As a crucial skill for any academic pursuing a research career, the ability to read and analyze scientific literature is a must-have. In this assignment I will choose two lab reports from the CCNY Library Database. which I will be subjecting to analysis using the eight elements described in chapter 19. The primary objective of this essay will be to examine how these reports compare and contrast with the standard format outlined in the chapter. Through annotation, the reports will be compared and contrasted to highlight any differences in structure, organization, and information presentation. Additionally, the essay will explore the reasons behind the authors’ choices in presenting information in a particular manner based on their major and academic interests. Overall, the analysis will enhance our understanding of the essential elements that make a lab report effective and the significance of scientific writing. The first lab reports I will be using are “Identification of Novel miRNAs, Targeting Genes, Signaling Pathway, and the Small Molecule for Overcoming Oxaliplatin Resistance of Metastatic Colorectal Cancer” and the second is “Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles”. The eight elements that I’ll be comparing and contrasting are title, abstract, introduction, materials, result, discussion, conclusion and acknowledgement.

The title of a lab report should be informative enough to enable readers to understand what thelab report is about. In the case of the two lab reports that I chose both accurately provide readers with titles that allow them to understand what the report is about. for example, the first lab report is called “identification of Novel miRNAs, Targeting Genes, Signaling Pathway, and the Small Molecule for Overcoming Oxaliplatin Resistance of Metastatic Colorectal Cancer”. These titles show both what the lab reports are going to be about and then go into specifications in detail. Which help reader to understand to better understand what the reports going to be about.

The introductions of lab reports 1 and 2 are both vastly similar because they both approach the introduction in similar fashion for example in lab report 1 the lab report immediately tells you about the subject in question that the lab report is going to be talking about. this can be seen in lab report too as well when they give you facts surrounding the subject. For example, in lab report one it states that” Colorectal cancer (CRC) is the third most common epithelial malignancy worldwide. According to the GLOBOCAN data source in 2020 in the United States, approximately 147,950 individuals were diagnosed with CRC and 53,200 patients died of this disease [1].–Surgery is the primary intervention measure for CRC patients at the primary stage of diagnosis; however, it is futile in patients who have developed distant metastasis. After surgery, approximately 20% of patients present metastatic (m)CRC micrometastasis [2, 3] …” (Misbah, M. Eat al.,2022).This shows the authors intent of educating the reader about the subject by explaining to the reader what the subject is and including various facts surrounding the subject. Another example is in lab report 2 where it states “Esophageal cancer is one of the malignant digestive system tumors with high lethality. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EACH) are the two most common histological types [1-3]. ESCC is a malignant tumor with hidden early symptoms and Chinese characteristics. The 5-year survival rate of early esophageal cancer can exceed 95%. But the overall 5-year survival rate is less than 20%, which seriously reduces the happiness of life of the people [4]. Precision medicine is a new medical concept and medical model based on the idea and technology of precision screening, diagnosis, and treatment…” (Xu, J et al., 2022). This is another clear example of the author of the lab report of lab 2 providing readers with background information in order to introduce the subject which is being reported on in the lab report.

