A Research

Proposal for
Admission Title –
Study design, the design of experiments and plan

in
of work for bacteriophages found in USA.

Postdoctora
l Degree. University – Recognized University Food Safety,
Agriculture and Health laboratory

By - Prashant SR Khemariya
Table of content
• Introduction ​
• Project approach ​
• Detection and Isolation of Phages
• Characterization of Phages​
• Suspension and growth studies ​
• Evaluation of study
• Improvement in the plan of work​
• Statistical analysis design
• ​My hands on Phage
• Future work​
• Laboratory Management​
• Discussion (Questions and Answers)
• References
Self-Introduction

At present I am working for Johnson &

Prashant is here, and I am delighted to be
Johnson and I looking for formulation of
here today to present my presentation for
drug products, process development and
the post-doctoral degree program in your
its validation, compliance of laboratory's
esteemed organization.
activities as per FDA, GMP and CLP

I have over 15 years of experience

in pharmaceutical biotech and
nutraceutical product I have completed my Bachelor and Master
development. I have developed more in Pharmacy and PhD in Biotechnology
than 65 products for different
regulatory markets.
Project's introduction

Phages

•Past
•Present
•Future
Phages

Phages, are viruses that infect and replicate within bacteria and archaea.

Bacteriophages are composed of proteins that encapsulate a DNA or RNA genome, and may have structures that are
either simple or elaborate

They are among the most common and diverse entities in the biosphere. Phages have been used since late 19th
century as an alternative to antibiotics in the former Soviet Union and Central Europe, as well as in France. They are
seen as a possible therapy against multi-drug-resistant strains of many bacteria.
Project's introduction History of Phage
Bacteria Eaters -Félix d'Herelle and Frederick Twort.

Phages were first used to treat bacterial infections over 100 years ago, to treat bacterial
infections in humans and animals.

Their effectiveness led to the establishment of phage therapy, a treatment method that
utilizes phages to target and eliminate specific pathogenic bacteria. Phages were also used to
control bacterial contaminants in food and water.

Their continued use in Georgia, Russia, and Poland—their use continued in those countries but
was largely discontinued elsewhere because of the availability of antibiotics.

The cautionary words from the discoverer of antibiotics, Alexander Fleming while accepting
the Nobel prize "I would like to sound one note of warning. The time may come when
penicillin can be bought by anyone in the shops and ignorant person may underdose himself
to non-lethal quantities of antibiotics making the microbes resistant"
History of Phage
In early of 19th century , there were two microbiologists who gave us Phages

(1915) Twort a British physician and microbiologist– twort was working on the growth of Micrococcus bacterial on agar plate but
bacteria were not growing even when subcultured.
Initially he concluded that an unknow substance is there which inhibit the growth of the bacterial,

Later on he further researched and he found that that substance is able to pass though the fine filter and cause the lysis of baceria.

Before Twort could conduct further experiments, the First World War interrupted his career and he joined Royal Army Medical Corps
and moved to Greece.
In 1917 d’Hérelle - French-Canadian microbiologist he was independently working on another research "enteric bacteria of dysentery
patients"
He said “invisible microbe that is antagonistic to the dysentery bacillus” the bacteriophage (a bacteria-eater, from the
Greek phagein meaning "to devour").
D’Hérelle concluded his paper with a few observations: that the bacteriophage is a “microbe of immunity;” it has specificity; and there
is a real potential to treat bacterial infections with phage therapy.
Health issue in the US
According to a 2019 report from the U.S. Center for Disease Control and Prevention on antibiotic threats in
the United States, each year over 2.8 million antibiotic resistant infections occur in the United States alone.
And, sadly, more than 35,000 people die in USA and 1.2 million people globally, as a result

In addition, according to the WHO, antimicrobial resistance is one of the top ten global health threats. So,
there is no doubt that this is a serious public health issue. To avoid bacterial resistance we need new
antibiotics and that is not easy.

If nothing changes, by 2050, 10 million people are expected to die from drug-resistant diseases every year.
Present condition of Phage
Over the years, phage therapy has evolved, Clinical trials are
ongoing to evaluate the efficacy and safety of phage therapy.

Despite their immense potential, there are also challenges

associated with the use of bacteriophages

Expanded access treatment - is a mechanism in which a physician is

permitted to use an investigational medical product.
Future of Phages

The future of phage therapy looks

The first clinical trial for
promising. The Food and Drug
intravenous (IV) phage therapy
Administration (FDA) continues to
gained FDA approval in 2019.
look into ways to regulate it.

