All bacterial genomes used in this analysis were retrieved from the Phage Annotation Tools and Methods server (Phantome server: http://www.phantome.org ). As of March 2010, the server contained 547 complete bacterial genomes (at most 20 contigs) of which only 41 bacterial genomes (Supplemental Table S1 ) had 190 manually annotated prophages. All other lytic and lysogenic phage genomes were also collected from the Phantome server.
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Biologic Function
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Lysogeny
Lysogeny
Lysogeny is a mode of viral reproduction in which the viral genome becomes integrated into the host cell's DNA, allowing the virus to replicate as part of the host's normal chromosomal DNA.
This process is an important aspect of many viral lifecycles and can have significant implications for the host organism.
The viral genome may remain dormant within the host cell for extended periods, only becoming activated under certain environmental or cellular conditions.
Understanding the mechanisms and dynamics of lysogeny is crucial for resaerch into viral pathogenesis, bacterial genetics, and the development of therapeutic interventions.
The PubCompare.ai platform can help optimize your lysogeny research by identifying the most effective protocols and procedures from the scientific literature, preprints, and patents using advanced AI-powered comparisons.
Experence reproducable results and enhance your lysogeny experiments with PubCompare's cutting-edge analysis tools.
This process is an important aspect of many viral lifecycles and can have significant implications for the host organism.
The viral genome may remain dormant within the host cell for extended periods, only becoming activated under certain environmental or cellular conditions.
Understanding the mechanisms and dynamics of lysogeny is crucial for resaerch into viral pathogenesis, bacterial genetics, and the development of therapeutic interventions.
The PubCompare.ai platform can help optimize your lysogeny research by identifying the most effective protocols and procedures from the scientific literature, preprints, and patents using advanced AI-powered comparisons.
Experence reproducable results and enhance your lysogeny experiments with PubCompare's cutting-edge analysis tools.
Most cited protocols related to «Lysogeny»
Bacteriophages
Genome
Genome, Bacterial
Lysogeny
Prophages
Wild-type MG1655 E. coli cells expressing cytoplasmic GFP and a kanamycin resistance cassette from plasmid pZS21-GFP (gift from Tom Silhavy, Princeton University) were labeled with the N-acetylglucosamine- and sialic acid-specific lectin Wheat Germ Agglutinin conjugated to Alexa-594 (Life Technologies). Five milliliters of cells were grown in lysogeny broth (LB) with shaking at 37 °C to exponential phase (optical density at 620 nm ∼ 0.5). One milliliter of cells was washed with fresh LB via centrifugation (10,000 g) and resuspension in 1 mL of LB and subsequently diluted 1:10 into 1 mL of fresh LB. Twenty-five microliters of a once-frozen 1 mg/mL fluorescent Wheat Germ Agglutinin stock solution were added, and the sample was briefly vortexed. Cells were incubated with the lectin for 20 min (approximately one cell cycle) with shaking at 37 °C in the dark. After incubation, cells were washed twice with fresh LB to remove excess lectin, and 5 μL of labeled cells were deposited onto a LB + 1% agarose pad, allowed to air dry on the pad, and promptly sealed with a #1.5 coverslip in a 125-μL FastWell (Grace BioLabs).
Labeled cells were imaged on a Nikon Eclipse Ti-E inverted fluorescence microscope with a 100X (NA 1.40) oil-immersion objective (Nikon Instruments). Images were collected using an Andor DU885 EMCCD camera (Andor Technology). Cells were maintained at 37 °C during imaging with an active-control environmental chamber (HaisonTech). Images were collected using μManager v. 1.3 [55 ].
Labeled cells were imaged on a Nikon Eclipse Ti-E inverted fluorescence microscope with a 100X (NA 1.40) oil-immersion objective (Nikon Instruments). Images were collected using an Andor DU885 EMCCD camera (Andor Technology). Cells were maintained at 37 °C during imaging with an active-control environmental chamber (HaisonTech). Images were collected using μManager v. 1.3 [55 ].
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Acetylglucosamine
Alexa594
Cell Cycle
Cells
Centrifugation
Cytoplasm
Escherichia coli
Freezing
Kanamycin Resistance
Lectin
Lysogeny
Microscopy, Fluorescence
N-Acetylneuraminic Acid
Plasmids
Sepharose
Submersion
Vision
Wheat Germ Agglutinins
MRE600 was grown in lysogeny broth, Miller (EMD) at 37 °C in a rotating culture tube. Genomic DNA was extracted from cells using the QIAamp DNA Mini Kit (Qiagen) according to the manufacturer’s instructions. DNA quality and quantity were determined using an Agilent 2200 TapeStation and Qubit dsDNA BR Assay (Life Technologies), respectively.
