FAIRLEIGH DICKINSON UNIVERSITY
SCHOOL OF NATURAL SCIENCES
BIOL 3225 General Microbiology
Literature review paper and presentation: 15%
Students are expected to write a literature review paper on a topic relevant to microbiology. The chosen topic may
not cover an event more than 5 years old. You are encouraged to start your research paper as early in the
semester as you possibly can. Your choice of topic may reflect your personal interests, support your career goals or
nurture your inherent intuition and curiosity. Have enough time to gather literature, write, revise, revise some more,
and turn in a scholarly paper. Maximum page limit is 10, double spaced, AMA (American Medical Association)
format. - Presentations should be 7-10 minutes long and should include all pertinent information as per their
The Scientific Literature Review
Background research is a vital component of the scientific research process. The students will be able to locate,
identify and critique key elements of scientific literature to discover what is known and what remains to be learned
about a topic.
Books and articles are categorized as either primary or secondary sources. It is always more desirable to use
primary sources whenever possible.
Primary sources are first-hand accounts of events
Secondary sources are second-hand accounts.
The competent researcher never relies on secondary sources but always reviews the primary source as a check
against possible errors. The researcher then makes records of the sources studied and summarizes the pertinent
information found in each.
The most common and useful method for recording bibliographical information is to write the complete information
for each publication on a separate 3X5 card (or file). These cards are kept in alphabetical order in a file to be a
ready source to cite relevant works in the body of the research paper. The researcher must develop an orderly and
systematic approach to coding their index cards. It is important to summarize an article or book using the same
format each time. This will enable quick comparisons.
For an article, examine the author’s credentials, scan the hypothesis, and focus on the methods of research
used (how the sample was selected and the data was analyzed). Read the conclusion and summary.
Retain sound and pertinent articles. To summarize and record the information, note author, title, and year
• Title of article
• Authors name(s) - all authors MUST be recorded.
• Full reference – year of publication, FULL name of the journal or book, # of issue or edition and
• Summary of information of interest NOTE: no everything may be of importance to your
research, concentrate only on the issues that are pertinent to your work.
REVIEWS For the past three or four years you have learned how to review a scientific paper, now is time to
learn how to use this information in a more productive form. Scientist must keep up with the advances on their
area of interest by constantly reading new publications. This will give them an overview of what is being
accomplished by the scientific community. Each individual paper you read will give you a piece of the puzzle.
During this exercise, you will learn how to put all the pieces of the puzzle together as a BIG PICTURE –
Scientific Literature Review.
ELEMENTS OF SCIENTIFIC LITERATURE
Title short, specific, clear
Introduction WHY are you doing this research?- state the propose of what you are expecting to find (Present
tense), review the individual literature and compile what information already exists on this subject (background
information reported by the papers you read regarding your topic)
Materials & Methods HOW was the research carried out? (Past tense) (design, target population, treatment,
analytical methods ---- brief explanation on how the different authors conducted their experiments) – compare their
methods), please NOTE that this may not be appropriated for your research.
Results WHAT kind of results were reported by the papers you read (past tense) again, this may not apply to your
research or it could be combine with your discussion and conclusion.
Discussion/Conclusions WHAT do the results published by the different researchers mean to you? (present
References / Literature cited
Paper Guidelines: The project will be based on new literature, at least seven original research articles from
scientific journals (primary source). Beside the new scientific literature (primary sources), background references
like books, popular science magazines or older articles from science journals should be used to complete your
work; to create the BIG PICTURE. (Minimum 10-12 references)
The steps required for the completion of the project are:
1. Sign-up for a topic provided by your instructor or if you have a particular topic or interest, you may clear it
with your instructor. Due (in class) by the 2nd week of class. Please note that no two person will be
allow to research the same topic.
• When deciding on a topic, you should ask yourself the question….. What do you want to know about
* Once you define your topic, you will not be allowed to change it.
Find primary references – at least 7 original research scientific articles from reputable scientific
journals (use the library services!). – NOTE: scientific reviews and mini-reviews are considered as
secondary source. -- Copies of the scientific papers PDF’s must be e-mailed to the instructor for
approval no later than September 23, 2018. late delivers will be penalized
NOTE that I cannot open any link! You must download the paper into your computer as a PDF
file and then forward the PDF as an email attachment.
