Rani anak Mat (212111)

BSM4301 SCL Assignment: The Deadly Dust

CASE REPORT 4
Your laboratory received a distress call from a hospital in Tuaran, Sabah. There was a reported
death through acute lung poisoning in a patient who opened a dubious letter. The patient
suffered from chills and shortness of breath, nausea, and vomiting for 2 days before being
admitted to Hospital Tuaran on 17 June 2023. He was also said to mutter the words “six...of
six...” before dying.
An autopsy revealed that there was an extraordinary inflammation of the lung and the
occurrence of a yellow mucosal membrane. The mucus was isolated, and a unique protein was
sequenced from the pathological examination. The result was as follows;
Protein X
Form: Mucus
Source: Lung
SEQ:
MIEVKTSELSDGEFNRGVFATRDIKKGELIHAAPVISYPNEQHEHIEKTLLADYAFEY
GINHTAILLGYGMLFNHSYTPNATYDIVFENHTFNFYAYKDIKAGEEILINYNGEVDN
DELLWF
Your team is convinced this protein is linked to a pathogen, and the lab director has insisted
your team generate a phylogenetic tree to infer its identity.

INSTRUCTIONS
You have assembled a team to analyze and determine the identity of the pathogen responsible
for the death of the patient using phylogenetic analysis. Your team is required to do the
following:
1. To generate the best tree, you must convert the protein sequence into its DNA sequence using
tBLASTn.
2. You must select six (6) sequences belonging to six (6) different species. Using one character-
building and distance-building method, build a phylogenetic tree using the DNA sequences
identified.
3. Using your team’s analysis, determine the pathogen(s) that may be responsible for the
infection based on the inference of phylogeny in your tree.
4. Prepare a simple report for the identification of the proteins, and what is most likely the
causal pathogen for the infection. In your report, include the alignments containing the
information you used to obtain the results.
RESULT
First, we analyzed the data by the guidelines provided. We utilized tblastn to compare the
protein query sequence against a nucleotide database because we had access to the protein
sequence. To find potential coding areas that could produce protein sequences similar to the
query protein, tBLASTn searches nucleotide databases. To do this, the query protein sequence
is translated into each of the six reading frames, and it is then compared to the nucleotide
database. When hunting for homologous genes or coding regions that are not annotated, this
strategy works quite well (Library Guides: NCBI Bioinformatics Resources: An
Introduction: BLAST: Compare & Identify Sequences, 2023). We estimate that more than
100 sequences produced substantial alignments based on the findings. From the results, we
choose six different species and then used MEGA to create the phylogenetic tree using
maximum likelihood techniques. The phylogenetic tree is displayed in Figure 1. We deduced
from Figure 1 that the sequence provided in Case Report 4 was virtually the same as
XM007365835.1 Dichomitus squalens.

Figure 1 shows our case group 4 first findings

Due to various factors, case report 4 group members decided against using the provided protein
sequence to look for the sequences with the same genomes in Blastp. A protein query sequence
is compared to a protein database, and Blastp is used to find similar or homologous protein
sequences. Using a heuristic method that finds local sequence alignments as fast as feasible,
BLASTp analyses query and database sequences (Library Guides: NCBI Bioinformatics
Resources: An Introduction: BLAST: Compare & Identify Sequences, 2023). We took six
sequences from the results and built a phylogenetic tree using the neighbor-joining method.
The phylogenetic tree created for the protein sequence mentioned in Case Report 4 is depicted
in Figure 2. The sequence we obtained from the phylogenetic tree matched WP142390998.1
Bacillus thuringiensis.

Figure 2 shows our group’s second result.

DISCUSSION
Two conclusions were drawn from the findings. The initial result (Figure 1) indicates that
Dichomitus squalens emerged because it matched the provided sequence. Unfortunately, our
brief investigation into the organisms revealed that Dichomitus squalens does not pose any
health risks to people. A type of wood-decaying fungus belonging to the Polyporaceae family
is called Dichomitus squalens. It is frequently called the "brown-rot fungus" or "pitted bracket."
This species, which is widespread around the world, is renowned for its ability to decompose
and disintegrate wood. It is not believed to be pathogenic or hazardous to people. There were
no papers that claimed it had any negative health consequences on people, including respiratory
issues (How Does Dichomitus Squalens Affect Human Health? 2023). Since Dichomitus
squalens is not the species we are looking for, we came to this conclusion.
In the following step, we just use the provided protein sequences in blastp without using the
nucleotide form. In the findings, we found several Bacillus-type organisms. Out of 100
sequences, we choose 6 different species, and then we used MEGA to create a phylogenetic
tree using the neighbor-joining tree method. Figure 2 led us to the conclusion that the species
we are looking for is WP 142390998.1 Bacillus thuringiensis. We can infer from several factors
that Bacillus thuringiensis WP 142390998.1 is the bacterium that fits our sequencing. By using
pairwise alignment, we first compared the case report 4 sequences to those of Bacillus
thuringiensis. Figure 3 results, which demonstrate the sequences’ complete similarity to one
another, were presented. Second, we used to look for Bacillus thuringiensis and discovered that
it affects human health in a few different ways. One of the publications describing how Bacillus
thuringiensis causes lung infection in people is shown in Figure 4 (Senesi, 2007). Thus, we
deduced that Bacillus thuringiensis was the pathogen responsible for the issue in our case report
no 4.

Figure 3 shows the pairwise alignment of Sequence X and Bacillus thuringiensis.

 Figure 4 shows the article about Bacillus thuringiensis that states its harmful to humans.
https://pubmed.ncbi.nlm.nih.gov/17387030/

REFERENCES
How does dichomitus squalens affect human health? (2023, January 6). scholar. Retrieved
June 24, 2023, from
https://scholar.google.com.my/scholar?hl=en&as_sdt=0,5&as_vis=1&qsp=1&q=%22
white+rot+fungus%22+dichomitus+squalens&qst=bb
Library Guides: NCBI Bioinformatics Resources: An Introduction: BLAST: Compare &
identify sequences. (2023, February 1). Library Guides at UC Berkeley. Retrieved
June 24, 2023, from https://guides.lib.berkeley.edu/ncbi/blast
Senesi, S. (2007). Bacillus thuringiensis pulmonary infection: a critical role for bacterial
membrane-damaging toxins and host neutrophils. PubMed. Retrieved June 24, 2023,
from https://pubmed.ncbi.nlm.nih.gov/17387030/