar solution (10% sucrose) in one vial, and a sugar and insecticide solution in another. Pyrethroid treatments resulted in the greatest mortality in the first hour at the lowest concentrations and spinosad consumption resulted in the least mortality. Biting midges were not deterred from feeding on the 1% ISB solutions despite the presence of an insecticide-free alternative source of sugar. PMID:26789534

  19. Draft Genome Sequence of Criibacterium bergeronii gen. nov., sp. nov., Strain CCRI-22567T, Isolated from a Vaginal Sample from a Woman with Bacterial Vaginosis.

    Science.gov (United States)

    Maheux, Andrée F; Bérubé, Ève; Boudreau, Dominique K; Raymond, Frédéric; Corbeil, Jacques; Roy, Paul H; Boissinot, Maurice; Omar, Rabeea F

    2016-01-01

    Criibacterium bergeronii gen. nov., sp. nov., CCRI-22567 is the type strain of the new genus Criibacterium The strain was isolated from a woman with bacterial vaginosis. The genome assembly comprised 2,384,460 bp, with 34.4% G+C content. This is the first genome announcement of a strain belonging to the genus Criibacterium. PMID:27587833

  20. Discovery of genes related to insecticide resistance in Bactrocera dorsalis by functional genomic analysis of a de novo assembled transcriptome.

    Directory of Open Access Journals (Sweden)

    Ju-Chun Hsu

    Full Text Available Insecticide resistance has recently become a critical concern for control of many insect pest species. Genome sequencing and global quantization of gene expression through analysis of the transcriptome can provide useful information relevant to this challenging problem. The oriental fruit fly, Bactrocera dorsalis, is one of the world's most destructive agricultural pests, and recently it has been used as a target for studies of genetic mechanisms related to insecticide resistance. However, prior to this study, the molecular data available for this species was largely limited to genes identified through homology. To provide a broader pool of gene sequences of potential interest with regard to insecticide resistance, this study uses whole transcriptome analysis developed through de novo assembly of short reads generated by next-generation sequencing (NGS. The transcriptome of B. dorsalis was initially constructed using Illumina's Solexa sequencing technology. Qualified reads were assembled into contigs and potential splicing variants (isotigs. A total of 29,067 isotigs have putative homologues in the non-redundant (nr protein database from NCBI, and 11,073 of these correspond to distinct D. melanogaster proteins in the RefSeq database. Approximately 5,546 isotigs contain coding sequences that are at least 80% complete and appear to represent B. dorsalis genes. We observed a strong correlation between the completeness of the assembled sequences and the expression intensity of the transcripts. The assembled sequences were also used to identify large numbers of genes potentially belonging to families related to insecticide resistance. A total of 90 P450-, 42 GST-and 37 COE-related genes, representing three major enzyme families involved in insecticide metabolism and resistance, were identified. In addition, 36 isotigs were discovered to contain target site sequences related to four classes of resistance genes. Identified sequence motifs were also

  1. Pyrethroid insecticides in municipal wastewater.

    Science.gov (United States)

    Weston, Donald P; Ramil, Heather L; Lydy, Michael J

    2013-11-01

    Pyrethroids are widely used insecticides, but minimal information has been published on their presence in municipal wastewater in the United States. Pyrethroids in wastewater from the Sacramento, California, USA, area consisted of permethrin, bifenthrin, cypermethrin, and cyhalothrin, with a combined concentration of 200 ng/L to 500 ng/L. Sampling within the wastewater collection system leading to the treatment plant suggested pyrethroids did not originate primarily from urban runoff, but could be from any of several drain disposal practices. Wastewater from residential areas was similar in pyrethroid composition and concentration to that from the larger metropolitan area as a whole. Secondary treatment removed approximately 90% of pyrethroids, but those remaining exceeded concentrations acutely toxic to sensitive species. Toxicity to the amphipod, Hyalella azteca, was consistently evident in the final effluent. The large river into which this particular plant discharged provided sufficient dilution such that pyrethroids were undetected in the river, and there was only slight toxicity of unknown cause in 1 river sample, but effects in receiving waters elsewhere will be site-specific. PMID:23893650

  2. Oxidative stress induced by chlorine dioxide as an insecticidal factor to the Indian meal moth, Plodia interpunctella.

    Science.gov (United States)

    Kumar, Sunil; Park, Jiyeong; Kim, Eunseong; Na, Jahyun; Chun, Yong Shik; Kwon, Hyeok; Kim, Wook; Kim, Yonggyun

    2015-10-01

    A novel fumigant, chlorine dioxide (ClO2) is a commercial bleaching and disinfection agent. Recent study indicates its insecticidal activity. However, its mode of action to kill insects is yet to be understood. This study set up a hypothesis that an oxidative stress induced by ClO2 is a main factor to kill insects. The Indian meal moth, Plodia interpunctella, is a lepidopteran insect pest infesting various stored grains. Larvae of P. interpunctella were highly susceptible to ClO2 gas, which exhibited an acute toxicity. Physiological damages by ClO2 were observed in hemocytes. At high doses, the larvae of P. interpunctella suffered significant reduction of total hemocytes. At low doses, ClO2 impaired hemocyte behaviors. The cytotoxicity of ClO2 was further analyzed using two insect cell lines, where Sf9 cells were more susceptible to ClO2 than High Five cells. The cells treated with ClO2 produced reactive oxygen species (ROS). The produced ROS amounts increased with an increase of the treated ClO2 amount. However, the addition of an antioxidant, vitamin E, significantly attenuated the cytotoxicity of ClO2 in a dose-dependent manner. To support the oxidative stress induced by ClO2, two antioxidant genes (superoxide dismutase (SOD) and thioredoxin-peroxidase (Tpx)) were identified from P. interpunctella EST library using ortholog sequences of Bombyx mori. Both SOD and Tpx were expressed in larvae of P. interpunctella especially under oxidative stress induced by bacterial challenge. Exposure to ClO2 gas significantly induced the gene expression of both SOD and Tpx. RNA interference of SOD or Tpx using specific double stranded RNAs significantly enhanced the lethality of P. interpunctella to ClO2 gas treatment as well as to the bacterial challenge. These results suggest that ClO2 induces the production of insecticidal ROS, which results in a fatal oxidative stress in P. interpunctella. PMID:26453230

  3. Examining marginal sequence similarities between bacterial type III secretion system components and Trypanosoma cruzi surface proteins: horizontal gene transfer or convergent evolution?

    OpenAIRE

    Silva, Danielle C. F.; Silva, Richard C.; Renata C Ferreira; Briones, Marcelo R. S.

    2013-01-01

    The cell invasion mechanism of Trypanosoma cruzi has similarities with some intracellular bacterial taxa especially regarding calcium mobilization. This mechanism is not observed in other trypanosomatids, suggesting that the molecules involved in this type of cell invasion were a product of (1) acquisition by horizontal gene transfer (HGT); (2) secondary loss in the other trypanosomatid lineages of the mechanism inherited since the bifurcation Bacteria-Neomura (1.9 billion to 900 million year...

  4. Genome Sequence of Bacillus thuringiensis subsp. kurstaki Strain HD-1

    OpenAIRE

    Day, Michael; Ibrahim, Mohamed; Dyer, David; Bulla, Lee

    2014-01-01

    We report here the complete genome sequence of Bacillus thuringiensis subsp. kurstaki strain HD-1, which serves as the primary U.S. reference standard for all commercial insecticidal formulations of B. thuringiensis manufactured around the world.

  5. Modeling global distribution of agricultural insecticides in surface waters

    International Nuclear Information System (INIS)

    Agricultural insecticides constitute a major driver of animal biodiversity loss in freshwater ecosystems. However, the global extent of their effects and the spatial extent of exposure remain largely unknown. We applied a spatially explicit model to estimate the potential for agricultural insecticide runoff into streams. Water bodies within 40% of the global land surface were at risk of insecticide runoff. We separated the influence of natural factors and variables under human control determining insecticide runoff. In the northern hemisphere, insecticide runoff presented a latitudinal gradient mainly driven by insecticide application rate; in the southern hemisphere, a combination of daily rainfall intensity, terrain slope, agricultural intensity and insecticide application rate determined the process. The model predicted the upper limit of observed insecticide exposure measured in water bodies (n = 82) in five different countries reasonably well. The study provides a global map of hotspots for insecticide contamination guiding future freshwater management and conservation efforts. - Highlights: • First global map on insecticide runoff through modelling. • Model predicts upper limit of insecticide exposure when compared to field data. • Water bodies in 40% of global land surface may be at risk of adverse effects. • Insecticide application rate, terrain slope and rainfall main drivers of exposure. - We provide the first global map on insecticide runoff to surface water predicting that water bodies in 40% of global land surface may be at risk of adverse effects

  6. Neurobehavioral toxicology of pyrethroid insecticides

    International Nuclear Information System (INIS)

    Pyrethroid insecticides are classified as either Type I or Type II based upon in vivo toxic signs, and neurophysiological and biochemical data. Both axonal sodium channels and the γ-aminobutyric acid (GABA) receptor complex have been proposed as the major site of action of the Type II pyrethroids. This investigation characterized the behavior and biochemical effects of low dosages of pyrethroids in rats. Type I and II pyrethroids were tested for effects on figure-eight maze activity and the acoustic startle response (ASR). All compounds decreased figure-eight maze activity. Interactions of Type I and II pyrethroids with the three major binding sites on the GABA complex were determined in vivo. Radioligand binding experiments assessed in vitro interactions of pyrethroids with the three major GABA-complex binding sites. None of the pyrethroids competed for [3H]-muscimol or [3H]-flunitrazepam binding. Only Type II pyrethroids inhibited binding of [35S]-t-butylbicyclophosphorothionate (TBPS) in cortical synaptosome preparations with K/sub i/ values of 5 to 10 μM. The [35S]-TBPS data implicate the TBPS/picrotoxinin binding site in the mechanism of Type II pyrethroid toxicity. The results of these experiments support the classification of pyrethroids into two classes, and demonstrate the utility of the figure-eight maze and the ASR in studies to elucidate neurotoxic mechanisms. The interaction of the Type II pyrethroids is probably restricted to the TBPS/picrotoxinin binding domain on the GABA complex as shown by both the in vivo and in vitro studies

  7. Design, synthesis and bioassay of new mosquito insecticides and repellents

    Science.gov (United States)

    New compounds and classes of compounds are needed to protect deployed military personnel from diseases transmitted by medically important arthropods. Historically, the synthetic insecticides and repellents have been effective tools for mosquito control. To develop new synthetic insecticides and repe...

  8. Differentially expressed genes of Coptotermes formosanus (Isoptera: Rhinotermitidae) challenged by chemical insecticides.

    Science.gov (United States)

    Zhang, Yi; Zhao, Yuanyuan; Qiu, Xuehong; Han, Richou

    2013-08-01

    Coptotermes formosanus Shiraki (Isoptera: Rhinotermitidae) termites are harmful social insects to wood constructions. The current control methods heavily depend on the chemical insecticides with increasing resistance. Analysis of the differentially expressed genes mediated by chemical insecticides will contribute to the understanding of the termite resistance to chemicals and to the establishment of alternative control measures. In the present article, a full-length cDNA library was constructed from the termites induced by a mixture of commonly used insecticides (0.01% sulfluramid and 0.01% triflumuron) for 24 h, by using the RNA ligase-mediated Rapid Amplification cDNA End method. Fifty-eight differentially expressed clones were obtained by polymerase chain reaction and confirmed by dot-blot hybridization. Forty-six known sequences were obtained, which clustered into 33 unique sequences grouped in 6 contigs and 27 singlets. Sixty-seven percent (22) of the sequences had counterpart genes from other organisms, whereas 33% (11) were undescribed. A Gene Ontology analysis classified 33 unique sequences into different functional categories. In general, most of the differential expression genes were involved in binding and catalytic activity. PMID:24020304

  9. Molecular and Insecticidal Characterization of a Cry1I Protein Toxic to Insects of the Families Noctuidae, Tortricidae, Plutellidae, and Chrysomelidae

    OpenAIRE

    Ruiz de Escudero, Iñigo; Estela, Anna; Porcar, Manuel; Martínez, Clara; Oguiza, José A.; Escriche, Baltasar; Ferré, Juan; Caballero, Primitivo

    2006-01-01

    The most notable characteristic of Bacillus thuringiensis is its ability to produce insecticidal proteins. More than 300 different proteins have been described with specific activity against insect species. We report the molecular and insecticidal characterization of a novel cry gene encoding a protein of the Cry1I group with toxic activity towards insects of the families Noctuidae, Tortricidae, Plutellidae, and Chrysomelidae. PCR analysis detected a DNA sequence with an open reading frame of...

  10. Electronic structure of pesticides: 1. Organochlorine insecticides

    Energy Technology Data Exchange (ETDEWEB)

    Novak, Igor, E-mail: inovak@csu.edu.au [Charles Sturt University, POB 883, Orange, NSW 2800 (Australia); Kovac, Branka [Physical Chemistry Division, ' R. Boskovic' Institute, HR-10000 Zagreb (Croatia)

    2011-11-15

    Highlights: {yields} Electronic structure of several organochlorine insecticides has been determined by UV photoelectron spectroscopy and high-level ab initio calculations. {yields} The electronic structure obtained from spectra has been related to their biological activity. {yields} The molecular modes of binding to appropriate receptors are rationalized in view of the molecule's electronic structure and conformational flexibility. - Abstract: The electronic structures of six organochlorine insecticides: {gamma}-lindane (I), aldrin (II), dieldrin (III), DDD (IV), DDE (V) and DDT (VI) have been investigated by UV photoelectron spectroscopy (UPS), quantum chemical calculations and comparison with molecular modelling studies. Their electronic and molecular structures are discussed in order to rationalize their biological activity. In this work we relate the biological activity of these insecticides to their experimentally observed electronic and molecular structures.

  11. Inhibition of aflatoxin production by selected insecticides.

    Science.gov (United States)

    Draughon, F A; Ayres, J C

    1981-04-01

    The insecticide naled completed inhibition production of aflatoxins B1, B2, G1, and G2 by and growth of Aspergillus parasiticus at a 100-ppm (100 microgram/ml) concentration. The insecticides dichlorvos, Landrin, pyrethrum, Sevin, malathion, and Diazinon significantly (P = 0.05) inhibited production of aflatoxins at a 100-ppm concentration. However, at a concentration of 10 ppm, significant inhibition in production of aflatoxins was found only with naled, dichlorvos, Sevin, Landrin, and pyrethrum. Dichlorvos, Landrin, Sevin, and naled inhibited growth of A. parasiticus by 28.9 , 18.9, 15.7, and 100%, respectively, at 100 ppm. Stimulation of growth was observed when diazinon was added to cultures. Aflatoxin B1 was most resistant to inhibition by insecticides, followed by G1, G2, and B2, respectively. PMID:6786222

  12. Amyloid fibril formation requires a chemically discriminating nucleation event: studies of an amyloidogenic sequence from the bacterial protein OsmB.

    Science.gov (United States)

    Jarrett, J T; Lansbury, P T

    1992-12-15

    The sequence of the Escherichia coli OsmB protein was found to resemble that of the C-terminal region of the beta amyloid protein of Alzheimer's disease, which seems to be the major determinant of its unusual structural and solubility properties. A peptide corresponding to residues 28-44 of the OsmB protein was synthesized, and its conformational properties and aggregation behavior were analyzed. The peptide OsmB(28-44) was shown to form amyloid fibrils, as did two sequence analogs designed to test the sequence specificity of fibril formation. These fibrils bound Congo red, and two of the peptides showed birefringence. The peptide fibrils were analyzed by electron microscopy and Fourier transform infrared spectroscopy. Subtle differences were observed which were not interpretable at the molecular level. The rate of fibril formation by each peptide was followed by monitoring the turbidity of supersaturated aqueous solutions. The kinetics of aggregation were characterized by a delay period during which the solution remained clear, followed by a nucleation event which led to a growth phase, during which the solution became viscous and turbid due to the presence of insoluble fibrils. The observation of a kinetic barrier to aggregation is typical of a crystallization event. The delay period could be eliminated by seeding the supersaturated solution with previously formed fibrils. Each peptide could be nucleated by fibrils formed from that same peptide, but not by fibrils from closely related sequences, suggesting that fibril growth requires specific hydrophobic interactions. It appears likely that this repeated sequence motif, which comprises most of the OsmB protein sequence, dictates the structure and possibly the function of that protein.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:1463722

  13. Sequence and transcription mapping of Bacillus subtilis competence genes comB and comA, one of which is related to a family of bacterial regulatory determinants.

    OpenAIRE

    Weinrauch, Y; Guillen, N.; Dubnau, D A

    1989-01-01

    The complete nucleotide sequences of the comA and comB loci of Bacillus subtilis were determined. The products of these genes are required for the development of competence in B. subtilis and for the expression of late-expressing competence genes. The major 5' termini of both the comA and comB transcripts were determined. The inferred promoters of both comA and comB contained sequences that were similar to those found at the -10 and -35 regions of promoters that are used by sigma A-RNA polyme...

  14. Composition and Metabolic Activities of the Bacterial Community in Shrimp Sauce at the Flavor-Forming Stage of Fermentation As Revealed by Metatranscriptome and 16S rRNA Gene Sequencings.

    Science.gov (United States)

    Duan, Shan; Hu, Xiaoxi; Li, Mengru; Miao, Jianyin; Du, Jinghe; Wu, Rongli

    2016-03-30

    The bacterial community and the metabolic activities involved at the flavor-forming stage during the fermentation of shrimp sauce were investigated using metatranscriptome and 16S rRNA gene sequencings. Results showed that the abundance of Tetragenococcus was 95.1%. Tetragenococcus halophilus was identified in 520 of 588 transcripts annotated in the Nr database. Activation of the citrate cycle and oxidative phosphorylation, along with the absence of lactate dehydrogenase gene expression, in T. halophilus suggests that T. halophilus probably underwent aerobic metabolism during shrimp sauce fermentation. The metabolism of amino acids, production of peptidase, and degradation of limonene and pinene were very active in T. halophilus. Carnobacterium, Pseudomonas, Escherichia, Staphylococcus, Bacillus, and Clostridium were also metabolically active, although present in very small populations. Enterococcus, Abiotrophia, Streptococcus, and Lactobacillus were detected in metatranscriptome sequencing, but not in 16S rRNA gene sequencing. Many minor taxa showed no gene expression, suggesting that they were in dormant status. PMID:26978261

  15. Complete Genome Sequence of a Gluconacetobacter hansenii ATCC 23769 Isolate, AY201, Producer of Bacterial Cellulose and Important Model Organism for the Study of Cellulose Biosynthesis

    Science.gov (United States)

    Mehta, Kalpa

    2016-01-01

    The cellulose producer and model organism used for the study of cellulose biosynthesis, Gluconacetobacter hansenii AY201, is a variant of G. hansenii ATCC 23769. We report here the complete nucleotide sequence of G. hansenii AY201, information which may be utilized to further the research into understanding the genes necessary for cellulose biosynthesis. PMID:27516506

  16. Draft Genome Sequence of a Copper-Resistant Marine Bacterium, Pantoea agglomerans Strain LMAE-2, a Bacterial Strain with Potential Use in Bioremediation.

    Science.gov (United States)

    Corsini, Gino; Valdés, Natalia; Pradel, Paulina; Tello, Mario; Cottet, Luis; Muiño, Laura; Karahanian, Eduardo; Castillo, Antonio; Gonzalez, Alex R

    2016-01-01

    Pantoea agglomerans LMAE-2 was isolated from seabed sediment moderately contaminated with Cu(2+) Here, we report its draft genome sequence, which has a size of 4.98 Mb. The presence of cop genes related with copper homeostasis in its genome may explain the resistance and strengthen its potential for use as bioremediation agent. PMID:27313292

  17. Complete Genome Sequence of a Gluconacetobacter hansenii ATCC 23769 Isolate, AY201, Producer of Bacterial Cellulose and Important Model Organism for the Study of Cellulose Biosynthesis.

    Science.gov (United States)

    Pfeffer, Sarah; Mehta, Kalpa; Brown, R Malcolm

    2016-01-01

    The cellulose producer and model organism used for the study of cellulose biosynthesis, Gluconacetobacter hansenii AY201, is a variant of G. hansenii ATCC 23769. We report here the complete nucleotide sequence of G. hansenii AY201, information which may be utilized to further the research into understanding the genes necessary for cellulose biosynthesis. PMID:27516506

  18. Effect of selected insecticides on SF9 insect cell line

    International Nuclear Information System (INIS)

    The toxic effect of three insecticides: dimethoate (organophosphate insecticide), acetamiprid (neonicotinoid insecticide) and deltamethrin (pyrethroid insecticide) were evaluated in vitro on cultured Sf9 cell line. Cell growth inhibition was measured by the 3- (4,5- dimethylthiazol - 2-yl) - 2,5 - diphenyl tetrazolium bromide (MTT) assay. Regression Analysis was used to estimate the 20% inhibition of cells growth (IC 20). The IC 20 values obtained for deltamethrin, acetamipridand dimethoate were: 46.8, 61.6 and 68.9 μM, respectively. The proportion of phagocytic cells was positively correlated with the applied concentrations of the insecticides. (author)

  19. Insecticide resistance selection in rice planthoppers

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ Brown planthopper (BPH, Nilaparvata lugens Stal) and white backed planthopper (WBPH, Sogatella furcifera Horvath) are the main insects on rice in China. The insecticide resistance of the two planthoppers have often been reported. Availability of the resistant population is a prerequisite for studying the resistance mechanism. In this paper, one method to select methamidophos resistance of the two planthoppers was recommended.

  20. Storage crambe seed treated with insecticides

    Directory of Open Access Journals (Sweden)

    Geraldo Cabral e Souza

    2014-02-01

    Full Text Available The use of low quality seeds with a lower physiological reflects one of the major causes of low productivity. Thus the storage conditions of seed must be taken into consideration. This research aimed to evaluate the influence of natural and synthetic insecticides on emergence and seed storage of crambe, as these substances are essential to prevent infestation of seeds of other species by harmful organisms. The experimental design was a randomized block in factorial 3 x 8 ( 8 substances and 3 storage times with 4 replications. We assessed the following natural insecticides: saffron, lime, ash, neem, diatomaceous earth, and synthetic: chlorpyrifos and deltamethrin; besides the control consisting of seeds without any treatment. We evaluated the percentage of emergence, speed of emergence index and time to reach 50 % of emergency. In all characteristics, it was found that no influence of neem on seed vigor. There are disadvantages in the application of the insecticides chlorpyrifos and diatomaceous earth, which interfered with the emergence rate of seeds of crambe. The seeds treated with other insecticides had different behavior of untreated seeds after 120 days of storage to assess the time that they take to reach 50 % germination.

  1. Possibilities of Botanical Insecticides in Plant Protection

    Czech Academy of Sciences Publication Activity Database

    Pavela, R.; Sajfrtová, Marie; Sovová, Helena; Bárnet, M.

    2008-01-01

    Roč. 2, č. 1 (2008), s. 16-23. ISSN 1313-2563 Grant ostatní: MŠk(CZ) 2B08049 Institutional support: RVO:67985858 Keywords : botanical insecticides * plant extracts * supercritical fluid extraction Subject RIV: GF - Plant Pathology, Vermin, Weed, Plant Protection

  2. Possibilities of Botanical Insecticides in Plant Protection

    Czech Academy of Sciences Publication Activity Database

    Pavela, R.; Sajfrtová, Marie; Sovová, Helena; Bárnet, M.

    2008-01-01

    Roč. 2, č. 1 (2008), s. 16-23. ISSN 1313-2563 Grant ostatní: GA MŠMT(CZ) 2B08049 Institutional research plan: CEZ:AV0Z40720504 Keywords : botanical insecticides * plant exctracts * supercritical fluid extraction Subject RIV: GF - Plant Pathology, Vermin, Weed, Plant Protection

  3. 16S rDNA sequence analysis of bacterial isolates from biodeteriorated mural paintings in the Servilia tomb (Necropolis of carmona, Seville, Spain).

    Science.gov (United States)

    Heyrman, J; Swings, J

    2001-11-01

    Bacteria were isolated from damaged mural paintings of the Servilia tomb (necropolis of Carmona, Seville, Spain). Selected strains, representative for different clusters of isolates with similar fatty acid profiles, were analysed by 16S rDNA sequence analysis. Bacillus is the dominant genus among the isolates: members of the rRNA species complexes of B. megaterium, B. pumilus and B. firmus were found as well as several other Bacillus species. One group of halotolerant isolates falls in the Bacillus sensu lato group, with closest relatedness to the genera Salibacillus and Virgibacillus. Other genera found are Artbrobacter, Micrococcus, Streptomyces, Sphingomonas, Paenibacillus, and a genus closely related to Paracraurococcus. Many isolates showed low 16S rDNA sequence similarities with the closest related database entries, a strong indication for the presence of several new species among the isolates. PMID:11822679

  4. Draft Genome Sequence of Flavobacterium sp. Strain TAB 87, Able To Inhibit the Growth of Cystic Fibrosis Bacterial Pathogens Belonging to the Burkholderia cepacia Complex.

    Science.gov (United States)

    Presta, Luana; Inzucchi, Ilaria; Bosi, Emanuele; Fondi, Marco; Perrin, Elena; Miceli, Elisangela; Tutino, Maria Luisa; Lo Giudice, Angelina; de Pascale, Donatella; Fani, Renato

    2016-01-01

    We report here the draft genome sequence of the Flavobacterium sp. TAB 87 strain, isolated from Antarctic seawater during a summer campaign near the French Antarctic station Dumont d'Urville (60°40'S, 40°01'E). It will allow for comparative genomics and the fulfillment of both fundamental and application-oriented investigations. It allowed the recognition of genes associated with the production of bioactive compounds and antibiotic resistance. PMID:27198032

  5. Insecticide-induced hormesis and arthropod pest management.

    Science.gov (United States)

    Guedes, Raul Narciso C; Cutler, G Christopher

    2014-05-01

    Ecological backlashes such as insecticide resistance, resurgence and secondary pest outbreaks are frequent problems associated with insecticide use against arthropod pest species. The last two have been particularly important in sparking interest in the phenomenon of insecticide-induced hormesis within entomology and acarology. Hormesis describes a biphasic dose-response relationship that is characterized by a reversal of response between low and high doses of a stressor (e.g. insecticides). Although the concept of insecticide-induced hormesis often does not receive sufficient attention, or has been subject to semantic confusion, it has been reported in many arthropod pest species and natural enemies, and has been linked to pest outbreaks and potential problems with insecticide resistance. The study of hormesis remains largely neglected in entomology and acarology. Here, we examined the concept of insecticide-induced hormesis in arthropods, its functional basis and potential fitness consequences, and its importance in arthropod pest management and other areas. PMID:24155227

  6. Bacterial Vaginosis

    Science.gov (United States)

    ... 586. Related Content STDs during Pregnancy Fact Sheet Pregnancy and HIV, Viral Hepatitis, and STD Prevention Pelvic Inflammatory Disease ( ... Bacterial Vaginosis (BV) Chlamydia Gonorrhea Genital Herpes Hepatitis HIV/AIDS & STDs Human Papillomavirus ... STDs See Also Pregnancy Reproductive ...

  7. Bacterial Meningitis

    Science.gov (United States)

    ... Schedules Preteen & Teen Vaccines Meningococcal Disease Sepsis Bacterial Meningitis Recommend on Facebook Tweet Share Compartir On this ... serious disease. Laboratory Methods for the Diagnosis of Meningitis This manual summarizes laboratory methods used to isolate, ...

  8. Prostatitis - bacterial

    Science.gov (United States)

    Any bacteria that can cause a urinary tract infection can cause acute bacterial prostatitis. Infections spread through sexual contact can cause prostatitis. These include chlamydia and gonorrhea . Sexually transmitted ...

  9. Bacterial Conjunctivitis

    OpenAIRE

    Köhle, Ülkü; Kükner, Şahap

    2003-01-01

    Conjunctivitis is an infection of the conjunctiva, generally characterized by irritation, itching, foreign body sensation, tearing and discharge. Bacterial conjunctivitis may be distinguished from other types of conjunctivitis by the presence of yellow–white mucopurulent discharge. It is the most common form of ocular infection all around the world. Staphylococcus species are the most common bacterial pathogenes, followed by Streptococcus pneumoniae and Haemophilus i...

  10. Identifying the fundamental units of bacterial diversity: A paradigm shift to incorporate ecology into bacterial systematics

    OpenAIRE

    Koeppel, Alexander; Perry, Elizabeth B.; Sikorski, Johannes; Krizanc, Danny; Warner, Andrew; Ward, David M.; Rooney, Alejandro P.; Brambilla, Evelyne; Connor, Nora; Ratcliff, Rodney M.; Nevo, Eviatar; Cohan, Frederick M

    2008-01-01

    The central questions of bacterial ecology and evolution require a method to consistently demarcate, from the vast and diverse set of bacterial cells within a natural community, the groups playing ecologically distinct roles (ecotypes). Because of a lack of theory-based guidelines, current methods in bacterial systematics fail to divide the bacterial domain of life into meaningful units of ecology and evolution. We introduce a sequence-based approach (“ecotype simulation”) to model the evolut...

  11. Cultivation-independent methods reveal differences among bacterial gut microbiota in triatomine vectors of Chagas disease.

    Directory of Open Access Journals (Sweden)

    Fabio Faria da Mota

    Full Text Available BACKGROUND: Chagas disease is a trypanosomiasis whose agent is the protozoan parasite Trypanosoma cruzi, which is transmitted to humans by hematophagous bugs known as triatomines. Even though insecticide treatments allow effective control of these bugs in most Latin American countries where Chagas disease is endemic, the disease still affects a large proportion of the population of South America. The features of the disease in humans have been extensively studied, and the genome of the parasite has been sequenced, but no effective drug is yet available to treat Chagas disease. The digestive tract of the insect vectors in which T. cruzi develops has been much less well investigated than blood from its human hosts and constitutes a dynamic environment with very different conditions. Thus, we investigated the composition of the predominant bacterial species of the microbiota in insect vectors from Rhodnius, Triatoma, Panstrongylus and Dipetalogaster genera. METHODOLOGY/PRINCIPAL FINDINGS: Microbiota of triatomine guts were investigated using cultivation-independent methods, i.e., phylogenetic analysis of 16s rDNA using denaturing gradient gel electrophoresis (DGGE and cloned-based sequencing. The Chao index showed that the diversity of bacterial species in triatomine guts is low, comprising fewer than 20 predominant species, and that these species vary between insect species. The analyses showed that Serratia predominates in Rhodnius, Arsenophonus predominates in Triatoma and Panstrongylus, while Candidatus Rohrkolberia predominates in Dipetalogaster. CONCLUSIONS/SIGNIFICANCE: The microbiota of triatomine guts represents one of the factors that may interfere with T. cruzi transmission and virulence in humans. The knowledge of its composition according to insect species is important for designing measures of biological control for T. cruzi. We found that the predominant species of the bacterial microbiota in triatomines form a group of low

  12. Insecticide tolerance of Culex nigripalpus in Florida.

    Science.gov (United States)

    Boike, A H; Rathburn, C B; Floore, T G; Rodriguez, H M; Coughlin, J S

    1989-12-01

    Larval susceptibility tests of Culex nigripalpus populations from various areas of Florida have shown resistance to several organophosphorus insecticides since 1984. Although the degree of resistance is low (2 to 7 times), it can be termed tolerance and appears to be the greatest for fenthion, followed by temephos, naled and malathion. It is suggested that pesticide runoff from lawns, golf courses and agricultural and urban areas may play a role in developing resistance in Florida mosquito populations. PMID:2614401

  13. Insecticide control in a Dengue epidemics model

    CERN Document Server

    Rodrigues, Helena Sofia; Torres, Delfim F M

    2010-01-01

    A model for the transmission of dengue disease is presented. It consists of eight mutually-exclusive compartments representing the human and vector dynamics. It also includes a control parameter (insecticide) in order to fight the mosquitoes. The main goal of this work is to investigate the best way to apply the control in order to effectively reduce the number of infected humans and mosquitoes. A case study, using data of the outbreak that occurred in 2009 in Cape Verde, is presented.

  14. Ryania Speciosa: an insecticide for organic orchards?

    OpenAIRE

    Kelderer, Markus; Sgarbossa, Manuela; Schönweger, Gudrun; Elias, Ellen; Roland, Zelger; Santer, Johann; Stuppner, Hermann

    2004-01-01

    Ryania speciosa is a grove belonging to the family Flacourtiacea, located in tropical climates in Central- and South- America. The Indigenous population used the plant, which contains toxic alkaloids, against cockroaches. In the forties the ground wood was used as insecticide against different pests. In the first version of annex 2b from the EC regulation 2092/91, Ryania was still listed, but it was subsequently cancelled due to its lack of registration as a pesticide in any Eu...

