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  • kubke 22:05 on August 15, 2014 Permalink | Reply
    Tags: embryology, lab life, research students,   

    H – Week 1 

    This week H started working in the lab. We had to wait until she had finished all of her compliance training and it was exciting to finally see her sitting at the dissecting microscope. We pulled a couple of embryos from my stock and off she went to try to see if she could do the dissection to expose the trigeminal nerve.

    The trigeminal nerve is the one that innervates areas of the face, for example the upper and lower jaw. It is relatively large and so is the ganglion which sits close to where the hindbrain meets the midbrain. One nice thing about the trigeminal is that the ganglion is easy to recognise – it is large and sort of heart shaped, so it is a good one to start with.

    I always like to see what approach comes naturally to students – it lets me see what are the habits that might need correcting, and also I am sometimes surprised with a way of doing things that I had not thought of and might be better in the way. So I sat watching her work, and enjoying her excitement.

    The dissections aren’t easy – and she stepped up to the mark. What is most difficult (and something that is almost impossible to teach) is to be able to “feel” the tension of the tissue through the forceps. At least for me, feeling the properties of the tissues is what tells me when I am applying too much or too little pressure or force, and what prevents me from damaging the structures I want to get to. For now, we are working with relatively large embryos (emphasis on relatively, they are about Hamburger and Hamilton stage 26) because at that age the nerves are better defined and it is important that she gets her head around the organisation of the hindbrain, how to better hold the forceps, how to adapt her hand control to what she is seeing under the microscope, how moving the light tubes provide different images, and so on.
    H was one of my students in 107 where she was taught a few of the things that she was working on today. What I always find amazing is the excitement of students who first dissect an embryo and they see that what I (we) taught her in class is actually a pretty good representation of reality.

    So, lesson learned? It doesn’t matter how many drawings, how many diagrams and movies I show the students it may be just by looking under the microscope that all that can eventually come to life. We were talking about this yesterday at #scichatnz – what *is* authentic learning. Well, I am glad to say, I saw that today. Although I have to also say that I am quite impressed that several years later she can still mentally refer to stuff I taught her in year 1. (Sure, she did go back to the notes before starting in the lab.) But it made me feel I must be doing something right.

  • kubke 22:19 on August 6, 2014 Permalink | Reply  

    Going open one research project at a time.

  • kubke 17:00 on October 8, 2013 Permalink | Reply  

    made a plot using R. Actually 4. All by myself and my cheatsheet. #babysteps

  • kubke 18:36 on October 7, 2013 Permalink | Reply  

    had to ask for an extension in the coursera computing for data analysis – this was a hard week!

  • kubke 13:15 on October 2, 2013 Permalink | Reply
    Tags: ABR development, ,   

    Developing ABRs Developing 

    managed to find the files in my hard drive – seem I have more than one copy of the files (I think people may call these backups) :)

    I now need to sort out the original files from those that have been processed and try to build some mechanim to track whatever changes are being made from the original files. Not sure where to do this – perhaps a wiki page might be the right place. OpenWetWare?

    All files have been moved to a shared Dropbox folder with Andy. So, step 1, file cleanup.

  • kubke 19:25 on September 27, 2013 Permalink | Reply
    Tags: , , data analysis,   

    Great week comes to an end on a high note 

    Ending the week with a chat with @nytowler aka Andy – it was way overdue. Hadn’t spoken to him in a while and it is great to be reminded what a great friend he is. Andy is one of the profs where I did my PhD. We had heaps of fun – and stayed in touch after I graduated. He connected me to the “net” (before there was an internet) and taught me electronics and programming. He has been a rock steady friend throughout all these years.
    But the high point (other than catching up and having a few laughs) was discussing liberating some data that we had intended to analyse a long while back. So we discussed how we would do that. He is happy to put the analysis out on github, and I would try to do some programming in R for the analysis.
    The motivation for this is that I signed up for a MOOC to learn R programming (two actually) and playing with this data would be a great opportunity for me to apply what I learn, and do it with someone that can help me solve any coding problems. And of course, the opportunity of working with Andy is just the cherry on the top, and to be honest the cupcake too.
    We both had a laugh, because as we were chatting (online of course) I pointed him to a few online tools, and servers that he hadn’t heard of. What a great opportunity to tease him about how the tables had turned.

    So, there will be more on that later. Right now my job is to create the repo on github, organise the data files, and start slowly trying to get things moving.
    Oh and I got him to open a twitter account. So hopefully this will just be the beginning. Wish us luck!

  • kubke 11:08 on September 26, 2013 Permalink | Reply  

    Morning tea: a chat with AMM about brain machine interfaces – an opprotunity for my lab work to move in that direction? Walked away with a long “to do” list. Nice!

