365 days of science: March

March was a month of many ups and downs. My UK holiday came to an end and I went back to work to find a lot of things had gone wrong. But by the end of the month things were looking up! So here is my month of March in science pics.

 

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365 days of science: January

After deciding to post a picture of science a day in 2018 I swiftly made an instagram account to do so from! See 365daysofscience on instagram if you are interested! In the first month, I have posted over 50 pictures and gained over 1000 followers already! It has been so nice to see people enjoying my science pics and asking questions, taking an interest and sharing their own pictures along with me. Here are just 24 of the pictures I posted in Jan 🙂 Cant wait for the next 11 months! In Feb I will be at conferences and overseas so get ready for pics in a whole new setting!
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365 days of science in 2018

365 days of science in 2018

Yep, guess who’s back at it again.

As some of you may know, in 2016 I read a paper a day every day of the year…. sort of. Check out some of my other blog posts if you want to know more about that. This year (2017) I haven’t done anything along those lines, but after being inspired by a number of scientists on twitter and Instagram I have set myself a new, and much easier challenge for 2018!

*drum roll please*

Next year starting on the 1st of Jan I will be sharing a photo/image each day that relates to something sciencey I did that day. It may be a photo of something I did in the lab, an image from something I read or me simply sharing the beautiful images some other scientists I know create. Thats 365 days of science photos for 2018!

While the aim of the 366 papers challenge I took on in 2016 was for me to get better at reading and digesting scientific literature, this time I want to use this challenge to try and engage with the general public and show people how cool science can be! Let’s trash this idea that science is boring and done in dark rooms by old white men and celebrate the beauty of science and diversity of the people within science!!

I will be sharing these images on this blog, on Instagram and on twitter all using the hashtag #365daysofscience

Here are the links to my twitter account and instagram account where you can follow me!!

Please feel free to join me and share your science pics too! The more people who get involved the better 🙂

How to read a scientific publication

One skill I think a lot of younger science students lack is the ability to read a paper quickly, dissect all the information and then decide whether the paper is good, bad or somewhere in between. Like many people, I have developed my own method for reading a research article, so I thought I would share it in the hopes of helping others to get through what can sometimes seem like a very daunting task.

  1. Read the title (duh)
    I realise this seems extremely obvious, and you probably did this to choose the paper in the first place. When I’m reading a paper that I really want to understand and remember I write notes on a blank piece of paper about it as I go. So naturally at the top of the page I write the title of the paper. Step 1 done!
  1. Read the abstract
    This gives you the general idea of the paper & what they have done/what you can expect from the paper. This is also the stage at which I decide whether I want to continue reading on.
  1. Read the last paragraph of the introduction
    I usually don’t even bother with the introduction of a paper unless I skim it very quickly. The exception to that is if I don’t know the field and I need a bit of background. But I always read the last paragraph of the intro as it is like a super brief summary of the whole intro, and usually states what question the authors are trying to address. At this stage I go back to my notes page and write down the question I think they are trying to answer/ the hypothesis they are testing.
  1. Skip straight to the figures in the results section
    Here I look at the figures, read the figure legends and write down what I think each of the figures shows. I then read the results section from start to finish to see if the authors and I have reached the same conclusions about the data. This is the best part in my opinion. Sometimes you think the data says exactly what the authors have said it does, sometimes you don’t. At the end of this section, I usually go back to my notes and write what the main points and ideas of the paper are. Sometimes it can be useful to re-draw the important figures in a more basic way- this helps me to wrap my head around some things I don’t get at the time.
  1. Read the methods section
    I tend to do this briefly, but this is often where you you can decide whether the paper is good or not (if you didn’t decide in the results). Here is where you can decide whether their experiments were designed well or not. After reading the methods I like to write down a few points about where they could have improved the study.
  1. Briefly read the discussion and then the conclusions
    I don’t really find the discussion section very helpful, however sometimes it can be interesting to read. The discussion tends to be the most biased part of the paper, and sometimes people make some huge leaps when interpreting their results and putting them in the perspective of the field. Remember when reading the discussion that often the references are there to support their conclusions. If the authors discuss papers that disagree with their results, kudos to them! I still like to read the discussion though. After reading the discussion and conclusion I like to write down the interesting points of the paper, what they showed and how (if possible) the work may relate to my own.
  1. Write your own conclusion about the paper you read
    Here I re-state what I think they were aiming to do and whether they did it. What was new, and what were their limitations in this study? I also write down the questions that I still have about the paper, and if I read the paper again in the future I go back to this notes page and try to answer those questions.
  1. Check if there are any references that you want to follow up on/may be of interest to you.

