What we have learned from

Current Topics in Molecular Biology classes

  1. Suteema Sawadpongpan        MBMG/M 603620555
  1. Contents
  2. Organization
  3. Graphics and technical supports
  1. Alliya Somnus                        MBMG/M 6036206
  1. Introduction
  2. Contents
  3. Conclusion and discussion
  1. Chit Care                                 MBMG/M 6036786
  1. Grammar and spelling
  2. Contents
  3. References
  1. Shalini Abeysinghe              MBMG/M 6037884
  1. Introduction
  2. Contents
  3. Conclusion and discussion

1. Introduction

A scientific research paper is what comes to mind when scientist deal with their research work.  Reading and understanding of a research paper is very important as we have to be critical on this deed. Since the pattern of each paper is different and also interpretation of the results with their own ideas may not always be true.  When we are reading a paper, 50% of our mind have to set questions on that “Are these results really believable?” as instructors told us and other 50% is focusing on reading in order to analyse the results critically.

However, learning this subject, “Current Topics in Molecular Biology” helps a great deal on guiding and practising our mind to read research papers in correct manner. Likewise, it is needed to highlight that this course is really helpful to improve our critical thinking and result interpretation and analysing skills.  After reading a paper, we found that it is very difficult to summarize even though we have understood about the paper. Nonetheless, throughout the guidance of this course, we have been able to summarized many papers in many categories such as Biochemistry, Microbiology, Medicine and Agriculture under deep understanding. Last but not least, at the end of this course, we have been improved to understand the standard quality of research paper along with pros and cons. This course helps to bring in a vast knowledge in broad spectrum that will be useful in future works. 

2. Contents

Aj. Sarin’s class

        This class we discussed about the techniques and methods used to treat the metastatic melanoma patients under the topic of “Genomic and transcriptomic features of response to anti-PD-1 therapy in Metastatic Melanoma.” In overall of this research study, simple techniques were used to obtain drastic results. In this research study, they blocked the PD-1 immune checkpoint to obtain the significant beneficial effects for melanoma patients. On the other hand, several methods such as transcriptomes and somatic mutanomes were used to identify the factors that influence both the sensitivity and the resistance to anti-PD-1 therapy. Contrastly, the results was found that high mutational levels associate with higher survival rate. Hence, the tumors of responding patients were enriched the mutations in DNA repair gene, BRCA2. This is controversial since we think that the higher mutations, the easier the cancers to be occured. However, this research indicated that biological processes that use IPRES or innate anti-PD-1 may improve the PD-1 response in melanoma and other cancer types. Moreover, the overall techniques and methods of analysis performed in this research was very clear and gathered extremely critical results with few techniques, showing that many techniques are not always needed to bring in the great results.       

Aj. Chalongrat’s class

        In this class, we played the game while we were discussing  the paper, “Scaffoldless engineered enzyme assembly for enhanced methanol utilization” in order to find out the winner who got the highest score of answering the questions. In addition, we also discussed together about the methods and strategies that used to improve the efficiency of enzyme to increase methanol utilization. Biological reaction was chosen to develop methanol utilization depending on conversion of methanol to formaldehyde by using methanol dehydrogenase (Mdh). Mdh was engineered to assemble with 3-hexulose-6-phosphate synthase (Hps) and 6-phospho-3-hexuloseisomerase (Phi) by using SH3 as the interaction pair to drive an activity of this enzyme complex faster and efficient by increasing kinetic trap. It provides stable enzyme structures, facilitates substrate channeling between active sites and prevents toxic intermediates production. The functional multienzyme complex enhanced the conversion of methanol to fructose 6-phosphate (F6P). Besides, NADH sink (Lactate dehydrogenase: LDH) was used to prevent reversion of formaldehyde to methanol to the extent of increasing F6P production. As the overall results of these two strategies, the capacity of the enzyme was improved to make more methanol utilization leading to be useful in the industry as well as we can apply for other fields to improvement of other enzyme functions.