  15. Bacterial carbonatogenesis

    International Nuclear Information System (INIS)

    Several series of experiments in the laboratory as well as in natural conditions teach that the production of carbonate particles by heterotrophic bacteria follows different ways. The 'passive' carbonatogenesis is generated by modifications of the medium that lead to the accumulation of carbonate and bicarbonate ions and to the precipitation of solid particles. The 'active' carbonatogenesis is independent of the metabolic pathways. The carbonate particles are produced by ionic exchanges through the cell membrane following still poorly known mechanisms. Carbonatogenesis appears to be the response of heterotrophic bacterial communities to an enrichment of the milieu in organic matter. The active carbonatogenesis seems to start first. It is followed by the passive one which induces the growth of initially produced particles. The yield of heterotrophic bacterial carbonatogenesis and the amounts of solid carbonates production by bacteria are potentially very high as compared to autotrophic or chemical sedimentation from marine, paralic or continental waters. Furthermore, the bacterial processes are environmentally very ubiquitous; they just require organic matter enrichment. Thus, apart from purely evaporite and autotrophic ones, all Ca and/or Mg carbonates must be considered as from heterotrophic bacterial origin. By the way, the carbon of carbonates comes from primary organic matter. Such considerations ask questions about some interpretations from isotopic data on carbonates. Finally, bacterial heterotrophic carbonatogenesis appears as a fundamental phase in the relationships between atmosphere and lithosphere and in the geo-biological evolution of Earth. (author)

  16. Insecticide resistance in Bemisia tabaci from Cyprus

    Institute of Scientific and Technical Information of China (English)

    Vassilis Vassiliou; Maria Emmanouilidou; Andreas Perrakis; Evangelia Morou; John Vontas; Anastasia Tsagkarakou; Emmanouil Roditakis

    2011-01-01

    A comprehensive study on the Bemisia tabaci(biotype B)resistance to neonicotinoid insecticides imidacloprid,acetamiprid and thiamethoxam,and pyrethroid bifenthrin was conducted in Cyprus.The resistance level to eight field-collected B.tabaci populations was investigated.The activities of enzymes involved in metabolic detoxification and the frequencies of pyrethroid and organophosphates target site resistance mutations were determined.Moderate to high levels of resistance were detected for imidacloprid(resistance factor[RF]77-392)and thiamethoxam(RF 50-164)while low resistance levels were observed for acetamiprid(RF 7-12).Uniform responses by the Cypriot whiteflies could be observed against all neonicotinoid insecticides.No cross-resistance between the neonicotinoids was detected as well as no association with the activity of the P450 microsomal oxidases.Only imidacloprid resistance correlated with carboxylesterase activity.Low to extremely high resistance was observed for insecticide bifenthrin(RF 49-1 243)which was associated with the frequency of the resistant allele in the sodium channel gene but not with the activity of the detoxification enzymes.Finally,the F331W mutation in the acetylcholinesterase enzyme ace1 gene was fixed in all B.tabaci populations from Cyprus.

  17. Insecticide Resistance and Management Strategies in Urban Ecosystems

    Science.gov (United States)

    Zhu, Fang; Lavine, Laura; O’Neal, Sally; Lavine, Mark; Foss, Carrie; Walsh, Douglas

    2016-01-01

    The increased urbanization of a growing global population makes imperative the development of sustainable integrated pest management (IPM) strategies for urban pest control. This emphasizes pests that are closely associated with the health and wellbeing of humans and domesticated animals. Concurrently there are regulatory requirements enforced to minimize inadvertent exposures to insecticides in the urban environment. Development of insecticide resistance management (IRM) strategies in urban ecosystems involves understanding the status and mechanisms of insecticide resistance and reducing insecticide selection pressure by combining multiple chemical and non-chemical approaches. In this review, we will focus on the commonly used insecticides and molecular and physiological mechanisms underlying insecticide resistance in six major urban insect pests: house fly, German cockroach, mosquitoes, red flour beetle, bed bugs and head louse. We will also discuss several strategies that may prove promising for future urban IPM programs. PMID:26751480

  18. Accepted 15 March 2012Available online 20 May 2012%Insecticidal, antimicrobial and antioxidant activities of bulb extracts of Allium sativum

    Institute of Scientific and Technical Information of China (English)

    Balaji Meriga; Ramgopal Mopuri; T MuraliKrishna

    2012-01-01

    ABSTRACT Objective:To evaluate the insecticidal, antimicrobial and antioxidant activities of bulb extracts ofAllium sativum(A. sativum).Methods:Dried bulbs ofA. sativum were extracted with different solvents and evaluated for insecticidal, antimicrobial and antioxidant activities.Results:Aqueous and methanol extracts showed highest insecticidal activity (mortality rate of81% and 64% respectively) against the larvae ofSpodoptera litura (S. litura) at a concentration of1 000 ppm. With regard to antimicrobial activity, aqueous extract exhibited antibacterial activity against gram positive (Bacillus subtilis, Staphylococcus aureu,) and gram negative (Escherichia coliandKlebsiella pneumonia) strains and antifungal activity againstCandida albicans. While methanol extract showed antimicrobial activity against all the tested micro organisms except two (Staphylococcus aureus andCandida albicans), the extracts of hexane, chloroform and ethyl acetate did not show any anti microbial activity. Minimum inhibitory concentration of aqueous and methanol extracts against tested bacterial and fungal strains was100-150 μg/mL. Antioxidant activity of the bulb extracts was evaluated in terms of inhibition of free radicals by 2, 2’-diphenly-1-picrylhydrazyl. Aqueous and methanol extracts exhibited strong antioxidant activity(80%-90% of the standard).Conclusions: Antioxidant and antimicrobial activity of A. sativum against the tested organisms therefore, provides scientific basis for its utilization in traditional and folk medicine. Also, our results demonstrated the insecticidal efficacy ofA. sativum againstS. litura, a polyphagous insect.

  19. Comprehensive phylogenetic analysis of bacterial reverse transcriptases.

    Directory of Open Access Journals (Sweden)

    Nicolás Toro

    Full Text Available Much less is known about reverse transcriptases (RTs in prokaryotes than in eukaryotes, with most prokaryotic enzymes still uncharacterized. Two surveys involving BLAST searches for RT genes in prokaryotic genomes revealed the presence of large numbers of diverse, uncharacterized RTs and RT-like sequences. Here, using consistent annotation across all sequenced bacterial species from GenBank and other sources via RAST, available from the PATRIC (Pathogenic Resource Integration Center platform, we have compiled the data for currently annotated reverse transcriptases from completely sequenced bacterial genomes. RT sequences are broadly distributed across bacterial phyla, but green sulfur bacteria and cyanobacteria have the highest levels of RT sequence diversity (≤85% identity per genome. By contrast, phylum Actinobacteria, for which a large number of genomes have been sequenced, was found to have a low RT sequence diversity. Phylogenetic analyses revealed that bacterial RTs could be classified into 17 main groups: group II introns, retrons/retron-like RTs, diversity-generating retroelements (DGRs, Abi-like RTs, CRISPR-Cas-associated RTs, group II-like RTs (G2L, and 11 other groups of RTs of unknown function. Proteobacteria had the highest potential functional diversity, as they possessed most of the RT groups. Group II introns and DGRs were the most widely distributed RTs in bacterial phyla. Our results provide insights into bacterial RT phylogeny and the basis for an update of annotation systems based on sequence/domain homology.

  20. Mixture for Controlling Insecticide-Resistant Malaria Vectors

    OpenAIRE

    Pennetier, Cédric; Costantini, Carlo; Corbel, Vincent; Licciardi, Séverine; Dabiré, Roch K.; Lapied, Bruno; Chandre, Fabrice; Hougard, Jean-Marc

    2008-01-01

    The spread of resistance to pyrethroids in the major Afrotropical malaria vectors Anopheles gambiae s.s. necessitates the development of new strategies to control resistant mosquito populations. To test the efficacy of nets treated with repellent and insecticide against susceptible and insecticide-resistant An. gambiae mosquito populations, we impregnated mosquito bed nets with an insect repellent mixed with a low dose of organophosphorous insecticide and tested them in a rice-growing area ne...

  1. Virus and calcium : an unexpected tandem to optimize insecticide efficacy

    OpenAIRE

    Apaire-Marchais, V; Ogliastro, M.; Chandre, Fabrice; Pennetier, Cédric; Raymond, V; Lapied, B

    2016-01-01

    The effective control of insect pests is based on the rational use of the most efficient and safe insecticide treatments. To increase the effects of classical insecticides and to avoid the ability of certain pest insects to develop resistance, it is essential to propose novel strategies. Previous studies have shown that calcium-dependent phosphorylation/dephosphorylation is now considered as a new cellular mechanism for increasing the target sensitivity to insecticides. Because it is known th...

  2. Innovative applications for insect viruses : towards insecticide sensitization

    OpenAIRE

    Lapied, B; Pennetier, Cédric; Apaire Marchais, V.; P. Licznar; Corbel, Vincent

    2009-01-01

    The effective management of emerging insect-borne disease is dependent on the use of safe and efficacious chemical insecticides. Given the inherent ability of insects to develop resistance, it is essential to propose innovative strategies because insecticides remain the most important element of integrated approaches to vector control. Recently, intracellular phosphorylation and dephosphorylation of membrane receptors and ion channels targeted by insecticides have been described as new proces...

  3. A critical review of neonicotinoid insecticides for developmental neurotoxicity

    OpenAIRE

    Sheets, Larry P.; Li, Abby A.; Minnema, Daniel J.; Collier, Richard H.; Creek, Moire R.; Peffer, Richard C.

    2015-01-01

    Abstract A comprehensive review of published and previously unpublished studies was performed to evaluate the neonicotinoid insecticides for evidence of developmental neurotoxicity (DNT). These insecticides have favorable safety profiles, due to their preferential affinity for nicotinic receptor (nAChR) subtypes in insects, poor penetration of the mammalian blood–brain barrier, and low application rates. Nevertheless, examination of this issue is warranted, due to their insecticidal mode of a...

  4. Fungal infection counters insecticide resistance in African malaria mosquitoes

    OpenAIRE

    Farenhorst, M.; J. C. Mouatcho; Kikankie, C.K.; Brooke, B.D.; Hunt, R. H.; M. B. Thomas; Koekemoer, L.L.; Knols, B.G.J.; M. Coetzee

    2009-01-01

    The evolution of insecticide resistance in mosquitoes is threatening the effectiveness and sustainability of malaria control programs in various parts of the world. Through their unique mode of action, entomopathogenic fungi provide promising alternatives to chemical control. However, potential interactions between fungal infection and insecticide resistance, such as cross-resistance, have not been investigated. We show that insecticide-resistant Anopheles mosquitoes remain susceptible to inf...

  5. Essential Oil Yield Pattern and Antibacterial and Insecticidal Activities of Trachyspermum ammi and Myristica fragrans.

    Science.gov (United States)

    Soni, Rajgovind; Sharma, Gaurav; Jasuja, Nakuleshwar Dut

    2016-01-01

    Two Indian spices, Trachyspermum ammi and Myristica fragrans, were studied for their essential oil (EO) yielding pattern, insecticidal activity, antibacterial activity, and composition. The essential oils (EOs) of T. ammi (1.94 ± 30 mL/100 gm) and M. fragrans (5.93 ± 90 mL/100 gm) were extracted using hydrodistillation method. In Gas Chromatography analysis, the beta-pinene, alpha-pinene, alpha-p-menth-1-en-4-ol, Limonene, and elemicin were found as major constituents of T. ammi essential oil whereas M. fragrans essential oil mostly contains Gamma-Terpinolene, p-Cymene, Thymol, and beta-pinene. The insecticidal activities of EO were demonstrated using LC50 values against Plodia interpunctella and EO of T. ammi was found comparatively more effective than EO of M. fragrans. Further, individual EO and combination of essential oil were examined for antibacterial activity against three Gram (-) bacterial strains (E. coli-MTCC 443, P. vulgaris-MTCC 1771, and K. pneumoniae-MTCC number 7028) and three Gram (+) bacterial strains (S. aureus-MTCC 3381, B. subtilis-MTCC 10619, and B. megaterium-MTCC 2412) by well agar diffusion method. The essential oil in combination (CEO) exhibited higher antibacterial activity as compared with individual essential oils. PMID:27190677

  6. Essential Oil Yield Pattern and Antibacterial and Insecticidal Activities of Trachyspermum ammi and Myristica fragrans

    Science.gov (United States)

    Sharma, Gaurav

    2016-01-01

    Two Indian spices, Trachyspermum ammi and Myristica fragrans, were studied for their essential oil (EO) yielding pattern, insecticidal activity, antibacterial activity, and composition. The essential oils (EOs) of T. ammi (1.94 ± 30 mL/100 gm) and M. fragrans (5.93 ± 90 mL/100 gm) were extracted using hydrodistillation method. In Gas Chromatography analysis, the beta-pinene, alpha-pinene, alpha-p-menth-1-en-4-ol, Limonene, and elemicin were found as major constituents of T. ammi essential oil whereas M. fragrans essential oil mostly contains Gamma-Terpinolene, p-Cymene, Thymol, and beta-pinene. The insecticidal activities of EO were demonstrated using LC50 values against Plodia interpunctella and EO of T. ammi was found comparatively more effective than EO of M. fragrans. Further, individual EO and combination of essential oil were examined for antibacterial activity against three Gram (−) bacterial strains (E. coli-MTCC 443, P. vulgaris-MTCC 1771, and K. pneumoniae-MTCC number 7028) and three Gram (+) bacterial strains (S. aureus-MTCC 3381, B. subtilis-MTCC 10619, and B. megaterium-MTCC 2412) by well agar diffusion method. The essential oil in combination (CEO) exhibited higher antibacterial activity as compared with individual essential oils. PMID:27190677

  7. The use of insecticides to control insect pests

    Directory of Open Access Journals (Sweden)

    M Wojciechowska

    2016-07-01

    Full Text Available Pesticides are used as plants protection products. Among those, insecticides serve as agents to control insects. When incorrectly applied, however these substances may negatively affect people's health and natural environment. Administration routes of insecticides depend on many factors and vary from spraying to fertilizers. These different methods influence how insects prey and how pests develop. Additionally, too frequent use of the same chemicals can lead to development of resistance of insects to these insecticides. In order to prevent occurrence of negative effects of insecticides on surroundings, the effects of these compounds should be studied

  8. Insecticide Mixtures Could Enhance the Toxicity of Insecticides in a Resistant Dairy Population of Musca domestica L

    OpenAIRE

    Hafiz Azhar Ali Khan; Waseem Akram; Sarfraz Ali Shad; Jong-Jin Lee

    2013-01-01

    House flies, Musca domestica L., are important pests of dairy operations worldwide, with the ability to adapt wide range of environmental conditions. There are a number of insecticides used for their management, but development of resistance is a serious problem. Insecticide mixtures could enhance the toxicity of insecticides in resistant insect pests, thus resulting as a potential resistance management tool. The toxicity of bifenthrin, cypermethrin, deltamethrin, chlorpyrifos, profenofos, em...

  9. Bacterial Adhesion & Blocking Bacterial Adhesion

    DEFF Research Database (Denmark)

    Vejborg, Rebecca Munk

    2008-01-01

    parameters, which influence the transition from a planktonic lifestyle to a sessile lifestyle, have been studied. Protein conditioning film formation was found to influence bacterial adhesion and subsequent biofilm formation considerable, and an aqueous extract of fish muscle tissue was shown to...... tract to the microbial flocs in waste water treatment facilities. Microbial biofilms may however also cause a wide range of industrial and medical problems, and have been implicated in a wide range of persistent infectious diseases, including implantassociated microbial infections. Bacterial adhesion is...... the first committing step in biofilm formation, and has therefore been intensely scrutinized. Much however, still remains elusive. Bacterial adhesion is a highly complex process, which is influenced by a variety of factors. In this thesis, a range of physico-chemical, molecular and environmental...

  10. Bacterial lipases

    NARCIS (Netherlands)

    Jaeger, Karl-Erich; Ransac, Stéphane; Dijkstra, Bauke W.; Colson, Charles; Heuvel, Margreet van; Misset, Onno

    1994-01-01

    Many different bacterial species produce lipases which hydrolyze esters of glycerol with preferably long-chain fatty acids. They act at the interface generated by a hydrophobic lipid substrate in a hydrophilic aqueous medium. A characteristic property of lipases is called interfacial activation, mea

  11. Bacterial Ecology

    DEFF Research Database (Denmark)

    Fenchel, Tom

    2011-01-01

    Bacterial ecology is concerned with the interactions between bacteria and their biological and nonbiological environments and with the role of bacteria in biogeochemical element cycling. Many fundamental properties of bacteria are consequences of their small size. Thus, they can efficiently exploit...

  12. Recent advances in bacterial heme protein biochemistry

    OpenAIRE

    Mayfield, Jeffery A.; Dehner, Carolyn A.; Dubois, Jennifer L.

    2011-01-01

    Recent progress in genetics, fed by the burst in genome sequence data, has led to the identification of a host of novel bacterial heme proteins that are now being characterized in structural and mechanistic terms. The following short review highlights very recent work with bacterial heme proteins involved in the uptake, biosynthesis, degradation, and use of heme in respiration and sensing.

  13. The insecticide resistance in two planthoppers from three areas to three insecticides

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    @@ Migrating insects brown planthopper (BPH), Nilaparata lugens Stal and white-backed planthopper (WBPH), Sogatellafurcifera Horvath are both most harmful insects on rice in China. Chemical control is thought to be the best way to manage them, but it may cause insecticide resistance.

  14. Characterization of insecticidal peptides from venom Australian funnel-web spiders

    Directory of Open Access Journals (Sweden)

    E. J. Vonorax

    2006-04-01

    Full Text Available Australian funnel-web spiders are relatively large primitive hunting spiders. Male Atrax robustus spiders have been responsible for a number of human deaths. Venom was collected from the species Hadronyche infensa (Hickman [female], H. formidabilis [male and female], H. versuta [female], and A. robustus (Cambridge [male] and was fractionated by high performance liquid chromatography. This resulted in the isolation and purification of a homologous series of 7 insecticidal peptides of relatively low molecular mass (approximately 4kDa. The amino acid sequences of these toxins consisted of 36 or 37 amino acids and were named atracotoxins. For the major bioassay of these toxins, we used the cotton bollworm, Helicoverpa armigera (Hubner, due to the great damage it causes to crops worldwide. These toxins, when injected subcutaneously into fifth or sixth instar larvae of Helicoverpa armigera,were lethal or caused an apparently irreversible writhing. The toxin from H. versuta venom showed no significant toxicity when subcutaneously injected into newborn mice. One of the toxins was found to have a free acid carboxyl terminus. These toxins have great potential as lead compounds for insecticide design or for incorporation in recombinant baculovirus insecticides.

  15. Isolation, characterization, and insecticidal activity of an endophyte of drunken horse grass, Achnatherum inebrians.

    Science.gov (United States)

    Shi, YingWu; Zhang, Xuebing; Lou, Kai

    2013-01-01

    Abstract Endophytic microorganisms reside within plant tissues and have often been found to promote plant growth. In this study, endophytic microorganisms were isolated from the roots, stems, leaves, and seeds of healthy drunken horse grass, Achnatherum inebrians (Hance) Keng (Poales: Poaceae), through the use of a grinding separation method and identified by a dual approach of morphological and physiological observation and 16S rRNA gene-based (for bacteria) and internal transcribed sequence-based (for fungi) molecular identification. The endophytes were then inoculated into liquid media for fermentation, and their crude extracts were employed for insecticidal activity tests using slide disc immersion and nebulization methods. A total of 89 bacteria species, which were classified into eight genera, Bacillus, Pseudomonas, Actinomyces, Corynebacterium, Acinetobacter, Sphingomonas, Paenibacillus, and Phyllobacterium, and two fungi, Claviceps and Chaetomium, were isolated. Of these species, isolates Streptomyces albus (Rossi-Doria) Waksman and Henrici (Actinomycetales: Streptomycetaceae) (GA) and Claviceps purpurea (Fr.) Tul. (Hypocreales: Clavicipitaceae) (PF-2) were shown to produce mortality rates of more than 90% in the cotton aphid, Aphis gossypii Glover (Hemiptera: Aphididae), after first and second screenings. The isolates PF-2 and GA associated with A. inebrians had significant insecticidal activities towards A. gossypii Glover (Hemiptera: Aphididae) and may provide a new biological resource for exploring a new microbial insecticide. PMID:24784492

  16. MITIGATION OF PYRETHROID INSECTICIDES IN A MISSISSIPPI DELTA CONSTRUCTED WETLAND

    Science.gov (United States)

    Pyrethroid insecticides are commonly used in intensively cultivated agricultural areas for crop pest control. During storm runoff events, these insecticides may be transported into aquatic receiving systems where they have the potential to damage fish and invertebrates. Constructed wetlands are on...

  17. ANDROGEN RECEPTOR ANTAGONISM BY THE ORGANOPHOSPHATE INSECTICIDE FENITROTHION

    Science.gov (United States)

    Androgen receptor antagonism by the organophosphate insecticide fenitrothion. Tamura, H., Maness, S.C., Reischmann, K. Dorman, D.C., Gray, L.E., and Gaido, K.W. (2000). Toxicol. Sci. Organophosphate insecticides represent one of the most widely used classes of pesticide...

  18. INSECTICIDE CONCENTRATIONS IN AIR AFTER APPLICATION OF PEST CONTROL STRIPS

    Science.gov (United States)

    Contamination of air in homes due to spraying of pesticides is of concern to the public. A pest control strip which kills creeping and crawling insects by contact is one method of reducing the amount of insecticide in the air. Several different insecticides are now available in t...

  19. Conifer flavonoid compounds inhibit detoxification enzymes and synergize insecticides.

    Science.gov (United States)

    Wang, Zhiling; Zhao, Zhong; Cheng, Xiaofei; Liu, Suqi; Wei, Qin; Scott, Ian M

    2016-02-01

    Detoxification by glutathione S-transferases (GSTs) and esterases are important mechanisms associated with insecticide resistance. Discovery of novel GST and esterase inhibitors from phytochemicals could provide potential new insecticide synergists. Conifer tree species contain flavonoids, such as taxifolin, that inhibit in vitro GST activity. The objectives were to test the relative effectiveness of taxifolin as an enzyme inhibitor and as an insecticide synergist in combination with the organophosphorous insecticide, Guthion (50% azinphos-methyl), and the botanical insecticide, pyrethrum, using an insecticide-resistant Colorado potato beetle (CPB) Leptinotarsa decemlineata (Say) strain. Both taxifolin and its isomer, quercetin, increased the mortality of 1(st) instar CPB larvae after 48h when combined with Guthion, but not pyrethrum. Taxifolin had greater in vitro esterase inhibition compared with the commonly used esterase inhibitor, S, S, S-tributyl phosphorotrithioate (DEF). An in vivo esterase and GST inhibition effect after ingestion of taxifolin was measured, however DEF caused a greater suppression of esterase activity. This study demonstrated that flavonoid compounds have both in vitro and in vivo esterase inhibition, which is likely responsible for the insecticide synergism observed in insecticide-resistant CPB. PMID:26821651

  20. Design, Synthesis and Insecticidal Activities of Novel Phenyl Substituted Isoxazolecarboxamides

    Institute of Scientific and Technical Information of China (English)

    LIU Peng-fei; ZHANG Ji-feng; YAN Tao; XIONG Li-xia; LI Zheng-ming

    2012-01-01

    Thirteen novel phenyl substituted isoxazolecarboxamides were synthesized,and their structures were characterized by 1H NMR,elementary analysis and high-resolution mass spectrometry(HRMS) techniques.Their evaluated insecticidal activities against oriental armyworm(Mythimna separata) indicate that the phcnyl substituted isoxazolecarboxamides exhibited moderate insecticidal activities,among which compounds 9c and 9k showed comparatively higher activities.

  1. Interactions of transgenic Bacillus thuringiensis insecticidal crops with spiders (Araneae)

    Science.gov (United States)

    Genetically modified crops expressing insecticidal proteins from Bacillus thuringiensis (Bt) have dramatically increased in acreage since their introduction in the mid-1990’s. Although the insecticidal mechanisms of Bt target specific pests, concerns persist regarding direct and indirect effects on...

  2. Effects of organophosphorus insecticides on sage grouse in southeastern Idaho

    Science.gov (United States)

    Blus, L.J.; Staley, C.S.; Henny, C.J.; Pendleton, G.W.; Craig, T.H.; Craig, E.H.; Halford, D.K.

    1989-01-01

    Unverified reports indicated die-offs of sage grouse have occurred since the 1970s in southeastern Idaho. Some verification that organophosphorus insecticides were involved was obtained in 1981 and 1983. A radio telemetry study indicated that dimethoate was responsible for most mortality. Methamidophos also acounted for mortality. Sage grouse populations may be adversely affected by organophosphorus insecticides.

  3. [Bacterial vaginosis].

    Science.gov (United States)

    Romero Herrero, Daniel; Andreu Domingo, Antonia

    2016-07-01

    Bacterial vaginosis (BV) is the main cause of vaginal dysbacteriosis in the women during the reproductive age. It is an entity in which many studies have focused for years and which is still open for discussion topics. This is due to the diversity of microorganisms that cause it and therefore, its difficult treatment. Bacterial vaginosis is probably the result of vaginal colonization by complex bacterial communities, many of them non-cultivable and with interdependent metabolism where anaerobic populations most likely play an important role in its pathogenesis. The main symptoms are an increase of vaginal discharge and the unpleasant smell of it. It can lead to serious consequences for women, such as an increased risk of contracting sexually transmitted infections including human immunodeficiency virus and upper genital tract and pregnancy complications. Gram stain is the gold standard for microbiological diagnosis of BV, but can also be diagnosed using the Amsel clinical criteria. It should not be considered a sexually transmitted disease but it is highly related to sex. Recurrence is the main problem of medical treatment. Apart from BV, there are other dysbacteriosis less characterized like aerobic vaginitis of which further studies are coming slowly but are achieving more attention and consensus among specialists. PMID:27474242

  4. Botanical insecticides inspired by plant-herbivore chemical interactions.

    Science.gov (United States)

    Miresmailli, Saber; Isman, Murray B

    2014-01-01

    Plants have evolved a plethora of secondary chemicals to protect themselves against herbivores and pathogens, some of which have been used historically for pest management. The extraction methods used by industry render many phytochemicals ineffective as insecticides despite their bioactivity in the natural context. In this review, we examine how plants use their secondary chemicals in nature and compare this with how they are used as insecticides to understand why the efficacy of botanical insecticides can be so variable. If the commercial production of botanical insecticides is to become a viable pest management option, factors such as production cost, resource availability, and extraction and formulation techniques need be considered alongside innovative application technologies to ensure consistent efficacy of botanical insecticides. PMID:24216132

  5. Insecticidal sesquiterpene from Alpinia oxyphylla against Drosophila melanogaster.

    Science.gov (United States)

    Miyazawa, M; Nakamura, Y; Ishikawa, Y

    2000-08-01

    In the course of screening for novel naturally occurring insecticides from Chinese crude drugs, an MeOH extract of Alpinia oxyphylla was found to possess insecticidal activity against larvae of Drosophila melanogaster Meigen. From the extract, an insecticidal compound was isolated by bioassay-guided fractionation and identified as nootkatone (1) by GC, GC-MS, and (1)H and (13)C NMR spectroscopy. In bioassays for insecticidal activity, 1 showed an LC(50) value of 11.5 micromol/mL of diet against larvae of D. melanogaster and an LD(50) value of 96 microg/adult against adults. Epinootkatol (1A), however, showed slight insecticidal activity in both assays, indicating that the carbonyl group at the 2-position in 1 was the important function for enhanced activity of 1. PMID:10956162

  6. An Operational Framework for Insecticide Resistance Management Planning

    Science.gov (United States)

    Chanda, Emmanuel; Thomsen, Edward K.; Musapa, Mulenga; Kamuliwo, Mulakwa; Brogdon, William G.; Norris, Douglas E.; Masaninga, Freddie; Wirtz, Robert; Sikaala, Chadwick H.; Muleba, Mbanga; Craig, Allen; Govere, John M.; Ranson, Hilary; Hemingway, Janet; Seyoum, Aklilu; Macdonald, Michael B.

    2016-01-01

    Arthropod vectors transmit organisms that cause many emerging and reemerging diseases, and their control is reliant mainly on the use of chemical insecticides. Only a few classes of insecticides are available for public health use, and the increased spread of insecticide resistance is a major threat to sustainable disease control. The primary strategy for mitigating the detrimental effects of insecticide resistance is the development of an insecticide resistance management plan. However, few examples exist to show how to implement such plans programmatically. We describe the formulation and implementation of a resistance management plan for mosquito vectors of human disease in Zambia. We also discuss challenges, steps taken to address the challenges, and directions for the future. PMID:27089119

  7. Averting a malaria disaster: will insecticide resistance derail malaria control?

    Science.gov (United States)

    Hemingway, Janet; Ranson, Hilary; Magill, Alan; Kolaczinski, Jan; Fornadel, Christen; Gimnig, John; Coetzee, Maureen; Simard, Frederic; Roch, Dabiré K; Hinzoumbe, Clément Kerah; Pickett, John; Schellenberg, David; Gething, Peter; Hoppé, Mark; Hamon, Nicholas

    2016-04-23

    World Malaria Day 2015 highlighted the progress made in the development of new methods of prevention (vaccines and insecticides) and treatment (single dose drugs) of the disease. However, increasing drug and insecticide resistance threatens the successes made with existing methods. Insecticide resistance has decreased the efficacy of the most commonly used insecticide class of pyrethroids. This decreased efficacy has increased mosquito survival, which is a prelude to rising incidence of malaria and fatalities. Despite intensive research efforts, new insecticides will not reach the market for at least 5 years. Elimination of malaria is not possible without effective mosquito control. Therefore, to combat the threat of resistance, key stakeholders need to rapidly embrace a multifaceted approach including a reduction in the cost of bringing new resistance management methods to market and the streamlining of associated development, policy, and implementation pathways to counter this looming public health catastrophe. PMID:26880124

  8. New perspectives on bacterial ferredoxin evolution

    Science.gov (United States)

    George, D. G.; Hunt, L. T.; Yeh, L.-S. L.; Barker, W. C.

    1985-01-01

    Ferredoxins are low-molecular-weight, nonheme, iron proteins which function as electron carriers in a wide variety of electron transport chains. Howard et al. (1983) have suggested that the amino end of Azotobacter vinelandii ferredoxin shows a greater similarity to the carboxyl end of ferredoxin from Chromatium vinosum and that their half-chain sequences are homologous when the half-chains of either species are considered in inverse order. Examination of this proposition has made it necessary to reevaluate previous conclusions concerning the evolution of bacterial ferredoxin. Attention is given to the properties of the bacterial ferredoxin sequences, and the evolution of the bacterial ferredoxins.

  9. A Bacillus thuringiensis insecticidal crystal protein with a high activity against members of the family Noctuidae.

    OpenAIRE

    Lambert, B.; Buysse, L; Decock, C.; Jansens, S.; Piens, C; Saey, B; Seurinck, J; Van Audenhove, K; Van Rie, J.; A. van Vliet; Peferoen, M.

    1996-01-01

    The full characterization of a novel insecticidal crystal protein, named Cry9Ca1 according to the revised nomenclature for Cry proteins, from Bacillus thuringiensis serovar tolworthi is reported. The crystal protein has 1,157 amino acids and a molecular mass of 129.8 kDa. It has the typical features of the Lepidoptera-active crystal proteins such as five conserved sequence blocks. Also, it is truncated upon trypsin digestion to a toxic fragment of 68.7 kDa by removal of 43 amino acids at the ...

  10. Molecular Characterization of Epiphytic Bacterial Communities on Charophycean Green Algae

    OpenAIRE

    Fisher, Madeline M.; Wilcox, Lee W.; Linda E Graham

    1998-01-01

    Epiphytic bacterial communities within the sheath material of three filamentous green algae, Desmidium grevillii, Hyalotheca dissiliens, and Spondylosium pulchrum (class Charophyceae, order Zygnematales), collected from a Sphagnum bog were characterized by PCR amplification, cloning, and sequencing of 16S ribosomal DNA. A total of 20 partial sequences and nine different sequence types were obtained, and one sequence type was recovered from the bacterial communities on all three algae. By phyl...

  11. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense.

    Directory of Open Access Journals (Sweden)

    Guoxia Liu

    Full Text Available Chemosensory proteins (CSPs are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1 was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde. This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity.

  12. Molecular basis of the remarkable species selectivity of an insecticidal sodium channel toxin from the African spider Augacephalus ezendami

    Science.gov (United States)

    Herzig, Volker; Ikonomopoulou, Maria; Smith, Jennifer J.; Dziemborowicz, Sławomir; Gilchrist, John; Kuhn-Nentwig, Lucia; Rezende, Fernanda Oliveira; Moreira, Luciano Andrade; Nicholson, Graham M.; Bosmans, Frank; King, Glenn F.