The abstract provides a condensed overview of the entire report and follows the same structure as the report itself, including the introduction, methods, results, discussion, and conclusion. However, due to space constraints, each section is represented by only a few sentences. As the abstract may reach a broader audience than the complete report, it is crucial to include enough information in the abstract to allow readers to decide quickly whether to seek out and read the full report. These qualities can be found in both of the lab reports. For example, in lab report one abstract section it states “One of the globally common cancers is colorectal cancer (CRC). At present, a surgical approach remains a good option for CRC patients; however, 20% of surgically treated CRC patients experience metastasis. Currently, even the first-line used drug, oxaliplatin, remains inadequate for treating metastatic CRC, and its side effect of neurotoxicity is a major problem when treating CRC. The Gene Omnibus GSE42387 database contains gene expression profiles of parental and oxaliplatin-resistant LoVo cell lines” (Misbah, M. Eat al.,2022). This shows how well written the abstracts for lab report one is because not only does lab report address what the subject is going to be about it also addresses what the issue the subject of the lab report is evolving around which in this case would be overcoming oxaliplatin resistance of metastatic colorectal cancer. Another example of a good abstract is in lab report 2 it states “Esophageal squamous cell carcinoma (ESCC) is one of the subtypes of esophageal cancer with Chinese characteristics, and its five-year survival rate is less than 20%. Early diagnosis is beneficial to improving the survival rate of ESCC significantly. Quantitative Real-Time Polymerase Chain Reaction is a high-throughput technique that can quantify tumor-related genes for early diagnosis. Its accuracy largely depends on the stability of the reference gene. There is no systematic scientific basis to demonstrate which reference gene expression is stable in ESCC and no consensus on the selection of internal reference. Therefore, this research used four software programs (The comparative delta-Ct method, GeNorm, NormFinder, and BestKeeper) to evaluate the expression stability of eight candidate reference genes commonly used in other tumor tissues and generated a comprehensive analysis by RefFinder” (Xu, J et al., 2022). This shows readers what the lab report overall will be about the way in which they do this is by first telling us about the subject which is ESCC then telling us what about that subject they’ll be talking about which is Reference genes. If you compare both lab reports, you can see that both lab reports have the same structure when it comes to addressing the abstract, they both include a intro sentence that allows the reader to know about what the subject is. For example, for both of the lab reports the intro sentence provides a fact surrounding the subject. In addition to this both lab reports also begin to elaborate to what the issue surrounding the subject is after they introduce the subject.

There is an element for writing a lab report called materials and methods. It purpose is to prove to the reader that the author approach to solving the issue that they are attempting to address in the lab report is appropriate and credible. This is typically done by describing the methods in which they did to perform their experiments in order for other scientists to perform those same experiments themselves. They also provide the materials that they used in said experiments such as databases used, and they describe procedures and conditions that said experiments had. In lab report one it sates “We used the GEO database (available at http://www-ncbi-nlm-nih-gov.ccny-proxy1.libr.ccny.cuny.edu/geo/) to identify DEGs. The gene expression profile of GSE42387 was downloaded from GEO which was sequenced on the GPL16297 platform of the Agilent-014850 Human Genome CGH Microarray 4x44K G4112F (Agilent Technologies, Santa Clara, CA, USA). Three colon cancer cell lines of HCT116, HT29, and LoVo present in the GSE42387 database were exposed to an increasing concentration of OXA or SN-38 for 9 months in vitro to generate subcell lines with acquired resistance. Gene expressions of the parental and resistant cell lines grown in drug-free media were compared to detect any differences linked to chemotherapeutic resistance” (Misbah, M. Eat al.,2022). This shows the author providing an example of sources that they used in order to formulate their research. Another example of the element lab report to where it states and method is in lab report to where states “To confirm the reliability of reference genes, transcriptome sequencing results were quantified. The expression level of each transcript was calculated according to the Transcripts Per Million reads (TPM) method based on the length of the gene and the number of reads mapped to the gene. RSEM (http://deweylab.biostat.wisc.edu/rsem/) was used to quantify gene abundances. The fold difference (FC)>2, p<0.05 was used as the standard to screen for expression difference analysis, and then the protein-protein interaction was performed from the differential genes to screen out the expression of important genes with significantly increased expression and more related to the pathogenesis of ESCC. Then, normalize the selected gene of a target with the two most stable and least stable reference genes[57, 58]. The qRT- PCR amplification conditions were as described, and the gene expression was calculated using the experimental group/control group=2^-??Ct . Calculate the relative expression levels of each reference gene and target gene, respectively, take the geometric mean of the two as the standardization result of double reference genes[59, 60], and use SPSS18 software for statistical analysis” (Xu, J et al., 2022). This shows the author of lab report to implementing a process in order to verify a piece of data they had collected. In the examples provided by both lab reports we can see that both lab reports used very different approaches to provide a materials and methods approach. for example, lab report one provided a database They used in order to identify something they needed for their research. Whereas in lab report two they provided a a process in which they use to verify a piece of data used for their specific research.

