Description
You are tasked with making an informational newsletter pertaining to 6 topics for someone with a high school education.Examples:I have some Newsletter examples from an upper division Microbiology course and so the topics are really different than what you are going to cover, but you can get an idea of what a newsletter looks like.These students obviously had some different requirements than you – some students put in some fun games (which are optional for you) and a personal perspective at the end (which is optional for you).So, while these are good examples of what a newsletter looks like (a cross between a newspaper and a magazine), you will still have to follow the instructions for your newsletter in terms of topics and length.
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W I N T E R
2 0 1 8 :
D E C E M B E R
E D I T I O N
the
Microbiome
And You
Let’s Explore!
Test your knowledge before diving
in!
1) Bacterial cells may be sphericalshaped coccus, rod-shaped bacillus,
and spiral.
A – True
B – False
2) Spherical shaped bacterial cells that
divide and remain attached in a
chainlike pattern are called:
A – Staphylococci C – Sarcinae
B – Streptobacilli
D – Streptococci
3) Living organisms are grouped
according to similar characteristics
and given a unique scientific name.
A – True
B – False
Answers: A, D, A
Do you know what’s in your
body?
Microorganisms play many roles in both land and water. They
are of critical importance to the sustainability of life, resources
for biotechnology, incredibly useful for research in
understanding biological interactions, and a part of our normal
microbiota. The human microbiome is a collection of
microorganisms that reside on or within the human body, and
is necessary to maintain good health.
Save the Date!
Conference
Event
Conference
3-4 December 2018
Water
Sustainability and
Reuse
Technologies
5-6 December 2018
5-7 December 2018
Exploring Human
Host – Microbiome
Interactions in
Health and Disease
Congress on
Clinical
Microbiology and
Infectious Diseases
THE MICROBIOME AND YOU
WINTER 2018
The Diversity of Microbes
Microbes can be found in varying shapes and
sizes, unique environments, and are useful in a
number of metabolic processes.
Caulobacter crescentus
A motile, gram-negative, oligotrophic bacterium, that is
able to live in environments that offer very low levels of
nutrients. It exists in two forms. The swarmer swims
around using its single flagellum, while the stalked uses
that flagellum to grow a stalk with an adhesive holdfast
to adhere to surfaces. When measured, this sticky
sugary substance produced is so strong it takes about 5
tonnes per square inch to remove. It generally doesn’t
cause disease.
Vibrio fischeri
Methanococcus jannaschii
This is a thermophillic methanogenic
archaea. It was discovered living in
extremely hot and oxygen-deprived waters at
the bottom of oceans in hypothermal vents.
Also, it’s the first archaeon to have its
genome fully sequenced. Methanogens are
crucial in anaerobic environments. They
convert organic compounds into methane,
allowing pathways for other compounds in
the environment to escape into the
atmosphere.
A unique bacterium that is motile, gram-negative, and
rod-shaped with bioluminescent properties. It is
frequently found in symbiotic relationships with marine
animals, such as the bobtail squid. These bacteria help
the squid glow, erasing the squids shadow, to protect it
from predators as it forages at night. In turn, the squid
provides shelter and a stable source of nutrients to the
bacteria.
Zaire ebolavirus
A species of the genus Ebolavirus that is threadlike and
cylindrical/tubular in shape. It contains a viral
envelope, matrix, and nucleocapsid components. Its
genomic material is composed of linear, single-stranded,
negative-sense RNA. This species is one of five to cause
the Ebola Virus Disease, a severe and often fatal
hemorrhagic fever in humans and other mammals. It is
transmitted to humans from wild animals and spread in
the human population via direct transmission of those
infected or deceased from the disease.
2
2
1
THE MICROBIOME AND YOU
WINTER 2018
New Advances in Gene Editing: What is
CRISPR?
What if one day somebody told you, you could
create your very own designer baby, select for
certain traits while inhibiting others. Would
you? This is just one of the ideas emerging from
the advances with CRISPR (Clustered
Regularly Interspaced Short Palindromic
Repeats) and its use in gene editing.
placed inside. This system would then serve as
a genetic memory, to help detect and destroy
future invaders.