    2016-01-01

    The inexorable decline in the armament of registered chemical insecticides has stimulated research into environmentally-friendly alternatives. Insecticidal spider-venom peptides are promising candidates for bioinsecticide development but it is challenging to find peptides that are specific for targeted pests. In the present study, we isolated an insecticidal peptide (Ae1a) from venom of the African spider Augacephalus ezendami (family Theraphosidae). Injection of Ae1a into sheep blowflies (Lucilia cuprina) induced rapid but reversible paralysis. In striking contrast, Ae1a was lethal to closely related fruit flies (Drosophila melanogaster) but induced no adverse effects in the recalcitrant lepidopteran pest Helicoverpa armigera. Electrophysiological experiments revealed that Ae1a potently inhibits the voltage-gated sodium channel BgNaV1 from the German cockroach Blattella germanica by shifting the threshold for channel activation to more depolarized potentials. In contrast, Ae1a failed to significantly affect sodium currents in dorsal unpaired median neurons from the American cockroach Periplaneta americana. We show that Ae1a interacts with the domain II voltage sensor and that sensitivity to the toxin is conferred by natural sequence variations in the S1–S2 loop of domain II. The phyletic specificity of Ae1a provides crucial information for development of sodium channel insecticides that target key insect pests without harming beneficial species. PMID:27383378

  13. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense

    Science.gov (United States)

    Liu, Guoxia; Ma, Hongmei; Xie, Hongyan; Xuan, Ning; Guo, Xia; Fan, Zhongxue; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François

    2016-01-01

    Chemosensory proteins (CSPs) are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1) was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde). This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity. PMID:27167733

  14. Biotype Characterization, Developmental Profiling, Insecticide Response and Binding Property of Bemisia tabaci Chemosensory Proteins: Role of CSP in Insect Defense.

    Science.gov (United States)

    Liu, Guoxia; Ma, Hongmei; Xie, Hongyan; Xuan, Ning; Guo, Xia; Fan, Zhongxue; Rajashekar, Balaji; Arnaud, Philippe; Offmann, Bernard; Picimbon, Jean-François

    2016-01-01

    Chemosensory proteins (CSPs) are believed to play a key role in the chemosensory process in insects. Sequencing genomic DNA and RNA encoding CSP1, CSP2 and CSP3 in the sweet potato whitefly Bemisia tabaci showed strong variation between B and Q biotypes. Analyzing CSP-RNA levels showed not only biotype, but also age and developmental stage-specific expression. Interestingly, applying neonicotinoid thiamethoxam insecticide using twenty-five different dose/time treatments in B and Q young adults showed that Bemisia CSP1, CSP2 and CSP3 were also differentially regulated over insecticide exposure. In our study one of the adult-specific gene (CSP1) was shown to be significantly up-regulated by the insecticide in Q, the most highly resistant form of B. tabaci. Correlatively, competitive binding assays using tryptophan fluorescence spectroscopy and molecular docking demonstrated that CSP1 protein preferentially bound to linoleic acid, while CSP2 and CSP3 proteins rather associated to another completely different type of chemical, i.e. α-pentyl-cinnamaldehyde (jasminaldehyde). This might indicate that some CSPs in whiteflies are crucial to facilitate the transport of fatty acids thus regulating some metabolic pathways of the insect immune response, while some others are tuned to much more volatile chemicals known not only for their pleasant odor scent, but also for their potent toxic insecticide activity. PMID:27167733

  15. Virus and calcium: an unexpected tandem to optimize insecticide efficacy.

    Science.gov (United States)

    Apaire-Marchais, Véronique; Ogliastro, Mylène; Chandre, Fabrice; Pennetier, Cédric; Raymond, Valérie; Lapied, Bruno

    2016-04-01

    The effective control of insect pests is based on the rational use of the most efficient and safe insecticide treatments. To increase the effects of classical insecticides and to avoid the ability of certain pest insects to develop resistance, it is essential to propose novel strategies. Previous studies have shown that calcium-dependent phosphorylation/dephosphorylation is now considered as a new cellular mechanism for increasing the target sensitivity to insecticides. Because it is known that virus entry is correlated with intracellular calcium concentration rise, this report attempts to present the most important data relevant to the feasibility of combining an insect virus such as baculovirus or densovirus with an insecticide. In this case, the insect virus is not used as a bioinsecticide but acts as a synergistic agent able to trigger calcium rise and to activate calcium-dependent intracellular signalling pathways involved in the increase of the membrane receptors and/or ion channels sensitivity to insecticides. This virus-insecticide mixture represents a promising alternative to optimize the efficacy of insecticides against insect pests while reducing the doses. PMID:26743399

  16. Radiotracer Approaches to Carbamate Insecticide Toxicology

    International Nuclear Information System (INIS)

    Methylcarbamates constitute one of the major groups of insecticides. Many unresolved problems in their toxicology may be readily approached with radiotracer studies. Dimethylcarbamates have been prepared with carbonyl-C14-labelling and methylcarbamates withmethyl-, carbonyl-and ring-labelling utilizing carbon-14. The pharmacological action of these.compounds presumably results from acetylcholinesterase inhibition and may involve carbamylation. Reaction of carbonyl- or methyl-labelled carbamates with purified cholinesterase or other esterases would allow a critical examination of this carbamylation reaction and the ease of spontaneous and induced reactivation or decarbamylation. The physiological significance of cholinesterase inhibition might be examined by administering acetate-C14 and analysis for radiolabelled acetylcholine accumulation in nervous tissue, or by utilizing acetyl-C14-choline as the substrate for in vitro determination of the degree of cholinesterase inhibition in tissues of poisoned animals with minimal dilution of the inhibitors and enzymes during analysis. Some progress has been made with radiolabelled materials in investigating the metabolism of carbamate insecticides. Sevin (1-naphthyl methylcarbamate) has been most extensively studied along with its potential hydrolysis products. The assumption that the metabolism of Sevin involves an initial hydrolysis and then further decomposition of the fragments was not supported by carbon-14 studies. The major detoxification mechanism in mammals, and probably also in insects, results from initial oxidative attack on the carbamate by the microsomes in the presence of reduced nicotinamide-adenine dinucleotide phosphate. Sevin is rapidly metabolized in mammals, but the fate of certain of the fragments has not been resolved. Some of the metabolites appear in the milk of lactating animals. One step in the metabolism appears to be formation of the N-methylol derivative. Preliminary studies on the metabolism

  17. Bacterial disease

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    2008241 Comparison of opa typing with Neisseria gonorrhoeae multi-antigen sequence typing for discrimination of Neisseria gonorrhoeae from patients and their sex partners.CHEN Hongxiang(陈宏翔),et al.Dept Dermatol Wuhan Union Hosp,Tongji Med Coll,Huazhong Sci & Technol Univ,Wuhan 4300022.Chin J Dermatol 2008;41(5):307-310.Objective To compare the potentiality of opa typing ersus Ncisseria gonorrhoeae multiantigen sequence typing(Ng-MAST)in discrimination of N.gonorrhoeae iso-lates,and to investigate the consistency of genotypes of

  18. The insecticide resistance in stripped stem borer, Chilo suppressalis (Walker)

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    @@ The stripped stem borer (SSB), Chilo suppressalis (Walker) is one of the major insect pests of rice in China. Chemical control has been a common practice in SSB management since 1950s. Insecticides used included BHC before 1983;organophosphorus insecticides (methyl-parathion, trichophon, methamidophos, and monocrotophos), and chlordimeform in mid-1970s-1980s; Shachongshuang (dimehypo) and Shachongdan (monousltap) since early 1980s. In recent years, SSB population and its damage to rice increased rapidly and failures on control has been reported. To find out the cause of failure and to put forward the suitable control methods, we studied the resistance of SSB to major insecticides used in China.

  19. EVALUATION OF SOME NOVEL INSECTICIDES AGAINST MYZUS PERSICAE (SULZER)

    OpenAIRE

    OMKAR GAVKARE; SURJEET KUMAR; NIKHIL SHARMA; Sharma, P L

    2013-01-01

    Realtive toxicity of some insecticides viz., acetamiprid, fipronil, imidacloprid, lambda cyhalothrin, malathionand thiamethoxam to apterous adults of the green peach aphid, Myzus persicae (Sulzer) was evaluated in thelaboratory using leaf dip method of bioassay. The LC50 values of these insecticides were calculated to be 17, 16.5,4.5, 15.4, 362.2 and 4.1 ppm, respectively. On the basis of LC50 values, thiamethoxam was found to be the mosttoxic insecticide with LC50 value of 4.1ppm, closely fo...

  20. Comparative efficacy of different insecticides against sucking pests of cotton

    International Nuclear Information System (INIS)

    Seven insecticides, viz. Mospilan 20SP, Confider 200SL, Talstar 10EC, Advantage 20EC, Actara 25WG, Polo 500EC and Tamaron 60SL were evaluated for their efficacy against jassid (Amarasca devastans Dist., (Whitefly (Bemisia tabaci (Genn.)) and thrips (Thrips tabaci Lind.) on cotton, at the University College of Agriculture, Bahauddin Zakariya University, Multan. The most effective insecticides for jassid, up to seven days were Confider and Mospilan, while Advantage was ineffective to control jassid population. Against whitefly the most effective insecticides were Mospilan and Actara, while Mospilan, Confidor and Tamaron were highly effective against thrips. (author)

  1. Antibacterial, Antifungal, and Insecticidal Potentials of Oxalis corniculata and Its Isolated Compounds

    Directory of Open Access Journals (Sweden)

    Azizur Rehman

    2015-01-01

    Full Text Available Oxalis corniculata is a common medicinal plant widely used against numerous infectious diseases. The agrochemical potential of methanolic extract, n-hexane, chloroform, ethyl acetate, and n-butanol fractions were assessed to measure the antibacterial, antifungal, and insecticidal activities of the plant. The crude, chloroform, and n-butanol soluble fractions showed excellent activities against Escherichia coli, Shigella dysenteriae, Salmonella typhi, and Bacillus subtilis but have no activity against Staphylococcus aureus. Similarly the crude, n-hexane, and chloroform fractions were also found to have significant activity against fungal strains including Fusarium solani, Aspergillus flexneri, and Aspergillus flavus and have no activity against Aspergillus niger. Chemical pesticides have shown very good results at the beginning, but with the passage of time the need was realized to use the natural plant sources for the safe control of insects. The current study will provide minor contribution towards it. High mortality rate was recorded for the crude extract and chloroform fraction against Tribolium castaneum. The two isolated compounds 5-hydroxy-6,7,8,4′-tetramethoxyflavone (1 and 5,7,4′-trihydroxy-6,8-dimethoxyflavone (2 were evaluated for antibacterial, antifungal, and insecticidal activities. The results showed that compound 2 was more active than compound 1 against the tested bacterial strains and insects.

  2. Antibacterial, Antifungal, and Insecticidal Potentials of Oxalis corniculata and Its Isolated Compounds.

    Science.gov (United States)

    Rehman, Azizur; Rehman, Ali; Ahmad, Ijaz

    2015-01-01

    Oxalis corniculata is a common medicinal plant widely used against numerous infectious diseases. The agrochemical potential of methanolic extract, n-hexane, chloroform, ethyl acetate, and n-butanol fractions were assessed to measure the antibacterial, antifungal, and insecticidal activities of the plant. The crude, chloroform, and n-butanol soluble fractions showed excellent activities against Escherichia coli, Shigella dysenteriae, Salmonella typhi, and Bacillus subtilis but have no activity against Staphylococcus aureus. Similarly the crude, n-hexane, and chloroform fractions were also found to have significant activity against fungal strains including Fusarium solani, Aspergillus flexneri, and Aspergillus flavus and have no activity against Aspergillus niger. Chemical pesticides have shown very good results at the beginning, but with the passage of time the need was realized to use the natural plant sources for the safe control of insects. The current study will provide minor contribution towards it. High mortality rate was recorded for the crude extract and chloroform fraction against Tribolium castaneum. The two isolated compounds 5-hydroxy-6,7,8,4'-tetramethoxyflavone (1) and 5,7,4'-trihydroxy-6,8-dimethoxyflavone (2) were evaluated for antibacterial, antifungal, and insecticidal activities. The results showed that compound 2 was more active than compound 1 against the tested bacterial strains and insects. PMID:25873973

  3. Bacterial hydrodynamics

    CERN Document Server

    Lauga, Eric

    2015-01-01

    Bacteria predate plants and animals by billions of years. Today, they are the world's smallest cells yet they represent the bulk of the world's biomass, and the main reservoir of nutrients for higher organisms. Most bacteria can move on their own, and the majority of motile bacteria are able to swim in viscous fluids using slender helical appendages called flagella. Low-Reynolds-number hydrodynamics is at the heart of the ability of flagella to generate propulsion at the micron scale. In fact, fluid dynamic forces impact many aspects of bacteriology, ranging from the ability of cells to reorient and search their surroundings to their interactions within mechanically and chemically-complex environments. Using hydrodynamics as an organizing framework, we review the biomechanics of bacterial motility and look ahead to future challenges.

  4. Insecticide Resistance in the Western Flower Thrips, Frankliniella occidentalis

    DEFF Research Database (Denmark)

    Jensen, Sten Erik

    assays used in this study appeared to have modest value for detecting resistance to methiocarb in field populations of F. occidentalis. The particular host plant of a polyphagous insect population may affect activity of detoxification enzymes and tolerance to insecticides. Another part of this study......The western flower thrips, Frankliniella occidentalis (Pergande) is a serious pest on a wide range of crops throughout the world. In Denmark F. occidentalis is a pest in greenhouses. F. occidentalis is difficult to control with insecticides because of its thigmokinetic behaviour and resistance to...... insecticides. Since F. occidentulis spread to become a worldwide pest in 1980’es, resistance to a number of different insecticides has been shown in many populations of F. occidentalis. This flower thrips has the potential of fast development of resistance owing to the short generation time, high fecundity...

  5. Federal Insecticide, Fungicide, and Rodenticide Act Section 18 Database

    Data.gov (United States)

    U.S. Environmental Protection Agency — Section 18 of Federal Insecticide, Fungicide, and Rodenticide Act (FIFRA) authorizes EPA to allow an unregistered use of a pesticide for a limited time if EPA...

  6. Co-application of herbicides and insecticides in dry bean

    OpenAIRE

    Peter H. Sikkema; Christy Shropshire; Robert E. Nurse; Nader Soltani

    2012-01-01

    Eight field trials were conducted from 2006 to 2008 at various locations in Ontario to evaluate the co-application of postemergence herbicides with cyhalothrin-lambda or dimethoate insecticides in cranberry and white bean. At 2 weeks after treatment, the addition of cyhalothrin-lambda or dimethoate insecticides to sethoxydim, quizalofop-p-ethyl, bentazon, fomesafen and bentazon plus fomesafen did not increase injury at the Exeter and Ridgetown locations except for bentazon plus dimethoate whi...

  7. The use of insecticides to control insect pests

    OpenAIRE

    Wojciechowska, M.; Stepnowski, P.; Gołębiowski, M.

    2016-01-01

    Pesticides are used as plants protection products. Among those, insecticides serve as agents to control insects. When incorrectly applied, however these substances may negatively affect people's health and natural environment. Administration routes of insecticides depend on many factors and vary from spraying to fertilizers. These different methods influence how insects prey and how pests develop. Additionally, too frequent use of the same chemicals can lead to development of resi...

  8. Insects, Insecticides and Hormesis: Evidence and Considerations for Study

    OpenAIRE

    Cutler, G. Christopher

    2012-01-01

    Insects are ubiquitous, crucial components of almost all terrestrial and fresh water ecosystems. In agricultural settings they are subjected to, intentionally or unintentionally, an array of synthetic pesticides and other chemical stressors. These ecological underpinnings, the amenability of insects to laboratory and field experiments, and our strong knowledgebase in insecticide toxicology, make the insect-insecticide model an excellent one to study many questions surrounding hormesis. Moreov...

  9. Impact and Selectivity of Insecticides to Predators and Parasitoids

    OpenAIRE

    Flávio Lemes Fernandes; Leandro Bacci; Maria Sena Fernandes

    2010-01-01

    Problems with the use of insecticides has brought losses, such as, negative impact on natural enemies. When these beneficial insects reduce cause the eruption of pests and resurgence it’s more common. Thus principles of conservation these arthropods are extremely important in the biological natural control of pests, so that these enemies may present a high performance. Because of the negative impacts caused by insecticides on agriculture and their harmful effects on natural enemies, the objec...

  10. Neural effects of insecticides in the honey bee

    OpenAIRE

    Belzunces, Luc; Tchamitchian, Sylvie; Brunet, Jean-Luc

    2012-01-01

    International audience During their foraging activity, honey bees are often exposed to direct and residual contacts with pesticides, especially insecticides, all substances specifically designed to kill, repel, attract or perturb the vital functions of insects. Insecticides may elicit lethal and sublethal effects of different natures that may affect various biological systems of the honey bee. The first step in the induction of toxicity by a chemical is the interaction between the toxic co...

  11. Efficacy of Selected Insecticides Applied to Hybrid Rice Seed

    OpenAIRE

    Adams, A.; Gore, J; Musser, F.; Cook, D; Catchot, A.; Walker, T.; Dobbins, C.

    2015-01-01

    Hybrid rice and insecticide seed treatments targeting rice water weevil, Lissorhoptrus oryzophilus Kuschel, have altered the landscape of rice production. The effect of reduced seeding rates on seed treatment efficacy in hybrid rice has not been studied. During 2011 and 2012, an experiment was conducted at seven locations to determine the relationship between low seeding rates used in hybrid rice and efficacy of selected insecticidal seed treatments as measured by rice water weevil densities ...

  12. Insecticide Resistance and Management Strategies in Urban Ecosystems

    OpenAIRE

    Fang Zhu; Laura Lavine; Sally O’Neal; Mark Lavine; Carrie Foss; Douglas Walsh

    2016-01-01

    The increased urbanization of a growing global population makes imperative the development of sustainable integrated pest management (IPM) strategies for urban pest control. This emphasizes pests that are closely associated with the health and wellbeing of humans and domesticated animals. Concurrently there are regulatory requirements enforced to minimize inadvertent exposures to insecticides in the urban environment. Development of insecticide resistance management (IRM) strategies in urban ...

  13. Measurement of overall insecticidal effects in experimental hut trials

    Directory of Open Access Journals (Sweden)

    Briët Olivier JT

    2012-11-01

    Full Text Available Abstract Background The ‘overall insecticidal effect’ is a key measure used to evaluate public health pesticides for indoor use in experimental hut trials. It depends on the proportion of mosquitoes that are killed out of those that enter the treated hut, intrinsic mortality in the control hut, and the ratio of mosquitoes entering the treatment hut to those entering the control hut. This paper critically examines the way the effect is defined, and discusses how it can be used to infer effectiveness of intervention programmes. Findings The overall insecticidal effect, as defined by the World Health Organization in 2006, can be negative when deterrence from entering the treated hut is high, even if all mosquitoes that enter are killed, wrongly suggesting that the insecticide enhances mosquito survival. Also in the absence of deterrence, even if the insecticide kills all mosquitoes in the treatment hut, the insecticidal effect is less than 100%, unless intrinsic mortality is nil. A proposed alternative definition for the measurement of the overall insecticidal effect has the desirable range of 0 to 1 (100%, provided mortality among non-repelled mosquitoes in the treated hut is less than the corresponding mortality in the control hut. This definition can be built upon to formulate the coverage-dependent insecticidal effectiveness of an intervention programme. Coverage-dependent population protection against feeding can be formulated similarly. Conclusions This paper shows that the 2006 recommended quantity for measuring the overall insecticidal effect is problematic, and proposes an alternative quantity with more desirable properties.

  14. Detoxification of organophosphate nerve agents by bacterial phosphotriesterase

    International Nuclear Information System (INIS)

    Organophosphates have been widely used as insecticides and chemical warfare agents. The health risks associated with these agents have necessitated the need for better detoxification and bioremediation tools. Bacterial enzymes capable of hydrolyzing the lethal organophosphate nerve agents are of special interest. Phosphotriesterase (PTE) isolated from the soil bacteria Pseudomonas diminuta displays a significant rate enhancement and substrate promiscuity for the hydrolysis of organophosphate triesters. Directed evolution and rational redesign of the active site of PTE have led to the identification of new variants with enhanced catalytic efficiency and stereoselectivity toward the hydrolysis of organophosphate neurotoxins. PTE has been utilized to protect against organophosphate poisoning in vivo. Biotechnological applications of PTE for detection and decontamination of insecticides and chemical warfare agents are developing into useful tools. In this review, the catalytic properties and potential applications of this remarkable enzyme are discussed

  15. Eco-Friendly Insecticide Discovery via Peptidomimetics: Design, Synthesis, and Aphicidal Activity of Novel Insect Kinin Analogues.

    Science.gov (United States)

    Zhang, Chuanliang; Qu, Yanyan; Wu, Xiaoqing; Song, Dunlun; Ling, Yun; Yang, Xinling

    2015-05-13

    Insect kinin neuropeptides are pleiotropic peptides that are involved in the regulation of hindgut contraction, diuresis, and digestive enzyme release. They share a common C-terminal pentapeptide sequence of Phe(1)-Xaa(2)-Yaa(3)-Trp(4)-Gly(5)-NH2 (where Xaa(2) = His, Asn, Phe, Ser, or Tyr; Yaa(3) = Pro, Ser, or Ala). Recently, the aphicidal activity of insect kinin analogues has attracted the attention of researchers. Our previous work demonstrated that the sequence-simplified insect kinin pentapeptide analogue Phe-Phe-[Aib]-Trp-Gly-NH2 could retain good aphicidal activity and be the lead compound for the further discovery of eco-friendly insecticides which encompassed a broad array of biochemicals derived from micro-organisms and other natural sources. Using the peptidomimetics strategy, we chose Phe-Phe-[Aib]-Trp-Gly-NH2 as the lead compound, and we designed and synthesized three series, including 31 novel insect kinin analogues. The aphicidal activity of the new analogues against soybean aphid was determined. The results showed that all of the analogues exhibited aphicidal activity. Of particular interest was the analogue II-1, which exhibited improved aphicidal activity with an LC50 of 0.019 mmol/L compared with the lead compound (LC50 = 0.045 mmol/L) or the commercial insecticide pymetrozine (LC50 = 0.034 mmol/L). This suggests that the analogue II-1 could be used as a new lead for the discovery of potential eco-friendly insecticides. PMID:25912216

  16. Impact of some selected insecticides application on soil microbial respiration.

    Science.gov (United States)

    Latif, M A; Razzaque, M A; Rahman, M M

    2008-08-15

    The aim of present study was to investigate the impact of selected insecticides used for controlling brinjal shoot and fruit borer on soil microorganisms and to find out the insecticides or nontoxic to soil microorganism the impact of nine selected insecticides on soil microbial respiration was studied in the laboratory. After injection of different insecticides solutions, the soil was incubated in the laboratory at room temperature for 32 days. The amount of CO2 evolved due to soil microbial respiration was determined at 2, 4, 8, 16, 24 and 32 days of incubation. Flubendiamide, nimbicidine, lambda-cyhalothrin, abamectin and thiodicarb had stimulatory effect on microbial respiration during the initial period of incubation. Chlorpyriphos, cartap and carbosulfan had inhibitory effect on microbial respiration and cypermethrin had no remarkable effect during the early stage of incubation. The negative effect of chlorpyriphos, cartap and carbosulfan was temporary, which was disappeared after 4 days of insecticides application. No effect of the selected insecticides on soil microorganisms was observed after 24 or 32 days of incubation. PMID:19266909

  17. Design, synthesis and insecticidal evaluation of aryloxy dihalopropene derivatives.

    Science.gov (United States)

    Yang, Ji-Chun; Li, Miao; Wu, Qiao; Liu, Chang-Ling; Chang, Xiu-Hui

    2016-02-01

    Plutella xylostella (P. xylostella) is a highly migratory, cosmopolitan species and one of the most important pest of cruciferous crops worldwide. Pyridalyl as a novel class of insecticides has good efficacy against P. xylostella. On the basis of the commercial insecticide pyridalyl, a series of new aryloxy dihalopropene derivatives were designed and synthesized by using Intermediate Derivatization Methods. Their chemical structures were confirmed by (1)H NMR, high-resolution mass spectrum (HRMS), and single-crystal X-ray diffraction analysis. The insecticidal activities of the new compounds against P. xylostella were evaluated. The results of bioassays indicated that most of the compounds showed moderate to high activities at the tested concentration, especially compounds 10e and 10g displayed more than 75% insecticidal activity against P. xylostella at 6.25mg/L, while pyridalyl showed 50% insecticidal activity at the same concentration. The field trials result of the insecticidal activities showed that compound 10e as a 10% emulsifiable concentrate (EC) was effective in the control of P. xylostella at 75-150g a.i./ha, and the mortality of P. xylostella for treatment with compound 10e at 75g a.i./ha was equivalent to pyridalyl at 105g a.i./ha. PMID:26432606

  18. Sublethal and transgenerational effects of insecticides in developing Trichogramma galloi (Hymenoptera: Trichogrammatidae) : toxicity of insecticides to Trichogramma galloi.

    Science.gov (United States)

    Costa, Mariana Abreu; Moscardini, Valéria Fonseca; da Costa Gontijo, Pablo; Carvalho, Geraldo Andrade; de Oliveira, Rodrigo Lopes; de Oliveira, Harley Nonato

    2014-10-01

    This study assessed the transgenerational effects of insecticides in developing Trichogramma galloi (Hymenoptera: Trichogrammatidae). Laboratory bioassays were performed in which five insecticides were sprayed on egg-larval, pre-pupal and pupal stages of the parasitoid. The interaction between insecticides and development stages of the parasitoid was not significant for the rate of F0 emergence. All insecticides significantly reduced the emergence of wasps, with the lowest emergence observed when they were applied to the pupal stage. For the sex ratio, only spinosad applied to the pre-pupal stage and triflumuron applied on the egg-larval and pre-pupal stages did not differ from the controls. Triflumuron applied to pre-pupae did not lead to any difference in the parasitism rate of the treated generation (F0) when compared to the control. There were no significant differences among survival curves for females of F0 when all insecticides were sprayed on the egg-larval stage. Both concentrations of lambda-cyhalothrin + thiamethoxam reduced female pre-pupal survival, and all treatments reduced female pupal survival. In addition, we observed a transgenerational effect of the insecticides on emergence and sex ratio of next generation (F1). Lambda-cyhalothrin + thiamethoxam (Min) applied to the pre-pupae and pupae, the maximum rate of the same insecticides applied to the egg-larvae and pre-pupae, and spinosad applied to pre-pupae all significantly reduced the adults emergence of T. galloi F1 generation. Only triflumuron did not alter the F1 sex ratio. These bioassays provide a basis for better understanding the effects of insecticide use on beneficial parasitoids. PMID:25011923

  19. Gene expression in gut symbiotic organ of stinkbug affected by extracellular bacterial symbiont.

    Directory of Open Access Journals (Sweden)

    Ryo Futahashi

    Full Text Available The bean bug Riptortus pedestris possesses a specialized symbiotic organ in a posterior region of the midgut, where numerous crypts harbor extracellular betaproteobacterial symbionts of the genus Burkholderia. Second instar nymphs orally acquire the symbiont from the environment, and the symbiont infection benefits the host by facilitating growth and by occasionally conferring insecticide resistance. Here we performed comparative transcriptomic analyses of insect genes expressed in symbiotic and non-symbiotic regions of the midgut dissected from Burkholderia-infected and uninfected R. pedestris. Expression sequence tag analysis of cDNA libraries and quantitative reverse transcription PCR identified a number of insect genes expressed in symbiosis- or aposymbiosis-associated patterns. For example, genes up-regulated in symbiotic relative to aposymbiotic individuals, including many cysteine-rich secreted protein genes and many cathepsin protease genes, are likely to play a role in regulating the symbiosis. Conversely, genes up-regulated in aposymbiotic relative to symbiotic individuals, including a chicken-type lysozyme gene and a defensin-like protein gene, are possibly involved in regulation of non-symbiotic bacterial infections. Our study presents the first transcriptomic data on gut symbiotic organ of a stinkbug, which provides initial clues to understanding of molecular mechanisms underlying the insect-bacterium gut symbiosis and sheds light on several intriguing commonalities between endocellular and extracellular symbiotic associations.

  20. AMPLIFICATION OF RIBOSOMAL RNA SEQUENCES

    Science.gov (United States)

    This book chapter offers an overview of the use of ribosomal RNA sequences. A history of the technology traces the evolution of techniques to measure bacterial phylogenetic relationships and recent advances in obtaining rRNA sequence information. The manual also describes procedu...

  1. Bacillus thuringiensis insecticidal Cry1Aa toxin binds to a highly conserved region of aminopeptidase N in the host insect leading to its evolutionary success.

    Science.gov (United States)

    Nakanishi, K; Yaoi, K; Shimada, N; Kadotani, T; Sato, R

    1999-06-15

    Bacillus thuringiensis insecticidal protein, Cry1Aa toxin, binds to a specific receptor in insect midguts and has insecticidal activity. Therefore, the structure of the receptor molecule is probably a key factor in determining the binding affinity of the toxin and insect susceptibility. The cDNA fragment (PX frg1) encoding the Cry1Aa toxin-binding region of an aminopeptidase N (APN) or an APN family protein from diamondback moth, Plutella xylostella midgut was cloned and sequenced. A comparison between the deduced amino acid sequence of PX frg1 and other insect APN sequences shows that Cry1Aa toxin binds to a highly conserved region of APN family protein. In this paper, we propose a model to explain the mechanism that causes B. thuringiensis evolutionary success and differing insect susceptibility to Cry1Aa toxin. PMID:10366728

  2. Insecticide mixtures could enhance the toxicity of insecticides in a resistant dairy population of Musca domestica L [corrected].

    Directory of Open Access Journals (Sweden)

    Hafiz Azhar Ali Khan

    Full Text Available House flies, Musca domestica L., are important pests of dairy operations worldwide, with the ability to adapt wide range of environmental conditions. There are a number of insecticides used for their management, but development of resistance is a serious problem. Insecticide mixtures could enhance the toxicity of insecticides in resistant insect pests, thus resulting as a potential resistance management tool. The toxicity of bifenthrin, cypermethrin, deltamethrin, chlorpyrifos, profenofos, emamectin benzoate and fipronil were assessed separately, and in mixtures against house flies. A field-collected population was significantly resistant to all the insecticides under investigation when compared with a laboratory susceptible strain. Most of the insecticide mixtures like one pyrethroid with other compounds evaluated under two conditions (1∶1-"A" and LC50: LC50-"B" significantly increased the toxicity of pyrethroids in the field population. Under both conditions, the combination indices of pyrethroids with other compounds, in most of the cases, were significantly below 1, suggesting synergism. The enzyme inhibitors, PBO and DEF, when used in combination with insecticides against the resistant population, toxicities of bifenthrin, cypermethrin, deltamethrin and emamectin were significantly increased, suggesting esterase and monooxygenase based resistance mechanism. The toxicities of bifenthrin, cypermethrin and deltamethrin in the resistant population of house flies could be enhanced by the combination with chlorpyrifos, profenofos, emamectin and fipronil. The findings of the present study might have practical significance for resistance management in house flies.

