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Identifying and Characterizing

Homologous Human Genetic
Information and Proteins with
Drosophila cDNA sequences
BIOL 230W LAB REPORT

TA: Mary McGoldrick & Ayesha Samad

Partner: Jake Purnell

2015/11/11

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Identifying and Characterizing Homologous Human Genetic Information

and Proteins with Drosophila cDNA sequences
1.0 Introduction
The study of human diseases caused by gene mutation is challenging and complicated.
Humans have long life cycle and various gene expressions. Disease-related proteins produced
via DNA expression involve a large number of structures and functions. Specific functions of
protein are revealed to the relationship with protein domains, which are conserved sequences
and are able to function independently [1]. In order to retrieve the coding DNA for those
proteins, cDNA technology is adapted. Complementary DNA (cDNA) is reversely transcribed
from mRNA. Compared with coding DNA strand, cDNA does not contain introns, so it is
directly related to translated mRNA and gene expression. A congregation of cDNA
representing all transcribed genes of a certain tissue or a certain period from a cell is called
genomic cDNA library, which is widely used in pathology [2].
Drosophila melanogaster, commonly known as fruit fly, is the model organism to study
human disease. Drosophila has a short lifecycle that is good for drug testing, and its genes
have been studied for hundreds of years [2]. According to relative study, Drosophila
homologs have 70% of the known human cancer genes and 60% of known genetic disorders
causing human diseases. The proteins of both human and Drosophila share many similarities
at the aspects of structures, functions, and pathologies. For instance, the GTP-dependent
phosphorylation activity depression is caused by the same mutation of GTPase domain and
kinase domain of human and Drosophila proteins. [1].

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Isolated Drosophila cDNA is unstable, so in order to conserve the cDNA libraries, cDNA
must be inserted into E. coli plasmid, small stable circular DNA. pNB40 plasmid carries and
stores cDNA library for further research [1].
Selection of studied E. coli is treated with ampicillin. Without antibiotic ampicillin,
anything can grow in media. If E. coli grows in ampicillin culture, only cells containing
resistance gene survive [3]. This step is essential in the overall experiment, because it
guarantees the purity of tested cDNA samples. Most of the contaminations and untargeted
genes are removed.
This experiment is designed to analyze the similarity of proteins and cDNA between
Drosophila and humans, to study the function of homologous proteins and the role in human
diseases, to indicate further understanding of the significant contribution of protein control to
human disease control. The specific purposes of the experiment are to identify Drosophila
proteins via the DNA sequence in the cDNA plasmid and their functions, the homologous
human proteins in Drosophila cDNA library, the relative human protein domains and their
functions, and the significance of studying Drosophila genomes contributing human diseases.
The hypotheses of this experiment are: the similarity of proteins and cDNA between
Drosophila and human is statistically high (estimated 80% or above). Homologous proteins
among Drosophila and humans widely exist, and they have similar functions. Also, protein
control is significant to human disease control.
2.0 Materials and Methods

To proceed this experiment, Drosophila were prepared to test; centrifuge and relative
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solutions were used to extract RNA; and then Master Mix reversely transcripts RNA into
cDNA; PCR machine was used to analyzed the cDNA data; and sterile water was kept as the
control group [1].
At the beginning, E. coli grew in liquid broth overnight and were shaken at 37, and
then stored at 4 for a week. 2 colonies of E. coli are selected from the media. The 2
colonies were put into 2 tubes by tooth picks and forceps marked as A and B containing Luria
Broth and ampicillin to kill the cell without antibiotics. After a while, coli suspension was
pipetted into QuickLyse Lysis to lyse cell membranes. Ice cold Complete Lysis Solution was
added and vibrated on vortex for a short period. Then cDNA was incubated at room
temperature for 5 min and centrifuged. Buffer QLW was added to the top of QuickLyse spin
column to wash the column. After wash, Buffer QLE was added into spin column. Finally, the
50l liquid containing plasmid for PCR and DNA was obtained [1]. 3 tubes were prepared for
2 plasmids from the 2 colonies, and negative control sterile water. All 3 tubes were pipetted
and added Mater Mix.
The DNA was analyzed by PCR. Agarose was placed into a flask and mixed with 1X TAE
buffer. The flask was heated for 40sec in microwave. Then the gel was put at room
temperature and cooled for 2 minutes. In order to view DNA ladder under UV light, ethidium
bromide dye was added into molten agarose. When casting the gel, agarose should harden for
10min.
The 12l samples were loaded into wells on in the gel. PCR DNA ladder was put in well
1. Plasmid A DNA was put in well 2. Plasmid A PCR product was put in well 3. Plasmid B

