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Relevant bibliographies by topics / Molecular sequences

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Academic literature on the topic 'Molecular sequences'

Author: Grafiati

Published: 4 June 2021

Last updated: 15 June 2025

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Journal articles on the topic "Molecular sequences"

1

Liu, B. Y., Z. Y. Wang, H. R. Wang, P. Hu, D. Xu, and Q. Wang. "Molecular profiling of bacterial species in the geese cecum." Czech Journal of Animal Science 56, No. 4 (2011): 192–203. http://dx.doi.org/10.17221/1433-cjas.

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The purpose of this study was to analyse the microbial diversity in the caecum of geese using a 16S ribosomal RNA gene (rRNA) clone library approach. A total of 160 clones and 124 clones were sequenced and phylogenetically analysed from the contents and mucosa of the caecum of Yang Zhou geese, respectively. The result indicated that there was a rich variety of bacteria in the caecum contents. Forty-six operational taxonomic units (OTUs) based on a 98% similarity criterion were classified in the contents of goose caecum, as compared to 29 OTUs based on a 97% similarity criterion in the mucosa of goose caecum. The sequences were assigned to 7 and 5 groups in the contents and mucosa of goose caecum, respectively. Contents of goose caecum were dominantly occupied by Clostridia-related species (58.7%) with other abundant sequences being related to Bacteroidetes (26.9%) and Erysipelotrichi (11.2%). Gammaproteobacteria (59.6%) and Clostridia (20.1%) were predominant in the mucosa of goose caecum.

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Bouchet, Valérie, Heather Huot, and Richard Goldstein. "Molecular Genetic Basis of Ribotyping." Clinical Microbiology Reviews 21, no. 2 (2008): 262–73. http://dx.doi.org/10.1128/cmr.00026-07.

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SUMMARY Nearly 2,000 ribotyping-based studies exist, ranging from epidemiology to phylogeny and taxonomy. None precisely reveals the molecular genetic basis, with many incorrectly attributing detected polymorphisms to rRNA gene sequences. Based on in silico genomics, we demonstrate that ribotype polymorphisms result from sequence variability in neutral housekeeping genes flanking rRNA operons, with rRNA gene sequences serving solely as conserved, flank-linked tags. We also reveal that from such an informatics perspective, it is readily feasible a priori to design an interpretable ribotyping scheme for a genomically sequenced microbial species, and we discuss limitations to the basic restriction fragment length polymorphism-based method as well as alternate PCR ribotyping-based schemes.

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Capesius, Ingrid, and Michael Stech. "Molecular relationships within mosses based on 18S rRNA gene sequences." Nova Hedwigia 64, no. 3-4 (1997): 525–33. http://dx.doi.org/10.1127/nova.hedwigia/64/1997/525.

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Landeweert, Renske, Paula Leeflang, Thom W. Kuyper, et al. "Molecular Identification of Ectomycorrhizal Mycelium in Soil Horizons." Applied and Environmental Microbiology 69, no. 1 (2003): 327–33. http://dx.doi.org/10.1128/aem.69.1.327-333.2003.

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ABSTRACT Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (≥99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had ≥98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.

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Val-Moraes, Silvana Pompéia, Eliamar Aparecida Nascimbem Pedrinho, Eliana Gertrudes Macedo Lemos, and Lucia Maria Carareto-Alves. "Molecular Identification of Fungal Communities in a Soil Cultivated with Vegetables and Soil Suppressiveness toRhizoctonia solani." Applied and Environmental Soil Science 2013 (2013): 1–7. http://dx.doi.org/10.1155/2013/268768.

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Fungi constitute an important part of the soil ecosystem, playing key roles in decomposition, cycling processes, and biotic interactions. Molecular methods have been used to assess fungal communities giving a more realistic view of their diversity. For this purpose, total DNA was extracted from bulk soils cultivated with tomato (STC), vegetables (SHC), and native forest (SMS) from three sites of the Taquara Branca river basin in Sumaré County, São Paulo State, Brazil. This metagenomic DNA was used as a template to amplify fungal 18S rDNA sequences, and libraries were constructed inEscherichia coliby cloning PCR products. The plasmid inserts were sequenced and compared to known rDNA sequences in the GenBank database. Of the sequenced clones, 22 were obtained from the SMS sample, 18 from the SHC sample, and 6 from the STC sample. Although most of the clone sequences did not match the sequences present in the database, individual amplified sequences matched with Glomeromycota (SMS), Fungi incertae sedis (SMS), and Neocallimastigomycota (SHC). Most of the sequences from the amplified taxa represent uncultured fungi. The molecular analysis of variance (AMOVA) indicated that fluctuations observed of haplotypes in the composition may be related to herbicide application.

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Ragan, Mark A., Guillaume Bernard, and Cheong Xin Chan. "Molecular phylogenetics before sequences." RNA Biology 11, no. 3 (2014): 176–85. http://dx.doi.org/10.4161/rna.27505.

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Gaduaa, Alaa A., and Ali A. Kareem. "Molecular Identification of Peach Fruit Fly Bactrocera zonata and its Symbionts in Karbala Province, Iraq." IOP Conference Series: Earth and Environmental Science 1214, no. 1 (2023): 012045. http://dx.doi.org/10.1088/1755-1315/1214/1/012045.

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Abstract Bactrocera zonata is a fruit tree pest that typically attacks and causes heavy damage in fruit production using its sucking mouth. Researchers have started to distinguish them through molecular characterization and sequencing to control this pest. Mitochondrial genes such as COI (mtCOI) are commonly used as barcoding for identifying eukaryotes and counting insects. In the current study, the mtCOI gene has been amplified. Three samples from five locations in Karbala city were sequenced using the Sanger sequencing method. Also, symbionts bacteria linked with this insect were molecularly identified by sequencing. Four different sequences of B. zonata showed genetic diversity, and three different endosymbionts, Pectobacterium carotovorum, Acidithiobacillus sp., and Bacterium symbiont of B. zonata were molecularly identified. Different computational tools were used to compare sequences with related sequences retrieved from databases. Associated species were identified through phylogenetic analysis using the MEGA X software and confirmed with available GenBank databases. Pairwise sequence alignment showed the sequence identity of about 99% with Bactrocera zonata.

