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Journal articles on the topic 'Open PHACTS'

Author: Grafiati

Published: 2 June 2025

Last updated: 31 July 2025

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1

Miller, Ryan A., Peter Woollard, Egon L. Willighagen, et al. "Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform." F1000Research 7 (January 17, 2018): 75. http://dx.doi.org/10.12688/f1000research.13197.1.

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Open PHACTS is a pre-competitive project to answer scientific questions developed recently by the pharmaceutical industry. Having high quality biological interaction information in the Open PHACTS Discovery Platform is needed to answer multiple pathway related questions. To address this, updated WikiPathways data has been added to the platform. This data includes information about biological interactions, such as stimulation and inhibition. The platform's Application Programming Interface (API) was extended with appropriate calls to reference these interactions. These new methods of the Open P

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Miller, Ryan A., Peter Woollard, Egon L. Willighagen, et al. "Explicit interaction information from WikiPathways in RDF facilitates drug discovery in the Open PHACTS Discovery Platform." F1000Research 7 (October 12, 2018): 75. http://dx.doi.org/10.12688/f1000research.13197.2.

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Open PHACTS is a pre-competitive project to answer scientific questions developed recently by the pharmaceutical industry. Having high quality biological interaction information in the Open PHACTS Discovery Platform is needed to answer multiple pathway related questions. To address this, updated WikiPathways data has been added to the platform. This data includes information about biological interactions, such as stimulation and inhibition. The platform's Application Programming Interface (API) was extended with appropriate calls to reference these interactions. These new methods of the Open P

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3

Williams, Antony J., Lee Harland, Paul Groth, et al. "Open PHACTS: semantic interoperability for drug discovery." Drug Discovery Today 17, no. 21-22 (2012): 1188–98. http://dx.doi.org/10.1016/j.drudis.2012.05.016.

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4

Bandaru, Santosh Panendra. "The Role of APIs in Modern Web Development: Enhancing System Integrations." International Journal of Computer Science and Mobile Computing 14, no. 3 (2025): 11–19. https://doi.org/10.47760/ijcsmc.2025.v14i03.002.

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Rapid growth and improvement in software development have prompted the use of cutting-edge designs, methodologies, techniques, and tools to provide software solutions of the highest calibre. However, guaranteeing dependable, practical, affordable, and high-quality software solutions requires more than just programming expertise. To improve software solutions, developers need to take into account many facets of the Software Development Life Cycle (SDLC). This entails having the ability to think critically and analytically, conceiving of practical business scenarios, and prioritising quality con

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5

Chichester, Christine, Lee Harald, and Tim Harder. "Mobile applications driven by Open PHACTS semantic web technology." EMBnet.journal 19, B (2013): 21. http://dx.doi.org/10.14806/ej.19.b.721.

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Groth, Paul, Antonis Loizou, Alasdair J. G. Gray, Carole Goble, Lee Harland, and Steve Pettifer. "API-centric Linked Data integration: The Open PHACTS Discovery Platform case study." Journal of Web Semantics 29 (December 2014): 12–18. http://dx.doi.org/10.1016/j.websem.2014.03.003.

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7

Ratnam, Joseline, Barbara Zdrazil, Daniela Digles, et al. "The Application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to Support Drug Discovery Research." PLoS ONE 9, no. 12 (2014): e115460. http://dx.doi.org/10.1371/journal.pone.0115460.

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Digles, D., B. Zdrazil, J. M. Neefs, et al. "Open PHACTS computational protocols for in silico target validation of cellular phenotypic screens: knowing the knowns." MedChemComm 7, no. 6 (2016): 1237–44. http://dx.doi.org/10.1039/c6md00065g.

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Barros, M., and F. M. Couto. "Knowledge Representation and Management: a Linked Data Perspective." Yearbook of Medical Informatics 25, no. 01 (2016): 178–83. http://dx.doi.org/10.15265/iy-2016-022.

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Summary Introduction: Biomedical research is increasingly becoming a data-intensive science in several areas, where prodigious amounts of data is being generated that has to be stored, integrated, shared and analyzed. In an effort to improve the accessibility of data and knowledge, the Linked Data initiative proposed a well-defined set of recommendations for exposing, sharing and integrating data, information and knowledge, using semantic web technologies. Objective: The main goal of this paper is to identify the current status and future trends of knowledge representation and management in Li

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10

Duangsri, Chanchanok, Tiina A. Salminen, Marion Alix, et al. "Characterization and Homology Modeling of Catalytically Active Recombinant PhaCAp Protein from Arthrospira platensis." Biology 12, no. 5 (2023): 751. http://dx.doi.org/10.3390/biology12050751.