After years of research and new developments
stemming from the idea behind CRISPR, it
was found that an enzyme, Cas9, could use
CRISPR sequences as a guide to recognize and
cleave specific strands of DNA that would be
complementary to the CRISPR sequence.
CRISPR/Cas9, a new technology, can now be
used to edit genes within organisms. This
allows researchers to easily alter DNA
sequences and modify gene function. It could
potentially correct genetic defects, improve
crops, and treat diseases.
How did it start? The idea arose from a
naturally occurring process in bacteria. In 1993,
it was proposed that CRISPRs served as a
bacterial immune system, to defend against
invading viruses. The fighting bacteria would
cut pieces of enzyme from the invading virus,
and store it within itself as a specific repeating
sequence with the genetic code of the virus
But what’s next? The author’s opinions…
There are many benefits from using CRISPR. In a laboratory setting, it is more cost effective and
precise because it is able to target specific DNA. In agriculture, it has been used in crops to
improve yield and drought tolerance. The possibility of using this system to some day cure disease
and cancer is beyond extraordinary. One potential application is to create gene drives. These are
genetic systems that can increase the chances of a particular trait being passed from parent to
offspring. It could possibly be used to control the spread of disease. But do we know what the
outcomes will be? Could there be a shift in genetic diversity? What happens when this tool gets
used for genetic modifications in human embryos? The use of this tool in its present time is
astounding, but its potential use in other aspects raises some ethical concerns.
3
THE MICROBIOME AND YOU
WINTER 2018
Microbial Biotechnology
Its importance in every day life
Antibiotics
Antibiotics are antimicrobial agents that are usually
produced naturally by a bacterium or fungus. It was
first discovered by Alexander Fleming, when he
exhibited inhibited growth of bacterium around the
mold Penicillium chrysogenum. The mold’s active
inhibitor was termed penicillin, and is an antibiotic
readily known today.
Consumer Goods
There are various bacteria and yeasts that carry out
catabolic reactions called fermentation. This process is
a crucial part of the production of many beverages and
foods consumed. Without these important microbes we
would not have delicious treats such as beer, wine,
cheese, yogurt, pickled vegetables, or soy sauce!
Vaccines
Vaccination is active immunity that is acquired
artificially. Vaccines introduce antigens to the body
when killed or inactivated bacteria get injected into the
body, which stimulates an immune response without
causing infection. This is the safest and most effective
means of controlling infectious diseases.
Wastewater Management
Sewage (wastewater) treatment is critical in preventing
raw, untreated sewage from being discharged into
rivers or oceans. There are a number of steps in the
treatment process. Microorganisms play an important
role in oxidizing the organic matter before the effluent
is disinfected by chlorination and released.
4
2
1
THE MICROBIOME AND YOU
WINTER 2018
Clostridioides difficile is a gram-positive, spore
forming, anaerobic, intestinal pathogen that
causes life-threatening diarrhea and colitis,
which mostly affects people who have had both
recent medical care and antibiotics. This
bacterium is highly contagious and resilient. In
it’s spore form, it is resistant to antibiotics and
can remain in the intestine, which allows for
recurrence even after treatment. Upon exposure
to the intestine, C. difficile germinates and with
resistance from the normal microbiota, it
colonizes the colon and produces toxins,
enterotoxin A and cytotoxin B. These toxins
inhibit actin polymerization, which eventually
leads to cell death. C. difficile then sporulates
and exits the body through diarrhea.
person. Poor infection control can increase the
spread within a facility, and also facility to
facility when an infected person is transferred. It
was also found that more than 100,000 infections
develop among those in nursing homes each year
and that women and Caucasians are at increased
risk. C. difficile is most common among patients,
healthcare workers, contaminated hospitals and
other healthcare related facility. The major risks
are antibiotic exposure within the preceding 2-3
months, advanced age (65 and older),
hospitalization, and long-term healthcare
facilities.
In recent studies, it has been suggested that these
traditional risk factors, antibiotics and
hospitalization, may no longer be the only
explanation. A researcher, Dr. Alice Guh,
discussed a study where a common food additive
could enhance virulence of C. difficile. She also
believes some common medications, such as
antacids, could disrupt the microbiome and also
play a role. The rate at which this infection is
rising causes alarm, and requires much of our
attention in assessing how to prevent this
infection from spreading.