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He, XY, VP Antao, D. Basila, JC Marx, and BR Davis. "Isolation and molecular characterization of the human CD34 gene." Blood 79, no. 9 (1992): 2296–302. http://dx.doi.org/10.1182/blood.v79.9.2296.2296.

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Abstract The human CD34 surface antigen is selectively expressed on hematopoietic stem/progenitor cells, suggesting that it plays an essential role in early hematopoiesis. Using a 1.5-kb partial human CD34 cDNA sequence, RNA-polymerase chain reaction (PCR), and rapid amplification of cDNA ends (RACE) methods, we cloned and sequenced the full-length (2.65 kb) cDNA. The cDNA encodes a type I transmembrane protein with no obvious homology to other known proteins. The entire CD34 gene of 28 kb was cloned, and the coding sequences mapped to eight exons. Mapping of the 5′ termini of mRNAs by 5′-RACE and RNAase protection analyses has indicated that the human CD34 gene uses multiple transcription initiation sites. Analysis of the upstream regulatory sequences revealed the absence of TATA and CAAT box sequences, and the presence of myb, myc, and ets-like DNA binding motifs. We have identified significant homology between human and mouse CD34 genes in 5′ and 3′ untranslated regions, amino acid coding sequences, and 5′ flanking sequences. This investigation of the CD34 gene should facilitate study of the function and regulation of this stem cell antigen.

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He, XY, VP Antao, D. Basila, JC Marx, and BR Davis. "Isolation and molecular characterization of the human CD34 gene." Blood 79, no. 9 (1992): 2296–302. http://dx.doi.org/10.1182/blood.v79.9.2296.bloodjournal7992296.

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The human CD34 surface antigen is selectively expressed on hematopoietic stem/progenitor cells, suggesting that it plays an essential role in early hematopoiesis. Using a 1.5-kb partial human CD34 cDNA sequence, RNA-polymerase chain reaction (PCR), and rapid amplification of cDNA ends (RACE) methods, we cloned and sequenced the full-length (2.65 kb) cDNA. The cDNA encodes a type I transmembrane protein with no obvious homology to other known proteins. The entire CD34 gene of 28 kb was cloned, and the coding sequences mapped to eight exons. Mapping of the 5′ termini of mRNAs by 5′-RACE and RNAase protection analyses has indicated that the human CD34 gene uses multiple transcription initiation sites. Analysis of the upstream regulatory sequences revealed the absence of TATA and CAAT box sequences, and the presence of myb, myc, and ets-like DNA binding motifs. We have identified significant homology between human and mouse CD34 genes in 5′ and 3′ untranslated regions, amino acid coding sequences, and 5′ flanking sequences. This investigation of the CD34 gene should facilitate study of the function and regulation of this stem cell antigen.

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Idris, A. M., and J. K. Brown. "Sinaloa Tomato Leaf Curl Geminivirus: Biological and Molecular Evidence for a New Subgroup III Virus." Phytopathology® 88, no. 7 (1998): 648–57. http://dx.doi.org/10.1094/phyto.1998.88.7.648.

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The biological and molecular properties of Sinaloa tomato leaf curl virus (STLCV) were investigated in line with the hypothesis that STLCV is a previously uncharacterized, whitefly-transmitted geminivirus from North America. STLCV causes yellow leaf curl symptoms in tomato and yellow-green foliar mottle in pepper. Five species belonging to two plant families were STLCV experimental hosts. STLCV had a persistent relationship with its whitefly vector, Bemisia tabaci. Polymerase chain reaction fragments of STLCV common region (CR) sequences of the A or B genomic components and the viral coat protein gene (AV1) were molecularly cloned and sequenced. The STLCV A- and B-component CR sequences (174 nucleotides each) shared 97.9% identity and contained identical cis elements putatively involved in transcriptional regulation and an origin of replication (the AC cleavage site within the loop of the hairpin structure and two direct repeat sequences thought to constitute the Rep binding motif), which collectively are diagnostic for subgroup III geminiviruses. The STLCV CR sequence shared 23.1 to 77.6% identity with CR sequences of representative geminiviridae, indicating the STLCV CR sequence is unique. Molecular phylogenetic analysis of CR or AV1 sequences of STLCV and the respective sequences of 31 familial members supported the placement of STLCV as a unique bipartite, subgroup III virus most closely related to other viruses from the Western Hemisphere. STLCV is provisionally described as a new species within the genus Begomovirus, family Geminiviridae.

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Dissertations / Theses on the topic "Molecular sequences"

1

Parsons, Jeremy David. "Computer analysis of molecular sequences." Thesis, University of Cambridge, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.282922.

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Kimothi, Dhananjay. "Learning representations for molecular sequences." Thesis, Queensland University of Technology, 2021. https://eprints.qut.edu.au/226106/1/Dhananjay_Kimothi_Thesis.pdf.

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This thesis explores the utility of representation learning for bioinformatics applications. It proposes approaches for generating low dimensional embeddings for molecular sequences, which proved effective for downstream bioinformatics tasks such as protein classification and protein-protein interaction prediction. One specific theme of this thesis is to develop a scalable and computationally effective solution for large scale sequence comparisons and two successful approaches – one based on a hierarchy of models, the other on a hybrid of two methods – are presented. The representation learning approaches proposed in this thesis are generic and can be adapted for similar problems within bioinformatics and other domains.

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Vázquez, García Ignacio. "Molecular evolution of biological sequences." Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/284174.