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Polyhydroxybutyrate (PHB) is a biocompatible and biodegradable polymer that has the potential to replace fossil-derived polymers. The enzymes involved in the biosynthesis of PHB are β-ketothiolase (PhaA), acetoacetyl-CoA reductase (PhaB), and PHA synthase (PhaC). PhaC in Arthrospira platensis is the key enzyme for PHB production. In this study, the recombinant E. cloni ®10G cells harboring A. platensis phaC (rPhaCAp) was constructed. The overexpressed and purified rPhaCAp with a predicted molecular mass of 69 kDa exhibited Vmax, Km, and kcat values of 24.5 ± 2 μmol/min/mg, 31.3 ± 2 µM and 412.

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Montanari, Floriane, Barbara Zdrazil, Daniela Digles, and Gerhard F. Ecker. "Selectivity profiling of BCRP versus P-gp inhibition: from automated collection of polypharmacology data to multi-label learning." Journal of Cheminformatics 8, no. 1 (2016): 7. https://doi.org/10.1186/s13321-016-0121-y.

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<strong>Background: </strong>The human ATP binding cassette transporters Breast Cancer Resistance Protein (BCRP) and Multidrug Resistance Protein 1 (P-gp) are co-expressed in many tissues and barriers, especially at the blood–brain barrier and at the hepatocyte canalicular membrane. Understanding their interplay in affecting the pharmacokinetics of drugs is of prime interest. <i>In silico</i> tools to predict inhibition and substrate profiles towards BCRP and P-gp might serve as early filters in the drug discovery and development process. However, to build such models, pharmacological data mus

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De Mastro, Francesco, Gennaro Brunetti, Claudio Cocozza, et al. "Dynamics of Pharmaceuticals in the Soil–Plant System: A Case Study on Mycorrhizal Artichoke." Soil Systems 9, no. 2 (2025): 51. https://doi.org/10.3390/soilsystems9020051.

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Contaminants of emerging concern, such as pharmaceuticals (PhACs), are continuously introduced into agro-ecosystems through irrigation with treated wastewater (TWW). While this practice is increasingly common in drought regions, only limited information is available on the fate of PhACs within the soil–plant system. For this purpose, a two-year study was conducted by irrigating artichokes, non-inoculated and inoculated with different arbuscular mycorrhizal fungi, with water containing PhACs at different concentrations. The experiment, conducted in both open field and pot conditions, aimed to e

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13

Matsusaki, Hiromi, Sumihide Manji, Kazunori Taguchi, Mikiya Kato, Toshiaki Fukui, and Yoshiharu Doi. "Cloning and Molecular Analysis of the Poly(3-hydroxybutyrate) and Poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) Biosynthesis Genes in Pseudomonas sp. Strain 61-3." Journal of Bacteriology 180, no. 24 (1998): 6459–67. http://dx.doi.org/10.1128/jb.180.24.6459-6467.1998.

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ABSTRACT Two types of polyhydroxyalkanoate (PHA) biosynthesis gene loci (phb and pha) of Pseudomonas sp. strain 61-3, which produces a blend of poly(3-hydroxybutyrate) [P(3HB)] homopolymer and a random copolymer {poly(3-hydroxybutyrate-co-3-hydroxyalkanoate) [P(3HB-co-3HA]} consisting of 3HA units of 4 to 12 carbon atoms, were cloned and analyzed at the molecular level. In thephb locus, three open reading frames encoding polyhydroxybutyrate (PHB) synthase (PhbCPs), β-ketothiolase (PhbAPs), and NADPH-dependent acetoacetyl coenzyme A reductase (PhbBPs) were found. The genetic organization showed

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Ravshanovna, Abdullaeva Khilola, and Allayarov Abdurakhman Nazaralievich. "THE PHENOLOGICAL PHASES AND RIPENING PERIOD OF STRAWBERRY FRUITS PLANTED IN THE OPEN FIELD AREAS." American Journal Of Agriculture And Horticulture Innovations 4, no. 3 (2024): 30–37. http://dx.doi.org/10.37547/ajahi/volume04issue03-06.

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In this article, the results of the study have been discussed on the cultivation of Uzbekistanskaya (st), Uzbekistan guzali (st), Redgauntlet (st), Zenga-Zengana, Medvey, Velikan, Dana varieties of strawberry that had been planted in experimental plots of strawberries in open field conditions at the scientific research institute of horticulture, viticulture andwinemaking named after Academician M. Mirzaev in Tashkent region. The duration of phenological phases and periods of ripening of berries in the varieties Vnuchka, Victoria and Zamposhniya were also monitored.As a result, the ripening of

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15

Hall, Brian, Jennifer Baldwin, Ho Gun Rhie, and Douglas Dennis. "Cloning of the Nocardia corallina polyhydroxyalkanoate synthase gene and production of poly-(3-hydroxybutyrate-co-3-hydroxyhexanoate) and poly-(3-hydroxyvalerate-co-3-hydroxyheptanoate)." Canadian Journal of Microbiology 44, no. 7 (1998): 687–91. http://dx.doi.org/10.1139/w98-048.

