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BIOL2319
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Practical 1: Literature search/Bioinformatics
BIOL XXXXXXXXXXSemester 2 2020
ONLINE LAB
INTRODUCTION
Reading and critically analysing scientific research articles is a special skill. In this online
lab session, You will get a chance to read a research article. There are many good ideas,
interesting hypothesis, innovative strategies and surprising outcomes published in
scientific journals. Surprisingly not all the journal articles published in a high-quality
journal are excellent. Some material is not reproducible, and they are not worth to read.
Experience may help in selecting the right article to obtain information on a specific topic.
The following questions will help you identify whether the chosen article is worth reading
or not.
Why was the study done/What is the aim of the study?
What hypothesis was tested in the specific study?
Was the study design appropriate?
Was the study method well designed with appropriate controls?
Was it reproducible/statistically analysed?
Were the results meaningful and aligned with the method and approach?
Are the discussion and conclusion valid?
Were ethics issues addressed in any way in the article?
OBJECTIVES/AIMS
In this lab session, you will
owse some websites to understand how to get valuable
information from different resources.
During this session, you should learn to identify and understand:
• Where to search for scientific research articles?
• What does “the authoritative research article” mean to me?
• Where to find the aim and hypothesis in a primary research article?
• How to summarise/write a short story from the information found in
a journal article?
This lab has two activities.
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ACTIVITY 1: Abstract writing
Cells and their internal organization is one of the major topics we will teach you in this
course (weeks 1 to 6). The literature provided in this activity will help to develop your
knowledge in the area and may support your learning contents.
1) Go to https:
www.ncbi.nlm.nih.gov/pubmed/ and select the keywords to find
out the following article according to your last name.
If your last name starts with A–F : Search an article by entering the following
detail.
migration and invasion
From the searched results find out the article published in 2014 by Justus CR.
et al.,
(The title of the article should be “In vitro Cell Migration and Invasion Assays”)
If your last name starts with G–M : Search the specific article by entering the
following detail.
Bernard O
From the searched results, find the article published in 2012 Sep
(The title of the article should be “Pharmacological inhibition of LIM kinase
stabilizes microtubules and inhibits neoplastic growth”)
If your last name starts with N–S : Search an article by entering the following
details.
SNARE and macrophages
Select the article published in 2008 by Achuthan A
(The title of the article should be “Regulation of the endosomal SNARE protein
syntaxin 7 by colony-stimulating factor 1 in macrophages”)
If your last name starts with T-Z : Search an article by entering the following
details.
Wee1 and adavosertib
Select the article published in 2020 July by Mugundu G.
(The title of the article should be “Effect of food on the pharmacokinetics of the
WEE1 inhibitor adavosertib (AZD1775) in patients with advanced solid tumors”)
Now, read the article that requested by your surname and in your own words write
a summary report (300 words maximum) which will cover the introduction, aim,
hypothesis, results and conclusion. (3 Marks).
https:
www.ncbi.nlm.nih.gov/pubmed
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ACTIVITY 2: Bioinformatics
Question #1 (total 1 mark)
If your last name starts with A – G: (a) Find out how many articles were published
y Yang C and Guan L in between XXXXXXXXXXmarks)? (b) How many of them
were in XXXXXXXXXXmarks)?
If your last name starts with H– M: Find out how many articles were published by
Kraft AS in between XXXXXXXXXX? How many of them were in 2015?
If your last name starts with N –S: Find out how many articles were published by
Piva TJ in between XXXXXXXXXX? How many of them were in 2017?
If your last name starts with T – Z: Find out how many articles were published by
Vlahos R in between XXXXXXXXXX? How many of them were in 2019?
Questions number 2 to 4 are based on the key proteins listed below.
• If your last name starts with A - G your protein to research is human BMP4.
• If your last name starts with H - M your protein to research is human N-cadherin.
• If your last name starts with N - S your protein to research is human Vimentin.
• If your last name starts with T – Z your protein to research is human Smad 2.
Question #2
Go to www.uniprot.org to explore the available resources of protein sequence and
functional information. Click on UniProtKB. Search for your protein (homo
sapiens). Tick the 1st selection box. Click on the Entry number. (a) Record the name
and or alternative names (if available) for your protein. (b) Record the length in
amino acids, and the molecular mass in Dalton of your protein. (c) Record the
published subcellular localisations of your protein. (1 Mark)
Question #3
Go to https:
www.proteinatlas.org Search for your protein. Record the general
information such as (a) gene name, (b) gene description, (c) protein class, and (d)
localisation within the cell. (0.5 Mark)
Question #4
Go to human genome resources at NCBI by clicking the following website,
https:
www.ncbi.nlm.nih.gov/projects/genome/guide/human/ search for your
gene (a) Record the chromosomal location. (b) Record the tissue that expressed a
higher level of this protein (mRNA XXXXXXXXXXMark)
https:
www.proteinatlas.org
https:
www.ncbi.nlm.nih.gov/projects/genome/guide/human
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Assessment submission date: 05/08/2020, 5:00 pm (Wednesday, week 3, 5:00 pm)
Assessment fraction: 6%
Submit the answers as described below.
Type your answers in a word document and save as .doc or docx.
The similarities will be checked. >30% similarities (for activity 1 only) will lose
marks.
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Practical 1: Report format
BIOL2319
Semester 2
2020 ONLINE LAB
ACTIVITY 1: Abstract writing
Write the abstract (a summary report) that requested by your surname and in your own words. This abstract should cover the introduction, aim, hypothesis, results and conclusion (300 words maximum). 3 Marks.
ACTIVITY 2: Bioinformatics
Write the answers that requested by your surname only. If not you will loose the marks.
Question #1 (total 1 mark)
Question #2 (total 1 mark)
Question #3 (total 0.5 mark)
Question #4 (total 0.5 mark)
BIOL2319
2018