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Evolution is an ubiquitous feature of living systems. The genetic composition of a population changes in response to the primary evolutionary forces: mutation, selection and genetic drift. Organisms undergoing rapid adaptation acquire multiple mutations that are physically linked in the genome, so their fates are mutually dependent and selection only acts on these loci in their entirety. This aspect has been largely overlooked in the study of asexual or somatic evolution and plays a major role in the evolution of bacterial and viral infections and cancer. In this thesis, we put forward a theoretical description for a minimal model of evolutionary dynamics to identify driver mutations, which carry a large positive fitness effect, among passenger mutations that hitchhike on successful genomes. We examine the effect this mode of selection has on genomic patterns of variation to infer the location of driver mutations and estimate their selection coefficient from time series of mutation frequencies. We then present a probabilistic model to reconstruct genotypically distinct lineages in mixed cell populations from DNA sequencing. This method uses Hidden Markov Models for the deconvolution of genetically diverse populations and can be applied to clonal admixtures of genomes in any asexual population, from evolving pathogens to the somatic evolution of cancer. To understand the effects of selection on rapidly adapting populations, we constructed sequence ensembles in a recombinant library of budding yeast (S. cerevisiae). Using DNA sequencing, we characterised the directed evolution of these populations under selective inhibition of rate-limiting steps of the cell cycle. We observed recurrent patterns of adaptive mutations and characterised common mutational processes, but the spectrum of mutations at the molecular level remained stochastic. Finally, we investigated the effect of genetic variation on the fate of new mutations, which gives rise to complex evolutionary dynamics. We demonstrate that the fitness variance of the population can set a selective threshold on new mutations, setting a limit to the efficiency of selection. In summary, we combined statistical analyses of genomic sequences, mathematical models of evolutionary dynamics and experiments in molecular evolution to advance our understanding of rapid adaptation. Our results open new avenues in our understanding of population dynamics that can be translated to a range of biological systems.

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Li, Juan, and 李娟. "Molecular characterization of chicken repetitive DNA sequences." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2003. http://hub.hku.hk/bib/B42577287.

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Li, Juan. "Molecular characterization of chicken repetitive DNA sequences." Click to view the E-thesis via HKUTO, 2003. http://sunzi.lib.hku.hk/hkuto/record/B42577287.

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Wu, Cunle. "cDNA clones contain autonomously replicating sequences." Thesis, McGill University, 1992. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=41041.

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We have shown that nine cDNA clones, which were derived from an oligo (dT) primed cDNA library of human embryonic lung fibroblast (IMR90), are capable of supporting autonomous replication of bacterial plasmid in mammalian (HeLa) cells. Two of these cDNA clones contain a region homologous to "O"-family middle repetitive sequences; the other seven clone hybridize with neither "O"-family nor Alu family sequences and are called NOA clones. Oligo (dT) primed cDNA of IMR90 has been demonstrated to be an enriched source for autonomously replicating sequences. Two out of three "O"-family homologous cDNA clones and seven out of ten NOA clones were capable of autonomous replication. In contrast, none of the five clones, which contained Alu repetitive sequences, demonstrated replicative potential. The two autonomously replicating, "O"-family homologous cDNA, 343 and 363, were characterized in the greatest detail. In particular, sequence and structural features of a 448 bp fragment of cDNA 343, which was capable of supporting autonomous replication activity, were: extensive asymmetrical A/T-rich regions; 10/11 match to yeast ARS consensus; scaffold attachment region consensus of Drosophila; bent DNA; a DNA unwinding element and an in vitro matrix binding activity. We have used a PCR-based mapping strategy to identify an in vivo initiation zone located in a region of approximately 1.6 kb which is inclusive of cDNA 343. The 343 sequence has been localized to the long arm (6q22-6qter) of human chromosome 6 by both Southern analysis of hamster-human cell hybrids and in situ hybridization. Transcripts homologous to 343 have been detected in both poly(A$ sp+$) and non-poly(A$ sp+$) RNA fractions to be 1.3 kb and 5 kb, respectively; the 1.3 kb transcript is greatly enriched in poly(A$ sp+$) RNA fraction, and the 5 kb transcript is present predominantly in non-poly(A$ sp+$) RNA fraction. The detailed characterization of 343 genomic locus demonstrated that the 343 sequence is conserv

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7

Greer, Peter Alan. "Molecular cloning of measles virus nucleic acid sequences." Thesis, McGill University, 1985. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=71952.

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A library of cDNA clones was prepared from measles virus infected cells. Six classes of viral specific cDNA sequences were identified by a combination of Northern and Southern blot hybridization analysis.<br>Clones corresponding to measles virus NP, P/C and M genes were initially identified by hybridization selection translation experiments. Restriction mapping analysis and comparison with the recently published nucleic acid sequences have confirmed the identities of these clones.<br>The cloned sequences corresponding to the NP and M genes were subcloned into a plasmid vector which contains the Salmonella phage SP6 promoter sequence. These constructions facilitated the in vitro synthesis of RNA. This cloned RNA was subsequently translated in vitro, giving rise to the measles virus NP and M proteins. In addition to the full length NP and M proteins, smaller peptides were observed in this in vitro expression system. The series of smaller peptides made from the cloned NP RNA appear to correlate with NP-related peptides which are seen in extracts prepared from infected cells.<br>The other three classes of viral specific clones could not be conclusively identified by hybridization selection translation experiments. However, northern blot hybridization analysis enabled a tentative assignment of these three cloned sequences to the measles virus HA, F and L genes. The clone corresponding to the F protein was subsequently expressed in vitro using the SP6 transcription vector system described above.

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Pethica, Ralph Brian. "Sequences, structures and biological functions of molecular evolution." Thesis, University of Bristol, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.546211.

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Richard, Catherine. "Deletion analysis of the sequences that regulate HEM13 expression." Thesis, McGill University, 1989. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=59289.