2. Read the papers (followed guide provided in the beginning of this assignment) and look for additional
scientific articles and background material (minimum 10 references should be included on your paper).
Prepare individual summary for each paper (like single pieces of a puzzle) write a two page
“resume” in your own words for each reference. E-mail then to the instructor no later than
October 6, 2018. – late delivers will be penalized
3. Compile all your information to give an overview of the studies done in a particular area of interest. “the
entire puzzle” -4. Start writing your scientific literature review. First draft must be e-mailed to your instructor no later
than 11:59pm October 27, 2018.
• You may re-submit via e-mail working drafts until November 17. NO MORE DRAFTS WILL BE
ACCEPTED AFTER THAT DAY. Make sure you have addressed all the recommendations and that
your paper is free of grammatical errors and of good scientific quality as per the guide provided at
the beginning of the assignment.
• Points to remember:
i. You are not to review each paper independently. DO NOT DESCRIBE INDIVIDUAL
RESEARCHES, YOU MUST SUMMARIZE AND COMPARE ALL THE PAPERS.
ii. You must compile all the information as a single unit
iii. Don’t forget to cite in text what each author have to say. When citing in text use author(s)
name(s) coma and year of publication. e.g. (Johnson, 2015) or (Johnson & Smith, 2016)
or if more than two authors use (Willey et al., 2014)
It MUST include:
o Title page -- (Title of your paper, your name and course number)
o Introduction (background information reported by the papers you read regarding your
o Material & Methods if appropriate to your topic (brief explanation on how the different
authors conducted their experiments) – compare their methods
o Result / Discussion what do the results published by the different researchers mean to
you. You may compare the data in tables, schemes or figures. BUT it has to be selfexplanatory and created by YOU. (do not copy them from the literature – that is considered
o Conclusion (what did you learn from your research)
o Reference -- In text references and literature cited.
In text references should be done by using the author(s) last name followed by a coma and the year of
publication (ex. Johns, 2016; Johns & Willian, 2016; if more than three authors use the first authors name
and et al. - Johns et al., 2016)
End of the paper reference (literature cited) can be written as follow…Make sure to write the name of all
authors here. -- do not use et al.!
Authors’ names (last name, Initial(s).and ; between the authors and before the last one)) Year of
publication. Article title (capitalize only the first letter of the first word and proper nouns), Journal name
(in italic), Volume number; full page numbers.
o Li, B.; Li, W.; Chen, X.; Jiang, M.; and Dong, M. (2012). In vitro antibiofilm activity of the
melanin from Auricularia auricula, an edible jelly mushroom. Annals of Microbiology, 62(4),
Article in an online journal: Author(s) (same as above). Year Title. Journal Name; volume (issue
NO.):inclusive pages. URL [provide the URL in this field; no need to use “URL:” preceding it]. Published
[date]. Updated [date]. Accessed [date].
o Drake A.J., Smith A., and Betts P.R., (2002). Type 2 Diabetes in Obese White Children.
Archives of Disease in Childhood 86(3), 207-208. http://vsearch.nlm.nih.gov/vivisimo/cgibin/query-meta?v:project=nlm-main-website&query=Archives+of+disease+in+childhood.
Accessed April 5, 2016.
o Langer, S., D. Schropp,, F. R. Bengelsdorf,, M. Othman, and M. Kazda. 2014. Dynamics of
biofilm formation during anaerobic digestion of organic waste. Anaerobe 29 , p 44-51.
http://dx.doi.org/10.1016/j.anaerobe.2013.11.013. Accessed April 5, 2016
When citing data from a Web site, include the following elements, if available, in the order shown
below: Author(s), if given (often, no authors are given). Title of the specific item cited (if none is given,
use the name of the organization responsible for the site). Name of the Web site. URL [provide URL
and verify that the link still works as close as possible to publication]. Published [date]. Updated [date].
o Living With Type 1 Diabetes. Diabetes.org. http://www.diabetes.org/living-withdiabetes/recently-diagnosed/living-with-type-1-diabetes.html. Published February 9, 2015.
Accessed April 7, 2015.
o Why Immunize? cdc.gov. http://www.cdc.gov/vaccines/vac-gen/why.htm. Updated September
23, 2014. Accessed April 7, 2015.
o Yale University. Science Daily. http://www.sciencedaily.com/relesases/2015/01/1501733950.
