quantitative-pcr-of-t7-bacteriophage-from-biopanning

Quantitative PCR of T7 Bacteriophage from Biopanning

This protocol describes the use of quantitative PCR (qPCR) to enumerate T7 phages from phage selection experiments (i.e., &#34;biopanning&#34;). qPCR is a ...

University of Texas at Austin

With the rise in antibiotic-resistant infections, non-invasive sensing of infectious diseases is increasingly important. Optical imaging, although safer and simpler, is less developed than other modalities such as radioimaging, due to low availability of target-specific molecular probes. Here we report carbon nanotubes (SWNTs) as bacterial probes for fluorescence imaging of pathogenic infections. We demonstrate that SWNTs functionalized using M13 bacteriophage (M13-SWNT) can distinguish between F'-positive and F'-negative bacterial strains. Moreover, through one-step modification, we attach an anti-bacterial antibody on M13-SWNT, making it easily tunable for sensing specific F'-negative bacteria. We illustrate detection of Staphylococcus aureus intramuscular infections, with ~3.4 × enhancement in fluorescence intensity over background. SWNT imaging presents lower signal spread ~0.08 × and higher signal amplification ~1.4 × , compared with conventional dyes. We show the probe offers greater ~5.7 × enhancement in imaging of S. aureus infective endocarditis. These biologically functionalized, aqueous-dispersed, actively targeted, modularly tunable SWNT probes offer new avenues for exploration of deeply buried infections. 

Carbon nanotubes as in vivo bacterial probes.

Mucus is a selective barrier to particles and molecules, preventing penetration to the epithelial surface of mucosal tissues. Significant advances in transmucosal drug delivery have recently been made and have emphasized that an understanding of the basic structure, viscoelastic properties, and interactions of mucus is of great value in the design of efficient drug delivery systems. Mucins, the primary non-aqueous component of mucus, are polymers carrying a complex and heterogeneous structure with domains that undergo a variety of molecular interactions, such as hydrophilic/hydrophobic, hydrogen bonds and electrostatic interactions. These properties are directly relevant to the numerous mucin-associated diseases, as well as delivering drugs across the mucus barrier. Therefore, in this review we discuss regional differences in mucus composition, mucus physicochemical properties, such as pore size, viscoelasticity, pH, and ionic strength. These factors are also discussed with respect to changes in mucus properties as a function of disease state. Collectively, the review seeks to provide a state of the art roadmap for researchers who must contend with this critical barrier to drug delivery.

Physicochemical properties of mucus and their impact on transmucosal drug delivery.

TaqMan and SYBR Green quantitative PCR (qPCR) methods were developed as DNA-based approaches to reproducibly enumerate M13 and T7 phages from phage display selection experiments individually and simultaneously. The genome copies of M13 and T7 phages were quantified by TaqMan or SYBR Green qPCR referenced against M13 and T7 DNA standard curves of known concentrations. TaqMan qPCR was capable of quantifying M13 and T7 phage DNA simultaneously with a detection range of 2.75*10-2.75*10genome copies(gc)/μL and 2.66*10-2.66*10 genome copies(gc)/μL respectively. TaqMan qPCR demonstrated an efficient amplification efficiency (E) of 0.97 and 0.90 for M13 and T7 phage DNA, respectively. SYBR Green qPCR was ten-fold more sensitive than TaqMan qPCR, able to quantify 2.75-2.75*10gc/μL and 2.66*10-2.66*10gc/μL of M13 and T7 phage DNA, with an amplification efficiency E of 1.06 and 0.78, respectively. Due to its superior sensitivity, SYBR Green qPCR was used to enumerate M13 and T7 phage display clones selected against a cell line, and quantified titers demonstrated accuracy comparable to titers from traditional double-layer plaque assay. Compared to enzyme linked immunosorbent assay, both qPCR methods exhibited increased detection sensitivity and reproducibility. These qPCR methods are reproducible, sensitive, and time-saving to determine their titers and to quantify a large number of phage samples individually or simultaneously, thus avoiding the need for time-intensive double-layer plaque assay. These findings highlight the attractiveness of qPCR for phage enumeration for applications ranging from selection to next-generation sequencing (NGS).

Quantification of M13 and T7 bacteriophages by TaqMan and SYBR green qPCR.

The severity of multidrug resistance to antibiotics has urged development of alternative treatment approaches, including bacteriophage therapy. Given the complexity of the bacteriophage structure, formulation and stability are primary concerns. Our present work optimized process and formulations of phage powder manufacturing and investigated the stability of lyophilized bacteriophage powders under ambient storage. The model phage M13 was formulated with trehalose, mannitol, sucrose and PEG and lyophilized in different conditions. Bacteriophage viability was examined by titering and was considered as the assessment of phage stability. Less titer loss of trehalose and sucrose formulations were observed compared to mannitol and PEG groups both immediately after lyophilization and upon long term storage. When evaluating lyophilization conditions, an additional 1 log titer was preserved by reduction of product drying stress. Trehalose was stabilized in the amorphous state whereas mannitol stayed in crystalline state in lyophilized powders. Increased moisture content was demonstrated to have a positive impact on viability of phage after lyophilization and upon storage. Overall, 2% trehalose or sucrose (w/v) can sufficiently stabilize phage during lyophilization process and storage in ambient conditions. There is a positive correlation between residual water and stability of phage. These collective findings highlight the potential of long-term, ambient storage of bacteriophage towards their successful use in diverse healthcare settings.

Manufacturing and ambient stability of shelf freeze dried bacteriophage powder formulations.

Peptides are small biological molecules that are attractive in drug delivery and materials engineering for applications including therapeutics, molecular building blocks and cell-targeting ligands. Peptides are small but can possess complexity and functionality as larger proteins. Due to their intrinsic properties, peptides are able to overcome the physiological and transport barriers presented by diseases. In this review, we discuss the progress of identifying and using peptides to shuttle across biological barriers and facilitate transport of drugs and drug delivery systems for improved therapy. Here, the focus of this review is on rationally designed, phage display peptides, and even endogenous peptides as carriers to penetrate biological barriers, specifically the blood-brain barrier(BBB), the gastrointestinal tract (GI), and the solid tumor microenvironment (T). We will discuss recent advances of peptides as drug carriers in these biological environments. From these findings, challenges and potential opportunities to iterate and improve peptide-based approaches will be discussed to translate their promise towards the clinic to deliver drugs for therapeutic efficacy.

Article	Year
Carbon nanotubes as in vivo bacterial probes. Nature communications\| PubMed ID: 25230005	2014
Physicochemical properties of mucus and their impact on transmucosal drug delivery. International journal of pharmaceutics\| PubMed ID: 28917986	2017
Quantification of M13 and T7 bacteriophages by TaqMan and SYBR green qPCR. Journal of virological methods\| PubMed ID: 29196210	2018
Manufacturing and ambient stability of shelf freeze dried bacteriophage powder formulations. International journal of pharmaceutics\| PubMed ID: 29486286	2018
Peptides as drug delivery vehicles across biological barriers. Journal of pharmaceutical investigation\| PubMed ID: 29963321	2018

Debadyuti Ghosh

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