  • kubke 11:07 on September 26, 2013 Permalink | Reply
    Tags: continuation, OA, Open access   

    You should be proud of what you have done and achieved, especially your work on #OA – sez continuation reviewer

    • kubke 11:08 on September 26, 2013 Permalink | Reply

      then again, who knows what the staffing committee will value :)

  • kubke 19:19 on September 25, 2013 Permalink | Reply
    Tags: , engagement, policy   

    So, there are subprofessorial memberships open for several university committees. Thinking that the Research, Library or Staffing would be ones where I could put in a good word or two for open science.
    #pondering. Do I really have the time?

  • kubke 15:15 on September 25, 2013 Permalink | Reply
    Tags: ,   

    Software being installed in the microscope – lets hope we can get that beast running again!

  • kubke 15:14 on September 25, 2013 Permalink | Reply  

    Congratulations Cherry 

    Today’s was Cherry’s graduation ceremony – wow – Congratulations.
    And in case you wonder whether us supervisors care, here is some proof of how happy it makes us to see students graduate!DSC02283

  • kubke 15:12 on September 22, 2013 Permalink | Reply
    Tags: , , lifelong learning,   

    Spent a large proportion of the weekend setting up the github repos. I feel like an absolute idiot at times but if I use it enough I am sure that even *I* can get a hang of it. Since I signed up for two coursera classes to learn R, I figured github would be a good place to keep the notes. One step at a time

    • kubke 21:56 on September 25, 2013 Permalink | Reply

      well – turns out that the code of conduct from coursera says I cannot share test questions and answers – so github is no a choice. Dang.

  • kubke 21:27 on September 21, 2013 Permalink | Reply
    Tags: , open research, , thoughts   

    A long chat with Mat Todd 

    After going to my first kiwi foo camp, i began noticing that Rob Inskeep was posting links on twitter to a social network called FriendFeed. Rob had organised getting a list of twitter handles prior to kiwi foo camp, which prompted me to sign up to twitter (yes, that is how it all started). So I joined FriendFeed and one evening I decided to search for “Open Access”. I suddenly found that there were heaps of people there discussing Open Access, Open Science and a whole lot of other things alike.

    It would be fair to say that if my original meeting with Nat Torkington back in 2008 changed my path, finding this community on FriendFeed was what would pave it. Hidden in the public view of FriendFeed was a community that was not just talking about changing the way we do and communicate science but were doing something about it. There were lots of disagreements, lots of trying to find common ground, lots of support, lots of ideas. This community was working together in ways I had never seen before. But for me, most importantly there was lots of learning.

    When FriendFeed got bought by Facebook and support for the platform slowly started to dwindle, the conversation moved to other platforms. But for me, none of them captured the spirit of the community I had found in 2009.

    I got the chance to meet a few of them in person as the years went by, and we have been able to keep up with what each of us were doing. Since then, a lot has changed. Things that were dreams became realities, other battles we lost and others we still keep fighting. I had a long chat with Mat Todd the other night. I discovered him on FriendFeed I don’t know when but probably at the beginning. I remember reading his insights with awe, admiring him from afar (or as afar as you can bee on an online social network).. I told him I always felt like I was stalking him, and what it had meant for me to meet him in person earlier this year. He chuckled and paraphrased a Charles Dickens quote, about moving on to sea and remembering the narrow river from where we came. I looked for that quote for days, and today I found it. The quote is priceless, but the paragraph it is embedded captures how I feel about everything that happened since that fateful day where I agreed to have a coffee with someone who identified himself as one Nat Torkington:

    “My dear Mrs Winter I have been much moved by your letter; and the pleasure it has given me has some little sorrowful ingredient in it. In the strife and struggle of this great world where most of us lose each other so strangely, it is impossible to be spoken to out of the old times without a softened emotion. You so belong to the days when the qualities that have done me most good since, were growing up in my boyish heart that I cannot end my answer to you lightly. […] We are all sailing away to the sea, and have a pleasure in thinking of the river we are upon, when it was very narrow and little.”

    (From Dickens, C. (2012). The Selected Letters of Charles Dickens. Oxford University Press.)