Patients at highest risk are those who take
antibiotics. Studies have shown that 30-50
percent of antibiotics prescribed in hospitals are
unnecessary or incorrect. When these
antibiotics are taken, the patient’s normal and
beneficial bacteria that can help protect against
infection may get suppressed for a period of
time. During this time is when patients may get
infected with C. difficile if they come into contact
with a contaminated surface or person to
5
2
1
THE MICROBIOME AND YOU
WINTER 2018
Time to perform an experiment!
Serial Dilutions
Let’s say you wanted to know the number of bacteria in a sample, such as milk. The number of
bacteria in this sample would far exceed that which can be directly counted on a single plate. A
common method is to use a viable plate count, which is obtained through serial dilutions. Samples are
taken from the dilution series and spread over an agar plate. After an incubation period, colonies will
form on the plate and can be counted. These colonies are colony forming units (CFU), which
represent an isolated cell from the inoculation solution. Viable plates, the ones that can be used to
accurately estimate the total number of microorganisms, are those that will contain 30-300 CFUs.
This number can then be used in a simple equation to determine the concentration of the sample in its
original form.
Steps:
1. Determine the dilutions of each dilution tube (this is the first series of dilutions)
Remove 1mL from the original culture and add to 9mL of sterile diluent to create a 1:10
dilution. Continue the dilution series by collecting 1mL from each preceding dilution and
continuing until the desired dilution is obtained. Transfer 0.1mL of each diluted sample onto
a plate. Incubate for a set amount of time.
2. Determine which plate is the countable plate
After the plates have grown CFUs, choose the least diluted plate that has 30-300 CFUs. In
this example it would be plate #3 with 70 colonies.
3. Calculate the concentration of the original sample
The number of colonies counted is divided by the final dilution (dilution factor x volume
plated). Therefore, the original sample in this experiment contains an estimated 700,000
CFU/mL.
6
THE MICROBIOME AND YOU
WINTER 2018
References:
Dalton, Clayton. “Dangerous Infection Tied To Hospitals Now Becoming Common Outside Them.”
Health News from NPR, NPR, 25 November 2018, https://www.npr.org/sections/healthshots/2018/11/25/657861409/dangerous-infection-tied-to-hospitals-now-becoming-common-outsidethem.
Dance, Amber. “Ten bacteria with real-life superpowers.” Earth, BBC, 29 July 2015,
http://www.bbc.com/earth/story/20150730-ten-bacteria-with-superpowers.
DeWeerdt, Sarah E. “The First Sequenced Extremophile.” Genome News Network, J. Craig Venter
Institute, 1 February 2002, http://www.genomenewsnetwork.org/articles/02_02/extremo1.shtml.
“Ebola virus disease.” World Health Organization, WHO, 12 February 2018, http://www.who.int/newsroom/fact-sheets/detail/ebola-virus-disease.
Heinlen, Latisha and Jimmy D. Ballard. “Clostridium difficile Infection.” NCBI, National Center for
Biotechnology Information, 1 September 2011,
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935936/.
“Nearly half a million Americans suffered from Clostridium difficile infections in a single year.” CDC
Newsroom, Centers for Disease Control and Prevention, 22 March 2017,
https://www.cdc.gov/media/releases/2015/p0225-clostridium-difficile.html.
O’Brien, Miles and Marsha Walton. “Glowing Squid.” Science Nation, National Science Foundation,
22 November 2010, https://www.nsf.gov/news/special_reports/science_nation/glowingsquid.jsp.
“Questions and Answers about CRISPR.” Broad Institute, Broad Institute, 2018,
https://www.broadinstitute.org/what-broad/areas-focus/project-spotlight/questions-and-answersabout-crispr.
Sandhu, Brindar, K. and Shonna M. McBride. “Clostridioides difficile.” Trends in Microbiology,
Elsevier, Inc., 1 December 2018, https://www.cell.com/trends/microbiology/fulltext/S0966842X(18)30200-2.