  3. Mutagenic and cytotoxic activities of benfuracarb insecticide.

    Science.gov (United States)

    Eren, Yasin; Erdoğmuş, Sevim Feyza; Akyıl, Dilek; Özkara, Arzu

    2016-08-01

    Benfuracarb is a carbamate insecticide used to control insect pests in vegetables and it has anti-acetylcholinesterase activity lower than other carbamates. Cytotoxic effects of benfuracarb were evaluated by using root growth inhibition (EC50), mitotic index (MI), and mitotic phase determinations on the root meristem cells of Allium cepa and mutagenic effects were determined in Salmonella typhymurium Ames test by TA98 and TA100 strains with and without metabolic activation. In Allium test, 1 % DMSO was used as negative control group and 10 ppm MMS was used as positive control group. 75 ppm concentration of benfuracarb was found as EC50. In MI and mitotic phases determination study, 37.5, 75 and 150 ppm doses of benfuracarb were used. Dose-dependent cytotoxic activity was found by root growth inhibition and MI studies. It was identified that mitotic inhibition activity of benfuracarb was higher than 10 ppm MMS. In Ames test, mutagenic activity was not observed and over 200 µg/plate of benfuracarb was determined as cytotoxic to S. typhymurium strains. Benfuracarb can be called as "mitotic inhibitor" but not called as mutagen. PMID:25381170

  4. Cell Culture for Production of Insecticidal Viruses.

    Science.gov (United States)

    Reid, Steven; Chan, Leslie C L; Matindoost, Leila; Pushparajan, Charlotte; Visnovsky, Gabriel

    2016-01-01

    While large-scale culture of insect cells will need to be conducted using bioreactors up to 10,000 l scale, many of the main challenges for cell culture-based production of insecticidal viruses can be studied using small-scale (20-500 ml) shaker/spinner flasks, either in free suspension or using microcarrier-based systems. These challenges still relate to the development of appropriate cell lines, stability of virus strains in culture, enhancing virus yields per cell, and the development of serum-free media and feeds for the desired production systems. Hence this chapter presents mainly the methods required to work with and analyze effectively insect cell systems using small-scale cultures. Outlined are procedures for quantifying cells and virus and for establishing frozen cells and virus stocks. The approach for maintaining cell cultures and the multiplicity of infection (MOI) and time of infection (TOI) parameters that should be considered for conducting infections are discussed.The methods described relate, in particular, to the suspension culture of Helicoverpa zea and Spodoptera frugiperda cell lines to produce the baculoviruses Helicoverpa armigera nucleopolyhedrovirus, HearNPV, and Anticarsia gemmatalis multicapsid nucleopolyhedrovirus, AgMNPV, respectively, and the production of the nonoccluded Oryctes nudivirus, OrNV, using an adherent coleopteran cell line. PMID:27565495

  5. Azobenzene Modified Imidacloprid Derivatives as Photoswitchable Insecticides: Steering Molecular Activity in a Controllable Manner

    Science.gov (United States)

    Xu, Zhiping; Shi, Lina; Jiang, Danping; Cheng, Jiagao; Shao, Xusheng; Li, Zhong

    2015-10-01

    Incorporating the photoisomerizable azobenzene into imidacloprid produced a photoswitchable insecticidal molecule as the first neonicotinoid example of remote control insecticide performance with spatiotemporal resolution. The designed photoswitchable insecticides showed distinguishable activity against Musca both in vivo and in vitro upon irradiation. Molecular docking study further suggested the binding difference of the two photoisomers. The generation of these photomediated insecticides provides novel insight into the insecticidal activity facilitating further investigation on the functions of insect nicotinic acetylcholine receptors and opens a novel way to control and study insect behavior on insecticide poisoning using light.

  6. Bacterial biogeography of the human digestive tract

    OpenAIRE

    Stearns, Jennifer C.; Michael D. J. Lynch; Senadheera, Dilani B.; Howard C. Tenenbaum; Michael B. Goldberg; Cvitkovitch, Dennis G.; Kenneth Croitoru; Gabriel Moreno-Hagelsieb; Neufeld, Josh D.

    2011-01-01

    We present bacterial biogeography as sampled from the human gastrointestinal tract of four healthy subjects. This study generated >32 million paired-end sequences of bacterial 16S rRNA genes (V3 region) representing >95,000 unique operational taxonomic units (OTUs; 97% similarity clusters), with >99% Good's coverage for all samples. The highest OTU richness and phylogenetic diversity was found in the mouth samples. The microbial communities of multiple biopsy sites within the colon were highl...

  7. Insights from Genomics into Bacterial Pathogen Populations

    OpenAIRE

    Wilson, DJ

    2012-01-01

    Bacterial pathogens impose a heavy burden of disease on human populations worldwide. The gravest threats are posed by highly virulent respiratory pathogens, enteric pathogens, and HIV-associated infections. Tuberculosis alone is responsible for the deaths of 1.5 million people annually. Treatment options for bacterial pathogens are being steadily eroded by the evolution and spread of drug resistance. However, population-level whole genome sequencing offers new hope in the fight against pathog...

  8. An evaluation of garlic lectin as an alternative carrier domain for insecticidal fusion proteins

    Institute of Scientific and Technical Information of China (English)

    Elaine Fitches; Judith Philip; Gareth Hinchliffe; Leisbeth Vercruysse; Nanasaheb Chougule; John A.Gatehouse

    2008-01-01

    The mannosc-binding lectin GNA(snowdrop lectin)is used as a"carrier"domain in insecticidal fusion proteins which cross the insect gut after oral ingestion.A similar lectin from garlic bulb,ASAII,has been evaluated as an altemative"carrieff".Recombinant ASAII delivered orally to larvae of cabbage moth(Mamestra brassica;Lepidoptera)Was subse-quently detected in haemolymph,demonstrating transport.Fusion proteins comprising an insect neurotoxin.ButaIT(Buthus tamulus insecticidal toxin;red scorpion toxin)linked to the C-terminal region of ASAII or GNA were produced as recombinant proteins(GNA/ButaIT and ASA/ButaIT)by expression in Pichia pastoris.In both cases the C-terminal sequence of the lectin was truncated to avoid post-translational proteolysis.The GNA-containing fusion protein was toxic by injection to cabbage moth larvae(LD50≈250μg/g),and when fed had a negative effect on survival and growth.It also decreased the survival of cereal aphids(Sitobion avenae;Homoptera)from neonate to adult by>70%when fed.In contrast,the ASA-ButaIT fusion protein was non-toxic to aphids,and had no effect on lepidopteran lalwae,either when injected or when fed.However,intact ASA-ButaIT fusion protein was present in the haemolymph of cabbage moth larvae following ingestion,showing that transport of the fusion had occurred.The stabilities of GNA/BUtaIT and ASA/ButaIT to proteolysis in vivo after injection or ingestion differed,and this may be a factor in determining insecticidal activities.

  9. ISOLATION AND CHARACTERIZATION OF BIFENTHRIN CATABOLIZING BACTERIAL STRAIN BACILLUS CIBI FROM SOIL FOR PYRETHROIDS BIODEGRADATION

    Directory of Open Access Journals (Sweden)

    Preeti Pandey

    2014-01-01

    Full Text Available Pyrethroids are commonly used in most parts of the world and are reported to have potential health risks. Bifenthrin, a third generation pyrethroid used as insecticide has caused potential effect on aquatic life and human health. Bioremediation is a practical approach to reduce pesticide in the environment and reports of microbial degradation of bifenthrin are meagre. This study was aimed at isolating and characterizing bacterial isolates for the efficient removal of bifenthrin residues in the environment. A bacterial strain PGS-4 isolated from sewage of pesticide industry was tested for growth at higher concentration of bifenthrin (800 mg L-1 and the optimum pH and temperature were determined. The strain utilized bifenthrin as sole carbon source for growth over a wide range of pH (4.0-9.0 and temperatures (16-37°C. On the basis of growth kinetics studies, the optimal conditions were determined to be pH 7.0-8.0 and 30°C. 16S rRNA gene sequence analysis showed that strain PGS-4 forms a distinct phylogenetic lineage within the evolutionary radiation encompassed by the genus Bacillus and showed 99% similarity to that of Bacillus cibi. This study depicts the ability of B. cibi to utilize bifenthrin at higher concentration under in vitro thereby can be used in eliminating bifenthrin from contaminated soils as a practical approach to reduce pyrethroid toxicity in the environment.

  10. Broad-range PCR, cloning and sequencing of the full 16S rRNA gene for detection of bacterial DNA in synovial fluid samples of Tunisian patients with reactive and undifferentiated arthritis

    OpenAIRE

    Siala, Mariam; Gdoura, Radhouane; Fourati, Hela; Rihl, Markus; Jaulhac, Benoit; Younes, Mohamed; Sibilia, Jean; Baklouti, Sofien; Bargaoui, Naceur; Sellami, Slaheddine; Sghir, Abdelghani; Hammami, Adnane

    2009-01-01

    Introduction Broad-range rDNA PCR provides an alternative, cultivation-independent approach for identifying bacterial DNA in reactive and other form of arthritis. The aim of this study was to use broad-range rDNA PCR targeting the 16S rRNA gene in patients with reactive and other forms of arthritis and to screen for the presence of DNA from any given bacterial species in synovial fluid (SF) samples. Methods We examined the SF samples from a total of 27 patients consisting of patients with rea...

  11. Insecticide cytotoxicology in China: Current status and challenges.

    Science.gov (United States)

    Zhong, Guohua; Cui, Gaofeng; Yi, Xin; Sun, Ranran; Zhang, Jingjing

    2016-09-01

    The insecticide cytotoxicology, as a new branch of toxicology, has rapidly developed in China. During the past twenty years, thousands of investigations have sprung up to evaluate the damages and clarify the mechanisms of insecticidal chemical substances to insect cells in vivo or in vitro. The mechanisms of necrosis, apoptosis or autophagy induced by synthetic or biogenic pesticides and virus infections have been systematically illuminated in many important models, including S2, BmN, SL-1, Sf21 and Sf9 cell lines. In addition, a variety of methods have also been applied to examine the effects of insecticides and elaborate the modes of action. As a result, many vital factors and pathways, such as cytochrome c, the Bcl-2 family and caspases, in mitochondrial signaling pathways, intracellular free calcium and lysosome signal pathways have been illuminated and drawn much attention. Benefiting from the application of insecticide cytotoxicology, natural products purifications, biological activities assessments of synthetic compounds and high throughput screening models have been accelerated in China. However, many questions remained, and there exist great challenges, especially in theory system, evaluation criterion, evaluation model, relationship between activity in vitro and effectiveness in vivo, and the toxicological mechanism. Fortunately, the generation of "omics" could bring opportunities for the development of insecticide cytotoxicology. PMID:27521907

  12. Insecticidal and Nematicidal Activities of Novel Mimosine Derivatives

    Directory of Open Access Journals (Sweden)

    Binh Cao Quan Nguyen

    2015-09-01

    Full Text Available Mimosine, a non-protein amino acid, is found in several tropical and subtropical plants, which has high value for medicine and agricultural chemicals. Here, in continuation of works aimed to development of natural product-based pesticidal agents, we present the first significant findings for insecticidal and nematicidal activities of novel mimosine derivatives. Interestingly, mimosinol and deuterated mimosinol (D-mimosinol from mimosine had strong insecticidal activity which could be a result of tyrosinase inhibition (IC50 = 31.4 and 46.1 μM, respectively. Of synthesized phosphoramidothionate derivatives from two these amino alcohols, two compounds (1a and 1b showed high insecticidal activity (LD50 = 0.5 and 0.7 μg/insect, respectively with 50%–60% mortality at 50 μg/mL which may be attributed to acetylcholinesterase inhibition. Compounds 1a and 1b also had strong nematicidal activity with IC50 = 31.8 and 50.2 μM, respectively. Our results suggest that the length of the alkyl chain and the functional group at the C5-position of phosphoramidothionates derived from mimosinol and d-mimosinol are essential for the insecticidal and nematicidal activities. These results reveal an unexplored scaffold as new insecticide and nematicide.

  13. Plant compounds insecticide activity against Coleoptera pests of stored products

    Energy Technology Data Exchange (ETDEWEB)

    Moreira, Marcio Dionizio; Picanco, Marcelo Coutinho; Guedes, Raul Narciso Carvalho; Campos, Mateus Ribeiro de; Silva, Gerson Adriano; Martins, Julio Claudio [Universidade Federal de Vicosa (UFV), MG (Brazil). Dept. de Biologia Animal]. E-mail: marcio.dionizio@gmail.com; picanco@ufv.br; guedes@ufv.br; mateusc3@yahoo.com.br; agronomiasilva@yahoo.com.br

    2007-07-15

    The objective of this work was to screen plants with insecticide activity, in order to isolate, identify and assess the bioactivity of insecticide compounds present in these plants, against Coleoptera pests of stored products: Oryzaephilus surinamensis L. (Silvanidae), Rhyzopertha dominica F. (Bostrichidae) and Sitophilus zeamais Mots. (Curculionidae). The plant species used were: basil (Ocimum selloi Benth.), rue (Ruta graveolens L.), lion's ear (Leonotis nepetifolia (L.) R.Br.), jimson weed (Datura stramonium L.), baleeira herb (Cordia verbenacea L.), mint (Mentha piperita L.), wild balsam apple (Mormodica charantia L.), and billy goat weed or mentrasto (Ageratum conyzoides L.). The insecticide activity of hexane and ethanol extracts from those plants on R. dominica was evaluated. Among them, only hexane extract of A. conyzoides showed insecticide activity; the hexane extract of this species was successively fractionated by silica gel column chromatography, for isolation and purification of the active compounds. Compounds 5,6,7,8,3',4',5'-heptamethoxyflavone; 5,6,7,8,3'-pentamethoxy-4',5'-methilenedioxyflavone and coumarin were identified. However, only coumarin showed insecticide activity against three insect pests (LD{sub 50} from 2.72 to 39.71 mg g{sup -1} a.i.). The increasing order of insects susceptibility to coumarin was R. dominica, S. zeamais and O. surinamensis. (author)

  14. Detection of arboviruses and other micro-organisms in experimentally infected mosquitoes using massively parallel sequencing.

    Directory of Open Access Journals (Sweden)

    Sonja Hall-Mendelin

    Full Text Available Human disease incidence attributed to arbovirus infection is increasing throughout the world, with effective control interventions limited by issues of sustainability, insecticide resistance and the lack of effective vaccines. Several promising control strategies are currently under development, such as the release of mosquitoes trans-infected with virus-blocking Wolbachia bacteria. Implementation of any control program is dependent on effective virus surveillance and a thorough understanding of virus-vector interactions. Massively parallel sequencing has enormous potential for providing comprehensive genomic information that can be used to assess many aspects of arbovirus ecology, as well as to evaluate novel control strategies. To demonstrate proof-of-principle, we analyzed Aedes aegypti or Aedes albopictus experimentally infected with dengue, yellow fever or chikungunya viruses. Random amplification was used to prepare sufficient template for sequencing on the Personal Genome Machine. Viral sequences were present in all infected mosquitoes. In addition, in most cases, we were also able to identify the mosquito species and mosquito micro-organisms, including the bacterial endosymbiont Wolbachia. Importantly, naturally occurring Wolbachia strains could be differentiated from strains that had been trans-infected into the mosquito. The method allowed us to assemble near full-length viral genomes and detect other micro-organisms without prior sequence knowledge, in a single reaction. This is a step toward the application of massively parallel sequencing as an arbovirus surveillance tool. It has the potential to provide insight into virus transmission dynamics, and has applicability to the post-release monitoring of Wolbachia in mosquito populations.

  15. Bioinformatic Comparison of Bacterial Secretomes

    Institute of Scientific and Technical Information of China (English)

    Catharine Song; Aseem Kumar; Mazen Saleh

    2009-01-01

    The rapid increasing number of completed bacterial genomes provides a good op-portunity to compare their proteomes. This study was undertaken to specifically compare and contrast their secretomes-the fraction of the proteome with pre-dicted N-terminal signal sequences, both type Ⅰ and type Ⅱ. A total of 176 theoreti-cal bacterial proteomes were examined using the ExProt program. Compared with the Gram-positives, the Gram-negative bacteria were found, on average, to con-tain a larger number of potential Sec-dependent sequences. In the Gram-negative bacteria but not in the others, there was a positive correlation between proteome size and secretome size, while there was no correlation between secretome size and pathogenicity. Within the Gram-negative bacteria, intracellular pathogens were found to have the smallest secretomes. However, the secretomes of certain bacte-ria did not fit into the observed pattern. Specifically, the secretome of Borrelia burgdoferi has an unusually large number of putative lipoproteins, and the signal peptides of mycoplasmas show closer sequence similarity to those of the Gram-negative bacteria. Our analysis also suggests that even for a theoretical minimal genome of 300 open reading frames, a fraction of this gene pool (up to a maximum of 20%) may code for proteins with Sec-dependent signal sequences.

  16. RESISTANCE OF THE TOXAPHENE INSECTICIDE IN SOIL

    Directory of Open Access Journals (Sweden)

    G MIRSATTARI

    2001-06-01

    Full Text Available Introduction. Toxaphene is resistant to degration and has been known as persistent bioaccumulator. In oder to understand the persistence and degradation phenomena of toxaphene in soil a series of tests were run. Methods. All experiments for dry and moist soil were conducted with 10 to 20 kg soil samples, contained in plastic tubs. The experiment was carried out in two parts. The five samples studied in each part are described below. Part I: "Dry samples". Soil control I soil amended with 10 percent gin trash/soil amended with 25 percent gin trash/soil amended with 10 percent gin trash and treated with 500 ppm toxaphene and soil treated with 500 ppm toxaphene. These samples were kept dry during the entire experimental period. Part II: "Moist samples". The samples were the same as described in part I, but they were kept moist by addition of water weekly during the experimental period. Periodically twenty grams of soil were analyzed using a gas chromatograph. Results. Chromatograms of dry and moist samples from soil containers (Part I and II analyzed up to 12 months after initiation of the experiments showed that no toxaphene degradation or dissipation had occurred. GLC profiles of extracts of 12 months soil samples were identical to those of 0 dry samples and almost 100 percent of toxaphene was recovered in all samples after one year regardless of whether samples were dry or moist I amended or not. Discussion. The results suggest that toxaphene dose not undergo degradation in soil" under aerobic condition, so it can be a persistent insecticide in soil under environmental condition.

  17. Influence of Pyrethroid Insecticides on Sodium and Calcium Influx in Neocortical Neurons

    Science.gov (United States)

    Pyrethroid insecticides bind to voltage-gated sodium channels and modify their gating kinetics, thereby disrupting neuronal function. Using murine neocortical neurons in primary culture, we have compared the ability of 11 structurally diverse pyrethroid insecticides to evoke Na+ ...

  18. Extraordinary resistance to insecticides reveals exotic Q biotype of Bemisia tabaci in the New World.

    Science.gov (United States)

    Dennehy, Timothy J; Degain, Benjamin A; Harpold, Virginia S; Zaborac, Marni; Morin, Shai; Fabrick, Jeffrey A; Nichols, Robert L; Brown, Judith K; Byrne, Frank J; Li, Xianchun

    2010-12-01

    A strain of the whitefly Bemisia tabaci (Gennadius) possessing unusually high levels of resistance to a wide range of insecticides was discovered in 2004 in the course of routine resistance monitoring in Arizona. The multiply resistant insects, collected from poinsettia (Euphorbia pulcherrima Willd. ex Klotzsch) plants purchased at a retail store in Tucson, were subjected to biotype analysis in three laboratories. Polyacrylamide gel electrophoresis of naphthyl esterases and sequencing of the mitochondrial cytochrome oxidase I gene (780 bp) confirmed the first detection of the Q biotype of B. tabaci in the New World. This U.S. Q biotype strain, referred to as Poinsettia'04, was highly resistant to two selective insect growth regulators, pyriproxyfen and buprofezin, and to mixtures of fenpropathrin and acephate. It was also unusually low in susceptibility to the neonicotinoid insecticides imidacloprid, acetamiprid, and thiamethoxam, relative to B biotype whiteflies. In 100 collections of whiteflies made in Arizona cotton (Gossypium spp.), vegetable, and melon (Cucumis melo L.) fields from 2001 to 2005, no Q biotypes were detected. Regions of the United States that were severely impacted by the introduction of the B biotype of B. tabaci in the 1980s would be well advised to promote measures that limit movement of the Q biotype from controlled environments into field systems and to formulate alternatives for managing this multiply-resistant biotype, in the event that it becomes more widely distributed. PMID:21309242

  19. Rhodnius prolixus supergene families of enzymes potentially associated with insecticide resistance.

    Science.gov (United States)

    Schama, Renata; Pedrini, Nicolás; Juárez, M Patricia; Nelson, David R; Torres, André Q; Valle, Denise; Mesquita, Rafael D

    2016-02-01

    Chagas disease or American trypanosomiasis, is a potentially life-threatening illness caused by the protozoan parasite, Trypanosoma cruzi. Once known as an endemic health problem of poor rural populations in Latin American countries, it has now spread worldwide. The parasite is transmitted by triatomine bugs, of which Rhodnius prolixus (Hemiptera, Reduviidae, Triatominae) is one of the vectors and a model organism. This species occurs mainly in Central and South American countries where the disease is endemic. Disease prevention focuses on vector control programs that, in general, rely intensely on insecticide use. However, the massive use of chemical insecticides can lead to resistance. One of the major mechanisms is known as metabolic resistance that is associated with an increase in the expression or activity of detoxification genes. Three of the enzyme families that are involved in this process - carboxylesterases (CCE), glutathione s-transferases (GST) and cytochrome P450s (CYP) - are analyzed in the R. prolixus genome. A similar set of detoxification genes to those of the Hemipteran Acyrthosiphon pisum but smaller than in most dipteran species was found in R. prolixus genome. All major CCE classes (43 genes found) are present but the pheromone/hormone processing class had fewer genes than usual. One main expansion was detected on the detoxification/dietary class. The phosphotriesterase family, recently associated with insecticide resistance, was also represented with one gene. One microsomal GST gene was found and the cytosolic GST gene count (14 genes) is extremely low when compared to the other hemipteran species with sequenced genomes. However, this is similar to Apis mellifera, a species known for its deficit in detoxification genes. In R. prolixus 88 CYP genes were found, with representatives in the four clans (CYP2, CYP3, CYP4 and mitochondrial) usually found in insects. R. prolixus seems to have smaller species-specific expansions of CYP genes than

  20. The insecticidal spider toxin SFI1 is a knottin peptide that blocks the pore of insect voltage-gated sodium channels via a large β-hairpin loop.

    Science.gov (United States)

    Bende, Niraj S; Dziemborowicz, Sławomir; Herzig, Volker; Ramanujam, Venkatraman; Brown, Geoffrey W; Bosmans, Frank; Nicholson, Graham M; King, Glenn F; Mobli, Mehdi

    2015-03-01

    Spider venoms contain a plethora of insecticidal peptides that act on neuronal ion channels and receptors. Because of their high specificity, potency and stability, these peptides have attracted much attention as potential environmentally friendly insecticides. Although many insecticidal spider venom peptides have been isolated, the molecular target, mode of action and structure of only a small minority have been explored. Sf1a, a 46-residue peptide isolated from the venom of the tube-web spider Segesteria florentina, is insecticidal to a wide range of insects, but nontoxic to vertebrates. In order to investigate its structure and mode of action, we developed an efficient bacterial expression system for the production of Sf1a. We determined a high-resolution solution structure of Sf1a using multidimensional 3D/4D NMR spectroscopy. This revealed that Sf1a is a knottin peptide with an unusually large β-hairpin loop that accounts for a third of the peptide length. This loop is delimited by a fourth disulfide bond that is not commonly found in knottin peptides. We showed, through mutagenesis, that this large loop is functionally critical for insecticidal activity. Sf1a was further shown to be a selective inhibitor of insect voltage-gated sodium channels, consistent with its 'depressant' paralytic phenotype in insects. However, in contrast to the majority of spider-derived sodium channel toxins that function as gating modifiers via interaction with one or more of the voltage-sensor domains, Sf1a appears to act as a pore blocker. PMID:25559770

  1. Modeling the integration of parasitoid, insecticide, and transgenic insecticidal crop for the long-term control of an insect pest.

    Science.gov (United States)

    Onstad, David W; Liu, Xiaoxia; Chen, Mao; Roush, Rick; Shelton, Anthony M

    2013-06-01

    The tools of insect pest management include host plant resistance, biological control, and insecticides and how they are integrated will influence the durability of each. We created a detailed model of the population dynamics and population genetics of the diamondback moth, Plutella xylostella L., and its parasitoid, Diadegma insulare (Cresson), to study long-term pest management in broccoli Brassica oleracea L. Given this pest's history of evolving resistance to various toxins, we also evaluated the evolution of resistance to transgenic insecticidal Bt broccoli (expressing Cry1Ac) and two types of insecticides. Simulations demonstrated that parasitism provided the most reliable, long-term control of P. xylostella populations. Use of Bt broccoli with a 10% insecticide-free refuge did not reduce the long-term contribution of parasitism to pest control. Small refuges within Bt broccoli fields can delay evolution of resistance > 30 generations if resistance alleles are rare in the pest population. However, the effectiveness of these refuges can be compromised by insecticide use. Rainfall mortality during the pest's egg and neonate stages significantly influences pest control but especially resistance management. Our model results support the idea that Bt crops and biological control can be integrated in integrated pest management and actually synergistically support each other. However, the planting and maintenance of toxin-free refuges are critical to this integration. PMID:23865173

  2. EVALUATION OF SOME NOVEL INSECTICIDES AGAINST MYZUS PERSICAE (SULZER

    Directory of Open Access Journals (Sweden)

    OMKAR GAVKARE

    2013-01-01

    Full Text Available Realtive toxicity of some insecticides viz., acetamiprid, fipronil, imidacloprid, lambda cyhalothrin, malathionand thiamethoxam to apterous adults of the green peach aphid, Myzus persicae (Sulzer was evaluated in thelaboratory using leaf dip method of bioassay. The LC50 values of these insecticides were calculated to be 17, 16.5,4.5, 15.4, 362.2 and 4.1 ppm, respectively. On the basis of LC50 values, thiamethoxam was found to be the mosttoxic insecticide with LC50 value of 4.1ppm, closely followed by imidacloprid with LC50 value as 4.5ppm.Malathion was found to be the least toxic with LC50 value of 362.2ppm

  3. Sublethal effects of some synthetic and botanical insecticides on Bemisia tabaci (Hemiptera: Aleyrodidae)

    OpenAIRE

    Esmaeily Saeideh; Samih Mohammad Amin; Zarabi Mehdi; Jafarbeigi Fatemeh

    2014-01-01

    In addition to direct mortality caused by insecticides, some biological traits of insects may also be affected by sublethal insecticide doses. In this study, we used the age-stage, two-sex life table method to evaluate the sublethal effects of the four synthetic insecticides: abamectin, imidacloprid, diazinon, and pymetrozin as well as the botanical insecticide taken from Calotropis procera (Asclepiadaceae) extract, on eggs of the cotton whitefly, Bemisia tabaci (Hem.: Aleyrodidae). The lowes...

  4. Status of insecticide resistance in high-risk malaria provinces in Afghanistan

    OpenAIRE

    Ahmad, Mushtaq; Buhler, Cyril; Pignatelli, Patricia; Ranson, Hilary; Nahzat, Sami Mohammad; Naseem, Mohammad; Sabawoon, Muhammad Farooq; Siddiqi, Abdul Majeed; Vink, Martijn

    2016-01-01

    Background Insecticide resistance seriously threatens the efficacy of vector control interventions in malaria endemic countries. In Afghanistan, the status of insecticide resistance is largely unknown while distribution of long-lasting insecticidal nets has intensified in recent years. The main objective of this study was thus to measure the level of resistance to four classes of insecticides in provinces with medium to high risk of malaria transmission. Methods Adult female mosquitoes were r...

  5. Optimal Cotton Insecticide Application Termination Timing: A Meta-Analysis.

    Science.gov (United States)

    Griffin, T W; Zapata, S D

    2016-08-01

    The concept of insecticide termination timing is generally accepted among cotton (Gossypium hirsutum) researchers; however, exact timings are often disputed. Specifically, there is uncertainty regarding the last economic insecticide application to control fruit-feeding pests including tarnished plant bug (Lygus lineolaris (Palisot de Beauvois)), boll weevil (Anthonomus grandis), bollworm (Helicoverpa zea), tobacco budworm (Heliothis virescens), and cotton fleahopper (Pseudatomoscelis seriatus). A systematic review of prior studies was conducted within a meta-analytic framework. Nine publicly available articles were amalgamated to develop an optimal timing principle. These prior studies reported 53 independent multiple means comparison field experiments for a total of 247 trial observations. Stochastic plateau theory integrated with econometric meta-analysis methodology was applied to the meta-database to determine the shape of the functional form of both the agronomic optimal insecticide termination timing and corresponding yield potential. Results indicated that current university insecticide termination timing recommendations are later than overall estimated timing suggested. The estimated 159 heat units (HU) after the fifth position above white flower (NAWF5) was found to be statistically different than the 194 HU termination used as the status quo recommended termination timing. Insecticides applied after 159 HU may have been applied in excess, resulting in unnecessary economic and environmental costs. Empirical results also suggested that extending the insecticide termination time by one unit resulted in a cotton lint yield increase of 0.27 kilograms per hectare up to the timing where the plateau began. Based on economic analyses, profit-maximizing producers may cease application as soon as 124 HU after NAWF5. These results provided insights useful to improve production systems by applying inputs only when benefits were expected to be in excess of the

  6. Insecticide resistance in vector Chagas disease: evolution, mechanisms and management.

    Science.gov (United States)

    Mougabure-Cueto, Gastón; Picollo, María Inés

    2015-09-01

    Chagas disease is a chronic parasitic infection restricted to America. The disease is caused by the protozoa Trypanosoma cruzi, which is transmitted to human through the feces of infected triatomine insects. Because no treatment is available for the chronic forms of the disease, vector chemical control represents the best way to reduce the incidence of the disease. Chemical control has been based principally on spraying dwellings with insecticide formulations and led to the reduction of triatomine distribution and consequent interruption of disease transmission in several areas from endemic region. However, in the last decade it has been repeatedly reported the presence triatomnes, mainly Triatoma infestans, after spraying with pyrethroid insecticides, which was associated to evolution to insecticide resistance. In this paper the evolution of insecticide resistance in triatomines is reviewed. The insecticide resistance was detected in 1970s in Rhodnius prolixus and 1990s in R. prolixus and T. infestans, but not until the 2000s resistance to pyrthroids in T. infestans associated to control failures was described in Argentina and Bolivia. The main resistance mechanisms (i.e. enhanced metabolism, altered site of action and reduced penetration) were described in the T. infestans resistant to pyrethrods. Different resistant profiles were demonstrated suggesting independent origin of the different resistant foci of Argentina and Bolivia. The deltamethrin resistance in T. infestans was showed to be controlled by semi-dominant, autosomally inherited factors. Reproductive and developmental costs were also demonstrated for the resistant T. infestans. A discussion about resistance and tolerance concepts and the persistence of T. infestans in Gran Chaco region are presented. In addition, theoretical concepts related to toxicological, evolutionary and ecological aspects of insecticide resistance are discussed in order to understand the particular scenario of pyrethroid

  7. Why insecticides are more toxic to insects than people: The unique toxicology of insects

    OpenAIRE

    Casida, J E; Quistad, G B

    2004-01-01

    The unique toxicology of insects provides the safety mechanisms for the major insecticides. The selectivity of insecticidal nerve poisons is attributable to structural differences in binding subsites (acetylcholinesterase and nicotinic receptor) or receptor subunit interfaces (gamma-aminobutyric acid receptor) or transmembrane regions (voltage-sensitive sodium channel) supplemented by metabolic activation and detoxification. Slow action limits the use of the remarkably selective insecticides ...

  8. Haematological parameters as bioindicators of insecticide exposure in teleosts.

    Science.gov (United States)

    Singh, Narendra Nath; Srivastava, Anil Kumar

    2010-06-01

    Haematological parameters, such as erythrocyte and leucocyte count, erythrocyte indices and thrombocyte number vis-a-vis coagulation of blood has been considered bioindicators of toxicosis in fish following exposure to organochlorine, organophosphate, carbamate and pyrethroid insecticides. This review deals with the effects of insecticides on the morphology of red blood cells, total erythrocyte count, haemoglobin content, haematocrit, mean corpuscular volume, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, erythrocyte sedimentation rate, total and differential leucocyte counts, thrombocyte count and clotting time in the peripheral blood of a number of teleosts. The review also takes stock of knowledge of the subject and explores prospects of additional research in the related area. PMID:20177774

  9. Characterization of an insecticidal toxin and pathogenicity of Pseudomonas taiwanensis against insects.

    Directory of Open Access Journals (Sweden)

    Wen-Jen Chen

    2014-08-01

    Full Text Available Pseudomonas taiwanensis is a broad-host-range entomopathogenic bacterium that exhibits insecticidal activity toward agricultural pests Plutella xylostella, Spodoptera exigua, Spodoptera litura, Trichoplusia ni and Drosophila melanogaster. Oral infection with different concentrations (OD = 0.5 to 2 of wild-type P. taiwanensis resulted in insect mortality rates that were not significantly different (92.7%, 96.4% and 94.5%. The TccC protein, a component of the toxin complex (Tc, plays an essential role in the insecticidal activity of P. taiwanensis. The ΔtccC mutant strain of P. taiwanensis, which has a knockout mutation in the tccC gene, only induced 42.2% mortality in P. xylostella, even at a high bacterial dose (OD = 2.0. TccC protein was cleaved into two fragments, an N-terminal fragment containing an Rhs-like domain and a C-terminal fragment containing a Glt symporter domain and a TraT domain, which might contribute to antioxidative stress activity and defense against macrophagosis, respectively. Interestingly, the primary structure of the C-terminal region of TccC in P. taiwanensis is unique among pathogens. Membrane localization of the C-terminal fragment of TccC was proven by flow cytometry. Sonicated pellets of P. taiwanensis ΔtccC strain had lower toxicity against the Sf9 insect cell line and P. xylostella larvae than the wild type. We also found that infection of Sf9 and LD652Y-5d cell lines with P. taiwanensis induced apoptotic cell death. Further, natural oral infection by P. taiwanensis triggered expression of host programmed cell death-related genes JNK-2 and caspase-3.