Biological Assay
DNA, Double-Stranded
Genome
Lysogeny
We developed BACPHLIP by first searching the Conserved Domain Database (Lu et al., 2020 (link)) (accessed: 03/2020) for protein domains that we hypothesized to be enriched in temperate phages (i.e. mechanistically involved in lysogeny). We searched the ‘description’ field using the following search terms: ‘integrase’, ‘excisionase’, ‘recombinase’, ‘transposase’, ‘lysogen’, and ‘temperate’. We additionally included a case sensitive search for ‘parA |ParA |parB |ParB’ due to its short length and potential overlap with many common words. These genes encode partitioning proteins that are frequently found on plasmids and in select temperate phage genomes, and were included in our search strategy due to their use in Mavrich & Hatfull (2017) (link), which brought their importance to our attention. We did not include a broad set of protein domains in our search strategy to ensure interpretability of our results and to limit the possibility of over-fitting.
Collectively, we identified 371 protein domains that formed the starting set of putatively useful protein domains. We stress that the ‘description’ field of the selected domains contained one or more of the above words at some point within it, but these domains may or may not actually be proteins or enzymes with any of the hypothesized functions. Some fraction of the initial set of 371 domains were thus likely to be unhelpful for the task of delineating temperate from virulent phages, due either to erroneous annotations or mis-classification via our simple keyword-based search strategy.
After removal of protein domains that were present in two or fewer training set phage genomes (see below for training set definitions) or which were actually more prevalent in the annotated virulent phage genomes (again, only considering phage genomes from the training dataset), we established a condensed dataset of 206 putatively useful lysogeny-associated protein domains. At this stage, we still did not know if any/all of these 206 domains would be useful for delineating temperate and virulent phages, which is why we next used this data as input into a Random Forest classifier that we hypothesized would disregard unimportant features (domains) and detect higher-level patterns in the data.
Collectively, we identified 371 protein domains that formed the starting set of putatively useful protein domains. We stress that the ‘description’ field of the selected domains contained one or more of the above words at some point within it, but these domains may or may not actually be proteins or enzymes with any of the hypothesized functions. Some fraction of the initial set of 371 domains were thus likely to be unhelpful for the task of delineating temperate from virulent phages, due either to erroneous annotations or mis-classification via our simple keyword-based search strategy.
After removal of protein domains that were present in two or fewer training set phage genomes (see below for training set definitions) or which were actually more prevalent in the annotated virulent phage genomes (again, only considering phage genomes from the training dataset), we established a condensed dataset of 206 putatively useful lysogeny-associated protein domains. At this stage, we still did not know if any/all of these 206 domains would be useful for delineating temperate and virulent phages, which is why we next used this data as input into a Random Forest classifier that we hypothesized would disregard unimportant features (domains) and detect higher-level patterns in the data.
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Attention
Bacteriophages
Enzymes
excisionase
Genes
Genome
Integrase
Lysogeny
Plasmids
Protein Domain
Proteins
Recombinase
SET Domain
SET protein, human
Staphylococcal Protein A
Transposase
All V. cholerae strains were derivatives of E7946, and all E. coli strains were derivatives of MG1655 and are described in detail in Table S1 in the supplemental material. The primers and recombinant DNA techniques used to generate these strains and plasmids are detailed in Table S2 in the supplemental material. Bacteria were commonly grown at 37°C in lysogeny broth (LB) and M9 minimal medium (M9 salts [Sigma-Aldrich], 2 mM MgSO4, and 100 µM CaCl2) supplemented with various carbon sources. Medium was supplemented with tetracycline (2 µg/ml), ampicillin (100 µg/ml), kanamycin (50 µg/ml), and/or spectinomycin (100 µg/ml) when appropriate.