Published January 7, 2015. Accessed April 5, 2015.
When referring to an entire book, not pages or specific sections, use the following format: References
should include the last name and first and middle initials of the author(s), italicized title case format for
all titles (capitalize all words except prepositions such as of, between, through), articles (such as a, the,
and an), and conjunctions (such as but, and, or; however, capitalize them if they begin the title or the
subtitle) the city and state of publication, the publisher, and the year of publication/creation.
o Silverstein A., Silverstein V.B., Nunn L.S. Cancer. Minneapolis, MN: Twenty-First Century
o Maul-Mellott, S.K. and Adams, J.N. Childhood Cancer: A Nursing Overview. Boston, MA:
Jones and Bartlett; 1987.
o Willey,J. M., L. M. Eherwood and C. J. Woolverton. Prescott’s MICROBIOLOGY 9th. Edition.
Chapters from books should be capitalized in the same format as journal articles (sentence case
format) and should not use quotation marks. Additionally, inclusive page numbers for the each chapter
should be provided. The title of the book, however, should be title cased and italicized, following the
print book format. A colon should follow the publication date and no space should be provided between
the colon or the page number(s) and hypen.
o Yagyu, S. and Iehara, T. MYCN nonamplified neuroblastoma: Detection of tumor-derived cellfree DNA in serum for predicting prognosis of neuroblastoma. In Hayat MA, ed. Pediatric
Cancer Diagnosis, Therapy, and Prognosis. Dordrecht, NY: Springer; 2013:11-17.
5. You must prepare the material to be presented to your classmates.
All Presentations (ppt, prezi, etc.. and an one page summary) regardless of your presentation date
are due via e-mail to your instructor on November 25, 2018 NO EXCEPTIONS. Points will be
deducted for late submissions
You will be presenting your topic during the class schedule time (based on the topic) and credit will
be given for the presentation and for answered questions.
Presentations should be 7-10 min. long and should include all pertinent information as per their
A summary (one page) of your presentation should be prepared and e-mailed to your instructor
before your presentation date for distribution to your classmates. All presentation materials will be
included in your final examination.
6. Final paper is to be submitted via Safe-Assignment by 11:59PM DECEMBER 1, 2018- Once you
submit it via Safe-assignment, you can no longer re-write it or fix it.
EVALUATION OF THE PROJECT (15%)
Primary references delivered on time (1 pt each)
Two page summary for each reference (2 pts each)
First draft complete and delivered on time
Final paper o Paper depth
o Spelling, paragraph and sentence structure,
grammar and punctuation
o One page summary
o Presentation content
o Timing + Question and answers
• Late submission(s)
• No approved topic or literature
• No drafts
• No oral presentation
- 50% of original pts.
- 50 pts
- 25 pts
- 30 pts.
SAMPLE LITERATURE REVIEW
Prion propagation and their effect in humans
Prions cause diseases like Creutzfeldt-Jakob disease (CJD), Gerstmann-Strässler-Scheinker syndrome (GSS), kuru,
and fatal familial insomnia in humans (Barbisin et al. 2014). Diseases caused by prions in animals include bovine spongiform
encephalopathy (BSE), also known as Mad Cow Disease, in cattle (Strom et al. 2014), scrapie in sheep, chronic wasting
disease (CWD) in cervids (which includes deer), transmissible mink encephalopathy, and feline spongiform encephalopathy
(Barbisin et al. 2014). Prion diseases are both fatal and currently incurable. These neurodegenerative diseases are collectively
referred to as transmissible spongiform encephalopathies (TSEs). Prions cannot be seen by the naked eye and are naturally
found in cells as normal, functional proteins. Their microbiological influence affects organisms on the cellular level, with
neurons as the primary focus for most studies………………………..
Materials and Methods
The researchers, Krejciova et al.(2014), simulated PrP conversion from the normal form to the abnormal form (that
would normally occur in cells) in vitro using a technique called protein misfolding cyclic amplification (PMCA). PMCA works by
incubating normally folded protein mixed with a small amount of misfolded protein. Then the conversion is sped up with a blast
of ultrasound. The cycle is repeated until the desired end result is achieved (Zou & Pierluigi, 2012)………………..