Tortora, Gerard, Funke, Berdell, Case, Christine. Microbiology an Introduction. Boston: Pearson, 2018.
Print
Vidyasagar, Aparna. “What is CRISPR?” Live Science, Purch, 20 April 2018,
https://www.livescience.com/58790-crispr-explained.html.
AUGUST 24th, 2022
Wednesday
Issue 01
PROTOZO-INE
M A KI N G M I C RO , M A C RO
ASEPTIC TECHNIQUE
WHAT’S
/ NEW /
PAGE 1
ASEPTIC TECHNIQUE
Caption: A masterful display of the streak plate method – with distinctive differences between the four
quadrants. Sterilization of the inoculation loop is important before, during and after plate treatment.
Subsequent streaks allow for the formation of colony forming units (CFU). Mixed sample specimens can
culture specific pure cultures by transfer to another plate – but requires the ability to recognize the
bacteria of interest on agar plate morphology.
POP QUIZ: ADVANCEMENTS IN
MICROBIOLOGY
Check your knowledge on PCR
————– CARY B. NULLIS
One of the most used molecular techniques
that we use to this day is polymerase chain
reaction (PCR). See if you know the answers
to the following questions and learn a little
more about how medical professionals
perform this technique and utilize the results!
Question #1: True or False
Kary B. Mullis was the founder of the PCR
technique.
Question #2:
What is PCR used for?
A. Detection of viral nucleic acids like
SARS-CoV-2
B. Diagnosing inherited diseases by
amount of gene
C. Studying concepts related to gene
expression
D. All the above
Question #3: True or False
PCR can be performed on RNA using an
enzyme called reverse transcriptase to make
cDNA template. This technique is called
reverse-transcription PCR (rtPCR).
1
Question #4:
Which of the following are
reagents used in PCR?
A. Primers/oligonucleotides
B. DNA polymerase
C. Deoxynucleotides
D. Target DNA/RNA
E. All of the above
Question #5:
All of the following is true except:
A. A high temperature is
during PCR needed to break
the hydrogen bond between
nucleotides in the target
DNA
B. PCR cycles between three
stages with varying
temperatures
C. DNA polymerase is use
because it’s an enzyme that
will not denature under high
temperatures
D. PCR can be performed at
an isothermal rate (constant
temperature)
POP QUIZ:
ADVANCEMENTS IN
MICROBIOLOGY
PAGE 2
RETREAT FROM THIS
SUMMER TREAT
CULTURE CORNER
(micro)
SAVINGS
PAGE 3
RECOMBINANT DNA:
HOW IT WORKS
SEAN’S SOAPBOX:
GET VAXXED
PAGE 4
WORKS CITED
Know the answers? Fill in your
responses on the feedback sheet
and enter a chance to win a small
prize!
Issue01
AUGUST 24th, 2022
CULTURE CORNER
Our favorite recipes for that
perfect specimen
————– PETRI DISH
MANNITOL SALT AGAR
Having trouble identifying S. aureus in
your primordial soup? We’ve got the
perfect agar recipe for that differential
media that you have been desperately
searching for! The only thing you’ll be
seeing are Staphylococcus and its species
because they tolerate high salt levels well.
Adjust the ingredient amount to your
liking but ensure that it’s balanced for a
7.5% salt concentration. Make sure you
have the following:
Caption: A microscopic menace, Listeria monocytogenes, was found to infect 23 individuals across a
total of 10 states. This is an example of vehicle transmission and most likely the result of being
produced in unsanitary conditions!
Retreat from this summer treat
Listeria outbreak from Big Olaf Icecream
————– EI SCREAM
The CDC, as of August 4th, has announced
a total recall of ice cream manufactured by
Big Olaf creamery due to contamination
with Listeria monocytogenes, the causative
agent of the disease listeriosis. This disease
is on the notifiable infectious diseases list,
meaning infections must be reported to the
federal level by law. The more information
known, such as the chain of transmission
allows for enactment of control plans for
disease mitigation like isolating infected
individuals or destroying the source of the
disease. Consumers are advised to discard
and stop consumption of all batches with
expiration date 6/30/2022 and rigorously
disinfect possible fomites like utensils that
touched the contaminant.