Ampicillin
Bacteria
Carbon
derivatives
Escherichia coli
Kanamycin
Lysogeny
Oligonucleotide Primers
Plasmids
Recombinant DNA
Salts
Spectinomycin
Strains
Sulfate, Magnesium
Tetracycline
Vibrio cholerae
Most recents protocols related to «Lysogeny»
Example 6
The living cells embedded in the SLMs were then exploited to develop a self-regenerating material. When a fragment of EC-SLM was introduced into selective lysogeny broth media, the SLM started to disperse and the cells self-replicated to form the turbid culture. After 24 h of culture, the cells were pelletized and casted onto the mold as per the same fabrication protocol described above. Ambient drying of the pellet for 24 h resulted in the second generation (denoted by Gen II) of EC-SLM fabricated from its first generation (denoted by Gen I,
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Cells
Fungus, Filamentous
Lysogeny
Parent
Regeneration
Example 1
Thuricide BT Caterpillar Control (Southern Ag) was used as the source of viable Bacillus thuringiensis spores (6 million spores/mg). The DEE chemical comprised of 1:200 bleach in water. This concentration corresponds to approximately 0.5 wt.-% bleach (Clorox) in water. Vegetative cells of BT were grown in lysogeny broth for 48 h at 30° C. The culture was diluted 1:100 with phosphate buffered saline and the DEE chemical composition (about 100 microliters) was added. In the case of spores, the DEE composition was added to achieve a 1:100 dilution of spores.
The spores and vegetative cells in a micro-centrifuge tube were then exposed to 2.45 GHz microwave radiation for 10 s. After exposure, the cells were centrifuged and washed to remove the DEE composition and then plated on Petrifilm and cultured. The plates were then cultured for 24 h at 30° C. This decontamination method resulted in 6-7 log reduction in BT vegetative cells. However, in the case of BT spores, only 4-5 log kill was realized. Increasing the microwave exposure time to 15-20 s yielded 6-7 log kill levels in the case of BT spores.
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Bacillus thuringiensis
Cells
chemical composition
Clorox
Decontamination
Lysogeny
Microwaves
Phosphates
Saline Solution
Spores
Technique, Dilution
Thuricide
Bacterial strains and plasmids used in this study are listed in Supplementary Data 1 . Bacteria were cultivated overnight at 37 °C with shaking at 200 rpm in lysogeny broth (LB) containing suitable antibiotics if necessary. If not otherwise stated, overnight cultures were diluted 1:20 into LB broth containing suitable antibiotics or additives like L -rhamnose and grown for 3 h at 37 °C and 200 rpm before sample collection for downstream analyses.
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Antibiotics, Antitubercular
Bacteria
Lysogeny
Plasmids
Rhamnose
Specimen Collection
Strains
Staphylococcus aureus (S. aureus) ATCC-6538 was cultured overnight at 37 °C in tryptic soy broth (TSB) in an orbital shaker (100–120 rpm). Escherichia coli (E. coli) 8099 and methicillin-resistant S. aureus (MRSA) (ATCC-44) were grown by the same procedure but substituting TSB with lysogeny broth (LB) and tryptic soy broth (TSB) with 5 mg/L tetracycline, respectively. Bacterial strains were grown to an initial concentration of 107–109 CFU (colony forming units)/mL. Cultures were pelleted via centrifugation (10,000 × g) for 10 min, the supernatant was decanted, and the bacteria were re-suspended in phosphate buffered saline (PBS; aqueous solution of 170 mM NaCl, 3.4 mM KCl, 10.0 mM Na2HPO4, 1.8 mM KH2PO4, pH 7.2) containing 0.05% Tween-80.
Bacteria
Centrifugation
Escherichia coli
Lysogeny
Methicillin-Resistant Staphylococcus aureus
Phosphates
Saline Solution
Sodium Chloride
Staphylococcus aureus Infection
Strains
Tetracycline
tryptic soy broth
Tween 80
Genomic DNA of the strains sequenced in this study was extracted and purified using Genomic-tips 100/G and a genomic DNA buffer set (Qiagen) from overnight cultures in lysogeny broth (LB) at 37 °C following the manufacturer’s protocol, with minor modifications including the addition of SDS (final concentration 1 %) after adding buffer B2 and incubation for 1 h at 50 °C. For short-read sequencing, libraries were prepared using the Nextera XT DNA sample prep kit (Illumina) or NEBNext Ultra II FS DNA library preparation kit (New England Biolabs) and sequenced using the Illumina MiSeq platform to generate paired-end sequence reads (301 bp ×2). Reads were trimmed by Platanus trim [27 (link)] with default parameters and assembled by Platanus_B_v1.3.1 [28 (link)]. Scaffolds ≥300 bp were used in this study.
