> Living Beings > Virus > Bacteriophages

Bacteriophages

Bacteriophages are viruses that infect and replicate within bacterial cells.
They are found in diverse environments and play a crucial role in microbial ecology and evolution.
Bacteriophages exhibit a wide range of morphologies and genome structures, and have been studied for their potential applications in phage therapy, bacterial detection, and biotechnology.
Reasearchers can leverae PubCompare.ai's AI-driven platform to optimize their bacteriophage research, locating protocols from literature, preprits, and patents with ease and identifying the best protocols and products through AI-driven comparisons.
PubCompare.ai's intuitive tools and analytics enable seamless, data-driven bacteriophage research exploration.

Most cited protocols related to «Bacteriophages»

Genetic Manipulation of E. coli

E. coli BW25141 (rrnB3 DElacZ4787 DEphoBR580 hsdR514 DE(araBAD)567 DE(rhaBAD)568 galU95 DEendA9::FRT DEuidA3::pir(wt) recA1 rph-1) was used for maintenance of the template plasmid pKD13 (GenBank™ Accession number AY048744). pKD46 (GenBank™ Accession number AY048746; Datsenko and Wanner, 2000 (link)) was made by PCR amplification of the Red recombinase genes from phage λ and cloning into pKD16, a derivative of INT-ts (Haldimann and Wanner, 2001 (link)) carrying araC and araBp from pBAD18 (Guzman et al, 1995 (link)).

Baba T., Ara T., Hasegawa M., Takai Y., Okumura Y., Baba M., Datsenko K.A., Tomita M., Wanner B.L, & Mori H. (2006). Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Molecular Systems Biology, 2, 2006.0008.

Publication 2006

Ara-C Bacteriophages Escherichia coli Gene Amplification Plasmids Recombinase

Automated Phage Sequence Annotation

PHAST accepts both raw DNA sequence and GenBank annotated genomes. If given a raw genomic sequence (FASTA format), PHAST identifies all ORFs using GLIMMER 3.02 (14 (link)). This ORF identification step takes about 45 s for an average bacterial genome of 5.0 Mb. The translated ORFs are then rapidly annotated via BLAST using PHAST's non-redundant bacterial protein library (∼2–3 min/genome). Because tRNA and tmRNA sites provide valuable information for identifying the attachment sites, they are calculated using the programs tRNAscan-SE (15 (link)) and ARAGORN (16 (link)). If an input (GenBank formatted) file is provided with complete protein and tRNA information, these steps are skipped. Phage or phage-like proteins are then identified by performing a BLAST search against PHAST's local phage/prophage sequence database along with specific keywords searches to facilitate further refinement and identification. Matched phage or phage-like sequences with BLAST e-values less than 10⁻⁴ are saved as hits and their positions tracked for subsequent evaluation for local phage density by DBSCAN (17 ).

Zhou Y., Liang Y., Lynch K.H., Dennis J.J, & Wishart D.S. (2011). PHAST: A Fast Phage Search Tool. Nucleic Acids Research, 39(Web Server issue), W347-W352.

Publication 2011

Bacterial Proteins Bacteriophages DNA Library Genome Genome, Bacterial Open Reading Frames Prophages Proteins tmRNA Transfer RNA

Antigen Prediction Using VaxiJen

The VaxiJen server [27 ] is implemented in Perl, with an interface written in HTML. VaxiJen identifies bacterial, viral and tumour antigens using three different models, derived in the present study. Protein sequences are uploaded as single or multiple files in plain or fasta format respectively. The results page reports antigen probability (as a fraction of unity) for each protein and a statement of antigen status ("probable Antigen" versus "Probable Non-Antigen").

Doytchinova I.A, & Flower D.R. (2007). VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8, 4.