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In the yeast Saccharomyces cerevisiae, HEM13 codes for coproporphyrinogen oxidase which catalyses the sixth enzymatic step in the heme biosynthetic pathway. Coproporphyrinogen oxidase synthesis has been shown to be regulated negatively by heme and oxygen at the transcriptional level. We are interested in defining the HEM13 cis-acting upstream sequences that mediate regulation by heme. HEM13-lacZ and HEM13-CYC1-lacZ hybrid fusions were made and expression of the resulting $ beta$-galactosidase activity was determined in vivo, under conditions of varying levels of heme. Deletion analysis of the HEM13 promoter revealed the existence of 3 upstream regulatory elements designated as UAS1, UAS2, and URS that span a region of 365 pb from nucleotides $-$640 to $-$275 with respect to the most upstream HEM13 transcriptional start site. The trans-acting factor HAP1 previously identified to activate expression of CYC1 and CTT1 genes in the presence of heme and oxygen, was found to be involved in the regulation of HEM13 expression. Measurements of HEM13-CYC1-lacZ fusions in a hap1 mutant strain indicated that HAP1 was required to fully induce and repress expression of the fusions under heme-deficient and heme-sufficient conditions respectively.

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Verlet, Jan Raf Rogier. "Controlling electronic and molecular dynamics using optical pulse sequences." Thesis, King's College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.397922.

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Books on the topic "Molecular sequences"

1

S, Waterman M., ed. Mathematical analysis of molecular sequences. Pergamon, 1989.

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2

Tashiro, Kentaro. Synthetic Molecular Sequences in Materials Science. Springer Japan, 2023. http://dx.doi.org/10.1007/978-4-431-56933-6.

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Erdmann, Volker A., and Jan Barciszewski, eds. From Nucleic Acids Sequences to Molecular Medicine. Springer Berlin Heidelberg, 2012. http://dx.doi.org/10.1007/978-3-642-27426-8.

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4

M, Miyamoto Michael, and Cracraft Joel, eds. Phylogenetic analysis of DNA sequences. Oxford University Press, 1991.

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Sillince, John A. A., and Maria Sillince. Molecular Databases for Protein Sequences and Structure Studies. Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-76809-5.

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Rodrigo, Allen G., and Gerald H. Learn, eds. Computational and Evolutionary Analysis of HIV Molecular Sequences. Springer US, 2001. http://dx.doi.org/10.1007/b112102.

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7

1960-, Rodrigo Allen G., and Learn Gerald H. 1948-, eds. Computational and evolutionary analysis of HIV molecular sequences. Kluwer Academic Publishers, 2001.

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1960-, Rodrigo Allen G., and Learn Gerald H. 1948-, eds. Computational and evolutionary analysis of HIV molecular sequences. Kluwer Academic Publishers, 2001.

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9

Berntson, Ewann Agenbroad. Evolutionary patterns within the Anthozoa (Phylum Cnidaria) reflected in ribosomal gene sequences. Massachusetts Institute of Technology, Woods Hole Oceanographic Institution, Joint Program in Oceanography/Applied Ocean Science and Engineering, 1998.

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Maroni, Gustavo. An atlas of Drosophila genes: Sequences and molecular features. Oxford University Press, 1993.

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Book chapters on the topic "Molecular sequences"

1

Eppstein, David, Zvi Galil, and Raffaele Giancarlo. "Efficient Algorithms with Applications to Molecular Biology." In Sequences. Springer New York, 1990. http://dx.doi.org/10.1007/978-1-4612-3352-7_5.

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Day, William H. E., and F. R. McMorris. "Discovering Consensus Molecular Sequences." In Information and Classification. Springer Berlin Heidelberg, 1993. http://dx.doi.org/10.1007/978-3-642-50974-2_40.

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Li, Wen-Hsiung, Chi-Cheng Luo, and Chung-I. Wu. "Evolution of DNA Sequences." In Molecular Evolutionary Genetics. Springer US, 1985. http://dx.doi.org/10.1007/978-1-4684-4988-4_1.

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Atri, Benu, and Olivier Lichtarge. "Computational Approaches to Studying Molecular Phylogenetics." In Bioinformatics: Sequences, Structures, Phylogeny. Springer Singapore, 2018. http://dx.doi.org/10.1007/978-981-13-1562-6_9.

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Petersen, Gitte. "Reading DNA Sequences." In Molecular Tools for Screening Biodiversity. Springer Netherlands, 1998. http://dx.doi.org/10.1007/978-94-009-0019-6_60.

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Devereux, Richard, and Stephanie G. Willis. "Amplification of ribosomal RNA sequences." In Molecular Microbial Ecology Manual. Springer Netherlands, 1995. http://dx.doi.org/10.1007/978-94-011-0351-0_19.

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Pohmann, Rolf. "Spatial Encoding – Basic Imaging Sequences." In Methods in Molecular Biology. Humana Press, 2011. http://dx.doi.org/10.1007/978-1-61779-219-9_2.

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Jorba, Jaume. "Phylogenetic Analysis of Poliovirus Sequences." In Methods in Molecular Biology. Springer New York, 2016. http://dx.doi.org/10.1007/978-1-4939-3292-4_11.

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Harrach, Balázs, and Mária Benko. "Phylogenetic Analysis of Adenovirus Sequences." In Methods in Molecular Medicine™. Humana Press, 2007. http://dx.doi.org/10.1007/978-1-59745-277-9_22.

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Powers, Thomas O., and Byron J. Adams. "Nucleotide Sequences in Nematode Systematics." In Advances in Molecular Plant Nematology. Springer US, 1994. http://dx.doi.org/10.1007/978-1-4757-9080-1_9.

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Conference papers on the topic "Molecular sequences"

1

Fida, Tekle, Luke Austin, Scott Leleika, Taylor Rambo, and Karen Crippen. "Development of Molecular Probe for Iron Reducing and Thiosulfate Reducing Bacteria." In CONFERENCE 2024. AMPP, 2024. https://doi.org/10.5006/c2024-20885.