  • kubke 23:17 on September 18, 2013 Permalink | Reply
    Tags: nottebohm,   

    Fernando Nottebohm Plenary, February 1, 2011 (Australian Neuroscience Conference, Auckland)


    • kubke 21:50 on September 21, 2013 Permalink | Reply

      “that which we hold true is most probably the next generation of unrefuted errors”

    • kubke 21:50 on September 21, 2013 Permalink | Reply

      ‘I wanted to make sure that neurogenesis was happening in nature because I am always afraid of laboratory artifacts’

    • kubke 21:50 on September 21, 2013 Permalink | Reply

      ‘these results were a reminder of how soon we become attached to our favourite interpretation’

    • kubke 21:51 on September 21, 2013 Permalink | Reply

      ‘just when we managed to develop a transgenic zebra finch we ran out of funding’

    • kubke 21:51 on September 21, 2013 Permalink | Reply

      ‘we invest millions to Study rats living in little plastic boxes pretending they are not only models for humans but also of humans living normal lives’

    • kubke 21:52 on September 21, 2013 Permalink | Reply

      ‘but try to study a natural phenomenon and it is not considered fundable . when will the coin drop and we will see what an idiotic decision this is’

  • kubke 10:30 on September 18, 2013 Permalink | Reply
    Tags: Einstein,   

    Every day I remind myself that my inner and outer life are based on the labors of other men, living and dead, and that I must exert myself in order to give in the same measure as I have received and am still receiving.

    Albert Einstein


  • kubke 16:21 on September 9, 2013 Permalink | Reply
    Tags: , ,   

    Almost 2 hours meeting with studentC. I can see the shift in the discussion from the “intellectual” to the “executive”. There is still a lot of domain language I need to learn. #morereadingtodo

  • kubke 14:21 on September 4, 2013 Permalink | Reply
    Tags: humour,   

  • kubke 12:44 on September 4, 2013 Permalink | Reply
    Tags: , , manuscripts   


    • kubke 12:48 on September 4, 2013 Permalink | Reply

      Perineuronal satellite neuroglia in the telencephalon of New Caledonian crows and other Passeriformes: evidence of satellite glial cells in the central nervous system of healthy birds?

      Felipe S. Medina, Gavin R. Hunt1, Russell D. Gray, J. Martin Wild, M. Fabiana Kubke

      Glia have been implicated in a variety of functions in the central nervous system, including the control of the neuronal extracellular space, synaptic plasticity and transmission, development and adult neurogenesis. Perineuronal glia forming groups around neurons are associated with both normal and pathological nervous tissue. Recent studies have linked reduction in the number of perineuronal oligodendrocytes in the prefrontal cortex with human schizophrenia and other psychiatric disorders. Therefore, perineuronal glia may play a decisive role in homeostasis and normal activity of the human nervous system.

      Here we report on the discovery of novel cell clusters in the telencephala of five healthy Passeriforme, one Psittaciform and one Charadriiforme bird species, which we refer to as Perineuronal Glial Clusters (PGCs). The aim of this study is to describe the structure and distribution of the PGCs in a number of avian species.

      PGCs were identified with the use of standard histological procedures. Heterochromatin masses visible inside the nuclei of these satellite glia suggest that they may correspond to oligodendrocytes. PGCs were found in the brains of nine New Caledonian crows, two Japanese jungle crows, two Australian magpies, two Indian mynah, three zebra finches (all Passeriformes), one Southern lapwing (Charadriiformes) and one monk parakeet (Psittaciformes). Microscopic survey of the brain tissue suggests that the largest PGCs are located in the hyperpallium densocellulare and mesopallium. No clusters were found in brain sections from one Gruiform (purple swamphen), one Strigiform (barn owl), one Trochiliform (green-backed firecrown), one Falconiform (chimango caracara), one Columbiform (pigeon) and one Galliform (chick).

      Our observations suggest that PGCs in Aves are brain region- and taxon-specific and that the presence of perineuronal glia in healthy human brains and the similar PGCs in avian gray matter is the result of convergent evolution. The discovery of PGCs in the zebra finch is of great importance because this species has the potential to become a robust animal model in which to study the function of neuron-glia interactions in healthy and diseased adult brains.

  • kubke 22:44 on June 2, 2013 Permalink | Reply
    Tags: , , publication   

    what a week! Sent 3 manuscripts out, sent out the review for on PLOS ONE paper, did the Women in Leadership workshop, organised the content for 2 courses in 2014, submitted the paper on recommendations for Open Access publishing for the Faculty, submitted the animal ethics protocol, registered for eResearch Symposium and, oh, yes, renegotiated the terms of my mortgage. All and all a very productive week! And monday is a holiday – Yay!

  • kubke 20:21 on May 18, 2013 Permalink | Reply
    Tags: Cereijido, ,   

    There is no need to promote science (it promotes itself)-but rather promoting a culture that is compatibel with science. Not knowing soemething about a process in nature does not mean we shoudl call it a miracle

    Marcelino Cereijido
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