  10. Bacterial diversity of soil under eucalyptus assessed by 16S rDNA sequencing analysis Diversidade bacteriana de solo sob eucaliptos obtida por seqüenciamento do 16S rDNA

    OpenAIRE

    Érico Leandro da Silveira; Rodrigo Matheus Pereira; Denilson César Scaquitto; Eliamar Aparecida Nascimbém Pedrinho; Silvana Pómpeia Val-Moraes; Ester Wickert; Lúcia Maria Carareto-Alves; Eliana Gertrudes Macedo Lemos

    2006-01-01

    Studies on the impact of Eucalyptus spp. on Brazilian soils have focused on soil chemical properties and isolating interesting microbial organisms. Few studies have focused on microbial diversity and ecology in Brazil due to limited coverage of traditional cultivation and isolation methods. Molecular microbial ecology methods based on PCR amplified 16S rDNA have enriched the knowledge of soils microbial biodiversity. The objective of this work was to compare and estimate the bacterial diversi...

  11. Biodiversity of Bacterial Ecosystems in Traditional Egyptian Domiati Cheese▿

    OpenAIRE

    El-Baradei, Gaber; Delacroix-Buchet, Agnès; Ogier, Jean-Claude

    2006-01-01

    Bacterial biodiversity occurring in traditional Egyptian soft Domiati cheese was studied by PCR-temporal temperature gel electrophoresis (TTGE) and PCR-denaturing gradient gel electrophoresis (DGGE). Bands were identified using a reference species database (J.-C. Ogier et al., Appl. Environ. Microbiol. 70:5628-5643, 2004); de novo bands having nonidentified migration patterns were identified by DNA sequencing. Results reveal a novel bacterial profile and extensive bacterial biodiversity in Do...

  12. Extraction of Bacterial RNA from Soil: Challenges and Solutions

    OpenAIRE

    Wang, Yong; Hayatsu, Masahito; Fujii, Takeshi

    2012-01-01

    Detection of bacterial gene expression in soil emerged in the early 1990s and provided information on bacterial responses in their original soil environments. As a key procedure in the detection, extraction of bacterial RNA from soil has attracted much interest, and many methods of soil RNA extraction have been reported in the past 20 years. In addition to various RT-PCR-based technologies, new technologies for gene expression analysis, such as microarrays and high-throughput sequencing techn...

  13. Xylella Genomics and Bacterial Pathogenicity to Plants

    OpenAIRE

    Dow, J. M.; Daniels, M. J.

    2000-01-01

    Xylella fastidiosa, a pathogen of citrus, is the first plant pathogenic bacterium for which the complete genome sequence has been published. Inspection of the sequence reveals high relatedness to many genes of other pathogens, notably Xanthomonas campestris. Based on this, we suggest that Xylella possesses certain easily testable properties that contribute to pathogenicity. We also present some general considerations for deriving information on pathogenicity from bacterial genomics.

  14. Impact of recombination on bacterial evolution

    OpenAIRE

    Didelot, Xavier; Maiden, Martin C. J.

    2010-01-01

    Genetic exchange plays a defining role in the evolution of many bacteria. The recent accumulation of nucleotide sequence data from multiple members of diverse bacterial genera has facilitated comparative studies that have revealed many features of this process. Here we focus on genetic exchange that has involved homologous recombination and illustrate how nucleotide sequence data have furthered our understanding of: (i) the frequency of recombination; (ii) the impact of recombination in diffe...

  15. Bacterial community analysis of Indonesian hot springs.

    Science.gov (United States)

    Baker, G C; Gaffar, S; Cowan, D A; Suharto, A R

    2001-06-12

    We report the first attempts to describe thermophilic bacterial communities in Indonesia's thermal springs using molecular phylogenetic analyses. 16S rRNA genes from laboratory cultures and DNA directly amplified from three hot springs in West Java were sequenced. The 22 sequences obtained were assignable to the taxa Proteobacteria, Bacillus and Flavobacterium, including a number of clades not normally associated with thermophily. PMID:11410357

  16. Identification of Genes Putatively Involved in Chitin Metabolism and Insecticide Detoxification in the Rice Leaf Folder (Cnaphalocrocis medinalis) Larvae through Transcriptomic Analysis

    OpenAIRE

    Hai-Zhong Yu; De-Fu Wen; Wan-Lin Wang; Lei Geng; Yan Zhang; Jia-Ping Xu

    2015-01-01

    The rice leaf roller (Cnaphalocrocis medinalis) is one of the most destructive agricultural pests. Due to its migratory behavior, it is difficult to control worldwide. To date, little is known about major genes of C. medinalis involved in chitin metabolism and insecticide detoxification. In order to obtain a comprehensive genome dataset of C. medinalis, we conducted de novo transcriptome sequencing which focused on the major feeding stage of fourth-instar larvae, and our work revealed usef...

  17. Bacterial Nail Infection (Paronychia)

    Science.gov (United States)

    ... of nail infection is often caused by a bacterial infection but may also be caused by herpes, a ... to a type of yeast called Candida , or bacterial infection, and this may lead to abnormal nail growth. ...

  18. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach that....... As such, adhesion represents the Achilles heel of crucial pathogenic functions. It follows that interference with adhesion can reduce bacterial virulence. Here, we illustrate this important topic with examples of techniques being developed that can inhibit bacterial adhesion. Some of these will...

  19. A new experimental approach for studying bacterial genomic island evolution identifies island genes with bacterial host-specific expression patterns

    OpenAIRE

    Nickerson Cheryl A; Wilson James W

    2006-01-01

    Abstract Background Genomic islands are regions of bacterial genomes that have been acquired by horizontal transfer and often contain blocks of genes that function together for specific processes. Recently, it has become clear that the impact of genomic islands on the evolution of different bacterial species is significant and represents a major force in establishing bacterial genomic variation. However, the study of genomic island evolution has been mostly performed at the sequence level usi...

  20. Role of cytochrome P450s in insecticide resistance: impact on the control of mosquito-borne diseases and use of insecticides on Earth

    OpenAIRE

    David, J.-P.; Ismail, H M; Chandor-Proust, A.; Paine, M. J. I.

    2013-01-01

    The fight against diseases spread by mosquitoes and other insects has enormous environmental, economic and social consequences. Chemical insecticides remain the first line of defence but the control of diseases, especially malaria and dengue fever, is being increasingly undermined by insecticide resistance. Mosquitoes have a large repertoire of P450s (over 100 genes). By pinpointing the key enzymes associated with insecticide resistance we can begin to develop new tools to aid the implementat...

  1. Impact of insecticides on wild fauna: a proposed toxicity index

    OpenAIRE

    Cooper, J.F.; Wynn, N.R.; Deuse, J.P.L.; Coste, C. M.; Zheng, S. Q.; Schiffers, Bruno

    1997-01-01

    The risks to fauna associated with the use of pesticides are generally known for individual pesticides. There exists, however, a lack of pub Iished material providing comparative coverage of all pesticides, although some partial compilations have been published. ln an attempt to redress this situation, we propose here a Toxicity Index covering fish, birds and bees for 169 currently available insecticides.

  2. Seed coating with a neonicotinoid insecticide negatively affects wild bees.

    Science.gov (United States)

    Rundlöf, Maj; Andersson, Georg K S; Bommarco, Riccardo; Fries, Ingemar; Hederström, Veronica; Herbertsson, Lina; Jonsson, Ove; Klatt, Björn K; Pedersen, Thorsten R; Yourstone, Johanna; Smith, Henrik G

    2015-05-01

    Understanding the effects of neonicotinoid insecticides on bees is vital because of reported declines in bee diversity and distribution and the crucial role bees have as pollinators in ecosystems and agriculture. Neonicotinoids are suspected to pose an unacceptable risk to bees, partly because of their systemic uptake in plants, and the European Union has therefore introduced a moratorium on three neonicotinoids as seed coatings in flowering crops that attract bees. The moratorium has been criticized for being based on weak evidence, particularly because effects have mostly been measured on bees that have been artificially fed neonicotinoids. Thus, the key question is how neonicotinoids influence bees, and wild bees in particular, in real-world agricultural landscapes. Here we show that a commonly used insecticide seed coating in a flowering crop can have serious consequences for wild bees. In a study with replicated and matched landscapes, we found that seed coating with Elado, an insecticide containing a combination of the neonicotinoid clothianidin and the non-systemic pyrethroid β-cyfluthrin, applied to oilseed rape seeds, reduced wild bee density, solitary bee nesting, and bumblebee colony growth and reproduction under field conditions. Hence, such insecticidal use can pose a substantial risk to wild bees in agricultural landscapes, and the contribution of pesticides to the global decline of wild bees may have been underestimated. The lack of a significant response in honeybee colonies suggests that reported pesticide effects on honeybees cannot always be extrapolated to wild bees. PMID:25901681

  3. Pyrethroid insecticides in urban salmon streams of the Pacific Northwest

    International Nuclear Information System (INIS)

    Urban streams of the Pacific Northwest provide spawning and rearing habitat for a variety of salmon species, and food availability for developing salmon could be adversely affected by pesticide residues in these waterbodies. Sediments from Oregon and Washington streams were sampled to determine if current-use pyrethroid insecticides from residential neighborhoods were reaching aquatic habitats, and if they were at concentrations acutely toxic to sensitive invertebrates. Approximately one-third of the 35 sediment samples contained measurable pyrethroids. Bifenthrin was the pyrethroid of greatest concern with regards to aquatic life toxicity, consistent with prior studies elsewhere. Toxicity to Hyalella azteca and/or Chironomus dilutus was found in two sediment samples at standard testing temperature (23 deg. C), and in one additional sample at a more environmentally realistic temperature (13 deg. C). Given the temperature dependency of pyrethroid toxicity, low temperatures typical of northwest streams can increase the potential for toxicity above that indicated by standard testing protocols. - Highlights: → Salmon-bearing creeks can be adversely impacted by insecticides from urban runoff. → Pyrethroid insecticides were found in one-third of the creeks in Washington and Oregon. → Two creeks contained concentrations acutely lethal to sensitive invertebrates. → Bifenthrin was of greatest concern, though less than in prior studies. → Standard toxicity testing underestimates the ecological risk of pyrethroids. - Pyrethroid insecticides are present in sediments of urban creeks of Oregon and Washington, though less commonly than in studies elsewhere in the U.S.

  4. Metaflumizone is a novel sodium channel blocker insecticide.

    Science.gov (United States)

    Salgado, V L; Hayashi, J H

    2007-12-15

    Metaflumizone is a novel semicarbazone insecticide, derived chemically from the pyrazoline sodium channel blocker insecticides (SCBIs) discovered at Philips-Duphar in the early 1970s, but with greatly improved mammalian safety. This paper describes studies confirming that the insecticidal action of metaflumizone is due to the state-dependent blockage of sodium channels. Larvae of the moth Spodoptera eridania injected with metaflumizone became paralyzed, concomitant with blockage of all nerve activity. Furthermore, tonic firing of abdominal stretch receptor organs from Spodoptera frugiperda was blocked by metaflumizone applied in the bath, consistent with the block of voltage-dependent sodium channels. Studies on native sodium channels, in primary-cultured neurons isolated from the CNS of the larvae of the moth Manduca sexta and on Para/TipE sodium channels heterologously expressed in Xenopus (African clawed frog) oocytes, confirmed that metaflumizone blocks sodium channels by binding selectively to the slow-inactivated state, which is characteristic of the SCBIs. The results confirm that metaflumizone is a novel sodium channel blocker insecticide. PMID:17959312

  5. Paraoxonase 1 (PON1) Status and Risk of Insecticide Exposure

    Energy Technology Data Exchange (ETDEWEB)

    Furlong, Clement E.; Cole, Toby B.; Walter, Betsy J.; Shih, Diana M.; Tward, Aaron; Lusis, Aldons J.; Timchalk, Chuck; Richter, Rebecca J.; Costa, Lucio G.

    2005-06-23

    Paraoxonase 1 (PON1) is an HDL associated enzyme that catalyzes a number of different reactions including the hydrolysis of the toxic oxon metabolites of the insecticides diazinon and chlorpyrifos. PON1 has also been implicated in the detoxication of oxidized lipids and the metabolism of a number of drugs, activating some, while inactivating others. There are two common PON1 coding region polymorphisms (L55M and Q192R). The latter determines the catalytic efficiency of hydrolysis of a number of substrates including chlorpyrifos oxon, but not diazoxon. Evidence for the physiological importance of PON1 in modulating exposures to these two insecticides comes from several different studies. Early studies noted that species with high levels of PON1 were much more resistant to certain organophosphorus (OP) insecticides than were species with low levels. Another early study by Main demonstrated that injected rabbit paraoxonase protected rats from paraoxon toxicity. Our research group began the development of a mouse model system for examining the importance of PON1 in the detoxication of OP insecticides.

  6. How heterogeneous is the involvement of ABC transporters against insecticides?

    Science.gov (United States)

    Porretta, Daniele; Epis, Sara; Mastrantonio, Valentina; Ferrari, Marco; Bellini, Romeo; Favia, Guido; Urbanelli, Sandra

    2016-05-01

    Understanding the molecular mechanisms underlying cellular defense against xenobiotic compounds is a main research issue in medical and veterinary entomology, as insecticide/acaricide resistance is a major threat in the control of arthropods. ABC transporters are recognized as a component of the detoxifying mechanism in arthropods. We investigated the possible involvement of ABC transporters in defense to the organophosphate insecticide temephos in the malarial vector Anopheles stephensi. We performed bioassays on larvae of An. stephensi, using insecticide alone and in combination with ABC-transporter inhibitors, to assess synergism between these compounds. Next, we investigated the expression profiles of six ABC transporter genes in larvae exposed to temephos. Surprisingly, neither bioassays nor gene expression analyses provided any evidence for a major role of ABC transporters in defense against temephos in An. stephensi. We thus decided to review existing literature to generate a record of other studies that failed to reveal a role for ABC transporters against particular insecticides/acaricides. A review of the scientific literature led to the recovery of 569 papers about ABC transporters; among these, 50 involved arthropods, and 10 reported negative results. Our study on An. stephensi and accompanying literature review highlight the heterogeneity that exists in ABC transporter involvement in defense/resistance mechanisms in arthropods. PMID:26855383

  7. Pyrethroid insecticides in urban salmon streams of the Pacific Northwest

    Energy Technology Data Exchange (ETDEWEB)

    Weston, D.P., E-mail: dweston@berkeley.edu [Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg., Berkeley, CA 94720-3140 (United States); Asbell, A.M., E-mail: aasbell@berkeley.edu [Department of Integrative Biology, University of California, 3060 Valley Life Sciences Bldg., Berkeley, CA 94720-3140 (United States); Hecht, S.A., E-mail: scott.hecht@noaa.gov [NOAA Fisheries, Office of Protected Resources, 510 Desmond Drive S.E., Lacey, WA 98503 (United States); Scholz, N.L., E-mail: nathaniel.scholz@noaa.gov [NOAA Fisheries, Northwest Fisheries Science Center, 2725 Montlake Blvd. E., Seattle, WA 98112 (United States); Lydy, M.J., E-mail: mlydy@siu.edu [Fisheries and Illinois Aquaculture Center and Department of Zoology, Southern Illinois University, 171 Life Sciences II, Carbondale, IL 62901 (United States)

    2011-10-15

    Urban streams of the Pacific Northwest provide spawning and rearing habitat for a variety of salmon species, and food availability for developing salmon could be adversely affected by pesticide residues in these waterbodies. Sediments from Oregon and Washington streams were sampled to determine if current-use pyrethroid insecticides from residential neighborhoods were reaching aquatic habitats, and if they were at concentrations acutely toxic to sensitive invertebrates. Approximately one-third of the 35 sediment samples contained measurable pyrethroids. Bifenthrin was the pyrethroid of greatest concern with regards to aquatic life toxicity, consistent with prior studies elsewhere. Toxicity to Hyalella azteca and/or Chironomus dilutus was found in two sediment samples at standard testing temperature (23 deg. C), and in one additional sample at a more environmentally realistic temperature (13 deg. C). Given the temperature dependency of pyrethroid toxicity, low temperatures typical of northwest streams can increase the potential for toxicity above that indicated by standard testing protocols. - Highlights: > Salmon-bearing creeks can be adversely impacted by insecticides from urban runoff. > Pyrethroid insecticides were found in one-third of the creeks in Washington and Oregon. > Two creeks contained concentrations acutely lethal to sensitive invertebrates. > Bifenthrin was of greatest concern, though less than in prior studies. > Standard toxicity testing underestimates the ecological risk of pyrethroids. - Pyrethroid insecticides are present in sediments of urban creeks of Oregon and Washington, though less commonly than in studies elsewhere in the U.S.

  8. Environmental insecticide residues from tsetse fly control measures in Uganda

    International Nuclear Information System (INIS)

    Up to June 1974 areas in Uganda totalling 8600km2 have been successfully reclaimed from tsetse fly infestation by ground spray of 3% dieldrin water emulsions. A search for equally effective but less persistent and toxic compounds against tsetse flies has been unsuccessful. Fourteen insecticide formulations have been tested for their persistence on tree bark surfaces and, therefore, their availability and toxicity to the target tsetse flies. Only those compounds with a high immediate insecticidal activity (some higher than dieldrin) like endosulfan, Chlorfenvinphos and propoxur could merit further consideration in tsetse control. While some were toxic to tsetse as fresh deposits, they lacked sufficient persistence. A study of the environmental implication from the continued use of the highly persistent and toxic dieldrin has provided useful data on residues likely to be found both in terrestrial and aquatic fauna and flora. These are generally low. Moreover, there is evidence of degradation in some fish species (Protopterus aethiopicus and Clarias). Also, dilution factors and adsorption involving the muddy nature of water run-off, etc., and controlled burning of grasses after tsetse eradication would tend to inactivate the residual insecticide and protect aquatic systems. The general findings have indicated less risk than anticipated of the environmental contamination from tsetse control by application of persistent and toxic insecticides. (author)

  9. Microbial minimalism: genome reduction in bacterial pathogens.

    Science.gov (United States)

    Moran, Nancy A

    2002-03-01

    When bacterial lineages make the transition from free-living or facultatively parasitic life cycles to permanent associations with hosts, they undergo a major loss of genes and DNA. Complete genome sequences are providing an understanding of how extreme genome reduction affects evolutionary directions and metabolic capabilities of obligate pathogens and symbionts. PMID:11893328

  10. Agricultural insecticides threaten surface waters at the global scale.

    Science.gov (United States)

    Stehle, Sebastian; Schulz, Ralf

    2015-05-01

    Compared with nutrient levels and habitat degradation, the importance of agricultural pesticides in surface water may have been underestimated due to a lack of comprehensive quantitative analysis. Increasing pesticide contamination results in decreasing regional aquatic biodiversity, i.e., macroinvertebrate family richness is reduced by ∼30% at pesticide concentrations equaling the legally accepted regulatory threshold levels (RTLs). This study provides a comprehensive metaanalysis of 838 peer-reviewed studies (>2,500 sites in 73 countries) that evaluates, for the first time to our knowledge on a global scale, the exposure of surface waters to particularly toxic agricultural insecticides. We tested whether measured insecticide concentrations (MICs; i.e., quantified insecticide concentrations) exceed their RTLs and how risks depend on insecticide development over time and stringency of environmental regulation. Our analysis reveals that MICs occur rarely (i.e., an estimated 97.4% of analyses conducted found no MICs) and there is a complete lack of scientific monitoring data for ∼90% of global cropland. Most importantly, of the 11,300 MICs, 52.4% (5,915 cases; 68.5% of the sites) exceeded the RTL for either surface water (RTLSW) or sediments. Thus, the biological integrity of global water resources is at a substantial risk. RTLSW exceedances depend on the catchment size, sampling regime, and sampling date; are significantly higher for newer-generation insecticides (i.e., pyrethroids); and are high even in countries with stringent environmental regulations. These results suggest the need for worldwide improvements to current pesticide regulations and agricultural pesticide application practices and for intensified research efforts on the presence and effects of pesticides under real-world conditions. PMID:25870271

  11. The rare bacterial biosphere.

    Science.gov (United States)

    Pedrós-Alió, Carlos

    2012-01-01

    All communities are dominated by a few species that account for most of the biomass and carbon cycling. On the other hand, a large number of species are represented by only a few individuals. In the case of bacteria, these rare species were until recently invisible. Owing to their low numbers, conventional molecular techniques could not retrieve them. Isolation in pure culture was the only way to identify some of them, but current culturing techniques are unable to isolate most of the bacteria in nature. The recent development of fast and cheap high-throughput sequencing has begun to allow access to the rare species. In the case of bacteria, the exploration of this rare biosphere has several points of interest. First, it will eventually produce a reasonable estimate of the total number of bacterial taxa in the oceans; right now, we do not even know the right order of magnitude. Second, it will answer the question of whether "everything is everywhere." Third, it will require hypothesizing and testing the ecological mechanisms that allow subsistence of many species in low numbers. And fourth, it will open an avenue of research into the immense reserve of genes with potential applications hidden in the rare biosphere. PMID:22457983

  12. Insecticidal genes of Yersinia spp.: taxonomical distribution, contribution to toxicity towards Manduca sexta and Galleria mellonella, and evolution

    Directory of Open Access Journals (Sweden)

    Schachtner Joachim

    2008-12-01

    Full Text Available Abstract Background Toxin complex (Tc proteins termed TcaABC, TcdAB, and TccABC with insecticidal activity are present in a variety of bacteria including the yersiniae. Results The tc gene sequences of thirteen Yersinia strains were compared, revealing a high degree of gene order conservation, but also remarkable differences with respect to pseudogenes, sequence variability and gene duplications. Outside the tc pathogenicity island (tc-PAIYe of Y. enterocolitica strain W22703, a pseudogene (tccC2'/3' encoding proteins with homology to TccC and similarity to tyrosine phosphatases at its C-terminus was identified. PCR analysis revealed the presence of the tc-PAIYe and of tccC2'/3'-homologues in all biotype 2–5 strains tested, and their absence in most representatives of biotypes 1A and 1B. Phylogenetic analysis of 39 TccC sequences indicates the presence of the tc-PAIYe in an ancestor of Yersinia. Oral uptake experiments with Manduca sexta revealed a higher larvae lethality of Yersinia strains harbouring the tc-PAIYe in comparison to strains lacking this island. Following subcutaneous infection of Galleria mellonella larvae with five non-human pathogenic Yersinia spp. and four Y. enterocolitica strains, we observed a remarkable variability of their insecticidal activity ranging from 20% (Y. kristensenii to 90% (Y. enterocolitica strain 2594 dead larvae after five days. Strain W22703 and its tcaA deletion mutant did not exhibit a significantly different toxicity towards G. mellonella. These data confirm a role of TcaA upon oral uptake only, and suggest the presence of further insecticidal determinants in Yersinia strains formerly unknown to kill insects. Conclusion This study investigated the tc gene distribution among yersiniae and the phylogenetic relationship between TccC proteins, thus contributing novel aspects to the current discussion about the evolution of insecticidal toxins in the genus Yersinia. The toxic potential of several Yersinia

  13. Bacterial sex in dental plaque

    Directory of Open Access Journals (Sweden)

    Ingar Olsen

    2013-06-01

    Full Text Available Genes are transferred between bacteria in dental plaque by transduction, conjugation, and transformation. Membrane vesicles can also provide a mechanism for horizontal gene transfer. DNA transfer is considered bacterial sex, but the transfer is not parallel to processes that we associate with sex in higher organisms. Several examples of bacterial gene transfer in the oral cavity are given in this review. How frequently this occurs in dental plaque is not clear, but evidence suggests that it affects a number of the major genera present. It has been estimated that new sequences in genomes established through horizontal gene transfer can constitute up to 30% of bacterial genomes. Gene transfer can be both inter- and intrageneric, and it can also affect transient organisms. The transferred DNA can be integrated or recombined in the recipient's chromosome or remain as an extrachromosomal inheritable element. This can make dental plaque a reservoir for antimicrobial resistance genes. The ability to transfer DNA is important for bacteria, making them better adapted to the harsh environment of the human mouth, and promoting their survival, virulence, and pathogenicity.

  14. Bacterial PCR in the diagnosis of joint infection

    OpenAIRE

    Jalava, J; Skurnik, M. (M.); Toivanen, A; P. Toivanen; Eerola, E

    2001-01-01

    OBJECTIVES—To evaluate the value of broad range bacterial PCR in the diagnosis of joint infection and to find out if there are bacteria causing arthritis which are not cultivable by the present methods.
METHODS—Polymerase chain reaction (PCR) with broad range bacterial primers and DNA sequencing (bacterial PCR) was used to analyse 154 synovial fluid (SF) samples from patients with different arthritic diseases.
RESULTS—Bacterial DNA was detected in 18 SF samples, including samples from six pat...

  15. Crossroads between Bacterial and Mammalian Glycosyltransferases

    Science.gov (United States)

    Brockhausen, Inka

    2014-01-01

    Bacterial glycosyltransferases (GT) often synthesize the same glycan linkages as mammalian GT; yet, they usually have very little sequence identity. Nevertheless, enzymatic properties, folding, substrate specificities, and catalytic mechanisms of these enzyme proteins may have significant similarity. Thus, bacterial GT can be utilized for the enzymatic synthesis of both bacterial and mammalian types of complex glycan structures. A comparison is made here between mammalian and bacterial enzymes that synthesize epitopes found in mammalian glycoproteins, and those found in the O antigens of Gram-negative bacteria. These epitopes include Thomsen–Friedenreich (TF or T) antigen, blood group O, A, and B, type 1 and 2 chains, Lewis antigens, sialylated and fucosylated structures, and polysialic acids. Many different approaches can be taken to investigate the substrate binding and catalytic mechanisms of GT, including crystal structure analyses, mutations, comparison of amino acid sequences, NMR, and mass spectrometry. Knowledge of the protein structures and functions helps to design GT for specific glycan synthesis and to develop inhibitors. The goals are to develop new strategies to reduce bacterial virulence and to synthesize vaccines and other biologically active glycan structures. PMID:25368613

  16. Insecticide-mediated shift in ecological dominance between two competing species of grain beetles.

    Science.gov (United States)

    Cordeiro, Erick Maurício G; Corrêa, Alberto S; Guedes, Raul Narciso C

    2014-01-01

    Competition is a driving force regulating communities often considered an intermittent phenomenon, difficult to verify and potentially driven by environmental disturbances. Insecticides are agents of environmental disturbance that can potentially change ecological relationships and competitive outcomes, but this subject has seldom been examined. As the co-existing cereal grain beetle species Sitophilus zeamais Motschulsky and Rhyzopertha dominica F. share a common realized niche, directly competing for the same resources, they were used as models in our study. Intraspecific competition experiments were performed with increasing insect densities and insecticide doses in additive and replacement series using various density combinations of both beetle species maintained on insecticide-free or -sprayed grains. Insecticide-mediated release from competitive stress was not observed in our study of intraspecific competition in grain beetles. The insecticide enhanced the effect of insect density, particularly for the maize weevil S. zeamais, further impairing population growth at high densities. Therefore, insecticide susceptibility increased with intraspecific competition favoring insecticide efficacy. However, the effect of insecticide exposure on competitive interaction extends beyond intraspecific competition, affecting interspecific competition as well. Sitophilus zeamais was the dominant species when in interspecific competition prevailing in natural conditions (without insecticide exposure), but the dominance and species prevalence shifted from S. zeamais to R. dominica under insecticide exposure. Therefore, high conspecific densities favored insecticide efficacy, but the strength of the relationship differs with the species. In addition, the insecticide mediated a shift in species dominance and competition outcome indicating that insecticides are relevant mediators of species interaction, potentially influencing community composition and raising management concerns

  17. Insecticide-mediated shift in ecological dominance between two competing species of grain beetles.

    Directory of Open Access Journals (Sweden)

    Erick Maurício G Cordeiro

    Full Text Available Competition is a driving force regulating communities often considered an intermittent phenomenon, difficult to verify and potentially driven by environmental disturbances. Insecticides are agents of environmental disturbance that can potentially change ecological relationships and competitive outcomes, but this subject has seldom been examined. As the co-existing cereal grain beetle species Sitophilus zeamais Motschulsky and Rhyzopertha dominica F. share a common realized niche, directly competing for the same resources, they were used as models in our study. Intraspecific competition experiments were performed with increasing insect densities and insecticide doses in additive and replacement series using various density combinations of both beetle species maintained on insecticide-free or -sprayed grains. Insecticide-mediated release from competitive stress was not observed in our study of intraspecific competition in grain beetles. The insecticide enhanced the effect of insect density, particularly for the maize weevil S. zeamais, further impairing population growth at high densities. Therefore, insecticide susceptibility increased with intraspecific competition favoring insecticide efficacy. However, the effect of insecticide exposure on competitive interaction extends beyond intraspecific competition, affecting interspecific competition as well. Sitophilus zeamais was the dominant species when in interspecific competition prevailing in natural conditions (without insecticide exposure, but the dominance and species prevalence shifted from S. zeamais to R. dominica under insecticide exposure. Therefore, high conspecific densities favored insecticide efficacy, but the strength of the relationship differs with the species. In addition, the insecticide mediated a shift in species dominance and competition outcome indicating that insecticides are relevant mediators of species interaction, potentially influencing community composition and raising

  18. The genome of the insecticidal Chromobacterium subtsugae PRAA4-1 and its comparison with that of Chromobacterium violaceum ATCC 12472.

    Science.gov (United States)

    Blackburn, Michael B; Sparks, Michael E; Gundersen-Rindal, Dawn E

    2016-12-01

    The genome of Chromobacterium subtsugae strain PRAA4-1, a betaproteobacterium producing insecticidal compounds, was sequenced and compared with the genome of C. violaceum ATCC 12472. The genome of C. subtsugae displayed a reduction in genes devoted to capsular and extracellular polysaccharide, possessed no genes encoding nitrate reductases, and exhibited many more phage-related sequences than were observed for C. violaceum. The genomes of both species possess a number of gene clusters predicted to encode biosynthetic complexes for secondary metabolites; these clusters suggest they produce overlapping, but distinct assortments of metabolites. PMID:27617206

  19. A comparison of bioinsecticide, Spinosad, the semi-synthetic insecticide, Spinetoram and synthetic insecticides as soil drenches for control of Tephritid fruit flies

    Science.gov (United States)

    Eight insecticides, including the natural bioinsecticide spinosad and the semi-synthetic insecticide spinetoram, as well as two synthetic pyrethroids, an insect growth regulator, an anthranilic diamide, and an organophosphate were evaluated as soil drench treatments for control of three economically...

  20. Vimentin in Bacterial Infections

    DEFF Research Database (Denmark)

    Mak, Tim N; Brüggemann, Holger

    2016-01-01

    -vimentin interactions are presented in this review: the role of vimentin in pathogen-binding on the cell surface and subsequent bacterial invasion and the interaction of cytosolic vimentin and intracellular pathogens with regards to innate immune signaling. Mechanistic insight is presented involving distinct bacterial......Despite well-studied bacterial strategies to target actin to subvert the host cell cytoskeleton, thus promoting bacterial survival, replication, and dissemination, relatively little is known about the bacterial interaction with other components of the host cell cytoskeleton, including intermediate...... filaments (IFs). IFs have not only roles in maintaining the structural integrity of the cell, but they are also involved in many cellular processes including cell adhesion, immune signaling, and autophagy, processes that are important in the context of bacterial infections. Here, we summarize the knowledge...

  1. Insecticide resistance in Culex quinquefasciatus from Zanzibar: implications for vector control programmes

    Directory of Open Access Journals (Sweden)

    Jones Christopher M

    2012-04-01

    Full Text Available Abstract Background Zanzibar has a long history of lymphatic filariasis (LF caused by the filarial parasite Wuchereria bancrofti, and transmitted by the mosquito Culex quinquefasciatus Say. The LF Programme in Zanzibar has successfully implemented mass drug administration (MDA to interrupt transmission, and is now in the elimination phase. Monitoring infections in mosquitoes, and assessing the potential role of interventions such as vector control, is important in case the disease re-emerges as a public health problem. Here, we examine Culex mosquito species from the two main islands to detect W. bancrofti infection and to determine levels of susceptibility to the insecticides used for vector control. Methods Culex mosquitoes collected during routine catches in Vitongoji, Pemba Island, and Makadara, Unguja Island were tested for W. bancrofti infection using PCR. Insecticide bioassays on Culex mosquitoes were performed to determine susceptibility to permethrin, deltamethrin, lambda-cyhalothrin, DDT and bendiocarb. Additional synergism assays with piperonyl butoxide (PBO were used for lambda-cyhalothrin. Pyrosequencing was used to determine the kdr genotype and sequencing of the mitochondrial cytochrome oxidase I (mtCOI subunit performed to identify ambiguous Culex species. Results None of the wild-caught Culex mosquitoes analysed were found to be positive for W. bancrofti. High frequencies of resistance to all insecticides were found in Wete, Pemba Island, whereas Culex from the nearby site of Tibirinzi (Pemba and in Kilimani, Unguja Island remained relatively susceptible. Species identification confirmed that mosquitoes from Wete were Culex quinquefasciatus. The majority of the Culex collected from Tibirinzi and all from Kilimani could not be identified to species by molecular assays. Two alternative kdr alleles, both resulting in a L1014F substitution were detected in Cx. quinquefasciatus from Wete with no homozygote susceptible detected

  2. Automatic sequences

    CERN Document Server

    Haeseler, Friedrich

    2003-01-01

    Automatic sequences are sequences which are produced by a finite automaton. Although they are not random they may look as being random. They are complicated, in the sense of not being not ultimately periodic, they may look rather complicated, in the sense that it may not be easy to name the rule by which the sequence is generated, however there exists a rule which generates the sequence. The concept automatic sequences has special applications in algebra, number theory, finite automata and formal languages, combinatorics on words. The text deals with different aspects of automatic sequences, in particular:· a general introduction to automatic sequences· the basic (combinatorial) properties of automatic sequences· the algebraic approach to automatic sequences· geometric objects related to automatic sequences.