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Abstract Microbiologically Influenced Corrosion (MIC) activities are mostly monitored by using canonical culture-based methods. However, these methods detect only culturable bacteria or require months of incubation to get results. To overcome this, molecular detection methods were developed for many of the MIC-causing microbes but were not available for Iron Reducing Bacteria (IRB) and Thiosulfate Reducing Bacteria (TRB). IRB and TRB are among the dominant group of microbes involved in corrosion and souring oil and gas infrastructures. In the present study, molecular probes were developed for IRB and TRB by targeting functional genes implicated in iron and thiosulfate reduction, respectively. Candidate gene sequences were retrieved from genome repository databases of pure isolates or metagenomic sequences. The sequences were aligned using bioinformatic software and primer-based probes were developed from conserved regions. Specificity and efficiency of the primers were validated by amplifying the sequences of target and non-target microbes using Quantitative Polymerase Chain Reaction (qPCR) methods. The probes successfully detected candidate microbes in biocorrosion samples collected from various gas processing facilities. The identified primer-based probes will help oil and gas industries to monitor MIC activities and develop timely management strategies to prevent undesirable microbial activities while improving system integrity and safety concerns.

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Ito, K., R. Matsuhashi, T. Kato, et al. "Potential Ennoblement of Stainless Steel by Marine Biofilm and Microbial Consortia Analysis." In CORROSION 2002. NACE International, 2002. https://doi.org/10.5006/c2002-02452.

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Abstract Ennoblement of open circuit potential (OCP) for stainless steel in natural seawater was analyzed. OCPs of platinum, gold, palladium, chromium, titanium and nickel ennobled in natural seawater as well as that of stainless steel, SUS304 (18Cr-8Ni). OCP ennoblement is not a specific phenomenon to only stainless steel. Microorganisms in marine biofilm caused OCP ennoblement. Cathodic polarization curves elucidated that synergistic effects of hydrogen peroxide and acidity by marine biofilm probably caused OCP ennoblement in natural seawater. Furthermore, we analyzed microbial consortia in the marine biofilm using molecular biological technique, PCR-DGGE. This made us possible to identify microorganisms in the microbial consortia based on DNA sequences without any microbial culture.

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Alabbas, Faisal M., Anthony E. Kakpovbia, John R. Spear, Brajendra Mishra, and David L. Olson. "Utilization of 454 Pyrosequencing of 16S rRNA for Biodiversity Investigations of Crude Oil Systems." In CORROSION 2014. NACE International, 2014. https://doi.org/10.5006/c2014-3827.

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Abstract Microbiologically influenced corrosion (MIC) is a major problem that impacts crude oil production, transportation and storage infrastructures. Indigenous microorganisms that naturally reside in oil reservoirs are able to induce localized changes in the aqueous environment and lead to catastrophic damages. The study herein applies molecular techniques to investigate the microbial communities associated with corrosion products collected from crude oil pipelines. Small subunit ribosomal rRNA gene pyrosequencing was used to identify microbial communities present in each system. The results indicated that that the microbial communities in the corrosion products obtained from both the sour oil pipeline and sweet crude pipelines were dominated by bacteria, though archaeal sequences (predominately Methanobacteriaceae and Methanomicrobiaceae) were also identified in the sweet and sour crude oil samples, respectively. The dominant bacterial phylotypes in the sour crude sample include members of the Thermoanaerobacterales, Synergistales, and Syntrophobacterales. In the sweet crude sample, the dominant phylotypes include members of Halothiobacillaceae. Interestingly, common bacterial phylotypes that are related to Thermotogaceae were identified in all investigated samples. The impacts of these microorganisms in MIC are presented in this paper. This work will increase the knowledge related to the complex microbial diversity associated with crude oil systems and guide future MIC research.

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Edgington, T. S., J. H. Morrissey, and H. Fakhrai. "MOLECULAR CLONING OF HUMAN TISSUE FACTOR cDNA." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1643740.

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Tissue factor (TF), the cell-surface receptor and allo-steric activator for factor Vll/VIIa, is important in hemostasis andinflammation. The TF apoprotein was purifiedfrom human brain using factor Vll-affinitychromatography and SDS gel electrophoresis,and was found to consist of a 47 kDa heavy chain plus a 12.5 kDa light chain. Approximately one-third of the heavy chain amino acid sequence was determined for four regions by microsequencing the intact protein and peptides derived from V8-protease digestion. A λgtll cDNA library, made from mRNA derived from the human fibroblastic cell line WI38,was screened with (a) affinity-purified rabbit antibodies to human tissue factor, and (b) a 45-mer oligonucleotide probe based on TF heavy chain amino acid sequence. Five overlapping cDNA clones were identifiedand sequenced which confirmed all four partial TF amino acid sequences. Together these clones span the entire heavy chain coding sequence as well as 5" and 3" nontranslated regions. The N-terminusof the TF heavy chain is preceded by an unusually long signal peptide which appears to be cleaved at alternative sites two amino acids apart. This results in two variants of TF heavy chains which differ slightly in length and amino-terminal sequence.The deduced protein sequence shows no major homology to known protein sequences. However,a relatively uncommon tripeptide sequence, Trp-Lys-Ser (WKS), appears three times in the TF heavy chain. This tripeptidesequence also occurs in HMW kininogen, factor VIII,von Willebrand"s factor andant ithrombin-III. Limited sequence similarity is observed in flanking sequences,andthis may indicate a possible functional domain for the recognition of members ofthe vitamin K-dependent serine protease famil.Supported by NIH grants HL-16411 andCA-41085.

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Dr. Carmen Morato and Dr. Juan I. Seijas. "Genetic Algorithms for Molecular Biology Sequences Analysis." In 2001 Sacramento, CA July 29-August 1,2001. American Society of Agricultural and Biological Engineers, 2001. http://dx.doi.org/10.13031/2013.7417.