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The polyhydroxyalkanoate (PHA) synthase gene (phaCNc) from Nocardia corallina was identified in a lambda library on a 6-kb BamHI fragment. A 2.8-kb XhoII subfragment was found to contain the ntact PHA synthase. This 2.8-kb fragment was subjected to DNA sequencing and was found to contain the coding region for the PHA synthase and a small downstream open reading frame of unknown function. On the basis of DNA sequence, phaCNc is closest in homology to the PHA synthases (phaCPaI and phaCPaII) of Pseudomonas aeruginosa (approximately 41% identity and 55% similarity). The 2.8-kb XhoII fragment cont

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16

Shamdasani, Sonu. "DESCENSUS AD INFERNOS: JUNG’S ‘SEASON IN HELL’." Phanês Journal For Jung History, no. 4 (December 4, 2021): 152–76. http://dx.doi.org/10.32724/phanes.2021.shamdasani.

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This article explores the linked themes of the descent into hell and divine madness, as articulated in Jung’s self-explorations between 1913 and 1930 and as portrayed in his Liber Novus: The Red Book, situating these with the history of these notions. This in turn open the question of the relation between Jung’s visionary experiences and his subsequent conceptual elaborations in his exoteric scholarly works. KEY WORDS Liber Novus, The Red Book, hell, divine madness, visionary experiences, esotericism, Jung, Blake, Dante, Swedenborg.

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17

Seguritan, Victor, I.-Wei Feng, Forest Rohwer, Mark Swift, and Anca M. Segall. "Genome Sequences of Two Closely Related Vibrio parahaemolyticus Phages, VP16T and VP16C." Journal of Bacteriology 185, no. 21 (2003): 6434–47. http://dx.doi.org/10.1128/jb.185.21.6434-6447.2003.

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ABSTRACT Two bacteriophages of an environmental isolate of Vibrio parahaemolyticus were isolated and sequenced. The VP16T and VP16C phages were separated from a mixed lysate based on plaque morphology and exhibit 73 to 88% sequence identity over about 80% of their genomes. Only about 25% of their predicted open reading frames are similar to genes with known functions in the GenBank database. Both phages have cos sites and open reading frames encoding proteins closely related to coliphage lambda's terminase protein (the large subunit). Like in coliphage lambda and other siphophages, a large ope

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18

Lin, Kate. "Two newly isolated phages infecting Vibrio parahaemolyticus." Young Scientist 3, no. 1 (2024): 1–8. https://doi.org/10.5281/zenodo.10934495.

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Vibrio is a bacterial genus that can be widely found in estuarine, coastal, and open-ocean waters around the globe. Vibrio alginolyticus and Vibrio parahaemolyticus specifically are known for being pathogenic, causing infections (known as 'vibriosis') in marine organisms and humans. Development of effective methods for treating Vibrio is essential. Considering the rapid development of antibiotic resistance, phage therapy emerges as a potentially more sustainable and effective solution, prompting continued efforts to isolate new phages that target pathogenic Vibrio species. For this research, w

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19

Briggiler Marcó, Mariángeles, Josiane E. Garneau, Denise Tremblay, Andrea Quiberoni, and Sylvain Moineau. "Characterization of Two Virulent Phages of Lactobacillus plantarum." Applied and Environmental Microbiology 78, no. 24 (2012): 8719–34. http://dx.doi.org/10.1128/aem.02565-12.

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ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phag

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20

Rousseau, Geneviève M., and Sylvain Moineau. "Evolution of Lactococcus lactis Phages within a Cheese Factory." Applied and Environmental Microbiology 75, no. 16 (2009): 5336–44. http://dx.doi.org/10.1128/aem.00761-09.

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ABSTRACT We have sequenced the double-stranded DNA genomes of six lactococcal phages (SL4, CB13, CB14, CB19, CB20, and GR7) from the 936 group that were isolated over a 9-year period from whey samples obtained from a Canadian cheese factory. These six phages infected the same two industrial Lactococcus lactis strains out of 30 tested. The CB14 and GR7 genomes were found to be 100% identical even though they were isolated 14 months apart, indicating that a phage can survive in a cheese plant for more than a year. The other four genomes were related but notably different. The length of the genom

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21

Falero, Alina, Andy Caballero, Beatriz Ferrán, Yovanny Izquierdo, Rafael Fando та Javier Campos. "DNA Binding Proteins of the Filamentous Phages CTXφ and VGJφ of Vibrio cholerae". Journal of Bacteriology 191, № 18 (2009): 5873–76. http://dx.doi.org/10.1128/jb.01206-08.