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DNA was put in well 4. Plasmid B PCR product was put in well 5. PCR negative control
(sterile water) was put in well 6. After the gel ran, the gel was put under UV light for
photographing [1].
Experimenter used Plasmid A and PCR A, and Jake Purnell handled plasmid B and PCR
B during the whole experiment [4].
3.0 Results
The group result was labeled section 014 group 6. The DNA sequences were
analyzed by PCR and MEGA software. Under UV light, the ladder on the gel was used to
determine the sizes of tetracycline resistant gene. The sizes were compared to identify the
gene and confirm the source. DNA sequences were displayed by MEGA in the form of peaks,
and the certain sequences were identified through NCBI website.

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Picture 1: Gel photo is blurry and ladders are invisible. All gel is in pale orange. The
wells are labeled in the picture.
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The DNA ladders were not clear. All gel appeared in pale orange. PCR DNA ladder was
in well 1. Plasmid A DNA was in well 2. Plasmid A PCR was in well 3. Plasmid B DNA was
in well 4. Plasmid B PCR was in well 5. PCR negative control was in well 6.

Picture 2: section 14 group 6 sample A MEGA picture

Sample A MEGA picture showing few overlaps and many sharp peaks was graphed
according to 14-6-A_SP6_E3_Oct-2-2015.ab1 on Angel. The cDNA sequence was found
related to both human and Drosophila and possessing similar structures and functions.
The information of mRNA and relative proteins of human and Drosophila are included in
the table.
mRNA and protein information
Request ID for nucleotide sequence

1AYZSRFH01R

mRNA Name

Drosophila melanogaster Reticulon-like 1

(Rtnl 1)

NCBI Reference Sequence of mRNA

NM_001169404.2
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Protein translated from mRNA

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Reticulon-like 1, isoform H [Drosophila

melanogaster]

NCBI Reference Sequence of protein

NP_001162875.1

Protein Domain in Drosophila protein

Reticulon

Homologous Human protein ID

1AZWW3P601R

Homologous
similarities

Human

proteins

and 64% Reticulon isoform q [Homo Sapiens]

64% TPA-truncated RTN3-A-D5 [Homo
Sapiens]
57% Chain A Human Nogo-A Functional
Domain: Noqo60 [Homo Sapiens]

Table 1: mRNA and protein information [5]

4.0 Discussion
Gel electrophoresis showed no DNA ladders. The problem was caused by the failure of
ethidium bromide dye stain to agarose. As a DNA interchelator, ethidium bromide dye inserts
between base pair of double helix to stain DNA. Since the DNA fragments are invisible under
UV light, not enough ethidium bromide dye was pipetted into gel [6].
MEGA shows a few overlaps in the diagram, which stands for the contamination of
cDNA. The cDNA sequence was analyzed via biological informatics website NCBI, and the
coded Drosophila protein is called Reticulon-like 1, isoform H; the homologous human
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proteins are Reticolun-3 isoform q with 64% similarity, TPA-truncated RTN3-A-D5 with 64%
similarity, and Chain A Human Hogo-A Functional Domain: Noqo60 with similarity of 57%.
We can conclude that not all Drosophila mRNA or proteins are homologous to human, but,
on the other hand, the homologous proteins do exist [5].
Reticolun protein is associated with the endoplasmic reticulum, the function is unknown
currently. Only one domain is found in this protein. Reticulon domain represents the
C-terminal domain of 3 reticolun isoforms [7]. The picture below shows the structure of
reticolun-4-interacting protein 4.