Barbisin et al. (2014) were also concerned about humans becoming infected with prions. They had worked under
certain assumptions. The primate Macaca fasicularis is known to be a good research subject for the understanding prion
diseases inflicting humans………. Another group of scientists (Belay et al. 2015) found that prion studying from RNA studies
had problems in maintaining RNA integrity, specifically from the heat produced using a rotating biopsy stamp when extracting
The findings of these studies indicate that prions continue to boggle the minds of researchers. These studies do,
however, give more insight to the capabilities of TSE-related prions…………………………….
Researchers Krejciova et al. (2014) have concluded that prions from cattle infected with BSE can effectively afflict
sheep of certain genotypes. However, the prion types found in these sheep have lost the capability to infect humans………….
Ultimately the ways prions propagate and influence cells and other microbes continues to elude researchers. The
current level of knowledge surrounding prions highlights that there is little information on how to protect livestock and people
from TSEs and other prion related neurodegenerative disorders……….
Barbisin, M., Silvia Vanni, Ann-Christin Schmädicke, Judith Montag, Dirk Motzkus, Lennart Opitz, Gabriela Salinas-Riester,
Giuseppe Legname (2014) Gene expression profiling of brains from bovine spongiform encephalopathy (BSE)infected cynomolgus macaques BMC Genomics. 2014; 15: 434. Published online 2014 Jun 5. doi: 10.1186/14712164-15-434
World Health Organization Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseas…
World Health Organization Estimates of the Global and
Regional Disease Burden of 22 Foodborne Bacterial,
Protozoal, and Viral Diseases, 2010: A Data Synthesis
Martyn D. Kirk
, Sara M. Pires, Robert E. Black, Marisa Caipo, John A. Crump, Brecht Devleesschauwer, Dörte Döpfer,
Aamir Fazil, Christa L. Fischer-Walker, Tine Hald, Aron J. Hall, Karen H. Keddy, Robin J. Lake, Claudio F. Lanata,
Paul R. Torgerson, Arie H. Havelaar, Frederick J. Angulo
Published: December 3, 2015
23 Dec 2015: Kirk MD, Pires SM, Black RE, Caipo M, Crump JA, et al. (2015) Correction: World Health Organization
Estimates of the Global and Regional Disease Burden of 22 Foodborne Bacterial, Protozoal, and Viral Diseases, 2010: A Data
Synthesis. PLOS Medicine 12(12): e1001940. https://doi.org/10.1371/journal.pmed.1001940 | View correction
Foodborne diseases are important worldwide, resulting in considerable morbidity and mortality. To our knowledge, we present the
first global and regional estimates of the disease burden of the most important foodborne bacterial, protozoal, and viral diseases.
Methods and Findings
We synthesized data on the number of foodborne illnesses, sequelae, deaths, and Disability Adjusted Life Years (DALYs), for all
diseases with sufficient data to support global and regional estimates, by age and region. The data sources included varied by
pathogen and included systematic reviews, cohort studies, surveillance studies and other burden of disease assessments. We
sought relevant data circa 2010, and included sources from 1990–2012. The number of studies per pathogen ranged from as few
as 5 studies for bacterial intoxications through to 494 studies for diarrheal pathogens. To estimate mortality for Mycobacterium bovis
infections and morbidity and mortality for invasive non-typhoidal Salmonella enterica infections, we excluded cases attributed to
HIV infection. We excluded stillbirths in our estimates. We estimate that the 22 diseases included in our study resulted in two billion
(95% uncertainty interval [UI] 1.5–2.9 billion) cases, over one million (95% UI 0.89–1.4 million) deaths, and 78.7 million (95% UI
65.0–97.7 million) DALYs in 2010. To estimate the burden due to contaminated food, we then applied proportions of infections that
were estimated to be foodborne from a global expert elicitation. Waterborne transmission of disease was not included. We estimate
that 29% (95% UI 23–36%) of cases caused by diseases in our study, or 582 million (95% UI 401–922 million), were transmitted by
contaminated food, resulting in 25.2 million (95% UI 17.5–37.0 million) DALYs. Norovirus was the leading cause of foodborne
illness causing 125 million (95% UI 70–251 million) cases, while Campylobacter spp. caused 96 million (95% UI 52–177 million)
foodborne illnesses. Of all fo ...
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