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ABSTRACT The native product of open reading frame 112 (orf112) and a recombinant variant of the RstB protein, encoded by Vibrio cholerae pathogen-specific bacteriophages VGJφ and CTXφ, respectively, were purified to more than 90% homogeneity. Orf112 protein was shown to specifically bind single-stranded genomic DNA of VGJφ; however, RstB protein unexpectedly bound double-stranded DNA in addition to the single-stranded genomic DNA. The DNA binding properties of these proteins may explain their requirement for the rolling circle replication of the respective phages and RstB's requirement for sin

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Kapfhammer, Dagmar, Julia Blass, Stefan Evers, and Joachim Reidl. "Vibrio cholerae Phage K139: Complete Genome Sequence and Comparative Genomics of Related Phages." Journal of Bacteriology 184, no. 23 (2002): 6592–601. http://dx.doi.org/10.1128/jb.184.23.6592-6601.2002.

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ABSTRACT In this report, we characterize the complete genome sequence of the temperate phage K139, which morphologically belongs to the Myoviridae phage family (P2 and 186). The prophage genome consists of 33,106 bp, and the overall GC content is 48.9%. Forty-four open reading frames were identified. Homology analysis and motif search were used to assign possible functions for the genes, revealing a close relationship to P2-like phages. By Southern blot screening of a Vibrio cholerae strain collection, two highly K139-related phage sequences were detected in non-O1, non-O139 strains. Combinato

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23

Berrahal, Chaker, and Fadili Abderrahim El. "Backstepping multiphase induction machine control impact in presence of open phases fault." International Journal of Power Electronics and Drive System 16, no. 1 (2025): 185–94. https://doi.org/10.11591/ijpeds.v16.i1.pp185-194.

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As power requirements increase, multiphase induction machines (MPIMs)present a promising alternative to conventional three-phase induction machines.These machines help reduce the current switched by the inverter and circulatingthrough the windings, which in turn mitigates torque ripple. Moreover, incorporatingmore than three phases enhances system reliability, allowing themachine to maintain operation even in the event of one or more phase failures.This makes MPIMs particularly suitable for high-reliability applications, such aselectric vehicles. While most previous studies have concentrated o

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Mahony, Jennifer, Walter Randazzo, Horst Neve, Luca Settanni, and Douwe van Sinderen. "Lactococcal 949 Group Phages Recognize a Carbohydrate Receptor on the Host Cell Surface." Applied and Environmental Microbiology 81, no. 10 (2015): 3299–305. http://dx.doi.org/10.1128/aem.00143-15.

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ABSTRACTLactococcal bacteriophages represent one of the leading causes of dairy fermentation failure and product inconsistencies. A new member of the lactococcal 949 phage group, named WRP3, was isolated from cheese whey from a Sicilian factory in 2011. The genome sequence of this phage was determined, and it constitutes the largest lactococcal phage genome currently known, at 130,008 bp. Detailed bioinformatic analysis of the genomic region encoding the presumed initiator complex and baseplate of WRP3 has aided in the functional assignment of several open reading frames (ORFs), particularly t

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Eraclio, Giovanni, Denise M. Tremblay, Alexia Lacelle-Côté, Simon J. Labrie, Maria Grazia Fortina, and Sylvain Moineau. "A Virulent Phage Infecting Lactococcus garvieae, with Homology to Lactococcus lactis Phages." Applied and Environmental Microbiology 81, no. 24 (2015): 8358–65. http://dx.doi.org/10.1128/aem.02603-15.

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ABSTRACTA new virulent phage belonging to theSiphoviridaefamily and able to infectLactococcus garvieaestrains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only twoL. garvieaestrains out of 73 tested. Phage GE1 has a double-stranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indi

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Chen, Feng, and Jingrang Lu. "Genomic Sequence and Evolution of Marine Cyanophage P60: a New Insight on Lytic and Lysogenic Phages." Applied and Environmental Microbiology 68, no. 5 (2002): 2589–94. http://dx.doi.org/10.1128/aem.68.5.2589-2594.2002.