Picture 3: Structure of reticolun-4-interacting protein 4

[8]
RTN-4 protein has the ability of inhibiting the axonal growth. Some study shows that
reticolun protein is related to neurodegeneration. Within the development of axons, the
neuron and sheath cover receive signals (ligand) to be activated and grow. The existence of
certain reticulon blocks the pathway of ligands and inhibits the growth of axons [9]. Currently,

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only little research focuses on the relationship between reticulon and neural diseases, so the
hypothesis indicating the causation is not credible. However, the homologous genes from
divergent evolution (i.e. same ancestor of human and Drosophila) and proteins of Drosophila
can be put into use of disease studies.
The errors in the experiments can be fixed by repeating steps. Ethidium bromide dye
should be added more than pervious. The contaminant might appear in the plasmid and PCR
tubes. To avoid the contamination, the equipment should be cleaned and sterilized. For
further experiment, other E. coli colony can be selected and tested.
Reviewing the primary goal for this experiment, the conclusion can be made: the
similarity of proteins and cDNA between Drosophila and human is statistically high,
approximately 60% similarity. Homologous proteins among Drosophila and human exist, and
they have similar functions. Lastly, protein control and disease are waiting for exploring
tighter links and more developed medical techniques in further research.

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References
[1] BIOL 230W: Biology of Molecules and Cells Laboratory Manual-Fall 2015. Penn State
University, 13Oct. 2015
[2] Herold, N., C. L. Will, E. Wolf, B. Kastner, H. Urlaub, and R. Luhrmann. "Conservation
of the Protein Composition and Electron Microscopy Structure of Drosophila
Melanogaster and Human Spliceosomal Complexes." Molecular and Cellular
Biology 29.1 (2008): 281-301. Web. 13Oct. 2015
[3] Karami, N., A. Martner, V. I. Enne, S. Swerkersson, I. Adlerberth, and A. E. Wold.
"Transfer of an Ampicillin Resistance Gene between Two Escherichia Coli Strains in the
Bowel Microbiota of an Infant Treated with Antibiotics." Journal of Antimicrobial
Chemotherapy 60.5 (2007): 1142-145. Web. 13Oct. 2015
[4] Jakes BIOL 230W: Biology of Molecules and Cells Laboratory Manual-Fall 2015. Penn
State University, pp. 38. 13Oct. 2015
[5] National Center for Biotechnology Information (NCBI), U.S. National Library of
Medicine8600 Rockville Pike, USA. 13 Oct. 2015.
[6] Ramana, M.m.v., Rahul Betkar, Amey Nimkar, Prasanna Ranade, Balaji Mundhe, and
Sachin Pardeshi. "In Vitro DNA Binding Studies of Antiretroviral Drug Nelfinavir Using
Ethidium Bromide as Fluorescence Probe." Journal of Photochemistry and
Photobiology B: Biology 151 (2015): 194-200. Web. 13 Oct. 2015.
[7] Brandizzi, Federica, and Giovanni Stefano. "Faculty of 1000 Evaluation for

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Reticulon-like-1, the Drosophila Ortholog of the Hereditary Spastic Paraplegia Gene

Reticulon 2, Is Required for Organization of Endoplasmic Reticulum and of Distal
Motor Axons." F1000 - Post-publication Peer Review of the Biomedical
Literature (2012): n. pag. Web. 13 Oct. 2015.
[8] Lomize, Andrei, Mikhail Lomize, and Irina Pogozheva. "2vn8 Reticulon-4-interacting
Protein 1." - Orientations of Proteins in Membranes (OPM) Database. University of
Michigan, 05 May 2013. Web. 13 Oct. 2015.
[9] Nziengui, Hugues, Karim Bouhidel, David Pillon, Christophe Der, Francis Marty, and
Benot Schoefs. "Reticulon-like Proteins in Arabidopsis Thaliana: Structural
Organization and ER Localization." FEBS Letters581.18 (2007): 3356-362. Web. 13Oct.
2015

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