In conclusion, while phage therapy

However, there are still challenges holds great potential, more
to overcome. research is needed before its use is
approved for people.
 Healing after 48hrs by my products

Healing after 48 hrs (other product)

 Outline of project study
How would I improve the
design to include the design
plan of work? Would I select
of experiments for each
different methods ?
phase of the plan of work.

Project
approach Outline of statistical analysis
design for the plan of work.
Complete attached logic
model template based on
the information.

What future work would I What equips I to hit the

like to do upon completing ground running and manage
this project? How would I the setup of the laboratory
further this research? and day to day operations ?

Questions and Answers.

Aim 1 - Determine the types of bacteriophages found in USA’s
agricultural environments and aquatic ecosystems.
Objective - Detection and Isolation of Lytic Bacteriophages from
Environmental Samples.

What are Lytic Bacteriophages?

What are replication methods ?

Why are Lytic Bacteriophages Important?

Environmental Factors Affecting

Bacteriophages in the Environment.

Methods for Detecting and Isolating Lytic

Bacteriophages from Environmental Samples.
 • Lytic bacteriophages, commonly referred
to as phages, are viruses that infect and
replicate within bacterial cells. These

Lytic viruses have a specific affinity for bacteria

and play a crucial role in regulating
bacterial populations in various
Bacteriophages environments. The term "lytic" refers to
the fact that these phages follow a lytic
lifecycle, ultimately causing the host
bacterial cell to burst (lyse) during the
process of viral replication.
Lytic Bacteriophages
• Since phages are still being studied and there is a lot that has not
be discovered, the information I am sharing may be seen as incomplete.
• There are many bacteriophage types, although a few we hear of more than
others. Bacteriophages are very complex viruses that have been around
since the earliest Earth history and have played a crucial role in maintaining
the balance over the population of bacteria on our planet.
• The term "lytic" refers to the fact that these phages follow a lytic lifecycle,
ultimately causing the host bacterial cell to burst (lyse) during the process
of viral replication
• There are so many bacteriophage types of all shapes and sizes, they are all
categorised into one of the two replication methods; lytic and lysogenic
The Lytic Cycle
The virus attaches
itself to a host cell
Attachment and injects its
genetic material
into its cytoplasm.

The virus's genetic

Entry & material takes

control of the host
cell and uses it to
Replication produce
more viruses.

New viruses
Assembly & emerge from
the host cell, often
Release destroying it in the
process.
The Lysogenic Cycle

The virus attaches itself to the

Attachment host cell and injects its genetic
material into the cell.

The virus integrates its genetic

Insertion material into the host cell's
DNA.

The virus lies dormant within

Dormancy the host cell, replicating along
with it.

Stressful conditions can trigger

Initiation of Lytic the virus to enter the lytic
cycle and start producing new
Cycle viruses.
Comparing Lytic and
Lysogenic Cycles
The lytic cycle is fast and efficient,
Speed with new viruses produced
quickly.

The lysogenic cycle allows viruses

to remain dormant for long
Latency periods, waiting for optimal
conditions for replication.

The lytic cycle destroys the host

cell, while the lysogenic cycle
Host Cell Damage often allows the host cell to
survive.

Lytic cycles typically lead to

immediate transmission, while
Transmission lysogenic cycles can spread
stealthily.
 Bacterial Disease Control

• Lytic bacteriophages offer a potential alternative to

antibiotics for treating bacterial infections by specifically
targeting pathogenic bacteria.

Food Safety

• By selectively targeting foodborne pathogens, lytic

bacteriophages could be used as natural antimicrobials to
reduce the risk of foodborne illnesses

Why are Lytic Biotechnology Applications

Bacteriophages • Bacteriophages can be utilized in various biotechnological

processes, including phage display, molecular cloning,
Important? and bacterial detection.
Environmental Factors
Affecting Bacteriophages in the
Environment.​
• Temperature
• Extreme temperatures can influence
bacteriophage activity, with some being more
active in warmer conditions, while others
thrive in colder environments.
• pH Levels
• The acidity or alkalinity of the environment can
impact bacteriophage survival and replication.
Some species prefer neutral pH, while others
thrive in acidic or alkaline conditions.
• Availability of Host Bacteria
• Bacteriophage populations are influenced by
the abundance and diversity of suitable host
bacteria in their environment.
This Photo by Unknown author is licensed under CC BY.
 Methods for Detecting and Isolation
of lytic Phages