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ABSTRACT The genome of cyanophage P60, a lytic virus which infects marine Synechococcus WH7803, was completely sequenced. The P60 genome contained 47,872 bp with 80 potential open reading frames that were mostly similar to the genes found in lytic phages like T7, phi-YeO3-12, and SIO1. The DNA replication system, consisting of primase-helicase and DNA polymerase, appeared to be more conserved in podoviruses than in siphoviruses and myoviruses, suggesting that DNA replication genes could be the critical elements for lytic phages. Strikingly high sequence similarities in the regions coding for n

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García, Pilar, Beatriz Martínez, José María Obeso, Rob Lavigne, Rudi Lurz, and Ana Rodríguez. "Functional Genomic Analysis of Two Staphylococcus aureus Phages Isolated from the Dairy Environment." Applied and Environmental Microbiology 75, no. 24 (2009): 7663–73. http://dx.doi.org/10.1128/aem.01864-09.

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ABSTRACT The genomes of the two lytic mutant Staphylococcus aureus bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (cos) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analys

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28

Samson, Julie E., and Sylvain Moineau. "Characterization of Lactococcus lactis Phage 949 and Comparison with Other Lactococcal Phages." Applied and Environmental Microbiology 76, no. 20 (2010): 6843–52. http://dx.doi.org/10.1128/aem.00796-10.

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ABSTRACT The virulent Lactococcus lactis phage 949 was isolated in 1975 from cheese whey in New Zealand. This phage is a member of the Siphoviridae family and of a rare lactococcal phage group that bears its name (949 group). It has an icosahedral capsid (79-nm diameter) and a very long noncontractile tail (length, 500 nm; width, 12 nm). It infected 7 of 59 tested L. lactis strains, a somewhat expanded host range for a rare lactococcal phage. The abortive phage infection defense mechanisms AbiQ and AbiT strongly inhibited the multiplication of phage 949, but AbiK and AbiV did not. Its double-s

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Quirk, Susan M., Deborah Bell-Pedersen, and Marlene Belfort. "Intron mobility in the T-even phages: High frequency inheritance of group I introns promoted by intron open reading frames." Cell 56, no. 3 (1989): 455–65. http://dx.doi.org/10.1016/0092-8674(89)90248-1.

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Kawato, Yasuhiko, Motoshige Yasuike, Yoji Nakamura, et al. "Complete Genome Sequence Analysis of Two Pseudomonas plecoglossicida Phages, Potential Therapeutic Agents." Applied and Environmental Microbiology 81, no. 3 (2014): 874–81. http://dx.doi.org/10.1128/aem.03038-14.

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ABSTRACTPseudomonas plecoglossicidais a lethal pathogen of ayu (Plecoglossus altivelis) in Japan and is responsible for substantial economic costs to ayu culture. Previously, we demonstrated the efficacy of phage therapy againstP. plecoglossicidainfection using two lytic phages (PPpW-3 and PPpW-4) (S. C. Park, I. Shimamura, M. Fukunaga, K. Mori, and T. Nakai, Appl Environ Microbiol 66:1416–1422, 2000,http://dx.doi.org/10.1128/AEM.66.4.1416-1422.2000; S. C. Park and T. Nakai, Dis Aquat Org 53:33–39, 2003,http://dx.doi.org/10.3354/dao053033). In the present study, the complete genome sequences o

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Santiago-Rodriguez, Tasha M., Patricia Marcos, Silvia Monteiro, Miguel Urdaneta, Ricardo Santos, and Gary A. Toranzos. "Evaluation of Enterococcus-infecting phages as indices of fecal pollution." Journal of Water and Health 11, no. 1 (2012): 51–63. http://dx.doi.org/10.2166/wh.2012.100.

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No microbial source tracking tool satisfies all the characteristics of an ideal indicator of human fecal pollution. For this reason, the potential of Enterococcus faecalis phages (enterophages) as markers of this type of contamination was tested by using eight Enterococcus type strains as the possible hosts. The prevalence of enterophages in animal feces and domestic sewage were determined, as were the inactivation rates in raw sewage at 4 °C and surface and tap waters at 22 °C. Enterophages were exclusively detected in raw sewage (up to 66.0 plaque forming units (PFU)/100 mL), suggesting a st

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Attai, Hedieh, and Pamela J. B. Brown. "Isolation and Characterization T4- and T7-Like Phages that Infect the Bacterial Plant Pathogen Agrobacterium tumefaciens." Viruses 11, no. 6 (2019): 528. http://dx.doi.org/10.3390/v11060528.

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In the rhizosphere, bacteria–phage interactions are likely to have important impacts on the ecology of microbial communities and microbe–plant interactions. To better understand the dynamics of Agrobacteria–phage interactions, we have isolated diverse bacteriophages which infect the bacterial plant pathogen, Agrobacterium tumefaciens. Here, we complete the genomic characterization of Agrobacterium tumefaciens phages Atu_ph04 and Atu_ph08. Atu_ph04—a T4-like phage belonging to the Myoviridae family—was isolated from waste water and has a 143,349 bp genome that encodes 223 predicted open reading

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Gutiérrez, Diana, Dieter Vandenheuvel, Beatriz Martínez, Ana Rodríguez, Rob Lavigne, and Pilar García. "Two Phages, phiIPLA-RODI and phiIPLA-C1C, Lyse Mono- and Dual-Species Staphylococcal Biofilms." Applied and Environmental Microbiology 81, no. 10 (2015): 3336–48. http://dx.doi.org/10.1128/aem.03560-14.

