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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 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 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 23:24 on December 6, 2012 Permalink | Reply
    Tags: , APR, metrics   

    Academic Performance Review 

    Every year, in December, we are expected to hand in our Academic Performance Reviews. It was due today, and I managed to get it finished 1 hour before midnight.
    One thing I like about the APR is the section where I am asked to set out my goals and objectives for the new year, and examine my year’s achievements against last years goals and objectives. It provides an opportunity to reflect on my career, how I spend my time, those things at which I failed and those at which I succeeded. In February I will be meeting with my Head of Department to discuss it.
    December is probably not a good time for this thoughtful process. I find myself trying to catch up with everything that needs to be done before year end, and sometimes getting things accomplished is a sluggish process because everyone is getting ready for the end of year and Christmas lunches, parties, drinks and dinners, and the closeness to the nearing summer break means that things dont work with the usual level of efficiency, And of course, everyone is trying to tie up the loose knots — so it can all become an uphill battle.
    I do my best thinking over the Christmas break. The University is closed and I can sit at home with my laptop enjoying the sun coming in through my window with no phone calls and few work-related email interruptions. I can think. I can turn the music on, and the change of pace is good.
    So I submitted the APR now, but I am sure I will be looking at it with a slightly different light over the break. I hope I will be allowed to provide a better version before the meeting.
    So what were my favoruite APR items this year?

    1. Engagement outside the University
    2. What we accomplished in New Zealand in the Open space throughout the year
    3. Tha the Open Research Conference is really happening.

    There were a few other things that made me smile as I was typing them: Being invited to join the blogging network at PLOS. Moving along with mentoring seccondary school science students. The manuscript submitted to PeerJ. The work done for PLOS ONE. Getting more work done in the lab. Not having given up on funding. The great student feedback on my teaching. The discussions about making what I teach better. The manuscripts that are almost there ready to submit. The success of my former PhD student. The friendships that developed with unexpected people. (Well, I didnt really type that last one!)

    And APRs are a good opportunity to discuss what I value with respects to “metrics” of my success. Unlike other evaluation processes, I can justify in the discussion why I choose not to offer the impact factor of the journals in which I publish, or why I think that one specific item is more important with respect to impact than another.

    Mainly, it is great to go through one of these APRs to find out that, for the most part the huge effort ends up paying off, and while the failures are there too, they are neither paralizing nor defining.

    Time for a pat on the back, and a good night sleep methinks.

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