Method Basis of detection/enumeration Duration Advantages Limitations

Simple, effective, “gold standard,”
Double agar overlay assay Slow, laborious, high standardization needed for
Virulent phage particles 1–2 days shows active virulence
(DLA) precise reproducibility

Transmission electron
Magnification of virus particles 2–3 day Works well with unknown phages Costly, laborious, high concentration needed
microscopy

Flow cytometry Viral particles 4–12 h Can detect different phages in a sample Expensive, low sensitivity, skilled operator needed

Nanoparticle detection by laser-illuminated optical

NanoSight 5–10 min Rapid runtime Can be used only on clear, concentrated samples
microscopy
2–6 h Overestimation of virulent particles (one
qPCR/RT-qPCR Viral nucleic acid Precise, reproducible
magnitude)

Droplet digital PCR (ddPCR) Viral nucleic acid 2–6 h No need for internal standards Could easily overestimate viral abundance

Time-consuming, surface protein mutants can give

Mass spectrometry Viral protein 2–3 days Accurate in determining PFU
false results
Significant amount of bioinformatics analysis
Illumina sequencing Viral nucleic acid library 3–4 days Not well suited for quantification
needed
PacBio sequencing Viral nucleic acid 2–5 days Prone to sequencing errors Long read lengths
NanoPore sequencing Viral nucleic acid (can be amplified if needed) 8–24 h Compact, rapid, multiple use Expensive, high rate of sequencing read error
Glassware
Test tubes, beakers, flasks, and other
glassware are required for sample
preparation.

Equipment
A spectrophotometer, centrifuge,
pipettes, and a biosafety cabinet are
essential tools for phage isolation.

Media and Reagents

Nutrient broth, agar, antifoam, and
chemicals such as chloroform and
Materials and
sodium chloride are commonly used.
Equipment
Collection of Sample
Seawater
Seawater samples are a common source of phages,
which can infect bacteria found in marine
environments.

Sewage Water
Sewage samples are rich in diverse bacterial
populations, thus useful for the isolation of phages.

Soil Samples
Phages are ubiquitous in soil, where they play a
significant role in bacterial population control.
Sample Preparation
• Quantification
• The concentration of bacteria in the
sample must be determined, usually
by measuring optical density.
• Filtering
• The sample is filtered to remove
bacterial debris and particles that may
interfere in phage isolation
• Storage
• The filtered sample is stored in a cold
environment until further use.
Bacterial Host Culture

E. coli Pseudomonas aeruginosa Staphylococcus Aureus

E. coli is commonly This bacterium is commonly This bacterium is commonly

used as a host for used as a host for the used as a host for the
phage propagation and isolation of phages that isolation of phages that
as a quality control for infect this particular infect this particular
phage purification. bacterium. bacterium.
Purification
Lysis - The sample containing bacteriophages is subjected to a lysis process,
resulting in the release of phages.

Centrifugation - Centrifugation is used to separate the debris and cellular

components from the phage-containing supernatant.

Chloroform Treatment -Chloroform treatment helps to eliminate remaining

bacterial debris and endotoxins that may interfere in phage isolation.

Concentration - The phage-containing supernatant is concentrated by

ultrafiltration or precipitation.
Aim 2: Characterize lytic bacteriophages isolated from
environmental samples.
Objective: Determine the host range and antibacterial
activity of isolates during the project’s first two to three
years.

Morphological Characterization
One-Step Growth Curve
Genetic Characterization
Phage Typing
Phage Receptor Identification
Phage DNA Restriction Analysis
Lysis Kinetics
Introduction
• It's important to note that the success of isolating and detecting lytic
bacteriophages from environmental samples depends on factors like sample
quality, the choice of host bacterium, and the presence of phages in the sample.
The process may require several iterations and optimizations to yield positive
results.
• After Isolation, characterizing lytic bacteriophages involves a series of laboratory
techniques and experiments to understand their properties, including host range,
morphology, and genetic makeup. Here are some common methods used for
characterizing lytic bacteriophages
• Morphological Characterization: Electron microscopy, such as transmission electron microscopy (TEM) or scanning
electron microscopy (SEM
• This research work will provide information about the phage's size, shape, and structural features.
• One-Step Growth Curve: This experiment will measure the phage's latent period (time before phage replication) and burst
size (number of phage particles released per infected host cell).
• This research step will involve infecting a bacterial culture and sampling at regular intervals to measure the increase in
phage concentration.
• Genetic Characterization: Phage DNA will be isolated and analyzed using techniques like polymerase chain reaction (PCR)
and DNA sequencing.
• This research work will provide insights into the phage's genetic composition, including its genome size, structure, and
potential genes involved in host recognition and lysis.
• Phage Typing: Phage typing involves characterizing phages based on their ability to produce distinct patterns of lysis on
different bacterial strains.
• This can be useful for identifying and classifying phages.
• Phage Receptor Identification: Understanding the receptors on the host cell that the phage attaches to can be crucial.
• Techniques like receptor blocking and adsorption inhibition assays can help identify these receptors.
• Phage DNA Restriction Analysis: Using restriction enzymes to digest phage DNA can provide information about its genetic
diversity.
• Lysis Kinetics:
• Measuring the time, it takes for a phage to lyse a population of host cells can provide insights into the phage's efficiency
and potency.
Methods for determining the
host range of lytic phage