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Sarkar, Arup, Bimal Kumar Sarkar, and Oldrich Zmeskal. "Topological entropy calculations on the molecular sequences." In 27TH INTERNATIONAL MEETING OF THERMOPHYSICS 2022. AIP Publishing, 2023. http://dx.doi.org/10.1063/5.0162854.

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Lopez, J. A., D. W. Chung, K. Fujikawa, F. S. Hagen, T. Papavannopoulou, and G. J. Roth. "MOLECULAR CLONING OF HUMAN PLATELET GLYCOPROTEIN Ib." In XIth International Congress on Thrombosis and Haemostasis. Schattauer GmbH, 1987. http://dx.doi.org/10.1055/s-0038-1642927.

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Glycoprotein Ib (GPIb) mediates von Willebrand factor-dependent platelet adhesion and participates in the resulting platelet activation process. In the present investigation, the primary structure of human platelet GPIb was studied. GPIb and its proteolytic fragment glycocalicin were purified to near homogeneity from human platelets by affinity chromatography using wheat germ agglutinin and anti-GPIb monoclonal antibody (D. Nugent, University of Washington) coupled to Sepharose. GPIba chain, β chain, and glycocalicin were isolated, reduced and carboxymethylated, and then fragmented by trypsin and S. aureus V8 protease. Peptides were isolated by HPLC and subjected to amino acid sequence analysis. Approximately 200 amino acid residues were identified. Affinity purified rabbit antibodies directed against the a chain, the ft chain, and glycocalicin were prepared and shown to be monospecific by Western blot analysis. Total RNA was prepared from human erythroleukemia cells grown in the presence of phorbol acetate. Poly(A)+ RNA was selected and used to prepare a cDNA library in λgt11. The library was screened with [125]I-labeled polyclonal antibody to glycocalicin. The clone with the largest cDNA insert was sequenced and shown to code for amino acid sequences corresponding to those determined by Edman degradation of glycocalicin. The predicted amino acid sequence contains at least six tandem repeats of 24 amino acids that are highly homologous with 13 repeats present in leucine rich α2 glycoprotein of human plasma. Another region in the protein contains a second repeat rich in threonine and serine, which shows some homology to a 9 amino acid repeat in the connecting region of human factor V. This region is probably the major site of attachment of clusters of O-linked carbohydrate in GPIbα. These results indicate that human platelet glycoprotein Ibα has a multi-domain structure composed of a number of repetitive sequences. Supported in part by grants from the American Heart Association, Robert Wood Johnson Foundation, Veterans Administration, and National Institutes of Health.

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Zhuang, Wei, Darius Abramavicius, and Shaul Mukamel. "Coherent Infrared Pulse Sequences for Probing Molecular Chirality." In International Conference on Ultrafast Phenomena. OSA, 2006. http://dx.doi.org/10.1364/up.2006.tuc3.

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Jayapriya, J., and Michael Arock. "A parallel GWO technique for aligning multiple molecular sequences." In 2015 International Conference on Advances in Computing, Communications and Informatics (ICACCI). IEEE, 2015. http://dx.doi.org/10.1109/icacci.2015.7275611.

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Kozyra, Jerzy, Harold Fellermann, Ben Shirt-Ediss, Annunziata Lopiccolo, and Natalio Krasnogor. "Optimizing nucleic acid sequences for a molecular data recorder." In GECCO '17: Genetic and Evolutionary Computation Conference. ACM, 2017. http://dx.doi.org/10.1145/3071178.3071345.

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Reports on the topic "Molecular sequences"

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Gerstein, Mark. Investigating Molecular Recognition Through Large-scale Analysis of Protein Sequences and Structures. Defense Technical Information Center, 2000. http://dx.doi.org/10.21236/ada383741.

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Gallego Sánchez, Gerardo J., Patricia Zapata, Oscar Castañeda, et al. Use of DNA sequences for identification of possible biotypes of the fruit borer Neoleucinodes elegantalis (Lepidoptera: Crambidae), an important pest of Andean solanaceous fruits. Centro Internacional de Agricultura Tropical (CIAT), 2015. http://dx.doi.org/10.21930/agrosavia.poster.2015.1.

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In Colombia, Venezuela, Ecuador, Brazil and Honduras, the tomato borer, Neoleucinodes elegantalis, is the most important fruit-related plague of the Solanaceae family. A suitable molecular characterization using a DNA barcoding system is necessary to clarify different issues inside the taxonomy of Neoleucinodes genus. Additionally, other DNA sequences used for molecular identification and phylogenetics studies, can be implemented to obtain a better understanding of the genetic variability across different animal groups and allows to acquire a enhanced description of the population s genetic variation. The main objectives of this study are: 1. Evaluate the performance of DNA barcoding sequences (COI gen and 18S rDNA gene), in the genetic characterization of populations of N. elegantalis, collected in different wild and cultivated solanaceous plants in Colombia and Ecuador. 2. Determination of possible haplotypes related with each population belonging to this species. 3.Identification of geographical patterns associated with the distribution of this insect.

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Davidson, Irit, Hsing-Jien Kung, and Richard L. Witter. Molecular Interactions between Herpes and Retroviruses in Dually Infected Chickens and Turkeys. United States Department of Agriculture, 2002. http://dx.doi.org/10.32747/2002.7575275.bard.