Advancements in molecular biology
now allow us the ability to whole
genome sequence, identifying all base
pairs in a bacterial genome and the
exact placement. This microbiological
fingerprint provides an excellent tool
to monitor epidemiology as a
reference genome can be matched
with individual genomes to
differentiate isolates as well as
monitor mutations that affect
pathogenicity. Development of the
whole genome sequence technique
has enabled testing of low –
moderate risk classified foods from
celery, apples, and ice cream in the
United States. Stay safe by following
CDC guidelines and reporting on
possible cases for a healthier
community!
Sodium Chloride…………….75.0 g
D- Mannitol……………………10.0 g
Casein Peptone……………. 5.0 g
Meat Peptone………………. 5.0 g
Beef Extract…………………. 1.0 g
Phenol Red…………..………..25.0 mg
Agar…………………………….. 15.0 g
Demineralized Water… 1000.0 mL
Disinfect your work area with 10% bleach.
Wear proper PPE to avoid contamination.
In a large saucepan, add agar and
demineralized water. Heat until agar is
dissolved. Stirring, add peptone, mannitol,
and salt to broth. Pour well mixed broth
into agar plate container, covering with
the agar plate lid slightly. Add sample and
spread gently over newly solidified agar
mixture. Incubate at 33-37 degrees Celsius
for 24-48 hours and observe for visual
changes.
d
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Issue01
AUGUST 24th, 2022
RECOMBINANT DNA: HOW IT WORKS
bacterium
0 Vector, such as a
:asmkl,is isola; .
0
e
DNA containing the gene o
interest from a different species is
cleaved by an enzyme into
fragments.
Plasmid
!— —-:a111~- – Bacterial
chromosome
ecombina t
{pla m· )
0 The desired gene is selected and inserted into a plasmid.
0 The plasmid is taken up by a cell,
such as a bacterium.
C) Cells with the gene of in erest are cloned
with either of ~o goals in mind.
~ Create and har:est
/
copies of a gen ✓
OR
‘-
~ Create and harvest
~ protein products of a gene.
Plasmid
RNA
Protein product
Gene encoding protein for
pest resistance is inserted
into plant cells.
Gene encoding degradative
enzyme to clean up toxic
waste is inse ed into
bacterial cells.
Amylase , cellulase, and other
enzymes prepare fabrics for
clothing manufacture.
Human growth hor mone
treats s unfed growth .
Caption: A generalized overview of how humans use genetically modified organisms to produce one of two pathways: 1) harvest multiple copies of
a gene or 2) harvest the protein created by the insert gene. The most used organisms for recombinant DNA are E. coli and S. cerevisiae. The
preferred organism for production of insulin is S. cerevisiae due to it’s ability for many post-translational modifications including phosphorylations,
acetylation and glycosylation. Post-translational modifiations are important as they make the synthesized structure biologically active. Adapted from
Microbiology: an Introduction (244) by G. Tortora., B. Funke., & C. Case, 2019, Pearson Education. Copyright 2019 by Pearson Education, Inc.
SEAN’S SOAPBOX:
GET VAXXED
Why it’s not only in your best
interest, but also for others
around you
————– SEAN ADVERSALO
3
Vaccination has been an
unnecessarily disputed topic in
today’s scientific discourse. My
opinion? If you haven’t already, do it!
It not only benefits you, but your
community as well. Many individuals
don’t have the opportunity to receive
as vaccine due to underlying
sickness or compromised immune
system. Taking a vaccine allows for
the development of herd immunity by
allowing those who take them
sufficient immunity to a specific
pathogen and prevent endemic
spread. Think of vaccines as practice
questions or office hours before a
midterm – they prepare your body to
recognize specific epitopes on
foreign micro-organisms that we
don’t want habituating in our body.
These train the adaptive immune
response in our body and one way
is by creating B cell II lymphocyte
memory cells that linger in our
circulatory system. They can rapidly
become antibody producing B cells
that secrete antibodies that bind to
the recognized antigen and prevent
cellular infection, and thus host
disease!
