20.109(S23):Journal article presentation

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20.109(S23): Laboratory Fundamentals of Biological Engineering

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Spring 2023 schedule        FYI        Assignments        Homework        Class data        Communication        Accessibility

       M1: Drug discovery        M2: Protein engineering        M3: Project design       


Overview and logistics

You will complete this assignment individually.

Please review the 20.109 statement on collaboration and integrity as you proceed.

In Module 1, you delivered a Research talk that was focused on your research project. For this assignment, you will present work completed by other scientists that has been peer-reviewed and published. Reading, understanding, and explaining research related to your project are all important skills that will be important as you flex your scientist muscles.

As you prepare your talk be sure to review the resources provided on the Communication tab. In addition, please use the following link to view the full video from Susan McConnell: Designing effective scientific presentations. Lastly, review the Journal club presentation Evaluation rubric (linked here)!

Method of submission

Please submit your completed Journal club slides 1 hr prior to your scheduled laboratory session time to Canvas, with filename Name_LabSection_JC.pptx (for example, ImaStudent_TR_JC.pptx).

Length and format of presentations

You will have 10 minutes to discuss the journal article you select. It may be very difficult, or impossible, to discuss all of the figures within the article adequately in only 10 minutes. Therefore, this assignment is not only to present the work, but also to identify the data that is most important to the conclusions. It is also critical to consider how your presentation 'flows' from one experiment to the next. As when you write your own research, you want to deliver a coherent story during your journal presentation.

Format considerations

The timing provided here is a guideline for a 10-minute presentation. Your presentation may vary depending on the content.

Section Minutes Number of slides DO DON'T
Introduction ~2 2-3
  • Introduce the key concepts that the audience will need to follow your presentation.
  • Briefly state the overall scope and significance of the study -- what is the central question and why is it interesting?
  • Try to summarize background material with a model slide rather than lines of text. If text is needed, bring in the details as you speak using PowerPoint animation.
  • Don't assume you are addressing an expert audience.
  • Don't give more information than is absolutely needed to understand the rest of your talk.
  • Don't put too much information on each slide.
Data ~7 4-6
  • Present the data in a logical sequence, letting each slide build upon the previous ones.
  • Include a title for each slide. The title should be the conclusion and should be unique to the information on the slide.
  • Make every element of your slide visible to the entire room. This means 20-point font or greater.
  • Interpret each slide thoroughly and carefully.
  • Point out strengths and weaknesses of the data along the way.
  • Don't read your talk. Similarly, do not read lists from slides.
  • Don't put much information on each slide. Each slide should make only one point.
  • Never say, "I know you can't read this, but...". Everything on each slide should be legible.
  • Don't be afraid to remind the audience how the data fits into the overall question
Summary ~1 1
  • Review each of your main messages.
  • Clearly state what the study contributed to the field.
  • Don't repeat experimental details.
Question & Answer ? 0
  • Answer the question being asked. If you are unclear about the question, ask for clarification.
  • Respect every question and questioner.
  • Don't take too long with one question. If the discussion is involved, suggest meeting after the talk to discuss it more.

Helpful hints

  • A 10-minute talk is NOT a 30-minute talk given while racing through slides and speaking very quickly.
  • Consider ways to transition from one slide to the next to ensure the information is tied together.
  • Practice your presentation in front of people rather than in a room by yourself and practice several times!
  • Familiarize yourself with using a laser pointer and/or slide changer if you will use one during the actual presentation.
  • If you do choose to use a pointer, use it to direct attention to specific elements on the screen, rather than constantly gesturing in the general vicinity of your slide; otherwise, the audience will not know what's important. When you later make your own slides and figures, the apparent need for a pointer may actually mean you need to make a clearer slide.

Article selection

You may choose to select a journal article from those provided by the teaching faculty or you can select an article that is related to your Module 2 research from any peer-reviewed journal.

  • If you choose an article from below, please "reserve" it by putting your (initials/lab section/team color) next to the listing here.
    • For visibility, please use the following format to sign up if possible, substituting in your own initials and team color: <font color = purple><b>[IS/WF/Purple]</b></font color>, which will look like [IS/WF/Purple]. Thanks!
  • If you would like to discuss a paper not on the list below, please email it (as .pdf) to the teaching faculty (Noreen, Becky, and Jamie) with a brief description of the work.
    • The list of papers below is provided as a guideline for the types of papers that might be relevant for your presentation. You are not limited to the primary research articles on this list. The list is provided simply to give you an idea of the kinds of subjects that could make suitable presentations for the class. Feel free to search PubMed yourself to find articles of interest to you.