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Tumors in commercial poultry are caused mainly by infection with avian herpes and retroviruses, the herpesvirus Marek's disease virus (MDV) and the retroviruses, reticuloendotheliosis (REV), lymphoid leukosis, subgroups A-I and J (ALV and ALV-J) in chickens, or Iymphoprolipherative disease (LPDV) in turkeys. Infection with one virus aggravates the clinical outcome of birds that are already infected by another oncogenic virus. As these viruses do not interfere for infection, MDV and one or more retroviruses can infect the same flock, the same bird and the same cell. While infecting the same cell, herpes and retroviruses might interact in at least three ways: a) Integration of retrovirus genomes, or genomic fragments (mainly the LTR) into MDV;b) alteration of LTR-driven expression of retroviral genes by MDV immediate- early genes, and c) by herpesvirus induced cellular transcriptional factors. The first type of molecular interaction have been demonstrated to happen efficiently in vitro by Dr. Kung, in cases multiple infection of cell cultures with MDV and REV or MDV and ALV. Moreover, Dr. Witter showed that an in vitro-created recombinant, RM1, had altered in vitro replication and in vivo biological properties. A more comprehensive characterization of RM1 was carried out in the present project. We sought to highlight whether events of such integrations occur also in the bird, in vivo. For that, we had first to determine the prevalence of dually-infected individual birds in commercial flocks, as no systematic survey has been yet reported. Surprisingly, about 25% of the commercial flocks infected with avian oncogenic viruses had a multiple virus infection and 5% of the total samples ana lysed had multiple virus sequences. Then, we aimed to evaluate and characterize biologically and molecularly the resulting recombinants, if formed, and to analyse the factors that affect these events (virus strains, type and age of birds and time interval between the infection with both viruses). The perception of retrovirus insertions into herpesviruses in vivo is not banal, as the in vivo and in vitro systems differ in the viral-target cells, lymphocytes or fibroblasts, in the MDV-replicative type, transforming or productive, and the immune system presence. We realized that previous methods employed to study in vitro created recombinant viruses were not adequate for the study of samples taken directly from the bird. Therefore, the Hot Spot-combined PCR was developed based on the molecularly known RM1 virus. Also, the PFGE that was used for tissue cultured-MDV separation was inefficient for separating MDV from organs, but useful with feather tips as a source of bird original MDV. Much attention was dedicated now to feathers, because if a recombinant virus would be formed in vivo, its biological significance would be evident by horizontal dissemination through the feathers. Major findings were: a) not only in vitro, but also in vivo MDV and retrovirus co-infections lead to LTR integrations into MDV. That was shown by the detection of chimeric molecules. These appeared in low quantities and as quasispecies, thus interfering with sequence analysis of cloned gel-purified chimeric molecules. Mainly inserts were located in the repeat long MDV fragments. In field birds chimeric molecules were detected at a lower frequency (2.5%) than in experimentally infected birds (30-50%). These could be transmitted experimentally to another birds by inoculation with chimeric molecules containing blood. Several types of chimeric molecules were formed, and same types were detected in birds infected by a second round. To reproduce viral integrations, in vivo infection trials were done with field inoculate that contained both viruses, but the chimeric molecule yield was undetectable.

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Taylor, Ronald C. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology. Office of Scientific and Technical Information (OSTI), 1991. http://dx.doi.org/10.2172/10108317.

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Robb, Frank T. Molecular Profiling of Microbial Communities from Contaminated Sources: Use of Subtractive Cloning Methods and rDNA Spacer Sequences. Office of Scientific and Technical Information (OSTI), 2001. http://dx.doi.org/10.2172/781022.

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Taylor, R. C. Automated insertion of sequences into a ribosomal RNA alignment: An application of computational linguistics in molecular biology. Office of Scientific and Technical Information (OSTI), 1991. http://dx.doi.org/10.2172/6057182.

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Robb, Frank T. Molecular Profiling of Microbial Communities from Contaminated Sources: Use of Subtractive Cloning Methods and rDNA Spacer Sequences. Office of Scientific and Technical Information (OSTI), 2000. http://dx.doi.org/10.2172/827425.

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Cohen, Yuval, Christopher A. Cullis, and Uri Lavi. Molecular Analyses of Soma-clonal Variation in Date Palm and Banana for Early Identification and Control of Off-types Generation. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7592124.bard.

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Date palm (Phoenix dactylifera L.) is the major fruit tree grown in arid areas in the Middle East and North Africa. In the last century, dates were introduced to new regions including the USA. Date palms are traditionally propagated through offshoots. Expansion of modern date palm groves led to the development of Tissue Culture propagation methods that generate a large number of homogenous plants, have no seasonal effect on plant source and provide tools to fight the expansion of date pests and diseases. The disadvantage of this procedure is the occurrence of off-type trees which differ from the original cultivar. In the present project we focused on two of the most common date palm off-types: (1) trees with reduced fruit setting, in which most of the flowers turn into three-carpel parthenocarpic fruits. In a severe form, multi-carpel flowers and fruitlets (with up to six or eight carpels instead of the normal three-carpel flowers) are also formed. (2) dwarf trees, having fewer and shorter leaves, very short trunk and are not bearing fruits at their expected age, compared to the normal trees. Similar off-types occur in other crop species propagated by tissue culture, like banana (mainly dwarf plants) or oil palm (with a common 'Mantled' phenotype with reduced fruit setting and occurrence of supernumerary carpels). Some off-types can only be detected several years after planting in the fields. Therefore, efficient methods for prevention of the generation of off-types, as well as methods for their detection and early removal, are required for date palms, as well as for other tissue culture propagated crops. This research is aimed at the understanding of the mechanisms by which off-types are generated, and developing markers for their early identification. Several molecular and genomic approaches were applied. Using Methylation Sensitive AFLP and bisulfite sequencing, we detected changes in DNA methylation patterns occurring in off-types. We isolated and compared the sequence and expression of candidate genes, genes related to vegetative growth and dwarfism and genes related to flower development. While no sequence variation were detected, changes in gene expression, associated with the severity of the "fruit set" phenotype were detected in two genes - PdDEF (Ortholog of rice SPW1, and AP3 B type MADS box gene), and PdDIF (a defensin gene, highly homologous to the oil palm gene EGAD). We applied transcriptomic analyses, using high throughput sequencing, to identify genes differentially expressed in the "palm heart" (the apical meristem and the region of embryonic leaves) of dwarf vs. normal trees. Among the differentially expressed genes we identified genes related to hormonal biosynthesis, perception and regulation, genes related to cell expansion, and genes related to DNA methylation. Using Representation Difference Analyses, we detected changes in the genomes of off-type trees, mainly chloroplast-derived sequences that were incorporated in the nuclear genome and sequences of transposable elements. Sequences previously identified as differing between normal and off-type trees of oil palms or banana, successfully identified variation among date palm off-types, suggesting that these represent highly labile regions of monocot genomes. The data indicate that the date palm genome, similarly to genomes of other monocot crops as oil palm and banana, is quite unstable when cells pass through a cycle of tissue culture and regeneration. Changes in DNA sequences, translocation of DNA fragments and alteration of methylation patterns occur. Consequently, patterns of gene expression are changed, resulting in abnormal phenotypes. The data can be useful for future development of tools for early identification of off-type as well as for better understanding the phenomenon of somaclonal variation during propagation in vitro.