So that’s how I read my papers when I want to really understand them and take notes. Many people will disagree with this method of reading a paper, but each to their own! Please let me know how you read a paper & if you have any other tips.

366 papers in 2016; looking back on a paper a day

In 2015 at the end of the year myself and a few others though it would be a good idea to read a scientific paper a day in 2016. So on the 1st of Jan 2016 I began this challenge, using the tag #366papers on twitter & listing each paper here on my website. Here are so pros, cons and my thoughts on this challenge:

Pros:

  • You get better at reading scientific papers and digesting them quickly
  • It is interesting, especially if you read widely (which I recommend)
  • It’s a neat challenge if you’re a scientist

Cons:

  • Starts to feel like a chore
  • A paper a day doesn’t leave a lot of time to really understand a paper in depth
  • Some days you want to read 5 papers and others you want to read 0, but that defeats the point of the exercise (I did this anyway)

All in all I wouldn’t do it again & I didn’t even do it properly this time. But I did read 366 papers (more really, but I didn’t list them all). As I was writing my thesis for a large chunk of the year it wasn’t that difficult to hit 366, however some days I just didn’t want to read a paper. I didn’t want to make reading papers feel like something I HAD to do, making it feel like a task, so I didn’t.

In retrospect I think 52 papers a year would be a better better goal. This gives you time to really understand the paper & means you don’t actually have to read one a day, which is not fun on holidays and weekends, or when you’re just flat out. So if you’re thinking of doing a similar challenge in 2017, perhaps think about cutting back to 1 paper a week….. Or try 1 a day, whatever suits you!

December: 366 papers in 2016

Dec 1:

Williams, Adam, Jorge Henao-Mejia, and Richard A. Flavell. “Editing the mouse genome using the CRISPR–Cas9 system.Cold Spring Harbor Protocols 2016, no. 2 (2016): pdb-top087536.

Dec 2:

Nicola, Nicos A., Warren S. Alexander, Douglas J. Hilton, and Ashley P. Ng. “In memoriam: Donald Metcalf (1929-2014)–A historical perspective of his contributions to hematology.Experimental hematology 43, no. 6 (2015): 425-427.

Dec 3:

Westerterp, Marit, Andrew J. Murphy, Mi Wang, Tamara A. Pagler, Yuliya Vengrenyuk, Mojdeh S. Kappus, Darren J. Gorman et al. “Deficiency of ATP-binding cassette transporters A1 and G1 in macrophages increases inflammation and accelerates atherosclerosis in mice.Circulation research 112, no. 11 (2013): 1456-1465.

Dec 4:

Baker, Paul J., Dave Boucher, Damien Bierschenk, Christina Tebartz, Paul G. Whitney, Damian B. D’Silva, Maria C. Tanzer et al. “NLRP3 inflammasome activation downstream of cytoplasmic LPS recognition by both caspase‐4 and caspase‐5.European journal of immunology 45, no. 10 (2015): 2918-2926.

Dec 5:

Kershaw, Nadia J., James M. Murphy, Nicholas PD Liau, Leila N. Varghese, Artem Laktyushin, Eden L. Whitlock, Isabelle S. Lucet, Nicos A. Nicola, and Jeffrey J. Babon. “SOCS3 binds specific receptor–JAK complexes to control cytokine signaling by direct kinase inhibition.Nature structural & molecular biology 20, no. 4 (2013): 469-476.