Bacterial • Simple method involving the exposure of

susceptibility various bacterial strains to the phage and
testing monitoring for lytic activity.

• Used for assessing the ability of a phage

Spot assays to lyse bacterial lawns by observing
distinct zones of clearing.

• Quantitative approach that allows

Plaque assays determination of phage infectivity and
visualization of individual plaques.
Importance of host range determination
Phage selection
Host range determination
allows researchers to identify
phages with high infectivity
against specific bacterial
strains, enabling precise
targeting and potential
therapeutic applications.
Bacteriophage
ecology
Understanding the host range
helps elucidate the dynamic
interactions between phages
and bacteria in diverse
environments, contributing to
our knowledge of microbial
ecosystems.
Biotechnological
applications
Knowledge of host range helps
in the development of phage-
based detection methods,
biocontrol agents, and as tools
in genetic engineering and
bioremediation.
 The presence of specific
Bacterial receptor receptors on the bacterial
surface determines phage
availability binding and subsequent
infection.

Phages possess receptor-

binding proteins that
Phage receptor match the receptors on
bacterial cells, enabling
recognition successful attachment

Factors and infection.

influencing Host defense

Bacterial defense systems,
such as CRISPR-Cas, can

host range mechanisms

act as barriers and limit
phage infection within
certain bacterial strains.
Antibacterial Activity

To assess the antibacterial activity of

In a time-kill curve assay, inoculate a
the phage, we can perform a time-
bacterial culture with the phage and
kill curve assay or measure the
monitor bacterial growth over time,
reduction in bacterial growth in the
will be studied.
presence of the phage.

Alternatively, we will measure the Finally collected data will be

optical density (OD) or colony- analyzed - to determine the host
forming units (CFUs) of the bacteria range of the phage and its
in the presence and absence of the antibacterial activity against
phage at various time points. different strains
Aim 3: To examine the interactions of lytic phage isolates with
foodborne pathogens in food matrices of significance to USA.
Objective: Conduct suspension and growth studies to examine
phage pathogen interactions and growth dynamics in years three
and four of the project.

• Foodborne Pathogens
• Role in Controlling Foodborne Pathogens
• Interactions Between Lytic Phages and Foodborne
Pathogens
• The Significance of Studying Interactions for Food
Safety
ExaminingLytic Phage
Interactions with
Foodborne Pathogens in
Food Matrices
As food safety challenges increase, understanding the interactions
between lytic phages and foodborne pathogens in food matrices
becomes increasingly important.
The interactions between lytic phage isolates and foodborne pathogens in
food matrices are of significant interest in the field of food safety and
microbiology.
Studying phage-pathogen interactions and growth dynamics through
suspension and growth studies will be a valuable approach during the
research to understand the dynamics of bacteriophages (phages) and their
impact on bacterial pathogens.

in third and fourth years of the project we will be able to understand insights
into phage therapy, phage ecology, and bacterial resistance mechanisms.
Below are some examinations of these interactions:

Foodborne Pathogens: Overview and Risks
Salmonella
A bacterium commonly found in
in contaminated food, causing
gastroenteritis and other illnesses.
illnesses. Salmonella is a leading
leading cause of foodborne illness
illness worldwide.
Listeria monocytogenes
A bacterium that can cause severe
severe infections in vulnerable
populations, including pregnant
pregnant women and
immunocompromised individuals.
individuals. Listeria is particularly
particularly concerning because it
because it can grow at refrigeration
refrigeration temperatures.
Salmonella, Shiga toxin-
producing E. coli,
Campylobacter, and
Listeria monocytogenes
Escherichia coli
A bacterium best known for
causing urinary tract infections, but
infections, but some strains can
can cause severe gastrointestinal
gastrointestinal symptoms. E. coli
coli infections can be particularly
particularly dangerous for young
young children and the elderly.
elderly.
Sample