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Levisohn, Sharon, Maricarmen Garcia, David Yogev, and Stanley Kleven. Targeted Molecular Typing of Pathogenic Avian Mycoplasmas. United States Department of Agriculture, 2006. http://dx.doi.org/10.32747/2006.7695853.bard.

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Intraspecies identification (DNA "fingerprinting") of pathogenic avian mycoplasmas is a powerful tool for epidemiological studies and monitoring strain identity. However the only widely method available for Mycoplasma gallisepticum (MG) and M. synoviae (MS)wasrandom amplified polymorphic DNA (RAPD). This project aimed to develop alternative and supplementary typing methods that will overcome the major constraints of RAPD, such as the need for isolation of the organism in pure culture and the lack of reproducibility intrinsic in the method. Our strategy focussed on recognition of molecular markers enabling identification of MG and MS vaccine strains and, by extension, pathogenic potential of field isolates. Our first aim was to develop PCR-based systems which will allow amplification of specific targeted genes directly from clinical material. For this purpose we evaluated the degree of intraspecies heterogeneity in genes encoding variable surface antigens uniquely found in MG all of which are putative pathogenicity factors. Phylogenic analysis of targeted sequences of selected genes (pvpA, gapA, mgc2, and lp) was employed to determine the relationship among MG strains.. This method, designated gene targeted sequencing (GTS), was successfully employed to identify strains and to establish epidemiologically-linked strain clusters. Diagnostic PCR tests were designed and validated for each of the target genes, allowing amplification of specific nucleotide sequences from clinical samples. An mgc2-PCR-RFLP test was designed for rapid differential diagnosis of MG vaccine strains in Israel. Addressing other project goals, we used transposon mutagenesis and in vivo and in vitro models for pathogenicity to correlated specific changes in target genes with biological properties that may impact the course of infection. An innovative method for specific detection and typing of MS strains was based on the hemagglutinin-encoding gene vlhA, uniquely found in this species. In parallel, we evaluated the application of amplified fragment length polymorphism (AFLP) in avian mycoplasmas. AFLP is a highly discriminatory method that scans the entire genome using infrequent restriction site PCR. As a first step the method was found to be highly correlated with other DNA typing methods for MG species and strain differentiation. The method is highly reproducible and relatively rapid, although it is necessary to isolate the strain to be tested. Both AFLP and GTS are readily to amenable to computer-assisted analysis of similarity and construction of a data-base resource. The availability of improved and diverse tools will help realize the full potential of molecular typing of avian mycoplasmas as an integral and essential part of mycoplasma control programs.

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Wackett, Lawrence, Raphi Mandelbaum, and Michael Sadowsky. Bacterial Mineralization of Atrazine as a Model for Herbicide Biodegradation: Molecular and Applied Aspects. United States Department of Agriculture, 1999. http://dx.doi.org/10.32747/1999.7695835.bard.

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Atrazine is a broadly used herbicide in agriculture and it was used here as a model to study the biodegradation of herbicides. The bacterium Pseudomonas sp. ADP metabolizes atrazine to carbon dioxide and ammonia and chloride. The genes encoding atrazine catabolism to cyanuric acid were cloned and expressed in Escherichia coli. The genes were designated atzA, atzB and atzC. Each gene was sequenced. The enzyme activities were characterized. AtzA is atrazine chlorohydrolase which takes atrazine to hydroxyatrizine. AtzB is hydroxyatrazine N-ethylaminohydrolase which produces N-isopropylammelide and N-ethylamine. AtzC is N-isopropylammelide N-isopropylaminohydrolase which produces cyanuric acid and N-isopropylamine. Each product was isolated and characterized to confirm their identity by chromatography and mass spectrometry. Sequence analysis indicated that each of the hydrolytic enzymes AtzA, AtzB and AtzC share identity which the aminohydrolase protein superfamily. Atrazine chlorohydrolase was purified to homogeneity. It was shown to have a kcat of 11 s-1 and a KM of 150 uM. It was shown to require a metal ion, either Fe(II), Mn(II) or Co(II), for activity. The atzA, atzB and atzC genes were shown to reside on a broad-host range plasmid in Pseudomonas sp. ADP. Six other recently isolated atrazine-degrading bacteria obtained from Europe and the United States contained homologs to the atz genes identified in Pseudomonas sp. ADP. The identity of the sequences were very high, being greater than 98% in all pairwise comparisons. This indicates that many atrazine-degrading bacteria worldwide metabolize atrazine via a pathway that proceeds through hydroxyatrazine, a metabolite which is non-phytotoxic and non-toxic to mammals. Enzymes were immobilized and used for degradation of atrazine in aqueous phases. The in-depth understanding of the genomics and biochemistry of the atrazine mineralization pathway enabled us to study factors affecting the prevalence of atrazine degradation in various agricultural soils under conservative and new agricultural practices. Moreover, Pseudomonas sp. ADP and/or its enzymes were added to atrazine-contaminated soils, aquifers and industrial wastewater to increase the rate and extent of atrazine biodegradation above that of untreated environments. Our studies enhance the ability to control the fate of regularly introduced pesticides in agriculture, or to reduce the environmental impact of unintentional releases.

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