CS 5974: Writing in Computer Science
Fall Semester, 2022

Sahar's Thesis Exercises

Jingyi's Solutions

  1. Since the outbreak of Severe Acute Respiratory Coronavirus 2 (SARs-CoV-2) in 2019, many studies have been carried out to gain a better understanding of the virus.
    • Severe Acute Respiratory Coronavirus 2 (SARs-CoV-2) *emerged* in 2019 and has since been *extensively studied*.
  2. In addition, viruses mutate to adapt to their surroundings and move from host to host more effectively.
    • *Furthermore*, viruses mutate to adapt to their surroundings and move from host to host more *efficiently*.
  3. Proteins with no known defining mutations were discarded.
    • We *excluded* proteins *without* known defining mutations.

Badhan's Solutions

  1. Selected 3 lines from ST:
    1. A mutation could help the virus gain traits that help it reproduce quickly or adhere better to the surface of human cells.
    2. Analysis of non-synonymous single-point mutations in SARS-CoV-2 variants and mimicry motifs may help us better understand their contribution to SARS-CoV-2 infectivity.
    3. To identify mechanisms of mimicry in SARS-CoV-2 and understand whether SliMs may play a role in pathogen invasion, as well as study the molecular effect of single amino acid variants on viral protein functions encoded by eukaryotic SliMs, we developed a protocol to identify co-occurrences of single point mutations and WLMs in SARS-Cov-2 protein sequences.
  2. Changing the 3 sentences.
    1. A mutation could help the virus gain traits that help it reproduce *rapidly *or adhere better to the surface of human cells.
    2. Analysis of non-synonymous single-point mutations in SARS-CoV-2 variants and mimicry motifs may help us better *determine* their contribution to SARS-CoV-2 infectivity.
    3. To identify mechanisms of mimicry in SARS-CoV-2 and understand whether SliMs may play a role in pathogen invasion, as well as study the molecular effect of single amino acid variants on viral protein functions encoded by eukaryotic SliMs, we *established* a protocol to identify co-occurrences of single point mutations and WLMs in SARS-Cov-2 protein sequences.
  3. Making these sentences concise.
    1. A mutation can help the virus gain traits that help it reproduce rapidly or adhere to the surface of human cells.
    2. Analysis of non-synonymous single-point mutations in SARS-CoV-2 variants and mimicry motifs can help determine their contribution to SARS-CoV-2 infectivity.
    3. We established a protocol to identify the co-existences of single-point mutations and ELMs in SARS-CoV-2 protein sequences for three reasons: identifying the mechanisms of mimicry in SARS-CoV-2, understanding the role of SliMs in pathogen invasion, and studying the molecular effect of single amino acid variants on viral protein functions encoded by eukaryotic SliMs.

Reza's Solutions

I have included my word alterations in braces in the first sentence (original) and my edited sentence as the second. Here are my selected sentences:
  1. It has been shown that some pathogens have evolved[developed], within their sequences, eukariotic SLiMs that mimic[imitate] host factors at the host-pathogen interface, thus hijacking[using] host pathways and cellular processes and promoting infection.
    • We know that some pathogens have eukariotic SLiMs that mimic the host's factors, which they use to hijack host pathways to promote infection.
  2. As a future prespective[extension], it could be possible to develop a tool for end-users so that they could obtain[calculate] some potential[possible] SLiM candidates for mimicry for their pathogen of interest.
    • This work can be extended into a simple tool to calculate imitating SLiM candidates for any host-pathogen pair.
  3. The next phase[step/process] would be fusion[merged] of the viral membrane with the host cell membrane and release[delivery] of the viral genome into the cell.
    • Thereafter, the viral and host membranes merge, and the virus releases its genome into the host's cell.

Yoonjin's Solutions

  1. Since the outbreak of Severe Acute Respiratory syndrome Coronavirus 2 (SARs-CoV-2) in 2019, many studies have been carried out to gain a better understanding of the virus.
    • Since the outbreak of Severe Acute Respiratory syndrome Coronavirus 2 (SARs-CoV-2) in 2019, many studies have been conducted to gain a better understanding of the virus.
    • Since the Severe Acute Respiratory syndrome Coronavirus 2 (SARs-CoV-2) in 2019, many studies have been conducted to better understand the virus.
  2. To identify mechanisms of mimicry in SARs-CoV-2 and understand whether SliMs may play a role in pathogen invasion, as well as study the molecular effect of single amino acid variants on viral protein functions encoded by eukaryotic SliMs, we developed a protocol to identify co-occurrences of single point mutations and ELMs in SARs-CoV-2 protein sequences.
    • To identify mechanisms of mimicry in SARs-CoV-2 and understand whether SliMs may play a role in pathogen invasion, as well as study the molecular effect of single amino acid variants on viral protein functions encoded by eukaryotic SliMs, we developed a procedure to analyze co-occurrences of single point mutations and ELMs in SARs-CoV-2 protein sequences.
    • We developed a procedure to examine the co-occurrences of single-point mutation and ELMs in SARs-CoV-2. This procedure will help us understand the role of mimicry in SARs-CoV-2 in pathogen invasion and the molecular effect of single amino acids variants on viral protein functions.
  3. (Initial phase of SARS-CoV-2 infection includes cell-entry) It is promoted with the interaction of Spike protein's receptor binding domain (RBD) with host angiotensin-converting enzyme 2 (ACE2) receptor.
    • (Initial phase of SARS-CoV-2 infection includes cell-entry). It is facilitated by the interaction of Spike protein's receptor binding domain (RBD) with host angiotensin-converting enzyme 2 (ACE2) receptor.
    • The interaction between spike protein's receptor binding domain (RBD) and host angiotensin-converting enzyme 2 (ACE2) receptor initiates cell entry of SARs-CoV-2 infection.

Xiao's Solutions

  1. Original: Since SLiMs are short and often degenerate, it is possible that some instances occur in protein sequences by pure chance
    • *As* SLiMs are short and *usually* degenerate, it is *likely* that *a number of* instances *appear* in protein sequences by *mere accident*
    • Some SLiMs can occur in protein sequences by chance since they are short and often degenerate.
  2. Original: It has been shown that some pathogens have evolved, within their sequences, eukaryotic SLiMs that mimic host factors at the host-pathogen interface, thus hijacking host pathways and cellular processes and promoting infection
    • It has been *demonstrated* that *certain* pathogens have evolved, within their sequences, eukaryotic SLiMs that mimic host factors at the host-pathogen interface, *thereby* hijacking host pathways and cellular processes and promoting infection
    • Some pathogens evolved eukaryotic SliMs within sequence to mimic host factors at the host-pathogen interface to hijack host pathways and cellular processes and promote infection
  3. Original: A mutation could help the virus gain traits that help it reproduce quickly or adhere better to the surface of human cells
    • A mutation *may* *aid* the virus *in acquiring* traits that help it *multiply* *rapidly* or adhere better to the surface of human cells
    • Virus can gain traits from mutations to reproduce quickly or adhere better to human cell surface