• a. Dairy Products: Milk, cheese, and yogurt are susceptible to contamination with pathogens like
Listeria and E. coli. Lytic phages can be added to these products to target and reduce pathogen
populations.
• b. Meat and Poultry: Raw and processed meats are often contaminated with Salmonella,
Campylobacter, and E. coli. Lytic phages can be applied as antimicrobial interventions during
processing to enhance food safety.
• c. Seafood: Seafood products, such as oysters and shrimp, can harbor Vibrio species, which are
harmful pathogens. Lytic phages specific to Vibrio can be used to reduce contamination.
• d. Fresh Produce: Fruits and vegetables can be contaminated with pathogens like E. coli and
Salmonella. Lytic phages can be employed in wash solutions or as post-harvest treatments to
reduce the risk of contamination.
 Interactions Between Lytic Phages and Foodborne Pathogens

Factors Influencing Interactions

The ability of phages to control foodborne pathogens depends on a variety of factors, including the
concentration and diversity of the bacterial community, the presence of phage-resistant mutants, and the
accessibility of bacteria to phages.
Experimental Approaches
Researchers use a variety of experimental methods to examine phage-bacteria interactions, including spot
testing, plaque assays, and high-throughput sequencing. These approaches can help identify effective phages
and optimal application methods.
Case Studies and Findings
Recent studies have shown promising results for the use of lytic phages in controlling foodborne pathogens in
dairy, meat, and produce. Examples include the use of phage cocktails to control L. monocytogenes in cheese
and the use of phage mixtures to control Salmonella and E. coli in meat products.
Aim 4: To examine the impact
of treatment duration,
concentration, and phage The impact of treatment duration
cocktails on phage pathogen
reduction. • Treatment Duration
Objective: Conduct studies to • Phage Concentration
evaluate the duration, • Phage Cocktails
concentration, and
combination of Data Analysis
phage treatment’s impact on
its ability to control foodborne
pathogen growth during years Reporting and Interpretation
three and four of the project.
 Short Duration: A shorter treatment duration may not
provide enough time for phages to replicate and reach
sufficient numbers to effectively reduce the pathogen
population. In some cases, it might lead to incomplete
pathogen clearance.

Treatment Optimal Duration: The optimal treatment duration can vary

depending on the specific phage-host system and the

Duration infection site. It is typically determined through empirical

studies and may range from a few days to several weeks.

Extended Duration: Prolonged treatment may increase the

risk of phage resistance development in bacteria. It may also
have practical limitations for patient compliance and cost.
Phage Concentration

• Low Concentration: Using a low phage concentration might not effectively reduce
the pathogen population, especially in cases of high bacterial load. It could result in
treatment failure.
• Optimal Concentration: The ideal phage concentration should be sufficient to infect
and replicate within the target bacteria rapidly. The concentration required can vary
widely based on the specific phage-bacteria interaction.
• High Concentration: Excessively high phage concentrations may not necessarily
improve pathogen reduction and can increase the risk of phage-resistant mutants
emerging.
Phage Cocktails

• Single Phage: Using a single phage strain in therapy can be effective when there is a
highly specific and well-characterized interaction between the phage and the target
pathogen. However, it carries a higher risk of resistance development.
• Phage Cocktails: Phage cocktails consist of multiple phage strains targeting the
same or different bacterial species. They can increase the spectrum of activity and
reduce the likelihood of resistance.
• Cocktail Composition: The selection of phages for a cocktail should be based on
their ability to work synergistically and cover a broad range of target bacteria. The
proportions of each phage in the cocktail can also affect treatment outcomes.
Reporting and Interpretation

• The detailed report will be prepared and summarized the experimental setup,
methods, results, and statistical analysis.
• Discussion will bae carried out on findings, including which treatment
conditions are most effective in controlling foodborne pathogen growth.
• Recommendations from the supervisor will be applicable for practical
applications of phage treatment in the food industry based on the study's
outcomes.
• Potential limitations and areas for future research will be considered
Data Analysis
The collected data will be
analyzed by using appropriate
statistical methods (e.g.,
ANOVA, t-tests) to compare
the different treatment
groups.
The treatment conditions will
be determined (duration,
concentration, and
combination) that result in the
most significant reduction in
pathogen counts.
 Outline of project study
design to include the How would I improve the
design of experiments for plan of work? Would I
each phase of the plan of select different methods ?
work.