To determine complete genome sequences, size selection of purified DNA was performed using magnetic beads (AMPure XP; Beckman Coulter) to obtain longer DNA fragments. Sequencing libraries were prepared using a rapid barcoding kit (SQK-RBK004), sequenced using the R9.4.1 flow cell with the Oxford Nanopore Technologies (ONT) MinION platform, and base-called using Guppy GPU ver. 3.4.5. (ONT). Reads were trimmed using NanoFilt [29 (link)] with the following parameters: minimum length=7 000 bp, minimum quality score=10 and 5'-terminal 100 bases cutting. For sequencing of three strains (93_161312, CEC13091 and F690), only≥15 kb reads were used for assembly to gain better results. For sequencing of strain F765, the minimum length was changed to 2000 bp to salvage its small plasmid sequence. ONT read assembly and polishing were performed using the microPIPE pipeline [30 (link)]. In brief, trimmed ONT reads were assembled using Flye (v2.8.3) [31 (link)] with the option ‘--plasmids’ and polished with ONT reads using four iterations of Racon (v1.4.20) [32 (link)] followed by one iteration of Medaka (v1.4.3) (GitHub –https://github.com/nanoporetech/medaka ). Output contigs were further refined with Illumina short reads using NextPolish (v1.3.1) (GitHub – https://github.com/Nextomics/NextPolish ). As the chromosome of strain 93_161312 and the plasmids of strain F690 were not circularized, manual curation was performed using Minimap2 [33 (link)], Integrative Genomics Viewer (igv ) [34 (link)] and GenomeMatcher v3.0.2 [35 (link)] to obtain their circular chromosome and plasmid sequences.
To determine complete genome sequences, size selection of purified DNA was performed using magnetic beads (AMPure XP; Beckman Coulter) to obtain longer DNA fragments. Sequencing libraries were prepared using a rapid barcoding kit (SQK-RBK004), sequenced using the R9.4.1 flow cell with the Oxford Nanopore Technologies (ONT) MinION platform, and base-called using Guppy GPU ver. 3.4.5. (ONT). Reads were trimmed using NanoFilt [29 (link)] with the following parameters: minimum length=7 000 bp, minimum quality score=10 and 5'-terminal 100 bases cutting. For sequencing of three strains (93_161312, CEC13091 and F690), only≥15 kb reads were used for assembly to gain better results. For sequencing of strain F765, the minimum length was changed to 2000 bp to salvage its small plasmid sequence. ONT read assembly and polishing were performed using the microPIPE pipeline [30 (link)]. In brief, trimmed ONT reads were assembled using Flye (v2.8.3) [31 (link)] with the option ‘--plasmids’ and polished with ONT reads using four iterations of Racon (v1.4.20) [32 (link)] followed by one iteration of Medaka (v1.4.3) (GitHub –
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Buffers
Chromosomes
DNA Library
Genome
Lebistes
Lysogeny
Oryziinae
Plasmids
Strains
Top products related to «Lysogeny»
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Lysogeny broth (LB) is a nutrient-rich growth medium used in microbiology and molecular biology laboratories. It provides essential nutrients to support the growth of various bacterial species. LB is a widely-used standard culture medium for cultivating and maintaining bacterial cultures.
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Kanamycin is a broad-spectrum antibiotic derived from the bacterium Streptomyces kanamyceticus. It is commonly used as a selective agent in molecular biology and microbiology laboratories for the growth and selection of bacteria that have been genetically modified to express a gene of interest.
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Ampicillin is a broad-spectrum antibiotic used in laboratory settings. It is a penicillin-based compound effective against a variety of gram-positive and gram-negative bacteria. Ampicillin functions by inhibiting cell wall synthesis, leading to bacterial cell lysis and death.
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Chloramphenicol is a bacteriostatic antibiotic that inhibits protein synthesis in bacteria. It is commonly used in microbiology laboratories for selective cultivation and identification of bacterial species.
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Lysogeny broth (LB) is a commonly used growth medium for cultivating bacteria. It provides the necessary nutrients and conditions for the propagation of bacterial cultures in a laboratory setting. LB is a complex medium that supports the growth of a wide range of bacterial species.
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Lysogeny broth (LB) is a nutrient-rich growth medium commonly used in microbiology and molecular biology laboratories for the cultivation of various bacterial species. It provides essential nutrients, such as amino acids, vitamins, and carbohydrates, to support the growth and proliferation of bacterial cultures.
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NaCl is a chemical compound commonly known as sodium chloride. It is a white, crystalline solid that is widely used in various industries, including pharmaceutical and laboratory settings. NaCl's core function is to serve as a basic, inorganic salt that can be used for a variety of applications in the lab environment.