Many vaccinations are available
that have been proven to be
clinically safe by clinical trials and
long-term measurement of adverse
side effects. One vaccine under
considerable scrutiny is the Covid19 vaccine.
The Pfizer-BioNTech Covid-19
vaccine was first approved for
emergency use under FDA
guidelines in the U.S. on December
11th, 2020. Less than a year after
that, it’s been moved to FDA
approval for adults and teens older
than 16 on August 23, 2021. It
continues to be authorized for
adolescent and even infant use
This harmless mRNA-based vaccine
does not linger and mutate host
DNA – it creates the viral spike
protein that allows disease to
happen but does not cause it.
Statistics collected by the CDC
report local infection symptoms in
48% of dose recipients and 0.72.9% of serious adverse effects in
the study cohorts. In a world where
variants continue to develop, I’m
willing to take these odds.
Issue01
Tuesday Sep 23, 20XX
WORKS CITED
Page 1
AAT Bioquest. (2022, February 4). How does temperature affect PCR? Retrieved August 28, 2022,
from https://www.aatbio.com/resources/faq-frequently-asked-questions/How-doestemperature-affect-PCR
Lenstra J. A. (1995). The applications of the polymerase chain reaction in the life sciences. Cellular
and molecular biology (Noisy-le-Grand, France), 41(5), 603–614.
National Human Genome Research Institute. (2020, August 17). Polymerase chain reaction (PCR)
fact sheet. Genome.gov. Retrieved August 28, 2022, from https://www.genome.gov/aboutgenomics/fact-sheets/Polymerase-Chain-Reaction-FactSheet#:~:text=How%20does%20PCR%20work%3F,the%20original%20strands%20as%20templa
tes.
Tankeshwar, A. (2022, August 19). Streak plate method: Principle, procedure, uses • microbe online.
Microbe Online. Retrieved August 27, 2022, from https://microbeonline.com/streak-platemethod-principle-purpose-procedure-results/
Tortora, G., Funke, B., & Case, C. (2019). Microbiology an introduction (13th ed.). Pearson Education.
Page 2
Buchanan, R. L., Gorris, L. G. M., Hayman, M. M., Jackson, T. C., & Whiting, R. C. (2017). A
review of listeria monocytogenes : An update on outbreaks, virulence, dose-response, ecology,
and risk assessments. Food Control, 75, 1–13. https://doi.org/10.1016/j.foodcont.2016.12.016
Center for Food Safety and Applied Nutrition. (n.d.). Big Olaf Creamery recalls ice cream because of
possible health risk. U.S. Food and Drug Administration. Retrieved August 27, 2022, from
https://www.fda.gov/safety/recalls-market-withdrawals-safety-alerts/big-olaf-creamery-recallsice-cream-because-possible-health-risk
Mannitol Salt Agar. Thermofisher. (2011, March 10). Retrieved August 28, 2022, from
https://tools.thermofisher.com/content/sfs/manuals/IFU1580.pdf
SmartLabel – Lysol® lysol® disinfectant spray – neutra air® 2 in 1 – tropical breeze. (n.d.). Retrieved
August 27, 2022, from http://rbnainfo.com/smart-label.php?productLineId=2692#ingredients
Tortora, G., Funke, B., & Case, C. (2019). Microbiology an introduction (13th ed.). Pearson Education.
Page 3
Centers for Disease Control and Prevention. (2022, June 21). Pfizer-biontech COVID-19 vaccine
reactions & adverse events. Centers for Disease Control and Prevention. Retrieved August
28, 2022, from https://www.cdc.gov/vaccines/covid-19/info-byproduct/pfizer/reactogenicity.html#:~:text=Solicited%20systemic%20adverse%20reactions%20
were,among%20ages%202%20%E2%80%93%204%20years.
Centers for Disease Control and Prevention. (2022, July 15). Understanding mrna COVID-19
vaccines. Centers for Disease Control and Prevention. Retrieved August 28, 2022, from
https://www.cdc.gov/coronavirus/2019-ncov/vaccines/different-vaccines/mrna.html
Tortora, G., Funke, B., & Case, C. (2019). Microbiology an introduction (13th ed.). Pearson Education.
4
Issue01
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