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ABSTRACTPhage therapy is a promising option for fighting against staphylococcal infections. Two lytic phages, vB_SauM_phiIPLA-RODI (phiIPLA-RODI) and vB_SepM_phiIPLA-C1C (phiIPLA-C1C), belonging to theMyoviridaefamily and exhibiting wide host ranges, were characterized in this study. The complete genome sequences comprised 142,348 bp and 140,961 bp and contained 213 and 203 open reading frames, respectively. The gene organization was typical ofSpounavirinaemembers, with long direct terminal repeats (LTRs), genes grouped into modules not clearly separated from each other, and several group I in

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Dupuis, Marie-Ã¯Â¿Â½ve, and Sylvain Moineau. "Genome Organization and Characterization of the Virulent Lactococcal Phage 1358 and Its Similarities to Listeria Phages." Applied and Environmental Microbiology 76, no. 5 (2010): 1623–32. http://dx.doi.org/10.1128/aem.02173-09.

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ABSTRACT Virulent phage 1358 is the reference member of a rare group of phages infecting Lactococcus lactis. Electron microscopy revealed a typical icosahedral capsid connected to one of the smallest noncontractile tails found in a lactococcal phage of the Siphoviridae family. Microbiological characterization identified a burst size of 72 virions released per infected host cell and a latent period of 90 min. The host range of phage 1358 was limited to 3 out of the 60 lactococcal strains tested. Moreover, this phage was insensitive to four Abi systems (AbiK, AbiQ, AbiT, and AbiV). The genome of

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Jiang, Tong, Cui Guo, Min Wang, et al. "Genome Analysis of Two Novel Synechococcus Phages That Lack Common Auxiliary Metabolic Genes: Possible Reasons and Ecological Insights by Comparative Analysis of Cyanomyoviruses." Viruses 12, no. 8 (2020): 800. http://dx.doi.org/10.3390/v12080800.

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The abundant and widespread unicellular cyanobacteria Synechococcus plays an important role in contributing to global phytoplankton primary production. In the present study, two novel cyanomyoviruses, S-N03 and S-H34 that infected Synechococcus MW02, were isolated from the coastal waters of the Yellow Sea. S-N03 contained a 167,069-bp genome comprising double-stranded DNA with a G + C content of 50.1%, 247 potential open reading frames and 1 tRNA; S-H34 contained a 167,040-bp genome with a G + C content of 50.1%, 246 potential open reading frames and 5 tRNAs. These two cyanophages contain fewe

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Zuber, Sophie, Catherine Ngom-Bru, Caroline Barretto, Anne Bruttin, Harald Brüssow, and Emmanuel Denou. "Genome Analysis of Phage JS98 Defines a Fourth Major Subgroup of T4-Like Phages in Escherichia coli." Journal of Bacteriology 189, no. 22 (2007): 8206–14. http://dx.doi.org/10.1128/jb.00838-07.

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ABSTRACT Numerous T4-like Escherichia coli phages were isolated from human stool and environmental wastewater samples in Bangladesh and Switzerland. The sequences of the major head gene (g23) revealed that these coliphages could be placed into four subgroups, represented by the phages T4, RB69, RB49, and JS98. Thus, JS98 defines a new major subgroup of E. coli T4-like phages. We conducted an analysis of the 169-kb JS98 genome sequence. Overall, 198 of the 266 JS98 open reading frames (ORFs) shared amino acid sequence identity with the reference T4 phage, 41 shared identity with other T4-like p

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Zablocki, Olivier, Lonnie van Zyl, Evelien M. Adriaenssens, et al. "High-Level Diversity of Tailed Phages, Eukaryote-Associated Viruses, and Virophage-Like Elements in the Metaviromes of Antarctic Soils." Applied and Environmental Microbiology 80, no. 22 (2014): 6888–97. http://dx.doi.org/10.1128/aem.01525-14.

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ABSTRACTThe metaviromes of two distinct Antarctic hyperarid desert soil communities have been characterized. Hypolithic communities, cyanobacterium-dominated assemblages situated on the ventral surfaces of quartz pebbles embedded in the desert pavement, showed higher virus diversity than surface soils, which correlated with previous bacterial community studies. Prokaryotic viruses (i.e., phages) represented the largest viral component (particularlyMycobacteriumphages) in both habitats, with an identical hierarchical sequence abundance of families of tailed phages (Siphoviridae>Myoviridae&gt

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Chia, Kok Hwee. "A general review on sexual awareness in children and adolescents with special needs. The Asian Educational Therapist." Asian Educational Therapist 2, no. 2 (2024): 12–20. https://doi.org/10.5281/zenodo.15221112.