Please review the articles before making your final selection to ensure it is a paper that you find interesting and that you are comfortable presenting!


Consequences of metal contamination

  1. Angele-Martinez, C., et. al. " Cobalt-mediated oxidative DNA damage and its prevention by polyphenol antioxidants." (2023) Journal of Inorganic Biochemistry. https://doi.org/10.1016/j.jinorgbio.2022.112024 [RM/TR/Orange] [VV/WF/Blue]
  2. Chen, C., et. al. " Comparative transcroptome analysis reveals gene network regulating cadmium uptake and translocation in peanut roots under iron deficiency." (2019) BMC Plant Biology. https://doi.org/10.1186/s12870-019-1654-9 [AG/TR/Pink]
  3. Cowell, M., et. al. " Intergenerational arsenic exposure on the mouse epigenome and metabolic physiology." (2022) Environmental and Molecular Mutagenesis. https://doi.org/10.1002/em.22526 [IL/TR/Blue][AK/WF/Red]
  4. Fan, S., et. al. Role of NF-κB in lead exposure-induced activation of astrocytes based on bioinformatics analysis of hippocampal proteomics." (2023) Chemico-Biological Interactions. https://doi.org/10.1016/j.cbi.2022.110310. [SM/TH/Red] [KA/WF/Yellow]
  5. Howard, J., et. al. Combating lead and cadmium exposure with an orally administered chitosan‑based chelating polymer." (2023) Scientific Reports. https://doi.org/10.1038/s41598-023-28968-4 [HJ/TR/Purple]
  6. Liu, Z., et. al. Effects of cadmium on transcription, physiology, and ultrastructure of two tobacco cultivars." (2023) Science of the Total Environment. http://dx.doi.org/10.1016/j.scitotenv.2023.161751 [JC/WF/Blue]
  7. Oyetibo, Z., et. al. Heavy metals assessment of ecosystem polluted with wastewaters and taxonomic profiling of multi-resistant bacteria with potential for petroleum hydrocarbon catabolism in nitrogen-limited medium." (2023) World Journal of Microbiology and Biotechnology. https://doi.org/10.1007/s11274-023-03524-4 [AW/WF/Orange]
  8. Huang, Q., et. al. Metagenomic analysis characterizes resistomes of an acidic, multimetal (loid)-enriched coal source mice drainage treatment system." (2023) World Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2023.130898
  9. Saha, J., et. al. Whole genome sequencing and comparative genomic analyses of Pseudomonas aeruginosa strain isolated from arable soil reveal novel insights into heavy metal resistance and codon biology." (2022) Current Genetics. https://doi.org/10.1007/s00294-022-01245-z [LD/TR/Yellow] [KE/WF/Pink]
  10. Wang, Z., et. al. Ferroptosis contributes to nickel-induced developmental neurotoxicity in zebrafish." (2023) Science of the Total Environment. http://dx.doi.org/10.1016/j.scitotenv.2022.160078 [ZL/TR/Orange] [AW/WF/Purple]
  11. Zheng, F., et. al. Cobalt induces neurodegenerative damages through Pin1 inactivation in mice and human neuroglioma cells." (2021) Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2021.126378 [SH/TR/Green] [JE/WF/Pink]