Full text: Click here

Publication 2007

Amino Acid Sequence Antigens Bacteriophages Proteins Tumor Antigens

Evaluating Viral Sequence Detection Tools

We first evaluated VirSorter results against the manually curated prophages from (Casjens, 2003 (link)). Each genome was processed with VirSorter, PhiSpy (Akhter, Aziz & Edwards, 2012 (link)), Phage_Finder (Fouts, 2006 (link)) and PHAST (Zhou et al., 2011 (link)). For each tool, a prophage was considered as “detected” when a prediction covered more than 75% of the known prophage. For a more detailed example case of prophage detection in a complete bacterial genome including both prophages and genomic islands, the same tools were applied to the manually annotated Pseudomonas aeruginosa LES B58 genome (Winstanley et al., 2009 (link)).
VirSorter was then compared with the same prophage detection tools on the set of simulated SAGs. In that case, a viral sequence was considered as detected if predicted as completely viral or as a prophage. All the additional detections were manually checked to verify if the region was indeed viral (originating from a prophage in one of the microbial genomes rather than from a viral genome) or a false positive. The same approach was used for the simulated microbial and viral metagenomes results.
For each set of predictions, two metrics are computed. First, the Recall value corresponds to the number of viral sequences correctly predicted divided by the total number of known viral sequences in the dataset, and reflects the ability of the tool to find every known viral sequence in the dataset. Second, the Precision value is computed as the total number of viral sequences correctly predicted divided by the total number of viral sequences predicted, and indicates how accurate the tool is in its identification of viral signal.

Roux S., Enault F., Hurwitz B.L, & Sullivan M.B. (2015). VirSorter: mining viral signal from microbial genomic data. PeerJ, 3, e985.

Full text: Click here

Publication 2015

Bacteriophages DMBT1 protein, human Genome Genome, Bacterial Genome, Microbial Genomic Islands Mental Recall Metagenome Prophages Pseudomonas aeruginosa Viral Genome

Comparative Analysis of T7-like Phages

The dataset used for benchmarking consisted of 60 T7-like phages genomes, from the Autographviridae family, downloaded from the GenBank RefSeq database [20 (link)]. These genomes were chosen because they are related, colinear and have an average genome size of 39.4 kbp (range: 31.5–41.7) and G + C mol% content of 50.7 (range: 42.6–61.8; Table S1). The testing dataset also contained the Pelagibacter phage HTVC011P genome, used as outlier for the T7-like phages. For this dataset of 61 phages, the intergenomic similarities were calculated with the following tools: Sequence Demarcation Tool (SDT) [10 (link)], pairwise sequence comparison (PASC) [8 (link)], OrthoANI [4 (link)], Gegenees [6 (link)], and VIRIDIC.
Additionally, two Salmonella phages (GE_vB_N5 and FE_vB_N8) were used for the illustration of genome and alignment length differences. The genome of the K155 strain of the T7 phage was used to test the effect of genome permutations and reverse complementarity on the intergenomic distances. Lastly, two artificial DNA sequences were generated by (i) scrambling the T7 genome with Shuffle DNA, part of the Sequence Manipulation Suite [21 (link)] and (ii) using Vladimír Čermák’s Random DNA Sequence Generator at http://www.molbiotools.com/randomsequencegenerator.html to generate a 39,937 bp (48.4% GC) sequence.

Moraru C., Varsani A, & Kropinski A.M. (2020). VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses. Viruses, 12(11), 1268.

Full text: Click here

Publication 2020

Bacteriophages Bacteriophage T7 Complement System Proteins Genome Salmonella Phages Strains

Most recents protocols related to «Bacteriophages»

Detecting Endogenous Bacteriophages in E. coli Nissle

Not available on PMC !

Example 56

Escherichia coli Nissle 1917 (E. coli Nissle) and engineered derivatives test positive for a low level presence of phage 3 in a validated bacteriophage plaque assay. Bacteriophage plaque assays were conducted to determine presence and levels of bacteriophage. In brief, supernatants from cultures of test bacteria that were grown overnight were mixed with a phage-sensitive indicator strain and plated in soft agar to detect the formation of plaques, indicative of the presence of bacteriophage. Polymerase chain reaction (PCR) primers were designed to detect the three different endogenous prophages identified in the bioinformatics analyses, and were used to assess plaques for the presence of phage-specific DNA.