Aj. Nitwara’s class

        In this class, we discussed about the effective tool for studying of virus entry to the cells from the topic of “Single-particle tracking of human immunodeficiency virus type 1 production entry into human primary macrophages.” We have learnt the new technique for studying virus entry that has better efficiency and sensitivity than existing techniques. This technique employed inorganic semiconductor nanocrystal quantum dots (QD) to label viral particles in a single-particle level and then viral infection was traced and visualized in real-time. It shows remarkable brightness and photostability, so it can demonstrate virus infection in longer time point. Moreover, this technique was used to follow HIV-1 virus entry and it revealed the entry step of HIV-1 virus to human macrophages. The viral entry pathway revealed from this technique will be useful to understand the HIV-1 virus infection pathway more than the past. Importantly, it may become a bridge to the development of HIV-1 virus entry inhibitors.

Aj. Albert’s class

        Basically, we learnt how to find out the take home messages and the important findings of the paper at a glance from Assoc. Prof Albert. We discussed the role of Glutathione transferase Omega 1 (GSTO1-1) from the paper “GSTO1-1 plays a pro-inflammatory role in models of inflammation, colitis and obesity.” We learnt GSTO1-1 involves in LPS response inflammatory pathway. On the other hand, obesity and type 2 diabetes mellitus (T2D) emerge as a global health problem recently. Insulin resistant T2D is related to obesity and systemic inflammation. Perhaps, we discussed about GSTO1-1 inhibitors could become new drug for obesity and T2D. In addition, we have learnt some knowledge about molecular docking between GSTO1-1 and ML175 which is the small molecular  inhibitor of GSTO1-1. To sum up, we gained the knowledge about GSTO1-1 as a target for development of new drugs for obesity and inflammatory related T2D, as well as the benefits of small molecular inhibitors such as low cost of production and high efficacy with potentially short half-life.

Aj. Poochit’s class

        In this session, we focused on the research in the topic of “Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing.” Because of increasing drug-resistant bacteria, using genetically engineered bacteriophage is the alternative approach to combat the pathogenic bacteria. A high-throughput phage-engineering platform was established by using yeast platform. Phage genome was engineered by using homology sequence with a yeast artificial chromosome (YAC) and gap repair mechanism to get the desired full phage genome. The host specificities of the functional phages were examined by plaque formation assays. This research found that the phage-engineering platform can change adaptable host ranges of specific phages that in turn the phages can infect targeted bacteria efficiently. Furthermore, phage cocktail with engineered host range can edit mixed bacterial population. It will be better or more ideal if only one engineered host range can edit mixed bacterial population instead using phage cocktail. In contrast, the establishment of a bacteriophage genome-engineering platform gives a strength to fight the emerging antibiotic-resistance  germ. The relationship between bacteriophages and targeted bacteria is still needed to understand.

Aj. Wipa’s class

        In this class, we discussed the research in the topic of “Identification of a Chlamydomonas plastidial 2-lysophosphatidic acid acyltransferase and its use to engineer microalgae with increased oil content.” As Chlamydomonas reinhardtii or microalgae is the alternative feedstock for bioenergy production, this research studied in depth in biosynthetic pathway of lipid in microalgae. The result showed that 2-lysophosphatidic acid acyltransferase (LPAAT1) which can acylate 2‐lysophosphatidic acid to form phosphatidic acid act as precursor of membrane and storage lipid, was targeted to chloroplast. In addition, they found that the overexpression of CrLPAAT1 in chloroplast causes the increased oil production under nitrogen starvation and this enzyme prefers using C16 as substrate rather than C18. Besides context discussion of this research, students learned about how to write the paper by using selling point of their own work in this class. Furthermore, the reader should consider the results  whether it was interpreted in the same way of  researcher or from the reader’s perspectives and the reader does not need to believe whatever the researcher have written in the paper.

Aj. Duncan’s class

        In this class, firstly, we got a priceless lesson not only for academic but also for our life. Because Prof. Duncan gave us the retracted paper “Subcutaneous injections of aluminum at vaccine adjuvant levels activate

innate immune genes in mouse brain that are homologous with biomarkers of autism.” However, no students noticed about that before. The paper supported that aluminium adjuvant to vaccines can cause neuro inflammatory of the brain leading to autism. Nevertheless, this paper was not a critical paper to believe in order not to be vaccinated. We discussed and found out the data and graphs that were edited to persuade the best desired results. After we had been given this message, Prof. Duncan showed the manipulated results i.e. photographes, bar graphs and western blot analysis from the different retracted papers. We could learn how to find out the manipulated photographs by looking at the patterns, how to trace the western blot analysis by searching the small dots and shadow as fingerprints of the protein bands and how to analyse the bar graphs by comparing with supporting results from different experiments. Eventually, we knew that we could not believe 100% the results that they showed in their paper albeit they expressed their selling point greatly.