  3. Horizontal gene transfer and bacterial diversity

    Indian Academy of Sciences (India)

    Chitra Dutta; Archana Pan

    2002-02-01

    Bacterial genomes are extremely dynamic and mosaic in nature. A substantial amount of genetic information is inserted into or deleted from such genomes through the process of horizontal transfer. Through the introduction of novel physiological traits from distantly related organisms, horizontal gene transfer often causes drastic changes in the ecological and pathogenic character of bacterial species and thereby promotes microbial diversification and speciation. This review discusses how the recent influx of complete chromosomal sequences of various microorganisms has allowed for a quantitative assessment of the scope, rate and impact of horizontally transmitted information on microbial evolution.

  4. Demonstrating Bacterial Flagella.

    Science.gov (United States)

    Porter, John R.; And Others

    1992-01-01

    Describes an effective laboratory method for demonstrating bacterial flagella that utilizes the Proteus mirabilis organism and a special harvesting technique. Includes safety considerations for the laboratory exercise. (MDH)

  5. Evaluation of insecticides for the control of Linepithema (Hymenoptera: Formicidae).

    Science.gov (United States)

    Nondillo, Aline; Chaves, Cindy Correa; Fialho, Flávio Bello; Bueno, Odair Correa; Botton, Marcos

    2014-02-01

    Linepithema micans (Forel) (Hymenoptera: Formicidae) is the main ant species responsible for the spreading of Eurhizococcus brasiliensis (Wille) (Hemiptera: Margarodidae), a soil scale that damages grapevine plants in southern Brazil. The effect of contact and ingestion of insecticides on the control of L. micans was evaluated in a greenhouse using grapevines (Vitis spp.) infested by L. micans. The insecticides thiamethoxam (250, 187.5, and 125 g/ha), fipronil (4, 5, and 50 ml/ha), and imidacloprid (650 g/ha) were sprayed on the ground, whereas toxic baits containing boric acid (0.5, 1.0, and 1.2%), pyriproxyfen (0.3 and 0.5%), and hydramethylnon (0.5%) were evaluated in different formulations. Hydramethylnon (toxic bait) and thiamethoxam (chemical barrier) were the most efficient active ingredients for the control of L. micans. PMID:24665704

  6. Typical Monoterpenes as Insecticides and Repellents against Stored Grain Pests

    Directory of Open Access Journals (Sweden)

    Suelen L. Reis

    2016-02-01

    Full Text Available Five monoterpenes naturally occurring in essential oils were tested for their insecticidal and repellent activities against the bruchid beetle Callosobruchus maculatus and the maize weevil Sitophilus zeamais. The monoterpenes were highly efficient as inducers of mortality or repellency against both insect species. They were more efficient in their fumigant activity against C. maculatus than against S. zeamais, while this profile of action was inverted when considering the repellent activities. Eugenol was one the most effective fumigants against both insects and one the most effective repellent against C. maculatus, while citronellal and geranial were one the most effective repellents against S. zeamais. Functional and positional isomerism of the monoterpenes pairs appears to exert little or no influence on theirs effects, especially in case of repellency. The validation of the insecticidal/repellent efficacy of isolated monoterpenes may permit a more advantageous, rapid, economic and optimized approach to the identification of promising oils for commercial formulations when combined with ethnobotanical strategies.

  7. Sorption and desorption of insecticides in Brazilian soils

    International Nuclear Information System (INIS)

    The sorption from aqueous solution of ten Brazilian soil types of four organochlorine, two organophosphorus and one carbamate insecticide was determined in the laboratory using gas chromatographic and radiometric techniques. Measurements showed that soils richest in organic matter, sorbed all substances except aldrin more strongly than the other soils. DDT was the most and aldrin the least sorbed organochlorine pesticide, being dieldrin sorbed two to four times more strongly than aldrin. Sorption of lindane varied in different soils. The organophosphate insecticides malathion and parathion were strongly sorbed in the soils richest in organic matter and weakly sorbed in the poorest soils heing moderately sorbed by the other soils. Sorption of carbaryl by all soils is small. Lindane was desorbed from the soil richest in organic matter and the extent of desorption was dependent on the sorption time. (Author)

  8. Resistance is not Futile: It Shapes Insecticide Discovery

    Directory of Open Access Journals (Sweden)

    Margaret C. Hardy

    2014-01-01

    Full Text Available Conventional chemical control compounds used for the management of insect pests have been much maligned, but still serve a critical role in protecting people and agricultural products from insect pests, as well as conserving biodiversity by eradicating invasive species. Although biological control can be an effective option for area-wide management of established pests, chemical control methods are important for use in integrated pest management (IPM programs, as well as in export treatments, eradicating recently arrived invasive species, and minimizing population explosions of vectors of human disease. Cogitated research and development programs have continued the innovation of insecticides, with a particular focus on combating insecticide resistance. Recent developments in the fields of human health, protecting the global food supply, and biosecurity will be highlighted.

  9. Synthesis and Insecticidal Activities of Novel Phthalic Acid Diamides

    Institute of Scientific and Technical Information of China (English)

    闫涛; 李玉新; 李永强; 王多义; 陈伟; 刘卓; 李正名

    2012-01-01

    In order to discover novel insecticides with the new action mode on ryanodine receptor (RyR), a series of novel phthalic acid diamide derivatives were designed and synthesized. All compounds were characterized by 1H NMR spectra and HRMS. The preliminary results of biological activity assessment indicated that some title compounds exhibited excellent insecticidal activities against Mythimna separata, Spodoptera exigua, and Plutella xylostella. The title compound 3-nitro-N-cyclopropyl-N'-[2-methyl-4-(perfluoropropan-2-yl)phenyl]phthalamidte (4a) was more efficient against diamondback moths than the control (chlorantraniliprole). The effects of some title compounds on intracellular calcium of neurons from the Spodoptera exigua proved that the title compounds were RyR activators.

  10. The impact of insecticides to local honey bee colony Apis cerana indica in laboratory condition

    Science.gov (United States)

    Putra, Ramadhani E.; Permana, Agus D.; Nuriyah, Syayidah

    2014-03-01

    Heavy use of insecticides considered as one of common practice at local farming systems. Even though many Indonesian researchers had stated the possible detrimental effect of insecticide on agriculture environment and biodiversity, researches on this subject had been neglected. Therefore, our purpose in this research is observing the impact of insecticides usage by farmer to non target organisme like local honey bee (Apis cerana indica), which commonly kept in area near agriculture system. This research consisted of field observations out at Ciburial, Dago Pakar, Bandung and laboratory tests at School of Life Sciences and Technology, Institut Teknologi Bandung. The field observations recorded visited agriculture corps and types of pollen carried by bees to the nest while laboratory test recorderd the effect of common insecticide to mortality and behavior of honey bees. Three types of insecticides used in this research were insecticides A with active agent Chlorantraniliprol 50 g/l, insecticide B with active agent Profenofos 500 g/l, and insecticides C with active agent Chlorantraniliprol 100 g/l and λ-cyhalotrin 50g/l. The results show that during one week visit, wild flower, Wedelia montana, visited by most honey bees with average visit 60 honey bees followed by corn, Zea mays, with 21 honey bees. The most pollen carried by foragers was Wedelia montana, Calliandra callothyrsus, and Zea mays. Preference test show that honeybees tend move to flowers without insecticides as the preference to insecticides A was 12.5%, insecticides B was 0%, and insecticides was C 4.2%. Mortality test showed that insecticides A has LD50 value 0.01 μg/μl, insecticide B 0.31 μg/μl, and insecticides C 0.09 μg/μl which much lower than suggested dosage recommended by insecticides producer. This research conclude that the use of insecticide could lower the pollination service provide by honey bee due to low visitation rate to flowers and mortality of foraging bees.

  11. Have Regulatory Efforts to Reduce Organophosphorus Insecticide Exposures Been Effective?

    OpenAIRE

    Clune, Alison L.; Ryan, P. Barry; Barr, Dana Boyd

    2012-01-01

    Background: The Food Quality Protection Act (FQPA) was signed into law in 1996 to strengthen the regulation of pesticide tolerances in food. Organophosphorus (OP) insecticides were the first group of pesticides reviewed by the U.S. Environmental Protection Agency (EPA) under the new law. Objective: Our goal was to determine whether urinary concentrations of dialkylphosphate (DAP) metabolites of OP pesticides declined between the National Health and Nutrition Examination Survey (NHANES) III an...

  12. Chemical Composition, Antifungal and Insecticidal Activities of Hedychium Essential Oils

    OpenAIRE

    Kanniah Rajasekaran; Jian Chen; BECNEL, JAMES J.; Natasha M. Agramonte; Bernier, Ulrich R.; Maia Tsikolia; Kemal Husnu Can Baser; Betul Demirci; David E. Wedge; Nurhayat Tabanca; Sampson, Blair J.; Hamidou F. Sakhanokho; James M. Spiers

    2013-01-01

    The antimicrobial properties of essential oils have been documented, and their use as “biocides” is gaining popularity. The aims of this study were to analyze the chemical composition and assess the biological activities of Hedychium essential oils. Oils from 19 Hedychium species and cultivars were analyzed by gas chromatography (GC) and gas chromatography-mass spectrometry (GC-MS) techniques. The antifungal and insecticidal activities of these oils were tested against Colletotrichum acutatum...

  13. Distribution of pyrethroid insecticides in secondary wastewater effluent

    OpenAIRE

    Parry, Emily; Young, Thomas M.

    2013-01-01

    Although the freely dissolved form of hydrophobic organic chemicals may best predict aquatic toxicity, differentiating between dissolved and particle bound forms is challenging at environmentally relevant concentrations for compounds with low toxicity thresholds such as pyrethroid insecticides. We investigated the distribution of pyrethroids among three forms: freely dissolved, complexed with dissolved organic carbon (DOC), and sorbed to suspended particulate matter, during a yearlong study a...

  14. Mixed function oxidases and insecticide resistance in medically important insects

    OpenAIRE

    A.A. Enayati; Ladonni, H

    2006-01-01

    MFOs are a large diverse superfamily of enzymes found in all insect tissues. They are involved in the metabolism of xenobiotics (e.g. drugs, pesticides and plant toxins) and endogenous compounds (e.g. ecdysteroids and juvenile hormones). They are also involved in bioactivation of phosphorothioate compounds such as organophosphorus insecticides. They have very diverse activities like hydroxylation, epoxidation, N-, O-or S-dealkylation, deamination, sulfoxidation, desulfuration and oxidative de...

  15. Usage Possibilities of Insecticide Effective Biocidals in Organic Agriculture

    OpenAIRE

    Şimşek, Muharrem; Yağcı, Mürşide; Erenler, Zuhal; Yaşarer, A. Haluk

    2015-01-01

    In conventional agriculture it is aimed that mainly increase in the amount of products, synthetic chemicals and fertilizers are used extensively to provide it. Today, terms such as safe food, human and environment health have become more important. Therefore, it is necessary to increase the share of organic agriculture which have less negative impacts to human health and environment, and sustainable use of natural resources. Herein environmentally insecticide effective biocidals to pest contr...

  16. Mechanism of action of organophosphorus and carbamate insecticides.

    OpenAIRE

    Fukuto, T R

    1990-01-01

    Organophosphorus and carbamate insecticides are toxic to insects and mammals by virtue of their ability to inactivate the enzyme acetylcholinesterase. This review addresses the mechanism of inhibition of acetylcholinesterase by organophosphorus and carbamate esters, focusing on structural requirements necessary for anticholinesterase activity. The inhibition of acetylcholinesterase by these compounds is discussed in terms of reactivity and steric effects. The role of metabolic activation or d...

  17. The Side Effects of Insecticide Efficient Biocidals to Beneficial Insects

    OpenAIRE

    Şimşek, Muharrem; ÖZKAN, Cem

    2015-01-01

    Unawares usage of biocidals effects not only natural resources, environment and human health but also can damage beneficial insects which suppresses pests. Herein, the side effects of insecticide efficient biocidals to important beneficial insects was handled and measures on sustainable biocidal usages was discussed. The side effects of Deltamethrin, Azadirachtin, Spinosad and Bacillus thuringinensis biocidals to certain important beneficial insects were evaluated with literature data. Negati...

  18. Bed bugs evolved unique adaptive strategy to resist pyrethroid insecticides

    OpenAIRE

    Fang Zhu; Hemant Gujar; Jennifer R. Gordon; Haynes, Kenneth F; Michael F. Potter; Palli, Subba R.

    2013-01-01

    Recent advances in genomic and post-genomic technologies have facilitated a genome-wide analysis of the insecticide resistance-associated genes in insects. Through bed bug, Cimex lectularius transcriptome analysis, we identified 14 molecular markers associated with pyrethroid resistance. Our studies revealed that most of the resistance-associated genes functioning in diverse mechanisms are expressed in the epidermal layer of the integument, which could prevent or slow down the toxin from reac...

  19. Insecticide residues cross-contamination of oilseeds during storage

    Directory of Open Access Journals (Sweden)

    Dauguet Sylvie

    2007-11-01

    Full Text Available Pesticide residues are found in oilseeds and crude oils: they are mainly organophosphate insecticides (pirimiphos-methyl, dichlorvos, malathion used in empty storage facilities and for application to stored cereal grains. Even if pests are found in stored oilseeds, French regulation does not permit use of these insecticides on stored oilseeds, as they have affinity for these lipophilic subtances. These residues arise from cross-contamination during mechanical contact with storage bins and grain handling equipment, and not from illegal use. This uptake of insecticide residues from their storage environment by oilseeds can lead to levels that exceed regulatory limits. An investigation of 11 grain storage companies allowed us to follow the course of 27 sunflower seeds batches, from reception at the storage facilities to outloading. Samples from each of these batches, made at outloading, were analysed content for insecticide residues. Traceability of sunflower seeds established by storers allowed us to identify the origine of observed cross-contamination cases. Substances discovered were dichlorvos, pirimiphos-methyl and malathion (and chlorpyriphos-methyl in a single case. Pirimiphos-methyl was most commonly detected, but most cases of non-accordance with regulatory levels were observed with dichlorvos and malathion. Main cross-contamination hazard resulted from treatment of cereals at outloading, just before sunflower seeds were outloaded, especially when these cereals treatments were frequent on that elevator. Other situations led to cross-contaminations, but generally of lower levels: outloading of sunflower seeds after outloading of cereal that was treated at the reception, several weeks or months before; sunflower seeds stored in bin that contained previously treated cereal; empty bins and handling equipment treated before receipt of sunflower seeds.

  20. Exogenous lipoid pneumonia induced by aspiration of insecticide.

    Science.gov (United States)

    Ishimatsu, Keisuke; Kamitani, Takeshi; Matsuo, Yoshio; Hatakenaka, Masamitsu; Sunami, Shunya; Jinnouchi, Mikako; Nagao, Michinobu; Yabuuchi, Hidetake; Honda, Hiroshi

    2012-01-01

    Exogenous lipoid pneumonia is a rare disorder caused by inhalation and/or aspiration of oil-based substances. The confirmed diagnosis of exogenous lipoid pneumonia is difficult, especially in cases for which it is impossible to ascertain a history of inhalation or aspiration. We present a case of exogenous lipoid pneumonia due to aspiration of insecticide, for which the computed tomography findings of fat attenuation within the lesion were helpful in reaching a correct diagnosis. PMID:21952608

  1. Insecticidal properties of a Chenopodium-based botanical.

    Science.gov (United States)

    Chiasson, H; Vincent, C; Bostanian, N J

    2004-08-01

    The emulsifiable concentrate UDA-245 based on an essential oil extract from Chenopodium ambrosioides variety near ambrosioides, a North American herbaceous plant, was compared with commercially available pesticides for their effectiveness to control green peach aphid, Myzus persicae (Sulzer) (Homoptera: Aphididae), western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), and greenhouse whitefly, Trialeurodes vaporariorium (Westwood) (Homoptera: Aleyrodidae). Side effects on the whitefly parasitoid Encarsia formosa Gahan (Hymenoptera: Aphelinidae) also were determined. With green peach aphid, UDA-245 at 0.5% concentration was significantly more effective than the control (water) treatment in a laboratory bioassay and significantly more effective than neem oil and the control treatment and as effective as insecticidal soap in a greenhouse assay. With the western flower thrips, UDA-245 at 0.5% was significantly more effective than neem oil, insecticidal soap and the control treatment in a laboratory bioassay, whereas in a greenhouse assay, UDA-245 at 1.0% was the only treatment that maintained control of the western flower thrips 2 wk after the last treatment period. UDA-245 at 0.5% (laboratory bioassay) was significantly more effective in managing greenhouse whitefly than neem oil, endosulfan, and the control treatment and as effective as insecticidal soap. Insecticidal soap proved to be toxic to the parasitoid E. formosa (71.9% mortality), whereas UDA-245 at 0.5% was not significantly more toxic than the control (11.2 and 4.6% mortality, respectively). Our results suggest that a greenhouse integrated pest management (IPM) program using a botanical such as UDA-245 could effectively control infestations of major pests present while having a negligible effect on biological control agents. PMID:15384351

  2. Typical Monoterpenes as Insecticides and Repellents against Stored Grain Pests

    OpenAIRE

    Reis, Suelen L; Anieli G. Mantello; Jeferson M. Macedo; Erica A. Gelfuso; da Silva, Cássio P.; Fachin, Ana L.; Alexandre M. Cardoso; Rene O. Beleboni

    2016-01-01

    Five monoterpenes naturally occurring in essential oils were tested for their insecticidal and repellent activities against the bruchid beetle Callosobruchus maculatus and the maize weevil Sitophilus zeamais. The monoterpenes were highly efficient as inducers of mortality or repellency against both insect species. They were more efficient in their fumigant activity against C. maculatus than against S. zeamais, while this profile of action was inverted when considering the repellent activities...

  3. Sucrose Improves Insecticide Activity Against Drosophila suzukii (Diptera: Drosophilidae).

    Science.gov (United States)

    Cowles, Richard S; Rodriguez-Saona, Cesar; Holdcraft, Robert; Loeb, Gregory M; Elsensohn, Johanna E; Hesler, Steven P

    2015-04-01

    The addition of sucrose to insecticides targeting spotted wing drosophila, Drosophila suzukii (Matsumura), enhanced lethality in laboratory, semifield, and field tests. In the laboratory, 0.1% sucrose added to a spray solution enhanced spotted wing drosophila feeding. Flies died 120 min earlier when exposed to spinosad residues at label rates enhanced with sucrose. Added sucrose reduced the LC50 for dried acetamiprid residues from 82 to 41 ppm in the spray solution. Laboratory bioassays of spotted wing drosophila mortality followed exposure to grape and blueberry foliage and/or fruit sprayed and aged in the field. On grape foliage, the addition of 2.4 g/liter of sugar with insecticide sprays resulted in an 11 and 6% increase of spotted wing drosophila mortality at 1 and 2 d exposures to residues, respectively, averaged over seven insecticides with three concentrations. In a separate experiment, spinetoram and cyantraniliprole reduced by 95-100% the larval infestation of blueberries, relative to the untreated control, 7 d after application at labeled rates when applied with 1.2 g/liter sucrose in a spray mixture, irrespective of rainfall; without sucrose infestation was reduced by 46-91%. Adding sugar to the organically acceptable spinosyn, Entrust, reduced larval infestation of strawberries by >50% relative to without sugar for five of the six sample dates during a season-long field trial. In a small-plot field test with blueberries, weekly applications in alternating sprays of sucrose plus reduced-risk insecticides, spinetoram or acetamiprid, reduced larval infestation relative to the untreated control by 76%; alternating bifenthrin and phosmet (without sucrose) reduced infestation by 65%. PMID:26470175

  4. Cloning and heterologous expression of a novel insecticidal gene (tccC1) from Xenorhabdus nematophilus strain

    International Nuclear Information System (INIS)

    We have identified and cloned a novel toxin gene (tccC1/xptB1) from Xenorhabdus nematophilus strain isolated from Korea-specific entomophagous nematode Steinernema glaseri MK. The DNA sequence of cloned toxin gene (3048 bp) has an open reading frame encoding 1016 amino acids with a predicted molecular mass of 111058 Da. The toxin sequence shares 50-96% identical amino acid residues with the previously reported tccC1 cloned from X. nematophilus (AJ308438), Photorhabdus luminescens W14 (AF346499) P. luminescens TTO1 (BX571873), and Yersinia pestis CO92 (NC003143). The toxin gene was successfully expressed in Escherichia coli, and the recombinant toxin protein caused a rapid cessation in mortality of Galleria mellonella larvae (80% death of larvae within 2 days). Conclusively, the heterologous expression of the novel gene tccC1 cloned into E. coli plasmid vector produced recombinant toxin with high insecticidal activity

  5. Biochemical and microbial soil functioning after application of the insecticide imidacloprid

    Institute of Scientific and Technical Information of China (English)

    Mariusz Cyco(n); Zofia Piotrowska-Seget

    2015-01-01

    Imidacloprid is one of the most commonly used insecticides in agricultural practice,and its application poses a potential risk for soil microorganisms.The objective of this study was to assess whether changes in the structure of the soil microbial community after imidacloprid application at the field rate (FR,1 mg/kg soil) and 10 times the FR (10× FR,10 mg/kg soil)may also have an impact on biochemical and microbial soil functioning.The obtained data showed a negative effect by imidacloprid applied at the FR dosage for substrate-induced respiration (SIR),the number of total bacteria,dehydrogenase (DHA),both phosphatases (PHOS-H and PHOS-OH),and urease (URE) at the beginning of the experiment.In 10× FR treated soil,decreased activity of SIR,DHA,PHOS-OH and PHOS-H was observed over the experimental period.Nitrifying and N2-fixing bacteria were the most sensitive to imidacloprid.The concentration of NO3-decreased in both imidacloprid-treated soils,whereas the concentration of NH4+ in soil with 10× FR was higher than in the control.Analysis of the bacterial growth strategy revealed that imidacloprid affected the r-or K-type bacterial classes as indicated also by the decreased eco-physiological (EP) index.Imidacloprid affected the physiological state of culturable bacteria and caused a reduction in the rate of colony formation as well as a prolonged time for growth.Principal component analysis showed that imidacloprid application significantly shifted the measured parameters,and the application of imidacloprid may pose a potential risk to the biochemical and microbial activity of soils.

  6. Potent Insecticidal Secondary Metabolites from the Medicinal Plant Acanthus montanus

    Directory of Open Access Journals (Sweden)

    Elham Amin

    2012-03-01

    Full Text Available Acanthus montanus (Nees T. Anders. (Family: Acanthaceae is a small shrub with sparse branches and soft stems, widespread in Africa, the Balkans, Romania, Greece and Eastern Mediterranean. Documented evidence showed that the leaves of the plant possess spasmolytic, analgesic, anti-inflammatory and antipyretic activities. In our ongoing research project; aimed at identifying new natural compounds with insecticidal activity, the alcohol extract of the aerial parts of A. montanus exhibited a significant activity against adult Aedes aegypti. Phytochemical study of the plant has resulted in isolation of nine compounds, eight of which exhibit variable degrees of insecticidal activity. β-sitosterol-3-O- β –D-glucoside (1 exhibited potent mosquitocidal activity (100% mortality against adult Aedes aegypti at 1.25 μg/mg concentration, followed by palmitic acid (2 (90%, linaroside (3 (80%, and acetoside (9 (70% respectively. It is noteworthy that this is the first report of insecticidal activity of β-sitosterol-3-O- β –D-glucoside, linaroside and acetoside.

  7. Minireview: Mode of action of meta-diamide insecticides.

    Science.gov (United States)

    Nakao, Toshifumi; Banba, Shinichi

    2015-06-01

    Meta-diamides [3-benzamido-N-(4-(perfluoropropan-2-yl)phenyl)benzamides] are a distinct class of RDL GABA receptor noncompetitive antagonists showing high insecticidal activity against Spodoptera litura. The mode of action of the meta-diamides was demonstrated to be distinct from that of conventional noncompetitive antagonists (NCAs) such as fipronil, picrotoxin, lindane, dieldrin, and α-endosulfan. It was suggested that meta-diamides act at or near G336 in the M3 region of the Drosophila RDL GABA receptor. Although the site of action of the meta-diamides appears to overlap with that of macrocyclic lactones including avermectins and milbemycins, differential effects of mutations on the actions of the meta-diamides and the macrocyclic lactones were observed. Molecular modeling studies revealed that the meta-diamides may bind to an inter-subunit pocket near G336 in the Drosophila RDL GABA receptor better when in the closed state, which is distinct from the NCA-binding site, which is in a channel formed by M2s. In contrast, the macrocyclic lactones were suggested to bind to an inter-subunit pocket near G336 in the Drosophila RDL GABA receptor when in the open state. Furthermore, mechanisms underlying the high selectivity of meta-diamides are discussed. This minireview highlights the unique features of novel meta-diamide insecticides and demonstrates why meta-diamides are anticipated to become prominent insecticides that are effective against pests resistant to cyclodienes and fipronil. PMID:26047110

  8. Neonicotinoid insecticides can serve as inadvertent insect contraceptives.

    Science.gov (United States)

    Straub, Lars; Villamar-Bouza, Laura; Bruckner, Selina; Chantawannakul, Panuwan; Gauthier, Laurent; Khongphinitbunjong, Kitiphong; Retschnig, Gina; Troxler, Aline; Vidondo, Beatriz; Neumann, Peter; Williams, Geoffrey R

    2016-07-27

    There is clear evidence for sublethal effects of neonicotinoid insecticides on non-target ecosystem service-providing insects. However, their possible impact on male insect reproduction is currently unknown, despite the key role of sex. Here, we show that two neonicotinoids (4.5 ppb thiamethoxam and 1.5 ppb clothianidin) significantly reduce the reproductive capacity of male honeybees (drones), Apis mellifera Drones were obtained from colonies exposed to the neonicotinoid insecticides or controls, and subsequently maintained in laboratory cages until they reached sexual maturity. While no significant effects were observed for male teneral (newly emerged adult) body mass and sperm quantity, the data clearly showed reduced drone lifespan, as well as reduced sperm viability (percentage living versus dead) and living sperm quantity by 39%. Our results demonstrate for the first time that neonicotinoid insecticides can negatively affect male insect reproductive capacity, and provide a possible mechanistic explanation for managed honeybee queen failure and wild insect pollinator decline. The widespread prophylactic use of neonicotinoids may have previously overlooked inadvertent contraceptive effects on non-target insects, thereby limiting conservation efforts. PMID:27466446

  9. Complexation of insecticide chlorantraniliprole with human serum albumin: Biophysical aspects

    International Nuclear Information System (INIS)

    Chlorantraniliprole is a novel insecticide belonging to the diamide class of selective ryanodine receptor agonists. A biophysical study on the binding interaction of a novel diamide insecticide, chlorantraniliprole, with staple in vivo transporter, human serum albumin (HSA) has been investigated utilizing a combination of steady-state and time-resolved fluorescence, circular dichroism (CD), and molecular modeling methods. The interaction of chlorantraniliprole with HSA gives rise to fluorescence quenching through static mechanism, this corroborates the fluorescence lifetime outcomes that the ground state complex formation and the predominant forces in the HSA-chlorantraniliprole conjugate are van der Waals forces and hydrogen bonds, as derived from thermodynamic analysis. The definite binding site of chlorantraniliprole in HSA has been identified from the denaturation of protein, competitive ligand binding, and molecular modeling, subdomain IIIA (Sudlow's site II) was designated to possess high-affinity binding site for chlorantraniliprole. Moreover, using synchronous fluorescence, CD, and three-dimensional fluorescence we testified some degree of HSA structure unfolding upon chlorantraniliprole binding. - Highlights: → Our study highlights for the first time how binding dynamics can predominate for the new diamide insecticide, chlorantraniliprole. → Chlorantraniliprole is situated within subdomain IIIA, Sudlow's site II, which is the same as that of indole-benzodiazepine site. → Biophysical and molecular modeling approaches are useful to resolve the ligand interaction with biomacromolecule. → It serves as a protective device in binding and in inactivating potential toxic compounds to which the body is exposed.

  10. Complexation of insecticide chlorantraniliprole with human serum albumin: Biophysical aspects

    Energy Technology Data Exchange (ETDEWEB)

    Ding Fei [Department of Chemistry, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193 (China); Liu Wei [College of Economics and Management, China Agricultural University, Beijing 100083 (China); Diao Jianxiong [Department of Chemistry, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193 (China); Yin Bin [Key Laboratory of Pesticide Chemistry and Application Technology, Ministry of Agriculture, Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Zhang Li, E-mail: zhli.work@gmail.co [Key Laboratory of Pesticide Chemistry and Application Technology, Ministry of Agriculture, Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Sun Ying, E-mail: sunying@cau.edu.c [Department of Chemistry, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193 (China)

    2011-07-15

    Chlorantraniliprole is a novel insecticide belonging to the diamide class of selective ryanodine receptor agonists. A biophysical study on the binding interaction of a novel diamide insecticide, chlorantraniliprole, with staple in vivo transporter, human serum albumin (HSA) has been investigated utilizing a combination of steady-state and time-resolved fluorescence, circular dichroism (CD), and molecular modeling methods. The interaction of chlorantraniliprole with HSA gives rise to fluorescence quenching through static mechanism, this corroborates the fluorescence lifetime outcomes that the ground state complex formation and the predominant forces in the HSA-chlorantraniliprole conjugate are van der Waals forces and hydrogen bonds, as derived from thermodynamic analysis. The definite binding site of chlorantraniliprole in HSA has been identified from the denaturation of protein, competitive ligand binding, and molecular modeling, subdomain IIIA (Sudlow's site II) was designated to possess high-affinity binding site for chlorantraniliprole. Moreover, using synchronous fluorescence, CD, and three-dimensional fluorescence we testified some degree of HSA structure unfolding upon chlorantraniliprole binding. - Highlights: {yields} Our study highlights for the first time how binding dynamics can predominate for the new diamide insecticide, chlorantraniliprole. {yields} Chlorantraniliprole is situated within subdomain IIIA, Sudlow's site II, which is the same as that of indole-benzodiazepine site. {yields} Biophysical and molecular modeling approaches are useful to resolve the ligand interaction with biomacromolecule. {yields} It serves as a protective device in binding and in inactivating potential toxic compounds to which the body is exposed.

  11. Neonicotinoid insecticides can serve as inadvertent insect contraceptives

    Science.gov (United States)

    Villamar-Bouza, Laura; Bruckner, Selina; Chantawannakul, Panuwan; Gauthier, Laurent; Khongphinitbunjong, Kitiphong; Retschnig, Gina; Troxler, Aline; Vidondo, Beatriz; Neumann, Peter; Williams, Geoffrey R.

    2016-01-01

    There is clear evidence for sublethal effects of neonicotinoid insecticides on non-target ecosystem service-providing insects. However, their possible impact on male insect reproduction is currently unknown, despite the key role of sex. Here, we show that two neonicotinoids (4.5 ppb thiamethoxam and 1.5 ppb clothianidin) significantly reduce the reproductive capacity of male honeybees (drones), Apis mellifera. Drones were obtained from colonies exposed to the neonicotinoid insecticides or controls, and subsequently maintained in laboratory cages until they reached sexual maturity. While no significant effects were observed for male teneral (newly emerged adult) body mass and sperm quantity, the data clearly showed reduced drone lifespan, as well as reduced sperm viability (percentage living versus dead) and living sperm quantity by 39%. Our results demonstrate for the first time that neonicotinoid insecticides can negatively affect male insect reproductive capacity, and provide a possible mechanistic explanation for managed honeybee queen failure and wild insect pollinator decline. The widespread prophylactic use of neonicotinoids may have previously overlooked inadvertent contraceptive effects on non-target insects, thereby limiting conservation efforts. PMID:27466446

  12. Dermal insecticide residues from birds inhabiting an orchard

    Science.gov (United States)

    Vyas, N.B.; Spann, J.W.; Hulse, C.S.; Gentry, S.; Borges, S.L.