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Sexual awareness in children and adolescents with special needs is a critical yet often overlooked aspect of their development. This paper explores the concept of sexual awareness, delineating it from sexuality and/or sexuality awareness. While sexuality encompasses a broad range of physical, emotional, and social aspects related to sex, sexual awareness pertains to recognizing one’s own and others’ sexual feelings and behaviors. Sexuality awareness extends this understanding to include societal norms and personal values about sexuality. The developmental trajectory of sexual aware

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Biswas, Sanjoy, Devendra Nath Tewari, Alok Kumar Chakrabarti, and Shanta Dutta. "Biological Characterization and Evaluation of the Therapeutic Value of Vibrio Phages 4141 and MJW Isolated from Clinical and Sewage Water Samples of Kolkata." Viruses 16, no. 11 (2024): 1741. http://dx.doi.org/10.3390/v16111741.

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The growing prevalence of antimicrobial resistance (AMR) necessitates the development of new treatment methods to combat diseases like cholera. Lytic bacteriophages are viruses that specifically target and lyse bacteria upon infection, making them a possible treatment option for multi-drug-resistant pathogens. The current study investigated the potential role of bacteriophages isolated from clinical stool and sewage water samples in treating multi-drug-resistant Vibrio cholerae infection, finding that over 95% of the strains were susceptible. Whole-genome sequencing (WGS) analysis revealed tha

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Schuch, Raymond, та Vincent A. Fischetti. "Detailed Genomic Analysis of the Wβ and γ Phages Infecting Bacillus anthracis: Implications for Evolution of Environmental Fitness and Antibiotic Resistance". Journal of Bacteriology 188, № 8 (2006): 3037–51. http://dx.doi.org/10.1128/jb.188.8.3037-3051.2006.

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ABSTRACT Phage-mediated lysis has been an essential laboratory tool for rapidly identifying Bacillus anthracis for more than 40 years, relying on the γ phage derivative of a Bacillus cereus prophage called W. The complete genomic sequences of the temperate W phage, referred to as Wβ, and its lytic variant γ were determined and found to encode 53 open reading frames each, spanning 40,864 bp and 37,373 bp, respectively. Direct comparison of the genomes showed that γ evolved through mutations at key loci controlling host recognition, lysogenic growth, and possibly host phenotypic modification. In

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Johnson, Matthew C., Kelsey B. Tatum, Jason S. Lynn та ін. "Sinorhizobium meliloti Phage ΦM9 Defines a New Group of T4 Superfamily Phages with Unusual Genomic Features but a Common T=16 Capsid". Journal of Virology 89, № 21 (2015): 10945–58. http://dx.doi.org/10.1128/jvi.01353-15.

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ABSTRACTRelatively little is known about the phages that infect agriculturally important nitrogen-fixing rhizobial bacteria. Here we report the genome and cryo-electron microscopy structure of theSinorhizobium meliloti-infecting T4 superfamily phage ΦM9. This phage and its close relativeRhizobiumphage vB_RleM_P10VF define a new group of T4 superfamily phages. These phages are distinctly different from the recently characterized cyanophage-likeS. melilotiphages of the ΦM12 group. Structurally, ΦM9 has a T=16 capsid formed from repeating units of an extended gp23-like subunit that assemble throu

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Crognale, Simona, Barbara Tonanzi, Francesco Valentino, Mauro Majone, and Simona Rossetti. "Microbiome dynamics and phaC synthase genes selected in a pilot plant producing polyhydroxyalkanoate from the organic fraction of urban waste." Science of The Total Environment 689 (June 26, 2019): 765–73. https://doi.org/10.1016/j.scitotenv.2019.06.491.

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This study analyses the bacterial population dynamics of a mixed microbial community (MMC) selected in a pilot plant producing polyhydroxyalkanoate (PHA) from the fermentation of the organic fraction of urban waste (OFMSW) and sewage sludge (SS). 16S rRNA gene high-throughput sequencing revealed the occurrence of a variety of PHA accumulating bacteria that ensured a stable PHA production in an open system operating with real substrates and without temperature control. The Volatile Fatty Acids (VFA) changes in the feed and the temperature variation affected the dynamics of the PHA-accumulating

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Groth, Paul Thomas, Antonis Loizou, Alasdair J. G. Gray, Carole Goble, Lee Harland, and Steve Pettifer. "Api-Centric Linked Data Integration: The Open Phacts Discovery Platform Case Study." SSRN Electronic Journal, 2014. http://dx.doi.org/10.2139/ssrn.3199140.