The result section of a lab report is the section in which evidence is presented in order to support the claims that will be made in the discussion section of the lab report. For example, in lab report 1 it states “We used the GeneMANIA online web tool to explore functional interactions of miRNA targets with each other and DEGs of the reactome. The PPAR pathway was used to analyze the functional roles of these molecules. The interaction network included 20 other related genes in addition to the two targets (PCK1 and IRS1 ) that were entered, and there were 144 links in total. Two interaction types were involved, and coexpression was the most frequent type of interaction (2.88%) (Figure 10(a)). High expressions of miR-7-5p, miR-20a-5p, and miR-636 targeting PCK1 suppressed OXA-resistant CRC through activation of the PPAR pathway. Overall interactions of miRNAs with target genes and their mechanisms are summarized in Figure 10(b)” (Misbah, M. Eat al.,2022).This shows an example of a result for a lab report. Another example is in lab report 2 where it states “It can be seen that the different algorithms and judgment standards between the software and the expression stability coefficients of the same reference gene obtained by different software were inconsistent. Finally, the eight candidate reference genes were comprehensively ranked using the stability comprehensive analysis software RefFinder [65] (Figure 6). The results illuminated that the two reference genes, PPIA and RPS18, were the most stably expressed under various conditions, and GUSB was the most erratically expressed gene. At the same time, PGK1 also performed instability in esophageal cancer samples and all esophageal samples, and HPRT1 was also unstable in normal esophageal samples. The use of multiple internal references can effectively reduce the test error. Under the conditions of this experiment, the combinations of two suitable internal reference genes of cancer esophageal tissues, normal esophageal tissues, and all samples were PPIA and RPS18” (Xu, J et al., 2022). Both lab reports demonstrate the implementation of the results section of a lab report similarly by both providing results from their research similar ways.

The discussion section in a lab report is the part of the lab report that discusses the results obtained from the experiment is very important. It allows the writer to explain the significance of the data and findings and present their conclusions. To write a strong discussion section, one needs to have critical thinking skills, attention to detail, and the ability to communicate effectively. For example in lab report one it states “ Our study revealed that PCK1 is an important antitumor mRNA and inhibitor of tumor progression. PCK1 was down- regulated in OXA-resistant CRC and functionally suppressed the drug-resistant phenotype. miR-20a-3p, miR-636, and miR-7-5p overexpression resensitized the OXA response by competitively binding the PCK1 mRNA 3′ UTR, leading to PPAR signaling of OXA-resistant CRC. In this study, previ- ously published mRNA expression datasets on OXA resis- tance of CRC in the GEO database were used to identify DEGs [42]. A computational analysis was performed by defining DEGs that were correlated with miRNAs. KEGG pathway enrichment analyses were identified and a PPI network was created to screen for hub genes. Furthermore, OS and DFS were evaluated to identify CRC patient survival biomarkers” (Misbah, M. Eat al.,2022). This example shows us how the writer explains the methodology used to arrive at these findings, including the use of previously published mRNA expression datasets on OXA resistance of CRC in the GEO database. Another example of the discussion section is in lab report 2 were it states “Esophageal squamous cell carcinoma is a malignant tumor with Chinese characteristics. Epidemiological characteristics are often related to factors such as diet (drinking, smoking, chewing betel nut, and drinking very hot beverages), BMI, and other factors [69-71]. After more than 70 years of development, China has made remarkable achievements in preventing and treating esophageal cancer and is now at the top level in the world. The early symptoms of this cancer are very subtle or lacking, so it is often diagnosed after the disease has deteriorated significantly, which makes the early diagnosis rate only 1.43%. With the development of bioinformatics, transcriptomic studies have found that some genes involved in tumorigenesis and metastasis are differentially expressed in tumor and normal tissues [72-75] (Xu, J et al., 2022). This example shows that Esophageal squamous cell carcinoma is a type of cancer that is prevalent in a certain part of the world, and its epidemiological characteristics are related to various factors such as diet, body weight, and others. Despite being a deadly disease with subtle or no early symptoms, significant progress has been made in preventing and treating this cancer, and its early diagnosis rate is very low. The advancement of bioinformatics has revealed differences in gene expression between tumor and normal tissues, which can help in research related to tumorigenesis and metastasis. If we compare the two we can see that there are a lot of differences . Lab report 1 discusses the findings of a study on PCK1 as an antitumor mRNA and inhibitor of tumor progression. The methodology used to arrive at the findings is explained, including the use of previously published mRNA expression datasets on OXA resistance of CRC in the GEO database. Lab report 2 focuses on Esophageal squamous cell carcinoma, discussing its epidemiological characteristics and progress in prevention and treatment. The use of bioinformatics in revealing gene expression differences between tumor and normal tissues is also highlighted.