Project
approach Outline of statistical
analysis design for the
Complete attached logic
model template based on
plan of work. the information.

What equips I to hit the

What future work would I
ground running and
like to do upon completing
manage the setup of the
this project? How would I
laboratory and day to day
further this research?
operations ?

Questions and Answers.

Question 2. How would I
improve the plan of work?
Would I select different
methods? If so, why?

The success of the Phages project hinges on an effective plan of work and
and carefully selected methods. Let's explore how we can achieve this!
Certainly, I can help to improve my research plan. To do so effectively, I'll need
to study in more details about our specific research methods, project and
feasibility. However, I can provide a general structure and tips to enhance our
research plan:
Literature Review:
· Summarize relevant research in our field.
· Identify gaps in the existing literature that our research will address.
· Show how our research builds on previous work.
Methodology:
· Describe our research methods in detail. This includes data collection and
analysis techniques.
· Justify our choice of methods. Explain why they are appropriate for our
research.
· Discuss any ethical considerations, including how we will obtain informed
consent if necessary.
Assessing the Current Plan of Work
1 Strengths & Weaknesses

We'll identify the strengths and weaknesses of the current plan to understand areas that
areas that need improvement.

2 Project Objectives & Milestones

By analyzing project objectives and milestones, we can ensure that they align with our
overall vision.
Identifying and Prioritizing Key Methods
Methods
Exploring Research Methods

We'll delve into various research methods that can be applied to the Phages project.

Feasibility & Efficiency

Considering factors like feasibility and efficiency, we'll assess which methods can yield the best
results.

Resource Requirements

Identifying the resources required for each method is crucial to ensure their successful
implementation.
Evaluating Pros and Cons
1 Advantages & Disadvantages

We'll carefully analyze the advantages and disadvantages of each method to make informed
decisions.

2 Impact on Project Outcomes

Considering the potential impact of each method on the Phages project outcomes will guide
our decision-making process.
Selecting the Most Suitable Methods
1 Alignment with Project Objectives

We'll ensure that the selected methods are aligned with the project's objectives and goals.

2 Compatibility with Resources

Assessing the compatibility of methods with the available resources will facilitate their
successful implementation.
Certainly, the selection of research methods can vary significantly depending on cost, time constraints, the nature
of the research, the research questions or objectives, and the available resources. The given methods will be
further studied to identify fulfilment. Before changing a new methods some other factors will be considered,
factors as like–
Ethical Considerations
Validity and Reliability
Reproducibility and validation of methods
Supervisor’s opinion
Cleaning Validation
Implementing and Monitoring Progress

1 Develop Timeline & Action Plan

Creating a detailed timeline and action plan will help us stay organized and focused on
achieving our goals.

2 Regularly Assess Progress

Consistently monitoring progress allows us to make necessary adjustments and ensure

that we're on track.

3 Make Necessary Adjustments

We'll make any adjustments needed along the way to improve the plan and enhance
project outcomes.
Conclusion
Recapping the Importance Highlighting Selected Methods

In conclusion, we'll recap the importance of We'll highlight the methods we've chosen and
improving the plan of work for the Phages discuss their potential impact on the Phages
project. project.
Laboratory Procedures:
Provide step-by-step protocols for laboratory experiments or analyses.
Include details about equipment, reagents, and materials required.
Highlight quality control measures to ensure data accuracy.

Data Analysis:
• Outline the statistical or analytical techniques we will employ.
• Explain how we will interpret and present our findings.
• Address any potential challenges or limitations in our analysis.
Timeline:
• Create a realistic timeline for our research, including milestones and deadlines.
• Consider potential setbacks and allocate time for unexpected delays.
Budget:
• Estimate the budget required for our research, including expenses for materials,
equipment, participant compensation, or travel.
•Review and Proofreading:
•Before finalizing our research plan, review it for clarity, coherence, and grammar.
•Seek feedback from peers or mentors to refine our plan further.
 Outline of project study
design to include the How would I improve the
design of experiments for plan of work? Would I
each phase of the plan of select different methods ?
work.

Project
approach Outline of statistical
analysis design for the
Complete attached logic
model template based on
plan of work. the information.

What equips I to hit the

What future work would I
ground running and
like to do upon completing
manage the setup of the
this project? How would I
laboratory and day to day
further this research?
operations ?

Questions and Answers.