Dec 6:

Jenkins, Misty R., Jesse A. Rudd-Schmidt, Jamie A. Lopez, Kelly M. Ramsbottom, Stuart I. Mannering, Daniel M. Andrews, Ilia Voskoboinik, and Joseph A. Trapani. “Failed CTL/NK cell killing and cytokine hypersecretion are directly linked through prolonged synapse time.The Journal of experimental medicine 212, no. 3 (2015): 307-317.

Dec 7:

Berry, Richard, Stephen J. Headey, Melissa J. Call, James McCluskey, Clive A. Tregaskes, Jim Kaufman, Ruide Koh, Martin J. Scanlon, Matthew E. Call, and Jamie Rossjohn. “Structure of the Chicken CD3ϵδ/γ Heterodimer and Its Assembly with the αβT Cell Receptor.Journal of Biological Chemistry 289, no. 12 (2014): 8240-8251.

Dec 8:

Ernst, Christina, Jeremy Pike, Sarah J. Aitken, Hannah K. Long, Nils Eling, Lovorka Stojic, Michelle C. Ward et al. “Successful transmission and transcriptional deployment of a human chromosome via mouse male meiosis.eLife 5 (2016): e20235.

Dec 9:

Gibson, Daniel G., Hamilton O. Smith, Clyde A. Hutchison III, J. Craig Venter, and Chuck Merryman. “Chemical synthesis of the mouse mitochondrial genome.” nature methods 7, no. 11 (2010): 901-903.

Dec 10:

Bank, Claudia, Sebastian Matuszewski, Ryan T. Hietpas, and Jeffrey D. Jensen. “On the (un-) predictability of a large intragenic fitness landscape.bioRxiv (2016): 048769.

Dec 11:

Rosenfeld, Lior, Michael Heyne, Julia M. Shifman, and Niv Papo. “Protein Engineering by Combined Computational and In Vitro Evolution Approaches.Trends in biochemical sciences 41, no. 5 (2016): 421-433.

Dec 12:

Rost, Fabian, Aida Rodrigo Albors, Vladimir Mazurov, Lutz Brusch, Andreas Deutsch, Elly M. Tanaka, and Osvaldo Chara. “Accelerated cell divisions drive the outgrowth of the regenerating spinal cord in axolotls.eLife 5 (2016): e20357.

Dec 13:

Suto, Nobuyoshi, Amanda Laque, Genna L. De Ness, Grant E. Wagner, Debbie Watry, Tony Kerr, Eisuke Koya, Mark R. Mayford, Bruce T. Hope, and Friedbert Weiss. “Distinct memory engrams in the infralimbic cortex of rats control opposing environmental actions on a learned behavior.eLife 5 (2016): e21920.

Dec 14:

Alcock, Felicity, Phillip J. Stansfeld, Hajra Basit, Johann Habersetzer, Matthew AB Baker, Tracy Palmer, Mark I. Wallace, and Ben C. Berks. “Assembling the Tat protein translocase.eLife 5 (2016): e20718.

Dec 15:

Wells, Michael F., Max R. Salick, Ole Wiskow, Daniel J. Ho, Kathleen A. Worringer, Robert J. Ihry, Sravya Kommineni et al. “Genetic ablation of AXL does not protect human neural progenitor cells and cerebral organoids from Zika virus infection.Cell Stem Cell 19, no. 6 (2016): 703-708.

Dec 16:

Hutchison, Clyde A., Ray-Yuan Chuang, Vladimir N. Noskov, Nacyra Assad-Garcia, Thomas J. Deerinck, Mark H. Ellisman, John Gill et al. “Design and synthesis of a minimal bacterial genome.Science 351, no. 6280 (2016): aad6253.

Dec 17:

Telenti, Amalio, Levi CT Pierce, William H. Biggs, Julia di Iulio, Emily HM Wong, Martin M. Fabani, Ewen F. Kirkness et al. “Deep sequencing of 10,000 human genomes.Proceedings of the National Academy of Sciences (2016): 201613365.