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Stierand, Katrin, Tim Harder, Lothar Wissler, Christian Lemmen, and Matthias Rarey. "Accessing Open PHACTS: interactive exploration of compounds and targets from the semantic web." Journal of Cheminformatics 6, S1 (2014). http://dx.doi.org/10.1186/1758-2946-6-s1-p52.

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Mohammadi, Mehrdad, Mahmood Saffari, Seyed Davar Siadat, et al. "Isolation, characterization, therapeutic potency, and genomic analysis of a novel bacteriophage vB_KshKPC-M against carbapenemase-producing Klebsiella pneumoniae strains (CRKP) isolated from Ventilator-associated pneumoniae (VAP) infection of COVID-19 patients." Annals of Clinical Microbiology and Antimicrobials 22, no. 1 (2023). http://dx.doi.org/10.1186/s12941-023-00567-1.

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Abstract Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a significant clinical problem, given the lack of therapeutic options. The CRKP strains have emerged as an essential worldwide healthcare issue during the last 10 years. Global expansion of the CRKP has made it a significant public health hazard. We must consider to novel therapeutic techniques. Bacteriophages are potent restorative cases against infections with multiple drug-resistant bacteria. The Phages offer promising prospects for the treatment of CRKP infections. Objective In this study, a novel K. pneumoniae phage

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"THE PRIEST, THE PSYCHIATRIST AND THE PROBLEM OF EVIL." Phanês Journal For Jung History, no. 2 (November 25, 2019): 101–40. http://dx.doi.org/10.32724/phanes.2019.miranda.

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This paper clusters around the problem of evil within the framework of depth psychology. The first part briefly introduces the narrative of the Book of Job as an example to contextualise how the ultimate question of God’s relation to evil remained unanswered and was left open-ended in Christian theology. The second part offers a historical reconstruction of the unresolved polemic over the nature of evil between Carl Jung and the English Dominican scholar and theologian Victor White (1902-1960). It explores their different speculations and formulations concerning evil and its psychological impl

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Pourcel, Christine, Cédric Midoux, Libera Latino, Marie-Agnès Petit, and Gilles Vergnaud. "Complete Genome Sequences of Pseudomonas aeruginosa Phages vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A." Genome Announcements 4, no. 6 (2016). http://dx.doi.org/10.1128/genomea.00916-16.

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vB_PaeP_PcyII-10_P3P1 and vB_PaeM_PcyII-10_PII10A are Pseudomonas aeruginosa bacteriophages belonging, respectively, to the Lit1virus genus of the Podoviridae family and the Pbunavirus genus of the Myoviridae family. Their genomes are 72,778 bp and 65,712 bp long, containing 94 and 93 predicted open reading frames, respectively.

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Hughes, Lee E., Christopher D. Shaffer, Vassie C. Ware, et al. "Eight Genome Sequences of Cluster BE1 Phages That Infect Streptomyces Species." Genome Announcements 6, no. 2 (2018). http://dx.doi.org/10.1128/genomea.01146-17.

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ABSTRACT Cluster BE1 Streptomyces bacteriophages belong to the Siphoviridae, with genome sizes over 130 kbp, and they contain direct terminal repeats of approximately 11 kbp. Eight newly isolated closely related cluster BE1 phages contain 43 to 48 tRNAs, one transfer-messenger RNA (tmRNA), and 216 to 236 predicted open reading frames (ORFs), but few of their genes are shared with other phages, including those infecting Streptomyces species.

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Zhang, Ruoshi, Milot Mirdita, Eli Levy Karin, Clovis Norroy, Clovis Galiez, and Johannes Söding. "SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts." Bioinformatics, April 1, 2021. http://dx.doi.org/10.1093/bioinformatics/btab222.

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Abstract Summary SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes. Availability and implementation Sp

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Doré, Laurie, Gabrielle Pageau, Françoise Bourque-Leblanc, et al. "Complete Genome Sequences of 10 Lactococcal Skunavirus Phages Isolated from Cheddar Cheese Whey Samples in Canada." Microbiology Resource Announcements 10, no. 15 (2021). http://dx.doi.org/10.1128/mra.00098-21.

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We report the complete genome sequences of 10 virulent phages of the Skunavirus genus ( Siphoviridae ) that infect Lactococcus lactis strains used for cheddar cheese production in Canada. Their linear genomes range from 28,969 bp to 31,042 bp with GC contents of 34.1 to 35.1% and 55 to 60 predicted open reading frames (ORFs).

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