Question-3 Outline
of statistical analysis
design for the
proposed plan of
work.
Now I will outline the statistical analysis design for the Phages
Project which aims to identify the role of phages in ecosystem
regulation.
• Designing a statistical analysis for the identification of phages that minimize foodborne illness and its associated public
health and economic losses is a complex task that involves several steps.

• Define Research Objectives and Hypotheses

• Clearly state the research objectives, such as identifying phages that are effective against specific foodborne pathogens.

• Formulate testable hypotheses, such as "Phages A, B, and C are more effective in reducing foodborne illness compared
to phages X, Y, and Z."

• Data Collection

• Collect data on foodborne pathogens, phage isolates, food samples, and relevant variables.

• Ensure the data is representative of the target population and is collected in a standardized manner.

• Experimental Design:

• Design experiments to evaluate the effectiveness of phages in reducing foodborne pathogens in different food matrices.

• Consider factors like phage concentration, exposure time, temperature, and food type.
 Identify

• Identify significant factors

• The statistical analysis design aims to identify
significant factors that affect the abundance and
diversity of phages and bacterial populations.

Objective of Model

Statistical • Model the interactions

• The statistical design aims to model the interactions
Analysis between phages, bacteria, and the environmental
factors that regulate them.
Design Predict

• Predict the outcomes

• The statistical design aims to predict the outcomes of
different scenarios that may influence the phages
and bacterial populations.
 Exploratory Analysis

Correlation
Analysis

Statistical
Analysis Regression Analysis
Techniques
• Exploratory Analysis
• Data exploration will be performed to understand the distribution,
skewness, and Kurtosis of the data.
• Correlation Analysis
• We will use correlation analysis to understand the relationship
between different variables and to identify significant factors that influence
the phages and bacterial populations.
• Regression Analysis
• Regression analysis will be used to model the interactions among variables
and to predict the outcomes of different scenarios.
 • Bacterial Growth Rates
Expected • Phage-Host Interactions

Outcomes and • Community Structure

Interpretation
Bacterial Growth Rates
Expected outcomes include
identifying the factors that
regulate bacterial and phage
populations and quantifying
their relative contribution to
ecosystem regulation.
Phage-Host Interactions
The statistical analysis will help
us understand the role of
phages in regulating bacterial
populations and how their
interactions with hosts affect
the ecosystem.
Community Structure
The statistical analysis will help
us understand the microbial
community structure and how
it is affected by environmental
factors and the interactions
among organisms.
 Metagenomics
• We will use metagenomics to extract DNA
and RNA from environmental samples which
allow us to understand the microbial
community structure and function.
Data Collection
Methods Environmental Factors
• We will measure environmental factors such
as temperature, pH, salinity, and nutrients
to understand how they influence the
abundance and diversity of phages and bacteria.

• Conclusion-
Conclusion
• The statistical analysis design for the Work Phages
Project aims to provide insights into the role of phages
in regulating bacterial populations and the ecological
processes that they participate in.
• This project is part of ongoing research into microbial
ecology, and we hope that the results will help us
create a better understanding of how ecosystems
function.
 Outline of project study
design to include the How would I improve the
design of experiments for plan of work? Would I
each phase of the plan of select different methods ?
work.

Project
approach Outline of statistical
analysis design for the
Complete attached logic
model template based on
plan of work. the information.

What equips I to hit the

What future work would I
ground running and
like to do upon completing
manage the setup of the
this project? How would I
laboratory and day to day
further this research?
operations ?

Questions and Answers.

Logic
Model

Word file
 Outline of project study
design to include the How would I improve the
design of experiments for plan of work? Would I
each phase of the plan of select different methods ?
work.

Project
approach Outline of statistical
analysis design for the
Complete attached logic
model template based on
plan of work. the information.

What equips I to hit the

What future work would I
ground running and
like to do upon completing
manage the setup of the
this project? How would I
laboratory and day to day
further this research?
operations ?

Questions and Answers.