Dec 18:

Zahn, Laura M., P. Mickey Williams, Jeremy P. Segal, Itay Tirosh, Benjamin Izar, Sanjay M. Prakadan, Marc H. Wadsworth II et al. “Single-cell expression profiles of melanoma.Science 183 (2016): 185.

Dec 19:

Telenti, Amalio, Brad A. Perkins, and J. Craig Venter. “Dynamics of an aging genome.Cell Metabolism 23, no. 6 (2016): 949-950.

Dec 20:

Vinson, Valda, Denes Hnisz, Abraham S. Weintraub, Daniel S. Day, Anne-Laure Valton, Rasmus O. Bak, Charles H. Li et al. “A proton pump in action.Science 351, no. 6280 (2016): 1411-1413.

Dec 21:

Tabebordbar, Mohammadsharif, Kexian Zhu, Jason KW Cheng, Wei Leong Chew, Jeffrey J. Widrick, Winston X. Yan, Claire Maesner et al. “In vivo gene editing in dystrophic mouse muscle and muscle stem cells.” Science 351, no. 6271 (2016): 407-411.

Dec 22:

Session, Adam M., Yoshinobu Uno, Taejoon Kwon, Jarrod A. Chapman, Atsushi Toyoda, Shuji Takahashi, Akimasa Fukui et al. “Genome evolution in the allotetraploid frog Xenopus laevis.Nature 538, no. 7625 (2016): 336-343.

Dec 23:

Chavez, Alejandro, Marcelle Tuttle, Benjamin W. Pruitt, Ben Ewen-Campen, Raj Chari, Dmitry Ter-Ovanesyan, Sabina J. Haque et al. “Comparative Analysis of Cas9 Activators Across Multiple Species.” (2016).

Dec 24:

Zhirnov, Victor, Reza M. Zadegan, Gurtej S. Sandhu, George M. Church, and William L. Hughes. “Nucleic acid memory.” Nature materials 15, no. 4 (2016): 366-370.

Dec 25:

Ostrov, Nili, Matthieu Landon, Marc Guell, Gleb Kuznetsov, Jun Teramoto, Natalie Cervantes, Minerva Zhou et al. “Design, synthesis, and testing toward a 57-codon genome.Science 353, no. 6301 (2016): 819-822.

Dec 26:

Shipman, Seth L., Jeff Nivala, Jeffrey D. Macklis, and George M. Church. “Molecular recordings by directed CRISPR spacer acquisition.Science (2016): aaf1175.

Dec 27:

Stranges, P. Benjamin, Mirkó Palla, Sergey Kalachikov, Jeff Nivala, Michael Dorwart, Shiv Kumar, Mintu Porel et al. “Design and characterization of a nanopore-coupled polymerase for single-molecule DNA sequencing by synthesis on an electrode array.Proceedings of the National Academy of Sciences 113, no. 44 (2016): E6749-E6756.

Dec 28:

Fuller, Carl W., Shiv Kumar, Mintu Porel, Minchen Chien, Arek Bibillo, P. Benjamin Stranges, Michael Dorwart et al. “Real-time single-molecule electronic DNA sequencing by synthesis using polymer-tagged nucleotides on a nanopore array.Proceedings of the National Academy of Sciences 113, no. 19 (2016): 5233-5238.

Dec 29:

Deamer, David, Mark Akeson, and Daniel Branton. “Three decades of nanopore sequencing.Nature biotechnology 34, no. 5 (2016): 518-524.

Dec 30:

Kasianowicz, John J., and Sergey M. Bezrukov. “On’three decades of nanopore sequencing’.” Nature biotechnology 34, no. 5 (2016): 481-482.

Dec 31:

van Gent, Dik C., and Roland Kanaar. “Exploiting DNA repair defects for novel cancer therapies.Molecular Biology of the Cell 27, no. 14 (2016): 2145-2148.