US11879123B2. Bacteria for the treatment of disorders (2024-01-23). Synlogic Operating Company, Inc. [US]. Inventors: Dean Falb [US], Adam B. Fisher [US], Vincent M. Isabella [US], Jonathan W. Kotula [US], David Lubkowicz [US], Paul F. Miller [US], Yves Millet [US], Sarah Elizabeth Rowe [US].

Full text: Click here

Patent 2024

Agar Bacteria Bacteriophage Plaque Assay Bacteriophages derivatives Escherichia coli Oligonucleotide Primers Polymerase Chain Reaction Prophages Senile Plaques Strains

PHESELECTOR Assay for Thiol Reactivity Evaluation

Not available on PMC !

Example 2

Bovine serum albumin (BSA), erbB2 extracellular domain (HER2) and streptavidin (100 μl of 2 μg/ml) were separately coated on Maxisorp 96 well plates. After blocking with 0.5% Tween-20 (in PBS), biotinylated and non-biotinylated hu4D5Fabv8-ThioFab-Phage (2×10¹⁰phage particles) were incubated for 1 hour at room temperature followed by incubation with horseradish peroxidase (HRP) labeled secondary antibody (anti-M13 phage coat protein, pVIII protein antibody). FIG. 8 illustrates the PHESELECTOR Assay by a schematic representation depicting the binding of Fab or ThioFab to HER2 (top) and biotinylated ThioFab to streptavidin (bottom).

Standard HRP reaction was carried out and the absorbance was measured at 450 nm. Thiol reactivity was measured by calculating the ratio between OD₄₅₀for streptavidin/OD₄₅₀for HER2. A thiol reactivity value of 1 indicates complete biotinylation of the cysteine thiol. In the case of Fab protein binding measurements, hu4D5Fabv8 (2-20 ng) was used followed by incubation with HRP labeled goat polyclonal anti-Fab antibodies.

US11873330B2. Cysteine engineered antibodies and conjugates (2024-01-16). Genentech, Inc. [None]. Inventors: Sunil Bhakta [US], Jagath R. Junutula [US].

Full text: Click here

Patent 2024

Anti-Antibodies Bacteriophage M13 Bacteriophages Biological Assay Biotinylation Cardiac Arrest Cysteine ERBB2 protein, human Goat herstatin protein, human Horseradish Peroxidase Immunoglobulins Proteins Serum Albumin, Bovine Streptavidin Sulfhydryl Compounds Tween 20

Llama Nanobody Isolation Protocol

Not available on PMC !

EXAMPLE 36

Peripheral blood mononuclear cells were prepared from blood samples obtained from llama No. 45 and No. 46 using Ficoll-Hypaque according to the manufacturer's instructions. Next, total RNA extracted was extracted from these cells and used as starting material for RT-PCR to amplify Nanobody encoding gene fragments. These fragments were cloned into phagemid vector pAX50. Phage was prepared according to standard methods (see for example the prior art and applications filed by applicant cited herein) and stored after filter sterilization at 4° C. for further use.

US11858997B2. Amino acid sequences that modulate the interaction between cells of the immune system (2024-01-02). Ablynx N.V. [BE]. Inventors: Guy Hermans [BE], Peter Verheesen [BE], Edward Dolk [NL], Hendricus Renerus Jacobus Mattheus Hoogenboom [NL], Michael John Scott Saunders [BE], Hans De Haard [NL], Renee de Bruin [NL].

Full text: Click here

Patent 2024

Bacteriophages BLOOD Cloning Vectors DNA Library Ficoll Genes Hypaque Llamas PBMC Peripheral Blood Mononuclear Cells Reverse Transcriptase Polymerase Chain Reaction Sterilization

Evaluating the Versatility of SpyTag002-SpyCatcher002 Reaction

Not available on PMC !