Future Work upon
Completing the
Phages Project:
Furthering the
Research
The future work after completing the Phages project. We will explore the
potential implications, current findings, further research, applications in
different fields, collaboration opportunities, challenges, and the
importance of continued research.
Potential Implications of the Phages
Project
Revolutionize Reduce Enhance Precision
Antibiotic Environmental Medicine
Resistance Impact
By utilizing phages,
Phages have the potential Phage therapy offers a personalized treatments
to combat antibiotic more targeted and can be developed to
resistance by targeting environmentally friendly specifically target bacteria
specific bacteria, opening solution compared to in individual patients.
doors for new treatments. traditional antibiotics.
Identifying Areas for Further
Research

Mechanisms of Genetic Modification Clinical Trials and

Phage Infection of Phages Efficacy Studies

Further investigation will Exploring the genetic Conducting rigorous clinical

needed to understand the modification of phages can trials and efficacy studies is
intricate mechanisms behind potentially enhance their essential to establish the
phage infection and replication effectiveness and expand their safety and efficacy of phage
processes. therapeutic applications. therapy.
Potential Applications in Different
Fields
Agriculture
Phage-based solutions can combat
agricultural pathogens, reduce
pesticide use, and promote
sustainable farming.
1 Medical Field
Phages hold promise for treating
bacterial infections, improving wound
2 healing, and managing chronic
conditions.
3 Food Industry
Phages offer a natural approach to
control foodborne pathogens, reducing
the risk of contamination and ensuring
food safety.
Collaboration Opportunities with
Organizations and Research Groups
Pharmaceutical Companies

Collaborating with pharmaceutical companies can accelerate the development and

commercialization of phage-based therapies.

Academic Institutions

Partnering with academic institutions allows for interdisciplinary research, knowledge exchange,
and access to specialized expertise.

Government Agencies

Collaboration with government agencies fosters regulatory support and paves the way for policy
changes promoting phage therapy.
Challenges and Limitations to
Overcome in Future Work
1 Bacteriophage Diversity

Unlocking the vast potential of diverse phage populations and harnessing their
unique traits poses a challenge.

2 Regulatory Approval

Navigating the complex regulatory landscape to secure necessary approvals for

phage therapies requires extensive research and collaboration.

3 Resistance Development

Anticipating and mitigating the development of phage resistance in target bacteria is

crucial for long-term effectiveness.
Conclusion and
Importance of Continued
Research
In conclusion, further research in phages is essential to unlock their full
potential, revolutionize treatments, combat antibiotic resistance, and
improve human and environmental health. Continued dedication to phage
research will shape the future of medicine and contribute to a healthier,
more sustainable world.
 Outline of project study
design to include the How would I improve the
design of experiments for plan of work? Would I
each phase of the plan of select different methods ?
work.

Project
approach Outline of statistical
analysis design for the
Complete attached logic
model template based on
plan of work. the information.

What equips I to hit the

What future work would I
ground running and
like to do upon completing
manage the setup of the
this project? How would I
laboratory and day to day
further this research?
operations ?

Questions and Answers.

What equips I to hit the
ground running and
manage the setup of the
laboratory and day to day
operations?
Uncover the secrets to supercharged laboratory management. From
assembling an extraordinary team to implementing cutting-edge
procedures.
Skills Required for Managing a
Laboratory Setup
Technical Expertise

Master in the scientific techniques and equipment involved in the laboratory setup.

Organizational Skills

Efficiently manage resources, schedules, and budgets for seamless operations.

Problem Solving

Tackle unexpected challenges and troubleshoot issues for smooth functioning.

 Understanding Laboratory
Operations and Regulations
Regulations

Operational Procedures Regulatory Compliance

Implement standard operating procedures Stay up-to-date with industry regulations and
(SOPs) for safety, efficiency, and compliance. maintain required certifications.
Establishing Standard Procedures and
and Protocols
1 Analyze Current Processes

Identify areas of improvement and develop standardized protocols.

2 Document SOPs

Create comprehensive standard operating procedures for consistent workflows.

3 Implement Training Programs

Train team members on SOPs to ensure proper execution and compliance.

Equipment and Resource Management

Inventory Control

Maintain an organized inventory system for efficient equipment and resource

management.

Preventive Maintenance

Schedule regular maintenance to ensure optimal performance of laboratory equipment.

Procurement Strategies

Implement cost-effective sourcing and purchasing strategies for necessary supplies.

Continual Performance
Evaluation and
Improvement

• Performance Monitoring
• Regularly assess individual
and team performance to
identify areas
of improvement.
• Implement Feedback Loops
• Encourage open
communication
and feedback to drive
continuous improvement.
Conclusion​

• Studying viruses has taught us a lot about the

human body and led to important
medical discoveries.
• Understanding these processes is crucial in
developing treatments and preventing future
outbreaks of viral infections.
• By understanding lytic and lysogenic cycles, we
can better appreciate the complexities of viral
infections. Studying viruses can lead to important
medical discoveries, and improved understanding
is crucial for developing treatments and
preventing future outbreaks.