Bioremediation approaches

  1. Acosta-Luque, M., et. al. " Remediation of Pb-contaminated soil using biochar-based slow-release P fertilizer and biomonitoring employing bioindicators." (2023). Scientific Reports. https://doi.org/10.1038/s41598-022-27043-8
  2. Carvajal, M., et. al. " Bioremoval of copper by filamentous fungi isolated from contaminated soils of Purchuncavi-Ventanas Central Chile." (2023). Scientific Reports. https://doi.org/10.1007/s10653-023-01493-z [TS/WF/Red]
  3. Henagamage, A., et. al. " Fungal-bacterial biofilm mediated heavy metal rhizo-remediation." (2022). World Journal of Microbiology and Biotechnology. https://doi.org/10.1007/s11274-022-03267-8 [LMS/WF/Yellow]
  4. Hu Z., et. al. " Synergy of surface adsorption and intracellular accumulation for removal of uranium with Stenotrophomonas sp: Performance and mechanisms." (2022). Environmental Research. https://doi.org/10.1016/j.envres.2022.115093 [AA/TR/Purple]
  5. Jakubczak, M., et. al. " Understanding the mechanism of Nb-MXene bioremediation with green microalgae." (2023). Scientific Reports. https://doi.org/10.1038/s41598-022-18154-3
  6. Leon-Vaz, A., et. al. " Enhanced wastewater bioremediation by a sulfur-based copolymer as scaffold for microalgae immobilization (AlgaPol)." (2019). Chemosphere. https://doi.org/10.1016/j.chemosphere.2023.137761 [DA/TR/GREEN] [CS/WF/BLUE]
  7. Li, J., et. al. " Efficient lead immobilization by bio-beads containing Pseudomonas rhodesiae and bone char." (2023). Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2023.130772 [JS/WF/Orange]
  8. Mao, Q., et. al. " Indigenous cyanobacteria enhances remediation of arsenic-contaminated soils by regulating physicochemical properties, microbial community structure and function in soil microenvironment." (2023). Science of the Total Environment. http://dx.doi.org/10.1016/j.scitotenv.2022.160543
  9. Lone, S., et. al. " Gelatin-chitosan hydrogel particles for efficient removal of Hg(II) from wastewater." (2019). Environmental Science. https://doi.org/10.1039/C8EW00678D [BL/TR/Red]
  10. Muduli, M., et. al. " Remediation and characterization of emerging and environmental pollutants from residential wastewater using a nature-based system." (2023). Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-023-25553-0
  11. Wu, C., et. al. " Bioremediation of mercury-polluted soil and water by the plant symbiotic fungus Metarhizium robertsii." (2022). PNAS. https://doi.org/10.1073/pnas.2214513119 [NH/WF/Purple], [KA/TR/Yellow]
  12. Wu, K., et. al. " Integrating FTIR 2D correlation analyses, regular and omics analyses studies on the interaction and algal toxicity mechanism between graphene oxide and cadmium." (2023). Journal of Hazardous Materials. https://doi.org/10.1016/j.jhazmat.2022.130298

Detection and analysis of contaminantion

  1. Bao, Q., et. al. In situ detection of heavy metal ions in sewage with screen-printed electrode-based portable electrochemical sensors." (2021) Analyst. https://10.1039/d1an01012c
  2. Eom, H., et. al. Improved toxicity analysis of heavy metal-contaminated water via a novel fermentative bacteria-based test kit." (2020) Chemosphere. https://doi.org/10.1016/j.chemosphere.2020.127412
  3. He, W., et. al. Colorimetric Sensor Array for Discrimination of Heavy Metal Ions in Aqueous Solution Based on Three Kinds of Thiols as Receptors." (2018) Analytical Chemistry. https://doi.org/10.1021/acs.analchem.8b00076
  4. Jeong, H., et. al. Characteristics of metal pollution and multi-isotopic signatures for C, Cu, Zn, and Pb in coastal sediments from special management areas in Korea." (2023) Marine Pollution Bulletin. https://doi.org/10.1016/j.marpolbul.2023.114642
  5. Landes, F., et. al. A Field Procedure To Screen Soil for Hazardous Lead." (2023) Analytical Chemistry. https://doi.org/10.1021/acs.analchem.9b00681
  6. Liu, Z., et. al. The effects of pollution by multiple metals derived from long-term smelting activities on soil mite communities in arable soils under different land use types in East China." (2023) Environmental Science and Pollution Research. https://doi.org/10.1007/s11356-023-25341-w
  7. Pan, S., et. al. Electron microscopic imaging and NanoSIMS investigation on physiological responses of Aspergillus niger under Pb(II) and Cd(II) stress." (2023) Frontiers in Bioengineering and Biotechnology. https://doi.org/10.3389/fbioe.2022.1096384
  8. Peralta, E., et. al. Heavy metal availability assessment using portable X-ray fluorescence and single extraction procedures on former vineyard polluted soils." (2020) Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2020.138670
  9. Wang, F., et. al. The high-dimensional geographic dataset revealed significant differences in the migration ability of cadmium from various sources in paddy fields." (2023) Scientific Reports. https://doi.org/10.1038/s41598-023-28812-9
  10. Wei, H., et. al. Decoding the metabolic response of Escherichia coli for sensing trace heavy metals in water." (2023) PNAS. https://doi.org/10.1073/pnas.2210061120 [AP/TR/Blue] [AH/WF/Green]
  11. Xu, D., et. al. Effects of soil properties on heavy metal bioavailability and accumulation in crop grains under different farmland use patterns." (2022) Scientific Reports. https://doi.org/10.1038/s41598-022-13140-1