Example 4

We tested the resilience of the reaction of SpyTag002 and SpyCatcher002 under a wide range of conditions. The above rate constants were calculated at pH 7, but reactivity was similar at pH 4 and slightly higher at pH 5 and 6 (FIG. 13A). Reaction was fast at 4, 25 and 37° C. (FIG. 13B). Reaction was relatively independent of buffer, with efficient reaction with phosphate, Tris or HEPES buffering, with relatively little dependence on specific monovalent or divalent anions or cations (FIG. 13C). Reaction of SpyTag002 and SpyCatcher002 tolerated well the presence of detergents Triton X-100 or Tween-20, giving a slight enhancement of reactivity (FIG. 13D). Reaction of SpyTag002 and SpyCatcher002 also tolerated over 3M urea (FIG. 13E).

SpyCatcher002 was selected on phage as an N-terminal fusion to pill. We confirmed that SpyCatcher002 also behaved well as a C-terminal fusion, showing efficient reaction of MBPx-SpyCatcher002 with SpyTag002-MBP (FIG. 14A). We validated that SpyTag002 reacted efficiently when fused at the N-terminus as SpyTag002-MBP (FIG. 12) or at the C-terminus as AffiEGFR-SpyTag002 (FIG. 14B).

US11873323B2. Proteins and peptide tags with enhanced rate of spontaneous isopeptide bond formation and uses thereof (2024-01-16). Oxford University Innovation Limited [GB]. Inventors: Mark Howarth [GB], Anthony Keeble [GB].

Full text: Click here

Patent 2024

Anions Bacteriophages Cations Contraceptives, Oral Detergents HEPES Phosphates Triton X-100 Tromethamine Tween 20 Urea

Llama Nanobody Library Generation

Not available on PMC !

EXAMPLE 12

Peripheral blood mononuclear cells were prepared from blood samples obtained from llama No. 146 and No. 147 using Ficoll-Hypaque according to the manufacturer's instructions. Next, total RNA extracted was extracted from these cells and used as starting material for RT-PCR to amplify Nanobody encoding gene fragments. These fragments were cloned into phagemid vector pAX50. Phage was prepared according to standard methods (see for example the prior art and applications filed by applicant cited herein) and stored after filter sterilization at 4° C. for further use.

Full text: Click here

Patent 2024

Bacteriophages BLOOD Cloning Vectors DNA Library Ficoll Genes Hypaque Llamas PBMC Peripheral Blood Mononuclear Cells Reverse Transcriptase Polymerase Chain Reaction Sterilization

Top products related to «Bacteriophages»

Miseq platform by Illumina

Sourced in United States, China, Germany, United Kingdom, Spain, Australia, Italy, Canada, Switzerland, France, Cameroon, India, Japan, Belgium, Ireland, Israel, Norway, Finland, Netherlands, Sweden, Singapore, Portugal, Poland, Czechia, Hong Kong, Brazil

The MiSeq platform is a benchtop sequencing system designed for targeted, amplicon-based sequencing applications. The system uses Illumina's proprietary sequencing-by-synthesis technology to generate sequencing data. The MiSeq platform is capable of generating up to 15 gigabases of sequencing data per run.

Phage dna isolation kit by Norgen Biotek

Sourced in Canada, United States

The Phage DNA Isolation Kit is a laboratory equipment designed to extract and purify DNA from bacteriophages, which are viruses that infect bacteria. The kit provides a streamlined process for isolating phage DNA from various sample types, allowing researchers to study the genetic composition and characteristics of these viruses.

Lipofectamine 2000 by Thermo Fisher Scientific

Sourced in United States, China, Germany, United Kingdom, Canada, Japan, France, Italy, Switzerland, Australia, Spain, Belgium, Denmark, Singapore, India, Netherlands, Sweden, New Zealand, Portugal, Poland, Israel, Lithuania, Hong Kong, Argentina, Ireland, Austria, Czechia, Cameroon, Taiwan, Province of China, Morocco

Lipofectamine 2000 is a cationic lipid-based transfection reagent designed for efficient and reliable delivery of nucleic acids, such as plasmid DNA and small interfering RNA (siRNA), into a wide range of eukaryotic cell types. It facilitates the formation of complexes between the nucleic acid and the lipid components, which can then be introduced into cells to enable gene expression or gene silencing studies.