    2007-01-01

    The US Environmental Protection Agency conducts risk assessments of insecticide applications to wild birds using a model that is limited to the dietary route of exposure. However, free-flying birds are also exposed to insecticides via the inhalation and dermal routes. We measured azinphos-methyl residues on the skin plus feathers and the feet of brown-headed cowbirds (Molothrus ater) in order to quantify dermal exposure to songbirds that entered and inhabited an apple (Malus x domestica) orchard following an insecticide application. Exposure to azinphos-methyl was measured by sampling birds from an aviary that was built around an apple tree. Birds sampled at 36 h and 7-day post-application were placed in the aviary within 1 h after the application whereas birds exposed for 3 days were released into the aviary 4-day post-application. Residues on vegetation and soil were also measured. Azinphos-methyl residues were detected from the skin plus feathers and the feet from all exposure periods. Our results underscore the importance of incorporating dermal exposure into avian pesticide risk assessments.

  13. BLANNOTATOR: enhanced homology-based function prediction of bacterial proteins

    Directory of Open Access Journals (Sweden)

    Kankainen Matti

    2012-02-01

    Full Text Available Abstract Background Automated function prediction has played a central role in determining the biological functions of bacterial proteins. Typically, protein function annotation relies on homology, and function is inferred from other proteins with similar sequences. This approach has become popular in bacterial genomics because it is one of the few methods that is practical for large datasets and because it does not require additional functional genomics experiments. However, the existing solutions produce erroneous predictions in many cases, especially when query sequences have low levels of identity with the annotated source protein. This problem has created a pressing need for improvements in homology-based annotation. Results We present an automated method for the functional annotation of bacterial protein sequences. Based on sequence similarity searches, BLANNOTATOR accurately annotates query sequences with one-line summary descriptions of protein function. It groups sequences identified by BLAST into subsets according to their annotation and bases its prediction on a set of sequences with consistent functional information. We show the results of BLANNOTATOR's performance in sets of bacterial proteins with known functions. We simulated the annotation process for 3090 SWISS-PROT proteins using a database in its state preceding the functional characterisation of the query protein. For this dataset, our method outperformed the five others that we tested, and the improved performance was maintained even in the absence of highly related sequence hits. We further demonstrate the value of our tool by analysing the putative proteome of Lactobacillus crispatus strain ST1. Conclusions BLANNOTATOR is an accurate method for bacterial protein function prediction. It is practical for genome-scale data and does not require pre-existing sequence clustering; thus, this method suits the needs of bacterial genome and metagenome researchers. The method and a

  14. Carvacrol importance in veterinary and human medicine as ecologic insecticide and acaricide

    Directory of Open Access Journals (Sweden)

    Vučinić Marijana

    2011-01-01

    Full Text Available Carvacrol is an active ingredient of essential oils from different plants, mainly from oregano and thyme species. It poseses biocidal activity agains many artropodes of the importance for veterinary and human medicine. Carvacrol acts as repelent, larvicide, insecticide and acaricide. It acts against pest artropodes such as those that serve as mechanical or biological vectors for many causal agents of viral, bacterial and parasitic diseases for animals and humans. Therefore, it may be used not only in pest arthropodes control but in vector borne diseases control, too. In the paper carvacrol bioactivity against mosquitoes, house flies, cockroaches, ticks and mites are described. Potencial modes of carvacrol action on artropodes are given, too. Carvacrol reachs its biotoxicity against arthropodes alone or in combination with other active ingredients from the same plant of its origin, such as tymol, cymen or others. The paper explains reasons for frequently investigations on essential oils and other natural products of plant origin to their biotoxicity against food stored pest or pest of medicinal importance, as well as, needs for their use in agriculture, veterinary and human medicine.

  15. Effects of neem-based insecticides on beet armyworm (Lepidoptera: Noctuidae)

    Institute of Scientific and Technical Information of China (English)

    SHOILM.GREENBERG; ALLANT.SHOWLER; TONG-XIANLIU

    2005-01-01

    Three commercial neem [Azadirachta indica A. Juss (Meliaceae)]-based insecticides, Agroneem, Ecozin, and Neemix, and a non-commercial neem leaf powder,were evaluated for oviposition deterrence, antifeedant effect on larvae, and toxicity to eggs and larvae of the beet armyworm, Spodoptera exigua (Hübner) (Lepidoptera: Noctuidae),on cotton leaves in the laboratory. Oviposition deterrence in no-choice, and two- and fivechoice assays, was observed for the neem-based insecticide treatments when compared with a non-treated control. Neem-based insecticides also deterred feeding by beet armyworm larvae. Direct contact with neem-based insecticides decreased the survival of beet armyworm eggs. Survival of beet armyworm larvae fed for 7 days on leaves treated with neembased insecticides was reduced to 27, 33, 60, and 61% for neem leaf powder, Ecozin,Agroneem, and Neemix, respectively. Possibilities for adoption of neem-based insecticides in commercial cotton for beet armyworm control are discussed.

  16. Optimized genotyping method for identification of bacterial contaminants in pharmaceutical industry

    Directory of Open Access Journals (Sweden)

    Stamatoski Borche

    2016-06-01

    Full Text Available Microbiological control is of crucial importance in the pharmaceutical industry regarding the possible bacterial contamination of the environment, water, raw materials and finished products. Molecular identification of bacterial contaminants based on DNA sequencing of the hypervariable 16SrRNA gene has been introduced recently. The aim of this study is to investigate the suitability of gene sequencing using our selection of PCR primers and conditions for rapid and accurate bacterial identification in pharmaceutical industry quality control.

  17. Identification and Characterization of Inhibitors of Bacterial Enoyl-Acyl Carrier Protein Reductase

    OpenAIRE

    Ling, Losee L.; Xian, Jun; Ali, Syed; Geng, Bolin; Fan, Jun; Mills, Debra M.; Arvanites, Anthony C.; Orgueira, Hernan; Ashwell, Mark A.; Carmel, Gilles; Xiang, Yibin; Moir, Donald T.

    2004-01-01

    Bacterial enoyl-acyl carrier protein reductase (ENR) catalyzes an essential step in fatty acid biosynthesis. ENR is an attractive target for narrow-spectrum antibacterial drug discovery because of its essential role in metabolism and its sequence conservation across many bacterial species. In addition, the bacterial ENR sequence and structural organization are distinctly different from those of mammalian fatty acid biosynthesis enzymes. High-throughput screening to identify inhibitors of Esch...

  18. Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

    OpenAIRE

    Cohan, Frederick M

    2006-01-01

    To completely understand the ecology of a bacterial community, we need to identify its ecologically distinct populations (ecotypes). The greatest promise for enumerating a community's constituent ecotypes is held by molecular approaches that identify bacterial ecotypes as DNA sequence clusters. These approaches succeed when ecotypes correspond with sequence clusters, but some models of bacterial speciation predict a one-to-many and others a many-to-one relationship between ecotypes and sequen...

  19. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome

    Science.gov (United States)

    Benoit, Joshua B.; Adelman, Zach N.; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C.; Szuter, Elise M.; Hagan, Richard W.; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M.; Nelson, David R.; Rosendale, Andrew J.; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M.; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R.; Ioannidis, Panagiotis; Waterhouse, Robert M.; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J. Spencer; Gondhalekar, Ameya D.; Scharf, Michael E.; Peterson, Brittany F.; Raje, Kapil R.; Hottel, Benjamin A.; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S. T.; Duncan, Elizabeth J.; Murali, Shwetha C.; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L.; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C.; Muzny, Donna M.; Wheeler, David; Panfilio, Kristen A.; Vargas Jentzsch, Iris M.; Vargo, Edward L.; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T.; Anderson, Michelle A. E.; Jones, Jeffery W.; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D.; Attardo, Geoffrey M.; Robertson, Hugh M.; Zdobnov, Evgeny M.; Ribeiro, Jose M. C.; Gibbs, Richard A.; Werren, John H.; Palli, Subba R.; Schal, Coby; Richards, Stephen

    2016-01-01

    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host–symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human–bed bug and symbiont–bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite. PMID:26836814

  20. Unique features of a global human ectoparasite identified through sequencing of the bed bug genome.

    Science.gov (United States)

    Benoit, Joshua B; Adelman, Zach N; Reinhardt, Klaus; Dolan, Amanda; Poelchau, Monica; Jennings, Emily C; Szuter, Elise M; Hagan, Richard W; Gujar, Hemant; Shukla, Jayendra Nath; Zhu, Fang; Mohan, M; Nelson, David R; Rosendale, Andrew J; Derst, Christian; Resnik, Valentina; Wernig, Sebastian; Menegazzi, Pamela; Wegener, Christian; Peschel, Nicolai; Hendershot, Jacob M; Blenau, Wolfgang; Predel, Reinhard; Johnston, Paul R; Ioannidis, Panagiotis; Waterhouse, Robert M; Nauen, Ralf; Schorn, Corinna; Ott, Mark-Christoph; Maiwald, Frank; Johnston, J Spencer; Gondhalekar, Ameya D; Scharf, Michael E; Peterson, Brittany F; Raje, Kapil R; Hottel, Benjamin A; Armisén, David; Crumière, Antonin Jean Johan; Refki, Peter Nagui; Santos, Maria Emilia; Sghaier, Essia; Viala, Sèverine; Khila, Abderrahman; Ahn, Seung-Joon; Childers, Christopher; Lee, Chien-Yueh; Lin, Han; Hughes, Daniel S T; Duncan, Elizabeth J; Murali, Shwetha C; Qu, Jiaxin; Dugan, Shannon; Lee, Sandra L; Chao, Hsu; Dinh, Huyen; Han, Yi; Doddapaneni, Harshavardhan; Worley, Kim C; Muzny, Donna M; Wheeler, David; Panfilio, Kristen A; Vargas Jentzsch, Iris M; Vargo, Edward L; Booth, Warren; Friedrich, Markus; Weirauch, Matthew T; Anderson, Michelle A E; Jones, Jeffery W; Mittapalli, Omprakash; Zhao, Chaoyang; Zhou, Jing-Jiang; Evans, Jay D; Attardo, Geoffrey M; Robertson, Hugh M; Zdobnov, Evgeny M; Ribeiro, Jose M C; Gibbs, Richard A; Werren, John H; Palli, Subba R; Schal, Coby; Richards, Stephen

    2016-01-01

    The bed bug, Cimex lectularius, has re-established itself as a ubiquitous human ectoparasite throughout much of the world during the past two decades. This global resurgence is likely linked to increased international travel and commerce in addition to widespread insecticide resistance. Analyses of the C. lectularius sequenced genome (650 Mb) and 14,220 predicted protein-coding genes provide a comprehensive representation of genes that are linked to traumatic insemination, a reduced chemosensory repertoire of genes related to obligate hematophagy, host-symbiont interactions, and several mechanisms of insecticide resistance. In addition, we document the presence of multiple putative lateral gene transfer events. Genome sequencing and annotation establish a solid foundation for future research on mechanisms of insecticide resistance, human-bed bug and symbiont-bed bug associations, and unique features of bed bug biology that contribute to the unprecedented success of C. lectularius as a human ectoparasite. PMID:26836814

  1. Jellyfish modulate bacterial dynamic and community structure.

    Directory of Open Access Journals (Sweden)

    Tinkara Tinta

    Full Text Available Jellyfish blooms have increased in coastal areas around the world and the outbreaks have become longer and more frequent over the past few decades. The Mediterranean Sea is among the heavily affected regions and the common bloom-forming taxa are scyphozoans Aurelia aurita s.l., Pelagia noctiluca, and Rhizostoma pulmo. Jellyfish have few natural predators, therefore their carcasses at the termination of a bloom represent an organic-rich substrate that supports rapid bacterial growth, and may have a large impact on the surrounding environment. The focus of this study was to explore whether jellyfish substrate have an impact on bacterial community phylotype selection. We conducted in situ jellyfish-enrichment experiment with three different jellyfish species. Bacterial dynamic together with nutrients were monitored to assess decaying jellyfish-bacteria dynamics. Our results show that jellyfish biomass is characterized by protein rich organic matter, which is highly bioavailable to 'jellyfish-associated' and 'free-living' bacteria, and triggers rapid shifts in bacterial population dynamics and composition. Based on 16S rRNA clone libraries and denaturing gradient gel electrophoresis (DGGE analysis, we observed a rapid shift in community composition from unculturable Alphaproteobacteria to culturable species of Gammaproteobacteria and Flavobacteria. The results of sequence analyses of bacterial isolates and of total bacterial community determined by culture independent genetic analysis showed the dominance of the Pseudoalteromonadaceae and the Vibrionaceae families. Elevated levels of dissolved proteins, dissolved organic and inorganic nutrient release, bacterial abundance and carbon production as well as ammonium concentrations characterized the degradation process. The biochemical composition of jellyfish species may influence changes in the amount of accumulated dissolved organic and inorganic nutrients. Our results can contribute insights into

  2. Identification of Genes Putatively Involved in Chitin Metabolism and Insecticide Detoxification in the Rice Leaf Folder (Cnaphalocrocis medinalis Larvae through Transcriptomic Analysis

    Directory of Open Access Journals (Sweden)

    Hai-Zhong Yu

    2015-09-01

    Full Text Available The rice leaf roller (Cnaphalocrocis medinalis is one of the most destructive agricultural pests. Due to its migratory behavior, it is difficult to control worldwide. To date, little is known about major genes of C. medinalis involved in chitin metabolism and insecticide detoxification. In order to obtain a comprehensive genome dataset of C. medinalis, we conducted de novo transcriptome sequencing which focused on the major feeding stage of fourth-instar larvae, and our work revealed useful information on chitin metabolism and insecticide detoxification and target genes of C. medinalis. We acquired 29,367,797 Illumina reads and assembled these reads into 63,174 unigenes with an average length of 753 bp. Among these unigenes, 31,810 were annotated against the National Center for Biotechnology Information non-redundant (NCBI nr protein database, resulting in 24,246, 8669 and 18,176 assigned to Swiss-Prot, clusters of orthologous group (COG, and gene ontology (GO, respectively. We were able to map 10,043 unigenes into 285 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG. Specifically, 16 genes, including five chitin deacetylases, two chitin synthases, five chitinases and four other related enzymes, were identified to be putatively involved in chitin biosynthesis and degradation, whereas 360 genes, including cytochrome P450s, glutathione S-transferases, esterases, and acetylcholinesterases, were found to be potentially involved in insecticide detoxification or as insecticide targets. The reliability of the transcriptome data was determined by reverse transcription quantitative PCR (RT-qPCR for the selected genes. Our data serves as a new and valuable sequence resource for genomic studies on C. medinalis. The findings should improve our understanding of C. medinalis genetics and contribute to management of this important agricultural pest.

  3. Identification of Genes Putatively Involved in Chitin Metabolism and Insecticide Detoxification in the Rice Leaf Folder (Cnaphalocrocis medinalis) Larvae through Transcriptomic Analysis

    Science.gov (United States)

    Yu, Hai-Zhong; Wen, De-Fu; Wang, Wan-Lin; Geng, Lei; Zhang, Yan; Xu, Jia-Ping

    2015-01-01

    The rice leaf roller (Cnaphalocrocis medinalis) is one of the most destructive agricultural pests. Due to its migratory behavior, it is difficult to control worldwide. To date, little is known about major genes of C. medinalis involved in chitin metabolism and insecticide detoxification. In order to obtain a comprehensive genome dataset of C. medinalis, we conducted de novo transcriptome sequencing which focused on the major feeding stage of fourth-instar larvae, and our work revealed useful information on chitin metabolism and insecticide detoxification and target genes of C. medinalis. We acquired 29,367,797 Illumina reads and assembled these reads into 63,174 unigenes with an average length of 753 bp. Among these unigenes, 31,810 were annotated against the National Center for Biotechnology Information non-redundant (NCBI nr) protein database, resulting in 24,246, 8669 and 18,176 assigned to Swiss-Prot, clusters of orthologous group (COG), and gene ontology (GO), respectively. We were able to map 10,043 unigenes into 285 pathways using the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG). Specifically, 16 genes, including five chitin deacetylases, two chitin synthases, five chitinases and four other related enzymes, were identified to be putatively involved in chitin biosynthesis and degradation, whereas 360 genes, including cytochrome P450s, glutathione S-transferases, esterases, and acetylcholinesterases, were found to be potentially involved in insecticide detoxification or as insecticide targets. The reliability of the transcriptome data was determined by reverse transcription quantitative PCR (RT-qPCR) for the selected genes. Our data serves as a new and valuable sequence resource for genomic studies on C. medinalis. The findings should improve our understanding of C. medinalis genetics and contribute to management of this important agricultural pest. PMID:26378520

  4. Blocking the evolution of insecticide-resistant malaria vectors with a microsporidian

    OpenAIRE

    Koella, Jacob C; Saddler, Adam; Karacs, Thomas P S

    2011-01-01

    Finding a way to block the evolution insecticide resistance would be a major breakthrough for the control of malaria. We suggest that this may be possible by introducing a stress into mosquito populations that restores the sensitivity of genetically resistant mosquitoes and that decreases their longevity when they are not exposed to insecticide. We use a mathematical model to show that, despite the intense selection pressure imposed by insecticides, moderate levels of stress might tip the evo...

  5. Insecticidal and repellent effect of extracts of Pluchea sericea (Nutt.) on adults of Bemisia tabaci (Genn.)

    OpenAIRE

    Carlos Enrique Ail-Catzim; Alejandro Manelik García-López; Rosalba Troncoso-Rojas; Rosario Esmeralda González-Rodríguez; Yuliana Sánchez-Segura

    2015-01-01

    T he use of repeated insecticide applications in agricultural crops to control Bemisia tabaci (Genn.) has resulted in resistance problems and environmental pollution. Inputs from plant species are an alternative to reduce this problem. Plants are a source of bioactive chemicals that can have insecticidal, repellent, attractant, anti-feeding or growth regulator effects. The aim of this study was to determine the insecticidal and repellent activity of ethanolic, acetonic and aqueous extracts of...

  6. Bystander Exposure to Ultra-Low-Volume Insecticide Applications Used for Adult Mosquito Management

    OpenAIRE

    Peterson, Robert K. D.; Jerome J. Schleier III; Preftakes, Collin J.

    2011-01-01

    A popular and effective management option for adult mosquitoes is the use of insecticides applied by ultra-low-volume (ULV) equipment. However, there is a paucity of data on human dermal exposure to insecticides applied by this method. The objective of the current study was to estimate dermal exposures to the insecticide active ingredient permethrin using water- (Aqua-Reslin®) and oil-based (Permanone® 30-30) formulations with passive dosimetry. No significant differences in deposition of per...

  7. Effects of Persistent Insecticides on Beneficial Soil Arthropod in Conventional Fields Compared to Organic Fields, Puducherry

    OpenAIRE

    Padmavathy Anbarashan; Poyyamoli Gopalswamy

    2013-01-01

    The usage of synthetic fertilizers/insecticides in conventional farming has dramatically increased over the past decades. The aim of the study was to compare the effects of bio-pesticides and insecticides/pesticides on selected beneficial non targeted arthropods. Orders Collembola, Arachinida/Opiliones, Oribatida and Coleoptera were the main groups of arthropods found in the organic fields and Coleoptera, Oribatida, Gamasida and Collembola in conventional fields. Pesticides/insecticides...

  8. Resistance to bio-insecticides or how to enhance their sustainability: a review

    OpenAIRE

    Myriam eSIEGWART; Benoit eGraillot; Christine eBlachère-Lopez; Samantha eBesse; Marc eBardin; Philippe eNicot; Miguel eLopez-Ferber

    2015-01-01

    After more than 70 years of chemical pesticide use, modern agriculture is increasingly using biological control products. Resistances to conventional insecticides are wide spread, while those to bio-insecticides have raised less attention, and resistance management is frequently neglected. However, a good knowledge of the limitations of a new technique often provides greater sustainability. In this review, we compile cases of resistance to widely used bio-insecticides and describe the associa...

  9. Various novel insecticides are less toxic to humans, more specific to key pests

    OpenAIRE

    Grafton-Cardwell, Elizabeth E.; Godfrey, Larry D.; Chaney, William E.; Bentley, Walter J.

    2005-01-01

    A number of novel insecticides have recently been registered for insect control in agriculture. A major advantage of these new products is that they act on insect biological processes that humans do not experience, such as molting. Many also have greater selectivity to target specific species, so they are less likely to harm natural enemies when compared with the broader spectrum organophosphate, carbamate, neonicotinoid and pyrethroid insecticides. Such novel insecticides currently in use in...

  10. Plant Essential Oils Synergize and Antagonize Toxicity of Different Conventional Insecticides against Myzus persicae (Hemiptera: Aphididae)

    OpenAIRE

    Nicoletta Faraone; N Kirk Hillier; G Christopher Cutler

    2015-01-01

    Plant-derived products can play an important role in pest management programs. Essential oils from Lavandula angustifolia (lavender) and Thymus vulgaris (thyme) and their main constituents, linalool and thymol, respectively, were evaluated for insecticidal activity and synergistic action in combination with insecticides against green peach aphid, Myzus persicae (Sulzer) (Hemiptera: Aphididae). The essential oils and their main constituents exerted similar insecticidal activity when aphids wer...

  11. Isolation of an Orally Active Insecticidal Toxin from the Venom of an Australian Tarantula

    OpenAIRE

    Hardy, Margaret C.; Daly, Norelle L.; Mehdi Mobli; Rodrigo A. V. Morales; Glenn F. King

    2013-01-01

    Many insect pests have developed resistance to existing chemical insecticides and consequently there is much interest in the development of new insecticidal compounds with novel modes of action. Although spiders have deployed insecticidal toxins in their venoms for over 250 million years, there is no evolutionary selection pressure on these toxins to possess oral activity since they are injected into prey and predators via a hypodermic needle-like fang. Thus, it has been assumed that spider-v...

  12. Insecticide susceptibility of Anopheles coluzzii and Anopheles gambiae mosquitoes in Ibadan, South-West Nigeria

    OpenAIRE

    Okorie, Patricia N.; Ademowo, George O.; Irving, Helen; Kelly-Hope, Louise A; Wondji, Charles S

    2014-01-01

    The emergence of insecticide resistance in Anopheles mosquitoes has great implications for malaria control in Nigeria. This study aimed to determine the dynamics of insecticide susceptibility levels and frequency of knockdown resistance (kdr) mutations (L1014F) in wild Anopheles coluzzii Coetzee & Wilkerson sp. n. and An. gambiae Giles ( (Diptera: Culicidae) from Ojoo and Bodija areas of Ibadan, South-West, Nigeria. Insecticide susceptibility to pyrethroids, organophosphates, carbamates and o...

  13. The evolutionary dynamics of insecticide resistance in the whitefly, Bemisia tabaci

    OpenAIRE

    Jones, Christopher Mark

    2011-01-01

    The whitefly Bemisia tabaci (Hempitera: Aleyrodidae), is one of most destructive insect pests of agriculture and horticulture worldwide. B. tabaci has an extensive host-plant range, transmits several plant viruses and is a highly invasive species. Managing B. tabaci is therefore extremely problematic and expensive, with a heavy burden placed upon insecticides. Despite a broad spectrum of insecticidal chemistry available for whitefly control, resistance is widespread and insecticide resistance...

  14. Isolation, characterisation and synthesis of insecticidal natural products of the Myrtaceae family

    OpenAIRE

    Beddie, David G.

    1998-01-01

    New insecticidal natural products are required to find compounds with higher intrinsic activities to lower field application rates, and with novel modes of action to combat insect pest species which have developed resistance to current commercial insecticides. Using a taxonomic approach, studies on plants of the Myrtaceae family led to the isolation and characterisation of a range of insecticidal natural products 1 - 9 (figure 1). These compounds are all structurally related as they conta...

  15. Shuffling bacterial metabolomes

    OpenAIRE

    Thomason, Brendan; Read, Timothy D.

    2006-01-01

    Horizontal gene transfer (HGT) has a far more significant role than gene duplication in bacterial evolution. This has recently been illustrated by work demonstrating the importance of HGT in the emergence of bacterial metabolic networks, with horizontally acquired genes being placed in peripheral pathways at the outer branches of the networks.

  16. Vimentin in Bacterial Infections.

    Science.gov (United States)

    Mak, Tim N; Brüggemann, Holger

    2016-01-01

    Despite well-studied bacterial strategies to target actin to subvert the host cell cytoskeleton, thus promoting bacterial survival, replication, and dissemination, relatively little is known about the bacterial interaction with other components of the host cell cytoskeleton, including intermediate filaments (IFs). IFs have not only roles in maintaining the structural integrity of the cell, but they are also involved in many cellular processes including cell adhesion, immune signaling, and autophagy, processes that are important in the context of bacterial infections. Here, we summarize the knowledge about the role of IFs in bacterial infections, focusing on the type III IF protein vimentin. Recent studies have revealed the involvement of vimentin in host cell defenses, acting as ligand for several pattern recognition receptors of the innate immune system. Two main aspects of bacteria-vimentin interactions are presented in this review: the role of vimentin in pathogen-binding on the cell surface and subsequent bacterial invasion and the interaction of cytosolic vimentin and intracellular pathogens with regards to innate immune signaling. Mechanistic insight is presented involving distinct bacterial virulence factors that target vimentin to subvert its function in order to change the host cell fate in the course of a bacterial infection. PMID:27096872

  17. Prevention of bacterial adhesion

    DEFF Research Database (Denmark)

    Klemm, Per; Vejborg, Rebecca Munk; Hancock, Viktoria

    2010-01-01

    Management of bacterial infections is becoming increasingly difficult due to the emergence and increasing prevalence of bacterial pathogens that are resistant to available antibiotics. Conventional antibiotics generally kill bacteria by interfering with vital cellular functions, an approach that ...... become valuable weapons for preventing pathogen contamination and fighting infectious diseases in the future....

  18. Vimentin in Bacterial Infections

    Directory of Open Access Journals (Sweden)

    Tim N. Mak

    2016-04-01

    Full Text Available Despite well-studied bacterial strategies to target actin to subvert the host cell cytoskeleton, thus promoting bacterial survival, replication, and dissemination, relatively little is known about the bacterial interaction with other components of the host cell cytoskeleton, including intermediate filaments (IFs. IFs have not only roles in maintaining the structural integrity of the cell, but they are also involved in many cellular processes including cell adhesion, immune signaling, and autophagy, processes that are important in the context of bacterial infections. Here, we summarize the knowledge about the role of IFs in bacterial infections, focusing on the type III IF protein vimentin. Recent studies have revealed the involvement of vimentin in host cell defenses, acting as ligand for several pattern recognition receptors of the innate immune system. Two main aspects of bacteria-vimentin interactions are presented in this review: the role of vimentin in pathogen-binding on the cell surface and subsequent bacterial invasion and the interaction of cytosolic vimentin and intracellular pathogens with regards to innate immune signaling. Mechanistic insight is presented involving distinct bacterial virulence factors that target vimentin to subvert its function in order to change the host cell fate in the course of a bacterial infection.

  19. The Use of Radioisotopes to Study the Absorption, Distribution and Elimination of Various Insecticides in Animals

    International Nuclear Information System (INIS)

    When insecticides are used against farm-animal parasites it is important to ensure that no harm is done to the health of the animal or the consumer. Radioisotopes provide a means of studying the behaviour of labelled insecticides in animal organisms and of obtaining extremely accurate data on residues of insecticides and insecticide decomposition products in meat and milk. The paper gives details on the rate at which DDT-C14, polychloropinene-Cl36 and chlorophos-P32 are absorbed through the skin, accumulated in the organs and tissues and eliminated from the organisms of farm and laboratory animals. (author)

  20. Indirect evidence that agricultural pesticides select for insecticide resistance in the malaria vector Anopheles gambiae.

    Science.gov (United States)

    Luc, Djogbénou S; Benoit, Assogba; Laurette, Djossou; Michel, Makoutode

    2016-06-01

    We investigated the possible relationship between the agricultural use of insecticides and the emergence of insecticide resistance. Bioassays were conducted using simulated mosquito larval habitats and well known Anopheles gambiae strains. Soil samples were collected from vegetable production areas in Benin, including one site with insecticide use, one site where insecticides had not been used for two months, and a third where insecticides had not been used. Pupation and emergence rates were very low in pyrethroid-susceptible strains when exposed to soil that had been recently exposed to insecticides. Pupation and emergence rates in strains with the kdr mutation alone or both the kdr and Ace-1 mutations were much higher. Overall, strains with the kdr mutation survived at higher rates compared to that without kdr mutation. Although this study is observational, we provide indirect evidence indicating that soils from agricultural areas contain insecticide residues that can play a role in the emergence of insecticide resistance in Anopheles. This aspect should be taken into account to better utilize the insecticide in the context of integrated pest management programs. PMID:27232122

  1. Ecotoxicity of binary mixtures of Microcystis aeruginosa and insecticides to Daphnia pulex

    International Nuclear Information System (INIS)

    In aquatic ecosystems, mixtures of chemical and natural stressors can occur which may significantly complicate risk assessment approaches. Here, we show that effects of binary combinations of four different insecticides and Microcystis aeruginosa, a toxic cyanobacteria, on Daphnia pulex exhibited distinct interaction patterns. Combinations with chlorpyrifos and tetradifon caused non-interactive effects, tebufenpyrad caused an antagonistic interaction and fenoyxcarb yielded patterns that depended on the reference model used (i.e. synergistic with independent action, additive with concentration addition). Our results demonstrate that interactive effects cannot be generalised across different insecticides, not even for those targeting the same biological pathway (i.e. tebufenpyrad and tetradifon both target oxidative phosphorylation). Also, the concentration addition reference model provided conservative predictions of effects in all investigated combinations for risk assessment. These predictions could, in absence of a full mechanistic understanding, provide a meaningful solution for managing water quality in systems impacted by both insecticides and cyanobacterial blooms. - Highlights:: • 2 of 4 insecticide-Microcystis combinations showed no interactive effect on Daphnia. • One insecticide showed antagonistic deviation patterns. • For one other insecticide the results depended on the reference model used. • Interactive effects between insecticides and Microcystis cannot be generalized. • The concentration addition model provides conservative estimates of mixture effects. - Interactive effects between insecticides and cyanobacterial stressors cannot be generalized, not even for insecticides with closely related known modes of action

  2. Current Perspectives on Plague Vector Control in Madagascar: Susceptibility Status of Xenopsylla cheopis to 12 Insecticides.

    Science.gov (United States)

    Miarinjara, Adélaïde; Boyer, Sébastien

    2016-02-01

    Plague is a rodent disease transmissible to humans by infected flea bites, and Madagascar is one of the countries with the highest plague incidence in the world. This study reports the susceptibility of the main plague vector Xenopsylla cheopis to 12 different insecticides belonging to 4 insecticide families (carbamates, organophosphates, pyrethroids and organochlorines). Eight populations from different geographical regions of Madagascar previously resistant to deltamethrin were tested with a World Health Organization standard bioassay. Insecticide susceptibility varied amongst populations, but all of them were resistant to six insecticides belonging to pyrethroid and carbamate insecticides (alphacypermethrin, lambdacyhalothrin, etofenprox, deltamethrin, bendiocarb and propoxur). Only one insecticide (dieldrin) was an efficient pulicide for all flea populations. Cross resistances were suspected. This study proposes at least three alternative insecticides (malathion, fenitrothion and cyfluthrin) to replace deltamethrin during plague epidemic responses, but the most efficient insecticide may be different for each population studied. We highlight the importance of continuous insecticide susceptibility surveillance in the areas of high plague risk in Madagascar. PMID:26844772

  3. Protective effect and economic impact of insecticide application methods on barley

    Directory of Open Access Journals (Sweden)

    Alfred Stoetzer

    2014-03-01

    Full Text Available The objective of this work was to evaluate the protective effect of different forms of insecticide application on the transmission of yellow dwarf disease in barley cultivars, as well as to determine the production costs and the net profit of these managements. The experiments were carried out during 2011 and 2012 growing seasons, using the following managements at main plots: T1, seed treatment with insecticide (ST + insecticide on shoots at 15-day interval; T2, just ST; T3, insecticide applied on shoots, when aphid control level (CL was reached; T4, without insecticide; and T5, ST + insecticide on shoots when CL was reached. Different barley cultivars - BRS Cauê, BRS Brau and MN 6021 - were arranged in the subplots. Insecticides lambda cyhalothrin (pyrethroid and thiamethoxam (neonicotinoid were used. There were differences on yellow dwarf disease index in both seasons for the different treatments, while damage to grain yield was influenced by year and aphid population. Production costs and net profit were different among treatments. Seed treatment with insecticide is sufficient to reduce the transmission of yellow dwarf disease in years with low aphid population pressure, while in years with larger populations, the application of insecticide on shoots is also required.

