ASSIGNMENT 1

BHLHE40

1. MUHAMAD FAIRUL IZWAN MAT ZAIN 1621195

2. MOHD AMIRUL SYAHMIN BIN ABDUL KARIM 1622141

3. MUHAMMAD SAUFI BIN AMIR 1621243

4. MOHAMAD SHAHRUL NUKMAN BIN SHAKIL 1627771

5. MUHAMMAD NAIM BIN MOHD RASHID 1622357

INSTRUCTOR: ASSOC. PROF. IR. DR. DR. AZRAN AZHIM

PROGRAM: BACHELOR OF PHYSICS (HONOURS)

SUBJECT: COMPUTER IN SCIENCE

SUBJECT CODE: KOS1110

SECTION: 4
TABLE OF CONTENTS

INTRODUCTION 3
METHOD 3

RESULT 4

DISCUSSION 6

CONCLUSION 8

REFERENCES 9

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1.0 INTRODUCTION

The main objective of this project is to acquire basic knowledge in understanding the methods

of gene feature identification, in which through identities percentage difference between

organisms that are close to human gene. The gene that assigned to us is BHLHE40 . On top of

that, this assignment aims to apply the techniques of multiple sequence alignment and create a

phylogenetic tree by using a specific computer program, CLC Sequence Viewer. In this

assignment, we were also assigned a task to introduce a recent journal paper regarding genetic

study which is related to extracellular matrix (ECM).

2.0`METHODS

The details of the gene were obtained from the database system provided by National Center

for Biotechnology Information (NCBI). NCBI also has a search program called BLAST

( Basic Local Alignment Search Tool ), which we use to search for sequence similarity of

nucleotide and protein . From that, we conducted a homology analysis. CLC Sequence Viewer

is used to construct a phylogenetic tree, meanwhile in order to find a recent journal paper, we

cited an article from PubMed.

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3.0 RESULT

3.1 GENE FEATURE IDENTIFICATION

Table 1: Gene Feature Identification

Official Symbol BHLHE40

Official Full Name Basic-Helix-Loop-Helix-Family Member E40
Gene Family E40
Primary Source HGNC:HGNC:1046
Gene Type protein coding
Lineage Eukaryota, Metazoa, Chordata, Craniata, Vertebrata, Euteleostomi,
Mammalia, Eutheria, Euarchontoglires, Primates, Haplorrhini,
Catarrhini, Hominidae and Homo.

Position 3p26.1

3.2 HOMOLOGY ANALYSIS

Table 2: Homology Analysis

Organisms Percentage identities (%)

Human 100
Sumateran orang Utan 100
Sunda Flying Lemur 95
Platypus 81
Vesperbat 89
Grey Mouse Lemur 87
Lesser Egyptian Jerboa 91

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3.3 PHYLOGENETIC TREE

Diagram 1: Phylogenetic Tree

3.4 RECENT JOURNAL PAPER ECM

Citation: Department of Circulation and Medical Imaging, Norwegian University of

Science and Technology, Trondheim, Norway. Ingrid.Eftedal@ntnu.no. Early genetic

responses in rat vascular tissue after simulated

diving http://physiolgenomics.physiology.org/content/44/24/1201

Published 15 December 2012 Vol. 44 no. 24, 1201-1207

4.0 DISCUSSION

4.1 The BRCA1 are normally expressed in the cell of breast and other tissue , where they

help to repair damage DNA or destroy cells if the DNA cannot be repaired . This gene provides

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instructions to make a protein that acts as a tumor suppressor. Tumor suppressor proteins help

prevent cells from growing and dividing too rapidly or in an uncontrolled way.

In the nucleus of many types of normal cells, the BRCA1 protein interacts with several

other proteins , DNA damage sensors and signal transducers to form a large multi-subunit

protein complex known as the BRCA1-associated genome surveillance complex (BASC) [to

mend breaks in DNA. These breaks can be caused by natural and medical radiation or other

environmental exposures, and they also occur when chromosomes exchange genetic material

in preparation for cell division. By helping to repair DNA, the BRCA1 protein plays a critical

role in maintaining the stability of a cell's genetic information.

Research suggests that the BRCA1 protein also regulates the activity of other genes and

plays an essential role in embryonic development. To carry out these functions, the BRCA1

protein interacts with many other proteins, including other tumor suppressors and proteins that

regulate cell division.