Mitomycin c by Merck Group

Sourced in United States, Germany, United Kingdom, Macao, Japan, France, Italy, Sao Tome and Principe, China, Australia, India

Mitomycin C is a laboratory reagent used in cell biology and cancer research. It is a potent DNA cross-linking agent that inhibits DNA synthesis and cell division. Mitomycin C is commonly used to study cellular processes and as a positive control in various cell-based assays.

Polybrene by Merck Group

Sourced in United States, Germany, China, Sao Tome and Principe, United Kingdom, Macao, Canada, France, Japan, Switzerland, Italy, Australia, Netherlands, Morocco, Israel, Ireland, Belgium, Denmark, Norway

Polybrene is a cationic polymer used as a transfection reagent in cell biology research. It facilitates the introduction of genetic material into cells by enhancing the efficiency of DNA or RNA uptake.

Hiseq 2500 by Illumina

Sourced in United States, China, Germany, United Kingdom, Canada, Switzerland, Sweden, Japan, Australia, France, India, Hong Kong, Spain, Cameroon, Austria, Denmark, Italy, Singapore, Brazil, Finland, Norway, Netherlands, Belgium, Israel

The HiSeq 2500 is a high-throughput DNA sequencing system designed for a wide range of applications, including whole-genome sequencing, targeted sequencing, and transcriptome analysis. The system utilizes Illumina's proprietary sequencing-by-synthesis technology to generate high-quality sequencing data with speed and accuracy.

Dnase 1 by Merck Group

Sourced in United States, Germany, Switzerland, United Kingdom, Italy, Japan, Macao, Canada, Sao Tome and Principe, China, France, Australia, Spain, Belgium, Netherlands, Israel, Sweden, India

DNase I is a laboratory enzyme that functions to degrade DNA molecules. It catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, effectively breaking down DNA strands.

Dnase 1 by Thermo Fisher Scientific

Sourced in United States, Germany, Lithuania, Canada, United Kingdom, China, Japan, Switzerland, Italy, France, Spain, Australia, Belgium, Denmark, Argentina, Sao Tome and Principe, Singapore, Poland, Finland, Austria, India, Netherlands, Ireland, Viet Nam

DNase I is an enzyme used in molecular biology laboratories to degrade DNA. It catalyzes the hydrolytic cleavage of phosphodiester linkages in the DNA backbone, effectively breaking down DNA molecules. This enzyme is commonly used to remove contaminating DNA from RNA preparations, allowing for more accurate downstream analysis of RNA.

Prism 8 by GraphPad

Sourced in United States, Austria, Canada, Belgium, United Kingdom, Germany, China, Japan, Poland, Israel, Switzerland, New Zealand, Australia, Spain, Sweden

Prism 8 is a data analysis and graphing software developed by GraphPad. It is designed for researchers to visualize, analyze, and present scientific data.

T4 dna ligase by New England Biolabs

Sourced in United States, China, United Kingdom, Germany, Japan, France, Canada, Morocco, Switzerland, Australia

T4 DNA ligase is an enzyme that catalyzes the formation of phosphodiester bonds between adjacent 3'-hydroxyl and 5'-phosphate termini in DNA. It is commonly used in molecular biology for the joining of DNA fragments.

What are the different types of bacteriophages?

Bacteriophages, or phages for short, exhibit a wide range of morphologies and genome structures. Some common types include: 1. Lytic phages: These phages infect and lyse (break open) bacterial cells, causing them to burst and release new phage particles. 2. Lysogenic phages: These phages can integrate their genetic material into the host bacterial genome, remaining dormant until certain conditions trigger them to enter the lytic cycle. 3. Filamentous phages: These phages have a long, thin, filamentous shape and do not lyse the host cell, instead continuously budding from the cell surface. 4. Myoviridae phages: These phages have a distinctive tail structure with a contractile sheath, which helps them inject their genetic material into the host cell.