  4. Effect of Botanical Insecticide of Macleya cordata on Physiology and Biochemistry of Cabbage (Brassica oleracea L.

    Directory of Open Access Journals (Sweden)

    Gong Li

    2013-06-01

    Full Text Available In order to improve the effect of Cyhalothrin and botanical insecticide of Macleya cordata in the Brassica oleracea L. investigated, the contents of proline, soluble sugar and soluble protein were determined. The results showed that under the stress of botanical insecticide of Macleya cordata at the same concentration, the contents of proline, soluble sugar and soluble protein were significantly lower than those with Cyhalothrin (p<0.05 except the proline content has not significant differences between Cyhalothrin and botanical insecticide of Macleya cordata with a dosage of 50×. The degree of damage with Cyhalothrin is greater than that of botanical insecticide of Macleya cordata.

  5. Two chitinase-like proteins abundantly accumulated in latex of mulberry show insecticidal activity

    Directory of Open Access Journals (Sweden)

    Komatsu Aino

    2010-01-01

    Full Text Available Abstract Background Plant latex is the cytoplasm of highly specialized cells known as laticifers, and is thought to have a critical role in defense against herbivorous insects. Proteins abundantly accumulated in latex might therefore be involved in the defense system. Results We purified latex abundant protein a and b (LA-a and LA-b from mulberry (Morus sp. and analyzed their properties. LA-a and LA-b have molecular masses of approximately 50 and 46 kDa, respectively, and are abundant in the soluble fraction of latex. Western blotting analysis suggested that they share sequence similarity with each other. The sequences of LA-a and LA-b, as determined by Edman degradation, showed chitin-binding domains of plant chitinases at the N termini. These proteins showed small but significant chitinase and chitosanase activities. Lectin RCA120 indicated that, unlike common plant chitinases, LA-a and LA-b are glycosylated. LA-a and LA-b showed insecticidal activities when fed to larvae of the model insect Drosophila melanogaster. Conclusions Our results suggest that the two LA proteins have a crucial role in defense against herbivorous insects, possibly by hydrolyzing their chitin.

  6. Cloning and characterization of an insecticidal crystal protein gene from Bacillus thuringiensis subspecies kenyae

    Indian Academy of Sciences (India)

    Hari S. Misra; Nivedita P. Khairnar; Manjula Mathur; N. Vijayalakshmi; Remesh S. Hire; T. K. Dongre; S. K. Mahajan

    2002-04-01

    A sporulating culture of Bacillus thuringiensis subsp. kenyae strain HD549 is toxic to larvae of lepidopteran insect species such as Spodoptera litura, Helicoverpa armigera and Phthorimaea operculella, and a dipteran insect, Culex fatigans. A 1.9-kb DNA fragment, PCR-amplified from HD549 using cryII-gene-specific primers, was cloned and expressed in E. coli. The recombinant protein produced 92% mortality in first-instar larvae of Spodoptera litura and 86% inhibition of adult emergence in Phthorimaea operculella, but showed very low toxicity against Helicoverpa armigera, and lower mortality against third-instar larvae of dipteran insects Culex fatigans, Anopheles stephensi and Aedes aegypti. The sequence of the cloned crystal protein gene showed almost complete homology with a mosquitocidal toxin gene from Bacillus thuringiensis var. kurstaki, with only five mutations scattered in different regions. Amino acid alignment with different insecticidal crystal proteins using the MUTALIN program suggested presence of the conserved block 3 region in the sequence of this protein. A mutation in codon 409 of this gene that changes a highly conserved phenylalanine residue to serine lies in this block.

  7. Cloning and characterization of an insecticidal crystal protein gene from Bacillus thuringiensis subspecies kenyae.

    Science.gov (United States)

    Misra, Hari S; Khairnar, Nivedita P; Mathur, Manjula; Vijayalakshmi, N; Hire, Ramesh S; Dongre, T K; Mahajan, S K

    2002-04-01

    A sporulating culture of Bacillus thuringiensis subsp. kenyae strain HD549 is toxic to larvae of lepidopteran insect species such as Spodoptera litura, Helicoverpa armigera and Phthorimaea operculella, and a dipteran insect, Culex fatigans. A 1.9-kb DNA fragment, PCR-amplified from HD549 using cryII-gene-specific primers, was cloned and expressed in E. coli. The recombinant protein produced 92% mortality in first-instar larvae of Spodoptera litura and 86% inhibition of adult emergence in Phthorimaea operculella, but showed very low toxicity against Helicoverpa armigera, and lower mortality against third-instar larvae of dipteran insects Culex fatigans, Anopheles stephensi and Aedes aegypti. The sequence of the cloned crystal protein gene showed almost complete homology with a mosquitocidal toxin gene from Bacillus thuringiensis var. kurstaki, with only five mutations scattered in different regions. Amino acid alignment with different insecticidal crystal proteins using the MUTALIN program suggested presence of the conserved block 3 region in the sequence of this protein. A mutation in codon 409 of this gene that changes a highly conserved phenylalanine residue to serine lies in this block. PMID:12357073

  8. Impact and Selectivity of Insecticides to Predators and Parasitoids

    Directory of Open Access Journals (Sweden)

    Flávio Lemes Fernandes

    2010-04-01

    Full Text Available Problems with the use of insecticides has brought losses, such as, negative impact on natural enemies. When these beneficial insects reduce cause the eruption of pests and resurgence it’s more common. Thus principles of conservation these arthropods are extremely important in the biological natural control of pests, so that these enemies may present a high performance. Because of the negative impacts caused by insecticides on agriculture and their harmful effects on natural enemies, the objective of this article is to approach two important subjects, divided into three parts. Part I relates to the description of the main crop pests and their natural enemies; Part II involves the impact of insecticides on predators and parasitoids and Part III focuses on the selectivity of several groups of insecticides to natural enemies. Before spraying insecticides, it is necessary to choose a product that is efficient to pests and selective to natural enemies. So, it is indispensable to identify correctly the groups and species of natural enemies, since insecticides have an impact on their survival, growth, development, reproduction (sexual ratio, fecundity, longevity and fertility, and behavior (motility, orientation, feeding, oviposition and learning of insects. The mechanisms of toxicity and selectivity of insecticides are related to the properties of higher or lower solubility and molecular weight. Besides, characteristics of the cuticular composition of the integument of natural enemies are extremely important in the selectivity of a product or the tolerance of a certain predator or parasitoid to this molecules.Impacto e Seletividade de Inseticidas para Predadores e ParasitóidesResumo.Dentre os problemas advindos do uso de inseticidas, a destruição de inimigos naturais é fator importante. Estes insetos benéficos podem reduzir problemas de erupção de pragas secundárias, ressurgência de pragas e manter a praga abaixo do nível de dano econ

  9. Insecticide Resistance and Metabolic Mechanisms Involved in Larval and Adult Stages of Aedes aegypti Insecticide-Resistant Reference Strains from Cuba.

    Science.gov (United States)

    Bisset, Juan Andrés; Rodríguez, María Magdalena; French, Leydis; Severson, David W; Gutiérrez, Gladys; Hurtado, Daymi; Fuentes, Ilario

    2014-12-01

    Studies were conducted to compare levels of insecticide resistance and to determine the metabolic resistance mechanisms in larval and adult stages of Aedes aegypti from Cuba. Three insecticide-resistant reference strains of Ae. aegypti from Cuba were examined. These strains were derived from a Santiago de Cuba strain isolated in 1997; it was previously subjected to a strong selection for resistance to temephos (SAN-F6), deltamethrin (SAN-F12), and propoxur (SAN-F13) and routinely maintained in the laboratory under selection pressure up to the present time, when the study was carried out. In addition, an insecticide-susceptible strain was used for comparison. The insecticide resistance in larvae and adults was determined using standard World Health Organization methodologies. Insecticide resistance mechanisms were determined by biochemical assays. The esterases (α EST and β EST) and mixed function oxidase (MFO) activities were significantly higher in adults than in the larvae of the three resistant strains studied. The association of resistance level with the biochemical mechanism for each insecticide was established for each stage. The observed differences between larval and adult stages of Ae. aegypti in their levels of insecticide resistance and the biochemical mechanisms involved should be included as part of monitoring and surveillance activities in Ae. aegypti vector control programs. PMID:25843136

  10. Carbaryl degradation by bacterial isolates from a soil ecosystem of the Gaza Strip

    Science.gov (United States)

    Hamada, Mazen; Matar, Ammar; Bashir, Abdallah

    2015-01-01

    Abstract Carbaryl is an important and widely used insecticide that pollutes soil and water systems. Bacteria from the local soil ecosystem of the Gaza Strip capable of utilizing carbaryl as the sole source of carbon and nitrogen were isolated and identified as belonging to Bacillus, Morganella, Pseudomonas, Aeromonas and Corynebacterium genera. Carbaryl biodegradation by Bacillus, Morganella and Corynebacterium isolates was analyzed in minimal liquid media supplemented with carbaryl as the only source of carbon and nitrogen. Bacillus and Morganella exhibited 94.6% and 87.3% carbaryl degradation, respectively, while Corynebacterium showed only moderate carbaryl degradation at 48.8%. These results indicate that bacterial isolates from a local soil ecosystem in the Gaza Strip are able to degrade carbaryl and can be used to decrease the risk of environmental contamination by this insecticide. PMID:26691466

  11. DIYA: a bacterial annotation pipeline for any genomics lab

    OpenAIRE

    Stewart, Andrew C.; Osborne, Brian; Read, Timothy D

    2009-01-01

    Summary:DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. The software is currently used to take DNA contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in Genbank file format as output. Availability: Distribution and source code are available at (https://sourceforge.net/projects/diyg/). Contact: tr...

  12. BAC ends library generation for Illumina sequencing

    OpenAIRE

    sprotocols

    2015-01-01

    Bacterial artificial chromosome (BAC) libraries are still a valuable tool for de novo assembly of complex genomes, such as many plants genomes. Shotgun sequencing of BACs, individually or by pools, produces first assemblies which usually need further improvement towards finished quality. We developed a new approach to obtain BAC ends libraries for Illumina sequencing (BES), overcoming the expensive and time consuming BAC ends Sanger sequencing. This new method could be useful for improving de...

  13. Bacterial small RNAs in the Genus Rickettsia

    OpenAIRE

    Schroeder, Casey L. C.; Narra, Hema P.; Rojas, Mark; Sahni, Abha; Patel, Jignesh; Khanipov, Kamil; Wood, Thomas G.; Fofanov, Yuriy; Sahni, Sanjeev K.

    2015-01-01

    Background Rickettsia species are obligate intracellular Gram-negative pathogenic bacteria and the etiologic agents of diseases such as Rocky Mountain spotted fever (RMSF), Mediterranean spotted fever, epidemic typhus, and murine typhus. Genome sequencing revealed that R. prowazekii has ~25 % non-coding DNA, the majority of which is thought to be either “junk DNA” or pseudogenes resulting from genomic reduction. These characteristics also define other Rickettsia genomes. Bacterial small RNAs,...

  14. Within-host evolution of bacterial pathogens.

    OpenAIRE

    Didelot, X.; Walker, AS; Peto, TE; Crook, DW; Wilson, DJ

    2016-01-01

    Whole-genome sequencing has opened the way for investigating the dynamics and genomic evolution of bacterial pathogens during the colonization and infection of humans. The application of this technology to the longitudinal study of adaptation in an infected host - in particular, the evolution of drug resistance and host adaptation in patients who are chronically infected with opportunistic pathogens - has revealed remarkable patterns of convergent evolution, suggestive of an inherent repeatab...

  15. Genome Sequence of the Spinosyns-Producing Bacterium Saccharopolyspora spinosa NRRL 18395 ▿

    Science.gov (United States)

    Pan, Yuanlong; Yang, Xi; Li, Jing; Zhang, Ruifen; Hu, Yongfei; Zhou, Yuguang; Wang, Jun; Zhu, Baoli

    2011-01-01

    Saccharopolyspora spinosa is a Gram-positive bacterium that produces spinosad, a well-known biodegradable insecticide that is used for agricultural pest control and has an excellent environmental and mammalian toxicological profile. Here, we present the first draft genome sequence of the type strain Saccharopolyspora spinosa NRRL 18395, which consists of 22 scaffolds. PMID:21478350

  16. Draft Genome Sequence of the Carbofuran-Mineralizing Novosphingobium sp. Strain KN65.2

    OpenAIRE

    Nguyen, Thi Phi Oanh; De Mot, René; Springael, Dirk

    2015-01-01

    Complete mineralization of the N-methylcarbamate insecticide carbofuran, including mineralization of the aromatic moiety, appears to be confined to sphingomonad isolates. Here, we report the first draft genome sequence of such a sphingomonad strain, i.e., Novosphingobium sp. KN65.2, isolated from carbofuran-exposed agricultural soil in Vietnam.

  17. Inhibition of voltage-gated calcium channels as common mode of action for (mixtures of) distinct classes of insecticides

    NARCIS (Netherlands)

    Meijer, Marieke; Dingemans, Milou M L; van den Berg, Martin; Westerink, Remco H S

    2014-01-01

    Humans are exposed to distinct structural classes of insecticides with different neurotoxic modes of action. Because calcium homeostasis is essential for proper neuronal function and development, we investigated the effects of insecticides from different classes (pyrethroid: (α-)cypermethrin; organo

  18. Jaburetox-2Ec: an insecticidal peptide derived from an isoform of urease from the plant Canavalia ensiformis.

    Science.gov (United States)

    Mulinari, F; Stanisçuaski, F; Bertholdo-Vargas, L R; Postal, M; Oliveira-Neto, O B; Rigden, D J; Grossi-de-Sá, M F; Carlini, C R

    2007-10-01

    Canatoxin, a urease isoform from Canavalia ensiformis seeds, shows insecticidal activity against different insect species. Its toxicity relies on an internal 10 kDa peptide (pepcanatox), released by hydrolysis of Canatoxin by cathepsins in the digestive system of susceptible insects. In the present work, based on the N-terminal sequence of pepcanatox, we have designed primers to amplify by PCR a 270-bp fragment corresponding to pepcanatox using JBURE-II cDNA (one of the urease isoforms cloned from C. ensiformis, with high identity to JBURE-I, the classical urease) as a template. This amplicon named jaburetox-2 was cloned into pET 101 vector to obtain heterologous expression in Escherichia coli of the recombinant protein in C-terminal fusion with V-5 epitope and 6-His tag. Jaburetox-2Ec was purified on Nickel-NTA resin and bioassayed in insect models. Dysdercus peruvianus larvae were fed on cotton seed meal diets containing 0.01% (w/w) Jaburetox-2Ec and, after 11 days, all individuals were dead. Jaburetox-2Ec was also tested against Spodoptera frugiperda larvae and caused 100% mortality. In contrast, high doses of Jaburetox-2Ec were innocuous when injected or ingested by mice and neonate rats. Modeling of Jaburetox-2Ec, in comparison with other peptide structures, revealed a prominent beta-hairpin motif consistent with an insecticidal activity based on either neurotoxicity or cell permeation. PMID:17875343

  19. Genome analysis of cytochrome P450s and their expression profiles in insecticide resistant mosquitoes, Culex quinquefasciatus.

    Directory of Open Access Journals (Sweden)

    Ting Yang

    Full Text Available Here we report a study of the 204 P450 genes in the whole genome sequence of larvae and adult Culex quinquefasciatus mosquitoes. The expression profiles of the P450 genes were compared for susceptible (S-Lab and resistant mosquito populations, two different field populations of mosquitoes (HAmCq and MAmCq, and field parental mosquitoes (HAmCq(G0 and MAmCq(G0 and their permethrin selected offspring (HAmCq(G8 and MAmCq(G6. While the majority of the P450 genes were expressed at a similar level between the field parental strains and their permethrin selected offspring, an up- or down-regulation feature in the P450 gene expression was observed following permethrin selection. Compared to their parental strains and the susceptible S-Lab strain, HAmCq(G8 and MAmCq(G6 were found to up-regulate 11 and 6% of total P450 genes in larvae and 7 and 4% in adults, respectively, while 5 and 11% were down-regulated in larvae and 4 and 2% in adults. Although the majority of these up- and down-regulated P450 genes appeared to be developmentally controlled, a few were either up- or down-regulated in both the larvae and adult stages. Interestingly, a different gene set was found to be up- or down-regulated in the HAmCq(G8 and MAmCq(G6 mosquito populations in response to insecticide selection. Several genes were identified as being up- or down-regulated in either the larvae or adults for both HAmCq(G8 and MAmCq(G6; of these, CYP6AA7 and CYP4C52v1 were up-regulated and CYP6BY3 was down-regulated across the life stages and populations of mosquitoes, suggesting a link with the permethrin selection in these mosquitoes. Taken together, the findings from this study indicate that not only are multiple P450 genes involved in insecticide resistance but up- or down-regulation of P450 genes may also be co-responsible for detoxification of insecticides, insecticide selection, and the homeostatic response of mosquitoes to changes in cellular environment.

  20. Molecular Analysis of Bacterial Microbiota on Brazilian Currency Note Surfaces

    Directory of Open Access Journals (Sweden)

    Tairacan Augusto Pereira da Fonseca

    2015-10-01

    Full Text Available Currency notes have been implicated as a vehicle for transmitting community-acquired bacterial infections. However, the overall diversity of the bacterial population residing on banknotes is still unknown in Brazil. In this study, we aimed to investigate the overall bacterial population from 150 different Brazilian Rial (R$ notes in circulation using a culture-independent Illumina massively parallel sequencing approach of the 16S rRNA genes. Samples were randomly collected from three different street markets or “feiras” in the metropolitan region of São Paulo. Taxonomical composition revealed the abundance of Proteobacteria phyla, followed by Firmicutes and Streptophyta, with a total of 1193 bacterial families and 3310 bacterial genera. Most of these bacterial genera are of human, animal, and environmental origins. Also, our analysis revealed the presence of some potential pathogenic bacterial genera including Salmonella, Staphylococcus, and Klebsiella. The results demonstrate that there is a tremendous diversity of bacterial contamination on currency notes, including organisms known to be opportunistic pathogens. One of the factors that may contribute to the richness of bacterial diversity in currency notes is personal hygiene. Thus, our results underscore the need to increase public awareness of the importance of personal hygiene of money handlers who also handle food.

  1. Bacterial Wound Culture

    Science.gov (United States)

    ... Home Visit Global Sites Search Help? Bacterial Wound Culture Share this page: Was this page helpful? Also known as: Aerobic Wound Culture; Anaerobic Wound Culture Formal name: Culture, wound Related ...

  2. Bacterial Meningitis in Infants

    Directory of Open Access Journals (Sweden)

    J Gordon Millichap

    2004-04-01

    Full Text Available A retrospective study of 80 infantile patients (ages 30-365 days; 47 male, 33 female with culture-proven bacterial meningitis seen over a 16 year period (1986-2001 is reported from Taiwan.

  3. Hepatopancreatic intoxication of lambda cyhalothrin insecticide on albino rats

    OpenAIRE

    Elhalwagy, Manal EA; Abd-Alrahman, Sherif H; Nahas, AA; Ziada, Reem M; Mohamady, Aziza H

    2015-01-01

    Background: Despite the known adverse effects of lambda cyhalothrin insecticide, little is known about its hepatopancreatic intoxication effects. The present study was carried out to elucidate sub-chronic effect of Karat 2.5% EC formulation of lambda cyhalothrin on male albino rats. Methods: To explore the effects of exposure to lambda cyhalothrin on rats and its mechanism, low (1/40 of LD50, 5 mg/kg/day) and high dose (1/4 of LD50, 50 mg/kg/day) lambda cyhalothrin were applied to rats via dr...

  4. A New Insecticidal Sesquiterpene Ester from Celastrus Angulatus

    Directory of Open Access Journals (Sweden)

    Shao-peng Wei

    2009-03-01

    Full Text Available A new sesquiterpene polyol ester with a β-dihydroagarofuran skeleton, NW37 (1, and three known compounds NW13 (2, NW16 (3 and NW35 (4 were isolated by bioassay-guided fractionation from the highly polar MeOH extracts of the root bark of Celastrus angulatus. Their chemical structures were elucidated mainly by analyses of MS and NMR spectral data. The insecticidal activity of compound 1 against 4th instar Mythimna separata larvae with a KD50 value of 252.3 μg·g-1 was demonstrated.

  5. Economic Consequences of Restricting the Use of Organochlorine Insecticides on Cotton, Corn, Peanuts, and Tobacco.

    Science.gov (United States)

    Davis, Velmar W.; And Others

    The Department of Agriculture continually reviews needs for insecticides and recommends those which are effective with least hazard to people and the environment. This report estimates the economic effects of reducing the use of organochlorine insecticides. Using data from a 1966 Economic Research Service Survey, the report concludes that these…

  6. Studies on the effect of organophosphorus insecticide (dichlorovos) on nucleic acids and its toxicity on mice

    International Nuclear Information System (INIS)

    The effect of organophosphorus insecticide dichlorovos on nucleic acids and its toxicity in mice was investigated. The studies carried out included distribution study of the insecticide in different organs of mice, its effect on acetyl cholinesterase both on blood and in brain and alkylation capability on guanine in urine and in intact DNA of mouse liver

  7. Residual toxicity of four insecticides to Aedes triseriatus in scrap tires.

    Science.gov (United States)

    Beehler, J W; Quick, T C; DeFoliart, G R

    1991-03-01

    Four insecticides were tested for residual activity to Aedes triseriatus in scrap tires. Abate (temephos) granules applied at 10 ppm (AI) resulted in 100% mortality of 4th instar larvae for more than one year. The other insecticides caused no mortality within 4 wk after application. PMID:2045803

  8. Fate and effects of the insecticide chlorpyrifos in outdoor plankton-dominated microcosms in Thailand.

    NARCIS (Netherlands)

    Daam, M.A.; Crum, S.J.H.; Brink, van den P.J.; Nogueira, A.J.A.

    2008-01-01

    The fate and effects of the insecticide chlorpyrifos were studied in plankton-dominated, freshwater microcosms in Thailand. Disappearance rates of chlorpyrifos from the water column in the present study were similar to those in temperate regions. Insecticide accumulation in the sediment was relative

  9. Relative toxicity and residual activity of insecticides used in blueberry pest management: mortality of natural enemies.

    Science.gov (United States)

    Roubos, Craig R; Rodriguez-Saona, Cesar; Holdcraft, Robert; Mason, Keith S; Isaacs, Rufus

    2014-02-01

    A series of bioassays were conducted to determine the relative toxicities and residual activities of insecticides labeled for use in blueberry (Vaccinium corymbosum L.) on natural enemies, to identify products with low toxicity or short duration effects on biological control agents. In total, 14 insecticides were evaluated using treated petri dishes and four commercially available natural enemies (Aphidius colemani Viereck, Orius insidiosus [Say], Chrysoperla rufilabris [Burmeister], and Hippodamia convergens [Guérin-Menéville]). Dishes were aged under greenhouse conditions for 0, 3, 7, or 14 d before introducing insects to test residual activity. Acute effects (combined mortality and knockdown) varied by insecticide, residue age, and natural enemy species. Broad-spectrum insecticides caused high mortality to all biocontrol agents, whereas products approved for use in organic agriculture had little effect. The reduced-risk insecticide acetamiprid consistently caused significant acute effects, even after aging for 14 d. Methoxyfenozide, novaluron, and chlorantraniliprole, which also are classified as reduced-risk insecticides, had low toxicity, and along with the organic products could be compatible with biological control. This study provides information to guide blueberry growers in their selection of insecticides. Further research will be needed to determine whether adoption of a pest management program based on the use of more selective insecticides will result in higher levels of biological control in blueberry. PMID:24665711

  10. Insecticide, Sugar and Diet Effects on Feeding and Mortality in Rhagoletis indifferens (Dipt., Tephritidae)

    Science.gov (United States)

    The effects of spinosad bait and various insecticides, the presence of sugar in insecticides, and diet on feeding responses and mortality in western cherry fruit fly, Rhagoletis indifferens Curran (Diptera: Tephritidae), were determined. Diet was defined as feeding on sugar only or yeast extract +...

  11. Collembola and macroarthropod community responses to carbamate, organophosphate and synthetic pyrethroid insecticides: direct and indirect effects

    NARCIS (Netherlands)

    Frampton, G.K.; Brink, van den P.J.

    2007-01-01

    Non-target effects on terrestrial arthropod communities of the broad-spectrum insecticides chlorpyrifos and cypermethrin and the selective insecticide pirimicarb were investigated in winter wheat fields in summer. Effects of chlorpyrifos on arthropod abundance and taxonomic richness were consistentl

  12. Liquid-Liquid Extraction of Insecticides from Juice: An Analytical Chemistry Laboratory Experiment

    Science.gov (United States)

    Radford, Samantha A.; Hunter, Ronald E., Jr.; Barr, Dana Boyd; Ryan, P. Barry

    2013-01-01

    A laboratory experiment was developed to target analytical chemistry students and to teach them about insecticides in food, sample extraction, and cleanup. Micro concentrations (sub-microgram/mL levels) of 12 insecticides spiked into apple juice samples are extracted using liquid-liquid extraction and cleaned up using either a primary-secondary…

  13. Insecticidal effect of furanocoumarins from fruits of Angelica archangelica L. against larvae Spodoptera littoralis Boisd

    Czech Academy of Sciences Publication Activity Database

    Pavela, R.; Vrchotová, Naděžda

    2013-01-01

    Roč. 43, MAY 2013 (2013), s. 33-39. ISSN 0926-6690 R&D Projects: GA MŠk(CZ) ED1.1.00/02.0073 Keywords : Angelica archangelica * furanocoumarins * essential oils * plant extracts * spodoptera littoralis * botanical insecticides * insecticidal activity Subject RIV: EH - Ecology, Behaviour Impact factor: 3.208, year: 2013

  14. Susceptibility of natural enemies of pests of agriculture to commonly applied insecticides in Honduras

    International Nuclear Information System (INIS)

    Insecticides are commonly used by Honduran farmers to control pest insects in agricultural crops such as corn, melons and tomatoes. However, the insecticides have the potential for toxicity to the natural enemies of the pest insects also. Therefore, efforts are being made to identify insecticides which, when used within the Inegerated Pest Management (IPM) programme, are selectively more toxic to the pest insects than their natural enemies. A number of selected chemical insecticides and a biological insecticide (NPV) were tested in three different tests to determine toxicity to two beneficial insects: Telenomus remus Nixon (Hymenoptera: Scelionidae) and Chrysoperla carnea Steph. (Neuroptera: Chrysopidae). All insecticides were toxic to T. remus which suffered high mortality. There was no significant difference in mortality of the insect due to the method of exposure to the insecticides. There were some differences in the toxicity of the insecticides to C. carnea, and abamectin, bifenthrin, cypermethrin, diafenthiuron, imidacloprid and fenpropathrin were relatively less toxic and could be used in IPM for the control of pest insects. (author)

  15. On-line Monitoring for Phosphorus Removal Process and Bacterial Community in Sequencing Batch Reactor%SBR工艺除磷过程与种群结构在线监测

    Institute of Scientific and Technical Information of China (English)

    崔有为; 王淑莹; 李晶

    2009-01-01

    For efficient energy consumption and control of effluent quality, the cycle duration for a sequencing batch reactor (SBR) needs to be adjusted by real-time control according to the characteristics and loading of waste-water. In this study, an on-line information system for phosphorus removal processes was established. Based on the analysis for four systems with different ecological community structures and two operation modes, anaerobic-aerobic process and anaerobic-anaerobic process, the characteristic patterns of oxidation-reduction potential (ORP) and pH were related to phosphorous dynamics in the anaerobic, anoxic and aerobic phases, for determination of the end of phosphorous removal. In the operation mode of anaerobic-aerobic process, the pH profile in the anaerobic phase was used to estimate the relative amount of phosphorous accumulating organisms (PAOs) and glycogen accumulat- ing organisms (GAOs), which is beneficial to early detection of ecology community shifts. The on-line sensor val-ue of pH and ORP may be used as the parameters to adjust the duration for phosphorous removal and community shifts to cope with influent variations and maintain appropriate operation conditions.

  16. High throughput direct end sequencing of BAC clones.

    OpenAIRE

    Kelley, J M; Field, C E; Craven, M B; Bocskai, D; Kim, U J; Rounsley, S D; Adams, M D

    1999-01-01

    Libraries constructed in bacterial artificial chromosome (BAC) vectors have become the choice for clone sets in high throughput genomic sequencing projects primarily because of their high stability. BAC libraries have been proposed as a source for minimally over-lapping clones for sequencing large genomic regions, and the use of BAC end sequences (i.e. sequences adjoining the insert sites) has been proposed as a primary means for selecting minimally overlapping clones for sequencing large gen...

  17. The bacterial communities of Drosophila suzukii collected from undamaged cherries

    OpenAIRE

    James Angus Chandler; James, Pamela M.; Guillaume Jospin; Lang, Jenna M.

    2014-01-01

    Drosophila suzukii is an introduced pest insect that feeds on undamaged, attached fruit. This diet is distinct from the fallen, discomposing fruits utilized by most other species of Drosophila. Since the bacterial microbiota of Drosophila, and of many other animals, is affected by diet, we hypothesized that the bacteria associated with D. suzukii are distinct from that of other Drosophila. Using 16S rDNA PCR and Illumina sequencing, we characterized the bacterial communities of larval and adu...

  18. Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes

    OpenAIRE

    Lieberman, Tami D; Michel, Jean-Baptiste; Aingaran, Mythili; Potter-Bynoe, Gail; Roux, Damien; Davis, Michael R.; Skurnik, David; Leiby, Nicholas; LiPuma, John J.; Goldberg, Joanna B.; McAdam, Alexander J.; Priebe, Gregory P.; Kishony, Roy

    2011-01-01

    Bacterial pathogens evolve during the infection of their human hosts 1-8 , but separating adaptive and neutral mutations remains challenging 9-11 . Here, we identify bacterial genes under adaptive evolution by tracking recurrent patterns of mutations in the same pathogenic strain during the infection of multiple patients. We conducted a retrospective study of a Burkholderia dolosa outbreak among people with cystic fibrosis, sequencing the genomes of 112 isolates collected from 14 individuals ...

  19. Sequence assembly

    DEFF Research Database (Denmark)

    Scheibye-Alsing, Karsten; Hoffmann, S.; Frankel, Annett Maria;

    2009-01-01

    Despite the rapidly increasing number of sequenced and re-sequenced genomes, many issues regarding the computational assembly of large-scale sequencing data have remain unresolved. Computational assembly is crucial in large genome projects as well for the evolving high-throughput technologies and...... plays an important role in processing the information generated by these methods. Here, we provide a comprehensive overview of the current publicly available sequence assembly programs. We describe the basic principles of computational assembly along with the main concerns, such as repetitive sequences...... in genomic DNA, highly expressed genes and alternative transcripts in EST sequences. We summarize existing comparisons of different assemblers and provide a detailed descriptions and directions for download of assembly programs at: http://genome.ku.dk/resources/assembly/methods.html....

  20. Potential exposure of pollinators to neonicotinoid insecticides from the use of insecticide seed treatments in the mid-southern United States.

    Science.gov (United States)

    Stewart, Scott D; Lorenz, Gus M; Catchot, Angus L; Gore, Jeff; Cook, Don; Skinner, John; Mueller, Thomas C; Johnson, Donald R; Zawislak, Jon; Barber, Jonathan

    2014-08-19

    Research was done during 2012 to evaluate the potential exposure of pollinators to neonicotinoid insecticides used as seed treatments on corn, cotton, and soybean. Samples were collected from small plot evaluations of seed treatments and from commercial fields in agricultural production areas in Arkansas, Mississippi, and Tennessee. In total, 560 samples were analyzed for concentrations of clothianidin, imidacloprid, thiamethoxam, and their metabolites. These included pollen from corn and cotton, nectar from cotton, flowers from soybean, honey bees, Apis mellifera L., and pollen carried by foragers returning to hives, preplanting and in-season soil samples, and wild flowers adjacent to recently planted fields. Neonicotinoid insecticides were detected at a level of 1 ng/g or above in 23% of wild flower samples around recently planted fields, with an average detection level of about 10 ng/g. We detected neonicotinoid insecticides in the soil of production fields prior to planting at an average concentration of about 10 ng/g, and over 80% of the samples having some insecticide present. Only 5% of foraging honey bees tested positive for the presence of neonicotinoid insecticides, and there was only one trace detection (bees. Soybean flowers, cotton pollen, and cotton nectar contained little or no neonicotinoids resulting from insecticide seed treatments. Average levels of neonicotinoid insecticides in corn pollen ranged from less than 1 to 6 ng/g. The highest neonicotinoid concentrations were found in soil collected during early flowering from insecticide seed treatment trials. However, these levels were generally not well correlated with neonicotinoid concentrations in flowers, pollen, or nectar. Concentrations in flowering structures were well below defined levels of concern thought to cause acute mortality in honey bees. The potential implications of our findings are discussed. PMID:25010122