4.2 Based on homology analysis, we selected 7 organisms which are Homo sapiens
Sumateran Orang Utan, Platypus ,Vesperbat, Lemur,Sunda Flying Lemur, Grey Mouse Lemur
and Lesser Egyptian Jerboa. We took Homo sapiens as reference and compare it to with the
other species. The percentage identities of all organisms are nearly the same because in their
gene, they have a certain DNA that are similar.

4.3 A phylogenetic tree, shows the evolutionary relationships among a set of organisms

based gene or protein make up. A sister group denotes the closest relatives and a clade is a

group of organisms that are descendent from a common ancestor. The reference gene in our

investigation is the Homo sapien (human) BHLHE40. Homology analysis is a test that

measures the similarities between a reference gene to a subject gene. Based on our findings,

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the homology analysis indicates that Sumateran orang Utan is 100% like Homo sapiens.

There is one sister group that shows that Sunda Flying Lemur is closely related. The furthest

organism that is found on the phylogenetic tree is the Platypus, with a 81% similarity to the

humans. Another statistical tool that we can use in constructing the phylogenetic tree is the

boot strap analysis; it indicates the confidence level that a common ancestor diverged at a

specific point. The tree indicates that the genus, Pan, Miopithecus, Nomascus and Pongo

share a common ancestor which diverged with a 47% chance. The tree also shows that

humans have a common ancestor with Gorilla, Bonobo, and Common Chimpanzee and that

the species diverged abruptly and recently.

4.4 (Ng et al., 2016) perform a comprehensive study on the effects of cartilaginous

extracellular matrix (ECM) components and culture regimen on cartilage formation by self-

assembling human MSCs in vitro and in vivo. The study is hoped to give insights that could

motivate new directions for engineering cartilage and bone via a cartilage template from self-

assembling MSCs. This study was done following a specific method; Human bone marrow-

derived MSCs (hMSCs) were seeded and compacted in 6.5-mm-diameter transwell inserts with

coated (type I, type II collagen) or uncoated (vehicle) membranes, at different densities (0.5

106, 1.0106, 1.5 106 per insert). Pellets were formed by aggregating hMSCs (0.25 106)

in round-bottomed wells. All tissues were cultured for up to 6 weeks for in vitro analyses. Discs

(cultured for 6, 8 or 10 weeks) and pellets (cultured for 10 weeks) were implanted

subcutaneously in immunocompromised mice to evaluate the cartilage stability in vivo. By

carefully analysing the data collected, they found that Type I and type II collagen coatings

enabled cartilage disc formation from self-assembling hMSCs. Without ECM coating, hMSCs

formed dome-shaped tissues resembling the pellets.

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 Type I collagen, expressed in the prechondrogenic mesenchyme, improved early

chondrogenesis versus type II collagen. In agreement with results at the phenotypic levels, the

expression of important cartilage markers (ACAN, COL2A1, C4ST, MAT3) was significantly

higher in the Col1 group than the Col2 group after 17 days of chondrogenic induction, but not

after 42 days High seeding density improved cartilage tissue properties but resulted in a lower

yield of disc formation. Discs and pellets exhibited compositional and organizational

differences in vitro and in vivo. Prolonged chondrogenic induction of the discs in vitro

expedited endochondral ossification in vivo.

5.0 CONCLUSION

As a conclusion, we have manage to fulfill the objectives of this assignment . BHLHE40 is a

protein coding gene. The gene feature of BHLHE40 is identified using BLAST whereby the

details were accessed directly from the database provided by National Centre for

Biotechnology (NCBI). We also able to come up with identities percentage between organisms

that are very close to human gene. Upon completing this task, we can reflect this assignment

with the Islamic teachings.

6.0 REFLECTION

Taha (20:50)

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Al-Muminun (23:115)

Allah is The Creator. Allah is the one who creates the universe and He also creates gene. Each

gene has its own functions. The function of the gene has already been fixed by Allah and the

gene will surely follow the fixation according to Allahs will. As a Muslim, we believe that

every creations has its own reasons and wisdom upon them. The study that have been made

should allow us to understand about Allahs creations thus will increase our faith to Allah.

7.0 REFERENCES

1.

2. National Centre for Biotechnology Information (http://www.ncbi.mlm.mih.gov)

3. Basic Local Alignment Search Tool (https://www.blast.ncbi.nlm.nih.gov/Blast.cgi)

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4. PubMed (https://www.ncbi.nlm.nih.gov/pubmed)

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