How can bacteriophages be used in biotechnology and research?

Bacteriophages have a wide range of applications in biotechnology and research, including: 1. Phage therapy: Using phages to treat bacterial infections, particularly in cases where antibiotics are ineffective. 2. Bacterial detection: Phages can be used to detect and identify specific bacterial strains, which is useful in food safety, clinical diagnostics, and environmental monitoring. 3. Phage display: Phages can be engineered to display peptides or proteins on their surface, which is a powerful tool for studying protein-protein interactions and identifying new therapeutic targets. 4. Bioremediation: Certain phages can be used to break down environmental pollutants or control the growth of harmful bacteria in industrial settings.

How can PubCompare.ai help with bacteriophage research?

PubCompare.ai's AI-driven platform can assist with bacteriophage research in several ways: 1. Efficient protocol screening: The platform allows you to quickly and easily search through the vast literature on bacteriophage protocols, helping you find the most relevant and effective ones for your research goals. 2. AI-driven insights: PubCompare.ai's AI algorithms can analyze and compare the efficacy of different bacteriophage protocols, highlighting key differences and enabling you to choose the best option for reproducibility and accuracy. 3. Seamless research exploration: The platform's intuitive tools and analytics provide a streamlined, data-driven approach to your bacteriophage research, saving you time and effort in the process. By leveraging PubCompare.ai, you can optimize your bacteriophage research and make more informed decisions about the protocols and products you use, ultimately leading to more successful and impactful studies.

What are some common challenges in working with bacteriophages?

Working with bacteriophages can present several challanges, including: 1. Host specificity: Many phages can only infect and replicate within specific bacterial hosts, which can make it difficult to find the right phage for a particular application. 2. Phage diversity: With the vast diversity of phages in the environment, it can be challenging to isolate and characterize the specific phages needed for your research or application. 3. Phage stability: Phages can be sensitive to environmental conditions, such as temperature, pH, and the presence of certain chemicals, which can affect their stability and viability. 4. Regulatory hurdles: The use of phages in clinical or industrial settings may require navigating complex regulatory frameworks, which can be time-consuming and resource-intensive.

More about "Bacteriophages"

Bacteriophages, also known as phages, are viruses that specifically infect and replicate within bacterial cells.
These unique microorganisms play a crucial role in microbial ecology and evolution, and have garnered significant interest for their potential applications in various fields.
Bacteriophages exhibit a wide range of morphologies, from simple icosahedral structures to more complex tail-containing virions.
Their genomes can also vary, with diverse structures and compositions, including single-stranded and double-stranded DNA or RNA.
This diversity allows phages to adapt to and infect a wide range of bacterial hosts.
Researchers have leveraged advanced technologies, such as the Illumina MiSeq and HiSeq 2500 platforms, to study the genomics and diversity of bacteriophages.
Techniques like Phage DNA Isolation Kits and T4 DNA ligase enable the extraction and manipulation of phage genetic material, while Mitomycin C and Polybrene can be used to induce phage production and enhance infection, respectively.
The potential applications of bacteriophages are vast and varied.
Phage therapy, where phages are used to target and eliminate specific bacterial infections, has shown promise as an alternative to traditional antibiotics.
Bacteriophages can also be utilized for bacterial detection and identification, as well as in biotechnological applications like bioremediation and enzyme production.
To optimize their bacteriophage research, scientists can utilize the AI-driven platform offered by PubCompare.ai.
This innovative tool allows researchers to easily locate relevant protocols from literature, preprints, and patents, and leverage AI-driven comparisons to identify the best protocols and products.
PubCompare.ai's intuitive tools and analytics enable seamless, data-driven exploration of the bacteriophage research landscape.
Whether you're studying phage ecology, exploring phage therapy, or investigating biotechnological applications, PubCompare.ai can help you navigate the complexities of bacteriophage research and unlock new possibilities.
Discover the power of AI-driven bacteriophage research with PubCompare.ai today!