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Yeast extract is a light-colored, water-soluble powder that is derived from the autolysis of baker's yeast. It serves as a nutrient source, providing a complex mixture of amino acids, vitamins, and other growth factors to support the cultivation of microbial cultures in various scientific and industrial applications.
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Tryptone is a complex organic compound derived from the enzymatic digestion of casein, a milk protein. It is commonly used as a nutrient source in microbial growth media for the cultivation of various types of bacteria. Tryptone provides a rich source of amino acids, peptides, and other essential nutrients required for the growth and proliferation of bacterial cultures in laboratory settings.
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Fetal Bovine Serum (FBS) is a cell culture supplement derived from the blood of bovine fetuses. FBS provides a source of proteins, growth factors, and other components that support the growth and maintenance of various cell types in in vitro cell culture applications.
More about "Lysogeny"
Lysogeny is a critical process in viral reproduction, where the viral genome integrates into the host cell's DNA, allowing the virus to replicate as part of the host's normal chromosomal DNA.
This lysogenic cycle is a fundamental aspect of many viral lifecycles and has significant implications for the host organism.
The viral genome may remain dormant within the host cell for extended periods, only becoming activated under specific environmental or cellular conditions.
Understanding the mechanisms and dynamics of lysogeny is crucial for research into viral pathogenesis, bacterial genetics, and the development of therapeutic interventions.
Lysogeny is closely related to the concept of a 'lysogenic cycle', where the viral genome is incorporated into the host's DNA.
This contrasts with the 'lytic cycle', where the virus replicates and lyses (breaks open) the host cell to release new viral particles.
The lysogenic cycle is an important survival strategy for many viruses, as it allows them to persist within the host without immediately causing cell death.
When studying lysogeny, researchers often utilize growth media like Lysogeny Broth (LB), which is a nutrient-rich medium commonly used for culturing bacteria and other microorganisms.
LB contains key ingredients such as tryptone (a enzymatic digest of casein), yeast extract, and sodium chloride (NaCl), which provide the necessary nutrients and osmotic balance for bacterial growth.
Antibiotics like kanamycin, ampicillin, and chloramphenicol are also frequently used to select for bacteria that have successfully incorporated the viral genome, as these antibiotics can kill or inhibit the growth of cells that lack the necessary resistance genes.
Fetal Bovine Serum (FBS) is another essential component in cell culture experiments related to lysogeny, as it provides the necessary growth factors and nutrients to support the proliferation of host cells, which is crucial for viral integration and replication.
By optimizing your lysogeny research with the cutting-edge analysis tools provided by PubCompare.ai, you can identify the most effective protocols and procedures from the scientific literature, preprints, and patents, leading to more reproducable and enhanced lysogeny experiments.
This lysogenic cycle is a fundamental aspect of many viral lifecycles and has significant implications for the host organism.
The viral genome may remain dormant within the host cell for extended periods, only becoming activated under specific environmental or cellular conditions.
Understanding the mechanisms and dynamics of lysogeny is crucial for research into viral pathogenesis, bacterial genetics, and the development of therapeutic interventions.
Lysogeny is closely related to the concept of a 'lysogenic cycle', where the viral genome is incorporated into the host's DNA.
This contrasts with the 'lytic cycle', where the virus replicates and lyses (breaks open) the host cell to release new viral particles.
The lysogenic cycle is an important survival strategy for many viruses, as it allows them to persist within the host without immediately causing cell death.
When studying lysogeny, researchers often utilize growth media like Lysogeny Broth (LB), which is a nutrient-rich medium commonly used for culturing bacteria and other microorganisms.
LB contains key ingredients such as tryptone (a enzymatic digest of casein), yeast extract, and sodium chloride (NaCl), which provide the necessary nutrients and osmotic balance for bacterial growth.
Antibiotics like kanamycin, ampicillin, and chloramphenicol are also frequently used to select for bacteria that have successfully incorporated the viral genome, as these antibiotics can kill or inhibit the growth of cells that lack the necessary resistance genes.
Fetal Bovine Serum (FBS) is another essential component in cell culture experiments related to lysogeny, as it provides the necessary growth factors and nutrients to support the proliferation of host cells, which is crucial for viral integration and replication.
By optimizing your lysogeny research with the cutting-edge analysis tools provided by PubCompare.ai, you can identify the most effective protocols and procedures from the scientific literature, preprints, and patents, leading to more reproducable and enhanced lysogeny experiments.