Aj. Apinunt’s class

             For this class, Aj. Apinunt has uploaded a paper titled “The Plaque of Plagiarism: Prevention and Cure!!!.” We will discuss about the serious problem of misconduct in science nowadays. We will learn how much plagiarism is important in every aspect. We will discuss different types of plagiarism including self-plagiarism, citation plagiarism, misappropriation of data and suppression. Hopefully, we will get a chance to discuss in order to avoid plagiarism by understanding its nature in scientific works based on the plagiarism developmental phenomena.

        

3. Conclusion

        Researcher would like to use the scientific research paper as the major tool to gain the knowledge as well as to share own original research work with others. In future, MGGE students to become outstanding and moral scientists and researchers in science, the Current topics in Molecular Biology course has been arranged. In each class, students were assigned to read the publication before attending the class. In this way, students had an opportunity to update their knowledge and information in various fields depending on the interest of each instructor. In addition, during the class, students have learnt how to read the paper more comprehensively by discussing with instructors. Moreover, students got opportunities to practise how to think critically as well as how to find the strength and weakness of each paper as the reader does not need to believe whatever the author wrote in the publication. Another major concern to students is the plagiarism issue for which each and every fact must be understood thoroughly. Lastly, we could learn how to use basecamp web server and google docs which are really useful tools for students’ group work in technical world.

In conclusion, this class practised students to get the essential skills to apply scientific research paper as a tool appropriately and developed critical thinking in lifelong which are important not only for being scientist but also in human life.

4. References

  1. Ando H, Lemire S, Pires DP, Lu TK. Engineering Modular Viral Scaffolds for Targeted Bacterial Population Editing. Cell Syst. 2015;1(3):187-96.

2.        Hugo W, Zaretsky JM, Sun L, Song C, Moreno BH, Hu-Lieskovan S,    et al. Genomic and Transcriptomic Features of Response to Anti-PD-1 Therapy in Metastatic Melanoma. Cell. 2016;165(1):35-44.

3.        Li D, Tomljenovic L, Li Y, Shaw CA. RETRACTED: Subcutaneous injections of aluminum at vaccine adjuvant levels activate innate immune genes in mouse brain that are homologous with biomarkers of autism. Journal of Inorganic Biochemistry. 2017;177:39-54.

4.        Li Q, Li W, Yin W, Guo J, Zhang ZP, Zeng D, et al. Single-Particle Tracking of Human Immunodeficiency Virus Type 1 Productive Entry into Human Primary Macrophages. ACS Nano. 2017;11(4):3890-903.

5.        Menon D, Innes A, Oakley AJ, Dahlstrom JE, Jensen LM, Brustle A, et al. GSTO1-1 plays a pro-inflammatory role in models of inflammation, colitis and obesity. Sci Rep. 2017;7(1):17832.

6.        Price JV, Chen L, Whitaker WB, Papoutsakis E, Chen W. Scaffoldless engineered enzyme assembly for enhanced methanol utilization. Proc Natl Acad Sci U S A. 2016;113(45):12691-6.

7.        Yamaoka Y, Achard D, Jang S, Legeret B, Kamisuki S, Ko D, et al. Identification of a Chlamydomonas plastidial 2-lysophosphatidic acid acyltransferase and its use to engineer microalgae with increased oil content. Plant Biotechnol J. 2016;14(11):2158-67.

8. Li, D., et al. (2017). "RETRACTED: Subcutaneous injections of aluminum at vaccine adjuvant levels activate innate immune genes in mouse brain that are homologous with biomarkers of autism." J Inorg Biochem 177: 39-54.

9. Khadilkar, S. S. (2018). "The Plague of Plagiarism: Prevention and Cure!!!" J Obstet Gynaecol India 68(6): 425-431.