The conclusion is a vital element in a lab report as it allows the writer to summarize the experiment’s findings, explain their significance, and draw final conclusions. In lab report two it sates “Lack of normalization may lead to an inaccurate conclusion, absolute quantification of reference genes is not recommended. This research systematically explored the applicability of candidate endogenous reference genes for normalization and performed a comprehensive assessment of reference gene required for qRT-PCR analysis of target gene expression in ESCC. It proved that RPS18 and PPIA are reference gene with a relatively stable expression before and after the onset of ESCC. Statistics are reliable(Xu, J et al., 2022). This shows the importance of normalization for accurate conclusions in qRT-PCR analysis of target gene expression in ESCC. The research conducted a systematic exploration of candidate endogenous reference genes for normalization and a comprehensive assessment of reference genes. The study found that RPS18 and PPIA were relatively stable reference genes with consistent expression before and after the onset of ESCC, making them suitable for qRT-PCR analysis. The example highlights the significance of using reliable statistics in the selection of reference genes for normalization to ensure the accuracy of the results obtained. Another example is in lab report 1 where it states “We concluded that miR-7-5p, miR-636, and miR-20a-3p target PCK1 in the PPAR signaling pathway and the small- molecule compound, mersalyl, might be involved in over- coming OXA-resistant CRC. Our findings may provide novel directions and strategies for CRC therapies” (Misbah, M. Eat al.,2022). This shows the conclusion of a study on the targeting of PCK1 in the PPAR signaling pathway in OXA-resistant colorectal cancer (CRC) and the potential involvement of mersalyl in overcoming drug resistance. The study found that miR-7-5p, miR-636, and miR-20a-3p target PCK1, which functions as an important antitumor mRNA and inhibitor of tumor progression. The use of mersalyl as a small-molecule compound may offer a novel strategy for the treatment of CRC. The conclusion suggests that the study has identified potential targets for therapy and provides direction for future research in the field. The two examples provided in the paragraph show different approaches to the conclusion element in lab reports. Lab report 2 focuses on the importance of normalization for accurate conclusions in qRT-PCR analysis of target gene expression in ESCC. The conclusion is drawn based on a systematic exploration and comprehensive assessment of reference genes. In contrast, Lab report 1 concludes a study on the targeting of PCK1 in the PPAR signaling pathway in OXA-resistant CRC and the potential involvement of mersalyl in overcoming drug resistance. The conclusion suggests that the study has identified potential targets for therapy and provides direction for future research in the field. While Lab report 2 emphasizes the significance of using reliable statistics, Lab report 1 highlights the identification of potential targets for therapy and the direction for future research.

The lab reports we analyzed had well-written titles that provided readers with an understanding of what the reports were about. The introductions of the lab reports were educational and informative, providing readers with background information on the subjects. Additionally, the abstracts provided condensed overviews of the entire report and included enough information to allow readers to decide quickly whether to seek out and read the full report. In conclusion, the lab reports we analyzed demonstrated the importance of following a standard format for effective scientific writing. By analyzing the eight elements, we were able to see the significance of structure, organization, and information presentation in scientific writing. The skills learned from analyzing lab reports can be applied to any research field, making it an essential skill for any academic pursuing a research career.

Reference List

Misbah, M., Kumar, M., Lee, K.-H., & Shen, S.-C. (2022). Identification of Novel miRNAs, Targeting Genes, Signaling Pathway, and the Small Molecule for Overcoming Oxaliplatin Resistance of Metastatic Colorectal Cancer. BioMed Research International, 2022, NA. https://link-gale-com.ccny-proxy1.libr.ccny.cuny.edu/apps/doc/A720581174/HRCA?u=cuny_ccny&sid=bookmark-HRCA&xid=670e11bb

Xu, J., Yang, M., Shao, A.-Z., Pan, H.-W., Fan, Y.-X., & Chen, K.-P. (2022). Identification and Validation of Common Reference Genes for Normalization of Esophageal Squamous Cell Carcinoma Gene Expression Profiles. BioMed Research International, 2022, NA. https://link-gale-com.ccny-proxy1.libr.ccny.cuny.edu/apps/doc/A728878967/HRCA?u=cuny_ccny&sid=bookmark-HRCA&xid=c938ac6a

This entry is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International license.

Digital

Lab Report

Need help with the Commons?